pax_global_header00006660000000000000000000000064141215206640014513gustar00rootroot0000000000000052 comment=f6b4c190aa360e20edb9659f179be2c3699e4b92 xtp-2021.2/000077500000000000000000000000001412152066400124145ustar00rootroot00000000000000xtp-2021.2/CHANGELOG.rst000066400000000000000000000253231412152066400144420ustar00rootroot00000000000000For more detailed information about the changes see the history of the `repository `__. Version 2021.2 (released 19.09.21) ================================== - no changes since v2021.1 Version 2021.1 (released 18.07.21) ================================== - no changes since v2021 Version 2021 (released 13.03.21) ================================ - fix CI on rawhide (#663) - add xtp_qmmm2qm to cmake install (#665) - add auto-cancel workflow to GitHub Actions (#674) Version 2021-rc.1 (released 15.01.21) ===================================== - G0W0 rpa energies are fixed in BSE (#383) - Hqp part of BSE can be separate from QP range (#388) - Fixed Cuda implementation (#391) - Plain, linear, and Anderson mixing in evGW - Use a general syntax to represent all QMPackages input (#318) - Remove support for both Gaussian and NWChem (#318) - Fixed executable path check (#400) - Usage of offdiagonal elements of Hqp in BSE optional, default: with offdiagonals (#402) - refactored MO reordering of external QMPackages (#406) - Add defaults to XML (#319, #413) - fix build with gcc-10 (#422, #424) - Add name command line argument (#426) - fix usage of PROJECT\_SOURCE\_DIR in cmake (#431) - check that temperature is positive for KMC (#432) - document cmake options and packages (#434) - remove long gone MKL option for gitlab-ci (#435) - add documentation using Sphinx (#433, #615) - add kokkos-based Ewald solver (#444, #446, #485) - allow multiple choices for the calculator options (#442, #445) - move bsecoupling defaults to xml (#451) - address missing includes (#452) - fix readjobfiles path (#453) - standardising include order and style in header files (#448) - changed to OpenMP reductions instead of hand crafted solutions (#466, #471, #493) - switch to GitHub Actions as CI (#467, #474, #477, #482, #500, #502, #518, #549, #637) - move tutorial to its own repo (#450) - removed share/packages folder (#475) - copy orca \*.gbw files in eqm (#472) - improve mkl support (#479) - add def2-tzvp, def2-tzvpp, def2-qzvp, def2-qzvpp for Rb,I,Ag,Xe (#480) - create a map between orca and libxc functional names (#461) - fix path to share/data (#486, #487) - remove special XML symbols (#488) - standardize includes in src files (#462) - add cmake exported target (#489) - update codacy badge (#490) - add mkl builds to CI (#496) - convert markdown to rst (#497) - enable CXX only in CMake (#499) - implement RPA correlation energy (#498) - added verbose option for rootfinder (#503) - fix orca pointcharges (#504) - remove constant cutoff from neighborlist (#508, #509) - fix default and flags properties issue (#511) - add more checks to the dft_parse_part (#510) - add NOSCF option for iqm in internal and external DFT (#483) - added versions to output files (#523) - write an empty state file if it does not exist yet (#526) - fix double unit conversion (#531) - Unittests can read input and reference values from files (#529) - fix double SCF in ORCA keyword line (#533) - xtp internally uses only single shells. (#539) - Refactor orbital reordering (#537) - fix build with clang-11 (#546) - Add a molden parser to xtp (#547) - Correct self-energy frequency derivative (#550) - fix multiline orca keyword (#552) - Contour Deformation Approach (CDA) for self-energy implemented (#4, #548) - BSE with perturbative dynamical screening (#3, #560) - Correction of full BSE energy contribution in analysis output (#560) - Bump required CMake version to 3.12 (#568) - Refactored calculator interface (#570) - Fixed boost test deprecation warnings (#569) - Refactored CUDA-OpenMP integration (#571) - replaced own integrals with the libint library (#559) - improved kmc output (#574) - fix build on Ubuntu 16.04 (#577) - use unique_ptr in factory (#581) - fix QMMM with QP (#590, #591) - fix bug in setCenter of AODipole (#593) - extra check in orca unit test (#594) - fixed atomid numbering while adding containers (#599) - added tool for automatic mapping file generation (#595) - Added GPU support for RPA (#601) - fixed int64 interface to RDKIT (#602) - remove kokkos dependent ewald (#612) - fixed Sphinx warnings (#609) - better error for exceeded angular momentum in libint (#613) - fixed wrong QP-QMMM energy with non-zero QPmin (#620) - fixed density analysis options (#627) - Use libint transformation matrices (#630) - Added script to extract orbitals from qmmm statefile (#629) - clean up XTP app message (#631) - fixed EXX 3c mode (#640) Version 1.6.4 (released 12.01.21) ================================= - fix build on openSUSE (#622) - refactored logger (#625) Version 1.6.3 (released 09.12.20) ================================= - switch to ghcr.io for CI (#555) - fixing Gaussian guess read keyword (#562, #563) - improved kmc output (#575) - use master .clang-format in format action (#582, #584) - strip windows line endings in readers (#596) Version 1.6.2 *SuperGitta* (released 22.08.20) ================================= - move CI to GitHub Actions (#512, #514, #516, #519) - add more checks to the dft_parse_part (#521) - make unit tests work in parallel (#530) Version 1.6.1 (released 21.06.20) ================================= - fix warnings on Ubuntu 20.04 (#438, #460) - remove obsolete boost define (#440) Version 1.6 *SuperPelagia* (released 17.04.20) ============================================== - fix 32-bit build (#381, #380) - remove duplicated basissets (#384, #386, #387) - fix clang-10 warnings (#394) - fix unit\_test\_eeinteractor on OpenSUSE (#341, #428) Version 1.6\_rc2 (released 10.02.20) ==================================== - fix remove giant logo from tarball (#337) - fix assertions related to GLIBCXX\_ASSERTIONS (#345) - remove unused boost serialisation (#346) - fix build on 32-bit archs (#347) - add ENABLE\_HIGH\_MEMORY\_TESTS cmake option (#356) - fix copyright (#363) - remove old doxygen target (#365) - fix some gcc10 warnings (#376) - Add external fields to dft calculations (#351, #353) - added def2 and cc basis sets (#355) - added apdft (#350) - added test to cubefile reader (#344) - fix state tracker (#333) - grid class refator (#335) - changed ppm screening (#371) Version 1.6\_rc1 (released 04.12.19) ==================================== - completely new statefile in hdf5 format for larger systems - new electrostatics with PCG solver - new QM/MM engine with freely configurable regions - exact GW-BSE for small systems - new iterative matrix solvers for large systems - CUDA support for parts of GW-BSE - full LAMMPS support - improved testing - new tutorial with more functionality - deleted netbeans support - removed old manual - Major CMake refactor Version 1.5.1 (released 20.11.19) ================================= - remove exit() calls in the library - fix build on CentOs7 Version 1.5 *SuperVictor* (released 31.01.19) ============================================= - enable gitlab CI Version 1.5\_rc3 (released 19.01.19) ==================================== - travis: fixed bug in building tags Version 1.5\_rc2 (released 16.01.19) ==================================== - fix parallel build of manual - fix usage on inkscape on arm arch - clean up namespace in header Version 1.5\_rc1 (released 28.12.18) ==================================== - optimized GW-BSE code and integral engine - added closed shell DFT code which supports hybrid functionals - removed ctp dependency - atm no support for site energy calculation - CHELPG fit for ground and excited states - merged igwbse and idft into one calculator - added unit and integration test - improved geometry optimiser - replaced ublas with Eigen3 - replaced boost serialisation with hdf5 files Version 1.4.1 (released 02.09.17) ================================= - fix pkg-config file Version 1.4 (released 29.10.16) =============================== - fixed a bug in gwbse - added missing copyright - cmake: fixed underlinking Version 1.4\_rc1 (released 26.09.16) ==================================== - include manual - an extension of the whole workflow from: electrons and holes, to singlet and triplet excitons - a fully functional GW-BSE code optimized for: molecular properties, including excited state geometry optimizsation - Inclusion of LIBXC to calculate Exchange correlation matrices - allowing interfacing GW-BSE with many quantum mechanical packages - support for ORCA DFT package - framework to use stochastic models to generate larger system - better performance of larger systems - new calculators: egwbse,igwbse,ewald,..... - support for intel mkl library and compilers for better performance - A periodic polarisation embedding: to calculate classical configuration energies without cutoffs - xtp\_update\_exciton to update state file to newest format - integration of moo and kmc into xtp for easier installation - kmc\_lifetime calculator to simulate exciton movement with lifetimes - partialcharges to extract atomic charges from qm calculation - renaming from ctp to xtp - many bugfixes Version 1.3 (released XX.09.15) =============================== - new executables: ctp\_tools, ctp\_dump, ctp\_parallel, xtp\_testsuite, xtp\_update - ctp\_tools wraps light-weight tools that assist e.g. in generating the system mapping file - ctp\_dump extracts information from the state file to human-readable format - ctp\_parallel wraps heavy-duty job-based calculators: allows synchronization across processes - ctp\_testsuite provides an easy-to-use environment to run: selected tests, individual calculators - ctp\_update updates an existent state file to the current version - new calculators: edft, idft, pdb2map, xqmultipole, ... - edft / idft: provide interfaces to the GAUSSIAN, TURBOMOLE & NWCHEM package, using packages computes: couplings, internal energies, partial charges - pdb2map (generates a system mapping file from an input coordinate file) - xqmultipole computes classical configuration energies of: charged clusters embedded in a molecular environment - enhanced usability via the command-line help, tutorial & test-suite - a GUI tutorial assists with the first practical steps in using VOTCA-CTP - an extended and homogenized help system provides: short infos on individual calculator options from the command line Version 1.0 (released 23.10.11) =============================== - parallel evaluation of site energies using: Thole model + GDMA - Tinker no longer required - much clearer input files (and many more checks for input errors) - most of calculators are parallel and can be used on a cluster - bug in zindo/ctp interface fixed - state file now contains: the atomistic trajectory, rigid fragments, conjugated segments - support for several MD frames xtp-2021.2/CMakeLists.txt000066400000000000000000000150101412152066400151510ustar00rootroot00000000000000cmake_minimum_required(VERSION 3.12) project(votca-xtp LANGUAGES CXX) set(PROJECT_VERSION "2021.2") string(REGEX REPLACE "[-.].*$" "" SOVERSION "${PROJECT_VERSION}") if (NOT ${SOVERSION} MATCHES "^[0-9]+$") message(FATAL_ERROR "Could not determine SOVERSION (${SOVERSION}) from ${PROJECT_VERSION}") endif (NOT ${SOVERSION} MATCHES "^[0-9]+$") set(PROJECT_CONTACT "https://github.com/votca/xtp/issues") # Cmake modules/macros are in a subdirectory to keep this file cleaner set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules) if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) #Release comes with -O3 by default set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) if(CMAKE_BUILD_TYPE STREQUAL Debug) add_definitions(-DDEBUG) endif() ###################################################################### # compiler tests # these need ot be done early (before further tests). ##################################################################### include(FeatureSummary) include(CheckCXXCompilerFlag) set(CMAKE_CXX_STANDARD 14) set(CMAKE_CXX_STANDARD_REQUIRED ON) set(CMAKE_CXX_EXTENSIONS OFF) #...without compiler extensions like gnu++11 #openmp with clang smaller version 10 and user defined reductions is buggy https://bugs.llvm.org/show_bug.cgi?id=44134 if (NOT CMAKE_CXX_COMPILER_ID STREQUAL "Clang" OR CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0) find_package(OpenMP 4.5) set_package_properties(OpenMP PROPERTIES TYPE RECOMMENDED PURPOSE "Used for thread parallelization in xtp") else() # in case OpenMP was detected somewhere else unset(OpenMP_FOUND) endif() ######################################################################## # User input options # ######################################################################## find_package(PkgConfig REQUIRED) set_package_properties(PkgConfig PROPERTIES TYPE RECOMMENDED PURPOSE "Used to detect libxc and libint package") pkg_check_modules(LIBXC REQUIRED IMPORTED_TARGET libxc) if(NOT TARGET PkgConfig::LIBINT) pkg_check_modules(LIBINT REQUIRED IMPORTED_TARGET libint2>=2.6) endif() find_package(HDF5 1.8 REQUIRED COMPONENTS CXX) set_package_properties(HDF5 PROPERTIES TYPE REQUIRED PURPOSE "Used to read/write HDF5 data files") if(HDF5_VERSION VERSION_GREATER 1.8) message(WARNING "HDF5 will be used such that it is compatible with version 1.8.") endif() # https://github.com/votca/xtp/issues/436, hdf5-1.10.4 generates a implicitly-declared operator warning if(HDF5_VERSION VERSION_GREATER_EQUAL 1.10.4 AND HDF5_VERSION VERSION_LESS_EQUAL 1.10.6) include(CheckCXXCompilerFlag) check_cxx_compiler_flag("-Wno-deprecated-copy" COMPILER_SUPPORTS_WNO_DEPRECATED_COPY) if(COMPILER_SUPPORTS_WNO_DEPRECATED_COPY) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated-copy") endif() endif() option(BUILD_SHARED_LIBS "Build shared libs" ON) include(GNUInstallDirs) option(USE_CUDA "Use a Nvidia GPU to speed up computations" OFF) add_feature_info(USE_CUDA USE_CUDA "Use CUDA for GPU acceleration") option(ENABLE_TESTING "Build and enable testing stuff" OFF) add_feature_info(ENABLE_TESTING ENABLE_TESTING "Enable unit tests") if(ENABLE_TESTING) enable_testing() endif(ENABLE_TESTING) ######################################################################## #Find external packages ######################################################################## if(IS_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/.git) find_package(Git) set_package_properties(Git PROPERTIES TYPE OPTIONAL PURPOSE "Generated version for development version") endif(IS_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/.git) find_package(Boost 1.57.0 REQUIRED COMPONENTS program_options filesystem system timer) find_package(Eigen3 3.3.0 REQUIRED NO_MODULE) if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR) set_package_properties(Boost PROPERTIES TYPE REQUIRED PURPOSE "Extended C++ libraries") set_package_properties(Eigen3 PROPERTIES TYPE REQUIRED PURPOSE "C++ vector data structures") endif() message(STATUS "Found Eigen3: ${Eigen3_DIR}") option(BUILD_MANPAGES "Build manpages (might lead to problem on system without rpath" OFF) add_feature_info(BUILD_MANPAGES BUILD_MANPAGES "Build manpages (disable for cross-compile)") #define this target here, so that individual man pages can append to it. if(NOT TARGET manpages) add_custom_target(manpages ALL) endif() find_package(VOTCA_TOOLS REQUIRED NO_MODULE) set_package_properties(VOTCA_TOOLS PROPERTIES TYPE REQUIRED PURPOSE "Votca base library") if(DEFINED VOTCA_TOOLS_VERSION AND NOT VOTCA_TOOLS_VERSION STREQUAL PROJECT_VERSION) message(FATAL_ERROR "Incompatible VOTCA Tools version found (needed ${PROJECT_VERSION}, found ${VOTCA_TOOLS_VERSION})") endif() message(STATUS "Found VOTCA_TOOLS: ${VOTCA_TOOLS_DIR}") find_package(VOTCA_CSG REQUIRED NO_MODULE) set_package_properties(VOTCA_TOOLS PROPERTIES TYPE REQUIRED PURPOSE "Votca csg library") if(DEFINED VOTCA_CSG_VERSION AND NOT VOTCA_CSG_VERSION STREQUAL PROJECT_VERSION) message(FATAL_ERROR "Incompatible VOTCA CSG version found (needed ${PROJECT_VERSION}, found ${VOTCA_CSG_VERSION})") endif() message(STATUS "Found VOTCA_CSG: ${VOTCA_CSG_DIR}") if(USE_CUDA) find_package(CUDA REQUIRED) set_package_properties(CUDA PROPERTIES TYPE REQUIRED PURPOSE "Used for GPU acceleration") endif(USE_CUDA) ######################################################################## # Checks what linear algebra packages are installed # ######################################################################## ######################################################################## # Basic system tests (standard libraries, headers, functions, types) # ######################################################################## include(CheckIncludeFileCXX) foreach(HEADER algorithm) check_include_file_cxx(${HEADER} FOUND_${HEADER}) if(NOT FOUND_${HEADER}) message(FATAL_ERROR "Could not find needed header - ${HEADER}") endif(NOT FOUND_${HEADER}) endforeach(HEADER) set(MATH_LIBRARIES "m" CACHE STRING "math library") mark_as_advanced( MATH_LIBRARIES ) ###################################### # Include the following subdirectory # ###################################### add_subdirectory(include/votca/xtp) add_subdirectory(scripts) add_subdirectory(src) add_subdirectory(share) if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR) feature_summary(INCLUDE_QUIET_PACKAGES WHAT ALL) endif (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR) xtp-2021.2/CMakeModules/000077500000000000000000000000001412152066400147255ustar00rootroot00000000000000xtp-2021.2/CMakeModules/gitscript.cmake000066400000000000000000000022211412152066400177340ustar00rootroot00000000000000if (GIT_EXECUTABLE) # refresh git index execute_process(COMMAND ${GIT_EXECUTABLE} update-index -q --refresh WORKING_DIRECTORY ${TOP_SOURCE_DIR} TIMEOUT 5 OUTPUT_QUIET ERROR_VARIABLE EXEC_ERR OUTPUT_STRIP_TRAILING_WHITESPACE ) #later use git describe here execute_process( COMMAND ${GIT_EXECUTABLE} rev-parse --short HEAD WORKING_DIRECTORY ${TOP_SOURCE_DIR} OUTPUT_VARIABLE THIS_GIT_ID OUTPUT_STRIP_TRAILING_WHITESPACE) execute_process( COMMAND ${GIT_EXECUTABLE} diff-index --name-only HEAD WORKING_DIRECTORY ${TOP_SOURCE_DIR} OUTPUT_VARIABLE _HAS_CHANGES OUTPUT_STRIP_TRAILING_WHITESPACE ERROR_QUIET) if (NOT "${_HAS_CHANGES}" STREQUAL "") set(THIS_GIT_ID "${THIS_GIT_ID} (dirty)") endif() message("Current git revision is ${THIS_GIT_ID}") set(THIS_GIT_ID "gitid: ${THIS_GIT_ID}") else() set (THIS_GIT_ID) endif() file(READ ${INPUT} CONTENT) string(REGEX REPLACE "#CSG_GIT_ID#" "${THIS_GIT_ID}" NEW_CONTENT "${CONTENT}") file(WRITE "${OUTPUT}.tmp" "${NEW_CONTENT}") execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different ${OUTPUT}.tmp ${OUTPUT}) execute_process(COMMAND ${CMAKE_COMMAND} -E remove ${OUTPUT}.tmp) xtp-2021.2/CMakeModules/gitversion.cmake000066400000000000000000000022741412152066400201250ustar00rootroot00000000000000if (GIT_EXECUTABLE) # refresh git index execute_process(COMMAND ${GIT_EXECUTABLE} update-index -q --refresh WORKING_DIRECTORY ${TOP_SOURCE_DIR} TIMEOUT 5 OUTPUT_QUIET ERROR_VARIABLE EXEC_ERR OUTPUT_STRIP_TRAILING_WHITESPACE ) #later use git describe here execute_process( COMMAND ${GIT_EXECUTABLE} rev-parse --short HEAD WORKING_DIRECTORY ${TOP_SOURCE_DIR} OUTPUT_VARIABLE THIS_GIT_ID OUTPUT_STRIP_TRAILING_WHITESPACE) execute_process( COMMAND ${GIT_EXECUTABLE} diff-index --name-only HEAD WORKING_DIRECTORY ${TOP_SOURCE_DIR} OUTPUT_VARIABLE _HAS_CHANGES OUTPUT_STRIP_TRAILING_WHITESPACE ERROR_QUIET) if (NOT "${_HAS_CHANGES}" STREQUAL "") set(THIS_GIT_ID "${THIS_GIT_ID} (dirty)") endif() message("Current git revision is ${THIS_GIT_ID}") set(THIS_GIT_ID "gitid: ${THIS_GIT_ID}") else() set (THIS_GIT_ID) endif() set (GIT_HEADER "gitversion.h") set (NEW_GIT_HEADER "new_gitversion.h") file(WRITE ${NEW_GIT_HEADER} "#include\nstatic const std::string gitversion = \"${THIS_GIT_ID}\";\n") execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different ${NEW_GIT_HEADER} ${GIT_HEADER}) execute_process(COMMAND ${CMAKE_COMMAND} -E remove ${NEW_GIT_HEADER}) xtp-2021.2/CODE_OF_CONDUCT.rst000066400000000000000000000063431412152066400154310ustar00rootroot00000000000000Contributor Covenant Code of Conduct ==================================== Our Pledge ---------- In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation. Our Standards ------------- Examples of behavior that contributes to creating a positive environment include: - Using welcoming and inclusive language - Being respectful of differing viewpoints and experiences - Gracefully accepting constructive criticism - Focusing on what is best for the community - Showing empathy towards other community members Examples of unacceptable behavior by participants include: - The use of sexualized language or imagery and unwelcome sexual attention or advances - Trolling, insulting/derogatory comments, and personal or political attacks - Public or private harassment - Publishing others' private information, such as a physical or electronic address, without explicit permission - Other conduct which could reasonably be considered inappropriate in a professional setting Our Responsibilities -------------------- Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. Scope ----- This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers. Enforcement ----------- Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at votca@googlegroups.com. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership. Attribution ----------- This Code of Conduct is adapted from the `Contributor Covenant `__, version 1.4, available at `http://contributor-covenant.org/version/1/4 `__ xtp-2021.2/LICENSE.rst000066400000000000000000000246431412152066400142410ustar00rootroot00000000000000:: Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1. Definitions. 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See the License for the specific language governing permissions and limitations under the License. xtp-2021.2/NOTICE.rst000066400000000000000000000004471412152066400141340ustar00rootroot00000000000000Versatile Object-oriented Toolkit for Coarse-graining Applications Copyright 2009-2020 The VOTCA Development Team This product includes software developed at The VOTCA Development Team (http://www.votca.org). This software contains code, which was derived from VOTCA KMC, MOO and CTP project. xtp-2021.2/README.rst000066400000000000000000000060171412152066400141070ustar00rootroot00000000000000|Codacy Badge| |codecov| |CI| |DOI| VOTCA-XTP is a library which allows you to calculate the electronic properties of organic materials, e.g. - excited state properties via GW-BSE - spectra using QM/MM in conjunction with excited state treatment via GW-BSE - energetic disorder for electrons/holes and excitons via QM/MM or fast MM/MM multipole methods - electron and hole mobilities using electronic couplings and kinetic Monte-Carlo - electron, hole, singlet and triplet diffusion constants using electronic couplings and kinetic Monte-Carlo Installation instructions and developer information can be found `here `__ For other questions, we provide an email list: `google group `__ and a slack channel: `Slack `__ We have no manual for the moment but we have a complete tutorial here: `Tutorial `__ The development of VOTCA is mainly funded by academic research grants. If you use this package, please cite the VOTCA papers: - Excited-State Electronic Structure of Molecules Using Many-Body Green’s Functions: Quasiparticles and Electron-Hole Excitations with VOTCA-XTP. Gianluca Tirimbò, Vivek Sundaram, Onur Çaylak, Wouter Scharpach, Javier Sijen, Christoph Junghans, Joshua Brown, Felipe Zapata Ruiz, Nicolas Renaud, Jens Wehner, Björn Baumeier, J. Chem. Phys. 152, 114103 (2020). - Electronic Excitations in Complex Molecular Environments: Many-Body Green’s Functions Theory in VOTCA-XTP. Jens Wehner, Lothar Brombacher, Joshua Brown, Christoph Junghans, Onur Caylak, Yuriy Khalak, Pranav Madhikar, Gianluca Tirimbo, Björn Baumeier, J. Chem. Theory Comput. 14, 6353 (2018). - Microscopic simulations of charge transport in disordered organic semiconductors. V. Ruehle, A. Lukyanov, F. May, M. Schrader, T. Vehoff, J. Kirkpatrick, B. Baumeier and D. Andrienko, J. Chem. Theo. Comp. 7, 3335-3345 (2011). - Versatile Object-oriented Toolkit for Coarse-graining Applications. V.Ruehle, C. Junghans, A. Lukyanov, K. Kremer, D. Andrienko, J. Chem. Theo. Comp. 5 (12), 3211 (2009). In case of questions, please post them in the google discussion group for votca at http://groups.google.com/group/votca-xtp You can contact the VOTCA Development Team at devs@votca.org. .. |Codacy Badge| image:: https://app.codacy.com/project/badge/Grade/b9c7170d5c3440b7a2327a667cb1ec59 :target: https://www.codacy.com/gh/votca/xtp?utm_source=github.com&utm_medium=referral&utm_content=votca/xtp&utm_campaign=Badge_Grade .. |codecov| image:: https://codecov.io/gh/votca/xtp/branch/master/graph/badge.svg :target: https://codecov.io/gh/votca/xtp .. |CI| image:: https://github.com/votca/votca/workflows/CI/badge.svg?branch=master :target: https://github.com/votca/votca/actions?query=workflow%3ACI+branch%3Amaster .. |DOI| image:: https://zenodo.org/badge/50048374.svg :target: https://zenodo.org/badge/latestdoi/50048374 xtp-2021.2/include/000077500000000000000000000000001412152066400140375ustar00rootroot00000000000000xtp-2021.2/include/votca/000077500000000000000000000000001412152066400151535ustar00rootroot00000000000000xtp-2021.2/include/votca/xtp/000077500000000000000000000000001412152066400157665ustar00rootroot00000000000000xtp-2021.2/include/votca/xtp/CMakeLists.txt000066400000000000000000000003741412152066400205320ustar00rootroot00000000000000configure_file(votca_xtp_config.h.in ${CMAKE_CURRENT_BINARY_DIR}/votca_xtp_config.h) file(GLOB_RECURSE VOTCA_HEADERS *.h ${CMAKE_CURRENT_BINARY_DIR}/votca_xtp_config.h) install(FILES ${VOTCA_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/votca/xtp) xtp-2021.2/include/votca/xtp/ERIs.h000066400000000000000000000066561412152066400167560ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_ERIS_H #define VOTCA_XTP_ERIS_H // Local VOTCA includes #include "threecenter.h" namespace votca { namespace xtp { /** * \brief Takes a density matrix and and an auxiliary basis set and calculates * the electron repulsion integrals. * */ class ERIs { public: void Initialize(const AOBasis& dftbasis, const AOBasis& auxbasis); void Initialize_4c(const AOBasis& dftbasis); Eigen::MatrixXd CalculateERIs_3c(const Eigen::MatrixXd& DMAT) const; std::array CalculateERIs_EXX_3c( const Eigen::MatrixXd& occMos, const Eigen::MatrixXd& DMAT) const { std::array result; result[0] = CalculateERIs_3c(DMAT); if (occMos.rows() > 0 && occMos.cols() > 0) { assert(occMos.rows() == DMAT.rows() && "occMos.rows()==DMAT.rows()"); result[1] = CalculateEXX_mos(occMos); } else { result[1] = CalculateEXX_dmat(DMAT); } return result; } Eigen::MatrixXd CalculateERIs_4c(const Eigen::MatrixXd& DMAT, double error) const { return Compute4c(DMAT, error)[0]; } std::array CalculateERIs_EXX_4c( const Eigen::MatrixXd& DMAT, double error) const { return Compute4c(DMAT, error); } Index Removedfunctions() const { return _threecenter.Removedfunctions(); } static double CalculateEnergy(const Eigen::MatrixXd& DMAT, const Eigen::MatrixXd& matrix_operator) { return matrix_operator.cwiseProduct(DMAT).sum(); } private: std::vector basis_; std::vector starts_; std::vector> shellpairs_; std::vector> shellpairdata_; Index maxnprim_; Index maxL_; Eigen::MatrixXd CalculateEXX_dmat(const Eigen::MatrixXd& DMAT) const; Eigen::MatrixXd CalculateEXX_mos(const Eigen::MatrixXd& occMos) const; std::vector> ComputeShellPairData( const std::vector& basis, const std::vector>& shellpairs) const; Eigen::MatrixXd ComputeSchwarzShells(const AOBasis& dftbasis) const; Eigen::MatrixXd ComputeShellBlockNorm(const Eigen::MatrixXd& dmat) const; template std::array Compute4c(const Eigen::MatrixXd& dmat, double error) const; TCMatrix_dft _threecenter; Eigen::MatrixXd schwarzscreen_; // Square matrix containing for all // shells }; // namespace xtp } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ERIS_H xtp-2021.2/include/votca/xtp/GaussianQuadratureBase.h000066400000000000000000000041441412152066400225450ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_GAUSSIANQUADRATUREBASE_H #define VOTCA_XTP_GAUSSIANQUADRATUREBASE_H // Local VOTCA includes #include "eigen.h" #include namespace votca { namespace xtp { class GaussianQuadratureBase { public: GaussianQuadratureBase() = default; void configure(Index order) { FillPoints(); FillAdaptedWeights(); CheckOrder(order, _map_points); CheckOrder(order, _map_AdaptedWeights); points_ = _map_points[order]; weights_ = _map_AdaptedWeights[order]; } virtual ~GaussianQuadratureBase() = default; Index Order() const { return points_.size(); } template double Integrate(const F& f) const { double result = 0.0; for (Index j = 0; j < Order(); ++j) { result += ScaledWeight(j) * f(j, ScaledPoint(j), UseSymmetry()); } return result; } virtual double ScaledPoint(Index i) const = 0; virtual double ScaledWeight(Index i) const = 0; private: void CheckOrder(Index order, const std::map& map) const; protected: Eigen::VectorXd points_; Eigen::VectorXd weights_; std::map _map_points; std::map _map_AdaptedWeights; virtual bool UseSymmetry() const = 0; virtual void FillPoints() = 0; virtual void FillAdaptedWeights() = 0; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_GAUSSIANQUADRATUREBASE_H xtp-2021.2/include/votca/xtp/ImaginaryAxisIntegration.h000066400000000000000000000040361412152066400231130ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #ifndef VOTCA_XTP_IMAGINARYAXISINTEGRATION_H #define VOTCA_XTP_IMAGINARYAXISINTEGRATION_H #include "eigen.h" #include "quadrature_factory.h" #include "rpa.h" #include // Computes the contribution from the Gauss-Laguerre quadrature to the // self-energy expectation matrix for given RPA and frequencies namespace votca { namespace xtp { class ImaginaryAxisIntegration { public: struct options { Index order; Index qptotal; Index qpmin; Index homo; Index rpamin; Index rpamax; std::string quadrature_scheme; double alpha; }; ImaginaryAxisIntegration(const Eigen::VectorXd& energies, const TCMatrix_gwbse& Mmn); void configure(options opt, const RPA& rpa, const Eigen::MatrixXd& kDielMxInv_zero); double SigmaGQDiag(double frequency, Index gw_level, double eta) const; private: options _opt; std::unique_ptr _gq = nullptr; // This function calculates and stores inverses of the microscopic dielectric // matrix in a matrix vector void CalcDielInvVector(const RPA& rpa, const Eigen::MatrixXd& kDielMxInv_zero); const Eigen::VectorXd& _energies; std::vector _dielinv_matrices_r; const TCMatrix_gwbse& _Mmn; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_IMAGINARYAXISINTEGRATION_H xtp-2021.2/include/votca/xtp/IndexParser.h000066400000000000000000000025261412152066400203700ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_INDEXPARSER_H #define VOTCA_XTP_INDEXPARSER_H // Standard includes #include #include // VOTCA includes #include /** * \brief Parser to read strings containing indexes in the format "1 2:7 8" * and returning a sorted expanded std::vector with only unique entries * It can also do the opposite */ namespace votca { namespace xtp { class IndexParser { public: std::vector CreateIndexVector(const std::string& Ids) const; std::string CreateIndexString(const std::vector& indeces) const; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_INDEXPARSER_H xtp-2021.2/include/votca/xtp/adiis.h000066400000000000000000000022751412152066400172360ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_ADIIS_H #define VOTCA_XTP_ADIIS_H // Standard includes #include #include // Local VOTCA includes #include "eigen.h" namespace votca { namespace xtp { class ADIIS { public: Eigen::VectorXd CalcCoeff(const std::vector& dmathist, const std::vector& mathist); bool Info() { return success; } private: bool success = true; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ADIIS_H xtp-2021.2/include/votca/xtp/adiis_costfunction.h000066400000000000000000000043471412152066400220360ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_ADIIS_COSTFUNCTION_H #define VOTCA_XTP_ADIIS_COSTFUNCTION_H // Local VOTCA includes #include "optimiser_costfunction.h" namespace votca { namespace xtp { class ADIIS_costfunction : public Optimiser_costfunction { public: ADIIS_costfunction(Eigen::VectorXd DiF, Eigen::MatrixXd DiFj) { _DiF = DiF; _DiFj = DiFj; } double EvaluateCost(const Eigen::VectorXd& parameters) override { Eigen::VectorXd c = parameters.cwiseAbs2(); double xnorm = c.sum(); c /= xnorm; return (2 * c.transpose() * _DiF + c.transpose() * _DiFj * c).value(); } Eigen::VectorXd EvaluateGradient(const Eigen::VectorXd& parameters) override { Eigen::VectorXd c = parameters.cwiseAbs2(); double xnorm = c.sum(); c /= xnorm; Eigen::VectorXd dEdc = 2.0 * _DiF + _DiFj * c + _DiFj.transpose() * c; Eigen::MatrixXd jac = Eigen::MatrixXd::Zero(c.size(), c.size()); for (Index i = 0; i < jac.rows(); i++) { for (Index j = 0; j < jac.cols(); j++) { jac(i, j) = -c(i) * 2.0 * parameters(j) / xnorm; } // Extra term on diagonal jac(i, i) += 2.0 * parameters(i) / xnorm; } return jac.transpose() * dEdc; } Index NumParameters() const override { return Index(_DiF.size()); } bool Converged(const Eigen::VectorXd&, double, const Eigen::VectorXd& gradient) override { return gradient.cwiseAbs().maxCoeff() < 1.e-7; } private: Eigen::VectorXd _DiF; Eigen::MatrixXd _DiFj; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ADIIS_COSTFUNCTION_H xtp-2021.2/include/votca/xtp/amplitude_integration.h000066400000000000000000000024601412152066400225300ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_AMPLITUDE_INTEGRATION_H #define VOTCA_XTP_AMPLITUDE_INTEGRATION_H // Local VOTCA includes #include "aobasis.h" #include "eigen.h" #include "regular_grid.h" namespace votca { namespace xtp { template class AmplitudeIntegration { public: explicit AmplitudeIntegration(const Grid& grid) : _grid(grid){}; std::vector > IntegrateAmplitude( const Eigen::VectorXd& amplitude); private: std::vector > SetupAmplitudeContainer(); const Grid _grid; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_AMPLITUDE_INTEGRATION_H xtp-2021.2/include/votca/xtp/anderson_mixing.h000066400000000000000000000035761412152066400213360ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_ANDERSON_MIXING_H #define VOTCA_XTP_ANDERSON_MIXING_H // Standard includes #include // Local VOTCA includes #include "eigen.h" namespace votca { namespace xtp { /** * \brief Anderson mixing as convergence acceleration in SCF/fixed point * problems * * Keeps a history of input and output solution vectors during a self-consistent * fixed-point procedure and determines a new solution from an optimized mixing. * Requires specification of the order of the method (maximum history to take) * and a mixing parameter. * * B. Baumeier, Diploma Thesis, Appendix C (2005) * * I. Ramiere and T. Helfer, Iterative Residual-Based Vector Methods to * Accelerate Fixed Point Iterations, Comput. Math. Appl. 70, 2210 (2015) */ class Anderson { public: const Eigen::VectorXd MixHistory(); void UpdateOutput(const Eigen::VectorXd &newOutput); void UpdateInput(const Eigen::VectorXd &newInput); void Configure(const Index order, const double alpha); private: std::vector _input; std::vector _output; double _alpha = 0.7; Index _order = 25; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ANDERSON_MIXING_H xtp-2021.2/include/votca/xtp/aobasis.h000066400000000000000000000050341412152066400175620ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_AOBASIS_H #define VOTCA_XTP_AOBASIS_H // Local VOTCA includes #include "aoshell.h" #include "checkpoint.h" #include "eigen.h" #include namespace votca { namespace xtp { class QMMolecule; class BasisSet; /** * \brief Container to hold Basisfunctions for all atoms * * It is constructed from a QMMolecule and a BasisSet. */ class AOBasis { public: void Fill(const BasisSet& bs, const QMMolecule& atoms); Index AOBasisSize() const { return _AOBasisSize; } using AOShellIterator = std::vector::const_iterator; AOShellIterator begin() const { return _aoshells.begin(); } AOShellIterator end() const { return _aoshells.end(); } const AOShell& getShell(Index idx) const { return _aoshells[idx]; } const std::vector getShellsofAtom(Index AtomId) const; Index getNumofShells() const { return Index(_aoshells.size()); } Index getMaxNprim() const; Index getMaxL() const; std::vector getMapToBasisFunctions() const; const std::vector& getFuncPerAtom() const { return _FuncperAtom; } std::vector GenerateLibintBasis() const; std::vector> ComputeShellPairs( double threshold = 1e-20) const; AOShell& addShell(const Shell& shell, const QMAtom& atom, Index startIndex); const std::string& Name() const { return _name; } void UpdateShellPositions(const QMMolecule& mol); void WriteToCpt(CheckpointWriter& w) const; void ReadFromCpt(CheckpointReader& r); void add(const AOBasis& other); friend std::ostream& operator<<(std::ostream& out, const AOBasis& aobasis); private: void FillFuncperAtom(); void clear(); std::string _name = ""; std::vector _aoshells; std::vector _FuncperAtom; Index _AOBasisSize; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_AOBASIS_H xtp-2021.2/include/votca/xtp/aomatrix.h000066400000000000000000000063331412152066400177700ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_AOMATRIX_H #define VOTCA_XTP_AOMATRIX_H // Local VOTCA includes #include "aobasis.h" namespace votca { namespace xtp { class AOMatrix { public: virtual void Fill(const AOBasis& aobasis) = 0; virtual Index Dimension() = 0; using MatrixLibInt = Eigen::Matrix; }; // derived class for kinetic energy class AOKinetic : public AOMatrix { public: void Fill(const AOBasis& aobasis) final; Index Dimension() final { return _aomatrix.rows(); } const Eigen::MatrixXd& Matrix() const { return _aomatrix; } private: Eigen::MatrixXd _aomatrix; }; // derived class for atomic orbital overlap class AOOverlap : public AOMatrix { public: void Fill(const AOBasis& aobasis) final; Index Dimension() final { return _aomatrix.rows(); } const Eigen::MatrixXd& Matrix() const { return _aomatrix; } Eigen::MatrixXd singleShellOverlap(const AOShell& shell) const; Index Removedfunctions() const { return removedfunctions; } double SmallestEigenValue() const { return smallestEigenvalue; } Eigen::MatrixXd Pseudo_InvSqrt(double etol); Eigen::MatrixXd Sqrt(); private: Index removedfunctions; double smallestEigenvalue; Eigen::MatrixXd _aomatrix; }; // derived class for atomic orbital Coulomb interaction class AOCoulomb : public AOMatrix { public: void Fill(const AOBasis& aobasis) final; Index Dimension() final { return _aomatrix.rows(); } const Eigen::MatrixXd& Matrix() const { return _aomatrix; } Eigen::MatrixXd Pseudo_InvSqrt_GWBSE(const AOOverlap& auxoverlap, double etol); Eigen::MatrixXd Pseudo_InvSqrt(double etol); Index Removedfunctions() const { return removedfunctions; } private: void computeCoulombIntegrals(const AOBasis& aobasis); Index removedfunctions; Eigen::MatrixXd _aomatrix; }; /* derived class for atomic orbital electrical dipole matrices, required for * electrical transition dipoles */ class AODipole : public AOMatrix { public: void Fill(const AOBasis& aobasis) final; Index Dimension() final { return _aomatrix[0].rows(); } const std::array& Matrix() const { return _aomatrix; } void setCenter(const Eigen::Vector3d& r) { for (Index i = 0; i < 3; i++) { _r[i] = r[i]; } } // definition of a center around which the moment should be calculated private: std::array _aomatrix; std::array _r = {0, 0, 0}; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_AOMATRIX_H xtp-2021.2/include/votca/xtp/aopotential.h000066400000000000000000000074301412152066400204620ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_AOPOTENTIAL_H #define VOTCA_XTP_AOPOTENTIAL_H // Local VOTCA includes #include "aobasis.h" #include "ecpaobasis.h" #include "staticsite.h" namespace votca { namespace xtp { class QMMolecule; // base class for 1D atomic orbital matrix types (overlap, Coulomb, ESP) template class AOPotential { public: Index Dimension() { return _aopotential.rows(); } const Eigen::Matrix& Matrix() const { return _aopotential; } protected: Eigen::Matrix Fill( const AOBasis& aobasis) const; virtual void FillBlock( Eigen::Block>& matrix, const AOShell& shell_row, const AOShell& shell_col) const = 0; Eigen::Matrix _aopotential; }; // derived class for Effective Core Potentials class AOECP : public AOPotential { public: void FillPotential(const AOBasis& aobasis, const ECPAOBasis& ecp); protected: void FillBlock(Eigen::Block& matrix, const AOShell& shell_row, const AOShell& shell_col) const override; private: Eigen::VectorXd ExpandContractions(const AOGaussianPrimitive& gaussian, const AOShell& shell) const; void setECP(const ECPAOBasis* ecp) { _ecp = ecp; } const ECPAOBasis* _ecp; Eigen::MatrixXd calcVNLmatrix( Index lmax_ecp, const Eigen::Vector3d& posC, const AOGaussianPrimitive& g_row, const AOGaussianPrimitive& g_col, const Eigen::Matrix& power_ecp, const Eigen::Matrix& gamma_ecp, const Eigen::Matrix& pref_ecp) const; void getBLMCOF(Index lmax_ecp, Index lmax_dft, const Eigen::Vector3d& pos, Eigen::Tensor& BLC, Eigen::Tensor& C) const; Eigen::VectorXd CalcNorms(double decay, Index size) const; Eigen::VectorXd CalcInt_r_exp(Index nmax, double decay) const; }; class AOMultipole : public AOPotential { public: void FillPotential(const AOBasis& aobasis, const QMMolecule& atoms); void FillPotential(const AOBasis& aobasis, const Eigen::Vector3d& r); void FillPotential( const AOBasis& aobasis, const std::vector>& externalsites); protected: void FillBlock(Eigen::Block& matrix, const AOShell& shell_row, const AOShell& shell_col) const override; private: void setSite(const StaticSite* site) { _site = site; }; const StaticSite* _site; }; class AOPlanewave : public AOPotential> { public: void FillPotential(const AOBasis& aobasis, const std::vector& kpoints); protected: void FillBlock(Eigen::Block& matrix, const AOShell& shell_row, const AOShell& shell_col) const override; private: void setkVector(const Eigen::Vector3d& k) { _k = k; }; Eigen::Vector3d _k; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_AOPOTENTIAL_H xtp-2021.2/include/votca/xtp/aoshell.h000066400000000000000000000114161412152066400175710ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_AOSHELL_H #define VOTCA_XTP_AOSHELL_H // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "basisset.h" #include "eigen.h" #include "qmatom.h" // include libint last otherwise it overrides eigen #include namespace votca { namespace xtp { class AOShell; class AOBasis; class AOGaussianPrimitive { friend AOShell; public: AOGaussianPrimitive(const GaussianPrimitive& gaussian, const AOShell& aoshell); AOGaussianPrimitive(const AOGaussianPrimitive& gaussian, const AOShell& aoshell); struct data { Index atomid; Index l; Index startindex; double decay; double contraction; double x; double y; double z; double scale; }; AOGaussianPrimitive(const AOGaussianPrimitive::data& d, const AOShell& aoshell) : _aoshell(aoshell) { _decay = d.decay; _contraction = d.contraction; _powfactor = CalcPowFactor(_decay); } void SetupCptTable(CptTable& table) const; void WriteData(data& d) const; double getPowfactor() const { return _powfactor; } double getDecay() const { return _decay; } double getContraction() const { return _contraction; } const AOShell& getShell() const { return _aoshell; } private: static double CalcPowFactor(double decay) { return std::pow(2.0 * decay / boost::math::constants::pi(), 0.75); } double _decay; double _contraction; const AOShell& _aoshell; double _powfactor; // used in evalspace to speed up DFT }; /* * shells in a Gaussian-basis expansion */ class AOShell { friend AOBasis; public: AOShell(const Shell& shell, const QMAtom& atom, Index startIndex); AOShell(const AOGaussianPrimitive::data& d) { _l = static_cast(d.l); _scale = d.scale; _startIndex = d.startindex; _atomindex = d.atomid; _pos = Eigen::Vector3d(d.x, d.y, d.z); _gaussians.push_back(AOGaussianPrimitive(d, *this)); } AOShell(const AOShell& shell); L getL() const { return _l; } Index getNumFunc() const { return NumFuncShell(_l); }; Index getCartesianNumFunc() const { return NumFuncShell_cartesian(_l); }; Index getStartIndex() const { return _startIndex; } Index getOffset() const { return OffsetFuncShell(_l); } Index getCartesianOffset() const { return OffsetFuncShell_cartesian(_l); } Index getAtomIndex() const { return _atomindex; } Index getSize() const { return _gaussians.size(); } libint2::Shell LibintShell() const; const Eigen::Vector3d& getPos() const { return _pos; } double getScale() const { return _scale; } void CalcMinDecay() { _mindecay = std::numeric_limits::max(); for (auto& gaussian : _gaussians) { _mindecay = std::min(_mindecay, gaussian.getDecay()); } } double getMinDecay() const { return _mindecay; } void EvalAOspace(Eigen::VectorBlock& AOvalues, const Eigen::Vector3d& grid_pos) const; void EvalAOspace(Eigen::VectorBlock& AOvalues, Eigen::Block& AODervalues, const Eigen::Vector3d& grid_pos) const; // iterator over pairs (decay constant; contraction coefficient) using GaussianIterator = std::vector::const_iterator; GaussianIterator begin() const { return _gaussians.begin(); } GaussianIterator end() const { return _gaussians.end(); } // adds a Gaussian void addGaussian(const GaussianPrimitive& gaussian) { _gaussians.push_back(AOGaussianPrimitive(gaussian, *this)); return; } void normalizeContraction(); friend std::ostream& operator<<(std::ostream& out, const AOShell& shell); private: L _l; // scaling factor double _scale; // number of functions in shell double _mindecay; Index _startIndex; Eigen::Vector3d _pos; Index _atomindex; // vector of pairs of decay constants and contraction coefficients std::vector _gaussians; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_AOSHELL_H xtp-2021.2/include/votca/xtp/aotransform.h000066400000000000000000000065771412152066400205110ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_AOTRANSFORM_H #define VOTCA_XTP_AOTRANSFORM_H // Local VOTCA includes #include "aoshell.h" #include "eigen.h" namespace votca { namespace xtp { // clang-format off //clang format puts one entry on each line namespace Cart{ enum Cart { s, // s x, y, z, // p xx, xy, xz, yy, yz, zz, // d xxx, xxy, xxz, xyy, xyz, xzz, yyy, yyz, yzz, zzz, // f xxxx, xxxy, xxxz, xxyy, xxyz, xxzz, xyyy, xyyz, xyzz, xzzz, yyyy, yyyz, yyzz, yzzz, zzzz, // g xxxxx, xxxxy, xxxxz, xxxyy, xxxyz, xxxzz, xxyyy, xxyyz, xxyzz, xxzzz, xyyyy, xyyyz, xyyzz, xyzzz, xzzzz, yyyyy, yyyyz, yyyzz, yyzzz, yzzzz, zzzzz, // h xxxxxx, xxxxxy, xxxxxz, xxxxyy, xxxxyz, xxxxzz, xxxyyy, xxxyyz, xxxyzz, xxxzzz, xxyyyy, xxyyyz, xxyyzz, xxyzzz, xxzzzz, xyyyyy, xyyyyz, xyyyzz, xyyzzz, xyzzzz, xzzzzz, yyyyyy, yyyyyz, yyyyzz, yyyzzz, yyzzzz, yzzzzz, zzzzzz, //i xxxxxxx, xxxxxxy, xxxxxxz, xxxxxyy, xxxxxyz, xxxxxzz, xxxxyyy, xxxxyyz, xxxxyzz, xxxxzzz, xxxyyyy, xxxyyyz, xxxyyzz, xxxyzzz, xxxzzzz, xxyyyyy, xxyyyyz, xxyyyzz, xxyyzzz, xxyzzzz, xxzzzzz, xyyyyyy, xyyyyyz, xyyyyzz, xyyyzzz, xyyzzzz, xyzzzzz, xzzzzzz, yyyyyyy, yyyyyyz, yyyyyzz, yyyyzzz, yyyzzzz, yyzzzzz, yzzzzzz, zzzzzzz, //j xxxxxxxx, xxxxxxxy, xxxxxxxz, xxxxxxyy, xxxxxxyz, xxxxxxzz, xxxxxyyy, xxxxxyyz, xxxxxyzz, xxxxxzzz, xxxxyyyy, xxxxyyyz, xxxxyyzz, xxxxyzzz, xxxxzzzz, xxxyyyyy, xxxyyyyz, xxxyyyzz, xxxyyzzz, xxxyzzzz, xxxzzzzz, xxyyyyyy, xxyyyyyz, xxyyyyzz, xxyyyzzz, xxyyzzzz, xxyzzzzz, xxzzzzzz, xyyyyyyy, xyyyyyyz, xyyyyyzz, xyyyyzzz, xyyyzzzz, xyyzzzzz, xyzzzzzz, xzzzzzzz, yyyyyyyy, yyyyyyyz, yyyyyyzz, yyyyyzzz, yyyyzzzz, yyyzzzzz, yyzzzzzz, yzzzzzzz, zzzzzzzz, //k }; } // clang-format on /* contains cartesian to spherical conversion */ class AOTransform { public: static std::array n_orbitals(); static std::array nx(); static std::array ny(); static std::array nz(); static std::array i_less_x(); static std::array i_less_y(); static std::array i_less_z(); static std::array i_more_x(); static std::array i_more_y(); static std::array i_more_z(); static Index getBlockSize(Index lmax); static Eigen::VectorXd XIntegrate(Index size, double U); static double getNorm(L l, const AOGaussianPrimitive& gaussian); /// transforms a cartesian shell to a spherical cartesian shell template static Matrix tform(L l_row, L l_col, const Matrix& cartesian); }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_AOTRANSFORM_H xtp-2021.2/include/votca/xtp/atom.h000066400000000000000000000051771412152066400171110ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ /// For earlier commit history see ctp commit /// 77795ea591b29e664153f9404c8655ba28dc14e9 #pragma once #ifndef VOTCA_XTP_ATOM_H #define VOTCA_XTP_ATOM_H // Standard includes #include #include #include // Local VOTCA includes #include "checkpointreader.h" #include "checkpointwriter.h" namespace votca { namespace xtp { class Atom { public: struct data { Index id; char* element; char* name; double x; double y; double z; Index resnr; }; Atom(Index resnr, std::string md_atom_name, Index atom_id, Eigen::Vector3d pos, std::string element); Atom(Index atom_id, std::string element, Eigen::Vector3d pos); Atom(data& d) { ReadData(d); } static std::string GetElementFromString(const std::string& MDName); Index getId() const { return _id; } const std::string& getName() const { return _name; } std::string getElement() const { return _element; } Index getResnr() const { return _resnr; } void setResnr(Index resnr) { _resnr = resnr; } void Translate(const Eigen::Vector3d& shift) { _pos = _pos + shift; } void Rotate(const Eigen::Matrix3d& R, const Eigen::Vector3d& refPos); const Eigen::Vector3d& getPos() const { return _pos; } void setPos(const Eigen::Vector3d& r) { _pos = r; } std::string identify() const { return "atom"; } friend std::ostream& operator<<(std::ostream& out, const Atom& atom) { out << atom.getId() << " " << atom.getName() << " " << atom.getElement() << " " << atom.getResnr(); out << " " << atom.getPos().x() << "," << atom.getPos().y() << "," << atom.getPos().z() << "\n"; return out; } void SetupCptTable(CptTable& table) const; void WriteData(data& d) const; void ReadData(const data& d); private: Index _id = -1; std::string _name = ""; std::string _element = ""; Index _resnr = -1; Eigen::Vector3d _pos = Eigen::Vector3d::Zero(); }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ATOM_H xtp-2021.2/include/votca/xtp/atomcontainer.h000066400000000000000000000127351412152066400210120ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_ATOMCONTAINER_H #define VOTCA_XTP_ATOMCONTAINER_H // Standard includes #include #include // VOTCA includes #include // Local VOTCA includes #include "checkpoint.h" #include "eigen.h" /** * \brief Basic Container for QMAtoms,PolarSites and Atoms * * * */ namespace votca { namespace xtp { template class AtomContainer { public: AtomContainer(std::string type, Index id) : _type(type), _id(id){}; AtomContainer(CheckpointReader& r) { this->ReadFromCpt(r); } virtual ~AtomContainer() = default; using iterator = typename std::vector::iterator; const std::string& getType() const { return _type; } void setType(std::string type) { _type = type; } Index getId() const { return _id; } Index size() const { return _atomlist.size(); } void push_back(const T& atom) { _atomlist.push_back(atom); calcPos(); } void push_back(T&& atom) { _atomlist.push_back(atom); calcPos(); } const T& at(Index index) const { return _atomlist.at(index); } T& at(Index index) { return _atomlist.at(index); } const T& operator[](Index index) const { return _atomlist[index]; } T& operator[](Index index) { return _atomlist[index]; } typename std::vector::iterator begin() { return _atomlist.begin(); } typename std::vector::iterator end() { return _atomlist.end(); } typename std::vector::const_iterator begin() const { return _atomlist.begin(); } typename std::vector::const_iterator end() const { return _atomlist.end(); } const Eigen::Vector3d& getPos() const { return _pos; } // calculates the lowest and highest point in the cube, sorrounding the // molecule std::pair CalcSpatialMinMax() const { std::pair result; Eigen::Vector3d min = std::numeric_limits::max() * Eigen::Vector3d::Ones(); Eigen::Vector3d max = std::numeric_limits::min() * Eigen::Vector3d::Ones(); for (const T& atom : _atomlist) { const Eigen::Vector3d& pos = atom.getPos(); if (pos.x() < min.x()) { min.x() = pos.x(); } if (pos.x() > max.x()) { max.x() = pos.x(); } if (pos.y() < min.y()) { min.y() = pos.y(); } if (pos.y() > max.y()) { max.y() = pos.y(); } if (pos.z() < min.z()) { min.z() = pos.z(); } if (pos.z() > max.z()) { max.z() = pos.z(); } } result.first = min; result.second = max; return result; } std::vector FindUniqueElements() const { std::vector result; for (const T& atom : _atomlist) { if (std::find(result.begin(), result.end(), atom.getElement()) == result.end()) { result.push_back(atom.getElement()); } } return result; } void Translate(const Eigen::Vector3d& shift) { for (T& atom : _atomlist) { atom.Translate(shift); } _pos += shift; } void Rotate(const Eigen::Matrix3d& R, const Eigen::Vector3d& ref_pos) { for (T& atom : _atomlist) { atom.Rotate(R, ref_pos); } calcPos(); } virtual void WriteToCpt(CheckpointWriter& w) const { w(_type, "type"); w(_id, "id"); w(int(_atomlist.size()), "size"); T element(0, "H", Eigen::Vector3d::Zero()); CptTable table = w.openTable(element.identify() + "s", element, _atomlist.size()); std::vector dataVec(_atomlist.size()); for (std::size_t i = 0; i < _atomlist.size(); ++i) { _atomlist[i].WriteData(dataVec[i]); } table.write(dataVec); } virtual void ReadFromCpt(CheckpointReader& r) { r(_type, "type"); r(_id, "id"); Index size = 0; r(size, "size"); if (size == 0) { return; } T element(0, "H", Eigen::Vector3d::Zero()); // dummy element to get // .identify for type CptTable table = r.openTable(element.identify() + "s", element); _atomlist.clear(); _atomlist.reserve(table.numRows()); std::vector dataVec(table.numRows()); table.read(dataVec); for (std::size_t i = 0; i < table.numRows(); ++i) { _atomlist.push_back(T(dataVec[i])); } calcPos(); } void calcPos() { tools::Elements element; Eigen::Vector3d pos = Eigen::Vector3d::Zero(); double totalmass = 0.0; for (const T& atom : _atomlist) { double mass = element.getMass(atom.getElement()); totalmass += mass; pos += mass * atom.getPos(); } _pos = pos / totalmass; } protected: std::vector _atomlist; std::string _type; Index _id; private: Eigen::Vector3d _pos = Eigen::Vector3d::Zero(); }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ATOMCONTAINER_H xtp-2021.2/include/votca/xtp/basisset.h000066400000000000000000000100311412152066400177470ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_BASISSET_H #define VOTCA_XTP_BASISSET_H // Standard includes #include #include #include #include #include // VOTCA includes #include namespace votca { namespace xtp { enum class L { S = 0, P = 1, D = 2, F = 3, G = 4, H = 5, I = 6 }; std::string EnumToString(L l); L StringToEnum(const std::string& type); L StringToEnum(char type); // shell type (S, P, D)) bool CheckShellType(const std::string& shelltype); Index OffsetFuncShell(L l); Index NumFuncShell(L l); Index NumFuncShell_cartesian(L l); Index OffsetFuncShell_cartesian(L l); // Gaussian function: contraction*exp(-decay*r^2) class GaussianPrimitive { public: GaussianPrimitive(double decay, double contraction) : _decay(decay), _contraction(contraction) {} double contraction() const { return _contraction; } double decay() const { return _decay; } private: double _decay; double _contraction; }; class Shell { public: Shell(L l, double scale) : _l(l), _scale(scale) { ; } L getL() const { return _l; } Index getnumofFunc() const { return NumFuncShell(_l); }; Index getOffset() const { return OffsetFuncShell(_l); } double getScale() const { return _scale; } Index getSize() const { return _gaussians.size(); } std::vector::const_iterator begin() const { return _gaussians.begin(); } std::vector::const_iterator end() const { return _gaussians.end(); } // adds a Gaussian GaussianPrimitive& addGaussian(double decay, double contraction); friend std::ostream& operator<<(std::ostream& out, const Shell& shell); private: L _l; // scaling factor double _scale; // vector of pairs of decay constants and contraction coefficients std::vector _gaussians; }; /* * A collection of shells associated with a specific element */ class Element { public: Element(std::string type) : _type(type) { ; } using ShellIterator = std::vector::const_iterator; ShellIterator begin() const { return _shells.begin(); } ShellIterator end() const { return _shells.end(); } const std::string& getType() const { return _type; } Shell& addShell(L l, double shellScale) { _shells.push_back(Shell(l, shellScale)); return _shells.back(); } Index NumOfShells() const { return _shells.size(); } friend std::ostream& operator<<(std::ostream& out, const Element& element); private: std::string _type; std::vector _shells; }; /* * A collection of elements and shells forms the basis set */ class BasisSet { public: void Load(const std::string& name); const Element& getElement(std::string element_type) const; std::map::iterator begin() { return _elements.begin(); } std::map::iterator end() { return _elements.end(); } std::map::const_iterator begin() const { return _elements.begin(); } std::map::const_iterator end() const { return _elements.end(); } friend std::ostream& operator<<(std::ostream& out, const BasisSet& basis); const std::string& Name() const { return _name; } private: Element& addElement(std::string elementType); std::string _name; std::map _elements; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_BASISSET_H xtp-2021.2/include/votca/xtp/bfgs_trm.h000066400000000000000000000054011412152066400177420ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_BFGS_TRM_H #define VOTCA_XTP_BFGS_TRM_H // Standard includes #include #include // Local VOTCA includes #include "logger.h" #include "optimiser_costfunction.h" namespace votca { namespace xtp { class BFGSTRM { public: BFGSTRM(Optimiser_costfunction& costfunction) : _costfunction(costfunction) { _hessian = Eigen::MatrixXd::Identity(costfunction.NumParameters(), costfunction.NumParameters()); } void setLog(Logger* pLog) { _pLog = pLog; } void setTrustRadius(double trust_radius) { _trust_radius = trust_radius; } double getTrustRadius() const { return _trust_radius; } void setCallbacks(const std::vector >& callbacks) { _callbacks = callbacks; } void setNumofIterations(Index iterations) { _max_iteration = iterations; } void Optimize(const Eigen::VectorXd& initialparameters); bool Success() const { return _success; } std::string getErrorMessage() const { return _errormessage; } double getCost() const { return _cost; } Index getIteration() const { return _iteration; } const Eigen::VectorXd getParameters() const { return _parameters; } void setInitialHessian(const Eigen::MatrixXd& hessian) { _hessian = hessian; } private: Optimiser_costfunction& _costfunction; void UpdateHessian(const Eigen::VectorXd& delta_pos, const Eigen::VectorXd& delta_gradient); double QuadraticEnergy(const Eigen::VectorXd& gradient, const Eigen::VectorXd& delta_pos) const; bool AcceptRejectStep(const Eigen::VectorXd& delta_pos, const Eigen::VectorXd& gradient, double energy_delta); std::string _errormessage; bool _success = true; Index _iteration = 0; std::vector > _callbacks; Eigen::MatrixXd _hessian; Eigen::VectorXd _parameters; double _cost = std::numeric_limits::max(); double _trust_radius = 0.1; Index _max_iteration = 200; Logger* _pLog; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_BFGS_TRM_H xtp-2021.2/include/votca/xtp/bse.h000066400000000000000000000123061412152066400167120ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_BSE_H #define VOTCA_XTP_BSE_H // Local VOTCA includes #include "logger.h" #include "orbitals.h" #include "qmstate.h" #include "threecenter.h" namespace votca { namespace xtp { struct BSE_Population; template class BSE_OPERATOR; typedef BSE_OPERATOR<1, 2, 1, 0> SingletOperator_TDA; typedef BSE_OPERATOR<1, 0, 1, 0> TripletOperator_TDA; template class QMFragment; class BSE { public: // BSE(Logger& log, TCMatrix_gwbse& Mmn, const Eigen::MatrixXd& Hqp_in) // : _log(log), _Mmn(Mmn), _Hqp_in(Hqp_in){}; BSE(Logger& log, TCMatrix_gwbse& Mmn) : _log(log), _Mmn(Mmn){}; struct options { bool useTDA = true; Index homo; Index rpamin; Index rpamax; Index qpmin; Index qpmax; Index vmin; Index cmax; Index nmax; // number of eigenvectors to calculate bool davidson; // use davidson to diagonalize the matrix bool matrixfree; // use matrix free method std::string davidson_correction; std::string davidson_ortho; std::string davidson_tolerance; std::string davidson_update; Index davidson_maxiter; double min_print_weight; // minimium contribution for state to print it bool use_Hqp_offdiag; Index max_dyn_iter; double dyn_tolerance; }; void configure(const options& opt, const Eigen::VectorXd& RPAEnergies, const Eigen::MatrixXd& Hqp_in); void Solve_singlets(Orbitals& orb) const; void Solve_triplets(Orbitals& orb) const; Eigen::MatrixXd getHqp() const { return _Hqp; }; SingletOperator_TDA getSingletOperator_TDA() const; TripletOperator_TDA getTripletOperator_TDA() const; void Analyze_singlets(std::vector > fragments, const Orbitals& orb) const; void Analyze_triplets(std::vector > fragments, const Orbitals& orb) const; void Perturbative_DynamicalScreening(const QMStateType& type, Orbitals& orb); private: options _opt; struct Interaction { Eigen::VectorXd exchange_contrib; Eigen::VectorXd direct_contrib; Eigen::VectorXd qp_contrib; }; struct ExpectationValues { Eigen::VectorXd direct_term; Eigen::VectorXd cross_term; }; Logger& _log; Index _bse_vmax; Index _bse_cmin; Index _bse_size; Index _bse_vtotal; Index _bse_ctotal; Index _max_dyn_iter; double _dyn_tolerance; Eigen::VectorXd _epsilon_0_inv; TCMatrix_gwbse& _Mmn; Eigen::MatrixXd _Hqp; tools::EigenSystem Solve_singlets_TDA() const; tools::EigenSystem Solve_singlets_BTDA() const; tools::EigenSystem Solve_triplets_TDA() const; tools::EigenSystem Solve_triplets_BTDA() const; void PrintWeights(const Eigen::VectorXd& weights) const; template void configureBSEOperator(BSE_OPERATOR& H) const; template tools::EigenSystem solve_hermitian(BSE_OPERATOR& h) const; template tools::EigenSystem Solve_nonhermitian(BSE_OPERATOR_ApB& apb, BSE_OPERATOR_AmB&) const; template tools::EigenSystem Solve_nonhermitian_Davidson(BSE_OPERATOR_A& Aop, BSE_OPERATOR_B& Bop) const; void printFragInfo(const std::vector >& frags, Index state) const; void printWeights(Index i_bse, double weight) const; void SetupDirectInteractionOperator(const Eigen::VectorXd& DFTenergies, double energy); Eigen::MatrixXd AdjustHqpSize(const Eigen::MatrixXd& Hqp_in, const Eigen::VectorXd& RPAInputEnergies); Interaction Analyze_eh_interaction(const QMStateType& type, const Orbitals& orb) const; template ExpectationValues ExpectationValue_Operator(const QMStateType& type, const Orbitals& orb, const BSE_OPERATOR& H) const; template ExpectationValues ExpectationValue_Operator_State(const QMStateType& type, const Orbitals& orb, const BSE_OPERATOR& H, const Index state) const; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_BSE_H xtp-2021.2/include/votca/xtp/bse_operator.h000066400000000000000000000051711412152066400206270ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_BSE_OPERATOR_H #define VOTCA_XTP_BSE_OPERATOR_H // Local VOTCA includes #include "eigen.h" #include "matrixfreeoperator.h" #include "threecenter.h" namespace votca { namespace xtp { struct BSEOperator_Options { Index homo; Index rpamin; Index qpmin; Index vmin; Index cmax; }; template class BSE_OPERATOR : public MatrixFreeOperator { public: BSE_OPERATOR(const Eigen::VectorXd& Hd_operator, const TCMatrix_gwbse& Mmn, const Eigen::MatrixXd& Hqp) : _epsilon_0_inv(Hd_operator), _Mmn(Mmn), _Hqp(Hqp){}; void configure(BSEOperator_Options opt); Eigen::RowVectorXd OperatorRow(Index index) const override; bool useBlock() const override { return cx != 0; } Index getBlocksize() const override { return Index(_bse_ctotal); } Eigen::MatrixXd OperatorBlock(Index row, Index col) const override; private: Eigen::RowVectorXd Hqp_row(Index index) const; Eigen::RowVectorXd Hd_row(Index index) const; Eigen::RowVectorXd Hd2_row(Index index) const; Eigen::MatrixXd HxBlock(Index row, Index col) const; BSEOperator_Options _opt; Index _bse_size; Index _bse_vtotal; Index _bse_ctotal; Index _bse_cmin; const Eigen::VectorXd& _epsilon_0_inv; const TCMatrix_gwbse& _Mmn; const Eigen::MatrixXd& _Hqp; }; // type defs for the different operators typedef BSE_OPERATOR<1, 2, 1, 0> SingletOperator_TDA; typedef BSE_OPERATOR<1, 0, 1, 0> TripletOperator_TDA; typedef BSE_OPERATOR<1, 4, 1, 1> SingletOperator_BTDA_ApB; typedef BSE_OPERATOR<1, 0, 1, 1> TripletOperator_BTDA_ApB; typedef BSE_OPERATOR<1, 0, 1, -1> Operator_BTDA_AmB; typedef BSE_OPERATOR<0, 2, 0, 1> SingletOperator_BTDA_B; typedef BSE_OPERATOR<1, 0, 0, 0> HqpOperator; typedef BSE_OPERATOR<0, 1, 0, 0> HxOperator; typedef BSE_OPERATOR<0, 0, 1, 0> HdOperator; typedef BSE_OPERATOR<0, 0, 0, 1> Hd2Operator; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_BSE_OPERATOR_H xtp-2021.2/include/votca/xtp/bse_population.h000066400000000000000000000037221412152066400211660ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_BSE_POPULATION_H #define VOTCA_XTP_BSE_POPULATION_H // Local VOTCA includes #include "checkpoint.h" #include "eigen.h" /** * \brief Small container to keep occupation of BSE states for each atom * * */ namespace votca { namespace xtp { struct BSE_Population { Eigen::VectorXd H; Eigen::VectorXd E; double Gs = 0; void Initialize(Index size) { H = Eigen::VectorXd::Zero(size); E = Eigen::VectorXd::Zero(size); Gs = 0; } void WriteToCpt(CheckpointWriter& w) const { w(H, "holeinfo"); w(E, "electroninfo"); w(Gs, "groundstate"); } void ReadFromCpt(CheckpointReader& r) { r(H, "holeinfo"); r(E, "electroninfo"); r(Gs, "groundstate"); } friend std::ostream& operator<<(std::ostream& out, const BSE_Population& pop) { if (pop.H.size() < 1) { return out; } Eigen::VectorXd diff = pop.H + pop.E; out << "GroundstateCharge:" << pop.Gs << "\n"; out << "Index hole electron dQ Qeff\n"; for (Index i = 0; i < pop.H.size(); ++i) { out << i << " " << pop.H(i) << " " << pop.E(i) << " " << diff(i) << " " << diff(i) + pop.Gs << "\n"; } return out; } }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_BSE_POPULATION_H xtp-2021.2/include/votca/xtp/bsecoupling.h000066400000000000000000000072121412152066400204530ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_BSECOUPLING_H #define VOTCA_XTP_BSECOUPLING_H // Local VOTCA includes #include "couplingbase.h" #include "qmstate.h" namespace votca { namespace xtp { /** * \brief Evaluates electronic coupling elements * * J. Wehner,B. Baumeier, * JCTC DOI: 10.1021/acs.jctc.6b00935 * */ class BSECoupling : public CouplingBase { public: void Initialize(tools::Property& options) override; std::string Identify() const { return "bsecoupling"; } void Addoutput(tools::Property& type_summary, const Orbitals& orbitalsA, const Orbitals& orbitalsB) const override; /** * \brief evaluates electronic couplings * * @param _orbitalsA molecular orbitals of molecule A * @param _orbitalsB molecular orbitals of molecule B * @param _orbitalsAB molecular orbitals of the dimer AB */ void CalculateCouplings(const Orbitals& orbitalsA, const Orbitals& orbitalsB, const Orbitals& orbitalsAB) override; private: void WriteToProperty(tools::Property& summary, const QMState& stateA, const QMState& stateB) const; double getSingletCouplingElement(Index levelA, Index levelB, Index methodindex) const; double getTripletCouplingElement(Index levelA, Index levelB, Index methodindex) const; Eigen::MatrixXd SetupCTStates(Index bseA_vtotal, Index bseB_vtotal, Index bseAB_vtotal, Index bseAB_ctotal, const Eigen::MatrixXd& A_AB, const Eigen::MatrixXd& B_AB) const; Eigen::MatrixXd ProjectFrenkelExcitons(const Eigen::MatrixXd& BSE_Coeffs, const Eigen::MatrixXd& X_AB, Index bseX_vtotal, Index bseX_ctotal, Index bseAB_vtotal, Index bseAB_ctotal) const; template std::array ProjectExcitons(Eigen::MatrixXd& FE_AB, Eigen::MatrixXd& CTStates, BSE_OPERATOR H) const; template Eigen::MatrixXd CalcJ_dimer(BSE_OPERATOR& H, Eigen::MatrixXd& projection) const; Eigen::MatrixXd OrthogonalizeCTs(Eigen::MatrixXd& FE_AB, Eigen::MatrixXd& CTStates) const; Eigen::MatrixXd Fulldiag(const Eigen::MatrixXd& J_dimer) const; Eigen::MatrixXd Perturbation(const Eigen::MatrixXd& J_dimer) const; std::array JAB_singlet; std::array JAB_triplet; bool _doTriplets = false; bool _doSinglets = false; bool _output_perturbation = true; Index _levA; Index _levB; Index _occA; Index _unoccA; Index _occB; Index _unoccB; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_BSECOUPLING_H xtp-2021.2/include/votca/xtp/bseoperator_btda.h000066400000000000000000000156671412152066400214750ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #ifndef VOTCA_XTP_BSEOPERATOR_BTDA_H #define VOTCA_XTP_BSEOPERATOR_BTDA_H // Local VOTCA includes #include "bse_operator.h" #include "eigen.h" namespace votca { namespace xtp { template class HamiltonianOperator; } } // namespace votca namespace Eigen { namespace internal { template struct traits< votca::xtp::HamiltonianOperator> : public Eigen::internal::traits {}; } // namespace internal } // namespace Eigen namespace votca { namespace xtp { template class HamiltonianOperator : public Eigen::EigenBase< HamiltonianOperator> { public: // Required typedefs, constants, and method: using Scalar = double; using RealScalar = double; using StorageIndex = votca::Index; enum { ColsAtCompileTime = Eigen::Dynamic, MaxColsAtCompileTime = Eigen::Dynamic, IsRowMajor = false }; HamiltonianOperator(const MatrixReplacementA& A, const MatrixReplacementB& B) : _A(A), _B(B) { _size = 2 * A.cols(); _diag = get_diagonal(); }; Eigen::Index rows() const { return this->_size; } Eigen::Index cols() const { return this->_size; } template Eigen::Product operator*( const Eigen::MatrixBase& x) const { return Eigen::Product( *this, x.derived()); } Eigen::VectorXd get_diagonal() const { Eigen::VectorXd diag = Eigen::VectorXd::Zero(_size); Index half = _size / 2; diag.head(half) = _A.diagonal(); diag.tail(half) = -diag.head(half); return diag; } Eigen::VectorXd diagonal() const { return _diag; } // get the full matrix if we have to Eigen::MatrixXd get_full_matrix() const { Eigen::MatrixXd matrix = Eigen::MatrixXd::Zero(_size, _size); Index half = _size / 2; matrix.topLeftCorner(half, half) = _A.get_full_matrix(); matrix.topRightCorner(half, half) = _B.get_full_matrix(); matrix.bottomLeftCorner(half, half) = -matrix.topRightCorner(half, half); matrix.bottomRightCorner(half, half) = -matrix.topLeftCorner(half, half); return matrix; } const MatrixReplacementA& _A; const MatrixReplacementB& _B; private: Index _size; Eigen::VectorXd _diag; }; } // namespace xtp } // namespace votca namespace Eigen { namespace internal { // replacement of the mat*vect operation template struct generic_product_impl< votca::xtp::HamiltonianOperator, Vtype, DenseShape, DenseShape, GemvProduct> : generic_product_impl_base< votca::xtp::HamiltonianOperator, Vtype, generic_product_impl, Vtype>> { typedef typename Product< votca::xtp::HamiltonianOperator, Vtype>::Scalar Scalar; template static void scaleAndAddTo(Dest& dst, const votca::xtp::HamiltonianOperator< MatrixReplacementA, MatrixReplacementB>& op, const Vtype& v, const Scalar& alpha) { // returns dst = alpha * op * v // alpha must be 1 here assert(alpha == Scalar(1) && "scaling is not implemented"); EIGEN_ONLY_USED_FOR_DEBUG(alpha); /**Instead of doing the (A B)*(v1) (-B -A) (v2) multiplication explicitly for each block we reshape v into (v1,v2) and multiply A*(v1,v2) and then sort the contributions into the resulting vector we do the same for B * **/ Map vmat(v.data(), v.size() / 2, 2); Index half = op.rows() / 2; MatrixX2d temp = op._A * vmat; dst.head(half) = temp.col(0); dst.tail(half) = -temp.col(1); temp = op._B * vmat; dst.head(half) += temp.col(1); dst.tail(half) -= temp.col(0); } }; // replacement of the mat*mat operation template struct generic_product_impl< votca::xtp::HamiltonianOperator, Mtype, DenseShape, DenseShape, GemmProduct> : generic_product_impl_base< votca::xtp::HamiltonianOperator, Mtype, generic_product_impl, Mtype>> { typedef typename Product< votca::xtp::HamiltonianOperator, Mtype>::Scalar Scalar; template static void scaleAndAddTo(Dest& dst, const votca::xtp::HamiltonianOperator< MatrixReplacementA, MatrixReplacementB>& op, const Mtype& m, const Scalar& alpha) { // returns dst = alpha * op * v // alpha must be 1 here assert(alpha == Scalar(1) && "scaling is not implemented"); EIGEN_ONLY_USED_FOR_DEBUG(alpha); Index half = op.rows() / 2; /**Instead of doing the (A B)*(M1) (-B -A) (M2) multiplication explicitly for each block we reshape M into (M1,M2) and multiply A*(M1,M2) and then sort the contributions into the resulting vector we do the same for B * **/ Map m_reshaped(m.data(), m.rows() / 2, m.cols() * 2); MatrixXd temp = op._A * m_reshaped; Map temp_unshaped(temp.data(), m.rows(), m.cols()); dst.topRows(half) = temp_unshaped.topRows(half); dst.bottomRows(half) = -temp_unshaped.bottomRows(half); temp = op._B * m_reshaped; dst.topRows(half) += temp_unshaped.bottomRows(half); dst.bottomRows(half) -= temp_unshaped.topRows(half); } }; } // namespace internal } // namespace Eigen #endif // VOTCA_XTP_BSEOPERATOR_BTDA_H xtp-2021.2/include/votca/xtp/calculatorfactory.h000066400000000000000000000025331412152066400216630ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_CALCULATORFACTORY_H #define VOTCA_XTP_CALCULATORFACTORY_H // Standard includes #include // VOTCA includes #include // Local VOTCA includes #include "qmcalculator.h" namespace votca { namespace xtp { class Calculatorfactory : public tools::ObjectFactory { private: Calculatorfactory() = default; public: static void RegisterAll(void); friend Calculatorfactory &Calculators(); }; inline Calculatorfactory &Calculators() { static Calculatorfactory instance; return instance; } } // namespace xtp } // namespace votca #endif // VOTCA_XTP_CALCULATORFACTORY_H xtp-2021.2/include/votca/xtp/chargecarrier.h000066400000000000000000000045521412152066400207460ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * * author: Kordt */ #pragma once #ifndef VOTCA_XTP_CHARGECARRIER_H #define VOTCA_XTP_CHARGECARRIER_H // Local VOTCA includes #include "glink.h" #include "gnode.h" namespace votca { namespace xtp { class Chargecarrier { public: Chargecarrier(Index id) : _id(id), lifetime(0.0), steps(0), _dr_travelled(Eigen::Vector3d::Zero()), node(nullptr){}; bool hasNode() { return (node != nullptr); } void updateLifetime(double dt) { lifetime += dt; } void updateOccupationtime(double dt) { node->UpdateOccupationTime(dt); } void updateSteps(Index t) { steps += t; } void resetCarrier() { lifetime = 0; steps = 0; _dr_travelled = Eigen::Vector3d::Zero(); } double getLifetime() const { return lifetime; } Index getSteps() const { return steps; } Index getCurrentNodeId() const { return node->getId(); } double getCurrentEnergy() const { return node->getSitenergy(); } const Eigen::Vector3d& getCurrentPosition() const { return node->getPos(); } double getCurrentEscapeRate() const { return node->getEscapeRate(); } GNode& getCurrentNode() const { return *node; } void ReleaseNode() { node->setOccupation(false); } void settoNote(GNode* newnode) { node = newnode; node->setOccupation(true); } void jumpAccordingEvent(const GLink& event) { ReleaseNode(); settoNote(event.getDestination()); _dr_travelled += event.getDeltaR(); } const Eigen::Vector3d& get_dRtravelled() const { return _dr_travelled; } Index getId() const { return _id; } void setId(Index id) { _id = id; } private: Index _id; double lifetime; Index steps; Eigen::Vector3d _dr_travelled; GNode* node; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_CHARGECARRIER_H xtp-2021.2/include/votca/xtp/checkpoint.h000066400000000000000000000033361412152066400202730ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_CHECKPOINT_H #define VOTCA_XTP_CHECKPOINT_H // Standard includes #include // Third party includes #include // Local VOTCA includes #include "checkpoint_utils.h" #include "checkpointreader.h" #include "checkpointtable.h" #include "checkpointwriter.h" namespace votca { namespace xtp { enum class CheckpointAccessLevel { READ = 0, // only read no write access MODIFY = 1, // if file exists, change it CREATE = 2 // create new file }; std::ostream& operator<<(std::ostream& s, CheckpointAccessLevel l); class CheckpointFile { public: CheckpointFile(std::string fN); CheckpointFile(std::string fN, CheckpointAccessLevel access); std::string getFileName(); std::string getVersion(); H5::H5File getHandle(); CheckpointWriter getWriter(); CheckpointWriter getWriter(const std::string _path); CheckpointReader getReader(); CheckpointReader getReader(const std::string _path); private: std::string _fileName; H5::H5File _fileHandle; CptLoc _rootLoc; CheckpointAccessLevel _accessLevel; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_CHECKPOINT_H xtp-2021.2/include/votca/xtp/checkpoint_utils.h000066400000000000000000000056121412152066400215120ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_CHECKPOINT_UTILS_H #define VOTCA_XTP_CHECKPOINT_UTILS_H // Standard includes #include #include #include // Third party includes #include // VOTCA includes #include namespace votca { namespace xtp { using CptLoc = H5::Group; namespace checkpoint_utils { H5::DataSpace str_scalar(H5::DataSpace(H5S_SCALAR)); inline H5::DataSpace StrScalar() { return H5::DataSpace(H5S_SCALAR); } // Declare some HDF5 data type inference stuff: // Adapted from // https://github.com/garrison/eigen3-hdf5/blob/2c782414251e75a2de9b0441c349f5f18fe929a2/eigen3-hdf5.hpp#L18 template struct InferDataType; template <> struct InferDataType { static const H5::DataType* get(void) { return &H5::PredType::NATIVE_FLOAT; } }; template <> struct InferDataType { static const H5::DataType* get(void) { return &H5::PredType::NATIVE_DOUBLE; } }; template <> struct InferDataType { static const H5::DataType* get(void) { return &H5::PredType::NATIVE_INT; } }; template <> struct InferDataType { static const H5::DataType* get(void) { return &H5::PredType::NATIVE_LONG; } }; template <> struct InferDataType { static const H5::DataType* get(void) { return &H5::PredType::NATIVE_UINT; } }; template <> struct InferDataType { static const H5::DataType* get(void) { #if (defined(__GNUC__) && defined(__clang__)) #pragma clang diagnostic push #pragma clang diagnostic ignored "-Wconversion" #elif (defined(__GNUC__) && !defined(__INTEL_COMPILER)) #pragma GCC diagnostic push #pragma GCC diagnostic ignored "-Wconversion" #elif (defined(__INTEL_COMPILER)) #pragma warning push #pragma warning(disable : 1682) // implicit conversion of a 64-bit integral // type to a smaller integral type #endif static const H5::StrType strtype(H5T_C_S1, H5T_VARIABLE); #if (defined(__GNUC__) && defined(__clang__)) #pragma clang diagnostic pop #elif (defined(__GNUC__) && !defined(__INTEL_COMPILER)) #pragma GCC diagnostic pop #elif (defined(__INTEL_COMPILER)) #pragma warning pop #endif return &strtype; } }; H5::DataSpace str_scalar(H5::DataSpace(H5S_SCALAR)); } // namespace checkpoint_utils } // namespace xtp } // namespace votca #endif // VOTCA_XTP_CHECKPOINT_UTILS_H xtp-2021.2/include/votca/xtp/checkpointreader.h000066400000000000000000000202361412152066400214540ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_CHECKPOINTREADER_H #define VOTCA_XTP_CHECKPOINTREADER_H // Standard includes #include #include #include #include // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "checkpoint_utils.h" #include "checkpointtable.h" #include "eigen.h" namespace votca { namespace xtp { using namespace checkpoint_utils; class CheckpointReader { public: CheckpointReader(const CptLoc& loc) : CheckpointReader(loc, "/"){}; CheckpointReader(const CptLoc& loc, const std::string path) : _loc(loc), _path(path){}; template typename std::enable_if::value>::type operator()( T& var, const std::string& name) const { try { ReadData(_loc, var, name); } catch (H5::Exception&) { std::stringstream message; message << "Could not read " << name << " from " << _loc.getFileName() << ":" << _path << std::endl; throw std::runtime_error(message.str()); } } template typename std::enable_if::value && !std::is_same::value>::type operator()(T& var, const std::string& name) const { try { ReadScalar(_loc, var, name); } catch (H5::Exception&) { std::stringstream message; message << "Could not read " << name << " from " << _loc.getFileName() << ":" << _path << "/" << std::endl; throw std::runtime_error(message.str()); } } void operator()(bool& v, const std::string& name) const { Index temp = Index(v); try { ReadScalar(_loc, temp, name); } catch (H5::Exception&) { std::stringstream message; message << "Could not read " << name << " from " << _loc.getFileName() << ":" << _path << std::endl; throw std::runtime_error(message.str()); } v = static_cast(temp); } void operator()(std::string& var, const std::string& name) const { try { ReadScalar(_loc, var, name); } catch (H5::Exception&) { std::stringstream message; message << "Could not read " << name << " from " << _loc.getFileName() << ":" << _path << std::endl; throw std::runtime_error(message.str()); } } CheckpointReader openChild(const std::string& childName) const { try { return CheckpointReader(_loc.openGroup(childName), _path + "/" + childName); } catch (H5::Exception&) { std::stringstream message; message << "Could not open " << _loc.getFileName() << ":/" << _path << "/" << childName << std::endl; throw std::runtime_error(message.str()); } } Index getNumDataSets() const { return _loc.getNumObjs(); } CptLoc getLoc() { return _loc; } template CptTable openTable(const std::string& name, const T& obj) { try { CptTable table = CptTable(name, sizeof(typename T::data), _loc); obj.SetupCptTable(table); return table; } catch (H5::Exception&) { std::stringstream message; message << "Could not open table " << name << " in " << _loc.getFileName() << ":" << _path << std::endl; throw std::runtime_error(message.str()); } } private: const CptLoc _loc; const std::string _path; void ReadScalar(const CptLoc& loc, std::string& var, const std::string& name) const { const H5::DataType* strType = InferDataType::get(); H5::Attribute attr = loc.openAttribute(name); H5std_string readbuf(""); attr.read(*strType, readbuf); var = readbuf; } template void ReadScalar(const CptLoc& loc, T& value, const std::string& name) const { H5::Attribute attr = loc.openAttribute(name); const H5::DataType* dataType = InferDataType::get(); attr.read(*dataType, &value); } template void ReadData(const CptLoc& loc, Eigen::MatrixBase& matrix, const std::string& name) const { const H5::DataType* dataType = InferDataType::get(); H5::DataSet dataset = loc.openDataSet(name); H5::DataSpace dp = dataset.getSpace(); hsize_t dims[2]; dp.getSimpleExtentDims(dims, nullptr); // ndims is always 2 for us hsize_t matRows = dims[0]; hsize_t matCols = dims[1]; matrix.derived().resize(matRows, matCols); if (matrix.size() == 0) { return; } hsize_t matColSize = matrix.derived().outerStride(); hsize_t fileRows = matCols; hsize_t fStride[2] = {1, fileRows}; hsize_t fCount[2] = {1, 1}; hsize_t fBlock[2] = {1, fileRows}; hsize_t mStride[2] = {matColSize, 1}; hsize_t mCount[2] = {1, 1}; hsize_t mBlock[2] = {matCols, 1}; hsize_t mDim[2] = {matCols, matColSize}; H5::DataSpace mspace(2, mDim); for (hsize_t i = 0; i < matRows; i++) { hsize_t fStart[2] = {i, 0}; hsize_t mStart[2] = {0, i}; dp.selectHyperslab(H5S_SELECT_SET, fCount, fStart, fStride, fBlock); mspace.selectHyperslab(H5S_SELECT_SET, mCount, mStart, mStride, mBlock); dataset.read(matrix.derived().data(), *dataType, mspace, dp); } } template typename std::enable_if::value>::type ReadData( const CptLoc& loc, std::vector& v, const std::string& name) const { H5::DataSet dataset = loc.openDataSet(name); H5::DataSpace dp = dataset.getSpace(); const H5::DataType* dataType = InferDataType::get(); hsize_t dims[2]; dp.getSimpleExtentDims(dims, nullptr); v.resize(dims[0]); if (v.empty()) { return; } try { dataset.read(&(v[0]), *dataType); } catch (H5::Exception&) { std::stringstream message; message << "Could not read " << name << " from " << _loc.getFileName() << ":" << _path << std::endl; throw std::runtime_error(message.str()); } } void ReadData(const CptLoc& loc, std::vector& v, const std::string& name) const { H5::DataSet dataset = loc.openDataSet(name); H5::DataSpace dp = dataset.getSpace(); const H5::DataType* dataType = InferDataType::get(); hsize_t dims[2]; dp.getSimpleExtentDims(dims, nullptr); std::vector temp(dims[0]); if (temp.empty()) { return; } try { dataset.read(temp.data(), *dataType); } catch (H5::Exception&) { std::stringstream message; message << "Could not read " << name << " from " << _loc.getFileName() << ":" << _path << std::endl; throw std::runtime_error(message.str()); } v.reserve(dims[0]); for (char* s : temp) { v.push_back(std::string(s)); free(s); } } void ReadData(const CptLoc& loc, tools::EigenSystem& sys, const std::string& name) const { CptLoc parent = loc.openGroup(name); ReadData(parent, sys.eigenvalues(), "eigenvalues"); ReadData(parent, sys.eigenvectors(), "eigenvectors"); ReadData(parent, sys.eigenvectors2(), "eigenvectors2"); Index info; ReadScalar(parent, info, "info"); sys.info() = static_cast(info); } void ReadData(const CptLoc& loc, std::vector& v, const std::string& name) const { CptLoc parent = loc.openGroup(name); size_t count = parent.getNumObjs(); v.resize(count); size_t c = 0; for (auto& vec : v) { ReadData(parent, vec, "ind" + std::to_string(c)); ++c; } } }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_CHECKPOINTREADER_H xtp-2021.2/include/votca/xtp/checkpointtable.h000066400000000000000000000134651412152066400213070ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_CHECKPOINTTABLE_H #define VOTCA_XTP_CHECKPOINTTABLE_H // Standard includes #include #include #include #include #include #include #include // Third party includes #include // Local VOTCA includes #include "checkpoint_utils.h" #define CPT_MEM_FROM_STRUCT(m, s) HOFFSET(s, m) #define CPT_MEMBER(m, s) HOFFSET(s, m) namespace votca { namespace xtp { using namespace checkpoint_utils; class CptTable { public: CptTable() = default; CptTable(const std::string& name, const std::size_t& rowSize, const std::size_t& nRows) : _name(name), _rowStructure(rowSize), _nRows(nRows), _props(H5::DSetCreatPropList(H5::DSetCreatPropList::DEFAULT)){}; CptTable(const std::string& name, const std::size_t& rowSize, const CptLoc& loc) : _name(name), _loc(loc), _inited(true), _rowStructure(rowSize) { _dataset = _loc.openDataSet(_name); _dp = _dataset.getSpace(); hsize_t dims[2]; _dp.getSimpleExtentDims(dims, nullptr); _nRows = dims[0]; } template typename std::enable_if::value>::type addCol( const U&, const std::string& name, const size_t& offset) { _rowStructure.insertMember(name, offset, *InferDataType::get()); } void addCol(const std::string&, const std::string& name, const size_t& offset) { _rowStructure.insertMember(name, offset, *InferDataType::get()); } void addCol(const char*, const std::string& name, const size_t& offset) { H5::DataType fixedWidth(H5T_STRING, MaxStringSize); _rowStructure.insertMember(name, offset, fixedWidth); } void initialize(const CptLoc& loc, bool compact) { // create the dataspace... if (_inited) { std::stringstream message; message << "Checkpoint tables cannot be reinitialized. " << _name << " has either already been initialized or already exists." << std::endl; throw std::runtime_error(message.str()); } _dims[0] = _nRows; _dims[1] = 1; _dp = H5::DataSpace(2, _dims); _loc = loc; if (compact) { _props.setLayout(H5D_layout_t::H5D_COMPACT); } try { _dataset = _loc.createDataSet(_name.c_str(), _rowStructure, _dp, _props); } catch (H5::Exception&) { std::stringstream message; message << "Could not write " << _name << " from " << _loc.getFileName(); throw std::runtime_error(message.str()); } _inited = true; } void write(void* buffer, const std::size_t& startIdx, const std::size_t& endIdx) { if (!_inited) { std::stringstream message; message << "Checkpoint table uninitialized." << std::endl; throw std::runtime_error(message.str()); } hsize_t s = (hsize_t)(startIdx); hsize_t e = (hsize_t)(endIdx); hsize_t l = e - s; hsize_t fStart[2] = {s, 0}; hsize_t fCount[2] = {l, 1}; hsize_t mStart[2] = {s, 0}; hsize_t mCount[2] = {l, 1}; hsize_t mDim[2] = {l, 1}; H5::DataSpace mspace(2, mDim); _dp.selectHyperslab(H5S_SELECT_SET, fCount, fStart); mspace.selectHyperslab(H5S_SELECT_SET, mCount, mStart); try { _dataset.write(buffer, _rowStructure, mspace, _dp); } catch (H5::Exception&) { std::stringstream message; message << "Could not write " << _name << " from " << _loc.getFileName(); throw std::runtime_error(message.str()); } } void writeToRow(void* buffer, const std::size_t idx) { write(buffer, idx, idx + 1); } template void write(std::vector& dataVec) { write(dataVec.data(), 0, dataVec.size()); } void read(void* buffer, const std::size_t& startIdx, const std::size_t& endIdx) { if (!_inited) { std::stringstream message; message << "Checkpoint table uninitialized." << std::endl; throw std::runtime_error(message.str()); } hsize_t s = (hsize_t)(startIdx); hsize_t e = (hsize_t)(endIdx); hsize_t l = e - s; hsize_t fStart[2] = {s, 0}; hsize_t fCount[2] = {l, 1}; hsize_t mStart[2] = {s, 0}; hsize_t mCount[2] = {l, 1}; hsize_t mDim[2] = {l, 1}; H5::DataSpace mspace(2, mDim); _dp.selectHyperslab(H5S_SELECT_SET, fCount, fStart); mspace.selectHyperslab(H5S_SELECT_SET, mCount, mStart); try { _dataset.read(buffer, _rowStructure, mspace, _dp); } catch (H5::Exception&) { std::stringstream message; message << "Could not read " << _name << " from " << _loc.getFileName(); throw std::runtime_error(message.str()); } } void readFromRow(void* buffer, const std::size_t& idx) { read(buffer, idx, idx + 1); } template void read(std::vector& dataVec) { read(dataVec.data(), 0, dataVec.size()); } std::size_t numRows() { return _nRows; } static const std::size_t MaxStringSize = 512; private: std::string _name; CptLoc _loc; bool _inited = false; H5::CompType _rowStructure; std::size_t _nRows; hsize_t _dims[2]; H5::DataSpace _dp; H5::DataSet _dataset; H5::DSetCreatPropList _props; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_CHECKPOINTTABLE_H xtp-2021.2/include/votca/xtp/checkpointwriter.h000066400000000000000000000227551412152066400215360ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_CHECKPOINTWRITER_H #define VOTCA_XTP_CHECKPOINTWRITER_H // Standard includes #include #include #include #include #include // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "checkpoint_utils.h" #include "checkpointtable.h" #include "eigen.h" namespace votca { namespace xtp { using namespace checkpoint_utils; class CheckpointWriter { public: CheckpointWriter(const CptLoc& loc) : CheckpointWriter(loc, "/"){}; CheckpointWriter(const CptLoc& loc, const std::string& path) : _loc(loc), _path(path){}; // see the following links for details // https://stackoverflow.com/a/8671617/1186564 template typename std::enable_if::value>::type operator()( const T& data, const std::string& name) const { try { WriteData(_loc, data, name); } catch (H5::Exception&) { std::stringstream message; message << "Could not write " << name << " to " << _loc.getFileName() << ":" << _path; throw std::runtime_error(message.str()); } } // Use this overload if T is a fundamental type // int, double, unsigned, etc, but not bool template typename std::enable_if::value && !std::is_same::value>::type operator()(const T& v, const std::string& name) const { try { WriteScalar(_loc, v, name); } catch (H5::Exception&) { std::stringstream message; message << "Could not write " << name << " to " << _loc.getFileName() << ":" << _path << std::endl; throw std::runtime_error(message.str()); } } void operator()(const bool& v, const std::string& name) const { Index temp = static_cast(v); try { WriteScalar(_loc, temp, name); } catch (H5::Exception&) { std::stringstream message; message << "Could not write " << name << " to " << _loc.getFileName() << ":" << _path << std::endl; throw std::runtime_error(message.str()); } } void operator()(const std::string& v, const std::string& name) const { try { WriteScalar(_loc, v, name); } catch (H5::Exception&) { std::stringstream message; message << "Could not write " << name << " to " << _loc.getFileName() << ":" << _path << std::endl; throw std::runtime_error(message.str()); } } CheckpointWriter openChild(const std::string& childName) const { try { return CheckpointWriter(_loc.openGroup(childName), _path + "/" + childName); } catch (H5::Exception&) { try { return CheckpointWriter(_loc.createGroup(childName), _path + "/" + childName); } catch (H5::Exception&) { std::stringstream message; message << "Could not open or create" << _loc.getFileName() << ":/" << _path << "/" << childName << std::endl; throw std::runtime_error(message.str()); } } } template CptTable openTable(const std::string& name, const T& obj, std::size_t nRows, bool compact = false) { CptTable table; try { table = CptTable(name, sizeof(typename T::data), _loc); obj.SetupCptTable(table); } catch (H5::Exception&) { try { table = CptTable(name, sizeof(typename T::data), nRows); obj.SetupCptTable(table); table.initialize(_loc, compact); } catch (H5::Exception&) { std::stringstream message; message << "Could not open table " << name << " in " << _loc.getFileName() << ":" << _path << std::endl; throw std::runtime_error(message.str()); } } return table; } private: const CptLoc _loc; const std::string _path; template void WriteScalar(const CptLoc& loc, const T& value, const std::string& name) const { hsize_t dims[1] = {1}; H5::DataSpace dp(1, dims); const H5::DataType* dataType = InferDataType::get(); H5::Attribute attr; try { attr = loc.createAttribute(name, *dataType, dp); } catch (H5::AttributeIException&) { attr = loc.openAttribute(name); } attr.write(*dataType, &value); } void WriteScalar(const CptLoc& loc, const std::string& value, const std::string& name) const { hsize_t dims[1] = {1}; H5::DataSpace dp(1, dims); const H5::DataType* strType = InferDataType::get(); H5::Attribute attr; try { attr = loc.createAttribute(name, *strType, dp); } catch (H5::AttributeIException&) { attr = loc.openAttribute(name); } attr.write(*strType, &value); } template void WriteData(const CptLoc& loc, const Eigen::MatrixBase& matrix, const std::string& name) const { hsize_t matRows = hsize_t(matrix.rows()); hsize_t matCols = hsize_t(matrix.cols()); hsize_t dims[2] = {matRows, matCols}; // eigen vectors are n,1 matrices if (dims[1] == 0) { dims[1] = 1; } H5::DataSpace dp(2, dims); const H5::DataType* dataType = InferDataType::get(); H5::DataSet dataset; try { dataset = loc.createDataSet(name.c_str(), *dataType, dp); } catch (H5::GroupIException&) { dataset = loc.openDataSet(name.c_str()); } hsize_t matColSize = matrix.derived().outerStride(); hsize_t fileRows = matCols; hsize_t fStride[2] = {1, fileRows}; hsize_t fCount[2] = {1, 1}; hsize_t fBlock[2] = {1, fileRows}; hsize_t mStride[2] = {matColSize, 1}; hsize_t mCount[2] = {1, 1}; hsize_t mBlock[2] = {matCols, 1}; hsize_t mDim[2] = {matCols, matColSize}; H5::DataSpace mspace(2, mDim); for (hsize_t i = 0; i < matRows; i++) { hsize_t fStart[2] = {i, 0}; hsize_t mStart[2] = {0, i}; dp.selectHyperslab(H5S_SELECT_SET, fCount, fStart, fStride, fBlock); mspace.selectHyperslab(H5S_SELECT_SET, mCount, mStart, mStride, mBlock); dataset.write(matrix.derived().data(), *dataType, mspace, dp); } } template typename std::enable_if::value>::type WriteData( const CptLoc& loc, const std::vector v, const std::string& name) const { hsize_t dims[2] = {(hsize_t)v.size(), 1}; const H5::DataType* dataType = InferDataType::get(); H5::DataSet dataset; H5::DataSpace dp(2, dims); try { dataset = loc.createDataSet(name.c_str(), *dataType, dp); } catch (H5::GroupIException&) { dataset = loc.openDataSet(name.c_str()); } dataset.write(v.data(), *dataType); } void WriteData(const CptLoc& loc, const std::vector& v, const std::string& name) const { hsize_t dims[1] = {(hsize_t)v.size()}; std::vector c_str_copy; c_str_copy.reserve(v.size()); for (const std::string& s : v) { c_str_copy.push_back(s.c_str()); } const H5::DataType* dataType = InferDataType::get(); H5::DataSet dataset; H5::DataSpace dp(1, dims); try { dataset = loc.createDataSet(name.c_str(), *dataType, dp); } catch (H5::GroupIException&) { dataset = loc.openDataSet(name.c_str()); } dataset.write(c_str_copy.data(), *dataType); } void WriteData(const CptLoc& loc, const std::vector& v, const std::string& name) const { size_t c = 0; std::string r; CptLoc parent; try { parent = loc.createGroup(name); } catch (H5::GroupIException&) { parent = loc.openGroup(name); } for (auto const& x : v) { r = std::to_string(c); WriteData(parent, x, "ind" + r); ++c; } } void WriteData(const CptLoc& loc, const tools::EigenSystem& sys, const std::string& name) const { CptLoc parent; try { parent = loc.createGroup(name); } catch (H5::GroupIException&) { parent = loc.openGroup(name); } WriteData(parent, sys.eigenvalues(), "eigenvalues"); WriteData(parent, sys.eigenvectors(), "eigenvectors"); WriteData(parent, sys.eigenvectors2(), "eigenvectors2"); WriteScalar(parent, Index(sys.info()), "info"); } template void WriteData(const CptLoc& loc, const std::map> map, const std::string& name) const { size_t c = 0; std::string r; // Iterate over the map and write map as a number of vectors with T1 as // index for (auto const& x : map) { r = std::to_string(c); CptLoc tempGr; try { tempGr = loc.createGroup(name); } catch (H5::GroupIException&) { tempGr = loc.openGroup(name); } WriteData(tempGr, x.second, "index" + r); ++c; } } }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_CHECKPOINTWRITER_H xtp-2021.2/include/votca/xtp/classicalsegment.h000066400000000000000000000035311412152066400214620ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_CLASSICALSEGMENT_H #define VOTCA_XTP_CLASSICALSEGMENT_H // Local VOTCA includes #include "atomcontainer.h" #include "polarsite.h" #include "staticsite.h" namespace votca { namespace xtp { template class ClassicalSegment : public AtomContainer { public: ClassicalSegment(std::string name, Index id) : AtomContainer(name, id){}; ClassicalSegment(CheckpointReader& r) : AtomContainer(r){}; void LoadFromFile(std::string filename); void WriteMPS(std::string filename, std::string header) const; double CalcTotalQ() const; std::string identify() const; Eigen::Vector3d CalcDipole() const; friend std::ostream& operator<<(std::ostream& out, const ClassicalSegment& container) { out << container.getId() << " " << container.identify() << " " << container.getType() << "\n"; for (const T& atom : container) { out << atom; } out << std::endl; return out; } }; using PolarSegment = ClassicalSegment; using StaticSegment = ClassicalSegment; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_CLASSICALSEGMENT_H xtp-2021.2/include/votca/xtp/convergenceacc.h000066400000000000000000000066071412152066400211150ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_CONVERGENCEACC_H #define VOTCA_XTP_CONVERGENCEACC_H // VOTCA includes #include // Local VOTCA includes #include "adiis.h" #include "aomatrix.h" #include "diis.h" #include "logger.h" namespace votca { namespace xtp { class ConvergenceAcc { public: enum KSmode { closed, open, fractional }; struct options { KSmode mode = KSmode::closed; bool usediis; bool noisy = false; Index histlength; bool maxout; double adiis_start; double diis_start; double levelshift; double levelshiftend; Index numberofelectrons; double mixingparameter; double Econverged; double error_converged; }; void Configure(const ConvergenceAcc::options& opt) { _opt = opt; if (_opt.mode == KSmode::closed) { _nocclevels = _opt.numberofelectrons / 2; } else if (_opt.mode == KSmode::open) { _nocclevels = _opt.numberofelectrons; } else if (_opt.mode == KSmode::fractional) { _nocclevels = 0; } _diis.setHistLength(_opt.histlength); } void setLogger(Logger* log) { _log = log; } void PrintConfigOptions() const; bool isConverged() const { if (_totE.size() < 2) { return false; } else { return std::abs(getDeltaE()) < _opt.Econverged && getDIIsError() < _opt.error_converged; } } double getDeltaE() const { if (_totE.size() < 2) { return 0; } else { return _totE.back() - _totE[_totE.size() - 2]; } } void setOverlap(AOOverlap& S, double etol); double getDIIsError() const { return _diiserror; } bool getUseMixing() const { return _usedmixing; } Eigen::MatrixXd Iterate(const Eigen::MatrixXd& dmat, Eigen::MatrixXd& H, tools::EigenSystem& MOs, double totE); tools::EigenSystem SolveFockmatrix(const Eigen::MatrixXd& H) const; void Levelshift(Eigen::MatrixXd& H, const Eigen::MatrixXd& MOs_old) const; Eigen::MatrixXd DensityMatrix(const tools::EigenSystem& MOs) const; private: options _opt; Eigen::MatrixXd DensityMatrixGroundState(const Eigen::MatrixXd& MOs) const; Eigen::MatrixXd DensityMatrixGroundState_unres( const Eigen::MatrixXd& MOs) const; Eigen::MatrixXd DensityMatrixGroundState_frac( const tools::EigenSystem& MOs) const; bool _usedmixing = true; double _diiserror = std::numeric_limits::max(); Logger* _log; const AOOverlap* _S; Eigen::MatrixXd Sminusahalf; std::vector _mathist; std::vector _dmatHist; std::vector _totE; Index _nocclevels; Index _maxerrorindex = 0; double _maxerror = 0.0; ADIIS _adiis; DIIS _diis; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_CONVERGENCEACC_H xtp-2021.2/include/votca/xtp/couplingbase.h000066400000000000000000000034741412152066400206220ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_COUPLINGBASE_H #define VOTCA_XTP_COUPLINGBASE_H // Third party includes #include // Local VOTCA includes #include "logger.h" #include "orbitals.h" namespace votca { namespace xtp { /** * \brief Base Class to derive DFT and BSE coupling from * */ class CouplingBase { public: virtual void CalculateCouplings(const Orbitals& orbitalsA, const Orbitals& orbitalsB, const Orbitals& orbitalsAB) = 0; virtual void Initialize(tools::Property&) = 0; virtual void Addoutput(tools::Property& type_summary, const Orbitals& orbitalsA, const Orbitals& orbitalsB) const = 0; void setLogger(Logger* pLog) { _pLog = pLog; } protected: Logger* _pLog; void CheckAtomCoordinates(const Orbitals& orbitalsA, const Orbitals& orbitalsB, const Orbitals& orbitalsAB) const; Eigen::MatrixXd CalculateOverlapMatrix(const Orbitals& orbitalsAB) const; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_COUPLINGBASE_H xtp-2021.2/include/votca/xtp/cubefile_writer.h000066400000000000000000000030541412152066400213130ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_CUBEFILE_WRITER_H #define VOTCA_XTP_CUBEFILE_WRITER_H // Local VOTCA includes #include "logger.h" #include "orbitals.h" #include "regular_grid.h" /** * \brief Writes an orbital file to a .cube file */ namespace votca { namespace xtp { class CubeFile_Writer { public: CubeFile_Writer(Eigen::Array steps, double padding, Logger& log) : _steps(steps), _padding(padding), _log(log){}; void WriteFile(const std::string& filename, const Orbitals& orb, QMState state, bool dostateonly) const; private: std::vector > CalculateValues( const Orbitals& orb, QMState state, bool dostateonly, const Regular_Grid& grid) const; Eigen::Array _steps; double _padding; Logger& _log; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_CUBEFILE_WRITER_H xtp-2021.2/include/votca/xtp/cudamatrix.h000066400000000000000000000045371412152066400203110ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #ifndef VOTCA_XTP_CUDAMATRIX_H #define VOTCA_XTP_CUDAMATRIX_H // CMake generated file #include "votca_xtp_config.h" #ifndef USE_CUDA #error Cuda not enabled #endif // Standard includes #include #include #include // Third party includes #include #include // Local VOTCA includes #include "eigen.h" /* * \brief Matrix Representation inside an Nvidia GPU */ namespace votca { namespace xtp { cudaError_t checkCuda(cudaError_t result); Index count_available_gpus(); class CudaMatrix { public: Index size() const { return _rows * _cols; }; Index rows() const { return _rows; }; Index cols() const { return _cols; }; double *data() const { return _data.get(); }; CudaMatrix(const Eigen::MatrixXd &matrix, const cudaStream_t &stream); // Allocate memory in the GPU for a matrix CudaMatrix(Index nrows, Index ncols, const cudaStream_t &stream); // Convert A Cudamatrix to an EigenMatrix operator Eigen::MatrixXd() const; void copy_to_gpu(const Eigen::MatrixXd &A); private: // Unique pointer with custom delete function using Unique_ptr_to_GPU_data = std::unique_ptr; Unique_ptr_to_GPU_data alloc_matrix_in_gpu(size_t size_arr) const; void throw_if_not_enough_memory_in_gpu(size_t requested_memory) const; size_t size_matrix() const { return this->size() * sizeof(double); } // Attributes of the matrix in the device Unique_ptr_to_GPU_data _data{nullptr, [](double *x) { checkCuda(cudaFree(x)); }}; cudaStream_t _stream = nullptr; Index _rows; Index _cols; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_CUDAMATRIX_H xtp-2021.2/include/votca/xtp/cudapipeline.h000066400000000000000000000047141412152066400206070ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #ifndef VOTCA_XTP_CUDAPIPELINE_H #define VOTCA_XTP_CUDAPIPELINE_H // CMake generated file #include "votca_xtp_config.h" #ifndef USE_CUDA #error Cuda not enabled #endif // Local VOTCA includes #include "cudamatrix.h" /* * \brief Perform Tensor-matrix multiplications in a GPU * * The `CudaPipeline` class handles the allocation and deallocation of arrays on * the GPU. */ namespace votca { namespace xtp { /* \brief The CudaPipeline class offload Eigen operations to an *Nvidia* GPU * using the CUDA language. The Cublas handle is the context manager for all the * resources needed by Cublas. While a stream is a queue of sequential * operations executed in the Nvidia device. */ class CudaPipeline { public: CudaPipeline(int deviceID) : _deviceID{deviceID} { checkCuda(cudaSetDevice(deviceID)); cublasCreate(&_handle); cudaStreamCreate(&_stream); } ~CudaPipeline(); CudaPipeline() = delete; CudaPipeline(const CudaPipeline &) = delete; CudaPipeline &operator=(const CudaPipeline &) = delete; // Invoke the ?gemm function of cublas void gemm(const CudaMatrix &A, const CudaMatrix &B, CudaMatrix &C, bool transpose_A = false, bool transpose_B = false, double beta = 0.0) const; // Invoke the multiplication with a diagonal matrix of cublas, diagonal matrix // B must have 1 column void diag_gemm(const CudaMatrix &A, const CudaMatrix &b, CudaMatrix &C) const; const cudaStream_t &get_stream() const { return _stream; }; int getDeviceId() const { return _deviceID; } private: int _deviceID = 0; // The cublas handles allocates hardware resources on the host and device. cublasHandle_t _handle; // Asynchronous stream cudaStream_t _stream; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_CUDAPIPELINE_H xtp-2021.2/include/votca/xtp/davidsonsolver.h000066400000000000000000000224321412152066400212040ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_DAVIDSONSOLVER_H #define VOTCA_XTP_DAVIDSONSOLVER_H // Standard includes #include #include #include // Third party includes #include // Local VOTCA includes #include "eigen.h" #include "logger.h" using boost::format; using std::flush; namespace votca { namespace xtp { /** * \brief Use Davidson algorithm to solve A*V=E*V **/ class DavidsonSolver { public: DavidsonSolver(Logger &log); void set_iter_max(Index N) { this->_iter_max = N; } void set_max_search_space(Index N) { this->_max_search_space = N; } void set_tolerance(std::string tol); void set_correction(std::string method); void set_ortho(std::string method); void set_size_update(std::string update_size); void set_matrix_type(std::string mt); Eigen::ComputationInfo info() const { return _info; } Eigen::VectorXd eigenvalues() const { return this->_eigenvalues; } Eigen::MatrixXd eigenvectors() const { return this->_eigenvectors; } Eigen::MatrixXd residues() const { return this->_res; } Index num_iterations() const { return this->_i_iter; } template void solve(const MatrixReplacement &A, Index neigen, Index size_initial_guess = 0) { if (_max_search_space < neigen) { _max_search_space = neigen * 5; } std::chrono::time_point start = std::chrono::system_clock::now(); Index op_size = A.rows(); checkOptions(op_size); printOptions(op_size); // initial guess size if (size_initial_guess == 0) { size_initial_guess = 2 * neigen; } // get the diagonal of the operator this->_Adiag = A.diagonal(); // target the lowest diagonal element ProjectedSpace proj = initProjectedSpace(neigen, size_initial_guess); RitzEigenPair rep; XTP_LOG(Log::error, _log) << TimeStamp() << " iter\tSearch Space\tNorm" << flush; for (_i_iter = 0; _i_iter < _iter_max; _i_iter++) { bool do_restart = (proj.search_space() > _max_search_space); if (do_restart) { restart(rep, proj, size_initial_guess); } updateProjection(A, proj); rep = getRitzEigenPairs(A, proj); bool converged = checkConvergence(rep, proj, neigen); printIterationData(rep, proj, neigen); bool last_iter = _i_iter == (_iter_max - 1); if (converged) { storeConvergedData(rep, neigen); break; } else if (last_iter) { storeNotConvergedData(rep, proj.root_converged, neigen); break; } extendProjection(rep, proj); } printTiming(start); } private: Logger &_log; Index _iter_max = 50; Index _i_iter = 0; double _tol = 1E-4; Index _max_search_space = 0; Eigen::VectorXd _Adiag; enum CORR { DPR, OLSEN }; CORR _davidson_correction = CORR::DPR; enum UPDATE { MIN, SAFE, MAX }; UPDATE _davidson_update = UPDATE::SAFE; enum ORTHO { GS, QR }; ORTHO _davidson_ortho = ORTHO::GS; enum MATRIX_TYPE { SYMM, HAM }; MATRIX_TYPE _matrix_type = MATRIX_TYPE::SYMM; Eigen::VectorXd _eigenvalues; Eigen::MatrixXd _eigenvectors; Eigen::VectorXd _res; Eigen::ComputationInfo _info = Eigen::ComputationInfo::NoConvergence; struct RitzEigenPair { Eigen::VectorXd lambda; // eigenvalues Eigen::MatrixXd q; // Ritz (or harmonic Ritz) eigenvectors Eigen::MatrixXd U; // eigenvectors of the small subspace Eigen::MatrixXd res; // residues of the pairs Eigen::ArrayXd res_norm() const { return res.colwise().norm(); } // norm of the residues }; struct ProjectedSpace { Eigen::MatrixXd V; // basis of vectors Eigen::MatrixXd AV; // A * V Eigen::MatrixXd T; // V.T * A * V Index search_space() const { return V.cols(); }; // size of the projection i.e. number of cols in V Index size_update; // size update ... std::vector root_converged; // keep track of which root have onverged }; template void updateProjection(const MatrixReplacement &A, ProjectedSpace &proj) const { if (_i_iter == 0 || _davidson_ortho == ORTHO::QR) { /* if we use QR we need to recompute the entire projection since QR will modify original subspace*/ proj.AV = A * proj.V; proj.T = proj.V.transpose() * proj.AV; } else if (_davidson_ortho == ORTHO::GS) { /* if we use a GS ortho we do not have to recompute the entire projection as GS doesn't change the original subspace*/ Index old_dim = proj.T.cols(); Index new_dim = proj.V.cols(); Index nvec = new_dim - old_dim; proj.AV.conservativeResize(Eigen::NoChange, new_dim); proj.AV.rightCols(nvec) = A * proj.V.rightCols(nvec); Eigen::MatrixXd VAV = proj.V.transpose() * proj.AV.rightCols(nvec); proj.T.conservativeResize(new_dim, new_dim); proj.T.rightCols(nvec) = VAV; proj.T.bottomLeftCorner(nvec, old_dim) = proj.T.topRightCorner(old_dim, nvec).transpose(); } } template RitzEigenPair getRitzEigenPairs(const MatrixReplacement &A, const ProjectedSpace &proj) const { // get the ritz vectors switch (this->_matrix_type) { case MATRIX_TYPE::SYMM: { return getRitz(proj); } case MATRIX_TYPE::HAM: { return getHarmonicRitz(A, proj); } } return RitzEigenPair(); } template RitzEigenPair getHarmonicRitz(const MatrixReplacement &A, const ProjectedSpace &proj) const { /* Compute the Harmonic Ritz vector following * Computing Interior Eigenvalues of Large Matrices * Ronald B Morgan * LINEAR ALGEBRA AND ITS APPLICATIONS 154-156:289-309 (1991) * https://cpb-us-w2.wpmucdn.com/sites.baylor.edu/dist/e/71/files/2015/05/InterEvals-1vgdz91.pdf */ RitzEigenPair rep; Eigen::MatrixXd B = proj.V.transpose() * (A * proj.AV); bool return_eigenvectors = true; Eigen::GeneralizedEigenSolver ges(proj.T, B, return_eigenvectors); ArrayXl idx = DavidsonSolver::argsort(ges.eigenvalues().real()); // smallest to largest idx = idx.reverse(); // we need the largest values, because this is the inverse value, so reverse // list rep.U = DavidsonSolver::extract_vectors(ges.eigenvectors().real(), idx); rep.U.colwise().normalize(); rep.lambda = (rep.U.transpose() * proj.T * rep.U).diagonal(); rep.q = proj.V * rep.U; // Ritz vectors rep.res = proj.AV * rep.U - rep.q * rep.lambda.asDiagonal(); // residues return rep; } RitzEigenPair getRitz(const ProjectedSpace &proj) const; Index getSizeUpdate(Index neigen) const; void checkOptions(Index operator_size); void printOptions(Index operator_size) const; void printTiming( const std::chrono::time_point &start) const; void printIterationData(const RitzEigenPair &rep, const ProjectedSpace &proj, Index neigen) const; ArrayXl argsort(const Eigen::VectorXd &V) const; Eigen::MatrixXd setupInitialEigenvectors(Index size_initial_guess) const; Eigen::MatrixXd extract_vectors(const Eigen::MatrixXd &V, const ArrayXl &idx) const; Eigen::MatrixXd orthogonalize(const Eigen::MatrixXd &V, Index nupdate); Eigen::MatrixXd qr(const Eigen::MatrixXd &A) const; Eigen::MatrixXd gramschmidt(const Eigen::MatrixXd &A, Index nstart); Eigen::VectorXd computeCorrectionVector(const Eigen::VectorXd &qj, double lambdaj, const Eigen::VectorXd &Aqj) const; Eigen::VectorXd dpr(const Eigen::VectorXd &r, double lambda) const; Eigen::VectorXd olsen(const Eigen::VectorXd &r, const Eigen::VectorXd &x, double lambda) const; ProjectedSpace initProjectedSpace(Index neigen, Index size_initial_guess) const; void extendProjection(const RitzEigenPair &rep, ProjectedSpace &proj); bool checkConvergence(const RitzEigenPair &rep, ProjectedSpace &proj, Index neigen); void restart(const RitzEigenPair &rep, ProjectedSpace &proj, Index size_restart) const; void storeConvergedData(const RitzEigenPair &rep, Index neigen); void storeNotConvergedData(const RitzEigenPair &rep, std::vector &root_converged, Index neigen); void storeEigenPairs(const RitzEigenPair &rep, Index neigen); }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_DAVIDSONSOLVER_H xtp-2021.2/include/votca/xtp/density_integration.h000066400000000000000000000034271412152066400222270ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_DENSITY_INTEGRATION_H #define VOTCA_XTP_DENSITY_INTEGRATION_H // Local VOTCA includes #include "aobasis.h" #include "eigen.h" #include "regular_grid.h" #include "vxc_grid.h" namespace votca { namespace xtp { struct Gyrationtensor { double mass; Eigen::Vector3d centroid; Eigen::Matrix3d gyration; }; template class DensityIntegration { public: explicit DensityIntegration(const Grid& grid) : _grid(grid){}; double IntegrateDensity(const Eigen::MatrixXd& density_matrix); double IntegratePotential(const Eigen::Vector3d& rvector) const; Eigen::Vector3d IntegrateField(const Eigen::Vector3d& rvector) const; Eigen::MatrixXd IntegratePotential(const AOBasis& externalbasis) const; Gyrationtensor IntegrateGyrationTensor(const Eigen::MatrixXd& density_matrix); const std::vector >& getDensities() const { return _densities; } private: void SetupDensityContainer(); const Grid _grid; std::vector > _densities; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_DENSITY_INTEGRATION_H xtp-2021.2/include/votca/xtp/dftcoupling.h000066400000000000000000000042431412152066400204600ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_DFTCOUPLING_H #define VOTCA_XTP_DFTCOUPLING_H // Local VOTCA includes #include "couplingbase.h" namespace votca { namespace xtp { /** * \brief Evaluates electronic coupling elements * * B. Baumeier, J. Kirkpatrick, D. Andrienko, * Phys. Chem. Chem. Phys., 12, 11103-11113, 2010 * */ class DFTcoupling : public CouplingBase { public: std::string Identify() const { return "dftcoupling"; } void CalculateCouplings(const Orbitals& orbitalsA, const Orbitals& orbitalsB, const Orbitals& orbitalsAB) override; void Initialize(tools::Property&) override; void Addoutput(tools::Property& type_summary, const Orbitals& orbitalsA, const Orbitals& orbitalsB) const override; private: void WriteToProperty(tools::Property& type_summary, const Orbitals& orbitalsA, const Orbitals& orbitalsB, Index a, Index b) const; double getCouplingElement(Index levelA, Index levelB, const Orbitals& orbitalsA, const Orbitals& orbitalsB) const; std::pair DetermineRangeOfStates(const Orbitals& orbital, Index numberofstates) const; Eigen::MatrixXd JAB; double _degeneracy = 0.0; Index _numberofstatesA = 1; Index _numberofstatesB = 1; std::pair Range_orbA; std::pair Range_orbB; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_DFTCOUPLING_H xtp-2021.2/include/votca/xtp/dftengine.h000066400000000000000000000110041412152066400200760ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_DFTENGINE_H #define VOTCA_XTP_DFTENGINE_H // VOTCA includes #include // Local VOTCA includes #include "ERIs.h" #include "convergenceacc.h" #include "ecpaobasis.h" #include "logger.h" #include "staticsite.h" #include "vxc_grid.h" #include "vxc_potential.h" namespace votca { namespace xtp { class Orbitals; /** * \brief Electronic ground-state via Density-Functional Theory * * Evaluates electronic ground state in molecular systems based on * density functional theory with Gaussian Orbitals. * */ class DFTEngine { public: void Initialize(tools::Property& options); void setLogger(Logger* pLog) { _pLog = pLog; } void setExternalcharges( std::vector >* externalsites) { _externalsites = externalsites; _addexternalsites = true; } bool Evaluate(Orbitals& orb); std::string getDFTBasisName() const { return _dftbasis_name; }; private: void Prepare(QMMolecule& mol); Vxc_Potential SetupVxc(const QMMolecule& mol); Eigen::MatrixXd OrthogonalizeGuess(const Eigen::MatrixXd& GuessMOs) const; void PrintMOs(const Eigen::VectorXd& MOEnergies, Log::Level level); void CalcElDipole(const Orbitals& orb) const; std::array CalcERIs_EXX(const Eigen::MatrixXd& MOCoeff, const Eigen::MatrixXd& Dmat, double error) const; Eigen::MatrixXd CalcERIs(const Eigen::MatrixXd& Dmat, double error) const; void ConfigOrbfile(Orbitals& orb); void SetupInvariantMatrices(); Mat_p_Energy SetupH0(const QMMolecule& mol) const; Mat_p_Energy IntegrateExternalMultipoles( const QMMolecule& mol, const std::vector >& multipoles) const; Mat_p_Energy IntegrateExternalDensity(const QMMolecule& mol, const Orbitals& extdensity) const; Eigen::MatrixXd IntegrateExternalField(const QMMolecule& mol) const; tools::EigenSystem IndependentElectronGuess(const Mat_p_Energy& H0) const; tools::EigenSystem ModelPotentialGuess( const Mat_p_Energy& H0, const QMMolecule& mol, const Vxc_Potential& vxcpotential) const; Eigen::MatrixXd AtomicGuess(const QMMolecule& mol) const; Eigen::MatrixXd RunAtomicDFT_unrestricted(const QMAtom& uniqueAtom) const; double NuclearRepulsion(const QMMolecule& mol) const; double ExternalRepulsion( const QMMolecule& mol, const std::vector >& multipoles) const; Eigen::MatrixXd SphericalAverageShells(const Eigen::MatrixXd& dmat, const AOBasis& dftbasis) const; Logger* _pLog; // basis sets std::string _auxbasis_name; std::string _dftbasis_name; std::string _ecp_name; AOBasis _dftbasis; AOBasis _auxbasis; ECPAOBasis _ecp; bool _with_ecp; std::string _four_center_method; // direct | cache // Pre-screening double _screening_eps; // numerical integration Vxc std::string _grid_name; // AO Matrices AOOverlap _dftAOoverlap; bool _with_guess; std::string _initial_guess; // Convergence Index _numofelectrons = 0; Index _max_iter; ConvergenceAcc::options _conv_opt; // DIIS variables ConvergenceAcc _conv_accelerator; // Electron repulsion integrals ERIs _ERIs; // external charges std::vector >* _externalsites; bool _addexternalsites = false; // exchange and correlation double _ScaHFX; std::string _xc_functional_name; bool _integrate_ext_density = false; // integrate external density std::string _orbfilename; std::string _gridquality; std::string _state; Eigen::Vector3d _extfield = Eigen::Vector3d::Zero(); bool _integrate_ext_field = false; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_DFTENGINE_H xtp-2021.2/include/votca/xtp/diis.h000066400000000000000000000024541412152066400170740ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_DIIS_H #define VOTCA_XTP_DIIS_H // Standard includes #include // Local VOTCA includes #include "eigen.h" namespace votca { namespace xtp { class DIIS { public: void Update(Index maxerrorindex, const Eigen::MatrixXd& errormatrix); Eigen::VectorXd CalcCoeff(); void setHistLength(Index length) { _histlength = length; } bool Info() { return success; } private: bool success = true; Index _histlength; std::vector > _Diis_Bs; std::vector _errormatrixhist; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_DIIS_H xtp-2021.2/include/votca/xtp/dipoledipoleinteraction.h000066400000000000000000000130671412152066400230570ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_DIPOLEDIPOLEINTERACTION_H #define VOTCA_XTP_DIPOLEDIPOLEINTERACTION_H // Local VOTCA includes #include "eeinteractor.h" #include "eigen.h" namespace votca { namespace xtp { class DipoleDipoleInteraction; } } // namespace votca namespace Eigen { namespace internal { // MatrixReplacement looks-like a SparseMatrix, so let's inherits its traits: template <> struct traits : public Eigen::internal::traits {}; } // namespace internal } // namespace Eigen namespace votca { namespace xtp { class DipoleDipoleInteraction : public Eigen::EigenBase { public: // Required typedefs, constants, and method: using Scalar = double; using RealScalar = double; using StorageIndex = votca::Index; enum { ColsAtCompileTime = Eigen::Dynamic, MaxColsAtCompileTime = Eigen::Dynamic, IsRowMajor = false }; DipoleDipoleInteraction(const eeInteractor& interactor, const std::vector& segs) : _interactor(interactor) { _size = 0; for (const PolarSegment& seg : segs) { _size += 3 * seg.size(); } _sites.reserve(_size / 3); for (const PolarSegment& seg : segs) { for (const PolarSite& site : seg) { _sites.push_back(&site); } } } class InnerIterator { public: InnerIterator(const DipoleDipoleInteraction& xpr, const Index& id) : _xpr(xpr), _id(id){}; InnerIterator& operator++() { _row++; return *this; } operator bool() const { return _row < _xpr._size; } // DO not use the size method, it returns linear dimension*linear // dimension i.e _size^2 double value() const { return _xpr(_row, _id); } Index row() const { return _row; } Index col() const { return _id; } Index index() const { return row(); } private: const DipoleDipoleInteraction& _xpr; const Index _id; Index _row = 0; }; Index rows() const { return this->_size; } Index cols() const { return this->_size; } Index outerSize() const { return this->_size; } template Eigen::Product operator*(const Eigen::MatrixBase& x) const { return Eigen::Product(*this, x.derived()); } // this is not a fast method const double& operator()(const Index i, const Index j) const { Index seg1id = Index(i / 3); Index xyz1 = Index(i % 3); Index seg2id = Index(j / 3); Index xyz2 = Index(j % 3); if (seg1id == seg2id) { return _sites[seg1id]->getPInv()(xyz1, xyz2); } else { const PolarSite& site1 = *_sites[seg1id]; const PolarSite& site2 = *_sites[seg2id]; return _interactor.FillTholeInteraction(site1, site2)(xyz1, xyz2); } }; Eigen::VectorXd multiply(const Eigen::VectorXd& v) const { assert(v.size() == _size && "input vector has the wrong size for multiply with operator"); const Index segment_size = Index(_sites.size()); Eigen::VectorXd result = Eigen::VectorXd::Zero(_size); #pragma omp parallel for schedule(dynamic) reduction(+ : result) for (Index i = 0; i < segment_size; i++) { const PolarSite& site1 = *_sites[i]; result.segment<3>(3 * i) += site1.getPInv() * v.segment<3>(3 * i); for (Index j = i + 1; j < segment_size; j++) { const PolarSite& site2 = *_sites[j]; Eigen::Matrix3d block = _interactor.FillTholeInteraction(site1, site2); result.segment<3>(3 * i) += block * v.segment<3>(3 * j); result.segment<3>(3 * j) += block.transpose() * v.segment<3>(3 * i); } } return result; } private: const eeInteractor& _interactor; std::vector _sites; Index _size; }; } // namespace xtp } // namespace votca namespace Eigen { namespace internal { // replacement of the mat*vect operation template struct generic_product_impl : generic_product_impl_base< votca::xtp::DipoleDipoleInteraction, Vtype, generic_product_impl> { typedef typename Product::Scalar Scalar; template static void scaleAndAddTo(Dest& dst, const votca::xtp::DipoleDipoleInteraction& op, const Vtype& v, const Scalar& alpha) { // returns dst = alpha * op * v // alpha must be 1 here assert(alpha == Scalar(1) && "scaling is not implemented"); EIGEN_ONLY_USED_FOR_DEBUG(alpha); Eigen::VectorXd temp = op.multiply(v); dst = temp.cast(); // tumbleweed fix do not delete } }; } // namespace internal } // namespace Eigen #endif // VOTCA_XTP_DIPOLEDIPOLEINTERACTION_H xtp-2021.2/include/votca/xtp/ecpaobasis.h000066400000000000000000000045001412152066400202470ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_ECPAOBASIS_H #define VOTCA_XTP_ECPAOBASIS_H // Local VOTCA includes #include "ecpaoshell.h" #include "eigen.h" namespace votca { namespace xtp { class QMMolecule; class ECPBasisSet; /** * \brief Container to hold ECPs for all atoms * * It is constructed from a vector of QMAtoms and an ECPBasisSet. */ class ECPAOBasis { public: // returns element names for which no ecp was found std::vector Fill(const ECPBasisSet& bs, QMMolecule& atoms); Index ECPAOBasisSize() const { return _AOBasisSize; } using ECPAOShellIterator = std::vector::const_iterator; ECPAOShellIterator begin() const { return _aoshells.begin(); } ECPAOShellIterator end() const { return _aoshells.end(); } const ECPAOShell& getShell(Index idx) const { return _aoshells[idx]; } const ECPAOShell& back() const { return _aoshells.back(); } std::vector > ShellsPerAtom() const; void AddECPChargeToMolecule(QMMolecule& mol) const; const std::string& Name() const { return _name; } void UpdateShellPositions(const QMMolecule& mol); void WriteToCpt(CheckpointWriter& w) const; void ReadFromCpt(CheckpointReader& r); void add(const ECPAOBasis& other); friend std::ostream& operator<<(std::ostream& out, const ECPAOBasis& ecp); private: void clear(); ECPAOShell& addShell(const ECPShell& shell, const QMAtom& atom, Index startIndex, L Lmax); std::vector _ncore_perAtom; std::vector _aoshells; std::string _name = ""; Index _AOBasisSize; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ECPAOBASIS_H xtp-2021.2/include/votca/xtp/ecpaoshell.h000066400000000000000000000075021412152066400202620ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_ECPAOSHELL_H #define VOTCA_XTP_ECPAOSHELL_H // VOTCA includes #include // Local VOTCA includes #include "ecpbasisset.h" #include "eigen.h" #include "qmatom.h" namespace votca { namespace xtp { class ECPAOShell; class ECPAOGaussianPrimitive { public: ECPAOGaussianPrimitive(const ECPGaussianPrimitive& gaussian) : _power(gaussian._power), _decay(gaussian._decay), _contraction(gaussian._contraction) { ; } struct data { Index atomid; Index l; Index lmax; Index startindex; Index power; double decay; double contraction; double x; double y; double z; }; ECPAOGaussianPrimitive(const ECPAOGaussianPrimitive::data& d) { _decay = d.decay; _contraction = d.contraction; _power = d.power; } void WriteData(data& d, const ECPAOShell& shell) const; void SetupCptTable(CptTable& table) const; Index getPower() const { return _power; } double getDecay() const { return _decay; } double getContraction() const { return _contraction; } private: Index _power = 0; double _decay = 0.0; double _contraction = 0.0; }; /* * shells in a Gaussian-basis expansion */ class ECPAOBasis; class ECPAOShell { friend ECPAOBasis; public: ECPAOShell(const ECPShell& shell, const QMAtom& atom, Index startIndex, L Lmax) : _L(shell.getL()), _startIndex(startIndex), _pos(atom.getPos()), _atomindex(atom.getId()), _Lmax_element(Lmax) { ; } ECPAOShell(const ECPAOGaussianPrimitive::data& d) { _L = static_cast(d.l); _Lmax_element = static_cast(d.lmax); _startIndex = d.startindex; _atomindex = d.atomid; _pos = Eigen::Vector3d(d.x, d.y, d.z); _gaussians.push_back(ECPAOGaussianPrimitive(d)); } Index getNumFunc() const { return NumFuncShell(_L); } Index getStartIndex() const { return _startIndex; } Index getOffset() const { return OffsetFuncShell(_L); } Index getAtomIndex() const { return _atomindex; } L getL() const { return _L; } L getLmaxElement() const { return _Lmax_element; } // Local part is with L=Lmax bool isNonLocal() const { return (_L < _Lmax_element); } const Eigen::Vector3d& getPos() const { return _pos; } Index getSize() const { return _gaussians.size(); } // iterator over pairs (decay constant; contraction coefficient) using ECPGaussianIterator = std::vector::const_iterator; ECPGaussianIterator begin() const { return _gaussians.begin(); } ECPGaussianIterator end() const { return _gaussians.end(); } // adds a Gaussian void addGaussian(const ECPGaussianPrimitive& gaussian) { _gaussians.push_back(ECPAOGaussianPrimitive(gaussian)); return; } friend std::ostream& operator<<(std::ostream& out, const ECPAOShell& shell); private: L _L; Index _startIndex; Eigen::Vector3d _pos; Index _atomindex; L _Lmax_element; // Lmax of the Element not the shell // vector of pairs of decay constants and contraction coefficients std::vector _gaussians; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ECPAOSHELL_H xtp-2021.2/include/votca/xtp/ecpbasisset.h000066400000000000000000000075371412152066400204600ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_ECPBASISSET_H #define VOTCA_XTP_ECPBASISSET_H // Local VOTCA includes #include "basisset.h" namespace votca { namespace xtp { class ECPGaussianPrimitive { public: ECPGaussianPrimitive(Index power, double decay, double contraction) : _power(power), _decay(decay), _contraction(contraction) { ; } Index _power; double _decay; double _contraction; }; class ECPShell { public: ECPShell(L l) : _l(l) { ; } L getL() const { return _l; } Index getnumofFunc() const { return NumFuncShell(_l); } Index getOffset() const { return OffsetFuncShell(_l); } Index getSize() const { return _gaussians.size(); } std::vector::const_iterator begin() const { return _gaussians.begin(); } std::vector::const_iterator end() const { return _gaussians.end(); } // adds a Gaussian of a pseudopotential ECPGaussianPrimitive& addGaussian(Index power, double decay, double contraction); friend std::ostream& operator<<(std::ostream& out, const ECPShell& shell); private: L _l; // vector of pairs of decay constants and contraction coefficients std::vector _gaussians; }; /* * A collection of shells associated with a specific element */ class ECPElement { public: ECPElement(std::string type, L lmax, Index ncore) : _type(type), _lmax(lmax), _ncore(ncore) { ; } using ECPShellIterator = std::vector::const_iterator; ECPShellIterator begin() const { return _shells.begin(); } ECPShellIterator end() const { return _shells.end(); } const std::string& getType() const { return _type; } L getLmax() const { return _lmax; } Index getNcore() const { return _ncore; } ECPShell& addShell(L l) { _shells.push_back(ECPShell(l)); return _shells.back(); } Index NumOfShells() const { return _shells.size(); } friend std::ostream& operator<<(std::ostream& out, const ECPElement& element); private: std::string _type; // applies to the highest angular momentum lmax L _lmax; // replaces ncore electrons Index _ncore; std::vector _shells; }; /* * A collection of elements and shells forms the basis set */ class ECPBasisSet { public: void Load(const std::string& name); ECPElement& addElement(std::string elementType, L lmax, Index ncore); const ECPElement& getElement(std::string element_type) const; std::map >::iterator begin() { return _elements.begin(); } std::map >::iterator end() { return _elements.end(); } const std::string& Name() const { return _name; } std::map >::const_iterator begin() const { return _elements.begin(); } std::map >::const_iterator end() const { return _elements.end(); } friend std::ostream& operator<<(std::ostream& out, const ECPBasisSet& basis); private: std::string _name; std::map > _elements; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ECPBASISSET_H xtp-2021.2/include/votca/xtp/eeinteractor.h000066400000000000000000000067051412152066400206330ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_EEINTERACTOR_H #define VOTCA_XTP_EEINTERACTOR_H // Local VOTCA includes #include "classicalsegment.h" #include "eigen.h" namespace votca { namespace xtp { enum Estatic : bool { noE_V = true, V = false, }; /** * \brief Mediates interaction between polar and static sites */ class eeInteractor { public: explicit eeInteractor() = default; explicit eeInteractor(double expdamping) : _expdamping(expdamping){}; Eigen::Matrix3d FillTholeInteraction(const PolarSite& site1, const PolarSite& site2) const; Eigen::VectorXd Cholesky_IntraSegment(const PolarSegment& seg) const; template double ApplyStaticField(const T& segment1, PolarSegment& segment2) const; template double ApplyInducedField(const PolarSegment& segment1, PolarSegment& segment2) const; template double CalcStaticEnergy(const S1& segment1, const S2& segment2) const; class E_terms { public: E_terms& operator+=(const E_terms& right) { this->_data += right._data; return *this; } E_terms operator+(E_terms right) const { right._data += this->_data; return right; } double sum() { return _data.sum(); } double& E_indu_indu() { return _data.x(); } double& E_indu_stat() { return _data.y(); } double& E_internal() { return _data.z(); } const Eigen::Vector3d& data() const { return _data; } private: Eigen::Vector3d _data = Eigen::Vector3d::Zero(); }; template E_terms CalcPolarEnergy(const S1& segment1, const S2& segment2) const; template double CalcStaticEnergy_IntraSegment(const S& seg) const; double CalcPolarEnergy_IntraSegment(const PolarSegment& seg) const; double CalcStaticEnergy_site(const StaticSite& site1, const StaticSite& site2) const; private: template Eigen::Matrix VSiteA(const StaticSite& site1, const StaticSite& site2) const; template double ApplyInducedField_site(const PolarSite& site1, PolarSite& site2) const; template double ApplyStaticField_site(const StaticSite& site1, PolarSite& site2) const; double CalcPolar_stat_Energy_site(const PolarSite& site1, const StaticSite& site2) const; E_terms CalcPolarEnergy_site(const PolarSite& site1, const StaticSite& site2) const; E_terms CalcPolarEnergy_site(const PolarSite& site1, const PolarSite& site2) const; double _expdamping = 0.39; // dimensionless }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_EEINTERACTOR_H xtp-2021.2/include/votca/xtp/eigen.h000066400000000000000000000105771412152066400172400ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_EIGEN_H #define VOTCA_XTP_EIGEN_H // CMake Generated file // clang-format off // order seems to matter here #include "votca_xtp_config.h" #include //clang-format on // VOTCA includes #include #include typedef Eigen::Matrix Vector9d; typedef Eigen::Matrix Matrix9d; typedef Eigen::Array ArrayXl; namespace votca { namespace xtp { inline bool XTP_HAS_MKL_OVERLOAD() { bool mkl_overload = false; #ifdef EIGEN_USE_MKL_ALL mkl_overload = true; #endif bool mkl_found = false; #ifdef MKL_FOUND mkl_found = true; #endif if (mkl_overload && mkl_found) { return true; } else { return false; } } // Stores matrix and energy together class Mat_p_Energy { public: Mat_p_Energy() : _energy(0.0), _matrix(Eigen::MatrixXd::Zero(0, 0)){}; Mat_p_Energy(Index rows, Index cols) : _energy(0.0), _matrix(Eigen::MatrixXd::Zero(rows, cols)){}; Mat_p_Energy(double e, const Eigen::MatrixXd& mat) : _energy(e), _matrix(mat){}; Mat_p_Energy(double e, Eigen::MatrixXd&& mat) : _energy(e), _matrix(std::move(mat)){}; Mat_p_Energy operator+(const Mat_p_Energy& other) const { Mat_p_Energy result = *this; result._energy += other._energy; result._matrix += other._matrix; return result; } Index rows() const { return _matrix.rows(); } Index cols() const { return _matrix.cols(); } Eigen::MatrixXd& matrix() { return _matrix; } double& energy() { return _energy; } const Eigen::MatrixXd& matrix() const { return _matrix; } double energy() const { return _energy; } private: double _energy; Eigen::MatrixXd _matrix; }; //Stores the diadicProduct of a vector with itself class AxA { public: AxA(const Eigen::Vector3d& a) { _data.segment<3>(0) = a.x() * a; _data.segment<2>(3) = a.y() * a.segment<2>(1); _data[5] = a.z() * a.z(); } inline const double& xx() const { return _data[0]; } inline const double& xy() const { return _data[1]; } inline const double& xz() const { return _data[2]; } inline const double& yy() const { return _data[3]; } inline const double& yz() const { return _data[4]; } inline const double& zz() const { return _data[5]; } private: Eigen::Matrix _data; }; #pragma omp declare reduction (+:Mat_p_Energy: omp_out=omp_out+omp_in)\ initializer(omp_priv=Mat_p_Energy(omp_orig.rows(),omp_orig.cols())) #pragma omp declare reduction (+: Eigen::VectorXd: omp_out=omp_out+omp_in)\ initializer(omp_priv=Eigen::VectorXd::Zero(omp_orig.size())) #pragma omp declare reduction (+: Eigen::MatrixXd: omp_out=omp_out+omp_in)\ initializer(omp_priv=Eigen::MatrixXd::Zero(omp_orig.rows(),omp_orig.cols())) #pragma omp declare reduction (+: Eigen::Matrix3d: omp_out=omp_out+omp_in)\ initializer(omp_priv=Eigen::Matrix3d::Zero()) #pragma omp declare reduction (+: Eigen::Vector3d: omp_out=omp_out+omp_in)\ initializer(omp_priv=Eigen::Vector3d::Zero()) namespace OPENMP { inline Index getMaxThreads() { Index nthreads = 1; #ifdef _OPENMP nthreads = Index(omp_get_max_threads()); #endif return nthreads; } inline bool InsideActiveParallelRegion(){ #ifdef _OPENMP return omp_in_parallel(); #endif return false; } inline Index getThreadId() { Index thread_id = 0; #ifdef _OPENMP thread_id = Index(omp_get_thread_num()); #endif return thread_id; } #ifdef _OPENMP inline void setMaxThreads(Index threads) { if (threads > 0) { omp_set_num_threads(int(threads)); } } #else inline void setMaxThreads(Index) {} #endif } // namespace OPENMP } // namespace xtp } // namespace votca #endif // VOTCA_XTP_EIGEN_H xtp-2021.2/include/votca/xtp/energy_costfunction.h000066400000000000000000000052261412152066400222330ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_ENERGY_COSTFUNCTION_H #define VOTCA_XTP_ENERGY_COSTFUNCTION_H // Local VOTCA includes #include "forces.h" #include "optimiser_costfunction.h" #include "orbitals.h" namespace votca { namespace xtp { class Energy_costfunction : public Optimiser_costfunction { public: struct conv_paras { double deltaE; double RMSForce; double MaxForce; double RMSStep; double MaxStep; Index maxforceindex = 0; Index maxstepindex = 0; }; Energy_costfunction(GWBSEEngine& gwbse_engine, StateTracker& tracker, Orbitals& orbitals, Forces& force_engine) : _gwbse_engine(gwbse_engine), _tracker(tracker), _orbitals(orbitals), _force_engine(force_engine){}; double EvaluateCost(const Eigen::VectorXd& parameters) override; Eigen::VectorXd EvaluateGradient(const Eigen::VectorXd& parameters) override; Index NumParameters() const override { return Index(_orbitals.QMAtoms().size() * 3); }; bool Converged(const Eigen::VectorXd& delta_parameters, double delta_cost, const Eigen::VectorXd& gradient) override; void ForcesReport() const { return _force_engine.Report(); } const conv_paras& getConvParas() const { return _convpara; } void setConvergenceParameters(const conv_paras& convergence) { _convpara = convergence; } void setLog(Logger* pLog) { _pLog = pLog; } void Report(const conv_paras& val); static void Vector2QMAtoms(const Eigen::VectorXd& pos, QMMolecule& atoms); static Eigen::VectorXd QMAtoms2Vector(QMMolecule& atoms); static Eigen::VectorXd Write3XMatrixToVector(const Eigen::MatrixX3d& matrix); private: static std::string Converged(double val, double limit); GWBSEEngine& _gwbse_engine; StateTracker& _tracker; Orbitals& _orbitals; Forces& _force_engine; Index _iteration = 0; double _energy; conv_paras _convpara; Logger* _pLog; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ENERGY_COSTFUNCTION_H xtp-2021.2/include/votca/xtp/energy_terms.h000066400000000000000000000053211412152066400206430ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_ENERGY_TERMS_H #define VOTCA_XTP_ENERGY_TERMS_H // Local VOTCA includes #include "eeinteractor.h" #include "eigen.h" /** * \brief Small container for the individual energy terms in a polar region * * */ namespace votca { namespace xtp { class Energy_terms { public: Energy_terms& operator+=(const Energy_terms& right) { this->_data += right._data; return *this; } Energy_terms operator+(Energy_terms right) const { right._data += this->_data; return right; } Energy_terms operator-(Energy_terms right) const { right._data *= (-1); right._data += this->_data; return right; } void addInternalPolarContrib(const eeInteractor::E_terms& induction_terms) { _data.segment<3>(0) += induction_terms.data(); } double Etotal() const { return _data.sum(); } // total energy double Epolar() const { return _data.segment<4>(0).sum(); } // all polar inside region and from outside contributions // dQ-dQ,Q-dQ,E_internal double Estatic() const { return _data.segment<2>(4).sum(); } // all static contributions Q-Q inside region and from outside double Eextern() const { return _data.segment<2>(3).sum(); } // all external contributions double Eintern() const { return Etotal() - Eextern(); } // all internal contributions double& E_indu_indu() { return _data[0]; } // dQ-dQ inside region double& E_indu_stat() { return _data[1]; } // dQ-Q inside region double& E_internal() { return _data[2]; } // e_internal double& E_polar_ext() { return _data[3]; } // dQ-Q and dQ-dQ from outside regions double& E_static_ext() { return _data[4]; } // Q-Q from outside regions double& E_static_static() { return _data[5]; } // Q-Q inside region const Eigen::Matrix& data() const { return _data; } Eigen::Matrix& data() { return _data; } private: Eigen::Matrix _data = Eigen::Matrix::Zero(); }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ENERGY_TERMS_H xtp-2021.2/include/votca/xtp/esp2multipole.h000066400000000000000000000043131412152066400207440ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_ESP2MULTIPOLE_H #define VOTCA_XTP_ESP2MULTIPOLE_H // Standard includes #include // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "classicalsegment.h" #include "espfit.h" #include "logger.h" #include "orbitals.h" namespace votca { namespace xtp { class Esp2multipole { public: Esp2multipole(Logger& log) : _log(log) { _pairconstraint.resize(0); _regionconstraint.resize(0); } std::string Identify() { return "esp2multipole"; } void Initialize(tools::Property& options); StaticSegment Extractingcharges(const Orbitals& orbitals) const; std::string GetStateString() const { return _state.ToString(); } private: void PrintDipoles(const Orbitals& orbitals, const StaticSegment& seg) const; QMState _state; std::string _method; std::string _gridsize; bool _use_mulliken; bool _use_lowdin; bool _use_CHELPG; bool _do_svd; double _conditionnumber; Logger& _log; std::vector > _pairconstraint; // pairconstraint[i] // is all the // atomindices which // have the same // charge std::vector > _regionconstraint; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ESP2MULTIPOLE_H xtp-2021.2/include/votca/xtp/espfit.h000066400000000000000000000047761412152066400174470ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_ESPFIT_H #define VOTCA_XTP_ESPFIT_H // Local VOTCA includes #include "classicalsegment.h" #include "logger.h" #include "qmfragment.h" /** * \brief Takes a list of atoms, and the corresponding density matrix and puts * out a table of partial charges */ namespace votca { namespace xtp { class Orbitals; class Grid; class QMState; class QMMolecule; class Espfit { public: Espfit(Logger& log) : _log(log) { _pairconstraint.resize(0); _regionconstraint.resize(0); } void setUseSVD(double conditionnumber) { _do_svd = true; _conditionnumber = conditionnumber; } void setPairConstraint(std::vector > pairconstraint) { _pairconstraint = pairconstraint; } void setRegionConstraint(std::vector > regionconstraint) { _regionconstraint = regionconstraint; } StaticSegment Fit2Density(const Orbitals& orbitals, const QMState& state, std::string gridsize); private: Logger& _log; bool _do_svd = true; double _conditionnumber = 1e-8; std::vector > _pairconstraint; // pairconstraint[i] // is all the // atomindices which // have the same // charge std::vector > _regionconstraint; void EvalNuclearPotential(const QMMolecule& atoms, Grid& grid); // Fits partial charges to Potential on a grid, constrains net charge StaticSegment FitPartialCharges(const Orbitals& orbitals, const Grid& grid, double netcharge); }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ESPFIT_H xtp-2021.2/include/votca/xtp/filterfactory.h000066400000000000000000000024251412152066400210170ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_FILTERFACTORY_H #define VOTCA_XTP_FILTERFACTORY_H // VOTCA includes #include // Local VOTCA includes #include "statefilter_base.h" namespace votca { namespace xtp { class FilterFactory : public tools::ObjectFactory { private: FilterFactory() = default; public: static void RegisterAll(void); friend FilterFactory &Filter(); }; inline FilterFactory &Filter() { static FilterFactory _instance; return _instance; } } // namespace xtp } // namespace votca #endif // VOTCA_XTP_FILTERFACTORY_H xtp-2021.2/include/votca/xtp/forces.h000066400000000000000000000034061412152066400174230ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_FORCES_H #define VOTCA_XTP_FORCES_H // Standard includes #include // Local VOTCA includes #include "gwbseengine.h" #include "logger.h" #include "qmatom.h" #include "segment.h" namespace votca { namespace xtp { class StateTracker; class Forces { public: Forces(GWBSEEngine& gwbse_engine, const StateTracker& tracker) : _gwbse_engine(gwbse_engine), _tracker(tracker){}; void Initialize(tools::Property& options); void Calculate(const Orbitals& orbitals); void setLog(Logger* pLog) { _pLog = pLog; } const Eigen::MatrixX3d& GetForces() const { return _forces; }; void Report() const; private: Eigen::Vector3d NumForceForward(Orbitals orbitals, Index atom_index); Eigen::Vector3d NumForceCentral(Orbitals orbitals, Index atom_index); void RemoveTotalForce(); double _displacement; std::string _force_method; GWBSEEngine& _gwbse_engine; const StateTracker& _tracker; bool _remove_total_force = true; Eigen::MatrixX3d _forces; Logger* _pLog; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_FORCES_H xtp-2021.2/include/votca/xtp/geometry_optimization.h000066400000000000000000000036751412152066400226130ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_GEOMETRY_OPTIMIZATION_H #define VOTCA_XTP_GEOMETRY_OPTIMIZATION_H // Standard includes #include // Local VOTCA includes #include "bfgs_trm.h" #include "energy_costfunction.h" #include "gwbseengine.h" #include "logger.h" #include "qmatom.h" #include "qmstate.h" namespace votca { namespace xtp { class GeometryOptimization { public: GeometryOptimization(GWBSEEngine& gwbse_engine, Orbitals& orbitals) : _gwbse_engine(gwbse_engine), _orbitals(orbitals){ }; void Initialize(tools::Property& options); void setLog(Logger* pLog) { _pLog = pLog; } void Evaluate(); private: static void Report(const BFGSTRM& bfgstrm, const Forces& forces, Logger& pLog); static void WriteTrajectory(const std::string& filename, QMMolecule& atoms, const BFGSTRM& bfgstrm); QMState _opt_state; std::string _optimizer; std::string _trajfile; GWBSEEngine& _gwbse_engine; Orbitals& _orbitals; Energy_costfunction::conv_paras _conv; Index _max_iteration; double _trust_radius; tools::Property _statetracker_options; tools::Property _force_options; Logger* _pLog; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_GEOMETRY_OPTIMIZATION_H xtp-2021.2/include/votca/xtp/glink.h000066400000000000000000000027761412152066400172570ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_GLINK_H #define VOTCA_XTP_GLINK_H // Local VOTCA includes #include "eigen.h" namespace votca { namespace xtp { class GNode; class GLink { public: GLink(GNode* dest, double rate, const Eigen::Vector3d& dr) : destination(dest), _rate(rate), _dr(dr){}; GLink(double rate) : _rate(rate), _decayevent(true){}; double getValue() const { return _rate; } double getRate() const { return _rate; } GNode* getDestination() const { assert(!_decayevent && "Decay event has no destination"); return destination; } const Eigen::Vector3d& getDeltaR() const { return _dr; } bool isDecayEvent() const { return _decayevent; } private: GNode* destination = nullptr; double _rate = 0.0; Eigen::Vector3d _dr = Eigen::Vector3d::Zero(); bool _decayevent = false; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_GLINK_H xtp-2021.2/include/votca/xtp/gnode.h000066400000000000000000000046531412152066400172430ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_GNODE_H #define VOTCA_XTP_GNODE_H // Local VOTCA includes #include "glink.h" #include "huffmantree.h" #include "qmpair.h" #include "segment.h" namespace votca { namespace xtp { class GNode { public: GNode(const Segment& seg, QMStateType carriertype, bool injectable) : _id(seg.getId()), _siteenergy(seg.getSiteEnergy(carriertype)), _position(seg.getPos()), _injectable(injectable){}; bool isOccupied() const { return _occupied; } void setOccupation(bool occupied) { _occupied = occupied; } bool isInjectable() const { return _injectable; } bool canDecay() const { return _hasdecay; } const Eigen::Vector3d& getPos() const { return _position; } Index getId() const { return _id; } void UpdateOccupationTime(double deltat) { _occupationtime += deltat; } const std::vector& Events() const { return _events; } double OccupationTime() const { return _occupationtime; } double getEscapeRate() const { return _escape_rate; } void InitEscapeRate(); void AddDecayEvent(double decayrate); void AddEventfromQmPair(const QMPair& pair, std::vector& nodes, double rate); double getSitenergy() const { return _siteenergy; } GLink* findHoppingDestination(double p) const; void MakeHuffTree(); void AddEvent(GNode* seg2, const Eigen::Vector3d& dr, double rate); private: Index _id = 0; bool _occupied = false; double _occupationtime = 0.0; double _escape_rate = 0.0; bool _hasdecay = false; double _siteenergy; Eigen::Vector3d _position; bool _injectable = true; std::vector _events; huffmanTree hTree; void organizeProbabilities(Index id, double add); void moveProbabilities(Index id); }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_GNODE_H xtp-2021.2/include/votca/xtp/grid.h000066400000000000000000000041651412152066400170720ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_GRID_H #define VOTCA_XTP_GRID_H // Standard includes #include #include // Local VOTCA includes #include "logger.h" #include "qmatom.h" #include "qmmolecule.h" /** * \brief Takes a list of atoms, and creates CHELPG grid. * * * */ namespace votca { namespace xtp { class Grid { public: const std::vector &getGridPositions() const { return _gridpoints; } Eigen::VectorXd &getGridValues() { return _gridvalues; } const Eigen::VectorXd &getGridValues() const { return _gridvalues; } Index size() { return Index(_gridpoints.size()); } void printGridtoxyzfile(std::string filename); void setupCHELPGGrid(const QMMolecule &Atomlist) { _padding = 3 * tools::conv::ang2bohr; // Additional distance from molecule // to set up grid according to CHELPG // paper [Journal of Computational // Chemistry 11, 361, 1990] _gridspacing = 0.3 * tools::conv::ang2bohr; // Grid spacing according to same paper _cutoff = 2.8 * tools::conv::ang2bohr; setupgrid(Atomlist); } private: void setupgrid(const QMMolecule &Atomlist); std::vector _gridpoints; Eigen::VectorXd _gridvalues; double _cutoff; double _gridspacing; double _padding; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_GRID_H xtp-2021.2/include/votca/xtp/grid_containers.h000066400000000000000000000030131412152066400213060ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_GRID_CONTAINERS_H #define VOTCA_XTP_GRID_CONTAINERS_H // Local VOTCA includes #include "aobasis.h" namespace votca { namespace xtp { class GridContainers { public: // containers for radial grids per element struct radial_grid { Eigen::VectorXd radius; Eigen::VectorXd weight; }; std::map radial_grids; // containers for spherical grids on a unit sphere per element struct spherical_grid { Eigen::VectorXd theta; Eigen::VectorXd phi; Eigen::VectorXd weight; }; std::map spherical_grids; // container for cartesian grid points and weights struct Cartesian_gridpoint { Eigen::Vector3d grid_pos; // bohr double grid_weight; }; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_GRID_CONTAINERS_H xtp-2021.2/include/votca/xtp/gridbox.h000066400000000000000000000063251412152066400176030ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_GRIDBOX_H #define VOTCA_XTP_GRIDBOX_H // Local VOTCA includes #include "aoshell.h" #include "grid_containers.h" namespace votca { namespace xtp { struct GridboxRange { Index start; Index size; }; class GridBox { public: void FindSignificantShells(const AOBasis& basis); Eigen::VectorXd CalcAOValue_and_Grad(Eigen::MatrixX3d& ao_grad, const Eigen::Vector3d& point) const; Eigen::VectorXd CalcAOValues(const Eigen::Vector3d& pos) const; const std::vector& getGridPoints() const { return grid_pos; } const std::vector& getGridWeights() const { return weights; } const std::vector& getShells() const { return significant_shells; } const std::vector& getAOranges() const { return aoranges; } Index size() const { return Index(grid_pos.size()); } Index Shellsize() const { return Index(significant_shells.size()); } Index Matrixsize() const { return matrix_size; } void addGridBox(const GridBox& box) { grid_pos.insert(grid_pos.end(), box.grid_pos.begin(), box.grid_pos.end()); weights.insert(weights.end(), box.weights.begin(), box.weights.end()); return; } void addGridPoint(const GridContainers::Cartesian_gridpoint& point) { grid_pos.push_back(point.grid_pos); weights.push_back(point.grid_weight); }; void addShell(const AOShell* shell) { significant_shells.push_back(shell); matrix_size += shell->getNumFunc(); }; void PrepareForIntegration(); Eigen::MatrixXd ReadFromBigMatrix(const Eigen::MatrixXd& bigmatrix) const; Eigen::VectorXd ReadFromBigVector(const Eigen::VectorXd& bigvector) const; void AddtoBigMatrix(Eigen::MatrixXd& bigmatrix, const Eigen::MatrixXd& smallmatrix) const; static bool compareGridboxes(GridBox& box1, GridBox& box2) { if (box1.Matrixsize() != box2.Matrixsize()) { return false; } if (box1.Shellsize() != box2.Shellsize()) { return false; } for (Index i = 0; i < Index(box1.significant_shells.size()); ++i) { if (box1.significant_shells[i] != box2.significant_shells[i]) { return false; } } return true; } private: Index matrix_size = 0; std::vector aoranges; std::vector ranges; std::vector inv_ranges; std::vector grid_pos; std::vector significant_shells; std::vector weights; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_GRIDBOX_H xtp-2021.2/include/votca/xtp/gw.h000066400000000000000000000121511412152066400165540ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_GW_H #define VOTCA_XTP_GW_H // Local VOTCA includes #include "logger.h" #include "orbitals.h" #include "rpa.h" #include "sigma_base.h" #include "threecenter.h" namespace votca { namespace xtp { class GW { public: GW(Logger& log, TCMatrix_gwbse& Mmn, const Eigen::MatrixXd& vxc, const Eigen::VectorXd& dft_energies) : _log(log), _Mmn(Mmn), _vxc(vxc), _dft_energies(dft_energies), _rpa(log, Mmn){}; struct options { Index homo; Index qpmin; Index qpmax; Index rpamin; Index rpamax; double eta; double g_sc_limit; Index g_sc_max_iterations; double gw_sc_limit; Index gw_sc_max_iterations; double shift = 0; double ScaHFX = 0.0; std::string sigma_integration; Index reset_3c; // how often the 3c integrals in iterate should be // rebuilt std::string qp_solver; double qp_solver_alpha = 0.75; Index qp_grid_steps; // Number of grid points double qp_grid_spacing; // Spacing of grid points in Ha Index gw_mixing_order; // mixing order double gw_mixing_alpha; // mixing alpha, also linear mixing std::string quadrature_scheme; // Kind of Gaussian-quadrature scheme to use Index order; // only needed for complex integration sigma CDA double alpha; // smooth tail in complex integration sigma CDA }; void configure(const options& opt); Eigen::VectorXd getGWAResults() const; // Calculates the diagonal elements up to self consistency void CalculateGWPerturbation(); // Calculated offdiagonal elements as well void CalculateHQP(); Eigen::MatrixXd getHQP() const; // Diagonalize QP particle Hamiltonian Eigen::SelfAdjointEigenSolver DiagonalizeQPHamiltonian() const; void PlotSigma(std::string filename, Index steps, double spacing, std::string states) const; Eigen::VectorXd RPAInputEnergies() const { return _rpa.getRPAInputEnergies(); } private: Index _qptotal; Eigen::MatrixXd _Sigma_x; Eigen::MatrixXd _Sigma_c; options _opt; std::unique_ptr _sigma = nullptr; Logger& _log; TCMatrix_gwbse& _Mmn; const Eigen::MatrixXd& _vxc; const Eigen::VectorXd& _dft_energies; RPA _rpa; // small class which calculates f(w) with and df/dw(w) // f=Sigma_c(w)+offset-w // offset= e_dft+Sigma_x-Vxc class QPFunc { public: QPFunc(Index gw_level, const Sigma_base& sigma, double offset) : _gw_level(gw_level), _offset(offset), _sigma_c_func(sigma){}; std::pair operator()(double frequency) const { std::pair result; result.first = value(frequency); result.second = deriv(frequency); return result; } double value(double frequency) const { return _sigma_c_func.CalcCorrelationDiagElement(_gw_level, frequency) + _offset - frequency; } double deriv(double frequency) const { return _sigma_c_func.CalcCorrelationDiagElementDerivative(_gw_level, frequency) - 1.0; } private: Index _gw_level; double _offset; const Sigma_base& _sigma_c_func; }; double SolveQP_Bisection(double lowerbound, double f_lowerbound, double upperbound, double f_upperbound, const QPFunc& f) const; double CalcHomoLumoShift(Eigen::VectorXd frequencies) const; Eigen::VectorXd ScissorShift_DFTlevel( const Eigen::VectorXd& dft_energies) const; void PrintQP_Energies(const Eigen::VectorXd& qp_diag_energies) const; void PrintGWA_Energies() const; Eigen::VectorXd SolveQP(const Eigen::VectorXd& frequencies) const; boost::optional SolveQP_Grid(double intercept0, double frequency0, Index gw_level) const; boost::optional SolveQP_FixedPoint(double intercept0, double frequency0, Index gw_level) const; boost::optional SolveQP_Linearisation(double intercept0, double frequency0, Index gw_level) const; bool Converged(const Eigen::VectorXd& e1, const Eigen::VectorXd& e2, double epsilon) const; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_GW_H xtp-2021.2/include/votca/xtp/gwbse.h000066400000000000000000000047431412152066400172560ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_GWBSE_H #define VOTCA_XTP_GWBSE_H // Standard includes #include // VOTCA includes #include // Local VOTCA includes #include "bse.h" #include "eigen.h" #include "gw.h" #include "logger.h" #include "qmfragment.h" namespace votca { namespace xtp { class Orbitals; class AOBasis; /** * \brief Electronic excitations from GW-BSE * * Evaluates electronic excitations in molecular systems based on * many-body Green's functions theory within the GW approximation and * the Bethe-Salpeter equation. Requires molecular orbitals * * B. Baumeier, Y. Ma, D. Andrienko, M. Rohlfing * J. Chem. Theory Comput. 8, 997-1002 (2012) * * B. Baumeier, D. Andrienko, M. Rohlfing * J. Chem. Theory Comput. 8, 2790-2795 (2012) * */ class GWBSE { public: GWBSE(Orbitals& orbitals) : _orbitals(orbitals){}; void Initialize(tools::Property& options); std::string Identify() { return "gwbse"; } void setLogger(Logger* pLog) { _pLog = pLog; } bool Evaluate(); void addoutput(tools::Property& summary); private: Eigen::MatrixXd CalculateVXC(const AOBasis& dftbasis); Index CountCoreLevels(); Logger* _pLog; Orbitals& _orbitals; // program tasks bool _do_gw = false; bool _do_bse_singlets = false; bool _do_bse_triplets = false; bool _do_dynamical_screening_bse = false; // options for own Vxc calculation std::string _functional; std::string _grid; GW::options _gwopt; BSE::options _bseopt; std::string _sigma_plot_states; Index _sigma_plot_steps; double _sigma_plot_spacing; std::string _sigma_plot_filename; // basis sets std::string _auxbasis_name; std::string _dftbasis_name; std::vector > _fragments; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_GWBSE_H xtp-2021.2/include/votca/xtp/gwbseengine.h000066400000000000000000000050071412152066400204360ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_GWBSEENGINE_H #define VOTCA_XTP_GWBSEENGINE_H // VOTCA includes #include // Local VOTCA includes #include "logger.h" namespace votca { namespace xtp { class QMPackage; class Orbitals; /** * \brief Electronic Excitations via Density-Functional Theory * * Evaluates electronic ground state in molecular systems based on * density functional theory with Gaussian Orbitals. * */ class GWBSEEngine { public: std::string Identify() { return "gwbse_engine"; } void Initialize(tools::Property& options, std::string archive_filename); void ExcitationEnergies(Orbitals& orbitals); void setLog(Logger* pLog) { _pLog = pLog; } void setQMPackage(QMPackage* qmpackage) { _qmpackage = qmpackage; } std::string GetDFTLog() const { return _dftlog_file; }; void setLoggerFile(std::string logger_file) { _logger_file = logger_file; }; void setRedirectLogger(bool redirect_logger) { _redirect_logger = redirect_logger; }; const tools::Property& ReportSummary() const { return _summary; }; private: QMPackage* _qmpackage; Logger* _pLog; // task options bool _do_guess = false; bool _do_dft_input = false; bool _do_dft_run = false; bool _do_dft_parse = false; bool _do_gwbse = false; bool _redirect_logger = false; // DFT log and MO file names std::string _MO_file; // file containing the MOs from qmpackage... std::string _dftlog_file; // file containing the Energies etc... from // qmpackage... std::string _logger_file; std::string _archive_file; std::string _guess_archiveA; std::string _guess_archiveB; // Options for GWBSE module tools::Property _gwbse_options; tools::Property _summary; void WriteLoggerToFile(Logger* pLog); }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_GWBSEENGINE_H xtp-2021.2/include/votca/xtp/gyration.h000066400000000000000000000030461412152066400177760ustar00rootroot00000000000000/* * Copyright 2016 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_GYRATION_H #define VOTCA_XTP_GYRATION_H // Standard includes #include // Local VOTCA includes #include "density_integration.h" #include "logger.h" #include "orbitals.h" namespace votca { namespace xtp { class Density2Gyration { public: Density2Gyration(Logger& log) : _log(log){}; std::string Identify() { return "density2gyration"; } void Initialize(tools::Property& options); void AnalyzeDensity(const Orbitals& orbitals); private: void ReportAnalysis(std::string label, const Gyrationtensor& gyro, const Eigen::SelfAdjointEigenSolver& es); void AnalyzeGeometry(const QMMolecule& atoms); QMState _state; bool _dostateonly; std::string _integrationmethod; std::string _gridsize; Logger& _log; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_GYRATION_H xtp-2021.2/include/votca/xtp/hist.h000066400000000000000000000061231412152066400171100ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_HIST_H #define VOTCA_XTP_HIST_H // Local VOTCA includes #include "checkpoint.h" #include "eigen.h" #include "energy_terms.h" /** * \brief Small container for convergence checking, stores current and last * value and gives the diff, or just the current value in the first iteration * * */ namespace votca { namespace xtp { template class hist { public: T getDiff() const { if (_filled > 1) { return _metric - _metric_old; } else if (_filled == 1) { return _metric; } else { throw std::runtime_error("hist is not filled yet"); } } const T& back() const { return _metric; } void push_back(const T& metric) { _metric_old = std::move(_metric); _metric = metric; _filled++; } void push_back(T&& metric) { _metric_old = std::move(_metric); _metric = std::move(metric); _filled++; } bool filled() const { return _filled > 0; } void WriteToCpt(CheckpointWriter& w) const { w(_filled, "filled"); if (_filled > 0) { WriteMetric(_metric, "metric", w); } if (_filled > 1) { WriteMetric(_metric_old, "metric_old", w); } } void ReadFromCpt(CheckpointReader& r) { r(_filled, "filled"); if (_filled > 0) { ReadMetric(_metric, "metric", r); } if (_filled > 1) { ReadMetric(_metric_old, "metric_old", r); } } private: void ReadMetric(T&, std::string tag, CheckpointReader& r); void WriteMetric(const T&, std::string tag, CheckpointWriter& w) const; Index _filled = 0; T _metric; T _metric_old; }; template inline void hist::ReadMetric(T& metric, std::string tag, CheckpointReader& r) { r(metric, tag); } template inline void hist::WriteMetric(const T& metric, std::string tag, CheckpointWriter& w) const { w(metric, tag); } template <> inline void hist::ReadMetric(Energy_terms& metric, std::string tag, CheckpointReader& r) { r(metric.data(), tag); } template <> inline void hist::WriteMetric(const Energy_terms& metric, std::string tag, CheckpointWriter& w) const { w(metric.data(), tag); } } // namespace xtp } // namespace votca #endif // VOTCA_XTP_HIST_H xtp-2021.2/include/votca/xtp/huffmantree.h000066400000000000000000000174261412152066400204550ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_HUFFMANTREE_H #define VOTCA_XTP_HUFFMANTREE_H // Standard includes #include #include #include #include namespace votca { namespace xtp { template class huffmanTree { public: void makeTree() { if (!events) { throw std::runtime_error( "Error in Huffmantree::makeTree : Pointer to Events not set!"); } // queue of the nodes, sorted by probability auto compare = [](huffmanNode *n1, huffmanNode *n2) { return n1->probability > n2->probability; }; // priority queues, because the algorithm always needs the element with the // smallest probability. Also, it keep adding nodes to it, so it would we // very inefficient to sort it in every iteration. std::priority_queue *, std::vector *>, decltype(compare)> queue(compare); htree = std::vector>( events->size() % 2 ? events->size() : events->size() - 1); auto comp2 = [](T *e1, T *e2) { return e1->getValue() > e2->getValue(); }; std::priority_queue, decltype(comp2)> eventQueue( comp2); sum_of_values = 0.0; Index firstEmptyFieldIndex = 0; for (T &e : *events) { eventQueue.push(&e); sum_of_values += e.getValue(); } while (eventQueue.size() > 1) { htree[firstEmptyFieldIndex].isOnLastLevel = true; htree[firstEmptyFieldIndex].leftLeaf = eventQueue.top(); eventQueue.pop(); htree[firstEmptyFieldIndex].rightLeaf = eventQueue.top(); eventQueue.pop(); htree[firstEmptyFieldIndex].probability = (htree[firstEmptyFieldIndex].leftLeaf->getValue() + htree[firstEmptyFieldIndex].rightLeaf->getValue()) / sum_of_values; queue.push(&(htree[firstEmptyFieldIndex])); firstEmptyFieldIndex++; } if (!eventQueue.empty()) { htree[firstEmptyFieldIndex].isOnLastLevel = true; htree[firstEmptyFieldIndex].rightLeaf = eventQueue.top(); htree[firstEmptyFieldIndex].leftLeaf = eventQueue.top(); htree[firstEmptyFieldIndex].probability = htree[firstEmptyFieldIndex].leftLeaf->getValue() / sum_of_values; queue.push(&(htree[firstEmptyFieldIndex])); firstEmptyFieldIndex++; } // now connect the hnodes, making a new one for every connection: // always take the two nodes with the smallest probability and "combine" // them, repeat, until just one node (the root) is left. huffmanNode *h1; huffmanNode *h2; while (queue.size() > 1) { h1 = queue.top(); queue.pop(); h2 = queue.top(); queue.pop(); htree[firstEmptyFieldIndex].probability = h1->probability + h2->probability; htree[firstEmptyFieldIndex].leftChild = h1; htree[firstEmptyFieldIndex].rightChild = h2; queue.push(&(htree[firstEmptyFieldIndex])); firstEmptyFieldIndex++; } // reorganize the probabilities: in every node, add the probability of one // subtree ("small") to all nodes of the other subtree. addProbabilityFromRightSubtreeToLeftSubtree(&htree[htree.size() - 1], 0); moveProbabilitiesFromRightSubtreesOneLevelUp(&htree[htree.size() - 1]); treeIsMade = true; } T *findHoppingDestination(double p) const { if (!treeIsMade) { throw std::runtime_error( "Tried to find Hopping Destination without initializing the " "Huffmantree first!"); } const huffmanNode *node = &htree.back(); while (!node->isOnLastLevel) { if (p > node->probability) { node = node->leftChild; } else { node = node->rightChild; } } return (p > node->probability ? node->leftLeaf : node->rightLeaf); } void setEvents(std::vector *v) { this->events = v; } private: template struct huffmanNode { // huffmanNode * for the inner nodes, T * for the nodes on the last level // before the leafs (The T themselves represent the "leaf" level) huffmanNode *leftChild; huffmanNode *rightChild; S *rightLeaf; S *leftLeaf; double probability; bool isOnLastLevel = false; }; void addProbabilityFromRightSubtreeToLeftSubtree(huffmanNode *n, double add) { // for each node, adds the probability of the right childnode to the left // childnode and every node under it. if the Tree would look like this (with // the Numbers representing the probability of every node) before calling // this function // 1.0 // ____||____ // | | // 0.4 0.6 // _||_ _||_ // | | | | // 0.25 0.15 0.35 0.25 // _||_ // | | // 0.1 0.05 // then it would look like this after calling it // 1.0 // ____||____ // | | // 1.0 0.6 // _||_ _||_ // | | | | // 1.0 0.75 0.6 0.25 // _||_ // | | // 0.75 0.65 // now the tree could be traversed with "while (!n.isLeaf()) // n=p>n.right.p?n.left:n.right" so in the function // moveProbabilitiesFromRightSubtreesOneLevelUp the numbers are moved one // level up to call n.p instead of n.right.p // adds "add" to the probability, then calls itself recursively. // this calculates the probabilities needed to traverse the tree quickly n->probability += add; // if leftId=-1 (=> node is leaf), returns if (n->isOnLastLevel) { return; } addProbabilityFromRightSubtreeToLeftSubtree( n->leftChild, add + n->rightChild->probability); addProbabilityFromRightSubtreeToLeftSubtree(n->rightChild, add); } void moveProbabilitiesFromRightSubtreesOneLevelUp(huffmanNode *n) { // moves the Probabilities on the right subtrees one level up. // if the Tree would look like this (with the Numbers representing the // probability of every node) before calling this function // 1.0 // ____||____ // | | // 1.0 0.6 // _||_ _||_ // | | | | // 1.0 0.75 0.6 0.25 // _||_ // | | // 0.75 0.65 // then it would look like this after calling it // 0. // ____||____ // | | // 0.75 0.25 // _||_ _||_ // | | | | // 1.0 0.65 0.6 0.25 // _||_ // | | // 0.75 0.65 // note, that now the probabilities on the leaf level are not needed anymore // to traverse the tree; the algorithm now is "while (!n.isLeaf()) // n=p>n.p?n.left:n.right" if (n->isOnLastLevel) { n->probability -= n->leftLeaf->getValue() / sum_of_values; } else { n->probability = n->rightChild->probability; moveProbabilitiesFromRightSubtreesOneLevelUp(n->rightChild); moveProbabilitiesFromRightSubtreesOneLevelUp(n->leftChild); } } std::vector> htree; bool treeIsMade = false; double sum_of_values = 0.0; std::vector *events = nullptr; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_HUFFMANTREE_H xtp-2021.2/include/votca/xtp/job.h000066400000000000000000000111501412152066400167070ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_JOB_H #define VOTCA_XTP_JOB_H // Standard includes #include #include #include // VOTCA includes #include namespace votca { namespace xtp { class Job { public: enum JobStatus { AVAILABLE, ASSIGNED, FAILED, COMPLETE }; Job(const tools::Property &prop); Job(Index id, const std::string &tag, const tools::Property &input, JobStatus status); std::string ConvertStatus(JobStatus) const; JobStatus ConvertStatus(std::string) const; class JobResult { public: void setStatus(JobStatus stat) { _status = stat; } void setOutput(std::string output) { _has_output = true; _output = tools::Property().add("output", output); } void setOutput(tools::Property &output) { _has_output = true; _output = output.get("output"); } JobStatus getStatus() const { return _status; } bool hasOutput() const { return _has_output; } const tools::Property &getOutput() const { return _output; } tools::Property &getOutput() { return _output; } bool hasError() const { return _has_error; } const std::string &getError() const { return _error; } void setError(std::string error) { _has_error = true; _error = error; } private: JobStatus _status; tools::Property _output; bool _has_output = false; std::string _error; bool _has_error = false; }; void Reset(); void ToStream(std::ofstream &ofs) const; void UpdateFrom(const Job &ext); void UpdateFromResult(const JobResult &res); Index getId() const { return _id; } std::string getTag() const { return _tag; } tools::Property &getInput() { return _input; } const tools::Property &getInput() const { return _input; } const JobStatus &getStatus() const { return _status; } std::string getStatusStr() const { return ConvertStatus(_status); } bool hasHost() const { return _has_host; } bool hasTime() const { return _has_time; } bool hasOutput() const { return _has_output; } bool hasError() const { return _has_error; } bool isAvailable() const { return (_status == AVAILABLE) ? true : false; } bool isAssigned() const { return (_status == ASSIGNED) ? true : false; } bool isFailed() const { return (_status == FAILED) ? true : false; } bool isComplete() const { return (_status == COMPLETE) ? true : false; } bool isFresh() const { return (_attemptsCount < 1) ? true : false; } void setStatus(JobStatus stat) { _status = stat; } void setStatus(std::string stat) { _status = ConvertStatus(stat); } void setTime(std::string time) { _time = time; _has_time = true; } void setHost(std::string host) { _host = host; _has_host = true; } void setOutput(std::string output) { _output = tools::Property().add("output", output); _has_output = true; } const std::string &getHost() const { assert(_has_host && "Job has no host"); return _host; } const std::string &getTime() const { assert(_has_time && "Job has no time"); return _time; } const tools::Property &getOutput() const { assert(_has_output && "Job has no output"); return _output; } const std::string &getError() const { assert(_has_error && "Job has no error"); return _error; } private: // Defined by user Index _id; std::string _tag; JobStatus _status; Index _attemptsCount = 0; tools::Property _input; // Generated during runtime std::string _host; bool _has_host = false; std::string _time; bool _has_time = false; tools::Property _output; bool _has_error = false; bool _has_output = false; std::string _error; }; // namespace xtp std::vector LOAD_JOBS(const std::string &xml_file); void WRITE_JOBS(const std::vector &jobs, const std::string &job_file); void UPDATE_JOBS(const std::vector &from, std::vector &to, const std::string &thisHost); } // namespace xtp } // namespace votca #endif // VOTCA_XTP_JOB_H xtp-2021.2/include/votca/xtp/jobapplication.h000066400000000000000000000031401412152066400211330ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #include #ifndef VOTCA_XTP_JOBAPPLICATION_H #define VOTCA_XTP_JOBAPPLICATION_H // Local VOTCA includes #include "jobcalculator.h" #include "progressobserver.h" #include "statesaver.h" #include "topology.h" #include "xtpapplication.h" namespace votca { namespace xtp { class JobApplication : public XtpApplication { public: JobApplication(); ~JobApplication() override = default; void Initialize() override; bool EvaluateOptions() override; void Run() override; void BeginEvaluate(Index nThreads, Index ompthread, ProgObserver > &jobs); bool EvaluateFrame(Topology &top); void SetCalculator(std::unique_ptr &&calculator); protected: bool _generate_input = false; bool _run = false; bool _import = false; std::unique_ptr _calculator; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_JOBAPPLICATION_H xtp-2021.2/include/votca/xtp/jobcalculator.h000066400000000000000000000037321412152066400207700ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ /// For an earlier history see ctp repo commit /// 77795ea591b29e664153f9404c8655ba28dc14e9 #pragma once #ifndef VOTCA_XTP_JOBCALCULATOR_H #define VOTCA_XTP_JOBCALCULATOR_H // VOTCA includes #include // Local VOTCA includes #include "job.h" #include "progressobserver.h" #include "topology.h" namespace votca { namespace xtp { class Topology; class JobCalculator : public tools::Calculator { public: JobCalculator() = default; ~JobCalculator() override = default; std::string Identify() override = 0; bool EvaluateFrame(const Topology &top) { return Evaluate(top); } void Initialize(const tools::Property &opt) final { tools::Property options = LoadDefaultsAndUpdateWithUserOptions("xtp", opt); ParseOptions(options); } virtual void WriteJobFile(const Topology &top) = 0; virtual void ReadJobFile(Topology &top) = 0; void setOpenMPThreads(Index ompthreads) { _openmp_threads = ompthreads; } void setProgObserver(ProgObserver > *obs) { _progObs = obs; } protected: virtual void ParseOptions(const tools::Property &opt) = 0; virtual bool Evaluate(const Topology &top) = 0; Index _openmp_threads; ProgObserver > *_progObs; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_JOBCALCULATOR_H xtp-2021.2/include/votca/xtp/jobcalculatorfactory.h000066400000000000000000000025751412152066400223640ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_JOBCALCULATORFACTORY_H #define VOTCA_XTP_JOBCALCULATORFACTORY_H // Standard includes #include // VOTCA includes #include // Local VOTCA includes #include "jobcalculator.h" namespace votca { namespace xtp { class JobCalculatorfactory : public tools::ObjectFactory { private: JobCalculatorfactory() = default; public: static void RegisterAll(void); friend JobCalculatorfactory &JobCalculators(); }; inline JobCalculatorfactory &JobCalculators() { static JobCalculatorfactory _instance; return _instance; } } // namespace xtp } // namespace votca #endif // VOTCA_XTP_JOBCALCULATORFACTORY_H xtp-2021.2/include/votca/xtp/jobtopology.h000066400000000000000000000075351412152066400205200ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_JOBTOPOLOGY_H #define VOTCA_XTP_JOBTOPOLOGY_H // Local VOTCA includes #include "job.h" #include "logger.h" #include "region.h" #include "topology.h" /** * \brief Class to set up the topology, e.g division of molecules into different * regions for a specific job. * * How energies are evaluated depends critically on the id of the region. * a) Lower ids means being evaluated later. So expensive regions should have * low ids, as they can then already incorporate partially converged results * from higher id regions b) The energy of a region, includes all interactions * with regions of higher ids. i.e. E(region0)=E0+E01+E02, whereas * E(region1)=E1+E12 and not E10 The reason is that DFT codes only return E0+ * all interaction energies and not the individual terms, this has to be changed * once we want to have multiple QM regions. */ namespace votca { namespace xtp { class SegId; class JobTopology { public: JobTopology(Job& job, Logger& log, std::string workdir) : _job(job), _log(log), _workdir(workdir){}; void BuildRegions(const Topology& top, tools::Property options); void WriteToHdf5(std::string filename) const; void WriteToPdb(std::string filename) const; std::vector >::iterator begin() { return _regions.begin(); } std::vector >::iterator end() { return _regions.end(); } const std::vector >& Regions() const { return _regions; } std::vector >& Regions() { return _regions; } Index size() const { return Index(_regions.size()); } std::vector >::const_iterator begin() const { return _regions.begin(); } std::vector >::const_iterator end() const { return _regions.end(); } private: std::vector > PartitionRegions( const std::vector& regions_def, const Topology& top) const; void CreateRegions(const tools::Property& options, const Topology& top, const std::vector >& region_seg_ids); void UpdateFromJobfile(tools::Property& options, const tools::Property& job_opt, const std::vector& paths) const; std::vector FindReplacePathsInOptions( const tools::Property& options, std::string tag) const; void ModifyOptionsByJobFile(std::vector& regions_def) const; void UpdateFromJobfile(tools::Property& options, const tools::Property& job_opt, const std::string& tag) const; template void ShiftPBC(const Topology& top, const Eigen::Vector3d& center, T& mol) const; void CheckEnumerationOfRegions( const std::vector& regions_def) const; void SortRegionsDefbyId(std::vector& regions_def) const; Job& _job; Logger& _log; std::vector > _regions; std::string _workdir = ""; static constexpr int jobtopology_version() { return 1; } }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_JOBTOPOLOGY_H xtp-2021.2/include/votca/xtp/kmccalculator.h000066400000000000000000000052761412152066400207750ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_KMCCALCULATOR_H #define VOTCA_XTP_KMCCALCULATOR_H // VOTCA includes #include #include #include // Local VOTCA includes #include "chargecarrier.h" #include "gnode.h" #include "logger.h" #include "qmcalculator.h" #include "qmstate.h" namespace votca { namespace xtp { class QMNBList; class KMCCalculator : public QMCalculator { public: ~KMCCalculator() override = default; void ParseOptions(const tools::Property& options) final { ParseCommonOptions(options); ParseSpecificOptions(options); } protected: virtual void ParseSpecificOptions(const tools::Property& options) = 0; QMStateType _carriertype; void LoadGraph(Topology& top); virtual void RunVSSM() = 0; void ParseCommonOptions(const tools::Property& options); double Promotetime(double cumulated_rate); void ResetForbiddenlist(std::vector& forbiddenid) const; void AddtoForbiddenlist(GNode& node, std::vector& forbiddenid) const; bool CheckForbidden(const GNode& node, const std::vector& forbiddenlist) const; bool CheckSurrounded(const GNode& node, const std::vector& forbiddendests) const; const GLink& ChooseHoppingDest(const GNode& node); Chargecarrier* ChooseAffectedCarrier(double cumulated_rate); void WriteOccupationtoFile(double simtime, std::string filename); void WriteRatestoFile(std::string filename, const QMNBList& nblist); void RandomlyCreateCharges(); void RandomlyAssignCarriertoSite(Chargecarrier& Charge); std::vector _nodes; std::vector _carriers; tools::Random _RandomVariable; std::string _injection_name; std::string _injectionmethod; Index _seed; Index _numberofcarriers; Eigen::Vector3d _field = Eigen::Vector3d::Zero(); double _maxrealtime; std::string _trajectoryfile; std::string _ratefile; std::string _occfile; Logger _log; double _temperature; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_KMCCALCULATOR_H xtp-2021.2/include/votca/xtp/logger.h000066400000000000000000000146561412152066400174320ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ /// For an earlier history see ctp repo commit /// 77795ea591b29e664153f9404c8655ba28dc14e9 #pragma once #ifndef VOTCA_XTP_LOGGER_H #define VOTCA_XTP_LOGGER_H // Standard includes #include #include #include // VOTCA includes #include namespace votca { namespace xtp { /* * Macros to use the Logger: XTP_LOG(level,logger) << message */ #define XTP_LOG(level, log) \ if (level > (log).getReportLevel()) \ ; \ else \ (log)(level) /* * Custom buffer to store messages */ class LogBuffer final : public std::stringbuf { public: LogBuffer() : std::stringbuf() { _LogLevel = Log::current_level; } // sets the log level (needed for output) void setLogLevel(Log::Level LogLevel) { _LogLevel = LogLevel; } // sets Multithreading (buffering required) void setMultithreading(bool maverick) { _maverick = maverick; } // sets preface strings for Log::error, Log::warning, ... void setPreface(Log::Level level, std::string preface) { switch (level) { case Log::Level::error: _errorPreface = preface; break; case Log::Level::warning: _warnPreface = preface; break; case Log::Level::info: _infoPreface = preface; break; case Log::Level::debug: _dbgPreface = preface; break; } } void EnablePreface() { _writePreface = true; } void DisablePreface() { _writePreface = false; } // flushes all collected messages void FlushBuffer() { std::cout << _stringStream.str(); _stringStream.str(""); } // returns the pointer to the collected messages std::string Messages() { std::string _messages = _stringStream.str(); _stringStream.str(""); return _messages; } private: // Log Level (WARNING, INFO, etc) Log::Level _LogLevel = Log::Level::error; // temporary buffer to store messages std::ostringstream _stringStream; // Multithreading bool _maverick = true; std::string _errorPreface = "\n ERROR "; std::string _warnPreface = "\n WARNING "; std::string _infoPreface = "\n "; std::string _dbgPreface = "\n DEBUG "; bool _writePreface = true; protected: int sync() { std::ostringstream _message; if (_writePreface) { switch (_LogLevel) { case Log::Level::error: _message << _errorPreface; break; case Log::Level::warning: _message << _warnPreface; break; case Log::Level::info: _message << _infoPreface; break; case Log::Level::debug: _message << _dbgPreface; break; } } if (!_maverick) { // collect all messages of one thread _stringStream << _message.str() << " " << str(); } else { // if only one thread outputs, flush immediately std::cout << _message.str() << " " << str() << std::flush; } _message.str(""); str(""); return 0; } }; /** \class Logger * \brief Logger is used for thread-safe output of messages * * Logger writes messages into LogBuffer. * Inheritance from ostream allows to use overloaded << and >> for writing. * Example: * * \code * #include * Logger log; // create a logger object * log.setReportLevel(Log::error); // output only log messages starting from a * level XTP_LOG(Log::error,*log) << "Error detected" << flush; // write to * the logger at an ERROR level cout << log; // output logger content to * standard output \endcode * * Logger has four predefined log levels: error, warning, info, * debug. */ class Logger final : public std::ostream { friend std::ostream &operator<<(std::ostream &log_out, Logger &logger) { log_out << logger.Messages(); return log_out; } public: Logger() : std::ostream(&_buffer), _ReportLevel(Log::current_level) { setMultithreading(_maverick); } Logger(Log::Level ReportLevel) : std::ostream(&_buffer), _ReportLevel(ReportLevel) { setMultithreading(_maverick); } Logger &operator()(Log::Level LogLevel) { _buffer.setLogLevel(LogLevel); return *this; } void setReportLevel(Log::Level ReportLevel) { _ReportLevel = ReportLevel; } void setMultithreading(bool maverick) { _maverick = maverick; _buffer.setMultithreading(_maverick); } bool isMaverick() const { return _maverick; } Log::Level getReportLevel() const { return _ReportLevel; } void setPreface(Log::Level level, const std::string &preface) { _buffer.setPreface(level, preface); } void setCommonPreface(const std::string &preface) { setPreface(Log::info, preface); setPreface(Log::error, preface); setPreface(Log::debug, preface); setPreface(Log::warning, preface); } void EnablePreface() { _buffer.EnablePreface(); } void DisablePreface() { _buffer.DisablePreface(); } private: LogBuffer _buffer; // at what level of detail output messages Log::Level _ReportLevel = Log::error; // if true, only a single processor job is executed bool _maverick = false; std::string Messages() { return _buffer.Messages(); } }; /** * \brief Timestamp returns the current time as a string * Example: cout << TimeStamp() */ class TimeStamp { public: friend std::ostream &operator<<(std::ostream &os, const TimeStamp &) { std::time_t now_time = std::chrono::system_clock::to_time_t(std::chrono::system_clock::now()); std::tm *timeinfo = std::localtime(&now_time); os << timeinfo->tm_year + 1900 << "-" << timeinfo->tm_mon + 1 << "-" << timeinfo->tm_mday << " " << timeinfo->tm_hour << ":" << timeinfo->tm_min << ":" << timeinfo->tm_sec; return os; } explicit TimeStamp() = default; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_LOGGER_H xtp-2021.2/include/votca/xtp/make_libint_work.h000066400000000000000000000017621412152066400214650ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_MAKE_LIBINT_WORK_H #define VOTCA_XTP_MAKE_LIBINT_WORK_H #ifndef LIBINT2_MAX_AM_default1 #define LIBINT2_MAX_AM_default1 LIBINT2_MAX_AM_default #endif #ifndef LIBINT2_MAX_AM_default2 #define LIBINT2_MAX_AM_default2 LIBINT2_MAX_AM_default #endif #endif // VOTCA_XTP_MAKE_LIBINT_WORK_Hxtp-2021.2/include/votca/xtp/matrixfreeoperator.h000066400000000000000000000142401412152066400220620ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_MATRIXFREEOPERATOR_H #define VOTCA_XTP_MATRIXFREEOPERATOR_H // Local VOTCA includes #include "eigen.h" namespace votca { namespace xtp { class MatrixFreeOperator; } } // namespace votca namespace Eigen { namespace internal { // MatrixReplacement looks-like a Matrix, so let's inherits its traits: template <> struct traits : public Eigen::internal::traits {}; } // namespace internal } // namespace Eigen namespace votca { namespace xtp { class MatrixFreeOperator : public Eigen::EigenBase { public: enum { ColsAtCompileTime = Eigen::Dynamic, MaxColsAtCompileTime = Eigen::Dynamic, IsRowMajor = false }; Index rows() const { return this->_size; } Index cols() const { return this->_size; } template Eigen::Product operator*( const Eigen::MatrixBase& x) const { return Eigen::Product( *this, x.derived()); } // convenience function Eigen::MatrixXd get_full_matrix() const; Eigen::VectorXd diagonal() const; Index size() const; void set_size(Index size); virtual bool useRow() const { return true; } virtual bool useBlock() const { return false; } virtual Index getBlocksize() const { return 0; } // extract row/col of the operator virtual Eigen::RowVectorXd OperatorRow(Index index) const; virtual Eigen::MatrixXd OperatorBlock(Index row, Index col) const; private: Index _size; }; } // namespace xtp } // namespace votca namespace Eigen { namespace internal { // replacement of the mat*vect operation template struct generic_product_impl : generic_product_impl_base< votca::xtp::MatrixFreeOperator, Vtype, generic_product_impl> { typedef typename Product::Scalar Scalar; template static void scaleAndAddTo(Dest& dst, const votca::xtp::MatrixFreeOperator& op, const Vtype& v, const Scalar& alpha) { // returns dst = alpha * op * v // alpha must be 1 here assert(alpha == Scalar(1) && "scaling is not implemented"); EIGEN_ONLY_USED_FOR_DEBUG(alpha); if (op.useRow()) { // make the mat vect product #pragma omp parallel for schedule(guided) for (Index i = 0; i < op.rows(); i++) { dst(i) = op.OperatorRow(i) * v; } } if (op.useBlock()) { Index blocksize = op.getBlocksize(); if (op.size() % blocksize != 0) { throw std::runtime_error("blocksize is not a multiple of matrix size"); } Index blocks = op.size() / blocksize; // this is inefficient if blocks struct generic_product_impl : generic_product_impl_base< votca::xtp::MatrixFreeOperator, Mtype, generic_product_impl> { typedef typename Product::Scalar Scalar; template static void scaleAndAddTo(Dest& dst, const votca::xtp::MatrixFreeOperator& op, const Mtype& m, const Scalar& alpha) { // returns dst = alpha * op * v // alpha must be 1 here assert(alpha == Scalar(1) && "scaling is not implemented"); EIGEN_ONLY_USED_FOR_DEBUG(alpha); // make the mat mat product if (op.useRow()) { #pragma omp parallel for for (Index i = 0; i < op.rows(); i++) { const Eigen::RowVectorXd row = op.OperatorRow(i) * m; dst.row(i) = row; } } if (op.useBlock()) { Index blocksize = op.getBlocksize(); if (op.size() % blocksize != 0) { throw std::runtime_error("blocksize is not a multiple of matrix size"); } Index blocks = op.size() / blocksize; // this uses the fact that all our matrices are symmetric, i.e we can // reuse half the blocks Eigen::MatrixXd result = Eigen::MatrixXd::Zero(dst.rows(), dst.cols()); #pragma omp declare reduction (+: Eigen::MatrixXd: omp_out=omp_out+omp_in)\ initializer(omp_priv=Eigen::MatrixXd::Zero(omp_orig.rows(),omp_orig.cols())) #pragma omp parallel for schedule(guided) reduction(+ : result) for (Index i_row = 0; i_row < blocks; i_row++) { for (Index i_col = i_row; i_col < blocks; i_col++) { const Eigen::MatrixXd blockmat = op.OperatorBlock(i_row, i_col); result.block(i_row * blocksize, 0, blocksize, dst.cols()) += blockmat * m.block(i_col * blocksize, 0, blocksize, m.cols()); if (i_row != i_col) { result.block(i_col * blocksize, 0, blocksize, dst.cols()) += blockmat.transpose() * m.block(i_row * blocksize, 0, blocksize, m.cols()); } } } dst += result; } } }; } // namespace internal } // namespace Eigen #endif // VOTCA_XTP_MATRIXFREEOPERATOR_H xtp-2021.2/include/votca/xtp/md2qmengine.h000066400000000000000000000030601412152066400203440ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_MD2QMENGINE_H #define VOTCA_XTP_MD2QMENGINE_H // VOTCA includes #include // Local VOTCA includes #include "topology.h" namespace votca { namespace xtp { class Md2QmEngine { public: Md2QmEngine(std::string mapfile) : _mapfile(mapfile){}; Topology map(const csg::Topology& top) const; private: void CheckMappingFile(tools::Property& topology_map) const; template bool SameValueForMultipleEntries(const std::vector& props, std::string tag) const; Index DetermineAtomNumOffset(const csg::Molecule* mol, const std::vector& atom_ids_map) const; void MakeSegmentsWholePBC(Topology& top) const; bool CheckMolWhole(const Topology& top, const Segment& seg) const; std::string _mapfile; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_MD2QMENGINE_H xtp-2021.2/include/votca/xtp/mmregion.h000066400000000000000000000050271412152066400177600ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_MMREGION_H #define VOTCA_XTP_MMREGION_H // Local VOTCA includes #include "classicalsegment.h" #include "region.h" namespace votca { namespace xtp { class QMRegion; class PolarRegion; class StaticRegion; template class MMRegion : public Region { public: MMRegion(Index id, Logger& log) : Region(id, log){}; void WriteToCpt(CheckpointWriter& w) const override; void ReadFromCpt(CheckpointReader& r) override; Index size() const override { return Index(_segments.size()); } using iterator = typename std::vector::iterator; void Initialize(const tools::Property& prop) override = 0; bool Converged() const override = 0; void Evaluate(std::vector >& regions) override = 0; std::string identify() const override = 0; const T& operator[](Index index) const { return _segments[index]; } T& operator[](Index index) { return _segments[index]; } typename std::vector::iterator begin() { return _segments.begin(); } typename std::vector::iterator end() { return _segments.end(); } typename std::vector::const_iterator begin() const { return _segments.begin(); } typename std::vector::const_iterator end() const { return _segments.end(); } double Etotal() const override = 0; void Reset() override = 0; double charge() const override; void WritePDB(csg::PDBWriter& writer) const override; void push_back(const T& seg) { _segments.push_back(seg); } protected: void AppendResult(tools::Property& prop) const override = 0; double InteractwithQMRegion(const QMRegion& region) override = 0; double InteractwithPolarRegion(const PolarRegion& region) override = 0; double InteractwithStaticRegion(const StaticRegion& region) override = 0; std::vector _segments; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_MMREGION_H xtp-2021.2/include/votca/xtp/molden.h000066400000000000000000000052051412152066400174170ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_MOLDEN_H #define VOTCA_XTP_MOLDEN_H // Local VOTCA includes #include "votca/xtp/logger.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/orbreorder.h" #include "votca/xtp/qmtool.h" #include namespace votca { namespace xtp { class Molden { public: Molden(Logger& log) : _log(log){}; ~Molden() = default; void WriteFile(const std::string& filename, const Orbitals& orbitals) const; void setBasissetInfo(const std::string& basisset_name, const std::string& aux_basisset_name) { _basisset_name = basisset_name; _aux_basisset_name = aux_basisset_name; } void parseMoldenFile(const std::string& filename, Orbitals& orbitals) const; private: // clang-format off Logger& _log; std::array _multipliers={{ 1, //s 1,1,1, //p 1,1,1,1,1, //d -1,1,1,1,1,1,-1, //f -1,-1,1,1,1,1,1,-1,-1, //g -1,-1,-1,1,1,1,1,1,-1,-1,-1, //h -1,-1,-1,-1,1,1,1,1,1,-1,-1,-1,-1 //i }}; std::array _reorderList={{ 0, //s 1,-1,0, //p 0,1,-1,2,-2, //d 0,1,-1,2,-2,3,-3, //f 0,1,-1,2,-2,3,-3,4,-4, //g 0,1,-1,2,-2,3,-3,4,-4,5,-5, //h 0,1,-1,2,-2,3,-3,4,-4,5,-5,6,-6 //i }}; // clang-format on std::string _basisset_name; std::string _aux_basisset_name; void writeAtoms(const Orbitals& orbitals, std::ofstream& outFile) const; void writeMOs(const Orbitals& orbitals, std::ofstream& outFile) const; void writeBasisSet(const Orbitals& orbitals, std::ofstream& outFile) const; std::string readAtoms(QMMolecule& mol, const std::string& units, std::ifstream& input_file) const; std::string readMOs(Orbitals& orbitals, std::ifstream& input_file) const; void addBasissetInfo(Orbitals& orbitals) const; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_MOLDEN_H xtp-2021.2/include/votca/xtp/nbo.h000066400000000000000000000017741412152066400167260ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_NBO_H #define VOTCA_XTP_NBO_H /** * \brief Takes a list of atoms, and the corresponding density and overlap * matrices and puts out a table of partial charges * * * */ namespace votca { namespace xtp { class NBO {}; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_NBO_H xtp-2021.2/include/votca/xtp/newton_rapson.h000066400000000000000000000042651412152066400210420ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_NEWTON_RAPSON_H #define VOTCA_XTP_NEWTON_RAPSON_H // VOTCA includes #include // Local VOTCA includes #include "eigen.h" namespace votca { namespace xtp { /** * \brief Newton Rapson rootfinder for 1d functions * * https://en.wikipedia.org/wiki/Newton%27s_method#Modified_Newton_methods * */ template class NewtonRapson { public: enum Errors { success, smalldenom, notconverged }; NewtonRapson(Index max_iterations, double tolerance) : _max_iterations(max_iterations), _tolerance(tolerance) {} NewtonRapson(Index max_iterations, double tolerance, double alpha) : _max_iterations(max_iterations), _tolerance(tolerance), _alpha(alpha) {} double FindRoot(const Func& f, double x0) { _info = Errors::notconverged; double x = x0; for (_iter = 0; _iter < _max_iterations; _iter++) { std::pair res = f(x); if (std::abs(res.second) < 1e-12) { _info = Errors::smalldenom; break; } double step = -_alpha * res.first / res.second; if (std::abs(step) < _tolerance) { _info = Errors::success; break; } x += step; } return x; } Errors getInfo() const { return _info; } Index getIterations() const { return _iter; } private: Errors _info = Errors::notconverged; Index _max_iterations; Index _iter; double _tolerance; double _alpha = 1.0; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_NEWTON_RAPSON_H xtp-2021.2/include/votca/xtp/openmp_cuda.h000066400000000000000000000060001412152066400204250ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_OPENMP_CUDA_H #define VOTCA_XTP_OPENMP_CUDA_H // Local VOTCA includes #include "eigen.h" #ifdef USE_CUDA #include "cudapipeline.h" #endif /** * \brief Supports operations on Matrices using OPENMP and * CUDA. * * Each operation works with 2-3 steps * 1) Allocate temporary matrices and move fixed data to the gpu before the * openmp region is created 2) Inside the openmp region, move the loop data to * the GPU and perform calculation there 3) For reduction operations, transfer * the GPU data back to the CPU after the loop is finished Each GPU is served by * one CPU thread, the other CPU threads perform the normal CPU based operations * If no GPU is present all CPUs simply do CPU work. * If this class is created inside an OPENMP region, it still ensures, that over * that OPENMP region not more threads access the GPUs then GPUs are present. * Otherwise it will work purely in serial. So this class does NOT work with * nested OPENMP */ namespace votca { namespace xtp { class OpenMP_CUDA { public: OpenMP_CUDA(); static Index UsingGPUs() { #ifdef USE_CUDA return count_available_gpus(); #else return 0; #endif } void setOperators(const std::vector& tensor, const Eigen::MatrixXd& rightoperator); void MultiplyRight(Eigen::MatrixXd& matrix); void setOperators(const Eigen::MatrixXd& leftoperator, const Eigen::MatrixXd& rightoperator); void MultiplyLeftRight(Eigen::MatrixXd& matrix); void createTemporaries(Index rows, Index cols); void A_TDA(const Eigen::MatrixXd& matrix, const Eigen::VectorXd& vec); Eigen::MatrixXd A_TDA_result(); private: const Eigen::MatrixXd* rightoperator_ = nullptr; const Eigen::MatrixXd* leftoperator_ = nullptr; std::vector reduction_; bool inside_Parallel_region_; Index threadID_parent_; #ifdef USE_CUDA std::vector gpuIDs_; std::vector> cuda_pips_; struct temporaries { std::unique_ptr A = nullptr; std::unique_ptr B = nullptr; std::unique_ptr C = nullptr; std::unique_ptr D = nullptr; std::unique_ptr E = nullptr; }; std::vector temp_; #endif }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_OPENMP_CUDA_H xtp-2021.2/include/votca/xtp/optimiser_costfunction.h000066400000000000000000000026301412152066400227510ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_OPTIMISER_COSTFUNCTION_H #define VOTCA_XTP_OPTIMISER_COSTFUNCTION_H // Local VOTCA includes #include "eigen.h" namespace votca { namespace xtp { class Optimiser_costfunction { public: virtual ~Optimiser_costfunction() = default; virtual double EvaluateCost(const Eigen::VectorXd& parameters) = 0; virtual Eigen::VectorXd EvaluateGradient( const Eigen::VectorXd& parameters) = 0; virtual Index NumParameters() const = 0; virtual bool Converged(const Eigen::VectorXd& delta_parameters, double delta_cost, const Eigen::VectorXd& gradient) = 0; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_OPTIMISER_COSTFUNCTION_H xtp-2021.2/include/votca/xtp/orbitals.h000066400000000000000000000305551412152066400177660ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_ORBITALS_H #define VOTCA_XTP_ORBITALS_H // VOTCA includes #include #include // Local VOTCA includes #include "aobasis.h" #include "checkpoint.h" #include "classicalsegment.h" #include "eigen.h" #include "qmmolecule.h" #include "qmstate.h" namespace votca { namespace xtp { /** * \brief container for molecular orbitals * * The Orbitals class stores orbital id, energy, MO coefficients, basis set * */ class Orbitals { public: Orbitals(); bool hasBasisSetSize() const { return (_basis_set_size > 0) ? true : false; } Index getBasisSetSize() const { return _basis_set_size; } void setBasisSetSize(Index basis_set_size) { _basis_set_size = basis_set_size; } Index getLumo() const { return _occupied_levels; } Index getHomo() const { return _occupied_levels - 1; } // access to DFT number of levels, new, tested bool hasNumberOfLevels() const { return ((_occupied_levels > 0) ? true : false); } void setNumberOfOccupiedLevels(Index occupied_levels) { _occupied_levels = occupied_levels; } // access to DFT number of electrons, new, tested bool hasNumberOfAlphaElectrons() const { return (_number_alpha_electrons > 0) ? true : false; } Index getNumberOfAlphaElectrons() const { return _number_alpha_electrons; }; void setNumberOfAlphaElectrons(Index electrons) { _number_alpha_electrons = electrons; } bool hasECPName() const { return (_ECP != "") ? true : false; } const std::string &getECPName() const { return _ECP; }; void setECPName(const std::string &ECP) { _ECP = ECP; }; // access to QM package name, new, tested bool hasQMpackage() const { return (!_qm_package.empty()); } const std::string &getQMpackage() const { return _qm_package; } void setQMpackage(const std::string &qmpackage) { _qm_package = qmpackage; } // access to DFT molecular orbital energies, new, tested bool hasMOs() const { return (_mos.eigenvalues().size() > 0) ? true : false; } const tools::EigenSystem &MOs() const { return _mos; } tools::EigenSystem &MOs() { return _mos; } // access to DFT molecular orbital energy of a specific level double getMOEnergy(Index level) const { if (level < _mos.eigenvalues().size()) { return _mos.eigenvalues()[level]; } else { throw std::runtime_error("Level index is outside array range"); } return 0; } // determine (pseudo-)degeneracy of a DFT molecular orbital std::vector CheckDegeneracy(Index level, double energy_difference) const; Index NumberofStates(QMStateType type) const { switch (type.Type()) { case QMStateType::Singlet: return Index(_BSE_singlet.eigenvalues().size()); break; case QMStateType::Triplet: return Index(_BSE_triplet.eigenvalues().size()); break; case QMStateType::KSstate: return Index(_mos.eigenvalues().size()); break; case QMStateType::PQPstate: return Index(_QPpert_energies.size()); break; case QMStateType::DQPstate: return Index(_QPdiag.eigenvalues().size()); break; default: return 1; break; } } bool hasQMAtoms() const { return (_atoms.size() > 0) ? true : false; } const QMMolecule &QMAtoms() const { return _atoms; } QMMolecule &QMAtoms() { return _atoms; } void setXCFunctionalName(std::string functionalname) { _functionalname = functionalname; } const std::string &getXCFunctionalName() const { return _functionalname; } // access to QM total energy, new, tested bool hasQMEnergy() const { return (_qm_energy != 0.0) ? true : false; } double getDFTTotalEnergy() const { return _qm_energy; } void setQMEnergy(double qmenergy) { _qm_energy = qmenergy; } // access to DFT basis set name bool hasDFTbasisName() const { return (!_dftbasis.empty()) ? true : false; } void setDFTbasisName(const std::string basis) { _dftbasis = basis; } const std::string &getDFTbasisName() const { return _dftbasis; } AOBasis SetupDftBasis() const { return SetupBasis(); } AOBasis SetupAuxBasis() const { return SetupBasis(); } /* * ======= GW-BSE related functions ======= */ // access to auxiliary basis set name bool hasAuxbasisName() const { return (!_auxbasis.empty()) ? true : false; } void setAuxbasisName(std::string basis) { _auxbasis = basis; } const std::string &getAuxbasisName() const { return _auxbasis; } // access to list of indices used in GWA bool hasGWAindices() const { return (_qpmax > 0) ? true : false; } void setGWindices(Index qpmin, Index qpmax) { _qpmin = qpmin; _qpmax = qpmax; } Index getGWAmin() const { return _qpmin; } Index getGWAmax() const { return _qpmax; } // access to list of indices used in RPA bool hasRPAindices() const { return (_rpamax > 0) ? true : false; } void setRPAindices(Index rpamin, Index rpamax) { _rpamin = rpamin; _rpamax = rpamax; } Index getRPAmin() const { return _rpamin; } Index getRPAmax() const { return _rpamax; } // access to list of indices used in BSE void setTDAApprox(bool usedTDA) { _useTDA = usedTDA; } bool getTDAApprox() const { return _useTDA; } bool hasBSEindices() const { return (_bse_cmax > 0) ? true : false; } void setBSEindices(Index vmin, Index cmax) { _bse_vmin = vmin; _bse_vmax = getHomo(); _bse_cmin = getLumo(); _bse_cmax = cmax; _bse_vtotal = _bse_vmax - _bse_vmin + 1; _bse_ctotal = _bse_cmax - _bse_cmin + 1; _bse_size = _bse_vtotal * _bse_ctotal; return; } Index getBSEvmin() const { return _bse_vmin; } Index getBSEvmax() const { return _bse_vmax; } Index getBSEcmin() const { return _bse_cmin; } Index getBSEcmax() const { return _bse_cmax; } double getScaHFX() const { return _ScaHFX; } void setScaHFX(double ScaHFX) { _ScaHFX = ScaHFX; } // access to perturbative QP energies bool hasRPAInputEnergies() const { return (_rpa_inputenergies.size() > 0); } const Eigen::VectorXd &RPAInputEnergies() const { return _rpa_inputenergies; } Eigen::VectorXd &RPAInputEnergies() { return _rpa_inputenergies; } // access to RPA input energies energies bool hasQPpert() const { return (_QPpert_energies.size() > 0) ? true : false; } const Eigen::VectorXd &QPpertEnergies() const { return _QPpert_energies; } Eigen::VectorXd &QPpertEnergies() { return _QPpert_energies; } // access to diagonalized QP energies and wavefunctions bool hasQPdiag() const { return (_QPdiag.eigenvalues().size() > 0) ? true : false; } const tools::EigenSystem &QPdiag() const { return _QPdiag; } tools::EigenSystem &QPdiag() { return _QPdiag; } bool hasBSETriplets() const { return (_BSE_triplet.eigenvectors().cols() > 0) ? true : false; } const tools::EigenSystem &BSETriplets() const { return _BSE_triplet; } tools::EigenSystem &BSETriplets() { return _BSE_triplet; } // access to singlet energies and wave function coefficients bool hasBSESinglets() const { return (_BSE_singlet.eigenvectors().cols() > 0) ? true : false; } const tools::EigenSystem &BSESinglets() const { return _BSE_singlet; } tools::EigenSystem &BSESinglets() { return _BSE_singlet; } // access to BSE energies with dynamical screening bool hasBSESinglets_dynamic() const { return (_BSE_singlet_energies_dynamic.size() > 0) ? true : false; } const Eigen::VectorXd &BSESinglets_dynamic() const { return _BSE_singlet_energies_dynamic; } Eigen::VectorXd &BSESinglets_dynamic() { return _BSE_singlet_energies_dynamic; } bool hasBSETriplets_dynamic() const { return (_BSE_triplet_energies_dynamic.size() > 0) ? true : false; } const Eigen::VectorXd &BSETriplets_dynamic() const { return _BSE_singlet_energies_dynamic; } Eigen::VectorXd &BSETriplets_dynamic() { return _BSE_singlet_energies_dynamic; } // access to transition dipole moments bool hasTransitionDipoles() const { return (_transition_dipoles.size() > 0) ? true : false; } const std::vector &TransitionDipoles() const { return _transition_dipoles; } Eigen::VectorXd Oscillatorstrengths() const; Eigen::Vector3d CalcElDipole(const QMState &state) const; // Calculates full electron density for state or transition density, if you // want to calculate only the density contribution of hole or electron use // DensityMatrixExcitedState Eigen::MatrixXd DensityMatrixFull(const QMState &state) const; // functions for calculating density matrices Eigen::MatrixXd DensityMatrixGroundState() const; std::array DensityMatrixExcitedState( const QMState &state) const; Eigen::MatrixXd DensityMatrixQuasiParticle(const QMState &state) const; Eigen::MatrixXd CalculateQParticleAORepresentation() const; double getTotalStateEnergy(const QMState &state) const; // Hartree double getExcitedStateEnergy(const QMState &state) const; // Hartree void OrderMOsbyEnergy(); void PrepareDimerGuess(const Orbitals &orbitalsA, const Orbitals &orbitalsB); void CalcCoupledTransition_Dipoles(); void WriteToCpt(const std::string &filename) const; void ReadFromCpt(const std::string &filename); void WriteToCpt(CheckpointWriter w) const; void ReadFromCpt(CheckpointReader r); bool GetFlagUseHqpOffdiag() const { return _use_Hqp_offdiag; }; void SetFlagUseHqpOffdiag(bool flag) { _use_Hqp_offdiag = flag; }; private: std::array CalcFreeTransition_Dipoles() const; // returns indeces of a re-sorted vector of energies from lowest to highest std::vector SortEnergies(); template AOBasis SetupBasis() const { BasisSet bs; if (dftbasis) { bs.Load(this->getDFTbasisName()); } else { bs.Load(this->getAuxbasisName()); } AOBasis basis; basis.Fill(bs, this->QMAtoms()); return basis; } void WriteToCpt(CheckpointFile f) const; void ReadFromCpt(CheckpointFile f); Eigen::MatrixXd TransitionDensityMatrix(const QMState &state) const; std::array DensityMatrixExcitedState_R( const QMState &state) const; std::array DensityMatrixExcitedState_AR( const QMState &state) const; Eigen::MatrixXd CalcAuxMat_cc(const Eigen::VectorXd &coeffs) const; Eigen::MatrixXd CalcAuxMat_vv(const Eigen::VectorXd &coeffs) const; Index _basis_set_size; Index _occupied_levels; Index _number_alpha_electrons; std::string _ECP = ""; bool _useTDA; tools::EigenSystem _mos; QMMolecule _atoms; double _qm_energy = 0; // new variables for GW-BSE storage Index _rpamin = 0; Index _rpamax = 0; Index _qpmin = 0; Index _qpmax = 0; Index _bse_vmin = 0; Index _bse_vmax = 0; Index _bse_cmin = 0; Index _bse_cmax = 0; Index _bse_size = 0; Index _bse_vtotal = 0; Index _bse_ctotal = 0; double _ScaHFX = 0; std::string _dftbasis = ""; std::string _auxbasis = ""; std::string _functionalname = ""; std::string _qm_package = ""; Eigen::VectorXd _rpa_inputenergies; // perturbative quasiparticle energies Eigen::VectorXd _QPpert_energies; // quasiparticle energies and coefficients after diagonalization tools::EigenSystem _QPdiag; tools::EigenSystem _BSE_singlet; std::vector _transition_dipoles; tools::EigenSystem _BSE_triplet; // singlet and triplet energies after perturbative dynamical screening Eigen::VectorXd _BSE_singlet_energies_dynamic; Eigen::VectorXd _BSE_triplet_energies_dynamic; bool _use_Hqp_offdiag = true; // Version 2: adds BSE energies after perturbative dynamical screening // Version 3 changed shell ordering static constexpr int orbitals_version() { return 3; } }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ORBITALS_H xtp-2021.2/include/votca/xtp/orbreorder.h000066400000000000000000000044541412152066400203130ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_ORBREORDER_H #define VOTCA_XTP_ORBREORDER_H #include #include #include "eigen.h" #include "votca/xtp/orbitals.h" namespace votca { namespace xtp { // structure to store a transposition using Transposition = std::pair; class OrbReorder { public: OrbReorder(std::array reorder, std::array multipliers, bool reverse = false); ~OrbReorder() = default; void reorderOrbitals(Eigen::MatrixXd& moCoefficients, const AOBasis& basis); void reorderOperator(Eigen::MatrixXd& Matrixoperator, const AOBasis& basis); private: // structure to store the transpositions for the first 7 shell types (i.e. // s=0, p, d, f, g, h, i=6) using OrbTranspositions = std::array, 7>; std::array _multipliers; std::array _reorder; // clang-format off // the ordering of the m quantumnumbers for every shell std::array _votcaOrder={{ 0, //s -1,0,1, //p -2,-1,0,1,2, //d -3,-2,-1,0,1,2,3, //f -4,-3,-2,-1,0,1,2,3,4, //g -5,-4,-3,-2,-1,0,1,2,3,4,5, // h -6,-5,-4,-3,-2,-1,0,1,2,3,4,5,6 // i }}; // clang-format on OrbTranspositions _transpositions; std::vector computeTranspositions( std::vector vStart, std::vector vTarget) const; std::vector copySegment(const std::array& input, Index start, Index size) const; bool _reverse; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ORBREORDER_H xtp-2021.2/include/votca/xtp/paircalculator.h000066400000000000000000000034561412152066400211540ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_PAIRCALCULATOR_H #define VOTCA_XTP_PAIRCALCULATOR_H // Local VOTCA includes #include "qmcalculator.h" namespace votca { namespace xtp { class PairCalculator : public QMCalculator { public: PairCalculator(){}; virtual ~PairCalculator(){}; bool EvaluateFrame(Topology *top); virtual void EvaluatePair(Topology *top, QMPair *pair){}; }; bool PairCalculator::EvaluateFrame(Topology *top) { // Rigidify if (a) not rigid yet (b) rigidification at all possible if (!top->isRigid()) { bool isRigid = top->Rigidify(); if (!isRigid) { return 0; } } else { std::cout << std::endl << "... ... System is already rigidified."; } std::cout << std::endl; QMNBList &nblist = top->NBList(); QMNBList::iterator pit; for (pit = nblist.begin(); pit != nblist.end(); pit++) { EvaluatePair(top, *pit); if ((*pit)->getId() == -1) { std::string pairId = boost::lexical_cast((*pit)->getId()); std::string pdbname = "Pair" + pairId + ".pdb"; } } return 1; } } // namespace xtp } // namespace votca #endif // VOTCA_XTP_PAIRCALCULATOR_H xtp-2021.2/include/votca/xtp/parallelxjobcalc.h000066400000000000000000000070271412152066400214470ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ /// For an earlier history see ctp repo commit /// 77795ea591b29e664153f9404c8655ba28dc14e9 #pragma once #ifndef VOTCA_XTP_PARALLELXJOBCALC_H #define VOTCA_XTP_PARALLELXJOBCALC_H // VOTCA includes #include // Local VOTCA includes #include "job.h" #include "jobcalculator.h" #include "progressobserver.h" #include "qmthread.h" /// PATHWAYS TO A NEW THREADED CALCULATOR /// ... 1 Define 'JobContainer' (needs to define iterator), 'pJob' ( = /// *iterator) /// ... 2 Derive new calculator as ': public /// ParallelXJobCalc' /// ... 3 Specialize XJOBS_FROM_TABLE< JobContainer, pJob> in xjob.cc /// ... 4 Register new calculator (see end of parallelxjobcalc.cc) /// REQUIRED MEMBERS FOR pJob /// pJob::JobResult (struct) namespace votca { namespace xtp { template class ParallelXJobCalc : public JobCalculator { public: class JobOperator; using Job = typename std::iterator_traits< typename JobContainer::iterator>::value_type; using Result = typename Job::JobResult; ParallelXJobCalc() = default; ~ParallelXJobCalc() override = default; std::string Identify() override = 0; void ParseOptions(const tools::Property &opt) final { ParseCommonOptions(opt); ParseSpecificOptions(opt); } bool Evaluate(const Topology &top) final; virtual void CustomizeLogger(QMThread &thread); virtual Result EvalJob(const Topology &top, Job &job, QMThread &thread) = 0; void LockCout() { _coutMutex.Lock(); } void UnlockCout() { _coutMutex.Unlock(); } void LockLog() { _logMutex.Lock(); } void UnlockLog() { _logMutex.Unlock(); } // ======================================== // // XJOB OPERATOR (THREAD) // // ======================================== // class JobOperator : public QMThread { public: JobOperator(Index id, const Topology &top, ParallelXJobCalc &master, Index openmp_threads) : _top(top), _master(master), _openmp_threads(openmp_threads) { setId(id); } // comes from baseclass so Id cannot be in initializer list ~JobOperator() override = default; void Run() override; private: const Topology &_top; ParallelXJobCalc &_master; Index _openmp_threads = 1; }; protected: virtual void ParseSpecificOptions(const tools::Property &options) = 0; // set the basis sets and functional in DFT package tools::Property UpdateDFTOptions(const tools::Property &options); // set the basis sets and functional in GWBSE tools::Property UpdateGWBSEOptions(const tools::Property &options); JobContainer _XJobs; tools::Mutex _coutMutex; tools::Mutex _logMutex; std::string _mapfile = ""; std::string _jobfile = ""; private: void ParseCommonOptions(const tools::Property &options); }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_PARALLELXJOBCALC_H xtp-2021.2/include/votca/xtp/polarregion.h000066400000000000000000000051171412152066400204640ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_POLARREGION_H #define VOTCA_XTP_POLARREGION_H // Local VOTCA includes #include "eeinteractor.h" #include "energy_terms.h" #include "hist.h" #include "mmregion.h" /** * \brief defines a polar region and of interacting electrostatic and induction * segments * * * */ namespace votca { namespace xtp { class QMRegion; class PolarRegion; class StaticRegion; class PolarRegion : public MMRegion { public: PolarRegion(Index id, Logger& log) : MMRegion(id, log) {} std::string identify() const override { return "polar"; } void Initialize(const tools::Property& prop) override; bool Converged() const override; void Evaluate(std::vector >& regions) override; void Reset() override; double Etotal() const override { return _E_hist.back().Etotal(); } void WriteToCpt(CheckpointWriter& w) const override; void ReadFromCpt(CheckpointReader& r) override; protected: void AppendResult(tools::Property& prop) const override; double InteractwithQMRegion(const QMRegion& region) override; double InteractwithPolarRegion(const PolarRegion& region) override; double InteractwithStaticRegion(const StaticRegion& region) override; private: void CalcInducedDipoles(); double StaticInteraction(); void PolarInteraction_scf(); double PolarEnergy_extern() const; eeInteractor::E_terms PolarEnergy() const; Index CalcPolDoF() const; Eigen::VectorXd CalcInducedDipoleInsideSegments() const; Eigen::VectorXd ReadInducedDipolesFromLastIteration() const; Eigen::VectorXd CalcInducedDipolesViaPCG( const Eigen::VectorXd& initial_guess); void WriteInducedDipolesToSegments(const Eigen::VectorXd& x); hist _E_hist; double _deltaE = 1e-5; double _deltaD = 1e-5; Index _max_iter = 100; double _exp_damp = 0.39; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_POLARREGION_H xtp-2021.2/include/votca/xtp/polarsite.h000066400000000000000000000105611412152066400201440ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_POLARSITE_H #define VOTCA_XTP_POLARSITE_H // Local VOTCA includes #include "eigen.h" #include "staticsite.h" namespace votca { namespace xtp { /** \brief Class to represent Atom/Site in electrostatic+polarization The units are atomic units, e.g. Bohr, Hartree. */ class PolarSite : public StaticSite { public: // delete these two functions because we do not want to be able to read // StaticSite::data but PolarSite::data void WriteData(StaticSite::data& d) const = delete; void ReadData(StaticSite::data& d) = delete; PolarSite(Index id, std::string element, Eigen::Vector3d pos); PolarSite(Index id, std::string element) : PolarSite(id, element, Eigen::Vector3d::Zero()){}; ~PolarSite() override = default; void setpolarization(const Eigen::Matrix3d& pol) override; Eigen::Matrix3d getpolarization() const { return _pinv.inverse(); } const Eigen::Matrix3d& getPInv() const { return _pinv; } // MULTIPOLES DEFINITION Eigen::Vector3d getDipole() const override; double getSqrtInvEigenDamp() const { return _eigendamp_invsqrt; } void Rotate(const Eigen::Matrix3d& R, const Eigen::Vector3d& ref_pos) override { StaticSite::Rotate(R, ref_pos); _pinv = R.transpose() * _pinv * R; } const Eigen::Vector3d& V() const { return _V; } Eigen::Vector3d& V() { return _V; } const Eigen::Vector3d& V_noE() const { return _V_noE; } Eigen::Vector3d& V_noE() { return _V_noE; } void Reset() { _V.setZero(); _V_noE.setZero(); } double deltaQ_V_ext() const { return _induced_dipole.dot(_V); } double InternalEnergy() const { return 0.5 * _induced_dipole.transpose() * _pinv * _induced_dipole; } const Eigen::Vector3d& Induced_Dipole() const { return _induced_dipole; } void setInduced_Dipole(const Eigen::Vector3d& induced_dipole) { _induced_dipole = induced_dipole; } struct data { Index id; char* element; double posX; double posY; double posZ; Index rank; double Q00; double Q11c; double Q11s; double Q10; double Q20; double Q21c; double Q21s; double Q22c; double Q22s; double Vx; double Vy; double Vz; double Vx_noE; double Vy_noE; double Vz_noE; double pxx; double pxy; double pxz; double pyy; double pyz; double pzz; double d_x_ind; double d_y_ind; double d_z_ind; }; // do not move up has to be below data definition PolarSite(const data& d); double DipoleChange() const; void SetupCptTable(CptTable& table) const override; void WriteData(data& d) const; void ReadData(const data& d); std::string identify() const override { return "polarsite"; } friend std::ostream& operator<<(std::ostream& out, const PolarSite& site) { out << site.getId() << " " << site.getElement() << " " << site.getRank(); out << " " << site.getPos().transpose() << " " << site.Induced_Dipole().transpose() << "\n"; return out; } private: std::string writepolarization() const override; // PolarSite has two external fields, // the first is used for interaction with regions, which are further out, i.e. // the interaction energy with it is included in the polar region energy Eigen::Vector3d _V = Eigen::Vector3d::Zero(); // the second is used for interaction with regions, which are further inside, // i.e. the interaction energy with it is included in the other region's // energy Eigen::Vector3d _V_noE = Eigen::Vector3d::Zero(); Eigen::Vector3d _induced_dipole = Eigen::Vector3d::Zero(); Eigen::Matrix3d _pinv = Eigen::Matrix3d::Zero(); double _eigendamp_invsqrt = 0.0; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_POLARSITE_H xtp-2021.2/include/votca/xtp/populationanalysis.h000066400000000000000000000034701412152066400221010ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_POPULATIONANALYSIS_H #define VOTCA_XTP_POPULATIONANALYSIS_H // Local VOTCA includes #include "aomatrix.h" #include "orbitals.h" #include "qmfragment.h" /** * \brief Takes a list of atoms, and the corresponding density matrix and puts * out a table of wavefunction partial charges * * * */ namespace votca { namespace xtp { template class Populationanalysis { public: StaticSegment CalcChargeperAtom(const Orbitals& orbitals, const QMState& state) const; void CalcChargeperFragment(std::vector >& frags, const Orbitals& orbitals, QMStateType type) const; private: Eigen::VectorXd CalcNucChargeperAtom(const QMMolecule& mol) const; Eigen::VectorXd CalcElecChargeperAtom(const Eigen::MatrixXd& dmat, AOOverlap& overlap, const AOBasis& basis) const; }; using Mulliken = Populationanalysis; using Lowdin = Populationanalysis; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_POPULATIONANALYSIS_H xtp-2021.2/include/votca/xtp/ppm.h000066400000000000000000000030341412152066400167330ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_PPM_H #define VOTCA_XTP_PPM_H // Local VOTCA includes #include "eigen.h" #include "rpa.h" namespace votca { namespace xtp { class PPM { public: PPM() : screening_r(0.0), screening_i(0.5){}; // This sets the screening frequencies for real and imaginary part in hartree void PPM_construct_parameters(const RPA& rpa); const Eigen::VectorXd& getPpm_weight() const { return _ppm_weight; } const Eigen::VectorXd& getPpm_freq() const { return _ppm_freq; } const Eigen::MatrixXd& getPpm_phi() const { return _ppm_phi; } void FreeMatrix() { _ppm_phi.resize(0, 0); } private: double screening_r; double screening_i; // PPM related variables and functions Eigen::MatrixXd _ppm_phi; Eigen::VectorXd _ppm_freq; Eigen::VectorXd _ppm_weight; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_PPM_H xtp-2021.2/include/votca/xtp/progressobserver.h000066400000000000000000000050111412152066400215500ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ /// For an earlier history see ctp repo commit /// 77795ea591b29e664153f9404c8655ba28dc14e9 #pragma once #ifndef VOTCA_XTP_PROGRESSOBSERVER_H #define VOTCA_XTP_PROGRESSOBSERVER_H // Standard includes #include // Third party includes #include #include // VOTCA includes #include #include namespace votca { namespace xtp { class QMThread; template class ProgObserver { using Job = typename std::iterator_traits< typename JobContainer::iterator>::value_type; using Result = typename Job::JobResult; public: void InitCmdLineOpts(const boost::program_options::variables_map &optsMap); void InitFromProgFile(std::string progFile, QMThread &thread); ProgObserver::Job *RequestNextJob(QMThread &thread); void ReportJobDone(Job &job, Result &res, QMThread &thread); void SyncWithProgFile(QMThread &thread); void LockProgFile(QMThread &thread); void ReleaseProgFile(QMThread &thread); std::string GenerateHost(); std::string GenerateTime(); private: std::string _lockFile = ""; std::string _progFile = ""; Index _cacheSize = -1; JobContainer _jobs; std::vector _jobsToProc; std::vector _jobsToSync; using iterator = typename JobContainer::iterator; iterator _metajit; using iterator_vec = typename std::vector::iterator; iterator_vec _nextjit; tools::Mutex _lockThread; std::unique_ptr _flock; std::map _restart_hosts; std::map _restart_stats; bool _restartMode = false; Index _jobsReported = 0; bool _moreJobsAvailable = false; Index _startJobsCount = 0; Index _maxJobs = 0; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_PROGRESSOBSERVER_H xtp-2021.2/include/votca/xtp/qmatom.h000066400000000000000000000046611412152066400174440ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_QMATOM_H #define VOTCA_XTP_QMATOM_H // VOTCA includes #include // Local VOTCA includes #include "checkpoint.h" namespace votca { namespace xtp { /** * \brief container for QM atoms * * Stores atom type, coordinates, charge */ class QMAtom { friend class ECPAOBasis; public: struct data { Index index; char* element; double x; double y; double z; Index nuccharge; Index ecpcharge; }; QMAtom(Index index, std::string element, Eigen::Vector3d pos); QMAtom(const data& d); const Eigen::Vector3d& getPos() const { return _pos; } void Translate(const Eigen::Vector3d& shift) { _pos += shift; } void Rotate(const Eigen::Matrix3d& R, const Eigen::Vector3d& refPos); void setPos(const Eigen::Vector3d& position) { _pos = position; } const std::string& getElement() const { return _element; } Index getId() const { return _index; } Index getNuccharge() const { return _nuccharge - _ecpcharge; } Index getElementNumber() const { return _nuccharge; } std::string identify() const { return "qmatom"; } friend std::ostream& operator<<(std::ostream& out, const QMAtom& atom) { out << atom.getId() << " " << atom.getElement(); out << " " << atom.getPos().x() << "," << atom.getPos().y() << "," << atom.getPos().z() << " " << atom.getNuccharge() << "\n"; return out; } private: Index _index; std::string _element; Eigen::Vector3d _pos; // Bohr Index _nuccharge = 0; Index _ecpcharge = 0; // ecp charge is set in ecpaobasis.fill public: void SetupCptTable(CptTable& table) const; void WriteData(data& d) const; void ReadData(const data& d); }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_QMATOM_H xtp-2021.2/include/votca/xtp/qmcalculator.h000066400000000000000000000025471412152066400206360ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_QMCALCULATOR_H #define VOTCA_XTP_QMCALCULATOR_H // VOTCA includes #include namespace votca { namespace xtp { class Topology; class QMCalculator : public tools::Calculator { public: QMCalculator() = default; ~QMCalculator() override = default; std::string Identify() override = 0; virtual bool WriteToStateFile() const = 0; bool EvaluateFrame(Topology& top); void Initialize(const tools::Property& opt) final; protected: virtual void ParseOptions(const tools::Property& opt) = 0; virtual bool Evaluate(Topology& top) = 0; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_QMCALCULATOR_H xtp-2021.2/include/votca/xtp/qmfragment.h000066400000000000000000000072051412152066400203040ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_QMFRAGMENT_H #define VOTCA_XTP_QMFRAGMENT_H // Local VOTCA includes #include "IndexParser.h" #include "bse_population.h" /** * \brief Container to define fragments of QMmolecules, containing atomindices, * no pointers to atoms, it also handles the parsing of strings etc.. Values * should have own destructor * * * */ namespace votca { namespace xtp { template class QMFragment { public: QMFragment(Index id, std::string atoms) : _id(id) { FillAtomIndices(atoms); } QMFragment() = default; QMFragment(CheckpointReader& r) { ReadFromCpt(r); } template void copy_withoutvalue(const QMFragment& frag) { _id = frag.getId(); _atomindices = frag.getIndices(); } void setId(Index id) { _id = id; } Index getId() const { return _id; } void FillFromString(std::string atoms) { FillAtomIndices(atoms); } const T& value() const { return _value; } T& value() { return _value; } Index size() const { return Index(_atomindices.size()); } const std::vector& getIndices() const { return _atomindices; } double ExtractFromVector(const Eigen::VectorXd& atomentries) const { double result = 0; for (Index index : _atomindices) { result += atomentries(index); } return result; } typename std::vector::const_iterator begin() const { return _atomindices.begin(); } typename std::vector::const_iterator end() const { return _atomindices.end(); } friend std::ostream& operator<<(std::ostream& out, const QMFragment& fragment) { out << "Fragment id:" << fragment._id << "\n"; out << "AtomIndices[" << fragment.size() << "]:"; for (Index id : fragment._atomindices) { out << id << " "; } out << "\nValue:" << fragment._value; out << "\n"; return out; }; void WriteToCpt(CheckpointWriter& w) const { w(_atomindices, "indices"); w(_id, "id"); WriteValue(w); } void ReadFromCpt(CheckpointReader& r) { r(_atomindices, "indices"); r(_id, "id"); ReadValue(r); } private: void WriteValue(CheckpointWriter& w) const; void ReadValue(CheckpointReader& r); void FillAtomIndices(const std::string& atoms) { IndexParser p; _atomindices = p.CreateIndexVector(atoms); } std::vector _atomindices; Index _id = -1; T _value{}; }; template inline void QMFragment::ReadValue(CheckpointReader& r) { r(_value, "value"); } template inline void QMFragment::WriteValue(CheckpointWriter& w) const { w(_value, "value"); } template <> inline void QMFragment::ReadValue(CheckpointReader& r) { CheckpointReader rr = r.openChild("BSE_pop"); _value.ReadFromCpt(rr); } template <> inline void QMFragment::WriteValue(CheckpointWriter& w) const { CheckpointWriter ww = w.openChild("BSE_pop"); _value.WriteToCpt(ww); } } // namespace xtp } // namespace votca #endif // VOTCA_XTP_QMFRAGMENT_H xtp-2021.2/include/votca/xtp/qmmolecule.h000066400000000000000000000036071412152066400203100ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_QMMOLECULE_H #define VOTCA_XTP_QMMOLECULE_H // Local VOTCA includes #include "atomcontainer.h" #include "qmatom.h" namespace votca { namespace xtp { class QMMolecule : public AtomContainer { public: QMMolecule(std::string name, Index id) : AtomContainer(name, id){}; QMMolecule(CheckpointReader& r) : AtomContainer(r){}; void LoadFromFile(std::string filename); void WriteXYZ(std::string filename, std::string header) const; void AddContainer(const AtomContainer& container) { Index offset = _atomlist.size(); _type += "_" + container.getType(); for (const auto& at : container) { // Update atom IDs to make sure they are unique QMAtom atom(at.getId() + offset, at.getElement(), at.getPos()); _atomlist.push_back(atom); } calcPos(); } friend std::ostream& operator<<(std::ostream& out, const QMMolecule& container) { out << container.getId() << " " << container.getType() << "\n"; for (const QMAtom& atom : container) { out << atom; } out << std::endl; return out; } }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_QMMOLECULE_H xtp-2021.2/include/votca/xtp/qmnblist.h000066400000000000000000000035421412152066400177740ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ /// For earlier commit history see ctp commit /// 77795ea591b29e664153f9404c8655ba28dc14e9 #pragma once #ifndef VOTCA_XTP_QMNBLIST_H #define VOTCA_XTP_QMNBLIST_H // VOTCA includes #include // Local VOTCA includes #include "qmpair.h" namespace votca { namespace xtp { class QMNBList : public csg::PairList { public: QMNBList() = default; ~QMNBList() override { csg::PairList::Cleanup(); } QMPair& Add(const Segment& seg1, const Segment& seg2, const Eigen::Vector3d& r); template void sortAndReindex(Compare comp); const QMPair* operator[](Index index) const { return _pairs[index]; } QMPair* operator[](Index index) { return _pairs[index]; } void WriteToCpt(CheckpointWriter& w) const; void ReadFromCpt(CheckpointReader& r, const std::vector& segments); protected: }; template inline void QMNBList::sortAndReindex(Compare comp) { std::sort(_pairs.begin(), _pairs.end(), comp); for (Index i = 0; i < Index(_pairs.size()); i++) { _pairs[i]->setId(i); } } } // namespace xtp } // namespace votca #endif // VOTCA_XTP_QMNBLIST_H xtp-2021.2/include/votca/xtp/qmpackage.h000066400000000000000000000106341412152066400200740ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_QMPACKAGE_H #define VOTCA_XTP_QMPACKAGE_H // VOTCA includes #include // Local VOTCA includes #include "aobasis.h" #include "classicalsegment.h" #include "logger.h" #include "settings.h" #include "staticsite.h" #include "votca/xtp/orbreorder.h" namespace votca { namespace xtp { class Orbitals; class QMPackage { public: virtual ~QMPackage() = default; virtual std::string getPackageName() const = 0; virtual void Initialize(const tools::Property& options) = 0; /// writes a coordinate file WITHOUT taking into account PBCs virtual bool WriteInputFile(const Orbitals& orbitals) = 0; virtual bool Run() = 0; virtual bool ParseLogFile(Orbitals& orbitals) = 0; virtual bool ParseMOsFile(Orbitals& orbitals) = 0; virtual void CleanUp() = 0; template void AddRegion(const MMRegion& mmregion) { using Segmenttype = typename std::iterator_traits::value_type; using Sitetype = typename std::iterator_traits< typename Segmenttype::iterator>::value_type; for (const Segmenttype& segment : mmregion) { for (const Sitetype& site : segment) { _externalsites.push_back( std::unique_ptr(new Sitetype(site))); } } if (_settings.get("write_charges")) { WriteChargeOption(); } } void setRunDir(const std::string& run_dir) { _run_dir = run_dir; } void setInputFileName(const std::string& input_file_name) { _input_file_name = input_file_name; } void setLogFileName(const std::string& log_file_name) { _log_file_name = log_file_name; } void setMOsFileName(const std::string& mo_file) { _mo_file_name = mo_file; } void setLog(Logger* pLog) { _pLog = pLog; } void setCharge(Index charge) { _charge = charge; _spin = std::abs(charge) + 1; } bool GuessRequested() const { return _settings.get("read_guess"); } virtual StaticSegment GetCharges() const = 0; virtual Eigen::Matrix3d GetPolarizability() const = 0; std::string getLogFile() const { return _log_file_name; }; std::string getMOFile() const { return _mo_file_name; }; protected: struct MinimalMMCharge { MinimalMMCharge(const Eigen::Vector3d& pos, double q) : _pos(pos), _q(q){}; Eigen::Vector3d _pos; double _q; }; tools::Property ParseCommonOptions(const tools::Property& options); std::string FindDefaultsFile() const; virtual void WriteChargeOption() = 0; std::vector SplitMultipoles(const StaticSite& site) const; void ReorderOutput(Orbitals& orbitals) const; Eigen::MatrixXd ReorderMOsBack(const Orbitals& orbitals) const; bool isLinker(std::string name, std::vector linker_names); std::vector GetLineAndSplit(std::ifstream& input_file, const std::string separators) const; // ShellReorder() and ShellMulitplier() specify the order for each // QMPackage. Some codes also use different normalisation conditions which // lead to other signs for some of the entries, which can be changed via the // multipliers. virtual const std::array& ShellMulitplier() const = 0; virtual const std::array& ShellReorder() const = 0; Settings _settings{"package"}; Index _charge; Index _spin; // 2S+1mem std::string _basisset_name; std::string _cleanup = ""; std::string _input_file_name; std::string _log_file_name; std::string _mo_file_name; std::string _options = ""; std::string _run_dir; std::string _scratch_dir; std::string _shell_file_name; Logger* _pLog; std::vector > _externalsites; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_QMPACKAGE_H xtp-2021.2/include/votca/xtp/qmpackagefactory.h000066400000000000000000000027201412152066400214610ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_QMPACKAGEFACTORY_H #define VOTCA_XTP_QMPACKAGEFACTORY_H // VOTCA includes #include // Local VOTCA includes #include "qmpackage.h" namespace votca { namespace xtp { class QMPackageFactory : public tools::ObjectFactory { private: QMPackageFactory() = default; public: QMPackageFactory(QMPackageFactory const &) = delete; void operator=(QMPackageFactory const &) = delete; QMPackageFactory(QMPackageFactory &&) = delete; void operator=(QMPackageFactory &&) = delete; static void RegisterAll(void); static QMPackageFactory &QMPackages() { static QMPackageFactory _instance; return _instance; } }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_QMPACKAGEFACTORY_H xtp-2021.2/include/votca/xtp/qmpair.h000066400000000000000000000075441412152066400174420ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ /// For earlier commit history see ctp commit /// 77795ea591b29e664153f9404c8655ba28dc14e9 #pragma once #ifndef VOTCA_XTP_QMPAIR_H #define VOTCA_XTP_QMPAIR_H // Standard includes #include // Local VOTCA includes #include "eigen.h" #include "qmstate.h" #include "segment.h" namespace votca { namespace xtp { class QMPair { public: enum PairType { Hopping = 0, Excitoncl = 1 }; static std::string get_name(PairType type) { switch (type) { case Hopping: return "Hopping"; case Excitoncl: return "Excitoncl"; // no default case to trigger compiler error } return ""; } struct data { Index id; Index Seg1Id; Index Seg2Id; double RX; double RY; double RZ; char* pair_type; double lambda0e; double lambda0h; double lambda0s; double lambda0t; double jeff2e; double jeff2h; double jeff2s; double jeff2t; }; static PairType get_Enum(std::string type) { if (type == "Hopping") { return PairType::Hopping; } else if (type == "Excitoncl") { return PairType::Excitoncl; } else { throw std::runtime_error("get_Enum input is invalid"); } } QMPair(Index id, const Segment* seg1, const Segment* seg2, const Eigen::Vector3d& delta_R); QMPair(const data& d, const std::vector& segments) { ReadData(d, segments); } Index getId() const { return _id; } void setId(Index id) { _id = id; } const Eigen::Vector3d& R() const { return _R; } double Dist() const { return _R.norm(); } void setLambdaO(double lO, QMStateType state) { _lambda0.setValue(lO, state); } double getLambdaO(QMStateType state) const { return _lambda0.getValue(state); } double getReorg12(QMStateType state) const { return _segments.first->getU_nX_nN(state) + _segments.second->getU_xN_xX(state); } // 1->2 double getReorg21(QMStateType state) const { return _segments.first->getU_xN_xX(state) + _segments.second->getU_nX_nN(state); } // 2->1 double getJeff2(QMStateType state) const { return _Jeff2.getValue(state); } void setJeff2(double Jeff2, QMStateType state) { _Jeff2.setValue(Jeff2, state); } double getdE12(QMStateType state) const { return _segments.first->getSiteEnergy(state) - _segments.second->getSiteEnergy(state); } Segment Seg2PbCopy() const; const Segment* Seg1() const { return _segments.first; } const Segment* Seg2() const { return _segments.second; } const Segment* first() { return _segments.first; } const Segment* second() { return _segments.second; } void setType(PairType pair_type) { _pair_type = pair_type; } const PairType& getType() const { return _pair_type; } void SetupCptTable(CptTable& table) const; void WriteData(data& d) const; void ReadData(const data& d, const std::vector& segments); private: Index _id = -1; std::pair _segments; Eigen::Vector3d _R = Eigen::Vector3d::Zero(); PairType _pair_type = PairType::Hopping; QMStateCarrierStorage _lambda0; QMStateCarrierStorage _Jeff2; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_QMPAIR_H xtp-2021.2/include/votca/xtp/qmregion.h000066400000000000000000000055411412152066400177650ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_QMREGION_H #define VOTCA_XTP_QMREGION_H // Local VOTCA includes #include "hist.h" #include "orbitals.h" #include "qmpackagefactory.h" #include "region.h" #include "statetracker.h" /** * \brief defines a qm region and runs dft and gwbse calculations * * * */ namespace votca { namespace xtp { class PolarRegion; class StaticRegion; class QMRegion : public Region { public: QMRegion(Index id, Logger& log, std::string workdir) : Region(id, log), _workdir(workdir) { QMPackageFactory::RegisterAll(); }; ~QMRegion() override = default; void Initialize(const tools::Property& prop) override; bool Converged() const override; void Evaluate(std::vector >& regions) override; void WriteToCpt(CheckpointWriter& w) const override; void ReadFromCpt(CheckpointReader& r) override; void ApplyQMFieldToPolarSegments(std::vector& segments) const; Index size() const override { return _size; } void WritePDB(csg::PDBWriter& writer) const override; std::string identify() const override { return "qm"; } void push_back(const QMMolecule& mol); void Reset() override; double charge() const override; double Etotal() const override { return _E_hist.back(); } protected: void AppendResult(tools::Property& prop) const override; double InteractwithQMRegion(const QMRegion& region) override; double InteractwithPolarRegion(const PolarRegion& region) override; double InteractwithStaticRegion(const StaticRegion& region) override; private: void AddNucleiFields(std::vector& segments, const StaticSegment& seg) const; Index _size = 0; Orbitals _orb; QMState _initstate; std::string _workdir = ""; std::unique_ptr _qmpackage = nullptr; std::string _grid_accuracy_for_ext_interaction = "medium"; hist _E_hist; hist _Dmat_hist; // convergence options double _DeltaD = 5e-5; double _DeltaE = 5e-5; bool _do_gwbse = false; tools::Property _dftoptions; tools::Property _gwbseoptions; StateTracker _statetracker; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_QMREGION_H xtp-2021.2/include/votca/xtp/qmstate.h000066400000000000000000000103241412152066400176150ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_QMSTATE_H #define VOTCA_XTP_QMSTATE_H // Standard includes #include // VOTCA includes #include // Local VOTCA includes #include "checkpointreader.h" #include "checkpointwriter.h" namespace votca { namespace xtp { class QMStateType { public: enum statetype { // never change the values Electron = 0, Hole = 1, Singlet = 2, Triplet = 3, Gstate = 4, PQPstate, DQPstate, KSstate }; QMStateType(const statetype& type) : _type(type) { ; } QMStateType() { ; } QMStateType(const std::string& s) { FromString(s); } statetype Type() const { return _type; } void FromString(const std::string& statetypestring); std::string ToString() const; std::string ToLongString() const; bool operator==(const QMStateType& rhs) const { return _type == rhs.Type(); } bool operator!=(const QMStateType& rhs) const { return _type != rhs.Type(); } bool operator==(const QMStateType::statetype& rhs) const { return _type == rhs; } bool operator!=(const QMStateType::statetype& rhs) const { return _type != rhs; } bool isExciton() const { return (_type == statetype::Singlet || _type == statetype::Triplet); } bool isKMCState() const { return (_type == statetype::Singlet || _type == statetype::Triplet || _type == statetype::Hole || _type == statetype::Electron); } bool isSingleParticleState() const { return (_type == statetype::PQPstate || _type == statetype::DQPstate || _type == KSstate); } bool isGWState() const { return (_type == statetype::PQPstate || _type == statetype::DQPstate); } private: statetype _type; }; /** * \brief Storage class for properties of QMStateTypes, which can be used in * KMC * * */ template class QMStateCarrierStorage { public: QMStateCarrierStorage() { _content = {0, 0, 0, 0}; } void setValue(T value, QMStateType t) { assert(t.isKMCState() && "QMStateCarrierStorage QMStateType is not for KMC simulations"); _content[t.Type()] = value; } T getValue(QMStateType t) const { assert(t.isKMCState() && "QMStateCarrierStorage QMStateType is not for KMC simulations"); return _content[t.Type()]; } private: std::array _content; }; /** * \brief Identifier for QMstates. Strings like S1 are converted into enum * +zero indexed int * * */ class QMState { public: QMState(const QMStateType::statetype& type, Index index, bool transition) : _type(QMStateType(type)), _index(index), _transition(transition) { ; } QMState(const QMStateType& type, Index index, bool transition) : _type(type), _index(index), _transition(transition) { ; } QMState() { ; } QMState(const std::string& statestring) { FromString(statestring); } void FromString(const std::string& statestring); std::string ToString() const; std::string ToLongString() const; const QMStateType& Type() const { return _type; } bool isTransition() const { return _transition; } Index StateIdx() const { return _index; } bool operator==(const QMState& rhs) const { return (_type == rhs.Type() && _index == rhs.StateIdx()); } bool operator!=(const QMState& rhs) const { return (_type != rhs.Type() || _index != rhs.StateIdx()); } private: Index DetermineIndex(const std::string& statestring); QMStateType DetermineType(const std::string& statestring); QMStateType _type; Index _index; bool _transition; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_QMSTATE_H xtp-2021.2/include/votca/xtp/qmthread.h000066400000000000000000000033501412152066400177450ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ /// For an earlier history see ctp repo commit /// 77795ea591b29e664153f9404c8655ba28dc14e9 #pragma once #ifndef VOTCA_XTP_QMTHREAD_H #define VOTCA_XTP_QMTHREAD_H // Standard includes #include #include #include // VOTCA includes #include #include // Local VOTCA includes #include "logger.h" namespace votca { namespace xtp { // ++++++++++++++++++++++++++++++++++++++ // // Thread class with local string stream // // ++++++++++++++++++++++++++++++++++++++ // class QMThread : public tools::Thread { public: QMThread() = default; QMThread(bool maverick) : _maverick(maverick) { ; } ~QMThread() override = default; Index getId() const { return _id; } void setId(Index id) { _id = id; } bool isMaverick() const { return _maverick; } Logger& getLogger() { return _logger; } void Run(void) override { ; } protected: Index _id; std::stringstream _ss; bool _maverick = false; Logger _logger; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_QMTHREAD_H xtp-2021.2/include/votca/xtp/qmtool.h000066400000000000000000000026711412152066400174600ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ /// For an earlier history see ctp repo commit /// 77795ea591b29e664153f9404c8655ba28dc14e9 #pragma once #ifndef VOTCA_XTP_QMTOOL_H #define VOTCA_XTP_QMTOOL_H // Third party includes #include // VOTCA includes #include #include namespace votca { namespace xtp { class QMTool : public tools::Calculator { public: QMTool() = default; ~QMTool() override = default; std::string Identify() override = 0; void Initialize(const tools::Property& options) final; bool Evaluate(); protected: virtual bool Run() = 0; virtual void ParseOptions(const tools::Property& opt) = 0; std::string _job_name = "votca"; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_QMTOOL_H xtp-2021.2/include/votca/xtp/quadrature_factory.h000066400000000000000000000025641412152066400220520ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_QUADRATURE_FACTORY_H #define VOTCA_XTP_QUADRATURE_FACTORY_H // Standard includes #include // VOTCA includes #include // Local VOTCA includes #include "GaussianQuadratureBase.h" namespace votca { namespace xtp { class QuadratureFactory : public tools::ObjectFactory { private: QuadratureFactory() = default; public: static void RegisterAll(void); friend QuadratureFactory &Quadratures(); }; inline QuadratureFactory &Quadratures() { static QuadratureFactory _instance; return _instance; } } // namespace xtp } // namespace votca #endif // VOTCA_XTP_QUADRATURE_FACTORY_H xtp-2021.2/include/votca/xtp/radial_euler_maclaurin_rule.h000066400000000000000000000353551412152066400236640ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_RADIAL_EULER_MACLAURIN_RULE_H #define VOTCA_XTP_RADIAL_EULER_MACLAURIN_RULE_H // VOTCA includes #include // Local VOTCA includes #include "basisset.h" #include "grid_containers.h" #include "qmatom.h" namespace votca { namespace xtp { class EulerMaclaurinGrid { public: EulerMaclaurinGrid() { FillGrids(); }; std::map CalculateAtomicRadialGrids( const AOBasis& aobasis, const QMMolecule& atoms, const std::string& type); std::vector CalculatePruningIntervals(const std::string& element); private: struct min_exp { double alpha; Index l; double range; }; std::map _element_ranges; std::map _pruning_set; std::map _BraggSlaterRadii; Index getGridParameters(const std::string& element, const std::string& type); double DetermineCutoff(double alpha, Index l, double eps); double CalcResidual(double alpha, Index l, double cutoff); double RadialIntegral(double alpha, Index l, double cutoff); void CalculateRadialCutoffs(const AOBasis& aobasis, const QMMolecule& atoms, const std::string& gridtype); void RefineElementRangeMap(const AOBasis& aobasis, const QMMolecule& atoms, double eps); void FillElementRangeMap(const AOBasis& aobasis, const QMMolecule& atoms, double eps); GridContainers::radial_grid CalculateRadialGridforAtom( const std::string& type, const std::pair& element); std::map MediumGrid; std::map CoarseGrid; std::map XcoarseGrid; std::map FineGrid; std::map XfineGrid; std::map Accuracy; inline void FillGrids() { FillBraggSlaterRadii(); FillPruningSet(); FillAccuracy(); FillMediumGrid(); FillCoarseGrid(); FillXcoarseGrid(); FillFineGrid(); FillXfineGrid(); } inline void FillBraggSlaterRadii() { const double ang2bohr = votca::tools::conv::ang2bohr; // _BraggSlaterRadii["H"] = 0.35 * ang2bohr; _BraggSlaterRadii["He"] = 0.35 * ang2bohr; // row of period system for 1st row elements taken from NWChem _BraggSlaterRadii["Li"] = 1.45 * ang2bohr; _BraggSlaterRadii["Be"] = 1.05 * ang2bohr; _BraggSlaterRadii["B"] = 0.85 * ang2bohr; _BraggSlaterRadii["C"] = 0.70 * ang2bohr; _BraggSlaterRadii["N"] = 0.65 * ang2bohr; _BraggSlaterRadii["O"] = 0.60 * ang2bohr; _BraggSlaterRadii["F"] = 0.50 * ang2bohr; _BraggSlaterRadii["Ne"] = 0.50 * ang2bohr; // row of period system for 2nd row elements taken from NWChem _BraggSlaterRadii["Na"] = 1.80 * ang2bohr; _BraggSlaterRadii["Mg"] = 1.5 * ang2bohr; _BraggSlaterRadii["Al"] = 1.25 * ang2bohr; _BraggSlaterRadii["Si"] = 1.1 * ang2bohr; _BraggSlaterRadii["P"] = 1.0 * ang2bohr; _BraggSlaterRadii["S"] = 1.0 * ang2bohr; _BraggSlaterRadii["Cl"] = 1.0 * ang2bohr; _BraggSlaterRadii["Ar"] = 1.0 * ang2bohr; // row of period system for 3rd row elements taken from NWChem _BraggSlaterRadii["K"] = 2.2 * ang2bohr; _BraggSlaterRadii["Ca"] = 1.8 * ang2bohr; _BraggSlaterRadii["Sc"] = 1.6 * ang2bohr; _BraggSlaterRadii["Ti"] = 1.4 * ang2bohr; _BraggSlaterRadii["V"] = 1.35 * ang2bohr; _BraggSlaterRadii["Cr"] = 1.4 * ang2bohr; _BraggSlaterRadii["Mn"] = 1.4 * ang2bohr; _BraggSlaterRadii["Fe"] = 1.4 * ang2bohr; _BraggSlaterRadii["Co"] = 1.35 * ang2bohr; _BraggSlaterRadii["Ni"] = 1.35 * ang2bohr; _BraggSlaterRadii["Cu"] = 1.35 * ang2bohr; _BraggSlaterRadii["Zn"] = 1.35 * ang2bohr; _BraggSlaterRadii["Ga"] = 1.30 * ang2bohr; _BraggSlaterRadii["Ge"] = 1.25 * ang2bohr; _BraggSlaterRadii["As"] = 1.15 * ang2bohr; _BraggSlaterRadii["Se"] = 1.15 * ang2bohr; _BraggSlaterRadii["Br"] = 1.15 * ang2bohr; _BraggSlaterRadii["Kr"] = 1.15 * ang2bohr; // 4th row (selection) _BraggSlaterRadii["Ag"] = 1.60 * ang2bohr; _BraggSlaterRadii["Rb"] = 2.35 * ang2bohr; _BraggSlaterRadii["Xe"] = 1.40 * ang2bohr; _BraggSlaterRadii["I"] = 1.40 * ang2bohr; /* Copied from grid_atom_type_info.F of NWChem * VALUES are in ANGSTROM Data BSrad/0.35,0.35,1.45,1.05,0.85,0.70,0.65,0.60,0.50,0.50, c Na Mg Al Si P S Cl Ar K Ca & 1.80,1.50,1.25,1.10,1.00,1.00,1.00,1.00,2.20,1.80, c Sc Ti V Cr Mn Fe Co Ni Cu Zn & 1.60,1.40,1.35,1.40,1.40,1.40,1.35,1.35,1.35,1.35, c Ga Ge As Se Br Kr Rb Sr Y Zr & 1.30,1.25,1.15,1.15,1.15,1.15,2.35,2.00,1.80,1.55, c Nb Mo Tc Ru Rh Pd Ag Cd In Sn & 1.45,1.45,1.35,1.30,1.35,1.40,1.60,1.55,1.55,1.45, c Sb Te I Xe Cs Ba La Ce Pr Nd & 1.45,1.40,1.40,1.40,2.60,2.15,1.95,1.85,1.85,1.85, c Pm Sm Eu Gd Tb Dy Ho Er Tm Yb & 1.85,1.85,1.85,1.80,1.75,1.75,1.75,1.75,1.75,1.75, c Lu Hf Ta W Re Os Ir Pt Au Hg & 1.75,1.55,1.45,1.35,1.35,1.30,1.35,1.35,1.35,1.50, c Tl Pb Bi Po At Rn Fr Ra Ac Th & 1.90,1.80,1.60,1.90,1.90,1.90,2.60,2.15,1.95,1.80, c Pa U Np Pu Am Cm Bk Cf Es Fm & 1.80,1.75,1.75,1.75,1.75,1.75,1.75,1.75,1.75,1.75, c Md No Lr Unq Unp & 1.75,1.75,1.75,1.55,1.55/ */ } inline void FillPruningSet() { // row of period system for H, He (not given in NWChem, assuming same as 1st // row) _pruning_set["H"] = 1; _pruning_set["He"] = 1; // row of period system for 1st row elements taken from NWChem _pruning_set["Li"] = 2; _pruning_set["Be"] = 2; _pruning_set["B"] = 2; _pruning_set["C"] = 2; _pruning_set["N"] = 2; _pruning_set["O"] = 2; _pruning_set["F"] = 2; _pruning_set["Ne"] = 2; // row of period system for 2nd row elements taken from NWChem _pruning_set["Na"] = 3; _pruning_set["Mg"] = 3; _pruning_set["Al"] = 3; _pruning_set["Si"] = 3; _pruning_set["P"] = 3; _pruning_set["S"] = 3; _pruning_set["Cl"] = 3; _pruning_set["Ar"] = 3; // row of period system for 3rd row elements taken from NWChem _pruning_set["K"] = 3; _pruning_set["Ca"] = 3; _pruning_set["Sc"] = 3; _pruning_set["Ti"] = 3; _pruning_set["V"] = 3; _pruning_set["Cr"] = 3; _pruning_set["Mn"] = 3; _pruning_set["Fe"] = 3; _pruning_set["Co"] = 3; _pruning_set["Ni"] = 3; _pruning_set["Cu"] = 3; _pruning_set["Zn"] = 3; _pruning_set["Ga"] = 3; _pruning_set["Ge"] = 3; _pruning_set["As"] = 3; _pruning_set["Se"] = 3; _pruning_set["Br"] = 3; _pruning_set["Kr"] = 3; // row of period system for 4th row elements taken from NWChem _pruning_set["Ag"] = 3; _pruning_set["Rb"] = 3; _pruning_set["I"] = 3; _pruning_set["Xe"] = 3; } inline void FillAccuracy() { Accuracy["xcoarse"] = 1e-4; Accuracy["coarse"] = 1e-5; Accuracy["medium"] = 1e-6; Accuracy["fine"] = 1e-7; Accuracy["xfine"] = 1e-8; } inline void FillMediumGrid() { // order for H, He (not given in NWChem, assuming same as 1st row) MediumGrid["H"] = 49; MediumGrid["He"] = 49; // orders for 1st row elements taken from NWChem MediumGrid["Li"] = 49; MediumGrid["Be"] = 49; MediumGrid["B"] = 49; MediumGrid["C"] = 49; MediumGrid["N"] = 49; MediumGrid["O"] = 49; MediumGrid["F"] = 49; MediumGrid["Ne"] = 49; // orders for 2nd row elements taken from NWChem MediumGrid["Na"] = 88; MediumGrid["Mg"] = 88; MediumGrid["Al"] = 88; MediumGrid["Si"] = 88; MediumGrid["P"] = 88; MediumGrid["S"] = 88; MediumGrid["Cl"] = 88; MediumGrid["Ar"] = 88; // orders for 3rd row elements taken from NWChem MediumGrid["K"] = 112; MediumGrid["Ca"] = 112; MediumGrid["Sc"] = 112; MediumGrid["Ti"] = 112; MediumGrid["V"] = 112; MediumGrid["Cr"] = 112; MediumGrid["Mn"] = 112; MediumGrid["Fe"] = 112; MediumGrid["Co"] = 112; MediumGrid["Ni"] = 112; MediumGrid["Cu"] = 112; MediumGrid["Zn"] = 112; MediumGrid["Ga"] = 112; MediumGrid["Ge"] = 112; MediumGrid["As"] = 112; MediumGrid["Se"] = 112; MediumGrid["Br"] = 112; MediumGrid["Kr"] = 112; // orders for 4th row elements (selected) MediumGrid["Ag"] = 123; MediumGrid["Rb"] = 123; MediumGrid["Xe"] = 123; MediumGrid["I"] = 123; } inline void FillFineGrid() { // order for H, He (not given in NWChem, assuming same as 1st row) FineGrid["H"] = 70; FineGrid["He"] = 70; // orders for 1st row elements taken from NWChem FineGrid["Li"] = 70; FineGrid["Be"] = 70; FineGrid["B"] = 70; FineGrid["C"] = 70; FineGrid["N"] = 70; FineGrid["O"] = 70; FineGrid["F"] = 70; FineGrid["Ne"] = 70; // orders for 2nd row elements taken from NWChem FineGrid["Na"] = 123; FineGrid["Mg"] = 123; FineGrid["Al"] = 123; FineGrid["Si"] = 123; FineGrid["P"] = 123; FineGrid["S"] = 123; FineGrid["Cl"] = 123; FineGrid["Ar"] = 123; // orders for 3rd row elements taken from NWChem FineGrid["K"] = 130; FineGrid["Ca"] = 130; FineGrid["Sc"] = 130; FineGrid["Ti"] = 130; FineGrid["V"] = 130; FineGrid["Cr"] = 130; FineGrid["Mn"] = 130; FineGrid["Fe"] = 130; FineGrid["Co"] = 130; FineGrid["Ni"] = 130; FineGrid["Cu"] = 130; FineGrid["Zn"] = 130; FineGrid["Ga"] = 130; FineGrid["Ge"] = 130; FineGrid["As"] = 130; FineGrid["Se"] = 130; FineGrid["Br"] = 130; FineGrid["Kr"] = 130; // 4th row (selected) FineGrid["Ag"] = 141; FineGrid["Rb"] = 141; FineGrid["I"] = 141; FineGrid["Xe"] = 141; } inline void FillXfineGrid() { // order for H, He (not given in NWChem, assuming same as 1st row) XfineGrid["H"] = 100; XfineGrid["He"] = 100; // orders for 1st row elements taken from NWChem XfineGrid["Li"] = 100; XfineGrid["Be"] = 100; XfineGrid["B"] = 100; XfineGrid["C"] = 100; XfineGrid["N"] = 100; XfineGrid["O"] = 100; XfineGrid["F"] = 100; XfineGrid["Ne"] = 100; // orders for 2nd row elements taken from NWChem XfineGrid["Na"] = 125; XfineGrid["Mg"] = 125; XfineGrid["Al"] = 125; XfineGrid["Si"] = 125; XfineGrid["P"] = 125; XfineGrid["S"] = 125; XfineGrid["Cl"] = 125; XfineGrid["Ar"] = 125; // orders for 3rd row elements taken from NWChem XfineGrid["K"] = 160; XfineGrid["Ca"] = 160; XfineGrid["Sc"] = 160; XfineGrid["Ti"] = 160; XfineGrid["V"] = 160; XfineGrid["Cr"] = 160; XfineGrid["Mn"] = 160; XfineGrid["Fe"] = 160; XfineGrid["Co"] = 160; XfineGrid["Ni"] = 160; XfineGrid["Cu"] = 160; XfineGrid["Zn"] = 160; XfineGrid["Ga"] = 160; XfineGrid["Ge"] = 160; XfineGrid["As"] = 160; XfineGrid["Se"] = 160; XfineGrid["Br"] = 160; XfineGrid["Kr"] = 160; // 4th row (selection) XfineGrid["Ag"] = 205; XfineGrid["Rb"] = 205; XfineGrid["I"] = 205; XfineGrid["Xe"] = 205; } inline void FillCoarseGrid() { // order for H, He (not given in NWChem, assuming same as 1st row) CoarseGrid["H"] = 35; CoarseGrid["He"] = 35; // orders for 1st row elements taken from NWChem CoarseGrid["Li"] = 35; CoarseGrid["Be"] = 35; CoarseGrid["B"] = 35; CoarseGrid["C"] = 35; CoarseGrid["N"] = 35; CoarseGrid["O"] = 35; CoarseGrid["F"] = 35; CoarseGrid["Ne"] = 35; // orders for 2nd row elements taken from NWChem CoarseGrid["Na"] = 70; CoarseGrid["Mg"] = 70; CoarseGrid["Al"] = 70; CoarseGrid["Si"] = 70; CoarseGrid["P"] = 70; CoarseGrid["S"] = 70; CoarseGrid["Cl"] = 70; CoarseGrid["Ar"] = 70; // orders for 3rd row elements taken from NWChem CoarseGrid["K"] = 95; CoarseGrid["Ca"] = 95; CoarseGrid["Sc"] = 95; CoarseGrid["Ti"] = 95; CoarseGrid["V"] = 95; CoarseGrid["Cr"] = 95; CoarseGrid["Mn"] = 95; CoarseGrid["Fe"] = 95; CoarseGrid["Co"] = 95; CoarseGrid["Ni"] = 95; CoarseGrid["Cu"] = 95; CoarseGrid["Zn"] = 95; CoarseGrid["Ga"] = 95; CoarseGrid["Ge"] = 95; CoarseGrid["As"] = 95; CoarseGrid["Se"] = 95; CoarseGrid["Br"] = 95; CoarseGrid["Kr"] = 95; // 4th row (selection) CoarseGrid["Ag"] = 104; CoarseGrid["Rb"] = 104; CoarseGrid["I"] = 104; CoarseGrid["Xe"] = 104; } inline void FillXcoarseGrid() { // order for H, He (not given in NWChem, assuming same as 1st row) XcoarseGrid["H"] = 21; XcoarseGrid["He"] = 21; // orders for 1st row elements taken from NWChem XcoarseGrid["Li"] = 21; XcoarseGrid["Be"] = 21; XcoarseGrid["B"] = 21; XcoarseGrid["C"] = 21; XcoarseGrid["N"] = 21; XcoarseGrid["O"] = 21; XcoarseGrid["F"] = 21; XcoarseGrid["Ne"] = 21; // orders for 2nd row elements taken from NWChem XcoarseGrid["Na"] = 42; XcoarseGrid["Mg"] = 42; XcoarseGrid["Al"] = 42; XcoarseGrid["Si"] = 42; XcoarseGrid["P"] = 42; XcoarseGrid["S"] = 42; XcoarseGrid["Cl"] = 42; XcoarseGrid["Ar"] = 42; // orders for 3rd row elements taken from NWChem XcoarseGrid["K"] = 75; XcoarseGrid["Ca"] = 75; XcoarseGrid["Sc"] = 75; XcoarseGrid["Ti"] = 75; XcoarseGrid["V"] = 75; XcoarseGrid["Cr"] = 75; XcoarseGrid["Mn"] = 75; XcoarseGrid["Fe"] = 75; XcoarseGrid["Co"] = 75; XcoarseGrid["Ni"] = 75; XcoarseGrid["Cu"] = 75; XcoarseGrid["Zn"] = 75; XcoarseGrid["Ga"] = 75; XcoarseGrid["Ge"] = 75; XcoarseGrid["As"] = 75; XcoarseGrid["Se"] = 75; XcoarseGrid["Br"] = 75; XcoarseGrid["Kr"] = 75; // 4th row (selection) XcoarseGrid["Ag"] = 84; XcoarseGrid["Rb"] = 84; XcoarseGrid["I"] = 84; XcoarseGrid["Xe"] = 84; } }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_RADIAL_EULER_MACLAURIN_RULE_H xtp-2021.2/include/votca/xtp/rate_engine.h000066400000000000000000000031621412152066400204210ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_RATE_ENGINE_H #define VOTCA_XTP_RATE_ENGINE_H // Local VOTCA includes #include "eigen.h" #include "qmpair.h" #include "qmstate.h" namespace votca { namespace xtp { class Rate_Engine { public: struct PairRates { double rate12 = 0.0; double rate21 = 0.0; }; Rate_Engine(double temperature, const Eigen::Vector3d& field) : _temperature(temperature), _field(field){}; PairRates Rate(const QMPair& pair, QMStateType carriertype) const; friend std::ostream& operator<<(std::ostream& out, const Rate_Engine& rate_engine); private: double Marcusrate(double Jeff2, double deltaG, double reorg) const; std::string _ratetype = "marcus"; double _temperature = 0.0; // units:Hartree Eigen::Vector3d _field = Eigen::Vector3d::Zero(); // units:Hartree/bohr }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_RATE_ENGINE_H xtp-2021.2/include/votca/xtp/region.h000066400000000000000000000052341412152066400174260ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_REGION_H #define VOTCA_XTP_REGION_H // Standard includes #include // VOTCA includes #include // Local VOTCA includes #include "checkpoint.h" #include "logger.h" /** * \brief base class to derive regions from * * * */ namespace votca { namespace xtp { class QMRegion; class PolarRegion; class StaticRegion; class Region { public: Region(Index id, Logger& log) : _id(id), _log(log){}; virtual ~Region() = default; virtual void WriteToCpt(CheckpointWriter& w) const = 0; virtual void ReadFromCpt(CheckpointReader& r) = 0; virtual void Initialize(const tools::Property& prop) = 0; virtual bool Converged() const = 0; virtual void Evaluate(std::vector >& regions) = 0; virtual Index size() const = 0; virtual std::string identify() const = 0; virtual void WritePDB(csg::PDBWriter& writer) const = 0; virtual void Reset() = 0; virtual double charge() const = 0; bool Successful() const { return _info; } std::string ErrorMsg() const { return _errormsg; } void AddResults(tools::Property& prop) const; Index getId() const { return _id; } virtual double Etotal() const = 0; friend std::ostream& operator<<(std::ostream& out, const Region& region) { out << "Id: " << region.getId() << " type: " << region.identify() << " size: " << region.size() << " charge[e]= " << region.charge(); return out; } protected: bool _info = true; std::string _errormsg = ""; std::vector ApplyInfluenceOfOtherRegions( std::vector >& regions); virtual void AppendResult(tools::Property& prop) const = 0; virtual double InteractwithQMRegion(const QMRegion& region) = 0; virtual double InteractwithPolarRegion(const PolarRegion& region) = 0; virtual double InteractwithStaticRegion(const StaticRegion& region) = 0; Index _id = -1; Logger& _log; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_REGION_H xtp-2021.2/include/votca/xtp/regular_grid.h000066400000000000000000000044641412152066400206150ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_REGULAR_GRID_H #define VOTCA_XTP_REGULAR_GRID_H // Local VOTCA includes #include "gridbox.h" namespace votca { namespace xtp { class QMMolecule; class aobasis; class Regular_Grid { public: void GridSetup(const Eigen::Array& steps, const Eigen::Array3d& padding, const QMMolecule& atoms, const AOBasis& basis); void GridSetup(const Eigen::Array3d& stepsize, const Eigen::Array3d& padding, const QMMolecule& atoms, const AOBasis& basis); Index getGridSize() const { return _totalgridsize; } Index getBoxesSize() const { return Index(_grid_boxes.size()); } const GridBox& operator[](Index index) const { return _grid_boxes[index]; } GridBox& operator[](Index index) { return _grid_boxes[index]; } std::vector::iterator begin() { return _grid_boxes.begin(); } std::vector::iterator end() { return _grid_boxes.end(); } std::vector::const_iterator begin() const { return _grid_boxes.begin(); } std::vector::const_iterator end() const { return _grid_boxes.end(); } Eigen::Array3d getStepSizes() const { return _stepsizes; } Eigen::Vector3d getStartingPoint() const { return _startingpoint; } Eigen::Array getSteps() const { return _steps; } private: Index _totalgridsize; std::vector _grid_boxes; Eigen::Array3d _stepsizes = Eigen::Array3d::Zero(); Eigen::Vector3d _startingpoint = Eigen::Vector3d::Zero(); Eigen::Array _steps = Eigen::Array::Zero(); }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_REGULAR_GRID_H xtp-2021.2/include/votca/xtp/rpa.h000066400000000000000000000054401412152066400167240ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_RPA_H #define VOTCA_XTP_RPA_H // Standard includes #include // Local VOTCA includes #include "eigen.h" #include "logger.h" namespace votca { namespace xtp { class TCMatrix_gwbse; class RPA { public: RPA(Logger& log, const TCMatrix_gwbse& Mmn) : _log(log), _Mmn(Mmn){}; void configure(Index homo, Index rpamin, Index rpamax) { _homo = homo; _rpamin = rpamin; _rpamax = rpamax; } double getEta() const { return _eta; } Eigen::MatrixXd calculate_epsilon_i(double frequency) const { return calculate_epsilon(frequency); } Eigen::MatrixXd calculate_epsilon_r(double frequency) const { return calculate_epsilon(frequency); } Eigen::MatrixXd calculate_epsilon_r(std::complex frequency) const; const Eigen::VectorXd& getRPAInputEnergies() const { return _energies; } void setRPAInputEnergies(const Eigen::VectorXd& rpaenergies) { _energies = rpaenergies; } // calculates full RPA vector of energies from gwa and dftenergies and qpmin // RPA energies have three parts, lower than qpmin: dftenergies,between qpmin // and qpmax:gwa_energies,above:dftenergies+homo-lumo shift void UpdateRPAInputEnergies(const Eigen::VectorXd& dftenergies, const Eigen::VectorXd& gwaenergies, Index qpmin); struct rpa_eigensolution { Eigen::VectorXd omega; // Eigenvalues Eigen::MatrixXd XpY; // Eigenvector components (X + Y) double ERPA_correlation; // total correlation energy }; rpa_eigensolution Diagonalize_H2p() const; private: Index _homo; // HOMO index with respect to dft energies Index _rpamin; Index _rpamax; const double _eta = 0.0001; Eigen::VectorXd _energies; Logger& _log; const TCMatrix_gwbse& _Mmn; template Eigen::MatrixXd calculate_epsilon(double frequency) const; Eigen::VectorXd Calculate_H2p_AmB() const; Eigen::MatrixXd Calculate_H2p_ApB() const; Eigen::SelfAdjointEigenSolver Diagonalize_H2p_C( const Eigen::MatrixXd& C) const; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_RPA_H xtp-2021.2/include/votca/xtp/segid.h000066400000000000000000000045751412152066400172450ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_SEGID_H #define VOTCA_XTP_SEGID_H // Standard includes #include // VOTCA includes #include // Local VOTCA includes #include "qmstate.h" /** * \brief Small wrapper for a segment id and the corresponding QMState or * filename * * * */ namespace votca { namespace xtp { class SegId { public: SegId(std::string input) { tools::Tokenizer tok(input, ":"); std::vector results = tok.ToVector(); if (results.size() != 2) { throw std::runtime_error("Malformed string '" + input + "' for segment"); } _id = std::stoi(results[0]); TestStringForQMState(results[1]); } SegId(Index id, std::string geometry) : _id(id) { TestStringForQMState(geometry); } Index Id() const { return _id; } bool hasFile() const { return _hasfilename; } std::string FileName() const { return _filename; } QMState getQMState() const { return _state; } private: void TestStringForQMState(const std::string& result) { std::string extension = tools::filesystem::GetFileExtension(result); if (extension == "pdb" || extension == "xyz" || extension == "mps") { _hasfilename = true; _filename = result; } else { try { _state = QMState(result); _hasfilename = false; } catch (std::runtime_error&) { throw std::runtime_error("'" + result + "' is neither a QMState nor a filename. Did " "you maybe forget the fileending"); } } } bool _hasfilename = false; Index _id; std::string _filename = ""; QMState _state; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_SEGID_H xtp-2021.2/include/votca/xtp/segment.h000066400000000000000000000065751412152066400176160ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_SEGMENT_H #define VOTCA_XTP_SEGMENT_H // Standard includes #include #include // Local VOTCA includes #include "atom.h" #include "atomcontainer.h" #include "qmstate.h" namespace votca { namespace xtp { class Segment : public AtomContainer { public: Segment(std::string name, Index id) : AtomContainer(name, id){}; // cannot use standard AtomContainer constructor because ReadFromCpt is // different. Segment(CheckpointReader& r) : AtomContainer("", 0) { ReadFromCpt(r); } ~Segment() override = default; /// Following notation can be observed in: /// [1. Victor, R. et al. Microscopic Simulations of Charge Transport in /// Disordered Organic Semiconductors. J. Chem. Theory Comput. 7, 3335–3345 /// (2011).] Labeling of the following methods follows the following /// semantics: U - Energy n - neutral geometry N - neutral state x - excited /// geometry X - excited state /// UxX - UnN void setU_xX_nN(double dU, QMStateType state) { _U_xX_nN.setValue(dU, state); } /// UnX - UnN void setU_nX_nN(double dU, QMStateType state) { _U_nX_nN.setValue(dU, state); } /// UxN - UxX void setU_xN_xX(double dU, QMStateType state) { _U_xN_xX.setValue(dU, state); } const Atom* getAtom(Index id) const; double getU_xX_nN(QMStateType state) const { return _U_xX_nN.getValue(state); } double getU_nX_nN(QMStateType state) const { return _U_nX_nN.getValue(state); } double getU_xN_xX(QMStateType state) const { return _U_xN_xX.getValue(state); } double getSiteEnergy(QMStateType state) const { return _site_eng.getValue(state) + _U_xX_nN.getValue(state); } double getEMpoles(QMStateType state) const { return _site_eng.getValue(state); } void setEMpoles(QMStateType state, double energy) { _site_eng.setValue(energy, state); } void AddMoleculeId(Index id) { _molecule_ids.push_back(int(id)); } const std::vector& getMoleculeIds() const { return _molecule_ids; } double getApproxSize() const; void WriteToCpt(CheckpointWriter& w) const override; void ReadFromCpt(CheckpointReader& r) override; friend std::ostream& operator<<(std::ostream& out, const Segment& container) { out << container.getId() << " " << container.getType() << "\n"; for (const Atom& atom : container) { out << atom; } out << std::endl; return out; } private: std::vector _molecule_ids = std::vector(0); QMStateCarrierStorage _U_xX_nN; QMStateCarrierStorage _U_nX_nN; QMStateCarrierStorage _U_xN_xX; QMStateCarrierStorage _site_eng; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_SEGMENT_H xtp-2021.2/include/votca/xtp/segmentmapper.h000066400000000000000000000104261412152066400210110ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_SEGMENTMAPPER_H #define VOTCA_XTP_SEGMENTMAPPER_H // Standard includes #include // VOTCA includes #include #include // Local VOTCA includes #include "classicalsegment.h" #include "logger.h" #include "qmmolecule.h" #include "segid.h" #include "topology.h" namespace votca { namespace xtp { template class SegmentMapper { public: SegmentMapper(Logger& log); void LoadMappingFile(const std::string& mapfile); AtomContainer map(const Segment& seg, const SegId& segid) const; AtomContainer map(const Segment& seg, QMState state) const; AtomContainer map(const Segment& seg, const std::string& coordfilename) const; private: using mapAtom = typename std::iterator_traits< typename AtomContainer::iterator>::value_type; typedef std::pair atom_id; struct FragInfo { std::vector _weights; std::vector _mapatom_ids; std::vector _mdatom_ids; std::vector _map_local_frame; }; struct Seginfo { std::pair minmax; std::vector mdatoms; std::vector fragments; bool map2md; std::string segname; std::vector weights; std::vector mapatoms; std::map coordfiles; }; std::map _mapatom_xml; std::map _segment_info; Index FindVectorIndexFromAtomId( Index atomid, const std::vector& fragment_mapatoms) const; void ParseFragment(Seginfo& seginfo, const tools::Property& frag); template Eigen::Vector3d CalcWeightedPos(const std::vector& weights, const T& atoms) const; void PlaceMapAtomonMD(const std::vector& fragment_mapatoms, const std::vector& fragment_mdatoms) const; void MapMapAtomonMD(const FragInfo& frag, const std::vector& fragment_mapatoms, const std::vector& fragment_mdatoms) const; Logger& _log; std::pair CalcAtomIdRange(const Segment& seg) const; std::pair CalcAtomIdRange(const std::vector& seg) const; atom_id StringToMapIndex(const std::string& map_string) const; atom_id StringToMDIndex(const std::string& md_string) const; Index getRank(const mapAtom& atom) const { return atom.getRank(); } std::vector getWeights(const tools::Property& frag) const; std::string getFrame(const tools::Property& frag) const { if (frag.exists(_mapatom_xml.at("frame"))) { return frag.get(_mapatom_xml.at("frame")).template as(); } return frag.get("localframe").template as(); } void FillMap() { _mapatom_xml["tag"] = "MP"; _mapatom_xml["name"] = "MPole"; _mapatom_xml["atoms"] = "mpoles"; _mapatom_xml["coords"] = "multipoles"; _mapatom_xml["weights"] = "mp_weights"; _mapatom_xml["frame"] = "mp_localframe"; } }; template <> inline void SegmentMapper::FillMap() { _mapatom_xml["tag"] = "QM"; _mapatom_xml["name"] = "QMAtom"; _mapatom_xml["atoms"] = "qmatoms"; _mapatom_xml["coords"] = "qmcoords"; _mapatom_xml["weights"] = "qm_weights"; _mapatom_xml["frame"] = "qm_localframe"; } template <> inline Index SegmentMapper::getRank(const QMAtom&) const { return 0; } using QMMapper = SegmentMapper; using StaticMapper = SegmentMapper; using PolarMapper = SegmentMapper; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_SEGMENTMAPPER_H xtp-2021.2/include/votca/xtp/settings.h000066400000000000000000000113341412152066400200010ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #ifndef VOTCA_XTP_SETTINGS_H #define VOTCA_XTP_SETTINGS_H // Standard includes #include #include #include #include #include #include #include // VOTCA includes #include /* * \brief Hierarchical representation of a QM Package input */ namespace votca { namespace xtp { class Settings { public: // Decompose a votca::tools::Property object into Settings Settings() = default; Settings(const std::string& root_key) : _root_key{root_key} {}; ~Settings() = default; /** * \brief Transform Properties into settings * @param Property object */ void read_property(const votca::tools::Property& properties, const std::string& key); /** * \brief read Settings from xml * @param path to the xml */ void load_from_xml(const std::string& path); /** * \brief Fill the missing values using another Settings instance * @param other Settings object */ void amend(const Settings& other); /** * \brief Add property * @param key to the property * @param value content of the property */ void add(const std::string& key, const std::string& value); /** * \brief Get a given key * @param key */ template T get(const std::string& key) const { auto delimiter = "."; std::string primary_key = key; std::string secondary_key; auto iter = key.find(delimiter); if (iter != std::string::npos) { primary_key = key.substr(0, key.find(delimiter)); secondary_key = key.substr(key.find(delimiter) + 1); } auto it = this->_nodes.find(primary_key); if (it == this->_nodes.end()) { std::ostringstream oss; oss << "Unknown keyword: " << key << "\n"; throw std::runtime_error(oss.str()); } else if (secondary_key.empty()) { return it->second.as(); } else { return it->second.get(secondary_key).as(); } } /** * \brief Retrieve property * @param key to property */ const votca::tools::Property& property(const std::string& key) const { return _nodes.at(key); } /** * \brief Check if a property exists * @param key */ bool has_key(const std::string& key) const; /** * \brief Check that the input is correct */ void validate() const; /** * \brief Convert a Settings object into a Property * @param root name */ tools::Property to_property(const std::string& name) const; friend std::ostream& operator<<(std::ostream& out, const Settings& sett); private: using Settings_map = std::unordered_map; Settings_map _nodes; // {Key, Property} Map std::string _root_key; std::string get_primary_key(const std::string& key) { return key.substr(0, key.find(".")); } void check_mandatory_keyword(const std::string& key) const; std::vector _general_properties = { "auxbasisset", // string "basisset", // string "charge", // index "cleanup", // string "convergence_tightness", // std::string "dipole_spacing", // boolean "ecp", // string "executable", // string // "external_charge", // Eigen::Vector9d "functional", // string "name", // string "optimize", // boolean "orca", // string "polarization", // boolean "read_guess", // boolean "spin", // index "scratch", // string "use_auxbasisset", // boolean "use_ecp", // boolean "write_charges", // boolean "xtpdft" // string }; std::vector _mandatory_keyword = { "functional", // string "name", // string, one of: orca }; std::unordered_map> _keyword_options{ {"name", {"orca"}}}; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_SETTINGS_H xtp-2021.2/include/votca/xtp/sigma_base.h000066400000000000000000000050721412152066400202350ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_SIGMA_BASE_H #define VOTCA_XTP_SIGMA_BASE_H // Local VOTCA includes #include "eigen.h" namespace votca { namespace xtp { class TCMatrix_gwbse; class RPA; class Sigma_base { public: Sigma_base(TCMatrix_gwbse& Mmn, const RPA& rpa) : _Mmn(Mmn), _rpa(rpa){}; virtual ~Sigma_base() = default; struct options { Index homo; Index qpmin; Index qpmax; Index rpamin; Index rpamax; double eta; std::string quadrature_scheme; // Gaussian-quadrature scheme to use in CDA Index order; // used in numerical integration of CDA Sigma double alpha; }; void configure(options opt) { _opt = opt; _qptotal = opt.qpmax - opt.qpmin + 1; _rpatotal = opt.rpamax - opt.rpamin + 1; } // Calculates full exchange matrix Eigen::MatrixXd CalcExchangeMatrix() const; // Calculates correlation diagonal Eigen::VectorXd CalcCorrelationDiag(const Eigen::VectorXd& frequencies) const; // Calculates correlation off-diagonal Eigen::MatrixXd CalcCorrelationOffDiag( const Eigen::VectorXd& frequencies) const; // Sets up the screening parametrisation virtual void PrepareScreening() = 0; // Calculates Sigma_c diagonal elements virtual double CalcCorrelationDiagElementDerivative( Index gw_level, double frequency) const = 0; virtual double CalcCorrelationDiagElement(Index gw_level, double frequency) const = 0; // Calculates Sigma_c off-diagonal elements virtual double CalcCorrelationOffDiagElement(Index gw_level1, Index gw_level2, double frequency1, double frequency2) const = 0; protected: options _opt; TCMatrix_gwbse& _Mmn; const RPA& _rpa; Index _qptotal = 0; Index _rpatotal = 0; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_SIGMA_BASE_H xtp-2021.2/include/votca/xtp/sigma_cda.h000066400000000000000000000065441412152066400200570ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #ifndef VOTCA_XTP_SIGMA_CDA_H #define VOTCA_XTP_SIGMA_CDA_H #include "votca/xtp/ImaginaryAxisIntegration.h" #include "votca/xtp/logger.h" #include "votca/xtp/rpa.h" #include "votca/xtp/sigma_base.h" #include // This computes the whole expectation matrix for the correlational part of the // self-energy with the Contour Deformation Approach according to Eqns 28 and 29 // of JCP 152, 114103 (2020). There are two contributions: // - from a numerical integration using Gaussian quadratures along the imaginary // frequncy axis (Eq. 28) // - from the residues included in the contours (Eq.29) // Both contributions contain term from a Gaussian tail with parameter alpha. namespace votca { namespace xtp { class Sigma_CDA : public Sigma_base { public: Sigma_CDA(TCMatrix_gwbse& Mmn, RPA& rpa) : Sigma_base(Mmn, rpa), _gq(rpa.getRPAInputEnergies(), Mmn){}; ~Sigma_CDA() = default; // Prepares the zero and imaginary frequency kappa matrices with // kappa(omega) = epsilon^-1(omega) - 1 needed in numerical // integration and for the Gaussian tail void PrepareScreening() final; // calculates the diagonal elements of the self-energy correlation part double CalcCorrelationDiagElement(Index gw_level, double frequency) const final; // numerical derivatice of the self-energy double CalcCorrelationDiagElementDerivative(Index gw_level, double frequency) const final { double h = 1e-3; double plus = CalcCorrelationDiagElement(gw_level, frequency + h); double minus = CalcCorrelationDiagElement(gw_level, frequency - h); return (plus - minus) / (2 * h); } // Calculates Sigma_c off-diagonal elements double CalcCorrelationOffDiagElement(Index, Index, double, double) const final { return 0; } private: // Theta-function weight of a residue double CalcResiduePrefactor(double e_f, double e_m, double frequency) const; // Sigma_c from all possible residues for given gw_level and frequency double CalcResidueContribution(double frequency, Index gw_level) const; // Sigma_c part from a single residue for a given gw_level and frequency double CalcDiagContribution(const Eigen::MatrixXd::ConstRowXpr& Imx_row, double delta, double eta) const; // Sigma_c part from Gaussian tail correction double CalcDiagContributionValue_tail( const Eigen::MatrixXd::ConstRowXpr& Imx_row, double delta, double alpha) const; ImaginaryAxisIntegration _gq; Eigen::MatrixXd _kDielMxInv_zero; // kappa = eps^-1 - 1 matrix }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_SIGMA_CDA_Hxtp-2021.2/include/votca/xtp/sigma_exact.h000066400000000000000000000036041412152066400204260ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #ifndef VOTCA_XTP_SIGMA_EXACT_H #define VOTCA_XTP_SIGMA_EXACT_H // Local VOTCA includes #include "rpa.h" #include "sigma_base.h" namespace votca { namespace xtp { class TCMatrix_gwbse; class RPA; class Sigma_Exact : public Sigma_base { public: Sigma_Exact(TCMatrix_gwbse& Mmn, RPA& rpa) : Sigma_base(Mmn, rpa){}; // Sets up the screening parametrisation void PrepareScreening() final; // Calculates Sigma_c diagonal elements double CalcCorrelationDiagElement(Index gw_level, double frequency) const final; double CalcCorrelationDiagElementDerivative(Index gw_level, double frequency) const final; // Calculates Sigma_c off-diagonal elements double CalcCorrelationOffDiagElement(Index gw_level1, Index gw_level2, double frequency1, double frequency2) const final; private: RPA::rpa_eigensolution _rpa_solution; // Eigenvalues, eigenvectors from RPA std::vector _residues; // Residues Eigen::MatrixXd CalcResidues(Index gw_level) const; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_SIGMA_EXACT_H xtp-2021.2/include/votca/xtp/sigma_ppm.h000066400000000000000000000033231412152066400201140ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_SIGMA_PPM_H #define VOTCA_XTP_SIGMA_PPM_H // Local VOTCA includes #include "ppm.h" #include "sigma_base.h" namespace votca { namespace xtp { class TCMatrix_gwbse; class RPA; class Sigma_PPM : public Sigma_base { public: Sigma_PPM(TCMatrix_gwbse& Mmn, RPA& rpa) : Sigma_base(Mmn, rpa){}; // Sets up the screening parametrisation void PrepareScreening() final; // Calculates Sigma_c diagonal elements double CalcCorrelationDiagElement(Index gw_level, double frequency) const final; double CalcCorrelationDiagElementDerivative(Index gw_level, double frequency) const final; // Calculates Sigma_c off-diagonal elements double CalcCorrelationOffDiagElement(Index gw_level1, Index gw_level2, double frequency1, double frequency2) const final; private: PPM _ppm; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_SIGMA_PPM_H xtp-2021.2/include/votca/xtp/sphere_lebedev_rule.h000066400000000000000000000122041412152066400221410ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_SPHERE_LEBEDEV_RULE_H #define VOTCA_XTP_SPHERE_LEBEDEV_RULE_H // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "grid_containers.h" #include "qmatom.h" namespace votca { namespace xtp { class LebedevGrid { public: LebedevGrid() { FillOrders(); FillOrder2Index(); FillIndex2Order(); }; std::map CalculateSphericalGrids( const QMMolecule &atoms, const std::string &type) const; GridContainers::spherical_grid CalculateUnitSphereGrid( const std::string &element, const std::string &type) const; GridContainers::spherical_grid CalculateUnitSphereGrid(Index order) const; Index Type2MaxOrder(const std::string &element, const std::string &type) const; Index getIndexFromOrder(Index order) const { if (Order2Index.count(order)) { return Order2Index.at(order); } else { throw std::runtime_error("No Index for Order " + std::to_string(order)); } } Index getOrderFromIndex(Index index) const { if (Index2Order.count(index)) { return Index2Order.at(index); } else { throw std::runtime_error("No Order for Index " + std::to_string(index)); } } private: Index Type2MaxOrder(const std::map &map, const std::string &element) const; Index available_table(Index rule) const; Index gen_oh(Index code, double a, double b, double v, double *x, double *y, double *z, double *w) const; Eigen::Matrix4Xd ld_by_order(Index order) const; void ld0006(double *x, double *y, double *z, double *w) const; void ld0014(double *x, double *y, double *z, double *w) const; void ld0026(double *x, double *y, double *z, double *w) const; void ld0038(double *x, double *y, double *z, double *w) const; void ld0050(double *x, double *y, double *z, double *w) const; void ld0074(double *x, double *y, double *z, double *w) const; void ld0086(double *x, double *y, double *z, double *w) const; void ld0110(double *x, double *y, double *z, double *w) const; void ld0146(double *x, double *y, double *z, double *w) const; void ld0170(double *x, double *y, double *z, double *w) const; void ld0194(double *x, double *y, double *z, double *w) const; void ld0230(double *x, double *y, double *z, double *w) const; void ld0266(double *x, double *y, double *z, double *w) const; void ld0302(double *x, double *y, double *z, double *w) const; void ld0350(double *x, double *y, double *z, double *w) const; void ld0434(double *x, double *y, double *z, double *w) const; void ld0590(double *x, double *y, double *z, double *w) const; void ld0770(double *x, double *y, double *z, double *w) const; void ld0974(double *x, double *y, double *z, double *w) const; void ld1202(double *x, double *y, double *z, double *w) const; void ld1454(double *x, double *y, double *z, double *w) const; void ld1730(double *x, double *y, double *z, double *w) const; void ld2030(double *x, double *y, double *z, double *w) const; void ld2354(double *x, double *y, double *z, double *w) const; void ld2702(double *x, double *y, double *z, double *w) const; void ld3074(double *x, double *y, double *z, double *w) const; void ld3470(double *x, double *y, double *z, double *w) const; void ld3890(double *x, double *y, double *z, double *w) const; void ld4334(double *x, double *y, double *z, double *w) const; void ld4802(double *x, double *y, double *z, double *w) const; void ld5294(double *x, double *y, double *z, double *w) const; void ld5810(double *x, double *y, double *z, double *w) const; Index precision_table(Index rule) const; Index order_table(Index rule) const; Eigen::Vector2d Cartesian2SphericalAngle( const Eigen::Vector3d &r) const; // phi=Vector[0] theta=Vector[1] std::map MediumOrder; std::map CoarseOrder; std::map XcoarseOrder; std::map FineOrder; std::map XfineOrder; std::map Order2Index; std::map Index2Order; void FillOrder2Index(); void FillIndex2Order(); void FillOrders(); void FillMediumOrder(); void FillFineOrder(); void FillXfineOrder(); void FillCoarseOrder(); void FillXcoarseOrder(); }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_SPHERE_LEBEDEV_RULE_H xtp-2021.2/include/votca/xtp/stateapplication.h000066400000000000000000000026121412152066400215040ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_STATEAPPLICATION_H #define VOTCA_XTP_STATEAPPLICATION_H // Local VOTCA includes #include "qmcalculator.h" #include "topology.h" #include "xtpapplication.h" namespace votca { namespace xtp { class StateApplication : public XtpApplication { public: StateApplication(); ~StateApplication() override = default; void Initialize() override; bool EvaluateOptions() override; void Run() override; void BeginEvaluate(Index nThreads); bool EvaluateFrame(Topology& top); void SetCalculator(std::unique_ptr&& calculator); protected: std::unique_ptr _calculator; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_STATEAPPLICATION_H xtp-2021.2/include/votca/xtp/statefilter_base.h000066400000000000000000000044441412152066400214650ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_STATEFILTER_BASE_H #define VOTCA_XTP_STATEFILTER_BASE_H // Standard includes #include // VOTCA includes #include #include // Local VOTCA includes #include "logger.h" #include "orbitals.h" namespace votca { namespace xtp { /** \brief Base Class for statefilter */ class StateFilter_base { public: StateFilter_base() = default; virtual ~StateFilter_base() = default; virtual std::string Identify() const = 0; virtual void Initialize(const tools::Property&) = 0; virtual void Info(Logger&) const = 0; virtual bool NeedsInitialState() const = 0; virtual void UpdateHist(const Orbitals&, QMState) = 0; virtual std::vector CalcIndeces(const Orbitals&, QMStateType) const = 0; virtual void WriteToCpt(CheckpointWriter&) = 0; virtual void ReadFromCpt(CheckpointReader&) = 0; protected: std::vector ReduceAndSortIndecesUp(const Eigen::VectorXd& overlap, Index offset, double threshold) const; std::vector ReduceAndSortIndecesDown(const Eigen::VectorXd& overlap, Index offset, double threshold) const; private: template std::vector ReduceAndSortIndeces(const Eigen::VectorXd& overlap, Index offset, double threshold) const; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_STATEFILTER_BASE_H xtp-2021.2/include/votca/xtp/statesaver.h000066400000000000000000000023751412152066400203270ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_STATESAVER_H #define VOTCA_XTP_STATESAVER_H // Standard includes #include #include // Local VOTCA includes #include "topology.h" namespace votca { namespace xtp { class StateSaver { public: StateSaver(std::string file) : _hdf5file(file){}; void WriteFrame(const Topology &top); Topology ReadFrame(Index frameid) const; std::vector getFrames() const; private: bool TopStepisinFrames(Index frameid) const; std::string _hdf5file; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_STATESAVER_H xtp-2021.2/include/votca/xtp/statetracker.h000066400000000000000000000040051412152066400206320ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_STATETRACKER_H #define VOTCA_XTP_STATETRACKER_H // Standard includes #include // Local VOTCA includes #include "logger.h" #include "orbitals.h" #include "qmstate.h" #include "statefilter_base.h" namespace votca { namespace xtp { /** * \brief Tracks from a spectrum of states the state, which fullfills certain * criteria * * */ class StateTracker { public: void Initialize(const tools::Property& options); void setLogger(Logger* log) { _log = log; } void setInitialState(const QMState& state) { _statehist.push_back(state); } void PrintInfo() const; QMState InitialState() const { return _statehist[0]; } QMState CalcStateAndUpdate(const Orbitals& orbitals); QMState CalcState(const Orbitals& orbitals) const; void WriteToCpt(CheckpointWriter& w) const; void ReadFromCpt(CheckpointReader& r); private: void UpdateLastCoeff(const Orbitals& orbitals); std::vector CollapseResults( std::vector >& results) const; std::vector ComparePairofVectors(std::vector& vec1, std::vector& vec2) const; Logger* _log; std::vector _statehist; std::vector > _filters; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_STATETRACKER_H xtp-2021.2/include/votca/xtp/staticregion.h000066400000000000000000000034441412152066400206370ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_STATICREGION_H #define VOTCA_XTP_STATICREGION_H // Local VOTCA includes #include "mmregion.h" namespace votca { namespace xtp { class QMRegion; class PolarRegion; class StaticRegion; class StaticRegion : public MMRegion { public: StaticRegion(Index id, Logger& log) : MMRegion(id, log) {} std::string identify() const override { return "static"; } void Initialize(const tools::Property&) override { return; } bool Converged() const override { return true; } double Etotal() const override { return 0.0; } void Evaluate(std::vector >&) override { return; } void Reset() override { return; }; protected: void ResetRegion() { return; } void AppendResult(tools::Property&) const override { return; } double InteractwithQMRegion(const QMRegion&) override { return 0.0; } double InteractwithPolarRegion(const PolarRegion&) override { return 0.0; } double InteractwithStaticRegion(const StaticRegion&) override { return 0.0; } private: }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_STATICREGION_H xtp-2021.2/include/votca/xtp/staticsite.h000066400000000000000000000072261412152066400203220ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. nn * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_STATICSITE_H #define VOTCA_XTP_STATICSITE_H // Local VOTCA includes #include "eigen.h" #include "qmatom.h" namespace votca { namespace xtp { /** \brief Class to represent Atom/Site in electrostatic The units are atomic units, e.g. Bohr, Hartree. */ class StaticSite { public: struct data { Index id; char* element; double posX; double posY; double posZ; Index rank; double Q00; double Q11c; double Q11s; double Q10; double Q20; double Q21c; double Q21s; double Q22c; double Q22s; }; StaticSite(Index id, std::string element, Eigen::Vector3d pos) : _id(id), _element(element), _pos(pos){}; StaticSite(Index id, std::string element) : StaticSite(id, element, Eigen::Vector3d::Zero()){}; StaticSite(const data& d) { ReadData(d); } StaticSite(const QMAtom& atom, double charge) : StaticSite(atom.getId(), atom.getElement(), atom.getPos()) { setCharge(charge); } virtual ~StaticSite() = default; protected: StaticSite() = default; public: Index getId() const { return _id; } Index getRank() const { return _rank; } const std::string& getElement() const { return _element; } const Eigen::Vector3d& getPos() const { return _pos; } void setMultipole(const Vector9d& multipole, Index rank) { _Q = multipole; _rank = rank; } // sets rank to 0 as well void setCharge(double q) { _Q(0) = q; _rank = 0; } void setPos(const Eigen::Vector3d& position) { _pos = position; } // COORDINATES TRANSFORMATION void Translate(const Eigen::VectorXd& shift); virtual void Rotate(const Eigen::Matrix3d& R, const Eigen::Vector3d& refPos); // MULTIPOLES DEFINITION double getCharge() const { return _Q(0); } const Vector9d& Q() const { return _Q; } // Q00,Q11c,Q11s,Q10,Q20, Q21c, Q21s, Q22c, Q22s,...[NOT following Stone // order for dipoles] virtual Eigen::Vector3d getDipole() const { return _Q.segment<3>(1); } Eigen::Matrix3d CalculateCartesianMultipole() const; static Eigen::VectorXd CalculateSphericalMultipole( const Eigen::Matrix3d& quad_cart); std::string WriteMpsLine(std::string unit = "bohr") const; virtual void SetupCptTable(CptTable& table) const; void WriteData(data& d) const; void ReadData(const data& d); virtual void setpolarization(const Eigen::Matrix3d&) { return; } virtual std::string identify() const { return "staticsite"; } friend std::ostream& operator<<(std::ostream& out, const StaticSite& site) { out << site.getId() << " " << site.getElement() << " " << site.getRank(); out << " " << site.getPos().transpose() << "\n"; return out; } protected: virtual std::string writepolarization() const; Index _id = -1; std::string _element = ""; Eigen::Vector3d _pos = Eigen::Vector3d::Zero(); Index _rank = 0; Vector9d _Q = Vector9d::Zero(); // Q00,Q11c,Q11s,Q10,Q20,Q21c,Q21s,Q22c,Q22s }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_STATICSITE_H xtp-2021.2/include/votca/xtp/symmetric_matrix.h000066400000000000000000000040541412152066400215420ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_SYMMETRIC_MATRIX_H #define VOTCA_XTP_SYMMETRIC_MATRIX_H // Standard includes #include #include // Local VOTCA includes #include "eigen.h" namespace votca { namespace xtp { /* * A symmetric matrix implementation for doubles, acces upper diagonal matrix */ class Symmetric_Matrix { public: Symmetric_Matrix(Index dim) { dimension = dim; data.resize((dim + 1) * dim / 2); } Symmetric_Matrix(const Eigen::MatrixXd& full); Index size() const { return dimension; } double TraceofProd(const Symmetric_Matrix& a) const; void AddtoEigenMatrix(Eigen::MatrixXd& full, double factor = 1.0) const; void AddtoEigenUpperMatrix( Eigen::SelfAdjointView& upper, double factor = 1.0) const; Eigen::MatrixXd FullMatrix() const; // returns a matrix where only the upper triangle part is filled, rest is set // to zero Eigen::MatrixXd UpperMatrix() const; double& operator()(Index i, Index j) { return data[index(i, j)]; }; const double& operator()(Index i, Index j) const { return data[index(i, j)]; }; friend std::ostream& operator<<(std::ostream& out, const Symmetric_Matrix& a); private: Index index(Index i, Index j) const; std::vector data; Index dimension; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_SYMMETRIC_MATRIX_H xtp-2021.2/include/votca/xtp/threecenter.h000066400000000000000000000072461412152066400204600ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_THREECENTER_H #define VOTCA_XTP_THREECENTER_H // Local VOTCA includes #include "aobasis.h" #include "eigen.h" #include "symmetric_matrix.h" /** * \brief Calculates three electron repulsion integrals for GW and DFT. * * * */ namespace libint2 { class Engine; } namespace votca { namespace xtp { // due to different requirements for the data format for DFT and GW we have two // different classes TCMatrix_gwbse and TCMatrix_dft which inherit from TCMatrix class TCMatrix { public: virtual ~TCMatrix() = default; Index Removedfunctions() const { return _removedfunctions; } protected: Index _removedfunctions = 0; Eigen::MatrixXd _inv_sqrt; }; class TCMatrix_dft final : public TCMatrix { public: void Fill(const AOBasis& auxbasis, const AOBasis& dftbasis); Index size() const { return Index(_matrix.size()); } Symmetric_Matrix& operator[](Index i) { return _matrix[i]; } const Symmetric_Matrix& operator[](Index i) const { return _matrix[i]; } private: std::vector _matrix; void FillBlock(std::vector& block, Index shellindex, const AOBasis& dftbasis, const AOBasis& auxbasis); }; class TCMatrix_gwbse final : public TCMatrix { public: // returns one level as a constant reference const Eigen::MatrixXd& operator[](Index i) const { return _matrix[i]; } // returns one level as a reference Eigen::MatrixXd& operator[](Index i) { return _matrix[i]; } // returns auxbasissize Index auxsize() const { return _auxbasissize; } Index get_mmin() const { return _mmin; } Index get_mmax() const { return _mmax; } Index get_nmin() const { return _nmin; } Index get_nmax() const { return _nmax; } Index msize() const { return _mtotal; } Index nsize() const { return _ntotal; } void Initialize(Index basissize, Index mmin, Index mmax, Index nmin, Index nmax); void Fill(const AOBasis& auxbasis, const AOBasis& dftbasis, const Eigen::MatrixXd& dft_orbitals); // Rebuilds ThreeCenterIntegrals, only works if the original basisobjects // still exist void Rebuild() { Fill(*_auxbasis, *_dftbasis, *_dft_orbitals); } void MultiplyRightWithAuxMatrix(const Eigen::MatrixXd& matrix); private: // store vector of matrices std::vector _matrix; // band summation indices Index _mmin; Index _mmax; Index _nmin; Index _nmax; Index _ntotal; Index _mtotal; Index _auxbasissize; const AOBasis* _auxbasis = nullptr; const AOBasis* _dftbasis = nullptr; const Eigen::MatrixXd* _dft_orbitals = nullptr; void Fill3cMO(const AOBasis& auxbasis, const AOBasis& dftbasis, const Eigen::MatrixXd& dft_orbitals); std::vector ComputeAO3cBlock(const libint2::Shell& auxshell, const AOBasis& dftbasis, libint2::Engine& engine) const; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_THREECENTER_H xtp-2021.2/include/votca/xtp/toolfactory.h000066400000000000000000000023731412152066400205110ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_TOOLFACTORY_H #define VOTCA_XTP_TOOLFACTORY_H // VOTCA includes #include // Local VOTCA includes #include "qmtool.h" namespace votca { namespace xtp { class QMToolFactory : public tools::ObjectFactory { private: QMToolFactory() = default; public: static void RegisterAll(void); friend QMToolFactory &QMTools(); }; inline QMToolFactory &QMTools() { static QMToolFactory _instance; return _instance; } } // namespace xtp } // namespace votca #endif // VOTCA_XTP_TOOLFACTORY_H xtp-2021.2/include/votca/xtp/topology.h000066400000000000000000000062141412152066400200160ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_TOPOLOGY_H #define VOTCA_XTP_TOPOLOGY_H // VOTCA includes #include #include #include #include // Local VOTCA includes #include "qmnblist.h" namespace votca { namespace xtp { class Segment; /** * \brief Container for segments and box * and atoms. */ class Topology { public: Topology() = default; Topology(const Topology &top); Topology &operator=(const Topology &top); // I do not have to manually make a move constructor or move assignment // operator or destructor because I only have to reassign pointers in qmnblist // object Segment &AddSegment(std::string segment_name); Segment &getSegment(Index id) { return _segments[id]; } const Segment &getSegment(Index id) const { return _segments[id]; } std::vector &Segments() { return _segments; } const std::vector &Segments() const { return _segments; } // Periodic boundary: Can be 'open', 'orthorhombic', 'triclinic' Eigen::Vector3d PbShortestConnect(const Eigen::Vector3d &r1, const Eigen::Vector3d &r2) const; const Eigen::Matrix3d &getBox() const { return _bc->getBox(); } double BoxVolume() const { return _bc->BoxVolume(); } void setBox(const Eigen::Matrix3d &box, csg::BoundaryCondition::eBoxtype boxtype = csg::BoundaryCondition::typeAuto); QMNBList &NBList() { return _nblist; } const QMNBList &NBList() const { return _nblist; } // Trajectory meta data: step number, time, frame (= Db ID) Index getStep() const { return _step; } void setStep(Index step) { _step = step; } double getTime() const { return _time; } void setTime(double time) { _time = time; } void WriteToCpt(CheckpointWriter &w) const; void WriteToPdb(std::string filename) const; void ReadFromCpt(CheckpointReader &r); double GetShortestDist(const Segment &seg1, const Segment &seg2) const; std::vector FindAllSegmentsOnMolecule( const Segment &seg1, const Segment &seg2) const; private: std::vector _segments; std::unique_ptr _bc = nullptr; QMNBList _nblist; double _time; Index _step; csg::BoundaryCondition::eBoxtype AutoDetectBoxType( const Eigen::Matrix3d &box); static constexpr int topology_version() { return 1; } }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_TOPOLOGY_H xtp-2021.2/include/votca/xtp/trustregion.h000066400000000000000000000046051412152066400205310ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_TRUSTREGION_H #define VOTCA_XTP_TRUSTREGION_H // Standard includes #include // Local VOTCA includes #include "eigen.h" // Solves the trustregion subproblem g^T*s+0.5*s^T H s = min with ||s||<=delta namespace votca { namespace xtp { class TrustRegion { public: Eigen::VectorXd CalculateStep(const Eigen::VectorXd& gradient, const Eigen::MatrixXd& Hessian, double delta) const; private: class TrustRegionFunction { public: TrustRegionFunction( const Eigen::VectorXd& factor, const Eigen::SelfAdjointEigenSolver& hessian, double trust_radius, Index startindex) : _factor(factor), _hessian(hessian), _trust_radius(trust_radius), _startindex(startindex) { ; } // Calculates \phi and \phi/\phi' std::pair Evaluate(double lambda) { Index size = _factor.size() - _startindex; Eigen::ArrayXd quotient = (_hessian.eigenvalues().array() + lambda).tail(size); const double p2 = (_factor.array().tail(size) / (quotient.pow(2))).sum(); const double p = std::sqrt(p2); const double q2 = (_factor.array().tail(size) / (quotient.pow(3))).sum(); std::pair result; result.first = 1 / _trust_radius - 1 / p; result.second = p2 / q2 * (p - _trust_radius) / _trust_radius; return result; } private: const Eigen::VectorXd& _factor; const Eigen::SelfAdjointEigenSolver& _hessian; double _trust_radius; Index _startindex; }; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_TRUSTREGION_H xtp-2021.2/include/votca/xtp/vc2index.h000066400000000000000000000030241412152066400176600ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_VC2INDEX_H #define VOTCA_XTP_VC2INDEX_H // VOTCA includes #include namespace votca { namespace xtp { /** * \brief This class transforms a pair of indices v,c into a compound index I, * via I=ctotal*v+c the fast dimension is c. If you have a choice iterate over c * and v not over I. * * */ class vc2index { public: vc2index(Index vmin, Index cmin, Index ctotal) : _vmin(vmin), _cmin(cmin), _ctotal(ctotal){}; inline Index I(Index v, Index c) const { return _ctotal * (v - _vmin) + (c - _cmin); } inline Index v(Index index) const { return (index / _ctotal + _vmin); } inline Index c(Index index) const { return (index % _ctotal + _cmin); } private: Index _vmin; Index _cmin; Index _ctotal; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_VC2INDEX_H xtp-2021.2/include/votca/xtp/version.h000066400000000000000000000020671412152066400176310ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_VERSION_H #define VOTCA_XTP_VERSION_H // Standard includes #include /** * \namespace votca::xtp * \brief Charge transport classes * * Classes used for charge and exciton transport simulations */ namespace votca { namespace xtp { const std::string &XtpVersionStr(); void HelpTextHeader(const std::string &tool_name); } // namespace xtp } // namespace votca #endif // VOTCA_XTP_VERSION_H xtp-2021.2/include/votca/xtp/votca_xtp_config.h.in000066400000000000000000000017641412152066400221100ustar00rootroot00000000000000/* * Copyright 2009-2019 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #ifndef VOTCA_XTP_CONFIG_H #define VOTCA_XTP_CONFIG_H /* OpenMP */ #if defined(_OPENMP) #include #endif /* Version number of package */ #define VERSION "@PROJECT_VERSION@" /* Contact address of package */ #define PACKAGE_BUGREPORT "@PROJECT_CONTACT@" #cmakedefine USE_CUDA #endif // _VOTCA_XTP_CONFIG_H xtp-2021.2/include/votca/xtp/vxc_functionals.h000066400000000000000000000271061412152066400213520ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_VXC_FUNCTIONALS_H #define VOTCA_XTP_VXC_FUNCTIONALS_H // Standard includes #include #include namespace votca { namespace xtp { /** \brief conversion of functional string into integer */ class Vxc_Functionals { public: Vxc_Functionals() { FillMaps(); }; int getID(std::string name) const { if (!_stringtoID.count(name)) { throw std::runtime_error("Functional " + name + " not supported"); } return _stringtoID.at(name); } private: std::map _stringtoID; inline void FillMaps() { FillstringtoID(); } inline void FillstringtoID() { _stringtoID["XC_LDA_X"] = 1; _stringtoID["XC_LDA_C_WIGNER"] = 2; _stringtoID["XC_LDA_C_RPA"] = 3; _stringtoID["XC_LDA_C_HL"] = 4; _stringtoID["XC_LDA_C_GL"] = 5; _stringtoID["XC_LDA_C_XALPHA"] = 6; _stringtoID["XC_LDA_C_VWN"] = 7; _stringtoID["XC_LDA_C_VWN_RPA"] = 8; _stringtoID["XC_LDA_C_PZ"] = 9; _stringtoID["XC_LDA_C_PZ_MOD"] = 10; _stringtoID["XC_LDA_C_OB_PZ"] = 11; _stringtoID["XC_LDA_C_PW"] = 12; _stringtoID["XC_LDA_C_PW_MOD"] = 13; _stringtoID["XC_LDA_C_OB_PW"] = 14; _stringtoID["XC_LDA_C_2D_AMGB"] = 15; _stringtoID["XC_LDA_C_2D_PRM"] = 16; _stringtoID["XC_LDA_C_vBH"] = 17; _stringtoID["XC_LDA_C_1D_CSC"] = 18; _stringtoID["XC_LDA_X_2D"] = 19; _stringtoID["XC_LDA_XC_TETER93"] = 20; _stringtoID["XC_LDA_X_1D"] = 21; _stringtoID["XC_LDA_C_ML1"] = 22; _stringtoID["XC_LDA_C_ML2"] = 23; _stringtoID["XC_LDA_C_GOMBAS"] = 24; _stringtoID["XC_LDA_C_PW_RPA"] = 25; _stringtoID["XC_LDA_C_1D_LOOS"] = 26; _stringtoID["XC_LDA_C_RC04"] = 27; _stringtoID["XC_LDA_C_VWN_1"] = 28; _stringtoID["XC_LDA_C_VWN_2"] = 29; _stringtoID["XC_LDA_C_VWN_3"] = 30; _stringtoID["XC_LDA_C_VWN_4"] = 31; _stringtoID["XC_LDA_K_TF"] = 50; _stringtoID["XC_LDA_K_LP"] = 51; _stringtoID["XC_GGA_C_Q2D"] = 47; _stringtoID["XC_GGA_X_Q2D"] = 48; _stringtoID["XC_GGA_X_PBE_MOL"] = 49; _stringtoID["XC_GGA_K_TFVW"] = 52; _stringtoID["XC_GGA_K_REVAPBEINT"] = 53; _stringtoID["XC_GGA_K_APBEINT"] = 54; _stringtoID["XC_GGA_K_REVAPBE"] = 55; _stringtoID["XC_GGA_X_AK13"] = 56; _stringtoID["XC_GGA_K_MEYER"] = 57; _stringtoID["XC_GGA_X_LV_RPW86"] = 58; _stringtoID["XC_GGA_X_PBE_TCA"] = 59; _stringtoID["XC_GGA_X_PBEINT"] = 60; _stringtoID["XC_GGA_C_ZPBEINT"] = 61; _stringtoID["XC_GGA_C_PBEINT"] = 62; _stringtoID["XC_GGA_C_ZPBESOL"] = 63; _stringtoID["XC_GGA_XC_OPBE_D"] = 65; _stringtoID["XC_GGA_XC_OPWLYP_D"] = 66; _stringtoID["XC_GGA_XC_OBLYP_D"] = 67; _stringtoID["XC_GGA_X_VMT84_GE"] = 68; _stringtoID["XC_GGA_X_VMT84_PBE"] = 69; _stringtoID["XC_GGA_X_VMT_GE"] = 70; _stringtoID["XC_GGA_X_VMT_PBE"] = 71; _stringtoID["XC_GGA_C_N12_SX"] = 79; _stringtoID["XC_GGA_C_N12"] = 80; _stringtoID["XC_GGA_X_N12"] = 82; _stringtoID["XC_GGA_C_VPBE"] = 83; _stringtoID["XC_GGA_C_OP_XALPHA"] = 84; _stringtoID["XC_GGA_C_OP_G96"] = 85; _stringtoID["XC_GGA_C_OP_PBE"] = 86; _stringtoID["XC_GGA_C_OP_B88"] = 87; _stringtoID["XC_GGA_C_FT97"] = 88; _stringtoID["XC_GGA_C_SPBE"] = 89; _stringtoID["XC_GGA_X_SSB_SW"] = 90; _stringtoID["XC_GGA_X_SSB"] = 91; _stringtoID["XC_GGA_X_SSB_D"] = 92; _stringtoID["XC_GGA_XC_HCTH_407P"] = 93; _stringtoID["XC_GGA_XC_HCTH_P76"] = 94; _stringtoID["XC_GGA_XC_HCTH_P14"] = 95; _stringtoID["XC_GGA_XC_B97_GGA1"] = 96; _stringtoID["XC_GGA_XC_HCTH_A"] = 97; _stringtoID["XC_GGA_X_BPCCAC"] = 98; _stringtoID["XC_GGA_C_REVTCA"] = 99; _stringtoID["XC_GGA_C_TCA"] = 100; _stringtoID["XC_GGA_X_PBE"] = 101; _stringtoID["XC_GGA_X_PBE_R"] = 102; _stringtoID["XC_GGA_X_B86"] = 103; _stringtoID["XC_GGA_X_HERMAN"] = 104; _stringtoID["XC_GGA_X_B86_MGC"] = 105; _stringtoID["XC_GGA_X_B88"] = 106; _stringtoID["XC_GGA_X_G96"] = 107; _stringtoID["XC_GGA_X_PW86"] = 108; _stringtoID["XC_GGA_X_PW91"] = 109; _stringtoID["XC_GGA_X_OPTX"] = 110; _stringtoID["XC_GGA_X_DK87_R1"] = 111; _stringtoID["XC_GGA_X_DK87_R2"] = 112; _stringtoID["XC_GGA_X_LG93"] = 113; _stringtoID["XC_GGA_X_FT97_A"] = 114; _stringtoID["XC_GGA_X_FT97_B"] = 115; _stringtoID["XC_GGA_X_PBE_SOL"] = 116; _stringtoID["XC_GGA_X_RPBE"] = 117; _stringtoID["XC_GGA_X_WC"] = 118; _stringtoID["XC_GGA_X_MPW91"] = 119; _stringtoID["XC_GGA_X_AM05"] = 120; _stringtoID["XC_GGA_X_PBEA"] = 121; _stringtoID["XC_GGA_X_MPBE"] = 122; _stringtoID["XC_GGA_X_XPBE"] = 123; _stringtoID["XC_GGA_X_2D_B86_MGC"] = 124; _stringtoID["XC_GGA_X_BAYESIAN"] = 125; _stringtoID["XC_GGA_X_PBE_JSJR"] = 126; _stringtoID["XC_GGA_X_2D_B88"] = 127; _stringtoID["XC_GGA_X_2D_B86"] = 128; _stringtoID["XC_GGA_X_2D_PBE"] = 129; _stringtoID["XC_GGA_C_PBE"] = 130; _stringtoID["XC_GGA_C_LYP"] = 131; _stringtoID["XC_GGA_C_P86"] = 132; _stringtoID["XC_GGA_C_PBE_SOL"] = 133; _stringtoID["XC_GGA_C_PW91"] = 134; _stringtoID["XC_GGA_C_AM05"] = 135; _stringtoID["XC_GGA_C_XPBE"] = 136; _stringtoID["XC_GGA_C_LM"] = 137; _stringtoID["XC_GGA_C_PBE_JRGX"] = 138; _stringtoID["XC_GGA_X_OPTB88_VDW"] = 139; _stringtoID["XC_GGA_X_PBEK1_VDW"] = 140; _stringtoID["XC_GGA_X_OPTPBE_VDW"] = 141; _stringtoID["XC_GGA_X_RGE2"] = 142; _stringtoID["XC_GGA_C_RGE2"] = 143; _stringtoID["XC_GGA_X_RPW86"] = 144; _stringtoID["XC_GGA_X_KT1"] = 145; _stringtoID["XC_GGA_XC_KT2"] = 146; _stringtoID["XC_GGA_C_WL"] = 147; _stringtoID["XC_GGA_C_WI"] = 148; _stringtoID["XC_GGA_X_MB88"] = 149; _stringtoID["XC_GGA_X_SOGGA"] = 150; _stringtoID["XC_GGA_X_SOGGA11"] = 151; _stringtoID["XC_GGA_C_SOGGA11"] = 152; _stringtoID["XC_GGA_C_WI0"] = 153; _stringtoID["XC_GGA_XC_TH1"] = 154; _stringtoID["XC_GGA_XC_TH2"] = 155; _stringtoID["XC_GGA_XC_TH3"] = 156; _stringtoID["XC_GGA_XC_TH4"] = 157; _stringtoID["XC_GGA_X_C09X"] = 158; _stringtoID["XC_GGA_C_SOGGA11_X"] = 159; _stringtoID["XC_GGA_X_LB"] = 160; _stringtoID["XC_GGA_XC_HCTH_93"] = 161; _stringtoID["XC_GGA_XC_HCTH_120"] = 162; _stringtoID["XC_GGA_XC_HCTH_147"] = 163; _stringtoID["XC_GGA_XC_HCTH_407"] = 164; _stringtoID["XC_GGA_XC_EDF1"] = 165; _stringtoID["XC_GGA_XC_XLYP"] = 166; _stringtoID["XC_GGA_XC_B97"] = 167; _stringtoID["XC_GGA_XC_B97_1"] = 168; _stringtoID["XC_GGA_XC_B97_2"] = 169; _stringtoID["XC_GGA_XC_B97_D"] = 170; _stringtoID["XC_GGA_XC_B97_K"] = 171; _stringtoID["XC_GGA_XC_B97_3"] = 172; _stringtoID["XC_GGA_XC_PBE1W"] = 173; _stringtoID["XC_GGA_XC_MPWLYP1W"] = 174; _stringtoID["XC_GGA_XC_PBELYP1W"] = 175; _stringtoID["XC_GGA_XC_SB98_1a"] = 176; _stringtoID["XC_GGA_XC_SB98_1b"] = 177; _stringtoID["XC_GGA_XC_SB98_1c"] = 178; _stringtoID["XC_GGA_XC_SB98_2a"] = 179; _stringtoID["XC_GGA_XC_SB98_2b"] = 180; _stringtoID["XC_GGA_XC_SB98_2c"] = 181; _stringtoID["XC_GGA_X_LBM"] = 182; _stringtoID["XC_GGA_X_OL2"] = 183; _stringtoID["XC_GGA_X_APBE"] = 184; _stringtoID["XC_GGA_K_APBE"] = 185; _stringtoID["XC_GGA_C_APBE"] = 186; _stringtoID["XC_GGA_K_TW1"] = 187; _stringtoID["XC_GGA_K_TW2"] = 188; _stringtoID["XC_GGA_K_TW3"] = 189; _stringtoID["XC_GGA_K_TW4"] = 190; _stringtoID["XC_GGA_X_HTBS"] = 191; _stringtoID["XC_GGA_X_AIRY"] = 192; _stringtoID["XC_GGA_X_LAG"] = 193; _stringtoID["XC_GGA_XC_MOHLYP"] = 194; _stringtoID["XC_GGA_XC_MOHLYP2"] = 195; _stringtoID["XC_GGA_XC_TH_FL"] = 196; _stringtoID["XC_GGA_XC_TH_FC"] = 197; _stringtoID["XC_GGA_XC_TH_FCFO"] = 198; _stringtoID["XC_GGA_XC_TH_FCO"] = 199; _stringtoID["XC_GGA_C_OPTC"] = 200; _stringtoID["XC_GGA_K_VW"] = 500; _stringtoID["XC_GGA_K_GE2"] = 501; _stringtoID["XC_GGA_K_GOLDEN"] = 502; _stringtoID["XC_GGA_K_YT65"] = 503; _stringtoID["XC_GGA_K_BALTIN"] = 504; _stringtoID["XC_GGA_K_LIEB"] = 505; _stringtoID["XC_GGA_K_ABSP1"] = 506; _stringtoID["XC_GGA_K_ABSP2"] = 507; _stringtoID["XC_GGA_K_GR"] = 508; _stringtoID["XC_GGA_K_LUDENA"] = 509; _stringtoID["XC_GGA_K_GP85"] = 510; _stringtoID["XC_GGA_K_PEARSON"] = 511; _stringtoID["XC_GGA_K_OL1"] = 512; _stringtoID["XC_GGA_K_OL2"] = 513; _stringtoID["XC_GGA_K_FR_B88"] = 514; _stringtoID["XC_GGA_K_FR_PW86"] = 515; _stringtoID["XC_GGA_K_DK"] = 516; _stringtoID["XC_GGA_K_PERDEW"] = 517; _stringtoID["XC_GGA_K_VSK"] = 518; _stringtoID["XC_GGA_K_VJKS"] = 519; _stringtoID["XC_GGA_K_ERNZERHOF"] = 520; _stringtoID["XC_GGA_K_LC94"] = 521; _stringtoID["XC_GGA_K_LLP"] = 522; _stringtoID["XC_GGA_K_THAKKAR"] = 523; _stringtoID["XC_GGA_X_WPBEH"] = 524; _stringtoID["XC_GGA_X_HJS_PBE"] = 525; _stringtoID["XC_GGA_X_HJS_PBE_SOL"] = 526; _stringtoID["XC_GGA_X_HJS_B88"] = 527; _stringtoID["XC_GGA_X_HJS_B97X"] = 528; _stringtoID["XC_GGA_X_ITYH"] = 529; _stringtoID["XC_GGA_X_SFAT"] = 530; _stringtoID["XC_HYB_GGA_X_N12_SX"] = 81; _stringtoID["XC_HYB_GGA_XC_B3PW91"] = 401; _stringtoID["XC_HYB_GGA_XC_B3LYP"] = 402; _stringtoID["XC_HYB_GGA_XC_B3P86"] = 403; _stringtoID["XC_HYB_GGA_XC_O3LYP"] = 404; _stringtoID["XC_HYB_GGA_XC_mPW1K"] = 405; _stringtoID["XC_HYB_GGA_XC_PBEH"] = 406; _stringtoID["XC_HYB_GGA_XC_B97"] = 407; _stringtoID["XC_HYB_GGA_XC_B97_1"] = 408; _stringtoID["XC_HYB_GGA_XC_B97_2"] = 410; _stringtoID["XC_HYB_GGA_XC_X3LYP"] = 411; _stringtoID["XC_HYB_GGA_XC_B1WC"] = 412; _stringtoID["XC_HYB_GGA_XC_B97_K"] = 413; _stringtoID["XC_HYB_GGA_XC_B97_3"] = 414; _stringtoID["XC_HYB_GGA_XC_MPW3PW"] = 415; _stringtoID["XC_HYB_GGA_XC_B1LYP"] = 416; _stringtoID["XC_HYB_GGA_XC_B1PW91"] = 417; _stringtoID["XC_HYB_GGA_XC_mPW1PW"] = 418; _stringtoID["XC_HYB_GGA_XC_MPW3LYP"] = 419; _stringtoID["XC_HYB_GGA_XC_SB98_1a"] = 420; _stringtoID["XC_HYB_GGA_XC_SB98_1b"] = 421; _stringtoID["XC_HYB_GGA_XC_SB98_1c"] = 422; _stringtoID["XC_HYB_GGA_XC_SB98_2a"] = 423; _stringtoID["XC_HYB_GGA_XC_SB98_2b"] = 424; _stringtoID["XC_HYB_GGA_XC_SB98_2c"] = 425; _stringtoID["XC_HYB_GGA_X_SOGGA11_X"] = 426; _stringtoID["XC_HYB_GGA_XC_HSE03"] = 427; _stringtoID["XC_HYB_GGA_XC_HSE06"] = 428; _stringtoID["XC_HYB_GGA_XC_HJS_PBE"] = 429; _stringtoID["XC_HYB_GGA_XC_HJS_PBE_SOL"] = 430; _stringtoID["XC_HYB_GGA_XC_HJS_B88"] = 431; _stringtoID["XC_HYB_GGA_XC_HJS_B97X"] = 432; _stringtoID["XC_HYB_GGA_XC_CAM_B3LYP"] = 433; _stringtoID["XC_HYB_GGA_XC_TUNED_CAM_B3LYP"] = 434; _stringtoID["XC_HYB_GGA_XC_BHANDH"] = 435; _stringtoID["XC_HYB_GGA_XC_BHANDHLYP"] = 436; _stringtoID["XC_HYB_GGA_XC_MB3LYP_RC04"] = 437; _stringtoID["XC_HYB_GGA_XC_MPWLYP1M"] = 453; _stringtoID["XC_HYB_GGA_XC_REVB3LYP"] = 454; _stringtoID["XC_HYB_GGA_XC_CAMY_BLYP"] = 455; _stringtoID["XC_HYB_GGA_XC_PBE0_13"] = 456; } }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_VXC_FUNCTIONALS_H xtp-2021.2/include/votca/xtp/vxc_grid.h000066400000000000000000000060561412152066400177530ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_VXC_GRID_H #define VOTCA_XTP_VXC_GRID_H // Local VOTCA includes #include "grid_containers.h" #include "gridbox.h" namespace votca { namespace xtp { class LebedevGrid; class QMMolecule; class aobasis; class Vxc_Grid { public: void GridSetup(const std::string& type, const QMMolecule& atoms, const AOBasis& basis); std::vector getGridpoints() const; std::vector getWeightedDensities() const; Index getGridSize() const { return _totalgridsize; } Index getBoxesSize() const { return Index(_grid_boxes.size()); } const GridBox& operator[](Index index) const { return _grid_boxes[index]; } GridBox& operator[](Index index) { return _grid_boxes[index]; } typename std::vector::iterator begin() { return _grid_boxes.begin(); } typename std::vector::iterator end() { return _grid_boxes.end(); } typename std::vector::const_iterator begin() const { return _grid_boxes.begin(); } typename std::vector::const_iterator end() const { return _grid_boxes.end(); } private: void FindSignificantShells(const AOBasis& basis); double erf1c(double x) const; void SortGridpointsintoBlocks( const std::vector >& grid); Eigen::MatrixXd CalcInverseAtomDist(const QMMolecule& atoms) const; Index UpdateOrder(LebedevGrid& sphericalgridofElement, Index maxorder, std::vector& PruningIntervals, double r) const; GridContainers::Cartesian_gridpoint CreateCartesianGridpoint( const Eigen::Vector3d& atomA_pos, GridContainers::radial_grid& radial_grid, GridContainers::spherical_grid& spherical_grid, Index i_rad, Index i_sph) const; Eigen::VectorXd SSWpartition(const Eigen::VectorXd& rq_i, const Eigen::MatrixXd& Rij) const; void SSWpartitionAtom( const QMMolecule& atoms, std::vector& atomgrid, Index i_atom, const Eigen::MatrixXd& Rij) const; Eigen::MatrixXd CalcDistanceAtomsGridpoints( const QMMolecule& atoms, std::vector& atomgrid) const; Index _totalgridsize; std::vector _grid_boxes; bool _density_set = false; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_VXC_GRID_H xtp-2021.2/include/votca/xtp/vxc_potential.h000066400000000000000000000036171412152066400210250ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_VXC_POTENTIAL_H #define VOTCA_XTP_VXC_POTENTIAL_H // Third party includes #include // Local VOTCA includes #include "grid_containers.h" #include "gridbox.h" #undef LOG namespace votca { namespace xtp { template class Vxc_Potential { public: explicit Vxc_Potential(const Grid& grid) : _grid(grid){}; ~Vxc_Potential(); static double getExactExchange(const std::string& functional); void setXCfunctional(const std::string& functional); Mat_p_Energy IntegrateVXC(const Eigen::MatrixXd& density_matrix) const; private: struct XC_entry { double f_xc = 0; // E_xc[n] = int{n(r)*eps_xc[n(r)] d3r} = int{ f_xc(r) d3r double df_drho = 0; // v_xc_rho(r) = df/drho double df_dsigma = 0; // df/dsigma ( df/dgrad(rho) = df/dsigma * // dsigma/dgrad(rho) = df/dsigma * 2*grad(rho)) }; XC_entry EvaluateXC(double rho, double sigma) const; const Grid _grid; int xfunc_id; bool _setXC = false; bool _use_separate; int cfunc_id; xc_func_type xfunc; // handle for exchange functional xc_func_type cfunc; // handle for correlation functional }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_VXC_POTENTIAL_H xtp-2021.2/include/votca/xtp/xtpapplication.h000066400000000000000000000024471412152066400212050ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_XTPAPPLICATION_H #define VOTCA_XTP_XTPAPPLICATION_H // Third party includes #include #include namespace votca { namespace xtp { class XtpApplication : public votca::tools::Application { public: XtpApplication(); ~XtpApplication() override = default; void Initialize() override; bool EvaluateOptions() override = 0; void Run(void) override = 0; void ShowHelpText(std::ostream &out) override; protected: votca::tools::Property _options; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_XTPAPPLICATION_H xtp-2021.2/scripts/000077500000000000000000000000001412152066400141035ustar00rootroot00000000000000xtp-2021.2/scripts/CMakeLists.txt000066400000000000000000000013031412152066400166400ustar00rootroot00000000000000foreach(SCRIPT xtp_update_mapfile xtp_basisset xtp_makeauxbasis xtp_autogen_mapping xtp_qmmm2qm) configure_file(${SCRIPT}.in ${CMAKE_CURRENT_BINARY_DIR}/${SCRIPT}.out @ONLY) add_custom_target(${SCRIPT}_build ALL DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/${SCRIPT}) add_custom_command(OUTPUT ${SCRIPT} COMMAND ${CMAKE_COMMAND} -DINPUT="${SCRIPT}.out" -DOUTPUT="${SCRIPT}" -DGIT_EXECUTABLE="${GIT_EXECUTABLE}" -DTOP_SOURCE_DIR="${CMAKE_SOURCE_DIR}" -P ${PROJECT_SOURCE_DIR}/CMakeModules/gitscript.cmake) set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_MAKE_CLEAN_FILES ${SCRIPT}) install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${SCRIPT} DESTINATION ${CMAKE_INSTALL_BINDIR}) endforeach(SCRIPT) xtp-2021.2/scripts/xtp_autogen_mapping.in000077500000000000000000000437451412152066400205230ustar00rootroot00000000000000#! /usr/bin/env python3 # # Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # import argparse import importlib import multiprocessing import os import shutil import subprocess import xml.etree.ElementTree as ET from collections import defaultdict from pathlib import Path from typing import Any, Dict, List, NamedTuple from xml.dom import minidom import numpy as np try: importlib.import_module("rdkit") except ModuleNotFoundError: exc = ModuleNotFoundError( """'xtp_autogen_mapping' requires the 'rdkit' package: https://anaconda.org/conda-forge/rdkit""" ) exc.__cause__ = None raise exc from rdkit import Chem from rdkit.Chem import AllChem VERSION = '@PROJECT_VERSION@ #CSG_GIT_ID#' # Hartree to eV H2EV = 27.21138 class JobMetadata(NamedTuple): """Create a namedtuple with the data to call Orca.""" name: str path_orca: str functional: str basis: str RI: bool def search_cores() -> int: """Try to find the number of cores in the system.""" cpuinfo = Path("/proc/cpuinfo") if not cpuinfo.exists(): return multiprocessing.cpu_count() with open(cpuinfo, 'r') as handler: for line in handler: if "cpu cores" in line: break return int(line.split()[-1]) def run_cmd(cmd: str): """Run a shell command.""" print("running: ", cmd) result = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True) if result.stderr: print("command error: ", result.stderr) def write_input( input_file_name: str, crg_spin_coord: str, meta: JobMetadata, optimize: bool = True): """Write Orca input file.""" # number of cores to use ncores = search_cores() # geometry optimization starts from MD structure for n, and n structure of e/h ri_string = ' RIJCOSX' if meta.RI else "" opt = "opt" if optimize else "" chelpg = "! CHELPG" if optimize else "" # Polar calculation polar = "% elprop\npolar 1\nSolver CG\nend\n" if optimize else "" # Input file inp = f"""{crg_spin_coord} %pal nprocs {ncores} end ! DFT {opt} {meta.functional} {meta.basis} {ri_string} SlowConv ! D3BJ {chelpg} {polar} """ with open(input_file_name, "w") as handler: handler.write(inp) def read_energies(logfile_name: str) -> List[float]: """parse SINGLE POINT ENERGIES.""" energies = [] with open(logfile_name, 'r') as logfile: for line in logfile.readlines(): if 'FINAL SINGLE POINT ENERGY' in line: energies.append(float(line.split()[-1])) return energies def optimize_geometry(state: str, meta: JobMetadata) -> List[float]: """Perform a geometry optimization using Orca.""" root = f"{meta.name}_{state}" input_file_name = f"{root}.inp" logfile_name = f"{root}.log" errfile_name = f"{root}.err" if state == 'n': crg_spin_coord = f'* xyzfile 0 1 {meta.name}_MD.xyz' elif state == 'e': crg_spin_coord = f'* xyzfile -1 2 {meta.name}_n.xyz' elif state == 'h': crg_spin_coord = f'* xyzfile 1 2 {meta.name}_n.xyz' # Write optimization Orca input write_input(input_file_name, crg_spin_coord, meta) # Call orca orca_command = f"{meta.path_orca} {input_file_name} > {logfile_name} 2> {errfile_name}" run_cmd(orca_command) return read_energies(logfile_name) def run_single_point(state: str, meta: JobMetadata): """Run a single point calculation with Orca.""" crg_spin_coord = f'* xyzfile 0 1 {meta.name}_{state}.xyz' root = f"{meta.name}_{state}" input_n_file_name = f"{root}_n.inp" write_input(input_n_file_name, crg_spin_coord, meta, optimize=False) # run ORCA again logfile_n_name = f"{root}_n.log" errfile_n_name = f"{root}_n.err" orca_command2 = f"{meta.path_orca} {input_n_file_name} > {logfile_n_name} 2> {errfile_n_name}" run_cmd(orca_command2) # parse SINGLE POINT ENERGIES return read_energies(logfile_n_name) def process_charges_and_polarization(root: str) -> None: """Read charges and compute polarization.""" # parse CHELPG charges logfile_name = f"{root}_log2mps.log" errfile_name = f"{root}_log2mps.err" log2mps_command = f"xtp_tools -e log2mps -n {root} > {logfile_name} 2> {errfile_name}" run_cmd(log2mps_command) # prep molpol.xml options = ET.Element('options') molpol = ET.SubElement(options, 'molpol') mode = ET.SubElement(molpol, 'mode') mode.text = 'qmpackage' logname = ET.SubElement(molpol, 'logfile') logname.text = f"{root}.log" molpol_xml_str = minidom.parseString( ET.tostring(options)).toprettyxml(indent=" ") with open("molpol.xml", "w") as f: f.write(molpol_xml_str) # run molpol logfile_name = f"{root}_molpol.log" errfile_name = f"{root}_molpol.err" molpol_command = f"xtp_tools -e molpol -o molpol.xml -n {root} > {logfile_name} 2> {errfile_name}" os.system(molpol_command) # copy oprimized MPS_FILE os.makedirs('../MP_FILES', exist_ok=True) mpsfile = f"{root}_polar.mps" mpsfile_store = f"../MP_FILES/{mpsfile}" shutil.copy(mpsfile, mpsfile_store) def optimize(state: str, meta: JobMetadata): """Optimize geometry, get CHELPG charges, polarizability tensor.""" root = f"{meta.name}_{state}" energies = optimize_geometry(state, meta) E_initial = energies[0] E_final = energies[-1] # copy optimized geometries os.makedirs('../QC_FILES', exist_ok=True) geofile = f"{root}.xyz" geofile_store = f'../QC_FILES/{geofile}' shutil.copy(geofile, geofile_store) process_charges_and_polarization(root) # if state is h or e, calculate a single energy for the neural molecule in the optimized geometry if state != 'n': energies = run_single_point(state, meta) E_cross = energies[0] else: E_cross = 0.0 names = [f"E_{state}_{kind}" for kind in ("init", "final", "cross")] return {name: value for name, value in zip(names, (E_initial, E_final, E_cross))} def optimize_geometry_in_state( mol: Chem.rdchem.Mol, states: List[str], meta: JobMetadata) -> Dict[str, float]: """Optimize the molecular geometry in the given staten.""" os.makedirs('generate', exist_ok=True) basedir = os.getcwd() os.chdir('generate') # read the initial PDB file mdXYZ_file_name = f'{meta.name}_MD.xyz' Chem.MolToXYZFile(mol, mdXYZ_file_name) # neutral energies = optimize('n', meta) # cation, if requested if 'h' in states: energies_h = optimize('h', meta) energies.update(energies_h) # anion, if requested if 'e' in states: energies_e = optimize('e', meta) energies.update(energies_e) os.chdir(basedir) return energies def generate_mapping(args: argparse.Namespace) -> None: """Generate the mapping files.""" # Read the molecule mol = Chem.MolFromPDBFile(args.pdbfile, removeHs=False) seg_name = Path(args.pdbfile).stem if not args.mdname: args.mdname = Chem.rdMolDescriptors.CalcMolFormula(mol) msg = """No *mdname* (-m, --mdname) has been specified, setting it to the molecular formula. If you used GROMACS, replace the entry in the generated mapping.xml with the name in topol.top (or similar). """ print(msg) if args.optimize: segment_name = Path(args.pdbfile).stem meta = JobMetadata( name=segment_name, path_orca=args.orca, functional=args.functional, basis=args.basis, RI=args.nori) energies = optimize_geometry_in_state(mol, args.states, meta) else: # The default energy for any key is 0 energies = defaultdict(lambda: 0.0) msg = """WARNING **The user didn't request an optimization**, therefore: 1. `qmcoords` and `multipoles` tags are going to be added to the mapping file but the *xyz and *mps files, and the QC_FILES and MP_FILES directories are not automatically generated, you must add them yourself. 2. Excitation and reorganization energies are all set to 0. You need to change those values. """ print(msg) # determine the rotatable bonds rotable_bond = Chem.MolFromSmarts('[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]') rbonds = mol.GetSubstructMatches(rotable_bond) bonds = [mol.GetBondBetweenAtoms(x, y).GetIdx() for x, y in rbonds] mol1 = Chem.Mol(mol) fragments = [] # fragment molecule based on the rotatable bonds if bonds == []: fragments.append(mol1) else: new_mol = Chem.FragmentOnBonds(mol1, bonds) fragments = Chem.GetMolFrags(new_mol, asMols=True) generate_xml_tree(mol, args.states, fragments, seg_name, energies, args.mdname) def generate_xml_tree( mol: Chem.rdchem.Mol, states: List[str], fragments: List[Any], seg_name: str, energies: Dict[str, float], md_name: str) -> None: topology = ET.Element('topology') molecules = ET.SubElement(topology, 'molecules') molecule = ET.SubElement(molecules, 'molecule') name = ET.SubElement(molecule, 'name') name.text = seg_name mdname = ET.SubElement(molecule, 'mdname') mdname.text = md_name segments = ET.SubElement(molecule, 'segments') segment = ET.SubElement(segments, 'segment') segment_name = ET.SubElement(segment, 'name') segment_name.text = seg_name # Add qmcoords, xyz, multipoles and polar files add_state_files('n', segment, seg_name) if 'h' in states: add_state_files('h', segment, seg_name) add_energies('h', segment, energies) if 'e' in states: add_state_files('e', segment, seg_name) add_energies('e', segment, energies) map2md = ET.SubElement(segment, 'map2md') map2md.text = '0' xmlfragments = ET.SubElement(segment, 'fragments') # add the fragments into the xml tree add_fragments(mol, fragments, xmlfragments) xml_str = minidom.parseString( ET.tostring(topology)).toprettyxml(indent=" ") with open("mapping.xml", "w") as f: f.write(xml_str) def add_state_files(state: str, segment: ET.Element, seg_name: str) -> None: """Add the files for each state.""" segment_coord = ET.SubElement(segment, f'qmcoords_{state}') segment_coord.text = f"QC_FILES/{seg_name}_{state}.xyz" segment_mpoles = ET.SubElement(segment, f'multipoles_{state}') segment_mpoles.text = f"MP_FILES/{seg_name}_{state}_polar.mps" def add_energies(state: str, segment: ET.Element, energies: Dict[str, float]) -> None: """Add the energies for the states.""" # adiabatic excitation energy segment_U_xX_nN = ET.SubElement(segment, f'U_xX_nN_{state}') segment_U_xX_nN.text = format_energy( energies, f"E_{state}_final", "E_n_final") # reorg energy deexcitation segment_U_nX_nN = ET.SubElement( segment, f'U_nX_nN_{state}') segment_U_nX_nN.text = format_energy( energies, f"E_{state}_cross", "E_n_final") # reorg energy excitation segment_U_xN_xX = ET.SubElement(segment, f'U_xN_xX_{state}') segment_U_xN_xX.text = format_energy( energies, f"E_{state}_init", f"E_{state}_final") def add_fragments( mol: Chem.rdchem.Mol, fragments: List[Chem.rdchem.Mol], xmlfragments: ET.Element) -> None: """Add fragments to the XML tree.""" for i, fragment in enumerate(fragments): i += 1 filename = f"fragment{i}.pdb" Chem.MolToPDBFile(fragment, filename) conf = fragment.GetConformer() xmlfragment = ET.SubElement(xmlfragments, 'fragment') frag_name = ET.SubElement(xmlfragment, 'name') frag_name.text = f'fragment{i}' mdatoms = ET.SubElement(xmlfragment, 'mdatoms') qmatoms = ET.SubElement(xmlfragment, 'qmatoms') mpoles = ET.SubElement(xmlfragment, 'mpoles') weights = ET.SubElement(xmlfragment, 'weights') localframe = ET.SubElement(xmlfragment, 'localframe') mdatoms_str = "" qmatoms_str = "" weights_str = "" localframe_str = "" idx = np.sort(check_collinear(fragment)) for atom in range(fragment.GetNumAtoms()): this_element = fragment.GetAtoms()[atom].GetSymbol() if this_element != "*": this_pos = conf.GetAtomPosition(atom) for index_atom in range(mol.GetNumAtoms()): full_atom = mol.GetAtoms()[index_atom] full_element = full_atom.GetPDBResidueInfo().GetName().replace(" ", "") full_element_qm = full_atom.GetSymbol() full_pos = mol.GetConformer().GetAtomPosition(index_atom) if all(getattr(full_pos, x) == getattr(this_pos, x) for x in {'x', 'y', 'z'}): mdatoms_str += f"0:{full_element}:{index_atom} " qmatoms_str += f"{index_atom}:{full_element_qm} " weights_str += f"{full_atom.GetMass()} " mdatoms.text = mdatoms_str qmatoms.text = qmatoms_str mpoles.text = qmatoms_str weights.text = weights_str for label in ["".join(c for c in qmatoms_str.split()[i] if c.isdigit()) for i in idx]: localframe_str += f"{label} " localframe.text = localframe_str def random_selection(fragment) -> np.ndarray: n_atoms = fragment.GetNumAtoms() # Choose 3 random idx (aka choose three random atoms in the fragment, excluding ghost atoms with symbol *) atomic_list = [a for a in range(n_atoms) if fragment.GetAtoms()[ a].GetSymbol() != '*'] # Divide this list in H-list and rest_of_the_atoms-list h_list = [a for a in atomic_list if fragment.GetAtoms()[ a].GetSymbol() == 'H'] rest_list = [a for a in atomic_list if fragment.GetAtoms()[ a].GetSymbol() != 'H'] size_sample = 0 # If the rest of the atoms are 3 or less if len(rest_list) < 4: # If there are no Hydrogens it spits out a sample size equal to the rest of the atoms list if len(h_list) < 1: size_sample = len(rest_list) # If there are Hydrogens and the rest of the atoms are less than 3 (2 or 1) if len(h_list) > 0 and len(rest_list) < 3: # If there are at least 3 H if len(h_list) > 2: new_items = np.random.choice( h_list, size=3 - len(rest_list), replace=False) for i in new_items: rest_list.append(i) size_sample = len(rest_list) # Otherwise just spit out the all atomic list # (this because you can have max 1 H and 2 rest of the atoms) else: rest_list = atomic_list size_sample = len(rest_list) # Else the rest of the atoms are more than 3 then sampling randomly # three of them it is fine else: size_sample = 3 idx = np.random.choice(rest_list, size=size_sample, replace=False) return idx def angle_fragment(idx: np.ndarray, fragment: Chem.rdchem.Mol) -> float: try: conformer = fragment.GetConformer() pos_1, pos_2, pos_3 = [ conformer.GetAtomPosition(idx[x].item()) for x in range(3)] vec1 = np.array([pos_1.x - pos_2.x, pos_1.y - pos_2.y, pos_1.z - pos_2.z]) vec2 = np.array([pos_1.x - pos_3.x, pos_1.y - pos_3.y, pos_1.z - pos_3.z]) # Sin(theta) with theta angle between vec1 and vec2 cp = np.linalg.norm(np.cross(vec1, vec2)) / \ (np.linalg.norm(vec1) * np.linalg.norm(vec2)) except ZeroDivisionError: # Just throw out a big value for the cp so check_collinear whill break immediatly cp = 1 return cp def check_collinear(fragment: Chem.rdchem.Mol) -> int: """Check if three random selected points are collinear.""" while True: idx = random_selection(fragment) cp_norm = angle_fragment(idx, fragment) if cp_norm > 0.6: break return idx def format_energy(energies: Dict[str, float], first: str, second: str) -> str: """Format the energy difference.""" diff = H2EV * (energies[first] - energies[second]) return str(diff) def main(): """Read the command line arguments.""" parser = argparse.ArgumentParser("xtp_autogen_mapping") # Add the arguments to the parser parser.add_argument("-pdb", "--pdbfile", required=True, type=exists, help="PDB coordinate file") parser.add_argument("-opt", "--optimize", action="store_true", help="optimization of XYZ and MPS files") parser.add_argument("-s", "--states", default="n", nargs="+", help="which states to optimize", choices=["n", "e", "h"]) parser.add_argument("-orca", "--orca", default="/opt/orca-4.2.1/orca", help="full path to orca executable") parser.add_argument("-f", "--functional", default="PBE0", help="DFT functional") parser.add_argument( "-b", "--basis", default="def2-tzvp", help="basis set") parser.add_argument("--nori", action="store_false", help="Do not to use the Resolution of Identity approximation") parser.add_argument("-m", "--mdname", default="", help="Name of the molecule in the MD topology") args = parser.parse_args() generate_mapping(args) def exists(input_file: str) -> str: """Check if the input file exists.""" path = Path(input_file) if not path.exists(): raise argparse.ArgumentTypeError(f"{input_file} doesn't exist!") return path.absolute().as_posix() if __name__ == "__main__": main() xtp-2021.2/scripts/xtp_basisset.in000077500000000000000000000212151412152066400171470ustar00rootroot00000000000000#! /usr/bin/env python3 # # Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # VERSION='@PROJECT_VERSION@ #CSG_GIT_ID#' import sys import os import time import numpy as np import lxml.etree as lxml import argparse PROGTITLE = 'THE VOTCA::XTP converter basissetfiles' PROGDESCR = 'Creates votca xml basissetfiles from NWCHEM basissetfiles' VOTCAHEADER = '''\ ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== {progtitle} please submit bugs to @PROJECT_CONTACT@ xtp_basisset, version {version} '''.format(version=VERSION, progtitle=PROGTITLE) def okquit(what=''): if what != '': print (what) sys.exit(0) def xxquit(what=''): if what != '': print("ERROR: {what}".format(what=what)) sys.exit(1) def sysexe(cmd, silent=False, devfile='/dev/null'): if VERBOSE: print("{0}@{1}$ {2}".format(USER, HOST, cmd)) if silent: cmd += ' >> {0} 2>> {0}'.format(devfile) cdx = os.system(cmd) #SYSCMDS.write('{cmd} = {cdx}\n'.format(cmd=cmd, cdx=cdx)) return cdx # ============================================================================= # PROGRAM OPTIONS # ============================================================================= class XtpHelpFormatter(argparse.HelpFormatter): def _format_usage(self, usage, action, group, prefix): return VOTCAHEADER progargs = argparse.ArgumentParser(prog='xtp_basisset', formatter_class=lambda prog: XtpHelpFormatter(prog,max_help_position=70), description=PROGDESCR) progargs.add_argument('-f', '--input', dest='input', action='store', required=False, type=str, default='', help='NWchem file containing the basisset or Turbomole folder with element names.') progargs.add_argument('-o', '--outputvotca', dest='outputfile', action='store', required=False, type=str, default='', help='Path of votca outputfile') progargs.add_argument('-t', '--turbomolebasisset', dest='turbobasis', action='store', required=False, type=str, default='', help='For turbomole specify the basisset that is supposed to be extracted from Files, for auxbasis sets the basisset the aux basisset is supposed to be used for.') OPTIONS = progargs.parse_args() if OPTIONS.input == '': progargs.print_help() okquit("\nQuit here, because: Inputfile not set (option -f/--input)") if OPTIONS.outputfile == '': progargs.print_help() okquit("\nQuit here, because: outputfile not set (option -o/--outputvotca)") def getelemententry(root,element): for e in root: #print e.get("name") if e.get("name")==element: return e return lxml.SubElement(root,"element",name=element) def convertofloat(floatstring): if "D" in floatstring: floatstring=floatstring.replace("D","E") try: a=float(floatstring) return a except ValueError: print("Cannot figure out what '{}' means".format(floatstring)) sys.exit() return False def turbomolegetcontributions(element,lines,basissetstringlist,basis,shells): newbasissets=[] start=False basissetfound=False for line in lines: if line[0]=="#": continue elif line in ["\n","\r\n"]: continue elif "$end" in line: continue if line[0]=="*" and basissetfound: #print start if start: #print "Breaking" break else: start=True continue if line.split()[0]==element: if line.split()[-1] in basissetstringlist and basissetfound==False: basissetfound=True continue if start and basissetfound: if "->" in line: newbasissets.append(line.split()[-1]) continue entries=line.split() if len(entries)==2: if entries[-1].upper() in shells: shelltype=entries[-1].upper() shell=lxml.SubElement(basis,"shell",type=shelltype,scale="1.0") else: constant=lxml.SubElement(shell,"constant",decay="{:1.6e}".format(convertofloat(entries[0]))) contraction=lxml.SubElement(constant,"contractions",type=shelltype,factor="{:1.6e}".format(convertofloat(entries[1]))) #contraction.text=" " else: print("Cannot figure out what line '{}' means".format(line)) sys.exit() if len(newbasissets)>0: turbomolegetcontributions(element,lines,newbasissets,basis,shells) return # ============================================================================= # PARSING NWCHEM FILE # ============================================================================= basissetname=os.path.splitext(os.path.basename(OPTIONS.outputfile))[0] basis = lxml.Element("basis",name=basissetname) basis.append(lxml.Comment("Basis set created by xtp_basisset from {} at {}".format(os.path.basename(OPTIONS.input),time.strftime("%c")))) elements=['H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'K', 'Ar', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Ni', 'Co', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'I', 'Te', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Pt', 'Ir', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Pa', 'Th', 'Np', 'U', 'Am', 'Pu', 'Bk', 'Cm', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Rf', 'Lr', 'Db', 'Bh', 'Sg', 'Mt', 'Ds', 'Rg', 'Hs', 'Uut', 'Uub', 'Uup', 'Uuq', 'Uuh', 'Uuo'] shells=["S","P","D","F","G","H","I"] if os.path.isfile(OPTIONS.input): print("File {} seems to be a NWCHEM file".format(OPTIONS.input)) keywords=["BASIS","end","basis","END"] with open(OPTIONS.input,'r') as f: for line in f.readlines(): if line[0]=="#": continue elif line in ["\n","\r\n"]: element=None continue entries=line.split() if entries[0] in keywords: element=None continue elif entries[0] in elements: element=getelemententry(basis,entries[0]) shelltype=entries[1] shell=lxml.SubElement(element,"shell",type=shelltype,scale="1.0") elif len(entries)>1 and shell!=None: constant=lxml.SubElement(shell,"constant",decay="{:1.6e}".format(convertofloat(entries[0]))) for contractionfactor,singleshell in zip(entries[1:],shelltype): contraction=lxml.SubElement(constant,"contractions",type=singleshell,factor="{:1.6e}".format(convertofloat(contractionfactor))) #contraction.text=" " else: okquit("\nCannot understand line in file:{}".format(line)) elif os.path.isdir(OPTIONS.input): print("Directory {} seems to be a Turbomole folder".format(OPTIONS.input)) if OPTIONS.turbobasis == '': progargs.print_help() okquit("\nQuit here, because: Turbomole basisset not set (option -t/--turbomolebasisset)") for ele in elements: if os.path.isfile(ele.lower()): print ("Opening {}".format(ele.lower())) with open(ele.lower(),'r') as f: lines=f.readlines() element=getelemententry(basis,ele) turbomolegetcontributions(ele.lower(),lines,OPTIONS.turbobasis,element,shells) else: print("File {} belonging to element not found. Skipping element!".format(ele.lower(),element)) print("Imported new basisset {} from {} written to file {} with xtp_basisset".format(basissetname,OPTIONS.input,OPTIONS.outputfile)) with open(OPTIONS.outputfile, 'wb') as f: f.write(lxml.tostring(basis, pretty_print=True)) sys.exit(0) xtp-2021.2/scripts/xtp_makeauxbasis.in000077500000000000000000000264701412152066400200170ustar00rootroot00000000000000#! /usr/bin/env python3 # # Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # VERSION='@PROJECT_VERSION@ #CSG_GIT_ID#' import sys import os import numpy as np import lxml.etree as lxml import time import argparse PROGTITLE = 'THE VOTCA::XTP creator aux-basissetfiles' PROGDESCR = 'Creates votca xml aux-basissetfiles from votca basissetfiles' VOTCAHEADER = '''\ ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== {progtitle} please submit bugs to @PROJECT_CONTACT@ xtp_makeauxbasis, version {version} '''.format(version=VERSION, progtitle=PROGTITLE) # ============================================================================= # PROGRAM OPTIONS # ============================================================================= class XtpHelpFormatter(argparse.HelpFormatter): def _format_usage(self, usage, action, group, prefix): return VOTCAHEADER progargs = argparse.ArgumentParser(prog='xtp_makeauxbasis', formatter_class=lambda prog: XtpHelpFormatter(prog,max_help_position=70), description=PROGDESCR) progargs.add_argument('-f', '--basisfile', action='store', required=True, type=argparse.FileType('r'), help='xtp basissetfile') progargs.add_argument('-o', '--outfile', type=str, default='', help='optional file to write basisset to') progargs.add_argument('-g', '--grouping', required=False, type=float, default=0.1, help='Cutoff at which basisfunctions are grouped together in deviation from the arithmetic mean; Default 0.1') progargs.add_argument('-c', '--cutoff', required=False, type=float, default=60, help='Cutoff for very localised basisfunctions; Default 60') progargs.add_argument('-e','--element', required=False, type=str, default="", help='Print out only the element specified') progargs.add_argument('-l', '--lmax', required=False, type=int, default=4, help='maximum angular momentum in aux basisset: Default:4') args=progargs.parse_args() outputfile=False if (args.outfile!=""): outputfile=args.outfile onlyoneelement=False if(args.element!=""): onlyoneelement=args.element if args.lmax>6: print ("ERROR: Higher order functions than H (L=6) are not implemented") sys.exit(1) class basisfunction(object): def __init__(self,decay,L): self.decay=decay self.L=L self.Ls=[] class collection(object): def __init__(self): self.functions=[] self.com=0 self.decay=0 def addbasisfunction(self,function): self.functions.append(function) self.calcmean() self.calcdecay() return def addcollection(self,collection): self.functions+=collection.functions self.calcmean() self.calcdecay() return def calcmean(self): mean=0 for i in self.functions: mean+=i.decay mean=mean/len(self.functions) self.com=mean return def size(self): return len(self.functions) def calcdecay(self): decay=1 for i in self.functions: decay=decay*i.decay self.decay=decay**(1/float(len(self.functions))) return def popbasisfunction(self): keep=[] pop=[] for i in self.functions: outside=isclose(i,self) if outside: pop.append(i) else: keep.append(i) self.functions=keep return pop def findLs(self): Ls=[] for f in self.functions: if f.L not in Ls: Ls.append(f.L) Ls.sort() self.Ls=Ls return def shellstring(self): self.findLs() string="" for l in self.Ls: string+=LtoShelltype(l) return string def checkcompleteness(self): return (len(self.Ls)==(self.Ls[-1]-self.Ls[0]+1)) def splitshell(self): newcollections=[] breakpointLs=[] if( not self.checkcompleteness()): if(len(self.Ls)>1): for Ls1,Ls2 in zip(self.Ls[:-1],self.Ls[1:]): if Ls1+1!=Ls2: breakpointLs.append(Ls1) for point in reversed(breakpointLs): keep=[] newcollection=collection() for function in self.functions: if function.L<=point: keep.append(function) else: newcollection.addbasisfunction(function) self.functions=keep newcollections.append(newcollection) self.calcmean() self.calcdecay() return newcollections def attachshelltoxml(self,child): shell=lxml.SubElement(child,"shell",type=self.shellstring(),scale="1.0") constant=lxml.SubElement(shell,"constant",decay="{:1.6e}".format(self.decay)) for l in self.Ls: contraction=lxml.SubElement(constant,"contractions",type=LtoShelltype(l),factor="1.0") def isclose(function,collection): inside=False for f in collection.functions: if (abs(np.log(function.decay)-np.log(f.decay))args.lmax): continue if(decay>args.cutoff): continue auxfunctions.append(basisfunction(decay,L)) print ("{} aux functions created".format(len(auxfunctions))) return auxfunctions def sortauxfunctions(auxfunctions): Lmax=0 for function in auxfunctions: if(function.L)>Lmax: Lmax=function.L print ("Maximum angular momentum in aux basisset is {}".format(Lmax)) functionsperL=[] for i in range(Lmax+1): functionsperL.append([]) for function in auxfunctions: functionsperL[function.L].append(function) for i,L in enumerate(functionsperL): print ("{} functions have L={}".format(len(L),i)) return functionsperL def readinbasisset(xmlfile): print ("Parsing {}\n".format(xmlfile)) parser=lxml.XMLParser(remove_comments=True) tree = lxml.parse(xmlfile,parser) root = tree.getroot() print ("Basisset name is {}".format(root.get("name"))) output = lxml.Element("basis",name="aux-"+root.get("name")) for element in root.iter('element'): if onlyoneelement==False or element.get("name")==onlyoneelement: output.append(processelement(element)) return output def clusterfunctionsperL(functions): functions.sort(key=lambda function: function.decay,reverse=True) collections=[] for function in functions: if not collections: #print "New" firstcollection=collection() firstcollection.addbasisfunction(function) collections.append(firstcollection) else: for col in collections: if isclose(function,col): #print "CLOSE",col.decay,function.decay col.addbasisfunction(function) break else: newcollection=collection() newcollection.addbasisfunction(function) collections.append(newcollection) print ("Reduced functions from {} to {}".format(len(functions),len(collections))) for i,col in enumerate(collections): print ("{} Functions: {} Decay {}".format(i,col.size(),col.decay)) return collections def clustercollections(collections): collections.sort(key=lambda col: col.decay,reverse=True) finalshells=[] for col in collections: if not finalshells: finalshells.append(col) else: for shell in finalshells: if isclosecol(shell,col): shell.addcollection(col) break else: finalshells.append(col) print ("Reduced functions from {} to {}".format(len(collections),len(finalshells))) for i,col in enumerate(finalshells): print ("{} Functions: {} Decay {} Type {}".format(i,col.size(),col.decay, col.shellstring())) return finalshells def processelement(elementxml): print("\nReading element {}".format(elementxml.get("name"))) basisfunctions=[] for shell in elementxml.iter('shell'): for constant in shell.iter('constant'): decay=float(constant.get("decay")) for contraction in constant.iter("contractions"): shelltype=contraction.get("type") basisfunctions.append(basisfunction(decay,ShelltypetoL(shelltype))) print("Found {} basisfunctions".format(len(basisfunctions))) auxfunctions=createauxfunctions(basisfunctions) functionsperL=sortauxfunctions(auxfunctions) collections=[] for L,functions in enumerate(functionsperL): print ("Clustering L={}".format(L)) collections+=clusterfunctionsperL(functions) print ("Collecting shells over Ls") shells=clustercollections(collections) print ("Collecting shells over Ls twice") finalshells=clustercollections(shells) splittshells=[] for shell in finalshells: splittshells+=shell.splitshell() finalshells+=splittshells outputxml = lxml.Element("element",name=elementxml.get("name"),help="Created by make-auxbasis.py with Lmax={},c={} and g={}".format(args.lmax,args.cutoff,args.grouping)) for shell in finalshells: shell.attachshelltoxml(outputxml) return outputxml outputxml=readinbasisset(args.basisfile) if outputfile==False: print (lxml.tostring(outputxml, pretty_print=True)) else: with open(outputfile, 'w') as f: f.write(lxml.tostring(outputxml, pretty_print=True)) xtp-2021.2/scripts/xtp_qmmm2qm.in000077500000000000000000000045711412152066400167270ustar00rootroot00000000000000#! /usr/bin/env python3 # # Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # import h5py import sys import os import argparse import importlib VERSION = '@PROJECT_VERSION@ #CSG_GIT_ID#' PROGTITLE = 'THE VOTCA::XTP QMMM orbfile converter' PROGDESCR = 'Convert QMMM orb file into a DFTGWBSE-like orb file usable by gencube,densityanalysis,...' VOTCAHEADER = '''\ ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== {progtitle} please submit bugs to @PROJECT_CONTACT@ xtp_qmmm2qm, version {version} '''.format(version=VERSION, progtitle=PROGTITLE) parser = argparse.ArgumentParser(prog='xtp_qmmm2qm') parser.add_argument("-f", "--file", help="Input File (String)") parser.add_argument("-r", "--region", help="QMMM region number (Index)") parser.add_argument('-v', '--verbosity', action="count", help="Verbose mode") args = parser.parse_args() region = "region_" + args.region file_name, ext = os.path.splitext(args.file) print (VOTCAHEADER) print("...Input file: ", args.file) print("...Selected region: ", region) with h5py.File(args.file, 'r') as data_qmmm: #Check if selected region exists in the database if region in data_qmmm.keys(): # Create database similar to the simple QM one new_file_name = file_name + "_QMlike" + ext with h5py.File(new_file_name,'w') as dataset: data_qmmm.copy(region+'/orbitals', dataset) dataset.move('orbitals','QMdata') if args.verbosity: print("...Checking keys") print(list(dataset["QMdata"].keys())) print("...Congrats! Your new file is ready with name: ", new_file_name) else: print("ERROR: The selcted region doesn't exist") print("Available regions: ", list(data_qmmm.keys())) xtp-2021.2/scripts/xtp_update_mapfile.in000077500000000000000000000106551412152066400203170ustar00rootroot00000000000000#! /usr/bin/env python3 # # Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # VERSION = '@PROJECT_VERSION@ #CSG_GIT_ID#' import sys import argparse import re import lxml.etree as lxml PROGTITLE = 'THE VOTCA::XTP MAPPING FILE UPDATER' PROGDESCR = 'Updates the CTP mapping file to VOTCA XTP' VOTCAHEADER = '''\ ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== {progtitle} please submit bugs to @PROJECT_CONTACT@ xtp_update_mapfile, version {version} '''.format(version=VERSION, progtitle=PROGTITLE) def okquit(what=''): if what != '': print(what) sys.exit(0) # ============================================================================= # PROGRAM OPTIONS # ============================================================================= class XtpHelpFormatter(argparse.HelpFormatter): def _format_usage(self, usage, action, group, prefix): return VOTCAHEADER progargs = argparse.ArgumentParser(prog='xtp_update_mapfile', formatter_class=lambda prog: XtpHelpFormatter( prog, max_help_position=70), description=PROGDESCR) progargs.add_argument('-sin', '--S_input', dest='S_input', action='store', required=True, type=argparse.FileType('r'), default='', help='Mapping file to update.') progargs.add_argument('-sout', '--S_output', dest='S_output', action='store', required=True, type=argparse.FileType('w'), default='', help='Filename of new Mapping file.') OPTIONS = progargs.parse_args() # ============================================================================= # LXML # ============================================================================= def RepresentsInt(s): try: int(s) return True except ValueError: return False def changeframe(localframetext): ids = localframetext.split() newids = [] for i in ids: if RepresentsInt(i): integer = int(i) else: print("Cannot convert {} to integer".format(i)) newinteger = integer-1 newids.append("{:d}".format(newinteger)) return ' '.join(newids) def changeids(atomidtext): re_s = re.compile(r'(\S+)') atoms_and_whitespaces = re_s.split(atomidtext) newstring = [] for atom in atoms_and_whitespaces: if not atom or atom.isspace(): newstring.append(atom) else: array = atom.split(":") atomtype = array[1] if RepresentsInt(array[0]): integer = int(array[0]) else: print("Cannot convert {} to integer".format(array[0])) newinteger = integer-1 newstring.append("{:d}:{}".format(newinteger, atomtype)) return ''.join(newstring) print("Reading in {}".format(OPTIONS.S_input.name)) Tree = lxml.parse(OPTIONS.S_input.name) Root = Tree.getroot() Molecules = Root.find("molecules") for molecule in Molecules.iter('molecule'): segments = molecule.find("segments") for segment in segments.iter('segment'): fragments = segment.find("fragments") for fragment in fragments.iter('fragment'): qmatoms = fragment.find("qmatoms") qmatoms.text = changeids(qmatoms.text) mpoles = fragment.find("mpoles") mpoles.text = changeids(mpoles.text) localframe = fragment.find("localframe") localframe.text = changeframe(localframe.text) print("Writing to {}".format(OPTIONS.S_output.name)) Tree.write(OPTIONS.S_output.name, pretty_print=True) sys.exit(0) xtp-2021.2/share/000077500000000000000000000000001412152066400135165ustar00rootroot00000000000000xtp-2021.2/share/CMakeLists.txt000066400000000000000000000002431412152066400162550ustar00rootroot00000000000000add_subdirectory(xtp/basis_sets) add_subdirectory(xtp/data) add_subdirectory(xtp/xml) add_subdirectory(xtp/ecps) add_subdirectory(benchmark) add_subdirectory(doc) xtp-2021.2/share/README.rst000066400000000000000000000004221412152066400152030ustar00rootroot00000000000000Content ======= This folder contains all the configuration files and documentation for the VOTCA-XTP package. Subfolders ---------- - **benchmark** Files to run a benchmark - **doc** Documentation files - **xtp** Data and configuration files for the VOTCA-XTP pacakge xtp-2021.2/share/benchmark/000077500000000000000000000000001412152066400154505ustar00rootroot00000000000000xtp-2021.2/share/benchmark/CMakeLists.txt000066400000000000000000000015321412152066400202110ustar00rootroot00000000000000file(GLOB_RECURSE VOTCA_XTP_XML *.xml) install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/ DESTINATION ${CMAKE_INSTALL_DATADIR}/votca/xtp/benchmark PATTERN "*.in" EXCLUDE PATTERN "CMake*" EXCLUDE) foreach(SCRIPT xtp_benchmark) configure_file(${SCRIPT}.in ${CMAKE_CURRENT_BINARY_DIR}/${SCRIPT}.out @ONLY) add_custom_target(${SCRIPT}_build ALL DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/${SCRIPT}) add_custom_command(OUTPUT ${SCRIPT} COMMAND ${CMAKE_COMMAND} -DINPUT="${SCRIPT}.out" -DOUTPUT="${SCRIPT}" -DGIT_EXECUTABLE="${GIT_EXECUTABLE}" -DTOP_SOURCE_DIR="${CMAKE_SOURCE_DIR}" -P ${PROJECT_SOURCE_DIR}/CMakeModules/gitscript.cmake) set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_MAKE_CLEAN_FILES ${SCRIPT}) install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${SCRIPT} DESTINATION ${CMAKE_INSTALL_DATADIR}/votca/xtp/benchmark/) endforeach(SCRIPT) xtp-2021.2/share/benchmark/Geometries_ThielSet/000077500000000000000000000000001412152066400213545ustar00rootroot00000000000000xtp-2021.2/share/benchmark/Geometries_ThielSet/aldehydes_ketones_and_amides/000077500000000000000000000000001412152066400272125ustar00rootroot00000000000000xtp-2021.2/share/benchmark/Geometries_ThielSet/aldehydes_ketones_and_amides/acetamide.xyz000066400000000000000000000005751412152066400317110ustar00rootroot000000000000009 acetamide H 1.173209 -1.735763 0.000000 H 2.035841 -0.226201 0.000000 H -2.121189 -0.156089 0.000000 H -1.310647 -1.472742 0.885504 H -1.310647 -1.472742 -0.885504 C 0.000000 0.000000 0.000000 C -1.267042 -0.831610 0.000000 O 0.000000 1.229439 0.000000 N 1.158967 -0.727718 0.000000 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xtp-2021.2/share/benchmark/Geometries_ThielSet/unsaturated_aliphatic_hydrocarbons/hexatriene.xyz000066400000000000000000000011141412152066400334130ustar00rootroot0000000000000014 hexatriene H -0.953777 1.207691 0.000000 H 0.953777 -1.207691 0.000000 H 2.155816 0.952317 0.000000 H -2.155816 -0.952317 0.000000 H 2.125769 3.402692 0.000000 H -2.125769 -3.402692 0.000000 H 0.275642 3.397162 0.000000 H -0.275642 -3.397162 0.000000 C 0.000000 0.676808 0.000000 C 0.000000 -0.676808 0.000000 C 1.204938 1.485654 0.000000 C -1.204938 -1.485654 0.000000 C 1.203567 2.831663 0.000000 C -1.203567 -2.831663 0.000000 xtp-2021.2/share/benchmark/Geometries_ThielSet/unsaturated_aliphatic_hydrocarbons/norbornadiene.xyz000066400000000000000000000011701412152066400341060ustar00rootroot0000000000000015 norbornadiene H 0.901419 0.000000 1.967823 H -0.901419 0.000000 1.967823 H 0.000000 2.156504 0.616597 H 0.000000 -2.156504 0.616597 H 1.924341 1.340999 -1.022814 H -1.924341 -1.340999 -1.022814 H -1.924341 1.340999 -1.022814 H 1.924341 -1.340999 -1.022814 C 0.000000 0.000000 1.346369 C 0.000000 1.119526 0.272221 C 0.000000 -1.119526 0.272221 C 1.235500 0.672374 -0.517602 C -1.235500 -0.672374 -0.517602 C -1.235500 0.672374 -0.517602 C 1.235500 -0.672374 -0.517602 xtp-2021.2/share/benchmark/Geometries_ThielSet/unsaturated_aliphatic_hydrocarbons/octatetraene.xyz000066400000000000000000000013621412152066400337420ustar00rootroot0000000000000018 octatetraene H 0.971328 1.220141 0.000000 H -0.971328 -1.220141 0.000000 H -2.098090 0.984719 0.000000 H 2.098090 -0.984719 0.000000 H -0.146884 3.418505 0.000000 H 0.146884 -3.418505 0.000000 H -2.193473 4.766086 0.000000 H 2.193473 -4.766086 0.000000 H -3.225698 3.230501 0.000000 H 3.225698 -3.230501 0.000000 C 0.000000 0.721498 0.000000 C 0.000000 -0.721498 0.000000 C 1.125020 -1.479523 0.000000 C -1.125020 1.479523 0.000000 C 1.121077 -2.928812 0.000000 C -1.121077 2.928812 0.000000 C 2.237388 -3.682282 0.000000 C -2.237388 3.682282 0.000000 xtp-2021.2/share/benchmark/dftgwbse.xml000066400000000000000000000015341412152066400200020ustar00rootroot00000000000000 user_input.xml energy system.orb system.xyz input,dft,parse,gwbse system_dft.orb system.gbw gwbse.xml 0 xtp-2021.2/share/benchmark/gwbse.xml000066400000000000000000000047671412152066400173170ustar00rootroot00000000000000 cc-pVTZ aux-cc-pVTZ full XC_HYB_GGA_XC_PBEH fine 0 evGW gw,singlets,triplets ppm 25 1 no 1 DPR normal GS safe 50 0 xtp-2021.2/share/benchmark/xtp_benchmark.in000066400000000000000000000151501412152066400206270ustar00rootroot00000000000000#! /usr/bin/env python3 # # Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # import sys import os import time import numpy as np import argparse import h5py import shutil import json VERSION = '@PROJECT_VERSION@ #CSG_GIT_ID#' PROGTITLE = 'THE VOTCA::XTP Benchmark' PROGDESCR = 'Runs a Thiel set benchmark' VOTCAHEADER = '''\ ================================================== ======== VOTCA (http://www.votca.org) ======== ================================================== {progtitle} please submit bugs to @PROJECT_CONTACT@ benchmark, version {version} '''.format(version=VERSION, progtitle=PROGTITLE) def xxquit(what=''): if what != '': print("ERROR: {what}".format(what=what)) sys.exit(1) def ReadEnergyFromHDF5(filename): orb = h5py.File(filename, 'r') a = orb['QMdata']['BSE_singlet']['eigenvalues'].value a.flatten() return a.flatten() def CheckforXMLFile(filename): print("Checking for '{}' file".format(filename)) if not os.path.isfile(filename): xxquit("'{}' file not found".format(filename)) class cd: """Context manager for changing the current working directory""" def __init__(self, newPath): self.newPath = os.path.expanduser(newPath) def __enter__(self): self.savedPath = os.getcwd() os.chdir(self.newPath) def __exit__(self, etype, value, traceback): os.chdir(self.savedPath) # ============================================================================= # PROGRAM OPTIONS # ============================================================================= class XtpHelpFormatter(argparse.HelpFormatter): def _format_usage(self, usage, action, group, prefix): return VOTCAHEADER progargs = argparse.ArgumentParser(prog='xtp_benchmark', formatter_class=lambda prog: XtpHelpFormatter( prog, max_help_position=70), description=PROGDESCR) progargs.add_argument('-t', '--threads', required=False, type=int, default=1, help='Number of OPENMP threads') progargs.add_argument('-r', '--run', action='store_const', const=1, default=0, help='Run benchmark') progargs.add_argument('-a', '--analyze', action='store_const', const=1, default=0, help='Show results') progargs.add_argument('--reset', action='store_const', const=1, default=0, help='Delete all benchmark run data') progargs.add_argument('--update', action='store_const', const=1, default=0, help='Update references') OPTIONS = progargs.parse_args() if OPTIONS.reset: print("Deleting 'RUN' directory") try: shutil.rmtree("RUN") except OSError as e: print("Error: %s - %s." % (e.filename, e.strerror)) if OPTIONS.run: print("Creating run directory") if os.path.isdir('RUN'): xxquit("Folder 'RUN' already exists") os.mkdir("RUN") CheckforXMLFile('dftgwbse.xml') CheckforXMLFile('gwbse.xml') CheckforXMLFile('xtpdft.xml') molecules = [] for folder in os.listdir("Geometries_ThielSet"): print("Reading geometries from folder '{}'".format(folder)) for geo in os.listdir("Geometries_ThielSet/"+folder): if os.path.splitext("Geometries_ThielSet/"+folder+"/"+geo)[1] == ".xyz": molname = os.path.splitext(geo)[0] print("Creating subfolder '{}'".format(molname)) dest = "RUN/{}".format(molname) molecules.append(molname) os.mkdir(dest) shutil.copyfile("Geometries_ThielSet/"+folder + "/"+geo, dest+"/system.xyz") shutil.copyfile('dftgwbse.xml', dest+'/dftgwbse.xml') shutil.copyfile('gwbse.xml', dest+'/gwbse.xml') shutil.copyfile('xtpdft.xml', dest+'/xtpdft.xml') print("\nStarting benchmark with {} threads".format(OPTIONS.threads)) print(30*"-") moldata = {} totaltime = time.time() referencedata = {} if os.path.isfile("references.json"): print("Loading reference data from 'references.json'") with open("references.json", 'r') as fp: referencedata = json.load(fp) for mol in molecules: print("Running {}".format(mol).ljust(30), end="\r") with cd("RUN/{}".format(mol)): start = time.time() cmd = 'xtp_tools -e dftgwbse -o dftgwbse.xml -t {} > dftgwbse.log'.format(OPTIONS.threads) os.system(cmd) dt = time.time() - start molinfo = {} molinfo["duration[s]"] = dt print("{}".format(mol).ljust(30)+" Duration: \t{:8.2f} seconds.".format(dt), end='') if not os.path.isfile("system.orb"): print(" Computation Failed") molinfo["Status"] = "Failed" else: S = ReadEnergyFromHDF5("system.orb") print(" S1 = {:3.6f}[Hrt]".format(S[0])) molinfo["Status"] = "Success" molinfo["S1[Hrt]"] = S[0] if referencedata and referencedata[mol]["Status"] == "Success": print(" S1_ref = {:3.6f}[Hrt]".format( referencedata[mol]["S1[Hrt]"])) moldata[mol] = molinfo print(30*"-") dttotal = time.time() - totaltime print("Total time: {:8.2f}".format(dttotal)) goodruns = 0 for _, result in moldata.items(): if result["Status"] == "Success": goodruns += 1 print("{:1.2f}% of runs completed successfully".format( float(goodruns)/float(len(moldata))*100.0)) print("Writing benchmark data to 'result.json'") with open('result.json', 'w') as fp: json.dump(moldata, fp, sort_keys=True, indent=4) xtp-2021.2/share/benchmark/xtpdft.xml000066400000000000000000000027031412152066400175050ustar00rootroot00000000000000 1 xtp 0 1e-7 DIIS 0.002 0.8 20 0.0 0.2 atom cc-pVTZ aux-cc-pVTZ fine XC_HYB_GGA_XC_PBEH 200 0 xtp-2021.2/share/doc/000077500000000000000000000000001412152066400142635ustar00rootroot00000000000000xtp-2021.2/share/doc/CMakeLists.txt000066400000000000000000000031131412152066400170210ustar00rootroot00000000000000if(VOTCA_SPHINX_DIR) file(GLOB RSTS ${CMAKE_CURRENT_SOURCE_DIR}/*.rst) set(MANUAL_RST_FILES) foreach(_RST ${RSTS}) get_filename_component(_FILE "${_RST}" NAME) add_custom_command(OUTPUT ${VOTCA_SPHINX_DIR}/xtp/${_FILE} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${_RST} ${VOTCA_SPHINX_DIR}/xtp/${_FILE} DEPENDS ${_RST}) list(APPEND MANUAL_RST_FILES ${VOTCA_SPHINX_DIR}/xtp/${_FILE}) endforeach() find_package(Python 3 COMPONENTS Interpreter) set_package_properties(Python PROPERTIES TYPE OPTIONAL PURPOSE "Used to build documentation files") if(Python_EXECUTABLE AND VOTCA_XML_PARSER) file(GLOB XMLS ${CMAKE_CURRENT_SOURCE_DIR}/../xtp/xml/*.xml) set(XML_RST_FILES) foreach(_XML ${XMLS}) get_filename_component(_FILE "${_XML}" NAME_WE) add_custom_command(OUTPUT ${VOTCA_SPHINX_DIR}/xtp/${_FILE}.rst COMMAND ${Python_EXECUTABLE} ${VOTCA_XML_PARSER} -i ${_XML} -o ${VOTCA_SPHINX_DIR}/xtp/${_FILE}.rst DEPENDS ${VOTCA_XML_PARSER} ${_XML}) list(APPEND XML_RST_FILES ${VOTCA_SPHINX_DIR}/xtp/${_FILE}.rst) endforeach() add_custom_command(OUTPUT ${VOTCA_SPHINX_DIR}/xtp/qmpackage_defaults.rst COMMAND ${Python_EXECUTABLE} ${VOTCA_XML_PARSER} -m qm -i ${CMAKE_CURRENT_SOURCE_DIR}/../xtp/data/qmpackage_defaults.xml -o ${VOTCA_SPHINX_DIR}/xtp/qmpackage_defaults.rst DEPENDS ${VOTCA_XML_PARSER} ${CMAKE_CURRENT_SOURCE_DIR}/../xtp/data/qmpackage_defaults.xml) list(APPEND XML_RST_FILES ${VOTCA_SPHINX_DIR}/xtp/qmpackage_defaults.rst) endif() add_custom_target(doc-xtp DEPENDS ${XML_RST_FILES} ${MANUAL_RST_FILES}) endif() xtp-2021.2/share/doc/XTP-MANUAL.rst000066400000000000000000000001701412152066400164410ustar00rootroot00000000000000********** XTP Manual ********** .. toctree:: xtp_introduction theory workflows_and_calculators qmpackages xtp-2021.2/share/doc/qmpackages.rst000066400000000000000000000007531412152066400171360ustar00rootroot00000000000000QM Packages ########### Currently two quantum mechanics packages are supported to compute the molecular orbitals: **XTP** and `ORCA `_. **XTP** refers to the built-in DFT engine shipped with VOTCA-XTP package. The following table, define the defaults use with the *QM Packages*, .. include:: qmpackage_defaults.rst .. note:: An *xml* file containing the QM packages defaults can be found at `$VOTCASHARE/xtp/data/qmpackage_defaults.xml` xtp-2021.2/share/doc/theory.rst000066400000000000000000000001601412152066400163240ustar00rootroot00000000000000Theory and Background ##################### DFT and GW-BSE ************** Hopping transport ***************** xtp-2021.2/share/doc/workflows_and_calculators.rst000066400000000000000000000002051412152066400222650ustar00rootroot00000000000000Workflow and Calculator Structure ################################# .. toctree:: xtp_map xtp_parallel xtp_run xtp_tools xtp-2021.2/share/doc/xtp_introduction.rst000066400000000000000000000000321412152066400204240ustar00rootroot00000000000000Introduction ############ xtp-2021.2/share/doc/xtp_map.rst000066400000000000000000000000201412152066400164550ustar00rootroot00000000000000xtp_map ####### xtp-2021.2/share/doc/xtp_parallel.rst000066400000000000000000000001201412152066400174750ustar00rootroot00000000000000xtp_parallel ############ .. toctree:: eqm iexcitoncl iqm qmmm xtp-2021.2/share/doc/xtp_run.rst000066400000000000000000000002651412152066400165170ustar00rootroot00000000000000xtp_run ####### The following calculators are available: .. toctree:: eanalyze einternal ianalyze kmclifetime kmcmultiple mapchecker neighborlist vaverage xtp-2021.2/share/doc/xtp_tools.rst000066400000000000000000000003471412152066400170540ustar00rootroot00000000000000xtp_tools ######### The following calculators are available: .. toctree:: apdft coupling densityanalysis dftgwbse excitoncoupling gencube log2mps molpol partialcharges spectrum orb2mol mol2orb xtp-2021.2/share/xtp/000077500000000000000000000000001412152066400143315ustar00rootroot00000000000000xtp-2021.2/share/xtp/README.rst000066400000000000000000000005411412152066400160200ustar00rootroot00000000000000Content ======= This folder contains data and configuration files for the **VOTCA-XTP** package. Subfolders ---------- - **basis\_sets** Basis sets definitions - **ecp** Efective Core Potentials data - **xml** Input and defaults values for the XTP calculators - **data** All the configurable data that do not belong in the previous categories xtp-2021.2/share/xtp/basis_sets/000077500000000000000000000000001412152066400164705ustar00rootroot00000000000000xtp-2021.2/share/xtp/basis_sets/3-21G.xml000066400000000000000000004007041412152066400177100ustar00rootroot00000000000000 xtp-2021.2/share/xtp/basis_sets/6-311++G(2p,2d).xml000066400000000000000000001561351412152066400210160ustar00rootroot00000000000000 xtp-2021.2/share/xtp/basis_sets/6-311++G.xml000066400000000000000000001265151412152066400201300ustar00rootroot00000000000000 xtp-2021.2/share/xtp/basis_sets/6-311+G(2d,p).xml000066400000000000000000001572241412152066400206610ustar00rootroot00000000000000 xtp-2021.2/share/xtp/basis_sets/6-311+G**.xml000066400000000000000000001516021412152066400201740ustar00rootroot00000000000000 xtp-2021.2/share/xtp/basis_sets/6-311G.xml000066400000000000000000000163771412152066400200060ustar00rootroot00000000000000 xtp-2021.2/share/xtp/basis_sets/6-31G**.xml000066400000000000000000002517701412152066400200470ustar00rootroot00000000000000 xtp-2021.2/share/xtp/basis_sets/6-31G.xml000066400000000000000000003232751412152066400177230ustar00rootroot00000000000000 xtp-2021.2/share/xtp/basis_sets/CMakeLists.txt000066400000000000000000000002011412152066400212210ustar00rootroot00000000000000file(GLOB_RECURSE VOTCA_XTP_XML *.xml) install(FILES ${VOTCA_XTP_XML} DESTINATION ${CMAKE_INSTALL_DATADIR}/votca/xtp/basis_sets) xtp-2021.2/share/xtp/basis_sets/Weigend_coulomb_fitting.xml000066400000000000000000010473571412152066400240610ustar00rootroot00000000000000 xtp-2021.2/share/xtp/basis_sets/ahlrichs_coulomb_fitting.xml000066400000000000000000006542341412152066400242710ustar00rootroot00000000000000 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xtp-2021.2/share/xtp/basis_sets/optaux-aug-cc-pvtz.xml000066400000000000000000001107571412152066400227030ustar00rootroot00000000000000 xtp-2021.2/share/xtp/basis_sets/ubecp.xml000066400000000000000000000227051412152066400203160ustar00rootroot00000000000000 / xtp-2021.2/share/xtp/basis_sets/ubecppol.xml000066400000000000000000000552451412152066400210360ustar00rootroot00000000000000 / xtp-2021.2/share/xtp/basis_sets/ubecppoldiff.xml000066400000000000000000000204271412152066400216610ustar00rootroot00000000000000 / xtp-2021.2/share/xtp/basis_sets/ubecppoldiff_s.xml000066400000000000000000000203241412152066400221770ustar00rootroot00000000000000 / xtp-2021.2/share/xtp/data/000077500000000000000000000000001412152066400152425ustar00rootroot00000000000000xtp-2021.2/share/xtp/data/CMakeLists.txt000066400000000000000000000001751412152066400200050ustar00rootroot00000000000000file(GLOB_RECURSE VOTCA_XTP_DATA *.xml) install(FILES ${VOTCA_XTP_DATA} DESTINATION ${CMAKE_INSTALL_DATADIR}/votca/xtp/data) xtp-2021.2/share/xtp/data/orca_functional_names.xml000066400000000000000000000005171412152066400223200ustar00rootroot00000000000000 B1LYP B3LYP PBE0 PBE PBE xtp-2021.2/share/xtp/data/qmpackage_defaults.xml000066400000000000000000000072501412152066400216100ustar00rootroot00000000000000 xtp 0 1 def2-tzvp aux-def2-tzvp false XC_HYB_GGA_XC_PBEH /tmp/qmpackage false 0.1 false false tight true 1e-9 RI 1e-7 DIIS 0.002 0.8 20 false 0.0 0.2 100 1e-7 0.7 atom medium xtp-2021.2/share/xtp/ecps/000077500000000000000000000000001412152066400152635ustar00rootroot00000000000000xtp-2021.2/share/xtp/ecps/CMakeLists.txt000066400000000000000000000001731412152066400200240ustar00rootroot00000000000000file(GLOB_RECURSE VOTCA_XTP_XML *.xml) install(FILES ${VOTCA_XTP_XML} DESTINATION ${CMAKE_INSTALL_DATADIR}/votca/xtp/ecps) xtp-2021.2/share/xtp/ecps/CRENBL_ECP.xml000066400000000000000000000041221412152066400174400ustar00rootroot00000000000000 xtp-2021.2/share/xtp/ecps/ECP2SDF.xml000066400000000000000000000017531412152066400170410ustar00rootroot00000000000000 xtp-2021.2/share/xtp/ecps/SBKJC_ECP.xml000066400000000000000000000024521412152066400173330ustar00rootroot00000000000000 xtp-2021.2/share/xtp/ecps/corelevels.xml000066400000000000000000000011171412152066400201500ustar00rootroot00000000000000 xtp-2021.2/share/xtp/ecps/def2-ecp.xml000066400000000000000000000161751412152066400174040ustar00rootroot00000000000000 xtp-2021.2/share/xtp/ecps/ecp.xml000066400000000000000000000121441412152066400165560ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/000077500000000000000000000000001412152066400151315ustar00rootroot00000000000000xtp-2021.2/share/xtp/xml/CMakeLists.txt000066400000000000000000000001721412152066400176710ustar00rootroot00000000000000file(GLOB_RECURSE VOTCA_XTP_XML *.xml) install(FILES ${VOTCA_XTP_XML} DESTINATION ${CMAKE_INSTALL_DATADIR}/votca/xtp/xml) xtp-2021.2/share/xtp/xml/apdft.xml000066400000000000000000000004231412152066400167500ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/coupling.xml000066400000000000000000000021711412152066400174740ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/densityanalysis.xml000066400000000000000000000006231412152066400210770ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/dftgwbse.xml000066400000000000000000000206261412152066400174660ustar00rootroot00000000000000 xtp false xtp-2021.2/share/xtp/xml/eanalyze.xml000066400000000000000000000016771412152066400174760ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/einternal.xml000066400000000000000000000004631412152066400176370ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/eqm.xml000066400000000000000000000150761412152066400164460ustar00rootroot00000000000000 false xtp-2021.2/share/xtp/xml/excitoncoupling.xml000066400000000000000000000031501412152066400210640ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/gencube.xml000066400000000000000000000014201412152066400172600ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/ianalyze.xml000066400000000000000000000012021412152066400174620ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/iexcitoncl.xml000066400000000000000000000006331412152066400200160ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/iqm.xml000066400000000000000000000171361412152066400164510ustar00rootroot00000000000000 false xtp-2021.2/share/xtp/xml/kmclifetime.xml000077500000000000000000000034011412152066400201450ustar00rootroot00000000000000 4000 xtp-2021.2/share/xtp/xml/kmcmultiple.xml000077500000000000000000000035621412152066400202120ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/log2mps.xml000066400000000000000000000003461412152066400172410ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/mapchecker.xml000066400000000000000000000012111412152066400177500ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/mol2orb.xml000066400000000000000000000003701412152066400172270ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/molpol.xml000066400000000000000000000021521412152066400171550ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/neighborlist.xml000066400000000000000000000013341412152066400203450ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/orb2mol.xml000066400000000000000000000001561412152066400172310ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/partialcharges.xml000066400000000000000000000012031412152066400206400ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/qmmm.xml000066400000000000000000000012201412152066400166150ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/spectrum.xml000066400000000000000000000015471412152066400175240ustar00rootroot00000000000000 xtp-2021.2/share/xtp/xml/vaverage.xml000066400000000000000000000004561412152066400174600ustar00rootroot00000000000000 xtp-2021.2/src/000077500000000000000000000000001412152066400132035ustar00rootroot00000000000000xtp-2021.2/src/CMakeLists.txt000066400000000000000000000001461412152066400157440ustar00rootroot00000000000000add_subdirectory(libxtp) add_subdirectory(tools) if(ENABLE_TESTING) add_subdirectory(tests) endif() xtp-2021.2/src/libxtp/000077500000000000000000000000001412152066400145055ustar00rootroot00000000000000xtp-2021.2/src/libxtp/CMakeLists.txt000066400000000000000000000052241412152066400172500ustar00rootroot00000000000000add_custom_target(gitversion-xtp COMMAND ${CMAKE_COMMAND} -DTOP_SOURCE_DIR="${CMAKE_SOURCE_DIR}" -DGIT_EXECUTABLE="${GIT_EXECUTABLE}" -P ${PROJECT_SOURCE_DIR}/CMakeModules/gitversion.cmake) set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_MAKE_CLEAN_FILES gitversion.h) file(GLOB_RECURSE VOTCA_SOURCES *.cc *.cpp) file(GLOB_RECURSE NOT_VOTCA_SOURCES cudapipeline.cc cudamatrix.cc) list(REMOVE_ITEM VOTCA_SOURCES ${NOT_VOTCA_SOURCES}) get_filename_component(_PARENT_PATH "${CMAKE_CURRENT_BINARY_DIR}" DIRECTORY) add_library(votca_xtp ${VOTCA_SOURCES}) set_target_properties(votca_xtp PROPERTIES SOVERSION ${SOVERSION}) set_target_properties(votca_xtp PROPERTIES VOTCA_SHARE ${PROJECT_SOURCE_DIR}/share) set_target_properties(votca_xtp PROPERTIES XTP_PATH ${_PARENT_PATH}/tools) add_dependencies(votca_xtp gitversion-xtp) target_link_libraries(votca_xtp PUBLIC VOTCA::votca_csg VOTCA::votca_tools Boost::boost Eigen3::Eigen ${HDF5_LIBRARIES} PRIVATE PkgConfig::LIBXC PkgConfig::LIBINT Boost::program_options Boost::filesystem Boost::system Boost::timer ) if(OpenMP_FOUND) target_link_libraries(votca_xtp PUBLIC OpenMP::OpenMP_CXX) endif() if(USE_CUDA) target_link_libraries(votca_xtp PUBLIC ${CUDA_LIBRARIES} ${CUDA_CUBLAS_LIBRARIES}) target_include_directories(votca_xtp PUBLIC ${CUDA_INCLUDE_DIRS}) target_sources(votca_xtp PRIVATE cudapipeline.cc cudamatrix.cc) endif() #CMAKE_CURRENT_BINARY_DIR for gitversion.h #PROJECT_BINARY_DIR/include/votca/xtp for votca_xtp_config.h target_include_directories(votca_xtp PRIVATE ${CMAKE_CURRENT_BINARY_DIR} $ PUBLIC $ ${HDF5_INCLUDE_DIRS} $ $ $) install(TARGETS votca_xtp EXPORT VOTCA_XTP_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) install(EXPORT VOTCA_XTP_Targets FILE VOTCA_XTP_Targets.cmake NAMESPACE VOTCA:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/VOTCA_XTP) include(CMakePackageConfigHelpers) write_basic_package_version_file("VOTCA_XTPConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion) configure_file(VOTCA_XTPConfig.cmake.in "${CMAKE_CURRENT_BINARY_DIR}/VOTCA_XTPConfig.cmake" @ONLY) install(FILES "${CMAKE_CURRENT_BINARY_DIR}/VOTCA_XTPConfig.cmake" "${CMAKE_CURRENT_BINARY_DIR}/VOTCA_XTPConfigVersion.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/VOTCA_XTP) add_library(VOTCA::votca_xtp ALIAS votca_xtp) xtp-2021.2/src/libxtp/GaussianQuadratureBase.cc000066400000000000000000000025111412152066400214160ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/GaussianQuadratureBase.h" namespace votca { namespace xtp { void GaussianQuadratureBase::CheckOrder( Index order, const std::map& map) const { if (map.count(order) == 0) { std::string keys = "{ "; for (const auto& pair : map) { keys += std::to_string(pair.first) + " "; } keys += "}"; throw std::invalid_argument("Order " + std::to_string(order) + " not in " + keys + ". Please " " select one of these numbers"); } } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/ImaginaryAxisIntegration.cc000066400000000000000000000070411412152066400217670ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #include "votca/xtp/ImaginaryAxisIntegration.h" #include "votca/xtp/quadrature_factory.h" #include "votca/xtp/threecenter.h" namespace votca { namespace xtp { ImaginaryAxisIntegration::ImaginaryAxisIntegration( const Eigen::VectorXd& energies, const TCMatrix_gwbse& Mmn) : _energies(energies), _Mmn(Mmn) {} void ImaginaryAxisIntegration::configure( options opt, const RPA& rpa, const Eigen::MatrixXd& kDielMxInv_zero) { _opt = opt; QuadratureFactory::RegisterAll(); _gq = std::unique_ptr( Quadratures().Create(_opt.quadrature_scheme)); _gq->configure(_opt.order); CalcDielInvVector(rpa, kDielMxInv_zero); } // This function calculates and stores inverses of the microscopic dielectric // matrix in a matrix vector void ImaginaryAxisIntegration::CalcDielInvVector( const RPA& rpa, const Eigen::MatrixXd& kDielMxInv_zero) { _dielinv_matrices_r.resize(_gq->Order()); for (Index j = 0; j < _gq->Order(); j++) { double newpoint = _gq->ScaledPoint(j); Eigen::MatrixXd eps_inv_j = rpa.calculate_epsilon_i(newpoint).inverse(); eps_inv_j.diagonal().array() -= 1.0; _dielinv_matrices_r[j] = -eps_inv_j + kDielMxInv_zero * std::exp(-std::pow(_opt.alpha * newpoint, 2)); } } class FunctionEvaluation { public: FunctionEvaluation(const Eigen::MatrixXd& Imx, const Eigen::ArrayXcd& DeltaE, const std::vector& dielinv_matrices_r) : _Imx(Imx), _DeltaE(DeltaE), _dielinv_matrices_r(dielinv_matrices_r){}; double operator()(Index j, double point, bool symmetry) const { Eigen::VectorXcd denominator; const std::complex cpoint(0.0, point); if (symmetry) { denominator = (_DeltaE + cpoint).cwiseInverse() + (_DeltaE - cpoint).cwiseInverse(); } else { denominator = (_DeltaE + cpoint).cwiseInverse(); } return 0.5 / tools::conv::Pi * ((_Imx * (_dielinv_matrices_r[j].conjugate())) .cwiseProduct(denominator.asDiagonal() * _Imx)) .sum() .real(); } private: const Eigen::MatrixXd& _Imx; const Eigen::ArrayXcd& _DeltaE; const std::vector& _dielinv_matrices_r; }; double ImaginaryAxisIntegration::SigmaGQDiag(double frequency, Index gw_level, double eta) const { Index lumo = _opt.homo + 1; const Index occ = lumo - _opt.rpamin; const Index unocc = _opt.rpamax - _opt.homo; Index gw_level_offset = gw_level + _opt.qpmin - _opt.rpamin; const Eigen::MatrixXd& Imx = _Mmn[gw_level_offset]; Eigen::ArrayXcd DeltaE = frequency - _energies.array(); DeltaE.imag().head(occ) = eta; DeltaE.imag().tail(unocc) = -eta; FunctionEvaluation f = FunctionEvaluation(Imx, DeltaE, _dielinv_matrices_r); return _gq->Integrate(f); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/IndexParser.cc000066400000000000000000000064311412152066400172440ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard inlcudes #include #include // Third party includes #include #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/IndexParser.h" namespace votca { namespace xtp { std::vector IndexParser::CreateIndexVector( const std::string& Ids) const { std::vector result; tools::Tokenizer tok(Ids, " ,\n\t"); std::vector results; tok.ToVector(results); const std::string delimiter = ":"; for (std::string s : results) { if (s.find(delimiter) != std::string::npos) { std::string copy_s = s; try { Index start = boost::lexical_cast(s.substr(0, s.find(delimiter))); Index stop = boost::lexical_cast( s.erase(0, s.find(delimiter) + delimiter.length())); for (Index i = start; i <= stop; i++) { result.push_back(i); } } catch (boost::bad_lexical_cast&) { throw std::runtime_error("Could not convert " + copy_s + " to range of integers."); } } else { try { result.push_back(boost::lexical_cast(s)); } catch (boost::bad_lexical_cast&) { throw std::runtime_error("Could not convert " + s + " to integer."); } } } // Eliminates duplicates and sorts the vector std::set s(result.begin(), result.end()); result.assign(s.begin(), s.end()); return result; } std::string IndexParser::CreateIndexString( const std::vector& indeces) const { std::set s(indeces.begin(), indeces.end()); std::vector sorted_unique(s.begin(), s.end()); std::string result = ""; if (sorted_unique.empty()) { return result; } std::vector difference(sorted_unique.size() + 1); difference.back() = 0; std::adjacent_difference(sorted_unique.begin(), sorted_unique.end(), difference.begin()); bool range_started = false; Index startindex; for (Index i = 0; i < Index(sorted_unique.size()); i++) { if (difference[i + 1] == 1) { if (range_started) { continue; } else { range_started = true; startindex = sorted_unique[i]; } } else { if (range_started) { result += std::to_string(startindex) + ":" + (std::to_string(sorted_unique[i])) + " "; range_started = false; } else { result += (std::to_string(sorted_unique[i])) + " "; } } } boost::trim(result); return result; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/VOTCA_XTPConfig.cmake.in000066400000000000000000000014001412152066400206440ustar00rootroot00000000000000include(CMakeFindDependencyMacro) if(@OpenMP_FOUND@) find_dependency(OpenMP 4.5) endif() find_dependency(PkgConfig REQUIRED) pkg_check_modules(LIBXC REQUIRED IMPORTED_TARGET libxc) find_dependency(HDF5 1.8 REQUIRED COMPONENTS CXX) find_dependency(Boost 1.57.0 REQUIRED COMPONENTS program_options filesystem system timer) find_dependency(Eigen3 3.3.0 REQUIRED NO_MODULE) find_dependency(VOTCA_CSG REQUIRED NO_MODULE) find_dependency(VOTCA_TOOLS REQUIRED NO_MODULE) if(@USE_CUDA@) find_dependency(CUDA REQUIRED) endif() include("${CMAKE_CURRENT_LIST_DIR}/VOTCA_XTP_Targets.cmake") set_target_properties(VOTCA::votca_xtp PROPERTIES VOTCA_SHARE "@CMAKE_INSTALL_DATADIR@/votca") set_target_properties(VOTCA::votca_xtp PROPERTIES XTP_PATH "@CMAKE_INSTALL_FULL_BINDIR@") xtp-2021.2/src/libxtp/anderson_mixing.cc000066400000000000000000000055451412152066400202110ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // Local VOTCA includes #include "votca/xtp/anderson_mixing.h" namespace votca { namespace xtp { void Anderson::Configure(const Index order, const double alpha) { _order = order + 1; _alpha = alpha; } void Anderson::UpdateOutput(const Eigen::VectorXd &newOutput) { // Check if max mixing history is reached and adding new step to history Index size = _output.size(); if (size > _order - 1) { _output.erase(_output.begin()); } _output.push_back(newOutput); } void Anderson::UpdateInput(const Eigen::VectorXd &newInput) { Index size = _output.size(); if (size > _order - 1) { _input.erase(_input.begin()); } _input.push_back(newInput); } const Eigen::VectorXd Anderson::MixHistory() { const Index iteration = _output.size(); const Index used_history = iteration - 1; Eigen::VectorXd OutMixed = _output.back(); Eigen::VectorXd InMixed = _input.back(); if (iteration > 1 && _order > 1) { Eigen::VectorXd DeltaN = OutMixed - InMixed; // Building Linear System for Coefficients Eigen::MatrixXd A = Eigen::MatrixXd::Zero(used_history, used_history); Eigen::VectorXd c = Eigen::VectorXd::Zero(used_history); for (Index m = 1; m < iteration; m++) { c(m - 1) = (DeltaN - _output[used_history - m] + _input[used_history - m]) .dot(DeltaN); for (Index j = 1; j < iteration; j++) { A(m - 1, j - 1) = (DeltaN - _output[used_history - m] + _input[used_history - m]) .dot((DeltaN - _output[used_history - j] + _input[used_history - j])); } } // Solving the System to obtain coefficients Eigen::VectorXd coefficients = A.fullPivHouseholderQr().solve(c); // Mixing the Potentials for (Index n = 1; n < iteration; n++) { OutMixed += coefficients(n - 1) * (_output[used_history - n] - _output[used_history]); InMixed += coefficients(n - 1) * (_input[used_history - n] - _input[used_history]); } } // Returning the linear Mix of Input and Output return _alpha * OutMixed + (1 - _alpha) * InMixed; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/aobasis.cc000066400000000000000000000163271412152066400164460ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/aobasis.h" #include "votca/xtp/basisset.h" #include "votca/xtp/make_libint_work.h" #include "votca/xtp/qmmolecule.h" // include libint last otherwise it overrides eigen #include namespace votca { namespace xtp { Index AOBasis::getMaxL() const { Index n = 0; for (const auto& shell : _aoshells) { n = std::max(static_cast(shell.getL()), n); } return n; } Index AOBasis::getMaxNprim() const { Index n = 0; for (const auto& shell : _aoshells) { n = std::max(shell.getSize(), n); } return n; } std::vector AOBasis::getMapToBasisFunctions() const { std::vector result; result.reserve(_aoshells.size()); Index n = 0; for (const auto& shell : _aoshells) { result.push_back(n); n += shell.getNumFunc(); } return result; } AOShell& AOBasis::addShell(const Shell& shell, const QMAtom& atom, Index startIndex) { _aoshells.push_back(AOShell(shell, atom, startIndex)); return _aoshells.back(); } const std::vector AOBasis::getShellsofAtom(Index AtomId) const { std::vector result; for (const auto& aoshell : _aoshells) { if (aoshell.getAtomIndex() == AtomId) { result.push_back(&aoshell); } } return result; } void AOBasis::add(const AOBasis& other) { Index atomindex_offset = Index(_FuncperAtom.size()); for (AOShell shell : other) { shell._atomindex += atomindex_offset; shell._startIndex = _AOBasisSize; _AOBasisSize += shell.getNumFunc(); _aoshells.push_back(shell); } FillFuncperAtom(); } void AOBasis::Fill(const BasisSet& bs, const QMMolecule& atoms) { clear(); _name = bs.Name(); // loop over atoms for (const QMAtom& atom : atoms) { Index atomfunc = 0; const std::string& name = atom.getElement(); const Element& element = bs.getElement(name); for (const Shell& shell : element) { Index numfuncshell = NumFuncShell(shell.getL()); AOShell& aoshell = addShell(shell, atom, _AOBasisSize); _AOBasisSize += numfuncshell; atomfunc += numfuncshell; for (const GaussianPrimitive& gaussian : shell) { aoshell.addGaussian(gaussian); } aoshell.CalcMinDecay(); aoshell.normalizeContraction(); } } FillFuncperAtom(); return; } void AOBasis::FillFuncperAtom() { _FuncperAtom.clear(); Index currentIndex = -1; for (const auto& shell : _aoshells) { if (shell.getAtomIndex() == currentIndex) { _FuncperAtom[shell.getAtomIndex()] += shell.getNumFunc(); } else { currentIndex = shell.getAtomIndex(); _FuncperAtom.push_back(shell.getNumFunc()); } } } std::vector AOBasis::GenerateLibintBasis() const { std::vector libintshells; libintshells.reserve(_aoshells.size()); for (const auto& shell : _aoshells) { libintshells.push_back(shell.LibintShell()); } return libintshells; } std::vector> AOBasis::ComputeShellPairs( double threshold) const { Index nthreads = OPENMP::getMaxThreads(); std::vector shells = GenerateLibintBasis(); // construct the 2-electron repulsion integrals engine std::vector engines; engines.reserve(nthreads); engines.emplace_back(libint2::Operator::overlap, getMaxNprim(), getMaxL(), 0); for (Index i = 1; i != nthreads; ++i) { engines.push_back(engines[0]); } std::vector> pairs(shells.size()); #pragma omp parallel for schedule(dynamic) for (Index s1 = 0; s1 < Index(shells.size()); ++s1) { Index thread_id = OPENMP::getThreadId(); libint2::Engine& engine = engines[thread_id]; const libint2::Engine::target_ptr_vec& buf = engine.results(); Index n1 = shells[s1].size(); for (Index s2 = 0; s2 <= s1; ++s2) { bool on_same_center = (shells[s1].O == shells[s2].O); bool significant = on_same_center; if (!on_same_center) { Index n2 = shells[s2].size(); engine.compute(shells[s1], shells[s2]); Eigen::Map buf_mat(buf[0], n1, n2); significant = (buf_mat.norm() >= threshold); } if (significant) { pairs[s1].push_back(s2); } } std::sort(pairs[s1].begin(), pairs[s1].end()); } return pairs; } void AOBasis::UpdateShellPositions(const QMMolecule& mol) { for (AOShell& shell : _aoshells) { shell._pos = mol[shell.getAtomIndex()].getPos(); } } void AOBasis::clear() { _name = ""; _aoshells.clear(); _FuncperAtom.clear(); _AOBasisSize = 0; } void AOBasis::WriteToCpt(CheckpointWriter& w) const { w(_name, "name"); w(_AOBasisSize, "basissize"); Index numofprimitives = 0; for (const auto& shell : _aoshells) { numofprimitives += shell.getSize(); } // this is all to make dummy AOGaussian Shell s(L::S, 0); GaussianPrimitive d(0.1, 0.1); QMAtom dummy(0, "H", Eigen::Vector3d::Zero()); AOShell s1(s, dummy, 0); s1.addGaussian(d); const AOGaussianPrimitive& dummy2 = *s1.begin(); CptTable table = w.openTable("Contractions", dummy2, numofprimitives); std::vector dataVec(numofprimitives); Index i = 0; for (const auto& shell : _aoshells) { for (const auto& gaussian : shell) { gaussian.WriteData(dataVec[i]); i++; } } table.write(dataVec); } void AOBasis::ReadFromCpt(CheckpointReader& r) { clear(); r(_name, "name"); r(_AOBasisSize, "basissize"); if (_AOBasisSize > 0) { // this is all to make dummy AOGaussian Shell s(L::S, 0); GaussianPrimitive d(0.1, 0.1); QMAtom dummy(0, "H", Eigen::Vector3d::Zero()); AOShell s1(s, dummy, 0); s1.addGaussian(d); const AOGaussianPrimitive& dummy2 = *s1.begin(); CptTable table = r.openTable("Contractions", dummy2); std::vector dataVec(table.numRows()); table.read(dataVec); Index laststartindex = -1; for (std::size_t i = 0; i < table.numRows(); ++i) { if (dataVec[i].startindex != laststartindex) { _aoshells.push_back(AOShell(dataVec[i])); laststartindex = dataVec[i].startindex; } else { _aoshells.back()._gaussians.push_back( AOGaussianPrimitive(dataVec[i], _aoshells.back())); } } FillFuncperAtom(); } } std::ostream& operator<<(std::ostream& out, const AOBasis& aobasis) { out << "Name:" << aobasis.Name() << "\n"; out << " Functions:" << aobasis.AOBasisSize() << " Shells:" << aobasis.getNumofShells() << "\n"; for (const auto& shell : aobasis) { out << shell; } return out; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/aomatrices/000077500000000000000000000000001412152066400166345ustar00rootroot00000000000000xtp-2021.2/src/libxtp/aomatrices/aoecp.cc000066400000000000000000001747621412152066400202530ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * *Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/aopotential.h" #include "votca/xtp/aotransform.h" namespace votca { namespace xtp { void AOECP::FillPotential(const AOBasis& aobasis, const ECPAOBasis& ecp) { this->setECP(&ecp); _aopotential = Fill(aobasis); } Eigen::VectorXd AOECP::ExpandContractions(const AOGaussianPrimitive& gaussian, const AOShell& shell) const { return Eigen::VectorXd::Constant(shell.getNumFunc(), gaussian.getContraction()); } void AOECP::FillBlock(Eigen::Block& matrix, const AOShell& shell_row, const AOShell& shell_col) const { /* * * Currently supported: * * S, P, D, F, G functions in DFT basis and non-local ECPs with l = 0, * 1, 2, 3 * * or * * S, P, D, F functions in DFT basis and non-local ECPs with l = 0, 1, * 2, 3, 4 * */ const Eigen::Vector3d& pos_row = shell_row.getPos(); const Eigen::Vector3d& pos_col = shell_col.getPos(); const Eigen::Vector3d diff = pos_row - pos_col; // initialize some helper double distsq = diff.squaredNorm(); for (const auto& gaussian_row : shell_row) { const double decay_row = gaussian_row.getDecay(); Eigen::VectorXd contractions_row = ExpandContractions(gaussian_row, shell_row); for (const auto& gaussian_col : shell_col) { // get decay constant const double decay_col = gaussian_col.getDecay(); const double fak = 0.5 / (decay_row + decay_col); const double fak2 = 2.0 * fak; double exparg = fak2 * decay_row * decay_col * distsq; // check if distance between positons is large, then skip step if (exparg > 30.0) { continue; } Eigen::VectorXd contractions_col = ExpandContractions(gaussian_col, shell_col); // for each atom and its pseudopotential, get a matrix for (const std::vector& shells_perAtom : _ecp->ShellsPerAtom()) { if (shells_perAtom.empty()) { continue; } Eigen::Matrix powermatrix = Eigen::Matrix::Zero(); // 4 fit components, non-local // ECPs l = 0, 1, 2, 3, 4 Eigen::Matrix decaymatrix = Eigen::Matrix::Zero(); Eigen::Matrix coefmatrix = Eigen::Matrix::Zero(); for (const ECPAOShell* shell_ecp : shells_perAtom) { // only do the non-local parts if (!shell_ecp->isNonLocal()) { // stop if local coefficient is not zero for (const auto& gaussian_ecp : *shell_ecp) { if (std::abs(gaussian_ecp.getContraction()) > 1e-5) { throw std::runtime_error( "ECPs with explicit local parts are not supported. Use " "external DFT instead."); } } continue; } Index index = 0; Index L = Index(shell_ecp->getL()); for (const auto& gaussian_ecp : *shell_ecp) { powermatrix(index, L) = int(gaussian_ecp.getPower()); decaymatrix(index, L) = gaussian_ecp.getDecay(); coefmatrix(index, L) = gaussian_ecp.getContraction(); index++; } } Eigen::MatrixXd VNL_ECP = calcVNLmatrix(Index(shells_perAtom[0]->getLmaxElement()), shells_perAtom[0]->getPos(), gaussian_row, gaussian_col, powermatrix, decaymatrix, coefmatrix); auto VNL_ECP_small = VNL_ECP.block(shell_row.getOffset(), shell_col.getOffset(), matrix.rows(), matrix.cols()); // consider contractions matrix += contractions_row.asDiagonal() * VNL_ECP_small * contractions_col.asDiagonal(); } } } } Eigen::MatrixXd AOECP::calcVNLmatrix( Index lmax_ecp, const Eigen::Vector3d& posC, const AOGaussianPrimitive& g_row, const AOGaussianPrimitive& g_col, const Eigen::Matrix& power_ecp, const Eigen::Matrix& gamma_ecp, const Eigen::Matrix& pref_ecp) const { /* calculate the contribution of the nonlocal * ECP of atom at posC with * decay constants in _gamma_ecp * coefficients in _pref_ecp * with angular momentum of max 4 * * to DFT basis shell pair * with decay alpha at posA * decay beta at posB */ const double conv = 1.e-9; // 1.e-8 const Index NMAX = 41; const double PI = boost::math::constants::pi(); double SQPI = sqrt(PI); double SQ2 = sqrt(2.); double SQ3 = sqrt(3.); double SQ5 = sqrt(5.); double SQ7 = sqrt(7.); double alpha = g_row.getDecay(); double beta = g_col.getDecay(); const Eigen::Vector3d& posA = g_row.getShell().getPos(); const Eigen::Vector3d& posB = g_col.getShell().getPos(); Index lmax_row = Index(g_row.getShell().getL()); Index lmax_col = Index(g_col.getShell().getL()); Index lmin = std::min({lmax_row, lmax_col, lmax_ecp}); Index lmax = std::max({lmax_row, lmax_col, lmax_ecp}); Index nsph_row = (lmax_row + 1) * (lmax_row + 1); Index nsph_col = (lmax_col + 1) * (lmax_col + 1); Eigen::Vector3d AVS = posA - posC; Eigen::Vector3d BVS = posB - posC; double AVS2 = AVS.squaredNorm(); double BVS2 = BVS.squaredNorm(); Index INULL = 0; if (AVS2 > 0.01) { INULL = 2; } if (BVS2 > 0.01) { INULL++; } Eigen::MatrixXd matrix = Eigen::MatrixXd::Zero(nsph_row, nsph_col); const Index nnonsep = gamma_ecp.rows(); Index nmax; if (INULL == 0) { nmax = 2 * lmin; } else if (INULL == 3) { nmax = 2 * NMAX + lmax_row + lmax_col; } else { nmax = NMAX + 2 * lmax; } Eigen::MatrixXd XI = Eigen::MatrixXd::Zero(lmax_ecp + 1, nmax + 1); double f_even_r0 = .5 * SQPI; double f_even_r1 = .5; double f_even_r2 = .25 * SQPI; for (Index N = 0; N <= nmax; N++) { if ((N % 2) == 0) { // N even, XI(L, odd N) never needed if (N > 0) { f_even_r0 = f_even_r2; // !! f_even_r1 = f_even_r1 * double(N / 2); f_even_r2 = .5 * f_even_r0 * double(N + 1); } double DFAK_r0 = .5 * double(N + 1); double DFAK_r1 = .5 * double(N + 2); double DFAK_r2 = .5 * double(N + 3); for (Index L = 0; L <= lmax_ecp; L++) { for (Index I = 0; I < nnonsep; I++) { Index power = power_ecp(I, L); double DLI = (alpha + beta + gamma_ecp(I, L)); if (power == 2) { XI(L, N) += f_even_r2 * pref_ecp(I, L) / std::pow(DLI, DFAK_r2); // r^2 terms } else if (power == 0) { XI(L, N) += f_even_r0 * pref_ecp(I, L) / std::pow(DLI, DFAK_r0); // r^0 terms } else if (power == 1) { XI(L, N) += f_even_r1 * pref_ecp(I, L) / std::pow(DLI, DFAK_r1); // r^1 terms } } } } // end if ( (N % 2) == 0 ) } /**** PREPARATIONS DONE, NOW START ******/ // some limit determinations double G1 = 1.; double AVSSQ = 0.; Index NMAX1 = 0; if (AVS2 > 0.01) { G1 = std::exp(-alpha * AVS2); AVSSQ = sqrt(AVS2); double AMAX = 0.0; double fak = 2.0 * alpha * AVSSQ; double Pow = 1.; double factorialNN = 1; for (Index NN = 0; NN <= NMAX; NN++) { if (NN != 0) { Pow = Pow * fak; factorialNN = factorialNN * double(NN); } double AF = G1 * Pow / factorialNN; if ((NN % 2) == 0) { Index ii = NN + 2 * lmax; switch (lmax_ecp) { case 0: AMAX = AF * XI(0, ii); break; case 1: AMAX = AF * std::max({XI(0, ii), XI(1, ii)}); break; case 2: AMAX = AF * std::max({XI(0, ii), XI(1, ii), XI(2, ii)}); break; case 3: AMAX = AF * std::max({XI(0, ii), XI(1, ii), XI(2, ii), XI(3, ii)}); break; case 4: AMAX = AF * std::max({XI(0, ii), XI(1, ii), XI(2, ii), XI(3, ii), XI(4, ii)}); break; } if (NMAX1 == 0 && AMAX <= conv) { NMAX1 = NN; } if (NMAX1 != 0 && AMAX > conv) { NMAX1 = 0; } } } if (NMAX1 == 0 && AMAX > conv) { NMAX1 = NMAX; } } // same story for B double G2 = 1.; double BVSSQ = 0.; Index NMAX2 = 0; if (BVS2 > 0.01) { G2 = std::exp(-beta * BVS2); BVSSQ = sqrt(BVS2); double BMAX = 0.0; double fak = 2.0 * beta * BVSSQ; double Pow = 1.; double factorialNN = 1; for (Index NN = 0; NN <= NMAX; NN++) { if (NN != 0) { Pow = Pow * fak; factorialNN = factorialNN * double(NN); } double BF = G2 * Pow / factorialNN; if ((NN % 2) == 0) { Index ii = NN + 2 * lmax; switch (lmax_ecp) { case 0: BMAX = BF * XI(0, ii); break; case 1: BMAX = BF * std::max({XI(0, ii), XI(1, ii)}); break; case 2: BMAX = BF * std::max({XI(0, ii), XI(1, ii), XI(2, ii)}); break; case 3: BMAX = BF * std::max({XI(0, ii), XI(1, ii), XI(2, ii), XI(3, ii)}); break; case 4: BMAX = BF * std::max({XI(0, ii), XI(1, ii), XI(2, ii), XI(3, ii), XI(4, ii)}); break; } if (NMAX2 == 0 && BMAX <= conv) { NMAX2 = NN; } if (NMAX2 != 0 && BMAX > conv) { NMAX2 = 0; } } } if (NMAX2 == 0 && BMAX > conv) { NMAX2 = NMAX; } } double GAUSS = G1 * G2; /****** ORIGINAL CKO SUBROUTINE **********/ Eigen::Tensor COEF(5, 5, 9, NMAX + 1); if (INULL != 0) { Index lmin_dft_ecp = 0; Index lmax_dft_ecp = 0; if (INULL == 2) { lmin_dft_ecp = std::min(lmax_row, lmax_ecp); lmax_dft_ecp = std::max(lmax_row, lmax_ecp); } else if (INULL == 1) { lmin_dft_ecp = std::min(lmax_col, lmax_ecp); lmax_dft_ecp = std::max(lmax_col, lmax_ecp); } else if (INULL == 3) { Index lmax_dft = std::max(lmax_row, lmax_col); lmin_dft_ecp = std::min(lmax_dft, lmax_ecp); lmax_dft_ecp = std::max(lmax_dft, lmax_ecp); } for (Index i4 = 0; i4 <= NMAX; i4++) { /********** ORIGINAL CKOEF SUBROUTINE *************************/ Index NU = i4 % 2; Index NG = (i4 + 1) % 2; double FN1 = double(i4 + 1); double FN2 = double(i4 + 2); double FN3 = double(i4 + 3); double FN4 = double(i4 + 4); double FN5 = double(i4 + 5); double FN6 = double(i4 + 6); double FN7 = double(i4 + 7); double FN8 = double(i4 + 8); COEF(0, 0, 4, i4) = double(NG) / FN1; // M0 Mn is a modified // spherical Bessel function of the first kind if (lmax_dft_ecp > 0) { double COEFF = double(NU) / FN2 * SQ3; // SQ(3) * M1 COEF(0, 1, 4, i4) = COEFF; COEF(1, 0, 4, i4) = COEFF; if (lmin_dft_ecp > 0) { COEF(1, 1, 4, i4) = double(NG) * 3.0 / FN3; // M0 + 2 * M2 COEFF = 3.0 / 2.0 * double(NG) * (1.0 / FN1 - 1.0 / FN3); // M0 - M2 COEF(1, 1, 3, i4) = COEFF; COEF(1, 1, 5, i4) = COEFF; } } if (lmax_dft_ecp > 1) { double COEFF = double(NG) / 2.0 * SQ5 * (3.0 / FN3 - 1.0 / FN1); // SQ(5) * M2 COEF(0, 2, 4, i4) = COEFF; COEF(2, 0, 4, i4) = COEFF; if (lmin_dft_ecp > 0) { COEFF = SQ3 * SQ5 / 2.0 * double(NG) * (3.0 / FN4 - 1.0 / FN2); // ( SQ(15)/5 ) * ( 2 * M1 + 3 * M3 ) COEF(1, 2, 4, i4) = COEFF; COEF(2, 1, 4, i4) = COEFF; COEFF = 3. * SQ5 / 2.0 * double(NU) * (1.0 / FN2 - 1.0 / FN4); // ( (3*SQ(5))/5 ) * ( M1 - M3 ) COEF(1, 2, 3, i4) = COEFF; COEF(1, 2, 5, i4) = COEFF; COEF(2, 1, 3, i4) = COEFF; COEF(2, 1, 5, i4) = COEFF; } if (lmin_dft_ecp > 1) { COEF(2, 2, 4, i4) = 5.0 / 4.0 * double(NG) * (9.0 / FN5 - 6.0 / FN3 + 1.0 / FN1); // (1/7) * ( 7 * M0 + 10 * // M2 + 18 * M4 ) COEFF = double(NG) * 15.0 / 2.0 * (1.0 / FN3 - 1.0 / FN5); // (1/7) * ( 7 * M0 + // 5 * M2 - 12 * M4 ) COEF(2, 2, 3, i4) = COEFF; COEF(2, 2, 5, i4) = COEFF; COEFF = 15.0 / 8.0 * double(NG) * (1.0 / FN1 - 2.0 / FN3 + 1.0 / FN5); // (1/7) * ( 7 * M0 - // 10 * M2 + 3 * M4 ) COEF(2, 2, 2, i4) = COEFF; COEF(2, 2, 6, i4) = COEFF; } } if (lmax_dft_ecp > 2) { double COEFF = double(NU) * .5 * SQ7 * (5. / FN4 - 3. / FN2); // SQ(7) * M3 COEF(0, 3, 4, i4) = COEFF; COEF(3, 0, 4, i4) = COEFF; if (lmin_dft_ecp > 0) { COEFF = double(NG) * .5 * SQ3 * SQ7 * (5. / FN5 - 3. / FN3); // ( SQ(21)/7 ) * ( 3 * M2 + 4 * M4 ) COEF(1, 3, 4, i4) = COEFF; COEF(3, 1, 4, i4) = COEFF; COEFF = double(NG) * .375 * SQ2 * SQ7 * (-5. / FN5 + 6. / FN3 - 1. / FN1); // ( (3*SQ(14))/7 ) * ( // M2 - M4 ) COEF(1, 3, 3, i4) = COEFF; COEF(1, 3, 5, i4) = COEFF; COEF(3, 1, 3, i4) = COEFF; COEF(3, 1, 5, i4) = COEFF; } if (lmin_dft_ecp > 1) { COEFF = double(NU) * .25 * SQ5 * SQ7 * (15. / FN6 - 14. / FN4 + 3. / FN2); // ( SQ(35)/105 ) * ( 27 * // M1 + 28 * M3 + 50 * M5 ) COEF(2, 3, 4, i4) = COEFF; COEF(3, 2, 4, i4) = COEFF; COEFF = double(NU) * .375 * SQ2 * SQ5 * SQ7 * (-5. / FN6 + 6. / FN4 - 1. / FN2); // ( SQ(70)/105 ) * ( 18 * M1 // + 7 * M3 - 25 * M5 ) COEF(2, 3, 3, i4) = COEFF; COEF(2, 3, 5, i4) = COEFF; COEF(3, 2, 3, i4) = COEFF; COEF(3, 2, 5, i4) = COEFF; COEFF = double(NU) * 1.875 * SQ7 * (1. / FN6 - 2. / FN4 + 1. / FN2); // ( SQ(7)/21 ) * ( 9 * M1 // - 14 * M3 + 5 * M5 ) COEF(2, 3, 2, i4) = COEFF; COEF(2, 3, 6, i4) = COEFF; COEF(3, 2, 2, i4) = COEFF; COEF(3, 2, 6, i4) = COEFF; } if (lmin_dft_ecp > 2) { COEF(3, 3, 4, i4) = double(NG) * 1.75 * (50. / FN7 - 30. / FN5 + 9. / FN3); // (1/33) * ( 33 * M0 + 44 * // M2 + 54 * M4 + 100 * M6 ) COEFF = double(NG) * 1.3125 * (-25. / FN7 + 35. / FN5 - 11. / FN3 + 1. / FN1); // (1/11) * ( 11 * M0 + 11 * M2 + 3 * M4 - 25 * M6 ) COEF(3, 3, 3, i4) = COEFF; COEF(3, 3, 5, i4) = COEFF; COEFF = double(NG) * 105 * .125 * (1. / FN7 - 2. / FN5 + 1. / FN3); // (1/11) * ( 11 * M0 - 21 // * M4 + 10 * M6 ) COEF(3, 3, 2, i4) = COEFF; COEF(3, 3, 6, i4) = COEFF; COEFF = double(NG) * 35 * .0625 * (-1. / FN7 + 3. / FN5 - 3. / FN3 + 1. / FN1); // (1/33) * ( 33 * M0 - 55 * M2 + 27 * M4 - 5 * M6 ) COEF(3, 3, 1, i4) = COEFF; COEF(3, 3, 7, i4) = COEFF; } } if (lmax_dft_ecp > 3) { double COEFF = double(NG) * .375 * (35. / FN5 - 30. / FN3 + 3. / FN1); // 3 * M4 COEF(0, 4, 4, i4) = COEFF; COEF(4, 0, 4, i4) = COEFF; if (lmin_dft_ecp > 0) { COEFF = double(NU) * .375 * SQ3 * (35. / FN6 - 30. / FN4 + 3. / FN2); // ( SQ(3)/3 ) * ( 4 * // M3 + 5 * M5 ) COEF(1, 4, 4, i4) = COEFF; COEF(4, 1, 4, i4) = COEFF; COEFF = double(NU) * .375 * SQ2 * SQ3 * SQ5 * (-7. / FN6 + 10. / FN4 - 3. / FN2); // ( SQ(30)/3 ) * ( M3 - // M5 ) COEF(1, 4, 3, i4) = COEFF; COEF(1, 4, 5, i4) = COEFF; COEF(4, 1, 3, i4) = COEFF; COEF(4, 1, 5, i4) = COEFF; } if (lmin_dft_ecp > 1) { COEFF = double(NG) * .1875 * SQ5 * (105. / FN7 - 125. / FN5 + 39. / FN3 - 3. / FN1); // ( (3*SQ(5))/77 ) * ( 22 * M2 + 20 * M4 + 35 * // M6 ) COEF(2, 4, 4, i4) = COEFF; COEF(4, 2, 4, i4) = COEFF; COEFF = double(NG) * 1.875 * SQ2 * SQ3 * (-7. / FN7 + 10. / FN5 - 3. / FN3); // ( (5*SQ(6))/77 ) * ( 11 * // M2 + 3 * M4 - 14 * M6 ) COEF(2, 4, 3, i4) = COEFF; COEF(2, 4, 5, i4) = COEFF; COEF(4, 2, 3, i4) = COEFF; COEF(4, 2, 5, i4) = COEFF; COEFF = double(NG) * .9375 * SQ3 * (7. / FN7 - 15. / FN5 + 9. / FN3 - 1. / FN1); // ( (5*SQ(3))/77 ) * ( 11 * M2 - 18 * M4 + 7 * M6 ) COEF(2, 4, 2, i4) = COEFF; COEF(2, 4, 6, i4) = COEFF; COEF(4, 2, 2, i4) = COEFF; COEF(4, 2, 6, i4) = COEFF; } if (lmin_dft_ecp > 2) { COEFF = double(NU) * .1875 * SQ7 * (175. / FN8 - 255. / FN6 + 105. / FN4 - 9. / FN2); // ( SQ(7)/1001 ) * ( 572 * M1 + 546 * M3 + 660 // * M5 + 1225 * M7) COEF(3, 4, 4, i4) = COEFF; COEF(4, 3, 4, i4) = COEFF; COEFF = double(NU) * 1.875 * SQ3 * SQ5 * SQ7 * (-35. / FN8 + 57. / FN6 - 25. / FN4 + 3. / FN2); // ( SQ(105))/1001 ) * ( 143 * M1 + 91 * M3 + 11 // * M5 - 245 * M7) COEF(3, 4, 3, i4) = COEFF; COEF(3, 4, 5, i4) = COEFF; COEF(4, 3, 3, i4) = COEFF; COEF(4, 3, 5, i4) = COEFF; COEFF = double(NU) * .9375 * SQ3 * SQ7 * (7. / FN8 - 15. / FN6 + 9. / FN4 - 1. / FN2); // ( SQ(21))/1001 ) * ( 286 * M1 - 91 * M3 - 440 // * M5 + 245 * M7) COEF(3, 4, 2, i4) = COEFF; COEF(3, 4, 6, i4) = COEFF; COEF(4, 3, 2, i4) = COEFF; COEF(4, 3, 6, i4) = COEFF; COEFF = double(NU) * 6.5625 * (-1. / FN8 + 3. / FN6 - 3. / FN4 + 1. / FN2); // ( 1/143 ) * ( 143 * M1 - 273 * M3 + 165 * M5 // - 35 * M7) COEF(3, 4, 1, i4) = COEFF; COEF(3, 4, 7, i4) = COEFF; COEF(4, 3, 1, i4) = COEFF; COEF(4, 3, 7, i4) = COEFF; } if (lmin_dft_ecp > 3) { throw std::runtime_error( "Sorry, not yet supported: Combination of G functions in DFT " "basis and ECPs with l = 4."); } } } // i4 loop (== CKO ) } // end if (INULL != 0) Eigen::Tensor BLMA; Eigen::Tensor CA; getBLMCOF(lmax_ecp, lmax_row, AVS, BLMA, CA); Eigen::Tensor BLMB; Eigen::Tensor CB; getBLMCOF(lmax_ecp, lmax_col, BVS, BLMB, CB); switch (INULL) { case 0: // AVSSQ <= 0.1 && BVSSQ <= 0.1 { for (Index i = 0; i < nsph_row; i++) { for (Index j = 0; j < nsph_col; j++) { for (Index L = 0; L <= lmin; L++) { double XI_L = XI(L, L + L); for (Index M = 4 - L; M <= 4 + L; M++) { matrix(i, j) += BLMA(i, L, M) * BLMB(j, L, M) * XI_L; } } } } break; } case 1: // AVSSQ <= 0.1 { Eigen::TensorFixedSize> SUMCI3; for (Index L = 0; L <= lmax_ecp; L++) { for (Index L2 = 0; L2 <= lmax_col; L2++) { Index range_M2 = std::min(L2, L); for (Index M2 = 4 - range_M2; M2 <= 4 + range_M2; M2++) { double VAR2 = 0.0; double fak = 2.0 * beta * BVSSQ; double pow = 1; double factorialNN = 1; for (Index NN = 0; NN <= NMAX2; NN++) { if (NN != 0) { pow = pow * fak; factorialNN = factorialNN * double(NN); } double XDUM = COEF(L, L2, M2, NN) * pow / factorialNN; VAR2 += XDUM * XI(L, NN + L + L2); } SUMCI3(L, L2, M2) = VAR2; } // end M2 } // end L2 } // end L for (Index i = 0; i < nsph_row; i++) { for (Index j = 0; j < nsph_col; j++) { for (Index L = 0; L <= std::min(lmax_row, lmax_ecp); L++) { for (Index L2 = 0; L2 <= lmax_col; L2++) { Index range_M2 = std::min(L2, L); for (Index M2 = 4 - range_M2; M2 <= 4 + range_M2; M2++) { for (Index M1 = 4 - L; M1 <= 4 + L; M1++) { matrix(i, j) += BLMA(i, L, M1) * BLMB(j, L2, M2) * SUMCI3(L, L2, M2) * CB(L, M1, M2); } } } } } } break; } case 2: // BVSSQ <= 0.1 { Eigen::TensorFixedSize> SUMCI3; for (Index L = 0; L <= lmax_ecp; L++) { for (Index L1 = 0; L1 <= lmax_row; L1++) { Index range_M1 = std::min(L1, L); for (Index M1 = 4 - range_M1; M1 <= 4 + range_M1; M1++) { double VAR1 = 0.0; double fak = 2.0 * alpha * AVSSQ; double pow = 1; double factorialN = 1; for (Index N = 0; N <= NMAX1; N++) { if (N != 0) { pow = pow * fak; factorialN = factorialN * double(N); } double XDUM = COEF(L, L1, M1, N) * pow / factorialN; VAR1 += XDUM * XI(L, N + L1 + L); } SUMCI3(L, L1, M1) = VAR1; } // end M1 } // end L1 } // end L for (Index i = 0; i < nsph_row; i++) { for (Index j = 0; j < nsph_col; j++) { for (Index L = 0; L <= std::min(lmax_col, lmax_ecp); L++) { for (Index L1 = 0; L1 <= lmax_row; L1++) { Index range_M1 = std::min(L1, L); for (Index M1 = 4 - range_M1; M1 <= 4 + range_M1; M1++) { for (Index M2 = 4 - L; M2 <= 4 + L; M2++) { matrix(i, j) += BLMA(i, L1, M1) * BLMB(j, L, M2) * SUMCI3(L, L1, M1) * CA(L, M2, M1); } } } } } } break; } case 3: { Eigen::TensorFixedSize> CC; CC.setZero(); for (Index L = 0; L <= lmax_ecp; L++) { Index range_M1 = std::min(lmax_row, Index(L)); Index range_M2 = std::min(lmax_col, Index(L)); for (Index M1 = 4 - range_M1; M1 <= 4 + range_M1; M1++) { for (Index M2 = 4 - range_M2; M2 <= 4 + range_M2; M2++) { for (Index M = 4 - L; M <= 4 + L; M++) { CC(L, M1, M2) += CA(L, M, M1) * CB(L, M, M2); } } } } Eigen::TensorFixedSize> SUMCI; SUMCI.setZero(); for (Index L = 0; L <= lmax_ecp; L++) { for (Index L1 = 0; L1 <= lmax_row; L1++) { Index range_M1 = std::min(L1, L); for (Index L2 = 0; L2 <= lmax_col; L2++) { Index range_M2 = std::min(L2, L); for (Index M1 = 4 - range_M1; M1 <= 4 + range_M1; M1++) { for (Index M2 = 4 - range_M2; M2 <= 4 + range_M2; M2++) { double fak1 = 2.0 * alpha * AVSSQ; double pow1 = 1; double factorialN = 1; for (Index N = 0; N <= NMAX1; N++) { if (N != 0) { pow1 = pow1 * fak1; factorialN = factorialN * double(N); } double VAR1 = COEF(L, L1, M1, N) * pow1 / factorialN; double VAR2 = 0.0; double fak2 = 2.0 * beta * BVSSQ; double pow2 = 1; double factorialNN = 1; for (Index NN = 0; NN <= NMAX2; NN++) { if (NN != 0) { pow2 = pow2 * fak2; factorialNN = factorialNN * double(NN); } double XDUM = COEF(L, L2, M2, NN) * pow2 / factorialNN; VAR2 += XDUM * XI(L, N + NN + L1 + L2); } SUMCI(L, L1, L2, M1, M2) += VAR1 * VAR2; } } // end M2 } // end M1 } // end L2 } // end L1 } // end L for (Index i = 0; i < nsph_row; i++) { for (Index j = 0; j < nsph_col; j++) { for (Index L = 0; L <= lmax_ecp; L++) { for (Index L1 = 0; L1 <= lmax_row; L1++) { Index range_M1 = std::min(L1, L); for (Index L2 = 0; L2 <= lmax_col; L2++) { Index range_M2 = std::min(L2, L); for (Index M1 = 4 - range_M1; M1 <= 4 + range_M1; M1++) { for (Index M2 = 4 - range_M2; M2 <= 4 + range_M2; M2++) { matrix(i, j) += BLMA(i, L1, M1) * BLMB(j, L2, M2) * SUMCI(L, L1, L2, M1, M2) * CC(L, M1, M2); } } } } } } } break; } default: throw std::runtime_error("AOECP::Wrong ECP summation mode"); } // switch // GET TRAFO HERE ALREADY Eigen::VectorXd NormA = CalcNorms(alpha, nsph_row); Eigen::VectorXd NormB = CalcNorms(beta, nsph_col); Eigen::MatrixXd copy = GAUSS * NormA.asDiagonal() * matrix * NormB.asDiagonal(); // FIXME use proper transformations class, this is a hack because nobody // understands aoecp // clang-format off std::array reorder = { 0, // s 2, 1, 3, // p 7, 5, 4, 6, 8, // d 14, 12, 10, 9, 11, 13, 15, // f 23, 21, 19, 17, 16, 18, 20, 22, 24, // g 34, 32, 30, 28, 26, 25, 27, 29, 31, 33, 35, // h 47, 45, 43, 41, 39, 37, 36, 38, 40, 42, 44, 46, 48 // i }; //clang-format on for (Index i = 0; i < matrix.rows(); i++) { for (Index j = 0; j < matrix.cols(); j++) { matrix(i, j) = copy(reorder[i], reorder[j]); } } return matrix; } Eigen::VectorXd AOECP::CalcNorms(double decay, Index size) const { Eigen::VectorXd Norms = Eigen::VectorXd(size); const double PI = boost::math::constants::pi(); double SQ2, SQ3, SQ5; double Norm_S = pow(2.0 * decay / PI, 0.75); double Norm_P = 0.0; Norms(0) = Norm_S; // Y 00 if (size > 1) { Norm_P = 2.0 * sqrt(decay) * Norm_S; Norms(1) = Norm_P; // Y 10 Norms(2) = Norm_P; // Y 1-1 Norms(3) = Norm_P; // Y 11 } if (size > 4) { SQ3 = sqrt(3.); double Norm_D = 4.00 * decay * Norm_S; Norms(4) = .5 * Norm_D / SQ3; // Y 20 Norms(5) = Norm_D; // Y 2-1 Norms(6) = Norm_D; // Y 21 Norms(7) = Norm_D; // Y 2-2 Norms(8) = .5 * Norm_D; // Y 22 } if (size > 9) { SQ2 = sqrt(2.); SQ5 = sqrt(5.); double Norm_F = 4.00 * decay * Norm_P; double Norm_F_1 = .5 * Norm_F / (SQ2 * SQ5); double Norm_F_3 = .5 * Norm_F / (SQ2 * SQ3); Norms(9) = .5 * Norm_F / (SQ3 * SQ5); // Y 30 Norms(10) = Norm_F_1; // Y 3-1 Norms(11) = Norm_F_1; // Y 31 Norms(12) = Norm_F; // Y 3-2 Norms(13) = .5 * Norm_F; // Y 32 Norms(14) = Norm_F_3; // Y 3-3 Norms(15) = Norm_F_3; // Y 33 } if (size > 16) { double SQ7 = sqrt(7.); double Norm_D = 0.0; double Norm_G = 4.00 * decay * Norm_D; double Norm_G_1 = .5 * Norm_G / (SQ2 * SQ3 * SQ7); double Norm_G_m2 = .5 * Norm_G / (SQ3 * SQ7); double Norm_G_3 = .5 * Norm_G / (SQ2 * SQ3); double Norm_G_m4 = .5 * Norm_G / SQ3; Norms(16) = .125 * Norm_G / (SQ3 * SQ5 * SQ7); // Y 40 Norms(17) = Norm_G_1; // Y 4-1 Norms(18) = Norm_G_1; // Y 41 Norms(19) = Norm_G_m2; // Y 4-2 Norms(20) = .5 * Norm_G_m2; // Y 42 Norms(21) = Norm_G_3; // Y 4-3 Norms(22) = Norm_G_3; // Y 43 Norms(23) = Norm_G_m4; // Y 4-4 Norms(24) = .25 * Norm_G_m4; // Y 44 } return Norms; } void AOECP::getBLMCOF(Index lmax_ecp, Index lmax_dft, const Eigen::Vector3d& pos, Eigen::Tensor& BLC, Eigen::Tensor& C) const { Index nsph = (lmax_dft + 1) * (lmax_dft + 1); Index lmax_dft_ecp = std::max(lmax_dft, lmax_ecp); Index lmin_dft_ecp = std::min(lmax_dft, lmax_ecp); BLC = Eigen::Tensor(nsph, 5, 9); BLC.setZero(); C = Eigen::Tensor(5, 9, 9); C.setZero(); Eigen::Tensor BLM(nsph, 5, 9); BLM.setZero(); const double PI = boost::math::constants::pi(); double SQPI = sqrt(PI); double SQ2 = sqrt(2.); double SQ2PI = SQ2 * SQPI; double SQ3 = sqrt(3.); double SQ5 = sqrt(5.); double SQ7 = sqrt(7.); double XS = 2. * SQPI; double XP, XD, XD_0, XD_p2; double XF_0, XF_1, XF_m2, XF_p2, XF_3; double BVS_X = pos(0); double BVS_Y = pos(1); double BVS_Z = pos(2); double BVS_XX = BVS_X * BVS_X; double BVS_YY = BVS_Y * BVS_Y; double BVS_ZZ = BVS_Z * BVS_Z; double BVS_RR = BVS_XX + BVS_YY + BVS_ZZ; double BVS_XY, BVS_XZ, BVS_YZ; BLM(0, 0, 4) = XS; // Y 00 if (lmax_dft > 0) { XP = XS / SQ3; BLM(1, 0, 4) = -BVS_Z * XS; // Y 10 BLM(1, 1, 4) = XP; BLM(2, 0, 4) = -BVS_Y * XS; // Y 1 -1 BLM(2, 1, 3) = XP; BLM(3, 0, 4) = -BVS_X * XS; // Y 11 BLM(3, 1, 5) = XP; } if (lmax_dft > 1) { BVS_XY = BVS_X * BVS_Y; BVS_XZ = BVS_X * BVS_Z; BVS_YZ = BVS_Y * BVS_Z; XD = XP / SQ5; XD_0 = 4.0 * SQPI / SQ5; XD_p2 = 2. * XD; BLM(4, 0, 4) = (3.0 * BVS_ZZ - BVS_RR) * XS; // Y 20 BLM(4, 1, 5) = 2.0 * BVS_X * XP; BLM(4, 1, 3) = 2.0 * BVS_Y * XP; BLM(4, 1, 4) = -4.0 * BVS_Z * XP; BLM(4, 2, 4) = XD_0; BLM(5, 0, 4) = BVS_YZ * XS; // Y 2 -1 BLM(5, 1, 3) = -BVS_Z * XP; BLM(5, 1, 4) = -BVS_Y * XP; BLM(5, 2, 3) = XD; BLM(6, 0, 4) = BVS_XZ * XS; // Y 21 BLM(6, 1, 5) = -BVS_Z * XP; BLM(6, 1, 4) = -BVS_X * XP; BLM(6, 2, 5) = XD; BLM(7, 0, 4) = BVS_XY * XS; // Y 2 -2 BLM(7, 1, 5) = -BVS_Y * XP; BLM(7, 1, 3) = -BVS_X * XP; BLM(7, 2, 2) = XD; BLM(8, 0, 4) = (BVS_XX - BVS_YY) * XS; // Y 22 BLM(8, 1, 5) = -2.0 * BVS_X * XP; BLM(8, 1, 3) = 2.0 * BVS_Y * XP; BLM(8, 2, 6) = XD_p2; } if (lmax_dft > 2) { XF_0 = 4. * SQPI / SQ7; XF_1 = 4. * SQ2PI / (SQ3 * SQ7); XF_m2 = 2. * SQPI / (SQ3 * SQ5 * SQ7); XF_p2 = 2. * XF_m2; XF_3 = 4. * SQ2PI / (SQ5 * SQ7); BLM(9, 0, 4) = (3. * BVS_RR - 5. * BVS_ZZ) * BVS_Z * XS; // Y 30 BLM(9, 1, 3) = -6. * BVS_YZ * XP; BLM(9, 1, 4) = 3. * (3. * BVS_ZZ - BVS_RR) * XP; BLM(9, 1, 5) = -6. * BVS_XZ * XP; BLM(9, 2, 3) = 6. * BVS_Y * XD; BLM(9, 2, 4) = -3. * BVS_Z * XD_0; BLM(9, 2, 5) = 6. * BVS_X * XD; BLM(9, 3, 4) = XF_0; BLM(10, 0, 4) = (BVS_RR - 5. * BVS_ZZ) * BVS_Y * XS; // Y 3 -1 BLM(10, 1, 3) = (4. * BVS_ZZ - BVS_XX - 3. * BVS_YY) * XP; BLM(10, 1, 4) = 8. * BVS_YZ * XP; BLM(10, 1, 5) = -2. * BVS_XY * XP; BLM(10, 2, 2) = 2. * BVS_X * XD; BLM(10, 2, 3) = -8. * BVS_Z * XD; BLM(10, 2, 4) = -2. * BVS_Y * XD_0; BLM(10, 2, 6) = -BVS_Y * XD_p2; BLM(10, 3, 3) = XF_1; BLM(11, 0, 4) = (BVS_RR - 5. * BVS_ZZ) * BVS_X * XS; // Y 31 BLM(11, 1, 3) = -2. * BVS_XY * XP; BLM(11, 1, 4) = 8. * BVS_XZ * XP; BLM(11, 1, 5) = (4. * BVS_ZZ - 3. * BVS_XX - BVS_YY) * XP; BLM(11, 2, 2) = 2. * BVS_Y * XD; BLM(11, 2, 4) = -2. * BVS_X * XD_0; BLM(11, 2, 5) = -8. * BVS_Z * XD; BLM(11, 2, 6) = BVS_X * XD_p2; BLM(11, 3, 5) = XF_1; BLM(12, 0, 4) = -BVS_XY * BVS_Z * XS; // Y 3 -2 BLM(12, 1, 3) = BVS_XZ * XP; BLM(12, 1, 4) = BVS_XY * XP; BLM(12, 1, 5) = BVS_YZ * XP; BLM(12, 2, 2) = -BVS_Z * XD; BLM(12, 2, 3) = -BVS_X * XD; BLM(12, 2, 5) = -BVS_Y * XD; BLM(12, 3, 2) = XF_m2; BLM(13, 0, 4) = (BVS_YY - BVS_XX) * BVS_Z * XS; // Y 32 BLM(13, 1, 3) = -2. * BVS_YZ * XP; BLM(13, 1, 4) = (BVS_XX - BVS_YY) * XP; BLM(13, 1, 5) = 2. * BVS_XZ * XP; BLM(13, 2, 3) = 2. * BVS_Y * XD; BLM(13, 2, 5) = -2. * BVS_X * XD; BLM(13, 2, 6) = -BVS_Z * XD_p2; BLM(13, 3, 6) = XF_p2; BLM(14, 0, 4) = (BVS_YY - 3. * BVS_XX) * BVS_Y * XS; // Y 3 -3 BLM(14, 1, 3) = 3. * (BVS_XX - BVS_YY) * XP; BLM(14, 1, 5) = 6. * BVS_XY * XP; BLM(14, 2, 2) = -6. * BVS_X * XD; BLM(14, 2, 6) = -3. * BVS_Y * XD_p2; BLM(14, 3, 1) = XF_3; BLM(15, 0, 4) = (3. * BVS_YY - BVS_XX) * BVS_X * XS; // Y 33 BLM(15, 1, 3) = -6. * BVS_XY * XP; BLM(15, 1, 5) = 3. * (BVS_XX - BVS_YY) * XP; BLM(15, 2, 2) = 6. * BVS_Y * XD; BLM(15, 2, 6) = -3. * BVS_X * XD_p2; BLM(15, 3, 7) = XF_3; } if (lmax_dft > 3) { double XG_0 = 16. * SQPI / 3.; double XG_1 = 4. * SQ2PI / (3. * SQ5); double XG_m2 = 4. * SQPI / (3. * SQ5); double XG_p2 = 2. * XG_m2; double XG_3 = 4. * SQ2PI / (3. * SQ5 * SQ7); double XG_m4 = 4. * SQPI / (3. * SQ5 * SQ7); double XG_p4 = 4. * XG_m4; BLM(16, 0, 4) = (35. * BVS_ZZ - 30. * BVS_ZZ * BVS_RR + 3. * BVS_RR * BVS_RR) * XS; // Y 40 BLM(16, 1, 3) = 12. * (5. * BVS_ZZ - BVS_RR) * BVS_Y * XP; BLM(16, 1, 4) = 16. * (3. * BVS_RR - 5. * BVS_ZZ) * BVS_Z * XP; BLM(16, 1, 5) = 12. * (5. * BVS_ZZ - BVS_RR) * BVS_X * XP; BLM(16, 2, 2) = -24. * BVS_XY * XD; BLM(16, 2, 3) = -96. * BVS_YZ * XD; BLM(16, 2, 4) = 12. * (3. * BVS_ZZ - BVS_RR) * XD_0; BLM(16, 2, 5) = -96. * BVS_XZ * XD; BLM(16, 2, 6) = 6. * (BVS_XX - BVS_YY) * XD_p2; BLM(16, 3, 3) = 12. * BVS_Y * XF_1; BLM(16, 3, 4) = -16. * BVS_Z * XF_0; BLM(16, 3, 5) = 12. * BVS_X * XF_1; BLM(16, 4, 4) = XG_0; BLM(17, 0, 4) = (7. * BVS_ZZ - 3. * BVS_RR) * BVS_YZ * XS; // Y 4 -1 BLM(17, 1, 3) = (3. * BVS_XX + 9. * BVS_YY - 4. * BVS_ZZ) * BVS_Z * XP; BLM(17, 1, 4) = 3. * (BVS_RR - 5. * BVS_ZZ) * BVS_Y * XP; BLM(17, 1, 5) = 6. * BVS_XY * BVS_Z * XP; BLM(17, 2, 2) = -6. * BVS_XZ * XD; BLM(17, 2, 3) = 3. * (4. * BVS_ZZ - BVS_XX - 3. * BVS_YY) * XD; BLM(17, 2, 4) = 6. * BVS_YZ * XD_0; BLM(17, 2, 5) = -6. * BVS_XY * XD; BLM(17, 2, 6) = 3. * BVS_YZ * XD_p2; BLM(17, 3, 2) = 6. * BVS_X * XF_m2; BLM(17, 3, 3) = -3. * BVS_Z * XF_1; BLM(17, 3, 4) = -2. * BVS_Y * XF_0; BLM(17, 3, 6) = -3. * BVS_Y * XF_p2; BLM(17, 4, 3) = XG_1; BLM(18, 0, 4) = (7. * BVS_ZZ - 3. * BVS_RR) * BVS_XZ * XS; // Y 41 BLM(18, 1, 3) = 6. * BVS_XY * BVS_Z * XP; BLM(18, 1, 4) = 3. * (BVS_RR - 5. * BVS_ZZ) * BVS_Y * XP; BLM(18, 1, 5) = (9. * BVS_XX + 3. * BVS_YY - 4. * BVS_ZZ) * BVS_Z * XP; BLM(18, 2, 2) = -6. * BVS_YZ * XD; BLM(18, 2, 3) = -6. * BVS_XY * XD; BLM(18, 2, 4) = 6. * BVS_XZ * XD_0; BLM(18, 2, 5) = 3. * (4. * BVS_ZZ - 3. * BVS_XX - BVS_YY) * XD; BLM(18, 2, 6) = -3. * BVS_XZ * XD_p2; BLM(18, 3, 2) = 6. * BVS_Y * XF_m2; BLM(18, 3, 4) = -2. * BVS_X * XF_0; BLM(18, 3, 5) = -3. * BVS_Z * XF_1; BLM(18, 3, 6) = 3. * BVS_X * XF_p2; BLM(18, 4, 5) = XG_1; BLM(19, 0, 4) = (7. * BVS_ZZ - BVS_RR) * BVS_XY * XS; // Y 4 -2 BLM(19, 1, 3) = (BVS_XX + 3. * BVS_YY - 6. * BVS_ZZ) * BVS_X * XP; BLM(19, 1, 4) = -12. * BVS_XY * BVS_Z * XP; BLM(19, 1, 5) = (3. * BVS_XX + BVS_YY - 6. * BVS_ZZ) * BVS_Y * XP; BLM(19, 2, 2) = 3. * (3. * BVS_ZZ - BVS_RR) * XD; BLM(19, 2, 3) = 12. * BVS_XZ * XD; BLM(19, 2, 4) = 3. * BVS_XY * XD_0; BLM(19, 2, 5) = 12. * BVS_YZ * XD; BLM(19, 3, 1) = .5 * BVS_X * XF_3; BLM(19, 3, 2) = -12. * BVS_Z * XF_m2; BLM(19, 3, 3) = -1.5 * BVS_X * XF_1; BLM(19, 3, 5) = -1.5 * BVS_Y * XF_1; BLM(19, 3, 7) = -.5 * BVS_Y * XF_3; BLM(19, 4, 2) = XG_m2; BLM(20, 0, 4) = (7. * BVS_ZZ - BVS_RR) * (BVS_XX - BVS_YY) * XS; // Y 42 BLM(20, 1, 3) = 4. * (3. * BVS_ZZ - BVS_YY) * BVS_Y * XP; BLM(20, 1, 4) = 12. * (BVS_YY - BVS_XX) * BVS_Z * XP; BLM(20, 1, 5) = 4. * (BVS_XX - 3. * BVS_ZZ) * BVS_X * XP; BLM(20, 2, 3) = -24. * BVS_YZ * XD; BLM(20, 2, 4) = 3. * (BVS_XX - BVS_YY) * XD_0; BLM(20, 2, 5) = 24. * BVS_XZ * XD; BLM(20, 2, 6) = 3. * (3. * BVS_ZZ - BVS_RR) * XD_p2; BLM(20, 3, 1) = BVS_Y * XF_3; BLM(20, 3, 3) = 3. * BVS_Y * XF_1; BLM(20, 3, 5) = -3. * BVS_X * XF_1; BLM(20, 3, 6) = -12. * BVS_Z * XF_m2; BLM(20, 3, 7) = BVS_X * XF_3; BLM(20, 4, 6) = XG_p2; BLM(21, 0, 4) = (3. * BVS_XX - BVS_YY) * BVS_YZ * XS; // Y 4 -3 BLM(21, 1, 3) = 3. * (BVS_YY - BVS_XX) * BVS_Z * XP; BLM(21, 1, 4) = (BVS_YY - 3. * BVS_XX) * BVS_Y * XP; BLM(21, 1, 5) = -6. * BVS_XY * BVS_Z * XP; BLM(21, 2, 2) = 6. * BVS_XZ * XD; BLM(21, 2, 3) = 3. * (BVS_XX - BVS_YY) * XD; BLM(21, 2, 5) = 6. * BVS_XY * XD; BLM(21, 2, 6) = 3. * BVS_YZ * XD_p2; BLM(21, 3, 1) = -BVS_Z * XF_3; BLM(21, 3, 2) = -6. * BVS_X * XF_m2; BLM(21, 3, 6) = -3. * BVS_Y * XF_p2; BLM(21, 4, 1) = XG_3; BLM(22, 0, 4) = (BVS_XX - 3. * BVS_YY) * BVS_XZ * XS; // Y 43 BLM(22, 1, 3) = 6. * BVS_XY * BVS_Z * XP; BLM(22, 1, 4) = (3. * BVS_YY - BVS_XX) * BVS_X * XP; BLM(22, 1, 5) = 3. * (BVS_YY - BVS_XX) * BVS_Z * XP; BLM(22, 2, 2) = -6. * BVS_YZ * XD; BLM(22, 2, 3) = -6. * BVS_XY * XD; BLM(22, 2, 5) = 3. * (BVS_XX - BVS_YY) * XD; BLM(22, 2, 6) = 3. * BVS_XZ * XD_p2; BLM(22, 3, 2) = 6. * BVS_Y * XF_m2; BLM(22, 3, 6) = -3. * BVS_X * XF_p2; BLM(22, 3, 7) = -BVS_Z * XF_3; BLM(22, 4, 7) = XG_3; BLM(23, 0, 4) = (BVS_XX - BVS_YY) * BVS_XY * XS; // Y 4 -4 BLM(23, 1, 3) = (3. * BVS_YY - BVS_XX) * BVS_X * XP; BLM(23, 1, 5) = (BVS_YY - 3. * BVS_XX) * BVS_Y * XP; BLM(23, 2, 2) = 3. * (BVS_XX - BVS_YY) * XD; BLM(23, 2, 6) = 3. * BVS_XY * XD_p2; BLM(23, 3, 1) = -BVS_X * XF_3; BLM(23, 3, 7) = -BVS_Y * XF_3; BLM(23, 4, 0) = XG_m4; BLM(24, 0, 4) = (BVS_XX * BVS_XX + BVS_YY * BVS_YY - 6. * BVS_XX * BVS_YY) * XS; // Y 4 4 BLM(24, 1, 3) = 4. * (3. * BVS_XX - BVS_YY) * BVS_Y * XP; BLM(24, 1, 5) = 4. * (3. * BVS_YY - BVS_XX) * BVS_X * XP; BLM(24, 2, 2) = -24. * BVS_XY * XD; BLM(24, 2, 6) = 6. * (BVS_XX - BVS_YY) * XD_p2; BLM(24, 3, 1) = 4. * BVS_Y * XF_3; BLM(24, 3, 7) = -4. * BVS_X * XF_3; BLM(24, 4, 8) = XG_p4; } double SXY = sqrt(BVS_XX + BVS_YY); // SXY = r * sin(theta) double SXYZ = sqrt(BVS_RR); // SXYZ = r double CP = 1.0; double SP = 0.0; if (SXY > 1.e-4) { CP = BVS_X / SXY; // CP = cos(phi) SP = BVS_Y / SXY; // SP = sin(phi) } if (SXYZ > 1.e-4) { double CT = BVS_Z / SXYZ; // CT = cos(theta) double ST = SXY / SXYZ; // ST = sin(theta) C(0, 4, 4) = 1.0; // 2*SQ(pi) * (Y 00) if (lmax_dft_ecp > 0) { C(1, 3, 4) = ST * SP; // 2*SQ(pi/3) * (Y 1-1) C(1, 4, 4) = CT; // 2*SQ(pi/3) * (Y 10) C(1, 5, 4) = ST * CP; // 2*SQ(pi/3) * (Y 11) Definition // of (Z lm) : if (lmin_dft_ecp > 0) { C(1, 3, 3) = CP; // 2*SQ(pi/3) * (Z 1-1) (Z lm) := ( // 1 / sin(theta) ) * ( d (Y lm) / d phi ) C(1, 3, 5) = CT * SP; // 2*SQ(pi/3) * (Y 1-1)' C(1, 4, 3) = 0.0; C(1, 4, 5) = -ST; // 2*SQ(pi/3) * (Y 10)' Differentiation with respect // to theta is denoted by an apostrophe: C(1, 5, 3) = -SP; // 2*SQ(pi/3) * (Z 11) C(1, 5, 5) = CT * CP; // 2*SQ(pi/3) * (Y 11)' f' := d // f / d theta } } if (lmax_dft_ecp > 1) { C(2, 2, 4) = SQ3 * ST * ST * CP * SP; // 2*SQ(pi/5) * (Y 2-2) C(2, 3, 4) = SQ3 * CT * ST * SP; // 2*SQ(pi/5) * (Y 2-1) C(2, 4, 4) = 1.5 * CT * CT - 0.5; // 2*SQ(pi/5) * (Y 20) C(2, 5, 4) = SQ3 * CT * ST * CP; // 2*SQ(pi/5) * (Y 21) C(2, 6, 4) = SQ3 * ST * ST * (CP * CP - .5); // 2*SQ(pi/5) * (Y 22) if (lmin_dft_ecp > 0) { C(2, 2, 3) = ST * (2.0 * CP * CP - 1.0); // 2*SQ(pi/15) * (Z 2-2) C(2, 2, 5) = 2.0 * CT * ST * CP * SP; // 2*SQ(pi/15) * (Y 2-2)' C(2, 3, 3) = CT * CP; // 2*SQ(pi/15) * (Z 2-1) C(2, 3, 5) = (2.0 * CT * CT - 1.0) * SP; // 2*SQ(pi/15) * (Y 2-1)' C(2, 4, 3) = 0.0; C(2, 4, 5) = -SQ3 * CT * ST; // 2*SQ(pi/15) * (Y 20)' C(2, 5, 3) = -CT * SP; // 2*SQ(pi/15) * (Z 21) C(2, 5, 5) = (2.0 * CT * CT - 1.0) * CP; // 2*SQ(pi/15) * (Y 21)' C(2, 6, 3) = -2.0 * ST * CP * SP; // 2*SQ(pi/15) * (Z 22) C(2, 6, 5) = CT * ST * (2.0 * CP * CP - 1.); // 2*SQ(pi/15) * (Y 22)' } if (lmin_dft_ecp > 1) { C(2, 2, 2) = CT * (2.0 * CP * CP - 1.0); // 2*SQ(pi/15) * (Z 2-2)' C(2, 2, 6) = (1.0 + CT * CT) * CP * SP; // 2*SQ(pi/15) * ( (Y 2-2)'' + 3*(Y 2-2) ) C(2, 3, 2) = -ST * CP; // 2*SQ(pi/15) * (Z 2-1)' C(2, 3, 6) = -CT * ST * SP; // 2*SQ(pi/15) * ( (Y 2-1)'' + 3*(Y 2-1) ) C(2, 4, 2) = 0.0; C(2, 4, 6) = .5 * SQ3 * ST * ST; // 2*SQ(pi/15) * ( (Y 20)'' + 3*(Y 20) ) C(2, 5, 2) = ST * SP; // 2*SQ(pi/15) * (Z 21)' C(2, 5, 6) = -CT * ST * CP; // 2*SQ(pi/15) * ( (Y 21)'' + 3*(Y 21) ) C(2, 6, 2) = -2.0 * CT * CP * SP; // 2*SQ(pi/15) * (Z 22)' C(2, 6, 6) = (1. + CT * CT) * (CP * CP - .5); // 2*SQ(pi/15) * ( (Y 22)'' + 3*(Y 22) ) } } if (lmax_dft_ecp > 2) { double f_phi, df_dphi; f_phi = (4. * CP * CP - 1.) * SP; // sin(3*phi) C(3, 1, 4) = (.5 * SQ5 / SQ2) * ST * ST * ST * f_phi; // 2*SQ(pi/7) * (Y 3-3) if (lmin_dft_ecp > 0) { df_dphi = 3. * (1. - 4. * SP * SP) * CP; C(3, 1, 3) = (.25 * SQ5 / SQ3) * ST * ST * df_dphi; // SQ((2*pi)/21) * (Z 3-3) C(3, 1, 5) = (.25 * SQ5 / SQ3) * 3. * ST * ST * CT * f_phi; // SQ((2*pi)/21) * (Y 3-3)' } if (lmin_dft_ecp > 1) { C(3, 1, 2) = (.5 / (SQ2 * SQ3)) * 2. * ST * CT * df_dphi; // 2*SQ(pi/105) * (Z 3-3)' C(3, 1, 6) = (.5 / (SQ2 * SQ3)) * 3. * (1. + CT * CT) * ST * f_phi; // 2*SQ(pi/105) * ( (Y 3-3)'' + 6*(Y 3-3) ) } if (lmin_dft_ecp > 2) { C(3, 1, 1) = (1. / 6.) * (.5 + 1.5 * CT * CT) * df_dphi; // (2/3)*SQ((2*pi)/35) * ( (5/2)*(Z 3-3) + (Z 3-3)'' ) C(3, 1, 7) = (1. / 6.) * 1.5 * (3. + CT * CT) * CT * f_phi; // (2/3)*SQ((2*pi)/35) * ( (5/2)*(Y 3-3)' + ( (Y // 3-3)'' + 6*(Y 3-3) )' ) } f_phi = CP * SP; // (1/2)*sin(2*phi) C(3, 2, 4) = (SQ3 * SQ5) * ST * ST * CT * f_phi; // 2*SQ(pi/7) * (Y 3-2) if (lmin_dft_ecp > 0) { df_dphi = 1. - 2. * SP * SP; C(3, 2, 3) = (SQ5 / SQ2) * ST * CT * df_dphi; // SQ((2*pi)/21) * (Z 3-2) C(3, 2, 5) = (SQ5 / SQ2) * (3. * CT * CT - 1.) * ST * f_phi; // SQ((2*pi)/21) * (Y 3-2)' } if (lmin_dft_ecp > 1) { C(3, 2, 2) = (1. - 2. * ST * ST) * df_dphi; // 2*SQ(pi/105) * (Z 3-2)' C(3, 2, 6) = (3. * CT * CT - 1.) * CT * f_phi; // 2*SQ(pi/105) * ( (Y 3-2)'' + 6*(Y 3-2) ) } if (lmin_dft_ecp > 2) { C(3, 2, 1) = (SQ2 / SQ3) * (-1.5) * ST * CT * df_dphi; // (2/3)*SQ((2*pi)/35) * ( (5/2)*(Z 3-2) + (Z 3-2)'' ) C(3, 2, 7) = (SQ2 / SQ3) * (-1.5) * (1. + CT * CT) * ST * f_phi; // (2/3)*SQ((2*pi)/35) * ( (5/2)*(Y 3-2)' + ( (Y // 3-2)'' + 6*(Y 3-2) )' ) } f_phi = SP; C(3, 3, 4) = (.5 * SQ3 / SQ2) * (5. * CT * CT - 1.) * ST * f_phi; // 2*SQ(pi/7) * (Y 3-1) if (lmin_dft_ecp > 0) { df_dphi = CP; C(3, 3, 3) = .25 * (5. * CT * CT - 1.) * df_dphi; // SQ((2*pi)/21) * (Z 3-1) C(3, 3, 5) = .25 * (4. - 15. * ST * ST) * CT * f_phi; // SQ((2*pi)/21) * (Y 3-1)' } if (lmin_dft_ecp > 1) { C(3, 3, 2) = (.5 / (SQ2 * SQ5)) * (-10.) * ST * CT * df_dphi; // 2*SQ(pi/105) * (Z 3-1)' C(3, 3, 6) = (.5 / (SQ2 * SQ5)) * (5. - 15. * CT * CT) * ST * f_phi; // 2*SQ(pi/105) * ( (Y 3-1)'' + 6*(Y 3-1) ) } if (lmin_dft_ecp > 2) { C(3, 3, 1) = (.5 / (SQ3 * SQ5)) * 7.5 * ST * ST * df_dphi; // (2/3)*SQ((2*pi)/35) * ( (5/2)*(Z 3-1) + (Z 3-1)'' ) C(3, 3, 7) = (.5 / (SQ3 * SQ5)) * 7.5 * ST * ST * CT * f_phi; // (2/3)*SQ((2*pi)/35) * ( (5/2)*(Y 3-1)' + ( (Y // 3-1)'' + 6*(Y 3-1) )' ) } C(3, 4, 4) = .5 * (5. * CT * CT - 3.) * CT; // 2*SQ(pi/7) * (Y 30) if (lmin_dft_ecp > 0) { C(3, 4, 3) = 0.; C(3, 4, 5) = (.5 / (SQ2 * SQ3)) * (3. - 15. * CT * CT) * ST; // SQ((2*pi)/21) * (Y 30)' } if (lmin_dft_ecp > 1) { C(3, 4, 2) = 0.; C(3, 4, 6) = (.5 / (SQ3 * SQ5)) * 15. * ST * ST * CT; // 2*SQ(pi/105) * ( (Y 30)'' + 6*(Y 30) ) } if (lmin_dft_ecp > 2) { C(3, 4, 1) = 0.; C(3, 4, 7) = (SQ2 / (6. * SQ5)) * (-7.5) * ST * ST * ST; // (2/3)*SQ((2*pi)/35) * ( (5/2)*(Y 30)' + ( (Y 30)'' // + 6*(Y 30) )' ) } f_phi = CP; C(3, 5, 4) = (.5 * SQ3 / SQ2) * (5. * CT * CT - 1.) * ST * f_phi; // 2*SQ(pi/7) * (Y 31) if (lmin_dft_ecp > 0) { df_dphi = -SP; C(3, 5, 3) = .25 * (5. * CT * CT - 1.) * df_dphi; // SQ((2*pi)/21) * (Z 31) C(3, 5, 5) = .25 * (4. - 15. * ST * ST) * CT * f_phi; // SQ((2*pi)/21) * (Y 31)' } if (lmin_dft_ecp > 1) { C(3, 5, 2) = (.5 / (SQ2 * SQ5)) * (-10.) * ST * CT * df_dphi; // 2*SQ(pi/105) * (Z 31)' C(3, 5, 6) = (.5 / (SQ2 * SQ5)) * (5. - 15. * CT * CT) * ST * f_phi; // 2*SQ(pi/105) * ( (Y 31)'' + 6*(Y 31) ) } if (lmin_dft_ecp > 2) { C(3, 5, 1) = (.5 / (SQ3 * SQ5)) * 7.5 * ST * ST * df_dphi; // (2/3)*SQ((2*pi)/35) * ( (5/2)*(Z 31) + (Z 31)'' ) C(3, 5, 7) = (.5 / (SQ3 * SQ5)) * 7.5 * ST * ST * CT * f_phi; // (2/3)*SQ((2*pi)/35) * ( (5/2)*(Y 31)' + ( (Y // 31)'' + 6*(Y 31) )' ) } f_phi = 1. - 2. * SP * SP; // cos(2*phi) C(3, 6, 4) = (.5 * SQ3 * SQ5) * ST * ST * CT * f_phi; // 2*SQ(pi/7) * (Y 32) if (lmin_dft_ecp > 0) { df_dphi = -4. * CP * SP; C(3, 6, 3) = (.5 * SQ5 / SQ2) * ST * CT * df_dphi; // SQ((2*pi)/21) * (Z 32) C(3, 6, 5) = (.5 * SQ5 / SQ2) * (3. * CT * CT - 1.) * ST * f_phi; // SQ((2*pi)/21) * (Y 32)' } if (lmin_dft_ecp > 1) { C(3, 6, 2) = .5 * (1. - 2. * ST * ST) * df_dphi; // 2*SQ(pi/105) * (Z 32)' C(3, 6, 6) = .5 * (3. * CT * CT - 1.) * CT * f_phi; // 2*SQ(pi/105) * ( (Y 32)'' + 6*(Y 32) ) } if (lmin_dft_ecp > 2) { C(3, 6, 1) = (1. / (SQ2 * SQ3)) * (-1.5) * ST * CT * df_dphi; // (2/3)*SQ((2*pi)/35) * ( (5/2)*(Z 32) + (Z 32)'' ) C(3, 6, 7) = (1. / (SQ2 * SQ3)) * (-1.5) * (1. + CT * CT) * ST * f_phi; // (2/3)*SQ((2*pi)/35) * ( (5/2)*(Y 32)' + ( (Y // 32)'' + 6*(Y 32) )' ) } f_phi = (1. - 4. * SP * SP) * CP; // cos(3*phi) C(3, 7, 4) = (.5 * SQ5 / SQ2) * ST * ST * ST * f_phi; // 2*SQ(pi/7) * (Y 33) if (lmin_dft_ecp > 0) { df_dphi = 3. * (1. - 4. * CP * CP) * SP; C(3, 7, 3) = (.25 * SQ5 / SQ3) * ST * ST * df_dphi; // SQ((2*pi)/21) * (Z 33) C(3, 7, 5) = (.25 * SQ5 / SQ3) * 3. * ST * ST * CT * f_phi; // SQ((2*pi)/21) * (Y 33)' } if (lmin_dft_ecp > 1) { C(3, 7, 2) = (.5 / (SQ2 * SQ3)) * 2. * ST * CT * df_dphi; // 2*SQ(pi/105) * (Z 33)' C(3, 7, 6) = (.5 / (SQ2 * SQ3)) * 3. * (1. + CT * CT) * ST * f_phi; // 2*SQ(pi/105) * ( (Y 33)'' + 6*(Y 33) ) } if (lmin_dft_ecp > 2) { C(3, 7, 1) = (1. / 6.) * (.5 + 1.5 * CT * CT) * df_dphi; // (2/3)*SQ((2*pi)/35) * ( (5/2)*(Z 33) + (Z 33)'' ) C(3, 7, 7) = (1. / 6.) * 1.5 * (3. + CT * CT) * CT * f_phi; // (2/3)*SQ((2*pi)/35) * ( (5/2)*(Y 33)' + ( (Y // 33)'' + 6*(Y 33) )' ) } } if (lmax_dft_ecp > 3) { double S2T = ST * ST; double C2T = CT * CT; double C2P = CP * CP; double S2P = SP * SP; double f_phi, df_dphi; f_phi = CP * SP * (C2P - S2P); // (1/4)*sin(4*phi) C(4, 0, 4) = (.5 * SQ5 * SQ7) * S2T * S2T * f_phi; // (2/3)*SQ(pi) * (Y 4-4) if (lmin_dft_ecp > 0) { df_dphi = (C2P - S2P) * (C2P - S2P) - 4. * C2P * S2P; C(4, 0, 3) = (1. / (SQ2 * SQ5)) * (.5 * SQ5 * SQ7) * S2T * ST * df_dphi; // (1/3)*SQ((2*pi)/5) * (Z 4-4) C(4, 0, 5) = (1. / (SQ2 * SQ5)) * (.5 * SQ5 * SQ7) * 4. * S2T * ST * CT * f_phi; // (1/3)*SQ((2*pi)/5) * (Y 4-4)' } if (lmin_dft_ecp > 1) { C(4, 0, 2) = (1. / (3. * SQ5)) * (.5 * SQ5 * SQ7) * 3. * S2T * CT * df_dphi; // (2/9)*SQ(pi/5) * (Z 4-4)' C(4, 0, 6) = (1. / (3. * SQ5)) * (.5 * SQ5 * SQ7) * 6. * (C2T + 1.) * S2T * f_phi; // (2/9)*SQ(pi/5) * ( (Y 4-4)'' + 10*(Y 4-4) ) } if (lmin_dft_ecp > 2) { C(4, 0, 1) = (SQ2 / (3. * SQ5 * SQ7)) * (.5 * SQ5 * SQ7) * (4.5 * C2T + 1.5) * ST * df_dphi; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Z 4-4) + (Z 4-4)'' ) C(4, 0, 7) = (SQ2 / (3. * SQ5 * SQ7)) * (.5 * SQ5 * SQ7) * 6. * (C2T + 3.) * ST * CT * f_phi; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Y 4-4)' + ( (Y // 4-4)'' + 10*(Y 4-4) )' ) } f_phi = (4. * C2P - 1.) * SP; // sin(3*phi) C(4, 1, 4) = (.5 * SQ5 * SQ7 / SQ2) * S2T * ST * CT * f_phi; // (2/3)*SQ(pi) * (Y 4-3) if (lmin_dft_ecp > 0) { df_dphi = 3. * (1. - 4. * SP * SP) * CP; C(4, 1, 3) = (1. / (SQ2 * SQ5)) * (.5 * SQ5 * SQ7 / SQ2) * S2T * CT * df_dphi; // (1/3)*SQ((2*pi)/5) * (Z 4-3) C(4, 1, 5) = (1. / (SQ2 * SQ5)) * (.5 * SQ5 * SQ7 / SQ2) * (4. * C2T - 1.) * S2T * f_phi; // (1/3)*SQ((2*pi)/5) * (Y 4-3)' } if (lmin_dft_ecp > 1) { C(4, 1, 2) = (1. / (3. * SQ5)) * (.5 * SQ5 * SQ7 / SQ2) * (3. * C2T - 1.) * ST * df_dphi; // (2/9)*SQ(pi/5) * (Z 4-3)' C(4, 1, 6) = (1. / (3. * SQ5)) * (.5 * SQ5 * SQ7 / SQ2) * 6. * C2T * CT * ST * f_phi; // (2/9)*SQ(pi/5) * ( (Y 4-3)'' + 10*(Y 4-3) ) } if (lmin_dft_ecp > 2) { C(4, 1, 1) = (SQ2 / (3. * SQ5 * SQ7)) * (.5 * SQ5 * SQ7 / SQ2) * (2. - 4.5 * S2T) * CT * df_dphi; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Z 4-3) + (Z 4-3)'' ) C(4, 1, 7) = (SQ2 / (3. * SQ5 * SQ7)) * (.5 * SQ5 * SQ7 / SQ2) * (6. * C2T * C2T - 4.5 * S2T) * f_phi; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Y 4-3)' + ( (Y // 4-3)'' + 10*(Y 4-3) )' ) } f_phi = CP * SP; // (1/2)*sin(2*phi) C(4, 2, 4) = (.5 * SQ5) * (7. * C2T - 1.) * S2T * f_phi; // (2/3)*SQ(pi) * (Y 4-2) if (lmin_dft_ecp > 0) { df_dphi = 1. - 2. * SP * SP; C(4, 2, 3) = (1. / (SQ2 * SQ5)) * (.5 * SQ5) * (7. * C2T - 1.) * ST * df_dphi; // (1/3)*SQ((2*pi)/5) * (Z 4-2) C(4, 2, 5) = (1. / (SQ2 * SQ5)) * (.5 * SQ5) * (14. * (C2T - S2T) - 2.) * ST * CT * f_phi; // (1/3)*SQ((2*pi)/5) * (Y 4-2)' } if (lmin_dft_ecp > 1) { C(4, 2, 2) = (1. / (3. * SQ5)) * (.5 * SQ5) * (6. - 21. * S2T) * CT * df_dphi; // (2/9)*SQ(pi/5) * (Z 4-2)' C(4, 2, 6) = (1. / (3. * SQ5)) * (.5 * SQ5) * 6. * (1. + C2T - 7. * S2T * C2T) * f_phi; // (2/9)*SQ(pi/5) * ( (Y 4-2)'' + 10*(Y 4-2) ) } if (lmin_dft_ecp > 2) { C(4, 2, 1) = (SQ2 / (3. * SQ5 * SQ7)) * (.5 * SQ5) * 10.5 * (1. - 3. * C2T) * ST * df_dphi; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Z 4-2) + (Z 4-2)'' ) C(4, 2, 7) = (SQ2 / (3. * SQ5 * SQ7)) * (.5 * SQ5) * (-42.) * C2T * CT * ST * f_phi; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Y 4-2)' + ( // (Y 4-2)'' + 10*(Y 4-2) )' ) } f_phi = SP; C(4, 3, 4) = (.5 * SQ5 / SQ2) * (7. * C2T - 3.) * ST * CT * f_phi; // (2/3)*SQ(pi) * (Y 4-1) if (lmin_dft_ecp > 0) { df_dphi = CP; C(4, 3, 3) = (1. / (SQ2 * SQ5)) * (.5 * SQ5 / SQ2) * (7. * C2T - 3.) * CT * df_dphi; // (1/3)*SQ((2*pi)/5) * (Z 4-1) C(4, 3, 5) = (1. / (SQ2 * SQ5)) * (.5 * SQ5 / SQ2) * (3. + (1. - 28. * S2T) * C2T) * f_phi; // (1/3)*SQ((2*pi)/5) * (Y 4-1)' } if (lmin_dft_ecp > 1) { C(4, 3, 2) = (1. / (3. * SQ5)) * (.5 * SQ5 / SQ2) * 3. * (1. - 7. * C2T) * ST * df_dphi; // (2/9)*SQ(pi/5) * (Z 4-1)' C(4, 3, 6) = (1. / (3. * SQ5)) * (.5 * SQ5 / SQ2) * 6. * (7. * S2T - 3.) * ST * CT * f_phi; // (2/9)*SQ(pi/5) * ( (Y 4-1)'' + 10*(Y 4-1) ) } if (lmin_dft_ecp > 2) { C(4, 3, 1) = (SQ2 / (3. * SQ5 * SQ7)) * (.5 * SQ5 / SQ2) * .5 * 63. * S2T * CT * df_dphi; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Z 4-1) + (Z 4-1)'' ) C(4, 3, 7) = (SQ2 / (3. * SQ5 * SQ7)) * (.5 * SQ5 / SQ2) * 21. * (1.5 - 2. * S2T) * S2T * f_phi; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Y 4-1)' + ( (Y // 4-1)'' + 10*(Y 4-1) )' ) } C(4, 4, 4) = .125 * ((35. * C2T - 30.) * C2T + 3.); // (2/3)*SQ(pi) * (Y 40) if (lmin_dft_ecp > 0) { C(4, 4, 3) = 0.; C(4, 4, 5) = (1. / (SQ2 * SQ5)) * .125 * 20. * (3. - 7. * C2T) * CT * ST; // (1/3)*SQ((2*pi)/5) * (Y 40)' } if (lmin_dft_ecp > 1) { C(4, 4, 2) = 0.; C(4, 4, 6) = (1. / (3. * SQ5)) * .125 * 30. * (7. * C2T - 1.) * S2T; // (2/9)*SQ(pi/5) * ( (Y 40)'' + 10*(Y 40) ) } if (lmin_dft_ecp > 2) { C(4, 4, 1) = 0.; C(4, 4, 7) = (SQ2 / (3. * SQ5 * SQ7)) * .125 * (-210.) * S2T * ST * CT; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Y 40)' + ( (Y 40)'' // + 10*(Y 40) )' ) } f_phi = CP; C(4, 5, 4) = (.5 * SQ5 / SQ2) * (7. * C2T - 3.) * ST * CT * f_phi; // (2/3)*SQ(pi) * (Y 41) if (lmin_dft_ecp > 0) { df_dphi = -SP; C(4, 5, 3) = (1. / (SQ2 * SQ5)) * (.5 * SQ5 / SQ2) * (7. * C2T - 3.) * CT * df_dphi; // (1/3)*SQ((2*pi)/5) * (Z 41) C(4, 5, 5) = (1. / (SQ2 * SQ5)) * (.5 * SQ5 / SQ2) * (3. + (1. - 28. * S2T) * C2T) * f_phi; // (1/3)*SQ((2*pi)/5) * (Y 41)' } if (lmin_dft_ecp > 1) { C(4, 5, 2) = (1. / (3. * SQ5)) * (.5 * SQ5 / SQ2) * 3. * (1. - 7. * C2T) * ST * df_dphi; // (2/9)*SQ(pi/5) * (Z 41)' C(4, 5, 6) = (1. / (3. * SQ5)) * (.5 * SQ5 / SQ2) * 6. * (7. * S2T - 3.) * ST * CT * f_phi; // (2/9)*SQ(pi/5) * ( (Y 41)'' + 10*(Y 41) ) } if (lmin_dft_ecp > 2) { C(4, 5, 1) = (SQ2 / (3. * SQ5 * SQ7)) * (.5 * SQ5 / SQ2) * .5 * 63. * S2T * CT * df_dphi; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Z 41) + (Z 41)'' ) C(4, 5, 7) = (SQ2 / (3. * SQ5 * SQ7)) * (.5 * SQ5 / SQ2) * 21. * (1.5 - 2. * S2T) * S2T * f_phi; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Y 41)' + ( (Y // 41)'' + 10*(Y 41) )' ) } f_phi = C2P - S2P; // cos(2*phi) C(4, 6, 4) = (.25 * SQ5) * (7. * C2T - 1.) * S2T * f_phi; // (2/3)*SQ(pi) * (Y 42) if (lmin_dft_ecp > 0) { df_dphi = -4. * CP * SP; C(4, 6, 3) = (1. / (SQ2 * SQ5)) * (.25 * SQ5) * (7. * C2T - 1.) * ST * df_dphi; // (1/3)*SQ((2*pi)/5) * (Z 42) C(4, 6, 5) = (1. / (SQ2 * SQ5)) * (.25 * SQ5) * (14. * (C2T - S2T) - 2.) * ST * CT * f_phi; // (1/3)*SQ((2*pi)/5) * (Y 42)' } if (lmin_dft_ecp > 1) { C(4, 6, 2) = (1. / (3. * SQ5)) * (.25 * SQ5) * (6. - 21. * S2T) * CT * df_dphi; // (2/9)*SQ(pi/5) * (Z 42)' C(4, 6, 6) = (1. / (3. * SQ5)) * (.25 * SQ5) * 6. * (1. + C2T - 7. * S2T * C2T) * f_phi; // (2/9)*SQ(pi/5) * ( (Y 42)'' + 10*(Y 42) ) } if (lmin_dft_ecp > 2) { C(4, 6, 1) = (SQ2 / (3. * SQ5 * SQ7)) * (.25 * SQ5) * 10.5 * (1. - 3. * C2T) * ST * df_dphi; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Z 42) + (Z 42)'' ) C(4, 6, 7) = (SQ2 / (3. * SQ5 * SQ7)) * (.25 * SQ5) * (-42.) * C2T * CT * ST * f_phi; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Y 42)' // + ( (Y 42)'' + 10*(Y 42) )' ) } f_phi = (1. - 4. * S2P) * CP; // cos(3*phi) C(4, 7, 4) = (.5 * SQ5 * SQ7 / SQ2) * S2T * ST * CT * f_phi; // (2/3)*SQ(pi) * (Y 43) if (lmin_dft_ecp > 0) { df_dphi = 3. * (1. - 4. * CP * CP) * SP; C(4, 7, 3) = (1. / (SQ2 * SQ5)) * (.5 * SQ5 * SQ7 / SQ2) * S2T * CT * df_dphi; // (1/3)*SQ((2*pi)/5) * (Z 43) C(4, 7, 5) = (1. / (SQ2 * SQ5)) * (.5 * SQ5 * SQ7 / SQ2) * (4. * C2T - 1.) * S2T * f_phi; // (1/3)*SQ((2*pi)/5) * (Y 43)' } if (lmin_dft_ecp > 1) { C(4, 7, 2) = (1. / (3. * SQ5)) * (.5 * SQ5 * SQ7 / SQ2) * (3. * C2T - 1.) * ST * df_dphi; // (2/9)*SQ(pi/5) * (Z 43)' C(4, 7, 6) = (1. / (3. * SQ5)) * (.5 * SQ5 * SQ7 / SQ2) * 6. * C2T * CT * ST * f_phi; // (2/9)*SQ(pi/5) * ( (Y 43)'' + 10*(Y 43) ) } if (lmin_dft_ecp > 2) { C(4, 7, 1) = (SQ2 / (3. * SQ5 * SQ7)) * (.5 * SQ5 * SQ7 / SQ2) * (2. - 4.5 * S2T) * CT * df_dphi; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Z 43) + (Z 43)'' ) C(4, 7, 7) = (SQ2 / (3. * SQ5 * SQ7)) * (.5 * SQ5 * SQ7 / SQ2) * (6. * C2T * C2T - 4.5 * S2T) * f_phi; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Y 43)' + ( (Y // 43)'' + 10*(Y 43) )' ) } f_phi = (C2P - S2P) * (C2P - S2P) - 4. * C2P * S2P; // cos(4*phi) C(4, 8, 4) = (.125 * SQ5 * SQ7) * S2T * S2T * f_phi; // (2/3)*SQ(pi) * (Y 44) if (lmin_dft_ecp > 0) { df_dphi = 16. * CP * SP * (S2P - C2P); C(4, 8, 3) = (1. / (SQ2 * SQ5)) * (.125 * SQ5 * SQ7) * S2T * ST * df_dphi; // (1/3)*SQ((2*pi)/5) * (Z 44) C(4, 8, 5) = (1. / (SQ2 * SQ5)) * (.125 * SQ5 * SQ7) * 4. * S2T * ST * CT * f_phi; // (1/3)*SQ((2*pi)/5) * (Y 44)' } if (lmin_dft_ecp > 1) { C(4, 8, 2) = (1. / (3. * SQ5)) * (.125 * SQ5 * SQ7) * 3. * S2T * CT * df_dphi; // (2/9)*SQ(pi/5) * (Z 44)' C(4, 8, 6) = (1. / (3. * SQ5)) * (.125 * SQ5 * SQ7) * 6. * (C2T + 1.) * S2T * f_phi; // (2/9)*SQ(pi/5) * ( (Y 44)'' + 10*(Y 44) ) } if (lmin_dft_ecp > 2) { C(4, 8, 1) = (SQ2 / (3. * SQ5 * SQ7)) * (.125 * SQ5 * SQ7) * (4.5 * C2T + 1.5) * ST * df_dphi; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Z 44) + (Z 44)'' ) C(4, 8, 7) = (SQ2 / (3. * SQ5 * SQ7)) * (.125 * SQ5 * SQ7) * 6. * (C2T + 3.) * ST * CT * f_phi; // (2/9)*SQ((2*pi)/35) * ( (9/2)*(Y 44)' + ( (Y // 44)'' + 10*(Y 44) )' ) } } for (Index I = 0; I < nsph; I++) { for (Index L = 0; L <= lmax_dft; L++) { for (Index M = 4 - L; M <= 4 + L; M++) { for (Index M1 = 4 - L; M1 <= 4 + L; M1++) { BLC(I, L, M) += BLM(I, L, M1) * C(L, M1, M); } } } } } else { for (Index L = 0; L <= lmax_dft_ecp; L++) { for (Index M = 4 - L; M <= 4 + L; M++) { C(L, M, M) = 1.; } } for (Index I = 0; I < nsph; I++) { for (Index L = 0; L <= lmax_dft; L++) { for (Index M = 4 - L; M <= 4 + L; M++) { BLC(I, L, M) = BLM(I, L, M); } } } } return; } // getBLMCOF } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/aomatrices/aomatrix.cc000066400000000000000000000242651412152066400210000ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "A_ol I_ol" BA_olI_ol, * WITHOUT WARRANTIE_ol OR CONDITION_ol OF ANY KIND, either express or implied. * _olee the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include "votca/xtp/make_libint_work.h" #include // Local VOTCA includes #include "votca/xtp/aomatrix.h" // include libint last otherwise it overrides eigen #include namespace votca { namespace xtp { template ::oper_params_type> std::array::nopers> computeOneBodyIntegrals(const AOBasis& aobasis, OperatorParams oparams = OperatorParams()) { Index nthreads = OPENMP::getMaxThreads(); std::vector shells = aobasis.GenerateLibintBasis(); std::vector> shellpair_list = aobasis.ComputeShellPairs(); Index nopers = static_cast(libint2::operator_traits::nopers); std::array::nopers> result; for (AOMatrix::MatrixLibInt& r : result) { r = AOMatrix::MatrixLibInt::Zero(aobasis.AOBasisSize(), aobasis.AOBasisSize()); } std::vector engines(nthreads); engines[0] = libint2::Engine(obtype, aobasis.getMaxNprim(), static_cast(aobasis.getMaxL()), 0); engines[0].set_params(oparams); for (Index i = 1; i < nthreads; ++i) { engines[i] = engines[0]; } std::vector shell2bf = aobasis.getMapToBasisFunctions(); #pragma omp parallel for schedule(dynamic) for (Index s1 = 0; s1 < aobasis.getNumofShells(); ++s1) { Index thread_id = OPENMP::getThreadId(); libint2::Engine& engine = engines[thread_id]; const libint2::Engine::target_ptr_vec& buf = engine.results(); Index bf1 = shell2bf[s1]; Index n1 = shells[s1].size(); for (Index s2 : shellpair_list[s1]) { engine.compute(shells[s1], shells[s2]); if (buf[0] == nullptr) { continue; // if all integrals screened out, skip to next shell set } Index bf2 = shell2bf[s2]; Index n2 = shells[s2].size(); for (unsigned int op = 0; op != nopers; ++op) { Eigen::Map buf_mat(buf[op], n1, n2); result[op].block(bf1, bf2, n1, n2) = buf_mat; if (s1 != s2) { // if s1 >= s2, copy {s1,s2} to the corresponding // {s2,s1} block, note the transpose! result[op].block(bf2, bf1, n2, n1) = buf_mat.transpose(); } } } } return result; } /*********************************** * KINETIC ***********************************/ void AOKinetic::Fill(const AOBasis& aobasis) { _aomatrix = computeOneBodyIntegrals(aobasis)[0]; } /*********************************** * OVERLAP ***********************************/ void AOOverlap::Fill(const AOBasis& aobasis) { _aomatrix = computeOneBodyIntegrals(aobasis)[0]; } Eigen::MatrixXd AOOverlap::singleShellOverlap(const AOShell& shell) const { libint2::Shell::do_enforce_unit_normalization(false); libint2::Operator obtype = libint2::Operator::overlap; try { libint2::Engine engine(obtype, shell.getSize(), static_cast(shell.getL()), 0); const libint2::Engine::target_ptr_vec& buf = engine.results(); libint2::Shell s = shell.LibintShell(); engine.compute(s, s); Eigen::Map buf_mat(buf[0], shell.getNumFunc(), shell.getNumFunc()); return buf_mat; } catch (const libint2::Engine::lmax_exceeded& error) { std::ostringstream oss; oss << "\nA libint error occured:\n" << error.what() << "\n" << "\nYou requested a computation for a shell with angular momentum " << error.lmax_requested() << ",\nbut your libint package only supports angular momenta upto " << error.lmax_limit() - 1 << ".\n" << "\nTo fix this error you will need to reinstall libint with " "support\n" "for higher angular momenta. If you installed your own libint it\n" "should be reconfigured and installed with the option " "--with-max-am=.\n" "If you installed libint with your OS package manager, you will\n" "need to setup you own libint installation with the \n" "--with-max-am= option set." << std::endl; throw std::runtime_error(oss.str()); } } Eigen::MatrixXd AOOverlap::Pseudo_InvSqrt(double etol) { Eigen::SelfAdjointEigenSolver es(_aomatrix); smallestEigenvalue = es.eigenvalues()(0); Eigen::VectorXd diagonal = Eigen::VectorXd::Zero(es.eigenvalues().size()); removedfunctions = 0; for (Index i = 0; i < diagonal.size(); ++i) { if (es.eigenvalues()(i) < etol) { removedfunctions++; } else { diagonal(i) = 1.0 / std::sqrt(es.eigenvalues()(i)); } } return es.eigenvectors() * diagonal.asDiagonal() * es.eigenvectors().transpose(); } Eigen::MatrixXd AOOverlap::Sqrt() { Eigen::SelfAdjointEigenSolver es(_aomatrix); smallestEigenvalue = es.eigenvalues()(0); return es.operatorSqrt(); } /*********************************** * COULOMB ***********************************/ void AOCoulomb::Fill(const AOBasis& aobasis) { computeCoulombIntegrals(aobasis); } void AOCoulomb::computeCoulombIntegrals(const AOBasis& aobasis) { Index nthreads = OPENMP::getMaxThreads(); std::vector shells = aobasis.GenerateLibintBasis(); std::vector shell2bf = aobasis.getMapToBasisFunctions(); Eigen::MatrixXd result = Eigen::MatrixXd::Zero(aobasis.AOBasisSize(), aobasis.AOBasisSize()); // build engines for each thread std::vector engines(nthreads); engines[0] = libint2::Engine(libint2::Operator::coulomb, aobasis.getMaxNprim(), static_cast(aobasis.getMaxL()), 0); engines[0].set(libint2::BraKet::xs_xs); for (Index i = 1; i != nthreads; ++i) { engines[i] = engines[0]; } #pragma omp parallel for schedule(dynamic) for (Index s1 = 0; s1 < aobasis.getNumofShells(); ++s1) { libint2::Engine& engine = engines[OPENMP::getThreadId()]; const libint2::Engine::target_ptr_vec& buf = engine.results(); Index bf1 = shell2bf[s1]; Index n1 = shells[s1].size(); // cannot use shellpairs because this is still a two-center integral and // overlap screening would give wrong result for (Index s2 = 0; s2 <= s1; ++s2) { engine.compute2( shells[s1], libint2::Shell::unit(), shells[s2], libint2::Shell::unit()); if (buf[0] == nullptr) { continue; // if all integrals screened out, skip to next shell set } Index bf2 = shell2bf[s2]; Index n2 = shells[s2].size(); Eigen::Map buf_mat(buf[0], n1, n2); result.block(bf1, bf2, n1, n2) = buf_mat; if (s1 != s2) { // if s1 >= s2, copy {s1,s2} to the corresponding // {s2,s1} block, note the transpose! result.block(bf2, bf1, n2, n1) = buf_mat.transpose(); } } } _aomatrix = result; } // This converts V into ((S-1/2 V S-1/2)-1/2 S-1/2)T, which is needed to // construct 4c integrals, Eigen::MatrixXd AOCoulomb::Pseudo_InvSqrt_GWBSE(const AOOverlap& auxoverlap, double etol) { Eigen::SelfAdjointEigenSolver eo(auxoverlap.Matrix()); removedfunctions = 0; Eigen::VectorXd diagonal_overlap = Eigen::VectorXd::Zero(eo.eigenvalues().size()); for (Index i = 0; i < diagonal_overlap.size(); ++i) { if (eo.eigenvalues()(i) < etol) { removedfunctions++; } else { diagonal_overlap(i) = 1.0 / std::sqrt(eo.eigenvalues()(i)); } } Eigen::MatrixXd Ssqrt = eo.eigenvectors() * diagonal_overlap.asDiagonal() * eo.eigenvectors().transpose(); Eigen::MatrixXd ortho = Ssqrt * _aomatrix * Ssqrt; Eigen::SelfAdjointEigenSolver es(ortho); Eigen::VectorXd diagonal = Eigen::VectorXd::Zero(es.eigenvalues().size()); for (Index i = 0; i < diagonal.size(); ++i) { if (es.eigenvalues()(i) < etol) { removedfunctions++; } else { diagonal(i) = 1.0 / std::sqrt(es.eigenvalues()(i)); } } Eigen::MatrixXd Vm1 = es.eigenvectors() * diagonal.asDiagonal() * es.eigenvectors().transpose(); Eigen::MatrixXd result = (Vm1 * Ssqrt).transpose(); return result; } Eigen::MatrixXd AOCoulomb::Pseudo_InvSqrt(double etol) { Eigen::SelfAdjointEigenSolver es(_aomatrix); Eigen::VectorXd diagonal = Eigen::VectorXd::Zero(es.eigenvalues().size()); removedfunctions = 0; for (Index i = 0; i < diagonal.size(); ++i) { if (es.eigenvalues()(i) < etol) { removedfunctions++; } else { diagonal(i) = 1.0 / std::sqrt(es.eigenvalues()(i)); } } return es.eigenvectors() * diagonal.asDiagonal() * es.eigenvectors().transpose(); } /*********************************** * DIPOLE ***********************************/ void AODipole::Fill(const AOBasis& aobasis) { auto results = computeOneBodyIntegrals>( aobasis, _r); for (Index i = 0; i < 3; i++) { _aomatrix[i] = results[1 + i]; // emultipole1 returns: overlap, x-dipole, // y-dipole, z-dipole } } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/aomatrices/aomultipole.cc000066400000000000000000003200421412152066400214760ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * *Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/aopotential.h" #include "votca/xtp/aotransform.h" #include "votca/xtp/qmmolecule.h" namespace votca { namespace xtp { void AOMultipole::FillBlock(Eigen::Block& matrix, const AOShell& shell_row, const AOShell& shell_col) const { const double pi = boost::math::constants::pi(); Index rank = _site->getRank(); if (rank < 1 && _site->getDipole().norm() > 1e-12) { rank = 1; } const double charge = _site->getCharge(); const Eigen::Vector3d dipole = _site->getDipole(); // factor 1.5 I am not sure about but then 6 monopoles and this tensor agree const Eigen::Matrix3d quadrupole = 1.5 * _site->CalculateCartesianMultipole(); // shell info, only lmax tells how far to go Index lmax_row = Index(shell_row.getL()); Index lmax_col = Index(shell_col.getL()); Index lsum = lmax_row + lmax_col; // set size of internal block for recursion Index nrows = AOTransform::getBlockSize(lmax_row); Index ncols = AOTransform::getBlockSize(lmax_col); std::array n_orbitals = AOTransform::n_orbitals(); std::array nx = AOTransform::nx(); std::array ny = AOTransform::ny(); std::array nz = AOTransform::nz(); std::array i_less_x = AOTransform::i_less_x(); std::array i_less_y = AOTransform::i_less_y(); std::array i_less_z = AOTransform::i_less_z(); // get shell positions const Eigen::Vector3d& pos_row = shell_row.getPos(); const Eigen::Vector3d& pos_col = shell_col.getPos(); const Eigen::Vector3d diff = pos_row - pos_col; // initialize some helper double distsq = diff.squaredNorm(); Eigen::MatrixXd cartesian = Eigen::MatrixXd::Zero( shell_row.getCartesianNumFunc(), shell_col.getCartesianNumFunc()); // iterate over Gaussians in this shell_row for (const auto& gaussian_row : shell_row) { // iterate over Gaussians in this shell_col // get decay constant const double decay_row = gaussian_row.getDecay(); for (const auto& gaussian_col : shell_col) { // get decay constant const double decay_col = gaussian_col.getDecay(); const double zeta = decay_row + decay_col; const double fak = 0.5 / zeta; const double fak2 = 2.0 * fak; const double xi = decay_row * decay_col * fak2; double exparg = xi * distsq; // some helpers const Eigen::Vector3d PmA = fak2 * (decay_row * pos_row + decay_col * pos_col) - pos_row; const Eigen::Vector3d PmB = fak2 * (decay_row * pos_row + decay_col * pos_col) - pos_col; const Eigen::Vector3d PmC = fak2 * (decay_row * pos_row + decay_col * pos_col) - _site->getPos(); const double U = zeta * PmC.squaredNorm(); // +3 quadrupole, +2 dipole, +1 nuclear attraction integrals const Eigen::VectorXd FmU = AOTransform::XIntegrate(lsum + rank + 1, U); Eigen::Tensor nuc3(nrows, ncols, lsum + 1); nuc3.setZero(); // (s-s element normiert ) double prefactor = 4. * sqrt(2. / pi) * pow(decay_row * decay_col, .75) * fak2 * exp(-exparg); for (Index m = 0; m < lsum + 1; m++) { nuc3(0, 0, m) = prefactor * FmU[m]; } //------------------------------------------------------ // Integrals p - s if (lmax_row > 0) { for (Index m = 0; m < lsum; m++) { nuc3(Cart::x, 0, m) = PmA(0) * nuc3(0, 0, m) - PmC(0) * nuc3(0, 0, m + 1); nuc3(Cart::y, 0, m) = PmA(1) * nuc3(0, 0, m) - PmC(1) * nuc3(0, 0, m + 1); nuc3(Cart::z, 0, m) = PmA(2) * nuc3(0, 0, m) - PmC(2) * nuc3(0, 0, m + 1); } } //------------------------------------------------------ // Integrals d - s if (lmax_row > 1) { for (Index m = 0; m < lsum - 1; m++) { double term = fak * (nuc3(0, 0, m) - nuc3(0, 0, m + 1)); nuc3(Cart::xx, 0, m) = PmA(0) * nuc3(Cart::x, 0, m) - PmC(0) * nuc3(Cart::x, 0, m + 1) + term; nuc3(Cart::xy, 0, m) = PmA(0) * nuc3(Cart::y, 0, m) - PmC(0) * nuc3(Cart::y, 0, m + 1); nuc3(Cart::xz, 0, m) = PmA(0) * nuc3(Cart::z, 0, m) - PmC(0) * nuc3(Cart::z, 0, m + 1); nuc3(Cart::yy, 0, m) = PmA(1) * nuc3(Cart::y, 0, m) - PmC(1) * nuc3(Cart::y, 0, m + 1) + term; nuc3(Cart::yz, 0, m) = PmA(1) * nuc3(Cart::z, 0, m) - PmC(1) * nuc3(Cart::z, 0, m + 1); nuc3(Cart::zz, 0, m) = PmA(2) * nuc3(Cart::z, 0, m) - PmC(2) * nuc3(Cart::z, 0, m + 1) + term; } } //------------------------------------------------------ // Integrals f - s if (lmax_row > 2) { for (Index m = 0; m < lsum - 2; m++) { nuc3(Cart::xxx, 0, m) = PmA(0) * nuc3(Cart::xx, 0, m) - PmC(0) * nuc3(Cart::xx, 0, m + 1) + 2 * fak * (nuc3(Cart::x, 0, m) - nuc3(Cart::x, 0, m + 1)); nuc3(Cart::xxy, 0, m) = PmA(1) * nuc3(Cart::xx, 0, m) - PmC(1) * nuc3(Cart::xx, 0, m + 1); nuc3(Cart::xxz, 0, m) = PmA(2) * nuc3(Cart::xx, 0, m) - PmC(2) * nuc3(Cart::xx, 0, m + 1); nuc3(Cart::xyy, 0, m) = PmA(0) * nuc3(Cart::yy, 0, m) - PmC(0) * nuc3(Cart::yy, 0, m + 1); nuc3(Cart::xyz, 0, m) = PmA(0) * nuc3(Cart::yz, 0, m) - PmC(0) * nuc3(Cart::yz, 0, m + 1); nuc3(Cart::xzz, 0, m) = PmA(0) * nuc3(Cart::zz, 0, m) - PmC(0) * nuc3(Cart::zz, 0, m + 1); nuc3(Cart::yyy, 0, m) = PmA(1) * nuc3(Cart::yy, 0, m) - PmC(1) * nuc3(Cart::yy, 0, m + 1) + 2 * fak * (nuc3(Cart::y, 0, m) - nuc3(Cart::y, 0, m + 1)); nuc3(Cart::yyz, 0, m) = PmA(2) * nuc3(Cart::yy, 0, m) - PmC(2) * nuc3(Cart::yy, 0, m + 1); nuc3(Cart::yzz, 0, m) = PmA(1) * nuc3(Cart::zz, 0, m) - PmC(1) * nuc3(Cart::zz, 0, m + 1); nuc3(Cart::zzz, 0, m) = PmA(2) * nuc3(Cart::zz, 0, m) - PmC(2) * nuc3(Cart::zz, 0, m + 1) + 2 * fak * (nuc3(Cart::z, 0, m) - nuc3(Cart::z, 0, m + 1)); } } //------------------------------------------------------ // Integrals g - s if (lmax_row > 3) { for (Index m = 0; m < lsum - 3; m++) { double term_xx = fak * (nuc3(Cart::xx, 0, m) - nuc3(Cart::xx, 0, m + 1)); double term_yy = fak * (nuc3(Cart::yy, 0, m) - nuc3(Cart::yy, 0, m + 1)); double term_zz = fak * (nuc3(Cart::zz, 0, m) - nuc3(Cart::zz, 0, m + 1)); nuc3(Cart::xxxx, 0, m) = PmA(0) * nuc3(Cart::xxx, 0, m) - PmC(0) * nuc3(Cart::xxx, 0, m + 1) + 3 * term_xx; nuc3(Cart::xxxy, 0, m) = PmA(1) * nuc3(Cart::xxx, 0, m) - PmC(1) * nuc3(Cart::xxx, 0, m + 1); nuc3(Cart::xxxz, 0, m) = PmA(2) * nuc3(Cart::xxx, 0, m) - PmC(2) * nuc3(Cart::xxx, 0, m + 1); nuc3(Cart::xxyy, 0, m) = PmA(0) * nuc3(Cart::xyy, 0, m) - PmC(0) * nuc3(Cart::xyy, 0, m + 1) + term_yy; nuc3(Cart::xxyz, 0, m) = PmA(1) * nuc3(Cart::xxz, 0, m) - PmC(1) * nuc3(Cart::xxz, 0, m + 1); nuc3(Cart::xxzz, 0, m) = PmA(0) * nuc3(Cart::xzz, 0, m) - PmC(0) * nuc3(Cart::xzz, 0, m + 1) + term_zz; nuc3(Cart::xyyy, 0, m) = PmA(0) * nuc3(Cart::yyy, 0, m) - PmC(0) * nuc3(Cart::yyy, 0, m + 1); nuc3(Cart::xyyz, 0, m) = PmA(0) * nuc3(Cart::yyz, 0, m) - PmC(0) * nuc3(Cart::yyz, 0, m + 1); nuc3(Cart::xyzz, 0, m) = PmA(0) * nuc3(Cart::yzz, 0, m) - PmC(0) * nuc3(Cart::yzz, 0, m + 1); nuc3(Cart::xzzz, 0, m) = PmA(0) * nuc3(Cart::zzz, 0, m) - PmC(0) * nuc3(Cart::zzz, 0, m + 1); nuc3(Cart::yyyy, 0, m) = PmA(1) * nuc3(Cart::yyy, 0, m) - PmC(1) * nuc3(Cart::yyy, 0, m + 1) + 3 * term_yy; nuc3(Cart::yyyz, 0, m) = PmA(2) * nuc3(Cart::yyy, 0, m) - PmC(2) * nuc3(Cart::yyy, 0, m + 1); nuc3(Cart::yyzz, 0, m) = PmA(1) * nuc3(Cart::yzz, 0, m) - PmC(1) * nuc3(Cart::yzz, 0, m + 1) + term_zz; nuc3(Cart::yzzz, 0, m) = PmA(1) * nuc3(Cart::zzz, 0, m) - PmC(1) * nuc3(Cart::zzz, 0, m + 1); nuc3(Cart::zzzz, 0, m) = PmA(2) * nuc3(Cart::zzz, 0, m) - PmC(2) * nuc3(Cart::zzz, 0, m + 1) + 3 * term_zz; } } //------------------------------------------------------ if (lmax_col > 0) { // Integrals s - p for (Index m = 0; m < lmax_col; m++) { nuc3(0, Cart::x, m) = PmB(0) * nuc3(0, 0, m) - PmC(0) * nuc3(0, 0, m + 1); nuc3(0, Cart::y, m) = PmB(1) * nuc3(0, 0, m) - PmC(1) * nuc3(0, 0, m + 1); nuc3(0, Cart::z, m) = PmB(2) * nuc3(0, 0, m) - PmC(2) * nuc3(0, 0, m + 1); } //------------------------------------------------------ // Integrals p - p if (lmax_row > 0) { for (Index m = 0; m < lmax_col; m++) { double term = fak * (nuc3(0, 0, m) - nuc3(0, 0, m + 1)); for (Index i = 1; i < 4; i++) { nuc3(i, Cart::x, m) = PmB(0) * nuc3(i, 0, m) - PmC(0) * nuc3(i, 0, m + 1) + nx[i] * term; nuc3(i, Cart::y, m) = PmB(1) * nuc3(i, 0, m) - PmC(1) * nuc3(i, 0, m + 1) + ny[i] * term; nuc3(i, Cart::z, m) = PmB(2) * nuc3(i, 0, m) - PmC(2) * nuc3(i, 0, m + 1) + nz[i] * term; } } } //------------------------------------------------------ // Integrals d - p f - p g - p for (Index m = 0; m < lmax_col; m++) { for (Index i = 4; i < n_orbitals[lmax_row]; i++) { int nx_i = nx[i]; int ny_i = ny[i]; int nz_i = nz[i]; int ilx_i = i_less_x[i]; int ily_i = i_less_y[i]; int ilz_i = i_less_z[i]; nuc3(i, Cart::x, m) = PmB(0) * nuc3(i, 0, m) - PmC(0) * nuc3(i, 0, m + 1) + nx_i * fak * (nuc3(ilx_i, 0, m) - nuc3(ilx_i, 0, m + 1)); nuc3(i, Cart::y, m) = PmB(1) * nuc3(i, 0, m) - PmC(1) * nuc3(i, 0, m + 1) + ny_i * fak * (nuc3(ily_i, 0, m) - nuc3(ily_i, 0, m + 1)); nuc3(i, Cart::z, m) = PmB(2) * nuc3(i, 0, m) - PmC(2) * nuc3(i, 0, m + 1) + nz_i * fak * (nuc3(ilz_i, 0, m) - nuc3(ilz_i, 0, m + 1)); } } //------------------------------------------------------ } // end if (lmax_col > 0) if (lmax_col > 1) { // Integrals s - d for (Index m = 0; m < lmax_col - 1; m++) { double term = fak * (nuc3(0, 0, m) - nuc3(0, 0, m + 1)); nuc3(0, Cart::xx, m) = PmB(0) * nuc3(0, Cart::x, m) - PmC(0) * nuc3(0, Cart::x, m + 1) + term; nuc3(0, Cart::xy, m) = PmB(0) * nuc3(0, Cart::y, m) - PmC(0) * nuc3(0, Cart::y, m + 1); nuc3(0, Cart::xz, m) = PmB(0) * nuc3(0, Cart::z, m) - PmC(0) * nuc3(0, Cart::z, m + 1); nuc3(0, Cart::yy, m) = PmB(1) * nuc3(0, Cart::y, m) - PmC(1) * nuc3(0, Cart::y, m + 1) + term; nuc3(0, Cart::yz, m) = PmB(1) * nuc3(0, Cart::z, m) - PmC(1) * nuc3(0, Cart::z, m + 1); nuc3(0, Cart::zz, m) = PmB(2) * nuc3(0, Cart::z, m) - PmC(2) * nuc3(0, Cart::z, m + 1) + term; } //------------------------------------------------------ // Integrals p - d d - d f - d g - d for (Index m = 0; m < lmax_col - 1; m++) { for (Index i = 1; i < n_orbitals[lmax_row]; i++) { int nx_i = nx[i]; int ny_i = ny[i]; int nz_i = nz[i]; int ilx_i = i_less_x[i]; int ily_i = i_less_y[i]; int ilz_i = i_less_z[i]; double term = fak * (nuc3(i, 0, m) - nuc3(i, 0, m + 1)); nuc3(i, Cart::xx, m) = PmB(0) * nuc3(i, Cart::x, m) - PmC(0) * nuc3(i, Cart::x, m + 1) + nx_i * fak * (nuc3(ilx_i, Cart::x, m) - nuc3(ilx_i, Cart::x, m + 1)) + term; nuc3(i, Cart::xy, m) = PmB(0) * nuc3(i, Cart::y, m) - PmC(0) * nuc3(i, Cart::y, m + 1) + nx_i * fak * (nuc3(ilx_i, Cart::y, m) - nuc3(ilx_i, Cart::y, m + 1)); nuc3(i, Cart::xz, m) = PmB(0) * nuc3(i, Cart::z, m) - PmC(0) * nuc3(i, Cart::z, m + 1) + nx_i * fak * (nuc3(ilx_i, Cart::z, m) - nuc3(ilx_i, Cart::z, m + 1)); nuc3(i, Cart::yy, m) = PmB(1) * nuc3(i, Cart::y, m) - PmC(1) * nuc3(i, Cart::y, m + 1) + ny_i * fak * (nuc3(ily_i, Cart::y, m) - nuc3(ily_i, Cart::y, m + 1)) + term; nuc3(i, Cart::yz, m) = PmB(1) * nuc3(i, Cart::z, m) - PmC(1) * nuc3(i, Cart::z, m + 1) + ny_i * fak * (nuc3(ily_i, Cart::z, m) - nuc3(ily_i, Cart::z, m + 1)); nuc3(i, Cart::zz, m) = PmB(2) * nuc3(i, Cart::z, m) - PmC(2) * nuc3(i, Cart::z, m + 1) + nz_i * fak * (nuc3(ilz_i, Cart::z, m) - nuc3(ilz_i, Cart::z, m + 1)) + term; } } //------------------------------------------------------ } // end if (lmax_col > 1) if (lmax_col > 2) { // Integrals s - f for (Index m = 0; m < lmax_col - 2; m++) { nuc3(0, Cart::xxx, m) = PmB(0) * nuc3(0, Cart::xx, m) - PmC(0) * nuc3(0, Cart::xx, m + 1) + 2 * fak * (nuc3(0, Cart::x, m) - nuc3(0, Cart::x, m + 1)); nuc3(0, Cart::xxy, m) = PmB(1) * nuc3(0, Cart::xx, m) - PmC(1) * nuc3(0, Cart::xx, m + 1); nuc3(0, Cart::xxz, m) = PmB(2) * nuc3(0, Cart::xx, m) - PmC(2) * nuc3(0, Cart::xx, m + 1); nuc3(0, Cart::xyy, m) = PmB(0) * nuc3(0, Cart::yy, m) - PmC(0) * nuc3(0, Cart::yy, m + 1); nuc3(0, Cart::xyz, m) = PmB(0) * nuc3(0, Cart::yz, m) - PmC(0) * nuc3(0, Cart::yz, m + 1); nuc3(0, Cart::xzz, m) = PmB(0) * nuc3(0, Cart::zz, m) - PmC(0) * nuc3(0, Cart::zz, m + 1); nuc3(0, Cart::yyy, m) = PmB(1) * nuc3(0, Cart::yy, m) - PmC(1) * nuc3(0, Cart::yy, m + 1) + 2 * fak * (nuc3(0, Cart::y, m) - nuc3(0, Cart::y, m + 1)); nuc3(0, Cart::yyz, m) = PmB(2) * nuc3(0, Cart::yy, m) - PmC(2) * nuc3(0, Cart::yy, m + 1); nuc3(0, Cart::yzz, m) = PmB(1) * nuc3(0, Cart::zz, m) - PmC(1) * nuc3(0, Cart::zz, m + 1); nuc3(0, Cart::zzz, m) = PmB(2) * nuc3(0, Cart::zz, m) - PmC(2) * nuc3(0, Cart::zz, m + 1) + 2 * fak * (nuc3(0, Cart::z, m) - nuc3(0, Cart::z, m + 1)); } //------------------------------------------------------ // Integrals p - f d - f f - f g - f for (Index m = 0; m < lmax_col - 2; m++) { for (Index i = 1; i < n_orbitals[lmax_row]; i++) { int nx_i = nx[i]; int ny_i = ny[i]; int nz_i = nz[i]; int ilx_i = i_less_x[i]; int ily_i = i_less_y[i]; int ilz_i = i_less_z[i]; double term_x = 2 * fak * (nuc3(i, Cart::x, m) - nuc3(i, Cart::x, m + 1)); double term_y = 2 * fak * (nuc3(i, Cart::y, m) - nuc3(i, Cart::y, m + 1)); double term_z = 2 * fak * (nuc3(i, Cart::z, m) - nuc3(i, Cart::z, m + 1)); nuc3(i, Cart::xxx, m) = PmB(0) * nuc3(i, Cart::xx, m) - PmC(0) * nuc3(i, Cart::xx, m + 1) + nx_i * fak * (nuc3(ilx_i, Cart::xx, m) - nuc3(ilx_i, Cart::xx, m + 1)) + term_x; nuc3(i, Cart::xxy, m) = PmB(1) * nuc3(i, Cart::xx, m) - PmC(1) * nuc3(i, Cart::xx, m + 1) + ny_i * fak * (nuc3(ily_i, Cart::xx, m) - nuc3(ily_i, Cart::xx, m + 1)); nuc3(i, Cart::xxz, m) = PmB(2) * nuc3(i, Cart::xx, m) - PmC(2) * nuc3(i, Cart::xx, m + 1) + nz_i * fak * (nuc3(ilz_i, Cart::xx, m) - nuc3(ilz_i, Cart::xx, m + 1)); nuc3(i, Cart::xyy, m) = PmB(0) * nuc3(i, Cart::yy, m) - PmC(0) * nuc3(i, Cart::yy, m + 1) + nx_i * fak * (nuc3(ilx_i, Cart::yy, m) - nuc3(ilx_i, Cart::yy, m + 1)); nuc3(i, Cart::xyz, m) = PmB(0) * nuc3(i, Cart::yz, m) - PmC(0) * nuc3(i, Cart::yz, m + 1) + nx_i * fak * (nuc3(ilx_i, Cart::yz, m) - nuc3(ilx_i, Cart::yz, m + 1)); nuc3(i, Cart::xzz, m) = PmB(0) * nuc3(i, Cart::zz, m) - PmC(0) * nuc3(i, Cart::zz, m + 1) + nx_i * fak * (nuc3(ilx_i, Cart::zz, m) - nuc3(ilx_i, Cart::zz, m + 1)); nuc3(i, Cart::yyy, m) = PmB(1) * nuc3(i, Cart::yy, m) - PmC(1) * nuc3(i, Cart::yy, m + 1) + ny_i * fak * (nuc3(ily_i, Cart::yy, m) - nuc3(ily_i, Cart::yy, m + 1)) + term_y; nuc3(i, Cart::yyz, m) = PmB(2) * nuc3(i, Cart::yy, m) - PmC(2) * nuc3(i, Cart::yy, m + 1) + nz_i * fak * (nuc3(ilz_i, Cart::yy, m) - nuc3(ilz_i, Cart::yy, m + 1)); nuc3(i, Cart::yzz, m) = PmB(1) * nuc3(i, Cart::zz, m) - PmC(1) * nuc3(i, Cart::zz, m + 1) + ny_i * fak * (nuc3(ily_i, Cart::zz, m) - nuc3(ily_i, Cart::zz, m + 1)); nuc3(i, Cart::zzz, m) = PmB(2) * nuc3(i, Cart::zz, m) - PmC(2) * nuc3(i, Cart::zz, m + 1) + nz_i * fak * (nuc3(ilz_i, Cart::zz, m) - nuc3(ilz_i, Cart::zz, m + 1)) + term_z; } } //------------------------------------------------------ } // end if (lmax_col > 2) if (lmax_col > 3) { // Integrals s - g for (Index m = 0; m < lmax_col - 3; m++) { double term_xx = fak * (nuc3(0, Cart::xx, m) - nuc3(0, Cart::xx, m + 1)); double term_yy = fak * (nuc3(0, Cart::yy, m) - nuc3(0, Cart::yy, m + 1)); double term_zz = fak * (nuc3(0, Cart::zz, m) - nuc3(0, Cart::zz, m + 1)); nuc3(0, Cart::xxxx, m) = PmB(0) * nuc3(0, Cart::xxx, m) - PmC(0) * nuc3(0, Cart::xxx, m + 1) + 3 * term_xx; nuc3(0, Cart::xxxy, m) = PmB(1) * nuc3(0, Cart::xxx, m) - PmC(1) * nuc3(0, Cart::xxx, m + 1); nuc3(0, Cart::xxxz, m) = PmB(2) * nuc3(0, Cart::xxx, m) - PmC(2) * nuc3(0, Cart::xxx, m + 1); nuc3(0, Cart::xxyy, m) = PmB(0) * nuc3(0, Cart::xyy, m) - PmC(0) * nuc3(0, Cart::xyy, m + 1) + term_yy; nuc3(0, Cart::xxyz, m) = PmB(1) * nuc3(0, Cart::xxz, m) - PmC(1) * nuc3(0, Cart::xxz, m + 1); nuc3(0, Cart::xxzz, m) = PmB(0) * nuc3(0, Cart::xzz, m) - PmC(0) * nuc3(0, Cart::xzz, m + 1) + term_zz; nuc3(0, Cart::xyyy, m) = PmB(0) * nuc3(0, Cart::yyy, m) - PmC(0) * nuc3(0, Cart::yyy, m + 1); nuc3(0, Cart::xyyz, m) = PmB(0) * nuc3(0, Cart::yyz, m) - PmC(0) * nuc3(0, Cart::yyz, m + 1); nuc3(0, Cart::xyzz, m) = PmB(0) * nuc3(0, Cart::yzz, m) - PmC(0) * nuc3(0, Cart::yzz, m + 1); nuc3(0, Cart::xzzz, m) = PmB(0) * nuc3(0, Cart::zzz, m) - PmC(0) * nuc3(0, Cart::zzz, m + 1); nuc3(0, Cart::yyyy, m) = PmB(1) * nuc3(0, Cart::yyy, m) - PmC(1) * nuc3(0, Cart::yyy, m + 1) + 3 * term_yy; nuc3(0, Cart::yyyz, m) = PmB(2) * nuc3(0, Cart::yyy, m) - PmC(2) * nuc3(0, Cart::yyy, m + 1); nuc3(0, Cart::yyzz, m) = PmB(1) * nuc3(0, Cart::yzz, m) - PmC(1) * nuc3(0, Cart::yzz, m + 1) + term_zz; nuc3(0, Cart::yzzz, m) = PmB(1) * nuc3(0, Cart::zzz, m) - PmC(1) * nuc3(0, Cart::zzz, m + 1); nuc3(0, Cart::zzzz, m) = PmB(2) * nuc3(0, Cart::zzz, m) - PmC(2) * nuc3(0, Cart::zzz, m + 1) + 3 * term_zz; } //------------------------------------------------------ // Integrals p - g d - g f - g g - g for (Index m = 0; m < lmax_col - 3; m++) { for (Index i = 1; i < n_orbitals[lmax_row]; i++) { int nx_i = nx[i]; int ny_i = ny[i]; int nz_i = nz[i]; int ilx_i = i_less_x[i]; int ily_i = i_less_y[i]; int ilz_i = i_less_z[i]; double term_xx = fak * (nuc3(i, Cart::xx, m) - nuc3(i, Cart::xx, m + 1)); double term_yy = fak * (nuc3(i, Cart::yy, m) - nuc3(i, Cart::yy, m + 1)); double term_zz = fak * (nuc3(i, Cart::zz, m) - nuc3(i, Cart::zz, m + 1)); nuc3(i, Cart::xxxx, m) = PmB(0) * nuc3(i, Cart::xxx, m) - PmC(0) * nuc3(i, Cart::xxx, m + 1) + nx_i * fak * (nuc3(ilx_i, Cart::xxx, m) - nuc3(ilx_i, Cart::xxx, m + 1)) + 3 * term_xx; nuc3(i, Cart::xxxy, m) = PmB(1) * nuc3(i, Cart::xxx, m) - PmC(1) * nuc3(i, Cart::xxx, m + 1) + ny_i * fak * (nuc3(ily_i, Cart::xxx, m) - nuc3(ily_i, Cart::xxx, m + 1)); nuc3(i, Cart::xxxz, m) = PmB(2) * nuc3(i, Cart::xxx, m) - PmC(2) * nuc3(i, Cart::xxx, m + 1) + nz_i * fak * (nuc3(ilz_i, Cart::xxx, m) - nuc3(ilz_i, Cart::xxx, m + 1)); nuc3(i, Cart::xxyy, m) = PmB(0) * nuc3(i, Cart::xyy, m) - PmC(0) * nuc3(i, Cart::xyy, m + 1) + nx_i * fak * (nuc3(ilx_i, Cart::xyy, m) - nuc3(ilx_i, Cart::xyy, m + 1)) + term_yy; nuc3(i, Cart::xxyz, m) = PmB(1) * nuc3(i, Cart::xxz, m) - PmC(1) * nuc3(i, Cart::xxz, m + 1) + ny_i * fak * (nuc3(ily_i, Cart::xxz, m) - nuc3(ily_i, Cart::xxz, m + 1)); nuc3(i, Cart::xxzz, m) = PmB(0) * nuc3(i, Cart::xzz, m) - PmC(0) * nuc3(i, Cart::xzz, m + 1) + nx_i * fak * (nuc3(ilx_i, Cart::xzz, m) - nuc3(ilx_i, Cart::xzz, m + 1)) + term_zz; nuc3(i, Cart::xyyy, m) = PmB(0) * nuc3(i, Cart::yyy, m) - PmC(0) * nuc3(i, Cart::yyy, m + 1) + nx_i * fak * (nuc3(ilx_i, Cart::yyy, m) - nuc3(ilx_i, Cart::yyy, m + 1)); nuc3(i, Cart::xyyz, m) = PmB(0) * nuc3(i, Cart::yyz, m) - PmC(0) * nuc3(i, Cart::yyz, m + 1) + nx_i * fak * (nuc3(ilx_i, Cart::yyz, m) - nuc3(ilx_i, Cart::yyz, m + 1)); nuc3(i, Cart::xyzz, m) = PmB(0) * nuc3(i, Cart::yzz, m) - PmC(0) * nuc3(i, Cart::yzz, m + 1) + nx_i * fak * (nuc3(ilx_i, Cart::yzz, m) - nuc3(ilx_i, Cart::yzz, m + 1)); nuc3(i, Cart::xzzz, m) = PmB(0) * nuc3(i, Cart::zzz, m) - PmC(0) * nuc3(i, Cart::zzz, m + 1) + nx_i * fak * (nuc3(ilx_i, Cart::zzz, m) - nuc3(ilx_i, Cart::zzz, m + 1)); nuc3(i, Cart::yyyy, m) = PmB(1) * nuc3(i, Cart::yyy, m) - PmC(1) * nuc3(i, Cart::yyy, m + 1) + ny_i * fak * (nuc3(ily_i, Cart::yyy, m) - nuc3(ily_i, Cart::yyy, m + 1)) + 3 * term_yy; nuc3(i, Cart::yyyz, m) = PmB(2) * nuc3(i, Cart::yyy, m) - PmC(2) * nuc3(i, Cart::yyy, m + 1) + nz_i * fak * (nuc3(ilz_i, Cart::yyy, m) - nuc3(ilz_i, Cart::yyy, m + 1)); nuc3(i, Cart::yyzz, m) = PmB(1) * nuc3(i, Cart::yzz, m) - PmC(1) * nuc3(i, Cart::yzz, m + 1) + ny_i * fak * (nuc3(ily_i, Cart::yzz, m) - nuc3(ily_i, Cart::yzz, m + 1)) + term_zz; nuc3(i, Cart::yzzz, m) = PmB(1) * nuc3(i, Cart::zzz, m) - PmC(1) * nuc3(i, Cart::zzz, m + 1) + ny_i * fak * (nuc3(ily_i, Cart::zzz, m) - nuc3(ily_i, Cart::zzz, m + 1)); nuc3(i, Cart::zzzz, m) = PmB(2) * nuc3(i, Cart::zzz, m) - PmC(2) * nuc3(i, Cart::zzz, m + 1) + nz_i * fak * (nuc3(ilz_i, Cart::zzz, m) - nuc3(ilz_i, Cart::zzz, m + 1)) + 3 * term_zz; } } //------------------------------------------------------ } // end if (lmax_col > 3) Eigen::MatrixXd multipole = charge * Eigen::Map(nuc3.data(), nrows, ncols); if (rank > 0) { Eigen::Tensor dip4(nrows, ncols, 3, lsum + 1); dip4.setZero(); // (s-s element normiert ) double _prefactor_dip = 2. * zeta * prefactor; for (Index m = 0; m < lsum + 1; m++) { dip4(0, 0, 0, m) = PmC(0) * _prefactor_dip * FmU[m + 1]; dip4(0, 0, 1, m) = PmC(1) * _prefactor_dip * FmU[m + 1]; dip4(0, 0, 2, m) = PmC(2) * _prefactor_dip * FmU[m + 1]; } //------------------------------------------------------ // Integrals p - s if (lmax_row > 0) { for (Index m = 0; m < lsum; m++) { for (Index k = 0; k < 3; k++) { dip4(Cart::x, 0, k, m) = PmA(0) * dip4(0, 0, k, m) - PmC(0) * dip4(0, 0, k, m + 1) + (k == 0) * nuc3(0, 0, m + 1); dip4(Cart::y, 0, k, m) = PmA(1) * dip4(0, 0, k, m) - PmC(1) * dip4(0, 0, k, m + 1) + (k == 1) * nuc3(0, 0, m + 1); dip4(Cart::z, 0, k, m) = PmA(2) * dip4(0, 0, k, m) - PmC(2) * dip4(0, 0, k, m + 1) + (k == 2) * nuc3(0, 0, m + 1); } } } //------------------------------------------------------ // Integrals d - s if (lmax_row > 1) { for (Index m = 0; m < lsum - 1; m++) { for (Index k = 0; k < 3; k++) { double term = fak * (dip4(0, 0, k, m) - dip4(0, 0, k, m + 1)); dip4(Cart::xx, 0, k, m) = PmA(0) * dip4(Cart::x, 0, k, m) - PmC(0) * dip4(Cart::x, 0, k, m + 1) + (k == 0) * nuc3(Cart::x, 0, m + 1) + term; dip4(Cart::xy, 0, k, m) = PmA(0) * dip4(Cart::y, 0, k, m) - PmC(0) * dip4(Cart::y, 0, k, m + 1) + (k == 0) * nuc3(Cart::y, 0, m + 1); dip4(Cart::xz, 0, k, m) = PmA(0) * dip4(Cart::z, 0, k, m) - PmC(0) * dip4(Cart::z, 0, k, m + 1) + (k == 0) * nuc3(Cart::z, 0, m + 1); dip4(Cart::yy, 0, k, m) = PmA(1) * dip4(Cart::y, 0, k, m) - PmC(1) * dip4(Cart::y, 0, k, m + 1) + (k == 1) * nuc3(Cart::y, 0, m + 1) + term; dip4(Cart::yz, 0, k, m) = PmA(1) * dip4(Cart::z, 0, k, m) - PmC(1) * dip4(Cart::z, 0, k, m + 1) + (k == 1) * nuc3(Cart::z, 0, m + 1); dip4(Cart::zz, 0, k, m) = PmA(2) * dip4(Cart::z, 0, k, m) - PmC(2) * dip4(Cart::z, 0, k, m + 1) + (k == 2) * nuc3(Cart::z, 0, m + 1) + term; } } } //------------------------------------------------------ // Integrals f - s if (lmax_row > 2) { for (Index m = 0; m < lsum - 2; m++) { for (Index k = 0; k < 3; k++) { dip4(Cart::xxx, 0, k, m) = PmA(0) * dip4(Cart::xx, 0, k, m) - PmC(0) * dip4(Cart::xx, 0, k, m + 1) + (k == 0) * nuc3(Cart::xx, 0, m + 1) + 2 * fak * (dip4(Cart::x, 0, k, m) - dip4(Cart::x, 0, k, m + 1)); dip4(Cart::xxy, 0, k, m) = PmA(1) * dip4(Cart::xx, 0, k, m) - PmC(1) * dip4(Cart::xx, 0, k, m + 1) + (k == 1) * nuc3(Cart::xx, 0, m + 1); dip4(Cart::xxz, 0, k, m) = PmA(2) * dip4(Cart::xx, 0, k, m) - PmC(2) * dip4(Cart::xx, 0, k, m + 1) + (k == 2) * nuc3(Cart::xx, 0, m + 1); dip4(Cart::xyy, 0, k, m) = PmA(0) * dip4(Cart::yy, 0, k, m) - PmC(0) * dip4(Cart::yy, 0, k, m + 1) + (k == 0) * nuc3(Cart::yy, 0, m + 1); dip4(Cart::xyz, 0, k, m) = PmA(0) * dip4(Cart::yz, 0, k, m) - PmC(0) * dip4(Cart::yz, 0, k, m + 1) + (k == 0) * nuc3(Cart::yz, 0, m + 1); dip4(Cart::xzz, 0, k, m) = PmA(0) * dip4(Cart::zz, 0, k, m) - PmC(0) * dip4(Cart::zz, 0, k, m + 1) + (k == 0) * nuc3(Cart::zz, 0, m + 1); dip4(Cart::yyy, 0, k, m) = PmA(1) * dip4(Cart::yy, 0, k, m) - PmC(1) * dip4(Cart::yy, 0, k, m + 1) + (k == 1) * nuc3(Cart::yy, 0, m + 1) + 2 * fak * (dip4(Cart::y, 0, k, m) - dip4(Cart::y, 0, k, m + 1)); dip4(Cart::yyz, 0, k, m) = PmA(2) * dip4(Cart::yy, 0, k, m) - PmC(2) * dip4(Cart::yy, 0, k, m + 1) + (k == 2) * nuc3(Cart::yy, 0, m + 1); dip4(Cart::yzz, 0, k, m) = PmA(1) * dip4(Cart::zz, 0, k, m) - PmC(1) * dip4(Cart::zz, 0, k, m + 1) + (k == 1) * nuc3(Cart::zz, 0, m + 1); dip4(Cart::zzz, 0, k, m) = PmA(2) * dip4(Cart::zz, 0, k, m) - PmC(2) * dip4(Cart::zz, 0, k, m + 1) + (k == 2) * nuc3(Cart::zz, 0, m + 1) + 2 * fak * (dip4(Cart::z, 0, k, m) - dip4(Cart::z, 0, k, m + 1)); } } } //------------------------------------------------------ // Integrals g - s if (lmax_row > 3) { for (Index m = 0; m < lsum - 3; m++) { for (Index k = 0; k < 3; k++) { double term_xx = fak * (dip4(Cart::xx, 0, k, m) - dip4(Cart::xx, 0, k, m + 1)); double term_yy = fak * (dip4(Cart::yy, 0, k, m) - dip4(Cart::yy, 0, k, m + 1)); double term_zz = fak * (dip4(Cart::zz, 0, k, m) - dip4(Cart::zz, 0, k, m + 1)); dip4(Cart::xxxx, 0, k, m) = PmA(0) * dip4(Cart::xxx, 0, k, m) - PmC(0) * dip4(Cart::xxx, 0, k, m + 1) + (k == 0) * nuc3(Cart::xxx, 0, m + 1) + 3 * term_xx; dip4(Cart::xxxy, 0, k, m) = PmA(1) * dip4(Cart::xxx, 0, k, m) - PmC(1) * dip4(Cart::xxx, 0, k, m + 1) + (k == 1) * nuc3(Cart::xxx, 0, m + 1); dip4(Cart::xxxz, 0, k, m) = PmA(2) * dip4(Cart::xxx, 0, k, m) - PmC(2) * dip4(Cart::xxx, 0, k, m + 1) + (k == 2) * nuc3(Cart::xxx, 0, m + 1); dip4(Cart::xxyy, 0, k, m) = PmA(0) * dip4(Cart::xyy, 0, k, m) - PmC(0) * dip4(Cart::xyy, 0, k, m + 1) + (k == 0) * nuc3(Cart::xyy, 0, m + 1) + term_yy; dip4(Cart::xxyz, 0, k, m) = PmA(1) * dip4(Cart::xxz, 0, k, m) - PmC(1) * dip4(Cart::xxz, 0, k, m + 1) + (k == 1) * nuc3(Cart::xxz, 0, m + 1); dip4(Cart::xxzz, 0, k, m) = PmA(0) * dip4(Cart::xzz, 0, k, m) - PmC(0) * dip4(Cart::xzz, 0, k, m + 1) + (k == 0) * nuc3(Cart::xzz, 0, m + 1) + term_zz; dip4(Cart::xyyy, 0, k, m) = PmA(0) * dip4(Cart::yyy, 0, k, m) - PmC(0) * dip4(Cart::yyy, 0, k, m + 1) + (k == 0) * nuc3(Cart::yyy, 0, m + 1); dip4(Cart::xyyz, 0, k, m) = PmA(0) * dip4(Cart::yyz, 0, k, m) - PmC(0) * dip4(Cart::yyz, 0, k, m + 1) + (k == 0) * nuc3(Cart::yyz, 0, m + 1); dip4(Cart::xyzz, 0, k, m) = PmA(0) * dip4(Cart::yzz, 0, k, m) - PmC(0) * dip4(Cart::yzz, 0, k, m + 1) + (k == 0) * nuc3(Cart::yzz, 0, m + 1); dip4(Cart::xzzz, 0, k, m) = PmA(0) * dip4(Cart::zzz, 0, k, m) - PmC(0) * dip4(Cart::zzz, 0, k, m + 1) + (k == 0) * nuc3(Cart::zzz, 0, m + 1); dip4(Cart::yyyy, 0, k, m) = PmA(1) * dip4(Cart::yyy, 0, k, m) - PmC(1) * dip4(Cart::yyy, 0, k, m + 1) + (k == 1) * nuc3(Cart::yyy, 0, m + 1) + 3 * term_yy; dip4(Cart::yyyz, 0, k, m) = PmA(2) * dip4(Cart::yyy, 0, k, m) - PmC(2) * dip4(Cart::yyy, 0, k, m + 1) + (k == 2) * nuc3(Cart::yyy, 0, m + 1); dip4(Cart::yyzz, 0, k, m) = PmA(1) * dip4(Cart::yzz, 0, k, m) - PmC(1) * dip4(Cart::yzz, 0, k, m + 1) + (k == 1) * nuc3(Cart::yzz, 0, m + 1) + term_zz; dip4(Cart::yzzz, 0, k, m) = PmA(1) * dip4(Cart::zzz, 0, k, m) - PmC(1) * dip4(Cart::zzz, 0, k, m + 1) + (k == 1) * nuc3(Cart::zzz, 0, m + 1); dip4(Cart::zzzz, 0, k, m) = PmA(2) * dip4(Cart::zzz, 0, k, m) - PmC(2) * dip4(Cart::zzz, 0, k, m + 1) + (k == 2) * nuc3(Cart::zzz, 0, m + 1) + 3 * term_zz; } } } //------------------------------------------------------ if (lmax_col > 0) { // Integrals s - p for (Index m = 0; m < lmax_col; m++) { for (Index k = 0; k < 3; k++) { dip4(0, Cart::x, k, m) = PmB(0) * dip4(0, 0, k, m) - PmC(0) * dip4(0, 0, k, m + 1) + (k == 0) * nuc3(0, 0, m + 1); dip4(0, Cart::y, k, m) = PmB(1) * dip4(0, 0, k, m) - PmC(1) * dip4(0, 0, k, m + 1) + (k == 1) * nuc3(0, 0, m + 1); dip4(0, Cart::z, k, m) = PmB(2) * dip4(0, 0, k, m) - PmC(2) * dip4(0, 0, k, m + 1) + (k == 2) * nuc3(0, 0, m + 1); } } //------------------------------------------------------ // Integrals p - p if (lmax_row > 0) { for (Index m = 0; m < lmax_col; m++) { for (Index i = 1; i < 4; i++) { for (Index k = 0; k < 3; k++) { double term = fak * (dip4(0, 0, k, m) - dip4(0, 0, k, m + 1)); dip4(i, Cart::x, k, m) = PmB(0) * dip4(i, 0, k, m) - PmC(0) * dip4(i, 0, k, m + 1) + (k == 0) * nuc3(i, 0, m + 1) + nx[i] * term; dip4(i, Cart::y, k, m) = PmB(1) * dip4(i, 0, k, m) - PmC(1) * dip4(i, 0, k, m + 1) + (k == 1) * nuc3(i, 0, m + 1) + ny[i] * term; dip4(i, Cart::z, k, m) = PmB(2) * dip4(i, 0, k, m) - PmC(2) * dip4(i, 0, k, m + 1) + (k == 2) * nuc3(i, 0, m + 1) + nz[i] * term; } } } } //------------------------------------------------------ // Integrals d - p f - p g - p for (Index m = 0; m < lmax_col; m++) { for (Index i = 4; i < n_orbitals[lmax_row]; i++) { int nx_i = nx[i]; int ny_i = ny[i]; int nz_i = nz[i]; int ilx_i = i_less_x[i]; int ily_i = i_less_y[i]; int ilz_i = i_less_z[i]; for (Index k = 0; k < 3; k++) { dip4(i, Cart::x, k, m) = PmB(0) * dip4(i, 0, k, m) - PmC(0) * dip4(i, 0, k, m + 1) + (k == 0) * nuc3(i, 0, m + 1) + nx_i * fak * (dip4(ilx_i, 0, k, m) - dip4(ilx_i, 0, k, m + 1)); dip4(i, Cart::y, k, m) = PmB(1) * dip4(i, 0, k, m) - PmC(1) * dip4(i, 0, k, m + 1) + (k == 1) * nuc3(i, 0, m + 1) + ny_i * fak * (dip4(ily_i, 0, k, m) - dip4(ily_i, 0, k, m + 1)); dip4(i, Cart::z, k, m) = PmB(2) * dip4(i, 0, k, m) - PmC(2) * dip4(i, 0, k, m + 1) + (k == 2) * nuc3(i, 0, m + 1) + nz_i * fak * (dip4(ilz_i, 0, k, m) - dip4(ilz_i, 0, k, m + 1)); } } } //------------------------------------------------------ } // end if (lmax_col > 0) if (lmax_col > 1) { // Integrals s - d for (Index m = 0; m < lmax_col - 1; m++) { for (Index k = 0; k < 3; k++) { double term = fak * (dip4(0, 0, k, m) - dip4(0, 0, k, m + 1)); dip4(0, Cart::xx, k, m) = PmB(0) * dip4(0, Cart::x, k, m) - PmC(0) * dip4(0, Cart::x, k, m + 1) + (k == 0) * nuc3(0, Cart::x, m + 1) + term; dip4(0, Cart::xy, k, m) = PmB(0) * dip4(0, Cart::y, k, m) - PmC(0) * dip4(0, Cart::y, k, m + 1) + (k == 0) * nuc3(0, Cart::y, m + 1); dip4(0, Cart::xz, k, m) = PmB(0) * dip4(0, Cart::z, k, m) - PmC(0) * dip4(0, Cart::z, k, m + 1) + (k == 0) * nuc3(0, Cart::z, m + 1); dip4(0, Cart::yy, k, m) = PmB(1) * dip4(0, Cart::y, k, m) - PmC(1) * dip4(0, Cart::y, k, m + 1) + (k == 1) * nuc3(0, Cart::y, m + 1) + term; dip4(0, Cart::yz, k, m) = PmB(1) * dip4(0, Cart::z, k, m) - PmC(1) * dip4(0, Cart::z, k, m + 1) + (k == 1) * nuc3(0, Cart::z, m + 1); dip4(0, Cart::zz, k, m) = PmB(2) * dip4(0, Cart::z, k, m) - PmC(2) * dip4(0, Cart::z, k, m + 1) + (k == 2) * nuc3(0, Cart::z, m + 1) + term; } } //------------------------------------------------------ // Integrals p - d d - d f - d g - d for (Index m = 0; m < lmax_col - 1; m++) { for (Index i = 1; i < n_orbitals[lmax_row]; i++) { int nx_i = nx[i]; int ny_i = ny[i]; int nz_i = nz[i]; int ilx_i = i_less_x[i]; int ily_i = i_less_y[i]; int ilz_i = i_less_z[i]; for (Index k = 0; k < 3; k++) { double term = fak * (dip4(i, 0, k, m) - dip4(i, 0, k, m + 1)); dip4(i, Cart::xx, k, m) = PmB(0) * dip4(i, Cart::x, k, m) - PmC(0) * dip4(i, Cart::x, k, m + 1) + (k == 0) * nuc3(i, Cart::x, m + 1) + nx_i * fak * (dip4(ilx_i, Cart::x, k, m) - dip4(ilx_i, Cart::x, k, m + 1)) + term; dip4(i, Cart::xy, k, m) = PmB(0) * dip4(i, Cart::y, k, m) - PmC(0) * dip4(i, Cart::y, k, m + 1) + (k == 0) * nuc3(i, Cart::y, m + 1) + nx_i * fak * (dip4(ilx_i, Cart::y, k, m) - dip4(ilx_i, Cart::y, k, m + 1)); dip4(i, Cart::xz, k, m) = PmB(0) * dip4(i, Cart::z, k, m) - PmC(0) * dip4(i, Cart::z, k, m + 1) + (k == 0) * nuc3(i, Cart::z, m + 1) + nx_i * fak * (dip4(ilx_i, Cart::z, k, m) - dip4(ilx_i, Cart::z, k, m + 1)); dip4(i, Cart::yy, k, m) = PmB(1) * dip4(i, Cart::y, k, m) - PmC(1) * dip4(i, Cart::y, k, m + 1) + (k == 1) * nuc3(i, Cart::y, m + 1) + ny_i * fak * (dip4(ily_i, Cart::y, k, m) - dip4(ily_i, Cart::y, k, m + 1)) + term; dip4(i, Cart::yz, k, m) = PmB(1) * dip4(i, Cart::z, k, m) - PmC(1) * dip4(i, Cart::z, k, m + 1) + (k == 1) * nuc3(i, Cart::z, m + 1) + ny_i * fak * (dip4(ily_i, Cart::z, k, m) - dip4(ily_i, Cart::z, k, m + 1)); dip4(i, Cart::zz, k, m) = PmB(2) * dip4(i, Cart::z, k, m) - PmC(2) * dip4(i, Cart::z, k, m + 1) + (k == 2) * nuc3(i, Cart::z, m + 1) + nz_i * fak * (dip4(ilz_i, Cart::z, k, m) - dip4(ilz_i, Cart::z, k, m + 1)) + term; } } } //------------------------------------------------------ } // end if (lmax_col > 1) if (lmax_col > 2) { // Integrals s - f for (Index m = 0; m < lmax_col - 2; m++) { for (Index k = 0; k < 3; k++) { dip4(0, Cart::xxx, k, m) = PmB(0) * dip4(0, Cart::xx, k, m) - PmC(0) * dip4(0, Cart::xx, k, m + 1) + (k == 0) * nuc3(0, Cart::xx, m + 1) + 2 * fak * (dip4(0, Cart::x, k, m) - dip4(0, Cart::x, k, m + 1)); dip4(0, Cart::xxy, k, m) = PmB(1) * dip4(0, Cart::xx, k, m) - PmC(1) * dip4(0, Cart::xx, k, m + 1) + (k == 1) * nuc3(0, Cart::xx, m + 1); dip4(0, Cart::xxz, k, m) = PmB(2) * dip4(0, Cart::xx, k, m) - PmC(2) * dip4(0, Cart::xx, k, m + 1) + (k == 2) * nuc3(0, Cart::xx, m + 1); dip4(0, Cart::xyy, k, m) = PmB(0) * dip4(0, Cart::yy, k, m) - PmC(0) * dip4(0, Cart::yy, k, m + 1) + (k == 0) * nuc3(0, Cart::yy, m + 1); dip4(0, Cart::xyz, k, m) = PmB(0) * dip4(0, Cart::yz, k, m) - PmC(0) * dip4(0, Cart::yz, k, m + 1) + (k == 0) * nuc3(0, Cart::yz, m + 1); dip4(0, Cart::xzz, k, m) = PmB(0) * dip4(0, Cart::zz, k, m) - PmC(0) * dip4(0, Cart::zz, k, m + 1) + (k == 0) * nuc3(0, Cart::zz, m + 1); dip4(0, Cart::yyy, k, m) = PmB(1) * dip4(0, Cart::yy, k, m) - PmC(1) * dip4(0, Cart::yy, k, m + 1) + (k == 1) * nuc3(0, Cart::yy, m + 1) + 2 * fak * (dip4(0, Cart::y, k, m) - dip4(0, Cart::y, k, m + 1)); dip4(0, Cart::yyz, k, m) = PmB(2) * dip4(0, Cart::yy, k, m) - PmC(2) * dip4(0, Cart::yy, k, m + 1) + (k == 2) * nuc3(0, Cart::yy, m + 1); dip4(0, Cart::yzz, k, m) = PmB(1) * dip4(0, Cart::zz, k, m) - PmC(1) * dip4(0, Cart::zz, k, m + 1) + (k == 1) * nuc3(0, Cart::zz, m + 1); dip4(0, Cart::zzz, k, m) = PmB(2) * dip4(0, Cart::zz, k, m) - PmC(2) * dip4(0, Cart::zz, k, m + 1) + (k == 2) * nuc3(0, Cart::zz, m + 1) + 2 * fak * (dip4(0, Cart::z, k, m) - dip4(0, Cart::z, k, m + 1)); } } //------------------------------------------------------ // Integrals p - f d - f f - f g - f for (Index m = 0; m < lmax_col - 2; m++) { for (Index i = 1; i < n_orbitals[lmax_row]; i++) { int nx_i = nx[i]; int ny_i = ny[i]; int nz_i = nz[i]; int ilx_i = i_less_x[i]; int ily_i = i_less_y[i]; int ilz_i = i_less_z[i]; for (Index k = 0; k < 3; k++) { double term_x = 2 * fak * (dip4(i, Cart::x, k, m) - dip4(i, Cart::x, k, m + 1)); double term_y = 2 * fak * (dip4(i, Cart::y, k, m) - dip4(i, Cart::y, k, m + 1)); double term_z = 2 * fak * (dip4(i, Cart::z, k, m) - dip4(i, Cart::z, k, m + 1)); dip4(i, Cart::xxx, k, m) = PmB(0) * dip4(i, Cart::xx, k, m) - PmC(0) * dip4(i, Cart::xx, k, m + 1) + (k == 0) * nuc3(i, Cart::xx, m + 1) + nx_i * fak * (dip4(ilx_i, Cart::xx, k, m) - dip4(ilx_i, Cart::xx, k, m + 1)) + term_x; dip4(i, Cart::xxy, k, m) = PmB(1) * dip4(i, Cart::xx, k, m) - PmC(1) * dip4(i, Cart::xx, k, m + 1) + (k == 1) * nuc3(i, Cart::xx, m + 1) + ny_i * fak * (dip4(ily_i, Cart::xx, k, m) - dip4(ily_i, Cart::xx, k, m + 1)); dip4(i, Cart::xxz, k, m) = PmB(2) * dip4(i, Cart::xx, k, m) - PmC(2) * dip4(i, Cart::xx, k, m + 1) + (k == 2) * nuc3(i, Cart::xx, m + 1) + nz_i * fak * (dip4(ilz_i, Cart::xx, k, m) - dip4(ilz_i, Cart::xx, k, m + 1)); dip4(i, Cart::xyy, k, m) = PmB(0) * dip4(i, Cart::yy, k, m) - PmC(0) * dip4(i, Cart::yy, k, m + 1) + (k == 0) * nuc3(i, Cart::yy, m + 1) + nx_i * fak * (dip4(ilx_i, Cart::yy, k, m) - dip4(ilx_i, Cart::yy, k, m + 1)); dip4(i, Cart::xyz, k, m) = PmB(0) * dip4(i, Cart::yz, k, m) - PmC(0) * dip4(i, Cart::yz, k, m + 1) + (k == 0) * nuc3(i, Cart::yz, m + 1) + nx_i * fak * (dip4(ilx_i, Cart::yz, k, m) - dip4(ilx_i, Cart::yz, k, m + 1)); dip4(i, Cart::xzz, k, m) = PmB(0) * dip4(i, Cart::zz, k, m) - PmC(0) * dip4(i, Cart::zz, k, m + 1) + (k == 0) * nuc3(i, Cart::zz, m + 1) + nx_i * fak * (dip4(ilx_i, Cart::zz, k, m) - dip4(ilx_i, Cart::zz, k, m + 1)); dip4(i, Cart::yyy, k, m) = PmB(1) * dip4(i, Cart::yy, k, m) - PmC(1) * dip4(i, Cart::yy, k, m + 1) + (k == 1) * nuc3(i, Cart::yy, m + 1) + ny_i * fak * (dip4(ily_i, Cart::yy, k, m) - dip4(ily_i, Cart::yy, k, m + 1)) + term_y; dip4(i, Cart::yyz, k, m) = PmB(2) * dip4(i, Cart::yy, k, m) - PmC(2) * dip4(i, Cart::yy, k, m + 1) + (k == 2) * nuc3(i, Cart::yy, m + 1) + nz_i * fak * (dip4(ilz_i, Cart::yy, k, m) - dip4(ilz_i, Cart::yy, k, m + 1)); dip4(i, Cart::yzz, k, m) = PmB(1) * dip4(i, Cart::zz, k, m) - PmC(1) * dip4(i, Cart::zz, k, m + 1) + (k == 1) * nuc3(i, Cart::zz, m + 1) + ny_i * fak * (dip4(ily_i, Cart::zz, k, m) - dip4(ily_i, Cart::zz, k, m + 1)); dip4(i, Cart::zzz, k, m) = PmB(2) * dip4(i, Cart::zz, k, m) - PmC(2) * dip4(i, Cart::zz, k, m + 1) + (k == 2) * nuc3(i, Cart::zz, m + 1) + nz_i * fak * (dip4(ilz_i, Cart::zz, k, m) - dip4(ilz_i, Cart::zz, k, m + 1)) + term_z; } } } //------------------------------------------------------ } // end if (lmax_col > 2) if (lmax_col > 3) { // Integrals s - g for (Index m = 0; m < lmax_col - 3; m++) { for (Index k = 0; k < 3; k++) { double term_xx = fak * (dip4(0, Cart::xx, k, m) - dip4(0, Cart::xx, k, m + 1)); double term_yy = fak * (dip4(0, Cart::yy, k, m) - dip4(0, Cart::yy, k, m + 1)); double term_zz = fak * (dip4(0, Cart::zz, k, m) - dip4(0, Cart::zz, k, m + 1)); dip4(0, Cart::xxxx, k, m) = PmB(0) * dip4(0, Cart::xxx, k, m) - PmC(0) * dip4(0, Cart::xxx, k, m + 1) + (k == 0) * nuc3(0, Cart::xxx, m + 1) + 3 * term_xx; dip4(0, Cart::xxxy, k, m) = PmB(1) * dip4(0, Cart::xxx, k, m) - PmC(1) * dip4(0, Cart::xxx, k, m + 1) + (k == 1) * nuc3(0, Cart::xxx, m + 1); dip4(0, Cart::xxxz, k, m) = PmB(2) * dip4(0, Cart::xxx, k, m) - PmC(2) * dip4(0, Cart::xxx, k, m + 1) + (k == 2) * nuc3(0, Cart::xxx, m + 1); dip4(0, Cart::xxyy, k, m) = PmB(0) * dip4(0, Cart::xyy, k, m) - PmC(0) * dip4(0, Cart::xyy, k, m + 1) + (k == 0) * nuc3(0, Cart::xyy, m + 1) + term_yy; dip4(0, Cart::xxyz, k, m) = PmB(1) * dip4(0, Cart::xxz, k, m) - PmC(1) * dip4(0, Cart::xxz, k, m + 1) + (k == 1) * nuc3(0, Cart::xxz, m + 1); dip4(0, Cart::xxzz, k, m) = PmB(0) * dip4(0, Cart::xzz, k, m) - PmC(0) * dip4(0, Cart::xzz, k, m + 1) + (k == 0) * nuc3(0, Cart::xzz, m + 1) + term_zz; dip4(0, Cart::xyyy, k, m) = PmB(0) * dip4(0, Cart::yyy, k, m) - PmC(0) * dip4(0, Cart::yyy, k, m + 1) + (k == 0) * nuc3(0, Cart::yyy, m + 1); dip4(0, Cart::xyyz, k, m) = PmB(0) * dip4(0, Cart::yyz, k, m) - PmC(0) * dip4(0, Cart::yyz, k, m + 1) + (k == 0) * nuc3(0, Cart::yyz, m + 1); dip4(0, Cart::xyzz, k, m) = PmB(0) * dip4(0, Cart::yzz, k, m) - PmC(0) * dip4(0, Cart::yzz, k, m + 1) + (k == 0) * nuc3(0, Cart::yzz, m + 1); dip4(0, Cart::xzzz, k, m) = PmB(0) * dip4(0, Cart::zzz, k, m) - PmC(0) * dip4(0, Cart::zzz, k, m + 1) + (k == 0) * nuc3(0, Cart::zzz, m + 1); dip4(0, Cart::yyyy, k, m) = PmB(1) * dip4(0, Cart::yyy, k, m) - PmC(1) * dip4(0, Cart::yyy, k, m + 1) + (k == 1) * nuc3(0, Cart::yyy, m + 1) + 3 * term_yy; dip4(0, Cart::yyyz, k, m) = PmB(2) * dip4(0, Cart::yyy, k, m) - PmC(2) * dip4(0, Cart::yyy, k, m + 1) + (k == 2) * nuc3(0, Cart::yyy, m + 1); dip4(0, Cart::yyzz, k, m) = PmB(1) * dip4(0, Cart::yzz, k, m) - PmC(1) * dip4(0, Cart::yzz, k, m + 1) + (k == 1) * nuc3(0, Cart::yzz, m + 1) + term_zz; dip4(0, Cart::yzzz, k, m) = PmB(1) * dip4(0, Cart::zzz, k, m) - PmC(1) * dip4(0, Cart::zzz, k, m + 1) + (k == 1) * nuc3(0, Cart::zzz, m + 1); dip4(0, Cart::zzzz, k, m) = PmB(2) * dip4(0, Cart::zzz, k, m) - PmC(2) * dip4(0, Cart::zzz, k, m + 1) + (k == 2) * nuc3(0, Cart::zzz, m + 1) + 3 * term_zz; } } //------------------------------------------------------ // Integrals p - g d - g f - g g - g for (Index m = 0; m < lmax_col - 3; m++) { for (Index i = 1; i < n_orbitals[lmax_row]; i++) { int nx_i = nx[i]; int ny_i = ny[i]; int nz_i = nz[i]; int ilx_i = i_less_x[i]; int ily_i = i_less_y[i]; int ilz_i = i_less_z[i]; for (Index k = 0; k < 3; k++) { double term_xx = fak * (dip4(i, Cart::xx, k, m) - dip4(i, Cart::xx, k, m + 1)); double term_yy = fak * (dip4(i, Cart::yy, k, m) - dip4(i, Cart::yy, k, m + 1)); double term_zz = fak * (dip4(i, Cart::zz, k, m) - dip4(i, Cart::zz, k, m + 1)); dip4(i, Cart::xxxx, k, m) = PmB(0) * dip4(i, Cart::xxx, k, m) - PmC(0) * dip4(i, Cart::xxx, k, m + 1) + (k == 0) * nuc3(i, Cart::xxx, m + 1) + nx_i * fak * (dip4(ilx_i, Cart::xxx, k, m) - dip4(ilx_i, Cart::xxx, k, m + 1)) + 3 * term_xx; dip4(i, Cart::xxxy, k, m) = PmB(1) * dip4(i, Cart::xxx, k, m) - PmC(1) * dip4(i, Cart::xxx, k, m + 1) + (k == 1) * nuc3(i, Cart::xxx, m + 1) + ny_i * fak * (dip4(ily_i, Cart::xxx, k, m) - dip4(ily_i, Cart::xxx, k, m + 1)); dip4(i, Cart::xxxz, k, m) = PmB(2) * dip4(i, Cart::xxx, k, m) - PmC(2) * dip4(i, Cart::xxx, k, m + 1) + (k == 2) * nuc3(i, Cart::xxx, m + 1) + nz_i * fak * (dip4(ilz_i, Cart::xxx, k, m) - dip4(ilz_i, Cart::xxx, k, m + 1)); dip4(i, Cart::xxyy, k, m) = PmB(0) * dip4(i, Cart::xyy, k, m) - PmC(0) * dip4(i, Cart::xyy, k, m + 1) + (k == 0) * nuc3(i, Cart::xyy, m + 1) + nx_i * fak * (dip4(ilx_i, Cart::xyy, k, m) - dip4(ilx_i, Cart::xyy, k, m + 1)) + term_yy; dip4(i, Cart::xxyz, k, m) = PmB(1) * dip4(i, Cart::xxz, k, m) - PmC(1) * dip4(i, Cart::xxz, k, m + 1) + (k == 1) * nuc3(i, Cart::xxz, m + 1) + ny_i * fak * (dip4(ily_i, Cart::xxz, k, m) - dip4(ily_i, Cart::xxz, k, m + 1)); dip4(i, Cart::xxzz, k, m) = PmB(0) * dip4(i, Cart::xzz, k, m) - PmC(0) * dip4(i, Cart::xzz, k, m + 1) + (k == 0) * nuc3(i, Cart::xzz, m + 1) + nx_i * fak * (dip4(ilx_i, Cart::xzz, k, m) - dip4(ilx_i, Cart::xzz, k, m + 1)) + term_zz; dip4(i, Cart::xyyy, k, m) = PmB(0) * dip4(i, Cart::yyy, k, m) - PmC(0) * dip4(i, Cart::yyy, k, m + 1) + (k == 0) * nuc3(i, Cart::yyy, m + 1) + nx_i * fak * (dip4(ilx_i, Cart::yyy, k, m) - dip4(ilx_i, Cart::yyy, k, m + 1)); dip4(i, Cart::xyyz, k, m) = PmB(0) * dip4(i, Cart::yyz, k, m) - PmC(0) * dip4(i, Cart::yyz, k, m + 1) + (k == 0) * nuc3(i, Cart::yyz, m + 1) + nx_i * fak * (dip4(ilx_i, Cart::yyz, k, m) - dip4(ilx_i, Cart::yyz, k, m + 1)); dip4(i, Cart::xyzz, k, m) = PmB(0) * dip4(i, Cart::yzz, k, m) - PmC(0) * dip4(i, Cart::yzz, k, m + 1) + (k == 0) * nuc3(i, Cart::yzz, m + 1) + nx_i * fak * (dip4(ilx_i, Cart::yzz, k, m) - dip4(ilx_i, Cart::yzz, k, m + 1)); dip4(i, Cart::xzzz, k, m) = PmB(0) * dip4(i, Cart::zzz, k, m) - PmC(0) * dip4(i, Cart::zzz, k, m + 1) + (k == 0) * nuc3(i, Cart::zzz, m + 1) + nx_i * fak * (dip4(ilx_i, Cart::zzz, k, m) - dip4(ilx_i, Cart::zzz, k, m + 1)); dip4(i, Cart::yyyy, k, m) = PmB(1) * dip4(i, Cart::yyy, k, m) - PmC(1) * dip4(i, Cart::yyy, k, m + 1) + (k == 1) * nuc3(i, Cart::yyy, m + 1) + ny_i * fak * (dip4(ily_i, Cart::yyy, k, m) - dip4(ily_i, Cart::yyy, k, m + 1)) + 3 * term_yy; dip4(i, Cart::yyyz, k, m) = PmB(2) * dip4(i, Cart::yyy, k, m) - PmC(2) * dip4(i, Cart::yyy, k, m + 1) + (k == 2) * nuc3(i, Cart::yyy, m + 1) + nz_i * fak * (dip4(ilz_i, Cart::yyy, k, m) - dip4(ilz_i, Cart::yyy, k, m + 1)); dip4(i, Cart::yyzz, k, m) = PmB(1) * dip4(i, Cart::yzz, k, m) - PmC(1) * dip4(i, Cart::yzz, k, m + 1) + (k == 1) * nuc3(i, Cart::yzz, m + 1) + ny_i * fak * (dip4(ily_i, Cart::yzz, k, m) - dip4(ily_i, Cart::yzz, k, m + 1)) + term_zz; dip4(i, Cart::yzzz, k, m) = PmB(1) * dip4(i, Cart::zzz, k, m) - PmC(1) * dip4(i, Cart::zzz, k, m + 1) + (k == 1) * nuc3(i, Cart::zzz, m + 1) + ny_i * fak * (dip4(ily_i, Cart::zzz, k, m) - dip4(ily_i, Cart::zzz, k, m + 1)); dip4(i, Cart::zzzz, k, m) = PmB(2) * dip4(i, Cart::zzz, k, m) - PmC(2) * dip4(i, Cart::zzz, k, m + 1) + (k == 2) * nuc3(i, Cart::zzz, m + 1) + nz_i * fak * (dip4(ilz_i, Cart::zzz, k, m) - dip4(ilz_i, Cart::zzz, k, m + 1)) + 3 * term_zz; } } } //------------------------------------------------------ } // end if (lmax_col > 3) multipole += dipole.x() * Eigen::Map(dip4.data(), nrows, ncols); size_t offset = nrows * ncols; multipole += dipole.y() * Eigen::Map( dip4.data() + offset, nrows, ncols); multipole += dipole.z() * Eigen::Map( dip4.data() + 2 * offset, nrows, ncols); if (rank > 1) { Eigen::Tensor quad4(nrows, ncols, 5, lsum + 1); quad4.setZero(); double fact = 1. / 3.; std::array fac0 = {fact, fact, 0., 2. * fact, 0.}; std::array fac1 = {fact, 0., fact, 0., 2. * fact}; std::array fac2 = {0., fact, fact, -2. * fact, -2. * fact}; std::array ind0 = {1, 2, 0, 0, 0}; std::array ind1 = {0, 0, 2, 0, 1}; std::array ind2 = {0, 0, 1, 2, 2}; // (s-s element normiert ) double prefactor_quad = (4. * zeta * zeta * prefactor) / 3.; for (Index m = 0; m < lsum + 1; m++) { quad4(0, 0, 0, m) = PmC(0) * PmC(1) * prefactor_quad * FmU[m + 2]; quad4(0, 0, 1, m) = PmC(0) * PmC(2) * prefactor_quad * FmU[m + 2]; quad4(0, 0, 2, m) = PmC(1) * PmC(2) * prefactor_quad * FmU[m + 2]; quad4(0, 0, 3, m) = (PmC(0) * PmC(0) - PmC(2) * PmC(2)) * prefactor_quad * FmU[m + 2]; quad4(0, 0, 4, m) = (PmC(1) * PmC(1) - PmC(2) * PmC(2)) * prefactor_quad * FmU[m + 2]; } //------------------------------------------------------ // Integrals p - s if (lmax_row > 0) { for (Index m = 0; m < lsum; m++) { for (Index k = 0; k < 5; k++) { quad4(Cart::x, 0, k, m) = PmA(0) * quad4(0, 0, k, m) - PmC(0) * quad4(0, 0, k, m + 1) + fac0[k] * dip4(0, 0, ind0[k], m + 1); quad4(Cart::y, 0, k, m) = PmA(1) * quad4(0, 0, k, m) - PmC(1) * quad4(0, 0, k, m + 1) + fac1[k] * dip4(0, 0, ind1[k], m + 1); quad4(Cart::z, 0, k, m) = PmA(2) * quad4(0, 0, k, m) - PmC(2) * quad4(0, 0, k, m + 1) + fac2[k] * dip4(0, 0, ind2[k], m + 1); } } } //------------------------------------------------------ // Integrals d - s if (lmax_row > 1) { for (Index m = 0; m < lsum - 1; m++) { for (Index k = 0; k < 5; k++) { double term = fak * (quad4(0, 0, k, m) - quad4(0, 0, k, m + 1)); quad4(Cart::xx, 0, k, m) = PmA(0) * quad4(Cart::x, 0, k, m) - PmC(0) * quad4(Cart::x, 0, k, m + 1) + fac0[k] * dip4(Cart::x, 0, ind0[k], m + 1) + term; quad4(Cart::xy, 0, k, m) = PmA(0) * quad4(Cart::y, 0, k, m) - PmC(0) * quad4(Cart::y, 0, k, m + 1) + fac0[k] * dip4(Cart::y, 0, ind0[k], m + 1); quad4(Cart::xz, 0, k, m) = PmA(0) * quad4(Cart::z, 0, k, m) - PmC(0) * quad4(Cart::z, 0, k, m + 1) + fac0[k] * dip4(Cart::z, 0, ind0[k], m + 1); quad4(Cart::yy, 0, k, m) = PmA(1) * quad4(Cart::y, 0, k, m) - PmC(1) * quad4(Cart::y, 0, k, m + 1) + fac1[k] * dip4(Cart::y, 0, ind1[k], m + 1) + term; quad4(Cart::yz, 0, k, m) = PmA(1) * quad4(Cart::z, 0, k, m) - PmC(1) * quad4(Cart::z, 0, k, m + 1) + fac1[k] * dip4(Cart::z, 0, ind1[k], m + 1); quad4(Cart::zz, 0, k, m) = PmA(2) * quad4(Cart::z, 0, k, m) - PmC(2) * quad4(Cart::z, 0, k, m + 1) + fac2[k] * dip4(Cart::z, 0, ind2[k], m + 1) + term; } } } //------------------------------------------------------ // Integrals f - s if (lmax_row > 2) { for (Index m = 0; m < lsum - 2; m++) { for (Index k = 0; k < 5; k++) { quad4(Cart::xxx, 0, k, m) = PmA(0) * quad4(Cart::xx, 0, k, m) - PmC(0) * quad4(Cart::xx, 0, k, m + 1) + fac0[k] * dip4(Cart::xx, 0, ind0[k], m + 1) + 2 * fak * (quad4(Cart::x, 0, k, m) - quad4(Cart::x, 0, k, m + 1)); quad4(Cart::xxy, 0, k, m) = PmA(1) * quad4(Cart::xx, 0, k, m) - PmC(1) * quad4(Cart::xx, 0, k, m + 1) + fac1[k] * dip4(Cart::xx, 0, ind1[k], m + 1); quad4(Cart::xxz, 0, k, m) = PmA(2) * quad4(Cart::xx, 0, k, m) - PmC(2) * quad4(Cart::xx, 0, k, m + 1) + fac2[k] * dip4(Cart::xx, 0, ind2[k], m + 1); quad4(Cart::xyy, 0, k, m) = PmA(0) * quad4(Cart::yy, 0, k, m) - PmC(0) * quad4(Cart::yy, 0, k, m + 1) + fac0[k] * dip4(Cart::yy, 0, ind0[k], m + 1); quad4(Cart::xyz, 0, k, m) = PmA(0) * quad4(Cart::yz, 0, k, m) - PmC(0) * quad4(Cart::yz, 0, k, m + 1) + fac0[k] * dip4(Cart::yz, 0, ind0[k], m + 1); quad4(Cart::xzz, 0, k, m) = PmA(0) * quad4(Cart::zz, 0, k, m) - PmC(0) * quad4(Cart::zz, 0, k, m + 1) + fac0[k] * dip4(Cart::zz, 0, ind0[k], m + 1); quad4(Cart::yyy, 0, k, m) = PmA(1) * quad4(Cart::yy, 0, k, m) - PmC(1) * quad4(Cart::yy, 0, k, m + 1) + fac1[k] * dip4(Cart::yy, 0, ind1[k], m + 1) + 2 * fak * (quad4(Cart::y, 0, k, m) - quad4(Cart::y, 0, k, m + 1)); quad4(Cart::yyz, 0, k, m) = PmA(2) * quad4(Cart::yy, 0, k, m) - PmC(2) * quad4(Cart::yy, 0, k, m + 1) + fac2[k] * dip4(Cart::yy, 0, ind2[k], m + 1); quad4(Cart::yzz, 0, k, m) = PmA(1) * quad4(Cart::zz, 0, k, m) - PmC(1) * quad4(Cart::zz, 0, k, m + 1) + fac1[k] * dip4(Cart::zz, 0, ind1[k], m + 1); quad4(Cart::zzz, 0, k, m) = PmA(2) * quad4(Cart::zz, 0, k, m) - PmC(2) * quad4(Cart::zz, 0, k, m + 1) + fac2[k] * dip4(Cart::zz, 0, ind2[k], m + 1) + 2 * fak * (quad4(Cart::z, 0, k, m) - quad4(Cart::z, 0, k, m + 1)); } } } //------------------------------------------------------ // Integrals g - s if (lmax_row > 3) { for (Index m = 0; m < lsum - 3; m++) { for (Index k = 0; k < 5; k++) { double term_xx = fak * (quad4(Cart::xx, 0, k, m) - quad4(Cart::xx, 0, k, m + 1)); double term_yy = fak * (quad4(Cart::yy, 0, k, m) - quad4(Cart::yy, 0, k, m + 1)); double term_zz = fak * (quad4(Cart::zz, 0, k, m) - quad4(Cart::zz, 0, k, m + 1)); quad4(Cart::xxxx, 0, k, m) = PmA(0) * quad4(Cart::xxx, 0, k, m) - PmC(0) * quad4(Cart::xxx, 0, k, m + 1) + fac0[k] * dip4(Cart::xxx, 0, ind0[k], m + 1) + 3 * term_xx; quad4(Cart::xxxy, 0, k, m) = PmA(1) * quad4(Cart::xxx, 0, k, m) - PmC(1) * quad4(Cart::xxx, 0, k, m + 1) + fac1[k] * dip4(Cart::xxx, 0, ind1[k], m + 1); quad4(Cart::xxxz, 0, k, m) = PmA(2) * quad4(Cart::xxx, 0, k, m) - PmC(2) * quad4(Cart::xxx, 0, k, m + 1) + fac2[k] * dip4(Cart::xxx, 0, ind2[k], m + 1); quad4(Cart::xxyy, 0, k, m) = PmA(0) * quad4(Cart::xyy, 0, k, m) - PmC(0) * quad4(Cart::xyy, 0, k, m + 1) + fac0[k] * dip4(Cart::xyy, 0, ind0[k], m + 1) + term_yy; quad4(Cart::xxyz, 0, k, m) = PmA(1) * quad4(Cart::xxz, 0, k, m) - PmC(1) * quad4(Cart::xxz, 0, k, m + 1) + fac1[k] * dip4(Cart::xxz, 0, ind1[k], m + 1); quad4(Cart::xxzz, 0, k, m) = PmA(0) * quad4(Cart::xzz, 0, k, m) - PmC(0) * quad4(Cart::xzz, 0, k, m + 1) + fac0[k] * dip4(Cart::xzz, 0, ind0[k], m + 1) + term_zz; quad4(Cart::xyyy, 0, k, m) = PmA(0) * quad4(Cart::yyy, 0, k, m) - PmC(0) * quad4(Cart::yyy, 0, k, m + 1) + fac0[k] * dip4(Cart::yyy, 0, ind0[k], m + 1); quad4(Cart::xyyz, 0, k, m) = PmA(0) * quad4(Cart::yyz, 0, k, m) - PmC(0) * quad4(Cart::yyz, 0, k, m + 1) + fac0[k] * dip4(Cart::yyz, 0, ind0[k], m + 1); quad4(Cart::xyzz, 0, k, m) = PmA(0) * quad4(Cart::yzz, 0, k, m) - PmC(0) * quad4(Cart::yzz, 0, k, m + 1) + fac0[k] * dip4(Cart::yzz, 0, ind0[k], m + 1); quad4(Cart::xzzz, 0, k, m) = PmA(0) * quad4(Cart::zzz, 0, k, m) - PmC(0) * quad4(Cart::zzz, 0, k, m + 1) + fac0[k] * dip4(Cart::zzz, 0, ind0[k], m + 1); quad4(Cart::yyyy, 0, k, m) = PmA(1) * quad4(Cart::yyy, 0, k, m) - PmC(1) * quad4(Cart::yyy, 0, k, m + 1) + fac1[k] * dip4(Cart::yyy, 0, ind1[k], m + 1) + 3 * term_yy; quad4(Cart::yyyz, 0, k, m) = PmA(2) * quad4(Cart::yyy, 0, k, m) - PmC(2) * quad4(Cart::yyy, 0, k, m + 1) + fac2[k] * dip4(Cart::yyy, 0, ind2[k], m + 1); quad4(Cart::yyzz, 0, k, m) = PmA(1) * quad4(Cart::yzz, 0, k, m) - PmC(1) * quad4(Cart::yzz, 0, k, m + 1) + fac1[k] * dip4(Cart::yzz, 0, ind1[k], m + 1) + term_zz; quad4(Cart::yzzz, 0, k, m) = PmA(1) * quad4(Cart::zzz, 0, k, m) - PmC(1) * quad4(Cart::zzz, 0, k, m + 1) + fac1[k] * dip4(Cart::zzz, 0, ind1[k], m + 1); quad4(Cart::zzzz, 0, k, m) = PmA(2) * quad4(Cart::zzz, 0, k, m) - PmC(2) * quad4(Cart::zzz, 0, k, m + 1) + fac2[k] * dip4(Cart::zzz, 0, ind2[k], m + 1) + 3 * term_zz; } } } //------------------------------------------------------ if (lmax_col > 0) { // Integrals s - p for (Index m = 0; m < lmax_col; m++) { for (Index k = 0; k < 5; k++) { quad4(0, Cart::x, k, m) = PmB(0) * quad4(0, 0, k, m) - PmC(0) * quad4(0, 0, k, m + 1) + fac0[k] * dip4(0, 0, ind0[k], m + 1); quad4(0, Cart::y, k, m) = PmB(1) * quad4(0, 0, k, m) - PmC(1) * quad4(0, 0, k, m + 1) + fac1[k] * dip4(0, 0, ind1[k], m + 1); quad4(0, Cart::z, k, m) = PmB(2) * quad4(0, 0, k, m) - PmC(2) * quad4(0, 0, k, m + 1) + fac2[k] * dip4(0, 0, ind2[k], m + 1); } } //------------------------------------------------------ // Integrals p - p if (lmax_row > 0) { for (Index m = 0; m < lmax_col; m++) { for (Index i = 1; i < 4; i++) { for (Index k = 0; k < 5; k++) { double term = fak * (quad4(0, 0, k, m) - quad4(0, 0, k, m + 1)); quad4(i, Cart::x, k, m) = PmB(0) * quad4(i, 0, k, m) - PmC(0) * quad4(i, 0, k, m + 1) + fac0[k] * dip4(i, 0, ind0[k], m + 1) + nx[i] * term; quad4(i, Cart::y, k, m) = PmB(1) * quad4(i, 0, k, m) - PmC(1) * quad4(i, 0, k, m + 1) + fac1[k] * dip4(i, 0, ind1[k], m + 1) + ny[i] * term; quad4(i, Cart::z, k, m) = PmB(2) * quad4(i, 0, k, m) - PmC(2) * quad4(i, 0, k, m + 1) + fac2[k] * dip4(i, 0, ind2[k], m + 1) + nz[i] * term; } } } } //------------------------------------------------------ // Integrals d - p f - p g - p for (Index m = 0; m < lmax_col; m++) { for (Index i = 4; i < n_orbitals[lmax_row]; i++) { int nx_i = nx[i]; int ny_i = ny[i]; int nz_i = nz[i]; int ilx_i = i_less_x[i]; int ily_i = i_less_y[i]; int ilz_i = i_less_z[i]; for (Index k = 0; k < 5; k++) { quad4(i, Cart::x, k, m) = PmB(0) * quad4(i, 0, k, m) - PmC(0) * quad4(i, 0, k, m + 1) + fac0[k] * dip4(i, 0, ind0[k], m + 1) + nx_i * fak * (quad4(ilx_i, 0, k, m) - quad4(ilx_i, 0, k, m + 1)); quad4(i, Cart::y, k, m) = PmB(1) * quad4(i, 0, k, m) - PmC(1) * quad4(i, 0, k, m + 1) + fac1[k] * dip4(i, 0, ind1[k], m + 1) + ny_i * fak * (quad4(ily_i, 0, k, m) - quad4(ily_i, 0, k, m + 1)); quad4(i, Cart::z, k, m) = PmB(2) * quad4(i, 0, k, m) - PmC(2) * quad4(i, 0, k, m + 1) + fac2[k] * dip4(i, 0, ind2[k], m + 1) + nz_i * fak * (quad4(ilz_i, 0, k, m) - quad4(ilz_i, 0, k, m + 1)); } } } //------------------------------------------------------ } // end if (lmax_col > 0) if (lmax_col > 1) { // Integrals s - d for (Index m = 0; m < lmax_col - 1; m++) { for (Index k = 0; k < 5; k++) { double term = fak * (quad4(0, 0, k, m) - quad4(0, 0, k, m + 1)); quad4(0, Cart::xx, k, m) = PmB(0) * quad4(0, Cart::x, k, m) - PmC(0) * quad4(0, Cart::x, k, m + 1) + fac0[k] * dip4(0, Cart::x, ind0[k], m + 1) + term; quad4(0, Cart::xy, k, m) = PmB(0) * quad4(0, Cart::y, k, m) - PmC(0) * quad4(0, Cart::y, k, m + 1) + fac0[k] * dip4(0, Cart::y, ind0[k], m + 1); quad4(0, Cart::xz, k, m) = PmB(0) * quad4(0, Cart::z, k, m) - PmC(0) * quad4(0, Cart::z, k, m + 1) + fac0[k] * dip4(0, Cart::z, ind0[k], m + 1); quad4(0, Cart::yy, k, m) = PmB(1) * quad4(0, Cart::y, k, m) - PmC(1) * quad4(0, Cart::y, k, m + 1) + fac1[k] * dip4(0, Cart::y, ind1[k], m + 1) + term; quad4(0, Cart::yz, k, m) = PmB(1) * quad4(0, Cart::z, k, m) - PmC(1) * quad4(0, Cart::z, k, m + 1) + fac1[k] * dip4(0, Cart::z, ind1[k], m + 1); quad4(0, Cart::zz, k, m) = PmB(2) * quad4(0, Cart::z, k, m) - PmC(2) * quad4(0, Cart::z, k, m + 1) + fac2[k] * dip4(0, Cart::z, ind2[k], m + 1) + term; } } //------------------------------------------------------ // Integrals p - d d - d f - d g - d for (Index m = 0; m < lmax_col - 1; m++) { for (Index i = 1; i < n_orbitals[lmax_row]; i++) { int nx_i = nx[i]; int ny_i = ny[i]; int nz_i = nz[i]; int ilx_i = i_less_x[i]; int ily_i = i_less_y[i]; int ilz_i = i_less_z[i]; for (Index k = 0; k < 5; k++) { double term = fak * (quad4(i, 0, k, m) - quad4(i, 0, k, m + 1)); quad4(i, Cart::xx, k, m) = PmB(0) * quad4(i, Cart::x, k, m) - PmC(0) * quad4(i, Cart::x, k, m + 1) + fac0[k] * dip4(i, Cart::x, ind0[k], m + 1) + nx_i * fak * (quad4(ilx_i, Cart::x, k, m) - quad4(ilx_i, Cart::x, k, m + 1)) + term; quad4(i, Cart::xy, k, m) = PmB(0) * quad4(i, Cart::y, k, m) - PmC(0) * quad4(i, Cart::y, k, m + 1) + fac0[k] * dip4(i, Cart::y, ind0[k], m + 1) + nx_i * fak * (quad4(ilx_i, Cart::y, k, m) - quad4(ilx_i, Cart::y, k, m + 1)); quad4(i, Cart::xz, k, m) = PmB(0) * quad4(i, Cart::z, k, m) - PmC(0) * quad4(i, Cart::z, k, m + 1) + fac0[k] * dip4(i, Cart::z, ind0[k], m + 1) + nx_i * fak * (quad4(ilx_i, Cart::z, k, m) - quad4(ilx_i, Cart::z, k, m + 1)); quad4(i, Cart::yy, k, m) = PmB(1) * quad4(i, Cart::y, k, m) - PmC(1) * quad4(i, Cart::y, k, m + 1) + fac1[k] * dip4(i, Cart::y, ind1[k], m + 1) + ny_i * fak * (quad4(ily_i, Cart::y, k, m) - quad4(ily_i, Cart::y, k, m + 1)) + term; quad4(i, Cart::yz, k, m) = PmB(1) * quad4(i, Cart::z, k, m) - PmC(1) * quad4(i, Cart::z, k, m + 1) + fac1[k] * dip4(i, Cart::z, ind1[k], m + 1) + ny_i * fak * (quad4(ily_i, Cart::z, k, m) - quad4(ily_i, Cart::z, k, m + 1)); quad4(i, Cart::zz, k, m) = PmB(2) * quad4(i, Cart::z, k, m) - PmC(2) * quad4(i, Cart::z, k, m + 1) + fac2[k] * dip4(i, Cart::z, ind2[k], m + 1) + nz_i * fak * (quad4(ilz_i, Cart::z, k, m) - quad4(ilz_i, Cart::z, k, m + 1)) + term; } } } //------------------------------------------------------ } // end if (lmax_col > 1) if (lmax_col > 2) { // Integrals s - f for (Index m = 0; m < lmax_col - 2; m++) { for (Index k = 0; k < 5; k++) { quad4(0, Cart::xxx, k, m) = PmB(0) * quad4(0, Cart::xx, k, m) - PmC(0) * quad4(0, Cart::xx, k, m + 1) + fac0[k] * dip4(0, Cart::xx, ind0[k], m + 1) + 2 * fak * (quad4(0, Cart::x, k, m) - quad4(0, Cart::x, k, m + 1)); quad4(0, Cart::xxy, k, m) = PmB(1) * quad4(0, Cart::xx, k, m) - PmC(1) * quad4(0, Cart::xx, k, m + 1) + fac1[k] * dip4(0, Cart::xx, ind1[k], m + 1); quad4(0, Cart::xxz, k, m) = PmB(2) * quad4(0, Cart::xx, k, m) - PmC(2) * quad4(0, Cart::xx, k, m + 1) + fac2[k] * dip4(0, Cart::xx, ind2[k], m + 1); quad4(0, Cart::xyy, k, m) = PmB(0) * quad4(0, Cart::yy, k, m) - PmC(0) * quad4(0, Cart::yy, k, m + 1) + fac0[k] * dip4(0, Cart::yy, ind0[k], m + 1); quad4(0, Cart::xyz, k, m) = PmB(0) * quad4(0, Cart::yz, k, m) - PmC(0) * quad4(0, Cart::yz, k, m + 1) + fac0[k] * dip4(0, Cart::yz, ind0[k], m + 1); quad4(0, Cart::xzz, k, m) = PmB(0) * quad4(0, Cart::zz, k, m) - PmC(0) * quad4(0, Cart::zz, k, m + 1) + fac0[k] * dip4(0, Cart::zz, ind0[k], m + 1); quad4(0, Cart::yyy, k, m) = PmB(1) * quad4(0, Cart::yy, k, m) - PmC(1) * quad4(0, Cart::yy, k, m + 1) + fac1[k] * dip4(0, Cart::yy, ind1[k], m + 1) + 2 * fak * (quad4(0, Cart::y, k, m) - quad4(0, Cart::y, k, m + 1)); quad4(0, Cart::yyz, k, m) = PmB(2) * quad4(0, Cart::yy, k, m) - PmC(2) * quad4(0, Cart::yy, k, m + 1) + fac2[k] * dip4(0, Cart::yy, ind2[k], m + 1); quad4(0, Cart::yzz, k, m) = PmB(1) * quad4(0, Cart::zz, k, m) - PmC(1) * quad4(0, Cart::zz, k, m + 1) + fac1[k] * dip4(0, Cart::zz, ind1[k], m + 1); quad4(0, Cart::zzz, k, m) = PmB(2) * quad4(0, Cart::zz, k, m) - PmC(2) * quad4(0, Cart::zz, k, m + 1) + fac2[k] * dip4(0, Cart::zz, ind2[k], m + 1) + 2 * fak * (quad4(0, Cart::z, k, m) - quad4(0, Cart::z, k, m + 1)); } } //------------------------------------------------------ // Integrals p - f d - f f - f g - f for (Index m = 0; m < lmax_col - 2; m++) { for (Index i = 1; i < n_orbitals[lmax_row]; i++) { int nx_i = nx[i]; int ny_i = ny[i]; int nz_i = nz[i]; int ilx_i = i_less_x[i]; int ily_i = i_less_y[i]; int ilz_i = i_less_z[i]; for (Index k = 0; k < 5; k++) { double term_x = 2 * fak * (quad4(i, Cart::x, k, m) - quad4(i, Cart::x, k, m + 1)); double term_y = 2 * fak * (quad4(i, Cart::y, k, m) - quad4(i, Cart::y, k, m + 1)); double term_z = 2 * fak * (quad4(i, Cart::z, k, m) - quad4(i, Cart::z, k, m + 1)); quad4(i, Cart::xxx, k, m) = PmB(0) * quad4(i, Cart::xx, k, m) - PmC(0) * quad4(i, Cart::xx, k, m + 1) + fac0[k] * dip4(i, Cart::xx, ind0[k], m + 1) + nx_i * fak * (quad4(ilx_i, Cart::xx, k, m) - quad4(ilx_i, Cart::xx, k, m + 1)) + term_x; quad4(i, Cart::xxy, k, m) = PmB(1) * quad4(i, Cart::xx, k, m) - PmC(1) * quad4(i, Cart::xx, k, m + 1) + fac1[k] * dip4(i, Cart::xx, ind1[k], m + 1) + ny_i * fak * (quad4(ily_i, Cart::xx, k, m) - quad4(ily_i, Cart::xx, k, m + 1)); quad4(i, Cart::xxz, k, m) = PmB(2) * quad4(i, Cart::xx, k, m) - PmC(2) * quad4(i, Cart::xx, k, m + 1) + fac2[k] * dip4(i, Cart::xx, ind2[k], m + 1) + nz_i * fak * (quad4(ilz_i, Cart::xx, k, m) - quad4(ilz_i, Cart::xx, k, m + 1)); quad4(i, Cart::xyy, k, m) = PmB(0) * quad4(i, Cart::yy, k, m) - PmC(0) * quad4(i, Cart::yy, k, m + 1) + fac0[k] * dip4(i, Cart::yy, ind0[k], m + 1) + nx_i * fak * (quad4(ilx_i, Cart::yy, k, m) - quad4(ilx_i, Cart::yy, k, m + 1)); quad4(i, Cart::xyz, k, m) = PmB(0) * quad4(i, Cart::yz, k, m) - PmC(0) * quad4(i, Cart::yz, k, m + 1) + fac0[k] * dip4(i, Cart::yz, ind0[k], m + 1) + nx_i * fak * (quad4(ilx_i, Cart::yz, k, m) - quad4(ilx_i, Cart::yz, k, m + 1)); quad4(i, Cart::xzz, k, m) = PmB(0) * quad4(i, Cart::zz, k, m) - PmC(0) * quad4(i, Cart::zz, k, m + 1) + fac0[k] * dip4(i, Cart::zz, ind0[k], m + 1) + nx_i * fak * (quad4(ilx_i, Cart::zz, k, m) - quad4(ilx_i, Cart::zz, k, m + 1)); quad4(i, Cart::yyy, k, m) = PmB(1) * quad4(i, Cart::yy, k, m) - PmC(1) * quad4(i, Cart::yy, k, m + 1) + fac1[k] * dip4(i, Cart::yy, ind1[k], m + 1) + ny_i * fak * (quad4(ily_i, Cart::yy, k, m) - quad4(ily_i, Cart::yy, k, m + 1)) + term_y; quad4(i, Cart::yyz, k, m) = PmB(2) * quad4(i, Cart::yy, k, m) - PmC(2) * quad4(i, Cart::yy, k, m + 1) + fac2[k] * dip4(i, Cart::yy, ind2[k], m + 1) + nz_i * fak * (quad4(ilz_i, Cart::yy, k, m) - quad4(ilz_i, Cart::yy, k, m + 1)); quad4(i, Cart::yzz, k, m) = PmB(1) * quad4(i, Cart::zz, k, m) - PmC(1) * quad4(i, Cart::zz, k, m + 1) + fac1[k] * dip4(i, Cart::zz, ind1[k], m + 1) + ny_i * fak * (quad4(ily_i, Cart::zz, k, m) - quad4(ily_i, Cart::zz, k, m + 1)); quad4(i, Cart::zzz, k, m) = PmB(2) * quad4(i, Cart::zz, k, m) - PmC(2) * quad4(i, Cart::zz, k, m + 1) + fac2[k] * dip4(i, Cart::zz, ind2[k], m + 1) + nz_i * fak * (quad4(ilz_i, Cart::zz, k, m) - quad4(ilz_i, Cart::zz, k, m + 1)) + term_z; } } } //------------------------------------------------------ } // end if (lmax_col > 2) if (lmax_col > 3) { // Integrals s - g for (Index m = 0; m < lmax_col - 3; m++) { for (Index k = 0; k < 5; k++) { double term_xx = fak * (quad4(0, Cart::xx, k, m) - quad4(0, Cart::xx, k, m + 1)); double term_yy = fak * (quad4(0, Cart::yy, k, m) - quad4(0, Cart::yy, k, m + 1)); double term_zz = fak * (quad4(0, Cart::zz, k, m) - quad4(0, Cart::zz, k, m + 1)); quad4(0, Cart::xxxx, k, m) = PmB(0) * quad4(0, Cart::xxx, k, m) - PmC(0) * quad4(0, Cart::xxx, k, m + 1) + fac0[k] * dip4(0, Cart::xxx, ind0[k], m + 1) + 3 * term_xx; quad4(0, Cart::xxxy, k, m) = PmB(1) * quad4(0, Cart::xxx, k, m) - PmC(1) * quad4(0, Cart::xxx, k, m + 1) + fac1[k] * dip4(0, Cart::xxx, ind1[k], m + 1); quad4(0, Cart::xxxz, k, m) = PmB(2) * quad4(0, Cart::xxx, k, m) - PmC(2) * quad4(0, Cart::xxx, k, m + 1) + fac2[k] * dip4(0, Cart::xxx, ind2[k], m + 1); quad4(0, Cart::xxyy, k, m) = PmB(0) * quad4(0, Cart::xyy, k, m) - PmC(0) * quad4(0, Cart::xyy, k, m + 1) + fac0[k] * dip4(0, Cart::xyy, ind0[k], m + 1) + term_yy; quad4(0, Cart::xxyz, k, m) = PmB(1) * quad4(0, Cart::xxz, k, m) - PmC(1) * quad4(0, Cart::xxz, k, m + 1) + fac1[k] * dip4(0, Cart::xxz, ind1[k], m + 1); quad4(0, Cart::xxzz, k, m) = PmB(0) * quad4(0, Cart::xzz, k, m) - PmC(0) * quad4(0, Cart::xzz, k, m + 1) + fac0[k] * dip4(0, Cart::xzz, ind0[k], m + 1) + term_zz; quad4(0, Cart::xyyy, k, m) = PmB(0) * quad4(0, Cart::yyy, k, m) - PmC(0) * quad4(0, Cart::yyy, k, m + 1) + fac0[k] * dip4(0, Cart::yyy, ind0[k], m + 1); quad4(0, Cart::xyyz, k, m) = PmB(0) * quad4(0, Cart::yyz, k, m) - PmC(0) * quad4(0, Cart::yyz, k, m + 1) + fac0[k] * dip4(0, Cart::yyz, ind0[k], m + 1); quad4(0, Cart::xyzz, k, m) = PmB(0) * quad4(0, Cart::yzz, k, m) - PmC(0) * quad4(0, Cart::yzz, k, m + 1) + fac0[k] * dip4(0, Cart::yzz, ind0[k], m + 1); quad4(0, Cart::xzzz, k, m) = PmB(0) * quad4(0, Cart::zzz, k, m) - PmC(0) * quad4(0, Cart::zzz, k, m + 1) + fac0[k] * dip4(0, Cart::zzz, ind0[k], m + 1); quad4(0, Cart::yyyy, k, m) = PmB(1) * quad4(0, Cart::yyy, k, m) - PmC(1) * quad4(0, Cart::yyy, k, m + 1) + fac1[k] * dip4(0, Cart::yyy, ind1[k], m + 1) + 3 * term_yy; quad4(0, Cart::yyyz, k, m) = PmB(2) * quad4(0, Cart::yyy, k, m) - PmC(2) * quad4(0, Cart::yyy, k, m + 1) + fac2[k] * dip4(0, Cart::yyy, ind2[k], m + 1); quad4(0, Cart::yyzz, k, m) = PmB(1) * quad4(0, Cart::yzz, k, m) - PmC(1) * quad4(0, Cart::yzz, k, m + 1) + fac1[k] * dip4(0, Cart::yzz, ind1[k], m + 1) + term_zz; quad4(0, Cart::yzzz, k, m) = PmB(1) * quad4(0, Cart::zzz, k, m) - PmC(1) * quad4(0, Cart::zzz, k, m + 1) + fac1[k] * dip4(0, Cart::zzz, ind1[k], m + 1); quad4(0, Cart::zzzz, k, m) = PmB(2) * quad4(0, Cart::zzz, k, m) - PmC(2) * quad4(0, Cart::zzz, k, m + 1) + fac2[k] * dip4(0, Cart::zzz, ind2[k], m + 1) + 3 * term_zz; } } //------------------------------------------------------ // Integrals p - g d - g f - g g - g for (Index m = 0; m < lmax_col - 3; m++) { for (Index i = 1; i < n_orbitals[lmax_row]; i++) { int nx_i = nx[i]; int ny_i = ny[i]; int nz_i = nz[i]; int ilx_i = i_less_x[i]; int ily_i = i_less_y[i]; int ilz_i = i_less_z[i]; for (Index k = 0; k < 5; k++) { double term_xx = fak * (quad4(i, Cart::xx, k, m) - quad4(i, Cart::xx, k, m + 1)); double term_yy = fak * (quad4(i, Cart::yy, k, m) - quad4(i, Cart::yy, k, m + 1)); double term_zz = fak * (quad4(i, Cart::zz, k, m) - quad4(i, Cart::zz, k, m + 1)); quad4(i, Cart::xxxx, k, m) = PmB(0) * quad4(i, Cart::xxx, k, m) - PmC(0) * quad4(i, Cart::xxx, k, m + 1) + fac0[k] * dip4(i, Cart::xxx, ind0[k], m + 1) + nx_i * fak * (quad4(ilx_i, Cart::xxx, k, m) - quad4(ilx_i, Cart::xxx, k, m + 1)) + 3 * term_xx; quad4(i, Cart::xxxy, k, m) = PmB(1) * quad4(i, Cart::xxx, k, m) - PmC(1) * quad4(i, Cart::xxx, k, m + 1) + fac1[k] * dip4(i, Cart::xxx, ind1[k], m + 1) + ny_i * fak * (quad4(ily_i, Cart::xxx, k, m) - quad4(ily_i, Cart::xxx, k, m + 1)); quad4(i, Cart::xxxz, k, m) = PmB(2) * quad4(i, Cart::xxx, k, m) - PmC(2) * quad4(i, Cart::xxx, k, m + 1) + fac2[k] * dip4(i, Cart::xxx, ind2[k], m + 1) + nz_i * fak * (quad4(ilz_i, Cart::xxx, k, m) - quad4(ilz_i, Cart::xxx, k, m + 1)); quad4(i, Cart::xxyy, k, m) = PmB(0) * quad4(i, Cart::xyy, k, m) - PmC(0) * quad4(i, Cart::xyy, k, m + 1) + fac0[k] * dip4(i, Cart::xyy, ind0[k], m + 1) + nx_i * fak * (quad4(ilx_i, Cart::xyy, k, m) - quad4(ilx_i, Cart::xyy, k, m + 1)) + term_yy; quad4(i, Cart::xxyz, k, m) = PmB(1) * quad4(i, Cart::xxz, k, m) - PmC(1) * quad4(i, Cart::xxz, k, m + 1) + fac1[k] * dip4(i, Cart::xxz, ind1[k], m + 1) + ny_i * fak * (quad4(ily_i, Cart::xxz, k, m) - quad4(ily_i, Cart::xxz, k, m + 1)); quad4(i, Cart::xxzz, k, m) = PmB(0) * quad4(i, Cart::xzz, k, m) - PmC(0) * quad4(i, Cart::xzz, k, m + 1) + fac0[k] * dip4(i, Cart::xzz, ind0[k], m + 1) + nx_i * fak * (quad4(ilx_i, Cart::xzz, k, m) - quad4(ilx_i, Cart::xzz, k, m + 1)) + term_zz; quad4(i, Cart::xyyy, k, m) = PmB(0) * quad4(i, Cart::yyy, k, m) - PmC(0) * quad4(i, Cart::yyy, k, m + 1) + fac0[k] * dip4(i, Cart::yyy, ind0[k], m + 1) + nx_i * fak * (quad4(ilx_i, Cart::yyy, k, m) - quad4(ilx_i, Cart::yyy, k, m + 1)); quad4(i, Cart::xyyz, k, m) = PmB(0) * quad4(i, Cart::yyz, k, m) - PmC(0) * quad4(i, Cart::yyz, k, m + 1) + fac0[k] * dip4(i, Cart::yyz, ind0[k], m + 1) + nx_i * fak * (quad4(ilx_i, Cart::yyz, k, m) - quad4(ilx_i, Cart::yyz, k, m + 1)); quad4(i, Cart::xyzz, k, m) = PmB(0) * quad4(i, Cart::yzz, k, m) - PmC(0) * quad4(i, Cart::yzz, k, m + 1) + fac0[k] * dip4(i, Cart::yzz, ind0[k], m + 1) + nx_i * fak * (quad4(ilx_i, Cart::yzz, k, m) - quad4(ilx_i, Cart::yzz, k, m + 1)); quad4(i, Cart::xzzz, k, m) = PmB(0) * quad4(i, Cart::zzz, k, m) - PmC(0) * quad4(i, Cart::zzz, k, m + 1) + fac0[k] * dip4(i, Cart::zzz, ind0[k], m + 1) + nx_i * fak * (quad4(ilx_i, Cart::zzz, k, m) - quad4(ilx_i, Cart::zzz, k, m + 1)); quad4(i, Cart::yyyy, k, m) = PmB(1) * quad4(i, Cart::yyy, k, m) - PmC(1) * quad4(i, Cart::yyy, k, m + 1) + fac1[k] * dip4(i, Cart::yyy, ind1[k], m + 1) + ny_i * fak * (quad4(ily_i, Cart::yyy, k, m) - quad4(ily_i, Cart::yyy, k, m + 1)) + 3 * term_yy; quad4(i, Cart::yyyz, k, m) = PmB(2) * quad4(i, Cart::yyy, k, m) - PmC(2) * quad4(i, Cart::yyy, k, m + 1) + fac2[k] * dip4(i, Cart::yyy, ind2[k], m + 1) + nz_i * fak * (quad4(ilz_i, Cart::yyy, k, m) - quad4(ilz_i, Cart::yyy, k, m + 1)); quad4(i, Cart::yyzz, k, m) = PmB(1) * quad4(i, Cart::yzz, k, m) - PmC(1) * quad4(i, Cart::yzz, k, m + 1) + fac1[k] * dip4(i, Cart::yzz, ind1[k], m + 1) + ny_i * fak * (quad4(ily_i, Cart::yzz, k, m) - quad4(ily_i, Cart::yzz, k, m + 1)) + term_zz; quad4(i, Cart::yzzz, k, m) = PmB(1) * quad4(i, Cart::zzz, k, m) - PmC(1) * quad4(i, Cart::zzz, k, m + 1) + fac1[k] * dip4(i, Cart::zzz, ind1[k], m + 1) + ny_i * fak * (quad4(ily_i, Cart::zzz, k, m) - quad4(ily_i, Cart::zzz, k, m + 1)); quad4(i, Cart::zzzz, k, m) = PmB(2) * quad4(i, Cart::zzz, k, m) - PmC(2) * quad4(i, Cart::zzz, k, m + 1) + fac2[k] * dip4(i, Cart::zzz, ind2[k], m + 1) + nz_i * fak * (quad4(ilz_i, Cart::zzz, k, m) - quad4(ilz_i, Cart::zzz, k, m + 1)) + 3 * term_zz; } } } //------------------------------------------------------ } // end if (lmax_col > 3) multipole += quadrupole(0, 1) * Eigen::Map(quad4.data(), nrows, ncols); multipole += quadrupole(0, 2) * Eigen::Map(quad4.data() + offset, nrows, ncols); multipole += quadrupole(1, 2) * Eigen::Map( quad4.data() + 2 * offset, nrows, ncols); multipole += 0.5 * quadrupole(0, 0) * Eigen::Map(quad4.data() + 3 * offset, nrows, ncols); multipole += 0.5 * quadrupole(1, 1) * Eigen::Map(quad4.data() + 4 * offset, nrows, ncols); } } // save to matrix cartesian += AOTransform::getNorm(shell_row.getL(), gaussian_row) * AOTransform::getNorm(shell_col.getL(), gaussian_col) * multipole.bottomRightCorner(shell_row.getCartesianNumFunc(), shell_col.getCartesianNumFunc()); } // shell_col Gaussians } // shell_row Gaussians matrix = AOTransform::tform(shell_row.getL(), shell_col.getL(), cartesian); } void AOMultipole::FillPotential(const AOBasis& aobasis, const Eigen::Vector3d& r) { StaticSite s = StaticSite(0, "", r); s.setCharge(1.0); setSite(&s); _aopotential = Fill(aobasis); } void AOMultipole::FillPotential(const AOBasis& aobasis, const QMMolecule& atoms) { _aopotential = Eigen::MatrixXd::Zero(aobasis.AOBasisSize(), aobasis.AOBasisSize()); for (const auto& atom : atoms) { StaticSite s = StaticSite(atom, double(atom.getNuccharge())); setSite(&s); _aopotential -= Fill(aobasis); } return; } void AOMultipole::FillPotential( const AOBasis& aobasis, const std::vector >& externalsites) { _aopotential = Eigen::MatrixXd::Zero(aobasis.AOBasisSize(), aobasis.AOBasisSize()); for (const std::unique_ptr& site : externalsites) { setSite(site.get()); _aopotential -= Fill(aobasis); } return; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/aomatrices/aoplanewave.cc000066400000000000000000001025161412152066400214520ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/aopotential.h" #include "votca/xtp/aotransform.h" namespace votca { namespace xtp { void AOPlanewave::FillBlock(Eigen::Block& matrix, const AOShell& shell_row, const AOShell& shell_col) const { // shell info, only lmax tells how far to go Index lmax_row = Index(shell_row.getL()); Index lmax_col = Index(shell_col.getL()); // set size of internal block for recursion Index nrows = AOTransform::getBlockSize(lmax_row); Index ncols = AOTransform::getBlockSize(lmax_col); if (lmax_col > 6 || lmax_row > 6) { throw std::runtime_error( "Orbitals higher than i are not yet implemented. This should not have " "happened!"); } // get shell positions const Eigen::Vector3d& pos_row = shell_row.getPos(); // get position R_{i} const Eigen::Vector3d& pos_col = shell_col.getPos(); // get position R_{j} const Eigen::Vector3d diff = pos_row - pos_col; // get difference r_{ij} const double distsq = diff.squaredNorm(); // get |R_{ij}|^2 // get kvector modulus const double kmodulus = _k.squaredNorm(); // get |k|^2 std::array n_orbitals = AOTransform::n_orbitals(); std::array nx = AOTransform::nx(); std::array ny = AOTransform::ny(); std::array nz = AOTransform::nz(); std::array i_less_x = AOTransform::i_less_x(); std::array i_less_y = AOTransform::i_less_y(); std::array i_less_z = AOTransform::i_less_z(); Eigen::MatrixXcd cartesian = Eigen::MatrixXcd::Zero( shell_row.getCartesianNumFunc(), shell_col.getCartesianNumFunc()); // iterate over Gaussians in this shell_row for (const auto& gaussian_row : shell_row) { // iterate over Gaussians in this shell_col // get decay constant const double decay_row = gaussian_row.getDecay(); for (const auto& gaussian_col : shell_col) { // get decay constant const double decay_col = gaussian_col.getDecay(); // some helpers const double fak = 0.5 / (decay_row + decay_col); const double fak2 = 2.0 * fak; double exparg = fak2 * decay_row * decay_col * distsq; // initialize local matrix block for unnormalized cartesians Eigen::MatrixXcd olk = Eigen::MatrixXcd::Zero(nrows, ncols); using COMPLEX = std::complex; // Define an abbreviation for // complex numbers Eigen::Vector3cd PmA; PmA.real() = fak2 * (decay_row * pos_row + decay_col * pos_col) - pos_row; PmA.imag() = fak * _k; Eigen::Vector3cd PmB; PmB.real() = fak2 * (decay_row * pos_row + decay_col * pos_col) - pos_col; PmB.imag() = fak * _k; const COMPLEX cfak(fak, 0.0); const COMPLEX cfak2(fak2, 0.0); // calculate s-s- overlap matrix element COMPLEX ssol(std::pow(4.0 * decay_row * decay_col, 0.75) * std::pow(fak2, 1.5) * std::exp(-exparg), 0.0); // s-s element // calculate s-W-s matrix element double kdotr_row = _k.dot(pos_row); double kdotr_col = _k.dot(pos_col); COMPLEX kexparg( fak2 * (-0.25) * (kmodulus), fak2 * (decay_row) * (kdotr_row) + fak2 * (decay_col) * (kdotr_col)); olk(0, 0) = ssol * (std::exp(kexparg)); // s-W-s element // Integral p-W-s if (lmax_row > 0) { olk(Cart::x, 0) = PmA(0) * olk(0, 0); olk(Cart::y, 0) = PmA(1) * olk(0, 0); olk(Cart::z, 0) = PmA(2) * olk(0, 0); } //------------------------------------------------------ // Integrals d - W - s if (lmax_row > 1) { COMPLEX term = (cfak) * (olk(0, 0)); olk(Cart::xx, 0) = PmA(0) * olk(Cart::x, 0) + term; olk(Cart::xy, 0) = PmA(0) * olk(Cart::y, 0); olk(Cart::xz, 0) = PmA(0) * olk(Cart::z, 0); olk(Cart::yy, 0) = PmA(1) * olk(Cart::y, 0) + term; olk(Cart::yz, 0) = PmA(1) * olk(Cart::z, 0); olk(Cart::zz, 0) = PmA(2) * olk(Cart::z, 0) + term; } //------------------------------------------------------ // Integrals f - W - s if (lmax_row > 2) { olk(Cart::xxx, 0) = PmA(0) * olk(Cart::xx, 0) + cfak2 * olk(Cart::x, 0); olk(Cart::xxy, 0) = PmA(1) * olk(Cart::xx, 0); olk(Cart::xxz, 0) = PmA(2) * olk(Cart::xx, 0); olk(Cart::xyy, 0) = PmA(0) * olk(Cart::yy, 0); olk(Cart::xyz, 0) = PmA(0) * olk(Cart::yz, 0); olk(Cart::xzz, 0) = PmA(0) * olk(Cart::zz, 0); olk(Cart::yyy, 0) = PmA(1) * olk(Cart::yy, 0) + cfak2 * olk(Cart::y, 0); olk(Cart::yyz, 0) = PmA(2) * olk(Cart::yy, 0); olk(Cart::yzz, 0) = PmA(1) * olk(Cart::zz, 0); olk(Cart::zzz, 0) = PmA(2) * olk(Cart::zz, 0) + cfak2 * olk(Cart::z, 0); } //------------------------------------------------------ // Integrals g - W - s if (lmax_row > 3) { COMPLEX term_xx = (cfak) * (olk(Cart::xx, 0)); COMPLEX term_yy = (cfak) * (olk(Cart::yy, 0)); COMPLEX term_zz = (cfak) * (olk(Cart::zz, 0)); olk(Cart::xxxx, 0) = PmA(0) * olk(Cart::xxx, 0) + 3.0 * term_xx; olk(Cart::xxxy, 0) = PmA(1) * olk(Cart::xxx, 0); olk(Cart::xxxz, 0) = PmA(2) * olk(Cart::xxx, 0); olk(Cart::xxyy, 0) = PmA(0) * olk(Cart::xyy, 0) + term_yy; olk(Cart::xxyz, 0) = PmA(1) * olk(Cart::xxz, 0); olk(Cart::xxzz, 0) = PmA(0) * olk(Cart::xzz, 0) + term_zz; olk(Cart::xyyy, 0) = PmA(0) * olk(Cart::yyy, 0); olk(Cart::xyyz, 0) = PmA(0) * olk(Cart::yyz, 0); olk(Cart::xyzz, 0) = PmA(0) * olk(Cart::yzz, 0); olk(Cart::xzzz, 0) = PmA(0) * olk(Cart::zzz, 0); olk(Cart::yyyy, 0) = PmA(1) * olk(Cart::yyy, 0) + 3.0 * term_yy; olk(Cart::yyyz, 0) = PmA(2) * olk(Cart::yyy, 0); olk(Cart::yyzz, 0) = PmA(1) * olk(Cart::yzz, 0) + term_zz; olk(Cart::yzzz, 0) = PmA(1) * olk(Cart::zzz, 0); olk(Cart::zzzz, 0) = PmA(2) * olk(Cart::zzz, 0) + 3.0 * term_zz; } //------------------------------------------------------ // Integrals h - W - s if (lmax_row > 4) { COMPLEX term_xxx = (cfak) * (olk(Cart::xxx, 0)); COMPLEX term_yyy = (cfak) * (olk(Cart::yyy, 0)); COMPLEX term_zzz = (cfak) * (olk(Cart::zzz, 0)); olk(Cart::xxxxx, 0) = PmA(0) * olk(Cart::xxxx, 0) + 4.0 * term_xxx; olk(Cart::xxxxy, 0) = PmA(1) * olk(Cart::xxxx, 0); olk(Cart::xxxxz, 0) = PmA(2) * olk(Cart::xxxx, 0); olk(Cart::xxxyy, 0) = PmA(1) * olk(Cart::xxxy, 0) + term_xxx; olk(Cart::xxxyz, 0) = PmA(1) * olk(Cart::xxxz, 0); olk(Cart::xxxzz, 0) = PmA(2) * olk(Cart::xxxz, 0) + term_xxx; olk(Cart::xxyyy, 0) = PmA(0) * olk(Cart::xyyy, 0) + term_yyy; olk(Cart::xxyyz, 0) = PmA(2) * olk(Cart::xxyy, 0); olk(Cart::xxyzz, 0) = PmA(1) * olk(Cart::xxzz, 0); olk(Cart::xxzzz, 0) = PmA(0) * olk(Cart::xzzz, 0) + term_zzz; olk(Cart::xyyyy, 0) = PmA(0) * olk(Cart::yyyy, 0); olk(Cart::xyyyz, 0) = PmA(0) * olk(Cart::yyyz, 0); olk(Cart::xyyzz, 0) = PmA(0) * olk(Cart::yyzz, 0); olk(Cart::xyzzz, 0) = PmA(0) * olk(Cart::yzzz, 0); olk(Cart::xzzzz, 0) = PmA(0) * olk(Cart::zzzz, 0); olk(Cart::yyyyy, 0) = PmA(1) * olk(Cart::yyyy, 0) + 4.0 * term_yyy; olk(Cart::yyyyz, 0) = PmA(2) * olk(Cart::yyyy, 0); olk(Cart::yyyzz, 0) = PmA(2) * olk(Cart::yyyz, 0) + term_yyy; olk(Cart::yyzzz, 0) = PmA(1) * olk(Cart::yzzz, 0) + term_zzz; olk(Cart::yzzzz, 0) = PmA(1) * olk(Cart::zzzz, 0); olk(Cart::zzzzz, 0) = PmA(2) * olk(Cart::zzzz, 0) + 4.0 * term_zzz; } //------------------------------------------------------ // Integrals i -W - s if (lmax_row > 5) { COMPLEX term_xxxx = (cfak) * (olk(Cart::xxxx, 0)); COMPLEX term_xyyy = (cfak) * (olk(Cart::xyyy, 0)); COMPLEX term_xzzz = (cfak) * (olk(Cart::xzzz, 0)); COMPLEX term_yyyy = (cfak) * (olk(Cart::yyyy, 0)); COMPLEX term_yyzz = (cfak) * (olk(Cart::yyzz, 0)); COMPLEX term_yzzz = (cfak) * (olk(Cart::yzzz, 0)); COMPLEX term_zzzz = (cfak) * (olk(Cart::zzzz, 0)); olk(Cart::xxxxxx, 0) = PmA(0) * olk(Cart::xxxxx, 0) + 5.0 * term_xxxx; olk(Cart::xxxxxy, 0) = PmA(1) * olk(Cart::xxxxx, 0); olk(Cart::xxxxxz, 0) = PmA(2) * olk(Cart::xxxxx, 0); olk(Cart::xxxxyy, 0) = PmA(1) * olk(Cart::xxxxy, 0) + term_xxxx; olk(Cart::xxxxyz, 0) = PmA(1) * olk(Cart::xxxxz, 0); olk(Cart::xxxxzz, 0) = PmA(2) * olk(Cart::xxxxz, 0) + term_xxxx; olk(Cart::xxxyyy, 0) = PmA(0) * olk(Cart::xxyyy, 0) + 2.0 * term_xyyy; olk(Cart::xxxyyz, 0) = PmA(2) * olk(Cart::xxxyy, 0); olk(Cart::xxxyzz, 0) = PmA(1) * olk(Cart::xxxzz, 0); olk(Cart::xxxzzz, 0) = PmA(0) * olk(Cart::xxzzz, 0) + 2.0 * term_xzzz; olk(Cart::xxyyyy, 0) = PmA(0) * olk(Cart::xyyyy, 0) + term_yyyy; olk(Cart::xxyyyz, 0) = PmA(2) * olk(Cart::xxyyy, 0); olk(Cart::xxyyzz, 0) = PmA(0) * olk(Cart::xyyzz, 0) + term_yyzz; olk(Cart::xxyzzz, 0) = PmA(1) * olk(Cart::xxzzz, 0); olk(Cart::xxzzzz, 0) = PmA(0) * olk(Cart::xzzzz, 0) + term_zzzz; olk(Cart::xyyyyy, 0) = PmA(0) * olk(Cart::yyyyy, 0); olk(Cart::xyyyyz, 0) = PmA(0) * olk(Cart::yyyyz, 0); olk(Cart::xyyyzz, 0) = PmA(0) * olk(Cart::yyyzz, 0); olk(Cart::xyyzzz, 0) = PmA(0) * olk(Cart::yyzzz, 0); olk(Cart::xyzzzz, 0) = PmA(0) * olk(Cart::yzzzz, 0); olk(Cart::xzzzzz, 0) = PmA(0) * olk(Cart::zzzzz, 0); olk(Cart::yyyyyy, 0) = PmA(1) * olk(Cart::yyyyy, 0) + 5.0 * term_yyyy; olk(Cart::yyyyyz, 0) = PmA(2) * olk(Cart::yyyyy, 0); olk(Cart::yyyyzz, 0) = PmA(2) * olk(Cart::yyyyz, 0) + term_yyyy; olk(Cart::yyyzzz, 0) = PmA(1) * olk(Cart::yyzzz, 0) + 2.0 * term_yzzz; olk(Cart::yyzzzz, 0) = PmA(1) * olk(Cart::yzzzz, 0) + term_zzzz; olk(Cart::yzzzzz, 0) = PmA(1) * olk(Cart::zzzzz, 0); olk(Cart::zzzzzz, 0) = PmA(2) * olk(Cart::zzzzz, 0) + 5.0 * term_zzzz; } //------------------------------------------------------ if (lmax_col > 0) { // Integrals s - W - p olk(0, Cart::x) = PmB(0) * olk(0, 0); olk(0, Cart::y) = PmB(1) * olk(0, 0); olk(0, Cart::z) = PmB(2) * olk(0, 0); //------------------------------------------------------ // Integrals p - W - p d - W - p f - W - p g - W - p h - // W - p i - W - p for (Index i = 1; i < n_orbitals[lmax_row]; i++) { // COMPLEX cnx(nx[i] * fak, 0.0); olk(i, Cart::x) = PmB(0) * olk(i, 0) + double(nx[i]) * cfak * olk(i_less_x[i], 0); // COMPLEX cny = (ny[i] * fak, 0.0); olk(i, Cart::y) = PmB(1) * olk(i, 0) + double(ny[i]) * cfak * olk(i_less_y[i], 0); // COMPLEX cnz = (nz[i] * fak, 0.0); olk(i, Cart::z) = PmB(2) * olk(i, 0) + double(nz[i]) * cfak * olk(i_less_z[i], 0); } //------------------------------------------------------ } // end if (lmax_col > 0) if (lmax_col > 1) { // Integrals s - W - d COMPLEX term = cfak * olk(0, 0); olk(0, Cart::xx) = PmB(0) * olk(0, Cart::x) + term; olk(0, Cart::xy) = PmB(0) * olk(0, Cart::y); olk(0, Cart::xz) = PmB(0) * olk(0, Cart::z); olk(0, Cart::yy) = PmB(1) * olk(0, Cart::y) + term; olk(0, Cart::yz) = PmB(1) * olk(0, Cart::z); olk(0, Cart::zz) = PmB(2) * olk(0, Cart::z) + term; //------------------------------------------------------ // Integrals p - W - d d - W - d f - W - d g - W - d h - // W - d i - W - d for (Index i = 1; i < n_orbitals[lmax_row]; i++) { COMPLEX term_loc = cfak * olk(i, 0); olk(i, Cart::xx) = PmB(0) * olk(i, Cart::x) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::x) + term_loc; olk(i, Cart::xy) = PmB(0) * olk(i, Cart::y) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::y); olk(i, Cart::xz) = PmB(0) * olk(i, Cart::z) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::z); olk(i, Cart::yy) = PmB(1) * olk(i, Cart::y) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::y) + term_loc; olk(i, Cart::yz) = PmB(1) * olk(i, Cart::z) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::z); olk(i, Cart::zz) = PmB(2) * olk(i, Cart::z) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::z) + term_loc; } //------------------------------------------------------ } // end if (lmax_col > 1) if (lmax_col > 2) { // Integrals s - W - f olk(0, Cart::xxx) = PmB(0) * olk(0, Cart::xx) + 2.0 * cfak * olk(0, Cart::x); olk(0, Cart::xxy) = PmB(1) * olk(0, Cart::xx); olk(0, Cart::xxz) = PmB(2) * olk(0, Cart::xx); olk(0, Cart::xyy) = PmB(0) * olk(0, Cart::yy); olk(0, Cart::xyz) = PmB(0) * olk(0, Cart::yz); olk(0, Cart::xzz) = PmB(0) * olk(0, Cart::zz); olk(0, Cart::yyy) = PmB(1) * olk(0, Cart::yy) + 2.0 * cfak * olk(0, Cart::y); olk(0, Cart::yyz) = PmB(2) * olk(0, Cart::yy); olk(0, Cart::yzz) = PmB(1) * olk(0, Cart::zz); olk(0, Cart::zzz) = PmB(2) * olk(0, Cart::zz) + 2.0 * cfak * olk(0, Cart::z); //------------------------------------------------------ // Integrals p - f d - f f - f g - f h - f i - f for (Index i = 1; i < n_orbitals[lmax_row]; i++) { COMPLEX term_x = 2.0 * cfak * olk(i, Cart::x); COMPLEX term_y = 2.0 * cfak * olk(i, Cart::y); COMPLEX term_z = 2.0 * cfak * olk(i, Cart::z); olk(i, Cart::xxx) = PmB(0) * olk(i, Cart::xx) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::xx) + term_x; olk(i, Cart::xxy) = PmB(1) * olk(i, Cart::xx) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::xx); olk(i, Cart::xxz) = PmB(2) * olk(i, Cart::xx) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::xx); olk(i, Cart::xyy) = PmB(0) * olk(i, Cart::yy) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::yy); olk(i, Cart::xyz) = PmB(0) * olk(i, Cart::yz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::yz); olk(i, Cart::xzz) = PmB(0) * olk(i, Cart::zz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::zz); olk(i, Cart::yyy) = PmB(1) * olk(i, Cart::yy) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::yy) + term_y; olk(i, Cart::yyz) = PmB(2) * olk(i, Cart::yy) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::yy); olk(i, Cart::yzz) = PmB(1) * olk(i, Cart::zz) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::zz); olk(i, Cart::zzz) = PmB(2) * olk(i, Cart::zz) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::zz) + term_z; } //------------------------------------------------------ } // end if (lmax_col > 2) if (lmax_col > 3) { // Integrals s - W - g COMPLEX term_xx = cfak * olk(0, Cart::xx); COMPLEX term_yy = cfak * olk(0, Cart::yy); COMPLEX term_zz = cfak * olk(0, Cart::zz); olk(0, Cart::xxxx) = PmB(0) * olk(0, Cart::xxx) + 3.0 * term_xx; olk(0, Cart::xxxy) = PmB(1) * olk(0, Cart::xxx); olk(0, Cart::xxxz) = PmB(2) * olk(0, Cart::xxx); olk(0, Cart::xxyy) = PmB(0) * olk(0, Cart::xyy) + term_yy; olk(0, Cart::xxyz) = PmB(1) * olk(0, Cart::xxz); olk(0, Cart::xxzz) = PmB(0) * olk(0, Cart::xzz) + term_zz; olk(0, Cart::xyyy) = PmB(0) * olk(0, Cart::yyy); olk(0, Cart::xyyz) = PmB(0) * olk(0, Cart::yyz); olk(0, Cart::xyzz) = PmB(0) * olk(0, Cart::yzz); olk(0, Cart::xzzz) = PmB(0) * olk(0, Cart::zzz); olk(0, Cart::yyyy) = PmB(1) * olk(0, Cart::yyy) + 3.0 * term_yy; olk(0, Cart::yyyz) = PmB(2) * olk(0, Cart::yyy); olk(0, Cart::yyzz) = PmB(1) * olk(0, Cart::yzz) + term_zz; olk(0, Cart::yzzz) = PmB(1) * olk(0, Cart::zzz); olk(0, Cart::zzzz) = PmB(2) * olk(0, Cart::zzz) + 3.0 * term_zz; //------------------------------------------------------ // Integrals p - g d - g f - g g - g h - g i - g for (Index i = 1; i < n_orbitals[lmax_row]; i++) { COMPLEX term_xx_loc = cfak * olk(i, Cart::xx); COMPLEX term_yy_loc = cfak * olk(i, Cart::yy); COMPLEX term_zz_loc = cfak * olk(i, Cart::zz); olk(i, Cart::xxxx) = PmB(0) * olk(i, Cart::xxx) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::xxx) + 3.0 * term_xx_loc; olk(i, Cart::xxxy) = PmB(1) * olk(i, Cart::xxx) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::xxx); olk(i, Cart::xxxz) = PmB(2) * olk(i, Cart::xxx) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::xxx); olk(i, Cart::xxyy) = PmB(0) * olk(i, Cart::xyy) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::xyy) + term_yy_loc; olk(i, Cart::xxyz) = PmB(1) * olk(i, Cart::xxz) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::xxz); olk(i, Cart::xxzz) = PmB(0) * olk(i, Cart::xzz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::xzz) + term_zz_loc; olk(i, Cart::xyyy) = PmB(0) * olk(i, Cart::yyy) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::yyy); olk(i, Cart::xyyz) = PmB(0) * olk(i, Cart::yyz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::yyz); olk(i, Cart::xyzz) = PmB(0) * olk(i, Cart::yzz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::yzz); olk(i, Cart::xzzz) = PmB(0) * olk(i, Cart::zzz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::zzz); olk(i, Cart::yyyy) = PmB(1) * olk(i, Cart::yyy) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::yyy) + 3.0 * term_yy_loc; olk(i, Cart::yyyz) = PmB(2) * olk(i, Cart::yyy) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::yyy); olk(i, Cart::yyzz) = PmB(1) * olk(i, Cart::yzz) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::yzz) + term_zz_loc; olk(i, Cart::yzzz) = PmB(1) * olk(i, Cart::zzz) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::zzz); olk(i, Cart::zzzz) = PmB(2) * olk(i, Cart::zzz) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::zzz) + 3.0 * term_zz_loc; } //------------------------------------------------------ } // end if (lmax_col > 3) if (lmax_col > 4) { // Integrals s - h COMPLEX term_xxx = cfak * olk(0, Cart::xxx); COMPLEX term_yyy = cfak * olk(0, Cart::yyy); COMPLEX term_zzz = cfak * olk(0, Cart::zzz); olk(0, Cart::xxxxx) = PmB(0) * olk(0, Cart::xxxx) + 4.0 * term_xxx; olk(0, Cart::xxxxy) = PmB(1) * olk(0, Cart::xxxx); olk(0, Cart::xxxxz) = PmB(2) * olk(0, Cart::xxxx); olk(0, Cart::xxxyy) = PmB(1) * olk(0, Cart::xxxy) + term_xxx; olk(0, Cart::xxxyz) = PmB(1) * olk(0, Cart::xxxz); olk(0, Cart::xxxzz) = PmB(2) * olk(0, Cart::xxxz) + term_xxx; olk(0, Cart::xxyyy) = PmB(0) * olk(0, Cart::xyyy) + term_yyy; olk(0, Cart::xxyyz) = PmB(2) * olk(0, Cart::xxyy); olk(0, Cart::xxyzz) = PmB(1) * olk(0, Cart::xxzz); olk(0, Cart::xxzzz) = PmB(0) * olk(0, Cart::xzzz) + term_zzz; olk(0, Cart::xyyyy) = PmB(0) * olk(0, Cart::yyyy); olk(0, Cart::xyyyz) = PmB(0) * olk(0, Cart::yyyz); olk(0, Cart::xyyzz) = PmB(0) * olk(0, Cart::yyzz); olk(0, Cart::xyzzz) = PmB(0) * olk(0, Cart::yzzz); olk(0, Cart::xzzzz) = PmB(0) * olk(0, Cart::zzzz); olk(0, Cart::yyyyy) = PmB(1) * olk(0, Cart::yyyy) + 4.0 * term_yyy; olk(0, Cart::yyyyz) = PmB(2) * olk(0, Cart::yyyy); olk(0, Cart::yyyzz) = PmB(2) * olk(0, Cart::yyyz) + term_yyy; olk(0, Cart::yyzzz) = PmB(1) * olk(0, Cart::yzzz) + term_zzz; olk(0, Cart::yzzzz) = PmB(1) * olk(0, Cart::zzzz); olk(0, Cart::zzzzz) = PmB(2) * olk(0, Cart::zzzz) + 4.0 * term_zzz; //------------------------------------------------------ // Integrals p - h d - h f - h g - h h - h i - h for (Index i = 1; i < n_orbitals[lmax_row]; i++) { COMPLEX term_xxx_loc = cfak * olk(i, Cart::xxx); COMPLEX term_yyy_loc = cfak * olk(i, Cart::yyy); COMPLEX term_zzz_loc = cfak * olk(i, Cart::zzz); olk(i, Cart::xxxxx) = PmB(0) * olk(i, Cart::xxxx) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::xxxx) + 4.0 * term_xxx_loc; olk(i, Cart::xxxxy) = PmB(1) * olk(i, Cart::xxxx) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::xxxx); olk(i, Cart::xxxxz) = PmB(2) * olk(i, Cart::xxxx) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::xxxx); olk(i, Cart::xxxyy) = PmB(1) * olk(i, Cart::xxxy) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::xxxy) + term_xxx_loc; olk(i, Cart::xxxyz) = PmB(1) * olk(i, Cart::xxxz) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::xxxz); olk(i, Cart::xxxzz) = PmB(2) * olk(i, Cart::xxxz) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::xxxz) + term_xxx_loc; olk(i, Cart::xxyyy) = PmB(0) * olk(i, Cart::xyyy) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::xyyy) + term_yyy_loc; olk(i, Cart::xxyyz) = PmB(2) * olk(i, Cart::xxyy) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::xxyy); olk(i, Cart::xxyzz) = PmB(1) * olk(i, Cart::xxzz) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::xxzz); olk(i, Cart::xxzzz) = PmB(0) * olk(i, Cart::xzzz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::xzzz) + term_zzz_loc; olk(i, Cart::xyyyy) = PmB(0) * olk(i, Cart::yyyy) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::yyyy); olk(i, Cart::xyyyz) = PmB(0) * olk(i, Cart::yyyz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::yyyz); olk(i, Cart::xyyzz) = PmB(0) * olk(i, Cart::yyzz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::yyzz); olk(i, Cart::xyzzz) = PmB(0) * olk(i, Cart::yzzz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::yzzz); olk(i, Cart::xzzzz) = PmB(0) * olk(i, Cart::zzzz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::zzzz); olk(i, Cart::yyyyy) = PmB(1) * olk(i, Cart::yyyy) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::yyyy) + 4.0 * term_yyy_loc; olk(i, Cart::yyyyz) = PmB(2) * olk(i, Cart::yyyy) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::yyyy); olk(i, Cart::yyyzz) = PmB(2) * olk(i, Cart::yyyz) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::yyyz) + term_yyy_loc; olk(i, Cart::yyzzz) = PmB(1) * olk(i, Cart::yzzz) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::yzzz) + term_zzz_loc; olk(i, Cart::yzzzz) = PmB(1) * olk(i, Cart::zzzz) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::zzzz); olk(i, Cart::zzzzz) = PmB(2) * olk(i, Cart::zzzz) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::zzzz) + 4.0 * term_zzz_loc; } //------------------------------------------------------ } // end if (lmax_col > 4) if (lmax_col > 5) { // Integrals s - W -i COMPLEX term_xxxx = cfak * olk(0, Cart::xxxx); COMPLEX term_xyyy = cfak * olk(0, Cart::xyyy); COMPLEX term_xzzz = cfak * olk(0, Cart::xzzz); COMPLEX term_yyyy = cfak * olk(0, Cart::yyyy); COMPLEX term_yyzz = cfak * olk(0, Cart::yyzz); COMPLEX term_yzzz = cfak * olk(0, Cart::yzzz); COMPLEX term_zzzz = cfak * olk(0, Cart::zzzz); olk(0, Cart::xxxxxx) = PmB(0) * olk(0, Cart::xxxxx) + 5.0 * term_xxxx; olk(0, Cart::xxxxxy) = PmB(1) * olk(0, Cart::xxxxx); olk(0, Cart::xxxxxz) = PmB(2) * olk(0, Cart::xxxxx); olk(0, Cart::xxxxyy) = PmB(1) * olk(0, Cart::xxxxy) + term_xxxx; olk(0, Cart::xxxxyz) = PmB(1) * olk(0, Cart::xxxxz); olk(0, Cart::xxxxzz) = PmB(2) * olk(0, Cart::xxxxz) + term_xxxx; olk(0, Cart::xxxyyy) = PmB(0) * olk(0, Cart::xxyyy) + 2.0 * term_xyyy; olk(0, Cart::xxxyyz) = PmB(2) * olk(0, Cart::xxxyy); olk(0, Cart::xxxyzz) = PmB(1) * olk(0, Cart::xxxzz); olk(0, Cart::xxxzzz) = PmB(0) * olk(0, Cart::xxzzz) + 2.0 * term_xzzz; olk(0, Cart::xxyyyy) = PmB(0) * olk(0, Cart::xyyyy) + term_yyyy; olk(0, Cart::xxyyyz) = PmB(2) * olk(0, Cart::xxyyy); olk(0, Cart::xxyyzz) = PmB(0) * olk(0, Cart::xyyzz) + term_yyzz; olk(0, Cart::xxyzzz) = PmB(1) * olk(0, Cart::xxzzz); olk(0, Cart::xxzzzz) = PmB(0) * olk(0, Cart::xzzzz) + term_zzzz; olk(0, Cart::xyyyyy) = PmB(0) * olk(0, Cart::yyyyy); olk(0, Cart::xyyyyz) = PmB(0) * olk(0, Cart::yyyyz); olk(0, Cart::xyyyzz) = PmB(0) * olk(0, Cart::yyyzz); olk(0, Cart::xyyzzz) = PmB(0) * olk(0, Cart::yyzzz); olk(0, Cart::xyzzzz) = PmB(0) * olk(0, Cart::yzzzz); olk(0, Cart::xzzzzz) = PmB(0) * olk(0, Cart::zzzzz); olk(0, Cart::yyyyyy) = PmB(1) * olk(0, Cart::yyyyy) + 5.0 * term_yyyy; olk(0, Cart::yyyyyz) = PmB(2) * olk(0, Cart::yyyyy); olk(0, Cart::yyyyzz) = PmB(2) * olk(0, Cart::yyyyz) + term_yyyy; olk(0, Cart::yyyzzz) = PmB(1) * olk(0, Cart::yyzzz) + 2.0 * term_yzzz; olk(0, Cart::yyzzzz) = PmB(1) * olk(0, Cart::yzzzz) + term_zzzz; olk(0, Cart::yzzzzz) = PmB(1) * olk(0, Cart::zzzzz); olk(0, Cart::zzzzzz) = PmB(2) * olk(0, Cart::zzzzz) + 5.0 * term_zzzz; //------------------------------------------------------ // Integrals p - W - i d - W - i f - W - i g - W -i h - // W - i i - W - i for (Index i = 1; i < n_orbitals[lmax_row]; i++) { COMPLEX term_xxxx_loc = cfak * olk(i, Cart::xxxx); COMPLEX term_xyyy_loc = cfak * olk(i, Cart::xyyy); COMPLEX term_xzzz_loc = cfak * olk(i, Cart::xzzz); COMPLEX term_yyyy_loc = cfak * olk(i, Cart::yyyy); COMPLEX term_yyzz_loc = cfak * olk(i, Cart::yyzz); COMPLEX term_yzzz_loc = cfak * olk(i, Cart::yzzz); COMPLEX term_zzzz_loc = cfak * olk(i, Cart::zzzz); olk(i, Cart::xxxxxx) = PmB(0) * olk(i, Cart::xxxxx) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::xxxxx) + 5.0 * term_xxxx_loc; olk(i, Cart::xxxxxy) = PmB(1) * olk(i, Cart::xxxxx) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::xxxxx); olk(i, Cart::xxxxxz) = PmB(2) * olk(i, Cart::xxxxx) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::xxxxx); olk(i, Cart::xxxxyy) = PmB(1) * olk(i, Cart::xxxxy) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::xxxxy) + term_xxxx_loc; olk(i, Cart::xxxxyz) = PmB(1) * olk(i, Cart::xxxxz) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::xxxxz); olk(i, Cart::xxxxzz) = PmB(2) * olk(i, Cart::xxxxz) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::xxxxz) + term_xxxx_loc; olk(i, Cart::xxxyyy) = PmB(0) * olk(i, Cart::xxyyy) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::xxyyy) + 2.0 * term_xyyy_loc; olk(i, Cart::xxxyyz) = PmB(2) * olk(i, Cart::xxxyy) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::xxxyy); olk(i, Cart::xxxyzz) = PmB(1) * olk(i, Cart::xxxzz) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::xxxzz); olk(i, Cart::xxxzzz) = PmB(0) * olk(i, Cart::xxzzz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::xxzzz) + 2.0 * term_xzzz_loc; olk(i, Cart::xxyyyy) = PmB(0) * olk(i, Cart::xyyyy) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::xyyyy) + term_yyyy_loc; olk(i, Cart::xxyyyz) = PmB(2) * olk(i, Cart::xxyyy) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::xxyyy); olk(i, Cart::xxyyzz) = PmB(0) * olk(i, Cart::xyyzz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::xyyzz) + term_yyzz_loc; olk(i, Cart::xxyzzz) = PmB(1) * olk(i, Cart::xxzzz) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::xxzzz); olk(i, Cart::xxzzzz) = PmB(0) * olk(i, Cart::xzzzz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::xzzzz) + term_zzzz_loc; olk(i, Cart::xyyyyy) = PmB(0) * olk(i, Cart::yyyyy) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::yyyyy); olk(i, Cart::xyyyyz) = PmB(0) * olk(i, Cart::yyyyz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::yyyyz); olk(i, Cart::xyyyzz) = PmB(0) * olk(i, Cart::yyyzz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::yyyzz); olk(i, Cart::xyyzzz) = PmB(0) * olk(i, Cart::yyzzz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::yyzzz); olk(i, Cart::xyzzzz) = PmB(0) * olk(i, Cart::yzzzz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::yzzzz); olk(i, Cart::xzzzzz) = PmB(0) * olk(i, Cart::zzzzz) + double(nx[i]) * cfak * olk(i_less_x[i], Cart::zzzzz); olk(i, Cart::yyyyyy) = PmB(1) * olk(i, Cart::yyyyy) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::yyyyy) + 5.0 * term_yyyy_loc; olk(i, Cart::yyyyyz) = PmB(2) * olk(i, Cart::yyyyy) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::yyyyy); olk(i, Cart::yyyyzz) = PmB(2) * olk(i, Cart::yyyyz) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::yyyyz) + term_yyyy_loc; olk(i, Cart::yyyzzz) = PmB(1) * olk(i, Cart::yyzzz) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::yyzzz) + 2.0 * term_yzzz_loc; olk(i, Cart::yyzzzz) = PmB(1) * olk(i, Cart::yzzzz) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::yzzzz) + term_zzzz_loc; olk(i, Cart::yzzzzz) = PmB(1) * olk(i, Cart::zzzzz) + double(ny[i]) * cfak * olk(i_less_y[i], Cart::zzzzz); olk(i, Cart::zzzzzz) = PmB(2) * olk(i, Cart::zzzzz) + double(nz[i]) * cfak * olk(i_less_z[i], Cart::zzzzz) + 5.0 * term_zzzz_loc; } //------------------------------------------------------ } // end if (lmax_col > 5) // save to matrix cartesian += AOTransform::getNorm(shell_row.getL(), gaussian_row) * AOTransform::getNorm(shell_col.getL(), gaussian_col) * olk.bottomRightCorner(shell_row.getCartesianNumFunc(), shell_col.getCartesianNumFunc()); } // close Gaussian shell_col } // close Gaussian shell_row matrix = AOTransform::tform(shell_row.getL(), shell_col.getL(), cartesian); } // End AOPlanewave void AOPlanewave::FillPotential(const AOBasis& aobasis, const std::vector& kpoints) { _aopotential = Eigen::MatrixXcd::Zero(aobasis.AOBasisSize(), aobasis.AOBasisSize()); for (const auto& kpoint : kpoints) { setkVector(kpoint); _aopotential += Fill(aobasis); } return; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/aomatrices/aopotential.cc000066400000000000000000000037441412152066400214720ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/aopotential.h" namespace votca { namespace xtp { template Eigen::Matrix AOPotential::Fill( const AOBasis& aobasis) const { typedef Eigen::Matrix MatrixXcdd; MatrixXcdd result = MatrixXcdd::Zero(aobasis.AOBasisSize(), aobasis.AOBasisSize()); // AOMatrix is symmetric, restrict explicit calculation of lower triangular // matrix #pragma omp parallel for schedule(guided) for (Index col = 0; col < aobasis.getNumofShells(); col++) { const AOShell& shell_col = aobasis.getShell(col); Index col_start = shell_col.getStartIndex(); for (Index row = col; row < aobasis.getNumofShells(); row++) { const AOShell& shell_row = aobasis.getShell(row); Index row_start = shell_row.getStartIndex(); // figure out the submatrix Eigen::Block block = result.block( row_start, col_start, shell_row.getNumFunc(), shell_col.getNumFunc()); // Fill block FillBlock(block, shell_row, shell_col); } } // Fill whole matrix by copying return result.template selfadjointView(); } template class AOPotential; template class AOPotential >; } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/aomatrices/aotransform.cc000066400000000000000000000303221412152066400214760ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * *Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/aotransform.h" #include "libint2/solidharmonics.h" namespace votca { namespace xtp { double AOTransform::getNorm(L l, const AOGaussianPrimitive& gaussian) { const double contraction = gaussian.getContraction(); const double decay = gaussian.getDecay(); switch (l) { case L::S: { return contraction; } case L::P: { return 2. * std::sqrt(decay) * contraction; } case L::D: { return 4. * decay * contraction / std::sqrt(3); } case L::F: { return 8 * std::pow(decay, 1.5) * contraction / std::sqrt(5 * 3); } case L::G: { return decay * decay * contraction * 16.0 / std::sqrt(5. * 3. * 7.); } default: throw std::runtime_error("No norms for shells higher than g (l=4)"); } return 0; } /// multiplies rows and columns of matrix cartesian, returns Matrix template Matrix AOTransform::tform(L l_row, L l_col, const Matrix& cartesian) { const auto& coefs_row = libint2::solidharmonics::SolidHarmonicsCoefficients::instance( int(l_row)); const auto& coefs_col = libint2::solidharmonics::SolidHarmonicsCoefficients::instance( int(l_col)); int npure_row = 2 * int(l_row) + 1; int npure_col = 2 * int(l_col) + 1; Matrix spherical = Matrix::Zero(npure_row, npure_col); // loop over row shg for (auto s1 = 0; s1 != npure_row; ++s1) { const auto nc1 = coefs_row.nnz(s1); // # of cartesians contributing to shg s1 const auto* c1_idxs = coefs_row.row_idx(s1); // indices of cartesians contributing to shg s1 const auto* c1_vals = coefs_row.row_values( s1); // coefficients of cartesians contributing to shg s1 // loop over col shg for (auto s2 = 0; s2 != npure_col; ++s2) { const auto nc2 = coefs_col.nnz(s2); // # of cartesians contributing to shg s2 const auto* c2_idxs = coefs_col.row_idx(s2); // indices of cartesians // contributing to shg s2 const auto* c2_vals = coefs_col.row_values( s2); // coefficients of cartesians contributing to shg s2 for (size_t ic1 = 0; ic1 != nc1; ++ic1) { // loop over contributing cartesians auto c1 = c1_idxs[ic1]; auto s1_c1_coeff = c1_vals[ic1]; for (size_t ic2 = 0; ic2 != nc2; ++ic2) { // loop over contributing cartesians auto c2 = c2_idxs[ic2]; auto s2_c2_coeff = c2_vals[ic2]; spherical(s1, s2) += cartesian(c1, c2) * s1_c1_coeff * s2_c2_coeff; } // cart2 } // cart1 } // shg2 } return spherical; } template Eigen::MatrixXd AOTransform::tform(L l_row, L l_col, const Eigen::MatrixXd& cartesian); template Eigen::MatrixXcd AOTransform::tform(L l_row, L l_col, const Eigen::MatrixXcd& cartesian); Eigen::VectorXd AOTransform::XIntegrate(Index size, double U) { Eigen::VectorXd FmU = Eigen::VectorXd::Zero(size); const Index mm = size - 1; const double pi = boost::math::constants::pi(); if (mm < 0) { throw std::runtime_error("mm is: " + std::to_string(mm) + " This should not have happened!"); } if (U < 0.0) { throw std::runtime_error("U is: " + std::to_string(U) + " This should not have happened!"); } if (U >= 10.0) { // forward iteration FmU[0] = 0.50 * std::sqrt(pi / U) * std::erf(std::sqrt(U)); const double expU = std::exp(-U); for (Index m = 1; m < FmU.size(); m++) { FmU[m] = (2.0 * double(m) - 1) * FmU[m - 1] / (2.0 * U) - expU / (2.0 * U); } } else if (U < 1e-10) { for (Index m = 0; m < FmU.size(); m++) { FmU[m] = 1.0 / (2.0 * double(m) + 1.0) - U / (2.0 * double(m) + 3.0); } } else if (U >= 1e-10 && U < 10.0) { // backward iteration double fm = 0.0; const double expU = std::exp(-U); for (Index m = 60; m >= mm; m--) { fm = (2.0 * U) / (2.0 * double(m) + 1.0) * (fm + expU / (2.0 * U)); } FmU[mm] = fm; for (Index m = mm - 1; m >= 0; m--) { FmU[m] = (2.0 * U) / (2.0 * double(m) + 1.0) * (FmU[m + 1] + expU / (2.0 * U)); } } return FmU; } Index AOTransform::getBlockSize(Index lmax) { // Each cartesian shells has (l+1)(l+2)/2 elements // Sum of all shells up to _lmax leads to blocksize=1+11/6 l+l^2+1/6 l^3 Index blocksize = 6 + 11 * lmax + 6 * lmax * lmax + lmax * lmax * lmax; blocksize /= 6; return blocksize; } // blockSize till l=8 std::array AOTransform::n_orbitals() { return {1, 4, 10, 20, 35, 56, 84, 120, 165}; } std::array AOTransform::nx() { return {0, 1, 0, 0, 2, 1, 1, 0, 0, 0, 3, 2, 2, 1, 1, 1, 0, 0, 0, 0, 4, 3, 3, 2, 2, 2, 1, 1, 1, 1, 0, 0, 0, 0, 0, 5, 4, 4, 3, 3, 3, 2, 2, 2, 2, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 6, 5, 5, 4, 4, 4, 3, 3, 3, 3, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 7, 6, 6, 5, 5, 5, 4, 4, 4, 4, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 8, 7, 7, 6, 6, 6, 5, 5, 5, 5, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0}; } std::array AOTransform::ny() { return {0, 0, 1, 0, 0, 1, 0, 2, 1, 0, 0, 1, 0, 2, 1, 0, 3, 2, 1, 0, 0, 1, 0, 2, 1, 0, 3, 2, 1, 0, 4, 3, 2, 1, 0, 0, 1, 0, 2, 1, 0, 3, 2, 1, 0, 4, 3, 2, 1, 0, 5, 4, 3, 2, 1, 0, 0, 1, 0, 2, 1, 0, 3, 2, 1, 0, 4, 3, 2, 1, 0, 5, 4, 3, 2, 1, 0, 6, 5, 4, 3, 2, 1, 0, 0, 1, 0, 2, 1, 0, 3, 2, 1, 0, 4, 3, 2, 1, 0, 5, 4, 3, 2, 1, 0, 6, 5, 4, 3, 2, 1, 0, 7, 6, 5, 4, 3, 2, 1, 0, 0, 1, 0, 2, 1, 0, 3, 2, 1, 0, 4, 3, 2, 1, 0, 5, 4, 3, 2, 1, 0, 6, 5, 4, 3, 2, 1, 0, 7, 6, 5, 4, 3, 2, 1, 0, 8, 7, 6, 5, 4, 3, 2, 1, 0}; } std::array AOTransform::nz() { return {0, 0, 0, 1, 0, 0, 1, 0, 1, 2, 0, 0, 1, 0, 1, 2, 0, 1, 2, 3, 0, 0, 1, 0, 1, 2, 0, 1, 2, 3, 0, 1, 2, 3, 4, 0, 0, 1, 0, 1, 2, 0, 1, 2, 3, 0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 0, 0, 1, 0, 1, 2, 0, 1, 2, 3, 0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 0, 1, 2, 3, 4, 5, 6, 0, 0, 1, 0, 1, 2, 0, 1, 2, 3, 0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 0, 1, 2, 3, 4, 5, 6, 0, 1, 2, 3, 4, 5, 6, 7, 0, 0, 1, 0, 1, 2, 0, 1, 2, 3, 0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 0, 1, 2, 3, 4, 5, 6, 0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7, 8}; } std::array AOTransform::i_less_x() { return {0, 0, 0, 0, 1, 2, 3, 0, 0, 0, 4, 5, 6, 7, 8, 9, 0, 0, 0, 0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 0, 0, 0, 0, 0, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 0, 0, 0, 0, 0, 0, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 0, 0, 0, 0, 0, 0, 0, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 0, 0, 0, 0, 0, 0, 0, 0, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 0, 0, 0, 0, 0, 0, 0, 0, 0}; } std::array AOTransform::i_less_y() { return {0, 0, 0, 0, 0, 1, 0, 2, 3, 0, 0, 4, 0, 5, 6, 0, 7, 8, 9, 0, 0, 10, 0, 11, 12, 0, 13, 14, 15, 0, 16, 17, 18, 19, 0, 0, 20, 0, 21, 22, 0, 23, 24, 25, 0, 26, 27, 28, 29, 0, 30, 31, 32, 33, 34, 0, 0, 35, 0, 36, 37, 0, 38, 39, 40, 0, 41, 42, 43, 44, 0, 45, 46, 47, 48, 49, 0, 50, 51, 52, 53, 54, 55, 0, 0, 56, 0, 57, 58, 0, 59, 60, 61, 0, 62, 63, 64, 65, 0, 66, 67, 68, 69, 70, 0, 71, 72, 73, 74, 75, 76, 0, 77, 78, 79, 80, 81, 82, 83, 0, 0, 84, 0, 85, 86, 0, 87, 88, 89, 0, 90, 91, 92, 93, 0, 94, 95, 96, 97, 98, 0, 99, 100, 101, 102, 103, 104, 0, 105, 106, 107, 108, 109, 110, 111, 0, 112, 113, 114, 115, 116, 117, 118, 119, 0}; } std::array AOTransform::i_less_z() { return {0, 0, 0, 0, 0, 0, 1, 0, 2, 3, 0, 0, 4, 0, 5, 6, 0, 7, 8, 9, 0, 0, 10, 0, 11, 12, 0, 13, 14, 15, 0, 16, 17, 18, 19, 0, 0, 20, 0, 21, 22, 0, 23, 24, 25, 0, 26, 27, 28, 29, 0, 30, 31, 32, 33, 34, 0, 0, 35, 0, 36, 37, 0, 38, 39, 40, 0, 41, 42, 43, 44, 0, 45, 46, 47, 48, 49, 0, 50, 51, 52, 53, 54, 55, 0, 0, 56, 0, 57, 58, 0, 59, 60, 61, 0, 62, 63, 64, 65, 0, 66, 67, 68, 69, 70, 0, 71, 72, 73, 74, 75, 76, 0, 77, 78, 79, 80, 81, 82, 83, 0, 0, 84, 0, 85, 86, 0, 87, 88, 89, 0, 90, 91, 92, 93, 0, 94, 95, 96, 97, 98, 0, 99, 100, 101, 102, 103, 104, 0, 105, 106, 107, 108, 109, 110, 111, 0, 112, 113, 114, 115, 116, 117, 118, 119}; } std::array AOTransform::i_more_x() { return {1, 4, 5, 6, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155}; } std::array AOTransform::i_more_y() { return {2, 5, 7, 8, 11, 13, 14, 16, 17, 18, 21, 23, 24, 26, 27, 28, 30, 31, 32, 33, 36, 38, 39, 41, 42, 43, 45, 46, 47, 48, 50, 51, 52, 53, 54, 57, 59, 60, 62, 63, 64, 66, 67, 68, 69, 71, 72, 73, 74, 75, 77, 78, 79, 80, 81, 82, 85, 87, 88, 90, 91, 92, 94, 95, 96, 97, 99, 100, 101, 102, 103, 105, 106, 107, 108, 109, 110, 112, 113, 114, 115, 116, 117, 118, 121, 123, 124, 126, 127, 128, 130, 131, 132, 133, 135, 136, 137, 138, 139, 141, 142, 143, 144, 145, 146, 148, 149, 150, 151, 152, 153, 154, 156, 157, 158, 159, 160, 161, 162, 163}; } std::array AOTransform::i_more_z() { return {3, 6, 8, 9, 12, 14, 15, 17, 18, 19, 22, 24, 25, 27, 28, 29, 31, 32, 33, 34, 37, 39, 40, 42, 43, 44, 46, 47, 48, 49, 51, 52, 53, 54, 55, 58, 60, 61, 63, 64, 65, 67, 68, 69, 70, 72, 73, 74, 75, 76, 78, 79, 80, 81, 82, 83, 86, 88, 89, 91, 92, 93, 95, 96, 97, 98, 100, 101, 102, 103, 104, 106, 107, 108, 109, 110, 111, 113, 114, 115, 116, 117, 118, 119, 122, 124, 125, 127, 128, 129, 131, 132, 133, 134, 136, 137, 138, 139, 140, 142, 143, 144, 145, 146, 147, 149, 150, 151, 152, 153, 154, 155, 157, 158, 159, 160, 161, 162, 163, 164}; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/aoshell.cc000066400000000000000000000335131412152066400164500ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/aoshell.h" #include "votca/xtp/aobasis.h" #include "votca/xtp/aomatrix.h" namespace votca { namespace xtp { AOGaussianPrimitive::AOGaussianPrimitive(const GaussianPrimitive& gaussian, const AOShell& aoshell) : _decay(gaussian.decay()), _contraction(gaussian.contraction()), _aoshell(aoshell) { _powfactor = CalcPowFactor(_decay); } AOGaussianPrimitive::AOGaussianPrimitive(const AOGaussianPrimitive& gaussian, const AOShell& aoshell) : _decay(gaussian._decay), _contraction(gaussian._contraction), _aoshell(aoshell), _powfactor(gaussian._powfactor) { ; } void AOGaussianPrimitive::SetupCptTable(CptTable& table) const { table.addCol(getShell().getAtomIndex(), "atomidx", HOFFSET(data, atomid)); table.addCol(static_cast(getShell().getL()), "L", HOFFSET(data, l)); table.addCol(getShell().getStartIndex(), "startidx", HOFFSET(data, startindex)); table.addCol(getDecay(), "decay", HOFFSET(data, decay)); table.addCol(getContraction(), "contr", HOFFSET(data, contraction)); table.addCol(getShell().getPos().x(), "pos.x", HOFFSET(data, x)); table.addCol(getShell().getPos().y(), "pos.y", HOFFSET(data, y)); table.addCol(getShell().getPos().z(), "pos.z", HOFFSET(data, z)); table.addCol(getShell().getScale(), "scale", HOFFSET(data, scale)); } void AOGaussianPrimitive::WriteData(data& d) const { d.atomid = getShell().getAtomIndex(); d.l = static_cast(getShell().getL()); d.startindex = getShell().getStartIndex(); d.decay = getDecay(); d.contraction = getContraction(); d.x = getShell().getPos().x(); d.y = getShell().getPos().y(); d.z = getShell().getPos().z(); d.scale = getShell().getScale(); } AOShell::AOShell(const Shell& shell, const QMAtom& atom, Index startIndex) : _l(shell.getL()), _scale(shell.getScale()), _startIndex(startIndex), _pos(atom.getPos()), _atomindex(atom.getId()) { ; } AOShell::AOShell(const AOShell& shell) { _l = shell._l; _scale = shell._scale; _mindecay = shell._mindecay; _startIndex = shell._startIndex; _pos = shell._pos; _atomindex = shell._atomindex; _gaussians.reserve(shell._gaussians.size()); for (const auto& gaus : shell._gaussians) { _gaussians.push_back(AOGaussianPrimitive(gaus, *this)); } } libint2::Shell AOShell::LibintShell() const { libint2::svector decays; libint2::svector contractions; const Eigen::Vector3d& pos = getPos(); libint2::Shell::Contraction contr; contr.l = static_cast(getL()); contr.pure = true; for (const auto& primitive : _gaussians) { decays.push_back(primitive.getDecay()); contr.coeff.push_back(primitive.getContraction()); } contractions.push_back(contr); std::array libintpos = {pos[0], pos[1], pos[2]}; return libint2::Shell(decays, contractions, libintpos); } void AOShell::normalizeContraction() { AOOverlap overlap; Eigen::MatrixXd block = overlap.singleShellOverlap(*this); double norm = std::sqrt(block(0, 0)); for (auto& gaussian : _gaussians) { gaussian._contraction /= norm; } return; } void AOShell::EvalAOspace(Eigen::VectorBlock& AOvalues, Eigen::Block& gradAOvalues, const Eigen::Vector3d& grid_pos) const { // need position of shell const Eigen::Vector3d center = (grid_pos - _pos); const double distsq = center.squaredNorm(); // iterate over Gaussians in this shell for (const AOGaussianPrimitive& gaussian : _gaussians) { const double alpha = gaussian.getDecay(); const double contraction = gaussian.getContraction(); const double expofactor = gaussian.getPowfactor() * std::exp(-alpha * distsq); const Eigen::Vector3d second_term = -2.0 * alpha * center; switch (_l) { case L::S: { double AOvalue = contraction * expofactor; AOvalues(0) += AOvalue; // s-function gradAOvalues.row(0) += second_term * AOvalue; // gradient of s-function } break; case L::P: { const double factor = 2. * sqrt(alpha) * contraction * expofactor; double AOvalue = factor * center.y(); // Y 1,-1 AOvalues(0) += AOvalue; gradAOvalues.row(0) += second_term * AOvalue; gradAOvalues(0, 1) += factor; AOvalue = factor * center.z(); // Y 1,0 AOvalues(1) += AOvalue; gradAOvalues.row(1) += second_term * AOvalue; gradAOvalues(1, 2) += factor; AOvalue = factor * center.x(); // Y 1,1 AOvalues(2) += AOvalue; gradAOvalues(2, 0) += factor; gradAOvalues.row(2) += second_term * AOvalue; // y gradient } break; case L::D: { const double factor = 2. * alpha * contraction * expofactor; const double factor_1 = factor / sqrt(3.); double AOvalue = 2. * factor * (center.x() * center.y()); // Y 2,-2 AOvalues(0) += AOvalue; Eigen::Array3d coeff = {2 * center.y(), 2 * center.x(), 0}; gradAOvalues.row(0) += factor * coeff.matrix() + second_term * AOvalue; AOvalue = 2. * factor * (center.y() * center.z()); // Y 2,-1 AOvalues(1) += AOvalue; coeff = {0, 2 * center.z(), 2 * center.y()}; gradAOvalues.row(1) += factor * coeff.matrix() + second_term * AOvalue; AOvalue = factor_1 * (3. * center.z() * center.z() - distsq); // Y 2,0 AOvalues(2) += AOvalue; coeff = {-2, -2, 4}; gradAOvalues.row(2) += (factor_1 * coeff * center.array()).matrix() + second_term * AOvalue; AOvalue = 2. * factor * (center.x() * center.z()); // Y 2,1 AOvalues(3) += AOvalue; coeff = {2 * center.z(), 0, 2 * center.x()}; gradAOvalues.row(3) += factor * coeff.matrix() + second_term * AOvalue; AOvalue = factor * (center.x() * center.x() - center.y() * center.y()); // Y 2,2 AOvalues(4) += AOvalue; coeff = {2 * center.x(), -2 * center.y(), 0}; gradAOvalues.row(4) += factor * coeff.matrix() + second_term * AOvalue; } break; case L::F: { const double factor = 2. * pow(alpha, 1.5) * contraction * expofactor; const double factor_1 = factor * 2. / sqrt(15.); const double factor_2 = factor * sqrt(2.) / sqrt(5.); const double factor_3 = factor * sqrt(2.) / sqrt(3.); AxA c(center); double AOvalue = factor_3 * center.y() * (3. * c.xx() - c.yy()); // Y 3,-3 AOvalues(0) += AOvalue; Eigen::Array3d coeff = {6. * c.xy(), 3. * (c.xx() - c.yy()), 0}; gradAOvalues.row(0) += factor_3 * coeff.matrix() + second_term * AOvalue; AOvalue = 4. * factor * center.x() * center.y() * center.z(); // Y 3,-2 AOvalues(1) += AOvalue; coeff = {c.yz(), c.xz(), c.xy()}; gradAOvalues.row(1) += 4 * factor * coeff.matrix() + second_term * AOvalue; AOvalue = factor_2 * center.y() * (5. * c.zz() - distsq); // Y 3,-1 AOvalues(2) += AOvalue; coeff = {-2. * c.xy(), 4. * c.zz() - c.xx() - 3. * c.yy(), 8. * c.yz()}; gradAOvalues.row(2) += factor_2 * coeff.matrix() + second_term * AOvalue; AOvalue = factor_1 * center.z() * (5. * c.zz() - 3. * distsq); // Y 3,0 AOvalues(3) += AOvalue; coeff = {-6. * c.xz(), -6. * c.yz(), 3. * (3. * c.zz() - distsq)}; gradAOvalues.row(3) += factor_1 * coeff.matrix() + second_term * AOvalue; AOvalue = factor_2 * center.x() * (5. * c.zz() - distsq); // Y 3,1 AOvalues(4) += AOvalue; coeff = {4. * c.zz() - c.yy() - 3. * c.xx(), -2. * c.xy(), 8. * c.xz()}; gradAOvalues.row(4) += factor_2 * coeff.matrix() + second_term * AOvalue; AOvalue = 2. * factor * center.z() * (c.xx() - c.yy()); // Y 3,2 AOvalues(5) += AOvalue; coeff = {2. * c.xz(), -2. * c.yz(), c.xx() - c.yy()}; gradAOvalues.row(5) += 2 * factor * coeff.matrix() + second_term * AOvalue; AOvalue = factor_3 * center.x() * (c.xx() - 3. * c.yy()); // Y 3,3 AOvalues(6) += AOvalue; coeff = {3. * (c.xx() - c.yy()), -6. * c.xy(), 0}; gradAOvalues.row(6) += factor_3 * coeff.matrix() + second_term * AOvalue; } break; case L::G: { const double factor = 2. / sqrt(3.) * alpha * alpha * contraction * expofactor; const double factor_1 = factor / sqrt(35.); const double factor_2 = factor * 4. / sqrt(14.); const double factor_3 = factor * 2. / sqrt(7.); const double factor_4 = factor * 2. * sqrt(2.); AxA c(center); double AOvalue = 4. * factor * c.xy() * (c.xx() - c.yy()); // Y 4,-4 AOvalues(0) += AOvalue; Eigen::Array3d coeff = {center.y() * (3. * c.xx() - c.yy()), center.x() * (c.xx() - 3. * c.yy()), 0}; gradAOvalues.row(0) += 4 * factor * coeff.matrix() + second_term * AOvalue; AOvalue = factor_4 * c.yz() * (3. * c.xx() - c.yy()); // Y 4,-3 AOvalues(1) += AOvalue; coeff = {6. * center.x() * c.yz(), 3. * center.z() * (c.xx() - c.yy()), center.y() * (3. * c.xx() - c.yy())}; gradAOvalues.row(1) += factor_4 * coeff.matrix() + second_term * AOvalue; AOvalue = 2. * factor_3 * c.xy() * (7. * c.zz() - distsq); // Y 4,-2 AOvalues(2) += AOvalue; coeff = {center.y() * (6. * c.zz() - 3. * c.xx() - c.yy()), center.x() * (6. * c.zz() - c.xx() - 3. * c.yy()), 12. * center.z() * c.xy()}; gradAOvalues.row(2) += 2 * factor_3 * coeff.matrix() + second_term * AOvalue; AOvalue = factor_2 * c.yz() * (7. * c.zz() - 3. * distsq); // Y 4,-1 AOvalues(3) += AOvalue; coeff = {(-6. * center.x() * c.yz()), center.z() * (4. * c.zz() - 3. * c.xx() - 9. * c.yy()), 3. * center.y() * (5. * c.zz() - distsq)}; gradAOvalues.row(3) += factor_2 * coeff.matrix() + second_term * AOvalue; AOvalue = factor_1 * (35. * c.zz() * c.zz() - 30. * c.zz() * distsq + 3. * distsq * distsq); // Y 4,0 AOvalues(4) += AOvalue; coeff = {12. * center.x() * (distsq - 5. * c.zz()), 12. * center.y() * (distsq - 5. * c.zz()), 16. * center.z() * (5. * c.zz() - 3. * distsq)}; gradAOvalues.row(4) += factor_1 * coeff.matrix() + second_term * AOvalue; AOvalue = factor_2 * c.xz() * (7. * c.zz() - 3. * distsq); // Y 4,1 AOvalues(5) += AOvalue; coeff = {center.z() * (4. * c.zz() - 9. * c.xx() - 3. * c.yy()), (-6. * center.y() * c.xz()), 3. * center.x() * (5. * c.zz() - distsq)}; gradAOvalues.row(5) += factor_2 * coeff.matrix() + second_term * AOvalue; AOvalue = factor_3 * (c.xx() - c.yy()) * (7. * c.zz() - distsq); // Y 4,2 AOvalues(6) += AOvalue; coeff = {4. * center.x() * (3. * c.zz() - c.xx()), 4. * center.y() * (c.yy() - 3. * c.zz()), 12. * center.z() * (c.xx() - c.yy())}; gradAOvalues.row(6) += factor_3 * coeff.matrix() + second_term * AOvalue; AOvalue = factor_4 * c.xz() * (c.xx() - 3. * c.yy()); // Y 4,3 AOvalues(7) += AOvalue; coeff = {3. * center.z() * (c.xx() - c.yy()), (-6. * center.y() * c.xz()), center.x() * (c.xx() - 3. * c.yy())}; gradAOvalues.row(7) += factor_4 * coeff.matrix() + second_term * AOvalue; AOvalue = factor * (c.xx() * c.xx() - 6. * c.xx() * c.yy() + c.yy() * c.yy()); // Y 4,4 AOvalues(8) += AOvalue; coeff = {center.x() * (c.xx() - 3. * c.yy()), center.y() * (c.yy() - 3. * c.xx()), 0}; gradAOvalues.row(8) += 4 * factor * coeff.matrix() + second_term * AOvalue; } break; default: throw std::runtime_error("Shell type:" + EnumToString(_l) + " not known"); break; } } // contractions return; } // namespace xtp void AOShell::EvalAOspace(Eigen::VectorBlock& AOvalues, const Eigen::Vector3d& grid_pos) const { Eigen::MatrixX3d temp = Eigen::MatrixX3d::Zero(AOvalues.size(), 3); Eigen::Block temp2 = temp.block(0, 0, temp.rows(), temp.cols()); EvalAOspace(AOvalues, temp2, grid_pos); } std::ostream& operator<<(std::ostream& out, const AOShell& shell) { out << "AtomIndex:" << shell.getAtomIndex(); out << " Shelltype:" << EnumToString(shell.getL()) << " StartIndex:" << shell.getStartIndex() << " Scale:" << shell.getScale() << " MinDecay:" << shell.getMinDecay() << "\n"; for (const auto& gaussian : shell) { out << " Gaussian Decay: " << gaussian.getDecay(); out << " Contraction: " << gaussian.getContraction(); out << "\n"; } return out; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/atom.cc000066400000000000000000000066411412152066400157630ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/atom.h" namespace votca { namespace xtp { Atom::Atom(Index resnr, std::string md_atom_name, Index atom_id, Eigen::Vector3d pos, std::string type) : _id(atom_id), _name(md_atom_name), _resnr(resnr), _pos(pos) { std::string elename = GetElementFromString(md_atom_name); std::string eletype = GetElementFromString(type); tools::Elements ele; bool found_element_name = true; bool found_element_type = true; try { ele.getMass(elename); } catch (std::runtime_error&) { found_element_name = false; } try { ele.getMass(eletype); } catch (std::runtime_error&) { found_element_type = false; } if (found_element_name && found_element_type) { if (elename != eletype) { throw std::runtime_error("Elements " + elename + " and" + eletype + " from atom name: " + md_atom_name + " and atom type:" + type + " do not match."); } _element = elename; } else if (found_element_name) { _element = elename; } else if (found_element_type) { _element = elename; } else { throw std::runtime_error("Could not get Element from atom name:" + md_atom_name + " or atom type:" + type); } } Atom::Atom(Index atom_id, std::string element, Eigen::Vector3d pos) : Atom(-1, element, atom_id, pos, element) {} std::string Atom::GetElementFromString(const std::string& MDName) { std::string element = MDName.substr(0, 1); if (MDName.size() > 1) { if (std::islower(MDName[1])) { element += MDName[1]; } } return element; } void Atom::Rotate(const Eigen::Matrix3d& R, const Eigen::Vector3d& refPos) { Eigen::Vector3d dir = _pos - refPos; dir = R * dir; _pos = refPos + dir; // Rotated Position } void Atom::SetupCptTable(CptTable& table) const { table.addCol(_id, "index", HOFFSET(data, id)); table.addCol(_element, "element", HOFFSET(data, element)); table.addCol(_name, "name", HOFFSET(data, name)); table.addCol(_pos[0], "pos.x", HOFFSET(data, x)); table.addCol(_pos[1], "pos.y", HOFFSET(data, y)); table.addCol(_pos[2], "pos.z", HOFFSET(data, z)); table.addCol(_resnr, "resnr", HOFFSET(data, resnr)); } void Atom::WriteData(data& d) const { d.id = _id; d.element = const_cast(_element.c_str()); d.name = const_cast(_name.c_str()); d.x = _pos[0]; d.y = _pos[1]; d.z = _pos[2]; d.resnr = _resnr; } void Atom::ReadData(const data& d) { _id = d.id; _element = std::string(d.element); free(d.element); _name = std::string(d.name); free(d.name); _pos[0] = d.x; _pos[2] = d.z; _pos[1] = d.y; _resnr = d.resnr; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/basisset.cc000066400000000000000000000155671412152066400166470ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/basisset.h" #include namespace votca { namespace xtp { L StringToEnum(const std::string& type) { assert(!type.empty() && "Shelltype must be non empty!"); assert(type.size() == 1 && "Shelltype size must be one"); const char t = type.back(); return StringToEnum(t); } L StringToEnum(char type) { L l; if (type == 'S') { l = L::S; } else if (type == 'P') { l = L::P; } else if (type == 'D') { l = L::D; } else if (type == 'F') { l = L::F; } else if (type == 'G') { l = L::G; } else if (type == 'H') { l = L::H; } else if (type == 'I') { l = L::I; } else { throw std::runtime_error("FindLmax: Shelltype '" + std::string(1, type) + "' not known"); } return l; } std::string EnumToString(L l) { switch (l) { case L::S: return "S"; case L::P: return "P"; case L::D: return "D"; case L::F: return "F"; case L::G: return "G"; case L::H: return "H"; case L::I: return "I"; } return ""; } Index OffsetFuncShell(L l) { switch (l) { case L::S: return 0; case L::P: return 1; case L::D: return 4; case L::F: return 9; case L::G: return 16; case L::H: return 25; case L::I: return 36; } return -1; } Index NumFuncShell(L l) { return 2 * Index(l) + 1; } Index NumFuncShell_cartesian(L l) { Index lindex = Index(l); return (lindex + 1) * (lindex + 2) / 2; } Index OffsetFuncShell_cartesian(L l) { switch (l) { case L::S: return 0; case L::P: return 1; case L::D: return 4; case L::F: return 10; case L::G: return 20; case L::H: return 35; case L::I: return 56; } return -1; } bool CheckShellType(const std::string& shelltype) { if (shelltype.empty()) { return false; } std::vector allowed_shells = {'S', 'P', 'D', 'F', 'G', 'H', 'I'}; std::vector::iterator it = std::find(allowed_shells.begin(), allowed_shells.end(), shelltype[0]); if (it == allowed_shells.end()) { return false; } else { Index index = std::distance(allowed_shells.begin(), it); for (Index i = 1; i < Index(shelltype.size()); i++) { if (index + i > Index(allowed_shells.size()) || shelltype[i] != allowed_shells[index + i]) { return false; } } } return true; } void BasisSet::Load(const std::string& name) { // if name contains .xml, assume a basisset .xml file is located in the // working directory std::size_t found_xml = name.find(".xml"); std::string xmlFile; if (found_xml != std::string::npos) { xmlFile = name; } else { xmlFile = tools::GetVotcaShare() + "/xtp/basis_sets/" + name + ".xml"; } tools::Property basis_property; basis_property.LoadFromXML(xmlFile); _name = basis_property.get("basis").getAttribute("name"); std::vector elementProps = basis_property.Select("basis.element"); for (tools::Property* elementProp : elementProps) { std::string elementName = elementProp->getAttribute("name"); Element& element = addElement(elementName); std::vector shellProps = elementProp->Select("shell"); for (tools::Property* shellProp : shellProps) { std::string shellType = shellProp->getAttribute("type"); if (!CheckShellType(shellType)) { throw std::runtime_error("Shelltype: '" + shellType + "' is not a valid shelltype!"); } for (char subtype : shellType) { double shellScale = shellProp->getAttribute("scale"); Shell& shell = element.addShell(StringToEnum(subtype), shellScale); std::vector constProps = shellProp->Select("constant"); for (tools::Property* constProp : constProps) { double decay = constProp->getAttribute("decay"); std::vector contrProps = constProp->Select("contractions"); double contraction = 0.0; for (tools::Property* contrProp : contrProps) { std::string contrType = contrProp->getAttribute("type"); if (contrType != std::string(1, subtype)) { continue; } contraction = contrProp->getAttribute("factor"); } shell.addGaussian(decay, contraction); } } } } return; } // adding an Element to a Basis Set Element& BasisSet::addElement(std::string elementType) { auto e = _elements.insert({elementType, Element(elementType)}); if (!e.second) { throw std::runtime_error("Inserting element into basisset failed!"); } return e.first->second; } const Element& BasisSet::getElement(std::string element_type) const { std::map::const_iterator itm = _elements.find(element_type); if (itm == _elements.end()) { throw std::runtime_error("Basis set " + _name + " does not have element of type " + element_type); } return itm->second; } std::ostream& operator<<(std::ostream& out, const Shell& shell) { out << "Type:" << EnumToString(shell.getL()) << " Scale:" << shell.getScale() << " Func: " << shell.getnumofFunc() << "\n"; for (const auto& gaussian : shell._gaussians) { out << " Gaussian Decay: " << gaussian.decay(); out << " Contraction: " << gaussian.contraction(); out << "\n"; } return out; } std::ostream& operator<<(std::ostream& out, const Element& element) { out << "Element:" << element.getType() << "\n"; for (const auto& shell : element) { out << shell; } return out; } std::ostream& operator<<(std::ostream& out, const BasisSet& basis) { out << "BasisSet:" << basis._name << "\n"; for (const auto& element : basis) { out << element.second; } out << std::flush; return out; } GaussianPrimitive& Shell::addGaussian(double decay, double contraction) { _gaussians.push_back(GaussianPrimitive(decay, contraction)); return _gaussians.back(); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/bfgs_trm.cc000066400000000000000000000126601412152066400166240ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // Local VOTCA includes #include "votca/xtp/atom.h" #include "votca/xtp/bfgs_trm.h" #include "votca/xtp/trustregion.h" namespace votca { namespace xtp { void BFGSTRM::Optimize(const Eigen::VectorXd& initialparameters) { _parameters = initialparameters; _cost = _costfunction.EvaluateCost(_parameters); double lastcost = _cost; Eigen::VectorXd gradient = _costfunction.EvaluateGradient(_parameters); for (auto& func : _callbacks) { func(); } Eigen::VectorXd delta_p_trial = Eigen::VectorXd::Zero(_parameters.size()); Eigen::VectorXd last_gradient = Eigen::VectorXd::Zero(_parameters.size()); double delta_cost = 0; for (_iteration = 1; _iteration <= _max_iteration; _iteration++) { for (Index i = 0; i < 100; i++) { TrustRegion subproblem; delta_p_trial = subproblem.CalculateStep(gradient, _hessian, _trust_radius); double trialcost = _costfunction.EvaluateCost(_parameters + delta_p_trial); delta_cost = trialcost - lastcost; bool step_accepted = AcceptRejectStep(delta_p_trial, gradient, delta_cost); if (step_accepted) { _cost = trialcost; _parameters += delta_p_trial; break; } } gradient = _costfunction.EvaluateGradient(_parameters); if (_iteration > 1) { UpdateHessian(delta_p_trial, gradient - last_gradient); } lastcost = _cost; last_gradient = gradient; for (auto& func : _callbacks) { func(); } if (_costfunction.Converged(delta_p_trial, delta_cost, gradient)) { break; } else if (_iteration == _max_iteration) { _success = false; XTP_LOG(Log::warning, *_pLog) << (boost::format("BFGS-TRM @iteration %1$d: not converged after " "%2$d iterations ") % _iteration % _max_iteration) .str() << std::flush; } } return; } /* Accept/reject the new geometry and adjust trust radius, if required */ bool BFGSTRM::AcceptRejectStep(const Eigen::VectorXd& delta_p, const Eigen::VectorXd& gradient, double cost_delta) { bool step_accepted = false; if (cost_delta > 0.0) { // total energy has unexpectedly increased, half the trust radius _trust_radius = 0.25 * _trust_radius; XTP_LOG(Log::warning, *_pLog) << (boost::format("BFGS-TRM @iteration %1$d: DeltaCost %2$2.4e step " "rejected ") % _iteration % cost_delta) .str() << std::flush; XTP_LOG(Log::warning, *_pLog) << (boost::format( "BFGS-TRM @iteration %1$d: new trust radius %2$2.4e") % _iteration % _trust_radius) .str() << std::flush; } else { // total energy has decreased, we accept the step but might update the trust // radius step_accepted = true; // adjust trust radius, if required double tr_check = cost_delta / QuadraticEnergy(gradient, delta_p); double norm_delta_p = delta_p.squaredNorm(); if (tr_check > 0.75 && 1.25 * norm_delta_p > _trust_radius * _trust_radius) { _trust_radius = 2.0 * _trust_radius; } else if (tr_check < 0.25) { _trust_radius = 0.25 * _trust_radius; } XTP_LOG(Log::warning, *_pLog) << (boost::format( "BFGS-TRM @iteration %1$d: DeltaCost/QuadraticApprox %2$2.4f " "step accepted ") % _iteration % tr_check) .str() << std::flush; XTP_LOG(Log::warning, *_pLog) << (boost::format( "BFGS-TRM @iteration %1$d: new trust radius %2$2.4e") % _iteration % _trust_radius) .str() << std::flush; } return step_accepted; } void BFGSTRM::UpdateHessian(const Eigen::VectorXd& delta_pos, const Eigen::VectorXd& delta_gradient) { // second term in BFGS update (needs current Hessian) _hessian -= _hessian * delta_pos * delta_pos.transpose() * _hessian.transpose() / (delta_pos.transpose() * _hessian * delta_pos).value(); // first term in BFGS update _hessian += (delta_gradient * delta_gradient.transpose()) / (delta_gradient.transpose() * delta_pos); // symmetrize Hessian (since d2E/dxidxj should be symmetric) _hessian = 0.5 * (_hessian + _hessian.transpose()); return; } /* Estimate energy change based on quadratic approximation */ double BFGSTRM::QuadraticEnergy(const Eigen::VectorXd& gradient, const Eigen::VectorXd& delta_pos) const { return (gradient.transpose() * delta_pos).value() + 0.5 * (delta_pos.transpose() * _hessian * delta_pos).value(); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/bsecoupling.cc000066400000000000000000000742371412152066400173430ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/aomatrix.h" #include "votca/xtp/bse.h" #include "votca/xtp/bse_operator.h" #include "votca/xtp/bsecoupling.h" namespace votca { namespace xtp { using namespace std; using boost::format; using namespace tools; void BSECoupling::Initialize(Property& options) { std::string key = Identify(); string spintype = options.ifExistsReturnElseThrowRuntimeError(key + ".spin"); if (spintype == "all") { _doSinglets = true; _doTriplets = true; } else if (spintype == "triplet") { _doTriplets = true; } else if (spintype == "singlet") { _doSinglets = true; } else { throw std::runtime_error( (boost::format( "Choice % for type not known. Available singlet,triplet,all") % spintype) .str()); } _output_perturbation = options.ifExistsReturnElseReturnDefault( key + ".use_perturbation", _output_perturbation); _levA = options.get(key + ".moleculeA.states").as(); _levB = options.get(key + ".moleculeB.states").as(); _occA = options.get(key + ".moleculeA.occLevels").as(); _occB = options.get(key + ".moleculeB.occLevels").as(); _unoccA = options.get(key + ".moleculeA.unoccLevels").as(); _unoccB = options.get(key + ".moleculeB.unoccLevels").as(); } void BSECoupling::WriteToProperty(Property& summary, const QMState& stateA, const QMState& stateB) const { Property& coupling_summary = summary.add("coupling", ""); double JAB_pert = 0; double JAB_diag = 0; if (stateA.Type() == QMStateType::Singlet) { JAB_pert = getSingletCouplingElement(stateA.StateIdx(), stateB.StateIdx(), 0); JAB_diag = getSingletCouplingElement(stateA.StateIdx(), stateB.StateIdx(), 1); } else if (stateA.Type() == QMStateType::Triplet) { JAB_pert = getTripletCouplingElement(stateA.StateIdx(), stateB.StateIdx(), 0); JAB_diag = getTripletCouplingElement(stateA.StateIdx(), stateB.StateIdx(), 1); } coupling_summary.setAttribute("stateA", stateA.ToString()); coupling_summary.setAttribute("stateB", stateB.ToString()); coupling_summary.setAttribute("j_pert", (format("%1$1.6e") % JAB_pert).str()); coupling_summary.setAttribute("j_diag", (format("%1$1.6e") % JAB_diag).str()); } void BSECoupling::Addoutput(Property& type_summary, const Orbitals&, const Orbitals&) const { tools::Property& bsecoupling = type_summary.add(Identify(), ""); string algorithm = "j_diag"; if (_output_perturbation) { algorithm = "j_pert"; } if (_doSinglets) { QMStateType singlet = QMStateType(QMStateType::Singlet); Property& singlet_summary = bsecoupling.add(singlet.ToLongString(), ""); singlet_summary.setAttribute("algorithm", algorithm); for (Index stateA = 0; stateA < _levA; ++stateA) { QMState qmstateA = QMState(singlet, stateA, false); for (Index stateB = 0; stateB < _levB; ++stateB) { QMState qmstateB = QMState(singlet, stateB, false); WriteToProperty(singlet_summary, qmstateA, qmstateB); } } } if (_doTriplets) { QMStateType triplet = QMStateType(QMStateType::Triplet); Property& triplet_summary = bsecoupling.add(triplet.ToLongString(), ""); triplet_summary.setAttribute("algorithm", algorithm); for (Index stateA = 0; stateA < _levA; ++stateA) { QMState qmstateA = QMState(triplet, stateA, false); for (Index stateB = 0; stateB < _levB; ++stateB) { QMState qmstateB = QMState(triplet, stateB, false); WriteToProperty(triplet_summary, qmstateA, qmstateB); } } } } double BSECoupling::getSingletCouplingElement(Index levelA, Index levelB, Index methodindex) const { return JAB_singlet[methodindex](levelA, levelB + _levA) * votca::tools::conv::hrt2ev; } double BSECoupling::getTripletCouplingElement(Index levelA, Index levelB, Index methodindex) const { return JAB_triplet[methodindex](levelA, levelB + _levA) * votca::tools::conv::hrt2ev; } Eigen::MatrixXd BSECoupling::SetupCTStates(Index bseA_vtotal, Index bseB_vtotal, Index bseAB_vtotal, Index bseAB_ctotal, const Eigen::MatrixXd& A_AB, const Eigen::MatrixXd& B_AB) const { Index noAB = _occA * _unoccB; Index noBA = _unoccA * _occB; Index bseAB_total = bseAB_vtotal + bseAB_ctotal; Index bseAB_size = bseAB_vtotal * bseAB_ctotal; Eigen::MatrixXd CTstates = Eigen::MatrixXd::Zero(bseAB_size, noAB + noBA); auto A_occ = A_AB.block(0, bseA_vtotal - _occA, bseAB_total, _occA); auto A_unocc = A_AB.block(0, bseA_vtotal, bseAB_total, _unoccA); auto B_occ = B_AB.block(0, bseB_vtotal - _occB, bseAB_total, _occB); auto B_unocc = B_AB.block(0, bseB_vtotal, bseAB_total, _unoccB); const Eigen::MatrixXd A_occ_occ = A_occ.topRows(bseAB_vtotal); const Eigen::MatrixXd B_unocc_unocc = B_unocc.bottomRows(bseAB_ctotal); // notation AB is CT states with A+B-, BA is the counterpart // Setting up CT-states: XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Setting up CT-states" << flush; // Number of A+B- states #pragma omp parallel for for (Index a_occ = 0; a_occ < _occA; a_occ++) { for (Index b_unocc = 0; b_unocc < _unoccB; b_unocc++) { Index index = a_occ * _unoccB + b_unocc; Eigen::MatrixXd Coeff = B_unocc_unocc.col(b_unocc) * A_occ_occ.col(a_occ).transpose(); CTstates.col(index) = Eigen::Map(Coeff.data(), bseAB_size); } } XTP_LOG(Log::error, *_pLog) << TimeStamp() << " " << noBA << " CT states A+B- created" << flush; const Eigen::MatrixXd A_unocc_unocc = A_unocc.bottomRows(bseAB_ctotal); const Eigen::MatrixXd B_occ_occ = B_occ.topRows(bseAB_vtotal); #pragma omp parallel for for (Index b_occ = 0; b_occ < _occB; b_occ++) { for (Index a_unocc = 0; a_unocc < _unoccA; a_unocc++) { Index index = b_occ * _unoccA + a_unocc + noAB; Eigen::MatrixXd Coeff = A_unocc_unocc.col(a_unocc) * B_occ_occ.col(b_occ).transpose(); CTstates.col(index) = Eigen::Map(Coeff.data(), bseAB_size); } } XTP_LOG(Log::error, *_pLog) << TimeStamp() << " " << noBA << " CT states A-B+ created" << flush; return CTstates; } Eigen::MatrixXd BSECoupling::ProjectFrenkelExcitons( const Eigen::MatrixXd& BSE_Coeffs, const Eigen::MatrixXd& X_AB, Index bseX_vtotal, Index bseX_ctotal, Index bseAB_vtotal, Index bseAB_ctotal) const { Index bseAB_size = bseAB_vtotal * bseAB_ctotal; auto X_occ = X_AB.leftCols(bseX_vtotal); auto X_unocc = X_AB.rightCols(bseX_ctotal); const Eigen::MatrixXd X_occ_occ = X_occ.topRows(bseAB_vtotal); const Eigen::MatrixXd X_unocc_unocc = X_unocc.bottomRows(bseAB_ctotal); Eigen::MatrixXd result = Eigen::MatrixXd::Zero(bseAB_size, BSE_Coeffs.cols()); // no pragma here because often we will only have one Coeff for (Index i = 0; i < BSE_Coeffs.cols(); i++) { Eigen::VectorXd coeff = BSE_Coeffs.col(i); Eigen::Map coeffmatrix = Eigen::Map(coeff.data(), bseX_ctotal, bseX_vtotal); Eigen::MatrixXd proj = X_unocc_unocc * coeffmatrix * X_occ_occ.transpose(); result.col(i) = Eigen::Map(proj.data(), proj.size()); } return result; } int GetSign(double value) { if (value < 0) { return -1; } else if (value > 0) { return 1; } return 0; } void BSECoupling::CalculateCouplings(const Orbitals& orbitalsA, const Orbitals& orbitalsB, const Orbitals& orbitalsAB) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Calculating exciton couplings" << flush; // set the parallelization XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Using " << OPENMP::getMaxThreads() << " threads" << flush; CheckAtomCoordinates(orbitalsA, orbitalsB, orbitalsAB); // constructing the direct product orbA x orbB Index basisB = orbitalsB.getBasisSetSize(); Index basisA = orbitalsA.getBasisSetSize(); if ((basisA == 0) || (basisB == 0)) { throw std::runtime_error("Basis set size is not stored in monomers"); } // get exciton information of molecule A Index bseA_cmax = orbitalsA.getBSEcmax(); Index bseA_cmin = orbitalsA.getBSEcmin(); Index bseA_vmax = orbitalsA.getBSEvmax(); Index bseA_vmin = orbitalsA.getBSEvmin(); Index bseA_vtotal = bseA_vmax - bseA_vmin + 1; Index bseA_ctotal = bseA_cmax - bseA_cmin + 1; Index bseA_total = bseA_vtotal + bseA_ctotal; Index bseA_size = bseA_vtotal * bseA_ctotal; Index bseA_singlet_exc = orbitalsA.BSESinglets().eigenvectors().cols(); Index bseA_triplet_exc = orbitalsA.BSETriplets().eigenvectors().cols(); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " molecule A has " << bseA_singlet_exc << " singlet excitons with dimension " << bseA_size << flush; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " molecule A has " << bseA_triplet_exc << " triplet excitons with dimension " << bseA_size << flush; // get exciton information of molecule B Index bseB_cmax = orbitalsB.getBSEcmax(); Index bseB_cmin = orbitalsB.getBSEcmin(); Index bseB_vmax = orbitalsB.getBSEvmax(); Index bseB_vmin = orbitalsB.getBSEvmin(); Index bseB_vtotal = bseB_vmax - bseB_vmin + 1; Index bseB_ctotal = bseB_cmax - bseB_cmin + 1; Index bseB_total = bseB_vtotal + bseB_ctotal; Index bseB_size = bseB_vtotal * bseB_ctotal; Index bseB_singlet_exc = orbitalsB.BSESinglets().eigenvectors().cols(); Index bseB_triplet_exc = orbitalsB.BSETriplets().eigenvectors().cols(); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " molecule B has " << bseB_singlet_exc << " singlet excitons with dimension " << bseB_size << flush; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " molecule B has " << bseB_triplet_exc << " triplet excitons with dimension " << bseB_size << flush; if (_levA > bseA_singlet_exc) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Number of excitons you want is greater than stored for molecule " "A. Setting to max number available" << flush; _levA = bseA_singlet_exc; } if (_levB > bseB_singlet_exc) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Number of excitons you want is greater than stored for molecule " "B. Setting to max number available" << flush; _levB = bseB_singlet_exc; } if (_levA > bseA_singlet_exc) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Number of Frenkel states you want is greater than stored for " "molecule A. Setting to max number available" << flush; _levA = bseA_singlet_exc; } if (_levB > bseB_singlet_exc) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Number of Frenkel states you want is greater than stored for " "molecule B. Setting to max number available" << flush; _levB = bseB_singlet_exc; } if (_unoccA > bseA_ctotal) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Number of occupied orbitals in molecule A for CT creation " "exceeds number of KS-orbitals in BSE" << flush; _unoccA = bseA_ctotal; } else if (_unoccA < 0) { _unoccA = bseA_ctotal; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Number of occupied orbitals in molecule B for CT creation " "exceeds number of KS-orbitals in BSE" << flush; } if (_unoccB > bseB_ctotal) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Number of occupied orbitals in molecule B for CT creation " "exceeds number of KS-orbitals in BSE" << flush; _unoccB = bseB_ctotal; } else if (_unoccB < 0) { _unoccB = bseB_ctotal; } if (_occA > bseA_vtotal) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Number of unoccupied orbitals in molecule A for CT creation " "exceeds number of KS-orbitals in BSE" << flush; _occA = bseA_vtotal; } else if (_occA < 0) { _occA = bseA_vtotal; } if (_occB > bseB_vtotal) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Number of unoccupied orbitals in molecule B for CT creation " "exceeds number of KS-orbitals in BSE" << flush; _occB = bseB_vtotal; } else if (_occB < 0) { _occB = bseB_vtotal; } // get exciton information of pair AB Index bseAB_cmax = orbitalsAB.getBSEcmax(); Index bseAB_cmin = orbitalsAB.getBSEcmin(); Index bseAB_vmax = orbitalsAB.getBSEvmax(); Index bseAB_vmin = orbitalsAB.getBSEvmin(); Index basisAB = orbitalsAB.getBasisSetSize(); Index bseAB_vtotal = bseAB_vmax - bseAB_vmin + 1; Index bseAB_ctotal = bseAB_cmax - bseAB_cmin + 1; Index bseAB_total = bseAB_vtotal + bseAB_ctotal; Index bseAB_size = bseAB_vtotal * bseAB_ctotal; // DFT levels of monomers can be reduced to those used in BSE XTP_LOG(Log::error, *_pLog) << TimeStamp() << " levels used for BSE of molA: " << bseA_vmin << " to " << bseA_cmax << " total: " << bseA_total << flush; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " levels used for BSE of molB: " << bseB_vmin << " to " << bseB_cmax << " total: " << bseB_total << flush; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " levels used for BSE of dimer AB: " << bseAB_vmin << " to " << bseAB_cmax << " total: " << bseAB_total << flush; Eigen::MatrixXd MOsA = orbitalsA.MOs().eigenvectors().block(0, bseA_vmin, basisA, bseA_total); Eigen::MatrixXd MOsB = orbitalsB.MOs().eigenvectors().block(0, bseB_vmin, basisB, bseB_total); Eigen::MatrixXd MOsAB = orbitalsAB.MOs().eigenvectors().block( 0, bseAB_vmin, basisAB, bseAB_total); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Calculating overlap matrix for basisset: " << orbitalsAB.getDFTbasisName() << flush; Eigen::MatrixXd overlap = CalculateOverlapMatrix(orbitalsAB) * MOsAB; XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Projecting monomers onto dimer orbitals" << flush; Eigen::MatrixXd A_AB = overlap.topRows(basisA).transpose() * MOsA; Eigen::MatrixXd B_AB = overlap.bottomRows(basisB).transpose() * MOsB; Eigen::VectorXd mag_A = A_AB.colwise().squaredNorm(); if (mag_A.any() < 0.95) { XTP_LOG(Log::error, *_pLog) << "\nWarning: " << "Projection of orbitals of monomer A on dimer is insufficient,mag=" << mag_A.minCoeff() << flush; } Eigen::VectorXd mag_B = B_AB.colwise().squaredNorm(); if (mag_B.any() < 0.95) { XTP_LOG(Log::error, *_pLog) << "\nWarning: " << "Projection of orbitals of monomer B on dimer is insufficient,mag=" << mag_B.minCoeff() << flush; } AOBasis dftbasis = orbitalsAB.SetupDftBasis(); AOBasis auxbasis = orbitalsAB.SetupAuxBasis(); TCMatrix_gwbse Mmn; // rpamin here, because RPA needs till rpamin Mmn.Initialize(auxbasis.AOBasisSize(), orbitalsAB.getRPAmin(), orbitalsAB.getGWAmax(), orbitalsAB.getRPAmin(), orbitalsAB.getRPAmax()); Mmn.Fill(auxbasis, dftbasis, orbitalsAB.MOs().eigenvectors()); const Eigen::MatrixXd& qpcoeff = orbitalsAB.QPdiag().eigenvectors(); Eigen::MatrixXd Hqp = qpcoeff * orbitalsAB.QPdiag().eigenvalues().asDiagonal() * qpcoeff.transpose(); BSE::options opt; opt.cmax = orbitalsAB.getBSEcmax(); opt.homo = orbitalsAB.getHomo(); opt.qpmin = orbitalsAB.getGWAmin(); opt.qpmax = orbitalsAB.getGWAmax(); opt.rpamax = orbitalsAB.getRPAmax(); opt.rpamin = orbitalsAB.getRPAmin(); opt.useTDA = true; opt.vmin = orbitalsAB.getBSEvmin(); opt.use_Hqp_offdiag = orbitalsAB.GetFlagUseHqpOffdiag(); BSE bse(*_pLog, Mmn); bse.configure(opt, orbitalsAB.RPAInputEnergies(), Hqp); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Setup BSE operator" << flush; // now the different spin types if (_doSinglets) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Evaluating singlets" << flush; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Setup Hamiltonian" << flush; Eigen::MatrixXd FE_AB = Eigen::MatrixXd::Zero(bseAB_size, _levA + _levB); const Eigen::MatrixXd bseA = orbitalsA.BSESinglets().eigenvectors().leftCols(_levA); FE_AB.leftCols(_levA) = ProjectFrenkelExcitons( bseA, A_AB, bseA_vtotal, bseA_ctotal, bseAB_vtotal, bseAB_ctotal); const Eigen::MatrixXd bseB = orbitalsB.BSESinglets().eigenvectors().leftCols(_levB); FE_AB.rightCols(_levB) = ProjectFrenkelExcitons( bseB, B_AB, bseB_vtotal, bseB_ctotal, bseAB_vtotal, bseAB_ctotal); Eigen::MatrixXd CTStates = SetupCTStates( bseA_vtotal, bseB_vtotal, bseAB_vtotal, bseAB_ctotal, A_AB, B_AB); JAB_singlet = ProjectExcitons(FE_AB, CTStates, bse.getSingletOperator_TDA()); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " calculated singlet couplings " << flush; } if (_doTriplets) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Evaluating triplets" << flush; Eigen::MatrixXd FE_AB = Eigen::MatrixXd::Zero(bseAB_size, _levA + _levB); const Eigen::MatrixXd bseA = orbitalsA.BSETriplets().eigenvectors().leftCols(_levA); FE_AB.leftCols(_levA) = ProjectFrenkelExcitons( bseA, A_AB, bseA_vtotal, bseA_ctotal, bseAB_vtotal, bseAB_ctotal); const Eigen::MatrixXd bseB = orbitalsB.BSETriplets().eigenvectors().leftCols(_levB); FE_AB.rightCols(_levB) = ProjectFrenkelExcitons( bseB, B_AB, bseB_vtotal, bseB_ctotal, bseAB_vtotal, bseAB_ctotal); Eigen::MatrixXd CTStates = SetupCTStates( bseA_vtotal, bseB_vtotal, bseAB_vtotal, bseAB_ctotal, A_AB, B_AB); JAB_triplet = ProjectExcitons(FE_AB, CTStates, bse.getTripletOperator_TDA()); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " calculated triplet couplings " << flush; } XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Done with exciton couplings" << flush; } Eigen::MatrixXd BSECoupling::OrthogonalizeCTs(Eigen::MatrixXd& FE_AB, Eigen::MatrixXd& CTStates) const { Index ct = CTStates.cols(); if (ct > 0) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Orthogonalizing CT-states with respect to FE-states" << flush; Eigen::MatrixXd correction = FE_AB * (FE_AB.transpose() * CTStates); CTStates -= correction; // normalize Eigen::VectorXd norm = CTStates.colwise().norm(); for (Index i = 0; i < CTStates.cols(); i++) { CTStates.col(i) /= norm(i); } Index minstateindex = 0; double minnorm = norm.minCoeff(&minstateindex); if (minnorm < 0.95) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " WARNING: CT-state " << minstateindex << " norm is only " << minnorm << flush; } } Index bse_exc = _levA + _levB; Index bseAB_size = CTStates.rows(); Eigen::MatrixXd projection(bseAB_size, bse_exc + ct); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " merging projections into one vector " << flush; projection.leftCols(bse_exc) = FE_AB; FE_AB.resize(0, 0); if (ct > 0) { projection.rightCols(ct) = CTStates; } CTStates.resize(0, 0); return projection; } template Eigen::MatrixXd BSECoupling::CalcJ_dimer(BSE_OPERATOR& H, Eigen::MatrixXd& projection) const { XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Setting up coupling matrix size " << projection.cols() << flush; // matrix _J // E_A J_AB J_A_ABCT J_A_BACT // J_BA E_B J_B_ABCT J_B_BACT // J_ABCT_A J_ABCT_B E_ABCT J_ABCT_BACT // J_BACT_A J_BACT_B J_BACT_ABCT E_BACT // this only works for hermitian/symmetric H so only in TDA Eigen::MatrixXd temp = H * projection; Eigen::MatrixXd J_dimer = projection.transpose() * temp; XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Setting up overlap matrix size " << projection.cols() << flush; Eigen::MatrixXd S_dimer = projection.transpose() * projection; projection.resize(0, 0); if (projection.cols()) { XTP_LOG(Log::debug, *_pLog) << "---------------------------------------" << flush; XTP_LOG(Log::debug, *_pLog) << "_J_dimer[Ryd]" << flush; XTP_LOG(Log::debug, *_pLog) << J_dimer << flush; XTP_LOG(Log::debug, *_pLog) << "_S_dimer" << flush; XTP_LOG(Log::debug, *_pLog) << S_dimer << flush; XTP_LOG(Log::debug, *_pLog) << "---------------------------------------" << flush; } Eigen::SelfAdjointEigenSolver es(S_dimer); Eigen::MatrixXd Sm1 = es.operatorInverseSqrt(); Eigen::MatrixXd J_ortho = Sm1 * J_dimer * Sm1; if (projection.cols()) { XTP_LOG(Log::debug, *_pLog) << "---------------------------------------" << flush; XTP_LOG(Log::debug, *_pLog) << "_J_ortho[Ryd]" << flush; XTP_LOG(Log::debug, *_pLog) << J_ortho << flush; XTP_LOG(Log::debug, *_pLog) << "_S-1/2" << flush; XTP_LOG(Log::debug, *_pLog) << Sm1 << flush; XTP_LOG(Log::debug, *_pLog) << "---------------------------------------" << flush; } XTP_LOG(Log::debug, *_pLog) << TimeStamp() << " Smallest value of dimer overlapmatrix is " << es.eigenvalues()(0) << flush; return J_ortho; } template std::array BSECoupling::ProjectExcitons( Eigen::MatrixXd& FE_AB, Eigen::MatrixXd& CTStates, BSE_OPERATOR H) const { Eigen::MatrixXd projection = OrthogonalizeCTs(FE_AB, CTStates); Eigen::MatrixXd J_ortho = CalcJ_dimer(H, projection); std::array J; XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Running Perturbation algorithm" << flush; J[0] = Perturbation(J_ortho); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Running Projection algorithm" << flush; J[1] = Fulldiag(J_ortho); XTP_LOG(Log::debug, *_pLog) << "---------------------------------------" << flush; XTP_LOG(Log::debug, *_pLog) << "Jeff_pert[Hrt]" << flush; XTP_LOG(Log::debug, *_pLog) << J[0] << flush; XTP_LOG(Log::debug, *_pLog) << "Jeff_diag[Hrt]" << flush; XTP_LOG(Log::debug, *_pLog) << J[1] << flush; XTP_LOG(Log::debug, *_pLog) << "---------------------------------------" << flush; return J; } Eigen::MatrixXd BSECoupling::Perturbation( const Eigen::MatrixXd& J_dimer) const { Index bse_exc = _levA + _levB; Index ct = J_dimer.rows() - bse_exc; Eigen::MatrixXd J_result = J_dimer; if (ct > 0) { Eigen::MatrixXd transformation = Eigen::MatrixXd::Identity(J_dimer.rows(), J_dimer.cols()); Eigen::MatrixXd Ct = J_dimer.bottomRightCorner(ct, ct); Eigen::SelfAdjointEigenSolver es(Ct); transformation.bottomRightCorner(ct, ct) = es.eigenvectors(); Ct.resize(0, 0); XTP_LOG(Log::debug, *_pLog) << "FE state hamiltonian" << flush; XTP_LOG(Log::debug, *_pLog) << J_dimer.topLeftCorner(bse_exc, bse_exc) << flush; if (ct > 0) { XTP_LOG(Log::debug, *_pLog) << "eigenvalues of CT states" << flush; XTP_LOG(Log::debug, *_pLog) << es.eigenvalues().transpose() << flush; } J_result = transformation.transpose() * J_dimer * transformation; XTP_LOG(Log::debug, *_pLog) << "---------------------------------------" << flush; XTP_LOG(Log::debug, *_pLog) << "_J_ortho[Hrt] CT-state diag" << flush; XTP_LOG(Log::debug, *_pLog) << J_result << flush; XTP_LOG(Log::debug, *_pLog) << "---------------------------------------" << flush; } Eigen::MatrixXd Jmatrix = Eigen::MatrixXd::Zero(bse_exc, bse_exc); for (Index stateA = 0; stateA < _levA; stateA++) { double Ea = J_result(stateA, stateA); for (Index stateB = 0; stateB < _levB; stateB++) { Index stateBd = stateB + _levA; XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Calculating coupling between exciton A" << stateA + 1 << " and exciton B" << stateB + 1 << flush; double J = J_result(stateA, stateBd); double Eb = J_result(stateBd, stateBd); for (Index k = bse_exc; k < (bse_exc + ct); k++) { double Eab = J_result(k, k); if (std::abs(Eab - Ea) < 0.001) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << "Energydifference between state A " << stateA + 1 << "and CT state " << k + 1 << " is " << Eab - Ea << "[Hrt]" << flush; } if (std::abs(Eab - Eb) < 0.001) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << "Energydifference between state B " << stateB + 1 << "and CT state " << k + 1 << " is " << Eab - Eb << "[Hrt]" << flush; } J += 0.5 * J_result(k, stateA) * J_result(k, stateBd) * (1 / (Ea - Eab) + 1 / (Eb - Eab)); // Have no clue why 0.5 } Jmatrix(stateA, stateBd) = J; Jmatrix(stateBd, stateA) = J; } } return Jmatrix; } Eigen::MatrixXd BSECoupling::Fulldiag(const Eigen::MatrixXd& J_dimer) const { Index bse_exc = _levA + _levB; Eigen::SelfAdjointEigenSolver es(J_dimer); XTP_LOG(Log::debug, *_pLog) << "---------------------------------------" << flush; XTP_LOG(Log::debug, *_pLog) << "Eigenvectors of J" << flush; XTP_LOG(Log::debug, *_pLog) << es.eigenvectors() << flush; XTP_LOG(Log::debug, *_pLog) << "J_eigenvalues[Hrt]" << flush; XTP_LOG(Log::debug, *_pLog) << es.eigenvalues() << flush; XTP_LOG(Log::debug, *_pLog) << "---------------------------------------" << flush; Eigen::MatrixXd Jmat = Eigen::MatrixXd::Zero(bse_exc, bse_exc); // Calculate projection on subspace for every pair of excitons separately for (Index stateA = 0; stateA < _levA; stateA++) { for (Index stateB = 0; stateB < _levB; stateB++) { Index stateBd = stateB + _levA; XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Calculating coupling between exciton A" << stateA + 1 << " and exciton B" << stateB + 1 << flush; std::array indexes; std::array signs; // Find the eigenstate state, which in an L2 is closed to A or B // respectively es.eigenvectors().row(stateA).cwiseAbs().maxCoeff(&indexes[0]); es.eigenvectors().row(stateBd).cwiseAbs().maxCoeff(&indexes[1]); if (indexes[0] == indexes[1]) { Eigen::RowVectorXd stateamplitudes = es.eigenvectors().row(stateBd).cwiseAbs(); stateamplitudes[indexes[1]] = 0.0; stateamplitudes.maxCoeff(&indexes[1]); } signs[0] = GetSign(es.eigenvectors()(stateA, indexes[0])); signs[1] = GetSign(es.eigenvectors()(stateBd, indexes[1])); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Order is: [Initial state n->nth eigenvalue]" << flush; XTP_LOG(Log::info, *_pLog) << " A" << stateA + 1 << ":" << stateA + 1 << "->" << indexes[0] + 1 << " "; XTP_LOG(Log::info, *_pLog) << " B" << stateB + 1 << ":" << stateBd + 1 << "->" << indexes[1] + 1 << " " << flush; // setting up transformation matrix Tmat and diagonal matrix Emat for the // eigenvalues; Eigen::Matrix2d Emat = Eigen::Matrix2d::Zero(); Eigen::Matrix2d Tmat = Eigen::Matrix2d::Zero(); // find the eigenvectors which are most similar to the initial states // row for (Index i = 0; i < 2; i++) { Index k = indexes[i]; double sign = signs[i]; Tmat(0, i) = sign * es.eigenvectors()(stateA, k); Tmat(1, i) = sign * es.eigenvectors()(stateBd, k); Emat(i, i) = es.eigenvalues()(k); } Tmat.colwise().normalize(); if (Tmat.determinant() < 0) { XTP_LOG(Log::info, *_pLog) << " Reduced state matrix is not in a right handed basis, " "multiplying second eigenvector by -1 " << flush; Tmat.col(1) *= -1; } XTP_LOG(Log::debug, *_pLog) << "---------------------------------------" << flush; XTP_LOG(Log::debug, *_pLog) << "_T" << flush; XTP_LOG(Log::debug, *_pLog) << Tmat << flush; Eigen::Matrix2d S_small = Tmat * Tmat.transpose(); XTP_LOG(Log::debug, *_pLog) << "S_small" << flush; XTP_LOG(Log::debug, *_pLog) << S_small << flush; // orthogonalize that matrix Eigen::SelfAdjointEigenSolver ss(S_small); Eigen::Matrix2d sm1 = ss.operatorInverseSqrt(); Emat = sm1 * Emat * sm1; XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Smallest value of dimer overlapmatrix is " << ss.eigenvalues()(0) << flush; XTP_LOG(Log::debug, *_pLog) << "S-1/2" << flush; XTP_LOG(Log::debug, *_pLog) << sm1 << flush; XTP_LOG(Log::debug, *_pLog) << "E_ortho" << flush; XTP_LOG(Log::debug, *_pLog) << Emat << flush; Tmat = Tmat * sm1; XTP_LOG(Log::debug, *_pLog) << "T_ortho" << flush; XTP_LOG(Log::debug, *_pLog) << Tmat << flush; XTP_LOG(Log::debug, *_pLog) << "---------------------------------------" << flush; Eigen::Matrix2d J_small = Tmat * Emat * Tmat.transpose(); XTP_LOG(Log::debug, *_pLog) << "T_ortho*E_ortho*T_ortho^T" << flush; XTP_LOG(Log::debug, *_pLog) << J_small << flush; Jmat(stateA, stateBd) = J_small(0, 1); Jmat(stateBd, stateA) = J_small(1, 0); } } return Jmat; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/calculators/000077500000000000000000000000001412152066400170215ustar00rootroot00000000000000xtp-2021.2/src/libxtp/calculators/eanalyze.cc000066400000000000000000000232341412152066400211440ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local private VOTCA includes #include "eanalyze.h" namespace votca { namespace xtp { void EAnalyze::ParseOptions(const tools::Property &options) { _resolution_pairs = options.get(".resolution_pairs").as(); _resolution_sites = options.get(".resolution_sites").as(); _resolution_spatial = options.get(".resolution_spatial").as(); _seg_pattern = options.get(".match_pattern").as(); std::string statestrings = options.get(".states").as(); tools::Tokenizer tok(statestrings, ",\n\t "); std::vector string_vec; tok.ToVector(string_vec); for (std::string &state : string_vec) { _states.push_back(QMStateType(state)); } _doenergy_landscape = options.get(".do_energy_landscape").as(); if (options.get(".do_distance_mode").as()) { std::string distancemode = options.get("distancemode").as(); if (distancemode == "centerofmass") { _atomdistances = false; } else { _atomdistances = true; } } } bool EAnalyze::Evaluate(Topology &top) { // Short-list segments according to pattern for (Segment &seg : top.Segments()) { std::string seg_name = seg.getType(); if (votca::tools::wildcmp(_seg_pattern, seg_name)) { _seg_shortlist.push_back(&seg); } } std::cout << std::endl << "... ... Short-listed " << _seg_shortlist.size() << " segments (pattern='" << _seg_pattern << "')" << std::flush; std::cout << std::endl << "... ... ... NOTE Statistics of site energies and spatial" << " correlations thereof are based on the short-listed segments only. " << std::flush; std::cout << std::endl << "... ... ... " << "Statistics of site-energy differences operate on the full list." << std::flush; // Calculate // ... Site-energy histogram, mean, width // ... Pair-energy histogram, mean, width // ... Site-energy correlation const QMNBList &nblist = top.NBList(); for (QMStateType state : _states) { std::cout << std::endl << "... ... excited state " << state.ToString() << std::flush; if (!_seg_shortlist.size()) { std::cout << std::endl << "... ... ... No segments short-listed. Skip ... " << std::flush; } else { SiteHist(state); SiteCorr(top, state); } if (!nblist.size()) { std::cout << std::endl << "... ... ... No pairs in topology. Skip ... " << std::flush; } else { PairHist(top, state); } } return true; } void EAnalyze::SiteHist(QMStateType state) const { std::vector Es; Es.reserve(_seg_shortlist.size()); for (Segment *seg : _seg_shortlist) { Es.push_back(seg->getSiteEnergy(state) * tools::conv::hrt2ev); } double MAX = *std::max_element(Es.begin(), Es.end()); double MIN = *std::min_element(Es.begin(), Es.end()); double sum = std::accumulate(Es.begin(), Es.end(), 0.0); double AVG = sum / double(Es.size()); double sq_sum = std::inner_product(Es.begin(), Es.end(), Es.begin(), 0.0); double STD = std::sqrt(sq_sum / double(Es.size()) - AVG * AVG); // Prepare bins Index BIN = Index((MAX - MIN) / _resolution_sites + 0.5) + 1; tools::HistogramNew hist; hist.Initialize(MIN, MAX, BIN); hist.ProcessRange::iterator>(Es.begin(), Es.end()); tools::Table &tab = hist.data(); tab.flags() = std::vector(tab.size(), ' '); std::string comment = (boost::format("EANALYZE: SITE-ENERGY HISTOGRAM[eV] \n # AVG %1$4.7f STD " "%2$4.7f MIN %3$4.7f MAX %4$4.7f") % AVG % STD % MIN % MAX) .str(); std::string filename = "eanalyze.sitehist_" + state.ToString() + ".out"; tab.set_comment(comment); tab.Save(filename); // Write "seg x y z energy" with atomic {x,y,z} if (_doenergy_landscape) { std::string filename2 = "eanalyze.landscape_" + state.ToString() + ".out"; std::ofstream out; out.open(filename2); if (!out) { throw std::runtime_error("error, cannot open file " + filename2); } for (Segment *seg : _seg_shortlist) { if (seg->getId() < _first_seg) { continue; } if (seg->getId() == _last_seg) { break; } double E = seg->getSiteEnergy(state); for (Atom &atm : *seg) { out << boost::format("%1$3s %2$4.7f %3$4.7f %4$4.7f %5$4.7f\n") % seg->getType() % atm.getPos().x() % atm.getPos().y() % atm.getPos().z() % E; } } out.close(); } } void EAnalyze::PairHist(const Topology &top, QMStateType state) const { const QMNBList &nblist = top.NBList(); std::string filenamelist = "eanalyze.pairlist_" + state.ToString() + ".out"; // Collect site-energy differences from neighbourlist std::vector dE; dE.reserve(2 * nblist.size()); std::ofstream out; out.open(filenamelist); if (!out) { throw std::runtime_error("error, cannot open file " + filenamelist); } for (QMPair *pair : nblist) { double deltaE = pair->getdE12(state) * tools::conv::hrt2ev; dE.push_back(deltaE); dE.push_back(-deltaE); out << boost::format("%1$5d %2$5d %3$4.7f \n") % pair->Seg1()->getId() % pair->Seg2()->getId() % deltaE; } out.close(); double MAX = *std::max_element(dE.begin(), dE.end()); double MIN = *std::min_element(dE.begin(), dE.end()); double sum = std::accumulate(dE.begin(), dE.end(), 0.0); double AVG = sum / double(dE.size()); double sq_sum = std::inner_product(dE.begin(), dE.end(), dE.begin(), 0.0); double STD = std::sqrt(sq_sum / double(dE.size()) - AVG * AVG); Index BIN = Index((MAX - MIN) / _resolution_pairs + 0.5) + 1; std::string filename2 = "eanalyze.pairhist_" + state.ToString() + ".out"; tools::HistogramNew hist; hist.Initialize(MIN, MAX, BIN); hist.ProcessRange::iterator>(dE.begin(), dE.end()); tools::Table &tab = hist.data(); std::string comment = (boost::format("EANALYZE: PAIR-ENERGY HISTOGRAM[eV] \n # AVG %1$4.7f STD " "%2$4.7f MIN %3$4.7f MAX %4$4.7f") % AVG % STD % MIN % MAX) .str(); tab.set_comment(comment); tab.flags() = std::vector(tab.size(), ' '); tab.Save(filename2); } void EAnalyze::SiteCorr(const Topology &top, QMStateType state) const { std::vector Es; Es.reserve(_seg_shortlist.size()); for (Segment *seg : _seg_shortlist) { Es.push_back(seg->getSiteEnergy(state) * tools::conv::hrt2ev); } double sum = std::accumulate(Es.begin(), Es.end(), 0.0); double AVG = sum / double(Es.size()); double sq_sum = std::inner_product(Es.begin(), Es.end(), Es.begin(), 0.0); double VAR = sq_sum / double(Es.size()) - AVG * AVG; double STD = std::sqrt(VAR); // Collect inter-site distances, correlation product tools::Table tabcorr; Index length = Index(_seg_shortlist.size()) * Index(_seg_shortlist.size() - 1) / 2; tabcorr.resize(length); Index index = 0; for (Index i = 0; i < Index(_seg_shortlist.size()); i++) { const Segment &segi = *_seg_shortlist[i]; for (Index j = i + 1; j < Index(_seg_shortlist.size()); j++) { const Segment &segj = *_seg_shortlist[j]; double R = 0; if (_atomdistances) { R = top.GetShortestDist(segi, segj); } else { R = (top.PbShortestConnect(segi.getPos(), segj.getPos())).norm(); } double C = (segi.getSiteEnergy(state) - AVG) * (segj.getSiteEnergy(state) - AVG); tabcorr.set(index, R * tools::conv::bohr2nm, C); index++; } } double MIN = tabcorr.x().minCoeff(); double MAX = tabcorr.x().maxCoeff(); // Prepare bins Index BIN = Index((MAX - MIN) / _resolution_spatial + 0.5) + 1; std::vector > histCs; histCs.resize(BIN); for (Index i = 0; i < tabcorr.size(); ++i) { Index bin = Index((tabcorr.x()[i] - MIN) / _resolution_spatial + 0.5); histCs[bin].push_back(tabcorr.y()[i]); } tools::Table histC; histC.SetHasYErr(true); // Calculate spatial correlation histC.resize(BIN); for (Index bin = 0; bin < BIN; ++bin) { double corr = 0.0; double dcorr2 = 0.0; for (double entry : histCs[bin]) { corr += entry / VAR; } corr = corr / double(histCs[bin].size()); for (Index i = 0; i < Index(histCs[bin].size()); ++i) { dcorr2 += (histCs[bin][i] / VAR / double(histCs[bin].size()) - corr) * (histCs[bin][i] / VAR / double(histCs[bin].size()) - corr); } // error on mean value dcorr2 = dcorr2 / double(histCs[bin].size()) / double(histCs[bin].size() - 1); double R = MIN + double(bin) * _resolution_spatial; histC.set(bin, R, corr, ' ', std::sqrt(dcorr2)); } std::string filename = "eanalyze.sitecorr_" + state.ToString() + ".out"; std::string comment = (boost::format("EANALYZE: DISTANCE[nm] SPATIAL SITE-ENERGY " "CORRELATION[eV] \n # AVG " "%1$4.7f STD %2$4.7f MIN %3$4.7f MAX %4$4.7f") % AVG % STD % MIN % MAX) .str(); histC.set_comment(comment); histC.Save(filename); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/calculators/eanalyze.h000066400000000000000000000036361412152066400210120ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_EANALYZE_H #define VOTCA_XTP_EANALYZE_H // Standard includes #include #include #include // VOTCA includes #include #include // Local VOTCA includes #include "votca/xtp/qmcalculator.h" #include "votca/xtp/qmstate.h" #include "votca/xtp/topology.h" namespace votca { namespace xtp { class EAnalyze final : public QMCalculator { public: EAnalyze() = default; ~EAnalyze() = default; bool WriteToStateFile() const { return false; } std::string Identify() { return "eanalyze"; } protected: void ParseOptions(const tools::Property &user_options); bool Evaluate(Topology &top); private: void SiteHist(QMStateType state) const; void PairHist(const Topology &top, QMStateType state) const; void SiteCorr(const Topology &top, QMStateType state) const; double _resolution_pairs; double _resolution_sites; double _resolution_spatial; bool _atomdistances = false; std::vector _states; bool _doenergy_landscape; Index _first_seg; Index _last_seg; std::string _seg_pattern; std::vector _seg_shortlist; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_EANALYZE_H xtp-2021.2/src/libxtp/calculators/einternal.cc000066400000000000000000000076011412152066400213150ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/topology.h" // Local private VOTCA includes #include "einternal.h" namespace votca { namespace xtp { void EInternal::ParseOptions(const tools::Property &options) { _energiesXML = options.get(".energiesXML").as(); } void EInternal::ParseEnergies() { std::cout << "\n... ... Site, reorg. energies from " << _energiesXML << ".\n"; tools::Property alloc; alloc.LoadFromXML(_energiesXML); std::string key = "topology.molecules.molecule"; std::vector mols = alloc.Select(key); for (tools::Property *molprop : mols) { key = "segments.segment"; std::vector segs = molprop->Select(key); for (tools::Property *segprop : segs) { std::string segName = segprop->get("name").as(); bool has_seg = true; QMStateCarrierStorage U_xX_nN; QMStateCarrierStorage U_nX_nN; QMStateCarrierStorage U_xN_xX; QMStateCarrierStorage has_state; double eV2hrt = tools::conv::ev2hrt; std::vector types = {QMStateType::Electron, QMStateType::Hole, QMStateType::Singlet, QMStateType::Triplet}; for (QMStateType type : types) { std::string u_xX_nN = "U_xX_nN_" + type.ToString(); std::string u_nX_nN = "U_nX_nN_" + type.ToString(); std::string u_xN_xX = "U_xN_xX_" + type.ToString(); if (segprop->exists(u_xX_nN) && segprop->exists(u_nX_nN) && segprop->exists(u_xN_xX)) { U_xX_nN.setValue(segprop->get(u_xX_nN).as() * eV2hrt, type); U_nX_nN.setValue(segprop->get(u_nX_nN).as() * eV2hrt, type); U_xN_xX.setValue(segprop->get(u_xN_xX).as() * eV2hrt, type); has_state.setValue(true, type); } } _seg_has_state[segName] = has_state; _seg_U_xX_nN[segName] = U_xX_nN; _seg_U_nX_nN[segName] = U_nX_nN; _seg_U_xN_xX[segName] = U_xN_xX; _has_seg[segName] = has_seg; } } } bool EInternal::Evaluate(Topology &top) { ParseEnergies(); Index count = 0; for (Segment &seg : top.Segments()) { std::string segName = seg.getType(); if (!_has_seg.count(segName)) { std::cout << std::endl << "... ... WARNING: No energy information for seg [" << segName << "]. Skipping... "; continue; } ++count; std::vector types = {QMStateType::Electron, QMStateType::Hole, QMStateType::Singlet, QMStateType::Triplet}; for (QMStateType type : types) { if (_seg_has_state[segName].getValue(type.Type())) { seg.setU_xX_nN(_seg_U_xX_nN[segName].getValue(type.Type()), type.Type()); seg.setU_nX_nN(_seg_U_nX_nN[segName].getValue(type.Type()), type.Type()); seg.setU_xN_xX(_seg_U_xN_xX[segName].getValue(type.Type()), type.Type()); } } } std::cout << std::endl << "... ... Read in site, reorg. energies for " << count << " segments. " << std::flush; return true; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/calculators/einternal.h000066400000000000000000000032071412152066400211550ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_EINTERNAL_H #define VOTCA_XTP_EINTERNAL_H // Local VOTCA includes #include "votca/xtp/qmcalculator.h" #include "votca/xtp/qmstate.h" namespace votca { namespace xtp { class EInternal final : public QMCalculator { public: EInternal() = default; ~EInternal() = default; std::string Identify() { return "einternal"; } bool WriteToStateFile() const { return true; } protected: void ParseOptions(const tools::Property &user_options); bool Evaluate(Topology &top); private: void ParseEnergies(); std::map > _seg_U_xX_nN; std::map > _seg_U_nX_nN; std::map > _seg_U_xN_xX; std::map > _seg_has_state; std::map _has_seg; std::string _energiesXML; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_EINTERNAL_H xtp-2021.2/src/libxtp/calculators/ianalyze.cc000066400000000000000000000154701412152066400211530ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/topology.h" // Local private VOTCA includes #include "ianalyze.h" namespace votca { namespace xtp { void IAnalyze::ParseOptions(const tools::Property &options) { std::string statestrings = options.get(".states").as(); tools::Tokenizer tok(statestrings, ",\n\t "); std::vector string_vec; tok.ToVector(string_vec); for (std::string &state : string_vec) { _states.push_back(QMStateType(state)); } _resolution_logJ2 = options.get(".resolution_logJ2").as(); if (options.get(".do_pairtype").as()) { _do_pairtype = true; std::string _store_stdstring = options.get(".pairtype").as(); if (_store_stdstring.find("Hopping") != std::string::npos) { _pairtype.push_back(QMPair::Hopping); } if (_store_stdstring.find("Excitoncl") != std::string::npos) { _pairtype.push_back(QMPair::Excitoncl); } if (!_pairtype.size()) { std::cout << "\n... ... No pairtypes recognized will output all pairs. "; _do_pairtype = false; } } if (options.get(".do_resolution_spatial").as()) { _resolution_spatial = options.get(".resolution_spatial").as(); if (_resolution_spatial != 0.0) { _do_IRdependence = true; } } } bool IAnalyze::Evaluate(Topology &top) { std::cout << std::endl; QMNBList &nblist = top.NBList(); if (!nblist.size()) { std::cout << std::endl << "... ... No pairs in topology. Skip..."; return false; } if (_do_pairtype) { bool pairs_exist = false; for (QMPair *pair : nblist) { QMPair::PairType pairtype = pair->getType(); if (std::find(_pairtype.begin(), _pairtype.end(), pairtype) != _pairtype.end()) { pairs_exist = true; break; } } if (!pairs_exist) { std::cout << std::endl << "... ... No pairs of given pairtypes in topology. Skip..."; return 0; } } for (QMStateType state : _states) { std::cout << "Calculating for state " << state.ToString() << " now." << std::endl; this->IHist(top, state); if (_do_IRdependence) { IRdependence(top, state); } } return true; } void IAnalyze::IHist(Topology &top, QMStateType state) { QMNBList &nblist = top.NBList(); // Collect J2s from pairs std::vector J2s; for (QMPair *pair : nblist) { if (_do_pairtype) { QMPair::PairType pairtype = pair->getType(); if (!(std::find(_pairtype.begin(), _pairtype.end(), pairtype) != _pairtype.end())) { continue; } } double test = pair->getJeff2(state) * tools::conv::hrt2ev * tools::conv::hrt2ev; if (test <= 0) { continue; } // avoid -inf in output double J2 = std::log10(test); J2s.push_back(J2); } if (J2s.size() < 1) { std::cout << "WARNING:" + state.ToLongString() + " Couplings are all zero. You have not yet imported them! " << std::endl; return; } double MAX = *std::max_element(J2s.begin(), J2s.end()); double MIN = *std::min_element(J2s.begin(), J2s.end()); double sum = std::accumulate(J2s.begin(), J2s.end(), 0.0); double AVG = sum / double(J2s.size()); double sq_sum = std::inner_product(J2s.begin(), J2s.end(), J2s.begin(), 0.0); double STD = std::sqrt(sq_sum / double(J2s.size()) - AVG * AVG); // Prepare bins Index BIN = Index((MAX - MIN) / _resolution_logJ2 + 0.5) + 1; tools::HistogramNew hist; hist.Initialize(MIN, MAX, BIN); hist.ProcessRange::iterator>(J2s.begin(), J2s.end()); tools::Table &tab = hist.data(); std::string comment = (boost::format("IANALYZE: PAIR-INTEGRAL J2 HISTOGRAM \n # AVG %1$4.7f " "STD %2$4.7f MIN %3$4.7f MAX %4$4.7f") % AVG % STD % MIN % MAX) .str(); std::string filename = "ianalyze.ihist_" + state.ToString() + ".out"; tab.set_comment(comment); tab.flags() = std::vector(tab.size(), ' '); tab.Save(filename); } void IAnalyze::IRdependence(Topology &top, QMStateType state) { QMNBList &nblist = top.NBList(); // Collect J2s from pairs std::vector J2s; J2s.reserve(nblist.size()); std::vector distances; distances.reserve(nblist.size()); for (QMPair *pair : nblist) { double test = pair->getJeff2(state) * tools::conv::hrt2ev * tools::conv::hrt2ev; if (test <= 0) { continue; } // avoid -inf in output double J2 = std::log10(test); double distance = pair->R().norm() * tools::conv::bohr2nm; distances.push_back(distance); J2s.push_back(J2); } double MAXR = *std::max_element(distances.begin(), distances.end()); double MINR = *std::min_element(distances.begin(), distances.end()); // Prepare R bins Index pointsR = Index((MAXR - MINR) / _resolution_spatial); std::vector > rJ2; rJ2.resize(pointsR); // Loop over distance for (Index i = 0; i < pointsR; ++i) { double thisMINR = MINR + double(i) * _resolution_spatial; double thisMAXR = MINR + double(i + 1) * _resolution_spatial; // now count Js that lie within this R range for (Index j = 0; j < Index(J2s.size()); ++j) { if (thisMINR < distances[j] && distances[j] < thisMAXR) { rJ2[i].push_back(J2s[j]); } } } tools::Table tab; tab.SetHasYErr(true); tab.resize(pointsR); // make plot values for (Index i = 0; i < Index(rJ2.size()); i++) { const std::vector &vec = rJ2[i]; double sum = std::accumulate(vec.begin(), vec.end(), 0.0); double AVG = sum / double(vec.size()); double thisR = MINR + (double(i) + 0.5) * _resolution_spatial; double sq_sum = std::inner_product(vec.begin(), vec.end(), vec.begin(), 0.0); double STD = std::sqrt(sq_sum / double(vec.size()) - AVG * AVG); tab.set(i, thisR, AVG, ' ', STD); } std::string filename = "ianalyze.ispatial_" + state.ToString() + ".out"; std::string comment = "# IANALYZE: SPATIAL DEPENDENCE OF log10(J2) " "[r[nm],log10(J)[eV^2],error]"; tab.setErrorDetails(comment); tab.Save(filename); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/calculators/ianalyze.h000066400000000000000000000030431412152066400210060ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_IANALYZE_H #define VOTCA_XTP_IANALYZE_H // Local VOTCA includes #include "votca/xtp/qmcalculator.h" #include "votca/xtp/qmpair.h" #include "votca/xtp/qmstate.h" namespace votca { namespace xtp { class IAnalyze final : public QMCalculator { public: std::string Identify() { return "ianalyze"; } bool WriteToStateFile() const { return false; } protected: void ParseOptions(const tools::Property &user_options); bool Evaluate(Topology &top); private: void IHist(Topology &top, QMStateType state); void IRdependence(Topology &top, QMStateType state); double _resolution_logJ2; std::vector _states; double _resolution_spatial; std::vector _pairtype; bool _do_pairtype = false; bool _do_IRdependence = false; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_IANALYZE_H xtp-2021.2/src/libxtp/calculators/kmclifetime.cc000066400000000000000000000320501412152066400216210ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include #include // Third party includes #include #include // VOTCA includes #include #include // Local VOTCA includes #include "votca/xtp/eigen.h" #include "votca/xtp/gnode.h" #include "votca/xtp/qmstate.h" #include "votca/xtp/topology.h" // Local private VOTCA includes #include "kmclifetime.h" namespace votca { namespace xtp { void KMCLifetime::ParseSpecificOptions(const tools::Property& options) { _insertions = options.get(".numberofinsertions").as(); _lifetimefile = options.get(".lifetimefile").as(); _probfile = options.ifExistsReturnElseReturnDefault( ".decayprobfile", ""); const tools::Property& carrier_options = options.get(".carrierenergy"); _do_carrierenergy = carrier_options.get(".run").as(); _energy_outputfile = carrier_options.get(".outputfile").as(); _alpha = carrier_options.get(".alpha").as(); _outputsteps = carrier_options.get(".outputsteps").as(); _log.setReportLevel(Log::current_level); _log.setCommonPreface("\n ..."); _carriertype = QMStateType(QMStateType::Singlet); XTP_LOG(Log::error, _log) << "carrier type:" << _carriertype.ToLongString() << std::flush; _field = Eigen::Vector3d::Zero(); } void KMCLifetime::WriteDecayProbability(std::string filename) { Eigen::VectorXd outrates = Eigen::VectorXd::Zero(_nodes.size()); Eigen::VectorXd inrates = Eigen::VectorXd::Zero(_nodes.size()); Eigen::VectorXd decayrates = Eigen::VectorXd::Ones(_nodes.size()); for (unsigned i = 0; i < _nodes.size(); i++) { GNode& node = _nodes[i]; if (node.canDecay()) { for (const GLink& event : node.Events()) { if (event.isDecayEvent()) { decayrates[i] = event.getRate(); } else { inrates[event.getDestination()->getId()] += event.getRate(); outrates[i] += event.getRate(); } } } } outrates = decayrates.cwiseQuotient(outrates + decayrates); inrates = decayrates.cwiseQuotient(inrates + decayrates); std::fstream probs; probs.open(filename, std::fstream::out); if (!probs.is_open()) { std::string error_msg = "Unable to write to file " + filename; throw std::runtime_error(error_msg); } probs << "#SiteID, Relative Prob outgoing, Relative Prob ingoing\n"; for (unsigned i = 0; i < _nodes.size(); i++) { probs << _nodes[i].getId() << " " << outrates[i] << " " << inrates[i] << std::endl; } probs.close(); return; } void KMCLifetime::ReadLifetimeFile(std::string filename) { tools::Property xml; xml.LoadFromXML(filename); std::vector jobProps = xml.Select("lifetimes.site"); if (jobProps.size() != _nodes.size()) { throw std::runtime_error( (boost::format("The number of sites in the topology: %i does not match " "the number in the lifetimefile: %i") % _nodes.size() % jobProps.size()) .str()); } for (tools::Property* prop : jobProps) { Index site_id = prop->getAttribute("id"); double lifetime = boost::lexical_cast(prop->value()); bool check = false; for (auto& node : _nodes) { if (node.getId() == site_id && !(node.canDecay())) { node.AddDecayEvent(1.0 / lifetime); check = true; break; } else if (node.getId() == site_id && node.canDecay()) { throw std::runtime_error( (boost::format("Node %i appears twice in your list") % site_id) .str()); } } if (!check) { throw std::runtime_error( (boost::format("Site from file with id: %i not found in state file") % site_id) .str()); } } for (auto& node : _nodes) { node.InitEscapeRate(); node.MakeHuffTree(); } return; } void KMCLifetime::WriteToTraj(std::fstream& traj, unsigned long insertioncount, double simtime, const Chargecarrier& affectedcarrier) const { const Eigen::Vector3d& dr_travelled = affectedcarrier.get_dRtravelled(); traj << simtime << "\t" << insertioncount << "\t" << affectedcarrier.getId() << "\t" << affectedcarrier.getLifetime() << "\t" << affectedcarrier.getSteps() << "\t" << affectedcarrier.getCurrentNodeId() + 1 << "\t" << dr_travelled.x() * tools::conv::bohr2nm << "\t" << dr_travelled.y() * tools::conv::bohr2nm << "\t" << dr_travelled.z() * tools::conv::bohr2nm << std::endl; } void KMCLifetime::RunVSSM() { std::chrono::time_point realtime_start = std::chrono::system_clock::now(); XTP_LOG(Log::error, _log) << "\nAlgorithm: VSSM for Multiple Charges with finite Lifetime\n" "number of charges: " << _numberofcarriers << "\nnumber of nodes: " << _nodes.size() << std::flush; if (_numberofcarriers > Index(_nodes.size())) { throw std::runtime_error( "ERROR in kmclifetime: specified number of charges is greater than the " "number of nodes. This conflicts with single occupation."); } std::fstream traj; std::fstream energyfile; XTP_LOG(Log::error, _log) << "Writing trajectory to " << _trajectoryfile << "." << std::flush; traj.open(_trajectoryfile, std::fstream::out); if (!traj.is_open()) { std::string error_msg = "Unable to write to file " + _trajectoryfile; throw std::runtime_error(error_msg); } traj << "#Simtime [s]\t Insertion\t Carrier ID\t Lifetime[s]\tSteps\t Last " "Segment\t x_travelled[nm]\t y_travelled[nm]\t z_travelled[nm]\n"; if (_do_carrierenergy) { XTP_LOG(Log::error, _log) << "Tracking the energy of one charge carrier and exponential average " "with alpha=" << _alpha << " to " << _energy_outputfile << std::flush; energyfile.open(_energy_outputfile, std::fstream::out); if (!energyfile.is_open()) { std::string error_msg = "Unable to write to file " + _energy_outputfile; throw std::runtime_error(error_msg); } energyfile << "Simtime [s]\tSteps\tCarrier ID\tEnergy_a=" << _alpha << "[eV]\n"; } // Injection XTP_LOG(Log::error, _log) << "\ninjection method: " << _injectionmethod << std::flush; RandomlyCreateCharges(); unsigned long insertioncount = 0; unsigned long step = 0; double simtime = 0.0; std::vector forbiddennodes; std::vector forbiddendests; time_t now = time(nullptr); tm* localtm = localtime(&now); XTP_LOG(Log::error, _log) << "Run started at " << asctime(localtm) << std::flush; double avlifetime = 0.0; double meanfreepath = 0.0; Eigen::Vector3d difflength_squared = Eigen::Vector3d::Zero(); double avgenergy = _carriers[0].getCurrentEnergy(); Index carrieridold = _carriers[0].getId(); while (insertioncount < _insertions) { std::chrono::duration elapsed_time = std::chrono::system_clock::now() - realtime_start; if (elapsed_time.count() > (_maxrealtime * 60. * 60.)) { XTP_LOG(Log::error, _log) << "\nReal time limit of " << _maxrealtime << " hours (" << Index(_maxrealtime * 60 * 60 + 0.5) << " seconds) has been reached. Stopping here.\n" << std::flush; break; } double cumulated_rate = 0; for (const auto& carrier : _carriers) { cumulated_rate += carrier.getCurrentEscapeRate(); } if (cumulated_rate == 0) { // this should not happen: no possible jumps // defined for a node throw std::runtime_error( "ERROR in kmclifetime: Incorrect rates in the database file. All the " "escape rates for the current setting are 0."); } // go forward in time double dt = Promotetime(cumulated_rate); if (_do_carrierenergy) { bool print = false; if (_carriers[0].getId() > carrieridold) { avgenergy = _carriers[0].getCurrentEnergy(); print = true; carrieridold = _carriers[0].getId(); } else if (step % _outputsteps == 0) { avgenergy = _alpha * _carriers[0].getCurrentEnergy() + (1 - _alpha) * avgenergy; print = true; } if (print) { energyfile << simtime << "\t" << step << "\t" << _carriers[0].getId() << "\t" << avgenergy * tools::conv::hrt2ev << std::endl; } } simtime += dt; step++; for (auto& carrier : _carriers) { carrier.updateLifetime(dt); carrier.updateSteps(1); carrier.updateOccupationtime(dt); } ResetForbiddenlist(forbiddennodes); bool secondlevel = true; while (secondlevel) { // determine which carrier will escape GNode* newnode = nullptr; Chargecarrier* affectedcarrier = ChooseAffectedCarrier(cumulated_rate); if (CheckForbidden(affectedcarrier->getCurrentNode(), forbiddennodes)) { continue; } // determine where it will jump to ResetForbiddenlist(forbiddendests); boost::progress_display progress(_insertions); while (true) { // LEVEL 2 newnode = nullptr; const GLink& event = ChooseHoppingDest(affectedcarrier->getCurrentNode()); if (event.isDecayEvent()) { const Eigen::Vector3d& dr_travelled = affectedcarrier->get_dRtravelled(); avlifetime += affectedcarrier->getLifetime(); meanfreepath += dr_travelled.norm(); difflength_squared += dr_travelled.cwiseAbs2(); WriteToTraj(traj, insertioncount, simtime, *affectedcarrier); ++progress; RandomlyAssignCarriertoSite(*affectedcarrier); affectedcarrier->resetCarrier(); insertioncount++; affectedcarrier->setId(_numberofcarriers - 1 + insertioncount); secondlevel = false; break; } else { newnode = event.getDestination(); } // check after the event if this was allowed if (CheckForbidden(*newnode, forbiddendests)) { continue; } // if the new segment is unoccupied: jump; if not: add to forbidden list // and choose new hopping destination if (newnode->isOccupied()) { if (CheckSurrounded(affectedcarrier->getCurrentNode(), forbiddendests)) { AddtoForbiddenlist(affectedcarrier->getCurrentNode(), forbiddennodes); break; // select new escape node (ends level 2 but without setting // level1step to 1) } AddtoForbiddenlist(*newnode, forbiddendests); continue; // select new destination } else { affectedcarrier->jumpAccordingEvent(event); secondlevel = false; break; // this ends LEVEL 2 , so that the time is updated and the // next MC step started } // END LEVEL 2 } // END LEVEL 1 } } XTP_LOG(Log::error, _log) << "\nTotal runtime:\t\t\t\t\t" << simtime << " s\n" "Total KMC steps:\t\t\t\t" << step << "\nAverage lifetime:\t\t\t\t" << avlifetime / double(insertioncount) << " s\n" << "Mean freepath\t l=<|r_x-r_o|> :\t\t" << (meanfreepath * tools::conv::bohr2nm / double(insertioncount)) << " nm\n" << "Average diffusionlength\t d=sqrt(<(r_x-r_o)^2>)\t" << std::sqrt(difflength_squared.norm() / double(insertioncount)) * tools::conv::bohr2nm << " nm\n" << std::flush; WriteOccupationtoFile(simtime, _occfile); traj.close(); if (_do_carrierenergy) { energyfile.close(); } return; } bool KMCLifetime::Evaluate(Topology& top) { XTP_LOG(Log::error, _log) << "\n-----------------------------------" "\n KMCLIFETIME started" "\n-----------------------------------\n" << std::flush; XTP_LOG(Log::info, _log) << "\nInitialising random number generator" << std::flush; _RandomVariable.init(_seed); LoadGraph(top); ReadLifetimeFile(_lifetimefile); if (!_probfile.empty()) { WriteDecayProbability(_probfile); } RunVSSM(); time_t now = time(nullptr); tm* localtm = localtime(&now); XTP_LOG(Log::info, _log) << " KMCLIFETIME finished at:" << asctime(localtm) << std::flush; std::cout << _log; return true; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/calculators/kmclifetime.h000066400000000000000000000032351412152066400214660ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_KMCLIFETIME_H #define VOTCA_XTP_KMCLIFETIME_H // Local VOTCA includes #include "votca/xtp/kmccalculator.h" namespace votca { namespace xtp { class KMCLifetime final : public KMCCalculator { public: KMCLifetime() = default; ~KMCLifetime() = default; bool WriteToStateFile() const { return false; } std::string Identify() { return "kmclifetime"; } protected: void ParseSpecificOptions(const tools::Property& user_options); bool Evaluate(Topology& top); private: void WriteDecayProbability(std::string filename); void RunVSSM(); void WriteToTraj(std::fstream& traj, unsigned long insertioncount, double simtime, const Chargecarrier& affectedcarrier) const; void ReadLifetimeFile(std::string filename); std::string _probfile; bool _do_carrierenergy; std::string _energy_outputfile; double _alpha; unsigned long _outputsteps; unsigned long _insertions; std::string _lifetimefile; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_KMCLIFETIME_H xtp-2021.2/src/libxtp/calculators/kmcmultiple.cc000066400000000000000000000411101412152066400216530ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include // Third party includes #include // VOTCA includes #include #include // Local VOTCA includes #include "votca/xtp/gnode.h" #include "votca/xtp/qmstate.h" #include "votca/xtp/topology.h" // Local private VOTCA includes #include "kmcmultiple.h" namespace votca { namespace xtp { void KMCMultiple::ParseSpecificOptions(const tools::Property& options) { _runtime = options.get(".runtime").as(); _field = options.get(".field").as(); double mtobohr = 1E9 * tools::conv::nm2bohr; _field *= (tools::conv::ev2hrt / mtobohr); // Converting from V/m to Hartree/bohr _outputtime = options.get(".outputtime").as(); _timefile = options.ifExistsReturnElseReturnDefault(".timefile", _timefile); std::string carriertype = options.get(".carriertype").as(); _carriertype = QMStateType(carriertype); if (!_carriertype.isKMCState()) { throw std::runtime_error("KMC cannot be run for state:" + _carriertype.ToLongString()); } _log.setReportLevel(Log::current_level); _log.setCommonPreface("\n ..."); } void KMCMultiple::PrintDiffandMu(const Eigen::Matrix3d& avgdiffusiontensor, double simtime, unsigned long step) { double absolute_field = _field.norm(); if (absolute_field == 0) { unsigned long diffusionsteps = step / _diffusionresolution; Eigen::Matrix3d result = avgdiffusiontensor / (double(diffusionsteps) * 2.0 * simtime * double(_numberofcarriers)); XTP_LOG(Log::error, _log) << "\nStep: " << step << " Diffusion tensor averaged over all carriers (nm^2/s):\n" << result * tools::conv::bohr2nm * tools::conv::bohr2nm << std::flush; } else { double average_mobility = 0; double bohr2Hrts_to_nm2Vs = tools::conv::bohr2nm * tools::conv::bohr2nm / tools::conv::hrt2ev; XTP_LOG(Log::error, _log) << "\nMobilities (nm^2/Vs): " << std::flush; for (Index i = 0; i < _numberofcarriers; i++) { Eigen::Vector3d velocity = _carriers[i].get_dRtravelled() / simtime; double mobility = velocity.dot(_field) / (absolute_field * absolute_field); XTP_LOG(Log::error, _log) << std::scientific << " carrier " << i + 1 << ": mu=" << mobility * bohr2Hrts_to_nm2Vs << std::flush; average_mobility += velocity.dot(_field) / (absolute_field * absolute_field); } average_mobility /= double(_numberofcarriers); XTP_LOG(Log::error, _log) << std::scientific << " Overall average mobility in field direction =" << average_mobility * bohr2Hrts_to_nm2Vs << " nm^2/Vs " << std::flush; } } void KMCMultiple::WriteToTrajectory(std::fstream& traj, std::vector& startposition, double simtime, unsigned long step) const { traj << simtime << "\t"; traj << step << "\t"; for (Index i = 0; i < _numberofcarriers; i++) { Eigen::Vector3d pos = startposition[i] + _carriers[i].get_dRtravelled(); traj << pos.x() * tools::conv::bohr2nm << "\t"; traj << pos.y() * tools::conv::bohr2nm << "\t"; traj << pos.z() * tools::conv::bohr2nm; if (i < _numberofcarriers - 1) { traj << "\t"; } else { traj << std::endl; } } } void KMCMultiple::WriteToEnergyFile(std::fstream& tfile, double simtime, unsigned long step) const { double absolute_field = _field.norm(); double currentenergy = 0; double currentmobility = 0; Eigen::Vector3d dr_travelled_current = Eigen::Vector3d::Zero(); double dr_travelled_field = 0.0; Eigen::Vector3d avgvelocity_current = Eigen::Vector3d::Zero(); if (absolute_field != 0) { for (const auto& carrier : _carriers) { dr_travelled_current += carrier.get_dRtravelled(); currentenergy += carrier.getCurrentEnergy(); } dr_travelled_current /= double(_numberofcarriers); currentenergy /= double(_numberofcarriers); avgvelocity_current = dr_travelled_current / simtime; currentmobility = avgvelocity_current.dot(_field) / (absolute_field * absolute_field); dr_travelled_field = dr_travelled_current.dot(_field) / absolute_field; } double bohr2Hrts_to_nm2Vs = tools::conv::bohr2nm * tools::conv::bohr2nm / tools::conv::hrt2ev; tfile << simtime << "\t" << step << "\t" << currentenergy * tools::conv::hrt2ev << "\t" << currentmobility * bohr2Hrts_to_nm2Vs << "\t" << dr_travelled_field * tools::conv::bohr2nm << "\t" << dr_travelled_current.norm() * tools::conv::bohr2nm << "\t" << std::endl; } void KMCMultiple::PrintDiagDandMu(const Eigen::Matrix3d& avgdiffusiontensor, double simtime, unsigned long step) { unsigned long diffusionsteps = step / _diffusionresolution; Eigen::Matrix3d result = avgdiffusiontensor / (double(diffusionsteps) * 2.0 * simtime * double(_numberofcarriers)); Eigen::SelfAdjointEigenSolver es; es.computeDirect(result); double bohr2_nm2 = tools::conv::bohr2nm * tools::conv::bohr2nm; XTP_LOG(Log::error, _log) << "\nEigenvalues:\n " << std::flush; for (Index i = 0; i < 3; i++) { XTP_LOG(Log::error, _log) << "Eigenvalue: " << es.eigenvalues()(i) * bohr2_nm2 << std::flush << "Eigenvector: " << es.eigenvectors().col(i).x() << " " << es.eigenvectors().col(i).y() << " " << es.eigenvectors().col(i).z() << "\n" << std::flush; } double bohr2Hrts_to_nm2Vs = tools::conv::bohr2nm * tools::conv::bohr2nm / tools::conv::hrt2ev; // calculate average mobility from the Einstein relation if (_field.norm() == 0) { XTP_LOG(Log::error, _log) << "The following value is calculated using the Einstein relation " "and assuming an isotropic medium" << std::flush; double avgD = 1. / 3. * es.eigenvalues().sum(); double average_mobility = std::abs(avgD / _temperature); XTP_LOG(Log::error, _log) << std::scientific << " Overall average mobility =" << average_mobility * bohr2Hrts_to_nm2Vs << " nm^2/Vs " << std::flush; } } void KMCMultiple::PrintChargeVelocity(double simtime) { Eigen::Vector3d avg_dr_travelled = Eigen::Vector3d::Zero(); for (Index i = 0; i < _numberofcarriers; i++) { XTP_LOG(Log::error, _log) << std::scientific << " carrier " << i + 1 << ": " << _carriers[i].get_dRtravelled().transpose() / simtime * tools::conv::bohr2nm << std::flush; avg_dr_travelled += _carriers[i].get_dRtravelled(); } avg_dr_travelled /= double(_numberofcarriers); Eigen::Vector3d avgvelocity = avg_dr_travelled / simtime; XTP_LOG(Log::error, _log) << std::scientific << " Overall average velocity (nm/s): " << avgvelocity.transpose() * tools::conv::bohr2nm << std::flush; } void KMCMultiple::RunVSSM() { std::chrono::time_point realtime_start = std::chrono::system_clock::now(); XTP_LOG(Log::error, _log) << "\nAlgorithm: VSSM for Multiple Charges" << std::flush; XTP_LOG(Log::error, _log) << "number of carriers: " << _numberofcarriers << std::flush; XTP_LOG(Log::error, _log) << "number of nodes: " << _nodes.size() << std::flush; bool checkifoutput = (_outputtime != 0); double nexttrajoutput = 0; unsigned long maxsteps = boost::numeric_cast(_runtime); unsigned long outputstep = boost::numeric_cast(_outputtime); bool stopontime = false; if (_runtime > 100) { XTP_LOG(Log::error, _log) << "stop condition: " << maxsteps << " steps." << std::flush; if (checkifoutput) { XTP_LOG(Log::error, _log) << "output frequency: "; XTP_LOG(Log::error, _log) << "every " << outputstep << " steps." << std::flush; } } else { stopontime = true; XTP_LOG(Log::error, _log) << "stop condition: " << _runtime << " seconds runtime." << std::flush; if (checkifoutput) { XTP_LOG(Log::error, _log) << "output frequency:\n " "every " << _outputtime << " seconds." << std::flush; } } XTP_LOG(Log::error, _log) << "(If you specify runtimes larger than 100 kmcmultiple assumes that " "you are specifying the number of steps for both runtime and " "outputtime.)" << std::flush; if (!stopontime && _outputtime != 0 && floor(_outputtime) != _outputtime) { throw std::runtime_error( "ERROR in kmcmultiple: runtime was specified in steps (>100) and " "outputtime in seconds (not an integer). Please use the same units for " "both input parameters."); } if (_numberofcarriers > Index(_nodes.size())) { throw std::runtime_error( "ERROR in kmcmultiple: specified number of carriers is greater than " "the " "number of nodes. This conflicts with single occupation."); } std::fstream traj; std::fstream tfile; if (checkifoutput) { XTP_LOG(Log::error, _log) << "Writing trajectory to " << _trajectoryfile << "." << std::flush; traj.open(_trajectoryfile, std::fstream::out); traj << "time[s]\tsteps\t"; for (Index i = 0; i < _numberofcarriers; i++) { traj << "carrier" << i + 1 << "_x\t"; traj << "carrier" << i + 1 << "_y\t"; traj << "carrier" << i + 1 << "_z"; if (i < _numberofcarriers - 1) { traj << "'\t"; } } traj << std::endl; if (!_timefile.empty()) { XTP_LOG(Log::error, _log) << "Writing time dependence of energy and mobility to " << _timefile << "." << std::flush; tfile.open(_timefile, std::fstream::out); tfile << "time[s]\t " "steps\tenergy_per_carrier[eV]\tmobility[nm**2/" "Vs]\tdistance_fielddirection[nm]\tdistance_absolute[nm]" << std::endl; } } RandomlyCreateCharges(); std::vector startposition(_numberofcarriers, Eigen::Vector3d::Zero()); for (Index i = 0; i < _numberofcarriers; i++) { startposition[i] = _carriers[i].getCurrentPosition(); } traj << 0 << "\t"; traj << 0 << "\t"; for (Index i = 0; i < _numberofcarriers; i++) { traj << startposition[i].x() * tools::conv::bohr2nm << "\t"; traj << startposition[i].y() * tools::conv::bohr2nm << "\t"; traj << startposition[i].z() * tools::conv::bohr2nm; if (i < _numberofcarriers - 1) { traj << "\t"; } else { traj << std::endl; } } std::vector forbiddennodes; std::vector forbiddendests; Eigen::Matrix3d avgdiffusiontensor = Eigen::Matrix3d::Zero(); double simtime = 0.0; unsigned long step = 0; while (((stopontime && simtime < _runtime) || (!stopontime && step < maxsteps))) { std::chrono::duration elapsed_time = std::chrono::system_clock::now() - realtime_start; if (elapsed_time.count() > (_maxrealtime * 60. * 60.)) { XTP_LOG(Log::error, _log) << "\nReal time limit of " << _maxrealtime << " hours (" << Index(_maxrealtime * 60 * 60 + 0.5) << " seconds) has been reached. Stopping here.\n" << std::flush; break; } double cumulated_rate = 0; for (const auto& carrier : _carriers) { cumulated_rate += carrier.getCurrentEscapeRate(); } if (cumulated_rate <= 0) { // this should not happen: no possible jumps // defined for a node throw std::runtime_error( "ERROR in kmcmultiple: Incorrect rates. All " "the escape rates for the current setting are 0."); } double dt = Promotetime(cumulated_rate); simtime += dt; step++; for (auto& carrier : _carriers) { carrier.updateOccupationtime(dt); } ResetForbiddenlist(forbiddennodes); bool level1step = true; while (level1step) { // determine which electron will escape GNode* newnode = nullptr; Chargecarrier* affectedcarrier = ChooseAffectedCarrier(cumulated_rate); if (CheckForbidden(affectedcarrier->getCurrentNode(), forbiddennodes)) { continue; } ResetForbiddenlist(forbiddendests); while (true) { // LEVEL 2 const GLink& event = ChooseHoppingDest(affectedcarrier->getCurrentNode()); newnode = event.getDestination(); if (newnode == nullptr) { AddtoForbiddenlist(affectedcarrier->getCurrentNode(), forbiddennodes); break; // select new escape node (ends level 2 but without setting // level1step to 1) } // check after the event if this was allowed if (CheckForbidden(*newnode, forbiddendests)) { continue; } // if the new segment is unoccupied: jump; if not: add to forbidden // list and choose new hopping destination if (newnode->isOccupied()) { if (CheckSurrounded(affectedcarrier->getCurrentNode(), forbiddendests)) { AddtoForbiddenlist(affectedcarrier->getCurrentNode(), forbiddennodes); break; // select new escape node (ends level 2 but without // setting level1step to 1) } AddtoForbiddenlist(*newnode, forbiddendests); continue; // select new destination } else { affectedcarrier->jumpAccordingEvent(event); level1step = false; break; // this ends LEVEL 2 , so that the time is updated and the // next MC step started } // END LEVEL 2 } // END LEVEL 1 } if (step % _diffusionresolution == 0) { for (const auto& carrier : _carriers) { avgdiffusiontensor += (carrier.get_dRtravelled()) * (carrier.get_dRtravelled()).transpose(); } } if (step != 0 && step % _intermediateoutput_frequency == 0) { PrintDiffandMu(avgdiffusiontensor, simtime, step); } if (checkifoutput) { bool outputsteps = (!stopontime && step % outputstep == 0); bool outputtime = (stopontime && simtime > nexttrajoutput); if (outputsteps || outputtime) { // write to trajectory file nexttrajoutput = simtime + _outputtime; WriteToTrajectory(traj, startposition, simtime, step); if (!_timefile.empty()) { WriteToEnergyFile(tfile, simtime, step); } } } } // KMC if (checkifoutput) { traj.close(); if (!_timefile.empty()) { tfile.close(); } } WriteOccupationtoFile(simtime, _occfile); XTP_LOG(Log::error, _log) << "\nfinished KMC simulation after " << step << " steps.\n" "simulated time " << simtime << " seconds.\n" << std::flush; PrintChargeVelocity(simtime); XTP_LOG(Log::error, _log) << "\nDistances travelled (nm): " << std::flush; for (Index i = 0; i < _numberofcarriers; i++) { XTP_LOG(Log::error, _log) << std::scientific << " carrier " << i + 1 << ": " << _carriers[i].get_dRtravelled().transpose() * tools::conv::bohr2nm << std::flush; } PrintDiffandMu(avgdiffusiontensor, simtime, step); PrintDiagDandMu(avgdiffusiontensor, simtime, step); return; } bool KMCMultiple::Evaluate(Topology& top) { XTP_LOG(Log::error, _log) << "\n-----------------------------------" "\n KMC FOR MULTIPLE CHARGES" "\n-----------------------------------\n" << std::flush; XTP_LOG(Log::info, _log) << "\nInitialising random number generator" << std::flush; _RandomVariable.init(_seed); LoadGraph(top); RunVSSM(); std::cout << _log; return true; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/calculators/kmcmultiple.h000066400000000000000000000040051412152066400215170ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_KMCMULTIPLE_H #define VOTCA_XTP_KMCMULTIPLE_H // Standard includes #include // Local VOTCA includes #include "votca/xtp/kmccalculator.h" namespace votca { namespace xtp { class KMCMultiple final : public KMCCalculator { public: KMCMultiple() = default; ~KMCMultiple() = default; bool WriteToStateFile() const { return false; } std::string Identify() { return "kmcmultiple"; } protected: void ParseSpecificOptions(const tools::Property& user_options); bool Evaluate(Topology& top); private: void RunVSSM(); void PrintChargeVelocity(double simtime); void PrintDiagDandMu(const Eigen::Matrix3d& avgdiffusiontensor, double simtime, unsigned long step); void WriteToEnergyFile(std::fstream& tfile, double simtime, unsigned long step) const; void WriteToTrajectory(std::fstream& traj, std::vector& startposition, double simtime, unsigned long step) const; void PrintDiffandMu(const Eigen::Matrix3d& avgdiffusiontensor, double simtime, unsigned long step); double _runtime; double _outputtime; std::string _timefile = ""; Index _intermediateoutput_frequency = 10000; unsigned long _diffusionresolution = 1000; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_KMCMULTIPLE_H xtp-2021.2/src/libxtp/calculators/mapchecker.h000066400000000000000000000124671412152066400213060ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_MAPCHECKER_H #define VOTCA_XTP_MAPCHECKER_H // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/qmcalculator.h" #include "votca/xtp/segmentmapper.h" namespace votca { namespace xtp { class MapChecker final : public QMCalculator { public: MapChecker() = default; ~MapChecker() = default; std::string Identify() { return "mapchecker"; } bool WriteToStateFile() const { return false; } protected: void ParseOptions(const tools::Property& user_options); bool Evaluate(Topology& top); private: std::string AddSteptoFilename(const std::string& filename, Index step) const; std::string AddStatetoFilename(const std::string& filename, QMState state) const; std::vector StringToStates(const std::string& states_string) const; std::string _segmentfile; std::string _qmfile; std::string _mpfile; std::string _mapfile = ""; std::vector _qmstates; std::vector _mdstates; }; void MapChecker::ParseOptions(const tools::Property& options) { _segmentfile = options.get(".md_pdbfile").as(); _qmfile = options.get(".qm_pdbfile").as(); _mpfile = options.get(".mp_pdbfile").as(); std::string output_qm = options.ifExistsReturnElseReturnDefault(".qm_states", ""); _qmstates = StringToStates(output_qm); std::string output_md = options.ifExistsReturnElseReturnDefault(".mp_states", ""); _mdstates = StringToStates(output_md); if (!(_qmstates.empty() && _mdstates.empty())) { _mapfile = options.get(".map_file").as(); } } std::vector MapChecker::StringToStates( const std::string& states_string) const { std::vector result; tools::Tokenizer tok_states(states_string, " \t\n"); std::vector states = tok_states.ToVector(); for (const std::string& s : states) { result.push_back(QMState(s)); } return result; } std::string MapChecker::AddStatetoFilename(const std::string& filename, QMState state) const { std::string base = tools::filesystem::GetFileBase(filename); std::string fileending = tools::filesystem::GetFileExtension(filename); std::string filename_comp = base + "_" + state.ToString() + "." + fileending; return filename_comp; } bool MapChecker::Evaluate(Topology& top) { std::cout << std::endl; std::string filename = AddSteptoFilename(_segmentfile, top.getStep()); std::cout << "Writing segments to " << filename << std::endl; top.WriteToPdb(filename); Logger log; log.setReportLevel(Log::current_level); log.setCommonPreface("\n... ..."); QMMapper map(log); for (QMState state : _qmstates) { map.LoadMappingFile(_mapfile); std::string filename_qm = AddStatetoFilename(_qmfile, state); csg::PDBWriter qmwriter; std::string filename_qm_state = AddSteptoFilename(filename_qm, top.getStep()); std::cout << "Writing qmmolecules to " << filename_qm_state << std::endl; qmwriter.Open(filename_qm_state, false); qmwriter.WriteHeader("QMFrame:" + std::to_string(top.getStep()) + " state:" + state.ToString()); qmwriter.WriteBox(top.getBox() * tools::conv::bohr2ang); for (const Segment& seg : top.Segments()) { QMMolecule mol = map.map(seg, state); qmwriter.WriteContainer(mol); } qmwriter.Close(); } PolarMapper mp(log); for (QMState state : _mdstates) { mp.LoadMappingFile(_mapfile); std::string filename_mp = AddStatetoFilename(_mpfile, state); csg::PDBWriter mpwriter; std::string filename_mp_state = AddSteptoFilename(filename_mp, top.getStep()); std::cout << "Writing polarsegments to " << filename_mp_state << std::endl; mpwriter.Open(filename_mp_state, false); mpwriter.WriteHeader("MPFrame:" + std::to_string(top.getStep()) + " state:" + state.ToString()); mpwriter.WriteBox(top.getBox() * tools::conv::bohr2ang); for (const Segment& seg : top.Segments()) { PolarSegment mol = mp.map(seg, state); mpwriter.WriteContainer(mol); } mpwriter.Close(); } return true; } std::string MapChecker::AddSteptoFilename(const std::string& filename, Index step) const { std::string base = tools::filesystem::GetFileBase(filename); std::string fileending = tools::filesystem::GetFileExtension(filename); std::string filename_comp = base + "_step_" + std::to_string(step) + "." + fileending; return filename_comp; } } // namespace xtp } // namespace votca #endif // VOTCA_XTP_MAPCHECKER_H xtp-2021.2/src/libxtp/calculators/neighborlist.cc000066400000000000000000000161271412152066400220300ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include #include // Local private VOTCA includes #include "neighborlist.h" namespace votca { namespace xtp { void Neighborlist::ParseOptions(const tools::Property& options) { std::vector segs = options.Select(".segments"); for (const tools::Property* segprop : segs) { std::string types = segprop->get("segmentname").as(); double cutoff = segprop->get("cutoff").as() * tools::conv::nm2bohr; tools::Tokenizer tok(types, " "); std::vector names; tok.ToVector(names); if (names.size() != 2) { throw std::runtime_error( "ERROR: Faulty pair definition for cut-off's: Need two segment names " "separated by a space"); } _cutoffs[names[0]][names[1]] = cutoff; _cutoffs[names[1]][names[0]] = cutoff; if (std::find(_included_segments.begin(), _included_segments.end(), names[0]) == _included_segments.end()) { _included_segments.push_back(names[0]); } if (std::find(_included_segments.begin(), _included_segments.end(), names[1]) == _included_segments.end()) { _included_segments.push_back(names[1]); } } const std::string& cutoff_type = options.get("cutoff_type").as(); if (cutoff_type == "constant") { _useConstantCutoff = true; _constantCutoff = options.get(".constant").as() * tools::conv::nm2bohr; } else { _useConstantCutoff = false; } if (options.get(".use_exciton_cutoff").as()) { _useExcitonCutoff = true; _excitonqmCutoff = options.get(".exciton_cutoff").as() * tools::conv::nm2bohr; } else { _useExcitonCutoff = false; } } Index Neighborlist::DetClassicalPairs(Topology& top) { Index classical_pairs = 0; #pragma omp parallel for for (Index i = 0; i < top.NBList().size(); i++) { const Segment* seg1 = top.NBList()[i]->Seg1(); const Segment* seg2 = top.NBList()[i]->Seg2(); if (top.GetShortestDist(*seg1, *seg2) > _excitonqmCutoff) { top.NBList()[i]->setType(QMPair::Excitoncl); #pragma omp critical { classical_pairs++; } } else { top.NBList()[i]->setType(QMPair::Hopping); } } // Type 3 Exciton_classical approx return classical_pairs; } bool Neighborlist::Evaluate(Topology& top) { double min = top.getBox().diagonal().minCoeff(); std::vector segs; for (Segment& seg : top.Segments()) { if (_useConstantCutoff || std::find(_included_segments.begin(), _included_segments.end(), seg.getType()) != _included_segments.end()) { segs.push_back(&seg); seg.getApproxSize(); } } std::cout << std::endl; std::cout << "Evaluating " << segs.size() << " segments for neighborlist. "; if ((top.Segments().size() - segs.size()) != 0) { std::cout << top.Segments().size() - segs.size() << " segments are not taken into account as specified" << std::endl; } else { std::cout << std::endl; } if (!_useConstantCutoff) { std::cout << "The following segments are used in the neigborlist creation" << std::endl; std::cout << "\t" << std::flush; for (const std::string& st : _included_segments) { std::cout << " " << st << std::flush; } std::cout << std::endl; } std::cout << "\r ... ... Evaluating " << std::flush; std::vector skippedpairs; top.NBList().Cleanup(); boost::progress_display progress(segs.size()); // cache approx sizes std::vector approxsize = std::vector(segs.size(), 0.0); #pragma omp parallel for for (Index i = 0; i < Index(segs.size()); i++) { approxsize[i] = segs[i]->getApproxSize(); } #pragma omp parallel for schedule(guided) for (Index i = 0; i < Index(segs.size()); i++) { Segment* seg1 = segs[i]; double cutoff = _constantCutoff; for (Index j = i + 1; j < Index(segs.size()); j++) { Segment* seg2 = segs[j]; if (!_useConstantCutoff) { try { cutoff = _cutoffs.at(seg1->getType()).at(seg2->getType()); } catch (const std::exception&) { std::string pairstring = seg1->getType() + "/" + seg2->getType(); if (std::find(skippedpairs.begin(), skippedpairs.end(), pairstring) == skippedpairs.end()) { #pragma omp critical { skippedpairs.push_back(pairstring); } } continue; } } if (cutoff > 0.5 * min) { throw std::runtime_error( (boost::format("Cutoff is larger than half the box size. Maximum " "allowed cutoff is %1$1.1f (nm)") % (tools::conv::bohr2nm * 0.5 * min)) .str()); } double cutoff2 = cutoff * cutoff; Eigen::Vector3d segdistance = top.PbShortestConnect(seg1->getPos(), seg2->getPos()); double segdistance2 = segdistance.squaredNorm(); double outside = cutoff + approxsize[i] + approxsize[j]; if (segdistance2 < cutoff2) { #pragma omp critical { top.NBList().Add(*seg1, *seg2, segdistance); } } else if (segdistance2 > (outside * outside)) { continue; } else { double R = top.GetShortestDist(*seg1, *seg2); if ((R * R) < cutoff2) { #pragma omp critical { top.NBList().Add(*seg1, *seg2, segdistance); } } } } /* exit loop seg2 */ #pragma omp critical { ++progress; } } /* exit loop seg1 */ if (skippedpairs.size() > 0) { std::cout << "WARNING: No cut-off specified for segment pairs of type " << std::endl; for (const std::string& st : skippedpairs) { std::cout << st << std::endl; } std::cout << "pairs were skipped" << std::endl; } std::cout << std::endl << " ... ... Created " << top.NBList().size() << " direct pairs."; if (_useExcitonCutoff) { std::cout << std::endl << " ... ... Determining classical pairs " << std::endl; Index classical_pairs = DetClassicalPairs(top); std::cout << " ... ... Found " << classical_pairs << " classical pairs " << std::endl; } // sort qmpairs by seg1id and then by seg2id then reindex the pair id // according to that. top.NBList().sortAndReindex([](QMPair* a, QMPair* b) { if (a->Seg1()->getId() != b->Seg1()->getId()) { return a->Seg1()->getId() < b->Seg1()->getId(); } return a->Seg2()->getId() < b->Seg2()->getId(); }); return true; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/calculators/neighborlist.h000066400000000000000000000031401412152066400216610ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_NEIGHBORLIST_H #define VOTCA_XTP_NEIGHBORLIST_H // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/atom.h" #include "votca/xtp/qmcalculator.h" #include "votca/xtp/qmnblist.h" #include "votca/xtp/topology.h" namespace votca { namespace xtp { class Neighborlist final : public QMCalculator { public: std::string Identify() { return "neighborlist"; } bool WriteToStateFile() const { return true; } protected: void ParseOptions(const tools::Property& user_options); bool Evaluate(Topology& top); private: Index DetClassicalPairs(Topology& top); std::vector _included_segments; std::map > _cutoffs; bool _useConstantCutoff; double _constantCutoff; bool _useExcitonCutoff; double _excitonqmCutoff; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_NEIGHBORLIST_H xtp-2021.2/src/libxtp/calculators/vaverage.cc000066400000000000000000000126611412152066400211360ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/topology.h" #include // Local private VOTCA includes #include "vaverage.h" namespace votca { namespace xtp { void VAverage::ParseOptions(const tools::Property& options) { _ratefile = options.get(".ratefile").as(); _occfile = options.get(".occfile").as(); _outputfile = options.get(".outputfile").as(); } std::vector VAverage::ReadOccfile(std::string filename) const { std::vector result; std::ifstream intt; intt.open(filename); if (!intt.is_open()) { throw std::runtime_error("File:" + filename + " could not be opened"); } std::string line; Index id = 0; while (intt.good()) { tools::getline(intt, line); std::vector split; tools::Tokenizer toker(line, " \t"); toker.ToVector(split); if (!split.size() || split[0] == "#" || split[0].substr(0, 1) == "#") { continue; } if (split.size() != 2) { throw std::runtime_error("Row should only contain id and occupation"); } Index id_readin = std::stoi(split[0]); if (id_readin != id) { throw std::runtime_error("Ids should be sorted and start at zero."); } id++; result.push_back(std::stod(split[1])); } return result; } std::vector VAverage::ReadRatefile( std::string filename) const { std::vector result; std::ifstream intt; intt.open(filename); if (!intt.is_open()) { throw std::runtime_error("File:" + filename + " could not be opened"); } Index id = 0; std::string line; while (intt.good()) { tools::getline(intt, line); std::vector split; tools::Tokenizer toker(line, " \t"); toker.ToVector(split); if (!split.size() || split[0] == "#" || split[0].substr(0, 1) == "#") { continue; } if (split.size() != 5) { throw std::runtime_error( "Row should only contain pairid,segid1,segid2 ,rate12,rate21"); } Index id_readin = std::stoi(split[0]); if (id_readin != id) { throw std::runtime_error("Ids should be sorted and start at zero."); } id++; Rate_Engine::PairRates pair; pair.rate12 = std::stod(split[3]); pair.rate21 = std::stod(split[4]); result.push_back(pair); } return result; } bool VAverage::Evaluate(Topology& top) { std::cout << std::endl << "... ... Computing velocity average for all sites\n"; std::cout << "Reading in site occupations from " << _occfile << std::endl; std::vector occ = ReadOccfile(_occfile); if (top.Segments().size() != occ.size()) { throw std::runtime_error( "Number of occupations is" + std::to_string(occ.size()) + " Topology has size:" + std::to_string(top.Segments().size())); } std::cout << "Reading in rates from " << _ratefile << std::endl; std::vector rates = ReadRatefile(_ratefile); if (top.NBList().size() != Index(rates.size())) { throw std::runtime_error( "Number of pairs in file is" + std::to_string(rates.size()) + " Topology has size:" + std::to_string(top.NBList().size())); } std::vector velocities = std::vector(occ.size(), Eigen::Vector3d::Zero()); for (const QMPair* pair : top.NBList()) { Index id1 = pair->Seg1()->getId(); Index id2 = pair->Seg1()->getId(); Index pairid = pair->getId(); double p1 = occ[id1]; double p2 = occ[id2]; double w12 = rates[pairid].rate12; double w21 = rates[pairid].rate21; const Eigen::Vector3d& dR12 = pair->R(); // points from seg. (1) to seg. (2) // Split current symmetrically among sites (1) and (2) Eigen::Vector3d v_12_21 = 0.5 * (p1 * w12 - p2 * w21) * dR12; velocities[id1] += v_12_21; velocities[id2] += v_12_21; } std::ofstream ofs; ofs.open(_outputfile, std::ofstream::out); if (!ofs.is_open()) { throw std::runtime_error("Bad file handle: " + _outputfile); } ofs << "# 1 | 2 | 3 4 5 | 6 7 8 |" << std::endl; ofs << "# ----|---------|--------------|-------------------|" << std::endl; ofs << "# ID | NAME | X Y Z [nm] | VX VY VZ [nm/s] |" << std::endl; for (const Segment& seg : top.Segments()) { const Eigen::Vector3d r = seg.getPos() * tools::conv::bohr2nm; const Eigen::Vector3d v = velocities[seg.getId()] * tools::conv::bohr2nm; ofs << (boost::format("%1$4d %2$-10s %3$+1.7e %4$+1.7e " "%5$+1.7e %6$+1.7e %7$+1.7e %8$+1.7e") % seg.getId() % seg.getType() % r.x() % r.y() % r.z() % v.x() % v.y() % v.z()) << std::endl; } std::cout << "Writing velocities to " << _outputfile << std::endl; return true; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/calculators/vaverage.h000066400000000000000000000031771412152066400210020ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_VAVERAGE_H #define VOTCA_XTP_VAVERAGE_H // Standard includes #include #include #include // Local VOTCA includes #include "votca/xtp/eigen.h" #include "votca/xtp/logger.h" #include "votca/xtp/qmcalculator.h" #include "votca/xtp/rate_engine.h" namespace votca { namespace xtp { class VAverage final : public QMCalculator { public: VAverage() = default; ~VAverage() = default; std::string Identify() { return "vaverage"; } bool WriteToStateFile() const { return false; } protected: void ParseOptions(const tools::Property& user_options); bool Evaluate(Topology& top); private: Logger _log; std::string _ratefile; std::string _occfile; std::string _outputfile; std::vector ReadOccfile(std::string filename) const; std::vector ReadRatefile(std::string filename) const; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_VAVERAGE_H xtp-2021.2/src/libxtp/checkpoint.cc000066400000000000000000000076211412152066400171510ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include #include #include #include #include #include #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/checkpoint.h" #include "votca/xtp/checkpointreader.h" #include "votca/xtp/checkpointwriter.h" #include "votca/xtp/votca_xtp_config.h" namespace votca { namespace xtp { using namespace checkpoint_utils; namespace bfs = boost::filesystem; std::ostream& operator<<(std::ostream& s, CheckpointAccessLevel l) { switch (l) { case CheckpointAccessLevel::READ: s << "read"; break; case CheckpointAccessLevel::MODIFY: s << "modify"; break; case CheckpointAccessLevel::CREATE: s << "create"; break; } return s; } bool FileExists(const std::string& fileName) { return bfs::exists(fileName); } CheckpointFile::CheckpointFile(std::string fN) : CheckpointFile(fN, CheckpointAccessLevel::MODIFY) {} CheckpointFile::CheckpointFile(std::string fN, CheckpointAccessLevel access) : _fileName(fN), _accessLevel(access) { try { H5::Exception::dontPrint(); hid_t fcpl_id = H5Pcreate(H5P_FILE_CREATE); H5::FileCreatPropList fcpList(fcpl_id); switch (_accessLevel) { case CheckpointAccessLevel::READ: _fileHandle = H5::H5File(_fileName, H5F_ACC_RDONLY); break; case CheckpointAccessLevel::CREATE: _fileHandle = H5::H5File(_fileName, H5F_ACC_TRUNC, fcpList); break; case CheckpointAccessLevel::MODIFY: if (!FileExists(_fileName)) { _fileHandle = H5::H5File(_fileName, H5F_ACC_TRUNC, fcpList); } else { _fileHandle = H5::H5File(_fileName, H5F_ACC_RDWR, fcpList); } } } catch (H5::Exception&) { std::stringstream message; message << "Could not access file " << _fileName; message << " with permission to " << _accessLevel << "." << std::endl; throw std::runtime_error(message.str()); } } std::string CheckpointFile::getFileName() { return _fileName; } H5::H5File CheckpointFile::getHandle() { return _fileHandle; } CheckpointWriter CheckpointFile::getWriter(const std::string _path) { if (_accessLevel == CheckpointAccessLevel::READ) { throw std::runtime_error("Checkpoint file opened as read only."); } try { return CheckpointWriter(_fileHandle.createGroup(_path), _path); } catch (H5::Exception&) { try { return CheckpointWriter(_fileHandle.openGroup(_path), _path); } catch (H5::Exception&) { std::stringstream message; message << "Could not create or open " << _fileName << ":" << _path << std::endl; throw std::runtime_error(message.str()); } } } CheckpointWriter CheckpointFile::getWriter() { return getWriter("/"); } CheckpointReader CheckpointFile::getReader(const std::string _path) { try { return CheckpointReader(_fileHandle.openGroup(_path), _path); } catch (H5::Exception&) { std::stringstream message; message << "Could not open " << _fileName << ":" << _path << std::endl; throw std::runtime_error(message.str()); } } CheckpointReader CheckpointFile::getReader() { return getReader("/"); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/classicalsegment.cc000066400000000000000000000145751412152066400203510ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // VOTCA includes #include #include #include // Local VOTCA includes #include "votca/xtp/atomcontainer.h" #include "votca/xtp/classicalsegment.h" namespace votca { namespace xtp { // MPS files have a weird format positions can be in bohr or angstroem, // multipoles are in q*bohr^k, with k rank of multipole and polarisabilities are // in angstroem^3 template void ClassicalSegment::LoadFromFile(std::string filename) { std::string line; std::ifstream intt; intt.open(filename); double unit_conversion = tools::conv::ang2bohr; Index readinmultipoles = 0; Index numberofmultipoles = 0; Vector9d multipoles = Vector9d::Zero(); Index rank = 0; if (!intt.is_open()) { throw std::runtime_error("File:" + filename + " could not be opened"); } while (intt.good()) { tools::getline(intt, line); tools::Tokenizer toker(line, " \t"); std::vector split = toker.ToVector(); if (!split.size() || split[0] == "!" || split[0].substr(0, 1) == "!") { continue; } // ! Interesting information here, e.g. // ! DCV2T opt // ! SP RB3LYP 6-311+G(d,p) // Units bohr // // C -4.2414603400 -3.8124751600 0.0017575736 Rank 2 // -0.3853409355 // -0.0002321905 0.2401559510 0.6602334308 // -0.7220625314 0.0004894995 -0.0003833545 0.4526409813 -0.50937399 // P 1.75 // Units used if (split[0] == "Units") { std::string units = split[1]; if (units != "bohr" && units != "angstrom") { throw std::runtime_error("Unit " + units + " in file " + filename + " not supported."); } if (units == "bohr") { unit_conversion = 1.0; } } else if (split.size() == 6) { // element, position, rank limit convert to bohr std::string name = split[0]; Eigen::Vector3d pos; Index id = Index(this->_atomlist.size()); pos[0] = boost::lexical_cast(split[1]); pos[1] = boost::lexical_cast(split[2]); pos[2] = boost::lexical_cast(split[3]); rank = boost::lexical_cast(split[5]); numberofmultipoles = (rank + 1) * (rank + 1); multipoles = Vector9d::Zero(); pos *= unit_conversion; this->_atomlist.push_back(T(id, name, pos)); } // 'P', dipole polarizability else if (split[0] == "P") { Eigen::Matrix3d p1; if (split.size() == 7) { double pxx = boost::lexical_cast(split[1]); double pxy = boost::lexical_cast(split[2]); double pxz = boost::lexical_cast(split[3]); double pyy = boost::lexical_cast(split[4]); double pyz = boost::lexical_cast(split[5]); double pzz = boost::lexical_cast(split[6]); p1 << pxx, pxy, pxz, pxy, pyy, pyz, pxz, pyz, pzz; } else if (split.size() == 2) { double pxx = boost::lexical_cast(split[1]); p1 = pxx * Eigen::Matrix3d::Identity(); } else { throw std::runtime_error("Invalid line in " + filename + ": " + line); } double unit_conversion_3 = std::pow(tools::conv::ang2bohr, 3); p1 = p1 * unit_conversion_3; this->_atomlist.back().setpolarization(p1); } // Multipole lines else { // stay in bohr for (const std::string& entry : split) { double qXYZ = boost::lexical_cast(entry); if (multipoles.size() < readinmultipoles) { throw std::runtime_error("ReadMpsFile: File" + filename + "is not properly formatted"); } multipoles(readinmultipoles) = qXYZ; readinmultipoles++; } if (readinmultipoles == numberofmultipoles) { Eigen::Vector3d temp_dipoles = multipoles.segment<3>(1); // mps format for dipoles is z x y // we need x y z multipoles(1) = temp_dipoles(1); multipoles(2) = temp_dipoles(2); multipoles(3) = temp_dipoles(0); this->_atomlist.back().setMultipole(multipoles, rank); readinmultipoles = 0; } } } this->calcPos(); } template double ClassicalSegment::CalcTotalQ() const { double Q = 0; for (const T& site : this->_atomlist) { Q += site.getCharge(); } return Q; } template Eigen::Vector3d ClassicalSegment::CalcDipole() const { Eigen::Vector3d dipole = Eigen::Vector3d::Zero(); Eigen::Vector3d CoM = this->getPos(); for (const T& site : this->_atomlist) { dipole += (site.getPos() - CoM) * site.getCharge(); dipole += site.getDipole(); } return dipole; } template void ClassicalSegment::WriteMPS(std::string filename, std::string header) const { std::ofstream ofs; ofs.open(filename, std::ofstream::out); if (!ofs.is_open()) { throw std::runtime_error("Bad file handle: " + filename); } ofs << (boost::format("! GENERATED BY VOTCA::XTP::%1$s\n") % header); ofs << (boost::format("! N=%2$d Q[e]=%1$+1.7f\n") % CalcTotalQ() % this->size()); ofs << boost::format("Units angstrom\n"); for (const T& site : this->_atomlist) { ofs << site.WriteMpsLine("angstrom"); } ofs.close(); } template std::string ClassicalSegment::identify() const { return ""; } template <> std::string ClassicalSegment::identify() const { return "PolarSegment"; } template <> std::string ClassicalSegment::identify() const { return "StaticSegment"; } template class ClassicalSegment; template class ClassicalSegment; } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/couplingbase.cc000066400000000000000000000050221412152066400174660ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/couplingbase.h" #include "votca/xtp/aomatrix.h" namespace votca { namespace xtp { Eigen::MatrixXd CouplingBase::CalculateOverlapMatrix( const Orbitals& orbitalsAB) const { AOBasis dftbasis = orbitalsAB.SetupDftBasis(); AOOverlap dftAOoverlap; dftAOoverlap.Fill(dftbasis); return dftAOoverlap.Matrix(); } void CouplingBase::CheckAtomCoordinates(const Orbitals& orbitalsA, const Orbitals& orbitalsB, const Orbitals& orbitalsAB) const { const QMMolecule& atomsA = orbitalsA.QMAtoms(); const QMMolecule& atomsB = orbitalsB.QMAtoms(); const QMMolecule& atomsAll = orbitalsAB.QMAtoms(); bool coordinates_agree = true; for (Index i = 0; i < atomsAll.size(); i++) { const QMAtom& dimer = atomsAll[i]; const QMAtom* monomer = nullptr; if (i < atomsA.size()) { monomer = &atomsA[i]; } else if (i < atomsB.size() + atomsA.size()) { monomer = &atomsB[i - atomsA.size()]; } else { // Linker XTP_LOG(Log::error, *_pLog) << (boost::format( "Neither Monomer A nor Monomer B contains " "atom %s on line %u. Hence, this atom is part of a linker.") % dimer.getElement() % (i + 1)) .str() << std::flush; continue; } if (!monomer->getPos().isApprox(dimer.getPos(), 0.001)) { coordinates_agree = false; } if (monomer->getElement() != dimer.getElement()) { throw std::runtime_error( "Atom types do not agree in dimer and monomers\n"); } } if (!coordinates_agree) { XTP_LOG(Log::error, *_pLog) << "======WARNING=======\n Coordinates of monomer " "and dimer atoms do not agree" << std::flush; } } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/cubefile_writer.cc000066400000000000000000000130041412152066400201640ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/cubefile_writer.h" #include "votca/xtp/amplitude_integration.h" #include "votca/xtp/density_integration.h" #include "votca/xtp/regular_grid.h" namespace votca { namespace xtp { std::vector> CubeFile_Writer::CalculateValues( const Orbitals& orb, QMState state, bool dostateonly, const Regular_Grid& grid) const { bool do_amplitude = (state.Type().isSingleParticleState()); if (do_amplitude) { Eigen::VectorXd amplitude; if (state.Type() == QMStateType::DQPstate) { Index amplitudeindex = state.StateIdx() - orb.getGWAmin(); amplitude = orb.CalculateQParticleAORepresentation().col(amplitudeindex); } else { amplitude = orb.MOs().eigenvectors().col(state.StateIdx()); } AmplitudeIntegration ampl(grid); return ampl.IntegrateAmplitude(amplitude); } else { Eigen::MatrixXd mat; if (state.Type().isExciton() && dostateonly) { std::array DMAT = orb.DensityMatrixExcitedState(state); mat = DMAT[1] - DMAT[0]; } else { mat = orb.DensityMatrixFull(state); } DensityIntegration density(grid); density.IntegrateDensity(mat); return density.getDensities(); } } std::vector FlattenValues( const std::vector>& gridvalues) { Index size = 0; for (const auto& box : gridvalues) { size += Index(box.size()); } std::vector result; result.reserve(size); for (const auto& box : gridvalues) { result.insert(result.end(), box.begin(), box.end()); } return result; } void CubeFile_Writer::WriteFile(const std::string& filename, const Orbitals& orb, QMState state, bool dostateonly) const { Regular_Grid grid; Eigen::Array3d padding = Eigen::Array3d::Ones() * _padding; AOBasis basis = orb.SetupDftBasis(); XTP_LOG(Log::info, _log) << " Loaded DFT Basis Set " << orb.getDFTbasisName() << std::flush; grid.GridSetup(_steps, padding, orb.QMAtoms(), basis); XTP_LOG(Log::info, _log) << " Calculating Gridvalues " << std::flush; auto temp = CalculateValues(orb, state, dostateonly, grid); std::vector grid_values = FlattenValues(temp); XTP_LOG(Log::info, _log) << " Calculated Gridvalues " << std::flush; bool do_amplitude = (state.Type().isSingleParticleState()); std::ofstream out(filename); if (!out.is_open()) { throw std::runtime_error("Bad file handle: " + filename); } // write cube header if (state.isTransition()) { out << boost::format("Transition state: %1$s \n") % state.ToString(); } else if (do_amplitude) { out << boost::format("%1$s with energy %2$f eV \n") % state.ToString() % (orb.getExcitedStateEnergy(state) * tools::conv::hrt2ev); } else { if (dostateonly) { out << boost::format( "Difference electron density of excited state %1$s \n") % state.ToString(); } else { out << boost::format("Total electron density of %1$s state\n") % state.ToString(); } } Eigen::Vector3d start = grid.getStartingPoint(); out << "Created by VOTCA-XTP \n"; if (do_amplitude) { out << boost::format("-%1$lu %2$f %3$f %4$f \n") % orb.QMAtoms().size() % start.x() % start.y() % start.z(); } else { out << boost::format("%1$lu %2$f %3$f %4$f \n") % orb.QMAtoms().size() % start.x() % start.y() % start.z(); } Eigen::Array steps = grid.getSteps(); Eigen::Array3d stepsizes = grid.getStepSizes(); out << boost::format("%1$d %2$f 0.0 0.0 \n") % steps.x() % stepsizes.x(); out << boost::format("%1$d 0.0 %2$f 0.0 \n") % steps.y() % stepsizes.y(); out << boost::format("%1$d 0.0 0.0 %2$f \n") % steps.z() % stepsizes.z(); tools::Elements elements; for (const QMAtom& atom : orb.QMAtoms()) { double x = atom.getPos().x(); double y = atom.getPos().y(); double z = atom.getPos().z(); std::string element = atom.getElement(); Index atnum = elements.getEleNum(element); Index crg = atom.getNuccharge(); out << boost::format("%1$d %2$d %3$f %4$f %5$f\n") % atnum % crg % x % y % z; } if (do_amplitude) { out << boost::format(" 1 %1$d \n") % (state.StateIdx() + 1); } Eigen::TensorMap> gridvalues( grid_values.data(), steps.z(), steps.y(), steps.x()); for (Index ix = 0; ix < steps.x(); ix++) { for (Index iy = 0; iy < steps.y(); iy++) { Index Nrecord = 0; for (Index iz = 0; iz < steps.z(); iz++) { out << boost::format("%1$E ") % gridvalues(iz, iy, ix); Nrecord++; if (Nrecord == 6 || iz == (steps.z() - 1)) { out << "\n"; Nrecord = 0; } } } } out.close(); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/cudamatrix.cc000066400000000000000000000066341412152066400171660ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * *Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/cudamatrix.h" namespace votca { namespace xtp { cudaError_t checkCuda(cudaError_t result) { if (result != cudaSuccess) { std::cerr << "CUDA Runtime Error: " << cudaGetErrorString(result) << "\n"; } return result; } Index count_available_gpus() { int count; cudaError_t err = cudaGetDeviceCount(&count); return (err != cudaSuccess) ? 0 : Index(count); } CudaMatrix::CudaMatrix(const Eigen::MatrixXd &matrix, const cudaStream_t &stream) : _rows{static_cast(matrix.rows())}, _cols{static_cast(matrix.cols())} { _data = alloc_matrix_in_gpu(size_matrix()); _stream = stream; cudaError_t err = cudaMemcpyAsync(_data.get(), matrix.data(), size_matrix(), cudaMemcpyHostToDevice, stream); if (err != 0) { throw std::runtime_error("Error copy arrays to device :" + std::string(cudaGetErrorString(err))); } } CudaMatrix::CudaMatrix(Index nrows, Index ncols, const cudaStream_t &stream) : _rows{static_cast(nrows)}, _cols{static_cast(ncols)} { _data = alloc_matrix_in_gpu(size_matrix()); _stream = stream; } CudaMatrix::operator Eigen::MatrixXd() const { Eigen::MatrixXd result = Eigen::MatrixXd::Zero(this->rows(), this->cols()); checkCuda(cudaMemcpyAsync(result.data(), this->data(), this->size_matrix(), cudaMemcpyDeviceToHost, this->_stream)); checkCuda(cudaStreamSynchronize(this->_stream)); return result; } void CudaMatrix::copy_to_gpu(const Eigen::MatrixXd &A) { size_t size_A = static_cast(A.size()) * sizeof(double); checkCuda(cudaMemcpyAsync(this->data(), A.data(), size_A, cudaMemcpyHostToDevice, _stream)); } CudaMatrix::Unique_ptr_to_GPU_data CudaMatrix::alloc_matrix_in_gpu( size_t size_arr) const { double *dmatrix; throw_if_not_enough_memory_in_gpu(size_arr); checkCuda(cudaMalloc(&dmatrix, size_arr)); Unique_ptr_to_GPU_data dev_ptr(dmatrix, [](double *x) { checkCuda(cudaFree(x)); }); return dev_ptr; } void CudaMatrix::throw_if_not_enough_memory_in_gpu( size_t requested_memory) const { size_t free, total; checkCuda(cudaMemGetInfo(&free, &total)); std::ostringstream oss; oss << "There were requested : " << requested_memory << "bytes Index the device\n"; oss << "Device Free memory (bytes): " << free << "\nDevice total Memory (bytes): " << total << "\n"; // Raise an error if there is not enough total or free memory in the device if (requested_memory > free) { oss << "There is not enough memory in the Device!\n"; throw std::runtime_error(oss.str()); } } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/cudapipeline.cc000066400000000000000000000076631412152066400174720ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * *Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/cudapipeline.h" #include namespace votca { namespace xtp { CudaPipeline::~CudaPipeline() { // destroy handle cublasDestroy(_handle); // destroy stream cudaStreamDestroy(_stream); } std::string cudaGetErrorEnum(cublasStatus_t error) { switch (error) { case CUBLAS_STATUS_SUCCESS: return "CUBLAS_STATUS_SUCCESS"; case CUBLAS_STATUS_NOT_INITIALIZED: return "CUBLAS_STATUS_NOT_INITIALIZED"; case CUBLAS_STATUS_ALLOC_FAILED: return "CUBLAS_STATUS_ALLOC_FAILED"; case CUBLAS_STATUS_INVALID_VALUE: return "CUBLAS_STATUS_INVALID_VALUE"; case CUBLAS_STATUS_ARCH_MISMATCH: return "CUBLAS_STATUS_ARCH_MISMATCH"; case CUBLAS_STATUS_MAPPING_ERROR: return "CUBLAS_STATUS_MAPPING_ERROR"; case CUBLAS_STATUS_EXECUTION_FAILED: return "CUBLAS_STATUS_EXECUTION_FAILED"; case CUBLAS_STATUS_INTERNAL_ERROR: return "CUBLAS_STATUS_INTERNAL_ERROR"; case CUBLAS_STATUS_NOT_SUPPORTED: return "CUBLAS_STATUS_NOT_SUPPORTED"; case CUBLAS_STATUS_LICENSE_ERROR: return "CUBLAS_STATUS_LICENSE_ERROR"; } return ""; } /* * Call the gemm function from cublas, resulting in the multiplication of the * two matrices */ void CudaPipeline::gemm(const CudaMatrix &A, const CudaMatrix &B, CudaMatrix &C, bool transpose_A, bool transpose_B, double beta) const { // Scalar constanst for calling blas double alpha = 1.; const double *palpha = α const double *pbeta = β cublasOperation_t transA = CUBLAS_OP_N; int k = int(A.cols()); if (transpose_A) { transA = CUBLAS_OP_T; k = int(A.rows()); } cublasOperation_t transB = CUBLAS_OP_N; int k2 = int(B.rows()); if (transpose_B) { transB = CUBLAS_OP_T; k2 = int(B.cols()); } if (k != k2) { throw std::runtime_error("Shape mismatch in cuda gemm"); } cublasSetStream(_handle, _stream); cublasStatus_t status = cublasDgemm(_handle, transA, transB, int(C.rows()), int(C.cols()), k, palpha, A.data(), int(A.rows()), B.data(), int(B.rows()), pbeta, C.data(), int(C.rows())); if (status != CUBLAS_STATUS_SUCCESS) { throw std::runtime_error("dgemm failed on gpu " + std::to_string(_deviceID) + " with errorcode:" + cudaGetErrorEnum(status)); } } void CudaPipeline::diag_gemm(const CudaMatrix &A, const CudaMatrix &b, CudaMatrix &C) const { if (b.cols() != 1) { throw std::runtime_error( "B Matrix in Cublas diag_gemm must have one column"); } if (A.rows() != b.rows()) { throw std::runtime_error("Shape mismatch in cuda diag_gemm"); } cublasSetStream(_handle, _stream); cublasStatus_t status = cublasDdgmm(_handle, CUBLAS_SIDE_LEFT, int(A.rows()), int(A.cols()), A.data(), int(A.rows()), b.data(), 1, C.data(), int(C.rows())); if (status != CUBLAS_STATUS_SUCCESS) { throw std::runtime_error("diag_gemm failed on gpu " + std::to_string(_deviceID) + " with errorcode:" + cudaGetErrorEnum(status)); } } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/davidsonsolver.cc000066400000000000000000000345031412152066400200630ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include #include // Local VOTCA includes #include "votca/xtp/davidsonsolver.h" #include "votca/xtp/eigen.h" using boost::format; using std::flush; namespace votca { namespace xtp { DavidsonSolver::DavidsonSolver(Logger &log) : _log(log) {} void DavidsonSolver::printTiming( const std::chrono::time_point &start) const { XTP_LOG(Log::error, _log) << TimeStamp() << "-----------------------------------" << flush; std::chrono::time_point end = std::chrono::system_clock::now(); std::chrono::duration elapsed_time = end - start; XTP_LOG(Log::error, _log) << TimeStamp() << "- Davidson ran for " << elapsed_time.count() << "secs." << flush; XTP_LOG(Log::error, _log) << TimeStamp() << "-----------------------------------" << flush; } void DavidsonSolver::checkOptions(Index operator_size) { //. search space exceeding the system size if (_max_search_space > operator_size) { XTP_LOG(Log::error, _log) << TimeStamp() << " == Warning : Max search space (" << _max_search_space << ") larger than system size (" << operator_size << ")" << flush; _max_search_space = operator_size; XTP_LOG(Log::error, _log) << TimeStamp() << " == Warning : Max search space set to " << operator_size << flush; this->_davidson_ortho = ORTHO::QR; XTP_LOG(Log::error, _log) << TimeStamp() << " == Warning : Orthogonalization set to QR for stabilty " << flush; XTP_LOG(Log::error, _log) << TimeStamp() << " == Warning : If problems appear, try asking for less than " << Index(operator_size / 10) << " eigenvalues" << flush; } if (this->_matrix_type == MATRIX_TYPE::HAM) { this->_davidson_ortho = ORTHO::QR; XTP_LOG(Log::error, _log) << TimeStamp() << " == Warning : Orthogonalization set to QR for non-symmetric matrix" << flush; } } void DavidsonSolver::printOptions(Index operator_size) const { XTP_LOG(Log::error, _log) << TimeStamp() << " Davidson Solver using " << OPENMP::getMaxThreads() << " threads." << flush; XTP_LOG(Log::error, _log) << TimeStamp() << " Tolerance : " << _tol << flush; switch (this->_davidson_correction) { case CORR::DPR: XTP_LOG(Log::error, _log) << TimeStamp() << " DPR Correction" << flush; break; case CORR::OLSEN: XTP_LOG(Log::error, _log) << TimeStamp() << " Olsen Correction" << flush; break; } switch (this->_davidson_ortho) { case ORTHO::GS: XTP_LOG(Log::error, _log) << TimeStamp() << " Gram-Schmidt Orthogonalization" << flush; break; case ORTHO::QR: XTP_LOG(Log::error, _log) << TimeStamp() << " QR Orthogonalization" << flush; break; } XTP_LOG(Log::error, _log) << TimeStamp() << " Matrix size : " << operator_size << 'x' << operator_size << flush; } void DavidsonSolver::printIterationData( const DavidsonSolver::RitzEigenPair &rep, const DavidsonSolver::ProjectedSpace &proj, Index neigen) const { Index converged_roots = 0; for (Index i = 0; i < neigen; i++) { converged_roots += proj.root_converged[i]; } double percent_converged = 100 * double(converged_roots) / double(neigen); XTP_LOG(Log::error, _log) << TimeStamp() << format(" %1$4d %2$12d \t %3$4.2e \t %4$5.2f%% converged") % _i_iter % proj.search_space() % rep.res_norm().head(neigen).maxCoeff() % percent_converged << flush; } void DavidsonSolver::set_matrix_type(std::string mt) { if (mt == "HAM") { this->_matrix_type = MATRIX_TYPE::HAM; } else if (mt == "SYMM") { this->_matrix_type = MATRIX_TYPE::SYMM; } else { throw std::runtime_error(mt + " is not a valid Davidson matrix type"); } } void DavidsonSolver::set_ortho(std::string method) { if (method == "GS") { this->_davidson_ortho = ORTHO::GS; } else if (method == "QR") { this->_davidson_ortho = ORTHO::QR; } else { throw std::runtime_error( method + " is not a valid Davidson orthogonalization method"); } } void DavidsonSolver::set_correction(std::string method) { if (method == "DPR") { this->_davidson_correction = CORR::DPR; } else if (method == "OLSEN") { this->_davidson_correction = CORR::OLSEN; } else { throw std::runtime_error(method + " is not a valid Davidson correction method"); } } void DavidsonSolver::set_tolerance(std::string tol) { if (tol == "loose") { this->_tol = 1E-3; } else if (tol == "normal") { this->_tol = 1E-4; } else if (tol == "strict") { this->_tol = 1E-5; } else { throw std::runtime_error(tol + " is not a valid Davidson tolerance"); } } void DavidsonSolver::set_size_update(std::string update_size) { if (update_size == "min") { this->_davidson_update = UPDATE::MIN; } else if (update_size == "safe") { this->_davidson_update = UPDATE::SAFE; } else if (update_size == "max") { this->_davidson_update = UPDATE::MAX; } else { throw std::runtime_error(update_size + " is not a valid Davidson update"); } } Index DavidsonSolver::getSizeUpdate(Index neigen) const { Index size_update; switch (this->_davidson_update) { case UPDATE::MIN: size_update = neigen; break; case UPDATE::SAFE: if (neigen < 20) { size_update = static_cast(1.5 * double(neigen)); } else { size_update = neigen + 10; } break; case UPDATE::MAX: size_update = 2 * neigen; break; default: size_update = 2 * neigen; break; } return size_update; } ArrayXl DavidsonSolver::argsort(const Eigen::VectorXd &V) const { /* \brief return the index of the sorted vector */ ArrayXl idx = ArrayXl::LinSpaced(V.rows(), 0, V.rows() - 1); std::sort(idx.data(), idx.data() + idx.size(), [&](Index i1, Index i2) { return V[i1] < V[i2]; }); return idx; } Eigen::MatrixXd DavidsonSolver::setupInitialEigenvectors( Index size_initial_guess) const { Eigen::MatrixXd guess = Eigen::MatrixXd::Zero(_Adiag.size(), size_initial_guess); ArrayXl idx = DavidsonSolver::argsort(_Adiag); switch (this->_matrix_type) { case MATRIX_TYPE::SYMM: /* \brief Initialize the guess eigenvector so that they 'target' the * smallest diagonal elements */ for (Index j = 0; j < size_initial_guess; j++) { guess(idx(j), j) = 1.0; } break; case MATRIX_TYPE::HAM: /* Initialize the guess eigenvector so that they 'target' the lowest * positive diagonal elements */ Index ind0 = _Adiag.size() / 2; for (Index j = 0; j < size_initial_guess; j++) { guess(idx(ind0 + j), j) = 1.0; } break; } return guess; } DavidsonSolver::RitzEigenPair DavidsonSolver::getRitz( const DavidsonSolver::ProjectedSpace &proj) const { DavidsonSolver::RitzEigenPair rep; Eigen::SelfAdjointEigenSolver es(proj.T); rep.lambda = es.eigenvalues(); rep.U = es.eigenvectors(); rep.q = proj.V * rep.U; // Ritz vectors rep.res = proj.AV * rep.U - rep.q * rep.lambda.asDiagonal(); // residues return rep; } DavidsonSolver::ProjectedSpace DavidsonSolver::initProjectedSpace( Index neigen, Index size_initial_guess) const { DavidsonSolver::ProjectedSpace proj; // initial vector basis proj.V = DavidsonSolver::setupInitialEigenvectors(size_initial_guess); // update variables proj.size_update = DavidsonSolver::getSizeUpdate(neigen); proj.root_converged = std::vector(proj.size_update, false); return proj; } bool DavidsonSolver::checkConvergence(const DavidsonSolver::RitzEigenPair &rep, DavidsonSolver::ProjectedSpace &proj, Index neigen) { Eigen::ArrayXd res_norm = rep.res_norm(); bool converged = true; for (Index j = 0; j < proj.size_update; j++) { proj.root_converged[j] = (res_norm[j] < _tol); if (j < neigen) { converged &= (res_norm[j] < _tol); } } return converged; } void DavidsonSolver::extendProjection(const DavidsonSolver::RitzEigenPair &rep, DavidsonSolver::ProjectedSpace &proj) { Index nupdate = 0; for (Index j = 0; j < proj.size_update; j++) { // skip the roots that have already converged if (proj.root_converged[j]) { continue; } nupdate++; // residue vector Eigen::VectorXd w = computeCorrectionVector(rep.q.col(j), rep.lambda(j), rep.res.col(j)); // append the correction vector to the search space proj.V.conservativeResize(Eigen::NoChange, proj.V.cols() + 1); proj.V.rightCols<1>() = w.normalized(); } proj.V = orthogonalize(proj.V, nupdate); } Eigen::MatrixXd DavidsonSolver::extract_vectors(const Eigen::MatrixXd &V, const ArrayXl &idx) const { Eigen::MatrixXd W = Eigen::MatrixXd::Zero(V.rows(), idx.size()); for (Index i = 0; i < idx.size(); i++) { W.col(i) = V.col(idx(i)); } return W; } Eigen::VectorXd DavidsonSolver::computeCorrectionVector( const Eigen::VectorXd &qj, double lambdaj, const Eigen::VectorXd &Aqj) const { /* compute correction vector with either DPR or OLSEN CORRECTION * For details on the method see : * Systematic Study of Selected Diagonalization Methods * for Configuration Interaction Matrices * M.L. Leininger et al . * Journal of Computational Chemistry Vol 22, No. 13 1574-1589 (2001) */ switch (this->_davidson_correction) { case CORR::DPR: { return dpr(Aqj, lambdaj); } case CORR::OLSEN: { return olsen(Aqj, qj, lambdaj); } } return Eigen::VectorXd::Zero(0); } Eigen::VectorXd DavidsonSolver::dpr(const Eigen::VectorXd &r, double lambda) const { /* \brief Compute the diagonal preconditoned residue : \delta = -r/(D - lambda) */ return (-r.array() / (_Adiag.array() - lambda)); } Eigen::VectorXd DavidsonSolver::olsen(const Eigen::VectorXd &r, const Eigen::VectorXd &x, double lambda) const { /* \brief Compute the olsen correction : \delta = (D-\lambda)^{-1} (-r + \epsilon x) */ Eigen::VectorXd delta = DavidsonSolver::dpr(r, lambda); double num = -x.transpose() * delta; double denom = -x.transpose() * dpr(x, lambda); double eps = num / denom; delta += eps * x; return delta; } Eigen::MatrixXd DavidsonSolver::orthogonalize(const Eigen::MatrixXd &V, Index nupdate) { switch (_davidson_ortho) { case ORTHO::GS: { return DavidsonSolver::gramschmidt(V, V.cols() - nupdate); } case ORTHO::QR: { return DavidsonSolver::qr(V); } } return Eigen::MatrixXd::Zero(0, 0); } Eigen::MatrixXd DavidsonSolver::qr(const Eigen::MatrixXd &A) const { Index nrows = A.rows(); Index ncols = A.cols(); ncols = std::min(nrows, ncols); Eigen::MatrixXd I = Eigen::MatrixXd::Identity(nrows, ncols); Eigen::HouseholderQR qr(A); return qr.householderQ() * I; } Eigen::MatrixXd DavidsonSolver::gramschmidt(const Eigen::MatrixXd &A, Index nstart) { Eigen::MatrixXd Q = A; for (Index j = nstart; j < A.cols(); ++j) { Q.col(j) -= Q.leftCols(j) * (Q.leftCols(j).transpose() * A.col(j)); Q.col(j).normalize(); // two is enough GS // http://stoppels.blog/posts/orthogonalization-performance Q.col(j) -= Q.leftCols(j) * (Q.leftCols(j).transpose() * Q.col(j)); if (Q.col(j).norm() <= 1E-12 * A.col(j).norm()) { _info = Eigen::ComputationInfo::NumericalIssue; throw std::runtime_error( "Linear dependencies in Gram-Schmidt. Switch to QR"); } Q.col(j).normalize(); } return Q; } void DavidsonSolver::restart(const DavidsonSolver::RitzEigenPair &rep, DavidsonSolver::ProjectedSpace &proj, Index size_restart) const { proj.V = rep.q.leftCols(size_restart); proj.AV = proj.AV * rep.U.leftCols(size_restart); // corresponds to replacing // V with q.leftCols proj.T = proj.V.transpose() * proj.AV; } void DavidsonSolver::storeConvergedData( const DavidsonSolver::RitzEigenPair &rep, Index neigen) { DavidsonSolver::storeEigenPairs(rep, neigen); XTP_LOG(Log::error, _log) << TimeStamp() << " Davidson converged after " << _i_iter << " iterations." << flush; _info = Eigen::ComputationInfo::Success; } void DavidsonSolver::storeNotConvergedData( const DavidsonSolver::RitzEigenPair &rep, std::vector &root_converged, Index neigen) { DavidsonSolver::storeEigenPairs(rep, neigen); double percent_converged = 0; for (Index i = 0; i < neigen; i++) { if (!root_converged[i]) { _eigenvalues(i) = 0; _eigenvectors.col(i).setZero(); } else { percent_converged += 1.; } } percent_converged /= double(neigen); percent_converged *= 100.; XTP_LOG(Log::error, _log) << TimeStamp() << "- Warning : Davidson " << format("%1$5.2f%%") % percent_converged << " converged after " << _i_iter << " iterations." << flush; _info = Eigen::ComputationInfo::NoConvergence; } void DavidsonSolver::storeEigenPairs(const DavidsonSolver::RitzEigenPair &rep, Index neigen) { // store the eigenvalues/eigenvectors this->_eigenvalues = rep.lambda.head(neigen); this->_eigenvectors = rep.q.leftCols(neigen); this->_eigenvectors.colwise().normalize(); this->_res = rep.res_norm().head(neigen); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/dftcoupling.cc000066400000000000000000000211111412152066400173260ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/aomatrix.h" #include "votca/xtp/dftcoupling.h" namespace votca { namespace xtp { using boost::format; using std::flush; void DFTcoupling::Initialize(tools::Property& options) { std::string key = ""; _degeneracy = options.ifExistsReturnElseReturnDefault( key + "degeneracy", _degeneracy); _degeneracy *= tools::conv::ev2hrt; _numberofstatesA = options.ifExistsReturnElseReturnDefault( key + "levA", _numberofstatesA); _numberofstatesB = options.ifExistsReturnElseReturnDefault( key + "levB", _numberofstatesB); } void DFTcoupling::WriteToProperty(tools::Property& type_summary, const Orbitals& orbitalsA, const Orbitals& orbitalsB, Index a, Index b) const { double J = getCouplingElement(a, b, orbitalsA, orbitalsB); tools::Property& coupling = type_summary.add("coupling", ""); coupling.setAttribute("levelA", a); coupling.setAttribute("levelB", b); coupling.setAttribute("j", (format("%1$1.6e") % J).str()); } void DFTcoupling::Addoutput(tools::Property& type_summary, const Orbitals& orbitalsA, const Orbitals& orbitalsB) const { tools::Property& dftcoupling = type_summary.add(Identify(), ""); dftcoupling.setAttribute("homoA", orbitalsA.getHomo()); dftcoupling.setAttribute("homoB", orbitalsB.getHomo()); tools::Property& hole_summary = dftcoupling.add("hole", ""); // hole hole for (Index a = Range_orbA.first; a <= orbitalsA.getHomo(); ++a) { for (Index b = Range_orbB.first; b <= orbitalsB.getHomo(); ++b) { WriteToProperty(hole_summary, orbitalsA, orbitalsB, a, b); } } tools::Property& electron_summary = dftcoupling.add("electron", ""); // electron-electron for (Index a = orbitalsA.getLumo(); a <= Range_orbA.first + Range_orbA.second - 1; ++a) { for (Index b = orbitalsB.getLumo(); b <= Range_orbB.first + Range_orbB.second - 1; ++b) { WriteToProperty(electron_summary, orbitalsA, orbitalsB, a, b); } } return; } std::pair DFTcoupling::DetermineRangeOfStates( const Orbitals& orbital, Index numberofstates) const { const Eigen::VectorXd& MOEnergies = orbital.MOs().eigenvalues(); if (std::abs(MOEnergies(orbital.getHomo()) - MOEnergies(orbital.getLumo())) < _degeneracy) { throw std::runtime_error( "Homo Lumo Gap is smaller than degeneracy. " "Either your degeneracy is too large or your Homo and Lumo are " "degenerate"); } Index minimal = orbital.getHomo() - numberofstates + 1; Index maximal = orbital.getLumo() + numberofstates - 1; std::vector deg_min = orbital.CheckDegeneracy(minimal, _degeneracy); minimal = *std::min_element(deg_min.begin(), deg_min.end()); std::vector deg_max = orbital.CheckDegeneracy(maximal, _degeneracy); maximal = *std::max_element(deg_max.begin(), deg_max.end()); std::pair result; result.first = minimal; // start result.second = maximal - minimal + 1; // size return result; } double DFTcoupling::getCouplingElement(Index levelA, Index levelB, const Orbitals& orbitalsA, const Orbitals& orbitalsB) const { Index levelsA = Range_orbA.second; if (_degeneracy != 0) { std::vector list_levelsA = orbitalsA.CheckDegeneracy(levelA, _degeneracy); std::vector list_levelsB = orbitalsB.CheckDegeneracy(levelB, _degeneracy); double JAB_sq = 0; for (Index iA : list_levelsA) { Index indexA = iA - Range_orbA.first; for (Index iB : list_levelsB) { Index indexB = iB - Range_orbB.first + levelsA; double JAB_one_level = JAB(indexA, indexB); JAB_sq += JAB_one_level * JAB_one_level; } } return std::sqrt(JAB_sq / double(list_levelsA.size() * list_levelsB.size())) * tools::conv::hrt2ev; } else { Index indexA = levelA - Range_orbA.first; Index indexB = levelB - Range_orbB.first + levelsA; return JAB(indexA, indexB) * tools::conv::hrt2ev; } } /** * \brief evaluates electronic couplings * @param _orbitalsA molecular orbitals of molecule A * @param _orbitalsB molecular orbitals of molecule B * @param _orbitalsAB molecular orbitals of the dimer AB */ void DFTcoupling::CalculateCouplings(const Orbitals& orbitalsA, const Orbitals& orbitalsB, const Orbitals& orbitalsAB) { XTP_LOG(Log::error, *_pLog) << "Calculating electronic couplings" << flush; CheckAtomCoordinates(orbitalsA, orbitalsB, orbitalsAB); // constructing the direct product orbA x orbB Index basisA = orbitalsA.getBasisSetSize(); Index basisB = orbitalsB.getBasisSetSize(); if ((basisA == 0) || (basisB == 0)) { throw std::runtime_error("Basis set size is not stored in monomers"); } Range_orbA = DetermineRangeOfStates(orbitalsA, _numberofstatesA); Range_orbB = DetermineRangeOfStates(orbitalsB, _numberofstatesB); Index levelsA = Range_orbA.second; Index levelsB = Range_orbB.second; XTP_LOG(Log::error, *_pLog) << "Levels:Basis A[" << levelsA << ":" << basisA << "]" << " B[" << levelsB << ":" << basisB << "]" << flush; if ((levelsA == 0) || (levelsB == 0)) { throw std::runtime_error( "No information about number of occupied/unoccupied levels is stored"); } // constructing merged orbitals auto MOsA = orbitalsA.MOs().eigenvectors().block(0, Range_orbA.first, basisA, Range_orbA.second); auto MOsB = orbitalsB.MOs().eigenvectors().block(0, Range_orbB.first, basisB, Range_orbB.second); XTP_LOG(Log::info, *_pLog) << "Calculating overlap matrix for basisset: " << orbitalsAB.getDFTbasisName() << flush; Eigen::MatrixXd overlap = CalculateOverlapMatrix(orbitalsAB) * orbitalsAB.MOs().eigenvectors(); XTP_LOG(Log::info, *_pLog) << "Projecting monomers onto dimer orbitals" << flush; Eigen::MatrixXd A_AB = MOsA.transpose() * overlap.topRows(basisA); Eigen::MatrixXd B_AB = MOsB.transpose() * overlap.bottomRows(basisB); Eigen::VectorXd mag_A = A_AB.rowwise().squaredNorm(); if (mag_A.any() < 0.95) { XTP_LOG(Log::error, *_pLog) << "\nWarning: " << "Projection of orbitals of monomer A on dimer is insufficient,mag=" << mag_A.minCoeff() << flush; } Eigen::VectorXd mag_B = B_AB.rowwise().squaredNorm(); if (mag_B.any() < 0.95) { XTP_LOG(Log::error, *_pLog) << "\nWarning: " << "Projection of orbitals of monomer B on dimer is insufficient,mag=" << mag_B.minCoeff() << flush; } Eigen::MatrixXd psi_AxB_dimer_basis(A_AB.rows() + B_AB.rows(), A_AB.cols()); psi_AxB_dimer_basis.topRows(A_AB.rows()) = A_AB; psi_AxB_dimer_basis.bottomRows(B_AB.rows()) = B_AB; XTP_LOG(Log::info, *_pLog) << "Projecting the Fock matrix onto the dimer basis" << flush; Eigen::MatrixXd JAB_dimer = psi_AxB_dimer_basis * orbitalsAB.MOs().eigenvalues().asDiagonal() * psi_AxB_dimer_basis.transpose(); XTP_LOG(Log::info, *_pLog) << "Constructing Overlap matrix" << flush; Eigen::MatrixXd S_AxB = psi_AxB_dimer_basis * psi_AxB_dimer_basis.transpose(); Eigen::SelfAdjointEigenSolver es(S_AxB); Eigen::MatrixXd Sm1 = es.operatorInverseSqrt(); XTP_LOG(Log::info, *_pLog) << "Smallest eigenvalue of overlap matrix is " << es.eigenvalues()(0) << flush; JAB = Sm1 * JAB_dimer * Sm1; XTP_LOG(Log::error, *_pLog) << "Done with electronic couplings" << flush; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/dftengine/000077500000000000000000000000001412152066400164505ustar00rootroot00000000000000xtp-2021.2/src/libxtp/dftengine/ERIs.cc000066400000000000000000000277111412152066400175710ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * *Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/ERIs.h" #include "votca/xtp/aobasis.h" #include "votca/xtp/make_libint_work.h" #include "votca/xtp/symmetric_matrix.h" // include libint last otherwise it overrides eigen #include namespace votca { namespace xtp { void ERIs::Initialize(const AOBasis& dftbasis, const AOBasis& auxbasis) { _threecenter.Fill(auxbasis, dftbasis); return; } void ERIs::Initialize_4c(const AOBasis& dftbasis) { basis_ = dftbasis.GenerateLibintBasis(); shellpairs_ = dftbasis.ComputeShellPairs(); starts_ = dftbasis.getMapToBasisFunctions(); maxnprim_ = dftbasis.getMaxNprim(); maxL_ = dftbasis.getMaxL(); shellpairdata_ = ComputeShellPairData(basis_, shellpairs_); schwarzscreen_ = ComputeSchwarzShells(dftbasis); return; } Eigen::MatrixXd ERIs::ComputeSchwarzShells(const AOBasis& basis) const { Index noshells = basis.getNumofShells(); Eigen::MatrixXd result = Eigen::MatrixXd::Zero(noshells, noshells); Index nthreads = OPENMP::getMaxThreads(); std::vector engines(nthreads); double epsilon = 0.0; engines[0] = libint2::Engine(libint2::Operator::coulomb, basis.getMaxNprim(), static_cast(basis.getMaxL()), 0, epsilon); for (Index i = 1; i < nthreads; ++i) { engines[i] = engines[0]; } std::vector shells = basis.GenerateLibintBasis(); using MatrixLibInt = Eigen::Matrix; #pragma omp parallel for schedule(dynamic) for (Index s1 = 0l; s1 < basis.getNumofShells(); ++s1) { Index thread_id = OPENMP::getThreadId(); libint2::Engine& engine = engines[thread_id]; const libint2::Engine::target_ptr_vec& buf = engine.results(); Index n1 = shells[s1].size(); for (Index s2 = 0l; s2 <= s1; ++s2) { Index n2 = shells[s2].size(); Index n12 = n1 * n2; engines[thread_id] .compute2( shells[s1], shells[s2], shells[s1], shells[s2]); Eigen::Map buf_mat(buf[0], n12, n12); result(s2, s1) = std::sqrt(buf_mat.cwiseAbs().maxCoeff()); } } return result.selfadjointView(); } std::vector> ERIs::ComputeShellPairData( const std::vector& basis, const std::vector>& shellpairs) const { std::vector> shellpairdata(basis.size()); const double ln_max_engine_precision = std::log(std::numeric_limits::epsilon() * 1e-10); #pragma omp parallel for schedule(dynamic) for (Index s1 = 0; s1 < Index(shellpairs.size()); s1++) { for (Index s2 : shellpairs[s1]) { shellpairdata[s1].emplace_back( libint2::ShellPair(basis[s1], basis[s2], ln_max_engine_precision)); } } return shellpairdata; } Eigen::MatrixXd ERIs::ComputeShellBlockNorm(const Eigen::MatrixXd& dmat) const { Eigen::MatrixXd result = Eigen::MatrixXd::Zero(starts_.size(), starts_.size()); #pragma omp parallel for schedule(dynamic) for (Index s1 = 0l; s1 < Index(basis_.size()); ++s1) { Index bf1 = starts_[s1]; Index n1 = basis_[s1].size(); for (Index s2 = 0l; s2 <= s1; ++s2) { Index bf2 = starts_[s2]; Index n2 = basis_[s2].size(); result(s2, s1) = dmat.block(bf2, bf1, n2, n1).cwiseAbs().maxCoeff(); } } return result.selfadjointView(); } template std::array ERIs::Compute4c(const Eigen::MatrixXd& dmat, double error) const { assert(schwarzscreen_.rows() > 0 && schwarzscreen_.cols() > 0 && "Please call Initialize_4c before running this"); Index nthreads = OPENMP::getMaxThreads(); Eigen::MatrixXd hartree = Eigen::MatrixXd::Zero(dmat.rows(), dmat.cols()); Eigen::MatrixXd exchange; if (with_exchange) { exchange = Eigen::MatrixXd::Zero(dmat.rows(), dmat.cols()); } Eigen::MatrixXd dnorm_block = ComputeShellBlockNorm(dmat); double fock_precision = error; // engine precision controls primitive truncation, assume worst-case scenario // (all primitive combinations add up constructively) Index max_nprim4 = maxnprim_ * maxnprim_ * maxnprim_ * maxnprim_; double engine_precision = std::min(fock_precision / dnorm_block.maxCoeff(), std::numeric_limits::epsilon()) / double(max_nprim4); std::vector engines(nthreads); engines[0] = libint2::Engine(libint2::Operator::coulomb, int(maxnprim_), int(maxL_), 0); engines[0].set_precision(engine_precision); // shellset-dependent precision // control will likely break // positive definiteness // stick with this simple recipe for (Index i = 1; i < nthreads; ++i) { engines[i] = engines[0]; } Index nshells = basis_.size(); #pragma omp parallel for schedule(dynamic)reduction(+ : hartree)reduction(+: exchange) for (Index s1 = 0; s1 < nshells; ++s1) { Index thread_id = OPENMP::getThreadId(); libint2::Engine& engine = engines[thread_id]; const auto& buf = engine.results(); Index start_1 = starts_[s1]; const libint2::Shell& shell1 = basis_[s1]; Index n1 = shell1.size(); auto sp12_iter = shellpairdata_[s1].begin(); for (Index s2 : shellpairs_[s1]) { Index start_2 = starts_[s2]; const libint2::Shell& shell2 = basis_[s2]; Index n2 = shell2.size(); double dnorm_12 = dnorm_block(s1, s2); const libint2::ShellPair* sp12 = &(*sp12_iter); ++sp12_iter; for (Index s3 = 0; s3 <= s1; ++s3) { Index start_3 = starts_[s3]; const libint2::Shell& shell3 = basis_[s3]; Index n3 = shell3.size(); auto sp34_iter = shellpairdata_[s3].begin(); double dnorm_123 = std::max(dnorm_block(s1, s3), std::max(dnorm_block(s2, s3), dnorm_12)); Index s4max = (s1 == s3) ? s2 : s3; for (Index s4 : shellpairs_[s3]) { if (s4 > s4max) { break; } // for each s3, s4 are stored in monotonically increasing // order const libint2::ShellPair* sp34 = &(*sp34_iter); // must update the iter even if going to skip s4 ++sp34_iter; double dnorm_1234 = std::max(dnorm_block(s1, s4), std::max(dnorm_block(s2, s4), std::max(dnorm_block(s3, s4), dnorm_123))); if (dnorm_1234 * schwarzscreen_(s1, s2) * schwarzscreen_(s3, s4) < fock_precision) { continue; } const libint2::Shell& shell4 = basis_[s4]; engine .compute2( shell1, shell2, shell3, shell4, sp12, sp34); const auto* buf_1234 = buf[0]; if (buf_1234 == nullptr) { continue; // if all integrals screened out, skip to next quartet } Index start_4 = starts_[s4]; Index n4 = shell4.size(); Index s12_deg = (s1 == s2) ? 1 : 2; Index s34_deg = (s3 == s4) ? 1 : 2; Index s12_34_deg = (s1 == s3) ? (s2 == s4 ? 1 : 2) : 2; Index s1234_deg = s12_deg * s34_deg * s12_34_deg; for (Index f1 = 0, f1234 = 0; f1 != n1; ++f1) { const Index bf1 = f1 + start_1; for (Index f2 = 0; f2 != n2; ++f2) { const Index bf2 = f2 + start_2; for (Index f3 = 0; f3 != n3; ++f3) { const Index bf3 = f3 + start_3; for (Index f4 = 0; f4 != n4; ++f4, ++f1234) { const Index bf4 = f4 + start_4; const double value = buf_1234[f1234]; const double value_scal_by_deg = value * double(s1234_deg); hartree(bf1, bf2) += dmat(bf3, bf4) * value_scal_by_deg; hartree(bf3, bf4) += dmat(bf1, bf2) * value_scal_by_deg; if (with_exchange) { exchange(bf1, bf3) -= dmat(bf2, bf4) * value_scal_by_deg; exchange(bf2, bf3) -= dmat(bf1, bf4) * value_scal_by_deg; exchange(bf2, bf4) -= dmat(bf1, bf3) * value_scal_by_deg; exchange(bf1, bf4) -= dmat(bf2, bf3) * value_scal_by_deg; } } } } } } } } } std::array result2; // 0.25=0.5(symmetrisation)*0.5(our dmat has a factor 2) result2[0] = 0.25 * (hartree + hartree.transpose()); if (with_exchange) { // prefactor result2[1] = 0.125 * (exchange + exchange.transpose()); } return result2; } template std::array ERIs::Compute4c( const Eigen::MatrixXd& dmat, double error) const; template std::array ERIs::Compute4c( const Eigen::MatrixXd& dmat, double error) const; Eigen::MatrixXd ERIs::CalculateERIs_3c(const Eigen::MatrixXd& DMAT) const { assert(_threecenter.size() > 0 && "Please call Initialize before running this"); Eigen::MatrixXd ERIs2 = Eigen::MatrixXd::Zero(DMAT.rows(), DMAT.cols()); Symmetric_Matrix dmat_sym = Symmetric_Matrix(DMAT); #pragma omp parallel for schedule(guided) reduction(+ : ERIs2) for (Index i = 0; i < _threecenter.size(); i++) { const Symmetric_Matrix& threecenter = _threecenter[i]; // Trace over prod::DMAT,I(l)=componentwise product over const double factor = threecenter.TraceofProd(dmat_sym); Eigen::SelfAdjointView m = ERIs2.selfadjointView(); threecenter.AddtoEigenUpperMatrix(m, factor); } return ERIs2.selfadjointView(); } Eigen::MatrixXd ERIs::CalculateEXX_dmat(const Eigen::MatrixXd& DMAT) const { assert(_threecenter.size() > 0 && "Please call Initialize before running this"); Eigen::MatrixXd EXX = Eigen::MatrixXd::Zero(DMAT.rows(), DMAT.cols()); #pragma omp parallel for schedule(guided) reduction(+ : EXX) for (Index i = 0; i < _threecenter.size(); i++) { const Eigen::MatrixXd threecenter = _threecenter[i].UpperMatrix(); EXX -= threecenter.selfadjointView() * DMAT * threecenter.selfadjointView(); } return EXX; } Eigen::MatrixXd ERIs::CalculateEXX_mos(const Eigen::MatrixXd& occMos) const { assert(_threecenter.size() > 0 && "Please call Initialize before running this"); Eigen::MatrixXd EXX = Eigen::MatrixXd::Zero(occMos.rows(), occMos.rows()); #pragma omp parallel for schedule(guided) reduction(+ : EXX) for (Index i = 0; i < _threecenter.size(); i++) { const Eigen::MatrixXd TCxMOs_T = occMos.transpose() * _threecenter[i].UpperMatrix().selfadjointView(); EXX -= TCxMOs_T.transpose() * TCxMOs_T; } return 2 * EXX; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/dftengine/adiis.cc000066400000000000000000000043361412152066400200560ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // Local VOTCA includes #include "votca/xtp/adiis.h" #include "votca/xtp/adiis_costfunction.h" #include "votca/xtp/bfgs_trm.h" #include "votca/xtp/logger.h" namespace votca { namespace xtp { Eigen::VectorXd ADIIS::CalcCoeff(const std::vector& dmathist, const std::vector& mathist) { success = true; Index size = dmathist.size(); const Eigen::MatrixXd& dmat = dmathist.back(); const Eigen::MatrixXd& H = mathist.back(); Eigen::VectorXd DiF = Eigen::VectorXd::Zero(size); Eigen::MatrixXd DiFj = Eigen::MatrixXd::Zero(size, size); for (Index i = 0; i < size; i++) { DiF(i) = ((dmathist[i]) - dmat).cwiseProduct(H).sum(); } for (Index i = 0; i < size; i++) { for (Index j = 0; j < size; j++) { DiFj(i, j) = ((dmathist[i]) - dmat).cwiseProduct((mathist[j]) - H).sum(); } } ADIIS_costfunction a_cost = ADIIS_costfunction(DiF, DiFj); BFGSTRM optimizer = BFGSTRM(a_cost); Logger log; optimizer.setLog(&log); optimizer.setNumofIterations(1000); optimizer.setTrustRadius(0.01); // Starting point: equal weights on all matrices Eigen::VectorXd coeffs = Eigen::VectorXd::Constant(size, 1.0 / double(size)); optimizer.Optimize(coeffs); success = optimizer.Success(); coeffs = optimizer.getParameters().cwiseAbs2(); double xnorm = coeffs.sum(); coeffs /= xnorm; if (std::abs(coeffs.tail(1).value()) < 0.001) { success = false; } return coeffs; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/dftengine/convergenceacc.cc000066400000000000000000000216271412152066400217340ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/convergenceacc.h" namespace votca { namespace xtp { void ConvergenceAcc::setOverlap(AOOverlap& S, double etol) { _S = &S; Sminusahalf = S.Pseudo_InvSqrt(etol); XTP_LOG(Log::error, *_log) << TimeStamp() << " Smallest value of AOOverlap matrix is " << _S->SmallestEigenValue() << std::flush; XTP_LOG(Log::error, *_log) << TimeStamp() << " Removed " << _S->Removedfunctions() << " basisfunction from inverse overlap matrix" << std::flush; return; } Eigen::MatrixXd ConvergenceAcc::Iterate(const Eigen::MatrixXd& dmat, Eigen::MatrixXd& H, tools::EigenSystem& MOs, double totE) { Eigen::MatrixXd H_guess = Eigen::MatrixXd::Zero(H.rows(), H.cols()); if (int(_mathist.size()) == _opt.histlength) { _totE.erase(_totE.begin() + _maxerrorindex); _mathist.erase(_mathist.begin() + _maxerrorindex); _dmatHist.erase(_dmatHist.begin() + _maxerrorindex); } _totE.push_back(totE); if (_opt.mode != KSmode::fractional) { double gap = MOs.eigenvalues()(_nocclevels) - MOs.eigenvalues()(_nocclevels - 1); if ((_diiserror > _opt.levelshiftend && _opt.levelshift > 0.0) || gap < 1e-6) { Levelshift(H, MOs.eigenvectors()); } } const Eigen::MatrixXd& S = _S->Matrix(); Eigen::MatrixXd errormatrix = Sminusahalf.transpose() * (H * dmat * S - S * dmat * H) * Sminusahalf; _diiserror = errormatrix.cwiseAbs().maxCoeff(); _mathist.push_back(H); _dmatHist.push_back(dmat); if (_opt.maxout) { if (_diiserror > _maxerror) { _maxerror = _diiserror; _maxerrorindex = _mathist.size() - 1; } } _diis.Update(_maxerrorindex, errormatrix); bool diis_error = false; XTP_LOG(Log::error, *_log) << TimeStamp() << " DIIs error " << getDIIsError() << std::flush; XTP_LOG(Log::error, *_log) << TimeStamp() << " Delta Etot " << getDeltaE() << std::flush; if ((_diiserror < _opt.adiis_start || _diiserror < _opt.diis_start) && _opt.usediis && _mathist.size() > 2) { Eigen::VectorXd coeffs; // use ADIIs if energy has risen a lot in current iteration if (_diiserror > _opt.diis_start || _totE.back() > 0.9 * _totE[_totE.size() - 2]) { coeffs = _adiis.CalcCoeff(_dmatHist, _mathist); diis_error = !_adiis.Info(); XTP_LOG(Log::warning, *_log) << TimeStamp() << " Using ADIIS for next guess" << std::flush; } else { coeffs = _diis.CalcCoeff(); diis_error = !_diis.Info(); XTP_LOG(Log::warning, *_log) << TimeStamp() << " Using DIIS for next guess" << std::flush; } if (diis_error) { XTP_LOG(Log::warning, *_log) << TimeStamp() << " (A)DIIS failed using mixing instead" << std::flush; H_guess = H; } else { for (Index i = 0; i < coeffs.size(); i++) { if (std::abs(coeffs(i)) < 1e-8) { continue; } H_guess += coeffs(i) * _mathist[i]; } } } else { H_guess = H; } MOs = SolveFockmatrix(H_guess); Eigen::MatrixXd dmatout = DensityMatrix(MOs); if (_diiserror > _opt.adiis_start || !_opt.usediis || diis_error || _mathist.size() <= 2) { _usedmixing = true; dmatout = _opt.mixingparameter * dmat + (1.0 - _opt.mixingparameter) * dmatout; XTP_LOG(Log::warning, *_log) << TimeStamp() << " Using Mixing with alpha=" << _opt.mixingparameter << std::flush; } else { _usedmixing = false; } return dmatout; } void ConvergenceAcc::PrintConfigOptions() const { XTP_LOG(Log::error, *_log) << TimeStamp() << " Convergence Options:" << std::flush; XTP_LOG(Log::error, *_log) << "\t\t Delta E [Ha]: " << _opt.Econverged << std::flush; XTP_LOG(Log::error, *_log) << "\t\t DIIS max error: " << _opt.error_converged << std::flush; if (_opt.usediis) { XTP_LOG(Log::error, *_log) << "\t\t DIIS histlength: " << _opt.histlength << std::flush; XTP_LOG(Log::error, *_log) << "\t\t ADIIS start: " << _opt.adiis_start << std::flush; XTP_LOG(Log::error, *_log) << "\t\t DIIS start: " << _opt.diis_start << std::flush; std::string del = "oldest"; if (_opt.maxout) { del = "largest"; } XTP_LOG(Log::error, *_log) << "\t\t Deleting " << del << " element from DIIS hist" << std::flush; } XTP_LOG(Log::error, *_log) << "\t\t Levelshift[Ha]: " << _opt.levelshift << std::flush; XTP_LOG(Log::error, *_log) << "\t\t Levelshift end: " << _opt.levelshiftend << std::flush; XTP_LOG(Log::error, *_log) << "\t\t Mixing Parameter alpha: " << _opt.mixingparameter << std::flush; } tools::EigenSystem ConvergenceAcc::SolveFockmatrix( const Eigen::MatrixXd& H) const { // transform to orthogonal for Eigen::MatrixXd H_ortho = Sminusahalf.transpose() * H * Sminusahalf; Eigen::SelfAdjointEigenSolver es(H_ortho); if (es.info() != Eigen::ComputationInfo::Success) { throw std::runtime_error("Matrix Diagonalisation failed. DiagInfo" + std::to_string(es.info())); } tools::EigenSystem result; result.eigenvalues() = es.eigenvalues(); result.eigenvectors() = Sminusahalf * es.eigenvectors(); return result; } void ConvergenceAcc::Levelshift(Eigen::MatrixXd& H, const Eigen::MatrixXd& MOs_old) const { if (_opt.levelshift < 1e-9) { return; } Eigen::VectorXd virt = Eigen::VectorXd::Zero(H.rows()); for (Index i = _nocclevels; i < H.rows(); i++) { virt(i) = _opt.levelshift; } XTP_LOG(Log::error, *_log) << TimeStamp() << " Using levelshift:" << _opt.levelshift << " Hartree" << std::flush; Eigen::MatrixXd vir = _S->Matrix() * MOs_old * virt.asDiagonal() * MOs_old.transpose() * _S->Matrix(); H += vir; return; } Eigen::MatrixXd ConvergenceAcc::DensityMatrix( const tools::EigenSystem& MOs) const { Eigen::MatrixXd result; if (_opt.mode == KSmode::closed) { result = DensityMatrixGroundState(MOs.eigenvectors()); } else if (_opt.mode == KSmode::open) { result = DensityMatrixGroundState_unres(MOs.eigenvectors()); } else if (_opt.mode == KSmode::fractional) { result = DensityMatrixGroundState_frac(MOs); } return result; } Eigen::MatrixXd ConvergenceAcc::DensityMatrixGroundState( const Eigen::MatrixXd& MOs) const { const Eigen::MatrixXd occstates = MOs.leftCols(_nocclevels); Eigen::MatrixXd dmatGS = 2.0 * occstates * occstates.transpose(); return dmatGS; } Eigen::MatrixXd ConvergenceAcc::DensityMatrixGroundState_unres( const Eigen::MatrixXd& MOs) const { if (_nocclevels == 0) { return Eigen::MatrixXd::Zero(MOs.rows(), MOs.rows()); } Eigen::MatrixXd occstates = MOs.leftCols(_nocclevels); Eigen::MatrixXd dmatGS = occstates * occstates.transpose(); return dmatGS; } Eigen::MatrixXd ConvergenceAcc::DensityMatrixGroundState_frac( const tools::EigenSystem& MOs) const { if (_opt.numberofelectrons == 0) { return Eigen::MatrixXd::Zero(MOs.eigenvectors().rows(), MOs.eigenvectors().rows()); } Eigen::VectorXd occupation = Eigen::VectorXd::Zero(MOs.eigenvalues().size()); std::vector > degeneracies; double buffer = 1e-4; degeneracies.push_back(std::vector{0}); for (Index i = 1; i < occupation.size(); i++) { if (MOs.eigenvalues()(i) < MOs.eigenvalues()(degeneracies[degeneracies.size() - 1][0]) + buffer) { degeneracies[degeneracies.size() - 1].push_back(i); } else { degeneracies.push_back(std::vector{i}); } } Index numofelec = _opt.numberofelectrons; for (const std::vector& deglevel : degeneracies) { Index numofpossibleelectrons = 2 * Index(deglevel.size()); if (numofpossibleelectrons <= numofelec) { for (Index i : deglevel) { occupation(i) = 2; } numofelec -= numofpossibleelectrons; } else { double occ = double(numofelec) / double(deglevel.size()); for (Index i : deglevel) { occupation(i) = occ; } break; } } Eigen::MatrixXd dmatGS = MOs.eigenvectors() * occupation.asDiagonal() * MOs.eigenvectors().transpose(); return dmatGS; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/dftengine/dftengine.cc000066400000000000000000001053271412152066400207320ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include #include // VOTCA includes #include #include // Local VOTCA includes #include "votca/xtp/aomatrix.h" #include "votca/xtp/aopotential.h" #include "votca/xtp/density_integration.h" #include "votca/xtp/dftengine.h" #include "votca/xtp/eeinteractor.h" #include "votca/xtp/logger.h" #include "votca/xtp/mmregion.h" #include "votca/xtp/orbitals.h" using boost::format; using namespace boost::filesystem; using namespace std; using std::flush; using namespace votca::tools; namespace votca { namespace xtp { void DFTEngine::Initialize(Property& options) { string key = "package"; const string key_xtpdft = "package.xtpdft"; _dftbasis_name = options.get(key + ".basisset").as(); if (options.get(key + ".use_auxbasisset").as()) { _auxbasis_name = options.get(key + ".auxbasisset").as(); } _four_center_method = options.get(key_xtpdft + ".four_center_method").as(); if (_four_center_method != "RI") { _screening_eps = options.get(key_xtpdft + ".screening_eps").as(); } if (options.get(key + ".use_ecp").as()) { _ecp_name = options.get(key + ".ecp").as(); _with_ecp = true; } else { _with_ecp = false; } _with_guess = options.get(key + ".read_guess").as(); _initial_guess = options.get(key_xtpdft + ".initial_guess").as(); _grid_name = options.get(key_xtpdft + ".integration_grid").as(); _xc_functional_name = options.get(key + ".functional").as(); if (options.get(key_xtpdft + ".use_external_density").as()) { _integrate_ext_density = true; _orbfilename = options.ifExistsReturnElseThrowRuntimeError( key_xtpdft + ".externaldensity.orbfile"); _gridquality = options.ifExistsReturnElseThrowRuntimeError( key_xtpdft + ".externaldensity.gridquality"); _state = options.ifExistsReturnElseThrowRuntimeError( key_xtpdft + ".externaldensity.state"); } if (options.get(key_xtpdft + ".use_external_field").as()) { _integrate_ext_field = true; _extfield = options.ifExistsReturnElseThrowRuntimeError( key_xtpdft + ".externalfield"); } _conv_opt.Econverged = options.get(key_xtpdft + ".convergence.energy").as(); _conv_opt.error_converged = options.get(key_xtpdft + ".convergence.error").as(); _max_iter = options.get(key_xtpdft + ".convergence.max_iterations").as(); string method = options.get(key_xtpdft + ".convergence.method").as(); if (method == "DIIS") { _conv_opt.usediis = true; } else if (method == "mixing") { _conv_opt.usediis = false; } if (!_conv_opt.usediis) { _conv_opt.histlength = 1; _conv_opt.maxout = false; } _conv_opt.mixingparameter = options.get(key_xtpdft + ".convergence.mixing").as(); _conv_opt.levelshift = options.get(key_xtpdft + ".convergence.levelshift").as(); _conv_opt.levelshiftend = options.get(key_xtpdft + ".convergence.levelshift_end").as(); _conv_opt.maxout = options.get(key_xtpdft + ".convergence.DIIS_maxout").as(); _conv_opt.histlength = options.get(key_xtpdft + ".convergence.DIIS_length").as(); _conv_opt.diis_start = options.get(key_xtpdft + ".convergence.DIIS_start").as(); _conv_opt.adiis_start = options.get(key_xtpdft + ".convergence.ADIIS_start").as(); return; } void DFTEngine::PrintMOs(const Eigen::VectorXd& MOEnergies, Log::Level level) { XTP_LOG(level, *_pLog) << " Orbital energies: " << flush; XTP_LOG(level, *_pLog) << " index occupation energy(Hartree) " << flush; for (Index i = 0; i < MOEnergies.size(); i++) { Index occupancy = 0; if (i < _numofelectrons / 2) { occupancy = 2; } XTP_LOG(level, *_pLog) << (boost::format(" %1$5d %2$1d %3$+1.10f") % i % occupancy % MOEnergies(i)) .str() << flush; } return; } void DFTEngine::CalcElDipole(const Orbitals& orb) const { QMState state = QMState("n"); Eigen::Vector3d result = orb.CalcElDipole(state); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Electric Dipole is[e*bohr]:\n\t\t dx=" << result[0] << "\n\t\t dy=" << result[1] << "\n\t\t dz=" << result[2] << flush; return; } std::array DFTEngine::CalcERIs_EXX( const Eigen::MatrixXd& MOCoeff, const Eigen::MatrixXd& Dmat, double error) const { if (_four_center_method == "RI") { if (_conv_accelerator.getUseMixing() || MOCoeff.rows() == 0) { return _ERIs.CalculateERIs_EXX_3c(Eigen::MatrixXd::Zero(0, 0), Dmat); } else { Eigen::MatrixXd occblock = MOCoeff.block(0, 0, MOCoeff.rows(), _numofelectrons / 2); return _ERIs.CalculateERIs_EXX_3c(occblock, Dmat); } } else { return _ERIs.CalculateERIs_EXX_4c(Dmat, error); } } Eigen::MatrixXd DFTEngine::CalcERIs(const Eigen::MatrixXd& Dmat, double error) const { if (_four_center_method == "RI") { return _ERIs.CalculateERIs_3c(Dmat); } else { return _ERIs.CalculateERIs_4c(Dmat, error); } } tools::EigenSystem DFTEngine::IndependentElectronGuess( const Mat_p_Energy& H0) const { return _conv_accelerator.SolveFockmatrix(H0.matrix()); } tools::EigenSystem DFTEngine::ModelPotentialGuess( const Mat_p_Energy& H0, const QMMolecule& mol, const Vxc_Potential& vxcpotential) const { Eigen::MatrixXd Dmat = AtomicGuess(mol); Mat_p_Energy e_vxc = vxcpotential.IntegrateVXC(Dmat); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Filled DFT Vxc matrix " << flush; Eigen::MatrixXd H = H0.matrix() + e_vxc.matrix(); if (_ScaHFX > 0) { std::array both = CalcERIs_EXX(Eigen::MatrixXd::Zero(0, 0), Dmat, 1e-12); H += both[0]; H += _ScaHFX * both[1]; } else { H += CalcERIs(Dmat, 1e-12); } return _conv_accelerator.SolveFockmatrix(H); } bool DFTEngine::Evaluate(Orbitals& orb) { Prepare(orb.QMAtoms()); Mat_p_Energy H0 = SetupH0(orb.QMAtoms()); tools::EigenSystem MOs; MOs.eigenvalues() = Eigen::VectorXd::Zero(H0.cols()); MOs.eigenvectors() = Eigen::MatrixXd::Zero(H0.rows(), H0.cols()); Vxc_Potential vxcpotential = SetupVxc(orb.QMAtoms()); ConfigOrbfile(orb); if (_with_guess) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Reading guess from orbitals object/file" << flush; MOs = orb.MOs(); MOs.eigenvectors() = OrthogonalizeGuess(MOs.eigenvectors()); } else { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Setup Initial Guess using: " << _initial_guess << flush; if (_initial_guess == "independent") { MOs = IndependentElectronGuess(H0); } else if (_initial_guess == "atom") { MOs = ModelPotentialGuess(H0, orb.QMAtoms(), vxcpotential); } else { throw std::runtime_error("Initial guess method not known/implemented"); } } Eigen::MatrixXd Dmat = _conv_accelerator.DensityMatrix(MOs); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Guess Matrix gives N=" << std::setprecision(9) << Dmat.cwiseProduct(_dftAOoverlap.Matrix()).sum() << " electrons." << flush; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " STARTING SCF cycle" << flush; XTP_LOG(Log::error, *_pLog) << " ----------------------------------------------" "----------------------------" << flush; for (Index this_iter = 0; this_iter < _max_iter; this_iter++) { XTP_LOG(Log::error, *_pLog) << flush; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Iteration " << this_iter + 1 << " of " << _max_iter << flush; Mat_p_Energy e_vxc = vxcpotential.IntegrateVXC(Dmat); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Filled DFT Vxc matrix " << flush; Eigen::MatrixXd H = H0.matrix() + e_vxc.matrix(); double Eone = Dmat.cwiseProduct(H0.matrix()).sum(); double Etwo = e_vxc.energy(); double exx = 0.0; if (_ScaHFX > 0) { std::array both = CalcERIs_EXX(MOs.eigenvectors(), Dmat, 1e-12); H += both[0]; Etwo += 0.5 * Dmat.cwiseProduct(both[0]).sum(); H += 0.5 * _ScaHFX * both[1]; exx = _ScaHFX / 4 * Dmat.cwiseProduct(both[1]).sum(); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Filled F+K matrix " << flush; } else { Eigen::MatrixXd Hartree = CalcERIs(Dmat, 1e-12); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Filled F matrix " << flush; H += Hartree; Etwo += 0.5 * Dmat.cwiseProduct(Hartree).sum(); } Etwo += exx; double totenergy = Eone + H0.energy() + Etwo; XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Single particle energy " << std::setprecision(12) << Eone << flush; XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Two particle energy " << std::setprecision(12) << Etwo << flush; XTP_LOG(Log::info, *_pLog) << TimeStamp() << std::setprecision(12) << " Local Exc contribution " << e_vxc.energy() << flush; if (_ScaHFX > 0) { XTP_LOG(Log::info, *_pLog) << TimeStamp() << std::setprecision(12) << " Non local Ex contribution " << exx << flush; } XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Total Energy " << std::setprecision(12) << totenergy << flush; Dmat = _conv_accelerator.Iterate(Dmat, H, MOs, totenergy); PrintMOs(MOs.eigenvalues(), Log::info); XTP_LOG(Log::info, *_pLog) << "\t\tGAP " << MOs.eigenvalues()(_numofelectrons / 2) - MOs.eigenvalues()(_numofelectrons / 2 - 1) << flush; if (_conv_accelerator.isConverged()) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Total Energy has converged to " << std::setprecision(9) << _conv_accelerator.getDeltaE() << "[Ha] after " << this_iter + 1 << " iterations. DIIS error is converged up to " << _conv_accelerator.getDIIsError() << flush; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Final Single Point Energy " << std::setprecision(12) << totenergy << " Ha" << flush; XTP_LOG(Log::error, *_pLog) << TimeStamp() << std::setprecision(12) << " Final Local Exc contribution " << e_vxc.energy() << " Ha" << flush; if (_ScaHFX > 0) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << std::setprecision(12) << " Final Non Local Ex contribution " << exx << " Ha" << flush; } PrintMOs(MOs.eigenvalues(), Log::error); orb.setQMEnergy(totenergy); orb.MOs() = MOs; CalcElDipole(orb); break; } else if (this_iter == _max_iter - 1) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " DFT calculation has not converged after " << _max_iter << " iterations. Use more iterations or another convergence " "acceleration scheme." << std::flush; return false; } } return true; } Mat_p_Energy DFTEngine::SetupH0(const QMMolecule& mol) const { AOKinetic dftAOkinetic; dftAOkinetic.Fill(_dftbasis); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Filled DFT Kinetic energy matrix ." << flush; AOMultipole dftAOESP; dftAOESP.FillPotential(_dftbasis, mol); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Filled DFT nuclear potential matrix." << flush; Eigen::MatrixXd H0 = dftAOkinetic.Matrix() + dftAOESP.Matrix(); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Constructed independent particle hamiltonian " << flush; double E0 = NuclearRepulsion(mol); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Nuclear Repulsion Energy is " << std::setprecision(9) << E0 << flush; if (_with_ecp) { AOECP dftAOECP; dftAOECP.FillPotential(_dftbasis, _ecp); H0 += dftAOECP.Matrix(); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Filled DFT ECP matrix" << flush; } if (_addexternalsites) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " " << _externalsites->size() << " External sites" << flush; if (_externalsites->size() < 200) { XTP_LOG(Log::error, *_pLog) << " Name Coordinates[a0] charge[e] dipole[e*a0] " " quadrupole[e*a0^2] " << flush; for (const std::unique_ptr& site : *_externalsites) { std::string output = (boost::format(" %1$s" " %2$+1.4f %3$+1.4f %4$+1.4f" " %5$+1.4f") % site->getElement() % site->getPos()[0] % site->getPos()[1] % site->getPos()[2] % site->getCharge()) .str(); const Eigen::Vector3d& dipole = site->getDipole(); output += (boost::format(" %1$+1.4f %2$+1.4f %3$+1.4f") % dipole[0] % dipole[1] % dipole[2]) .str(); if (site->getRank() > 1) { Eigen::VectorXd quadrupole = site->Q().tail<5>(); output += (boost::format( " %1$+1.4f %2$+1.4f %3$+1.4f %4$+1.4f %5$+1.4f") % quadrupole[0] % quadrupole[1] % quadrupole[2] % quadrupole[3] % quadrupole[4]) .str(); } XTP_LOG(Log::error, *_pLog) << output << flush; } } Mat_p_Energy ext_multipoles = IntegrateExternalMultipoles(mol, *_externalsites); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Nuclei-external site interaction energy " << std::setprecision(9) << ext_multipoles.energy() << flush; E0 += ext_multipoles.energy(); H0 += ext_multipoles.matrix(); } if (_integrate_ext_density) { Orbitals extdensity; extdensity.ReadFromCpt(_orbfilename); Mat_p_Energy extdensity_result = IntegrateExternalDensity(mol, extdensity); E0 += extdensity_result.energy(); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Nuclei-external density interaction energy " << std::setprecision(9) << extdensity_result.energy() << flush; H0 += extdensity_result.matrix(); } if (_integrate_ext_field) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Integrating external electric field with F[Hrt]=" << _extfield.transpose() << flush; H0 += IntegrateExternalField(mol); } return Mat_p_Energy(E0, H0); } void DFTEngine::SetupInvariantMatrices() { _dftAOoverlap.Fill(_dftbasis); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Filled DFT Overlap matrix." << flush; _conv_opt.numberofelectrons = _numofelectrons; _conv_accelerator.Configure(_conv_opt); _conv_accelerator.setLogger(_pLog); _conv_accelerator.setOverlap(_dftAOoverlap, 1e-8); _conv_accelerator.PrintConfigOptions(); if (_four_center_method == "RI") { // prepare invariant part of electron repulsion integrals _ERIs.Initialize(_dftbasis, _auxbasis); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Inverted AUX Coulomb matrix, removed " << _ERIs.Removedfunctions() << " functions from aux basis" << flush; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Setup invariant parts of Electron Repulsion integrals " << flush; } else { XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Calculating 4c diagonals. " << flush; _ERIs.Initialize_4c(_dftbasis); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Calculated 4c diagonals. " << flush; } return; } Eigen::MatrixXd DFTEngine::RunAtomicDFT_unrestricted( const QMAtom& uniqueAtom) const { bool with_ecp = _with_ecp; if (uniqueAtom.getElement() == "H" || uniqueAtom.getElement() == "He") { with_ecp = false; } QMMolecule atom = QMMolecule("individual_atom", 0); atom.push_back(uniqueAtom); BasisSet basisset; basisset.Load(_dftbasis_name); AOBasis dftbasis; dftbasis.Fill(basisset, atom); Vxc_Grid grid; grid.GridSetup(_grid_name, atom, dftbasis); Vxc_Potential gridIntegration(grid); gridIntegration.setXCfunctional(_xc_functional_name); ECPAOBasis ecp; if (with_ecp) { ECPBasisSet ecps; ecps.Load(_ecp_name); ecp.Fill(ecps, atom); } Index numofelectrons = uniqueAtom.getNuccharge(); Index alpha_e = 0; Index beta_e = 0; if ((numofelectrons % 2) != 0) { alpha_e = numofelectrons / 2 + numofelectrons % 2; beta_e = numofelectrons / 2; } else { alpha_e = numofelectrons / 2; beta_e = alpha_e; } AOOverlap dftAOoverlap; AOKinetic dftAOkinetic; AOMultipole dftAOESP; AOECP dftAOECP; ERIs ERIs_atom; // DFT AOOverlap matrix dftAOoverlap.Fill(dftbasis); dftAOkinetic.Fill(dftbasis); dftAOESP.FillPotential(dftbasis, atom); ERIs_atom.Initialize_4c(dftbasis); ConvergenceAcc Convergence_alpha; ConvergenceAcc Convergence_beta; ConvergenceAcc::options opt_alpha = _conv_opt; opt_alpha.mode = ConvergenceAcc::KSmode::open; opt_alpha.histlength = 20; opt_alpha.levelshift = 0.1; opt_alpha.levelshiftend = 0.0; opt_alpha.usediis = true; opt_alpha.adiis_start = 0.0; opt_alpha.diis_start = 0.0; opt_alpha.numberofelectrons = alpha_e; ConvergenceAcc::options opt_beta = opt_alpha; opt_beta.numberofelectrons = beta_e; Logger log; Convergence_alpha.Configure(opt_alpha); Convergence_alpha.setLogger(&log); Convergence_alpha.setOverlap(dftAOoverlap, 1e-8); Convergence_beta.Configure(opt_beta); Convergence_beta.setLogger(&log); Convergence_beta.setOverlap(dftAOoverlap, 1e-8); /**** Construct initial density ****/ Eigen::MatrixXd H0 = dftAOkinetic.Matrix() + dftAOESP.Matrix(); if (with_ecp) { dftAOECP.FillPotential(dftbasis, ecp); H0 += dftAOECP.Matrix(); } tools::EigenSystem MOs_alpha = Convergence_alpha.SolveFockmatrix(H0); Eigen::MatrixXd dftAOdmat_alpha = Convergence_alpha.DensityMatrix(MOs_alpha); if (uniqueAtom.getElement() == "H") { return dftAOdmat_alpha; } tools::EigenSystem MOs_beta = Convergence_beta.SolveFockmatrix(H0); Eigen::MatrixXd dftAOdmat_beta = Convergence_beta.DensityMatrix(MOs_beta); Index maxiter = 80; for (Index this_iter = 0; this_iter < maxiter; this_iter++) { Eigen::MatrixXd H_alpha = H0; Eigen::MatrixXd H_beta = H_alpha; double E_two_alpha = 0.0; double E_two_beta = 0.0; if (_ScaHFX > 0) { std::array both_alpha = ERIs_atom.CalculateERIs_EXX_4c(dftAOdmat_alpha, 1e-15); std::array both_beta = ERIs_atom.CalculateERIs_EXX_4c(dftAOdmat_beta, 1e-15); Eigen::MatrixXd Hartree = both_alpha[0] + both_beta[0]; E_two_alpha += Hartree.cwiseProduct(dftAOdmat_alpha).sum(); E_two_beta += Hartree.cwiseProduct(dftAOdmat_beta).sum(); E_two_alpha += 0.5 * both_alpha[1].cwiseProduct(dftAOdmat_alpha).sum(); E_two_beta += 0.5 * both_beta[1].cwiseProduct(dftAOdmat_beta).sum(); H_alpha += Hartree + _ScaHFX * both_alpha[1]; H_beta += Hartree + _ScaHFX * both_beta[1]; } else { Eigen::MatrixXd Hartree = ERIs_atom.CalculateERIs_4c(dftAOdmat_alpha + dftAOdmat_beta, 1e-15); E_two_alpha += Hartree.cwiseProduct(dftAOdmat_alpha).sum(); E_two_beta += Hartree.cwiseProduct(dftAOdmat_beta).sum(); H_alpha += Hartree; H_beta += Hartree; } Mat_p_Energy e_vxc_alpha = gridIntegration.IntegrateVXC(dftAOdmat_alpha); H_alpha += e_vxc_alpha.matrix(); E_two_alpha += e_vxc_alpha.energy(); Mat_p_Energy e_vxc_beta = gridIntegration.IntegrateVXC(dftAOdmat_beta); H_beta += e_vxc_beta.matrix(); E_two_beta += e_vxc_beta.energy(); double E_one_alpha = dftAOdmat_alpha.cwiseProduct(H0).sum(); double E_one_beta = dftAOdmat_beta.cwiseProduct(H0).sum(); double E_alpha = E_one_alpha + E_two_alpha; double E_beta = E_one_beta + E_two_beta; double totenergy = E_alpha + E_beta; // evolve alpha dftAOdmat_alpha = Convergence_alpha.Iterate(dftAOdmat_alpha, H_alpha, MOs_alpha, E_alpha); // evolve beta dftAOdmat_beta = Convergence_beta.Iterate(dftAOdmat_beta, H_beta, MOs_beta, E_beta); XTP_LOG(Log::debug, *_pLog) << TimeStamp() << " Iter " << this_iter << " of " << maxiter << " Etot " << totenergy << " diise_a " << Convergence_alpha.getDIIsError() << " diise_b " << Convergence_beta.getDIIsError() << "\n\t\t a_gap " << MOs_alpha.eigenvalues()(alpha_e) - MOs_alpha.eigenvalues()(alpha_e - 1) << " b_gap " << MOs_beta.eigenvalues()(beta_e) - MOs_beta.eigenvalues()(beta_e - 1) << " Nalpha=" << dftAOoverlap.Matrix().cwiseProduct(dftAOdmat_alpha).sum() << " Nbeta=" << dftAOoverlap.Matrix().cwiseProduct(dftAOdmat_beta).sum() << flush; bool converged = Convergence_alpha.isConverged() && Convergence_beta.isConverged(); if (converged || this_iter == maxiter - 1) { if (converged) { XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Converged after " << this_iter + 1 << " iterations" << flush; } else { XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Not converged after " << this_iter + 1 << " iterations. Unconverged density.\n\t\t\t" << " DIIsError_alpha=" << Convergence_alpha.getDIIsError() << " DIIsError_beta=" << Convergence_beta.getDIIsError() << flush; } break; } } Eigen::MatrixXd avgmatrix = SphericalAverageShells(dftAOdmat_alpha + dftAOdmat_beta, dftbasis); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Atomic density Matrix for " << uniqueAtom.getElement() << " gives N=" << std::setprecision(9) << avgmatrix.cwiseProduct(dftAOoverlap.Matrix()).sum() << " electrons." << flush; return avgmatrix; } Eigen::MatrixXd DFTEngine::AtomicGuess(const QMMolecule& mol) const { std::vector elements = mol.FindUniqueElements(); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Scanning molecule of size " << mol.size() << " for unique elements" << flush; QMMolecule uniqueelements = QMMolecule("uniqueelements", 0); for (auto element : elements) { uniqueelements.push_back(QMAtom(0, element, Eigen::Vector3d::Zero())); } XTP_LOG(Log::info, *_pLog) << TimeStamp() << " " << uniqueelements.size() << " unique elements found" << flush; std::vector uniqueatom_guesses; for (QMAtom& unique_atom : uniqueelements) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Calculating atom density for " << unique_atom.getElement() << flush; Eigen::MatrixXd dmat_unrestricted = RunAtomicDFT_unrestricted(unique_atom); uniqueatom_guesses.push_back(dmat_unrestricted); } Eigen::MatrixXd guess = Eigen::MatrixXd::Zero(_dftbasis.AOBasisSize(), _dftbasis.AOBasisSize()); Index start = 0; for (const QMAtom& atom : mol) { Index index = 0; for (; index < uniqueelements.size(); index++) { if (atom.getElement() == uniqueelements[index].getElement()) { break; } } Eigen::MatrixXd& dmat_unrestricted = uniqueatom_guesses[index]; guess.block(start, start, dmat_unrestricted.rows(), dmat_unrestricted.cols()) = dmat_unrestricted; start += dmat_unrestricted.rows(); } return guess; } void DFTEngine::ConfigOrbfile(Orbitals& orb) { if (_with_guess) { if (orb.hasDFTbasisName()) { if (orb.getDFTbasisName() != _dftbasis_name) { throw runtime_error( (boost::format("Basisset Name in guess orb file " "and in dftengine option file differ %1% vs %2%") % orb.getDFTbasisName() % _dftbasis_name) .str()); } } else { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " WARNING: " "Orbital file has no basisset information," "using it as a guess might work or not for calculation with " << _dftbasis_name << flush; } } orb.setDFTbasisName(_dftbasis_name); orb.setBasisSetSize(_dftbasis.AOBasisSize()); orb.setXCFunctionalName(_xc_functional_name); orb.setScaHFX(_ScaHFX); if (_with_ecp) { orb.setECPName(_ecp_name); } if (_four_center_method == "RI") { orb.setAuxbasisName(_auxbasis_name); } if (_with_guess) { if (orb.hasECPName() || _with_ecp) { if (orb.getECPName() != _ecp_name) { throw runtime_error( (boost::format("ECPs in orb file: %1% and options %2% differ") % orb.getECPName() % _ecp_name) .str()); } } if (orb.getNumberOfAlphaElectrons() != _numofelectrons / 2) { throw runtime_error( (boost::format("Number of electron in guess orb file: %1% and in " "dftengine: %2% differ.") % orb.getNumberOfAlphaElectrons() % (_numofelectrons / 2)) .str()); } if (orb.getBasisSetSize() != _dftbasis.AOBasisSize()) { throw runtime_error((boost::format("Number of levels in guess orb file: " "%1% and in dftengine: %2% differ.") % orb.getBasisSetSize() % _dftbasis.AOBasisSize()) .str()); } } else { orb.setNumberOfAlphaElectrons(_numofelectrons / 2); orb.setNumberOfOccupiedLevels(_numofelectrons / 2); } return; } void DFTEngine::Prepare(QMMolecule& mol) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Using " << OPENMP::getMaxThreads() << " threads" << flush; if (XTP_HAS_MKL_OVERLOAD()) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Using MKL overload for Eigen " << flush; } else { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Using native Eigen implementation, no BLAS overload " << flush; } XTP_LOG(Log::error, *_pLog) << " Molecule Coordinates [A] " << flush; for (const QMAtom& atom : mol) { const Eigen::Vector3d pos = atom.getPos() * tools::conv::bohr2ang; std::string output = (boost::format(" %1$s" " %2$+1.4f %3$+1.4f %4$+1.4f") % atom.getElement() % pos[0] % pos[1] % pos[2]) .str(); XTP_LOG(Log::error, *_pLog) << output << flush; } BasisSet dftbasisset; dftbasisset.Load(_dftbasis_name); _dftbasis.Fill(dftbasisset, mol); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Loaded DFT Basis Set " << _dftbasis_name << " with " << _dftbasis.AOBasisSize() << " functions" << flush; if (_four_center_method == "RI") { BasisSet auxbasisset; auxbasisset.Load(_auxbasis_name); _auxbasis.Fill(auxbasisset, mol); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Loaded AUX Basis Set " << _auxbasis_name << " with " << _auxbasis.AOBasisSize() << " functions" << flush; } if (_with_ecp) { ECPBasisSet ecpbasisset; ecpbasisset.Load(_ecp_name); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Loaded ECP library " << _ecp_name << flush; std::vector results = _ecp.Fill(ecpbasisset, mol); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Filled ECP Basis of size " << _ecp.ECPAOBasisSize() << flush; if (results.size() > 0) { std::string message = ""; for (const std::string& element : results) { message += " " + element; } XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Found no ECPs for elements" << message << flush; } } for (const QMAtom& atom : mol) { _numofelectrons += atom.getNuccharge(); } // here number of electrons is actually the total number, everywhere else in // votca it is just alpha_electrons XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Total number of electrons: " << _numofelectrons << flush; SetupInvariantMatrices(); return; } Vxc_Potential DFTEngine::SetupVxc(const QMMolecule& mol) { _ScaHFX = Vxc_Potential::getExactExchange(_xc_functional_name); if (_ScaHFX > 0) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Using hybrid functional with alpha=" << _ScaHFX << flush; } Vxc_Grid grid; grid.GridSetup(_grid_name, mol, _dftbasis); Vxc_Potential vxc(grid); vxc.setXCfunctional(_xc_functional_name); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Setup numerical integration grid " << _grid_name << " for vxc functional " << _xc_functional_name << flush; XTP_LOG(Log::info, *_pLog) << "\t\t " << " with " << grid.getGridSize() << " points" << " divided into " << grid.getBoxesSize() << " boxes" << flush; return vxc; } double DFTEngine::NuclearRepulsion(const QMMolecule& mol) const { double E_nucnuc = 0.0; for (Index i = 0; i < mol.size(); i++) { const Eigen::Vector3d& r1 = mol[i].getPos(); double charge1 = double(mol[i].getNuccharge()); for (Index j = 0; j < i; j++) { const Eigen::Vector3d& r2 = mol[j].getPos(); double charge2 = double(mol[j].getNuccharge()); E_nucnuc += charge1 * charge2 / (r1 - r2).norm(); } } return E_nucnuc; } // spherically average the density matrix belonging to two shells Eigen::MatrixXd DFTEngine::SphericalAverageShells( const Eigen::MatrixXd& dmat, const AOBasis& dftbasis) const { Eigen::MatrixXd avdmat = Eigen::MatrixXd::Zero(dmat.rows(), dmat.cols()); for (const AOShell& shellrow : dftbasis) { Index size_row = shellrow.getNumFunc(); Index start_row = shellrow.getStartIndex(); for (const AOShell& shellcol : dftbasis) { Index size_col = shellcol.getNumFunc(); Index start_col = shellcol.getStartIndex(); Eigen::MatrixXd shelldmat = dmat.block(start_row, start_col, size_row, size_col); if (shellrow.getL() == shellcol.getL()) { double diagavg = shelldmat.diagonal().sum() / double(shelldmat.rows()); Index offdiagelements = shelldmat.rows() * shelldmat.cols() - shelldmat.cols(); double offdiagavg = (shelldmat.sum() - shelldmat.diagonal().sum()) / double(offdiagelements); avdmat.block(start_row, start_col, size_row, size_col).array() = offdiagavg; avdmat.block(start_row, start_col, size_row, size_col) .diagonal() .array() = diagavg; } else { double avg = shelldmat.sum() / double(shelldmat.size()); avdmat.block(start_row, start_col, size_row, size_col).array() = avg; } } } return avdmat; } double DFTEngine::ExternalRepulsion( const QMMolecule& mol, const std::vector >& multipoles) const { if (multipoles.size() == 0) { return 0; } double E_ext = 0; eeInteractor interactor; for (const QMAtom& atom : mol) { StaticSite nucleus = StaticSite(atom, double(atom.getNuccharge())); for (const std::unique_ptr& site : *_externalsites) { if ((site->getPos() - nucleus.getPos()).norm() < 1e-7) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " External site sits on nucleus, " "interaction between them is ignored." << flush; continue; } E_ext += interactor.CalcStaticEnergy_site(*site, nucleus); } } return E_ext; } Eigen::MatrixXd DFTEngine::IntegrateExternalField(const QMMolecule& mol) const { AODipole dipole; dipole.setCenter(mol.getPos()); dipole.Fill(_dftbasis); Eigen::MatrixXd result = Eigen::MatrixXd::Zero(dipole.Dimension(), dipole.Dimension()); for (Index i = 0; i < 3; i++) { result -= dipole.Matrix()[i] * _extfield[i]; } return result; } Mat_p_Energy DFTEngine::IntegrateExternalMultipoles( const QMMolecule& mol, const std::vector >& multipoles) const { Mat_p_Energy result(_dftbasis.AOBasisSize(), _dftbasis.AOBasisSize()); AOMultipole dftAOESP; dftAOESP.FillPotential(_dftbasis, multipoles); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Filled DFT external multipole potential matrix" << flush; result.matrix() = dftAOESP.Matrix(); result.energy() = ExternalRepulsion(mol, multipoles); return result; } Mat_p_Energy DFTEngine::IntegrateExternalDensity( const QMMolecule& mol, const Orbitals& extdensity) const { BasisSet basis; basis.Load(extdensity.getDFTbasisName()); AOBasis aobasis; aobasis.Fill(basis, extdensity.QMAtoms()); Vxc_Grid grid; grid.GridSetup(_gridquality, extdensity.QMAtoms(), aobasis); DensityIntegration numint(grid); Eigen::MatrixXd dmat = extdensity.DensityMatrixFull(_state); numint.IntegrateDensity(dmat); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Calculated external density" << flush; Eigen::MatrixXd e_contrib = numint.IntegratePotential(_dftbasis); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Calculated potential from electron density" << flush; AOMultipole esp; esp.FillPotential(_dftbasis, extdensity.QMAtoms()); double nuc_energy = 0.0; for (const QMAtom& atom : mol) { nuc_energy += numint.IntegratePotential(atom.getPos()) * double(atom.getNuccharge()); for (const QMAtom& extatom : extdensity.QMAtoms()) { const double dist = (atom.getPos() - extatom.getPos()).norm(); nuc_energy += double(atom.getNuccharge()) * double(extatom.getNuccharge()) / dist; } } XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Calculated potential from nuclei" << flush; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Electrostatic: " << nuc_energy << flush; return Mat_p_Energy(nuc_energy, e_contrib + esp.Matrix()); } Eigen::MatrixXd DFTEngine::OrthogonalizeGuess( const Eigen::MatrixXd& GuessMOs) const { Eigen::MatrixXd nonortho = GuessMOs.transpose() * _dftAOoverlap.Matrix() * GuessMOs; Eigen::SelfAdjointEigenSolver es(nonortho); Eigen::MatrixXd result = GuessMOs * es.operatorInverseSqrt(); return result; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/dftengine/diis.cc000066400000000000000000000056301412152066400177130ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include // Local VOTCA includes #include "votca/xtp/diis.h" namespace votca { namespace xtp { void DIIS::Update(Index maxerrorindex, const Eigen::MatrixXd& errormatrix) { if (int(_errormatrixhist.size()) == _histlength) { _errormatrixhist.erase(_errormatrixhist.begin() + maxerrorindex); _Diis_Bs.erase(_Diis_Bs.begin() + maxerrorindex); for (std::vector& subvec : _Diis_Bs) { subvec.erase(subvec.begin() + maxerrorindex); } } _errormatrixhist.push_back(errormatrix); std::vector Bijs; for (Index i = 0; i < Index(_errormatrixhist.size()) - 1; i++) { double value = errormatrix.cwiseProduct((_errormatrixhist[i]).transpose()).sum(); Bijs.push_back(value); _Diis_Bs[i].push_back(value); } Bijs.push_back(errormatrix.cwiseProduct(errormatrix.transpose()).sum()); _Diis_Bs.push_back(Bijs); return; } Eigen::VectorXd DIIS::CalcCoeff() { success = true; const Index size = Index(_errormatrixhist.size()); // C2-DIIS Eigen::MatrixXd B = Eigen::MatrixXd::Zero(size, size); for (Index i = 0; i < B.rows(); i++) { for (Index j = 0; j <= i; j++) { B(i, j) = _Diis_Bs[i][j]; if (i != j) { B(j, i) = B(i, j); } } } Eigen::SelfAdjointEigenSolver es(B); Eigen::MatrixXd eigenvectors = Eigen::MatrixXd::Zero(size, size); for (Index i = 0; i < es.eigenvectors().cols(); i++) { double norm = es.eigenvectors().col(i).sum(); eigenvectors.col(i) = es.eigenvectors().col(i) / norm; } // Choose solution by picking out solution with smallest absolute error Eigen::VectorXd errors = (eigenvectors.transpose() * B * eigenvectors).diagonal().cwiseAbs(); double MaxWeight = 10.0; Index mincoeff = 0; success = false; for (Index i = 0; i < errors.size(); i++) { errors.minCoeff(&mincoeff); if (std::abs(eigenvectors.col(mincoeff).maxCoeff()) > MaxWeight) { errors[mincoeff] = std::numeric_limits::max(); } else { success = true; break; } } Eigen::VectorXd coeffs = eigenvectors.col(mincoeff); if (std::abs(coeffs[coeffs.size() - 1]) < 0.001) { success = false; } return coeffs; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/ecpaobasis.cc000066400000000000000000000127251412152066400171340ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include // Local VOTCA includes #include "votca/xtp/ecpaobasis.h" #include "votca/xtp/ecpbasisset.h" #include "votca/xtp/qmmolecule.h" namespace votca { namespace xtp { ECPAOShell& ECPAOBasis::addShell(const ECPShell& shell, const QMAtom& atom, Index startIndex, L Lmax) { _aoshells.push_back(ECPAOShell(shell, atom, startIndex, Lmax)); return _aoshells.back(); } std::vector > ECPAOBasis::ShellsPerAtom() const { std::vector > result(_ncore_perAtom.size()); for (const ECPAOShell& shell : _aoshells) { result[shell.getAtomIndex()].push_back(&shell); } return result; } void ECPAOBasis::AddECPChargeToMolecule(QMMolecule& mol) const { for (Index i = 0; i < mol.size(); i++) { mol[i]._ecpcharge = _ncore_perAtom[i]; } } void ECPAOBasis::clear() { _name = ""; _aoshells.clear(); _ncore_perAtom.clear(); _AOBasisSize = 0; } void ECPAOBasis::UpdateShellPositions(const QMMolecule& mol) { for (ECPAOShell& shell : _aoshells) { shell._pos = mol[shell.getAtomIndex()].getPos(); } } void ECPAOBasis::add(const ECPAOBasis& other) { Index atomindex_offset = Index(_ncore_perAtom.size()); for (ECPAOShell shell : other) { shell._atomindex += atomindex_offset; shell._startIndex = _AOBasisSize; _AOBasisSize += shell.getNumFunc(); _aoshells.push_back(shell); } _ncore_perAtom.insert(_ncore_perAtom.end(), other._ncore_perAtom.begin(), other._ncore_perAtom.end()); } std::vector ECPAOBasis::Fill(const ECPBasisSet& bs, QMMolecule& atoms) { _AOBasisSize = 0; _aoshells.clear(); _ncore_perAtom.clear(); _name = bs.Name(); std::vector non_ecp_elements; Index index = 0; for (QMAtom& atom : atoms) { std::string name = atom.getElement(); bool element_exists = true; try { bs.getElement(name); } catch (std::runtime_error& error) { element_exists = false; if (std::find(non_ecp_elements.begin(), non_ecp_elements.end(), name) != non_ecp_elements.end()) { non_ecp_elements.push_back(name); } } if (element_exists) { const ECPElement& element = bs.getElement(name); _ncore_perAtom.push_back(element.getNcore()); L lmax = element.getLmax(); for (const ECPShell& shell : element) { ECPAOShell& aoshell = addShell(shell, atom, _AOBasisSize, lmax); index++; _AOBasisSize += NumFuncShell(shell.getL()); for (const ECPGaussianPrimitive& gaussian : shell) { aoshell.addGaussian(gaussian); } } } else { _ncore_perAtom.push_back(0); } } AddECPChargeToMolecule(atoms); return non_ecp_elements; } void ECPAOBasis::WriteToCpt(CheckpointWriter& w) const { w(_name, "name"); w(_AOBasisSize, "basissize"); w(_ncore_perAtom, "atomic ecp charges"); Index numofprimitives = 0; for (const auto& shell : _aoshells) { numofprimitives += shell.getSize(); } // this is all to make dummy ECPAOGaussian ECPGaussianPrimitive d(2, 0.1, 0.1); ECPAOGaussianPrimitive dummy2(d); CptTable table = w.openTable("Contractions", dummy2, numofprimitives); std::vector dataVec(numofprimitives); Index i = 0; for (const auto& shell : _aoshells) { for (const auto& gaussian : shell) { gaussian.WriteData(dataVec[i], shell); i++; } } table.write(dataVec); } void ECPAOBasis::ReadFromCpt(CheckpointReader& r) { clear(); r(_name, "name"); r(_AOBasisSize, "basissize"); if (_AOBasisSize > 0) { r(_ncore_perAtom, "atomic ecp charges"); // this is all to make dummy ECPAOGaussian ECPGaussianPrimitive d(2, 0.1, 0.1); ECPAOGaussianPrimitive dummy2(d); CptTable table = r.openTable("Contractions", dummy2); std::vector dataVec(table.numRows()); table.read(dataVec); Index laststartindex = -1; for (std::size_t i = 0; i < table.numRows(); ++i) { if (dataVec[i].startindex != laststartindex) { _aoshells.push_back(ECPAOShell(dataVec[i])); laststartindex = dataVec[i].startindex; } else { _aoshells.back()._gaussians.push_back( ECPAOGaussianPrimitive(dataVec[i])); } } } } std::ostream& operator<<(std::ostream& out, const ECPAOBasis& ecp) { out << "Name:" << ecp.Name() << "\n"; out << " Functions:" << ecp.ECPAOBasisSize() << " Shells:" << ecp._aoshells.size() << "\n"; for (const auto& shell : ecp) { out << shell; } out << "\n" << " Atomcharges:"; for (Index i = 0; i < Index(ecp._ncore_perAtom.size()); i++) { out << i << " " << ecp._ncore_perAtom[i] << " "; } return out; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/ecpaoshell.cc000066400000000000000000000046541412152066400171440ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/ecpaoshell.h" #include "votca/xtp/aomatrix.h" #include "votca/xtp/basisset.h" #include "votca/xtp/ecpaobasis.h" namespace votca { namespace xtp { void ECPAOGaussianPrimitive::WriteData(data& d, const ECPAOShell& shell) const { d.atomid = shell.getAtomIndex(); d.l = static_cast(shell.getL()); d.startindex = shell.getStartIndex(); d.decay = getDecay(); d.contraction = getContraction(); d.power = _power; d.x = shell.getPos().x(); d.y = shell.getPos().y(); d.z = shell.getPos().z(); d.lmax = static_cast(shell.getLmaxElement()); } void ECPAOGaussianPrimitive::SetupCptTable(CptTable& table) const { Index i = 0; double d = 0.0; table.addCol(i, "atomidx", HOFFSET(data, atomid)); table.addCol(i, "L", HOFFSET(data, l)); table.addCol(i, "startidx", HOFFSET(data, startindex)); table.addCol(i, "power", HOFFSET(data, power)); table.addCol(d, "decay", HOFFSET(data, decay)); table.addCol(d, "contr", HOFFSET(data, contraction)); table.addCol(d, "pos.x", HOFFSET(data, x)); table.addCol(d, "pos.y", HOFFSET(data, y)); table.addCol(d, "pos.z", HOFFSET(data, z)); table.addCol(i, "lmax", HOFFSET(data, lmax)); } std::ostream& operator<<(std::ostream& out, const ECPAOShell& shell) { out << "AtomIndex:" << shell.getAtomIndex(); out << " Shelltype:" << xtp::EnumToString(shell.getL()) << " L:" << Index(shell.getL()) << " NonLocal:" << shell.isNonLocal() << " Func:" << shell.getNumFunc() << "\n"; for (const auto& gaussian : shell) { out << " Gaussian Decay: " << gaussian.getDecay(); out << " Power: " << gaussian.getPower(); out << " Contractions: " << gaussian.getContraction() << "\n"; } return out; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/ecpbasisset.cc000066400000000000000000000113201412152066400173160ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // VOTCA includes #include // Local VOTCA includes #include "votca/tools/globals.h" #include "votca/xtp/basisset.h" #include "votca/xtp/ecpbasisset.h" namespace votca { namespace xtp { void ECPBasisSet::Load(const std::string& name) { tools::Property basis_property; // if name contains .xml, assume a ecp .xml file is located in the working // directory std::size_t found_xml = name.find(".xml"); std::string xmlFile; if (found_xml != std::string::npos) { xmlFile = name; } else { xmlFile = tools::GetVotcaShare() + "/xtp/ecps/" + name + ".xml"; } basis_property.LoadFromXML(xmlFile); _name = basis_property.get("pseudopotential").getAttribute("name"); std::vector elementProps = basis_property.Select("pseudopotential.element"); for (tools::Property* elementProp : elementProps) { std::string elementName = elementProp->getAttribute("name"); Index lmax = elementProp->getAttribute("lmax"); if (lmax > Index(L::I)) { throw std::runtime_error("In ecps lmax larger " + std::to_string(Index(L::I)) + " is not allowed"); } Index ncore = elementProp->getAttribute("ncore"); ECPElement& element = addElement(elementName, static_cast(lmax), ncore); std::vector shellProps = elementProp->Select("shell"); for (tools::Property* shellProp : shellProps) { std::string shellType = shellProp->getAttribute("type"); if (shellType.size() > 1) { throw std::runtime_error( "In ecps no combined shells e.g. SP are allowed. Here:" + shellType); } ECPShell& shell = element.addShell(StringToEnum(shellType)); std::vector constProps = shellProp->Select("constant"); for (tools::Property* constProp : constProps) { Index power = constProp->getAttribute("power"); double decay = constProp->getAttribute("decay"); double contraction = constProp->getAttribute("contraction"); shell.addGaussian(power, decay, contraction); } } } return; } // adding an Element to a Pseudopotential Library ECPElement& ECPBasisSet::addElement(std::string elementType, L lmax, Index ncore) { std::shared_ptr element(new ECPElement(elementType, lmax, ncore)); _elements[elementType] = element; return *element; } const ECPElement& ECPBasisSet::getElement(std::string element_type) const { std::map >::const_iterator itm = _elements.find(element_type); if (itm == _elements.end()) { throw std::runtime_error("Basis set " + _name + " does not have element of type " + element_type); } const ECPElement& element = *((*itm).second); return element; } std::ostream& operator<<(std::ostream& out, const ECPShell& shell) { out << "Type:" << xtp::EnumToString(shell.getL()) << " Func: " << shell.getnumofFunc() << "\n"; for (const auto& gaussian : shell._gaussians) { out << " Gaussian Decay: " << gaussian._decay; out << " Contraction:" << gaussian._contraction << "\n"; } return out; } std::ostream& operator<<(std::ostream& out, const ECPElement& element) { out << "Element:" << element.getType() << " Lmax:" << element.getLmax() << " Ncore:" << element.getNcore() << "\n"; for (const auto& shell : element) { out << shell; } return out; } std::ostream& operator<<(std::ostream& out, const ECPBasisSet& basis) { out << "BasisSet:" << basis._name << "\n"; for (const auto& element : basis) { out << (*element.second); } out << std::flush; return out; } // adds a Gaussian of a pseudopotential ECPGaussianPrimitive& ECPShell::addGaussian(Index power, double decay, double contraction) { _gaussians.push_back(ECPGaussianPrimitive(power, decay, contraction)); return _gaussians.back(); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/eeinteractor.cc000066400000000000000000000322751412152066400175110ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/eeinteractor.h" namespace votca { namespace xtp { template Eigen::Matrix eeInteractor::VSiteA( const StaticSite& siteA, const StaticSite& siteB) const { const Eigen::Vector3d& posA = siteA.getPos(); const Eigen::Vector3d& posB = siteB.getPos(); Index rankB = siteB.getRank(); Eigen::Vector3d a = posB - posA; // Vector of the distance between polar sites const double R = a.norm(); const double fac1 = 1.0 / R; a *= fac1; // unit vector pointing from A to B Eigen::Matrix V; V(0) = fac1 * siteB.getCharge(); if (N > 1 || rankB > 0) { const double fac2 = std::pow(fac1, 2); // Dipole-Charge Interaction if (N > 1) { V.segment(1, 3) = fac2 * a * siteB.getCharge(); // T_1alpha,00 (alpha=x,y,z) } // Charge-Dipole Interaction if (rankB > 0) { V(0) -= fac2 * a.dot(siteB.Q().segment<3>(1)); // T_00,1alpha (alpha=x,y,z) } const double fac3 = std::pow(fac1, 3); if (N > 1 && rankB > 0) { // Dipole-Dipole Interaction Eigen::Vector3d result = -3 * a * (a.transpose() * siteB.Q().segment<3>(1)); result += siteB.Q().segment<3>(1); result *= fac3; V.segment(1, 3) += result; // T_1alpha,1beta // (alpha,beta=x,y,z) } if (N > 4 || rankB > 1) { const double sqr3 = std::sqrt(3); const AxA r(a); { // Quadrupole-Charge interaction Eigen::Matrix Qq; Qq(0) = 1.5 * r.zz() - 0.5; // T20,00 Qq(1) = r.xz(); // T21c,00 Qq(2) = r.yz(); // T21s,000 Qq(3) = 0.5 * (r.xx() - r.yy()); // T22c,00 Qq(4) = r.xy(); // T22s,00 Qq.tail<4>() *= sqr3; if (N > 4) { V.segment(4, 5) = fac3 * Qq.transpose() * siteB.getCharge(); } if (rankB > 1) { V(0) += fac3 * Qq * siteB.Q().segment<5>(4); } } if ((N > 4 || rankB > 0) || (N > 1 || rankB > 1)) { Eigen::Matrix dQ; const double fac4 = std::pow(fac1, 4); // Quadrupole-Dipole Interaction const Eigen::Vector3d afac = a * fac4; dQ.col(0) = (1.5 - 7.5 * r.zz()) * afac; dQ.col(0).z() += 3 * afac.z(); // T20-1beta (beta=x,y,z) dQ.col(1) = -5 * r.xz() * afac; dQ.col(1).z() += afac.x(); dQ.col(1).x() += afac.z(); // T21c-1beta (beta=x,y,z) dQ.col(2) = -5 * r.yz() * afac; dQ.col(2).z() += afac.y(); dQ.col(2).y() += afac.z(); dQ.col(3) = -2.5 * (r.xx() - r.yy()) * afac; dQ.col(3).x() += afac.x(); dQ.col(3).y() -= afac.y(); // T22c-1beta (beta=x,y,z) dQ.col(4) = -5 * r.xy() * afac; dQ.col(4).y() += afac.x(); dQ.col(4).x() += afac.y(); // T22s-1beta (beta=x,y,z) dQ.rightCols<4>() *= sqr3; if (N > 4) { V.segment(4, 5) += dQ.transpose() * siteB.Q().segment<3>(1); } if (rankB > 1) { V.segment(1, 3) -= dQ * siteB.Q().segment<5>(4); } } if (N > 4 && rankB > 1) { // Quadrupole-Quadrupole Interaction Eigen::Matrix QQ; QQ(0, 0) = 0.75 * ((35 * r.zz() - 30) * r.zz() + 3); // T20,20 double temp = 0.5 * sqr3 * (35 * r.zz() - 15); QQ(1, 0) = temp * r.xz(); // T20,21c QQ(2, 0) = temp * r.yz(); // T20,21s temp = 5 * (7 * r.zz() - 1); QQ(3, 0) = sqr3 * 0.25 * temp * (r.xx() - r.yy()); // T20,22c QQ(4, 0) = sqr3 * 0.5 * temp * r.xy(); // T20,22s QQ(1, 1) = 35 * r.zz() * r.xx() - 5 * (r.xx() + r.zz()) + 1; // T21c,21c QQ(2, 1) = r.xy() * temp; // T21c,21s QQ(3, 1) = 0.5 * r.xz() * (35 * (r.xx() - r.yy()) - 10); // T21c,22c QQ(4, 1) = r.yz() * 5 * (7 * r.xx() - 1); // T21c,22s QQ(2, 2) = 5 * (7 * r.yy() * r.zz() - (r.yy() + r.zz())) + 1; // T21s,21s QQ(3, 2) = 0.5 * r.yz() * (35 * (r.xx() - r.yy()) + 10); // T21s,22c QQ(4, 2) = r.xz() * 5 * (7 * r.yy() - 1); // T21s,22s QQ(3, 3) = 8.75 * std::pow(r.xx() - r.yy(), 2) - 5 * (r.xx() + r.yy()) + 1; // T22c,22c QQ(4, 3) = 17.5 * r.xy() * (r.xx() - r.yy()); // T22c,22s QQ(4, 4) = 5 * (7 * r.xx() * r.yy() - (r.xx() + r.yy())) + 1; // T22s,22s const double fac5 = std::pow(fac1, 5); V.segment(4, 5) += fac5 * QQ.selfadjointView() * siteB.Q().segment<5>(4); } } } return V; } Eigen::Matrix3d eeInteractor::FillTholeInteraction( const PolarSite& site1, const PolarSite& site2) const { const Eigen::Vector3d& posB = site2.getPos(); const Eigen::Vector3d& posA = site1.getPos(); Eigen::Vector3d a = posB - posA; // Vector of the distance between polar sites const double R = a.norm(); // Norm of distance vector const double fac1 = 1 / R; a *= fac1; // unit vector pointing from A to B double lambda3 = std::pow(fac1, 3); double lambda5 = lambda3; const double au3 = _expdamping * std::pow(R, 3) * site1.getSqrtInvEigenDamp() * site2.getSqrtInvEigenDamp(); // au3 is dimensionless if (au3 < 40) { const double exp_ua = std::exp(-au3); lambda3 *= (1 - exp_ua); lambda5 *= (1 - (1 + au3) * exp_ua); } Eigen::Matrix3d result = -3 * lambda5 * a * a.transpose(); result.diagonal().array() += lambda3; return result; // T_1alpha,1beta (alpha,beta=x,y,z) } template double eeInteractor::ApplyStaticField_site(const StaticSite& site1, PolarSite& site2) const { Eigen::Vector3d V = Eigen::Vector3d::Zero(); double e = 0.0; if (site2.getRank() < 2) { const Eigen::Vector4d V_full = VSiteA<4>(site2, site1); V = V_full.segment<3>(1); e = V_full.dot(site2.Q().head<4>()); } else { const Eigen::Matrix V_full = VSiteA<9>(site2, site1); V = V_full.segment<3>(1); e = V_full.dot(site2.Q()); } if (CE == Estatic::noE_V) { site2.V_noE() += V; } else { site2.V() += V; } return e; } template double eeInteractor::ApplyInducedField_site(const PolarSite& site1, PolarSite& site2) const { const Eigen::Matrix3d tTab = FillTholeInteraction(site1, site2); const Eigen::Vector3d V = tTab.transpose() * site1.Induced_Dipole(); double e = 0.0; if (CE == Estatic::noE_V) { site2.V_noE() += V; } else { site2.V() += V; e = CalcPolar_stat_Energy_site(site1, site2); } return e; } double eeInteractor::CalcStaticEnergy_site(const StaticSite& site1, const StaticSite& site2) const { double e = 0.0; if (site2.getRank() < 2) { const Eigen::Vector4d V_full = VSiteA<4>(site2, site1); e = V_full.dot(site2.Q().head<4>()); } else { const Eigen::Matrix V_full = VSiteA<9>(site2, site1); e = V_full.dot(site2.Q()); } return e; } double eeInteractor::CalcPolar_stat_Energy_site(const PolarSite& site1, const StaticSite& site2) const { const Eigen::Vector4d V_full = VSiteA<4>(site1, site2); return V_full.tail<3>().dot(site1.Induced_Dipole()); } eeInteractor::E_terms eeInteractor::CalcPolarEnergy_site( const PolarSite& site1, const StaticSite& site2) const { eeInteractor::E_terms val; val.E_indu_stat() = CalcPolar_stat_Energy_site(site1, site2); return val; } eeInteractor::E_terms eeInteractor::CalcPolarEnergy_site( const PolarSite& site1, const PolarSite& site2) const { // contributions are stat-induced, induced-stat and induced induced eeInteractor::E_terms val; val.E_indu_indu() = site1.Induced_Dipole().transpose() * FillTholeInteraction(site1, site2) * site2.Induced_Dipole(); val.E_indu_stat() = CalcPolar_stat_Energy_site(site1, site2); val.E_indu_stat() += CalcPolar_stat_Energy_site(site2, site1); return val; } template double eeInteractor::ApplyStaticField(const T& segment1, PolarSegment& segment2) const { double e = 0.0; for (PolarSite& s2 : segment2) { for (const auto& s1 : segment1) { e += ApplyStaticField_site(s1, s2); } } return e; } template double eeInteractor::ApplyStaticField( const StaticSegment& seg1, PolarSegment& seg2) const; template double eeInteractor::ApplyStaticField( const StaticSegment& seg1, PolarSegment& seg2) const; template double eeInteractor::ApplyStaticField( const PolarSegment& seg1, PolarSegment& seg2) const; template double eeInteractor::ApplyStaticField( const PolarSegment& seg1, PolarSegment& seg2) const; template double eeInteractor::ApplyInducedField(const PolarSegment& segment1, PolarSegment& segment2) const { double e = 0; for (PolarSite& s2 : segment2) { for (const PolarSite& s1 : segment1) { e += ApplyInducedField_site(s1, s2); } } return e; } template double eeInteractor::ApplyInducedField( const PolarSegment& seg1, PolarSegment& seg2) const; template double eeInteractor::ApplyInducedField( const PolarSegment& seg1, PolarSegment& seg2) const; template double eeInteractor::CalcStaticEnergy(const S1& segment1, const S2& segment2) const { double e = 0; for (const auto& s1 : segment2) { for (const auto& s2 : segment1) { e += CalcStaticEnergy_site(s2, s1); } } return e; } template double eeInteractor::CalcStaticEnergy(const StaticSegment& seg1, const PolarSegment& seg2) const; template double eeInteractor::CalcStaticEnergy(const StaticSegment& seg1, const StaticSegment& seg2) const; template double eeInteractor::CalcStaticEnergy(const PolarSegment& seg1, const PolarSegment& seg2) const; template double eeInteractor::CalcStaticEnergy(const PolarSegment& seg1, const StaticSegment& seg2) const; template double eeInteractor::CalcStaticEnergy_IntraSegment(const S& seg) const { double e = 0; for (Index i = 0; i < seg.size(); i++) { for (Index j = 0; j < i; j++) { e += CalcStaticEnergy_site(seg[i], seg[j]); } } return e; } template double eeInteractor::CalcStaticEnergy_IntraSegment( const PolarSegment& seg1) const; template double eeInteractor::CalcStaticEnergy_IntraSegment( const StaticSegment& seg2) const; template eeInteractor::E_terms eeInteractor::CalcPolarEnergy(const S1& segment1, const S2& segment2) const { eeInteractor::E_terms e; for (const auto& s1 : segment2) { for (const auto& s2 : segment1) { e += CalcPolarEnergy_site(s2, s1); } } return e; } template eeInteractor::E_terms eeInteractor::CalcPolarEnergy( const PolarSegment& seg1, const PolarSegment& seg2) const; template eeInteractor::E_terms eeInteractor::CalcPolarEnergy( const PolarSegment& seg1, const StaticSegment& seg2) const; double eeInteractor::CalcPolarEnergy_IntraSegment( const PolarSegment& seg) const { double e = 0; for (Index i = 0; i < seg.size(); i++) { for (Index j = 0; j < i; j++) { e += seg[i].Induced_Dipole().transpose() * FillTholeInteraction(seg[i], seg[j]) * seg[j].Induced_Dipole(); } } return e; } Eigen::VectorXd eeInteractor::Cholesky_IntraSegment( const PolarSegment& seg) const { Index size = 3 * seg.size(); Eigen::MatrixXd A = Eigen::MatrixXd::Zero(size, size); for (Index i = 1; i < seg.size(); i++) { for (Index j = 0; j < i; j++) { A.block<3, 3>(3 * i, 3 * j) = FillTholeInteraction(seg[i], seg[j]); } } for (Index i = 0; i < seg.size(); i++) { A.block<3, 3>(3 * i, 3 * i) = seg[i].getPInv(); } Eigen::VectorXd b = Eigen::VectorXd(size); for (Index i = 0; i < seg.size(); i++) { const Eigen::Vector3d V = seg[i].V() + seg[i].V_noE(); b.segment<3>(3 * i) = -V; } Eigen::LLT> lltOfA(A); return lltOfA.solve(b); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/energy_costfunction.cc000066400000000000000000000136741412152066400211160ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/energy_costfunction.h" #include "votca/xtp/qmatom.h" #include "votca/xtp/statetracker.h" namespace votca { namespace xtp { double Energy_costfunction::EvaluateCost(const Eigen::VectorXd& parameters) { Vector2QMAtoms(parameters, _orbitals.QMAtoms()); _gwbse_engine.setRedirectLogger(true); std::string logger_file; if (_iteration == 0) { logger_file = "gwbse_iteration_" + (boost::format("%1%") % _iteration).str() + ".log"; _iteration++; } else { logger_file = "gwbse_iteration_" + (boost::format("%1%") % _iteration).str() + ".log"; } _gwbse_engine.setLoggerFile(logger_file); _gwbse_engine.ExcitationEnergies(_orbitals); _gwbse_engine.setRedirectLogger(false); _energy = _orbitals.getTotalStateEnergy( _tracker.CalcStateAndUpdate(_orbitals)); // in Hartree return _energy; } Eigen::VectorXd Energy_costfunction::EvaluateGradient( const Eigen::VectorXd& parameters) { Vector2QMAtoms(parameters, _orbitals.QMAtoms()); _force_engine.Calculate(_orbitals); Eigen::VectorXd gradient = Write3XMatrixToVector(-_force_engine.GetForces()); return gradient; } bool Energy_costfunction::Converged(const Eigen::VectorXd& delta_parameters, double delta_cost, const Eigen::VectorXd& gradient) { _iteration++; bool energy_converged = false; bool RMSForce_converged = false; bool MaxForce_converged = false; bool RMSStep_converged = false; bool MaxStep_converged = false; Energy_costfunction::conv_paras convval; convval.deltaE = delta_cost; convval.RMSForce = std::sqrt(gradient.cwiseAbs2().sum()) / double(gradient.size()); convval.MaxForce = gradient.cwiseAbs().maxCoeff(&convval.maxforceindex); convval.RMSStep = std::sqrt(delta_parameters.cwiseAbs2().sum()) / double(delta_parameters.size()); convval.MaxStep = delta_parameters.cwiseAbs().maxCoeff(&convval.maxstepindex); if (std::abs(convval.deltaE) < _convpara.deltaE) { energy_converged = true; } if (convval.RMSForce < _convpara.RMSForce) { RMSForce_converged = true; } if (convval.MaxForce < _convpara.MaxForce) { MaxForce_converged = true; } if (convval.RMSStep < _convpara.RMSStep) { RMSStep_converged = true; } if (convval.MaxStep < _convpara.MaxStep) { MaxStep_converged = true; } Report(convval); if (energy_converged && RMSForce_converged && MaxForce_converged && RMSStep_converged && MaxStep_converged) { return true; } return false; } void Energy_costfunction::Report(const Energy_costfunction::conv_paras& val) { const Energy_costfunction::conv_paras& paras = getConvParas(); XTP_LOG(Log::error, *_pLog) << (boost::format(" energy change: %1$12.8f Hartree %2$s") % val.deltaE % Converged(val.deltaE, paras.deltaE)) .str() << std::flush; XTP_LOG(Log::error, *_pLog) << (boost::format(" RMS force: %1$12.8f Hartree/Bohr %2$s") % val.RMSForce % Converged(val.RMSForce, paras.RMSForce)) .str() << std::flush; XTP_LOG(Log::error, *_pLog) << (boost::format(" Max force: %1$12.8f Hartree/Bohr %2$s") % val.MaxForce % Converged(val.MaxForce, paras.MaxForce)) .str() << std::flush; XTP_LOG(Log::error, *_pLog) << (boost::format(" RMS step: %1$12.8f Bohr %2$s") % val.RMSStep % Converged(val.RMSStep, paras.RMSStep)) .str() << std::flush; XTP_LOG(Log::error, *_pLog) << (boost::format(" Max step: %1$12.8f Bohr %2$s") % val.MaxStep % Converged(val.MaxStep, paras.MaxStep)) .str() << std::flush; XTP_LOG(Log::error, *_pLog) << (boost::format(" ++++++++++++++++++++++++++++++++++++++++++" "++++++++++++++++++++++++ ")) .str() << std::flush; XTP_LOG(Log::error, *_pLog) << std::flush; } std::string Energy_costfunction::Converged(double val, double limit) { if (std::abs(val) < limit) { return (boost::format("Converged (%1%)") % limit).str(); } else { return (boost::format("Not converged (%1%)") % limit).str(); } } void Energy_costfunction::Vector2QMAtoms(const Eigen::VectorXd& pos, QMMolecule& atoms) { for (Index i = 0; i < atoms.size(); i++) { Eigen::Vector3d pos_displaced; pos_displaced << pos(3 * i), pos(3 * i + 1), pos(3 * i + 2); atoms[i].setPos(pos_displaced); } } Eigen::VectorXd Energy_costfunction::QMAtoms2Vector(QMMolecule& atoms) { Eigen::VectorXd result = Eigen::VectorXd::Zero(3 * atoms.size()); for (Index i = 0; i < atoms.size(); i++) { result(3 * i) = atoms[i].getPos().x(); result(3 * i + 1) = atoms[i].getPos().y(); result(3 * i + 2) = atoms[i].getPos().z(); } return result; } Eigen::VectorXd Energy_costfunction::Write3XMatrixToVector( const Eigen::MatrixX3d& matrix) { Eigen::VectorXd vec = Eigen::VectorXd::Zero(matrix.rows() * matrix.cols()); for (Index i_cart = 0; i_cart < 3; i_cart++) { for (Index i_atom = 0; i_atom < matrix.rows(); i_atom++) { Index idx = 3 * i_atom + i_cart; vec(idx) = matrix(i_atom, i_cart); } } return vec; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/esp2multipole.cc000066400000000000000000000115311412152066400176210ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // Local VOTCA includes #include "votca/xtp/esp2multipole.h" #include "votca/xtp/espfit.h" #include "votca/xtp/nbo.h" #include "votca/xtp/populationanalysis.h" namespace votca { namespace xtp { using std::flush; void Esp2multipole::Initialize(tools::Property& options) { std::string key = Identify(); _do_svd = false; _use_mulliken = false; _use_CHELPG = false; _use_lowdin = false; std::string statestring = options.get(key + ".state").as(); _state.FromString(statestring); _method = options.get(key + ".method").as(); if (_method == "mulliken") { _use_mulliken = true; } else if (_method == "loewdin") { _use_lowdin = true; } else if (_method == "CHELPG") { _use_CHELPG = true; } if (options.exists(key + ".constraints")) { if (options.exists(key + ".constraints.regions")) { std::vector prop_region = options.Select(key + ".constraints.regions.region"); Index index = 0; for (tools::Property* prop : prop_region) { std::string indices = prop->get("indices").as(); QMFragment reg = QMFragment(index, indices); index++; reg.value() = prop->get("charge").as(); _regionconstraint.push_back(reg); XTP_LOG(Log::error, _log) << "Fit constrained by Region" << flush; XTP_LOG(Log::error, _log) << reg; } } if (options.exists(key + ".constraints.pairs")) { std::vector prop_pair = options.Select(key + ".constraints.pairs.pair"); for (tools::Property* prop : prop_pair) { std::string pairstring = prop->as(); tools::Tokenizer tok(pairstring, "\n\t ,"); std::vector pairvec; tok.ConvertToVector(pairvec); std::pair pair; pair.first = pairvec[0]; pair.second = pairvec[1]; _pairconstraint.push_back(pair); XTP_LOG(Log::error, _log) << "Charges " << pair.first << " " << pair.second << " constrained to be equal." << flush; } } } _gridsize = options.ifExistsReturnElseReturnDefault( key + ".gridsize", "medium"); if (options.exists(key + ".svd")) { _do_svd = options.get(key + ".svd.do_svd").as(); _conditionnumber = options.get(key + ".svd.conditionnumber").as(); } return; } void Esp2multipole::PrintDipoles(const Orbitals& orbitals, const StaticSegment& seg) const { Eigen::Vector3d classical_dip = seg.CalcDipole(); XTP_LOG(Log::error, _log) << "El Dipole from fitted charges [e*bohr]:\n\t\t" << boost::format( " dx = %1$+1.4f dy = %2$+1.4f dz = %3$+1.4f |d|^2 = %4$+1.4f") % classical_dip.x() % classical_dip.y() % classical_dip.z() % classical_dip.squaredNorm() << flush; Eigen::Vector3d qm_dip = orbitals.CalcElDipole(_state); XTP_LOG(Log::error, _log) << "El Dipole from exact qm density [e*bohr]:\n\t\t" << boost::format( " dx = %1$+1.4f dy = %2$+1.4f dz = %3$+1.4f |d|^2 = %4$+1.4f") % qm_dip.x() % qm_dip.y() % qm_dip.z() % qm_dip.squaredNorm() << flush; } StaticSegment Esp2multipole::Extractingcharges(const Orbitals& orbitals) const { XTP_LOG(Log::error, _log) << "===== Running on " << OPENMP::getMaxThreads() << " threads ===== " << flush; StaticSegment result("result", 0); if (_use_mulliken) { Mulliken mulliken; result = mulliken.CalcChargeperAtom(orbitals, _state); } else if (_use_lowdin) { Lowdin lowdin; result = lowdin.CalcChargeperAtom(orbitals, _state); } else if (_use_CHELPG) { Espfit esp = Espfit(_log); if (_pairconstraint.size() > 0) { esp.setPairConstraint(_pairconstraint); } if (_regionconstraint.size() > 0) { esp.setRegionConstraint(_regionconstraint); } if (_do_svd) { esp.setUseSVD(_conditionnumber); } result = esp.Fit2Density(orbitals, _state, _gridsize); } PrintDipoles(orbitals, result); return result; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/espfit.cc000066400000000000000000000217511412152066400163140ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/aomatrix.h" #include "votca/xtp/density_integration.h" #include "votca/xtp/espfit.h" #include "votca/xtp/grid.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/vxc_grid.h" namespace votca { namespace xtp { using std::flush; StaticSegment Espfit::Fit2Density(const Orbitals& orbitals, const QMState& state, std::string gridsize) { const Eigen::MatrixXd dmat = orbitals.DensityMatrixFull(state); // setting up grid Grid grid; grid.setupCHELPGGrid(orbitals.QMAtoms()); XTP_LOG(Log::info, _log) << TimeStamp() << " Done setting up CHELPG grid with " << grid.size() << " points " << flush; // Calculating nuclear potential at gridpoints AOBasis basis = orbitals.SetupDftBasis(); AOOverlap overlap; overlap.Fill(basis); double N_comp = dmat.cwiseProduct(overlap.Matrix()).sum(); Vxc_Grid numintgrid; numintgrid.GridSetup(gridsize, orbitals.QMAtoms(), basis); XTP_LOG(Log::info, _log) << TimeStamp() << " Setup " << gridsize << " Numerical Grid with " << numintgrid.getGridSize() << " gridpoints." << flush; DensityIntegration numway(numintgrid); double N = numway.IntegrateDensity(dmat); XTP_LOG(Log::error, _log) << TimeStamp() << " Calculated Densities at Numerical Grid, Number of electrons is " << N << flush; if (std::abs(N - N_comp) > 0.001) { XTP_LOG(Log::error, _log) << "=======================" << flush; XTP_LOG(Log::error, _log) << "WARNING: Calculated Densities at Numerical Grid, Number of " "electrons " << N << " is far away from the the real value " << N_comp << ", you should increase the accuracy of the integration grid." << flush; N = N_comp; XTP_LOG(Log::error, _log) << "WARNING: Electronnumber set to " << N << flush; XTP_LOG(Log::error, _log) << "=======================" << flush; } XTP_LOG(Log::error, _log) << TimeStamp() << " Calculating ESP at CHELPG grid points" << flush; #pragma omp parallel for for (Index i = 0; i < grid.size(); i++) { grid.getGridValues()(i) = numway.IntegratePotential(grid.getGridPositions()[i]); } XTP_LOG(Log::info, _log) << TimeStamp() << " Electron contribution calculated" << flush; double netcharge = 0.0; if (!state.isTransition()) { EvalNuclearPotential(orbitals.QMAtoms(), grid); Index Znuc = 0; for (const QMAtom& atom : orbitals.QMAtoms()) { Znuc += atom.getNuccharge(); } netcharge = double(Znuc) - N; } netcharge = std::round(netcharge); XTP_LOG(Log::error, _log) << TimeStamp() << " Netcharge constrained to " << netcharge << flush; return FitPartialCharges(orbitals, grid, netcharge); ; } void Espfit::EvalNuclearPotential(const QMMolecule& atoms, Grid& grid) { const std::vector& gridpoints = grid.getGridPositions(); Eigen::VectorXd& gridvalues = grid.getGridValues(); XTP_LOG(Log::info, _log) << TimeStamp() << " Calculating ESP of nuclei at CHELPG grid points" << flush; for (Index i = 0; i < Index(gridpoints.size()); i++) { for (Index j = 0; j < atoms.size(); j++) { const Eigen::Vector3d& posatom = atoms[j].getPos(); Index Znuc = atoms[j].getNuccharge(); double dist_j = (gridpoints[i] - posatom).norm(); gridvalues(i) += double(Znuc) / dist_j; } } return; } StaticSegment Espfit::FitPartialCharges(const Orbitals& orbitals, const Grid& grid, double netcharge) { const QMMolecule& atomlist = orbitals.QMAtoms(); const Index NoOfConstraints = 1 + Index(_regionconstraint.size()) + Index(_pairconstraint.size()); const Index matrixSize = atomlist.size() + NoOfConstraints; XTP_LOG(Log::info, _log) << TimeStamp() << " Setting up Matrices for fitting of size " << matrixSize << " x " << matrixSize << flush; const std::vector& gridpoints = grid.getGridPositions(); const Eigen::VectorXd& potential = grid.getGridValues(); XTP_LOG(Log::info, _log) << TimeStamp() << " Using " << atomlist.size() << " Fittingcenters and " << gridpoints.size() << " Gridpoints." << flush; Eigen::MatrixXd Amat = Eigen::MatrixXd::Zero(matrixSize, matrixSize); Eigen::VectorXd Bvec = Eigen::VectorXd::Zero(matrixSize); // setting up _Amat #pragma omp parallel for for (Index i = 0; i < atomlist.size(); i++) { for (Index j = i; j < atomlist.size(); j++) { for (const auto& gridpoint : gridpoints) { double dist_i = (atomlist[i].getPos() - gridpoint).norm(); double dist_j = (atomlist[j].getPos() - gridpoint).norm(); Amat(i, j) += 1.0 / dist_i / dist_j; } Amat(j, i) = Amat(i, j); } } // setting up Bvec #pragma omp parallel for for (Index i = 0; i < atomlist.size(); i++) { for (Index j = 0; j < Index(gridpoints.size()); j++) { double dist_i = (atomlist[i].getPos() - gridpoints[j]).norm(); Bvec(i) += potential(j) / dist_i; } } // Total charge constraint for (Index i = 0; i < atomlist.size() + 1; i++) { Amat(i, atomlist.size()) = 1.0; Amat(atomlist.size(), i) = 1.0; } Amat(atomlist.size(), atomlist.size()) = 0.0; Bvec(atomlist.size()) = netcharge; // netcharge!!!! // Pairconstraint for (Index i = 0; i < Index(_pairconstraint.size()); i++) { const std::pair& pair = _pairconstraint[i]; Amat(pair.first, atomlist.size() + 1 + i) = 1.0; Amat(atomlist.size() + 1 + i, pair.first) = 1.0; Amat(pair.second, atomlist.size() + 1 + i) = -1.0; Amat(atomlist.size() + 1 + i, pair.second) = -1.0; } // Regionconstraint for (Index i = 0; i < Index(_regionconstraint.size()); i++) { const QMFragment& reg = _regionconstraint[i]; for (Index index : reg) { Amat(index, atomlist.size() + i + 1 + _pairconstraint.size()) = 1.0; Amat(atomlist.size() + i + 1 + _pairconstraint.size(), index) = 1.0; } Bvec(atomlist.size() + i + 1 + _pairconstraint.size()) = reg.value(); } XTP_LOG(Log::info, _log) << TimeStamp() << " Solving linear Equation " << flush; Eigen::VectorXd charges; if (_do_svd) { Eigen::JacobiSVD svd; svd.setThreshold(_conditionnumber); svd.compute(Amat, Eigen::ComputeThinU | Eigen::ComputeThinV); charges = svd.solve(Bvec); XTP_LOG(Log::info, _log) << TimeStamp() << " SVD Done. " << flush; if ((Bvec.size() - svd.nonzeroSingularValues()) != 0) { XTP_LOG(Log::error, _log) << TimeStamp() << Bvec.size() - svd.nonzeroSingularValues() << " Sites could not be fitted and are set to zero." << flush; } } else { Eigen::ColPivHouseholderQR QR(Amat); if (QR.info() != Eigen::ComputationInfo::Success) { throw std::runtime_error( "Espfit: Solving the constrained equation failed. Maybe try SVD."); } charges = QR.solve(Bvec); XTP_LOG(Log::info, _log) << TimeStamp() << " Solved linear least square fit ." << flush; } // remove constraints from charges charges.conservativeResize(atomlist.size()); StaticSegment seg = StaticSegment(orbitals.QMAtoms().getType(), orbitals.QMAtoms().getId()); XTP_LOG(Log::error, _log) << " Sum of fitted charges: " << charges.sum() << flush; for (Index i = 0; i < atomlist.size(); i++) { seg.push_back(StaticSite(atomlist[i], charges(i))); } // get RMSE double rmse = 0.0; double totalPotSq = 0.0; for (Index k = 0; k < Index(gridpoints.size()); k++) { double temp = 0.0; for (const StaticSite& atom : seg) { double dist = (gridpoints[k] - atom.getPos()).norm(); temp += atom.getCharge() / dist; } rmse += (potential(k) - temp) * (potential(k) - temp); totalPotSq += potential(k) * potential(k); } XTP_LOG(Log::error, _log) << " RMSE of fit: " << std::sqrt(rmse / double(gridpoints.size())) << flush; XTP_LOG(Log::error, _log) << " RRMSE of fit: " << std::sqrt(rmse / totalPotSq) << flush; return seg; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/factories/000077500000000000000000000000001412152066400164645ustar00rootroot00000000000000xtp-2021.2/src/libxtp/factories/calculatorfactory.cc000066400000000000000000000031141412152066400225130ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/calculatorfactory.h" // Local private VOTCA includes #include "calculators/eanalyze.h" #include "calculators/einternal.h" #include "calculators/ianalyze.h" #include "calculators/kmclifetime.h" #include "calculators/kmcmultiple.h" #include "calculators/mapchecker.h" #include "calculators/neighborlist.h" #include "calculators/vaverage.h" namespace votca { namespace xtp { void Calculatorfactory::RegisterAll(void) { Calculators().Register("neighborlist"); Calculators().Register("mapchecker"); Calculators().Register("ianalyze"); Calculators().Register("eanalyze"); Calculators().Register("einternal"); Calculators().Register("kmclifetime"); Calculators().Register("kmcmultiple"); Calculators().Register("vaverage"); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/factories/filterfactory.cc000066400000000000000000000025771412152066400216630ustar00rootroot00000000000000 /* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include // Local private VOTCA includes #include "statefilters/DeltaQ_filter.h" #include "statefilters/Density_filter.h" #include "statefilters/Localisation_filter.h" #include "statefilters/OscillatorStrength_filter.h" #include "statefilters/Overlap_filter.h" namespace votca { namespace xtp { void FilterFactory::RegisterAll(void) { Filter().Register("chargetransfer"); Filter().Register("density"); Filter().Register("localisation"); Filter().Register("oscillatorstrength"); Filter().Register("overlap"); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/factories/jobcalculatorfactory.cc000066400000000000000000000023251412152066400232110ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/jobcalculatorfactory.h" // Local private VOTCA includes #include "jobcalculators/eqm.h" #include "jobcalculators/iexcitoncl.h" #include "jobcalculators/iqm.h" #include "jobcalculators/qmmm.h" namespace votca { namespace xtp { void JobCalculatorfactory::RegisterAll(void) { JobCalculators().Register("iqm"); JobCalculators().Register("eqm"); JobCalculators().Register("iexcitoncl"); JobCalculators().Register("qmmm"); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/factories/qmpackagefactory.cc000066400000000000000000000020351412152066400223140ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/qmpackagefactory.h" // Local private VOTCA includes #include "qmpackages/orca.h" #include "qmpackages/xtpdft.h" namespace votca { namespace xtp { void QMPackageFactory::RegisterAll(void) { QMPackages().Register("orca"); QMPackages().Register("xtp"); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/factories/quadrature_factory.cc000066400000000000000000000025401412152066400227000ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/quadrature_factory.h" // Local private VOTCA includes #include "gaussian_quadrature/gauss_hermite_quadrature.h" #include "gaussian_quadrature/gauss_laguerre_quadrature.h" #include "gaussian_quadrature/gauss_legendre_quadrature.h" namespace votca { namespace xtp { void QuadratureFactory::RegisterAll(void) { Quadratures().Register("laguerre"); Quadratures().Register("legendre"); Quadratures().Register( "modified_legendre"); Quadratures().Register("hermite"); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/factories/toolfactory.cc000066400000000000000000000035301412152066400213410ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/toolfactory.h" // Local private VOTCA includes #include "tools/apdft.h" #include "tools/coupling.h" #include "tools/densityanalysis.h" #include "tools/dftgwbse.h" #include "tools/excitoncoupling.h" #include "tools/gencube.h" #include "tools/log2mps.h" #include "tools/mol2orb.h" #include "tools/molpol.h" #include "tools/orb2mol.h" #include "tools/partialcharges.h" #include "tools/qmsandbox.h" #include "tools/spectrum.h" namespace votca { namespace xtp { void QMToolFactory::RegisterAll(void) { QMTools().Register("log2mps"); QMTools().Register("dftgwbse"); QMTools().Register("qmsandbox"); QMTools().Register("spectrum"); QMTools().Register("excitoncoupling"); QMTools().Register("gencube"); QMTools().Register("partialcharges"); QMTools().Register("densityanalysis"); QMTools().Register("coupling"); QMTools().Register("molpol"); QMTools().Register("apdft"); QMTools().Register("mol2orb"); QMTools().Register("orb2mol"); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/forces.cc000066400000000000000000000130671412152066400163040ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/atom.h" #include "votca/xtp/forces.h" #include "votca/xtp/statetracker.h" namespace votca { namespace xtp { using std::flush; void Forces::Initialize(tools::Property& options) { std::vector choices = {"forward", "central"}; _force_method = options.ifExistsAndinListReturnElseThrowRuntimeError( ".method", choices); _displacement = options.ifExistsReturnElseReturnDefault( ".displacement", 0.001); // Angstrom _displacement *= tools::conv::ang2bohr; _remove_total_force = options.ifExistsReturnElseReturnDefault( ".CoMforce_removal", _remove_total_force); return; } void Forces::Calculate(const Orbitals& orbitals) { Index natoms = orbitals.QMAtoms().size(); _forces = Eigen::MatrixX3d::Zero(natoms, 3); for (Index atom_index = 0; atom_index < natoms; atom_index++) { XTP_LOG(Log::debug, *_pLog) << "FORCES--DEBUG working on atom " << atom_index << flush; Eigen::Vector3d atom_force = Eigen::Vector3d::Zero(); // Calculate Force on this atom if (_force_method == "forward") { atom_force = NumForceForward(orbitals, atom_index); } if (_force_method == "central") { atom_force = NumForceCentral(orbitals, atom_index); } _forces.row(atom_index) = atom_force.transpose(); } if (_remove_total_force) { RemoveTotalForce(); } return; } void Forces::Report() const { XTP_LOG(Log::error, *_pLog) << (boost::format(" ---- FORCES (Hartree/Bohr) ")).str() << flush; XTP_LOG(Log::error, *_pLog) << (boost::format(" %1$s differences ") % _force_method).str() << flush; XTP_LOG(Log::error, *_pLog) << (boost::format(" displacement %1$1.4f Angstrom ") % (_displacement * tools::conv::bohr2ang)) .str() << flush; XTP_LOG(Log::error, *_pLog) << (boost::format(" Atom\t x\t y\t z ")).str() << flush; for (Index i = 0; i < _forces.rows(); i++) { XTP_LOG(Log::error, *_pLog) << (boost::format("%1$4d %2$+1.4f %3$+1.4f %4$+1.4f") % i % _forces(i, 0) % _forces(i, 1) % _forces(i, 2)) .str() << flush; } return; } Eigen::Vector3d Forces::NumForceForward(Orbitals orbitals, Index atom_index) { Eigen::Vector3d force = Eigen::Vector3d::Zero(); // get this atoms's current coordinates double energy_center = orbitals.getTotalStateEnergy(_tracker.CalcState(orbitals)); const Eigen::Vector3d current_pos = orbitals.QMAtoms()[atom_index].getPos(); for (Index i_cart = 0; i_cart < 3; i_cart++) { Eigen::Vector3d displacement_vec = Eigen::Vector3d::Zero(); displacement_vec[i_cart] = _displacement; // update the coordinate Eigen::Vector3d pos_displaced = current_pos + displacement_vec; orbitals.QMAtoms()[atom_index].setPos(pos_displaced); _gwbse_engine.ExcitationEnergies(orbitals); double energy_displaced = orbitals.getTotalStateEnergy(_tracker.CalcState(orbitals)); force(i_cart) = (energy_center - energy_displaced) / _displacement; orbitals.QMAtoms()[atom_index].setPos( current_pos); // restore original coordinate into segment } // Cartesian directions return force; } Eigen::Vector3d Forces::NumForceCentral(Orbitals orbitals, Index atom_index) { Eigen::Vector3d force = Eigen::Vector3d::Zero(); const Eigen::Vector3d current_pos = orbitals.QMAtoms()[atom_index].getPos(); for (Index i_cart = 0; i_cart < 3; i_cart++) { XTP_LOG(Log::debug, *_pLog) << "FORCES--DEBUG Cartesian component " << i_cart << flush; Eigen::Vector3d displacement_vec = Eigen::Vector3d::Zero(); displacement_vec[i_cart] = _displacement; // update the coordinate Eigen::Vector3d pos_displaced = current_pos + displacement_vec; orbitals.QMAtoms()[atom_index].setPos(pos_displaced); _gwbse_engine.ExcitationEnergies(orbitals); double energy_displaced_plus = orbitals.getTotalStateEnergy(_tracker.CalcState(orbitals)); // update the coordinate pos_displaced = current_pos - displacement_vec; orbitals.QMAtoms()[atom_index].setPos(pos_displaced); _gwbse_engine.ExcitationEnergies(orbitals); double energy_displaced_minus = orbitals.getTotalStateEnergy(_tracker.CalcState(orbitals)); force(i_cart) = 0.5 * (energy_displaced_minus - energy_displaced_plus) / _displacement; orbitals.QMAtoms()[atom_index].setPos( current_pos); // restore original coordinate into orbital } return force; } void Forces::RemoveTotalForce() { Eigen::Vector3d avgtotal_force = _forces.colwise().sum() / double(_forces.rows()); for (Index i_atom = 0; i_atom < _forces.rows(); i_atom++) { _forces.row(i_atom) -= avgtotal_force; } return; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gaussian_quadrature/000077500000000000000000000000001412152066400205545ustar00rootroot00000000000000xtp-2021.2/src/libxtp/gaussian_quadrature/gauss_hermite_quadrature.cc000066400000000000000000000740171412152066400261700ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSe-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include "gauss_hermite_quadrature.h" // Gauss-Hermite quadrature points and adapted weights as exported from // https://keisan.casio.com/exec/system/1329114617 // with 50 digits namespace votca { namespace xtp { void Gauss_Hermite_Quadrature::FillPoints() { Eigen::VectorXd points_8(8); points_8 << -2.9306374202572440192235027052435991461994485855216, -1.9816567566958429258546306397693095686949116340382, -1.1571937124467801947207657790631002434520047595976, -0.38118699020732211685471888558369141763186003151966, 0.38118699020732211685471888558369141763186003151966, 1.1571937124467801947207657790631002434520047595976, 1.9816567566958429258546306397693095686949116340382, 2.9306374202572440192235027052435991461994485855216; _map_points[8] = points_8; Eigen::VectorXd points_10(10); points_10 << -3.4361591188377376033267254943191213848406783093902, -2.5327316742327897964089607977547934803078465081567, -1.7566836492998817734514012201061567632954744937389, -1.0366108297895136541774919167592090162982561106572, -0.34290132722370460878916502555725803120830265867773, 0.34290132722370460878916502555725803120830265867773, 1.0366108297895136541774919167592090162982561106572, 1.7566836492998817734514012201061567632954744937389, 2.5327316742327897964089607977547934803078465081567, 3.4361591188377376033267254943191213848406783093902; _map_points[10] = points_10; Eigen::VectorXd points_12(12); points_12 << -3.8897248978697819192716427472441917601481810141665, -3.0206370251208897717106793751767636460038065983103, -2.279507080501059900187728569424341135039156593214, -1.5976826351526047967096627709045767082402869887687, -0.94778839124016374370457813106013651367915379591455, -0.31424037625435911127661163409533712897211083832271, 0.3142403762543591112766116340953371289721108383227, 0.94778839124016374370457813106013651367915379591455, 1.5976826351526047967096627709045767082402869887687, 2.279507080501059900187728569424341135039156593214, 3.0206370251208897717106793751767636460038065983103, 3.8897248978697819192716427472441917601481810141665; _map_points[12] = points_12; Eigen::VectorXd points_14(14); points_14 << -4.3044485704736318126212981003689427253218103879463, -3.4626569336022705502089173611504324421390765376615, -2.7484707249854025686249985241464309299737954499322, -2.0951832585077168157349727263032374554797833544483, -1.4766827311411408705835065442050785826659377346378, -0.87871378732939941611467931186079607260338557501491, -0.29174551067256207844611307579938114089108844043221, 0.29174551067256207844611307579938114089108844043221, 0.87871378732939941611467931186079607260338557501491, 1.4766827311411408705835065442050785826659377346378, 2.0951832585077168157349727263032374554797833544483, 2.7484707249854025686249985241464309299737954499322, 3.4626569336022705502089173611504324421390765376615, 4.3044485704736318126212981003689427253218103879463; _map_points[14] = points_14; Eigen::VectorXd points_16(16); points_16 << -4.6887389393058183646884986487456108906323917275435, -3.8694479048601226987194240980148123970065994702497, -3.176999161979956026813994559263696476791667372742, -2.5462021578474813621593287054458941245194651994058, -1.9517879909162539774346554149598874927683260586599, -1.3802585391988807963720896696945820384406817699701, -0.82295144914465589258245449673394264076350817254127, -0.2734810461381524521582804019650150339298178803279, 0.2734810461381524521582804019650150339298178803279, 0.82295144914465589258245449673394264076350817254127, 1.3802585391988807963720896696945820384406817699701, 1.9517879909162539774346554149598874927683260586599, 2.5462021578474813621593287054458941245194651994058, 3.1769991619799560268139945592636964767916673727419, 3.8694479048601226987194240980148123970065994702497, 4.6887389393058183646884986487456108906323917275435; _map_points[16] = points_16; Eigen::VectorXd points_18(18); points_18 << -5.0483640088744667683720375788536521210964511478335, -4.2481178735681264630234201609020812454613481259571, -3.5737690684862660795006759937718894579393109766802, -2.9613775055316068447786325490618382146613988430531, -2.3862990891666860002645930142399451367070333328477, -1.8355316042616288922538394440906011492669936367257, -1.3009208583896173656662655543926105802181346396612, -0.7766829192674116613166594622838522947287132144905, -0.25826775051909675925811609871057963300171513532774, 0.2582677505190967592581160987105796330017151353277, 0.7766829192674116613166594622838522947287132144905, 1.3009208583896173656662655543926105802181346396612, 1.8355316042616288922538394440906011492669936367257, 2.3862990891666860002645930142399451367070333328477, 2.9613775055316068447786325490618382146613988430531, 3.5737690684862660795006759937718894579393109766802, 4.248117873568126463023420160902081245461348125957, 5.0483640088744667683720375788536521210964511478335; _map_points[18] = points_18; Eigen::VectorXd points_20(20); points_20 << -5.3874808900112328620169004106811207539962864490659, -4.6036824495507442730776752489783475851133984877619, -3.944764040115625210375628800524411807149768127888, -3.3478545673832163269149245229964636985104785902937, -2.788806058428130480525033756403185410670698887902, -2.2549740020892755230823333447345651280822653160264, -1.7385377121165862067808656621364064429514094196004, -1.2340762153953230078858183469594102295854459300694, -0.7374737285453943587056051442521042290772162039768, -0.24534070830090124990383653063361662396613385130349, 0.24534070830090124990383653063361662396613385130349, 0.73747372854539435870560514425210422907721620397679, 1.2340762153953230078858183469594102295854459300694, 1.7385377121165862067808656621364064429514094196004, 2.2549740020892755230823333447345651280822653160264, 2.788806058428130480525033756403185410670698887902, 3.3478545673832163269149245229964636985104785902937, 3.9447640401156252103756288005244118071497681278883, 4.603682449550744273077675248978347585113398487762, 5.3874808900112328620169004106811207539962864490659; _map_points[20] = points_20; Eigen::VectorXd points_40(40); points_40 << -8.098761139250850052012636369630536203159878558411, -7.4115825314854688094393004346606137838517548859766, -6.8402373052493554178458239138344048541844776615676, -6.3282553512200819556569910907660684038833769829979, -5.8540950560304001080427055883267519292216187560587, -5.406654247970127608400173980753063275682274386632, -4.9792609785452558716265182296182638236429580903587, -4.567502072844394855169482293577938174854843489872, -4.1682570668325002015364923207359804227827976573906, -3.779206753435223493119356115842927618490199421049, -3.3985582658596283462937862596982787619977026521078, -3.024879883901284437677049325341784266908327117963, -2.6569959984428957949808471006826969983518444487154, -2.2939171418750834218850495645276828751185935391695, -1.9347914722822957932979370652209982676235065775805, -1.5788698949316138862584512814687415071154993234949, -1.2254801090462890309490863830460385618165976626906, -0.87400661235708807743789879817524989268743615719011, -0.52387471383227719261491711165465674591655953342785, -0.1745372145975823834894506883588453187290397479542, 0.1745372145975823834894506883588453187290397479542, 0.52387471383227719261491711165465674591655953342785, 0.87400661235708807743789879817524989268743615719011, 1.2254801090462890309490863830460385618165976626906, 1.5788698949316138862584512814687415071154993234949, 1.9347914722822957932979370652209982676235065775805, 2.2939171418750834218850495645276828751185935391695, 2.6569959984428957949808471006826969983518444487154, 3.024879883901284437677049325341784266908327117963, 3.3985582658596283462937862596982787619977026521078, 3.779206753435223493119356115842927618490199421049, 4.168257066832500201536492320735980422782797657391, 4.567502072844394855169482293577938174854843489872, 4.9792609785452558716265182296182638236429580903587, 5.406654247970127608400173980753063275682274386632, 5.8540950560304001080427055883267519292216187560587, 6.3282553512200819556569910907660684038833769829979, 6.8402373052493554178458239138344048541844776615676, 7.4115825314854688094393004346606137838517548859766, 8.0987611392508500520126363696305362031598785584111; _map_points[40] = points_40; Eigen::VectorXd points_100(100); points_100 << -13.406487338144910138498015358651607145889756981295, -12.82379974948780890633912881377721549748456726861, -12.342964222859674295102740266870727507684215885999, -11.915061943114165801984797918762777070787192719624, -11.521415400787030241694215193615806787762300833732, -11.15240438558512526489903525035673867121886647691, -10.80226075368471459482166754925048490352246777013, -10.46718542134281214178313316357805048536805919779, -10.144509941292845469888588301440455941004734121264, -9.8322698077779690943551615313409315780947453926671, -9.5289658233901148046970657443074887808291687384498, -9.2334208902191615504779366283532133797467520910863, -8.944689217325474478798596807541288507747329552581, -8.6619961681345177143760754560127444328156251045127, -8.3846969404162650750860155396074513179782321306247, -8.112247311162791917211692013817029356168170316702, -7.84418238446082116879207953051081085258829182278, -7.5801008078574888842858087147798508005952446740541, -7.3196528223045353163320619830886983154201857246218, -7.0625310602488654374655227313402111369558533713012, -6.808463352858796414478980904321988789367313784202, -6.5572070319215393159801431092748363242153412136856, -6.308544361112135121638817415387415841889996789733, -6.06227883261430263866518460107768521940501572821, -5.818232135203517047362269817047869590598875519347, -5.5762416493299241033034851100970939533372038220982, -5.3361583601383604972771152654631793693757767432758, -5.09784510508913624700009193939928820181483169172, -4.861175091791210210046066849049651598903759210722, -4.6260306357871557730740379959854765524883917545046, -4.3923020786826840167447755690930260111118164084445, -4.1598868551310305400680411225876429394973862403352, -3.9286886834276709720095023242871466851524016002606, -3.6986168593184919397969539485760535948752486554752, -3.4695856364185891697681598371294103733559227855906, -3.2415136796310129503587732945183130796639221482042, -3.0143235803311555167151651485231965602581338238536, -2.7879414239819893131903676217409219127677228740981, -2.5622964023726080250560245984515873668232679322664, -2.3373204639068785050126227798659529280851747489535, -2.1129479963711879520297712999877086865700732258921, -1.8891155374270083714936395268915260054134381371616, -1.6657615087415094698666537171307433322798696612353, -1.442825970215932787702577716776781467558992104909, -1.2202503912189530588204931976741636515776285057147, -0.9979774360981052439241030610879289945935713461451, -0.7759507615401457819750658338752050281515312263498, -0.55411482359161698823299767239979854264076384558092, -0.33241469234223180704589884489338884776779165908485, -0.11079587242243948288755989392835521073522875550516, 0.11079587242243948288755989392835521073522875550516, 0.33241469234223180704589884489338884776779165908485, 0.55411482359161698823299767239979854264076384558092, 0.7759507615401457819750658338752050281515312263498, 0.9979774360981052439241030610879289945935713461451, 1.2202503912189530588204931976741636515776285057147, 1.442825970215932787702577716776781467558992104909, 1.6657615087415094698666537171307433322798696612353, 1.8891155374270083714936395268915260054134381371616, 2.1129479963711879520297712999877086865700732258921, 2.3373204639068785050126227798659529280851747489535, 2.5622964023726080250560245984515873668232679322664, 2.7879414239819893131903676217409219127677228740981, 3.0143235803311555167151651485231965602581338238536, 3.2415136796310129503587732945183130796639221482042, 3.4695856364185891697681598371294103733559227855906, 3.6986168593184919397969539485760535948752486554752, 3.9286886834276709720095023242871466851524016002606, 4.1598868551310305400680411225876429394973862403352, 4.392302078682684016744775569093026011111816408444, 4.6260306357871557730740379959854765524883917545046, 4.861175091791210210046066849049651598903759210722, 5.09784510508913624700009193939928820181483169172, 5.3361583601383604972771152654631793693757767432758, 5.576241649329924103303485110097093953337203822098, 5.818232135203517047362269817047869590598875519347, 6.0622788326143026386651846010776852194050157282098, 6.308544361112135121638817415387415841889996789733, 6.557207031921539315980143109274836324215341213686, 6.808463352858796414478980904321988789367313784202, 7.062531060248865437465522731340211136955853371301, 7.3196528223045353163320619830886983154201857246218, 7.580100807857488884285808714779850800595244674054, 7.84418238446082116879207953051081085258829182278, 8.1122473111627919172116920138170293561681703167016, 8.3846969404162650750860155396074513179782321306247, 8.6619961681345177143760754560127444328156251045127, 8.944689217325474478798596807541288507747329552581, 9.2334208902191615504779366283532133797467520910863, 9.5289658233901148046970657443074887808291687384498, 9.8322698077779690943551615313409315780947453926671, 10.144509941292845469888588301440455941004734121264, 10.46718542134281214178313316357805048536805919779, 10.80226075368471459482166754925048490352246777013, 11.152404385585125264899035250356738671218866476907, 11.521415400787030241694215193615806787762300833732, 11.915061943114165801984797918762777070787192719624, 12.342964222859674295102740266870727507684215885999, 12.82379974948780890633912881377721549748456726861, 13.4064873381449101384980153586516071458897569812959; _map_points[100] = points_100; } void Gauss_Hermite_Quadrature::FillAdaptedWeights() { Eigen::VectorXd AdaptedWeights_8(8); AdaptedWeights_8 << 1.0719301442479797564640154828686192710583035011087, 0.8667526065633812222177945178444721007823603317873, 0.7928900483864012509056467065099944670699652191022, 0.7645441286517291990713914850625153797906970121608, 0.7645441286517291990713914850625153797906970121608, 0.7928900483864012509056467065099944670699652191022, 0.8667526065633812222177945178444721007823603317873, 1.0719301442479797564640154828686192710583035011087; _map_AdaptedWeights[8] = AdaptedWeights_8; Eigen::VectorXd AdaptedWeights_10(10); AdaptedWeights_10 << 1.0254516913657372330206021439998001007206764041771, 0.820666126404816614571910879903882294986432537887, 0.7414419319435649700820477018891891603635366640119, 0.70329632310490617009834172682079856333223356450024, 0.68708185395127336268656718422692784453580030087846, 0.6870818539512733626865671842269278445358003008785, 0.7032963231049061700983417268207985633322335645002, 0.7414419319435649700820477018891891603635366640119, 0.8206661264048166145719108799038822949864325378872, 1.0254516913657372330206021439998001007206764041771; _map_AdaptedWeights[10] = AdaptedWeights_10; Eigen::VectorXd AdaptedWeights_12(12); AdaptedWeights_12 << 0.989699047092298099365013260061309904979902995276, 0.7866439394633224644915380743541227886372855230251, 0.7052203661122197557556715481998492923710656431374, 0.662662773266871319239255150461100359348980754644, 0.63962123202025660066934991623180131877302719880201, 0.62930787436949282103571883185136329069537833837549, 0.62930787436949282103571883185136329069537833837549, 0.639621232020256600669349916231801318773027198802, 0.66266277326687131923925515046110035934898075464401, 0.70522036611221975575567154819984929237106564313742, 0.7866439394633224644915380743541227886372855230251, 0.9896990470922980993650132600613099049799029952755; _map_AdaptedWeights[12] = AdaptedWeights_12; Eigen::VectorXd AdaptedWeights_14(14); AdaptedWeights_14 << 0.960878703025659256530957856273245078574670135086, 0.7599870873975660800632761513147237493826116686251, 0.677706759192397010397799872260068292400349536379, 0.63290060647233309082923787100002824017391731693, 0.6063797391260974872052603343591461156764643412857, 0.59110666704316242483025610616840494300223021601381, 0.58406169052199623900075832593066558843366126221565, 0.5840616905219962390007583259306655884336612622156, 0.59110666704316242483025610616840494300223021601381, 0.6063797391260974872052603343591461156764643412857, 0.6329006064723330908292378710000282401739173169296, 0.677706759192397010397799872260068292400349536379, 0.75998708739756608006327615131472374938261166862506, 0.960878703025659256530957856273245078574670135086; _map_AdaptedWeights[14] = AdaptedWeights_14; Eigen::VectorXd AdaptedWeights_16(16); AdaptedWeights_16 << 0.936874492884069357470004849342561171325068702881, 0.738245622277681359882790450735840033408093284309, 0.6557556728761177064705989221774875270966151707271, 0.6097369582559972856242997148163131018517144433067, 0.58124727540086389202624422184292731510412746076873, 0.5632178290881998377123686952648505613118715089659, 0.55244195736745939041573957443504654808920309409138, 0.54737520503784399928196163481039041583828307915463, 0.54737520503784399928196163481039041583828307915463, 0.55244195736745939041573957443504654808920309409138, 0.5632178290881998377123686952648505613118715089659, 0.5812472754008638920262442218429273151041274607687, 0.6097369582559972856242997148163131018517144433067, 0.65575567287611770647059892217748752709661517072711, 0.738245622277681359882790450735840033408093284309, 0.936874492884069357470004849342561171325068702881; _map_AdaptedWeights[16] = AdaptedWeights_16; Eigen::VectorXd AdaptedWeights_18(18); AdaptedWeights_18 << 0.9163935375519155947662880291953182438433621949995, 0.719993383105314144400021542382132236413335255132, 0.637630172006160187495403399833138046386032910798, 0.5909530034631081328753352419791538626101162669642, 0.561279045549804538746093740280135250066751747336, 0.54157867866213244558778798431831136530920994802962, 0.5285894429188008800743612444401935861230623382277, 0.5206349466760646162215527041692833691475359172075, 0.5168458364816212822612399422473770735127756668207, 0.5168458364816212822612399422473770735127756668207, 0.52063494667606461622155270416928336914753591720746, 0.5285894429188008800743612444401935861230623382277, 0.5415786786621324455877879843183113653092099480296, 0.561279045549804538746093740280135250066751747336, 0.590953003463108132875335241979153862610116266964, 0.637630172006160187495403399833138046386032910798, 0.7199933831053141444000215423821322364133352551319, 0.916393537551915594766288029195318243843362194999; _map_AdaptedWeights[18] = AdaptedWeights_18; Eigen::VectorXd AdaptedWeights_20(20); AdaptedWeights_20 << 0.898591961453191416420545454828522781943430553196, 0.7043329611769424087138204002833519583892017111602, 0.622278696191412280649317396569296403505856898279, 0.575262442852503182139156253731619647430862573735, 0.544851742364520005199359051276235186443829263999, 0.524080350948557612676557263766842812596750345434, 0.50967902711745800667286665991982639104787118706115, 0.4999208713362905172649779639324870322555667062887, 0.49384338527205292781460899199861133161984929633202, 0.49092150066674582427959429560835390391359129040998, 0.49092150066674582427959429560835390391359129040998, 0.493843385272052927814608991998611331619849296332, 0.4999208713362905172649779639324870322555667062887, 0.5096790271174580066728666599198263910478711870611, 0.5240803509485576126765572637668428125967503454339, 0.544851742364520005199359051276235186443829263999, 0.575262442852503182139156253731619647430862573735, 0.622278696191412280649317396569296403505856898279, 0.70433296117694240871382040028335195838920171116, 0.898591961453191416420545454828522781943430553196; _map_AdaptedWeights[20] = AdaptedWeights_20; Eigen::VectorXd AdaptedWeights_40(40); AdaptedWeights_40 << 0.79217343042479188987800095748798411535774567837, 0.613953703878935383944246291689536142504787739962, 0.536616531144795196536723170248508610918146786087, 0.490665384575827574543390365654021705490497311997, 0.459424375107941603710371577218345173808391179699, 0.436537482189441642164328468470713683872015807784, 0.4189698708431732031240293469237776265259205587382, 0.405060349154516337882290585279197190300142034582, 0.3938118403658963050929861777821223128111093983517, 0.384584951523524201762130019349088370018133158048, 0.376948948361650239259741281290406302051303489467, 0.3706026146575434159283205942344419468957845295787, 0.3653292765749101735525280685904706175318557190108, 0.3609698396280510762801426398148467820351636833947, 0.3574059229232464112539845210821416756728513979189, 0.3545489531398290125116992047959251509182701267523, 0.3523329389876451331367093201797921020267727439583, 0.35070961650094071619709743385068413742301776785814, 0.34964518840941309218045459186871590112941250662274, 0.34911818842117296421961593485789636945260602763304, 0.349118188421172964219615934857896369452606027633, 0.3496451884094130921804545918687159011294125066227, 0.35070961650094071619709743385068413742301776785814, 0.3523329389876451331367093201797921020267727439583, 0.3545489531398290125116992047959251509182701267523, 0.3574059229232464112539845210821416756728513979189, 0.3609698396280510762801426398148467820351636833947, 0.3653292765749101735525280685904706175318557190108, 0.3706026146575434159283205942344419468957845295787, 0.376948948361650239259741281290406302051303489467, 0.384584951523524201762130019349088370018133158048, 0.393811840365896305092986177782122312811109398352, 0.405060349154516337882290585279197190300142034582, 0.4189698708431732031240293469237776265259205587382, 0.436537482189441642164328468470713683872015807784, 0.459424375107941603710371577218345173808391179699, 0.490665384575827574543390365654021705490497311997, 0.536616531144795196536723170248508610918146786087, 0.61395370387893538394424629168953614250478773996, 0.79217343042479188987800095748798411535774567837; _map_AdaptedWeights[40] = AdaptedWeights_40; Eigen::VectorXd AdaptedWeights_100(100); AdaptedWeights_100 << 0.6743535524209081439144025322357969381272017071, 0.518506807270200187726050665111323503038427962204, 0.4499931710544165907648101872521147551333758224, 0.40868865844190154714613837503957915906257950342, 0.38013743880057595596193666992410590336797709384, 0.3588184090711120834491848927844103303232485607, 0.34208926231424714546011050858620558080828493449, 0.32849948464545747856020223747214567572843775586, 0.31717511097185385937581657915597613681593413933, 0.307552728501673729425021966433176174327683014141, 0.299249958039079093578440327494018648052919217681, 0.291996563960276082259823793494679455502968596256, 0.2855952145313678849370074481368712583044532496687, 0.279897872545084658580480609338457328739955191921, 0.274790938326829146069468993027033265118124824608, 0.27018554353399078770286477498189887309588469265, 0.266011005285956696413087151450559093401633842281, 0.262210289443758959517549614653266828478241448795, 0.258736790904380865770764353737768989580456052256, 0.255552000562019435279616540371000633519831808597, 0.252623783391417573284153133498430447377859549676, 0.249925086601289282222331416606355747401733716912, 0.247432956126835293415851674773995121032599185583, 0.245127777913567834895395123882781470007877207313, 0.242992685579107730478061435462116976292893659945, 0.241013092922387224180078423754952089502145990545, 0.239176321299559035958881946763582668655766586888, 0.237471299920461647510524395875446862597050976355, 0.235888322794699254658347185155053993143790400688, 0.234418850121758228317060808304373017810627782989, 0.233055344869710310073633127854054318689174911742, 0.2317911374537038421006636685636535230105612914491, 0.230620313034512848757842867301380704437147086747, 0.229537617164869894480798355881041685000969115206, 0.2285383764262468035420204238669485174237681995155, 0.2276184313984020656428194886871545920347032826, 0.22677407984368572366352959998646567756517227542359, 0.226002028407800085009415685138971573253587753407, 0.2252993514677081961876097873053529240523027388728, 0.2246634560172451970005387549736599871520685064234, 0.2240920516877911097339302674236748167112933999977, 0.2235831251671776091962776632918640772865666868697, 0.2231349184139684965646673456144631502542687237661, 0.2227459101733572351354113660822711481187881733362, 0.22241480039054435089974751581529092250163484713076, 0.2221404971917734901660652328308870403188519987264, 0.2219221061654981101361923007519455534479680431397, 0.2217589217290237858046220853815951121613060743657, 0.2216504204115155471103158805118085904679336523634, 0.22159625592418327022113796043197491110732147551622, 0.22159625592418327022113796043197491110732147551622, 0.22165042041151554711031588051180859046793365236339, 0.2217589217290237858046220853815951121613060743657, 0.22192210616549811013619230075194555344796804313971, 0.22214049719177349016606523283088704031885199872643, 0.2224148003905443508997475158152909225016348471308, 0.2227459101733572351354113660822711481187881733362, 0.22313491841396849656466734561446315025426872376614, 0.22358312516717760919627766329186407728656668686975, 0.2240920516877911097339302674236748167112933999977, 0.2246634560172451970005387549736599871520685064234, 0.2252993514677081961876097873053529240523027388728, 0.2260020284078000850094156851389715732535877534075, 0.226774079843685723663529599986465677565172275424, 0.2276184313984020656428194886871545920347032826002, 0.2285383764262468035420204238669485174237681995155, 0.229537617164869894480798355881041685000969115206, 0.2306203130345128487578428673013807044371470867471, 0.2317911374537038421006636685636535230105612914491, 0.233055344869710310073633127854054318689174911742, 0.234418850121758228317060808304373017810627782989, 0.235888322794699254658347185155053993143790400688, 0.237471299920461647510524395875446862597050976355, 0.2391763212995590359588819467635826686557665868877, 0.241013092922387224180078423754952089502145990545, 0.242992685579107730478061435462116976292893659945, 0.245127777913567834895395123882781470007877207313, 0.247432956126835293415851674773995121032599185583, 0.249925086601289282222331416606355747401733716912, 0.252623783391417573284153133498430447377859549676, 0.2555520005620194352796165403710006335198318085972, 0.258736790904380865770764353737768989580456052256, 0.262210289443758959517549614653266828478241448795, 0.266011005285956696413087151450559093401633842281, 0.270185543533990787702864774981898873095884692651, 0.274790938326829146069468993027033265118124824608, 0.279897872545084658580480609338457328739955191921, 0.2855952145313678849370074481368712583044532496687, 0.291996563960276082259823793494679455502968596256, 0.299249958039079093578440327494018648052919217681, 0.307552728501673729425021966433176174327683014141, 0.31717511097185385937581657915597613681593413933, 0.32849948464545747856020223747214567572843775586, 0.34208926231424714546011050858620558080828493449, 0.358818409071112083449184892784410330323248560695, 0.38013743880057595596193666992410590336797709384, 0.408688658441901547146138375039579159062579503416, 0.44999317105441659076481018725211475513337582239, 0.518506807270200187726050665111323503038427962204, 0.6743535524209081439144025322357969381272017071; _map_AdaptedWeights[100] = AdaptedWeights_100; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gaussian_quadrature/gauss_hermite_quadrature.h000066400000000000000000000027511412152066400260260ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #ifndef VOTCA_XTP_GAUSS_HERMITE_QUADRATURE_H #define VOTCA_XTP_GAUSS_HERMITE_QUADRATURE_H #include "votca/xtp/GaussianQuadratureBase.h" namespace votca { namespace xtp { class Gauss_Hermite_Quadrature : public GaussianQuadratureBase { public: double ScaledPoint(Index i) const final { return points_[i]; } double ScaledWeight(Index i) const final { return weights_[i]; } protected: // The hermite quadrature method is suitable for integration limits a = // -infty b = +infty. Here we don't do any modification to the original // hermite quadrature method. Points and weights are not transformed bool UseSymmetry() const final { return false; } void FillPoints() final; void FillAdaptedWeights() final; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_GAUSS_HERMITE_QUADRATURE_H xtp-2021.2/src/libxtp/gaussian_quadrature/gauss_laguerre_quadrature.cc000066400000000000000000000732741412152066400263450ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSe-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include "gauss_laguerre_quadrature.h" // Gauss-Laguerre quadrature points and adapted weights as exported from // https://keisan.casio.com/exec/system/1329114617 // with 50 digits, alpha=0 namespace votca { namespace xtp { void Gauss_Laguerre_Quadrature::FillPoints() { Eigen::VectorXd points_8(8); points_8 << 0.17027963230510099978886185660829724468251824708548, 0.9037017767993799121860202235550898922166525972985, 2.2510866298661306893071183669686351538381871358948, 4.2667001702876587936494218269006396344821222793532, 7.0459054023934656972793254821193584980087387492524, 10.758516010180995224059956788032034147832602219141, 15.740678641278004578028761158402835874146032041614, 22.863131736889264105700534297413109554793146730361; _map_points[8] = points_8; Eigen::VectorXd points_10(10); points_10 << 0.1377934705404924308307725056527111881079916807458, 0.7294545495031704981603731216760787810760727333122, 1.8083429017403160482329200757506088332830602823715, 3.4014336978548995144825322214083906792731566142035, 5.5524961400638036324175584868687628579740642873178, 8.330152746764496700238767197274522182709438972031, 11.843785837900065564918538919141613985802816909465, 16.279257831378102099532653935833622335255995603033, 21.996585811980761951277090195594493976806732340002, 29.920697012273891559908793340799195179710670577518; _map_points[10] = points_10; Eigen::VectorXd points_12(12); points_12 << 0.11572211735802067526719642824049422371981805287062, 0.6117574845151306653916300530416698801066213555077, 1.512610269776418786781737926866697246973609916394, 2.8337513377435072286274717765721434586744749567016, 4.5992276394183484846057292248505333063864850146524, 6.8445254531151773477543304184938407896643044488694, 9.6213168424568670439123823492309910941421457731566, 13.006054993306347720346052429401001984505838945536, 17.116855187462255728184052800759193917914019230472, 22.151090379397005669921895083663788010407725298709, 28.48796725098400031256860723252153419851162040233, 37.099121044466920336638914276358111888993336604802; _map_points[12] = points_12; Eigen::VectorXd points_14(14); points_14 << 0.0997475070325975745736829452514337328496035798394, 0.5268576488519028964045834515021405172634500388511, 1.3006291212514964817084202211569857435644440547503, 2.4308010787308446361699975103839831795758034729374, 3.93210282229321888213134366777639017436772314625, 5.825536218301708419338999838984992693945922492875, 8.1402401415651450300597804605200400135811494427105, 10.916499507366018840813051090408562918776029134103, 14.210805011161288683105978082509492366054109733828, 18.104892220218098412554627208297871875299155685169, 22.723381628269624823228088698478093397573388953516, 28.272981723248205695415892321792259432913212010101, 35.149443660592426582864312136374578367282950253361, 44.366081711117423041631242366563175586953058001708; _map_points[14] = points_14; Eigen::VectorXd points_16(16); points_16 << 0.0876494104789278403601980973401034621419572269307, 0.462696328915080831880838260664253790647713617829, 1.141057774831226856877945018105178437344393273812, 2.129283645098380616326159070658178825103674723855, 3.437086633893206645235107016751850636368112142398, 5.0780186145497679129230583081419290650410566835825, 7.0703385350482341303959894708013377973907115507906, 9.4383143363919387839472467291128233157596833315712, 12.214223368866158736939124608824202825826006388601, 15.441527368781617076764774162213510172456158693868, 19.18015685675313485466314094973963152074358424594, 23.515905693991908531823187275156254224431439633643, 28.578729742882140367520613709877699560720238612648, 34.583398702286625814527687177752583364021196976611, 41.940452647688332635472233025186596374902502248119, 51.7011603395433183643426971196738666271015706498; _map_points[16] = points_16; Eigen::VectorXd points_18(18); points_18 << 0.0781691666697054712986747615334420233702209795519, 0.4124900852591292910391015365358187181177146313242, 1.0165201796235396891909368618668855701206401569414, 1.894888509969760914267278319541264842564557062806, 3.054353113202659751152411307188873720946276545317, 4.5042055388898928263379557145489659831509941873015, 6.2567250739491114527420911632631325424397973997244, 8.3278251566056300217047026156366702569736425802806, 10.73799004775760933521790333966296316427852438555, 13.513656207555089819086381210822127397981969779753, 16.689306281930105937818398416274447581466477919728, 20.310767626267742856131376455327358444583306013385, 24.44068135928370276564422579804482604635135712019, 29.168208662579616131298067780459902617589068898445, 34.627927065660172145401242943827329353360610031535, 41.041816772808758139294861428387138227755853533312, 48.833922716086522748658609329001988025490585699449, 59.090546435901250703715781018076865483458403075406; _map_points[18] = points_18; Eigen::VectorXd points_20(20); points_20 << 0.0705398896919887533666890045842150958693606298353, 0.3721268180016114437942413887611466366740282101562, 0.916582102483273564667716277074183187205604198043, 1.7073065310283438806876896674130507061879399482153, 2.7491992553094321296450304604948133842756169174058, 4.0489253138508869223749533691333321965066524470376, 5.6151749708616165141045398856518923479177568766444, 7.4590174536710633097688602183718175953844771201739, 9.594392869581096772473672734282798378150637894214, 12.038802546964316309623409298865515868227553873675, 14.814293442630739978512679710047975674250757105644, 17.948895520519376017365790992612509648678004429199, 21.47878824028501097573517036959466921620975569711, 25.451702793186905503518677484641541838163511223646, 29.932554631700612006713656135165823251660560350598, 35.013434240479000006284935906688139581765928732597, 40.8330570567285710620295677078075526717076597492, 47.619994047346502139941627152851121113143970342575, 55.810795750063898890750773444497235628385311248334, 66.524416525615753818640318791460665979634913005697; _map_points[20] = points_20; Eigen::VectorXd points_40(40); points_40 << 0.0357003943088883851220844712866008554471707628149, 0.18816228315869851600358934621909591394293666113791, 0.462694281314576453564937524561190364453607375302, 0.859772963972934922257272224688722412787336248772, 1.3800108205273371864980003295952655980266946580187, 2.024209135922826733442066002800130755138249586785, 2.79336935350681645765351448602664039646411766026, 3.688702677908270209591526351908686985322684278108, 4.7116411465549726936187228362774736997704383014234, 5.863850878343718114273164237995829873706333665906, 7.147247908102288250685691951979423627162742562622, 8.564017017586163762718522042088132329834223235875, 10.116634048451939406849629656395244803078763144976, 11.80789229400458484284158670436063044361624976829, 13.640933712537087228371676360650120272664977583724, 15.619285893339073837201963652188014575529877065963, 17.74690595009566304257387749542437728612928336178, 20.028232834574890529612614810175117254644494661203, 22.468249983498418351371786228994536610130643377903, 25.072560772426203794396086209400976984928647204804, 27.84748000916886272075170414045579970497710334522, 30.800145739445462700754385196191111466806525240079, 33.938657084913719609098858586281999025873238496244, 37.272245880476004328320760990607420709008825810101, 40.811492823886920466155675581600642667953251587249, 44.568603175334462707123020634498355945521081304283, 48.557763533059992280962048806706793661448765941115, 52.795611187216932969352021137391763864681330119913, 57.301863323393627495033746995892165165394807293789, 62.100179072775111612168199057898992128296274498277, 67.219370927126998799080277551888705482491990862762, 72.695158847612462117521927724261938587543180945972, 78.572802911571309280543896833481259682513746165071, 84.911231135704984542701564709666318673805455422378, 91.789874671236376992337193480627315365272611690889, 99.32080871744680825010905416548681232546713909599, 107.67244063938827252079676761132266456489436636241, 117.12230951269068880765064412355070215650915273018, 128.20184198825565119254110438963126356905018343001, 142.28004446915999788834883535954176420971149849241; _map_points[40] = points_40; Eigen::VectorXd points_100(100); points_100 << 0.014386146995419669464436032421084281688512050966, 0.075803612023357124642993170677619621890564537719, 0.186314102057187173711460039042000603546202143312, 0.345969180991429090805378304989176665916272749467, 0.554810937580915509598340862968475972057253331879, 0.812891284115668845038081302089693108916678219316, 1.120273835007540148567503208138516870987060387277, 1.4770343299238270697185615900119702038820488303, 1.883260826342394705801824648360138069613386116537, 2.339053849646034171844423329865789475081345368214, 2.844526542755359066517119246955045643779362386548, 3.399804827445711944287159094946990679966759356644, 4.005027581758652017464900403271417436365020069786, 4.6603468355689084595040280266228479367781522394339, 5.3659279855851170148835307002113124177735600130764, 6.121950030804019789061373794621522567393863248656, 6.928605829376173055020578689898725880965610515716, 7.786102377862517434336654189095964321122329875985, 8.69466111392216798920445606412688315055307201065, 9.654518243555080727805574157972236574607597645112, 10.665925094121675550534495350158743760803952603248, 11.729148494472225071619721912253497544647053283665, 12.844471183641030571565638150584109591717836412828, 14.012192249694274648964132308316289629464199959767, 15.23262760046669784302041550956226051576480325499, 16.506110468081989594185016055271767580375606202441, 17.832991949326387429842546114269676532212047749239, 19.213641584136066684901496749658987824327097324692, 20.648447974668349519654447808348566296686549680439, 22.137819447656704406552716077390543723572214396682, 23.682184763002376100171887646238319774521954316415, 25.281993871834041538775185811767894692106599605973, 26.937718727574264943554420821563356298284635311442, 28.64985415389129217109679221074678696489104285425, 30.418918773790942919595713617048104452697898639485, 32.245456004520665842270490683432751487625800550655, 34.130035123421516471287278120181406582083089466876, 36.07325241037997322620358475807515539192546120546, 38.07573237310709319104533518730924429731326579851, 40.138129062115545763233678737698828135667518753993, 42.261127482984794178411494933871743845349357073648, 44.445445114311806077478838491178111032087024891251, 46.691833540651539419116010770581151491879821535361, 49.001080210772436956028200619659191741327940749713, 51.37401033270399452135984751304564700967634136002, 53.811488918355660438291791945942420574999135872589, 56.314422991961708237686384235697436356533205469116, 58.883763978282090293706081105456788791980697773486, 61.520510288396142646799262555210088301307405134792, 64.225710123101560166967699113534070019919296344492, 67.000464516419311596764254278099751432705630830302, 69.845930644558374286446832951544745923856156790577, 72.763325428974586256338515260247046548202678094156, 75.753929465939936192709187121887367163951952654792, 78.81909131941147219953449711916410052905582603643, 81.960232219060124004406034433922871748963999777354, 85.17885121121890019965819425201152285085863371472, 88.47653081739461122166173313351549931817562325053, 91.85494326304930893124588349974424058207792737754, 95.31585734883172060708188049803719081708348511971, 98.861146047613527716885852139755277900476209073942, 102.49279492391656096335151490724171601197400288973, 106.21291148804681620553193500890842029564387560101, 110.02373561603091696044095567254651297506815777452, 113.92765118897162371111095615952688206853431374889, 117.92719913257322683566930153317598472314768078915, 122.0250920704416210770071192771802129977882374398, 126.22423084475038757481282514568521751638696104949, 130.52772320679941326555235618477155948740904346682, 134.93890504022740757717591916185365596931353150412, 139.46136455424015676483735784559273942265772179158, 144.0989699772127241580660709688897260659410534834, 148.85590139775824946113745249503385376533217593335, 153.73668754797303061104508345523147446924144789121, 158.74624851171310443390313484523534639226550232703, 163.88994558258723283156168509187096508290147957381, 169.17363981000302458051369125544383162038737281778, 174.60376118237662671452586450128250401592779770557, 180.18739094024569619468544567349296547541064513326, 185.93236023966697143161396472939190679919308665195, 191.84736937224832912467163514693758170098662143982, 197.94213310214325740605535167367820592237967945187, 204.22755956703050772080095334034491093971825741861, 210.71597286157694337066830974235388351439277499162, 217.42139327200148109611632514213232315501173179011, 224.35989478887460814536094305461044256748650339089, 231.550068025172484218832989049761250273162951332, 239.01362975131492446798893533792714879336168509609, 246.77624096724849045732253704645704530192569180271, 254.86862925704743027863842226837592454026841223628, 263.32816846915789310981244461061198767500418420254, 272.20117002409253682587551568880510333756002327315, 281.54632828389738879914802558930339720242714802028, 291.44013361637710726069724339449220378847267906566, 301.98585525163915366574517831621556837970610886064, 313.3295340040755243411836472127284809659746476805, 325.69126343702652000203534998873955161221810012847, 339.43510192344961653520496673232150915962334632322, 355.26131188853413247248270949708161897245257424477, 374.98411283434267870488403679649642050330116428623; _map_points[100] = points_100; } void Gauss_Laguerre_Quadrature::FillAdaptedWeights() { Eigen::VectorXd AdaptedWeights_8(8); AdaptedWeights_8 << 0.4377234104929113732325975801238703103376631775236, 1.033869347665597642499265855827602461954335024897, 1.6697097656587757491539220177008427856051063662388, 2.3769247017585994809591690994750058720662557571753, 3.2085409133479262842483918457600300070144929506379, 4.268575510825132198584121630659636092804766871837, 5.81808336867192192828814196198241067161659726355, 8.906226215292211406501042881028511446149064456402; _map_AdaptedWeights[8] = AdaptedWeights_8; Eigen::VectorXd AdaptedWeights_10(10); AdaptedWeights_10 << 0.354009738606996308762226891442067608352461375232, 0.8319023010435807381098296581278495772769414887138, 1.3302885617493281787527921943939936989529079083161, 1.8630639031111309897639887354824669365659029551084, 2.4502555580830101660726937316575225674840723086896, 3.122764155135182496150818263314554723390177279479, 3.934152695561521098655812459248230777449846058056, 4.99241487219302310201148565243315445132156715098, 6.57220248513080297518766871037611234659532162923, 9.7846958403746306947700866387185981389150975238; _map_AdaptedWeights[10] = AdaptedWeights_10; Eigen::VectorXd AdaptedWeights_12(12); AdaptedWeights_12 << 0.29720963604441079779198122036754357695062747309614, 0.6964629804305972306780669558553119367200522247323, 1.1077813946157521533394673801418981284103516456771, 1.5384642390428291247940386335053805911722249486239, 1.9983276062742427651969640965367302175914220369978, 2.5007457691008668747508706633043160797088609808069, 3.065321518282386236204603418051038424900531165525, 3.723289110782771599995609779712930189226527287525, 4.529814029981735062093311912367881036129552807779, 5.5972584618353210926905239085094747371049317491765, 7.2129954609258770081711351665202483272292177775714, 10.543837461910081111715846770154439584665010094888; _map_AdaptedWeights[12] = AdaptedWeights_12; Eigen::VectorXd AdaptedWeights_14(14); AdaptedWeights_14 << 0.25613115473690945367155604137236094757882153053717, 0.5991704774951183385157662720719434606317389384044, 0.9499715024749579869125484270936094947507661292047, 1.3128078114661639384270884248489802423178192160109, 1.6932659907519653529745410676462360050266873059999, 2.098409084271843687773502577270101983723504094644, 2.5376326549353938448820099657512096366218759469362, 3.0241599177032399386467951716218970800189870315433, 3.577804355719859916426068792226390777216598510176, 4.230565034906432048949948938499946279885083169143, 5.0394133684635116188297693664760942153547229583944, 6.120947928329725523704405649801959608037466565982, 7.7742953670060321174893698342712637506928074474584, 11.21683421670331968972355415696472732866015480776; _map_AdaptedWeights[14] = AdaptedWeights_14; Eigen::VectorXd AdaptedWeights_16(16); AdaptedWeights_16 << 0.2250363148642472519066007573814144458690185247157, 0.5258360527623424536145694105195410860858136585704, 0.831961391687087087665388515060005798365531503267, 1.1460992409637517046479569302568902959453778405277, 1.471751316966808588743042045866684543762434226604, 1.813134687381348164887396108630316034513537481787, 2.1755175196946074520626708322288638779797078925836, 2.565762750165029209248616884561986932692202919775, 2.993215086371375165178025151565561897712713600071, 3.471234483102090290873868627597548190602231270141, 4.020044086444668866478284115357455952539428504624, 4.672516607732854267365709256517417593833911905772, 5.48742065798615247120752800022638302859933708972, 6.58536123328921366083470226903840093817534637811, 8.27635798436423448649507548525324886996687288917, 11.82427755165843478668777351092777039548497478358; _map_AdaptedWeights[16] = AdaptedWeights_16; Eigen::VectorXd AdaptedWeights_18(18); AdaptedWeights_18 << 0.2006779892089060424567117353858677921357410065508, 0.4685526868918793123451038404723618531476174159314, 0.7402656826535084821328848952165180073326729046531, 1.0175917173039668575733601963884569464681833491062, 1.3028787020654185274613294165010989084158853049221, 1.598862139757241971464163626319250748097864369331, 1.908813906969691449405383185790548603253747095167, 2.236777877856928862808745488037440092537055724348, 2.587924166792750465265463240542766432247187473213, 2.969102377726253026889997545139828219911420194409, 3.389748873854004693214943133356206203447866755699, 3.863462276042960583502177219572994264901461070218, 4.4109368969663167872945574616798809600665149029142, 5.0659315146113905979769671798325064724279803521, 5.888946263673389544438677676632267647722417256986, 7.00435926919015216807565159336225208655434075251, 8.73234485076647154208563069167393633193242434362, 12.379906492173747450634250720326202919731298778298; _map_AdaptedWeights[18] = AdaptedWeights_18; Eigen::VectorXd AdaptedWeights_20(20); AdaptedWeights_20 << 0.1810800624189892554516754059131106442274690763912, 0.4225567678785639745203441725664581975475829520687, 0.6669095467018481503734821149925159278667309548724, 0.91535237278307367267060468477186806700815510543294, 1.169539707195545973801478222395774760596840666293, 1.4313549859282059863684499489151433158764096086852, 1.7029811379850227240253326163320672029093050496994, 1.9870158907927472141092183927512902068826472595247, 2.2866357812534307854622285468149565116091533479661, 2.605834727553833332694989509540333237056796189593, 2.949783734213950866002354168272859510783865111907, 3.325395782009319552369519374217511185662934568037, 3.742255470589810921117072932653778117460980980766, 4.214236710251880419868080637824787464513838141909, 4.7625184614902092969529219783909637106473444797488, 5.42172604424557430380308297989981779213794759508, 6.254012356932421292895184903007075421492954607332, 7.38731438905443455194030019196464791168876917979, 9.1513287309874796079434824255295052861521913541, 12.89338864593999667102628712874852788017020483556; _map_AdaptedWeights[20] = AdaptedWeights_20; Eigen::VectorXd AdaptedWeights_40(40); AdaptedWeights_40 << 0.0916254711574598973115116980801374830365200986836, 0.213420584905012080007193367121512341186179067974, 0.3357181166802846738805107016162921911147717694494, 0.458540935033497560385432380376452497081119061553, 0.582068165779105168990996365401543283733186743579, 0.706495216367219392989830015673016682193654834516, 0.832026903003485238099112947978349523568841199324, 0.958878198794443111448122679676028906726062837454, 1.087276162030549715753869333172026615810409829194, 1.217462327977780978954277850665609480465428924915, 1.349695491356765307923938594423945197288932007748, 1.484254929776846711205611786129787199493824011776, 1.621444162811821978023168843164545274346126922021, 1.761595374676769611184242204209815983710518506098, 1.905074665894799676682993205972793710682835087884, 2.052288347261716717601995822729474548137376825858, 2.203690553245095889098283443281405707821460447477, 2.359792538523203323540373753789014974182625221262, 2.52117414037643299165313690287422820905783991025, 2.688498055408842264159505447063746594807941918888, 2.86252781321044881203476395983104311306154633077, 3.044150665311517100410439679543336703973242206997, 3.23440709726353194177490239428867111728031920006, 3.434529398427748092203984818916024646916862068008, 3.645992824994089072389656466994904343809662531182, 3.87058459721651656808475320213444338362887384907, 4.110498680432822655835822472639515778885674143888, 4.368468723254063474508083382729450258024161759933, 4.647958984074466882993033998838839914922868269628, 4.953446112409893262186961507855627211243793964933, 5.29084840590073657468737365718858968797061461384, 5.6682046090329767700073052902326379530552220105, 6.09679641474342030593376010859198806113486222265, 6.5931088610399995379442966420629489948229766364, 7.18249599553689315064429801626699574805948127705, 7.90666631138422877369310742310586595207240931369, 8.8408924928103465207912559506302679230302350146, 10.140899265621169483909460030694046881974765591424, 12.2100212992046038985226485875881108283678273395, 16.7055206420242974052468774398573553754649199408; _map_AdaptedWeights[40] = AdaptedWeights_40; Eigen::VectorXd AdaptedWeights_100(100); AdaptedWeights_100 << 0.036919939314547993881411785214888485896408070178, 0.085951345725921354135990924868356400493487728672, 0.135076347286164061380903423701488222323509920067, 0.18424069956500730763515611045153438123420901536, 0.233451446141280421726906433541098297782059647888, 0.28271984378164452166765828810799230979069262623, 0.332057878360216896843505523780141522959956311767, 0.381477785290452047783996464882101347652677523895, 0.4309919593063252143972900109238281606554216676206, 0.480612941774710562374542466481313693916004476049, 0.530353428454059705976212135958878058886203752295, 0.580226284010330321332297246994356768853677882931, 0.63024455934702059951914237468401709830071704533, 0.68042151046961384158215799299580215089372074938, 0.730770618450149419897166429251690351648882034684, 0.781305610360941494961702615201237067787428097553, 0.832040481168061617092076323421497989838424916826, 0.882989516630006835954003431788219599674293552765, 0.934167317275462090638034483929486051066217574924, 0.985588823551736637706762160364386467486652955625, 1.0372693422487070230494163082479985350150057702521, 1.089224574314770659472812292635101126468618318508, 1.141470644192765260846350193420878561006121196887, 1.194024130815760643630623389727696108291878550321, 1.246902100415515737648505971195490501063080698034, 1.300122141310523765763021097644413083208941452559, 1.353702400856200406404346064734008611910072522262, 1.407661624757148877662670634449416711756276873725, 1.462019198960816763259891977082157114019744626717, 1.516795194373519038111937959022904946132806912385, 1.57201041466404978255907267231170589495260804105, 1.6276864474472926795735582160956270956033979368468, 1.683845719170769181037062706048741254899306968308, 1.74051155406139488512397405993551058588800738583, 1.79770823752838185465489271776462776700539093959, 1.85546108446184368636142438074010649734772712993, 1.913796512915946137866124553334737389568205110832, 1.9727421237212305102695270688534115024955631232, 2.03232678663398894964699721426813759067704816851, 2.092580733702422741127790667525935681511769901181, 2.153535660611092763626554412553049029424553589998, 2.21522483685843270335206736771632828878904007948, 2.277683225728673326560951980410239299471364901114, 2.34094761514158333504710567029468641076319619039, 2.40505676060352910278329872190109014853553100971, 2.47005154164453003175936905334214490878499684225, 2.535975133311854335028037539441752220500758674359, 2.602873194505578443435540234848129523033281189732, 2.67079407519059121350487787156041193967117731043, 2.73978904480897194900172018389199775325192879835, 2.809912544553994824809190226076611155801321069926, 2.88122246656126652759829186429290041522720167509, 2.953780463534681133761979169028734526486376056522, 3.02765229286837076391544591428890651083221240119, 3.10290819996702722873408871139926032371457466251, 3.179623346225993050324893810613027585606588759611, 3.257878288034191592106495855475619784103229735143, 3.33775951423803577760395212328103289475657186609, 3.419360050791192654002128918178660903797399824829, 3.50278014286134288006695937350393743001467680905, 3.58812802653100352895504815759839456814914074701, 3.67552080449106105248863502792598863378447655371, 3.76508544287940603301012089832773991633022777601, 3.85695990978628010269605292991101785239883526691, 3.95129448009112296084307036672160806471066926881, 4.0482532364178323226774084353033824824584795888, 4.148015802363327800283217965659424505144203627, 4.25077935211810823679244285911473002867150328221, 4.35676095061938881015332624766758181161075110746, 4.4662002910728123140682652081693688026931978903, 4.5793629128737134860710534049674256082614409809, 4.69654400377203816014949848028435319129961819588, 4.818072917085036874367185628110070458006756218799, 4.9443185699788779059690863394992470599680683382, 5.07569593525772318594608473360804631585257908599, 5.2126739008686592812700632612806578879833718487, 5.3557848543812506505899489634111827300758848891, 5.50563646260515840395904881800378313745499826371, 5.66292627184206617136093917590945315654921401784, 5.8284599707478626267550272499964217588615910285, 6.0031744637308038046675056588524992684773765788, 6.1881673418494502515482985241631252441776326098, 6.38473497877833257922556337937364859708426786636, 6.59442243137378965949994484175831143637091800474, 6.8190897678626761187705731803546190954400691021, 7.0610016850025108248539626653847334668443258116, 7.3229508340958450093743595039249411445506666067, 7.6084310939560134731201323844713799936804871328, 7.9218868481886084532598211126972930825882055048, 8.26908150662496626475912882963165557215374477667, 8.6576598589739272079300448307223675419606791724, 9.0980388945229258193407011282410192762091851171, 9.6048835568654946122141762477038050760639011679483, 10.1996888715856386588309545606214683570029238436, 10.9156175227240176758109193524478890157747729336, 11.8073985027212477121628818445333081213822488404, 12.9741341509108123920094390653061654897178622626, 14.6215810644517865930437346381411571489579913595, 17.2847396480859001324847059640491782072314462628, 23.1715523384710306176727561011713184686190876643; _map_AdaptedWeights[100] = AdaptedWeights_100; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gaussian_quadrature/gauss_laguerre_quadrature.h000066400000000000000000000027231412152066400261760ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #ifndef VOTCA_XTP_GAUSS_LAGUERRE_QUADRATURE_H #define VOTCA_XTP_GAUSS_LAGUERRE_QUADRATURE_H #include "votca/xtp/GaussianQuadratureBase.h" namespace votca { namespace xtp { class Gauss_Laguerre_Quadrature : public GaussianQuadratureBase { public: double ScaledPoint(Index i) const final { return points_[i]; } double ScaledWeight(Index i) const final { return weights_[i]; } protected: // The laguerre method is suitable for integration limits a = 0 b = // +infty. Here we have value1 and value2 because we split the original // integral from -infty to +infty in two parts bool UseSymmetry() const final { return true; } void FillPoints() final; void FillAdaptedWeights() final; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_GAUSS_LAGUERRE_QUADRATURE_H xtp-2021.2/src/libxtp/gaussian_quadrature/gauss_legendre_quadrature.cc000066400000000000000000000750031412152066400263140ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSe-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include "gauss_legendre_quadrature.h" // Gauss-Legendre quadrature points and adapted weights as exported from // https://keisan.casio.com/exec/system/1329114617 // with 50 digits namespace votca { namespace xtp { void Gauss_Legendre_Quadrature_Base::FillPoints() { Eigen::VectorXd points_8(8); points_8 << -0.96028985649753623168356086856947299042823523430145, -0.79666647741362673959155393647583043683717173161597, -0.52553240991632898581773904918924634904196424312039, -0.18343464249564980493947614236018398066675781291297, 0.18343464249564980493947614236018398066675781291297, 0.52553240991632898581773904918924634904196424312039, 0.79666647741362673959155393647583043683717173161597, 0.96028985649753623168356086856947299042823523430145; _map_points[8] = points_8; Eigen::VectorXd points_10(10); points_10 << -0.97390652851717172007796401208445205342826994669238, -0.86506336668898451073209668842349304852754301496533, -0.67940956829902440623432736511487357576929471183481, -0.43339539412924719079926594316578416220007183765625, -0.14887433898163121088482600112971998461756485942069, 0.14887433898163121088482600112971998461756485942069, 0.43339539412924719079926594316578416220007183765625, 0.67940956829902440623432736511487357576929471183481, 0.86506336668898451073209668842349304852754301496533, 0.97390652851717172007796401208445205342826994669238; _map_points[10] = points_10; Eigen::VectorXd points_12(12); points_12 << -0.98156063424671925069054909014928082296015519981373, -0.9041172563704748566784658661190961925375967092133, -0.76990267419430468703689383321281807598492575001893, -0.58731795428661744729670241894053428036909851404805, -0.36783149899818019375269153664371756125636014133541, -0.12523340851146891547244136946385312998339691630544, 0.12523340851146891547244136946385312998339691630544, 0.36783149899818019375269153664371756125636014133541, 0.58731795428661744729670241894053428036909851404805, 0.76990267419430468703689383321281807598492575001893, 0.9041172563704748566784658661190961925375967092133, 0.98156063424671925069054909014928082296015519981373; _map_points[12] = points_12; Eigen::VectorXd points_14(14); points_14 << -0.98628380869681233884159726670405280167609140723923, -0.92843488366357351733639113937787426447703921040984, -0.82720131506976499318979474265039496103970110147508, -0.68729290481168547014801980301933413753840121274717, -0.51524863635815409196529071855118866230888528256931, -0.31911236892788976043567182416847546683426120353384, -0.10805494870734366206624465021983474761195160547424, 0.10805494870734366206624465021983474761195160547424, 0.31911236892788976043567182416847546683426120353384, 0.51524863635815409196529071855118866230888528256931, 0.68729290481168547014801980301933413753840121274717, 0.82720131506976499318979474265039496103970110147508, 0.92843488366357351733639113937787426447703921040984, 0.98628380869681233884159726670405280167609140723923; _map_points[14] = points_14; Eigen::VectorXd points_16(16); points_16 << -0.98940093499164993259615417345033262742627407165765, -0.94457502307323257607798841553460834509113927259107, -0.86563120238783174388046789771239313238733538484753, -0.7554044083550030338951011948474422683538136564575, -0.61787624440264374844667176404879101899188221776566, -0.45801677765722738634241944298357757354003161303552, -0.2816035507792589132304605014604961064860694907706, -0.09501250983763744018531933542495806313035305568907, 0.09501250983763744018531933542495806313035305568907, 0.2816035507792589132304605014604961064860694907706, 0.4580167776572273863424194429835775735400316130355, 0.6178762444026437484466717640487910189918822177657, 0.7554044083550030338951011948474422683538136564575, 0.86563120238783174388046789771239313238733538484753, 0.94457502307323257607798841553460834509113927259107, 0.98940093499164993259615417345033262742627407165765; _map_points[16] = points_16; Eigen::VectorXd points_18(18); points_18 << -0.99156516842093094673001600470615077025257893684544, -0.95582394957139775518119589292977630997284413481131, -0.8926024664975557392060605911271455154078952713523, -0.80370495897252311568241745501459079710329892161192, -0.69168704306035320787489108128884838945227057281751, -0.55977083107394753460787154852532913692762648577071, -0.41175116146284264603593179383305163707898968212003, -0.2518862256915055095889728548779112301628617656596, -0.08477501304173530124226185293578381173331738690609, 0.08477501304173530124226185293578381173331738690609, 0.2518862256915055095889728548779112301628617656596, 0.41175116146284264603593179383305163707898968212003, 0.5597708310739475346078715485253291369276264857707, 0.69168704306035320787489108128884838945227057281751, 0.80370495897252311568241745501459079710329892161192, 0.8926024664975557392060605911271455154078952713523, 0.95582394957139775518119589292977630997284413481131, 0.99156516842093094673001600470615077025257893684544; _map_points[18] = points_18; Eigen::VectorXd points_20(20); points_20 << -0.99312859918509492478612238847132027822264713090166, -0.96397192727791379126766613119727722191206032780619, -0.91223442825132590586775244120329811304918479742369, -0.83911697182221882339452906170152068532962936506564, -0.74633190646015079261430507035564159031073067956918, -0.63605368072651502545283669622628593674338911679937, -0.51086700195082709800436405095525099842549132920243, -0.37370608871541956067254817702492723739574632170568, -0.22778585114164507808049619536857462474308893768293, -0.0765265211334973337546404093988382110047962668135, 0.0765265211334973337546404093988382110047962668135, 0.22778585114164507808049619536857462474308893768293, 0.3737060887154195606725481770249272373957463217057, 0.5108670019508270980043640509552509984254913292024, 0.63605368072651502545283669622628593674338911679937, 0.74633190646015079261430507035564159031073067956918, 0.83911697182221882339452906170152068532962936506564, 0.91223442825132590586775244120329811304918479742369, 0.96397192727791379126766613119727722191206032780619, 0.99312859918509492478612238847132027822264713090166; _map_points[20] = points_20; Eigen::VectorXd points_40(40); points_40 << -0.99823770971055920034962270242058649233577038159505, -0.99072623869945700645305435222137215496222208135109, -0.97725994998377426266337028371290380697866793203799, -0.95791681921379165580454099945275928509488349060275, -0.93281280827867653336085216684520571643475357528269, -0.90209880696887429672825333086849310358448808105767, -0.8659595032122595038207818083546199635705465530111, -0.82461223083331166319632023066609877390724038424299, -0.77830565142651938769497154550649484802069131612689, -0.72731825518992710328099645175493054855737867353333, -0.67195668461417954837935451496149410997032598138385, -0.61255388966798023795261245023069487738012378168315, -0.54946712509512820207593130552951797023397510159565, -0.48307580168617871290856657424482300459902239553311, -0.41377920437160500152487974580371368297409962405292, -0.34199409082575847300749248117919431006695362002733, -0.26815218500725368114118434480859618342480437323625, -0.19269758070137109971551685206514989481409202110521, -0.11608407067525520848345128440802411376872853085422, -0.03877241750605082193319344402462329467936463438314, 0.03877241750605082193319344402462329467936463438314, 0.11608407067525520848345128440802411376872853085422, 0.19269758070137109971551685206514989481409202110521, 0.2681521850072536811411843448085961834248043732362, 0.34199409082575847300749248117919431006695362002733, 0.41377920437160500152487974580371368297409962405292, 0.48307580168617871290856657424482300459902239553311, 0.54946712509512820207593130552951797023397510159565, 0.61255388966798023795261245023069487738012378168315, 0.67195668461417954837935451496149410997032598138385, 0.72731825518992710328099645175493054855737867353333, 0.77830565142651938769497154550649484802069131612689, 0.82461223083331166319632023066609877390724038424299, 0.8659595032122595038207818083546199635705465530111, 0.90209880696887429672825333086849310358448808105767, 0.93281280827867653336085216684520571643475357528269, 0.95791681921379165580454099945275928509488349060275, 0.97725994998377426266337028371290380697866793203799, 0.99072623869945700645305435222137215496222208135109, 0.99823770971055920034962270242058649233577038159505; _map_points[40] = points_40; Eigen::VectorXd points_100(100); points_100 << -0.9997137267734412336782284693423006767183495273084, -0.99849195063959581840016335918634916230485485042057, -0.99629513473312514918613173224113103543643128814043, -0.99312493703744345965200989284878347073177145886652, -0.98898439524299174800441874580773663183933363710695, -0.9838775407060570154961001555110081673443670168508, -0.97780935848691828855378108842920192863523449426625, -0.97078577576370633193089785789750538855055719947821, -0.96281365425581552729365932603016638643733150673041, -0.95390078292549174284933693089435764464522145101467, -0.9440558701362559779627747064152187467397203733821, -0.93328853504307954592433366813086250408354607429702, -0.9216092981453339526669513284819874591245827977322, -0.90902957098252969046712633778914606444327728958459, -0.89556164497072698669852102243022776984818176899772, -0.88121867938501841557331682542780558244549441102126, -0.86601468849716462341073996967624296638031483930559, -0.84996452787959128429336259142010465407379077950067, -0.83308387988840082354291583384475567990749483030996, -0.8153892383391762543939887586492580053825503765137, -0.79689789239031447638957288218324598288952685596429, -0.7776279096494954756275513868344901065385397999361, -0.75759811851970717603566796443840077231310897190004, -0.73682808980202070551242771482010100284327844624712, -0.7153381175730564464599671227043659640843978385956, -0.6931491993558019659486479416754372655870000179307, -0.67028301560314101580258701432322661366980568402882, -0.6467619085141292798326303044586304350197337842485, -0.6226088602037077716041908451723122446538177322898, -0.59784747024717872126480654514934063639489919232049, -0.57250193262138119131687044352572544896003394967556, -0.5465970120650941674679942571817499039562417759375, -0.52015801988176305664681574945520853076893769042009, -0.49321078920819093356930879344933399099072332535856, -0.46578164977335804224921662339575458161165111021221, -0.4378974021720315131089780436221959621257017634841, -0.4095852916783015425288684000571577014953643891648, -0.38087298162462995676336254886958740374970726512371, -0.35178852637242172097234382954897056524931809638907, -0.3223603439005291517224765823983254274021916230231, -0.29261718803847196473755588823549438456153898917258, -0.2625881203715034791689293362549821411320226945355, -0.23230248184497396964950996320796411069750977150714, -0.20178986409573599723604885953039646294369200355905, -0.17108008053860327488753237470708980746585972511807, -0.14020313723611397320751460468240551661687300626336, -0.10918920358006111500342600657938488688489962996916, -0.07806858281343663669481737120155257397635002744853, -0.04687168242159163161492391293384830953706539908602, -0.015628984421543082872216699997429340147756182855562, 0.01562898442154308287221669999742934014775618285556, 0.04687168242159163161492391293384830953706539908602, 0.07806858281343663669481737120155257397635002744853, 0.10918920358006111500342600657938488688489962996916, 0.14020313723611397320751460468240551661687300626336, 0.17108008053860327488753237470708980746585972511807, 0.20178986409573599723604885953039646294369200355905, 0.23230248184497396964950996320796411069750977150714, 0.26258812037150347916892933625498214113202269453552, 0.29261718803847196473755588823549438456153898917258, 0.32236034390052915172247658239832542740219162302309, 0.35178852637242172097234382954897056524931809638907, 0.38087298162462995676336254886958740374970726512371, 0.4095852916783015425288684000571577014953643891648, 0.4378974021720315131089780436221959621257017634841, 0.4657816497733580422492166233957545816116511102122, 0.49321078920819093356930879344933399099072332535856, 0.52015801988176305664681574945520853076893769042009, 0.54659701206509416746799425718174990395624177593753, 0.57250193262138119131687044352572544896003394967556, 0.59784747024717872126480654514934063639489919232049, 0.62260886020370777160419084517231224465381773228982, 0.64676190851412927983263030445863043501973378424853, 0.67028301560314101580258701432322661366980568402882, 0.69314919935580196594864794167543726558700001793073, 0.71533811757305644645996712270436596408439783859563, 0.73682808980202070551242771482010100284327844624712, 0.75759811851970717603566796443840077231310897190004, 0.77762790964949547562755138683449010653853979993608, 0.79689789239031447638957288218324598288952685596429, 0.8153892383391762543939887586492580053825503765137, 0.83308387988840082354291583384475567990749483030996, 0.84996452787959128429336259142010465407379077950067, 0.86601468849716462341073996967624296638031483930559, 0.88121867938501841557331682542780558244549441102126, 0.89556164497072698669852102243022776984818176899772, 0.90902957098252969046712633778914606444327728958459, 0.9216092981453339526669513284819874591245827977322, 0.93328853504307954592433366813086250408354607429702, 0.9440558701362559779627747064152187467397203733821, 0.95390078292549174284933693089435764464522145101467, 0.96281365425581552729365932603016638643733150673041, 0.97078577576370633193089785789750538855055719947821, 0.97780935848691828855378108842920192863523449426625, 0.9838775407060570154961001555110081673443670168508, 0.98898439524299174800441874580773663183933363710695, 0.99312493703744345965200989284878347073177145886652, 0.99629513473312514918613173224113103543643128814043, 0.99849195063959581840016335918634916230485485042057, 0.9997137267734412336782284693423006767183495273084; _map_points[100] = points_100; } void Gauss_Legendre_Quadrature_Base::FillAdaptedWeights() { Eigen::VectorXd AdaptedWeights_8(8); AdaptedWeights_8 << 0.10122853629037625915253135430996219011539409105169, 0.22238103445337447054435599442624088443013087005125, 0.31370664587788728733796220198660131326032899900273, 0.36268378337836198296515044927719561219414603989433, 0.3626837833783619829651504492771956121941460398943, 0.3137066458778872873379622019866013132603289990027, 0.2223810344533744705443559944262408844301308700512, 0.10122853629037625915253135430996219011539409105169; _map_AdaptedWeights[8] = AdaptedWeights_8; Eigen::VectorXd AdaptedWeights_10(10); AdaptedWeights_10 << 0.066671344308688137593568809893331792857864834320158, 0.14945134915058059314577633965769733240255663966943, 0.21908636251598204399553493422816319245877187052268, 0.2692667193099963550912269215694693528597599384609, 0.29552422471475287017389299465133832942104671702685, 0.2955242247147528701738929946513383294210467170269, 0.2692667193099963550912269215694693528597599384609, 0.2190863625159820439955349342281631924587718705227, 0.14945134915058059314577633965769733240255663966943, 0.06667134430868813759356880989333179285786483432016; _map_AdaptedWeights[10] = AdaptedWeights_10; Eigen::VectorXd AdaptedWeights_12(12); AdaptedWeights_12 << 0.04717533638651182719461596148501706031702907399485, 0.10693932599531843096025471819399622421457017347033, 0.16007832854334622633465252954335907187201173049086, 0.2031674267230659217490644558097983765065181472746, 0.2334925365383548087608498989248780562594099721998, 0.24914704581340278500056243604295121083046090256962, 0.2491470458134027850005624360429512108304609025696, 0.2334925365383548087608498989248780562594099721998, 0.2031674267230659217490644558097983765065181472746, 0.1600783285433462263346525295433590718720117304909, 0.1069393259953184309602547181939962242145701734703, 0.04717533638651182719461596148501706031702907399485; _map_AdaptedWeights[12] = AdaptedWeights_12; Eigen::VectorXd AdaptedWeights_14(14); AdaptedWeights_14 << 0.035119460331751863031832876138191780619705609277127, 0.08015808715976020980563327706285430958369778539459, 0.1215185706879031846894148090724766259566693456901, 0.15720316715819353456960193862384215660566803733732, 0.1855383974779378137417165901251570362489226029373, 0.20519846372129560396592406566121805571033906130942, 0.21526385346315779019587644331626003527499755805413, 0.2152638534631577901958764433162600352749975580541, 0.2051984637212956039659240656612180557103390613094, 0.1855383974779378137417165901251570362489226029373, 0.1572031671581935345696019386238421566056680373373, 0.12151857068790318468941480907247662595666934569008, 0.08015808715976020980563327706285430958369778539459, 0.0351194603317518630318328761381917806197056092771; _map_AdaptedWeights[14] = AdaptedWeights_14; Eigen::VectorXd AdaptedWeights_16(16); AdaptedWeights_16 << 0.02715245941175409485178057245601810351226737556676, 0.06225352393864789286284383699437769427498650835291, 0.09515851168249278480992510760224622635526350318371, 0.1246289712555338720524762821920164201448868592222, 0.14959598881657673208150173054747854897049106820784, 0.16915651939500253818931207903035996221163947341603, 0.1826034150449235888667636679692199393835562236546, 0.1894506104550684962853967232082831051469089883959, 0.1894506104550684962853967232082831051469089883959, 0.18260341504492358886676366796921993938355622365465, 0.16915651939500253818931207903035996221163947341603, 0.1495959888165767320815017305474785489704910682078, 0.1246289712555338720524762821920164201448868592222, 0.0951585116824927848099251076022462263552635031837, 0.0622535239386478928628438369943776942749865083529, 0.02715245941175409485178057245601810351226737556676; _map_AdaptedWeights[16] = AdaptedWeights_16; Eigen::VectorXd AdaptedWeights_18(18); AdaptedWeights_18 << 0.02161601352648331031334271026645246938768523147559, 0.04971454889496979645333494620263864168086624612891, 0.076425730254889056529129677616636525605317906208358, 0.10094204410628716556281398492483460706280113888768, 0.12255520671147846018451912680020155522816389733344, 0.14064291467065065120473130375194722809550241033097, 0.15468467512626524492541800383637477219321839626735, 0.16427648374583272298605377646592759041233895399735, 0.1691423829631435918406564701349866103341058193703, 0.1691423829631435918406564701349866103341058193703, 0.16427648374583272298605377646592759041233895399735, 0.1546846751262652449254180038363747721932183962674, 0.140642914670650651204731303751947228095502410331, 0.1225552067114784601845191268002015552281638973334, 0.10094204410628716556281398492483460706280113888768, 0.07642573025488905652912967761663652560531790620836, 0.0497145488949697964533349462026386416808662461289, 0.02161601352648331031334271026645246938768523147559; _map_AdaptedWeights[18] = AdaptedWeights_18; Eigen::VectorXd AdaptedWeights_20(20); AdaptedWeights_20 << 0.01761400713915211831186196235185281636214310554334, 0.04060142980038694133103995227493210987909063998995, 0.06267204833410906356950653518704160635160107657844, 0.08327674157670474872475814322204620610017782858316, 0.10193011981724043503675013548034987616669165602339, 0.11819453196151841731237737771138228700504121954897, 0.13168863844917662689849449974816313491611051114698, 0.14209610931838205132929832506716493303451541339202, 0.1491729864726037467878287370019694366926799040814, 0.1527533871307258506980843319550975934919486451124, 0.15275338713072585069808433195509759349194864511238, 0.14917298647260374678782873700196943669267990408137, 0.14209610931838205132929832506716493303451541339202, 0.131688638449176626898494499748163134916110511147, 0.11819453196151841731237737771138228700504121954897, 0.10193011981724043503675013548034987616669165602339, 0.0832767415767047487247581432220462061001778285832, 0.06267204833410906356950653518704160635160107657844, 0.04060142980038694133103995227493210987909063999, 0.017614007139152118311861962351852816362143105543337; _map_AdaptedWeights[20] = AdaptedWeights_20; Eigen::VectorXd AdaptedWeights_40(40); AdaptedWeights_40 << 0.00452127709853319125847173287818533272783111019971, 0.0104982845311528136147421710672796523767926213158, 0.01642105838190788871286348488236392729234229334696, 0.02224584919416695726150432418420857320703319667935, 0.02793700698002340109848915750772107730255086205077, 0.033460195282547847392678183086410848977241786653764, 0.03878216797447201763997203129044616225345921123203, 0.04387090818567327199167468604171549581100683717024, 0.04869580763507223206143416044814638806784302737712, 0.05322784698393682435499647977226050455532117182201, 0.05743976909939155136661773091042598560010483585445, 0.06130624249292893916653799640839859590259376351117, 0.06480401345660103807455452956675273003269296420849, 0.06791204581523390382569010823192398598419723837929, 0.0706116473912867796954836308552868323595591039956, 0.0728865823958040590605106834425178358575590809858, 0.07472316905796826420018933626132467319120293442036, 0.07611036190062624237155807592249482301255955384507, 0.07703981816424796558830753428381024852443975416394, 0.07750594797842481126372396295832632696366865278811, 0.07750594797842481126372396295832632696366865278811, 0.07703981816424796558830753428381024852443975416394, 0.07611036190062624237155807592249482301255955384507, 0.07472316905796826420018933626132467319120293442036, 0.0728865823958040590605106834425178358575590809858, 0.07061164739128677969548363085528683235955910399559, 0.06791204581523390382569010823192398598419723837929, 0.06480401345660103807455452956675273003269296420849, 0.06130624249292893916653799640839859590259376351117, 0.0574397690993915513666177309104259856001048358545, 0.053227846983936824354996479772260504555321171822, 0.0486958076350722320614341604481463880678430273771, 0.0438709081856732719916746860417154958110068371702, 0.03878216797447201763997203129044616225345921123203, 0.03346019528254784739267818308641084897724178665376, 0.0279370069800234010984891575077210773025508620508, 0.0222458491941669572615043241842085732070331966794, 0.016421058381907888712863484882363927292342293346958, 0.0104982845311528136147421710672796523767926213158, 0.00452127709853319125847173287818533272783111019971; _map_AdaptedWeights[40] = AdaptedWeights_40; Eigen::VectorXd AdaptedWeights_100(100); AdaptedWeights_100 << 7.34634490505671730406320658330336390670473562483e-4, 0.001709392653518105239529358371491195243731385491463, 0.002683925371553482419439590429001120081931114951, 0.00365596120132637518234245872752519569920656740515, 0.0046244500634221193510957890829784766503524952949, 0.00558842800386551515721194634843921073131869400808, 0.00654694845084532276415210333149526369993836336648, 0.00749907325546471157882874401639778316358347894815, 0.0084438714696689714026208349023010019346444598841, 0.0093804196536944579514182376608121187307870432387, 0.0103078025748689695857821017278353779760583438414, 0.0112251140231859771172215733663335847772264195644, 0.01213145766297949740774479244874817073696312331126, 0.01302594789297154228555858375890179013496473584175, 0.01390771070371877268795414910800463779518081214312, 0.0147758845274413017688799875203542571693887431146, 0.01562962107754600272393686595379192555246997980994, 0.0164680861761452126431049800882107808211676616038, 0.01729046056832358243934419836674167481162350856517, 0.01809594072212811666439075142049303134757874495839, 0.01888373961337490455294116588154323429711127634742, 0.019653087494435305865381470245444065555269599491251, 0.02040323264620943276683885165758377060570969930262, 0.02113344211252764154267230044096968163532972887451, 0.0218430024162473863139537413043980247653489998232, 0.02253122025633627270179697093167396234015893534871, 0.02319742318525412162248885418272728845115448573609, 0.0238409602659682059625604119022834321447074490926, 0.024461202707957052719975023349772890646295732397804, 0.02505754448157958970376422562092326422383855852793, 0.02562940291020811607564200986215087092697767002027, 0.02617621923954567634230874175730188501127513119069, 0.02669745918357096266038466418633635063465575039001, 0.027192613446576880136491567802170692266987896012, 0.02766119822079238829420415587042645529240035866422, 0.02810275565910117331764833018699455045141809940021, 0.028516854322395097990936762864457873259842725484, 0.028903089601125203134876228134515265315607868055261, 0.02926108411063827662011902349564095444308419504535, 0.0295904880599126425117545106788365851728062850714, 0.029890979593332830916836806668595827658091414260799, 0.0301622651051691449190686816104792326571023257827, 0.030404079526454820016507859818825176605607248310117, 0.0306161865839804484964594432620531928530860237891, 0.03079837903115259042771390303055976009497083447037, 0.03095047885049098823406346347074792738298717776694, 0.031072337427566516587810170242918034845915436348, 0.0311638356962099067838183212171866533438363686839, 0.03122488425484935773237649864809813488180274068218, 0.03125542345386335694764247438619802878783383672609, 0.03125542345386335694764247438619802878783383672609, 0.0312248842548493577323764986480981348818027406822, 0.03116383569620990678381832121718665334383636868393, 0.03107233742756651658781017024291803484591543634796, 0.0309504788504909882340634634707479273829871777669, 0.0307983790311525904277139030305597600949708344704, 0.03061618658398044849645944326205319285308602378906, 0.0304040795264548200165078598188251766056072483101, 0.03016226510516914491906868161047923265710232578271, 0.0298909795933328309168368066685958276580914142608, 0.0295904880599126425117545106788365851728062850714, 0.0292610841106382766201190234956409544430841950453, 0.02890308960112520313487622813451526531560786805526, 0.02851685432239509799093676286445787325984272548397, 0.0281027556591011733176483301869945504514180994002, 0.02766119822079238829420415587042645529240035866422, 0.027192613446576880136491567802170692266987896012, 0.02669745918357096266038466418633635063465575039001, 0.0261762192395456763423087417573018850112751311907, 0.02562940291020811607564200986215087092697767002027, 0.02505754448157958970376422562092326422383855852793, 0.0244612027079570527199750233497728906462957323978, 0.0238409602659682059625604119022834321447074490926, 0.0231974231852541216224888541827272884511544857361, 0.0225312202563362727017969709316739623401589353487, 0.0218430024162473863139537413043980247653489998232, 0.0211334421125276415426723004409696816353297288745, 0.02040323264620943276683885165758377060570969930262, 0.01965308749443530586538147024544406555526959949125, 0.01888373961337490455294116588154323429711127634742, 0.01809594072212811666439075142049303134757874495839, 0.0172904605683235824393441983667416748116235085652, 0.0164680861761452126431049800882107808211676616038, 0.0156296210775460027239368659537919255524699798099, 0.0147758845274413017688799875203542571693887431146, 0.01390771070371877268795414910800463779518081214312, 0.01302594789297154228555858375890179013496473584175, 0.01213145766297949740774479244874817073696312331126, 0.01122511402318597711722157336633358477722641956438, 0.0103078025748689695857821017278353779760583438414, 0.00938041965369445795141823766081211873078704323867, 0.0084438714696689714026208349023010019346444598841, 0.0074990732554647115788287440163977831635834789481, 0.00654694845084532276415210333149526369993836336648, 0.0055884280038655151572119463484392107313186940081, 0.00462445006342211935109578908297847665035249529489, 0.00365596120132637518234245872752519569920656740515, 0.002683925371553482419439590429001120081931114951, 0.00170939265351810523952935837149119524373138549146, 7.34634490505671730406320658330336390670473562483E-4; _map_AdaptedWeights[100] = AdaptedWeights_100; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gaussian_quadrature/gauss_legendre_quadrature.h000066400000000000000000000051771412152066400261630ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #ifndef VOTCA_XTP_GAUSS_LEGENDRE_QUADRATURE_H #define VOTCA_XTP_GAUSS_LEGENDRE_QUADRATURE_H #include "votca/xtp/GaussianQuadratureBase.h" #include namespace votca { namespace xtp { class Gauss_Legendre_Quadrature_Base : public GaussianQuadratureBase { protected: void FillPoints() final; void FillAdaptedWeights() final; }; class Gauss_modified_Legendre_Quadrature : public Gauss_Legendre_Quadrature_Base { public: double ScaledPoint(Index i) const final { return 0.5 * (1.0 + points_(i)) / (1.0 - points_(i)); } double ScaledWeight(Index i) const final { double den = (1.0 - points_(i)) * (1.0 - points_(i)); return weights_(i) / den; } protected: // The modified legendre method is suitable for integration limits a = 0 b = // +infty. Here we have value1 and value2 because we split the original // integral from -infty to +infty in two parts. Original legendre quadrature // is meant for integral with integration limits of -1 and 1. To overcome // this we use the transformation x' = 0.5 * (1+x/1-x) bool UseSymmetry() const final { return true; } }; class Gauss_Legendre_Quadrature : public Gauss_Legendre_Quadrature_Base { public: double ScaledPoint(Index i) const final { return std::tan(0.5 * votca::tools::conv::Pi * points_(i)); } double ScaledWeight(Index i) const final { const double halfpi = 0.5 * tools::conv::Pi; double den = std::cos(halfpi * points_[i]) * std::cos(halfpi * points_[i]); return weights_(i) * halfpi / den; } protected: // This particular legendre quadrature is suitable for integration limits a // = -infty b = +infty. Original Legendre quadrature is meant for // integration limits -1 and +1. The change of variables is x' = tan (pi/2 * // x). When x=-1 we have x'=-infty. When x=1 we have x'=+infty bool UseSymmetry() const final { return false; } }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_GAUSS_LEGENDRE_QUADRATURE_Hxtp-2021.2/src/libxtp/geometry_optimization.cc000066400000000000000000000156671412152066400214740ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include "functional" // Local VOTCA includes #include "votca/xtp/bfgs_trm.h" #include "votca/xtp/energy_costfunction.h" #include "votca/xtp/forces.h" #include "votca/xtp/geometry_optimization.h" #include "votca/xtp/statetracker.h" namespace votca { namespace xtp { void GeometryOptimization::Initialize(tools::Property& options) { std::string statestring = options.get(".state").as(); _opt_state.FromString(statestring); if (!_opt_state.Type().isExciton()) { throw std::runtime_error( "At the moment only excitonic states can be optimized"); } // default convergence parameters from ORCA _conv.deltaE = options.get(".convergence.energy").as(); // Hartree _conv.RMSForce = options.get(".convergence.RMSForce").as(); // Hartree/Bohr _conv.MaxForce = options.get(".convergence.MaxForce").as(); // Hartree/Bohr _conv.RMSStep = options.get(".convergence.RMSStep").as(); // Bohr _conv.MaxStep = options.get(".convergence.MaxStep").as(); // Bohr _trust_radius = options.get("optimizer.trust").as(); // Angstrom _trust_radius *= tools::conv::ang2bohr; // initial trust radius in a.u. _max_iteration = options.get(".maxiter").as(); _trajfile = options.get(".trajectory_file").as(); _optimizer = options.get(".optimizer.method").as(); _force_options = options.get(".forces"); _statetracker_options = options.get(".statetracker"); } void GeometryOptimization::Evaluate() { XTP_LOG(Log::error, *_pLog) << "Requested geometry optimization of excited state " << _opt_state.ToString() << std::flush; StateTracker tracker; tracker.Initialize(_statetracker_options); tracker.setInitialState(_opt_state); tracker.setLogger(_pLog); tracker.PrintInfo(); // get a force object Forces force_engine(_gwbse_engine, tracker); force_engine.Initialize(_force_options); force_engine.setLog(_pLog); XTP_LOG(Log::error, *_pLog) << (boost::format("Convergence of total energy: %1$8.6f Hartree ") % _conv.deltaE) .str() << std::flush; XTP_LOG(Log::error, *_pLog) << (boost::format("Convergence of RMS Force: %1$8.6f Hartree/Bohr ") % _conv.RMSForce) .str() << std::flush; XTP_LOG(Log::error, *_pLog) << (boost::format("Convergence of Max Force: %1$8.6f Hartree/Bohr ") % _conv.MaxForce) .str() << std::flush; XTP_LOG(Log::error, *_pLog) << (boost::format("Convergence of RMS Step: %1$8.6f Bohr ") % _conv.RMSStep) .str() << std::flush; XTP_LOG(Log::error, *_pLog) << (boost::format("Convergence of Max Step: %1$8.6f Bohr ") % _conv.MaxStep) .str() << std::flush; XTP_LOG(Log::error, *_pLog) << (boost::format("Initial trust radius: %1$8.6f Bohr") % _trust_radius) .str() << std::flush; Energy_costfunction e_cost = Energy_costfunction(_gwbse_engine, tracker, _orbitals, force_engine); e_cost.setConvergenceParameters(_conv); e_cost.setLog(_pLog); // get the optimizer if (_optimizer == "BFGS-TRM") { BFGSTRM bfgstrm(e_cost); std::vector > callbacks; std::function reporting = std::bind( Report, std::cref(bfgstrm), std::cref(force_engine), std::ref(*_pLog)); callbacks.push_back(reporting); std::function filewrite = std::bind( WriteTrajectory, _trajfile, _orbitals.QMAtoms(), std::cref(bfgstrm)); callbacks.push_back(filewrite); bfgstrm.setCallbacks(callbacks); bfgstrm.setNumofIterations(_max_iteration); bfgstrm.setTrustRadius(_trust_radius); bfgstrm.setLog(_pLog); bfgstrm.Optimize(Energy_costfunction::QMAtoms2Vector(_orbitals.QMAtoms())); } return; } void GeometryOptimization::Report(const BFGSTRM& bfgstrm, const Forces& forces, Logger& pLog) { XTP_LOG(Log::error, pLog) << std::flush; XTP_LOG(Log::error, pLog) << (boost::format("=========== OPTIMIZATION SUMMARY " "================================= ")) .str() << std::flush; XTP_LOG(Log::error, pLog) << "At iteration " << bfgstrm.getIteration() << std::flush; XTP_LOG(Log::error, pLog) << (boost::format(" ---- POSITIONS (Angstrom) ")).str() << std::flush; XTP_LOG(Log::error, pLog) << (boost::format(" Atom\t x\t y\t z ")).str() << std::flush; const Eigen::VectorXd& atomvec = bfgstrm.getParameters(); for (Index i = 0; i < atomvec.size(); i += 3) { XTP_LOG(Log::error, pLog) << (boost::format("%1$4d %2$+1.4f %3$+1.4f %4$+1.4f") % (i / 3) % (atomvec(i) * votca::tools::conv::bohr2ang) % (atomvec(i + 1) * votca::tools::conv::bohr2ang) % (atomvec(i + 2) * votca::tools::conv::bohr2ang)) .str() << std::flush; } XTP_LOG(Log::error, pLog) << (boost::format(" Total energy: %1$12.8f Hartree ") % bfgstrm.getCost()) .str() << std::flush; XTP_LOG(Log::error, pLog) << (boost::format(" Trust radius: %1$12.8f Bohr ") % bfgstrm.getTrustRadius()) .str() << std::flush; forces.Report(); return; } void GeometryOptimization::WriteTrajectory(const std::string& filename, QMMolecule& atoms, const BFGSTRM& bfgstrm) { std::ofstream ofs; if (bfgstrm.getIteration() == 0) { ofs.open(filename, std::ofstream::out); } else { ofs.open(filename, std::ofstream::app); } if (!ofs.is_open()) { throw std::runtime_error("Bad file handle: " + filename); } // write coordinates as xyz file ofs << atoms.size() << std::endl; ofs << "iteration " << bfgstrm.getIteration() << " energy " << bfgstrm.getCost() << " Hartree" << std::endl; Energy_costfunction::Vector2QMAtoms(bfgstrm.getParameters(), atoms); for (const QMAtom& atom : atoms) { const Eigen::Vector3d pos = atom.getPos() * tools::conv::bohr2ang; ofs << atom.getElement() << " " << pos.x() << " " << pos.y() << " " << pos.z() << std::endl; } ofs.close(); return; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gnode.cc000066400000000000000000000034161412152066400161140ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include // Local VOTCA includes #include "votca/xtp/gnode.h" using namespace std; namespace votca { namespace xtp { void GNode::AddDecayEvent(double decayrate) { _events.push_back(GLink(decayrate)); _hasdecay = true; } void GNode::AddEvent(GNode* seg2, const Eigen::Vector3d& dr, double rate) { _events.push_back(GLink(seg2, rate, dr)); } void GNode::InitEscapeRate() { _escape_rate = 0.0; for (const auto& event : _events) { _escape_rate += event.getRate(); } } GLink* GNode::findHoppingDestination(double p) const { return hTree.findHoppingDestination(p); } void GNode::MakeHuffTree() { hTree.setEvents(&_events); hTree.makeTree(); } void GNode::AddEventfromQmPair(const QMPair& pair, std::vector& nodes, double rate) { Index destination = 0; Eigen::Vector3d dr = Eigen::Vector3d::Zero(); if (_id == pair.Seg1()->getId()) { destination = pair.Seg2()->getId(); dr = pair.R(); } else { destination = pair.Seg1()->getId(); dr = -pair.R(); } AddEvent(&nodes[destination], dr, rate); return; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/grids/000077500000000000000000000000001412152066400156155ustar00rootroot00000000000000xtp-2021.2/src/libxtp/grids/grid.cc000066400000000000000000000060241412152066400170530ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include /* ceil */ // VOTCA includes #include #include // Local VOTCA includes #include "votca/xtp/grid.h" namespace votca { namespace xtp { void Grid::printGridtoxyzfile(std::string filename) { // unit is Angstrom in xyz file std::ofstream points; points.open(filename, std::ofstream::out); points << _gridpoints.size() << std::endl; points << std::endl; for (const auto& point : _gridpoints) { points << "X " << point.x() * tools::conv::bohr2ang << " " << point.y() * tools::conv::bohr2ang << " " << point.z() * tools::conv::bohr2ang << std::endl; } points.close(); return; } void Grid::setupgrid(const QMMolecule& Atomlist) { tools::Elements elements; std::pair extension = Atomlist.CalcSpatialMinMax(); Eigen::Array3d min = extension.first.array(); Eigen::Array3d max = extension.second.array(); Eigen::Array3d doublesteps = (max - min + 2 * _padding) / _gridspacing; Eigen::Array steps = (doublesteps.ceil()).cast(); // needed to symmetrize grid around molecule Eigen::Array3d padding = (doublesteps - steps.cast()) * _gridspacing * 0.5 + _padding; Eigen::Array3d minpos = min - padding; for (Index i = 0; i <= steps.x(); i++) { double x = minpos.x() + double(i) * _gridspacing; for (Index j = 0; j <= steps.y(); j++) { double y = minpos.y() + double(j) * _gridspacing; for (Index k = 0; k <= steps.z(); k++) { double z = minpos.z() + double(k) * _gridspacing; bool is_valid = false; Eigen::Vector3d gridpos(x, y, z); for (const QMAtom& atom : Atomlist) { const Eigen::Vector3d& atompos = atom.getPos(); double distance2 = (gridpos - atompos).squaredNorm(); double atomcutoff = elements.getVdWChelpG(atom.getElement()) * tools::conv::ang2bohr; if (distance2 < (atomcutoff * atomcutoff)) { is_valid = false; break; } else if (distance2 < (_cutoff * _cutoff)) { is_valid = true; } } if (is_valid) { _gridpoints.push_back(gridpos); } } } } _gridvalues = Eigen::VectorXd::Zero(_gridpoints.size()); return; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/grids/gridbox.cc000066400000000000000000000115561412152066400175720ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/gridbox.h" namespace votca { namespace xtp { void GridBox::FindSignificantShells(const AOBasis& basis) { for (const AOShell& store : basis) { const double decay = store.getMinDecay(); const Eigen::Vector3d& shellpos = store.getPos(); for (const auto& point : grid_pos) { Eigen::Vector3d dist = shellpos - point; double distsq = dist.squaredNorm(); // if contribution is smaller than -ln(1e-10), add shell to list if ((decay * distsq) < 20.7) { addShell(&store); break; } } } } Eigen::VectorXd GridBox::CalcAOValue_and_Grad( Eigen::MatrixX3d& ao_grad, const Eigen::Vector3d& point) const { Eigen::VectorXd ao = Eigen::VectorXd::Zero(Matrixsize()); for (Index j = 0; j < Shellsize(); ++j) { Eigen::Block grad_block = ao_grad.block(aoranges[j].start, 0, aoranges[j].size, 3); Eigen::VectorBlock ao_block = ao.segment(aoranges[j].start, aoranges[j].size); significant_shells[j]->EvalAOspace(ao_block, grad_block, point); } return ao; } Eigen::VectorXd GridBox::CalcAOValues(const Eigen::Vector3d& pos) const { Eigen::VectorXd ao = Eigen::VectorXd::Zero(Matrixsize()); for (Index j = 0; j < Shellsize(); ++j) { Eigen::VectorBlock ao_block = ao.segment(aoranges[j].start, aoranges[j].size); significant_shells[j]->EvalAOspace(ao_block, pos); } return ao; } void GridBox::AddtoBigMatrix(Eigen::MatrixXd& bigmatrix, const Eigen::MatrixXd& smallmatrix) const { for (Index i = 0; i < Index(ranges.size()); i++) { for (Index j = 0; j < Index(ranges.size()); j++) { bigmatrix.block(ranges[i].start, ranges[j].start, ranges[i].size, ranges[j].size) += smallmatrix.block(inv_ranges[i].start, inv_ranges[j].start, inv_ranges[i].size, inv_ranges[j].size); } } return; } Eigen::MatrixXd GridBox::ReadFromBigMatrix( const Eigen::MatrixXd& bigmatrix) const { Eigen::MatrixXd matrix = Eigen::MatrixXd(matrix_size, matrix_size); for (Index i = 0; i < Index(ranges.size()); i++) { for (Index j = 0; j < Index(ranges.size()); j++) { matrix.block(inv_ranges[i].start, inv_ranges[j].start, inv_ranges[i].size, inv_ranges[j].size) = bigmatrix.block(ranges[i].start, ranges[j].start, ranges[i].size, ranges[j].size); } } return matrix; } Eigen::VectorXd GridBox::ReadFromBigVector( const Eigen::VectorXd& bigvector) const { Eigen::VectorXd vector = Eigen::VectorXd(matrix_size); for (Index i = 0; i < Index(ranges.size()); i++) { vector.segment(inv_ranges[i].start, inv_ranges[i].size) = bigvector.segment(ranges[i].start, ranges[i].size); } return vector; } void GridBox::PrepareForIntegration() { Index index = 0; aoranges = std::vector(0); ranges = std::vector(0); inv_ranges = std::vector(0); std::vector start; std::vector end; for (const auto shell : significant_shells) { GridboxRange temp; temp.size = shell->getNumFunc(); temp.start = index; aoranges.push_back(temp); index += shell->getNumFunc(); start.push_back(shell->getStartIndex()); end.push_back(shell->getStartIndex() + shell->getNumFunc()); } std::vector startindex; std::vector endindex; if (start.size() > 1) { startindex.push_back(start[0]); for (Index i = 0; i < Index(start.size()) - 1; ++i) { if (end[i] != start[i + 1]) { startindex.push_back(start[i + 1]); endindex.push_back(end[i]); } } endindex.push_back(end[end.size() - 1]); } else { startindex = start; endindex = end; } Index shellstart = 0; for (Index i = 0; i < Index(startindex.size()); ++i) { Index size = endindex[i] - startindex[i]; GridboxRange temp; temp.size = size; temp.start = startindex[i]; ranges.push_back(temp); GridboxRange temp2; temp2.size = size; temp2.start = shellstart; inv_ranges.push_back(temp2); shellstart += size; } return; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/grids/radial_euler_maclaurin_rule.cc000066400000000000000000000227651412152066400236520ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "A_ol I_ol" BA_olI_ol, * WITHOUT WARRANTIE_ol OR CONDITION_ol OF ANY KIND, either express or implied. * _olee the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // Local VOTCA includes #include "votca/xtp/aobasis.h" #include "votca/xtp/aomatrix.h" #include "votca/xtp/qmmolecule.h" #include "votca/xtp/radial_euler_maclaurin_rule.h" namespace votca { namespace xtp { std::vector EulerMaclaurinGrid::CalculatePruningIntervals( const std::string& element) { std::vector r; // get Bragg-Slater Radius for this element double BSradius = _BraggSlaterRadii.at(element); // row type of element Index RowType = _pruning_set.at(element); if (RowType == 1) { r.push_back(0.25 * BSradius); r.push_back(0.5 * BSradius); r.push_back(1.0 * BSradius); r.push_back(4.5 * BSradius); } else if (RowType == 2) { r.push_back(0.1667 * BSradius); r.push_back(0.5 * BSradius); r.push_back(0.9 * BSradius); r.push_back(3.5 * BSradius); } else if (RowType == 3) { r.push_back(0.1 * BSradius); r.push_back(0.4 * BSradius); r.push_back(0.8 * BSradius); r.push_back(2.5 * BSradius); } else { throw std::runtime_error( "EulerMaclaurinGrid::CalculatePruningIntervals:Pruning unsupported for " "RowType"); } return r; } void EulerMaclaurinGrid::FillElementRangeMap(const AOBasis& aobasis, const QMMolecule& atoms, double eps) { std::map::iterator it; for (const QMAtom& atom : atoms) { std::string name = atom.getElement(); // is this element already in map? it = _element_ranges.find(name); // only proceed, if element data does not exist yet if (it == _element_ranges.end()) { min_exp this_atom; double range_max = std::numeric_limits::min(); double decaymin = std::numeric_limits::max(); Index lvalue = std::numeric_limits::min(); const std::vector shells = aobasis.getShellsofAtom(atom.getId()); // and loop over all shells to figure out minimum decay constant and // angular momentum of this function for (const AOShell* shell : shells) { Index lmax = Index(shell->getL()); if (shell->getMinDecay() < decaymin) { decaymin = shell->getMinDecay(); lvalue = lmax; } double range = DetermineCutoff(2 * decaymin, 2 * lvalue + 2, eps); if (range > range_max) { this_atom.alpha = decaymin; this_atom.l = lvalue; this_atom.range = range; range_max = range; } } // shells _element_ranges[name] = this_atom; } // new element } // atoms } void EulerMaclaurinGrid::RefineElementRangeMap(const AOBasis& aobasis, const QMMolecule& atoms, double eps) { AOOverlap overlap; overlap.Fill(aobasis); // get collapsed index list std::vector idxstart; const std::vector& idxsize = aobasis.getFuncPerAtom(); Index start = 0; for (Index size : idxsize) { idxstart.push_back(start); start += size; } // refining by going through all atom combinations for (Index i = 0; i < atoms.size(); ++i) { const QMAtom& atom_a = atoms[i]; Index a_start = idxstart[i]; Index a_size = idxsize[i]; double range_max = std::numeric_limits::min(); // get preset values for this atom type double alpha_a = _element_ranges.at(atom_a.getElement()).alpha; Index l_a = _element_ranges.at(atom_a.getElement()).l; const Eigen::Vector3d& pos_a = atom_a.getPos(); // Cannot iterate only over j 1e-5) { double range = DetermineCutoff( alpha_a + _element_ranges.at(atom_b.getElement()).alpha, l_a + _element_ranges.at(atom_b.getElement()).l + 2, eps); // now do some update trickery from Gaussian product formula double dist = (pos_b - pos_a).norm(); double shift_2g = dist * alpha_a / (alpha_a + _element_ranges.at(atom_b.getElement()).alpha); range += (shift_2g + dist); if (range > range_max) { range_max = range; } } } if (std::round(range_max) > _element_ranges.at(atom_a.getElement()).range) { _element_ranges.at(atom_a.getElement()).range = std::round(range_max); } } } void EulerMaclaurinGrid::CalculateRadialCutoffs(const AOBasis& aobasis, const QMMolecule& atoms, const std::string& gridtype) { double eps = Accuracy[gridtype]; FillElementRangeMap(aobasis, atoms, eps); RefineElementRangeMap(aobasis, atoms, eps); return; } std::map EulerMaclaurinGrid::CalculateAtomicRadialGrids(const AOBasis& aobasis, const QMMolecule& atoms, const std::string& type) { CalculateRadialCutoffs(aobasis, atoms, type); std::map result; for (const auto& element : _element_ranges) { result[element.first] = CalculateRadialGridforAtom(type, element); } return result; } GridContainers::radial_grid EulerMaclaurinGrid::CalculateRadialGridforAtom( const std::string& type, const std::pair& element) { GridContainers::radial_grid result; Index np = getGridParameters(element.first, type); double cutoff = element.second.range; result.radius = Eigen::VectorXd::Zero(np); result.weight = Eigen::VectorXd::Zero(np); double alpha = -cutoff / (log(1.0 - std::pow((1.0 + double(np)) / (2.0 + double(np)), 3))); double factor = 3.0 / (1.0 + double(np)); for (Index i = 0; i < np; i++) { double q = double(i + 1) / (double(np) + 1.0); double r = -alpha * std::log(1.0 - std::pow(q, 3)); double w = factor * alpha * r * r / (1.0 - std::pow(q, 3)) * std::pow(q, 2); result.radius[i] = r; result.weight[i] = w; } return result; } double EulerMaclaurinGrid::DetermineCutoff(double alpha, Index l, double eps) { // determine norm of function /* For a function f(r) = r^k*exp(-alpha*r^2) determine the radial distance r such that the fraction of the function norm that is neglected if the 3D volume integration is terminated at a distance r is less than or equal to eps. */ double cutoff = 1.0; // initial value double increment = 0.5; // increment while (increment > 0.01) { double residual = CalcResidual(alpha, l, cutoff); if (residual > eps) { cutoff += increment; } else { cutoff -= increment; if (cutoff < 0.0) { cutoff = 0.0; } increment = 0.5 * increment; cutoff += increment; } } return cutoff; } double EulerMaclaurinGrid::CalcResidual(double alpha, Index l, double cutoff) { return RadialIntegral(alpha, l + 2, cutoff) / RadialIntegral(alpha, l + 2, 0.0); } double EulerMaclaurinGrid::RadialIntegral(double alpha, Index l, double cutoff) { const double pi = boost::math::constants::pi(); Index ilo = l % 2; double value = 0.0; double valexp; if (ilo == 0) { double expo = std::sqrt(alpha) * cutoff; if (expo <= 40.0) { value = 0.5 * std::sqrt(pi / alpha) * std::erfc(expo); } } double exponent = alpha * cutoff * cutoff; if (exponent > 500.0) { valexp = 0.0; value = 0.0; } else { valexp = std::exp(-exponent); value = valexp / 2.0 / alpha; } for (Index i = ilo + 2; i <= l; i += 2) { value = (double(i - 1) * value + std::pow(cutoff, i - 1) * valexp) / 2.0 / alpha; } return value; } Index EulerMaclaurinGrid::getGridParameters(const std::string& element, const std::string& type) { if (type == "medium") { return MediumGrid.at(element); } else if (type == "coarse") { return CoarseGrid.at(element); } else if (type == "xcoarse") { return XcoarseGrid.at(element); } else if (type == "fine") { return FineGrid.at(element); } else if (type == "xfine") { return XfineGrid.at(element); } throw std::runtime_error("Grid type " + type + " is not implemented"); return -1; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/grids/regular_grid.cc000066400000000000000000000062741412152066400206030ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/regular_grid.h" #include "votca/xtp/qmmolecule.h" #include "votca/xtp/radial_euler_maclaurin_rule.h" #include "votca/xtp/sphere_lebedev_rule.h" namespace votca { namespace xtp { void Regular_Grid::GridSetup(const Eigen::Array3d& stepsizes, const Eigen::Array3d& padding, const QMMolecule& atoms, const AOBasis& basis) { std::pair extension = atoms.CalcSpatialMinMax(); Eigen::Array3d min = extension.first.array(); Eigen::Array3d max = extension.second.array(); Eigen::Array3d doublesteps = (max - min + 2 * padding) / stepsizes + 1.0; Eigen::Array steps = (doublesteps.ceil()).cast(); // needed to symmetrize grid around molecule Eigen::Array3d padding_sym = (doublesteps - steps.cast()) * stepsizes * 0.5 + padding; GridSetup(steps, padding_sym, atoms, basis); } void Regular_Grid::GridSetup(const Eigen::Array& steps, const Eigen::Array3d& padding, const QMMolecule& atoms, const AOBasis& basis) { std::pair extension = atoms.CalcSpatialMinMax(); Eigen::Array3d min = extension.first.array(); Eigen::Array3d max = extension.second.array(); _startingpoint = min - padding; _stepsizes = (max - min + 2 * padding) / (steps - 1).cast(); _steps = steps; const Index gridboxsize = 500; GridBox gridbox; for (Index i = 0; i < steps.x(); i++) { double x = _startingpoint.x() + double(i) * _stepsizes.x(); for (Index j = 0; j < steps.y(); j++) { double y = _startingpoint.y() + double(j) * _stepsizes.y(); for (Index k = 0; k < steps.z(); k++) { double z = _startingpoint.z() + double(k) * _stepsizes.z(); GridContainers::Cartesian_gridpoint point; point.grid_weight = 1.0; point.grid_pos = Eigen::Vector3d(x, y, z); gridbox.addGridPoint(point); if (gridbox.size() == gridboxsize) { _grid_boxes.push_back(gridbox); gridbox = GridBox(); } } } } if (gridbox.size() > 0) { _grid_boxes.push_back(gridbox); } #pragma omp parallel for for (Index i = 0; i < getBoxesSize(); i++) { _grid_boxes[i].FindSignificantShells(basis); _grid_boxes[i].PrepareForIntegration(); } _totalgridsize = 0; for (auto& box : _grid_boxes) { _totalgridsize += box.size(); } } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/grids/sphere_lebedev_rule.cc000066400000000000000000006574601412152066400221510ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "A_ol I_ol" BA_olI_ol, * WITHOUT WARRANTIE_ol OR CONDITION_ol OF ANY KIND, either express or implied. * _olee the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/sphere_lebedev_rule.h" #include "votca/xtp/grid_containers.h" #include "votca/xtp/qmmolecule.h" #include "votca/xtp/qmpackage.h" namespace votca { namespace xtp { std::map LebedevGrid::CalculateSphericalGrids(const QMMolecule &atoms, const std::string &type) const { std::vector unique_atoms = atoms.FindUniqueElements(); std::map result; for (const std::string &atomname : unique_atoms) { result[atomname] = CalculateUnitSphereGrid(atomname, type); } return result; } GridContainers::spherical_grid LebedevGrid::CalculateUnitSphereGrid( const std::string &element, const std::string &type) const { Index order = Type2MaxOrder(element, type); return CalculateUnitSphereGrid(order); } GridContainers::spherical_grid LebedevGrid::CalculateUnitSphereGrid( Index order) const { const double fourpi = 4 * tools::conv::Pi; GridContainers::spherical_grid result; result.phi = Eigen::VectorXd::Zero(order); result.theta = Eigen::VectorXd::Zero(order); result.weight = Eigen::VectorXd::Zero(order); Eigen::Matrix4Xd xyzw = ld_by_order(order); for (Index i = 0; i < order; i++) { Eigen::Vector3d xyz = xyzw.col(i).head<3>(); Eigen::Vector2d spherical = this->Cartesian2SphericalAngle(xyz); result.phi[i] = spherical[0]; result.theta[i] = spherical[1]; result.weight[i] = fourpi * xyzw.col(i)[3]; } return result; } Index LebedevGrid::Type2MaxOrder(const std::map &map, const std::string &element) const { if (map.count(element)) { return map.at(element); } else { throw std::runtime_error("Element type " + element + " for LebedevGrid not found"); } return -1; } Index LebedevGrid::Type2MaxOrder(const std::string &element, const std::string &type) const { if (type == "medium") { return Type2MaxOrder(MediumOrder, element); } else if (type == "coarse") { return Type2MaxOrder(CoarseOrder, element); } else if (type == "xcoarse") { return Type2MaxOrder(XcoarseOrder, element); } else if (type == "fine") { return Type2MaxOrder(FineOrder, element); } else if (type == "xfine") { return Type2MaxOrder(XfineOrder, element); } throw std::runtime_error("Grid type " + type + " is not implemented"); return -1; } //****************************************************************************80 Index LebedevGrid::available_table(Index rule) const //****************************************************************************80 // // Purpose: // // AVAILABLE_TABLE returns the availability of a Lebedev rule. // // Modified: // // 12 September 2010 // // Author: // // John Burkardt // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Input, Index RULE, the index of the rule, between 1 and 65. // // Output, Index AVAILABLE_TABLE, the availability of the rule. // * -1, there is no such rule; // * 0, there is such a rule, but it is not available in this library. // * 1, the rule is available in this library. // { Index rule_max = 65; Index table[65] = {1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1}; Index value; if (rule < 1) { value = -1; } else if (rule_max < rule) { value = -1; } else { value = table[rule - 1]; } return value; } //****************************************************************************80 Index LebedevGrid::gen_oh(Index code, double a, double b, double v, double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // GEN_OH generates points under OH symmetry. // // Discussion: // // Given a point on a sphere, specified by A and B, this routine generates // all the equivalent points under OH symmetry, making grid points with // weight V. // // The variable NUM is increased by the number of different points // generated. // // Depending on CODE, there are from 6 to 48 different but equivalent // points that are generated: // // CODE=1: (0,0,1) etc ( 6 points) // CODE=2: (0,A,A) etc, A=1/sqrt(2) ( 12 points) // CODE=3: (A,A,A) etc, A=1/sqrt(3) ( 8 points) // CODE=4: (A,A,B) etc, B=sqrt(1-2 A^2) ( 24 points) // CODE=5: (A,B,0) etc, B=sqrt(1-A^2), A input ( 24 points) // CODE=6: (A,B,C) etc, C=sqrt(1-A^2-B^2), A, B input ( 48 points) // // Modified: // // 11 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Input, Index CODE, selects the symmetry group. // // Input/output, Index &NUM, the number of points. This is incremented // upon output by the number of points generated on this call. // // Input, double A, B, information that may be needed to // generate the coordinates of the points (for code = 5 or 6 only). // // Input, double V, the weight to be assigned the points. // // Output, double X[*], Y[*], Z[*], W[*], the coordinates // and weights of the symmetric points generated on this call. // // Output, Index GEN_OH, the number of points generated on this call. // { double c; Index num; if (code == 1) { a = 1.0; x[0] = a; y[0] = 0.0; z[0] = 0.0; w[0] = v; x[1] = -a; y[1] = 0.0; z[1] = 0.0; w[1] = v; x[2] = 0.0; y[2] = a; z[2] = 0.0; w[2] = v; x[3] = 0.0; y[3] = -a; z[3] = 0.0; w[3] = v; x[4] = 0.0; y[4] = 0.0; z[4] = a; w[4] = v; x[5] = 0.0; y[5] = 0.0; z[5] = -a; w[5] = v; num = 6; } else if (code == 2) { a = sqrt(0.5); x[0] = 0; y[0] = a; z[0] = a; w[0] = v; x[1] = 0; y[1] = -a; z[1] = a; w[1] = v; x[2] = 0; y[2] = a; z[2] = -a; w[2] = v; x[3] = 0; y[3] = -a; z[3] = -a; w[3] = v; x[4] = a; y[4] = 0; z[4] = a; w[4] = v; x[5] = -a; y[5] = 0; z[5] = a; w[5] = v; x[6] = a; y[6] = 0; z[6] = -a; w[6] = v; x[7] = -a; y[7] = 0; z[7] = -a; w[7] = v; x[8] = a; y[8] = a; z[8] = 0; w[8] = v; x[9] = -a; y[9] = a; z[9] = 0; w[9] = v; x[10] = a; y[10] = -a; z[10] = 0; w[10] = v; x[11] = -a; y[11] = -a; z[11] = 0; w[11] = v; num = 12; } else if (code == 3) { a = sqrt(1.0 / 3.0); x[0] = a; y[0] = a; z[0] = a; w[0] = v; x[1] = -a; y[1] = a; z[1] = a; w[1] = v; x[2] = a; y[2] = -a; z[2] = a; w[2] = v; x[3] = -a; y[3] = -a; z[3] = a; w[3] = v; x[4] = a; y[4] = a; z[4] = -a; w[4] = v; x[5] = -a; y[5] = a; z[5] = -a; w[5] = v; x[6] = a; y[6] = -a; z[6] = -a; w[6] = v; x[7] = -a; y[7] = -a; z[7] = -a; w[7] = v; num = 8; } else if (code == 4) { b = sqrt(1.0 - 2.0 * a * a); x[0] = a; y[0] = a; z[0] = b; w[0] = v; x[1] = -a; y[1] = a; z[1] = b; w[1] = v; x[2] = a; y[2] = -a; z[2] = b; w[2] = v; x[3] = -a; y[3] = -a; z[3] = b; w[3] = v; x[4] = a; y[4] = a; z[4] = -b; w[4] = v; x[5] = -a; y[5] = a; z[5] = -b; w[5] = v; x[6] = a; y[6] = -a; z[6] = -b; w[6] = v; x[7] = -a; y[7] = -a; z[7] = -b; w[7] = v; x[8] = a; y[8] = b; z[8] = a; w[8] = v; x[9] = -a; y[9] = b; z[9] = a; w[9] = v; x[10] = a; y[10] = -b; z[10] = a; w[10] = v; x[11] = -a; y[11] = -b; z[11] = a; w[11] = v; x[12] = a; y[12] = b; z[12] = -a; w[12] = v; x[13] = -a; y[13] = b; z[13] = -a; w[13] = v; x[14] = a; y[14] = -b; z[14] = -a; w[14] = v; x[15] = -a; y[15] = -b; z[15] = -a; w[15] = v; x[16] = b; y[16] = a; z[16] = a; w[16] = v; x[17] = -b; y[17] = a; z[17] = a; w[17] = v; x[18] = b; y[18] = -a; z[18] = a; w[18] = v; x[19] = -b; y[19] = -a; z[19] = a; w[19] = v; x[20] = b; y[20] = a; z[20] = -a; w[20] = v; x[21] = -b; y[21] = a; z[21] = -a; w[21] = v; x[22] = b; y[22] = -a; z[22] = -a; w[22] = v; x[23] = -b; y[23] = -a; z[23] = -a; w[23] = v; num = 24; } else if (code == 5) { b = sqrt(1.0 - a * a); x[0] = a; y[0] = b; z[0] = 0; w[0] = v; x[1] = -a; y[1] = b; z[1] = 0; w[1] = v; x[2] = a; y[2] = -b; z[2] = 0; w[2] = v; x[3] = -a; y[3] = -b; z[3] = 0; w[3] = v; x[4] = b; y[4] = a; z[4] = 0; w[4] = v; x[5] = -b; y[5] = a; z[5] = 0; w[5] = v; x[6] = b; y[6] = -a; z[6] = 0; w[6] = v; x[7] = -b; y[7] = -a; z[7] = 0; w[7] = v; x[8] = a; y[8] = 0; z[8] = b; w[8] = v; x[9] = -a; y[9] = 0; z[9] = b; w[9] = v; x[10] = a; y[10] = 0; z[10] = -b; w[10] = v; x[11] = -a; y[11] = 0; z[11] = -b; w[11] = v; x[12] = b; y[12] = 0; z[12] = a; w[12] = v; x[13] = -b; y[13] = 0; z[13] = a; w[13] = v; x[14] = b; y[14] = 0; z[14] = -a; w[14] = v; x[15] = -b; y[15] = 0; z[15] = -a; w[15] = v; x[16] = 0; y[16] = a; z[16] = b; w[16] = v; x[17] = 0; y[17] = -a; z[17] = b; w[17] = v; x[18] = 0; y[18] = a; z[18] = -b; w[18] = v; x[19] = 0; y[19] = -a; z[19] = -b; w[19] = v; x[20] = 0; y[20] = b; z[20] = a; w[20] = v; x[21] = 0; y[21] = -b; z[21] = a; w[21] = v; x[22] = 0; y[22] = b; z[22] = -a; w[22] = v; x[23] = 0; y[23] = -b; z[23] = -a; w[23] = v; num = 24; } else if (code == 6) { c = sqrt(1.0 - a * a - b * b); x[0] = a; y[0] = b; z[0] = c; w[0] = v; x[1] = -a; y[1] = b; z[1] = c; w[1] = v; x[2] = a; y[2] = -b; z[2] = c; w[2] = v; x[3] = -a; y[3] = -b; z[3] = c; w[3] = v; x[4] = a; y[4] = b; z[4] = -c; w[4] = v; x[5] = -a; y[5] = b; z[5] = -c; w[5] = v; x[6] = a; y[6] = -b; z[6] = -c; w[6] = v; x[7] = -a; y[7] = -b; z[7] = -c; w[7] = v; x[8] = a; y[8] = c; z[8] = b; w[8] = v; x[9] = -a; y[9] = c; z[9] = b; w[9] = v; x[10] = a; y[10] = -c; z[10] = b; w[10] = v; x[11] = -a; y[11] = -c; z[11] = b; w[11] = v; x[12] = a; y[12] = c; z[12] = -b; w[12] = v; x[13] = -a; y[13] = c; z[13] = -b; w[13] = v; x[14] = a; y[14] = -c; z[14] = -b; w[14] = v; x[15] = -a; y[15] = -c; z[15] = -b; w[15] = v; x[16] = b; y[16] = a; z[16] = c; w[16] = v; x[17] = -b; y[17] = a; z[17] = c; w[17] = v; x[18] = b; y[18] = -a; z[18] = c; w[18] = v; x[19] = -b; y[19] = -a; z[19] = c; w[19] = v; x[20] = b; y[20] = a; z[20] = -c; w[20] = v; x[21] = -b; y[21] = a; z[21] = -c; w[21] = v; x[22] = b; y[22] = -a; z[22] = -c; w[22] = v; x[23] = -b; y[23] = -a; z[23] = -c; w[23] = v; x[24] = b; y[24] = c; z[24] = a; w[24] = v; x[25] = -b; y[25] = c; z[25] = a; w[25] = v; x[26] = b; y[26] = -c; z[26] = a; w[26] = v; x[27] = -b; y[27] = -c; z[27] = a; w[27] = v; x[28] = b; y[28] = c; z[28] = -a; w[28] = v; x[29] = -b; y[29] = c; z[29] = -a; w[29] = v; x[30] = b; y[30] = -c; z[30] = -a; w[30] = v; x[31] = -b; y[31] = -c; z[31] = -a; w[31] = v; x[32] = c; y[32] = a; z[32] = b; w[32] = v; x[33] = -c; y[33] = a; z[33] = b; w[33] = v; x[34] = c; y[34] = -a; z[34] = b; w[34] = v; x[35] = -c; y[35] = -a; z[35] = b; w[35] = v; x[36] = c; y[36] = a; z[36] = -b; w[36] = v; x[37] = -c; y[37] = a; z[37] = -b; w[37] = v; x[38] = c; y[38] = -a; z[38] = -b; w[38] = v; x[39] = -c; y[39] = -a; z[39] = -b; w[39] = v; x[40] = c; y[40] = b; z[40] = a; w[40] = v; x[41] = -c; y[41] = b; z[41] = a; w[41] = v; x[42] = c; y[42] = -b; z[42] = a; w[42] = v; x[43] = -c; y[43] = -b; z[43] = a; w[43] = v; x[44] = c; y[44] = b; z[44] = -a; w[44] = v; x[45] = -c; y[45] = b; z[45] = -a; w[45] = v; x[46] = c; y[46] = -b; z[46] = -a; w[46] = v; x[47] = -c; y[47] = -b; z[47] = -a; w[47] = v; num = 48; } else { throw std::runtime_error( "GEN_OH - Fatal error!\n Illegal value of code.\n"); } return num; } //****************************************************************************80 Eigen::Matrix4Xd LebedevGrid::ld_by_order(Index order) const // Purpose: // // LD_BY_ORDER returns a Lebedev angular grid given its order. // // Discussion: // // Only a certain set of such rules are available through this function. // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // { Eigen::VectorXd x = Eigen::VectorXd::Zero(order); Eigen::VectorXd y = Eigen::VectorXd::Zero(order); Eigen::VectorXd z = Eigen::VectorXd::Zero(order); Eigen::VectorXd w = Eigen::VectorXd::Zero(order); switch (order) { case 6: ld0006(x.data(), y.data(), z.data(), w.data()); break; case 14: ld0014(x.data(), y.data(), z.data(), w.data()); break; case 26: ld0026(x.data(), y.data(), z.data(), w.data()); break; case 38: ld0038(x.data(), y.data(), z.data(), w.data()); break; case 50: ld0050(x.data(), y.data(), z.data(), w.data()); break; case 74: ld0074(x.data(), y.data(), z.data(), w.data()); break; case 86: ld0086(x.data(), y.data(), z.data(), w.data()); break; case 110: ld0110(x.data(), y.data(), z.data(), w.data()); break; case 146: ld0146(x.data(), y.data(), z.data(), w.data()); break; case 170: ld0170(x.data(), y.data(), z.data(), w.data()); break; case 194: ld0194(x.data(), y.data(), z.data(), w.data()); break; case 230: ld0230(x.data(), y.data(), z.data(), w.data()); break; case 266: ld0266(x.data(), y.data(), z.data(), w.data()); break; case 302: ld0302(x.data(), y.data(), z.data(), w.data()); break; case 350: ld0350(x.data(), y.data(), z.data(), w.data()); break; case 434: ld0434(x.data(), y.data(), z.data(), w.data()); break; case 590: ld0590(x.data(), y.data(), z.data(), w.data()); break; case 770: ld0770(x.data(), y.data(), z.data(), w.data()); break; case 974: ld0974(x.data(), y.data(), z.data(), w.data()); break; case 1202: ld1202(x.data(), y.data(), z.data(), w.data()); break; case 1454: ld1454(x.data(), y.data(), z.data(), w.data()); break; case 1730: ld1730(x.data(), y.data(), z.data(), w.data()); break; case 2030: ld2030(x.data(), y.data(), z.data(), w.data()); break; case 2354: ld2354(x.data(), y.data(), z.data(), w.data()); break; case 2702: ld2702(x.data(), y.data(), z.data(), w.data()); break; case 3074: ld3074(x.data(), y.data(), z.data(), w.data()); break; case 3470: ld3470(x.data(), y.data(), z.data(), w.data()); break; case 3890: ld3890(x.data(), y.data(), z.data(), w.data()); break; case 4334: ld4334(x.data(), y.data(), z.data(), w.data()); break; case 4802: ld4802(x.data(), y.data(), z.data(), w.data()); break; case 5294: ld5294(x.data(), y.data(), z.data(), w.data()); break; case 5810: ld5810(x.data(), y.data(), z.data(), w.data()); break; default: throw std::runtime_error( "LD_BY_ORDER - Fatal error! Unexpected value of ORDER."); break; } Eigen::Matrix4Xd result = Eigen::Matrix4Xd::Zero(4, order); result.row(0) = x; result.row(1) = y; result.row(2) = z; result.row(3) = w; return result; } //****************************************************************************80 void LebedevGrid::ld0006(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0006 computes the 6 point Lebedev angular grid. // // Modified: // // 11 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.1666666666666667; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); return; } //****************************************************************************80 void LebedevGrid::ld0014(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0014 computes the 14 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.6666666666666667e-1; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.7500000000000000e-1; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0026(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0026 computes the 26 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.4761904761904762e-1; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.3809523809523810e-1; n = n + gen_oh(2, a, b, v, x + n, y + n, z + n, w + n); v = 0.3214285714285714e-1; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0038(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0038 computes the 38 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.9523809523809524e-2; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.3214285714285714e-1; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.4597008433809831; v = 0.2857142857142857e-1; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0050(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0050 computes the 50 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.1269841269841270e-1; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.2257495590828924e-1; n = n + gen_oh(2, a, b, v, x + n, y + n, z + n, w + n); v = 0.2109375000000000e-1; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.3015113445777636; v = 0.2017333553791887e-1; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0074(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0074 computes the 74 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.5130671797338464e-3; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.1660406956574204e-1; n = n + gen_oh(2, a, b, v, x + n, y + n, z + n, w + n); v = -0.2958603896103896e-1; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.4803844614152614; v = 0.2657620708215946e-1; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3207726489807764; v = 0.1652217099371571e-1; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0086(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0086 computes the 86 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.1154401154401154e-1; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.1194390908585628e-1; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.3696028464541502; v = 0.1111055571060340e-1; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6943540066026664; v = 0.1187650129453714e-1; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3742430390903412; v = 0.1181230374690448e-1; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0110(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0110 computes the 110 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.3828270494937162e-2; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.9793737512487512e-2; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.1851156353447362; v = 0.8211737283191111e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6904210483822922; v = 0.9942814891178103e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3956894730559419; v = 0.9595471336070963e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4783690288121502; v = 0.9694996361663028e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0146(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0146 computes the 146 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.5996313688621381e-3; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.7372999718620756e-2; n = n + gen_oh(2, a, b, v, x + n, y + n, z + n, w + n); v = 0.7210515360144488e-2; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.6764410400114264; v = 0.7116355493117555e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4174961227965453; v = 0.6753829486314477e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1574676672039082; v = 0.7574394159054034e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1403553811713183; b = 0.4493328323269557; v = 0.6991087353303262e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0170(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0170 computes the 170 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.5544842902037365e-2; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.6071332770670752e-2; n = n + gen_oh(2, a, b, v, x + n, y + n, z + n, w + n); v = 0.6383674773515093e-2; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.2551252621114134; v = 0.5183387587747790e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6743601460362766; v = 0.6317929009813725e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4318910696719410; v = 0.6201670006589077e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2613931360335988; v = 0.5477143385137348e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.4990453161796037; b = 0.1446630744325115; v = 0.5968383987681156e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0194(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0194 computes the 194 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.1782340447244611e-2; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.5716905949977102e-2; n = n + gen_oh(2, a, b, v, x + n, y + n, z + n, w + n); v = 0.5573383178848738e-2; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.6712973442695226; v = 0.5608704082587997e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2892465627575439; v = 0.5158237711805383e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4446933178717437; v = 0.5518771467273614e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1299335447650067; v = 0.4106777028169394e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3457702197611283; v = 0.5051846064614808e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1590417105383530; b = 0.8360360154824589; v = 0.5530248916233094e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0230(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0230 computes the 230 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = -0.5522639919727325e-1; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.4450274607445226e-2; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.4492044687397611; v = 0.4496841067921404e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2520419490210201; v = 0.5049153450478750e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6981906658447242; v = 0.3976408018051883e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6587405243460960; v = 0.4401400650381014e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4038544050097660e-1; v = 0.1724544350544401e-1; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5823842309715585; v = 0.4231083095357343e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3545877390518688; v = 0.5198069864064399e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2272181808998187; b = 0.4864661535886647; v = 0.4695720972568883e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0266(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0266 computes the 266 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = -0.1313769127326952e-2; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = -0.2522728704859336e-2; n = n + gen_oh(2, a, b, v, x + n, y + n, z + n, w + n); v = 0.4186853881700583e-2; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.7039373391585475; v = 0.5315167977810885e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1012526248572414; v = 0.4047142377086219e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4647448726420539; v = 0.4112482394406990e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3277420654971629; v = 0.3595584899758782e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6620338663699974; v = 0.4256131351428158e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.8506508083520399; v = 0.4229582700647240e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3233484542692899; b = 0.1153112011009701; v = 0.4080914225780505e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2314790158712601; b = 0.5244939240922365; v = 0.4071467593830964e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0302(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0302 computes the 302 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.8545911725128148e-3; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.3599119285025571e-2; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.3515640345570105; v = 0.3449788424305883e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6566329410219612; v = 0.3604822601419882e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4729054132581005; v = 0.3576729661743367e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.9618308522614784e-1; v = 0.2352101413689164e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2219645236294178; v = 0.3108953122413675e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7011766416089545; v = 0.3650045807677255e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2644152887060663; v = 0.2982344963171804e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5718955891878961; v = 0.3600820932216460e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2510034751770465; b = 0.8000727494073952; v = 0.3571540554273387e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1233548532583327; b = 0.4127724083168531; v = 0.3392312205006170e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0350(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0350 computes the 350 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.3006796749453936e-2; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.3050627745650771e-2; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.7068965463912316; v = 0.1621104600288991e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4794682625712025; v = 0.3005701484901752e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1927533154878019; v = 0.2990992529653774e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6930357961327123; v = 0.2982170644107595e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3608302115520091; v = 0.2721564237310992e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6498486161496169; v = 0.3033513795811141e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1932945013230339; v = 0.3007949555218533e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3800494919899303; v = 0.2881964603055307e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2899558825499574; b = 0.7934537856582316; v = 0.2958357626535696e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.9684121455103957e-1; b = 0.8280801506686862; v = 0.3036020026407088e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1833434647041659; b = 0.9074658265305127; v = 0.2832187403926303e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0434(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0434 computes the 434 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.5265897968224436e-3; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.2548219972002607e-2; n = n + gen_oh(2, a, b, v, x + n, y + n, z + n, w + n); v = 0.2512317418927307e-2; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.6909346307509111; v = 0.2530403801186355e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1774836054609158; v = 0.2014279020918528e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4914342637784746; v = 0.2501725168402936e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6456664707424256; v = 0.2513267174597564e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2861289010307638; v = 0.2302694782227416e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7568084367178018e-1; v = 0.1462495621594614e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3927259763368002; v = 0.2445373437312980e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.8818132877794288; v = 0.2417442375638981e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.9776428111182649; v = 0.1910951282179532e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2054823696403044; b = 0.8689460322872412; v = 0.2416930044324775e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5905157048925271; b = 0.7999278543857286; v = 0.2512236854563495e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5550152361076807; b = 0.7717462626915901; v = 0.2496644054553086e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.9371809858553722; b = 0.3344363145343455; v = 0.2236607760437849e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0590(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0590 computes the 590 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.3095121295306187e-3; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.1852379698597489e-2; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.7040954938227469; v = 0.1871790639277744e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6807744066455243; v = 0.1858812585438317e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6372546939258752; v = 0.1852028828296213e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5044419707800358; v = 0.1846715956151242e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4215761784010967; v = 0.1818471778162769e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3317920736472123; v = 0.1749564657281154e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2384736701421887; v = 0.1617210647254411e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1459036449157763; v = 0.1384737234851692e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6095034115507196e-1; v = 0.9764331165051050e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6116843442009876; v = 0.1857161196774078e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3964755348199858; v = 0.1705153996395864e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1724782009907724; v = 0.1300321685886048e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5610263808622060; b = 0.3518280927733519; v = 0.1842866472905286e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4742392842551980; b = 0.2634716655937950; v = 0.1802658934377451e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5984126497885380; b = 0.1816640840360209; v = 0.1849830560443660e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3791035407695563; b = 0.1720795225656878; v = 0.1713904507106709e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2778673190586244; b = 0.8213021581932511e-1; v = 0.1555213603396808e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5033564271075117; b = 0.8999205842074875e-1; v = 0.1802239128008525e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0770(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0770 computes the 770 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.2192942088181184e-3; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.1436433617319080e-2; n = n + gen_oh(2, a, b, v, x + n, y + n, z + n, w + n); v = 0.1421940344335877e-2; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.5087204410502360e-1; v = 0.6798123511050502e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1228198790178831; v = 0.9913184235294912e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2026890814408786; v = 0.1180207833238949e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2847745156464294; v = 0.1296599602080921e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3656719078978026; v = 0.1365871427428316e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4428264886713469; v = 0.1402988604775325e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5140619627249735; v = 0.1418645563595609e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6306401219166803; v = 0.1421376741851662e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6716883332022612; v = 0.1423996475490962e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6979792685336881; v = 0.1431554042178567e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1446865674195309; v = 0.9254401499865368e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3390263475411216; v = 0.1250239995053509e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5335804651263506; v = 0.1394365843329230e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.6944024393349413e-1; b = 0.2355187894242326; v = 0.1127089094671749e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2269004109529460; b = 0.4102182474045730; v = 0.1345753760910670e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.8025574607775339e-1; b = 0.6214302417481605; v = 0.1424957283316783e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1467999527896572; b = 0.3245284345717394; v = 0.1261523341237750e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1571507769824727; b = 0.5224482189696630; v = 0.1392547106052696e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2365702993157246; b = 0.6017546634089558; v = 0.1418761677877656e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.7714815866765732e-1; b = 0.4346575516141163; v = 0.1338366684479554e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3062936666210730; b = 0.4908826589037616; v = 0.1393700862676131e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3822477379524787; b = 0.5648768149099500; v = 0.1415914757466932e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld0974(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD0974 computes the 974 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.1438294190527431e-3; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.1125772288287004e-2; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.4292963545341347e-1; v = 0.4948029341949241e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1051426854086404; v = 0.7357990109125470e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1750024867623087; v = 0.8889132771304384e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2477653379650257; v = 0.9888347838921435e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3206567123955957; v = 0.1053299681709471e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3916520749849983; v = 0.1092778807014578e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4590825874187624; v = 0.1114389394063227e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5214563888415861; v = 0.1123724788051555e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6253170244654199; v = 0.1125239325243814e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6637926744523170; v = 0.1126153271815905e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6910410398498301; v = 0.1130286931123841e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7052907007457760; v = 0.1134986534363955e-2; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1236686762657990; v = 0.6823367927109931e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2940777114468387; v = 0.9454158160447096e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.4697753849207649; v = 0.1074429975385679e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.6334563241139567; v = 0.1129300086569132e-2; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5974048614181342e-1; b = 0.2029128752777523; v = 0.8436884500901954e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1375760408473636; b = 0.4602621942484054; v = 0.1075255720448885e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3391016526336286; b = 0.5030673999662036; v = 0.1108577236864462e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1271675191439820; b = 0.2817606422442134; v = 0.9566475323783357e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2693120740413512; b = 0.4331561291720157; v = 0.1080663250717391e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1419786452601918; b = 0.6256167358580814; v = 0.1126797131196295e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6709284600738255e-1; b = 0.3798395216859157; v = 0.1022568715358061e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.7057738183256172e-1; b = 0.5517505421423520; v = 0.1108960267713108e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2783888477882155; b = 0.6029619156159187; v = 0.1122790653435766e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1979578938917407; b = 0.3589606329589096; v = 0.1032401847117460e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2087307061103274; b = 0.5348666438135476; v = 0.1107249382283854e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4055122137872836; b = 0.5674997546074373; v = 0.1121780048519972e-2; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld1202(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD1202 computes the 1202 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.1105189233267572e-3; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.9205232738090741e-3; n = n + gen_oh(2, a, b, v, x + n, y + n, z + n, w + n); v = 0.9133159786443561e-3; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.3712636449657089e-1; v = 0.3690421898017899e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.9140060412262223e-1; v = 0.5603990928680660e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1531077852469906; v = 0.6865297629282609e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2180928891660612; v = 0.7720338551145630e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2839874532200175; v = 0.8301545958894795e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3491177600963764; v = 0.8686692550179628e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4121431461444309; v = 0.8927076285846890e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4718993627149127; v = 0.9060820238568219e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5273145452842337; v = 0.9119777254940867e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6209475332444019; v = 0.9128720138604181e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6569722711857291; v = 0.9130714935691735e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6841788309070143; v = 0.9152873784554116e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7012604330123631; v = 0.9187436274321654e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1072382215478166; v = 0.5176977312965694e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2582068959496968; v = 0.7331143682101417e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.4172752955306717; v = 0.8463232836379928e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5700366911792503; v = 0.9031122694253992e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.9827986018263947; b = 0.1771774022615325; v = 0.6485778453163257e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.9624249230326228; b = 0.2475716463426288; v = 0.7435030910982369e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.9402007994128811; b = 0.3354616289066489; v = 0.7998527891839054e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.9320822040143202; b = 0.3173615246611977; v = 0.8101731497468018e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.9043674199393299; b = 0.4090268427085357; v = 0.8483389574594331e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.8912407560074747; b = 0.3854291150669224; v = 0.8556299257311812e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.8676435628462708; b = 0.4932221184851285; v = 0.8803208679738260e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.8581979986041619; b = 0.4785320675922435; v = 0.8811048182425720e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.8396753624049856; b = 0.4507422593157064; v = 0.8850282341265444e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.8165288564022188; b = 0.5632123020762100; v = 0.9021342299040653e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.8015469370783529; b = 0.5434303569693900; v = 0.9010091677105086e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.7773563069070351; b = 0.5123518486419871; v = 0.9022692938426915e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.7661621213900394; b = 0.6394279634749102; v = 0.9158016174693465e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.7553584143533510; b = 0.6269805509024392; v = 0.9131578003189435e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.7344305757559503; b = 0.6031161693096310; v = 0.9107813579482705e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.7043837184021765; b = 0.5693702498468441; v = 0.9105760258970126e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld1454(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD1454 computes the 1454 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.7777160743261247e-4; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.7557646413004701e-3; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.3229290663413854e-1; v = 0.2841633806090617e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.8036733271462222e-1; v = 0.4374419127053555e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1354289960531653; v = 0.5417174740872172e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1938963861114426; v = 0.6148000891358593e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2537343715011275; v = 0.6664394485800705e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3135251434752570; v = 0.7025039356923220e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3721558339375338; v = 0.7268511789249627e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4286809575195696; v = 0.7422637534208629e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4822510128282994; v = 0.7509545035841214e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5320679333566263; v = 0.7548535057718401e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6172998195394274; v = 0.7554088969774001e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6510679849127481; v = 0.7553147174442808e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6777315251687360; v = 0.7564767653292297e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6963109410648741; v = 0.7587991808518730e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7058935009831749; v = 0.7608261832033027e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.9955546194091857; v = 0.4021680447874916e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.9734115901794209; v = 0.5804871793945964e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.9275693732388626; v = 0.6792151955945159e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.8568022422795103; v = 0.7336741211286294e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.7623495553719372; v = 0.7581866300989608e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5707522908892223; b = 0.4387028039889501; v = 0.7538257859800743e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5196463388403083; b = 0.3858908414762617; v = 0.7483517247053123e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4646337531215351; b = 0.3301937372343854; v = 0.7371763661112059e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4063901697557691; b = 0.2725423573563777; v = 0.7183448895756934e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3456329466643087; b = 0.2139510237495250; v = 0.6895815529822191e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2831395121050332; b = 0.1555922309786647; v = 0.6480105801792886e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2197682022925330; b = 0.9892878979686097e-1; v = 0.5897558896594636e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1564696098650355; b = 0.4598642910675510e-1; v = 0.5095708849247346e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6027356673721295; b = 0.3376625140173426; v = 0.7536906428909755e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5496032320255096; b = 0.2822301309727988; v = 0.7472505965575118e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4921707755234567; b = 0.2248632342592540; v = 0.7343017132279698e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4309422998598483; b = 0.1666224723456479; v = 0.7130871582177445e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3664108182313672; b = 0.1086964901822169; v = 0.6817022032112776e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2990189057758436; b = 0.5251989784120085e-1; v = 0.6380941145604121e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6268724013144998; b = 0.2297523657550023; v = 0.7550381377920310e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5707324144834607; b = 0.1723080607093800; v = 0.7478646640144802e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5096360901960365; b = 0.1140238465390513; v = 0.7335918720601220e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4438729938312456; b = 0.5611522095882537e-1; v = 0.7110120527658118e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6419978471082389; b = 0.1164174423140873; v = 0.7571363978689501e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5817218061802611; b = 0.5797589531445219e-1; v = 0.7489908329079234e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld1730(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD1730 computes the 1730 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.6309049437420976e-4; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.6398287705571748e-3; n = n + gen_oh(2, a, b, v, x + n, y + n, z + n, w + n); v = 0.6357185073530720e-3; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.2860923126194662e-1; v = 0.2221207162188168e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7142556767711522e-1; v = 0.3475784022286848e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1209199540995559; v = 0.4350742443589804e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1738673106594379; v = 0.4978569136522127e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2284645438467734; v = 0.5435036221998053e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2834807671701512; v = 0.5765913388219542e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3379680145467339; v = 0.6001200359226003e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3911355454819537; v = 0.6162178172717512e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4422860353001403; v = 0.6265218152438485e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4907781568726057; v = 0.6323987160974212e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5360006153211468; v = 0.6350767851540569e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6142105973596603; v = 0.6354362775297107e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6459300387977504; v = 0.6352302462706235e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6718056125089225; v = 0.6358117881417972e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6910888533186254; v = 0.6373101590310117e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7030467416823252; v = 0.6390428961368665e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.8354951166354646e-1; v = 0.3186913449946576e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2050143009099486; v = 0.4678028558591711e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3370208290706637; v = 0.5538829697598626e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.4689051484233963; v = 0.6044475907190476e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5939400424557334; v = 0.6313575103509012e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1394983311832261; b = 0.4097581162050343e-1; v = 0.4078626431855630e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1967999180485014; b = 0.8851987391293348e-1; v = 0.4759933057812725e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2546183732548967; b = 0.1397680182969819; v = 0.5268151186413440e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3121281074713875; b = 0.1929452542226526; v = 0.5643048560507316e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3685981078502492; b = 0.2467898337061562; v = 0.5914501076613073e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4233760321547856; b = 0.3003104124785409; v = 0.6104561257874195e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4758671236059246; b = 0.3526684328175033; v = 0.6230252860707806e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5255178579796463; b = 0.4031134861145713; v = 0.6305618761760796e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5718025633734589; b = 0.4509426448342351; v = 0.6343092767597889e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2686927772723415; b = 0.4711322502423248e-1; v = 0.5176268945737826e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3306006819904809; b = 0.9784487303942695e-1; v = 0.5564840313313692e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3904906850594983; b = 0.1505395810025273; v = 0.5856426671038980e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4479957951904390; b = 0.2039728156296050; v = 0.6066386925777091e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5027076848919780; b = 0.2571529941121107; v = 0.6208824962234458e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5542087392260217; b = 0.3092191375815670; v = 0.6296314297822907e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6020850887375187; b = 0.3593807506130276; v = 0.6340423756791859e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4019851409179594; b = 0.5063389934378671e-1; v = 0.5829627677107342e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4635614567449800; b = 0.1032422269160612; v = 0.6048693376081110e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5215860931591575; b = 0.1566322094006254; v = 0.6202362317732461e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5758202499099271; b = 0.2098082827491099; v = 0.6299005328403779e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6259893683876795; b = 0.2618824114553391; v = 0.6347722390609353e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5313795124811891; b = 0.5263245019338556e-1; v = 0.6203778981238834e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5893317955931995; b = 0.1061059730982005; v = 0.6308414671239979e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6426246321215801; b = 0.1594171564034221; v = 0.6362706466959498e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6511904367376113; b = 0.5354789536565540e-1; v = 0.6375414170333233e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld2030(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD2030 computes the 2030 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.4656031899197431e-4; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.5421549195295507e-3; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.2540835336814348e-1; v = 0.1778522133346553e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6399322800504915e-1; v = 0.2811325405682796e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1088269469804125; v = 0.3548896312631459e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1570670798818287; v = 0.4090310897173364e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2071163932282514; v = 0.4493286134169965e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2578914044450844; v = 0.4793728447962723e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3085687558169623; v = 0.5015415319164265e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3584719706267024; v = 0.5175127372677937e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4070135594428709; v = 0.5285522262081019e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4536618626222638; v = 0.5356832703713962e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4979195686463577; v = 0.5397914736175170e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5393075111126999; v = 0.5416899441599930e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6115617676843916; v = 0.5419308476889938e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6414308435160159; v = 0.5416936902030596e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6664099412721607; v = 0.5419544338703164e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6859161771214913; v = 0.5428983656630975e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6993625593503890; v = 0.5442286500098193e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7062393387719380; v = 0.5452250345057301e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7479028168349763e-1; v = 0.2568002497728530e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1848951153969366; v = 0.3827211700292145e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3059529066581305; v = 0.4579491561917824e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.4285556101021362; v = 0.5042003969083574e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5468758653496526; v = 0.5312708889976025e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.6565821978343439; v = 0.5438401790747117e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1253901572367117; b = 0.3681917226439641e-1; v = 0.3316041873197344e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1775721510383941; b = 0.7982487607213301e-1; v = 0.3899113567153771e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2305693358216114; b = 0.1264640966592335; v = 0.4343343327201309e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2836502845992063; b = 0.1751585683418957; v = 0.4679415262318919e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3361794746232590; b = 0.2247995907632670; v = 0.4930847981631031e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3875979172264824; b = 0.2745299257422246; v = 0.5115031867540091e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4374019316999074; b = 0.3236373482441118; v = 0.5245217148457367e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4851275843340022; b = 0.3714967859436741; v = 0.5332041499895321e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5303391803806868; b = 0.4175353646321745; v = 0.5384583126021542e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5726197380596287; b = 0.4612084406355461; v = 0.5411067210798852e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2431520732564863; b = 0.4258040133043952e-1; v = 0.4259797391468714e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3002096800895869; b = 0.8869424306722721e-1; v = 0.4604931368460021e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3558554457457432; b = 0.1368811706510655; v = 0.4871814878255202e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4097782537048887; b = 0.1860739985015033; v = 0.5072242910074885e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4616337666067458; b = 0.2354235077395853; v = 0.5217069845235350e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5110707008417874; b = 0.2842074921347011; v = 0.5315785966280310e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5577415286163795; b = 0.3317784414984102; v = 0.5376833708758905e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6013060431366950; b = 0.3775299002040700; v = 0.5408032092069521e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3661596767261781; b = 0.4599367887164592e-1; v = 0.4842744917904866e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4237633153506581; b = 0.9404893773654421e-1; v = 0.5048926076188130e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4786328454658452; b = 0.1431377109091971; v = 0.5202607980478373e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5305702076789774; b = 0.1924186388843570; v = 0.5309932388325743e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5793436224231788; b = 0.2411590944775190; v = 0.5377419770895208e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6247069017094747; b = 0.2886871491583605; v = 0.5411696331677717e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4874315552535204; b = 0.4804978774953206e-1; v = 0.5197996293282420e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5427337322059053; b = 0.9716857199366665e-1; v = 0.5311120836622945e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5943493747246700; b = 0.1465205839795055; v = 0.5384309319956951e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6421314033564943; b = 0.1953579449803574; v = 0.5421859504051886e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6020628374713980; b = 0.4916375015738108e-1; v = 0.5390948355046314e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6529222529856881; b = 0.9861621540127005e-1; v = 0.5433312705027845e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld2354(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD2354 computes the 2354 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.3922616270665292e-4; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.4703831750854424e-3; n = n + gen_oh(2, a, b, v, x + n, y + n, z + n, w + n); v = 0.4678202801282136e-3; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.2290024646530589e-1; v = 0.1437832228979900e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5779086652271284e-1; v = 0.2303572493577644e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.9863103576375984e-1; v = 0.2933110752447454e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1428155792982185; v = 0.3402905998359838e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1888978116601463; v = 0.3759138466870372e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2359091682970210; v = 0.4030638447899798e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2831228833706171; v = 0.4236591432242211e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3299495857966693; v = 0.4390522656946746e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3758840802660796; v = 0.4502523466626247e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4204751831009480; v = 0.4580577727783541e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4633068518751051; v = 0.4631391616615899e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5039849474507313; v = 0.4660928953698676e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5421265793440747; v = 0.4674751807936953e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6092660230557310; v = 0.4676414903932920e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6374654204984869; v = 0.4674086492347870e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6615136472609892; v = 0.4674928539483207e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6809487285958127; v = 0.4680748979686447e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6952980021665196; v = 0.4690449806389040e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7041245497695400; v = 0.4699877075860818e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6744033088306065e-1; v = 0.2099942281069176e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1678684485334166; v = 0.3172269150712804e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2793559049539613; v = 0.3832051358546523e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3935264218057639; v = 0.4252193818146985e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5052629268232558; v = 0.4513807963755000e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.6107905315437531; v = 0.4657797469114178e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1135081039843524; b = 0.3331954884662588e-1; v = 0.2733362800522836e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1612866626099378; b = 0.7247167465436538e-1; v = 0.3235485368463559e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2100786550168205; b = 0.1151539110849745; v = 0.3624908726013453e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2592282009459942; b = 0.1599491097143677; v = 0.3925540070712828e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3081740561320203; b = 0.2058699956028027; v = 0.4156129781116235e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3564289781578164; b = 0.2521624953502911; v = 0.4330644984623263e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4035587288240703; b = 0.2982090785797674; v = 0.4459677725921312e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4491671196373903; b = 0.3434762087235733; v = 0.4551593004456795e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4928854782917489; b = 0.3874831357203437; v = 0.4613341462749918e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5343646791958988; b = 0.4297814821746926; v = 0.4651019618269806e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5732683216530990; b = 0.4699402260943537; v = 0.4670249536100625e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2214131583218986; b = 0.3873602040643895e-1; v = 0.3549555576441708e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2741796504750071; b = 0.8089496256902013e-1; v = 0.3856108245249010e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3259797439149485; b = 0.1251732177620872; v = 0.4098622845756882e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3765441148826891; b = 0.1706260286403185; v = 0.4286328604268950e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4255773574530558; b = 0.2165115147300408; v = 0.4427802198993945e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4727795117058430; b = 0.2622089812225259; v = 0.4530473511488561e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5178546895819012; b = 0.3071721431296201; v = 0.4600805475703138e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5605141192097460; b = 0.3508998998801138; v = 0.4644599059958017e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6004763319352512; b = 0.3929160876166931; v = 0.4667274455712508e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3352842634946949; b = 0.4202563457288019e-1; v = 0.4069360518020356e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3891971629814670; b = 0.8614309758870850e-1; v = 0.4260442819919195e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4409875565542281; b = 0.1314500879380001; v = 0.4408678508029063e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4904893058592484; b = 0.1772189657383859; v = 0.4518748115548597e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5375056138769549; b = 0.2228277110050294; v = 0.4595564875375116e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5818255708669969; b = 0.2677179935014386; v = 0.4643988774315846e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6232334858144959; b = 0.3113675035544165; v = 0.4668827491646946e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4489485354492058; b = 0.4409162378368174e-1; v = 0.4400541823741973e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5015136875933150; b = 0.8939009917748489e-1; v = 0.4514512890193797e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5511300550512623; b = 0.1351806029383365; v = 0.4596198627347549e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5976720409858000; b = 0.1808370355053196; v = 0.4648659016801781e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6409956378989354; b = 0.2257852192301602; v = 0.4675502017157673e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5581222330827514; b = 0.4532173421637160e-1; v = 0.4598494476455523e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6074705984161695; b = 0.9117488031840314e-1; v = 0.4654916955152048e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6532272537379033; b = 0.1369294213140155; v = 0.4684709779505137e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6594761494500487; b = 0.4589901487275583e-1; v = 0.4691445539106986e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld2702(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD2702 computes the 2702 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.2998675149888161e-4; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.4077860529495355e-3; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.2065562538818703e-1; v = 0.1185349192520667e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5250918173022379e-1; v = 0.1913408643425751e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.8993480082038376e-1; v = 0.2452886577209897e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1306023924436019; v = 0.2862408183288702e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1732060388531418; v = 0.3178032258257357e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2168727084820249; v = 0.3422945667633690e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2609528309173586; v = 0.3612790520235922e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3049252927938952; v = 0.3758638229818521e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3483484138084404; v = 0.3868711798859953e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3908321549106406; v = 0.3949429933189938e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4320210071894814; v = 0.4006068107541156e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4715824795890053; v = 0.4043192149672723e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5091984794078453; v = 0.4064947495808078e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5445580145650803; v = 0.4075245619813152e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6072575796841768; v = 0.4076423540893566e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6339484505755803; v = 0.4074280862251555e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6570718257486958; v = 0.4074163756012244e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6762557330090709; v = 0.4077647795071246e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6911161696923790; v = 0.4084517552782530e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7012841911659961; v = 0.4092468459224052e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7064559272410020; v = 0.4097872687240906e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6123554989894765e-1; v = 0.1738986811745028e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1533070348312393; v = 0.2659616045280191e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2563902605244206; v = 0.3240596008171533e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3629346991663361; v = 0.3621195964432943e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.4683949968987538; v = 0.3868838330760539e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5694479240657952; v = 0.4018911532693111e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.6634465430993955; v = 0.4089929432983252e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1033958573552305; b = 0.3034544009063584e-1; v = 0.2279907527706409e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1473521412414395; b = 0.6618803044247135e-1; v = 0.2715205490578897e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1924552158705967; b = 0.1054431128987715; v = 0.3057917896703976e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2381094362890328; b = 0.1468263551238858; v = 0.3326913052452555e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2838121707936760; b = 0.1894486108187886; v = 0.3537334711890037e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3291323133373415; b = 0.2326374238761579; v = 0.3700567500783129e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3736896978741460; b = 0.2758485808485768; v = 0.3825245372589122e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4171406040760013; b = 0.3186179331996921; v = 0.3918125171518296e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4591677985256915; b = 0.3605329796303794; v = 0.3984720419937579e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4994733831718418; b = 0.4012147253586509; v = 0.4029746003338211e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5377731830445096; b = 0.4403050025570692; v = 0.4057428632156627e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5737917830001331; b = 0.4774565904277483; v = 0.4071719274114857e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2027323586271389; b = 0.3544122504976147e-1; v = 0.2990236950664119e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2516942375187273; b = 0.7418304388646328e-1; v = 0.3262951734212878e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3000227995257181; b = 0.1150502745727186; v = 0.3482634608242413e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3474806691046342; b = 0.1571963371209364; v = 0.3656596681700892e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3938103180359209; b = 0.1999631877247100; v = 0.3791740467794218e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4387519590455703; b = 0.2428073457846535; v = 0.3894034450156905e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4820503960077787; b = 0.2852575132906155; v = 0.3968600245508371e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5234573778475101; b = 0.3268884208674639; v = 0.4019931351420050e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5627318647235282; b = 0.3673033321675939; v = 0.4052108801278599e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5996390607156954; b = 0.4061211551830290; v = 0.4068978613940934e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3084780753791947; b = 0.3860125523100059e-1; v = 0.3454275351319704e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3589988275920223; b = 0.7928938987104867e-1; v = 0.3629963537007920e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4078628415881973; b = 0.1212614643030087; v = 0.3770187233889873e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4549287258889735; b = 0.1638770827382693; v = 0.3878608613694378e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5000278512957279; b = 0.2065965798260176; v = 0.3959065270221274e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5429785044928199; b = 0.2489436378852235; v = 0.4015286975463570e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5835939850491711; b = 0.2904811368946891; v = 0.4050866785614717e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6216870353444856; b = 0.3307941957666609; v = 0.4069320185051913e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4151104662709091; b = 0.4064829146052554e-1; v = 0.3760120964062763e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4649804275009218; b = 0.8258424547294755e-1; v = 0.3870969564418064e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5124695757009662; b = 0.1251841962027289; v = 0.3955287790534055e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5574711100606224; b = 0.1679107505976331; v = 0.4015361911302668e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5998597333287227; b = 0.2102805057358715; v = 0.4053836986719548e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6395007148516600; b = 0.2518418087774107; v = 0.4073578673299117e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5188456224746252; b = 0.4194321676077518e-1; v = 0.3954628379231406e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5664190707942778; b = 0.8457661551921499e-1; v = 0.4017645508847530e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6110464353283153; b = 0.1273652932519396; v = 0.4059030348651293e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6526430302051563; b = 0.1698173239076354; v = 0.4080565809484880e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6167551880377548; b = 0.4266398851548864e-1; v = 0.4063018753664651e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6607195418355383; b = 0.8551925814238349e-1; v = 0.4087191292799671e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld3074(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD3074 computes the 3074 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.2599095953754734e-4; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.3603134089687541e-3; n = n + gen_oh(2, a, b, v, x + n, y + n, z + n, w + n); v = 0.3586067974412447e-3; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.1886108518723392e-1; v = 0.9831528474385880e-4; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4800217244625303e-1; v = 0.1605023107954450e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.8244922058397242e-1; v = 0.2072200131464099e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1200408362484023; v = 0.2431297618814187e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1595773530809965; v = 0.2711819064496707e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2002635973434064; v = 0.2932762038321116e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2415127590139982; v = 0.3107032514197368e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2828584158458477; v = 0.3243808058921213e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3239091015338138; v = 0.3349899091374030e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3643225097962194; v = 0.3430580688505218e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4037897083691802; v = 0.3490124109290343e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4420247515194127; v = 0.3532148948561955e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4787572538464938; v = 0.3559862669062833e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5137265251275234; v = 0.3576224317551411e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5466764056654611; v = 0.3584050533086076e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6054859420813535; v = 0.3584903581373224e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6308106701764562; v = 0.3582991879040586e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6530369230179584; v = 0.3582371187963125e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6718609524611158; v = 0.3584353631122350e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6869676499894013; v = 0.3589120166517785e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6980467077240748; v = 0.3595445704531601e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7048241721250522; v = 0.3600943557111074e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5591105222058232e-1; v = 0.1456447096742039e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1407384078513916; v = 0.2252370188283782e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2364035438976309; v = 0.2766135443474897e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3360602737818170; v = 0.3110729491500851e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.4356292630054665; v = 0.3342506712303391e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5321569415256174; v = 0.3491981834026860e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.6232956305040554; v = 0.3576003604348932e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.9469870086838469e-1; b = 0.2778748387309470e-1; v = 0.1921921305788564e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1353170300568141; b = 0.6076569878628364e-1; v = 0.2301458216495632e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1771679481726077; b = 0.9703072762711040e-1; v = 0.2604248549522893e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2197066664231751; b = 0.1354112458524762; v = 0.2845275425870697e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2624783557374927; b = 0.1750996479744100; v = 0.3036870897974840e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3050969521214442; b = 0.2154896907449802; v = 0.3188414832298066e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3472252637196021; b = 0.2560954625740152; v = 0.3307046414722089e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3885610219026360; b = 0.2965070050624096; v = 0.3398330969031360e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4288273776062765; b = 0.3363641488734497; v = 0.3466757899705373e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4677662471302948; b = 0.3753400029836788; v = 0.3516095923230054e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5051333589553359; b = 0.4131297522144286; v = 0.3549645184048486e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5406942145810492; b = 0.4494423776081795; v = 0.3570415969441392e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5742204122576457; b = 0.4839938958841502; v = 0.3581251798496118e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1865407027225188; b = 0.3259144851070796e-1; v = 0.2543491329913348e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2321186453689432; b = 0.6835679505297343e-1; v = 0.2786711051330776e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2773159142523882; b = 0.1062284864451989; v = 0.2985552361083679e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3219200192237254; b = 0.1454404409323047; v = 0.3145867929154039e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3657032593944029; b = 0.1854018282582510; v = 0.3273290662067609e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4084376778363622; b = 0.2256297412014750; v = 0.3372705511943501e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4499004945751427; b = 0.2657104425000896; v = 0.3448274437851510e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4898758141326335; b = 0.3052755487631557; v = 0.3503592783048583e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5281547442266309; b = 0.3439863920645423; v = 0.3541854792663162e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5645346989813992; b = 0.3815229456121914; v = 0.3565995517909428e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5988181252159848; b = 0.4175752420966734; v = 0.3578802078302898e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2850425424471603; b = 0.3562149509862536e-1; v = 0.2958644592860982e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3324619433027876; b = 0.7330318886871096e-1; v = 0.3119548129116835e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3785848333076282; b = 0.1123226296008472; v = 0.3250745225005984e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4232891028562115; b = 0.1521084193337708; v = 0.3355153415935208e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4664287050829722; b = 0.1921844459223610; v = 0.3435847568549328e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5078458493735726; b = 0.2321360989678303; v = 0.3495786831622488e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5473779816204180; b = 0.2715886486360520; v = 0.3537767805534621e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5848617133811376; b = 0.3101924707571355; v = 0.3564459815421428e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6201348281584888; b = 0.3476121052890973; v = 0.3578464061225468e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3852191185387871; b = 0.3763224880035108e-1; v = 0.3239748762836212e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4325025061073423; b = 0.7659581935637135e-1; v = 0.3345491784174287e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4778486229734490; b = 0.1163381306083900; v = 0.3429126177301782e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5211663693009000; b = 0.1563890598752899; v = 0.3492420343097421e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5623469504853703; b = 0.1963320810149200; v = 0.3537399050235257e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6012718188659246; b = 0.2357847407258738; v = 0.3566209152659172e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6378179206390117; b = 0.2743846121244060; v = 0.3581084321919782e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4836936460214534; b = 0.3895902610739024e-1; v = 0.3426522117591512e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5293792562683797; b = 0.7871246819312640e-1; v = 0.3491848770121379e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5726281253100033; b = 0.1187963808202981; v = 0.3539318235231476e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6133658776169068; b = 0.1587914708061787; v = 0.3570231438458694e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6515085491865307; b = 0.1983058575227646; v = 0.3586207335051714e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5778692716064976; b = 0.3977209689791542e-1; v = 0.3541196205164025e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6207904288086192; b = 0.7990157592981152e-1; v = 0.3574296911573953e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6608688171046802; b = 0.1199671308754309; v = 0.3591993279818963e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6656263089489130; b = 0.4015955957805969e-1; v = 0.3595855034661997e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld3470(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD3470 computes the 3470 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.2040382730826330e-4; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.3178149703889544e-3; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.1721420832906233e-1; v = 0.8288115128076110e-4; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4408875374981770e-1; v = 0.1360883192522954e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7594680813878681e-1; v = 0.1766854454542662e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1108335359204799; ; v = 0.2083153161230153e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1476517054388567; v = 0.2333279544657158e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1856731870860615; v = 0.2532809539930247e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2243634099428821; v = 0.2692472184211158e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2633006881662727; v = 0.2819949946811885e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3021340904916283; v = 0.2920953593973030e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3405594048030089; v = 0.2999889782948352e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3783044434007372; v = 0.3060292120496902e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4151194767407910; v = 0.3105109167522192e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4507705766443257; v = 0.3136902387550312e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4850346056573187; v = 0.3157984652454632e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5176950817792470; v = 0.3170516518425422e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5485384240820989; v = 0.3176568425633755e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6039117238943308; v = 0.3177198411207062e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6279956655573113; v = 0.3175519492394733e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6493636169568952; v = 0.3174654952634756e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6677644117704504; v = 0.3175676415467654e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6829368572115624; v = 0.3178923417835410e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6946195818184121; v = 0.3183788287531909e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7025711542057026; v = 0.3188755151918807e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7066004767140119; v = 0.3191916889313849e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5132537689946062e-1; v = 0.1231779611744508e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1297994661331225; v = 0.1924661373839880e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2188852049401307; v = 0.2380881867403424e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3123174824903457; v = 0.2693100663037885e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.4064037620738195; v = 0.2908673382834366e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.4984958396944782; v = 0.3053914619381535e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5864975046021365; v = 0.3143916684147777e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.6686711634580175; v = 0.3187042244055363e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.8715738780835950e-1; b = 0.2557175233367578e-1; v = 0.1635219535869790e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1248383123134007; b = 0.5604823383376681e-1; v = 0.1968109917696070e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1638062693383378; b = 0.8968568601900765e-1; v = 0.2236754342249974e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2035586203373176; b = 0.1254086651976279; v = 0.2453186687017181e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2436798975293774; b = 0.1624780150162012; v = 0.2627551791580541e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2838207507773806; b = 0.2003422342683208; v = 0.2767654860152220e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3236787502217692; b = 0.2385628026255263; v = 0.2879467027765895e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3629849554840691; b = 0.2767731148783578; v = 0.2967639918918702e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4014948081992087; b = 0.3146542308245309; v = 0.3035900684660351e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4389818379260225; b = 0.3519196415895088; v = 0.3087338237298308e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4752331143674377; b = 0.3883050984023654; v = 0.3124608838860167e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5100457318374018; b = 0.4235613423908649; v = 0.3150084294226743e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5432238388954868; b = 0.4574484717196220; v = 0.3165958398598402e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5745758685072442; b = 0.4897311639255524; v = 0.3174320440957372e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1723981437592809; b = 0.3010630597881105e-1; v = 0.2182188909812599e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2149553257844597; b = 0.6326031554204694e-1; v = 0.2399727933921445e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2573256081247422; b = 0.9848566980258631e-1; v = 0.2579796133514652e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2993163751238106; b = 0.1350835952384266; v = 0.2727114052623535e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3407238005148000; b = 0.1725184055442181; v = 0.2846327656281355e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3813454978483264; b = 0.2103559279730725; v = 0.2941491102051334e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4209848104423343; b = 0.2482278774554860; v = 0.3016049492136107e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4594519699996300; b = 0.2858099509982883; v = 0.3072949726175648e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4965640166185930; b = 0.3228075659915428; v = 0.3114768142886460e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5321441655571562; b = 0.3589459907204151; v = 0.3143823673666223e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5660208438582166; b = 0.3939630088864310; v = 0.3162269764661535e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5980264315964364; b = 0.4276029922949089; v = 0.3172164663759821e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2644215852350733; b = 0.3300939429072552e-1; v = 0.2554575398967435e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3090113743443063; b = 0.6803887650078501e-1; v = 0.2701704069135677e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3525871079197808; b = 0.1044326136206709; v = 0.2823693413468940e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3950418005354029; b = 0.1416751597517679; v = 0.2922898463214289e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4362475663430163; b = 0.1793408610504821; v = 0.3001829062162428e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4760661812145854; b = 0.2170630750175722; v = 0.3062890864542953e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5143551042512103; b = 0.2545145157815807; v = 0.3108328279264746e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5509709026935597; b = 0.2913940101706601; v = 0.3140243146201245e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5857711030329428; b = 0.3274169910910705; v = 0.3160638030977130e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6186149917404392; b = 0.3623081329317265; v = 0.3171462882206275e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3586894569557064; b = 0.3497354386450040e-1; v = 0.2812388416031796e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4035266610019441; b = 0.7129736739757095e-1; v = 0.2912137500288045e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4467775312332510; b = 0.1084758620193165; v = 0.2993241256502206e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4883638346608543; b = 0.1460915689241772; v = 0.3057101738983822e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5281908348434601; b = 0.1837790832369980; v = 0.3105319326251432e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5661542687149311; b = 0.2212075390874021; v = 0.3139565514428167e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6021450102031452; b = 0.2580682841160985; v = 0.3161543006806366e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6360520783610050; b = 0.2940656362094121; v = 0.3172985960613294e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4521611065087196; b = 0.3631055365867002e-1; v = 0.2989400336901431e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4959365651560963; b = 0.7348318468484350e-1; v = 0.3054555883947677e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5376815804038283; b = 0.1111087643812648; v = 0.3104764960807702e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5773314480243768; b = 0.1488226085145408; v = 0.3141015825977616e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6148113245575056; b = 0.1862892274135151; v = 0.3164520621159896e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6500407462842380; b = 0.2231909701714456; v = 0.3176652305912204e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5425151448707213; b = 0.3718201306118944e-1; v = 0.3105097161023939e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5841860556907931; b = 0.7483616335067346e-1; v = 0.3143014117890550e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6234632186851500; b = 0.1125990834266120; v = 0.3168172866287200e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6602934551848843; b = 0.1501303813157619; v = 0.3181401865570968e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6278573968375105; b = 0.3767559930245720e-1; v = 0.3170663659156037e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6665611711264577; b = 0.7548443301360158e-1; v = 0.3185447944625510e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld3890(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD3890 computes the 3890 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.1807395252196920e-4; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.2848008782238827e-3; n = n + gen_oh(2, a, b, v, x + n, y + n, z + n, w + n); v = 0.2836065837530581e-3; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.1587876419858352e-1; v = 0.7013149266673816e-4; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4069193593751206e-1; v = 0.1162798021956766e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7025888115257997e-1; v = 0.1518728583972105e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1027495450028704; v = 0.1798796108216934e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1371457730893426; v = 0.2022593385972785e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1727758532671953; v = 0.2203093105575464e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2091492038929037; v = 0.2349294234299855e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2458813281751915; v = 0.2467682058747003e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2826545859450066; v = 0.2563092683572224e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3191957291799622; v = 0.2639253896763318e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3552621469299578; v = 0.2699137479265108e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3906329503406230; v = 0.2745196420166739e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4251028614093031; v = 0.2779529197397593e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4584777520111870; v = 0.2803996086684265e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4905711358710193; v = 0.2820302356715842e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5212011669847385; v = 0.2830056747491068e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5501878488737995; v = 0.2834808950776839e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6025037877479342; v = 0.2835282339078929e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6254572689549016; v = 0.2833819267065800e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6460107179528248; v = 0.2832858336906784e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6639541138154251; v = 0.2833268235451244e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6790688515667495; v = 0.2835432677029253e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6911338580371512; v = 0.2839091722743049e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6999385956126490; v = 0.2843308178875841e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7053037748656896; v = 0.2846703550533846e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4732224387180115e-1; v = 0.1051193406971900e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1202100529326803; v = 0.1657871838796974e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2034304820664855; v = 0.2064648113714232e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2912285643573002; v = 0.2347942745819741e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3802361792726768; v = 0.2547775326597726e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.4680598511056146; v = 0.2686876684847025e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5528151052155599; v = 0.2778665755515867e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.6329386307803041; v = 0.2830996616782929e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.8056516651369069e-1; b = 0.2363454684003124e-1; v = 0.1403063340168372e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1156476077139389; b = 0.5191291632545936e-1; v = 0.1696504125939477e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1520473382760421; b = 0.8322715736994519e-1; v = 0.1935787242745390e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1892986699745931; b = 0.1165855667993712; v = 0.2130614510521968e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2270194446777792; b = 0.1513077167409504; v = 0.2289381265931048e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2648908185093273; b = 0.1868882025807859; v = 0.2418630292816186e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3026389259574136; b = 0.2229277629776224; v = 0.2523400495631193e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3400220296151384; b = 0.2590951840746235; v = 0.2607623973449605e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3768217953335510; b = 0.2951047291750847; v = 0.2674441032689209e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4128372900921884; b = 0.3307019714169930; v = 0.2726432360343356e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4478807131815630; b = 0.3656544101087634; v = 0.2765787685924545e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4817742034089257; b = 0.3997448951939695; v = 0.2794428690642224e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5143472814653344; b = 0.4327667110812024; v = 0.2814099002062895e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5454346213905650; b = 0.4645196123532293; v = 0.2826429531578994e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5748739313170252; b = 0.4948063555703345; v = 0.2832983542550884e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1599598738286342; b = 0.2792357590048985e-1; v = 0.1886695565284976e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1998097412500951; b = 0.5877141038139065e-1; v = 0.2081867882748234e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2396228952566202; b = 0.9164573914691377e-1; v = 0.2245148680600796e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2792228341097746; b = 0.1259049641962687; v = 0.2380370491511872e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3184251107546741; b = 0.1610594823400863; v = 0.2491398041852455e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3570481164426244; b = 0.1967151653460898; v = 0.2581632405881230e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3949164710492144; b = 0.2325404606175168; v = 0.2653965506227417e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4318617293970503; b = 0.2682461141151439; v = 0.2710857216747087e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4677221009931678; b = 0.3035720116011973; v = 0.2754434093903659e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5023417939270955; b = 0.3382781859197439; v = 0.2786579932519380e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5355701836636128; b = 0.3721383065625942; v = 0.2809011080679474e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5672608451328771; b = 0.4049346360466055; v = 0.2823336184560987e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5972704202540162; b = 0.4364538098633802; v = 0.2831101175806309e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2461687022333596; b = 0.3070423166833368e-1; v = 0.2221679970354546e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2881774566286831; b = 0.6338034669281885e-1; v = 0.2356185734270703e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3293963604116978; b = 0.9742862487067941e-1; v = 0.2469228344805590e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3697303822241377; b = 0.1323799532282290; v = 0.2562726348642046e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4090663023135127; b = 0.1678497018129336; v = 0.2638756726753028e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4472819355411712; b = 0.2035095105326114; v = 0.2699311157390862e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4842513377231437; b = 0.2390692566672091; v = 0.2746233268403837e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5198477629962928; b = 0.2742649818076149; v = 0.2781225674454771e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5539453011883145; b = 0.3088503806580094; v = 0.2805881254045684e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5864196762401251; b = 0.3425904245906614; v = 0.2821719877004913e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6171484466668390; b = 0.3752562294789468; v = 0.2830222502333124e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3350337830565727; b = 0.3261589934634747e-1; v = 0.2457995956744870e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3775773224758284; b = 0.6658438928081572e-1; v = 0.2551474407503706e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4188155229848973; b = 0.1014565797157954; v = 0.2629065335195311e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4586805892009344; b = 0.1368573320843822; v = 0.2691900449925075e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4970895714224235; b = 0.1724614851951608; v = 0.2741275485754276e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5339505133960747; b = 0.2079779381416412; v = 0.2778530970122595e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5691665792531440; b = 0.2431385788322288; v = 0.2805010567646741e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6026387682680377; b = 0.2776901883049853; v = 0.2822055834031040e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6342676150163307; b = 0.3113881356386632; v = 0.2831016901243473e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4237951119537067; b = 0.3394877848664351e-1; v = 0.2624474901131803e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4656918683234929; b = 0.6880219556291447e-1; v = 0.2688034163039377e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5058857069185980; b = 0.1041946859721635; v = 0.2738932751287636e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5443204666713996; b = 0.1398039738736393; v = 0.2777944791242523e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5809298813759742; b = 0.1753373381196155; v = 0.2806011661660987e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6156416039447128; b = 0.2105215793514010; v = 0.2824181456597460e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6483801351066604; b = 0.2450953312157051; v = 0.2833585216577828e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5103616577251688; b = 0.3485560643800719e-1; v = 0.2738165236962878e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5506738792580681; b = 0.7026308631512033e-1; v = 0.2778365208203180e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5889573040995292; b = 0.1059035061296403; v = 0.2807852940418966e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6251641589516930; b = 0.1414823925236026; v = 0.2827245949674705e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6592414921570178; b = 0.1767207908214530; v = 0.2837342344829828e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5930314017533384; b = 0.3542189339561672e-1; v = 0.2809233907610981e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6309812253390175; b = 0.7109574040369549e-1; v = 0.2829930809742694e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6666296011353230; b = 0.1067259792282730; v = 0.2841097874111479e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6703715271049922; b = 0.3569455268820809e-1; v = 0.2843455206008783e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld4334(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD4334 computes the 4334 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.1449063022537883e-4; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.2546377329828424e-3; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.1462896151831013e-1; v = 0.6018432961087496e-4; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3769840812493139e-1; v = 0.1002286583263673e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6524701904096891e-1; v = 0.1315222931028093e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.9560543416134648e-1; v = 0.1564213746876724e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1278335898929198; v = 0.1765118841507736e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1613096104466031; v = 0.1928737099311080e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1955806225745371; v = 0.2062658534263270e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2302935218498028; v = 0.2172395445953787e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2651584344113027; v = 0.2262076188876047e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2999276825183209; v = 0.2334885699462397e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3343828669718798; v = 0.2393355273179203e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3683265013750518; v = 0.2439559200468863e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4015763206518108; v = 0.2475251866060002e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4339612026399770; v = 0.2501965558158773e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4653180651114582; v = 0.2521081407925925e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4954893331080803; v = 0.2533881002388081e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5243207068924930; v = 0.2541582900848261e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5516590479041704; v = 0.2545365737525860e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6012371927804176; v = 0.2545726993066799e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6231574466449819; v = 0.2544456197465555e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6429416514181271; v = 0.2543481596881064e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6604124272943595; v = 0.2543506451429194e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6753851470408250; v = 0.2544905675493763e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6876717970626160; v = 0.2547611407344429e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6970895061319234; v = 0.2551060375448869e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7034746912553310; v = 0.2554291933816039e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7067017217542295; v = 0.2556255710686343e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4382223501131123e-1; v = 0.9041339695118195e-4; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1117474077400006; v = 0.1438426330079022e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1897153252911440; v = 0.1802523089820518e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2724023009910331; v = 0.2060052290565496e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3567163308709902; v = 0.2245002248967466e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.4404784483028087; v = 0.2377059847731150e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5219833154161411; v = 0.2468118955882525e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5998179868977553; v = 0.2525410872966528e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.6727803154548222; v = 0.2553101409933397e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.7476563943166086e-1; b = 0.2193168509461185e-1; v = 0.1212879733668632e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1075341482001416; b = 0.4826419281533887e-1; v = 0.1472872881270931e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1416344885203259; b = 0.7751191883575742e-1; v = 0.1686846601010828e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1766325315388586; b = 0.1087558139247680; v = 0.1862698414660208e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2121744174481514; b = 0.1413661374253096; v = 0.2007430956991861e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2479669443408145; b = 0.1748768214258880; v = 0.2126568125394796e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2837600452294113; b = 0.2089216406612073; v = 0.2224394603372113e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3193344933193984; b = 0.2431987685545972; v = 0.2304264522673135e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3544935442438745; b = 0.2774497054377770; v = 0.2368854288424087e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3890571932288154; b = 0.3114460356156915; v = 0.2420352089461772e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4228581214259090; b = 0.3449806851913012; v = 0.2460597113081295e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4557387211304052; b = 0.3778618641248256; v = 0.2491181912257687e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4875487950541643; b = 0.4099086391698978; v = 0.2513528194205857e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5181436529962997; b = 0.4409474925853973; v = 0.2528943096693220e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5473824095600661; b = 0.4708094517711291; v = 0.2538660368488136e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5751263398976174; b = 0.4993275140354637; v = 0.2543868648299022e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1489515746840028; b = 0.2599381993267017e-1; v = 0.1642595537825183e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1863656444351767; b = 0.5479286532462190e-1; v = 0.1818246659849308e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2238602880356348; b = 0.8556763251425254e-1; v = 0.1966565649492420e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2612723375728160; b = 0.1177257802267011; v = 0.2090677905657991e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2984332990206190; b = 0.1508168456192700; v = 0.2193820409510504e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3351786584663333; b = 0.1844801892177727; v = 0.2278870827661928e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3713505522209120; b = 0.2184145236087598; v = 0.2348283192282090e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4067981098954663; b = 0.2523590641486229; v = 0.2404139755581477e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4413769993687534; b = 0.2860812976901373; v = 0.2448227407760734e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4749487182516394; b = 0.3193686757808996; v = 0.2482110455592573e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5073798105075426; b = 0.3520226949547602; v = 0.2507192397774103e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5385410448878654; b = 0.3838544395667890; v = 0.2524765968534880e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5683065353670530; b = 0.4146810037640963; v = 0.2536052388539425e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5965527620663510; b = 0.4443224094681121; v = 0.2542230588033068e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2299227700856157; b = 0.2865757664057584e-1; v = 0.1944817013047896e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2695752998553267; b = 0.5923421684485993e-1; v = 0.2067862362746635e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3086178716611389; b = 0.9117817776057715e-1; v = 0.2172440734649114e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3469649871659077; b = 0.1240593814082605; v = 0.2260125991723423e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3845153566319655; b = 0.1575272058259175; v = 0.2332655008689523e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4211600033403215; b = 0.1912845163525413; v = 0.2391699681532458e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4567867834329882; b = 0.2250710177858171; v = 0.2438801528273928e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4912829319232061; b = 0.2586521303440910; v = 0.2475370504260665e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5245364793303812; b = 0.2918112242865407; v = 0.2502707235640574e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5564369788915756; b = 0.3243439239067890; v = 0.2522031701054241e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5868757697775287; b = 0.3560536787835351; v = 0.2534511269978784e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6157458853519617; b = 0.3867480821242581; v = 0.2541284914955151e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3138461110672113; b = 0.3051374637507278e-1; v = 0.2161509250688394e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3542495872050569; b = 0.6237111233730755e-1; v = 0.2248778513437852e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3935751553120181; b = 0.9516223952401907e-1; v = 0.2322388803404617e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4317634668111147; b = 0.1285467341508517; v = 0.2383265471001355e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4687413842250821; b = 0.1622318931656033; v = 0.2432476675019525e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5044274237060283; b = 0.1959581153836453; v = 0.2471122223750674e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5387354077925727; b = 0.2294888081183837; v = 0.2500291752486870e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5715768898356105; b = 0.2626031152713945; v = 0.2521055942764682e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6028627200136111; b = 0.2950904075286713; v = 0.2534472785575503e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6325039812653463; b = 0.3267458451113286; v = 0.2541599713080121e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3981986708423407; b = 0.3183291458749821e-1; v = 0.2317380975862936e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4382791182133300; b = 0.6459548193880908e-1; v = 0.2378550733719775e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4769233057218166; b = 0.9795757037087952e-1; v = 0.2428884456739118e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5140823911194238; b = 0.1316307235126655; v = 0.2469002655757292e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5496977833862983; b = 0.1653556486358704; v = 0.2499657574265851e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5837047306512727; b = 0.1988931724126510; v = 0.2521676168486082e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6160349566926879; b = 0.2320174581438950; v = 0.2535935662645334e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6466185353209440; b = 0.2645106562168662; v = 0.2543356743363214e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4810835158795404; b = 0.3275917807743992e-1; v = 0.2427353285201535e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5199925041324341; b = 0.6612546183967181e-1; v = 0.2468258039744386e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5571717692207494; b = 0.9981498331474143e-1; v = 0.2500060956440310e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5925789250836378; b = 0.1335687001410374; v = 0.2523238365420979e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6261658523859670; b = 0.1671444402896463; v = 0.2538399260252846e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6578811126669331; b = 0.2003106382156076; v = 0.2546255927268069e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5609624612998100; b = 0.3337500940231335e-1; v = 0.2500583360048449e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5979959659984670; b = 0.6708750335901803e-1; v = 0.2524777638260203e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6330523711054002; b = 0.1008792126424850; v = 0.2540951193860656e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6660960998103972; b = 0.1345050343171794; v = 0.2549524085027472e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6365384364585819; b = 0.3372799460737052e-1; v = 0.2542569507009158e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6710994302899275; b = 0.6755249309678028e-1; v = 0.2552114127580376e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld4802(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD4802 computes the 4802 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.9687521879420705e-4; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.2307897895367918e-3; n = n + gen_oh(2, a, b, v, x + n, y + n, z + n, w + n); v = 0.2297310852498558e-3; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.2335728608887064e-1; v = 0.7386265944001919e-4; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4352987836550653e-1; v = 0.8257977698542210e-4; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6439200521088801e-1; v = 0.9706044762057630e-4; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.9003943631993181e-1; v = 0.1302393847117003e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1196706615548473; v = 0.1541957004600968e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1511715412838134; v = 0.1704459770092199e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1835982828503801; v = 0.1827374890942906e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2165081259155405; v = 0.1926360817436107e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2496208720417563; v = 0.2008010239494833e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2827200673567900; v = 0.2075635983209175e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3156190823994346; v = 0.2131306638690909e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3481476793749115; v = 0.2176562329937335e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3801466086947226; v = 0.2212682262991018e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4114652119634011; v = 0.2240799515668565e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4419598786519751; v = 0.2261959816187525e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4714925949329543; v = 0.2277156368808855e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4999293972879466; v = 0.2287351772128336e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5271387221431248; v = 0.2293490814084085e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5529896780837761; v = 0.2296505312376273e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6000856099481712; v = 0.2296793832318756e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6210562192785175; v = 0.2295785443842974e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6401165879934240; v = 0.2295017931529102e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6571144029244334; v = 0.2295059638184868e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6718910821718863; v = 0.2296232343237362e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6842845591099010; v = 0.2298530178740771e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6941353476269816; v = 0.2301579790280501e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7012965242212991; v = 0.2304690404996513e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7056471428242644; v = 0.2307027995907102e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4595557643585895e-1; v = 0.9312274696671092e-4; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1049316742435023; v = 0.1199919385876926e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1773548879549274; v = 0.1598039138877690e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2559071411236127; v = 0.1822253763574900e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3358156837985898; v = 0.1988579593655040e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.4155835743763893; v = 0.2112620102533307e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.4937894296167472; v = 0.2201594887699007e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5691569694793316; v = 0.2261622590895036e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.6405840854894251; v = 0.2296458453435705e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.7345133894143348e-1; b = 0.2177844081486067e-1; v = 0.1006006990267000e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1009859834044931; b = 0.4590362185775188e-1; v = 0.1227676689635876e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1324289619748758; b = 0.7255063095690877e-1; v = 0.1467864280270117e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1654272109607127; b = 0.1017825451960684; v = 0.1644178912101232e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1990767186776461; b = 0.1325652320980364; v = 0.1777664890718961e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2330125945523278; b = 0.1642765374496765; v = 0.1884825664516690e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2670080611108287; b = 0.1965360374337889; v = 0.1973269246453848e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3008753376294316; b = 0.2290726770542238; v = 0.2046767775855328e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3344475596167860; b = 0.2616645495370823; v = 0.2107600125918040e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3675709724070786; b = 0.2941150728843141; v = 0.2157416362266829e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4001000887587812; b = 0.3262440400919066; v = 0.2197557816920721e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4318956350436028; b = 0.3578835350611916; v = 0.2229192611835437e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4628239056795531; b = 0.3888751854043678; v = 0.2253385110212775e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4927563229773636; b = 0.4190678003222840; v = 0.2271137107548774e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5215687136707969; b = 0.4483151836883852; v = 0.2283414092917525e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5491402346984905; b = 0.4764740676087880; v = 0.2291161673130077e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5753520160126075; b = 0.5034021310998277; v = 0.2295313908576598e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1388326356417754; b = 0.2435436510372806e-1; v = 0.1438204721359031e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1743686900537244; b = 0.5118897057342652e-1; v = 0.1607738025495257e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2099737037950268; b = 0.8014695048539634e-1; v = 0.1741483853528379e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2454492590908548; b = 0.1105117874155699; v = 0.1851918467519151e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2807219257864278; b = 0.1417950531570966; v = 0.1944628638070613e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3156842271975842; b = 0.1736604945719597; v = 0.2022495446275152e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3502090945177752; b = 0.2058466324693981; v = 0.2087462382438514e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3841684849519686; b = 0.2381284261195919; v = 0.2141074754818308e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4174372367906016; b = 0.2703031270422569; v = 0.2184640913748162e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4498926465011892; b = 0.3021845683091309; v = 0.2219309165220329e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4814146229807701; b = 0.3335993355165720; v = 0.2246123118340624e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5118863625734701; b = 0.3643833735518232; v = 0.2266062766915125e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5411947455119144; b = 0.3943789541958179; v = 0.2280072952230796e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5692301500357246; b = 0.4234320144403542; v = 0.2289082025202583e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5958857204139576; b = 0.4513897947419260; v = 0.2294012695120025e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2156270284785766; b = 0.2681225755444491e-1; v = 0.1722434488736947e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2532385054909710; b = 0.5557495747805614e-1; v = 0.1830237421455091e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2902564617771537; b = 0.8569368062950249e-1; v = 0.1923855349997633e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3266979823143256; b = 0.1167367450324135; v = 0.2004067861936271e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3625039627493614; b = 0.1483861994003304; v = 0.2071817297354263e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3975838937548699; b = 0.1803821503011405; v = 0.2128250834102103e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4318396099009774; b = 0.2124962965666424; v = 0.2174513719440102e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4651706555732742; b = 0.2445221837805913; v = 0.2211661839150214e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4974752649620969; b = 0.2762701224322987; v = 0.2240665257813102e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5286517579627517; b = 0.3075627775211328; v = 0.2262439516632620e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5586001195731895; b = 0.3382311089826877; v = 0.2277874557231869e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5872229902021319; b = 0.3681108834741399; v = 0.2287854314454994e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6144258616235123; b = 0.3970397446872839; v = 0.2293268499615575e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2951676508064861; b = 0.2867499538750441e-1; v = 0.1912628201529828e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3335085485472725; b = 0.5867879341903510e-1; v = 0.1992499672238701e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3709561760636381; b = 0.8961099205022284e-1; v = 0.2061275533454027e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4074722861667498; b = 0.1211627927626297; v = 0.2119318215968572e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4429923648839117; b = 0.1530748903554898; v = 0.2167416581882652e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4774428052721736; b = 0.1851176436721877; v = 0.2206430730516600e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5107446539535904; b = 0.2170829107658179; v = 0.2237186938699523e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5428151370542935; b = 0.2487786689026271; v = 0.2260480075032884e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5735699292556964; b = 0.2800239952795016; v = 0.2277098884558542e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6029253794562866; b = 0.3106445702878119; v = 0.2287845715109671e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6307998987073145; b = 0.3404689500841194; v = 0.2293547268236294e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3752652273692719; b = 0.2997145098184479e-1; v = 0.2056073839852528e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4135383879344028; b = 0.6086725898678011e-1; v = 0.2114235865831876e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4506113885153907; b = 0.9238849548435643e-1; v = 0.2163175629770551e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4864401554606072; b = 0.1242786603851851; v = 0.2203392158111650e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5209708076611709; b = 0.1563086731483386; v = 0.2235473176847839e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5541422135830122; b = 0.1882696509388506; v = 0.2260024141501235e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5858880915113817; b = 0.2199672979126059; v = 0.2277675929329182e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6161399390603444; b = 0.2512165482924867; v = 0.2289102112284834e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6448296482255090; b = 0.2818368701871888; v = 0.2295027954625118e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4544796274917948; b = 0.3088970405060312e-1; v = 0.2161281589879992e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4919389072146628; b = 0.6240947677636835e-1; v = 0.2201980477395102e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5279313026985183; b = 0.9430706144280313e-1; v = 0.2234952066593166e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5624169925571135; b = 0.1263547818770374; v = 0.2260540098520838e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5953484627093287; b = 0.1583430788822594; v = 0.2279157981899988e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6266730715339185; b = 0.1900748462555988; v = 0.2291296918565571e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6563363204278871; b = 0.2213599519592567; v = 0.2297533752536649e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5314574716585696; b = 0.3152508811515374e-1; v = 0.2234927356465995e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5674614932298185; b = 0.6343865291465561e-1; v = 0.2261288012985219e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6017706004970264; b = 0.9551503504223951e-1; v = 0.2280818160923688e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6343471270264178; b = 0.1275440099801196; v = 0.2293773295180159e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6651494599127802; b = 0.1593252037671960; v = 0.2300528767338634e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6050184986005704; b = 0.3192538338496105e-1; v = 0.2281893855065666e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6390163550880400; b = 0.6402824353962306e-1; v = 0.2295720444840727e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6711199107088448; b = 0.9609805077002909e-1; v = 0.2303227649026753e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6741354429572275; b = 0.3211853196273233e-1; v = 0.2304831913227114e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld5294(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD5294 computes the 5294 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.9080510764308163e-4; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.2084824361987793e-3; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.2303261686261450e-1; v = 0.5011105657239616e-4; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3757208620162394e-1; v = 0.5942520409683854e-4; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5821912033821852e-1; v = 0.9564394826109721e-4; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.8403127529194872e-1; v = 0.1185530657126338e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1122927798060578; v = 0.1364510114230331e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1420125319192987; v = 0.1505828825605415e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1726396437341978; v = 0.1619298749867023e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2038170058115696; v = 0.1712450504267789e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2352849892876508; v = 0.1789891098164999e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2668363354312461; v = 0.1854474955629795e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2982941279900452; v = 0.1908148636673661e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3295002922087076; v = 0.1952377405281833e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3603094918363593; v = 0.1988349254282232e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3905857895173920; v = 0.2017079807160050e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4202005758160837; v = 0.2039473082709094e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4490310061597227; v = 0.2056360279288953e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4769586160311491; v = 0.2068525823066865e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5038679887049750; v = 0.2076724877534488e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5296454286519961; v = 0.2081694278237885e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5541776207164850; v = 0.2084157631219326e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5990467321921213; v = 0.2084381531128593e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6191467096294587; v = 0.2083476277129307e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6375251212901849; v = 0.2082686194459732e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6540514381131168; v = 0.2082475686112415e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6685899064391510; v = 0.2083139860289915e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6810013009681648; v = 0.2084745561831237e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6911469578730340; v = 0.2087091313375890e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6988956915141736; v = 0.2089718413297697e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7041335794868720; v = 0.2092003303479793e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7067754398018567; v = 0.2093336148263241e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3840368707853623e-1; v = 0.7591708117365267e-4; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.9835485954117399e-1; v = 0.1083383968169186e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1665774947612998; v = 0.1403019395292510e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2405702335362910; v = 0.1615970179286436e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3165270770189046; v = 0.1771144187504911e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3927386145645443; v = 0.1887760022988168e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.4678825918374656; v = 0.1973474670768214e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5408022024266935; v = 0.2033787661234659e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.6104967445752438; v = 0.2072343626517331e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.6760910702685738; v = 0.2091177834226918e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.6655644120217392e-1; b = 0.1936508874588424e-1; v = 0.9316684484675566e-4; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.9446246161270182e-1; b = 0.4252442002115869e-1; v = 0.1116193688682976e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1242651925452509; b = 0.6806529315354374e-1; v = 0.1298623551559414e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1553438064846751; b = 0.9560957491205369e-1; v = 0.1450236832456426e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1871137110542670; b = 0.1245931657452888; v = 0.1572719958149914e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2192612628836257; b = 0.1545385828778978; v = 0.1673234785867195e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2515682807206955; b = 0.1851004249723368; v = 0.1756860118725188e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2838535866287290; b = 0.2160182608272384; v = 0.1826776290439367e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3159578817528521; b = 0.2470799012277111; v = 0.1885116347992865e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3477370882791392; b = 0.2781014208986402; v = 0.1933457860170574e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3790576960890540; b = 0.3089172523515731; v = 0.1973060671902064e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4097938317810200; b = 0.3393750055472244; v = 0.2004987099616311e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4398256572859637; b = 0.3693322470987730; v = 0.2030170909281499e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4690384114718480; b = 0.3986541005609877; v = 0.2049461460119080e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4973216048301053; b = 0.4272112491408562; v = 0.2063653565200186e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5245681526132446; b = 0.4548781735309936; v = 0.2073507927381027e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5506733911803888; b = 0.4815315355023251; v = 0.2079764593256122e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5755339829522475; b = 0.5070486445801855; v = 0.2083150534968778e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1305472386056362; b = 0.2284970375722366e-1; v = 0.1262715121590664e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1637327908216477; b = 0.4812254338288384e-1; v = 0.1414386128545972e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1972734634149637; b = 0.7531734457511935e-1; v = 0.1538740401313898e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2308694653110130; b = 0.1039043639882017; v = 0.1642434942331432e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2643899218338160; b = 0.1334526587117626; v = 0.1729790609237496e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2977171599622171; b = 0.1636414868936382; v = 0.1803505190260828e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3307293903032310; b = 0.1942195406166568; v = 0.1865475350079657e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3633069198219073; b = 0.2249752879943753; v = 0.1917182669679069e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3953346955922727; b = 0.2557218821820032; v = 0.1959851709034382e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4267018394184914; b = 0.2862897925213193; v = 0.1994529548117882e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4573009622571704; b = 0.3165224536636518; v = 0.2022138911146548e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4870279559856109; b = 0.3462730221636496; v = 0.2043518024208592e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5157819581450322; b = 0.3754016870282835; v = 0.2059450313018110e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5434651666465393; b = 0.4037733784993613; v = 0.2070685715318472e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5699823887764627; b = 0.4312557784139123; v = 0.2077955310694373e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5952403350947741; b = 0.4577175367122110; v = 0.2081980387824712e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2025152599210369; b = 0.2520253617719557e-1; v = 0.1521318610377956e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2381066653274425; b = 0.5223254506119000e-1; v = 0.1622772720185755e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2732823383651612; b = 0.8060669688588620e-1; v = 0.1710498139420709e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3080137692611118; b = 0.1099335754081255; v = 0.1785911149448736e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3422405614587601; b = 0.1399120955959857; v = 0.1850125313687736e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3758808773890420; b = 0.1702977801651705; v = 0.1904229703933298e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4088458383438932; b = 0.2008799256601680; v = 0.1949259956121987e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4410450550841152; b = 0.2314703052180836; v = 0.1986161545363960e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4723879420561312; b = 0.2618972111375892; v = 0.2015790585641370e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5027843561874343; b = 0.2920013195600270; v = 0.2038934198707418e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5321453674452458; b = 0.3216322555190551; v = 0.2056334060538251e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5603839113834030; b = 0.3506456615934198; v = 0.2068705959462289e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5874150706875146; b = 0.3789007181306267; v = 0.2076753906106002e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6131559381660038; b = 0.4062580170572782; v = 0.2081179391734803e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2778497016394506; b = 0.2696271276876226e-1; v = 0.1700345216228943e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3143733562261912; b = 0.5523469316960465e-1; v = 0.1774906779990410e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3501485810261827; b = 0.8445193201626464e-1; v = 0.1839659377002642e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3851430322303653; b = 0.1143263119336083; v = 0.1894987462975169e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4193013979470415; b = 0.1446177898344475; v = 0.1941548809452595e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4525585960458567; b = 0.1751165438438091; v = 0.1980078427252384e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4848447779622947; b = 0.2056338306745660; v = 0.2011296284744488e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5160871208276894; b = 0.2359965487229226; v = 0.2035888456966776e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5462112185696926; b = 0.2660430223139146; v = 0.2054516325352142e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5751425068101757; b = 0.2956193664498032; v = 0.2067831033092635e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6028073872853596; b = 0.3245763905312779; v = 0.2076485320284876e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6291338275278409; b = 0.3527670026206972; v = 0.2081141439525255e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3541797528439391; b = 0.2823853479435550e-1; v = 0.1834383015469222e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3908234972074657; b = 0.5741296374713106e-1; v = 0.1889540591777677e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4264408450107590; b = 0.8724646633650199e-1; v = 0.1936677023597375e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4609949666553286; b = 0.1175034422915616; v = 0.1976176495066504e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4944389496536006; b = 0.1479755652628428; v = 0.2008536004560983e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5267194884346086; b = 0.1784740659484352; v = 0.2034280351712291e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5577787810220990; b = 0.2088245700431244; v = 0.2053944466027758e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5875563763536670; b = 0.2388628136570763; v = 0.2068077642882360e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6159910016391269; b = 0.2684308928769185; v = 0.2077250949661599e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6430219602956268; b = 0.2973740761960252; v = 0.2082062440705320e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4300647036213646; b = 0.2916399920493977e-1; v = 0.1934374486546626e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4661486308935531; b = 0.5898803024755659e-1; v = 0.1974107010484300e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5009658555287261; b = 0.8924162698525409e-1; v = 0.2007129290388658e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5344824270447704; b = 0.1197185199637321; v = 0.2033736947471293e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5666575997416371; b = 0.1502300756161382; v = 0.2054287125902493e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5974457471404752; b = 0.1806004191913564; v = 0.2069184936818894e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6267984444116886; b = 0.2106621764786252; v = 0.2078883689808782e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6546664713575417; b = 0.2402526932671914; v = 0.2083886366116359e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5042711004437253; b = 0.2982529203607657e-1; v = 0.2006593275470817e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5392127456774380; b = 0.6008728062339922e-1; v = 0.2033728426135397e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5726819437668618; b = 0.9058227674571398e-1; v = 0.2055008781377608e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6046469254207278; b = 0.1211219235803400; v = 0.2070651783518502e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6350716157434952; b = 0.1515286404791580; v = 0.2080953335094320e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6639177679185454; b = 0.1816314681255552; v = 0.2086284998988521e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5757276040972253; b = 0.3026991752575440e-1; v = 0.2055549387644668e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6090265823139755; b = 0.6078402297870770e-1; v = 0.2071871850267654e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6406735344387661; b = 0.9135459984176636e-1; v = 0.2082856600431965e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6706397927793709; b = 0.1218024155966590; v = 0.2088705858819358e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6435019674426665; b = 0.3052608357660639e-1; v = 0.2083995867536322e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6747218676375681; b = 0.6112185773983089e-1; v = 0.2090509712889637e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 void LebedevGrid::ld5810(double *x, double *y, double *z, double *w) const //****************************************************************************80 // // Purpose: // // LD5810 computes the 5810 point Lebedev angular grid. // // Modified: // // 12 September 2010 // // Author: // // Dmitri Laikov // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Output, double X[N], Y[N], Z[N], W[N], the coordinates // and weights of the points. // { double a = 0.0; double b = 0.0; Index n; double v; n = 0; v = 0.9735347946175486e-5; n = n + gen_oh(1, a, b, v, x + n, y + n, z + n, w + n); v = 0.1907581241803167e-3; n = n + gen_oh(2, a, b, v, x + n, y + n, z + n, w + n); v = 0.1901059546737578e-3; n = n + gen_oh(3, a, b, v, x + n, y + n, z + n, w + n); a = 0.1182361662400277e-1; v = 0.3926424538919212e-4; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3062145009138958e-1; v = 0.6667905467294382e-4; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5329794036834243e-1; v = 0.8868891315019135e-4; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7848165532862220e-1; v = 0.1066306000958872e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1054038157636201; v = 0.1214506743336128e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1335577797766211; v = 0.1338054681640871e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1625769955502252; v = 0.1441677023628504e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.1921787193412792; v = 0.1528880200826557e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2221340534690548; v = 0.1602330623773609e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2522504912791132; v = 0.1664102653445244e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.2823610860679697; v = 0.1715845854011323e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3123173966267560; v = 0.1758901000133069e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3419847036953789; v = 0.1794382485256736e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3712386456999758; v = 0.1823238106757407e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3999627649876828; v = 0.1846293252959976e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4280466458648093; v = 0.1864284079323098e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4553844360185711; v = 0.1877882694626914e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.4818736094437834; v = 0.1887716321852025e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5074138709260629; v = 0.1894381638175673e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5319061304570707; v = 0.1898454899533629e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5552514978677286; v = 0.1900497929577815e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.5981009025246183; v = 0.1900671501924092e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6173990192228116; v = 0.1899837555533510e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6351365239411131; v = 0.1899014113156229e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6512010228227200; v = 0.1898581257705106e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6654758363948120; v = 0.1898804756095753e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6778410414853370; v = 0.1899793610426402e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6881760887484110; v = 0.1901464554844117e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.6963645267094598; v = 0.1903533246259542e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7023010617153579; v = 0.1905556158463228e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.7059004636628753; v = 0.1907037155663528e-3; n = n + gen_oh(4, a, b, v, x + n, y + n, z + n, w + n); a = 0.3552470312472575e-1; v = 0.5992997844249967e-4; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.9151176620841283e-1; v = 0.9749059382456978e-4; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.1566197930068980; v = 0.1241680804599158e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2265467599271907; v = 0.1437626154299360e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.2988242318581361; v = 0.1584200054793902e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.3717482419703886; v = 0.1694436550982744e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.4440094491758889; v = 0.1776617014018108e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5145337096756642; v = 0.1836132434440077e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.5824053672860230; v = 0.1876494727075983e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.6468283961043370; v = 0.1899906535336482e-3; n = n + gen_oh(5, a, b, v, x + n, y + n, z + n, w + n); a = 0.6095964259104373e-1; b = 0.1787828275342931e-1; v = 0.8143252820767350e-4; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.8811962270959388e-1; b = 0.3953888740792096e-1; v = 0.9998859890887728e-4; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1165936722428831; b = 0.6378121797722990e-1; v = 0.1156199403068359e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1460232857031785; b = 0.8985890813745037e-1; v = 0.1287632092635513e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1761197110181755; b = 0.1172606510576162; v = 0.1398378643365139e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2066471190463718; b = 0.1456102876970995; v = 0.1491876468417391e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2374076026328152; b = 0.1746153823011775; v = 0.1570855679175456e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2682305474337051; b = 0.2040383070295584; v = 0.1637483948103775e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2989653312142369; b = 0.2336788634003698; v = 0.1693500566632843e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3294762752772209; b = 0.2633632752654219; v = 0.1740322769393633e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3596390887276086; b = 0.2929369098051601; v = 0.1779126637278296e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3893383046398812; b = 0.3222592785275512; v = 0.1810908108835412e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4184653789358347; b = 0.3512004791195743; v = 0.1836529132600190e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4469172319076166; b = 0.3796385677684537; v = 0.1856752841777379e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4745950813276976; b = 0.4074575378263879; v = 0.1872270566606832e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5014034601410262; b = 0.4345456906027828; v = 0.1883722645591307e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5272493404551239; b = 0.4607942515205134; v = 0.1891714324525297e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5520413051846366; b = 0.4860961284181720; v = 0.1896827480450146e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5756887237503077; b = 0.5103447395342790; v = 0.1899628417059528e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1225039430588352; b = 0.2136455922655793e-1; v = 0.1123301829001669e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1539113217321372; b = 0.4520926166137188e-1; v = 0.1253698826711277e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1856213098637712; b = 0.7086468177864818e-1; v = 0.1366266117678531e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2174998728035131; b = 0.9785239488772918e-1; v = 0.1462736856106918e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2494128336938330; b = 0.1258106396267210; v = 0.1545076466685412e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2812321562143480; b = 0.1544529125047001; v = 0.1615096280814007e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3128372276456111; b = 0.1835433512202753; v = 0.1674366639741759e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3441145160177973; b = 0.2128813258619585; v = 0.1724225002437900e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3749567714853510; b = 0.2422913734880829; v = 0.1765810822987288e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4052621732015610; b = 0.2716163748391453; v = 0.1800104126010751e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4349335453522385; b = 0.3007127671240280; v = 0.1827960437331284e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4638776641524965; b = 0.3294470677216479; v = 0.1850140300716308e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4920046410462687; b = 0.3576932543699155; v = 0.1867333507394938e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5192273554861704; b = 0.3853307059757764; v = 0.1880178688638289e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5454609081136522; b = 0.4122425044452694; v = 0.1889278925654758e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5706220661424140; b = 0.4383139587781027; v = 0.1895213832507346e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5946286755181518; b = 0.4634312536300553; v = 0.1898548277397420e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.1905370790924295; b = 0.2371311537781979e-1; v = 0.1349105935937341e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2242518717748009; b = 0.4917878059254806e-1; v = 0.1444060068369326e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2577190808025936; b = 0.7595498960495142e-1; v = 0.1526797390930008e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2908724534927187; b = 0.1036991083191100; v = 0.1598208771406474e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3236354020056219; b = 0.1321348584450234; v = 0.1659354368615331e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3559267359304543; b = 0.1610316571314789; v = 0.1711279910946440e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3876637123676956; b = 0.1901912080395707; v = 0.1754952725601440e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4187636705218842; b = 0.2194384950137950; v = 0.1791247850802529e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4491449019883107; b = 0.2486155334763858; v = 0.1820954300877716e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4787270932425445; b = 0.2775768931812335; v = 0.1844788524548449e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5074315153055574; b = 0.3061863786591120; v = 0.1863409481706220e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5351810507738336; b = 0.3343144718152556; v = 0.1877433008795068e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5619001025975381; b = 0.3618362729028427; v = 0.1887444543705232e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5875144035268046; b = 0.3886297583620408; v = 0.1894009829375006e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6119507308734495; b = 0.4145742277792031; v = 0.1897683345035198e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2619733870119463; b = 0.2540047186389353e-1; v = 0.1517327037467653e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.2968149743237949; b = 0.5208107018543989e-1; v = 0.1587740557483543e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3310451504860488; b = 0.7971828470885599e-1; v = 0.1649093382274097e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3646215567376676; b = 0.1080465999177927; v = 0.1701915216193265e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3974916785279360; b = 0.1368413849366629; v = 0.1746847753144065e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4295967403772029; b = 0.1659073184763559; v = 0.1784555512007570e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4608742854473447; b = 0.1950703730454614; v = 0.1815687562112174e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4912598858949903; b = 0.2241721144376724; v = 0.1840864370663302e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5206882758945558; b = 0.2530655255406489; v = 0.1860676785390006e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5490940914019819; b = 0.2816118409731066; v = 0.1875690583743703e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5764123302025542; b = 0.3096780504593238; v = 0.1886453236347225e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6025786004213506; b = 0.3371348366394987; v = 0.1893501123329645e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6275291964794956; b = 0.3638547827694396; v = 0.1897366184519868e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3348189479861771; b = 0.2664841935537443e-1; v = 0.1643908815152736e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.3699515545855295; b = 0.5424000066843495e-1; v = 0.1696300350907768e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4042003071474669; b = 0.8251992715430854e-1; v = 0.1741553103844483e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4375320100182624; b = 0.1112695182483710; v = 0.1780015282386092e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4699054490335947; b = 0.1402964116467816; v = 0.1812116787077125e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5012739879431952; b = 0.1694275117584291; v = 0.1838323158085421e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5315874883754966; b = 0.1985038235312689; v = 0.1859113119837737e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5607937109622117; b = 0.2273765660020893; v = 0.1874969220221698e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5888393223495521; b = 0.2559041492849764; v = 0.1886375612681076e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6156705979160163; b = 0.2839497251976899; v = 0.1893819575809276e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6412338809078123; b = 0.3113791060500690; v = 0.1897794748256767e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4076051259257167; b = 0.2757792290858463e-1; v = 0.1738963926584846e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4423788125791520; b = 0.5584136834984293e-1; v = 0.1777442359873466e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4760480917328258; b = 0.8457772087727143e-1; v = 0.1810010815068719e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5085838725946297; b = 0.1135975846359248; v = 0.1836920318248129e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5399513637391218; b = 0.1427286904765053; v = 0.1858489473214328e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5701118433636380; b = 0.1718112740057635; v = 0.1875079342496592e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5990240530606021; b = 0.2006944855985351; v = 0.1887080239102310e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6266452685139695; b = 0.2292335090598907; v = 0.1894905752176822e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6529320971415942; b = 0.2572871512353714; v = 0.1898991061200695e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.4791583834610126; b = 0.2826094197735932e-1; v = 0.1809065016458791e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5130373952796940; b = 0.5699871359683649e-1; v = 0.1836297121596799e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5456252429628476; b = 0.8602712528554394e-1; v = 0.1858426916241869e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5768956329682385; b = 0.1151748137221281; v = 0.1875654101134641e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6068186944699046; b = 0.1442811654136362; v = 0.1888240751833503e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6353622248024907; b = 0.1731930321657680; v = 0.1896497383866979e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6624927035731797; b = 0.2017619958756061; v = 0.1900775530219121e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5484933508028488; b = 0.2874219755907391e-1; v = 0.1858525041478814e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.5810207682142106; b = 0.5778312123713695e-1; v = 0.1876248690077947e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6120955197181352; b = 0.8695262371439526e-1; v = 0.1889404439064607e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6416944284294319; b = 0.1160893767057166; v = 0.1898168539265290e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6697926391731260; b = 0.1450378826743251; v = 0.1902779940661772e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6147594390585488; b = 0.2904957622341456e-1; v = 0.1890125641731815e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6455390026356783; b = 0.5823809152617197e-1; v = 0.1899434637795751e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6747258588365477; b = 0.8740384899884715e-1; v = 0.1904520856831751e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); a = 0.6772135750395347; b = 0.2919946135808105e-1; v = 0.1905534498734563e-3; n = n + gen_oh(6, a, b, v, x + n, y + n, z + n, w + n); n = n - 1; return; } //****************************************************************************80 Index LebedevGrid::order_table(Index rule) const //****************************************************************************80 // // Purpose: // // ORDER_TABLE returns the order of a Lebedev rule. // // Modified: // // 11 September 2010 // // Author: // // John Burkardt // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Input, Index RULE, the index of the rule, between 1 and 65. // // Output, Index ORDER_TABLE, the order of the rule. // { Index rule_max = 65; Index table[65] = {6, 14, 26, 38, 50, 74, 86, 110, 146, 170, 194, 230, 266, 302, 350, 386, 434, 482, 530, 590, 650, 698, 770, 830, 890, 974, 1046, 1118, 1202, 1274, 1358, 1454, 1538, 1622, 1730, 1814, 1910, 2030, 2126, 2222, 2354, 2450, 2558, 2702, 2810, 2930, 3074, 3182, 3314, 3470, 3590, 3722, 3890, 4010, 4154, 4334, 4466, 4610, 4802, 4934, 5090, 5294, 5438, 5606, 5810}; Index value; if (rule < 1) { throw std::runtime_error("ORDER_TABLE - Fatal error!\n RULE < 1.\n"); } else if (rule_max < rule) { throw std::runtime_error("ORDER_TABLE - Fatal error!\n RULE_MAX < RULE.\n"); } value = table[rule - 1]; return value; } //****************************************************************************80 Index LebedevGrid::precision_table(Index rule) const //****************************************************************************80 // // Purpose: // // PRECISION_TABLE returns the precision of a Lebedev rule. // // Modified: // // 11 September 2010 // // Author: // // John Burkardt // // Reference: // // Vyacheslav Lebedev, Dmitri Laikov, // A quadrature formula for the sphere of the 131st // algebraic order of accuracy, // Russian Academy of Sciences Doklady Mathematics, // Volume 59, Number 3, 1999, pages 477-481. // // Parameters: // // Input, Index RULE, the index of the rule, between 1 and 65. // // Output, Index PRECISION_TABLE, the precision of the rule. // { Index rule_max = 65; Index table[65] = {3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131}; Index value; if (rule < 1) { throw std::runtime_error("PRECISION_TABLE - Fatal error!\n RULE < 1.\n"); } else if (rule_max < rule) { throw std::runtime_error( "PRECISION_TABLE - Fatal error!\n RULE_MAX < RULE.\n"); } value = table[rule - 1]; return value; } Eigen::Vector2d LebedevGrid::Cartesian2SphericalAngle( const Eigen::Vector3d &r) const { // phi=Vector[0] theta=Vector[1] Eigen::Vector2d result; result[0] = std::acos(r(2)); result[1] = std::atan2(r(1), r(0)); return result; } void LebedevGrid::FillOrder2Index() { Order2Index[38] = 1; Order2Index[50] = 2; Order2Index[74] = 3; Order2Index[86] = 4; Order2Index[110] = 5; Order2Index[146] = 6; Order2Index[170] = 7; Order2Index[194] = 8; Order2Index[230] = 9; Order2Index[266] = 10; Order2Index[302] = 11; Order2Index[350] = 12; Order2Index[434] = 13; Order2Index[590] = 14; Order2Index[770] = 15; Order2Index[974] = 16; Order2Index[1202] = 17; Order2Index[1454] = 18; Order2Index[1730] = 19; Order2Index[2030] = 20; Order2Index[2354] = 21; Order2Index[2702] = 22; Order2Index[3074] = 23; Order2Index[3470] = 24; Order2Index[3890] = 25; Order2Index[4334] = 26; Order2Index[4802] = 27; Order2Index[5294] = 28; Order2Index[5810] = 29; } void LebedevGrid::FillIndex2Order() { Index2Order[1] = 38; Index2Order[2] = 50; Index2Order[3] = 74; Index2Order[4] = 86; Index2Order[5] = 110; Index2Order[6] = 146; Index2Order[7] = 170; Index2Order[8] = 194; Index2Order[9] = 230; Index2Order[10] = 266; Index2Order[11] = 302; Index2Order[12] = 350; Index2Order[13] = 434; Index2Order[14] = 590; Index2Order[15] = 770; Index2Order[16] = 974; Index2Order[17] = 1202; Index2Order[18] = 1454; Index2Order[19] = 1730; Index2Order[20] = 2030; Index2Order[21] = 2354; Index2Order[22] = 2702; Index2Order[23] = 3074; Index2Order[24] = 3470; Index2Order[25] = 3890; Index2Order[26] = 4334; Index2Order[27] = 4802; Index2Order[28] = 5294; Index2Order[29] = 5810; } void LebedevGrid::FillOrders() { FillMediumOrder(); FillCoarseOrder(); FillXcoarseOrder(); FillFineOrder(); FillXfineOrder(); } void LebedevGrid::FillMediumOrder() { // order for H, He (not given in NWChem, assuming same as 1st row) MediumOrder["H"] = 434; MediumOrder["He"] = 434; // orders for 1st row elements taken from NWChem MediumOrder["Li"] = 434; MediumOrder["Be"] = 434; MediumOrder["B"] = 434; MediumOrder["C"] = 434; MediumOrder["N"] = 434; MediumOrder["O"] = 434; MediumOrder["F"] = 434; MediumOrder["Ne"] = 434; // orders for 2nd row elements taken from NWChem MediumOrder["Na"] = 434; MediumOrder["Mg"] = 434; MediumOrder["Al"] = 434; MediumOrder["Si"] = 434; MediumOrder["P"] = 434; MediumOrder["S"] = 434; MediumOrder["Cl"] = 434; MediumOrder["Ar"] = 434; // orders for 3rd row elements taken from NWChem MediumOrder["K"] = 590; MediumOrder["Ca"] = 590; MediumOrder["Sc"] = 590; MediumOrder["Ti"] = 590; MediumOrder["V"] = 590; MediumOrder["Cr"] = 590; MediumOrder["Mn"] = 590; MediumOrder["Fe"] = 590; MediumOrder["Co"] = 590; MediumOrder["Ni"] = 590; MediumOrder["Cu"] = 590; MediumOrder["Zn"] = 590; MediumOrder["Ga"] = 590; MediumOrder["Ge"] = 590; MediumOrder["As"] = 590; MediumOrder["Se"] = 590; MediumOrder["Br"] = 590; MediumOrder["Kr"] = 590; // 4th row (selection) MediumOrder["Ag"] = 590; MediumOrder["Rb"] = 590; MediumOrder["I"] = 590; MediumOrder["Xe"] = 590; } void LebedevGrid::FillFineOrder() { // order for H, He (not given in NWChem, assuming same as 1st row) FineOrder["H"] = 590; FineOrder["He"] = 590; // orders for 1st row elements taken from NWChem FineOrder["Li"] = 590; FineOrder["Be"] = 590; FineOrder["B"] = 590; FineOrder["C"] = 590; FineOrder["N"] = 590; FineOrder["O"] = 590; FineOrder["F"] = 590; FineOrder["Ne"] = 590; // orders for 2nd row elements taken from NWChem FineOrder["Na"] = 770; FineOrder["Mg"] = 770; FineOrder["Al"] = 770; FineOrder["Si"] = 770; FineOrder["P"] = 770; FineOrder["S"] = 770; FineOrder["Cl"] = 770; FineOrder["Ar"] = 770; // orders for 3rd row elements taken from NWChem FineOrder["K"] = 974; FineOrder["Ca"] = 974; FineOrder["Sc"] = 974; FineOrder["Ti"] = 974; FineOrder["V"] = 974; FineOrder["Cr"] = 974; FineOrder["Mn"] = 974; FineOrder["Fe"] = 974; FineOrder["Co"] = 974; FineOrder["Ni"] = 974; FineOrder["Cu"] = 974; FineOrder["Zn"] = 974; FineOrder["Ga"] = 974; FineOrder["Ge"] = 974; FineOrder["As"] = 974; FineOrder["Se"] = 974; FineOrder["Br"] = 974; FineOrder["Kr"] = 974; // 4th row FineOrder["Ag"] = 974; FineOrder["Rb"] = 974; FineOrder["I"] = 974; FineOrder["Xe"] = 974; } void LebedevGrid::FillXfineOrder() { // order for H, He (not given in NWChem, assuming same as 1st row) XfineOrder["H"] = 1202; XfineOrder["He"] = 1202; // orders for 1st row elements taken from NWChem XfineOrder["Li"] = 1202; XfineOrder["Be"] = 1202; XfineOrder["B"] = 1202; XfineOrder["C"] = 1202; XfineOrder["N"] = 1202; XfineOrder["O"] = 1202; XfineOrder["F"] = 1202; XfineOrder["Ne"] = 1202; // orders for 2nd row elements taken from NWChem XfineOrder["Na"] = 1454; XfineOrder["Mg"] = 1454; XfineOrder["Al"] = 1454; XfineOrder["Si"] = 1454; XfineOrder["P"] = 1454; XfineOrder["S"] = 1454; XfineOrder["Cl"] = 1454; XfineOrder["Ar"] = 1454; // orders for 3rd row elements taken from NWChem XfineOrder["K"] = 1454; XfineOrder["Ca"] = 1454; XfineOrder["Sc"] = 1454; XfineOrder["Ti"] = 1454; XfineOrder["V"] = 1454; XfineOrder["Cr"] = 1454; XfineOrder["Mn"] = 1454; XfineOrder["Fe"] = 1454; XfineOrder["Co"] = 1454; XfineOrder["Ni"] = 1454; XfineOrder["Cu"] = 1454; XfineOrder["Zn"] = 1454; XfineOrder["Ga"] = 1454; XfineOrder["Ge"] = 1454; XfineOrder["As"] = 1454; XfineOrder["Se"] = 1454; XfineOrder["Br"] = 1454; XfineOrder["Kr"] = 1454; // 4th row XfineOrder["Ag"] = 1454; XfineOrder["Rb"] = 1454; XfineOrder["I"] = 1454; XfineOrder["Xe"] = 1454; } void LebedevGrid::FillCoarseOrder() { // order for H, He (not given in NWChem, assuming same as 1st row) CoarseOrder["H"] = 302; CoarseOrder["He"] = 302; // orders for 1st row elements taken from NWChem CoarseOrder["Li"] = 302; CoarseOrder["Be"] = 302; CoarseOrder["B"] = 302; CoarseOrder["C"] = 302; CoarseOrder["N"] = 302; CoarseOrder["O"] = 302; CoarseOrder["F"] = 302; CoarseOrder["Ne"] = 302; // orders for 2nd row elements taken from NWChem CoarseOrder["Na"] = 302; CoarseOrder["Mg"] = 302; CoarseOrder["Al"] = 302; CoarseOrder["Si"] = 302; CoarseOrder["P"] = 302; CoarseOrder["S"] = 302; CoarseOrder["Cl"] = 302; CoarseOrder["Ar"] = 302; // orders for 3rd row elements taken from NWChem CoarseOrder["K"] = 302; CoarseOrder["Ca"] = 302; CoarseOrder["Sc"] = 302; CoarseOrder["Ti"] = 302; CoarseOrder["V"] = 302; CoarseOrder["Cr"] = 302; CoarseOrder["Mn"] = 302; CoarseOrder["Fe"] = 302; CoarseOrder["Co"] = 302; CoarseOrder["Ni"] = 302; CoarseOrder["Cu"] = 302; CoarseOrder["Zn"] = 302; CoarseOrder["Ga"] = 302; CoarseOrder["Ge"] = 302; CoarseOrder["As"] = 302; CoarseOrder["Se"] = 302; CoarseOrder["Br"] = 302; CoarseOrder["Kr"] = 302; // 4th row CoarseOrder["Ag"] = 302; CoarseOrder["Rb"] = 302; CoarseOrder["I"] = 302; CoarseOrder["Xe"] = 302; } void LebedevGrid::FillXcoarseOrder() { // order for H, He (not given in NWChem, assuming same as 1st row) XcoarseOrder["H"] = 194; XcoarseOrder["He"] = 194; // orders for 1st row elements taken from NWChem XcoarseOrder["Li"] = 194; XcoarseOrder["Be"] = 194; XcoarseOrder["B"] = 194; XcoarseOrder["C"] = 194; XcoarseOrder["N"] = 194; XcoarseOrder["O"] = 194; XcoarseOrder["F"] = 194; XcoarseOrder["Ne"] = 194; // orders for 2nd row elements taken from NWChem XcoarseOrder["Na"] = 194; XcoarseOrder["Mg"] = 194; XcoarseOrder["Al"] = 194; XcoarseOrder["Si"] = 194; XcoarseOrder["P"] = 194; XcoarseOrder["S"] = 194; XcoarseOrder["Cl"] = 194; XcoarseOrder["Ar"] = 194; // orders for 3rd row elements taken from NWChem XcoarseOrder["K"] = 194; XcoarseOrder["Ca"] = 194; XcoarseOrder["Sc"] = 194; XcoarseOrder["Ti"] = 194; XcoarseOrder["V"] = 194; XcoarseOrder["Cr"] = 194; XcoarseOrder["Mn"] = 194; XcoarseOrder["Fe"] = 194; XcoarseOrder["Co"] = 194; XcoarseOrder["Ni"] = 194; XcoarseOrder["Cu"] = 194; XcoarseOrder["Zn"] = 194; XcoarseOrder["Ga"] = 194; XcoarseOrder["Ge"] = 194; XcoarseOrder["As"] = 194; XcoarseOrder["Se"] = 194; XcoarseOrder["Br"] = 194; XcoarseOrder["Kr"] = 194; // 4th row XcoarseOrder["Ag"] = 194; XcoarseOrder["Rb"] = 194; XcoarseOrder["I"] = 194; XcoarseOrder["Xe"] = 194; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/grids/vxc_grid.cc000066400000000000000000000305621412152066400177370ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/vxc_grid.h" #include "votca/xtp/qmmolecule.h" #include "votca/xtp/radial_euler_maclaurin_rule.h" #include "votca/xtp/sphere_lebedev_rule.h" namespace votca { namespace xtp { void Vxc_Grid::SortGridpointsintoBlocks( const std::vector >& grid) { const double boxsize = 1; // 1 bohr Eigen::Array3d min = Eigen::Array3d::Ones() * std::numeric_limits::max(); Eigen::Array3d max = Eigen::Array3d::Ones() * std::numeric_limits::min(); for (const auto& atom_grid : grid) { for (const auto& gridpoint : atom_grid) { const Eigen::Vector3d& pos = gridpoint.grid_pos; max = max.max(pos.array()).eval(); min = min.min(pos.array()).eval(); } } Eigen::Array3d molextension = max - min; Eigen::Array numberofboxes = (molextension / boxsize).ceil().cast(); std::vector > > > boxes; // creating temparray for (Index i = 0; i < numberofboxes.x(); i++) { std::vector< std::vector > > boxes_yz; for (Index j = 0; j < numberofboxes.y(); j++) { std::vector > boxes_z; for (Index k = 0; k < numberofboxes.z(); k++) { std::vector box; box.reserve(100); boxes_z.push_back(box); } boxes_yz.push_back(boxes_z); } boxes.push_back(boxes_yz); } for (const auto& atomgrid : grid) { for (const auto& gridpoint : atomgrid) { Eigen::Array3d pos = gridpoint.grid_pos - min.matrix(); Eigen::Array index = (pos / boxsize).floor().cast(); boxes[index.x()][index.y()][index.z()].push_back(&gridpoint); } } for (auto& boxes_xy : boxes) { for (auto& boxes_z : boxes_xy) { for (auto& box : boxes_z) { if (box.empty()) { continue; } GridBox gridbox; for (const auto& point : box) { gridbox.addGridPoint(*point); } _grid_boxes.push_back(gridbox); } } } return; } void Vxc_Grid::FindSignificantShells(const AOBasis& basis) { #pragma omp parallel for for (Index i = 0; i < getBoxesSize(); i++) { _grid_boxes[i].FindSignificantShells(basis); } std::vector grid_boxes_copy; // use vector of bool to indicate if a gridbox has already been merged into // another std::vector Merged = std::vector(_grid_boxes.size(), false); for (Index i = 0; i < Index(_grid_boxes.size()); i++) { if (Merged[i]) { continue; } GridBox box = _grid_boxes[i]; if (box.Shellsize() < 1) { continue; } Merged[i] = true; for (Index j = i + 1; j < Index(_grid_boxes.size()); j++) { if (GridBox::compareGridboxes(_grid_boxes[i], _grid_boxes[j])) { Merged[j] = true; box.addGridBox(_grid_boxes[j]); } } grid_boxes_copy.push_back(box); } _totalgridsize = 0; for (auto& box : grid_boxes_copy) { _totalgridsize += box.size(); box.PrepareForIntegration(); } _grid_boxes = grid_boxes_copy; } std::vector Vxc_Grid::getGridpoints() const { std::vector gridpoints; gridpoints.reserve(this->getGridSize()); for (const auto& box : _grid_boxes) { const std::vector& points = box.getGridPoints(); for (const Eigen::Vector3d& point : points) { gridpoints.push_back(&point); } } return gridpoints; } Eigen::MatrixXd Vxc_Grid::CalcInverseAtomDist(const QMMolecule& atoms) const { Eigen::MatrixXd result = Eigen::MatrixXd::Zero(atoms.size(), atoms.size()); #pragma omp parallel for for (Index i = 0; i < atoms.size(); ++i) { const Eigen::Vector3d& pos_a = atoms[i].getPos(); for (Index j = 0; j < i; ++j) { const Eigen::Vector3d& pos_b = atoms[j].getPos(); result(j, i) = 1 / (pos_a - pos_b).norm(); } } return result + result.transpose(); } Index Vxc_Grid::UpdateOrder(LebedevGrid& sphericalgridofElement, Index maxorder, std::vector& PruningIntervals, double r) const { Index order; Index maxindex = sphericalgridofElement.getIndexFromOrder(maxorder); if (maxindex == 1) { // smallest possible grid anyway, nothing to do order = maxorder; } else if (maxindex == 2) { // only three intervals if (r < PruningIntervals[0]) { order = sphericalgridofElement.getOrderFromIndex(1); // 1; } else if ((r >= PruningIntervals[0]) && (r < PruningIntervals[3])) { order = sphericalgridofElement.getOrderFromIndex(2); } else { order = sphericalgridofElement.getOrderFromIndex(1); } // maxorder == 2 } else { // five intervals if (r < PruningIntervals[0]) { order = sphericalgridofElement.getOrderFromIndex(2); } else if ((r >= PruningIntervals[0]) && (r < PruningIntervals[1])) { order = sphericalgridofElement.getOrderFromIndex(4); } else if ((r >= PruningIntervals[1]) && (r < PruningIntervals[2])) { constexpr Index maximum = 4; order = sphericalgridofElement.getOrderFromIndex( std::max(maxindex - 1, maximum)); } else if ((r >= PruningIntervals[2]) && (r < PruningIntervals[3])) { order = maxorder; } else { constexpr Index maximum = 1; order = sphericalgridofElement.getOrderFromIndex( std::max(maxindex - 1, maximum)); } } return order; } GridContainers::Cartesian_gridpoint Vxc_Grid::CreateCartesianGridpoint( const Eigen::Vector3d& atomA_pos, GridContainers::radial_grid& radial_grid, GridContainers::spherical_grid& spherical_grid, Index i_rad, Index i_sph) const { GridContainers::Cartesian_gridpoint gridpoint; double p = spherical_grid.phi[i_sph]; double t = spherical_grid.theta[i_sph]; const Eigen::Vector3d s = Eigen::Vector3d{sin(p) * cos(t), sin(p) * sin(t), cos(p)}; double r = radial_grid.radius[i_rad]; gridpoint.grid_pos = atomA_pos + r * s; gridpoint.grid_weight = radial_grid.weight[i_rad] * spherical_grid.weight[i_sph]; return gridpoint; } Eigen::MatrixXd Vxc_Grid::CalcDistanceAtomsGridpoints( const QMMolecule& atoms, std::vector& atomgrid) const { Eigen::MatrixXd result = Eigen::MatrixXd::Zero(atoms.size(), atomgrid.size()); #pragma omp parallel for for (Index i = 0; i < atoms.size(); ++i) { const Eigen::Vector3d& atom_pos = atoms[i].getPos(); for (Index j = 0; j < Index(atomgrid.size()); ++j) { const auto& gridpoint = atomgrid[j]; result(i, j) = (atom_pos - gridpoint.grid_pos).norm(); } } return result; } void Vxc_Grid::SSWpartitionAtom( const QMMolecule& atoms, std::vector& atomgrid, Index i_atom, const Eigen::MatrixXd& Rij) const { Eigen::MatrixXd AtomGridDist = CalcDistanceAtomsGridpoints(atoms, atomgrid); #pragma omp parallel for schedule(guided) for (Index i_grid = 0; i_grid < Index(atomgrid.size()); i_grid++) { Eigen::VectorXd p = SSWpartition(AtomGridDist.col(i_grid), Rij); // check weight sum double wsum = p.sum(); if (wsum != 0.0) { // update the weight of this grid point atomgrid[i_grid].grid_weight *= p[i_atom] / wsum; } else { std::cerr << "\nSum of partition weights of grid point " << i_grid << " of atom " << i_atom << " is zero! "; throw std::runtime_error("\nThis should never happen!"); } } // partition weight for each gridpoint } void Vxc_Grid::GridSetup(const std::string& type, const QMMolecule& atoms, const AOBasis& basis) { GridContainers initialgrids; // get radial grid per element EulerMaclaurinGrid radialgridofElement; initialgrids.radial_grids = radialgridofElement.CalculateAtomicRadialGrids( basis, atoms, type); // this checks out 1:1 with NWChem results! AWESOME LebedevGrid sphericalgridofElement; initialgrids.spherical_grids = sphericalgridofElement.CalculateSphericalGrids(atoms, type); // for the partitioning, we need all inter-center distances later, stored in // matrix Eigen::MatrixXd Rij = CalcInverseAtomDist(atoms); std::vector > grid; for (Index i_atom = 0; i_atom < atoms.size(); ++i_atom) { const QMAtom& atom = atoms[i_atom]; const Eigen::Vector3d& atomA_pos = atom.getPos(); const std::string& name = atom.getElement(); GridContainers::radial_grid radial_grid = initialgrids.radial_grids.at(name); GridContainers::spherical_grid spherical_grid = initialgrids.spherical_grids.at(name); // maximum order (= number of points) in spherical integration grid Index maxorder = sphericalgridofElement.Type2MaxOrder(name, type); // for pruning of integration grid, get interval boundaries for this element std::vector PruningIntervals = radialgridofElement.CalculatePruningIntervals(name); Index current_order = 0; // for each radial value std::vector atomgrid; for (Index i_rad = 0; i_rad < radial_grid.radius.size(); i_rad++) { double r = radial_grid.radius[i_rad]; // which Lebedev order for this point? Index order = UpdateOrder(sphericalgridofElement, maxorder, PruningIntervals, r); // get new spherical grid, if order changed if (order != current_order) { spherical_grid = sphericalgridofElement.CalculateUnitSphereGrid(order); current_order = order; } for (Index i_sph = 0; i_sph < spherical_grid.phi.size(); i_sph++) { GridContainers::Cartesian_gridpoint gridpoint = CreateCartesianGridpoint(atomA_pos, radial_grid, spherical_grid, i_rad, i_sph); atomgrid.push_back(gridpoint); } // spherical gridpoints } // radial gridpoint SSWpartitionAtom(atoms, atomgrid, i_atom, Rij); // now remove points from the grid with negligible weights std::vector atomgrid_cleanedup; for (const auto& point : atomgrid) { if (point.grid_weight > 1e-13) { atomgrid_cleanedup.push_back(point); } } grid.push_back(atomgrid_cleanedup); } // atoms SortGridpointsintoBlocks(grid); FindSignificantShells(basis); return; } Eigen::VectorXd Vxc_Grid::SSWpartition(const Eigen::VectorXd& rq_i, const Eigen::MatrixXd& Rij) const { const double ass = 0.725; // initialize partition vector to 1.0 Eigen::VectorXd p = Eigen::VectorXd::Ones(rq_i.size()); const double tol_scr = 1e-10; const double leps = 1e-6; // go through centers for (Index i = 1; i < rq_i.size(); i++) { double rag = rq_i(i); // through all other centers (one-directional) for (Index j = 0; j < i; j++) { if ((std::abs(p[i]) > tol_scr) || (std::abs(p[j]) > tol_scr)) { double mu = (rag - rq_i(j)) * Rij(j, i); if (mu > ass) { p[i] = 0.0; } else if (mu < -ass) { p[j] = 0.0; } else { double sk; if (std::abs(mu) < leps) { sk = -1.88603178008 * mu + 0.5; } else { sk = erf1c(mu); } if (mu > 0.0) { sk = 1.0 - sk; } p[j] = p[j] * sk; p[i] = p[i] * (1.0 - sk); } } } } return p; } double Vxc_Grid::erf1c(double x) const { const static double alpha_erf1 = 1.0 / 0.30; return 0.5 * std::erfc(std::abs(x / (1.0 - x * x)) * alpha_erf1); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gwbse/000077500000000000000000000000001412152066400156145ustar00rootroot00000000000000xtp-2021.2/src/libxtp/gwbse/bse.cc000066400000000000000000000714501412152066400167030ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/bse.h" #include "votca/xtp/bse_operator.h" #include "votca/xtp/bseoperator_btda.h" #include "votca/xtp/davidsonsolver.h" #include "votca/xtp/populationanalysis.h" #include "votca/xtp/qmfragment.h" #include "votca/xtp/rpa.h" #include "votca/xtp/vc2index.h" using boost::format; using std::flush; namespace votca { namespace xtp { void BSE::configure(const options& opt, const Eigen::VectorXd& RPAInputEnergies, const Eigen::MatrixXd& Hqp_in) { _opt = opt; _bse_vmax = _opt.homo; _bse_cmin = _opt.homo + 1; _bse_vtotal = _bse_vmax - _opt.vmin + 1; _bse_ctotal = _opt.cmax - _bse_cmin + 1; _bse_size = _bse_vtotal * _bse_ctotal; _max_dyn_iter = _opt.max_dyn_iter; _dyn_tolerance = _opt.dyn_tolerance; if (_opt.use_Hqp_offdiag) { _Hqp = AdjustHqpSize(Hqp_in, RPAInputEnergies); } else { _Hqp = AdjustHqpSize(Hqp_in, RPAInputEnergies).diagonal().asDiagonal(); } SetupDirectInteractionOperator(RPAInputEnergies, 0.0); } Eigen::MatrixXd BSE::AdjustHqpSize(const Eigen::MatrixXd& Hqp, const Eigen::VectorXd& RPAInputEnergies) { Index hqp_size = _bse_vtotal + _bse_ctotal; Index gwsize = _opt.qpmax - _opt.qpmin + 1; Index RPAoffset = _opt.vmin - _opt.rpamin; Eigen::MatrixXd Hqp_BSE = Eigen::MatrixXd::Zero(hqp_size, hqp_size); if (_opt.vmin >= _opt.qpmin) { Index start = _opt.vmin - _opt.qpmin; if (_opt.cmax <= _opt.qpmax) { Hqp_BSE = Hqp.block(start, start, hqp_size, hqp_size); } else { Index virtoffset = gwsize - start; Hqp_BSE.topLeftCorner(virtoffset, virtoffset) = Hqp.block(start, start, virtoffset, virtoffset); Index virt_extra = _opt.cmax - _opt.qpmax; Hqp_BSE.diagonal().tail(virt_extra) = RPAInputEnergies.segment(RPAoffset + virtoffset, virt_extra); } } if (_opt.vmin < _opt.qpmin) { Index occ_extra = _opt.qpmin - _opt.vmin; Hqp_BSE.diagonal().head(occ_extra) = RPAInputEnergies.segment(RPAoffset, occ_extra); Hqp_BSE.block(occ_extra, occ_extra, gwsize, gwsize) = Hqp; if (_opt.cmax > _opt.qpmax) { Index virtoffset = occ_extra + gwsize; Index virt_extra = _opt.cmax - _opt.qpmax; Hqp_BSE.diagonal().tail(virt_extra) = RPAInputEnergies.segment(RPAoffset + virtoffset, virt_extra); } } return Hqp_BSE; } void BSE::SetupDirectInteractionOperator( const Eigen::VectorXd& RPAInputEnergies, double energy) { RPA rpa = RPA(_log, _Mmn); rpa.configure(_opt.homo, _opt.rpamin, _opt.rpamax); rpa.setRPAInputEnergies(RPAInputEnergies); Eigen::SelfAdjointEigenSolver es( rpa.calculate_epsilon_r(energy)); _Mmn.MultiplyRightWithAuxMatrix(es.eigenvectors()); _epsilon_0_inv = Eigen::VectorXd::Zero(es.eigenvalues().size()); for (Index i = 0; i < es.eigenvalues().size(); ++i) { if (es.eigenvalues()(i) > 1e-8) { _epsilon_0_inv(i) = 1 / es.eigenvalues()(i); } } } template void BSE::configureBSEOperator(BSE_OPERATOR& H) const { BSEOperator_Options opt; opt.cmax = _opt.cmax; opt.homo = _opt.homo; opt.qpmin = _opt.qpmin; opt.rpamin = _opt.rpamin; opt.vmin = _opt.vmin; H.configure(opt); } tools::EigenSystem BSE::Solve_triplets_TDA() const { TripletOperator_TDA Ht(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(Ht); return solve_hermitian(Ht); } void BSE::Solve_singlets(Orbitals& orb) const { orb.setTDAApprox(_opt.useTDA); if (_opt.useTDA) { orb.BSESinglets() = Solve_singlets_TDA(); } else { orb.BSESinglets() = Solve_singlets_BTDA(); } orb.CalcCoupledTransition_Dipoles(); } void BSE::Solve_triplets(Orbitals& orb) const { orb.setTDAApprox(_opt.useTDA); if (_opt.useTDA) { orb.BSETriplets() = Solve_triplets_TDA(); } else { orb.BSETriplets() = Solve_triplets_BTDA(); } } tools::EigenSystem BSE::Solve_singlets_TDA() const { SingletOperator_TDA Hs(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(Hs); XTP_LOG(Log::error, _log) << TimeStamp() << " Setup TDA singlet hamiltonian " << flush; return solve_hermitian(Hs); } SingletOperator_TDA BSE::getSingletOperator_TDA() const { SingletOperator_TDA Hs(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(Hs); return Hs; } TripletOperator_TDA BSE::getTripletOperator_TDA() const { TripletOperator_TDA Ht(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(Ht); return Ht; } template tools::EigenSystem BSE::solve_hermitian(BSE_OPERATOR& h) const { std::chrono::time_point start, end; std::chrono::time_point hstart, hend; std::chrono::duration elapsed_time; start = std::chrono::system_clock::now(); tools::EigenSystem result; if (_opt.davidson) { DavidsonSolver DS(_log); DS.set_correction(_opt.davidson_correction); DS.set_tolerance(_opt.davidson_tolerance); DS.set_ortho(_opt.davidson_ortho); DS.set_size_update(_opt.davidson_update); DS.set_iter_max(_opt.davidson_maxiter); DS.set_max_search_space(10 * _opt.nmax); if (_opt.matrixfree) { XTP_LOG(Log::error, _log) << TimeStamp() << " Using matrix free method" << flush; DS.solve(h, _opt.nmax); } else { XTP_LOG(Log::error, _log) << TimeStamp() << " Using full matrix method" << flush; // get the full matrix hstart = std::chrono::system_clock::now(); Eigen::MatrixXd hfull = h.get_full_matrix(); hend = std::chrono::system_clock::now(); elapsed_time = hend - hstart; XTP_LOG(Log::info, _log) << TimeStamp() << " Full matrix assembled in " << elapsed_time.count() << " secs" << flush; // solve theeigenalue problem hstart = std::chrono::system_clock::now(); DS.solve(hfull, _opt.nmax); hend = std::chrono::system_clock::now(); elapsed_time = hend - hstart; XTP_LOG(Log::info, _log) << TimeStamp() << " Davidson solve done in " << elapsed_time.count() << " secs" << flush; } result.eigenvalues() = DS.eigenvalues(); result.eigenvectors() = DS.eigenvectors(); } else { XTP_LOG(Log::error, _log) << TimeStamp() << " Lapack Diagonalization" << flush; hstart = std::chrono::system_clock::now(); Eigen::MatrixXd hfull = h.get_full_matrix(); hend = std::chrono::system_clock::now(); elapsed_time = hend - hstart; XTP_LOG(Log::info, _log) << TimeStamp() << " Full matrix assembled in " << elapsed_time.count() << " secs" << flush; hstart = std::chrono::system_clock::now(); result = tools::linalg_eigenvalues(hfull, _opt.nmax); hend = std::chrono::system_clock::now(); elapsed_time = hend - hstart; XTP_LOG(Log::info, _log) << TimeStamp() << " Lapack solve done in " << elapsed_time.count() << " secs" << flush; } end = std::chrono::system_clock::now(); elapsed_time = end - start; XTP_LOG(Log::info, _log) << TimeStamp() << " Diagonalization done in " << elapsed_time.count() << " secs" << flush; return result; } tools::EigenSystem BSE::Solve_singlets_BTDA() const { if (_opt.davidson) { SingletOperator_TDA A(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(A); SingletOperator_BTDA_B B(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(B); XTP_LOG(Log::error, _log) << TimeStamp() << " Setup Full singlet hamiltonian " << flush; return Solve_nonhermitian_Davidson(A, B); } else { SingletOperator_BTDA_ApB Hs_ApB(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(Hs_ApB); Operator_BTDA_AmB Hs_AmB(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(Hs_AmB); XTP_LOG(Log::error, _log) << TimeStamp() << " Setup Full singlet hamiltonian " << flush; return Solve_nonhermitian(Hs_ApB, Hs_AmB); } } tools::EigenSystem BSE::Solve_triplets_BTDA() const { if (_opt.davidson) { TripletOperator_TDA A(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(A); Hd2Operator B(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(B); XTP_LOG(Log::error, _log) << TimeStamp() << " Setup Full triplet hamiltonian " << flush; return Solve_nonhermitian_Davidson(A, B); } else { TripletOperator_BTDA_ApB Ht_ApB(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(Ht_ApB); Operator_BTDA_AmB Ht_AmB(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(Ht_AmB); XTP_LOG(Log::error, _log) << TimeStamp() << " Setup Full triplet hamiltonian " << flush; return Solve_nonhermitian(Ht_ApB, Ht_AmB); } } template tools::EigenSystem BSE::Solve_nonhermitian(BSE_OPERATOR_ApB& apb, BSE_OPERATOR_AmB& amb) const { // For details of the method, see EPL,78(2007)12001, // Nuclear Physics A146(1970)449, Nuclear Physics A163(1971)257. // setup resonant (A) and RARC blocks (B) // corresponds to // _ApB = (_eh_d +_eh_qp + _eh_d2 + 4.0 * _eh_x); // _AmB = (_eh_d +_eh_qp - _eh_d2); std::chrono::time_point start, end; std::chrono::time_point hstart, hend; std::chrono::duration elapsed_time; start = std::chrono::system_clock::now(); Eigen::MatrixXd ApB = apb.get_full_matrix(); Eigen::MatrixXd AmB = amb.get_full_matrix(); XTP_LOG(Log::error, _log) << TimeStamp() << " Setup singlet hamiltonian " << flush; XTP_LOG(Log::error, _log) << TimeStamp() << " Lapack Diagonalization" << flush; // calculate Cholesky decomposition of A-B = LL^T. It throws an error if not // positive definite //(A-B) is not needed any longer and can be overwritten XTP_LOG(Log::info, _log) << TimeStamp() << " Trying Cholesky decomposition of KAA-KAB" << flush; Eigen::LLT > L(AmB); for (Index i = 0; i < AmB.rows(); ++i) { for (Index j = i + 1; j < AmB.cols(); ++j) { AmB(i, j) = 0; } } if (L.info() != Eigen::ComputationInfo::Success) { XTP_LOG(Log::error, _log) << TimeStamp() << " Cholesky decomposition of KAA-KAB was unsucessful. Try a smaller " "basisset. This can indicate a triplet instability." << flush; throw std::runtime_error("Cholesky decompostion failed"); } else { XTP_LOG(Log::info, _log) << TimeStamp() << " Cholesky decomposition of KAA-KAB was successful" << flush; } ApB = AmB.transpose() * ApB * AmB; XTP_LOG(Log::info, _log) << TimeStamp() << " Calculated H = L^T(A+B)L " << flush; XTP_LOG(Log::error, _log) << TimeStamp() << " Solving for first " << _opt.nmax << " eigenvectors" << flush; hstart = std::chrono::system_clock::now(); tools::EigenSystem eigensys = tools::linalg_eigenvalues(ApB, _opt.nmax); hend = std::chrono::system_clock::now(); elapsed_time = hend - hstart; XTP_LOG(Log::info, _log) << TimeStamp() << " Lapack solve done in " << elapsed_time.count() << " secs" << flush; if (eigensys.info() != Eigen::ComputationInfo::Success) { XTP_LOG(Log::error, _log) << TimeStamp() << " Could not solve problem" << flush; } else { XTP_LOG(Log::info, _log) << TimeStamp() << " Solved HR_l = eps_l^2 R_l " << flush; } ApB.resize(0, 0); if ((eigensys.eigenvalues().array() < 0).any()) { throw std::runtime_error("Negative eigenvalues in BTDA"); } Eigen::VectorXd energies = eigensys.eigenvalues().cwiseSqrt(); // has to stay otherwise mkl // complains tools::EigenSystem result; result.eigenvalues() = energies; // reconstruct real eigenvectors X_l = 1/2 [sqrt(eps_l) (L^T)^-1 + // 1/sqrt(eps_l)L ] R_l // Y_l = 1/2 [sqrt(eps_l) (L^T)^-1 - // 1/sqrt(eps_l)L ] R_l // 1/sqrt(eps_l)L ] R_l // determine inverse of L^T Eigen::MatrixXd LmT = AmB.inverse().transpose(); Index dim = LmT.rows(); result.eigenvectors().resize(dim, _opt.nmax); // resonant part (_X_evec) result.eigenvectors2().resize(dim, _opt.nmax); // anti-resonant part (_Y_evec) for (Index level = 0; level < _opt.nmax; level++) { double sqrt_eval = std::sqrt(energies(level)); // get l-th reduced EV result.eigenvectors().col(level) = (0.5 / sqrt_eval * (energies(level) * LmT + AmB) * eigensys.eigenvectors().col(level)); result.eigenvectors2().col(level) = (0.5 / sqrt_eval * (energies(level) * LmT - AmB) * eigensys.eigenvectors().col(level)); } end = std::chrono::system_clock::now(); elapsed_time = end - start; XTP_LOG(Log::info, _log) << TimeStamp() << " Diagonalization done in " << elapsed_time.count() << " secs" << flush; return result; } template tools::EigenSystem BSE::Solve_nonhermitian_Davidson(BSE_OPERATOR_A& Aop, BSE_OPERATOR_B& Bop) const { std::chrono::time_point start, end; std::chrono::time_point hstart, hend; std::chrono::duration elapsed_time; start = std::chrono::system_clock::now(); // operator HamiltonianOperator Hop(Aop, Bop); // Davidson solver DavidsonSolver DS(_log); DS.set_correction(_opt.davidson_correction); DS.set_tolerance(_opt.davidson_tolerance); DS.set_ortho(_opt.davidson_ortho); DS.set_size_update(_opt.davidson_update); DS.set_iter_max(_opt.davidson_maxiter); DS.set_max_search_space(10 * _opt.nmax); DS.set_matrix_type("HAM"); if (_opt.matrixfree) { XTP_LOG(Log::error, _log) << TimeStamp() << " Using matrix free method" << flush; DS.solve(Hop, _opt.nmax); } else { XTP_LOG(Log::error, _log) << TimeStamp() << " Using full matrix method" << flush; // get the full matrix hstart = std::chrono::system_clock::now(); Eigen::MatrixXd hfull = Hop.get_full_matrix(); hend = std::chrono::system_clock::now(); elapsed_time = hend - hstart; XTP_LOG(Log::info, _log) << TimeStamp() << " Full matrix assembled in " << elapsed_time.count() << " secs" << flush; // solve theeigenalue problem hstart = std::chrono::system_clock::now(); DS.solve(hfull, _opt.nmax); hend = std::chrono::system_clock::now(); elapsed_time = hend - hstart; XTP_LOG(Log::info, _log) << TimeStamp() << " Davidson solve done in " << elapsed_time.count() << " secs" << flush; } // results tools::EigenSystem result; result.eigenvalues() = DS.eigenvalues(); Eigen::MatrixXd _tmpX = DS.eigenvectors().topRows(Aop.size()); Eigen::MatrixXd _tmpY = DS.eigenvectors().bottomRows(Aop.size()); // // normalization so that eigenvector^2 - eigenvector2^2 = 1 Eigen::VectorXd normX = _tmpX.colwise().squaredNorm(); Eigen::VectorXd normY = _tmpY.colwise().squaredNorm(); Eigen::ArrayXd sqinvnorm = (normX - normY).array().inverse().cwiseSqrt(); result.eigenvectors() = _tmpX * sqinvnorm.matrix().asDiagonal(); result.eigenvectors2() = _tmpY * sqinvnorm.matrix().asDiagonal(); end = std::chrono::system_clock::now(); elapsed_time = end - start; XTP_LOG(Log::info, _log) << TimeStamp() << " Diagonalization done in " << elapsed_time.count() << " secs" << flush; return result; } void BSE::printFragInfo(const std::vector >& frags, Index state) const { for (const QMFragment& frag : frags) { double dq = frag.value().H[state] + frag.value().E[state]; double qeff = dq + frag.value().Gs; XTP_LOG(Log::error, _log) << format( " Fragment %1$4d -- hole: %2$5.1f%% electron: " "%3$5.1f%% dQ: %4$+5.2f Qeff: %5$+5.2f") % int(frag.getId()) % (100.0 * frag.value().H[state]) % (-100.0 * frag.value().E[state]) % dq % qeff << flush; } return; } void BSE::PrintWeights(const Eigen::VectorXd& weights) const { vc2index vc = vc2index(_opt.vmin, _bse_cmin, _bse_ctotal); for (Index i_bse = 0; i_bse < _bse_size; ++i_bse) { double weight = weights(i_bse); if (weight > _opt.min_print_weight) { XTP_LOG(Log::error, _log) << format(" HOMO-%1$-3d -> LUMO+%2$-3d : %3$3.1f%%") % (_opt.homo - vc.v(i_bse)) % (vc.c(i_bse) - _opt.homo - 1) % (100.0 * weight) << flush; } } return; } void BSE::Analyze_singlets(std::vector > fragments, const Orbitals& orb) const { Interaction act; QMStateType singlet = QMStateType(QMStateType::Singlet); Eigen::VectorXd oscs = orb.Oscillatorstrengths(); act = Analyze_eh_interaction(singlet, orb); if (fragments.size() > 0) { Lowdin low; low.CalcChargeperFragment(fragments, orb, singlet); } const Eigen::VectorXd& energies = orb.BSESinglets().eigenvalues(); double hrt2ev = tools::conv::hrt2ev; XTP_LOG(Log::error, _log) << " ====== singlet energies (eV) ====== " << flush; for (Index i = 0; i < _opt.nmax; ++i) { Eigen::VectorXd weights = orb.BSESinglets().eigenvectors().col(i).cwiseAbs2(); if (!orb.getTDAApprox()) { weights -= orb.BSESinglets().eigenvectors2().col(i).cwiseAbs2(); } double osc = oscs[i]; XTP_LOG(Log::error, _log) << format( " S = %1$4d Omega = %2$+1.12f eV lamdba = %3$+3.2f nm " "= %4$+1.4f = %5$+1.4f = %6$+1.4f") % (i + 1) % (hrt2ev * energies(i)) % (1240.0 / (hrt2ev * energies(i))) % (hrt2ev * act.qp_contrib(i)) % (hrt2ev * act.exchange_contrib(i)) % (hrt2ev * act.direct_contrib(i)) << flush; const Eigen::Vector3d& trdip = orb.TransitionDipoles()[i]; XTP_LOG(Log::error, _log) << format( " TrDipole length gauge[e*bohr] dx = %1$+1.4f dy = " "%2$+1.4f dz = %3$+1.4f |d|^2 = %4$+1.4f f = %5$+1.4f") % trdip[0] % trdip[1] % trdip[2] % (trdip.squaredNorm()) % osc << flush; PrintWeights(weights); if (fragments.size() > 0) { printFragInfo(fragments, i); } XTP_LOG(Log::error, _log) << flush; } return; } void BSE::Analyze_triplets(std::vector > fragments, const Orbitals& orb) const { Interaction act; QMStateType triplet = QMStateType(QMStateType::Triplet); act = Analyze_eh_interaction(triplet, orb); if (fragments.size() > 0) { Lowdin low; low.CalcChargeperFragment(fragments, orb, triplet); } const Eigen::VectorXd& energies = orb.BSETriplets().eigenvalues(); XTP_LOG(Log::error, _log) << " ====== triplet energies (eV) ====== " << flush; for (Index i = 0; i < _opt.nmax; ++i) { Eigen::VectorXd weights = orb.BSETriplets().eigenvectors().col(i).cwiseAbs2(); if (!orb.getTDAApprox()) { weights -= orb.BSETriplets().eigenvectors2().col(i).cwiseAbs2(); } XTP_LOG(Log::error, _log) << format( " T = %1$4d Omega = %2$+1.12f eV lamdba = %3$+3.2f nm " "= %4$+1.4f = %5$+1.4f") % (i + 1) % (tools::conv::hrt2ev * energies(i)) % (1240.0 / (tools::conv::hrt2ev * energies(i))) % (tools::conv::hrt2ev * act.qp_contrib(i)) % (tools::conv::hrt2ev * act.direct_contrib(i)) << flush; PrintWeights(weights); if (fragments.size() > 0) { printFragInfo(fragments, i); } XTP_LOG(Log::error, _log) << format(" ") << flush; } return; } template BSE::ExpectationValues BSE::ExpectationValue_Operator( const QMStateType& type, const Orbitals& orb, const BSE_OPERATOR& H) const { const tools::EigenSystem& BSECoefs = (type == QMStateType::Singlet) ? orb.BSESinglets() : orb.BSETriplets(); ExpectationValues expectation_values; expectation_values.direct_term = BSECoefs.eigenvectors() .cwiseProduct((H * BSECoefs.eigenvectors())) .colwise() .sum() .transpose(); if (!orb.getTDAApprox()) { expectation_values.direct_term += BSECoefs.eigenvectors2() .cwiseProduct((H * BSECoefs.eigenvectors2())) .colwise() .sum() .transpose(); expectation_values.cross_term = 2 * BSECoefs.eigenvectors2() .cwiseProduct((H * BSECoefs.eigenvectors())) .colwise() .sum() .transpose(); } else { expectation_values.cross_term = Eigen::VectorXd::Zero(0); } return expectation_values; } template BSE::ExpectationValues BSE::ExpectationValue_Operator_State( const QMStateType& type, const Orbitals& orb, const BSE_OPERATOR& H, const Index state) const { const tools::EigenSystem& BSECoefs = (type == QMStateType::Singlet) ? orb.BSESinglets() : orb.BSETriplets(); ExpectationValues expectation_values; const Eigen::MatrixXd& BSECoefs_state = BSECoefs.eigenvectors().col(state); expectation_values.direct_term = BSECoefs_state.cwiseProduct((H * BSECoefs_state)) .colwise() .sum() .transpose(); if (!orb.getTDAApprox()) { const Eigen::MatrixXd& BSECoefs2_state = BSECoefs.eigenvectors2().col(state); expectation_values.direct_term += BSECoefs2_state.cwiseProduct((H * BSECoefs2_state)) .colwise() .sum() .transpose(); expectation_values.cross_term = 2 * BSECoefs2_state.cwiseProduct((H * BSECoefs_state)) .colwise() .sum() .transpose(); } else { expectation_values.cross_term = Eigen::VectorXd::Zero(0); } return expectation_values; } // Composition of the excitation energy in terms of QP, direct (screened), // and exchance contributions in the BSE // Full BSE: // // | A* | | H K | | A | // | -B* | | -K -H | | B | = A*.H.A + B*.H.B + 2A*.K.B // // with: H = H_qp + H_d + eta.H_x // K = H_d2 + eta.H_x // // reports composition for FULL BSE as // = A*.H_qp.A + B*.H_qp.B // = eta.(A*.H_x.A + B*.H_x.B + 2A*.H_x.B) // = A*.H_d.A + B*.H_d.B + 2A*.H_d2.B BSE::Interaction BSE::Analyze_eh_interaction(const QMStateType& type, const Orbitals& orb) const { Interaction analysis; ExpectationValues expectation_values; HqpOperator hqp(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(hqp); expectation_values = ExpectationValue_Operator(type, orb, hqp); analysis.qp_contrib = expectation_values.direct_term; HdOperator hd(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(hd); expectation_values = ExpectationValue_Operator(type, orb, hd); analysis.direct_contrib = expectation_values.direct_term; if (!orb.getTDAApprox()) { Hd2Operator hd2(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(hd2); expectation_values = ExpectationValue_Operator(type, orb, hd2); analysis.direct_contrib += expectation_values.cross_term; } if (type == QMStateType::Singlet) { HxOperator hx(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(hx); expectation_values = ExpectationValue_Operator(type, orb, hx); analysis.exchange_contrib = 2.0 * expectation_values.direct_term; if (!orb.getTDAApprox()) { analysis.exchange_contrib += 2.0 * expectation_values.cross_term; } } else { analysis.exchange_contrib = Eigen::VectorXd::Zero(0); } return analysis; } // Dynamical Screening in BSE as perturbation to static excitation energies // as in Phys. Rev. B 80, 241405 (2009) for the TDA case void BSE::Perturbative_DynamicalScreening(const QMStateType& type, Orbitals& orb) { const tools::EigenSystem& BSECoefs = (type == QMStateType::Singlet) ? orb.BSESinglets() : orb.BSETriplets(); const Eigen::VectorXd& RPAInputEnergies = orb.RPAInputEnergies(); ExpectationValues expectation_values; // static case as reference SetupDirectInteractionOperator(RPAInputEnergies, 0.0); HdOperator Hd_static(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(Hd_static); expectation_values = ExpectationValue_Operator(type, orb, Hd_static); Eigen::VectorXd Hd_static_contribution = expectation_values.direct_term; if (!orb.getTDAApprox()) { Hd2Operator Hd2_static(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(Hd2_static); expectation_values = ExpectationValue_Operator(type, orb, Hd2_static); Hd_static_contribution += expectation_values.cross_term; } const Eigen::VectorXd& BSEenergies = BSECoefs.eigenvalues(); // initial copy of static BSE energies to dynamic Eigen::VectorXd BSEenergies_dynamic = BSEenergies; // recalculate Hd at the various energies for (Index i_exc = 0; i_exc < BSEenergies.size(); i_exc++) { XTP_LOG(Log::info, _log) << "Dynamical Screening BSE, Excitation " << i_exc << " static " << BSEenergies(i_exc) << flush; for (Index iter = 0; iter < _max_dyn_iter; iter++) { // setup the direct operator with the last energy as screening frequency double old_energy = BSEenergies_dynamic(i_exc); SetupDirectInteractionOperator(RPAInputEnergies, old_energy); HdOperator Hd_dyn(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(Hd_dyn); // get the contribution of Hd for the dynamic case expectation_values = ExpectationValue_Operator_State(type, orb, Hd_dyn, i_exc); Eigen::VectorXd Hd_dynamic_contribution = expectation_values.direct_term; if (!orb.getTDAApprox()) { Hd2Operator Hd2_dyn(_epsilon_0_inv, _Mmn, _Hqp); configureBSEOperator(Hd2_dyn); expectation_values = ExpectationValue_Operator_State(type, orb, Hd2_dyn, i_exc); Hd_dynamic_contribution += expectation_values.cross_term; } // new energy perturbatively BSEenergies_dynamic(i_exc) = BSEenergies(i_exc) + Hd_static_contribution(i_exc) - Hd_dynamic_contribution(0); XTP_LOG(Log::info, _log) << "Dynamical Screening BSE, excitation " << i_exc << " iteration " << iter << " dynamic " << BSEenergies_dynamic(i_exc) << flush; // check tolerance if (std::abs(BSEenergies_dynamic(i_exc) - old_energy) < _dyn_tolerance) { break; } } } double hrt2ev = tools::conv::hrt2ev; if (type == QMStateType::Singlet) { orb.BSESinglets_dynamic() = BSEenergies_dynamic; XTP_LOG(Log::error, _log) << " ====== singlet energies with perturbative " "dynamical screening (eV) ====== " << flush; Eigen::VectorXd oscs = orb.Oscillatorstrengths(); for (Index i = 0; i < _opt.nmax; ++i) { double osc = oscs[i]; XTP_LOG(Log::error, _log) << format( " S(dynamic) = %1$4d Omega = %2$+1.12f eV lamdba = %3$+3.2f " "nm f " "= %4$+1.4f") % (i + 1) % (hrt2ev * BSEenergies_dynamic(i)) % (1240.0 / (hrt2ev * BSEenergies_dynamic(i))) % (osc * BSEenergies_dynamic(i) / BSEenergies(i)) << flush; } } else { orb.BSETriplets_dynamic() = BSEenergies_dynamic; XTP_LOG(Log::error, _log) << " ====== triplet energies with perturbative " "dynamical screening (eV) ====== " << flush; for (Index i = 0; i < _opt.nmax; ++i) { XTP_LOG(Log::error, _log) << format( " T(dynamic) = %1$4d Omega = %2$+1.12f eV lamdba = %3$+3.2f " "nm ") % (i + 1) % (hrt2ev * BSEenergies_dynamic(i)) % (1240.0 / (hrt2ev * BSEenergies_dynamic(i))) << flush; } } } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gwbse/bse_operator.cc000066400000000000000000000112151412152066400206070ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/bse_operator.h" #include "votca/xtp/vc2index.h" namespace votca { namespace xtp { template void BSE_OPERATOR::configure(BSEOperator_Options opt) { _opt = opt; Index bse_vmax = _opt.homo; _bse_cmin = _opt.homo + 1; _bse_vtotal = bse_vmax - _opt.vmin + 1; _bse_ctotal = _opt.cmax - _bse_cmin + 1; _bse_size = _bse_vtotal * _bse_ctotal; this->set_size(_bse_size); } template Eigen::RowVectorXd BSE_OPERATOR::OperatorRow( Index index) const { Eigen::RowVectorXd row = Eigen::RowVectorXd::Zero(_bse_size); if (cd != 0) { row += cd * Hd_row(index); } if (cd2 != 0) { row += cd2 * Hd2_row(index); } if (cqp != 0) { row += cqp * Hqp_row(index); } return row; } template Eigen::MatrixXd BSE_OPERATOR::OperatorBlock(Index row, Index col) const { return cx * HxBlock(row, col); } template Eigen::MatrixXd BSE_OPERATOR::HxBlock(Index row, Index col) const { Index auxsize = _Mmn.auxsize(); Index vmin = _opt.vmin - _opt.rpamin; Index cmin = _bse_cmin - _opt.rpamin; Index v1 = row + vmin; Index v2 = col + vmin; return _Mmn[v1].block(cmin, 0, _bse_ctotal, auxsize) * _Mmn[v2].block(cmin, 0, _bse_ctotal, auxsize).transpose(); } template Eigen::RowVectorXd BSE_OPERATOR::Hd_row(Index index) const { Index auxsize = _Mmn.auxsize(); vc2index vc = vc2index(0, 0, _bse_ctotal); Index vmin = _opt.vmin - _opt.rpamin; Index cmin = _bse_cmin - _opt.rpamin; Index v1 = vc.v(index); Index c1 = vc.c(index); const Eigen::MatrixXd Mmn1T = -(_Mmn[v1 + vmin].block(vmin, 0, _bse_vtotal, auxsize) * _epsilon_0_inv.asDiagonal()) .transpose(); const Eigen::MatrixXd& Mmn2 = _Mmn[c1 + cmin]; Eigen::MatrixXd Mmn2xMmn1T = Mmn2.block(cmin, 0, _bse_ctotal, auxsize) * Mmn1T; return Eigen::Map(Mmn2xMmn1T.data(), Mmn2xMmn1T.size()); } template Eigen::RowVectorXd BSE_OPERATOR::Hqp_row(Index index) const { vc2index vc = vc2index(0, 0, _bse_ctotal); Index v1 = vc.v(index); Index c1 = vc.c(index); Eigen::MatrixXd Result = Eigen::MatrixXd::Zero(_bse_ctotal, _bse_vtotal); Index cmin = _bse_vtotal; // v->c Result.col(v1) += _Hqp.col(c1 + cmin).segment(cmin, _bse_ctotal); // c-> v Result.row(c1) -= _Hqp.col(v1).head(_bse_vtotal); return Eigen::Map(Result.data(), Result.size()); } template Eigen::RowVectorXd BSE_OPERATOR::Hd2_row(Index index) const { Index auxsize = _Mmn.auxsize(); vc2index vc = vc2index(0, 0, _bse_ctotal); const Index vmin = _opt.vmin - _opt.rpamin; const Index cmin = _bse_cmin - _opt.rpamin; Index v1 = vc.v(index); Index c1 = vc.c(index); const Eigen::MatrixXd Mmn2T = -(_Mmn[c1 + cmin].block(vmin, 0, _bse_vtotal, auxsize) * _epsilon_0_inv.asDiagonal()) .transpose(); const Eigen::MatrixXd& Mmn1 = _Mmn[v1 + vmin]; Eigen::MatrixXd Mmn1xMmn2T = Mmn1.block(cmin, 0, _bse_ctotal, auxsize) * Mmn2T; return Eigen::Map(Mmn1xMmn2T.data(), Mmn1xMmn2T.size()); } template class BSE_OPERATOR<1, 2, 1, 0>; template class BSE_OPERATOR<1, 0, 1, 0>; template class BSE_OPERATOR<1, 4, 1, 1>; template class BSE_OPERATOR<1, 0, 1, 1>; template class BSE_OPERATOR<1, 0, 1, -1>; template class BSE_OPERATOR<1, 0, 0, 0>; template class BSE_OPERATOR<0, 1, 0, 0>; template class BSE_OPERATOR<0, 0, 1, 0>; template class BSE_OPERATOR<0, 0, 0, 1>; template class BSE_OPERATOR<0, 2, 0, 1>; } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gwbse/gw.cc000066400000000000000000000413471412152066400165510ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include #include // Local VOTCA includes #include "votca/xtp/IndexParser.h" #include "votca/xtp/anderson_mixing.h" #include "votca/xtp/gw.h" #include "votca/xtp/newton_rapson.h" #include "votca/xtp/rpa.h" #include "votca/xtp/sigma_cda.h" #include "votca/xtp/sigma_exact.h" #include "votca/xtp/sigma_ppm.h" namespace votca { namespace xtp { void GW::configure(const options& opt) { _opt = opt; _qptotal = _opt.qpmax - _opt.qpmin + 1; _rpa.configure(_opt.homo, _opt.rpamin, _opt.rpamax); if (_opt.sigma_integration == "exact") { _sigma = std::make_unique(_Mmn, _rpa); } else if (_opt.sigma_integration == "cda") { _sigma = std::make_unique(_Mmn, _rpa); } else if (_opt.sigma_integration == "ppm") { _sigma = std::make_unique(_Mmn, _rpa); } Sigma_base::options sigma_opt; sigma_opt.homo = _opt.homo; sigma_opt.qpmax = _opt.qpmax; sigma_opt.qpmin = _opt.qpmin; sigma_opt.rpamin = _opt.rpamin; sigma_opt.rpamax = _opt.rpamax; sigma_opt.eta = _opt.eta; sigma_opt.alpha = _opt.alpha; sigma_opt.quadrature_scheme = _opt.quadrature_scheme; sigma_opt.order = _opt.order; _sigma->configure(sigma_opt); _Sigma_x = Eigen::MatrixXd::Zero(_qptotal, _qptotal); _Sigma_c = Eigen::MatrixXd::Zero(_qptotal, _qptotal); } double GW::CalcHomoLumoShift(Eigen::VectorXd frequencies) const { double DFTgap = _dft_energies(_opt.homo + 1) - _dft_energies(_opt.homo); double QPgap = frequencies(_opt.homo + 1 - _opt.qpmin) - frequencies(_opt.homo - _opt.qpmin); return QPgap - DFTgap; } Eigen::MatrixXd GW::getHQP() const { return _Sigma_x + _Sigma_c - _vxc + Eigen::MatrixXd( _dft_energies.segment(_opt.qpmin, _qptotal).asDiagonal()); } Eigen::SelfAdjointEigenSolver GW::DiagonalizeQPHamiltonian() const { Eigen::SelfAdjointEigenSolver qpdiag(getHQP()); PrintQP_Energies(qpdiag.eigenvalues()); return qpdiag; } void GW::PrintGWA_Energies() const { Eigen::VectorXd gwa_energies = getGWAResults(); double shift = CalcHomoLumoShift(gwa_energies); XTP_LOG(Log::error, _log) << (boost::format( " ====== Perturbative quasiparticle energies (Hartree) ====== ")) .str() << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" DeltaHLGap = %1$+1.6f Hartree") % shift).str() << std::flush; for (Index i = 0; i < _qptotal; i++) { std::string level = " Level"; if ((i + _opt.qpmin) == _opt.homo) { level = " HOMO "; } else if ((i + _opt.qpmin) == _opt.homo + 1) { level = " LUMO "; } XTP_LOG(Log::error, _log) << level << (boost::format(" = %1$4d DFT = %2$+1.4f VXC = %3$+1.4f S-X = " "%4$+1.4f S-C = %5$+1.4f GWA = %6$+1.4f") % (i + _opt.qpmin) % _dft_energies(i + _opt.qpmin) % _vxc(i, i) % _Sigma_x(i, i) % _Sigma_c(i, i) % gwa_energies(i)) .str() << std::flush; } return; } void GW::PrintQP_Energies(const Eigen::VectorXd& qp_diag_energies) const { Eigen::VectorXd gwa_energies = getGWAResults(); XTP_LOG(Log::error, _log) << TimeStamp() << " Full quasiparticle Hamiltonian " << std::flush; XTP_LOG(Log::error, _log) << (boost::format( " ====== Diagonalized quasiparticle energies (Hartree) " "====== ")) .str() << std::flush; for (Index i = 0; i < _qptotal; i++) { std::string level = " Level"; if ((i + _opt.qpmin) == _opt.homo) { level = " HOMO "; } else if ((i + _opt.qpmin) == _opt.homo + 1) { level = " LUMO "; } XTP_LOG(Log::error, _log) << level << (boost::format(" = %1$4d PQP = %2$+1.6f DQP = %3$+1.6f ") % (i + _opt.qpmin) % gwa_energies(i) % qp_diag_energies(i)) .str() << std::flush; } return; } Eigen::VectorXd GW::ScissorShift_DFTlevel( const Eigen::VectorXd& dft_energies) const { Eigen::VectorXd shifted_energies = dft_energies; shifted_energies.segment(_opt.homo + 1, dft_energies.size() - _opt.homo - 1) .array() += _opt.shift; return shifted_energies; } void GW::CalculateGWPerturbation() { _Sigma_x = (1 - _opt.ScaHFX) * _sigma->CalcExchangeMatrix(); XTP_LOG(Log::error, _log) << TimeStamp() << " Calculated Hartree exchange contribution" << std::flush; // dftenergies has size aobasissize // rpaenergies/Mmn have size rpatotal // gwaenergies/frequencies have size qptotal // homo index is relative to dft_energies XTP_LOG(Log::error, _log) << TimeStamp() << " Scissor shifting DFT energies by: " << _opt.shift << " Hrt" << std::flush; Eigen::VectorXd dft_shifted_energies = ScissorShift_DFTlevel(_dft_energies); _rpa.setRPAInputEnergies( dft_shifted_energies.segment(_opt.rpamin, _opt.rpamax - _opt.rpamin + 1)); Eigen::VectorXd frequencies = dft_shifted_energies.segment(_opt.qpmin, _qptotal); Anderson _mixing; _mixing.Configure(_opt.gw_mixing_order, _opt.gw_mixing_alpha); for (Index i_gw = 0; i_gw < _opt.gw_sc_max_iterations; ++i_gw) { if (i_gw % _opt.reset_3c == 0 && i_gw != 0) { _Mmn.Rebuild(); XTP_LOG(Log::info, _log) << TimeStamp() << " Rebuilding 3c integrals" << std::flush; } _sigma->PrepareScreening(); XTP_LOG(Log::info, _log) << TimeStamp() << " Calculated screening via RPA" << std::flush; XTP_LOG(Log::info, _log) << TimeStamp() << " Solving QP equations " << std::flush; if (_opt.gw_mixing_order > 0 && i_gw > 0) { _mixing.UpdateInput(frequencies); } frequencies = SolveQP(frequencies); if (_opt.gw_sc_max_iterations > 1) { Eigen::VectorXd rpa_energies_old = _rpa.getRPAInputEnergies(); if (_opt.gw_mixing_order > 0 && i_gw > 0) { if (_opt.gw_mixing_order == 1) { XTP_LOG(Log::debug, _log) << "GWSC using linear mixing with alpha: " << _opt.gw_mixing_alpha << std::flush; } else { XTP_LOG(Log::debug, _log) << "GWSC using Anderson mixing with history " << _opt.gw_mixing_order << ", alpha: " << _opt.gw_mixing_alpha << std::flush; } _mixing.UpdateOutput(frequencies); Eigen::VectorXd mixed_frequencies = _mixing.MixHistory(); _rpa.UpdateRPAInputEnergies(_dft_energies, mixed_frequencies, _opt.qpmin); frequencies = mixed_frequencies; } else { XTP_LOG(Log::debug, _log) << "GWSC using plain update " << std::flush; _rpa.UpdateRPAInputEnergies(_dft_energies, frequencies, _opt.qpmin); } for (int i = 0; i < frequencies.size(); i++) { XTP_LOG(Log::debug, _log) << "... GWSC iter " << i_gw << " state " << i << " " << std::setprecision(9) << frequencies(i) << std::flush; } XTP_LOG(Log::info, _log) << TimeStamp() << " GW_Iteration:" << i_gw << " Shift[Hrt]:" << CalcHomoLumoShift(frequencies) << std::flush; if (Converged(_rpa.getRPAInputEnergies(), rpa_energies_old, _opt.gw_sc_limit)) { XTP_LOG(Log::info, _log) << TimeStamp() << " Converged after " << i_gw + 1 << " GW iterations." << std::flush; break; } else if (i_gw == _opt.gw_sc_max_iterations - 1) { XTP_LOG(Log::error, _log) << TimeStamp() << " WARNING! GW-self-consistency cycle not converged after " << _opt.gw_sc_max_iterations << " iterations." << std::flush; XTP_LOG(Log::error, _log) << TimeStamp() << " Run continues. Inspect results carefully!" << std::flush; break; } } } _Sigma_c.diagonal() = _sigma->CalcCorrelationDiag(frequencies); PrintGWA_Energies(); } Eigen::VectorXd GW::getGWAResults() const { return _Sigma_x.diagonal() + _Sigma_c.diagonal() - _vxc.diagonal() + _dft_energies.segment(_opt.qpmin, _qptotal); } Eigen::VectorXd GW::SolveQP(const Eigen::VectorXd& frequencies) const { const Eigen::VectorXd intercepts = _dft_energies.segment(_opt.qpmin, _qptotal) + _Sigma_x.diagonal() - _vxc.diagonal(); Eigen::VectorXd frequencies_new = frequencies; Eigen::Array converged = Eigen::Array::Zero(_qptotal); #ifdef _OPENMP Index use_threads = OPENMP::getMaxThreads() > _qptotal ? _qptotal : OPENMP::getMaxThreads(); #endif #pragma omp parallel for schedule(dynamic) num_threads(use_threads) for (Index gw_level = 0; gw_level < _qptotal; ++gw_level) { double initial_f = frequencies[gw_level]; double intercept = intercepts[gw_level]; boost::optional newf; if (_opt.qp_solver == "fixedpoint") { newf = SolveQP_FixedPoint(intercept, initial_f, gw_level); } if (newf) { frequencies_new[gw_level] = newf.value(); converged[gw_level] = true; } else { newf = SolveQP_Grid(intercept, initial_f, gw_level); if (newf) { frequencies_new[gw_level] = newf.value(); converged[gw_level] = true; } else { newf = SolveQP_Linearisation(intercept, initial_f, gw_level); if (newf) { frequencies_new[gw_level] = newf.value(); } } } } if (!converged.all()) { std::vector states; for (Index s = 0; s < converged.size(); s++) { if (!converged[s]) { states.push_back(s); } } IndexParser rp; XTP_LOG(Log::error, _log) << TimeStamp() << " Not converged PQP states are:" << rp.CreateIndexString(states) << std::flush; XTP_LOG(Log::error, _log) << TimeStamp() << " Increase the grid search interval" << std::flush; } return frequencies_new; } boost::optional GW::SolveQP_Linearisation(double intercept0, double frequency0, Index gw_level) const { boost::optional newf = boost::none; double sigma = _sigma->CalcCorrelationDiagElement(gw_level, frequency0); double dsigma_domega = _sigma->CalcCorrelationDiagElementDerivative(gw_level, frequency0); double Z = 1.0 - dsigma_domega; if (std::abs(Z) > 1e-9) { newf = frequency0 + (intercept0 - frequency0 + sigma) / Z; } return newf; } boost::optional GW::SolveQP_Grid(double intercept0, double frequency0, Index gw_level) const { std::vector> roots; const double range = _opt.qp_grid_spacing * double(_opt.qp_grid_steps - 1) / 2.0; boost::optional newf = boost::none; double freq_prev = frequency0 - range; QPFunc fqp(gw_level, *_sigma.get(), intercept0); double targ_prev = fqp.value(freq_prev); double qp_energy = 0.0; double gradient_max = std::numeric_limits::max(); bool pole_found = false; for (Index i_node = 1; i_node < _opt.qp_grid_steps; ++i_node) { double freq = freq_prev + _opt.qp_grid_spacing; double targ = fqp.value(freq); if (targ_prev * targ < 0.0) { // Sign change double f = SolveQP_Bisection(freq_prev, targ_prev, freq, targ, fqp); double gradient = fqp.deriv(f); double qp_weight = -1.0 / gradient; roots.push_back(std::make_pair(f, qp_weight)); if (std::abs(gradient) < gradient_max) { gradient_max = std::abs(gradient); qp_energy = f; pole_found = true; } } freq_prev = freq; targ_prev = targ; } if (Log::current_level > Log::error) { #pragma omp critical { if (!pole_found) { XTP_LOG(Log::info, _log) << " No roots found for qplevel:" << gw_level << std::flush; } else { XTP_LOG(Log::info, _log) << " Roots found for qplevel:" << gw_level << " (qpenergy:qpweight)\n\t\t"; for (auto& root : roots) { XTP_LOG(Log::info, _log) << std::setprecision(5) << root.first << ":" << root.second << " "; } XTP_LOG(Log::info, _log) << "Root chosen " << qp_energy << std::flush; } } } if (pole_found) { newf = qp_energy; } return newf; } boost::optional GW::SolveQP_FixedPoint(double intercept0, double frequency0, Index gw_level) const { boost::optional newf = boost::none; QPFunc f(gw_level, *_sigma.get(), intercept0); NewtonRapson newton = NewtonRapson( _opt.g_sc_max_iterations, _opt.g_sc_limit, _opt.qp_solver_alpha); double freq_new = newton.FindRoot(f, frequency0); if (newton.getInfo() == NewtonRapson::success) { newf = freq_new; } return newf; } // https://en.wikipedia.org/wiki/Bisection_method double GW::SolveQP_Bisection(double lowerbound, double f_lowerbound, double upperbound, double f_upperbound, const QPFunc& f) const { if (f_lowerbound * f_upperbound > 0) { throw std::runtime_error( "Bisection needs a postive and negative function value"); } double zero = 0.0; while (true) { double c = 0.5 * (lowerbound + upperbound); if (std::abs(upperbound - lowerbound) < _opt.g_sc_limit) { zero = c; break; } double y_c = f.value(c); if (std::abs(y_c) < _opt.g_sc_limit) { zero = c; break; } if (y_c * f_lowerbound > 0) { lowerbound = c; f_lowerbound = y_c; } else { upperbound = c; f_upperbound = y_c; } } return zero; } bool GW::Converged(const Eigen::VectorXd& e1, const Eigen::VectorXd& e2, double epsilon) const { Index state = 0; bool energies_converged = true; double diff_max = (e1 - e2).cwiseAbs().maxCoeff(&state); if (diff_max > epsilon) { energies_converged = false; } XTP_LOG(Log::info, _log) << TimeStamp() << " E_diff max=" << diff_max << " StateNo:" << state << std::flush; return energies_converged; } void GW::CalculateHQP() { Eigen::VectorXd diag_backup = _Sigma_c.diagonal(); _Sigma_c = _sigma->CalcCorrelationOffDiag(getGWAResults()); _Sigma_c.diagonal() = diag_backup; } void GW::PlotSigma(std::string filename, Index steps, double spacing, std::string states) const { Eigen::VectorXd frequencies = _rpa.getRPAInputEnergies().segment(_opt.qpmin - _opt.rpamin, _qptotal); std::vector state_inds; IndexParser rp; std::vector parsed_states = rp.CreateIndexVector(states); for (Index gw_level : parsed_states) { if (gw_level >= _opt.qpmin && gw_level <= _opt.qpmax) { state_inds.push_back(gw_level); } } XTP_LOG(Log::error, _log) << TimeStamp() << " PQP(omega) written to '" << filename << "' for states " << rp.CreateIndexString(state_inds) << std::flush; const Index num_states = state_inds.size(); const Eigen::VectorXd intercept = _dft_energies.segment(_opt.qpmin, _qptotal) + _Sigma_x.diagonal() - _vxc.diagonal(); Eigen::MatrixXd mat = Eigen::MatrixXd::Zero(steps, 2 * num_states); #pragma omp parallel for schedule(dynamic) for (Index grid_point = 0; grid_point < steps; grid_point++) { const double offset = ((double)grid_point - ((double)(steps - 1) / 2.0)) * spacing; for (Index i = 0; i < num_states; i++) { const Index gw_level = state_inds[i]; const double omega = frequencies(gw_level) + offset; double sigma = _sigma->CalcCorrelationDiagElement(gw_level, omega); mat(grid_point, 2 * i) = omega; mat(grid_point, 2 * i + 1) = sigma + intercept[gw_level]; } } std::ofstream out; out.open(filename); for (Index i = 0; i < num_states; i++) { const Index gw_level = state_inds[i]; out << boost::format("#%1$somega_%2$d\tE_QP(omega)_%2$d") % (i == 0 ? "" : "\t") % gw_level; } out << std::endl; boost::format numFormat("%+1.6f"); Eigen::IOFormat matFormat(Eigen::StreamPrecision, 0, "\t", "\n"); out << numFormat % mat.format(matFormat) << std::endl; out.close(); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gwbse/gwbse.cc000066400000000000000000000663301412152066400172420ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include #include #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/bse.h" #include "votca/xtp/ecpbasisset.h" #include "votca/xtp/gwbse.h" #include "votca/xtp/logger.h" #include "votca/xtp/openmp_cuda.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/vxc_grid.h" #include "votca/xtp/vxc_potential.h" using boost::format; using namespace boost::filesystem; using std::flush; namespace votca { namespace xtp { Index GWBSE::CountCoreLevels() { Index ignored_corelevels = 0; if (!_orbitals.hasECPName()) { ECPBasisSet basis; basis.Load("corelevels"); Index coreElectrons = 0; for (const auto& atom : _orbitals.QMAtoms()) { coreElectrons += basis.getElement(atom.getElement()).getNcore(); } ignored_corelevels = coreElectrons / 2; } return ignored_corelevels; } void GWBSE::Initialize(tools::Property& options) { std::string key = Identify(); // getting level ranges Index rpamax = 0; Index rpamin = 0; // never changes Index qpmin = 0; Index qpmax = 0; Index bse_vmin = 0; Index bse_cmax = 0; Index homo = _orbitals.getHomo(); // indexed from 0 Index num_of_levels = _orbitals.getBasisSetSize(); Index num_of_occlevels = _orbitals.getNumberOfAlphaElectrons(); std::string ranges = options.get(key + ".ranges").as(); // now check validity, and get rpa, qp, and bse level ranges accordingly if (ranges == "factor") { double rpamaxfactor = options.get(key + ".rpamax").as(); rpamax = Index(rpamaxfactor * double(num_of_levels)) - 1; // total number of levels double qpminfactor = options.get(key + ".qpmin").as(); qpmin = num_of_occlevels - Index(qpminfactor * double(num_of_occlevels)) - 1; double qpmaxfactor = options.get(key + ".qpmax").as(); qpmax = num_of_occlevels + Index(qpmaxfactor * double(num_of_occlevels)) - 1; double bseminfactor = options.get(key + ".bsemin").as(); bse_vmin = num_of_occlevels - Index(bseminfactor * double(num_of_occlevels)) - 1; double bsemaxfactor = options.get(key + ".bsemax").as(); bse_cmax = num_of_occlevels + Index(bsemaxfactor * double(num_of_occlevels)) - 1; } else if (ranges == "explicit") { // get explicit numbers rpamax = options.get(key + ".rpamax").as(); qpmin = options.get(key + ".qpmin").as(); qpmax = options.get(key + ".qpmax").as(); bse_vmin = options.get(key + ".bsemin").as(); bse_cmax = options.get(key + ".bsemax").as(); } else if (ranges == "default") { rpamax = num_of_levels - 1; qpmin = 0; qpmax = 3 * homo + 1; bse_vmin = 0; bse_cmax = 3 * homo + 1; } else if (ranges == "full") { rpamax = num_of_levels - 1; qpmin = 0; qpmax = num_of_levels - 1; bse_vmin = 0; bse_cmax = num_of_levels - 1; } std::string ignore_corelevels = options.get(key + ".ignore_corelevels").as(); if (ignore_corelevels == "RPA" || ignore_corelevels == "GW" || ignore_corelevels == "BSE") { Index ignored_corelevels = CountCoreLevels(); if (ignore_corelevels == "RPA") { rpamin = ignored_corelevels; } if (ignore_corelevels == "GW" || ignore_corelevels == "RPA") { if (qpmin < ignored_corelevels) { qpmin = ignored_corelevels; } } if (ignore_corelevels == "GW" || ignore_corelevels == "RPA" || ignore_corelevels == "BSE") { if (bse_vmin < ignored_corelevels) { bse_vmin = ignored_corelevels; } } XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Ignoring " << ignored_corelevels << " core levels for " << ignore_corelevels << " and beyond." << flush; } // check maximum and minimum sizes if (rpamax > num_of_levels) { rpamax = num_of_levels - 1; } if (qpmax > num_of_levels) { qpmax = num_of_levels - 1; } if (bse_cmax > num_of_levels) { bse_cmax = num_of_levels - 1; } if (bse_vmin < 0) { bse_vmin = 0; } if (qpmin < 0) { qpmin = 0; } _gwopt.homo = homo; _gwopt.qpmin = qpmin; _gwopt.qpmax = qpmax; _gwopt.rpamin = rpamin; _gwopt.rpamax = rpamax; _bseopt.vmin = bse_vmin; _bseopt.cmax = bse_cmax; _bseopt.homo = homo; _bseopt.qpmin = qpmin; _bseopt.qpmax = qpmax; _bseopt.rpamin = rpamin; _bseopt.rpamax = rpamax; _orbitals.setRPAindices(rpamin, rpamax); _orbitals.setGWindices(qpmin, qpmax); _orbitals.setBSEindices(bse_vmin, bse_cmax); _orbitals.SetFlagUseHqpOffdiag(_bseopt.use_Hqp_offdiag); Index bse_vmax = homo; Index bse_cmin = homo + 1; Index bse_vtotal = bse_vmax - bse_vmin + 1; Index bse_ctotal = bse_cmax - bse_cmin + 1; Index bse_size = bse_vtotal * bse_ctotal; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " RPA level range [" << rpamin << ":" << rpamax << "]" << flush; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " GW level range [" << qpmin << ":" << qpmax << "]" << flush; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " BSE level range occ[" << bse_vmin << ":" << bse_vmax << "] virt[" << bse_cmin << ":" << bse_cmax << "]" << flush; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " BSE Hamiltonian has size " << bse_size << "x" << bse_size << flush; _gwopt.reset_3c = options.get(key + ".rebuild_threecenter_freq").as(); _bseopt.nmax = options.get(key + ".exctotal").as(); if (_bseopt.nmax > bse_size || _bseopt.nmax < 0) { _bseopt.nmax = bse_size; } // eigensolver options _bseopt.davidson = options.get(key + ".eigensolver.dodavidson").as(); if (_bseopt.davidson) { _bseopt.matrixfree = options.get(key + ".eigensolver.domatrixfree").as(); _bseopt.davidson_correction = options.get(key + ".eigensolver.davidson_correction").as(); _bseopt.davidson_ortho = options.get(key + ".eigensolver.davidson_ortho").as(); _bseopt.davidson_tolerance = options.get(key + ".eigensolver.davidson_tolerance").as(); _bseopt.davidson_update = options.get(key + ".eigensolver.davidson_update").as(); _bseopt.davidson_maxiter = options.get(key + ".eigensolver.davidson_maxiter").as(); // check size if (_bseopt.nmax > bse_size / 4) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Warning : Too many eigenvalues required for Davidson. Default " "to Lapack diagonalization" << flush; _bseopt.davidson = false; } } _bseopt.useTDA = options.get(key + ".useTDA").as(); _orbitals.setTDAApprox(_bseopt.useTDA); if (!_bseopt.useTDA) { XTP_LOG(Log::error, *_pLog) << " BSE type: full" << flush; } else { XTP_LOG(Log::error, *_pLog) << " BSE type: TDA" << flush; } _bseopt.use_Hqp_offdiag = options.get(key + ".use_Hqp_offdiag").as(); if (!_bseopt.use_Hqp_offdiag) { XTP_LOG(Log::error, *_pLog) << " BSE without Hqp offdiagonal elements" << flush; } else { XTP_LOG(Log::error, *_pLog) << " BSE with Hqp offdiagonal elements" << flush; } _bseopt.max_dyn_iter = options.get(key + ".dynamical_screening_max_iterations").as(); _bseopt.dyn_tolerance = options.get(key + ".dynamical_screening_tolerance").as(); if (_bseopt.max_dyn_iter > 0) { _do_dynamical_screening_bse = true; } _functional = options.get(key + ".vxc.functional").as(); _grid = options.get(key + ".vxc.grid").as(); _auxbasis_name = options.get(key + ".auxbasisset").as(); _dftbasis_name = options.get(key + ".basisset").as(); if (_dftbasis_name != _orbitals.getDFTbasisName()) { throw std::runtime_error( "Name of the Basisset from .orb file: " + _orbitals.getDFTbasisName() + " and from GWBSE optionfile " + _dftbasis_name + " do not agree."); } std::string mode = options.get(key + ".mode").as(); if (mode == "G0W0") { _gwopt.gw_sc_max_iterations = 1; } else if (mode == "evGW") { _gwopt.g_sc_limit = 0.1 * _gwopt.gw_sc_limit; _gwopt.eta = 0.1; } // Check if the exact exchange of the functional matches the exact exchange in // orb file. If not display a warning. double ScaHFX_temp = Vxc_Potential::getExactExchange(_functional); if (ScaHFX_temp != _orbitals.getScaHFX()) { XTP_LOG(Log::error, *_pLog) << (boost::format( "WARNING: GWBSE exact exchange a=%s differs from qmpackage " "exact exchange a=%s, \n probably your functionals are " "inconsistent \n or dft orbitals were loaded from a package" " other than votca or orca. \n The GWBSE exact exchange will " "be used.") % ScaHFX_temp % _orbitals.getScaHFX()) .str() << std::flush; _orbitals.setScaHFX(ScaHFX_temp); } XTP_LOG(Log::error, *_pLog) << " Running GW as: " << mode << flush; _gwopt.ScaHFX = _orbitals.getScaHFX(); _gwopt.shift = options.get(key + ".scissor_shift").as(); _gwopt.g_sc_limit = options.get(key + ".g_sc_limit").as(); // convergence criteria // for qp iteration // [Hartree]] _gwopt.g_sc_max_iterations = options.get(key + ".g_sc_max_iterations").as(); // convergence // criteria for qp // iteration // [Hartree]] if (mode == "evGW") { _gwopt.gw_sc_max_iterations = options.get(key + ".gw_sc_max_iterations").as(); } _gwopt.gw_sc_limit = options.get(key + ".gw_sc_limit").as(); // convergence criteria // for shift it XTP_LOG(Log::error, *_pLog) << " g_sc_limit [Hartree]: " << _gwopt.g_sc_limit << flush; if (_gwopt.gw_sc_max_iterations > 1) { XTP_LOG(Log::error, *_pLog) << " gw_sc_limit [Hartree]: " << _gwopt.gw_sc_limit << flush; } _bseopt.min_print_weight = options.get(key + ".bse_print_weight").as(); // print exciton WF composition weight larger than minimum // possible tasks std::string tasks_string = options.get(key + ".tasks").as(); boost::algorithm::to_lower(tasks_string); if (tasks_string.find("all") != std::string::npos) { _do_gw = true; _do_bse_singlets = true; _do_bse_triplets = true; } if (tasks_string.find("gw") != std::string::npos) { _do_gw = true; } if (tasks_string.find("singlets") != std::string::npos) { _do_bse_singlets = true; } if (tasks_string.find("triplets") != std::string::npos) { _do_bse_triplets = true; } XTP_LOG(Log::error, *_pLog) << " Tasks: " << flush; if (_do_gw) { XTP_LOG(Log::error, *_pLog) << " GW " << flush; } if (_do_bse_singlets) { XTP_LOG(Log::error, *_pLog) << " singlets " << flush; } if (_do_bse_triplets) { XTP_LOG(Log::error, *_pLog) << " triplets " << flush; } XTP_LOG(Log::error, *_pLog) << " Store: " << flush; if (_do_gw) { XTP_LOG(Log::error, *_pLog) << " GW " << flush; } if (options.exists(key + ".fragments")) { std::vector prop_region = options.Select(key + ".fragments.fragment"); Index index = 0; for (tools::Property* prop : prop_region) { std::string indices = prop->ifExistsReturnElseThrowRuntimeError("indices"); _fragments.push_back(QMFragment(index, indices)); index++; } } _gwopt.sigma_integration = options.get(key + ".sigma_integrator").as(); XTP_LOG(Log::error, *_pLog) << " Sigma integration: " << _gwopt.sigma_integration << flush; _gwopt.eta = options.get(key + ".eta").as(); XTP_LOG(Log::error, *_pLog) << " eta: " << _gwopt.eta << flush; if (_gwopt.sigma_integration == "exact") { XTP_LOG(Log::error, *_pLog) << " RPA Hamiltonian size: " << (homo + 1 - rpamin) * (rpamax - homo) << flush; } _gwopt.order = options.get(key + ".quadrature_order").as(); XTP_LOG(Log::error, *_pLog) << " Quadrature integration order : " << _gwopt.order << flush; _gwopt.quadrature_scheme = options.get(key + ".quadrature_scheme").as(); XTP_LOG(Log::error, *_pLog) << " Quadrature integration scheme : " << _gwopt.quadrature_scheme << flush; _gwopt.alpha = options.get(key + ".alpha").as(); XTP_LOG(Log::error, *_pLog) << " Alpha smoothing parameter : " << _gwopt.alpha << flush; _gwopt.qp_solver = options.get(key + ".qp_solver").as(); _gwopt.qp_grid_steps = options.get(key + ".qp_grid_steps").as(); _gwopt.qp_grid_spacing = options.get(key + ".qp_grid_spacing").as(); XTP_LOG(Log::error, *_pLog) << " QP solver: " << _gwopt.qp_solver << flush; if (_gwopt.qp_solver == "grid") { XTP_LOG(Log::error, *_pLog) << " QP grid steps: " << _gwopt.qp_grid_steps << flush; XTP_LOG(Log::error, *_pLog) << " QP grid spacing: " << _gwopt.qp_grid_spacing << flush; } _gwopt.gw_mixing_order = options.get(key + ".gw_mixing_order").as(); // max history in // mixing (0: plain, // 1: linear, >1 // Anderson) _gwopt.gw_mixing_alpha = options.get(key + ".gw_mixing_alpha").as(); if (mode == "evGW") { if (_gwopt.gw_mixing_order == 0) { XTP_LOG(Log::error, *_pLog) << " evGW with plain update " << std::flush; } else if (_gwopt.gw_mixing_order == 1) { XTP_LOG(Log::error, *_pLog) << " evGW with linear update using alpha " << _gwopt.gw_mixing_alpha << std::flush; } else { XTP_LOG(Log::error, *_pLog) << " evGW with Anderson update with history " << _gwopt.gw_mixing_order << " using alpha " << _gwopt.gw_mixing_alpha << std::flush; } } _sigma_plot_states = options.get(key + ".sigma_plot_states").as(); _sigma_plot_steps = options.get(key + ".sigma_plot_steps").as(); _sigma_plot_spacing = options.get(key + ".sigma_plot_spacing").as(); _sigma_plot_filename = options.get(key + ".sigma_plot_filename").as(); if (!_sigma_plot_states.empty()) { XTP_LOG(Log::error, *_pLog) << " Sigma plot states: " << _sigma_plot_states << flush; XTP_LOG(Log::error, *_pLog) << " Sigma plot steps: " << _sigma_plot_steps << flush; XTP_LOG(Log::error, *_pLog) << " Sigma plot spacing: " << _sigma_plot_spacing << flush; XTP_LOG(Log::error, *_pLog) << " Sigma plot filename: " << _sigma_plot_filename << flush; } } void GWBSE::addoutput(tools::Property& summary) { const double hrt2ev = tools::conv::hrt2ev; tools::Property& gwbse_summary = summary.add("GWBSE", ""); if (_do_gw) { gwbse_summary.setAttribute("units", "eV"); gwbse_summary.setAttribute( "DFTEnergy", (format("%1$+1.6f ") % (_orbitals.getDFTTotalEnergy() * hrt2ev)).str()); tools::Property& dft_summary = gwbse_summary.add("dft", ""); dft_summary.setAttribute("HOMO", _gwopt.homo); dft_summary.setAttribute("LUMO", _gwopt.homo + 1); for (Index state = 0; state < _gwopt.qpmax + 1 - _gwopt.qpmin; state++) { tools::Property& level_summary = dft_summary.add("level", ""); level_summary.setAttribute("number", state + _gwopt.qpmin); level_summary.add( "dft_energy", (format("%1$+1.6f ") % (_orbitals.MOs().eigenvalues()(state + _gwopt.qpmin) * hrt2ev)) .str()); level_summary.add( "gw_energy", (format("%1$+1.6f ") % (_orbitals.QPpertEnergies()(state) * hrt2ev)) .str()); level_summary.add("qp_energy", (format("%1$+1.6f ") % (_orbitals.QPdiag().eigenvalues()(state) * hrt2ev)) .str()); } } if (_do_bse_singlets) { tools::Property& singlet_summary = gwbse_summary.add("singlets", ""); for (Index state = 0; state < _bseopt.nmax; ++state) { tools::Property& level_summary = singlet_summary.add("level", ""); level_summary.setAttribute("number", state + 1); level_summary.add( "omega", (format("%1$+1.6f ") % (_orbitals.BSESinglets().eigenvalues()(state) * hrt2ev)) .str()); if (_orbitals.hasTransitionDipoles()) { const Eigen::Vector3d& dipoles = (_orbitals.TransitionDipoles())[state]; double f = 2 * dipoles.squaredNorm() * _orbitals.BSESinglets().eigenvalues()(state) / 3.0; level_summary.add("f", (format("%1$+1.6f ") % f).str()); tools::Property& dipol_summary = level_summary.add( "Trdipole", (format("%1$+1.4f %2$+1.4f %3$+1.4f") % dipoles.x() % dipoles.y() % dipoles.z()) .str()); dipol_summary.setAttribute("unit", "e*bohr"); dipol_summary.setAttribute("gauge", "length"); } } } if (_do_bse_triplets) { tools::Property& triplet_summary = gwbse_summary.add("triplets", ""); for (Index state = 0; state < _bseopt.nmax; ++state) { tools::Property& level_summary = triplet_summary.add("level", ""); level_summary.setAttribute("number", state + 1); level_summary.add( "omega", (format("%1$+1.6f ") % (_orbitals.BSETriplets().eigenvalues()(state) * hrt2ev)) .str()); } } return; } /* * Many-body Green's fuctions theory implementation * * data required from orbitals file * - atomic coordinates * - DFT molecular orbitals (energies and coeffcients) * - DFT exchange-correlation potential matrix in atomic orbitals * - number of electrons, number of levels */ Eigen::MatrixXd GWBSE::CalculateVXC(const AOBasis& dftbasis) { if (_orbitals.getXCFunctionalName().empty()) { _orbitals.setXCFunctionalName(_functional); } else { if (!(_functional == _orbitals.getXCFunctionalName())) { throw std::runtime_error("Functionals from DFT " + _orbitals.getXCFunctionalName() + " GWBSE " + _functional + " differ!"); } } Vxc_Grid grid; grid.GridSetup(_grid, _orbitals.QMAtoms(), dftbasis); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Setup grid for integration with gridsize: " << _grid << " with " << grid.getGridSize() << " points, divided into " << grid.getBoxesSize() << " boxes" << flush; Vxc_Potential vxcpotential(grid); vxcpotential.setXCfunctional(_functional); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Integrating Vxc in VOTCA with functional " << _functional << flush; Eigen::MatrixXd DMAT = _orbitals.DensityMatrixGroundState(); Mat_p_Energy e_vxc_ao = vxcpotential.IntegrateVXC(DMAT); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Calculated Vxc in VOTCA" << flush; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Set hybrid exchange factor: " << _orbitals.getScaHFX() << flush; Index qptotal = _gwopt.qpmax - _gwopt.qpmin + 1; Index basissize = Index(_orbitals.MOs().eigenvectors().rows()); Eigen::MatrixXd mos = _orbitals.MOs().eigenvectors().block(0, _gwopt.qpmin, basissize, qptotal); Eigen::MatrixXd vxc = mos.transpose() * e_vxc_ao.matrix() * mos; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Calculated exchange-correlation expectation values " << flush; return vxc; } bool GWBSE::Evaluate() { // set the parallelization XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Using " << OPENMP::getMaxThreads() << " threads" << flush; if (XTP_HAS_MKL_OVERLOAD()) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Using MKL overload for Eigen " << flush; } else { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Using native Eigen implementation, no BLAS overload " << flush; } Index nogpus = OpenMP_CUDA::UsingGPUs(); if (nogpus > 0) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Using CUDA support for tensor multiplication with " << nogpus << " GPUs." << flush; } XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Molecule Coordinates [A] " << flush; for (QMAtom& atom : _orbitals.QMAtoms()) { std::string output = (boost::format("%5d" "%5s" " %1.4f %1.4f %1.4f") % atom.getId() % atom.getElement() % (atom.getPos().x() * tools::conv::bohr2ang) % (atom.getPos().y() * tools::conv::bohr2ang) % (atom.getPos().z() * tools::conv::bohr2ang)) .str(); XTP_LOG(Log::error, *_pLog) << output << flush; } std::string dft_package = _orbitals.getQMpackage(); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " DFT data was created by " << dft_package << flush; BasisSet dftbs; dftbs.Load(_dftbasis_name); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Loaded DFT Basis Set " << _dftbasis_name << flush; // fill DFT AO basis by going through all atoms AOBasis dftbasis; dftbasis.Fill(dftbs, _orbitals.QMAtoms()); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Filled DFT Basis of size " << dftbasis.AOBasisSize() << flush; // load auxiliary basis set (element-wise information) from xml file BasisSet auxbs; auxbs.Load(_auxbasis_name); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Loaded Auxbasis Set " << _auxbasis_name << flush; // fill auxiliary AO basis by going through all atoms AOBasis auxbasis; auxbasis.Fill(auxbs, _orbitals.QMAtoms()); _orbitals.setAuxbasisName(_auxbasis_name); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Filled Auxbasis of size " << auxbasis.AOBasisSize() << flush; if ((_do_bse_singlets || _do_bse_triplets) && _fragments.size() > 0) { for (const auto& frag : _fragments) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Fragment " << frag.getId() << " size:" << frag.size() << flush; } } if (!_do_gw && !_orbitals.hasQPdiag()) { throw std::runtime_error( "You want no GW calculation but the orb file has no QPcoefficients for " "BSE"); } TCMatrix_gwbse Mmn; // rpamin here, because RPA needs till rpamin Index max_3c = std::max(_bseopt.cmax, _gwopt.qpmax); Mmn.Initialize(auxbasis.AOBasisSize(), _gwopt.rpamin, max_3c, _gwopt.rpamin, _gwopt.rpamax); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Calculating Mmn_beta (3-center-repulsion x orbitals) " << flush; Mmn.Fill(auxbasis, dftbasis, _orbitals.MOs().eigenvectors()); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Removed " << Mmn.Removedfunctions() << " functions from Aux Coulomb matrix to avoid near linear dependencies" << flush; XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Calculated Mmn_beta (3-center-repulsion x orbitals) " << flush; Eigen::MatrixXd Hqp; if (_do_gw) { Eigen::MatrixXd vxc = CalculateVXC(dftbasis); GW gw = GW(*_pLog, Mmn, vxc, _orbitals.MOs().eigenvalues()); gw.configure(_gwopt); gw.CalculateGWPerturbation(); if (!_sigma_plot_states.empty()) { gw.PlotSigma(_sigma_plot_filename, _sigma_plot_steps, _sigma_plot_spacing, _sigma_plot_states); } // store perturbative QP energy data in orbitals object (DFT, S_x,S_c, V_xc, // E_qp) _orbitals.QPpertEnergies() = gw.getGWAResults(); _orbitals.RPAInputEnergies() = gw.RPAInputEnergies(); XTP_LOG(Log::info, *_pLog) << TimeStamp() << " Calculating offdiagonal part of Sigma " << flush; gw.CalculateHQP(); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Calculated offdiagonal part of Sigma " << flush; Hqp = gw.getHQP(); Eigen::SelfAdjointEigenSolver es = gw.DiagonalizeQPHamiltonian(); if (es.info() == Eigen::ComputationInfo::Success) { XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Diagonalized QP Hamiltonian " << flush; } _orbitals.QPdiag().eigenvectors() = es.eigenvectors(); _orbitals.QPdiag().eigenvalues() = es.eigenvalues(); } else { if (_orbitals.getGWAmax() != _gwopt.qpmax || _orbitals.getGWAmin() != _gwopt.qpmin || _orbitals.getRPAmax() != _gwopt.rpamax || _orbitals.getRPAmin() != _gwopt.rpamin) { throw std::runtime_error( "The ranges for GW and RPA do not agree with the ranges from the " ".orb file, rerun your GW calculation"); } const Eigen::MatrixXd& qpcoeff = _orbitals.QPdiag().eigenvectors(); Hqp = qpcoeff * _orbitals.QPdiag().eigenvalues().asDiagonal() * qpcoeff.transpose(); } // proceed only if BSE requested if (_do_bse_singlets || _do_bse_triplets) { BSE bse = BSE(*_pLog, Mmn); bse.configure(_bseopt, _orbitals.RPAInputEnergies(), Hqp); // store the direct contribution to the static BSE results Eigen::VectorXd Hd_static_contrib_triplet; Eigen::VectorXd Hd_static_contrib_singlet; if (_do_bse_triplets) { bse.Solve_triplets(_orbitals); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Solved BSE for triplets " << flush; bse.Analyze_triplets(_fragments, _orbitals); } if (_do_bse_singlets) { bse.Solve_singlets(_orbitals); XTP_LOG(Log::error, *_pLog) << TimeStamp() << " Solved BSE for singlets " << flush; bse.Analyze_singlets(_fragments, _orbitals); } // do perturbative dynamical screening in BSE if (_do_dynamical_screening_bse) { if (_do_bse_triplets) { bse.Perturbative_DynamicalScreening(QMStateType(QMStateType::Triplet), _orbitals); } if (_do_bse_singlets) { bse.Perturbative_DynamicalScreening(QMStateType(QMStateType::Singlet), _orbitals); } } } XTP_LOG(Log::error, *_pLog) << TimeStamp() << " GWBSE calculation finished " << flush; return true; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gwbse/gwbseengine.cc000066400000000000000000000126771412152066400204350ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include #include // Local VOTCA includes #include "votca/xtp/gwbse.h" #include "votca/xtp/gwbseengine.h" #include "votca/xtp/logger.h" #include "votca/xtp/qmpackage.h" using boost::format; using namespace boost::filesystem; using std::flush; namespace votca { namespace xtp { // +++++++++++++++++++++++++++++ // // GWBSEENGINE MEMBER FUNCTIONS // // +++++++++++++++++++++++++++++ // void GWBSEEngine::Initialize(tools::Property& options, std::string archive_filename) { _archive_file = archive_filename; std::string tasks_string = options.get(".tasks").as(); if (tasks_string.find("guess") != std::string::npos) { _do_guess = true; } if (tasks_string.find("input") != std::string::npos) { _do_dft_input = true; } if (tasks_string.find("dft") != std::string::npos) { _do_dft_run = true; } if (tasks_string.find("parse") != std::string::npos) { _do_dft_parse = true; } if (tasks_string.find("gwbse") != std::string::npos) { _do_gwbse = true; } // XML option file for GWBSE if (_do_gwbse) { _gwbse_options = options.get(".gwbse_options"); } // DFT log and MO file names _MO_file = _qmpackage->getMOFile(); _dftlog_file = _qmpackage->getLogFile(); // Logger redirection _redirect_logger = options.ifExistsReturnElseReturnDefault( ".redirect_logger", _redirect_logger); _logger_file = "gwbse.log"; // for requested merged guess, two archived orbitals objects are needed if (_do_guess) { _guess_archiveA = options.ifExistsReturnElseThrowRuntimeError(".archiveA"); _guess_archiveB = options.ifExistsReturnElseThrowRuntimeError(".archiveB"); } return; } /* * CALL DFT and GWBSE modules to get excitation energies * */ void GWBSEEngine::ExcitationEnergies(Orbitals& orbitals) { // redirect log, if required // define own logger for GW-BSE that is written into a runFolder logfile Logger gwbse_engine_logger(_pLog->getReportLevel()); Logger* logger = _pLog; if (_redirect_logger) { gwbse_engine_logger.setMultithreading(false); gwbse_engine_logger.setPreface(Log::info, "\n ..."); gwbse_engine_logger.setPreface(Log::error, "\n ..."); gwbse_engine_logger.setPreface(Log::warning, "\n ..."); gwbse_engine_logger.setPreface(Log::debug, "\n ..."); logger = &gwbse_engine_logger; } _qmpackage->setLog(logger); if (_do_dft_input) { // required for merged guess if (_qmpackage->GuessRequested() && _do_guess) { // do not want to do an // SCF loop for a dimer XTP_LOG(Log::error, *logger) << "Guess requested, reading molecular orbitals" << flush; Orbitals orbitalsA, orbitalsB; orbitalsA.ReadFromCpt(_guess_archiveA); orbitalsB.ReadFromCpt(_guess_archiveB); orbitals.PrepareDimerGuess(orbitalsA, orbitalsB); } _qmpackage->WriteInputFile(orbitals); } if (_do_dft_run) { bool run_success = _qmpackage->Run(); if (!run_success) { throw std::runtime_error("\n DFT-run failed. Stopping!"); } } // parse DFT data, if required if (_do_dft_parse) { XTP_LOG(Log::error, *logger) << "Parsing DFT data from " << _dftlog_file << " and " << _MO_file << flush; _qmpackage->setLogFileName(_dftlog_file); _qmpackage->setMOsFileName(_MO_file); bool Logfile_parse = _qmpackage->ParseLogFile(orbitals); if (!Logfile_parse) { throw std::runtime_error("\n Parsing DFT logfile " + _dftlog_file + " failed. Stopping!"); } bool Orbfile_parse = _qmpackage->ParseMOsFile(orbitals); if (!Orbfile_parse) { throw std::runtime_error("\n Parsing DFT orbfile " + _MO_file + " failed. Stopping!"); } _qmpackage->CleanUp(); } // if no parsing of DFT data is requested, reload serialized orbitals object if (!_do_dft_parse && _do_gwbse) { XTP_LOG(Log::error, *logger) << "Loading serialized data from " << _archive_file << flush; orbitals.ReadFromCpt(_archive_file); } tools::Property& output_summary = _summary.add("output", ""); if (_do_gwbse) { GWBSE gwbse = GWBSE(orbitals); gwbse.setLogger(logger); gwbse.Initialize(_gwbse_options); gwbse.Evaluate(); gwbse.addoutput(output_summary); } if (_redirect_logger) { WriteLoggerToFile(logger); } return; } void GWBSEEngine::WriteLoggerToFile(Logger* pLog) { std::ofstream ofs; ofs.open(_logger_file, std::ofstream::out); if (!ofs.is_open()) { throw std::runtime_error("Bad file handle: " + _logger_file); } ofs << (*pLog) << std::endl; ofs.close(); return; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gwbse/ppm.cc000066400000000000000000000035771412152066400167330ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include // Local VOTCA includes #include "votca/xtp/ppm.h" namespace votca { namespace xtp { void PPM::PPM_construct_parameters(const RPA& rpa) { // Solve Eigensystem Eigen::SelfAdjointEigenSolver es( rpa.calculate_epsilon_r(screening_r)); _ppm_phi = es.eigenvectors(); // store PPM weights from eigenvalues _ppm_weight = 1 - es.eigenvalues().array().inverse(); // a) phi^t * epsilon(1) * phi e.g. transform epsilon(1) to the same space as // epsilon(0) Eigen::MatrixXd ortho = _ppm_phi.transpose() * rpa.calculate_epsilon_i(screening_i) * _ppm_phi; Eigen::MatrixXd epsilon_1_inv = ortho.inverse(); // determine PPM frequencies _ppm_freq.resize(es.eigenvalues().size()); #pragma omp parallel for for (Index i = 0; i < es.eigenvalues().size(); i++) { if (_ppm_weight(i) < 1.e-5) { _ppm_weight(i) = 0.0; _ppm_freq(i) = 0.5; // Hartree continue; } else { double nom = epsilon_1_inv(i, i) - 1.0; double frac = -1.0 * nom / (nom + _ppm_weight(i)) * screening_i * screening_i; _ppm_freq(i) = std::sqrt(std::abs(frac)); } } return; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gwbse/rpa.cc000066400000000000000000000202131412152066400167030ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/rpa.h" #include "votca/xtp/aomatrix.h" #include "votca/xtp/openmp_cuda.h" #include "votca/xtp/threecenter.h" #include "votca/xtp/vc2index.h" namespace votca { namespace xtp { void RPA::UpdateRPAInputEnergies(const Eigen::VectorXd& dftenergies, const Eigen::VectorXd& gwaenergies, Index qpmin) { Index rpatotal = _rpamax - _rpamin + 1; _energies = dftenergies.segment(_rpamin, rpatotal); Index gwsize = Index(gwaenergies.size()); Index lumo = _homo + 1; Index qpmax = qpmin + gwsize - 1; _energies.segment(qpmin - _rpamin, gwsize) = gwaenergies; Eigen::VectorXd corrections_occ = _energies.segment(qpmin - _rpamin, lumo - qpmin) - dftenergies.segment(qpmin - _rpamin, lumo - qpmin); Eigen::VectorXd corrections_virt = _energies.segment(lumo - qpmin, gwsize - (lumo - qpmin)) - dftenergies.segment(lumo - qpmin, gwsize - (lumo - qpmin)); double max_correction_occ = (corrections_occ.cwiseAbs()).maxCoeff(); double max_correction_virt = (corrections_virt.cwiseAbs()).maxCoeff(); Index levelaboveqpmax = _rpamax - qpmax; Index levelbelowqpmin = qpmin - _rpamin; _energies.segment(0, levelbelowqpmin).array() -= max_correction_occ; _energies.segment(qpmax + 1 - _rpamin, levelaboveqpmax).array() += max_correction_virt; } template Eigen::MatrixXd RPA::calculate_epsilon(double frequency) const { const Index size = _Mmn.auxsize(); const Index lumo = _homo + 1; const Index n_occ = lumo - _rpamin; const Index n_unocc = _rpamax - lumo + 1; const double freq2 = frequency * frequency; const double eta2 = _eta * _eta; OpenMP_CUDA transform; transform.createTemporaries(n_unocc, size); #pragma omp parallel for schedule(dynamic) for (Index m_level = 0; m_level < n_occ; m_level++) { const double qp_energy_m = _energies(m_level); const Eigen::MatrixXd Mmn_RPA = _Mmn[m_level].bottomRows(n_unocc); const Eigen::ArrayXd deltaE = _energies.tail(n_unocc).array() - qp_energy_m; Eigen::VectorXd denom; if (imag) { denom = 4 * deltaE / (deltaE.square() + freq2); } else { Eigen::ArrayXd deltEf = deltaE - frequency; Eigen::ArrayXd sum = deltEf / (deltEf.square() + eta2); deltEf = deltaE + frequency; sum += deltEf / (deltEf.square() + eta2); denom = 2 * sum; } transform.A_TDA(Mmn_RPA, denom); } Eigen::MatrixXd result = transform.A_TDA_result(); result.diagonal().array() += 1.0; return result; } template Eigen::MatrixXd RPA::calculate_epsilon(double frequency) const; template Eigen::MatrixXd RPA::calculate_epsilon(double frequency) const; Eigen::MatrixXd RPA::calculate_epsilon_r(std::complex frequency) const { const Index size = _Mmn.auxsize(); const Index lumo = _homo + 1; const Index n_occ = lumo - _rpamin; const Index n_unocc = _rpamax - lumo + 1; OpenMP_CUDA transform; transform.createTemporaries(n_unocc, size); #pragma omp parallel for schedule(dynamic) for (Index m_level = 0; m_level < n_occ; m_level++) { const double qp_energy_m = _energies(m_level); const Eigen::MatrixXd Mmn_RPA = _Mmn[m_level].bottomRows(n_unocc); const Eigen::ArrayXd deltaE = _energies.tail(n_unocc).array() - qp_energy_m; Eigen::ArrayXd deltaEm = frequency.real() - deltaE; Eigen::ArrayXd deltaEp = frequency.real() + deltaE; double sigma_1 = std::pow(frequency.imag() + _eta, 2); double sigma_2 = std::pow(frequency.imag() - _eta, 2); Eigen::VectorXd chi = deltaEm * (deltaEm.cwiseAbs2() + sigma_1).cwiseInverse() - deltaEp * (deltaEp.cwiseAbs2() + sigma_2).cwiseInverse(); transform.A_TDA(Mmn_RPA, chi); } Eigen::MatrixXd result = -2 * transform.A_TDA_result(); result.diagonal().array() += 1.0; return result; } RPA::rpa_eigensolution RPA::Diagonalize_H2p() const { const Index lumo = _homo + 1; const Index n_occ = lumo - _rpamin; const Index n_unocc = _rpamax - lumo + 1; const Index rpasize = n_occ * n_unocc; Eigen::VectorXd AmB = Calculate_H2p_AmB(); Eigen::MatrixXd ApB = Calculate_H2p_ApB(); RPA::rpa_eigensolution sol; sol.ERPA_correlation = -0.25 * (ApB.trace() + AmB.sum()); // C = AmB^1/2 * ApB * AmB^1/2 Eigen::MatrixXd& C = ApB; C.applyOnTheLeft(AmB.cwiseSqrt().asDiagonal()); C.applyOnTheRight(AmB.cwiseSqrt().asDiagonal()); Eigen::SelfAdjointEigenSolver es = Diagonalize_H2p_C(C); // Do not remove this line! It has to be there for MKL to not crash sol.omega = Eigen::VectorXd::Zero(es.eigenvalues().size()); sol.omega = es.eigenvalues().cwiseSqrt(); sol.ERPA_correlation += 0.5 * sol.omega.sum(); XTP_LOG(Log::info, _log) << TimeStamp() << " Lowest neutral excitation energy (eV): " << tools::conv::hrt2ev * sol.omega.minCoeff() << std::flush; // RPA correlation energy calculated from Eq.9 of J. Chem. Phys. 132, 234114 // (2010) XTP_LOG(Log::error, _log) << TimeStamp() << " RPA correlation energy (Hartree): " << sol.ERPA_correlation << std::flush; sol.XpY = Eigen::MatrixXd(rpasize, rpasize); Eigen::VectorXd AmB_sqrt = AmB.cwiseSqrt(); Eigen::VectorXd Omega_sqrt_inv = sol.omega.cwiseSqrt().cwiseInverse(); for (int s = 0; s < rpasize; s++) { sol.XpY.col(s) = Omega_sqrt_inv(s) * AmB_sqrt.cwiseProduct(es.eigenvectors().col(s)); } return sol; } Eigen::VectorXd RPA::Calculate_H2p_AmB() const { const Index lumo = _homo + 1; const Index n_occ = lumo - _rpamin; const Index n_unocc = _rpamax - lumo + 1; const Index rpasize = n_occ * n_unocc; vc2index vc = vc2index(0, 0, n_unocc); Eigen::VectorXd AmB = Eigen::VectorXd::Zero(rpasize); for (Index v = 0; v < n_occ; v++) { Index i = vc.I(v, 0); AmB.segment(i, n_unocc) = _energies.segment(n_occ, n_unocc).array() - _energies(v); } return AmB; } Eigen::MatrixXd RPA::Calculate_H2p_ApB() const { const Index lumo = _homo + 1; const Index n_occ = lumo - _rpamin; const Index n_unocc = _rpamax - lumo + 1; const Index rpasize = n_occ * n_unocc; const Index auxsize = _Mmn.auxsize(); vc2index vc = vc2index(0, 0, n_unocc); Eigen::MatrixXd ApB = Eigen::MatrixXd::Zero(rpasize, rpasize); #pragma omp parallel for schedule(guided) for (Index v2 = 0; v2 < n_occ; v2++) { Index i2 = vc.I(v2, 0); const Eigen::MatrixXd Mmn_v2T = _Mmn[v2].block(n_occ, 0, n_unocc, auxsize).transpose(); for (Index v1 = v2; v1 < n_occ; v1++) { Index i1 = vc.I(v1, 0); // Multiply with factor 2 to sum over both (identical) spin states ApB.block(i1, i2, n_unocc, n_unocc) = 2 * 2 * _Mmn[v1].block(n_occ, 0, n_unocc, auxsize) * Mmn_v2T; } } ApB.diagonal() += Calculate_H2p_AmB(); return ApB; } Eigen::SelfAdjointEigenSolver RPA::Diagonalize_H2p_C( const Eigen::MatrixXd& C) const { XTP_LOG(Log::error, _log) << TimeStamp() << " Diagonalizing two-particle Hamiltonian " << std::flush; Eigen::SelfAdjointEigenSolver es(C); // Uses lower triangle XTP_LOG(Log::error, _log) << TimeStamp() << " Diagonalization done " << std::flush; double minCoeff = es.eigenvalues().minCoeff(); if (minCoeff <= 0.0) { XTP_LOG(Log::error, _log) << TimeStamp() << " Detected non-positive eigenvalue: " << minCoeff << std::flush; throw std::runtime_error("Detected non-positive eigenvalue."); } return es; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gwbse/sigma_base.cc000066400000000000000000000053301412152066400202160ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/sigma_base.h" #include "votca/xtp/threecenter.h" namespace votca { namespace xtp { Eigen::MatrixXd Sigma_base::CalcExchangeMatrix() const { Eigen::MatrixXd result = Eigen::MatrixXd::Zero(_qptotal, _qptotal); Index occlevel = _opt.homo - _opt.rpamin + 1; Index qpmin = _opt.qpmin - _opt.rpamin; #pragma omp parallel for schedule(dynamic) for (Index gw_level1 = 0; gw_level1 < _qptotal; gw_level1++) { const Eigen::MatrixXd& Mmn1 = _Mmn[gw_level1 + qpmin]; for (Index gw_level2 = gw_level1; gw_level2 < _qptotal; gw_level2++) { const Eigen::MatrixXd& Mmn2 = _Mmn[gw_level2 + qpmin]; double sigma_x = -(Mmn1.topRows(occlevel).cwiseProduct(Mmn2.topRows(occlevel))).sum(); result(gw_level2, gw_level1) = sigma_x; } } result = result.selfadjointView(); return result; } Eigen::VectorXd Sigma_base::CalcCorrelationDiag( const Eigen::VectorXd& frequencies) const { Eigen::VectorXd result = Eigen::VectorXd::Zero(_qptotal); #pragma omp parallel for schedule(dynamic) for (Index gw_level = 0; gw_level < _qptotal; gw_level++) { result(gw_level) = CalcCorrelationDiagElement(gw_level, frequencies[gw_level]); } return result; } Eigen::MatrixXd Sigma_base::CalcCorrelationOffDiag( const Eigen::VectorXd& frequencies) const { Eigen::MatrixXd result = Eigen::MatrixXd::Zero(_qptotal, _qptotal); #pragma omp parallel for schedule(dynamic) for (Index gw_level1 = 0; gw_level1 < _qptotal; gw_level1++) { for (Index gw_level2 = gw_level1 + 1; gw_level2 < _qptotal; gw_level2++) { double sigma_c = CalcCorrelationOffDiagElement( gw_level1, gw_level2, frequencies[gw_level1], frequencies[gw_level2]); result(gw_level2, gw_level1) = sigma_c; } } result = result.selfadjointView(); return result; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gwbse/sigma_cda.cc000066400000000000000000000121761412152066400200410ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #include #include namespace votca { namespace xtp { // Prepares the zero and imaginary frequency kappa matrices with // kappa(omega) = epsilon^-1(omega) - 1 needed in numerical // integration and for the Gaussian tail void Sigma_CDA::PrepareScreening() { ImaginaryAxisIntegration::options opt; opt.homo = _opt.homo; opt.order = _opt.order; opt.qptotal = _qptotal; opt.qpmin = _opt.qpmin; opt.rpamax = _opt.rpamax; opt.rpamin = _opt.rpamin; opt.alpha = _opt.alpha; opt.quadrature_scheme = _opt.quadrature_scheme; // prepare the zero frequency inverse for Gaussian tail _kDielMxInv_zero = _rpa.calculate_epsilon_r(std::complex(0.0, 0.0)).inverse(); _kDielMxInv_zero.diagonal().array() -= 1.0; _gq.configure(opt, _rpa, _kDielMxInv_zero); } // This function is used in the calculation of the residues and // calculates the real part of the dielectric function for a complex // frequency of the kind omega = delta + i*eta. Instead of explicit // inversion and multiplication with and Imx vector, a linear system // is solved. double Sigma_CDA::CalcDiagContribution( const Eigen::MatrixXd::ConstRowXpr& Imx_row, double delta, double eta) const { std::complex delta_eta(delta, eta); Eigen::MatrixXd DielMxInv = _rpa.calculate_epsilon_r(delta_eta); Eigen::VectorXd x = DielMxInv.partialPivLu().solve(Imx_row.transpose()) - Imx_row.transpose(); return x.dot(Imx_row.transpose()); } // Step-function prefactor for the residues double Sigma_CDA::CalcResiduePrefactor(double e_f, double e_m, double frequency) const { double factor = 0.0; double tolerance = 1e-10; if (e_f < e_m && e_m < frequency) { factor = 1.0; } else if (e_f > e_m && e_m > frequency) { factor = -1.0; } else if (std::abs(e_m - frequency) < tolerance && e_f > e_m) { factor = -0.5; } else if (std::abs(e_m - frequency) < tolerance && e_f < e_m) { factor = 0.5; } return factor; } // Calculates the contribution of residues to the correlation // part of the self-energy of a fixed gw_level double Sigma_CDA::CalcResidueContribution(double frequency, Index gw_level) const { const Eigen::VectorXd& rpa_energies = _rpa.getRPAInputEnergies(); Index rpatotal = rpa_energies.size(); Index gw_level_offset = gw_level + _opt.qpmin - _opt.rpamin; double sigma_c = 0.0; double sigma_c_tail = 0.0; Index homo = _opt.homo - _opt.rpamin; Index lumo = homo + 1; double fermi_rpa = (rpa_energies(lumo) + rpa_energies(homo)) / 2.0; const Eigen::MatrixXd& Imx = _Mmn[gw_level_offset]; for (Index i = 0; i < rpatotal; ++i) { double delta = rpa_energies(i) - frequency; double abs_delta = std::abs(delta); double factor = CalcResiduePrefactor(fermi_rpa, rpa_energies(i), frequency); // Only considering the terms with a abs(prefactor) > 0. // The prefactor can be 1,-1,0.5,-0.5 or 0. We avoid calculating the // diagonal contribution if the prefactor is 0. We want to calculate it for // all the other cases. if (std::abs(factor) > 1e-10) { sigma_c += factor * CalcDiagContribution(Imx.row(i), abs_delta, _rpa.getEta()); } // adds the contribution from the Gaussian tail if (abs_delta > 1e-10) { sigma_c_tail += CalcDiagContributionValue_tail(Imx.row(i), delta, _opt.alpha); } } return sigma_c + sigma_c_tail; } // Calculates the correlation part of the self-energy for a fixed // gw_level and frequence by evaluating the numerical integration // and residue contributions double Sigma_CDA::CalcCorrelationDiagElement(Index gw_level, double frequency) const { double sigma_c_residue = CalcResidueContribution(frequency, gw_level); double sigma_c_integral = _gq.SigmaGQDiag(frequency, gw_level, _rpa.getEta()); return sigma_c_residue + sigma_c_integral; } // Calculates the contribuion of the tail correction to the // residue term double Sigma_CDA::CalcDiagContributionValue_tail( const Eigen::MatrixXd::ConstRowXpr& Imx_row, double delta, double alpha) const { double erfc_factor = 0.5 * std::copysign(1.0, delta) * std::exp(std::pow(alpha * delta, 2)) * std::erfc(std::abs(alpha * delta)); double value = (Imx_row * _kDielMxInv_zero).dot(Imx_row); return value * erfc_factor; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gwbse/sigma_exact.cc000066400000000000000000000117761412152066400204230ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/sigma_exact.h" #include "votca/xtp/rpa.h" #include "votca/xtp/threecenter.h" #include "votca/xtp/vc2index.h" namespace votca { namespace xtp { void Sigma_Exact::PrepareScreening() { _rpa_solution = _rpa.Diagonalize_H2p(); _residues = std::vector(_qptotal); #pragma omp parallel for schedule(dynamic) for (Index gw_level = 0; gw_level < _qptotal; gw_level++) { _residues[gw_level] = CalcResidues(gw_level); } return; } double Sigma_Exact::CalcCorrelationDiagElement(Index gw_level, double frequency) const { const double eta2 = _opt.eta * _opt.eta; const Index lumo = _opt.homo + 1; const Index n_occ = lumo - _opt.rpamin; const Index n_unocc = _opt.rpamax - _opt.homo; double sigma = 0.0; for (Index s = 0; s < _rpa_solution.omega.size(); s++) { const double eigenvalue = _rpa_solution.omega(s); const Eigen::ArrayXd res_12 = _residues[gw_level].col(s).cwiseAbs2(); Eigen::ArrayXd temp = -_rpa.getRPAInputEnergies().array() + frequency; temp.segment(0, n_occ) += eigenvalue; temp.segment(n_occ, n_unocc) -= eigenvalue; const Eigen::ArrayXd denom = temp.abs2() + eta2; sigma += (res_12 * temp / denom).sum(); } return 2 * sigma; } double Sigma_Exact::CalcCorrelationDiagElementDerivative( Index gw_level, double frequency) const { const double eta2 = _opt.eta * _opt.eta; const Index lumo = _opt.homo + 1; const Index n_occ = lumo - _opt.rpamin; const Index n_unocc = _opt.rpamax - _opt.homo; double dsigma_domega = 0.0; for (Index s = 0; s < _rpa_solution.omega.size(); s++) { const double eigenvalue = _rpa_solution.omega(s); const Eigen::ArrayXd res_12 = _residues[gw_level].col(s).cwiseAbs2(); Eigen::ArrayXd temp = -_rpa.getRPAInputEnergies().array() + frequency; temp.segment(0, n_occ) += eigenvalue; temp.segment(n_occ, n_unocc) -= eigenvalue; const Eigen::ArrayXd denom = temp.abs2() + eta2; dsigma_domega += ((eta2 - temp.abs2()) * res_12 / denom.abs2()).sum(); } return 2 * dsigma_domega; } double Sigma_Exact::CalcCorrelationOffDiagElement(Index gw_level1, Index gw_level2, double frequency1, double frequency2) const { const double eta2 = _opt.eta * _opt.eta; const Index lumo = _opt.homo + 1; const Index n_occ = lumo - _opt.rpamin; const Index n_unocc = _opt.rpamax - _opt.homo; const Index rpasize = _rpa_solution.omega.size(); double sigma_c = 0.0; for (Index s = 0; s < rpasize; s++) { const double eigenvalue = _rpa_solution.omega(s); const Eigen::VectorXd& res1 = _residues[gw_level1].col(s); const Eigen::VectorXd& res2 = _residues[gw_level2].col(s); const Eigen::VectorXd res_12 = res1.cwiseProduct(res2); Eigen::ArrayXd temp1 = -_rpa.getRPAInputEnergies().array(); temp1.segment(0, n_occ) += eigenvalue; temp1.segment(n_occ, n_unocc) -= eigenvalue; const Eigen::ArrayXd temp2 = temp1 + frequency2; temp1 += frequency1; const Eigen::ArrayXd numer1 = res_12.array() * temp1; const Eigen::ArrayXd numer2 = res_12.array() * temp2; const Eigen::ArrayXd denom1 = temp1.abs2() + eta2; const Eigen::ArrayXd denom2 = temp2.abs2() + eta2; sigma_c += 0.5 * ((numer1 / denom1) + (numer2 / denom2)).sum(); } // Multiply with factor 2.0 to sum over both (identical) spin states return 2.0 * sigma_c; } Eigen::MatrixXd Sigma_Exact::CalcResidues(Index gw_level) const { const Index lumo = _opt.homo + 1; const Index n_occ = lumo - _opt.rpamin; const Index n_unocc = _opt.rpamax - _opt.homo; const Index rpasize = n_occ * n_unocc; const Index qpoffset = _opt.qpmin - _opt.rpamin; const Index auxsize = _Mmn.auxsize(); vc2index vc = vc2index(0, 0, n_unocc); const Eigen::MatrixXd& Mmn_i = _Mmn[gw_level + qpoffset]; Eigen::MatrixXd res = Eigen::MatrixXd::Zero(_rpatotal, rpasize); for (Index v = 0; v < n_occ; v++) { // Sum over v auto Mmn_v = _Mmn[v].block(n_occ, 0, n_unocc, auxsize); const Eigen::MatrixXd fc = Mmn_v * Mmn_i.transpose(); // Sum over chi auto XpY_v = _rpa_solution.XpY.block(vc.I(v, 0), 0, n_unocc, rpasize); res += fc.transpose() * XpY_v; // Sum over c } return res; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gwbse/sigma_ppm.cc000066400000000000000000000116101412152066400200760ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // VOTCA includes #include #include // Local VOTCA includes #include "votca/xtp/ppm.h" #include "votca/xtp/sigma_ppm.h" #include "votca/xtp/threecenter.h" namespace votca { namespace xtp { void Sigma_PPM::PrepareScreening() { _ppm.PPM_construct_parameters(_rpa); _Mmn.MultiplyRightWithAuxMatrix(_ppm.getPpm_phi()); } double Sigma_PPM::CalcCorrelationDiagElement(Index gw_level, double frequency) const { const Index lumo = _opt.homo + 1; const double eta2 = _opt.eta * _opt.eta; const Index levelsum = _Mmn.nsize(); // total number of bands const Index qpmin_offset = _opt.qpmin - _opt.rpamin; double sigma = 0.0; for (Index i_aux = 0; i_aux < _Mmn.auxsize(); i_aux++) { // the ppm_weights smaller 1.e-5 are set to zero in rpa.cc // PPM_construct_parameters if (_ppm.getPpm_weight()(i_aux) < 1.e-9) { continue; } const double ppm_freq = _ppm.getPpm_freq()(i_aux); const double fac = 0.5 * _ppm.getPpm_weight()(i_aux) * ppm_freq; const Eigen::ArrayXd Mmn2 = _Mmn[gw_level + qpmin_offset].col(i_aux).cwiseAbs2(); Eigen::ArrayXd temp = frequency - _rpa.getRPAInputEnergies().array(); temp.segment(0, lumo) += ppm_freq; temp.segment(lumo, levelsum - lumo) -= ppm_freq; Eigen::ArrayXd denom = temp.abs2() + eta2; sigma += fac * (Mmn2 * temp / denom).sum(); } return sigma; } double Sigma_PPM::CalcCorrelationDiagElementDerivative(Index gw_level, double frequency) const { const Index lumo = _opt.homo + 1; const double eta2 = _opt.eta * _opt.eta; const Index levelsum = _Mmn.nsize(); // total number of bands const Index qpmin_offset = _opt.qpmin - _opt.rpamin; double dsigma_domega = 0.0; for (Index i_aux = 0; i_aux < _Mmn.auxsize(); i_aux++) { // the ppm_weights smaller 1.e-5 are set to zero in rpa.cc // PPM_construct_parameters if (_ppm.getPpm_weight()(i_aux) < 1.e-9) { continue; } const double ppm_freq = _ppm.getPpm_freq()(i_aux); const double fac = 0.5 * _ppm.getPpm_weight()(i_aux) * ppm_freq; const Eigen::ArrayXd Mmn2 = _Mmn[gw_level + qpmin_offset].col(i_aux).cwiseAbs2(); Eigen::ArrayXd temp = frequency - _rpa.getRPAInputEnergies().array(); temp.segment(0, lumo) += ppm_freq; temp.segment(lumo, levelsum - lumo) -= ppm_freq; Eigen::ArrayXd denom = temp.abs2() + eta2; dsigma_domega += fac * ((eta2 - temp.abs2()) * Mmn2 / denom.abs2()).sum(); } return dsigma_domega; } double Sigma_PPM::CalcCorrelationOffDiagElement(Index gw_level1, Index gw_level2, double frequency1, double frequency2) const { const Index lumo = _opt.homo + 1; const double eta2 = _opt.eta * _opt.eta; const Index levelsum = _Mmn.nsize(); // total number of bands const Index auxsize = _Mmn.auxsize(); // size of the GW basis const Eigen::VectorXd ppm_weight = _ppm.getPpm_weight(); const Eigen::VectorXd ppm_freqs = _ppm.getPpm_freq(); const Index qpmin_offset = _opt.qpmin - _opt.rpamin; const Eigen::VectorXd RPAEnergies = _rpa.getRPAInputEnergies(); double sigma_c = 0; for (Index i_aux = 0; i_aux < auxsize; i_aux++) { // the ppm_weights smaller 1.e-5 are set to zero in rpa.cc // PPM_construct_parameters if (ppm_weight(i_aux) < 1.e-9) { continue; } const double ppm_freq = ppm_freqs(i_aux); const double fac = 0.25 * ppm_weight(i_aux) * ppm_freq; const Eigen::MatrixXd& Mmn1 = _Mmn[gw_level1 + qpmin_offset]; const Eigen::MatrixXd& Mmn2 = _Mmn[gw_level2 + qpmin_offset]; const Eigen::ArrayXd Mmn1xMmn2 = Mmn1.col(i_aux).cwiseProduct(Mmn2.col(i_aux)); Eigen::ArrayXd temp1 = RPAEnergies; temp1.segment(0, lumo) -= ppm_freq; temp1.segment(lumo, levelsum - lumo) += ppm_freq; Eigen::ArrayXd temp2 = (frequency2 - temp1); temp1 = (frequency1 - temp1); sigma_c += fac * ((temp1 / (temp1.abs2() + eta2) + temp2 / (temp2.abs2() + eta2)) * Mmn1xMmn2) .sum(); } return sigma_c; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/gyration.cc000066400000000000000000000175731412152066400166650ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/gyration.h" #include "votca/xtp/vxc_grid.h" using namespace votca::tools; namespace votca { namespace xtp { void Density2Gyration::Initialize(tools::Property& options) { std::string key = Identify(); std::string statestring = options.get(key + ".state").as(); _state.FromString(statestring); _dostateonly = options.ifExistsReturnElseReturnDefault( key + ".difference_to_groundstate", false); _gridsize = options.ifExistsReturnElseReturnDefault( key + ".gridsize", "medium"); } void Density2Gyration::AnalyzeDensity(const Orbitals& orbitals) { XTP_LOG(Log::error, _log) << "===== Running on " << OPENMP::getMaxThreads() << " threads ===== " << std::flush; const QMMolecule& Atomlist = orbitals.QMAtoms(); BasisSet bs; bs.Load(orbitals.getDFTbasisName()); AOBasis basis; basis.Fill(bs, Atomlist); AnalyzeGeometry(Atomlist); // setup numerical integration grid Vxc_Grid grid; grid.GridSetup(_gridsize, Atomlist, basis); DensityIntegration numway(grid); if (!_dostateonly) { Eigen::MatrixXd DMAT_tot = orbitals.DensityMatrixFull(_state); Gyrationtensor gyro = numway.IntegrateGyrationTensor(DMAT_tot); Eigen::SelfAdjointEigenSolver es; es.computeDirect(gyro.gyration); XTP_LOG(Log::error, _log) << TimeStamp() << " Converting to Eigenframe " << std::flush; XTP_LOG(Log::error, _log) << TimeStamp() << " Reporting " << std::flush; ReportAnalysis(_state.ToLongString(), gyro, es); } else { // hole density first std::array DMAT = orbitals.DensityMatrixExcitedState(_state); Gyrationtensor gyro_hole = numway.IntegrateGyrationTensor(DMAT[0]); Eigen::SelfAdjointEigenSolver es_h; es_h.computeDirect(gyro_hole.gyration); XTP_LOG(Log::error, _log) << TimeStamp() << " Converting to Eigenframe " << std::flush; XTP_LOG(Log::error, _log) << TimeStamp() << " Reporting " << std::flush; ReportAnalysis("hole", gyro_hole, es_h); // electron density Gyrationtensor gyro_electron = numway.IntegrateGyrationTensor(DMAT[1]); Eigen::SelfAdjointEigenSolver es_e; es_e.computeDirect(gyro_electron.gyration); XTP_LOG(Log::error, _log) << TimeStamp() << " Converting to Eigenframe " << std::flush; XTP_LOG(Log::error, _log) << TimeStamp() << " Reporting " << std::flush; ReportAnalysis("electron", gyro_electron, es_e); } return; } void Density2Gyration::AnalyzeGeometry(const QMMolecule& atoms) { tools::Elements elements; double mass = 0.0; Eigen::Vector3d centroid = Eigen::Vector3d::Zero(); Eigen::Matrix3d gyration = Eigen::Matrix3d::Zero(); for (const QMAtom& atom : atoms) { double m = elements.getMass(atom.getElement()); const Eigen::Vector3d& pos = atom.getPos(); mass += m; centroid += m * pos; gyration += m * pos * pos.transpose(); } centroid /= mass; gyration /= mass; gyration -= centroid * centroid.transpose(); Gyrationtensor gyro; gyro.mass = mass; gyro.centroid = centroid; gyro.gyration = gyration; Eigen::SelfAdjointEigenSolver es; es.computeDirect(gyro.gyration); ReportAnalysis("geometry", gyro, es); } void Density2Gyration::ReportAnalysis( std::string label, const Gyrationtensor& gyro, const Eigen::SelfAdjointEigenSolver& es) { XTP_LOG(Log::error, _log) << "---------------- " << label << " ----------------" << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Norm = %1$9.4f ") % (gyro.mass)) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Centroid x = %1$9.4f Ang") % (gyro.centroid.x() * tools::conv::bohr2ang)) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Centroid y = %1$9.4f Ang") % (gyro.centroid.y() * tools::conv::bohr2ang)) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Centroid y = %1$9.4f Ang") % (gyro.centroid.z() * tools::conv::bohr2ang)) << std::flush; double RA2 = tools::conv::bohr2ang * tools::conv::bohr2ang; XTP_LOG(Log::error, _log) << (boost::format(" Gyration Tensor xx = %1$9.4f Ang^2") % (gyro.gyration(0, 0) * RA2)) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Gyration Tensor xy = %1$9.4f Ang^2") % (gyro.gyration(0, 1) * RA2)) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Gyration Tensor xz = %1$9.4f Ang^2") % (gyro.gyration(0, 2) * RA2)) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Gyration Tensor yy = %1$9.4f Ang^2") % (gyro.gyration(1, 1) * RA2)) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Gyration Tensor yz = %1$9.4f Ang^2") % (gyro.gyration(1, 2) * RA2)) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Gyration Tensor zz = %1$9.4f Ang^2") % (gyro.gyration(2, 2) * RA2)) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Gyration Tensor D1 = %1$9.4f Ang^2") % (es.eigenvalues()[0] * RA2)) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Gyration Tensor D2 = %1$9.4f Ang^2") % (es.eigenvalues()[1] * RA2)) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Gyration Tensor D3 = %1$9.4f Ang^2") % (es.eigenvalues()[2] * RA2)) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Radius of Gyration = %1$9.4f Ang") % (std::sqrt(es.eigenvalues().sum()) * tools::conv::bohr2ang)) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Tensor EF Axis 1 1 = %1$9.4f ") % es.eigenvectors().col(0).x()) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Tensor EF Axis 1 2 = %1$9.4f ") % es.eigenvectors().col(0).y()) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Tensor EF Axis 1 3 = %1$9.4f ") % es.eigenvectors().col(0).z()) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Tensor EF Axis 2 1 = %1$9.4f ") % es.eigenvectors().col(1).x()) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Tensor EF Axis 2 2 = %1$9.4f ") % es.eigenvectors().col(1).y()) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Tensor EF Axis 2 3 = %1$9.4f ") % es.eigenvectors().col(1).z()) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Tensor EF Axis 3 1 = %1$9.4f ") % es.eigenvectors().col(2).x()) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Tensor EF Axis 3 2 = %1$9.4f ") % es.eigenvectors().col(2).y()) << std::flush; XTP_LOG(Log::error, _log) << (boost::format(" Tensor EF Axis 3 3 = %1$9.4f ") % es.eigenvectors().col(2).z()) << std::flush; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/job.cc000066400000000000000000000135771412152066400156030ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ /// For an earlier history see ctp repo commit /// 77795ea591b29e664153f9404c8655ba28dc14e9 // Third party includes #include #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/job.h" namespace votca { namespace xtp { using boost::format; Job::Job(const tools::Property &prop) { // DEFINED BY USER _id = prop.get("id").as(); _tag = prop.get("tag").as(); _input = prop.get("input"); if (prop.exists("status")) { _status = ConvertStatus(prop.get("status").as()); } else { _status = AVAILABLE; } // GENERATED DURING RUNTIME if (prop.exists("host")) { _host = prop.get("host").as(); _has_host = true; } if (prop.exists("time")) { _time = prop.get("time").as(); _has_time = true; } if (prop.exists("output")) { _output = prop.get("output"); _has_output = true; } if (prop.exists("error")) { _error = prop.get("error").as(); _has_error = true; } } Job::Job(Index id, const std::string &tag, const tools::Property &input, JobStatus status) { _id = id; _tag = tag; _input = input.get("input"); _status = status; } std::string Job::ConvertStatus(JobStatus status) const { std::string converted; switch (status) { case AVAILABLE: converted = "AVAILABLE"; break; case ASSIGNED: converted = "ASSIGNED"; break; case FAILED: converted = "FAILED"; break; case COMPLETE: converted = "COMPLETE"; break; default: throw std::runtime_error("Incomprehensible status (enum)"); } return converted; } Job::JobStatus Job::ConvertStatus(std::string status) const { JobStatus converted; if (status == "AVAILABLE") { converted = AVAILABLE; } else if (status == "ASSIGNED") { converted = ASSIGNED; } else if (status == "FAILED") { converted = FAILED; } else if (status == "COMPLETE") { converted = COMPLETE; } else { throw std::runtime_error("Incomprehensible status: " + status); } return converted; } void Job::Reset() { _output = tools::Property(); _has_output = false; _error = ""; _has_error = false; return; } void Job::ToStream(std::ofstream &ofs) const { tools::PropertyIOManipulator iomXML(tools::PropertyIOManipulator::XML, 0, "\t\t"); std::string tab = "\t"; ofs << tab << "\n"; ofs << tab << tab << (format("%1$d\n") % _id).str(); ofs << tab << tab << (format("%1$s\n") % _tag).str(); ofs << iomXML << _input; ofs << tab << tab << (format("%1$s\n") % ConvertStatus(_status)).str(); if (_has_host) { ofs << tab << tab << (format("%1$s\n") % _host).str(); } if (_has_time) { ofs << tab << tab << (format("\n") % _time).str(); } if (_has_output) { ofs << iomXML << _output; } if (_has_error) { ofs << tab << tab << (format("%1$s\n") % _error).str(); } ofs << tab << "\n"; return; } void Job::UpdateFrom(const Job &ext) { _status = ext.getStatus(); if (ext.hasHost()) { _has_host = true; _host = ext.getHost(); } if (ext.hasTime()) { _has_time = true; _time = ext.getTime(); } if (ext.hasOutput()) { _has_output = true; _output = ext.getOutput(); } if (ext.hasError()) { _has_error = true; _error = ext.getError(); } return; } void Job::UpdateFromResult(const JobResult &res) { _status = res.getStatus(); if (res.hasOutput()) { _output = res.getOutput(); _has_output = true; } if (res.hasError()) { _error = res.getError(); _has_error = true; } _attemptsCount++; return; } std::vector LOAD_JOBS(const std::string &job_file) { tools::Property xml; xml.LoadFromXML(job_file); std::vector jobProps = xml.Select("jobs.job"); std::vector jobs; jobs.reserve(jobProps.size()); for (tools::Property *prop : jobProps) { jobs.push_back(Job(*prop)); } return jobs; } void WRITE_JOBS(const std::vector &jobs, const std::string &job_file) { std::ofstream ofs; ofs.open(job_file, std::ofstream::out); if (!ofs.is_open()) { throw std::runtime_error("Bad file handle: " + job_file); } ofs << "" << std::endl; for (auto &job : jobs) { job.ToStream(ofs); } ofs << "" << std::endl; ofs.close(); return; } void UPDATE_JOBS(const std::vector &from, std::vector &to, const std::string &thisHost) { std::vector::iterator it_int; std::vector::const_iterator it_ext; if (to.size() != from.size()) { throw std::runtime_error("Progress file out of sync (::size), abort."); } for (it_int = to.begin(), it_ext = from.begin(); it_int != to.end(); ++it_int, ++it_ext) { Job &job_int = *it_int; const Job &job_ext = *it_ext; if (job_int.getId() != job_ext.getId()) { throw std::runtime_error("Progress file out of sync (::id), abort."); } if (job_ext.hasHost() && job_ext.getHost() != thisHost) { job_int.UpdateFrom(job_ext); } } return; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/jobapplication.cc000066400000000000000000000132441412152066400200160ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // Local VOTCA includes #include "votca/xtp/jobapplication.h" #include "votca/xtp/jobcalculatorfactory.h" #include "votca/xtp/version.h" namespace votca { namespace xtp { JobApplication::JobApplication() { JobCalculatorfactory::RegisterAll(); } void JobApplication::Initialize(void) { XtpApplication::Initialize(); JobCalculatorfactory::RegisterAll(); namespace propt = boost::program_options; AddProgramOptions()("file,f", propt::value(), " hdf5 state file, *.hdf5"); AddProgramOptions()("first-frame,i", propt::value()->default_value(0), " start from this frame"); AddProgramOptions()("nframes,n", propt::value()->default_value(1), " number of frames to process"); AddProgramOptions()("nthreads,t", propt::value()->default_value(1), " number of threads to create"); AddProgramOptions()("ompthreads,p", propt::value()->default_value(1), " number of openmp threads to create in each thread"); AddProgramOptions()("save,s", propt::value()->default_value(true), " whether or not to save changes to state file"); AddProgramOptions()("restart,r", propt::value()->default_value(""), " restart pattern: 'host(pc1:234) stat(FAILED)'"); AddProgramOptions()("cache,c", propt::value()->default_value(8), " assigns jobs in blocks of this size"); AddProgramOptions()("jobs,j", propt::value()->default_value("run"), " task(s) to perform: write, run, read"); AddProgramOptions()("maxjobs,m", propt::value()->default_value(-1), " maximum number of jobs to process (-1 = inf)"); } bool JobApplication::EvaluateOptions(void) { CheckRequired("options", "Please provide an xml file with calculator options"); CheckRequired("file", "Please provide the state file"); std::string jobstr = _op_vm["jobs"].as(); _generate_input = (jobstr == "write"); _run = (jobstr == "run"); _import = (jobstr == "read"); return true; } void JobApplication::Run() { std::string name = ProgramName(); if (VersionString() != "") { name = name + ", version " + VersionString(); } xtp::HelpTextHeader(name); // EVALUATE OPTIONS Index nThreads = OptionsMap()["nthreads"].as(); Index ompThreads = OptionsMap()["ompthreads"].as(); Index nframes = OptionsMap()["nframes"].as(); Index fframe = OptionsMap()["first-frame"].as(); bool save = OptionsMap()["save"].as(); // STATESAVER & PROGRESS OBSERVER std::string statefile = OptionsMap()["file"].as(); _options.LoadFromXML(OptionsMap()["options"].as()); ProgObserver> progObs = ProgObserver>(); progObs.InitCmdLineOpts(OptionsMap()); // INITIALIZE & RUN CALCULATORS std::cout << "Initializing calculator " << std::endl; BeginEvaluate(nThreads, ompThreads, progObs); StateSaver statsav(statefile); std::vector frames = statsav.getFrames(); std::cout << frames.size() << " frames in statefile, Ids are: "; for (Index frame : frames) { std::cout << frame << " "; } std::cout << std::endl; if (fframe < Index(frames.size())) { std::cout << "Starting at frame " << frames[fframe] << std::endl; } else { std::cout << "First frame:" << fframe << " is larger than number of frames:" << Index(frames.size()) << std::endl; return; } if ((fframe + nframes) > Index(frames.size())) { nframes = Index(frames.size()) - fframe; } for (Index i = fframe; i < nframes; i++) { std::cout << "Evaluating frame " << frames[i] << std::endl; Topology top = statsav.ReadFrame(frames[i]); EvaluateFrame(top); if (save && _import) { statsav.WriteFrame(top); } else { std::cout << "Changes have not been written to state file." << std::endl; } } } void JobApplication::SetCalculator( std::unique_ptr&& calculator) { _calculator = std::move(calculator); } void JobApplication::BeginEvaluate(Index nThreads, Index ompThreads, ProgObserver>& jobs) { std::cout << "... " << _calculator->Identify() << " "; _calculator->setnThreads(nThreads); _calculator->setOpenMPThreads(ompThreads); _calculator->setProgObserver(&jobs); _calculator->Initialize(_options); std::cout << std::endl; } bool JobApplication::EvaluateFrame(Topology& top) { std::cout << "... " << _calculator->Identify() << " " << std::flush; if (_generate_input) { _calculator->WriteJobFile(top); } else if (_run) { _calculator->EvaluateFrame(top); } else if (_import) { _calculator->ReadJobFile(top); } else { ; } std::cout << std::endl; return true; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/jobcalculators/000077500000000000000000000000001412152066400175145ustar00rootroot00000000000000xtp-2021.2/src/libxtp/jobcalculators/eqm.cc000066400000000000000000000247721412152066400206210ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include #include #include // Local VOTCA includes #include "votca/xtp/esp2multipole.h" #include "votca/xtp/segmentmapper.h" // Local private VOTCA includes #include "eqm.h" using boost::format; using namespace boost::filesystem; namespace votca { namespace xtp { void EQM::ParseSpecificOptions(const tools::Property& options) { QMPackageFactory::RegisterAll(); // job tasks std::string _tasks_string = options.get(".tasks").as(); if (_tasks_string.find("input") != std::string::npos) { _do_dft_input = true; } if (_tasks_string.find("dft") != std::string::npos) { _do_dft_run = true; } if (_tasks_string.find("parse") != std::string::npos) { _do_dft_parse = true; } if (_tasks_string.find("gwbse") != std::string::npos) { _do_gwbse = true; } if (_tasks_string.find("esp") != std::string::npos) { _do_esp = true; } // set the basis sets and functional for DFT and GWBSE _gwbse_options = this->UpdateGWBSEOptions(options); _package_options = this->UpdateDFTOptions(options); _esp_options = options.get(".esp_options"); } void EQM::WriteJobFile(const Topology& top) { std::cout << "\n... ... Writing job file: " << _jobfile << std::flush; std::ofstream ofs; ofs.open(_jobfile, std::ofstream::out); if (!ofs.is_open()) { throw std::runtime_error("\nERROR: bad file handle: " + _jobfile); } ofs << "" << std::endl; Index jobCount = 0; const std::vector& segments = top.Segments(); for (const Segment& segment : segments) { Index id = segment.getId(); std::string tag = ""; tools::Property Input; tools::Property& pInput = Input.add("input", ""); tools::Property& pSegment = pInput.add("segment", (format("%1$s") % segment.getId()).str()); pSegment.setAttribute("type", segment.getType()); pSegment.setAttribute("id", segment.getId()); Job job(id, tag, Input, Job::AVAILABLE); job.ToStream(ofs); jobCount++; } ofs << "" << std::endl; ofs.close(); std::cout << jobCount << " jobs" << std::flush; } void EQM::SetJobToFailed(Job::JobResult& jres, Logger& pLog, const std::string& errormessage) { XTP_LOG(Log::error, pLog) << errormessage << std::flush; std::cout << pLog; jres.setError(errormessage); jres.setStatus(Job::FAILED); } void EQM::WriteLoggerToFile(const std::string& logfile, Logger& logger) { std::ofstream ofs; ofs.open(logfile, std::ofstream::out); if (!ofs.is_open()) { throw std::runtime_error("Bad file handle: " + logfile); } ofs << logger << std::endl; ofs.close(); } Job::JobResult EQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { Orbitals orbitals; Job::JobResult jres = Job::JobResult(); tools::Property _job_input = job.getInput(); std::vector lSegments = _job_input.Select("segment"); Index segId = lSegments.front()->getAttribute("id"); std::string segType = lSegments.front()->getAttribute("type"); std::string qmgeo_state = "n"; if (lSegments.front()->exists("qm_geometry")) { qmgeo_state = lSegments.front()->getAttribute("qm_geometry"); } QMState state(qmgeo_state); const Segment& seg = top.getSegment(segId); Logger& pLog = opThread.getLogger(); QMMapper mapper(pLog); mapper.LoadMappingFile(_mapfile); orbitals.QMAtoms() = mapper.map(seg, state); XTP_LOG(Log::error, pLog) << TimeStamp() << " Evaluating site " << seg.getId() << std::flush; // directories and files boost::filesystem::path arg_path; std::string eqm_work_dir = "OR_FILES"; std::string frame_dir = "frame_" + boost::lexical_cast(top.getStep()); std::string orb_file = (format("%1%_%2%%3%") % "molecule" % segId % ".orb").str(); std::string mol_dir = (format("%1%%2%%3%") % "molecule" % "_" % segId).str(); std::string package_append = "workdir_" + Identify(); std::string work_dir = (arg_path / eqm_work_dir / package_append / frame_dir / mol_dir) .generic_string(); tools::Property job_summary; tools::Property& output_summary = job_summary.add("output", ""); tools::Property& segment_summary = output_summary.add("segment", ""); std::string segName = seg.getType(); segId = seg.getId(); segment_summary.setAttribute("id", segId); segment_summary.setAttribute("type", segName); if (_do_dft_input || _do_dft_run || _do_dft_parse) { XTP_LOG(Log::error, pLog) << "Running DFT" << std::flush; Logger dft_logger(votca::Log::current_level); dft_logger.setMultithreading(false); dft_logger.setPreface(Log::info, (format("\nDFT INF ...")).str()); dft_logger.setPreface(Log::error, (format("\nDFT ERR ...")).str()); dft_logger.setPreface(Log::warning, (format("\nDFT WAR ...")).str()); dft_logger.setPreface(Log::debug, (format("\nDFT DBG ...")).str()); std::string dft_key = "package"; std::string package = _package_options.get(dft_key + ".name").as(); std::unique_ptr qmpackage = std::unique_ptr( QMPackageFactory::QMPackages().Create(package)); qmpackage->setLog(&dft_logger); qmpackage->setRunDir(work_dir); qmpackage->Initialize(_package_options); // create input for DFT if (_do_dft_input) { boost::filesystem::create_directories(work_dir); qmpackage->WriteInputFile(orbitals); } if (_do_dft_run) { bool run_dft_status = qmpackage->Run(); if (!run_dft_status) { std::string output = "DFT run failed"; SetJobToFailed(jres, pLog, output); return jres; } } // parse the log/orbitals files if (_do_dft_parse) { bool parse_log_status = qmpackage->ParseLogFile(orbitals); if (!parse_log_status) { std::string output = "log incomplete; "; SetJobToFailed(jres, pLog, output); return jres; } bool parse_orbitals_status = qmpackage->ParseMOsFile(orbitals); if (!parse_orbitals_status) { std::string output = "orbfile failed; "; SetJobToFailed(jres, pLog, output); return jres; } // additionally copy *.gbw files for orca (-> iqm guess) if (qmpackage->getPackageName() == "orca") { std::string DIR = eqm_work_dir + "/molecules/" + frame_dir; boost::filesystem::create_directories(DIR); std::string gbw_file = (format("%1%_%2%%3%") % "molecule" % segId % ".gbw").str(); std::string GBWFILE = DIR + "/" + gbw_file; XTP_LOG(Log::error, pLog) << "Copying MO data to " << gbw_file << std::flush; std::string GBWFILE_workdir = work_dir + "/system.gbw"; boost::filesystem::copy_file( GBWFILE_workdir, GBWFILE, boost::filesystem::copy_option::overwrite_if_exists); } } // end of the parse orbitals/log qmpackage->CleanUp(); WriteLoggerToFile(work_dir + "/dft.log", dft_logger); } if (!_do_dft_parse && (_do_gwbse || _do_esp)) { // load the DFT data from serialized orbitals object std::string ORB_FILE = eqm_work_dir + "/molecules/" + frame_dir + "/" + orb_file; XTP_LOG(Log::error, pLog) << TimeStamp() << " Loading DFT data from " << ORB_FILE << std::flush; orbitals.ReadFromCpt(ORB_FILE); } if (_do_gwbse) { XTP_LOG(Log::error, pLog) << "Running GWBSE" << std::flush; try { GWBSE gwbse = GWBSE(orbitals); Logger gwbse_logger(votca::Log::current_level); gwbse_logger.setMultithreading(false); gwbse_logger.setPreface(Log::info, (format("\nGWBSE INF ...")).str()); gwbse_logger.setPreface(Log::error, (format("\nGWBSE ERR ...")).str()); gwbse_logger.setPreface(Log::warning, (format("\nGWBSE WAR ...")).str()); gwbse_logger.setPreface(Log::debug, (format("\nGWBSE DBG ...")).str()); gwbse.setLogger(&gwbse_logger); gwbse.Initialize(_gwbse_options); gwbse.Evaluate(); gwbse.addoutput(segment_summary); WriteLoggerToFile(work_dir + "/gwbse.log", gwbse_logger); } catch (std::runtime_error& error) { std::string errormessage(error.what()); SetJobToFailed(jres, pLog, "GWBSE:" + errormessage); return jres; } } if (_do_esp) { XTP_LOG(Log::error, pLog) << "Running ESPFIT" << std::flush; try { Esp2multipole esp2multipole = Esp2multipole(pLog); esp2multipole.Initialize(_esp_options); std::string ESPDIR = "MP_FILES/" + frame_dir + "/" + esp2multipole.GetStateString(); StaticSegment seg2 = esp2multipole.Extractingcharges(orbitals); std::string mps_file = (format("%1%_%2%_%3%.mps") % segType % segId % esp2multipole.GetStateString()) .str(); boost::filesystem::create_directories(ESPDIR); seg2.WriteMPS(ESPDIR + "/" + mps_file, "Generated by eqm:" + esp2multipole.GetStateString()); XTP_LOG(Log::error, pLog) << "Written charges to " << (ESPDIR + "/" + mps_file) << std::flush; segment_summary.add("partialcharges", (ESPDIR + "/" + mps_file)); } catch (std::runtime_error& error) { std::string errormessage(error.what()); SetJobToFailed(jres, pLog, "ESPFIT:" + errormessage); return jres; } } XTP_LOG(Log::error, pLog) << TimeStamp() << " Finished evaluating site " << seg.getId() << std::flush; if (_do_dft_parse || _do_gwbse) { XTP_LOG(Log::error, pLog) << "Saving data to " << orb_file << std::flush; std::string DIR = eqm_work_dir + "/molecules/" + frame_dir; boost::filesystem::create_directories(DIR); std::string ORBFILE = DIR + "/" + orb_file; orbitals.WriteToCpt(ORBFILE); } // output of the JOB jres.setOutput(job_summary); jres.setStatus(Job::COMPLETE); return jres; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/jobcalculators/eqm.h000066400000000000000000000037341412152066400204560ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_EQM_H #define VOTCA_XTP_EQM_H // Local VOTCA includes #include "votca/xtp/gwbse.h" #include "votca/xtp/parallelxjobcalc.h" #include "votca/xtp/qmpackagefactory.h" #include "votca/xtp/segment.h" namespace votca { namespace xtp { /** * \brief Run DFT/GWBSE calculations * * Evaluates DFT and GWBSE for all molecules * Requires a first-principles package, i.e. ORCA * */ class EQM final : public ParallelXJobCalc > { public: std::string Identify() { return "eqm"; } Job::JobResult EvalJob(const Topology &top, Job &job, QMThread &opThread); void CleanUp() { ; } void WriteJobFile(const Topology &top); void ReadJobFile(Topology &) { return; } protected: void ParseSpecificOptions(const tools::Property &user_options); private: void WriteLoggerToFile(const std::string &logfile, Logger &logger); void SetJobToFailed(Job::JobResult &jres, Logger &pLog, const std::string &errormessage); tools::Property _package_options; tools::Property _gwbse_options; tools::Property _esp_options; // what to do bool _do_dft_input = false; bool _do_dft_run = false; bool _do_dft_parse = false; bool _do_gwbse = false; bool _do_esp = false; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_EQM_H xtp-2021.2/src/libxtp/jobcalculators/iexcitoncl.cc000066400000000000000000000241641412152066400221730ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include #include // VOTCA includes #include #include // Local VOTCA includes #include "votca/xtp/eeinteractor.h" #include "votca/xtp/logger.h" #include "votca/xtp/segmentmapper.h" // Local private VOTCA includes #include "iexcitoncl.h" using namespace boost::filesystem; using namespace votca::tools; namespace votca { namespace xtp { // +++++++++++++++++++++++++++++ // // IEXCITON MEMBER FUNCTIONS // // +++++++++++++++++++++++++++++ // void IEXCITON::ParseSpecificOptions(const tools::Property& options) { if (options.get(".use_states").as()) { std::string parse_string = options.get(".states").as(); _statemap = FillParseMaps(parse_string); } } std::map IEXCITON::FillParseMaps( const std::string& Mapstring) { Tokenizer split_options(Mapstring, ", \t\n"); std::map type2level; for (const std::string& substring : split_options) { std::vector segmentpnumber; Tokenizer tok(substring, ":"); tok.ToVector(segmentpnumber); if (segmentpnumber.size() != 2) { throw std::runtime_error("Parser iqm: Segment and exciton labels:" + substring + "are not separated properly"); } QMState state = QMState(segmentpnumber[1]); if (!state.isTransition()) { throw std::runtime_error("State to calculate must be a transition state"); } std::string segmentname = segmentpnumber[0]; type2level[segmentname] = state; } return type2level; } Job::JobResult IEXCITON::EvalJob(const Topology& top, Job& job, QMThread& opThread) { // report back to the progress observer Job::JobResult jres = Job::JobResult(); // get the logger from the thread Logger& pLog = opThread.getLogger(); // get the information about the job executed by the thread Index job_ID = job.getId(); Property job_input = job.getInput(); std::vector segment_list = job_input.Select("segment"); Index ID_A = segment_list.front()->getAttribute("id"); std::string type_A = segment_list.front()->getAttribute("type"); std::string mps_fileA = segment_list.front()->getAttribute("mps_file"); Index ID_B = segment_list.back()->getAttribute("id"); std::string type_B = segment_list.back()->getAttribute("type"); std::string mps_fileB = segment_list.back()->getAttribute("mps_file"); const Segment& seg_A = top.getSegment(ID_A); if (type_A != seg_A.getType()) { throw std::runtime_error("SegmentA: type " + seg_A.getType() + " and type in jobfile " + type_A + " do not agree for ID:" + std::to_string(ID_A)); } const Segment& seg_B = top.getSegment(ID_B); if (type_B != seg_B.getType()) { throw std::runtime_error("SegmentB: type " + seg_B.getType() + " and type in jobfile " + type_B + " do not agree for ID:" + std::to_string(ID_B)); } const QMNBList& nblist = top.NBList(); const QMPair* pair = nblist.FindPair(&seg_A, &seg_B); if (pair == nullptr) { throw std::runtime_error( "pair between segments " + std::to_string(seg_A.getId()) + ":" + std::to_string(seg_B.getId()) + " not found in neighborlist "); } XTP_LOG(Log::error, pLog) << TimeStamp() << " Evaluating pair " << job_ID << " [" << ID_A << ":" << ID_B << "]" << std::flush; StaticMapper map(pLog); map.LoadMappingFile(_mapfile); StaticSegment seg1 = map.map(*(pair->Seg1()), mps_fileA); StaticSegment seg2 = map.map(pair->Seg2PbCopy(), mps_fileB); eeInteractor actor; double JAB = actor.CalcStaticEnergy(seg1, seg2); _cutoff = 0; Property job_summary; Property& job_output = job_summary.add("output", ""); Property& pair_summary = job_output.add("pair", ""); std::string nameA = seg_A.getType(); std::string nameB = seg_B.getType(); pair_summary.setAttribute("idA", ID_A); pair_summary.setAttribute("idB", ID_B); pair_summary.setAttribute("typeA", nameA); pair_summary.setAttribute("typeB", nameB); Property& coupling_summary = pair_summary.add("Coupling", ""); coupling_summary.setAttribute("jABstatic", JAB * tools::conv::hrt2ev); jres.setOutput(job_summary); jres.setStatus(Job::COMPLETE); return jres; } QMState IEXCITON::GetElementFromMap(const std::string& elementname) const { QMState state; try { state = _statemap.at(elementname); } catch (std::out_of_range&) { std::string errormessage = "Map does not have segment of type: " + elementname; errormessage += "\n segments in map are:"; for (const auto& s : _statemap) { errormessage += "\n\t" + s.first; } throw std::runtime_error(errormessage); } return state; } void IEXCITON::WriteJobFile(const Topology& top) { std::cout << "\n... ... Writing job file " << _jobfile << std::flush; std::ofstream ofs; ofs.open(_jobfile, std::ofstream::out); if (!ofs.is_open()) { throw std::runtime_error("\nERROR: bad file handle: " + _jobfile); } const QMNBList& nblist = top.NBList(); Index jobCount = 0; if (nblist.size() == 0) { std::cout << "\n... ... No pairs in neighbor list, skip." << std::flush; return; } ofs << "\n"; std::string tag = ""; for (const QMPair* pair : nblist) { if (pair->getType() == QMPair::PairType::Excitoncl) { Index id1 = pair->Seg1()->getId(); std::string name1 = pair->Seg1()->getType(); Index id2 = pair->Seg2()->getId(); std::string name2 = pair->Seg2()->getType(); Index id = jobCount; QMState state1 = GetElementFromMap(name1); QMState state2 = GetElementFromMap(name2); std::string mps_file1 = (boost::format("MP_FILES/%s_%s.mps") % name1 % state1.ToString()) .str(); std::string mps_file2 = (boost::format("MP_FILES/%s_%s.mps") % name2 % state2.ToString()) .str(); Property Input; Property& pInput = Input.add("input", ""); Property& pSegment1 = pInput.add("segment", boost::lexical_cast(id1)); pSegment1.setAttribute("type", name1); pSegment1.setAttribute("id", id1); pSegment1.setAttribute("mps_file", mps_file1); Property& pSegment2 = pInput.add("segment", boost::lexical_cast(id2)); pSegment2.setAttribute("type", name2); pSegment2.setAttribute("id", id2); pSegment2.setAttribute("mps_file", mps_file2); Job job(id, tag, Input, Job::AVAILABLE); job.ToStream(ofs); jobCount++; } } // CLOSE STREAM ofs << "\n"; ofs.close(); std::cout << "\n... ... In total " << jobCount << " jobs" << std::flush; } void IEXCITON::ReadJobFile(Topology& top) { Property xml; std::vector records; // gets the neighborlist from the topology QMNBList& nblist = top.NBList(); Index number_of_pairs = nblist.size(); Index current_pairs = 0; Logger log; log.setReportLevel(Log::current_level); // load the QC results in a vector indexed by the pair ID xml.LoadFromXML(_jobfile); std::vector jobProps = xml.Select("jobs.job"); records.resize(number_of_pairs + 1); // to skip pairs which are not in the jobfile for (auto& record : records) { record = nullptr; } // loop over all jobs = pair records in the job file for (Property* prop : jobProps) { // if job produced an output, then continue with analysis if (prop->exists("output") && prop->exists("output.pair")) { current_pairs++; Property& poutput = prop->get("output.pair"); Index idA = poutput.getAttribute("idA"); Index idB = poutput.getAttribute("idB"); Segment& segA = top.getSegment(idA); Segment& segB = top.getSegment(idB); QMPair* qmp = nblist.FindPair(&segA, &segB); if (qmp == nullptr) { XTP_LOG(Log::error, log) << "No pair " << idA << ":" << idB << " found in the neighbor list. Ignoring" << std::flush; } else { records[qmp->getId()] = &(prop->get("output.pair")); } } else { Property thebadone = prop->get("id"); throw std::runtime_error( "\nERROR: Job file incomplete.\n Job with id " + thebadone.as() + " is not finished. Check your job file for FAIL, " "AVAILABLE, or ASSIGNED. Exiting\n"); } } // finished loading from the file // loop over all pairs in the neighbor list XTP_LOG(Log::error, log) << "Neighborlist size " << top.NBList().size() << std::flush; for (QMPair* pair : top.NBList()) { if (records[pair->getId()] == nullptr) { continue; // skip pairs which are not in the jobfile } if (pair->getType() == QMPair::Excitoncl) { Property* pair_property = records[pair->getId()]; const Property& pCoupling = pair_property->get("Coupling"); double jAB = pCoupling.getAttribute("jABstatic"); double Jeff2 = jAB * jAB * tools::conv::ev2hrt * tools::conv::ev2hrt; pair->setJeff2(Jeff2, QMStateType::Singlet); } } XTP_LOG(Log::error, log) << "Pairs [total:updated] " << number_of_pairs << ":" << current_pairs << std::flush; std::cout << log; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/jobcalculators/iexcitoncl.h000066400000000000000000000035411412152066400220310ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_IEXCITONCL_H #define VOTCA_XTP_IEXCITONCL_H // Third party includes #include #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/parallelxjobcalc.h" #include "votca/xtp/qmstate.h" namespace votca { namespace xtp { /** * \brief Evaluates Transition Charge distributions classically * * Evaluates the electrostatic classical coupling between molecules in * their excited states. * Callname: iexcitoncl */ class IEXCITON final : public ParallelXJobCalc > { public: std::string Identify() { return "iexcitoncl"; } Job::JobResult EvalJob(const Topology &top, Job &job, QMThread &opThread); void WriteJobFile(const Topology &top); void ReadJobFile(Topology &top); protected: void ParseSpecificOptions(const tools::Property &user_options); private: QMState GetElementFromMap(const std::string &elementname) const; std::map FillParseMaps(const std::string &Mapstring); double _cutoff; std::map _statemap; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_IEXCITONCL_H xtp-2021.2/src/libxtp/jobcalculators/iqm.cc000066400000000000000000000707031412152066400206200ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include #include #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/atom.h" #include "votca/xtp/logger.h" #include "votca/xtp/qmpackagefactory.h" #include "votca/xtp/segmentmapper.h" // Local private VOTCA includes #include "iqm.h" using boost::format; using namespace boost::filesystem; namespace votca { namespace xtp { void IQM::ParseSpecificOptions(const tools::Property& options) { QMPackageFactory::RegisterAll(); // job tasks std::string tasks_string = options.get(".tasks").as(); if (tasks_string.find("input") != std::string::npos) { _do_dft_input = true; } if (tasks_string.find("dft") != std::string::npos) { _do_dft_run = true; } if (tasks_string.find("parse") != std::string::npos) { _do_dft_parse = true; } if (tasks_string.find("dftcoupling") != std::string::npos) { _do_dftcoupling = true; } if (tasks_string.find("gw") != std::string::npos) { _do_gwbse = true; } if (tasks_string.find("bsecoupling") != std::string::npos) { _do_bsecoupling = true; } // storage options std::string store_string = options.get(".store").as(); if (store_string.find("dft") != std::string::npos) { _store_dft = true; } if (store_string.find("gw") != std::string::npos) { _store_gw = true; } _dftpackage_options = this->UpdateDFTOptions(options); _gwbse_options = this->UpdateGWBSEOptions(options); _dftcoupling_options = options.get(".dftcoupling_options"); tools::Property& prop_bsecoupling = _bsecoupling_options.add("bsecoupling", ""); prop_bsecoupling = options.get("bsecoupling"); // read linker groups std::string linker = options.ifExistsReturnElseReturnDefault(".linker_names", ""); tools::Tokenizer toker(linker, ", \t\n"); std::vector linkers = toker.ToVector(); for (const std::string& link : linkers) { tools::Tokenizer toker2(link, ":"); std::vector link_split = toker2.ToVector(); if (link_split.size() != 2) { throw std::runtime_error( "Linker molecule has to be defined NAME:STATEGEO .e.g. DCV5T:n"); } _linkers[link_split[0]] = QMState(link_split[1]); } // options for parsing data into state file std::string key_read = ".readjobfile"; if (options.exists(key_read + ".singlet")) { std::string parse_string_s = options.get(key_read + ".singlet").as(); _singlet_levels = FillParseMaps(parse_string_s); } if (options.exists(key_read + ".triplet")) { std::string parse_string_t = options.get(key_read + ".triplet").as(); _triplet_levels = FillParseMaps(parse_string_t); } if (options.exists(key_read + ".hole")) { std::string parse_string_h = options.get(key_read + ".hole").as(); _hole_levels = FillParseMaps(parse_string_h); } if (options.exists(key_read + ".electron")) { std::string parse_string_e = options.get(key_read + ".electron").as(); _electron_levels = FillParseMaps(parse_string_e); } } std::map IQM::FillParseMaps( const std::string& Mapstring) { tools::Tokenizer split_options(Mapstring, ", \t\n"); std::map type2level; for (const std::string& substring : split_options) { std::vector segmentpnumber; tools::Tokenizer tok(substring, ":"); tok.ToVector(segmentpnumber); if (segmentpnumber.size() != 2) { throw std::runtime_error("Parser iqm: Segment and exciton labels:" + substring + "are not separated properly"); } QMState state = QMState(segmentpnumber[1]); std::string segmentname = segmentpnumber[0]; type2level[segmentname] = state; } return type2level; } void IQM::addLinkers(std::vector& segments, const Topology& top) { std::vector result; const Segment* seg1 = segments[0]; const Segment* seg2 = segments[1]; std::vector segmentsInMolecule = top.FindAllSegmentsOnMolecule(*seg1, *seg2); for (const Segment* segment : segmentsInMolecule) { Index idIterator = segment->getId(); if (idIterator != seg1->getId() && idIterator != seg2->getId() && isLinker(segment->getType())) { segments.push_back(segment); } } } bool IQM::isLinker(const std::string& name) { return _linkers.count(name) == 1; } void IQM::SetJobToFailed(Job::JobResult& jres, Logger& pLog, const std::string& errormessage) { XTP_LOG(Log::error, pLog) << errormessage << std::flush; std::cout << pLog; jres.setError(errormessage); jres.setStatus(Job::FAILED); } void IQM::WriteLoggerToFile(const std::string& logfile, Logger& logger) { std::ofstream ofs; ofs.open(logfile, std::ofstream::out); if (!ofs.is_open()) { throw std::runtime_error("Bad file handle: " + logfile); } ofs << logger << std::endl; ofs.close(); } Job::JobResult IQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { // report back to the progress observer Job::JobResult jres = Job::JobResult(); std::string iqm_work_dir = "OR_FILES"; std::string eqm_work_dir = "OR_FILES"; std::string frame_dir = "frame_" + boost::lexical_cast(top.getStep()); Logger& pLog = opThread.getLogger(); QMMapper mapper(pLog); mapper.LoadMappingFile(_mapfile); // get the information about the job executed by the thread Index job_ID = job.getId(); tools::Property job_input = job.getInput(); std::vector segment_list = job_input.Select("segment"); Index ID_A = segment_list.front()->getAttribute("id"); std::string type_A = segment_list.front()->getAttribute("type"); Index ID_B = segment_list.back()->getAttribute("id"); std::string type_B = segment_list.back()->getAttribute("type"); std::string qmgeo_state_A = "n"; if (segment_list.front()->exists("qm_geometry")) { qmgeo_state_A = segment_list.front()->getAttribute("qm_geometry"); } std::string qmgeo_state_B = "n"; if (segment_list.back()->exists("qm_geometry")) { qmgeo_state_B = segment_list.back()->getAttribute("qm_geometry"); } QMState stateA(qmgeo_state_A); QMState stateB(qmgeo_state_B); // set the folders std::string pair_dir = (format("%1%%2%%3%%4%%5%") % "pair" % "_" % ID_A % "_" % ID_B).str(); boost::filesystem::path arg_path, arg_pathA, arg_pathB, arg_pathAB; std::string orbFileA = (arg_pathA / eqm_work_dir / "molecules" / frame_dir / (format("%1%_%2%%3%") % "molecule" % ID_A % ".orb").str()) .generic_string(); ; std::string orbFileB = (arg_pathB / eqm_work_dir / "molecules" / frame_dir / (format("%1%_%2%%3%") % "molecule" % ID_B % ".orb").str()) .generic_string(); ; std::string orbFileAB = (arg_pathAB / iqm_work_dir / "pairs_iqm" / frame_dir / (format("%1%%2%%3%%4%%5%") % "pair_" % ID_A % "_" % ID_B % ".orb").str()) .generic_string(); ; std::string orb_dir = (arg_path / iqm_work_dir / "pairs_iqm" / frame_dir).generic_string(); ; const Segment& seg_A = top.getSegment(ID_A); const Segment& seg_B = top.getSegment(ID_B); const QMNBList& nblist = top.NBList(); const QMPair* pair = nblist.FindPair(&seg_A, &seg_B); XTP_LOG(Log::error, pLog) << TimeStamp() << " Evaluating pair " << job_ID << " [" << ID_A << ":" << ID_B << "] out of " << (top.NBList()).size() << std::flush; std::string package_append = "workdir_" + Identify(); std::vector segments; segments.push_back(&seg_A); segments.push_back(&seg_B); std::string work_dir = (arg_path / iqm_work_dir / package_append / frame_dir / pair_dir) .generic_string(); if (_linkers.size() > 0) { addLinkers(segments, top); } Orbitals orbitalsAB; // if a pair object is available and is not linked take into account PBC, // otherwise write as is if (pair == nullptr || segments.size() > 2) { if (pair == nullptr) { XTP_LOG(Log::warning, pLog) << "PBCs are not taken into account when writing the coordinate file!" << std::flush; } orbitalsAB.QMAtoms() = mapper.map(*(segments[0]), stateA); orbitalsAB.QMAtoms().AddContainer(mapper.map(*(segments[1]), stateB)); for (Index i = 2; i < Index(segments.size()); i++) { QMState linker_state = _linkers.at(segments[i]->getType()); orbitalsAB.QMAtoms().AddContainer( mapper.map(*(segments[i]), linker_state)); } } else { const Segment* seg1 = pair->Seg1(); orbitalsAB.QMAtoms() = mapper.map(*seg1, stateA); Segment seg2 = pair->Seg2PbCopy(); orbitalsAB.QMAtoms().AddContainer(mapper.map(seg2, stateB)); } if (_do_dft_input || _do_dft_run || _do_dft_parse) { std::string qmpackage_work_dir = (arg_path / iqm_work_dir / package_append / frame_dir / pair_dir) .generic_string(); Logger dft_logger(Log::current_level); dft_logger.setMultithreading(false); dft_logger.setPreface(Log::info, (format("\nDFT INF ...")).str()); dft_logger.setPreface(Log::error, (format("\nDFT ERR ...")).str()); dft_logger.setPreface(Log::warning, (format("\nDFT WAR ...")).str()); dft_logger.setPreface(Log::debug, (format("\nDFT DBG ...")).str()); std::string dftname = "package.name"; std::string package = _dftpackage_options.get(dftname).as(); std::unique_ptr qmpackage = std::unique_ptr( QMPackageFactory::QMPackages().Create(package)); qmpackage->setLog(&dft_logger); qmpackage->setRunDir(qmpackage_work_dir); qmpackage->Initialize(_dftpackage_options); // if asked, prepare the input files if (_do_dft_input) { boost::filesystem::create_directories(qmpackage_work_dir); if (qmpackage->GuessRequested()) { if (_linkers.size() > 0) { throw std::runtime_error( "Error: You are using a linker and want " "to use a monomer guess for the dimer. These are mutually " "exclusive."); } XTP_LOG(Log::error, pLog) << "Guess requested, reading molecular orbitals" << std::flush; if (qmpackage->getPackageName() == "orca") { XTP_LOG(Log::info, pLog) << "Copying monomer .gbw files to pair folder" << std::flush; std::string gbwFileA = (arg_pathA / eqm_work_dir / "molecules" / frame_dir / (format("%1%_%2%%3%") % "molecule" % ID_A % ".gbw").str()) .generic_string(); ; std::string gbwFileB = (arg_pathB / eqm_work_dir / "molecules" / frame_dir / (format("%1%_%2%%3%") % "molecule" % ID_B % ".gbw").str()) .generic_string(); ; std::string gbwFileA_workdir = (boost::filesystem::path(qmpackage_work_dir) / "molA.gbw") .generic_string(); ; std::string gbwFileB_workdir = (boost::filesystem::path(qmpackage_work_dir) / "molB.gbw") .generic_string(); ; boost::filesystem::copy_file( gbwFileA, gbwFileA_workdir, boost::filesystem::copy_option::overwrite_if_exists); boost::filesystem::copy_file( gbwFileB, gbwFileB_workdir, boost::filesystem::copy_option::overwrite_if_exists); } else { Orbitals orbitalsB; Orbitals orbitalsA; try { XTP_LOG(Log::error, pLog) << "Reading MoleculeA from " << orbFileA << std::flush; orbitalsA.ReadFromCpt(orbFileA); } catch (std::runtime_error&) { SetJobToFailed( jres, pLog, "Do input: failed loading orbitals from " + orbFileA); return jres; } try { XTP_LOG(Log::error, pLog) << "Reading MoleculeB from " << orbFileB << std::flush; orbitalsB.ReadFromCpt(orbFileB); } catch (std::runtime_error&) { SetJobToFailed( jres, pLog, "Do input: failed loading orbitals from " + orbFileB); return jres; } XTP_LOG(Log::info, pLog) << "Constructing the guess for dimer orbitals" << std::flush; orbitalsAB.PrepareDimerGuess(orbitalsA, orbitalsB); } } else { XTP_LOG(Log::info, pLog) << "No Guess requested, starting from DFT starting Guess" << std::flush; } qmpackage->WriteInputFile(orbitalsAB); } if (_do_dft_run) { XTP_LOG(Log::error, pLog) << "Running DFT" << std::flush; bool _run_dft_status = qmpackage->Run(); if (!_run_dft_status) { SetJobToFailed(jres, pLog, qmpackage->getPackageName() + " run failed"); WriteLoggerToFile(work_dir + "/dft.log", dft_logger); return jres; } } if (_do_dft_parse) { bool parse_log_status = qmpackage->ParseLogFile(orbitalsAB); if (!parse_log_status) { SetJobToFailed(jres, pLog, "LOG parsing failed"); return jres; } bool parse_orbitals_status = qmpackage->ParseMOsFile(orbitalsAB); if (!parse_orbitals_status) { SetJobToFailed(jres, pLog, "Orbitals parsing failed"); return jres; } } // end of the parse orbitals/log qmpackage->CleanUp(); WriteLoggerToFile(work_dir + "/dft.log", dft_logger); } else { try { orbitalsAB.ReadFromCpt(orbFileAB); } catch (std::runtime_error&) { SetJobToFailed(jres, pLog, "Do input: failed loading orbitals from " + orbFileAB); return jres; } } tools::Property job_summary; tools::Property& job_output = job_summary.add("output", ""); if (_do_dftcoupling) { DFTcoupling dftcoupling; dftcoupling.setLogger(&pLog); dftcoupling.Initialize(_dftcoupling_options); Orbitals orbitalsB; Orbitals orbitalsA; try { orbitalsA.ReadFromCpt(orbFileA); } catch (std::runtime_error&) { SetJobToFailed(jres, pLog, "Do input: failed loading orbitals from " + orbFileA); return jres; } try { orbitalsB.ReadFromCpt(orbFileB); } catch (std::runtime_error&) { SetJobToFailed(jres, pLog, "Do input: failed loading orbitals from " + orbFileB); return jres; } try { dftcoupling.CalculateCouplings(orbitalsA, orbitalsB, orbitalsAB); dftcoupling.Addoutput(job_output, orbitalsA, orbitalsB); } catch (std::runtime_error& error) { std::string errormessage(error.what()); SetJobToFailed(jres, pLog, errormessage); return jres; } } // do excited states calculation if (_do_gwbse) { try { XTP_LOG(Log::error, pLog) << "Running GWBSE" << std::flush; Logger gwbse_logger(Log::current_level); gwbse_logger.setMultithreading(false); gwbse_logger.setPreface(Log::info, (format("\nGWBSE INF ...")).str()); gwbse_logger.setPreface(Log::error, (format("\nGWBSE ERR ...")).str()); gwbse_logger.setPreface(Log::warning, (format("\nGWBSE WAR ...")).str()); gwbse_logger.setPreface(Log::debug, (format("\nGWBSE DBG ...")).str()); GWBSE gwbse = GWBSE(orbitalsAB); gwbse.setLogger(&gwbse_logger); gwbse.Initialize(_gwbse_options); gwbse.Evaluate(); WriteLoggerToFile(work_dir + "/gwbse.log", gwbse_logger); } catch (std::runtime_error& error) { std::string errormessage(error.what()); SetJobToFailed(jres, pLog, errormessage); return jres; } } // end of excited state calculation, exciton data is in _orbitalsAB // calculate the coupling if (_do_bsecoupling) { XTP_LOG(Log::error, pLog) << "Running BSECoupling" << std::flush; BSECoupling bsecoupling; // orbitals must be loaded from a file if (!_do_gwbse) { try { orbitalsAB.ReadFromCpt(orbFileAB); } catch (std::runtime_error&) { SetJobToFailed(jres, pLog, "Do input: failed loading orbitals from " + orbFileAB); return jres; } } Orbitals orbitalsB; Orbitals orbitalsA; try { orbitalsA.ReadFromCpt(orbFileA); } catch (std::runtime_error&) { SetJobToFailed(jres, pLog, "Do input: failed loading orbitals from " + orbFileA); return jres; } try { orbitalsB.ReadFromCpt(orbFileB); } catch (std::runtime_error&) { SetJobToFailed(jres, pLog, "Do input: failed loading orbitals from " + orbFileB); return jres; } try { Logger bsecoupling_logger(Log::current_level); bsecoupling_logger.setMultithreading(false); bsecoupling_logger.setPreface(Log::info, (format("\nBSECOU INF ...")).str()); bsecoupling_logger.setPreface(Log::error, (format("\nBSECOU ERR ...")).str()); bsecoupling_logger.setPreface(Log::warning, (format("\nBSECOU WAR ...")).str()); bsecoupling_logger.setPreface(Log::debug, (format("\nBSECOU DBG ...")).str()); bsecoupling.setLogger(&bsecoupling_logger); bsecoupling.Initialize(_bsecoupling_options); bsecoupling.CalculateCouplings(orbitalsA, orbitalsB, orbitalsAB); bsecoupling.Addoutput(job_output, orbitalsA, orbitalsB); WriteLoggerToFile(work_dir + "/bsecoupling.log", bsecoupling_logger); } catch (std::runtime_error& error) { std::string errormessage(error.what()); SetJobToFailed(jres, pLog, errormessage); return jres; } } tools::PropertyIOManipulator iomXML(tools::PropertyIOManipulator::XML, 1, ""); std::stringstream sout; sout << iomXML << job_summary; XTP_LOG(Log::error, pLog) << TimeStamp() << " Finished evaluating pair " << ID_A << ":" << ID_B << std::flush; if (_store_dft || _store_gw) { boost::filesystem::create_directories(orb_dir); XTP_LOG(Log::error, pLog) << "Saving orbitals to " << orbFileAB << std::flush; if (!_store_dft) { orbitalsAB.MOs().clear(); } if (!_store_gw) { orbitalsAB.QPdiag().clear(); orbitalsAB.QPpertEnergies().resize(0); } orbitalsAB.WriteToCpt(orbFileAB); } else { XTP_LOG(Log::error, pLog) << "Orb file is not saved according to options " << std::flush; } jres.setOutput(job_summary); jres.setStatus(Job::COMPLETE); return jres; } void IQM::WriteJobFile(const Topology& top) { std::cout << std::endl << "... ... Writing job file " << _jobfile << std::flush; std::ofstream ofs; ofs.open(_jobfile, std::ofstream::out); if (!ofs.is_open()) { throw std::runtime_error("\nERROR: bad file handle: " + _jobfile); } const QMNBList& nblist = top.NBList(); Index jobCount = 0; if (nblist.size() == 0) { std::cout << std::endl << "... ... No pairs in neighbor list, skip." << std::flush; return; } ofs << "" << std::endl; std::string tag = ""; for (const QMPair* pair : nblist) { if (pair->getType() == QMPair::Excitoncl) { continue; } Index id1 = pair->Seg1()->getId(); std::string name1 = pair->Seg1()->getType(); Index id2 = pair->Seg2()->getId(); std::string name2 = pair->Seg2()->getType(); Index id = jobCount; tools::Property Input; tools::Property& pInput = Input.add("input", ""); tools::Property& pSegmentA = pInput.add("segment", boost::lexical_cast(id1)); pSegmentA.setAttribute("type", name1); pSegmentA.setAttribute("id", id1); tools::Property& pSegmentB = pInput.add("segment", boost::lexical_cast(id2)); pSegmentB.setAttribute("type", name2); pSegmentB.setAttribute("id", id2); Job job(id, tag, Input, Job::AVAILABLE); job.ToStream(ofs); jobCount++; } // CLOSE STREAM ofs << "" << std::endl; ofs.close(); std::cout << std::endl << "... ... In total " << jobCount << " jobs" << std::flush; return; } double IQM::GetDFTCouplingFromProp(tools::Property& dftprop, Index stateA, Index stateB) { double J = 0; bool found = false; for (tools::Property* state : dftprop.Select("coupling")) { Index state1 = state->getAttribute("levelA"); Index state2 = state->getAttribute("levelB"); if (state1 == stateA && state2 == stateB) { J = state->getAttribute("j") * tools::conv::ev2hrt; found = true; break; } } if (found) { return J * J; } else { return -1; } } double IQM::GetBSECouplingFromProp(tools::Property& bseprop, const QMState& stateA, const QMState& stateB) { double J = 0; std::string algorithm = bseprop.getAttribute("algorithm"); bool found = false; for (tools::Property* state : bseprop.Select("coupling")) { QMState state1; state1.FromString(state->getAttribute("stateA")); QMState state2; state2.FromString(state->getAttribute("stateB")); if (state1 == stateA && state2 == stateB) { J = state->getAttribute(algorithm) * tools::conv::ev2hrt; found = true; break; } } if (found) { return J * J; } else { return -1; } } QMState IQM::GetElementFromMap(const std::map& elementmap, const std::string& elementname) const { QMState state; try { state = elementmap.at(elementname); } catch (std::out_of_range&) { std::string errormessage = "Map does not have segment of type: " + elementname; errormessage += "\n segments in map are:"; for (const auto& s : elementmap) { errormessage += "\n\t" + s.first; } throw std::runtime_error(errormessage); } return state; } void IQM::ReadJobFile(Topology& top) { // gets the neighborlist from the topology QMNBList& nblist = top.NBList(); Index number_of_pairs = nblist.size(); Index dft_h = 0; Index dft_e = 0; Index bse_s = 0; Index bse_t = 0; Index incomplete_jobs = 0; Logger log; log.setReportLevel(Log::current_level); tools::Property xml; // load the QC results in a vector indexed by the pair ID xml.LoadFromXML(_jobfile); std::vector jobProps = xml.Select("jobs.job"); std::vector records = std::vector(nblist.size() + 1, nullptr); // loop over all jobs = pair records in the job file for (tools::Property* job : jobProps) { if (!job->exists("status")) { throw std::runtime_error( "Jobfile is malformed. tag missing on job."); } if (job->get("status").as() != "COMPLETE" || !job->exists("output")) { incomplete_jobs++; continue; } // get the output records tools::Property poutput = job->get("output"); // job file is stupid, because segment ids are only in input have to get // them out l std::vector segmentprobs = job->Select("input.segment"); std::vector id; for (tools::Property* segment : segmentprobs) { id.push_back(segment->getAttribute("id")); } if (id.size() != 2) { throw std::runtime_error( "Getting pair ids from jobfile failed, check jobfile."); } Index idA = id[0]; Index idB = id[1]; // segments which correspond to these ids Segment& segA = top.getSegment(idA); Segment& segB = top.getSegment(idB); // pair that corresponds to the two segments QMPair* qmp = nblist.FindPair(&segA, &segB); // output using logger if (qmp == nullptr) { // there is no pair in the neighbor list with this // name XTP_LOG(Log::error, log) << "No pair " << idA << ":" << idB << " found in the neighbor list. Ignoring" << std::flush; } else { records[qmp->getId()] = &(job->get("output")); } } // finished loading from the file for (QMPair* pair : top.NBList()) { if (records[pair->getId()] == nullptr) { continue; // skip pairs which are not in the jobfile } const Segment* segmentA = pair->Seg1(); const Segment* segmentB = pair->Seg2(); QMPair::PairType ptype = pair->getType(); if (ptype != QMPair::PairType::Hopping) { XTP_LOG(Log::error, log) << "WARNING Pair " << pair->getId() << " is not of any of the " "Hopping type. Skipping pair" << std::flush; continue; } tools::Property* pair_property = records[pair->getId()]; if (pair_property->exists("dftcoupling")) { tools::Property& dftprop = pair_property->get("dftcoupling"); Index homoA = dftprop.getAttribute("homoA"); Index homoB = dftprop.getAttribute("homoB"); QMStateType hole = QMStateType(QMStateType::Hole); if (dftprop.exists(hole.ToLongString())) { tools::Property& holes = dftprop.get(hole.ToLongString()); QMState stateA = GetElementFromMap(_hole_levels, segmentA->getType()); QMState stateB = GetElementFromMap(_hole_levels, segmentB->getType()); Index levelA = homoA - stateA.StateIdx(); // h1 is is homo; Index levelB = homoB - stateB.StateIdx(); double J2 = GetDFTCouplingFromProp(holes, levelA, levelB); if (J2 >= 0) { pair->setJeff2(J2, hole); dft_h++; } } QMStateType electron = QMStateType(QMStateType::Electron); if (dftprop.exists(electron.ToLongString())) { tools::Property& electrons = dftprop.get(electron.ToLongString()); QMState stateA = GetElementFromMap(_electron_levels, segmentA->getType()); QMState stateB = GetElementFromMap(_electron_levels, segmentB->getType()); Index levelA = homoA + 1 + stateA.StateIdx(); // e1 is lumo; Index levelB = homoB + 1 + stateB.StateIdx(); double J2 = GetDFTCouplingFromProp(electrons, levelA, levelB); if (J2 >= 0) { pair->setJeff2(J2, electron); dft_e++; } } } if (pair_property->exists("bsecoupling")) { tools::Property& bseprop = pair_property->get("bsecoupling"); QMStateType singlet = QMStateType(QMStateType::Singlet); if (bseprop.exists(singlet.ToLongString())) { tools::Property& singlets = bseprop.get(singlet.ToLongString()); QMState stateA = GetElementFromMap(_singlet_levels, segmentA->getType()); QMState stateB = GetElementFromMap(_singlet_levels, segmentB->getType()); double J2 = GetBSECouplingFromProp(singlets, stateA, stateB); if (J2 >= 0) { pair->setJeff2(J2, singlet); bse_s++; } } QMStateType triplet = QMStateType(QMStateType::Triplet); if (bseprop.exists(triplet.ToLongString())) { tools::Property& triplets = bseprop.get(triplet.ToLongString()); QMState stateA = GetElementFromMap(_triplet_levels, segmentA->getType()); QMState stateB = GetElementFromMap(_triplet_levels, segmentB->getType()); double J2 = GetBSECouplingFromProp(triplets, stateA, stateB); if (J2 >= 0) { pair->setJeff2(J2, triplet); bse_t++; } } } } XTP_LOG(Log::error, log) << "Pairs [total:updated(e,h,s,t)] " << number_of_pairs << ":(" << dft_e << "," << dft_h << "," << bse_s << "," << bse_t << ") Incomplete jobs: " << incomplete_jobs << "\n" << std::flush; return; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/jobcalculators/iqm.h000066400000000000000000000063371412152066400204640ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_IQM_H #define VOTCA_XTP_IQM_H // Third party includes #include #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/bsecoupling.h" #include "votca/xtp/dftcoupling.h" #include "votca/xtp/gwbse.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/parallelxjobcalc.h" namespace votca { namespace xtp { /** * \brief DFT & GWBSE-based coupling elements * * Evaluates DFT & GWBSE-based coupling elements for all conjugated * segments from the neighbor list. Requires molecular orbitals of two monomers * and a dimer in ORCA format. * * Callname: iqm */ class IQM final : public ParallelXJobCalc > { public: std::string Identify() { return "iqm"; } Job::JobResult EvalJob(const Topology& top, Job& job, QMThread& opThread); void WriteJobFile(const Topology& top); void ReadJobFile(Topology& top); protected: void ParseSpecificOptions(const tools::Property& user_options); private: double GetBSECouplingFromProp(tools::Property& bseprop, const QMState& stateA, const QMState& stateB); double GetDFTCouplingFromProp(tools::Property& dftprop, Index stateA, Index stateB); void SetJobToFailed(Job::JobResult& jres, Logger& pLog, const std::string& errormessage); void WriteLoggerToFile(const std::string& logfile, Logger& logger); void addLinkers(std::vector& segments, const Topology& top); bool isLinker(const std::string& name); std::map FillParseMaps(const std::string& Mapstring); QMState GetElementFromMap(const std::map& elementmap, const std::string& elementname) const; tools::Property _dftpackage_options; tools::Property _gwbse_options; tools::Property _bsecoupling_options; tools::Property _dftcoupling_options; // what to do bool _do_dft_input = false; bool _do_dft_run = false; bool _do_dft_parse = false; bool _do_dftcoupling = false; bool _do_gwbse = false; bool _do_bsecoupling = false; std::map _linkers; // what to write in the storage bool _store_dft = false; bool _store_gw = false; // parsing options std::map _singlet_levels; std::map _triplet_levels; std::map _hole_levels; std::map _electron_levels; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_IQM_H xtp-2021.2/src/libxtp/jobcalculators/qmmm.cc000066400000000000000000000263551412152066400210050ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/jobtopology.h" #include "votca/xtp/qmregion.h" // Local private VOTCA includes #include "qmmm.h" namespace votca { namespace xtp { void QMMM::ParseSpecificOptions(const tools::Property& options) { _print_regions_pdb = options.get(".print_regions_pdb").as(); _max_iterations = options.get(".max_iterations").as(); _regions_def = options.get(".regions"); _regions_def.add("mapfile", _mapfile); std::string states = options.get(".write_parse.states").as(); tools::Tokenizer tok(states, " ,;\n\t"); std::vector statestrings = tok.ToVector(); _states.reserve(statestrings.size()); for (std::string s : statestrings) { _states.push_back(QMState(s)); } bool groundstate_found = false; for (const QMState& state : _states) { if (state.Type() == QMStateType::Gstate) { groundstate_found = true; } } if (!groundstate_found) { _states.push_back(QMState("n")); } } Job::JobResult QMMM::EvalJob(const Topology& top, Job& job, QMThread& Thread) { std::chrono::time_point start = std::chrono::system_clock::now(); std::string qmmm_work_dir = "QMMM"; if (!this->hasQMRegion()) { qmmm_work_dir = "MMMM"; } std::string frame_dir = "frame_" + boost::lexical_cast(top.getStep()); std::string job_dir = "job_" + std::to_string(job.getId()) + "_" + job.getTag(); boost::filesystem::path arg_path; std::string workdir = (arg_path / qmmm_work_dir / frame_dir / job_dir).generic_string(); boost::filesystem::create_directories(workdir); Job::JobResult jres = Job::JobResult(); Logger& pLog = Thread.getLogger(); JobTopology jobtop = JobTopology(job, pLog, workdir); jobtop.BuildRegions(top, _regions_def); if (_print_regions_pdb) { std::string pdb_filename = "regions.pdb"; XTP_LOG(Log::error, pLog) << TimeStamp() << " Writing jobtopology to " << (workdir + "/" + pdb_filename) << std::flush; jobtop.WriteToPdb(workdir + "/" + pdb_filename); } Index no_static_regions = 0; for (std::unique_ptr& region : jobtop) { no_static_regions += region->Converged(); } bool no_top_scf = false; if (jobtop.size() - no_static_regions < 2) { XTP_LOG(Log::error, pLog) << TimeStamp() << " Only " << jobtop.size() - no_static_regions << " scf region is used. The remaining regions are static. So no " "inter regions scf is required. " << std::flush; no_top_scf = true; _max_iterations = 1; } Index iteration = 0; for (; iteration < _max_iterations; iteration++) { XTP_LOG(Log::error, pLog) << TimeStamp() << " --Inter Region SCF Iteration " << iteration + 1 << " of " << _max_iterations << std::flush; for (std::unique_ptr& region : jobtop) { XTP_LOG(Log::error, pLog) << TimeStamp() << " Evaluating " << region->identify() << " " << region->getId() << std::flush; region->Reset(); region->Evaluate(jobtop.Regions()); if (!region->Successful()) { jres.setStatus(Job::JobStatus::FAILED); jres.setError(region->ErrorMsg()); return jres; } } std::string checkpointfilename = "checkpoint_iter_" + std::to_string(iteration + 1) + ".hdf5"; XTP_LOG(Log::error, pLog) << TimeStamp() << " Writing checkpoint to " << checkpointfilename << std::flush; jobtop.WriteToHdf5(workdir + "/" + checkpointfilename); if (!no_top_scf) { std::vector converged_regions; for (std::unique_ptr& region : jobtop) { converged_regions.push_back(region->Converged()); } double etot = 0.0; for (const std::unique_ptr& reg : jobtop) { etot += reg->Etotal(); } XTP_LOG(Log::error, pLog) << TimeStamp() << " --Total Energy all regions " << etot << std::flush; bool all_regions_converged = std::all_of(converged_regions.begin(), converged_regions.end(), [](bool i) { return i; }); if (all_regions_converged) { XTP_LOG(Log::error, pLog) << TimeStamp() << " Job converged after " << iteration + 1 << " iterations." << std::flush; jres.setStatus(Job::JobStatus::COMPLETE); break; } if (iteration == _max_iterations - 1) { XTP_LOG(Log::error, pLog) << TimeStamp() << " Job did not converge after " << iteration + 1 << " iterations.\n Writing results to jobfile." << std::flush; jres.setStatus(Job::JobStatus::FAILED); jres.setError("Inter Region SCF did not converge in " + std::to_string(_max_iterations) + " iterations."); } } else { jres.setStatus(Job::JobStatus::COMPLETE); } } tools::Property results; tools::Property& jobresult = results.add("output", ""); tools::Property& regionsresults = jobresult.add("regions", ""); double etot = 0.0; double charge = 0.0; for (const std::unique_ptr& reg : jobtop) { reg->AddResults(regionsresults); etot += reg->Etotal(); charge += reg->charge(); } std::chrono::time_point end = std::chrono::system_clock::now(); std::chrono::duration elapsed_time = end - start; jobresult.add("E_tot", std::to_string(etot * tools::conv::hrt2ev)); jobresult.add("Compute_Time", std::to_string(Index(elapsed_time.count()))); jobresult.add("Total_Charge", std::to_string(charge)); if (!no_top_scf) { jobresult.add("Iterations", std::to_string(iteration + 1)); } jres.setOutput(results); return jres; } bool QMMM::hasQMRegion() const { Logger log; QMRegion QMdummy(0, log, ""); bool found_qm = false; std::vector regions_def = _regions_def.Select("region"); for (const tools::Property* reg : regions_def) { std::string type = reg->ifExistsReturnElseThrowRuntimeError("type"); if (QMdummy.identify() == type) { found_qm = true; break; } } return found_qm; } void QMMM::WriteJobFile(const Topology& top) { if (!_write_parse) { throw std::runtime_error( "Cannot write jobfile, please add e " "s1 to your options."); } std::cout << std::endl << "... ... Writing job file " << _jobfile << std::flush; bool hasQMRegion = this->hasQMRegion(); std::ofstream ofs; ofs.open(_jobfile, std::ofstream::out); if (!ofs.is_open()) { throw std::runtime_error("\nERROR: bad file handle: " + _jobfile); } ofs << "" << std::endl; Index jobid = 0; for (const Segment& seg : top.Segments()) { for (const QMState& state : _states) { std::string marker = std::to_string(seg.getId()) + ":" + state.ToString(); std::string tag = seg.getType() + "_" + marker; tools::Property Input; tools::Property& pInput = Input.add("input", ""); pInput.add("site_energies", marker); tools::Property& regions = pInput.add("regions", ""); tools::Property& region = regions.add("region", ""); region.add("id", "0"); if (hasQMRegion) { region.add("state", state.ToString()); } region.add("segments", marker); Job job(jobid, tag, Input, Job::AVAILABLE); job.ToStream(ofs); jobid++; } } ofs << "" << std::endl; ofs.close(); std::cout << std::endl << "... ... In total " << jobid + 1 << " jobs" << std::flush; return; } void QMMM::ReadJobFile(Topology& top) { if (!_write_parse) { throw std::runtime_error( "Cannot read jobfile, please add n e " "h to your options."); } Index incomplete_jobs = 0; Eigen::Matrix energies = Eigen::Matrix::Zero(top.Segments().size(), 5); Eigen::Matrix found = Eigen::Matrix::Zero(top.Segments().size(), 5); tools::Property xml; xml.LoadFromXML(_jobfile); std::vector jobProps = xml.Select("jobs.job"); for (tools::Property* job : jobProps) { Index jobid = job->get("id").as(); if (!job->exists("status")) { throw std::runtime_error( "Jobfile is malformed. tag missing for job " + std::to_string(jobid)); } if (job->get("status").as() != "COMPLETE" || !job->exists("output")) { incomplete_jobs++; continue; } std::string marker = job->get("input.site_energies").as(); tools::Tokenizer tok(marker, ":"); std::vector split = tok.ToVector(); Index segid = std::stoi(split[0]); if (segid < 0 || segid >= Index(top.Segments().size())) { throw std::runtime_error("JobSegment id" + std::to_string(segid) + " is not in topology for job " + std::to_string(jobid)); } QMState state; try { state.FromString(split[1]); } catch (std::runtime_error& e) { std::stringstream message; message << e.what() << " for job " << jobid; throw std::runtime_error(message.str()); } double energy = job->get("output.E_tot").as() * tools::conv::ev2hrt; if (found(segid, state.Type().Type()) != 0) { throw std::runtime_error("There are two entries in jobfile for segment " + std::to_string(segid) + " state:" + state.ToString()); } energies(segid, state.Type().Type()) = energy; found(segid, state.Type().Type()) = 1; } Eigen::Matrix found_states = found.colwise().sum(); std::cout << std::endl; for (Index i = 0; i < 5; i++) { if (found_states(i) > 0) { QMStateType type(static_cast(i)); std::cout << "Found " << found_states(i) << " states of type " << type.ToString() << std::endl; } } if (incomplete_jobs > 0) { std::cout << incomplete_jobs << " incomplete jobs found." << std::endl; } for (Segment& seg : top.Segments()) { Index segid = seg.getId(); for (Index i = 0; i < 4; i++) { QMStateType type(static_cast(i)); if (found(segid, i) && found(segid, 4)) { double energy = energies(segid, i) - energies(segid, 4); seg.setEMpoles(type, energy); } } } } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/jobcalculators/qmmm.h000066400000000000000000000031371412152066400206400ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_QMMM_H #define VOTCA_XTP_QMMM_H // Local VOTCA includes #include "votca/xtp/parallelxjobcalc.h" namespace votca { namespace xtp { /** * \brief QM/MM with different regions around * * Calculates properties of different regions inside a multiregion calculation * * Callname: qmmm */ class QMMM final : public ParallelXJobCalc > { public: std::string Identify() { return "qmmm"; } Job::JobResult EvalJob(const Topology& top, Job& job, QMThread& Thread); void WriteJobFile(const Topology& top); void ReadJobFile(Topology& top); protected: void ParseSpecificOptions(const tools::Property& user_options); private: bool hasQMRegion() const; tools::Property _regions_def; Index _max_iterations; bool _print_regions_pdb = false; bool _write_parse = true; std::vector _states; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_QMMM_H xtp-2021.2/src/libxtp/jobtopology.cc000066400000000000000000000313421412152066400173660ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include // Local VOTCA includes #include "votca/xtp/checkpoint.h" #include "votca/xtp/jobtopology.h" #include "votca/xtp/polarregion.h" #include "votca/xtp/qmregion.h" #include "votca/xtp/segmentmapper.h" #include "votca/xtp/staticregion.h" #include "votca/xtp/version.h" namespace votca { namespace xtp { void JobTopology::SortRegionsDefbyId( std::vector& regions_def) const { std::sort(regions_def.begin(), regions_def.end(), [](const tools::Property* A, const tools::Property* B) { return (A->get("id").as()) < (B->get("id").as()); }); } void JobTopology::ModifyOptionsByJobFile( std::vector& regions_def) const { const tools::Property& jobinput = _job.getInput(); std::vector regions_def_job = jobinput.Select("regions.region"); std::string tag = "jobfile"; for (tools::Property* prop : regions_def) { Index id = prop->get("id").as(); std::vector paths = FindReplacePathsInOptions(*prop, tag); if (!paths.empty()) { XTP_LOG(Log::info, _log) << " Region " << std::to_string(id) << " is modified by jobfile" << std::flush; XTP_LOG(Log::info, _log) << " Replacing the following paths with jobfile entries" << std::flush; for (const std::string& path : paths) { XTP_LOG(Log::info, _log) << " - " << path << std::flush; } bool found_region_in_jobfile = false; const tools::Property* job_prop = nullptr; for (const tools::Property* prop_job : regions_def_job) { Index id2 = prop_job->get("id").as(); if (id2 == id) { job_prop = prop_job; found_region_in_jobfile = true; } } if (!found_region_in_jobfile) { throw std::runtime_error("Region " + std::to_string(id) + " was not found in jobfile."); } UpdateFromJobfile(*prop, *job_prop, paths); } } } void JobTopology::BuildRegions(const Topology& top, tools::Property options) { std::vector regions_def = options.Select("region"); CheckEnumerationOfRegions(regions_def); SortRegionsDefbyId(regions_def); ModifyOptionsByJobFile(regions_def); std::vector > region_seg_ids = PartitionRegions(regions_def, top); // around this point the whole jobtopology will be centered CreateRegions(options, top, region_seg_ids); XTP_LOG(Log::error, _log) << " Regions created" << std::flush; for (const auto& region : _regions) { XTP_LOG(Log::error, _log) << *region << std::flush; } return; } std::vector JobTopology::FindReplacePathsInOptions( const tools::Property& options, std::string tag) const { std::vector result; std::string options_path = "options.qmmm.regions.region"; for (const tools::Property& sub : options) { if (sub.HasChildren()) { std::vector subresult = FindReplacePathsInOptions(sub, tag); result.insert(result.end(), subresult.begin(), subresult.end()); } else if (sub.value() == tag) { std::string path = sub.path() + "." + sub.name(); std::size_t pos = path.find(options_path); if (pos != std::string::npos) { path.replace(pos, options_path.size(), ""); } result.push_back(path); } } return result; } void JobTopology::UpdateFromJobfile( tools::Property& options, const tools::Property& job_opt, const std::vector& paths) const { for (const std::string& path : paths) { if (job_opt.exists(path)) { options.set(path, job_opt.get(path).value()); } else { throw std::runtime_error("Jobfile does not contain options for " + path); } } } template void JobTopology::ShiftPBC(const Topology& top, const Eigen::Vector3d& center, T& mol) const { Eigen::Vector3d r_pbc = top.PbShortestConnect(center, mol.getPos()); Eigen::Vector3d r = mol.getPos() - center; Eigen::Vector3d shift = r_pbc - r; if (shift.norm() > 1e-9) { mol.Translate(shift); } } void JobTopology::CreateRegions( const tools::Property& options, const Topology& top, const std::vector >& region_seg_ids) { std::string mapfile = options.ifExistsReturnElseThrowRuntimeError("mapfile"); std::vector regions_def = options.Select("region"); // around this point the whole jobtopology will be centered for removing pbc Eigen::Vector3d center = top.getSegment(region_seg_ids[0][0].Id()).getPos(); for (const tools::Property* region_def : regions_def) { Index id = region_def->ifExistsReturnElseThrowRuntimeError("id"); const std::vector& seg_ids = region_seg_ids[id]; std::string type = region_def->ifExistsReturnElseThrowRuntimeError("type"); std::unique_ptr region; QMRegion QMdummy(0, _log, ""); StaticRegion Staticdummy(0, _log); PolarRegion Polardummy(0, _log); if (type == QMdummy.identify()) { std::unique_ptr qmregion = std::unique_ptr(new QMRegion(id, _log, _workdir)); QMMapper qmmapper(_log); qmmapper.LoadMappingFile(mapfile); for (const SegId& seg_index : seg_ids) { const Segment& segment = top.getSegment(seg_index.Id()); QMMolecule mol = qmmapper.map(segment, seg_index); mol.setType("qm" + std::to_string(id)); ShiftPBC(top, center, mol); qmregion->push_back(mol); } region = std::move(qmregion); } else if (type == Polardummy.identify()) { std::unique_ptr polarregion = std::unique_ptr(new PolarRegion(id, _log)); PolarMapper polmap(_log); polmap.LoadMappingFile(mapfile); for (const SegId& seg_index : seg_ids) { const Segment& segment = top.getSegment(seg_index.Id()); PolarSegment mol = polmap.map(segment, seg_index); ShiftPBC(top, center, mol); mol.setType("mm" + std::to_string(id)); polarregion->push_back(mol); } region = std::move(polarregion); } else if (type == Staticdummy.identify()) { std::unique_ptr staticregion = std::unique_ptr(new StaticRegion(id, _log)); StaticMapper staticmap(_log); staticmap.LoadMappingFile(mapfile); for (const SegId& seg_index : seg_ids) { const Segment& segment = top.getSegment(seg_index.Id()); StaticSegment mol = staticmap.map(segment, seg_index); mol.setType("mm" + std::to_string(id)); ShiftPBC(top, center, mol); staticregion->push_back(mol); } region = std::move(staticregion); } else { throw std::runtime_error("Region type not known!"); } region->Initialize(*region_def); _regions.push_back(std::move(region)); } } void JobTopology::WriteToPdb(std::string filename) const { csg::PDBWriter writer; writer.Open(filename, false); writer.WriteHeader("Job:" + std::to_string(this->_job.getId())); for (const std::unique_ptr& reg : _regions) { reg->WritePDB(writer); } writer.Close(); } std::vector > JobTopology::PartitionRegions( const std::vector& regions_def, const Topology& top) const { std::vector explicitly_named_segs_per_region; std::vector > segids_per_region; std::vector processed_segments = std::vector(top.Segments().size(), false); for (const tools::Property* region_def : regions_def) { if (!region_def->exists("segments") && !region_def->exists("cutoff")) { throw std::runtime_error( "Region definition needs either segments or a cutoff to find " "segments"); } std::vector seg_ids; if (region_def->exists("segments")) { std::string seg_ids_string = region_def->get("segments").as(); tools::Tokenizer tok(seg_ids_string, " \n\t"); for (const std::string& seg_id_string : tok.ToVector()) { seg_ids.push_back(SegId(seg_id_string)); } for (const SegId& seg_id : seg_ids) { if (seg_id.Id() > Index(top.Segments().size() - 1)) { throw std::runtime_error("Segment id is not in topology"); } processed_segments[seg_id.Id()] = true; } } explicitly_named_segs_per_region.push_back(int(seg_ids.size())); if (region_def->exists("cutoff")) { double cutoff = tools::conv::nm2bohr * region_def->ifExistsReturnElseThrowRuntimeError( "cutoff.radius"); std::string seg_geometry = region_def->ifExistsReturnElseReturnDefault( "cutoff.geometry", "n"); double min = top.getBox().diagonal().minCoeff(); if (cutoff > 0.5 * min) { throw std::runtime_error( (boost::format("Cutoff is larger than half the box size. Maximum " "allowed cutoff is %1$1.1f") % (tools::conv::bohr2nm * 0.5 * min)) .str()); } std::vector center = seg_ids; if (region_def->exists("cutoff.region")) { Index id = region_def->get("cutoff.region").as(); bool only_explicit = region_def->ifExistsReturnElseReturnDefault( "cutoff.relative_to_explicit_segs", false); if (id < Index(segids_per_region.size())) { center = segids_per_region[id]; if (only_explicit) { Index no_of_segs = explicitly_named_segs_per_region[id]; if (no_of_segs == 0) { throw std::runtime_error("Region with id '" + std::to_string(id) + "' does not have"); } center.resize(no_of_segs, SegId(0, "n")); // need the second argument because resize can also increase // capacity of vector and then needs a constructor, // here we shrink, so should not happen } } else { throw std::runtime_error("Region with id '" + std::to_string(id) + "' used for cutoff does not exist"); } } if (center.empty()) { throw std::runtime_error( "Region needs either a segment or another region to which to apply " "the cutoff"); } for (const SegId& segid : center) { const Segment& center_seg = top.getSegment(segid.Id()); for (const Segment& otherseg : top.Segments()) { if (center_seg.getId() == otherseg.getId() || processed_segments[otherseg.getId()]) { continue; } if (top.PbShortestConnect(center_seg.getPos(), otherseg.getPos()) .norm() < cutoff) { seg_ids.push_back(SegId(otherseg.getId(), seg_geometry)); processed_segments[otherseg.getId()] = true; } } } } segids_per_region.push_back(seg_ids); } return segids_per_region; } void JobTopology::CheckEnumerationOfRegions( const std::vector& regions_def) const { std::vector reg_ids; for (const tools::Property* region_def : regions_def) { reg_ids.push_back( region_def->ifExistsReturnElseThrowRuntimeError("id")); } std::vector v(reg_ids.size()); std::iota(v.begin(), v.end(), 0); if (!std::is_permutation(reg_ids.begin(), reg_ids.end(), v.begin())) { throw std::runtime_error( "Region id definitions are not clear. You must start at id 0 and then " "ascending order. i.e. 0 1 2 3."); } } void JobTopology::WriteToHdf5(std::string filename) const { CheckpointFile cpf(filename, CheckpointAccessLevel::CREATE); CheckpointWriter a = cpf.getWriter(); a(_job.getId(), "jobid"); a(XtpVersionStr(), "XTPVersion"); a(jobtopology_version(), "version"); for (const auto& region : _regions) { CheckpointWriter w = cpf.getWriter("region_" + std::to_string(region->getId())); region->WriteToCpt(w); } } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/kmccalculator.cc000066400000000000000000000224421412152066400176440ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/gnode.h" #include "votca/xtp/kmccalculator.h" #include "votca/xtp/logger.h" #include "votca/xtp/qmstate.h" #include "votca/xtp/rate_engine.h" #include "votca/xtp/topology.h" using namespace std; namespace votca { namespace xtp { void KMCCalculator::ParseCommonOptions(const tools::Property& options) { _seed = options.get(".seed").as(); _numberofcarriers = options.get(".numberofcarriers").as(); _injection_name = options.get(".injectionpattern").as(); _maxrealtime = options.get(".maxrealtime").as(); _trajectoryfile = options.get(".trajectoryfile").as(); _temperature = options.get(".temperature").as(); _temperature *= (tools::conv::kB * tools::conv::ev2hrt); _occfile = options.get(".occfile").as(); _ratefile = options.get(".ratefile").as(); _injectionmethod = options.get(".injectionmethod").as(); } void KMCCalculator::LoadGraph(Topology& top) { std::vector& segs = top.Segments(); if (segs.size() < 1) { throw std::runtime_error("Your state file contains no segments!"); } _nodes.reserve(segs.size()); for (Segment& seg : segs) { bool injectable = false; if (tools::wildcmp(_injection_name, seg.getType())) { injectable = true; } _nodes.push_back(GNode(seg, _carriertype, injectable)); } QMNBList& nblist = top.NBList(); if (nblist.size() < 1) { throw std::runtime_error("neighborlist contains no pairs!"); } if (_temperature <= 0) { throw std::runtime_error( "Your Temperature is negative or zero, please specify the temperature " "in Kelvin."); } Rate_Engine rate_engine(_temperature, _field); XTP_LOG(Log::error, _log) << "\nCalculating initial rates." << std::flush; XTP_LOG(Log::error, _log) << rate_engine << std::flush; XTP_LOG(Log::error, _log) << " carriertype: " << _carriertype.ToLongString() << std::flush; for (const QMPair* pair : nblist) { Rate_Engine::PairRates rates = rate_engine.Rate(*pair, _carriertype); _nodes[pair->Seg1()->getId()].AddEventfromQmPair(*pair, _nodes, rates.rate12); _nodes[pair->Seg2()->getId()].AddEventfromQmPair(*pair, _nodes, rates.rate21); } _RandomVariable.setMaxInt(Index(_nodes.size())); XTP_LOG(Log::error, _log) << " Rates for " << _nodes.size() << " sites are computed." << std::flush; WriteRatestoFile(_ratefile, nblist); Index events = 0; Index max = std::numeric_limits::min(); Index min = std::numeric_limits::max(); double minlength = std::numeric_limits::max(); double maxlength = 0; for (const auto& node : _nodes) { Index size = Index(node.Events().size()); for (const auto& event : node.Events()) { if (event.isDecayEvent()) { continue; } double dist = event.getDeltaR().norm(); if (dist > maxlength) { maxlength = dist; } else if (dist < minlength) { minlength = dist; } } events += size; if (size == 0) { XTP_LOG(Log::info, _log) << "Node " << node.getId() << " has 0 jumps" << std::flush; } else if (size < min) { min = size; } else if (size > max) { max = size; } } double avg = double(events) / double(_nodes.size()); double deviation = 0.0; for (const auto& node : _nodes) { double size = double(node.Events().size()); deviation += (size - avg) * (size - avg); } deviation = std::sqrt(deviation / double(_nodes.size())); XTP_LOG(Log::error, _log) << "Nblist has " << nblist.size() << " pairs. Nodes contain " << events << " jump events\n" << "with avg=" << avg << " std=" << deviation << " max=" << max << " min=" << min << " jumps per site\n" << "Minimum jumpdistance =" << minlength * tools::conv::bohr2nm << " nm Maximum distance =" << maxlength * tools::conv::bohr2nm << " nm\n" << std::flush; double conv = std::pow(tools::conv::bohr2nm, 3); XTP_LOG(Log::error, _log) << "spatial carrier density: " << double(_numberofcarriers) / (top.BoxVolume() * conv) << " nm^-3" << std::flush; for (auto& node : _nodes) { node.InitEscapeRate(); node.MakeHuffTree(); } return; } void KMCCalculator::ResetForbiddenlist( std::vector& forbiddenlist) const { forbiddenlist.clear(); return; } void KMCCalculator::AddtoForbiddenlist( GNode& node, std::vector& forbiddenlist) const { forbiddenlist.push_back(&node); return; } bool KMCCalculator::CheckForbidden( const GNode& node, const std::vector& forbiddenlist) const { bool forbidden = false; for (const GNode* fnode : forbiddenlist) { if (&node == fnode) { forbidden = true; break; } } return forbidden; } bool KMCCalculator::CheckSurrounded( const GNode& node, const std::vector& forbiddendests) const { bool surrounded = true; for (const auto& event : node.Events()) { bool thisevent_possible = true; for (const GNode* fnode : forbiddendests) { if (event.getDestination() == fnode) { thisevent_possible = false; break; } } if (thisevent_possible == true) { surrounded = false; break; } } return surrounded; } void KMCCalculator::RandomlyCreateCharges() { XTP_LOG(Log::error, _log) << "looking for injectable nodes..." << std::flush; for (Index i = 0; i < _numberofcarriers; i++) { Chargecarrier newCharge(i); RandomlyAssignCarriertoSite(newCharge); XTP_LOG(Log::error, _log) << "starting position for charge " << i << ": segment " << newCharge.getCurrentNodeId() << std::flush; _carriers.push_back(newCharge); } return; } void KMCCalculator::RandomlyAssignCarriertoSite(Chargecarrier& Charge) { Index nodeId_guess = -1; do { nodeId_guess = _RandomVariable.rand_uniform_int(); } while (_nodes[nodeId_guess].isOccupied() || _nodes[nodeId_guess].isInjectable() == false); // maybe already occupied? or maybe not injectable? if (Charge.hasNode()) { Charge.ReleaseNode(); } Charge.settoNote(&_nodes[nodeId_guess]); return; } double KMCCalculator::Promotetime(double cumulated_rate) { double dt = 0; double rand_u = 1 - _RandomVariable.rand_uniform(); dt = -1 / cumulated_rate * std::log(rand_u); return dt; } const GLink& KMCCalculator::ChooseHoppingDest(const GNode& node) { double u = 1 - _RandomVariable.rand_uniform(); return *(node.findHoppingDestination(u)); } Chargecarrier* KMCCalculator::ChooseAffectedCarrier(double cumulated_rate) { if (_carriers.size() == 1) { return &_carriers[0]; } Chargecarrier* carrier = nullptr; double u = 1 - _RandomVariable.rand_uniform(); for (Index i = 0; i < _numberofcarriers; i++) { u -= _carriers[i].getCurrentEscapeRate() / cumulated_rate; if (u <= 0 || i == _numberofcarriers - 1) { carrier = &_carriers[i]; break; } } return carrier; } void KMCCalculator::WriteRatestoFile(std::string filename, const QMNBList& nblist) { XTP_LOG(Log::error, _log) << "\nRates are written to " << filename << std::flush; fstream ratefs; ratefs.open(filename, fstream::out); ratefs << "#PairID,SiteID1,SiteID2, ,rate12[1/s],rate21[1/s] at " << _temperature * tools::conv::hrt2ev / tools::conv::kB << "K for carrier:" << _carriertype.ToString() << endl; Rate_Engine rate_engine(_temperature, _field); for (const QMPair* pair : nblist) { Rate_Engine::PairRates rates = rate_engine.Rate(*pair, _carriertype); ratefs << pair->getId() << " " << pair->Seg1()->getId() << " " << pair->Seg2()->getId() << " " << rates.rate12 << " " << rates.rate21 << "\n"; } ratefs << std::flush; ratefs.close(); } void KMCCalculator::WriteOccupationtoFile(double simtime, std::string filename) { XTP_LOG(Log::error, _log) << "\nOccupations are written to " << filename << std::flush; fstream probs; probs.open(filename, fstream::out); probs << "#SiteID, Occupation prob at " << _temperature * tools::conv::hrt2ev / tools::conv::kB << "K for carrier:" << _carriertype.ToString() << endl; for (const GNode& node : _nodes) { double occupationprobability = node.OccupationTime() / simtime; probs << node.getId() << "\t" << occupationprobability << endl; } probs.close(); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/matrixfreeoperator.cc000066400000000000000000000054641412152066400207470ustar00rootroot00000000000000 /* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/matrixfreeoperator.h" namespace votca { namespace xtp { Eigen::RowVectorXd MatrixFreeOperator::OperatorRow(Index) const { return Eigen::RowVectorXd::Zero(0); } Eigen::MatrixXd MatrixFreeOperator::OperatorBlock(Index, Index) const { return Eigen::MatrixXd::Zero(0, 0); } Eigen::VectorXd MatrixFreeOperator::diagonal() const { Eigen::VectorXd D = Eigen::VectorXd::Zero(_size); if (useRow()) { #pragma omp parallel for schedule(guided) for (Index i = 0; i < _size; i++) { Eigen::RowVectorXd row_data = this->OperatorRow(i); D(i) = row_data(i); } } if (useBlock()) { Index blocksize = getBlocksize(); if (size() % blocksize != 0) { throw std::runtime_error("blocksize is not a multiple of matrix size"); } Index blocks = size() / blocksize; // this is inefficient if blocksOperatorRow(i); } } if (useBlock()) { Index blocksize = getBlocksize(); if (size() % blocksize != 0) { throw std::runtime_error("blocksize is not a multiple of matrix size"); } Index blocks = size() / blocksize; // this is inefficient if blocks_size; } // set the size void MatrixFreeOperator::set_size(Index size) { this->_size = size; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/md2qmengine.cc000066400000000000000000000206051412152066400172250ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/md2qmengine.h" namespace votca { namespace xtp { void Md2QmEngine::CheckMappingFile(tools::Property& topology_map) const { std::string molkey = "topology.molecules.molecule"; std::vector molecules = topology_map.Select(molkey); if (SameValueForMultipleEntries(molecules, "mdname")) { throw std::runtime_error("Multiple molecules have same mdname"); } std::string segkey = "segments.segment"; std::vector segments_all; for (tools::Property* mol : molecules) { std::vector segments = mol->Select(segkey); if (SameValueForMultipleEntries(segments, "name")) { throw std::runtime_error("Multiple segments in molecule:" + mol->get("mdname").as() + " have same name"); } segments_all.insert(segments_all.end(), segments.begin(), segments.end()); for (tools::Property* seg : segments) { std::string fragkey = "fragments.fragment"; std::vector fragments = seg->Select(fragkey); if (SameValueForMultipleEntries(fragments, "name")) { throw std::runtime_error( "Multiple fragments have same name in molecule " + mol->get("mdname").as() + " segment " + seg->get("name").as()); } std::vector atomnames_seg; for (tools::Property* frag : fragments) { std::string mdatoms = frag->get("mdatoms").as(); tools::Tokenizer tok_md_atoms(mdatoms, " \t\n"); std::vector atomnames = tok_md_atoms.ToVector(); atomnames_seg.insert(atomnames_seg.end(), atomnames.begin(), atomnames.end()); } std::sort(atomnames_seg.begin(), atomnames_seg.end()); // O(N log N) if (adjacent_find(atomnames_seg.begin(), atomnames_seg.end()) != atomnames_seg.end()) { throw std::runtime_error( "Multiple mdatoms have same identifier in molecule " + mol->get("mdname").as() + " segment " + seg->get("name").as()); } } } if (SameValueForMultipleEntries(segments_all, "name")) { throw std::runtime_error("Multiple segments have same name"); } } Index Md2QmEngine::DetermineAtomNumOffset( const csg::Molecule* mol, const std::vector& atom_ids_map) const { std::vector IDs; IDs.reserve(mol->BeadCount()); for (const csg::Bead* bead : mol->Beads()) { IDs.push_back(bead->getId()); } std::sort(IDs.begin(), IDs.end()); Index offset = IDs[0] - atom_ids_map[0]; for (Index i = 1; i < Index(IDs.size()); i++) { if (IDs[i] - atom_ids_map[i] != offset) { throw std::runtime_error( "AtomIds offset could not be determined, either our MD trajectory or " "your mapping file have wrong Atom ids"); } } return offset; } bool Md2QmEngine::CheckMolWhole(const Topology& top, const Segment& seg) const { Eigen::Vector3d CoM = seg.getPos(); bool whole = true; for (const Atom& a : seg) { Eigen::Vector3d r = a.getPos() - CoM; Eigen::Vector3d r_pbc = top.PbShortestConnect(CoM, a.getPos()); Eigen::Vector3d shift = r_pbc - r; if (shift.norm() > 1e-9) { whole = false; break; } } return whole; } void Md2QmEngine::MakeSegmentsWholePBC(Topology& top) const { for (Segment& seg : top.Segments()) { seg.calcPos(); while (!CheckMolWhole(top, seg)) { Eigen::Vector3d CoM = seg.getPos(); for (Atom& a : seg) { Eigen::Vector3d r = a.getPos() - CoM; Eigen::Vector3d r_pbc = top.PbShortestConnect(CoM, a.getPos()); Eigen::Vector3d shift = r_pbc - r; if (shift.norm() > 1e-9) { a.Translate(shift); } } seg.calcPos(); } } } Topology Md2QmEngine::map(const csg::Topology& top) const { tools::Property topology_map; topology_map.LoadFromXML(_mapfile); CheckMappingFile(topology_map); Topology xtptop; xtptop.setStep(top.getStep()); xtptop.setTime(top.getTime()); xtptop.setBox(top.getBox() * tools::conv::nm2bohr, top.getBoxType()); // which segmentname does an atom belong to molname atomid std::map > MolToSegMap; // which atomids belong to molname std::map > MolToAtomIds; // names of segments in one molecule; std::map > SegsinMol; std::string molkey = "topology.molecules.molecule"; std::vector molecules = topology_map.Select(molkey); std::string segkey = "segments.segment"; for (tools::Property* mol : molecules) { std::string molname = mol->get("mdname").as(); std::vector segments = mol->Select(segkey); std::vector segnames; std::vector atomids; for (tools::Property* seg : segments) { std::string segname = seg->get("name").as(); segnames.push_back(segname); std::string fragkey = "fragments.fragment"; std::vector fragments = seg->Select(fragkey); for (tools::Property* frag : fragments) { std::string mdatoms = frag->get("mdatoms").as(); tools::Tokenizer tok_md_atoms(mdatoms, " \t\n"); std::vector atomnames; tok_md_atoms.ToVector(atomnames); for (const std::string& atomname : atomnames) { tools::Tokenizer tok_atom_name(atomname, ":"); std::vector entries = tok_atom_name.ToVector(); if (entries.size() != 3) { throw std::runtime_error("Atom entry " + atomname + " is not well formatted"); } // format should be RESNUM:ATOMNAME:ATOMID we do not care about the // first two Index atomid = 0; try { atomid = std::stoi(entries[2]); } catch (std::invalid_argument& e) { throw std::runtime_error("Atom entry " + atomname + " is not well formatted"); } atomids.push_back(atomid); MolToSegMap[molname][atomid] = segname; } } } std::sort(atomids.begin(), atomids.end()); MolToAtomIds[molname] = atomids; SegsinMol[molname] = segnames; } for (const csg::Molecule* mol : top.Molecules()) { const std::vector segnames = SegsinMol[mol->getName()]; std::map segments; // we first add them to topology // and then modify them via // pointers; for (const std::string& segname : segnames) { segments[segname] = &xtptop.AddSegment(segname); segments[segname]->AddMoleculeId(mol->getId()); } Index IdOffset = DetermineAtomNumOffset(mol, MolToAtomIds[mol->getName()]); for (const csg::Bead* bead : mol->Beads()) { Segment* seg = segments[MolToSegMap[mol->getName()][bead->getId() - IdOffset]]; Atom atom(bead->getResnr(), bead->getName(), bead->getId(), bead->getPos() * tools::conv::nm2bohr, bead->getType()); seg->push_back(atom); } } MakeSegmentsWholePBC(xtptop); return xtptop; } template bool Md2QmEngine::SameValueForMultipleEntries( const std::vector& props, std::string valuetag) const { std::vector entries; for (tools::Property* prop : props) { entries.push_back(prop->get(valuetag).as()); } std::sort(entries.begin(), entries.end()); // O(N log N) return adjacent_find(entries.begin(), entries.end()) != entries.end(); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/mmregion.cc000066400000000000000000000040461412152066400166350ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/mmregion.h" namespace votca { namespace xtp { template double MMRegion::charge() const { double charge = 0.0; for (const auto& seg : _segments) { for (const auto& site : seg) { charge += site.getCharge(); } } return charge; } template void MMRegion::WritePDB(csg::PDBWriter& writer) const { for (const auto& seg : _segments) { writer.WriteContainer(seg); } } template void MMRegion::WriteToCpt(CheckpointWriter& w) const { w(_id, "id"); w(identify(), "type"); Index size = Index(_segments.size()); w(size, "size"); CheckpointWriter ww = w.openChild("segments"); for (const auto& seg : _segments) { CheckpointWriter www = ww.openChild(seg.identify() + "_" + std::to_string(seg.getId())); seg.WriteToCpt(www); } } template void MMRegion::ReadFromCpt(CheckpointReader& r) { r(_id, "id"); Index size; r(size, "size"); _segments.clear(); _segments.reserve(size); T dummy("dummy", 0); CheckpointReader rr = r.openChild("segments"); for (Index i = 0; i < size; i++) { CheckpointReader rrr = rr.openChild(dummy.identify() + "_" + std::to_string(i)); _segments.push_back(T(rrr)); } } template class MMRegion; template class MMRegion; } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/molden.cc000066400000000000000000000206411412152066400162750ustar00rootroot00000000000000#include #include "votca/xtp/basisset.h" #include "votca/xtp/molden.h" #include namespace votca { namespace xtp { void Molden::writeAtoms(const Orbitals& orbitals, std::ofstream& outFile) const { for (const auto& atom : orbitals.QMAtoms()) { const Eigen::Vector3d& pos = atom.getPos(); outFile << boost::format("%-4s %5d %5d %22.12e %22.10e %22.10e\n") % atom.getElement() % (atom.getId() + 1) % atom.getElementNumber() % pos[0] % pos[1] % pos[2]; } } void Molden::writeMOs(const Orbitals& orbitals, std::ofstream& outFile) const { Eigen::VectorXd energies = orbitals.MOs().eigenvalues(); bool fromVotcaToExternal = true; OrbReorder reorder(_reorderList, _multipliers, fromVotcaToExternal); Eigen::MatrixXd moCoefficients = orbitals.MOs().eigenvectors(); reorder.reorderOrbitals(moCoefficients, orbitals.SetupDftBasis()); for (Index i = 0; i < orbitals.getBasisSetSize(); i++) { // over columns outFile << "Sym= \n"; outFile << boost::format("Ene= %-20.12e\n") % energies[i]; outFile << "Spin= Alpha\n"; outFile << boost::format("Occup= %-5.2f\n") % (2 * (i < orbitals.getLumo())); for (Index j = 0; j < orbitals.getBasisSetSize(); j++) { outFile << boost::format("%5d %22.12e\n") % (j + 1) % moCoefficients(j, i); } } } void Molden::writeBasisSet(const Orbitals& orbitals, std::ofstream& outFile) const { AOBasis basis = orbitals.SetupDftBasis(); for (const auto& atom : orbitals.QMAtoms()) { // The 0 in the format string of the next line is meaningless it // is included for backwards compatibility of molden files outFile << boost::format("%4d 0 \n") % (atom.getId() + 1); const std::vector shells = basis.getShellsofAtom(atom.getId()); for (const AOShell* shell : shells) { // The 1.0 at the end of the next line is meaningless it // is included for backwards compatibility of molden files outFile << boost::format("%-3s %4d %3.1f \n") % boost::to_lower_copy(EnumToString(shell->getL())) % shell->getSize() % 1.0; for (const AOGaussianPrimitive& gaussian : *shell) { outFile << boost::format("%22.10e %22.10e\n") % gaussian.getDecay() % gaussian.getContraction(); } } outFile << " \n"; } } void Molden::WriteFile(const std::string& filename, const Orbitals& orbitals) const { if (!orbitals.hasDFTbasisName()) { throw std::runtime_error(".orb file does not contain a basisset name"); } std::ofstream outFile(filename); if (outFile.is_open()) { XTP_LOG(Log::error, _log) << "Writing data to " << filename << std::flush; // print Header outFile << "[Molden Format]\n"; outFile << "[Title]\n"; outFile << "Molden file created by VOTCA-XTP\n"; outFile << " \n"; outFile << "[Atoms] AU\n"; writeAtoms(orbitals, outFile); outFile << "[GTO] \n"; writeBasisSet(orbitals, outFile); // indicate spherical D F and G functions outFile << "[5D] \n[7F] \n[9G] \n"; outFile << "[MO]\n"; writeMOs(orbitals, outFile); XTP_LOG(Log::error, _log) << "Finished writing to molden file." << std::flush; } } std::string Molden::readAtoms(QMMolecule& mol, const std::string& units, std::ifstream& input_file) const { std::string line; std::istringstream iss(" "); while (std::getline(input_file, line)) { boost::trim(line); if (line == "" || line[0] == '[') { return line; } iss.str(line); iss.clear(); // extract data double x, y, z; Index atom_id; std::string junk; std::string atom_type; iss >> atom_type >> atom_id >> junk >> x >> y >> z; atom_id = atom_id - 1; // molden uses indexing from 1, we use indexing from 0 // Add data to orbitals object Eigen::Vector3d pos(x, y, z); if (units == "Angs") { pos = tools::conv::ang2bohr * pos; } mol.push_back(QMAtom(atom_id, atom_type, pos)); } return ""; } // The returned string contains the line with the next section header // or, if it is the last section, an empty string. std::string Molden::readMOs(Orbitals& orbitals, std::ifstream& input_file) const { // setup space to store everything Index basis_size = orbitals.getBasisSetSize(); Index number_of_electrons = 0; if (basis_size == 0) { throw std::runtime_error( "Basis size not set, atoms were not parsed first."); } orbitals.MOs().eigenvalues().resize(basis_size); orbitals.MOs().eigenvectors().resize(basis_size, basis_size); // actual parsing std::string line; std::string tempStr; double tempDouble; Index tempIndex; std::istringstream iss(" "); for (Index i = 0; i < basis_size; i++) { // loop over mo's std::getline(input_file, line); // skip symmetry label // energy line std::getline(input_file, line); iss.str(line); iss.clear(); iss >> tempStr >> tempDouble; orbitals.MOs().eigenvalues()[i] = tempDouble; // spin channel line std::getline(input_file, line); iss.str(line); iss.clear(); iss >> tempStr >> tempStr; if (tempStr == "Beta") { throw std::runtime_error( "Open shell systems are currently not supported"); } // occupation line std::getline(input_file, line); iss.str(line); iss.clear(); iss >> tempStr >> tempDouble; number_of_electrons += (int)tempDouble; // MO coefficients for (int j = 0; j < basis_size; j++) { // loop over ao's std::getline(input_file, line); iss.str(line); iss.clear(); iss >> tempIndex >> tempDouble; orbitals.MOs().eigenvectors()(j, i) = tempDouble; } } orbitals.setNumberOfAlphaElectrons(number_of_electrons); orbitals.setNumberOfOccupiedLevels(number_of_electrons / 2); OrbReorder reorder(_reorderList, _multipliers); reorder.reorderOrbitals(orbitals.MOs().eigenvectors(), orbitals.SetupDftBasis()); getline(input_file, line); return line; } void Molden::addBasissetInfo(Orbitals& orbitals) const { orbitals.setDFTbasisName(_basisset_name); orbitals.setBasisSetSize(orbitals.SetupDftBasis().AOBasisSize()); orbitals.setAuxbasisName(_aux_basisset_name); } void Molden::parseMoldenFile(const std::string& filename, Orbitals& orbitals) const { if (_basisset_name == "") { throw std::runtime_error( "Basisset names should be set before reading the molden file."); } std::ifstream input_file(filename); // Check if succesfull if (input_file.fail()) { throw std::runtime_error("Could not open molden file."); } std::string line; std::getline(input_file, line); while (input_file) { boost::trim(line); if (line[0] != '[') { // ignore non-relevant lines std::getline(input_file, line); continue; } // Extract the part between square brackets long unsigned close = line.find("]"); std::string sectionType = line.substr(1, close - 1); // Import data from relevant sections if (sectionType == "Atoms") { std::string units = line.substr(close + 1); boost::trim(units); XTP_LOG(Log::error, _log) << "Reading atoms using " << units << " units." << std::flush; line = readAtoms(orbitals.QMAtoms(), units, input_file); addBasissetInfo(orbitals); } else if (sectionType == "GTO") { XTP_LOG(Log::error, _log) << "Basisset specification is ignored." << std::flush; XTP_LOG(Log::error, _log) << "Basissets are specified via the mol2orb.xml options file." << std::flush; std::getline(input_file, line); } else if (sectionType == "MO") { if (orbitals.QMAtoms().size() == 0) { throw std::runtime_error( "Atoms should be specified before MO coefficients."); } else { XTP_LOG(Log::error, _log) << "Reading molecular orbital coefficients" << std::flush; line = readMOs(orbitals, input_file); } } else if (sectionType == "STO") { throw std::runtime_error( "Slater Type Orbitals (STOs) are not supported in VOTCA-XTP."); } else { std::getline(input_file, line); } } XTP_LOG(Log::error, _log) << "Done parsing molden file" << std::flush; } } // namespace xtp } // namespace votcaxtp-2021.2/src/libxtp/nbo.cc000066400000000000000000000014661412152066400156010ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/nbo.h" namespace votca { namespace xtp {} // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/numerical_integration/000077500000000000000000000000001412152066400210675ustar00rootroot00000000000000xtp-2021.2/src/libxtp/numerical_integration/amplitude_integration.cc000066400000000000000000000040741412152066400257720ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/amplitude_integration.h" #include "votca/xtp/aopotential.h" namespace votca { namespace xtp { template std::vector > AmplitudeIntegration::IntegrateAmplitude( const Eigen::VectorXd& amplitude) { auto result = SetupAmplitudeContainer(); #pragma omp parallel for schedule(guided) for (Index i = 0; i < _grid.getBoxesSize(); ++i) { const GridBox& box = _grid[i]; if (!box.Matrixsize()) { continue; } const Eigen::VectorXd amplitude_here = box.ReadFromBigVector(amplitude); const std::vector& points = box.getGridPoints(); const std::vector& weights = box.getGridWeights(); // iterate over gridpoints for (Index p = 0; p < box.size(); p++) { Eigen::VectorXd ao = box.CalcAOValues(points[p]); result[i][p] = weights[p] * amplitude_here.dot(ao); } } return result; } template std::vector > AmplitudeIntegration::SetupAmplitudeContainer() { std::vector > amplitudes = std::vector >(_grid.getBoxesSize()); for (Index i = 0; i < _grid.getBoxesSize(); i++) { amplitudes[i] = std::vector(_grid[i].size(), 0.0); } return amplitudes; } template class AmplitudeIntegration; } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/numerical_integration/density_integration.cc000066400000000000000000000123501412152066400254610ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/density_integration.h" #include "votca/xtp/aopotential.h" namespace votca { namespace xtp { template double DensityIntegration::IntegratePotential( const Eigen::Vector3d& rvector) const { double result = 0.0; assert(!_densities.empty() && "Density not calculated"); for (Index i = 0; i < _grid.getBoxesSize(); i++) { const std::vector& points = _grid[i].getGridPoints(); const std::vector& densities = _densities[i]; for (Index j = 0; j < _grid[i].size(); j++) { double dist = (points[j] - rvector).norm(); result -= densities[j] / dist; } } return result; } template Eigen::Vector3d DensityIntegration::IntegrateField( const Eigen::Vector3d& rvector) const { Eigen::Vector3d result = Eigen::Vector3d::Zero(); assert(!_densities.empty() && "Density not calculated"); for (Index i = 0; i < _grid.getBoxesSize(); i++) { const std::vector& points = _grid[i].getGridPoints(); const std::vector& densities = _densities[i]; for (Index j = 0; j < _grid[i].size(); j++) { Eigen::Vector3d r = points[j] - rvector; result -= densities[j] * r / std::pow(r.norm(), 3); // x,y,z } } return result; } template void DensityIntegration::SetupDensityContainer() { _densities = std::vector >(_grid.getBoxesSize()); for (Index i = 0; i < _grid.getBoxesSize(); i++) { _densities[i] = std::vector(_grid[i].size(), 0.0); } } template double DensityIntegration::IntegrateDensity( const Eigen::MatrixXd& density_matrix) { double N = 0.0; SetupDensityContainer(); #pragma omp parallel for schedule(guided) reduction(+ : N) for (Index i = 0; i < _grid.getBoxesSize(); ++i) { const GridBox& box = _grid[i]; if (!box.Matrixsize()) { continue; } const Eigen::MatrixXd DMAT_here = box.ReadFromBigMatrix(density_matrix); const std::vector& points = box.getGridPoints(); const std::vector& weights = box.getGridWeights(); // iterate over gridpoints for (Index p = 0; p < box.size(); p++) { Eigen::VectorXd ao = box.CalcAOValues(points[p]); double rho = (ao.transpose() * DMAT_here * ao)(0, 0) * weights[p]; _densities[i][p] = rho; N += rho; } } return N; } template Gyrationtensor DensityIntegration::IntegrateGyrationTensor( const Eigen::MatrixXd& density_matrix) { double N = 0.0; Eigen::Vector3d centroid = Eigen::Vector3d::Zero(); Eigen::Matrix3d gyration = Eigen::Matrix3d::Zero(); SetupDensityContainer(); #pragma omp parallel for schedule(guided)reduction(+:N)reduction(+:centroid)reduction(+:gyration) for (Index i = 0; i < _grid.getBoxesSize(); ++i) { const GridBox& box = _grid[i]; if (!box.Matrixsize()) { continue; } const Eigen::MatrixXd DMAT_here = box.ReadFromBigMatrix(density_matrix); const std::vector& points = box.getGridPoints(); const std::vector& weights = box.getGridWeights(); // iterate over gridpoints for (Index p = 0; p < box.size(); p++) { Eigen::VectorXd ao = box.CalcAOValues(points[p]); double rho = (ao.transpose() * DMAT_here * ao).value() * weights[p]; _densities[i][p] = rho; N += rho; centroid += rho * points[p]; gyration += rho * points[p] * points[p].transpose(); } } // Normalize centroid = centroid / N; gyration = gyration / N; gyration = gyration - centroid * centroid.transpose(); Gyrationtensor gyro; gyro.mass = N; gyro.centroid = centroid; gyro.gyration = gyration; return gyro; } template Eigen::MatrixXd DensityIntegration::IntegratePotential( const AOBasis& externalbasis) const { Eigen::MatrixXd Potential = Eigen::MatrixXd::Zero( externalbasis.AOBasisSize(), externalbasis.AOBasisSize()); assert(!_densities.empty() && "Density not calculated"); for (Index i = 0; i < _grid.getBoxesSize(); i++) { const std::vector& points = _grid[i].getGridPoints(); const std::vector& densities = _densities[i]; for (Index j = 0; j < _grid[i].size(); j++) { if (densities[j] < 1e-12) { continue; } AOMultipole esp; esp.FillPotential(externalbasis, points[j]); Potential += densities[j] * esp.Matrix(); } } return Potential; } template class DensityIntegration; template class DensityIntegration; } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/numerical_integration/vxc_potential.cc000066400000000000000000000152761412152066400242700ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/vxc_functionals.h" #include "votca/xtp/vxc_grid.h" #include "votca/xtp/vxc_potential.h" namespace votca { namespace xtp { template Vxc_Potential::~Vxc_Potential() { if (_setXC) { xc_func_end(&xfunc); if (_use_separate) { xc_func_end(&cfunc); } } } template double Vxc_Potential::getExactExchange(const std::string& functional) { double exactexchange = 0.0; Vxc_Functionals map; tools::Tokenizer tok(functional, " "); std::vector functional_names = tok.ToVector(); if (functional_names.size() > 2) { throw std::runtime_error("Too many functional names"); } else if (functional_names.size() < 1) { throw std::runtime_error("Specify at least one functional"); } for (const std::string& functional_name : functional_names) { int func_id = map.getID(functional_name); if (func_id < 0) { exactexchange = 0.0; break; } xc_func_type func; if (xc_func_init(&func, func_id, XC_UNPOLARIZED) != 0) { throw std::runtime_error( (boost::format("Functional %s not found\n") % functional_name).str()); } if (exactexchange > 0 && func.cam_alpha > 0) { throw std::runtime_error( "You have specified two functionals with exact exchange"); } exactexchange += func.cam_alpha; xc_func_end(&func); } return exactexchange; } template void Vxc_Potential::setXCfunctional(const std::string& functional) { Vxc_Functionals map; std::vector strs; tools::Tokenizer tok(functional, " ,\n\t"); tok.ToVector(strs); xfunc_id = 0; _use_separate = false; cfunc_id = 0; if (strs.size() == 1) { xfunc_id = map.getID(strs[0]); } else if (strs.size() == 2) { xfunc_id = map.getID(strs[0]); cfunc_id = map.getID(strs[1]); _use_separate = true; } else { throw std::runtime_error( "LIBXC. Please specify one combined or an exchange and a correlation " "functionals"); } if (xc_func_init(&xfunc, xfunc_id, XC_UNPOLARIZED) != 0) { throw std::runtime_error( (boost::format("Functional %s not found\n") % strs[0]).str()); } if (xfunc.info->kind != 2 && !_use_separate) { throw std::runtime_error( "Your functional misses either correlation or exchange, please specify " "another functional, separated by whitespace"); } if (_use_separate) { if (xc_func_init(&cfunc, cfunc_id, XC_UNPOLARIZED) != 0) { throw std::runtime_error( (boost::format("Functional %s not found\n") % strs[1]).str()); } if ((xfunc.info->kind + cfunc.info->kind) != 1) { throw std::runtime_error( "Your functionals are not one exchange and one correlation"); } } _setXC = true; return; } template typename Vxc_Potential::XC_entry Vxc_Potential::EvaluateXC( double rho, double sigma) const { Vxc_Potential::XC_entry result; switch (xfunc.info->family) { case XC_FAMILY_LDA: xc_lda_exc_vxc(&xfunc, 1, &rho, &result.f_xc, &result.df_drho); break; case XC_FAMILY_GGA: case XC_FAMILY_HYB_GGA: xc_gga_exc_vxc(&xfunc, 1, &rho, &sigma, &result.f_xc, &result.df_drho, &result.df_dsigma); break; } if (_use_separate) { typename Vxc_Potential::XC_entry temp; // via libxc correlation part only switch (cfunc.info->family) { case XC_FAMILY_LDA: xc_lda_exc_vxc(&cfunc, 1, &rho, &temp.f_xc, &temp.df_drho); break; case XC_FAMILY_GGA: case XC_FAMILY_HYB_GGA: xc_gga_exc_vxc(&cfunc, 1, &rho, &sigma, &temp.f_xc, &temp.df_drho, &temp.df_dsigma); break; } result.f_xc += temp.f_xc; result.df_drho += temp.df_drho; result.df_dsigma += temp.df_dsigma; } return result; } template Mat_p_Energy Vxc_Potential::IntegrateVXC( const Eigen::MatrixXd& density_matrix) const { Mat_p_Energy vxc = Mat_p_Energy(density_matrix.rows(), density_matrix.cols()); #pragma omp parallel for schedule(guided) reduction(+ : vxc) for (Index i = 0; i < _grid.getBoxesSize(); ++i) { const GridBox& box = _grid[i]; if (!box.Matrixsize()) { continue; } double EXC_box = 0.0; const Eigen::MatrixXd DMAT_here = box.ReadFromBigMatrix(density_matrix); const Eigen::MatrixXd DMAT_symm = DMAT_here + DMAT_here.transpose(); double cutoff = 1.e-40 / double(density_matrix.rows()) / double(density_matrix.rows()); if (DMAT_here.cwiseAbs2().maxCoeff() < cutoff) { continue; } Eigen::MatrixXd Vxc_here = Eigen::MatrixXd::Zero(DMAT_here.rows(), DMAT_here.cols()); const std::vector& points = box.getGridPoints(); const std::vector& weights = box.getGridWeights(); // iterate over gridpoints for (Index p = 0; p < box.size(); p++) { Eigen::MatrixX3d ao_grad = Eigen::MatrixX3d::Zero(box.Matrixsize(), 3); Eigen::VectorXd ao = box.CalcAOValue_and_Grad(ao_grad, points[p]); const double rho = 0.5 * (ao.transpose() * DMAT_symm * ao).value(); const double weight = weights[p]; if (rho * weight < 1.e-20) { continue; // skip the rest, if density is very small } const Eigen::Vector3d rho_grad = ao.transpose() * DMAT_symm * ao_grad; const double sigma = (rho_grad.transpose() * rho_grad).value(); const Eigen::VectorXd grad = ao_grad * rho_grad; typename Vxc_Potential::XC_entry xc = EvaluateXC(rho, sigma); EXC_box += weight * rho * xc.f_xc; auto addXC = weight * (0.5 * xc.df_drho * ao + 2.0 * xc.df_dsigma * grad); Vxc_here.noalias() += addXC * ao.transpose(); } box.AddtoBigMatrix(vxc.matrix(), Vxc_here); vxc.energy() += EXC_box; } return Mat_p_Energy(vxc.energy(), vxc.matrix() + vxc.matrix().transpose()); } template class Vxc_Potential; } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/openmp_cuda.cc000066400000000000000000000200561412152066400173110ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/openmp_cuda.h" namespace votca { namespace xtp { OpenMP_CUDA::OpenMP_CUDA() { inside_Parallel_region_ = OPENMP::InsideActiveParallelRegion(); threadID_parent_ = OPENMP::getThreadId(); #ifdef USE_CUDA Index no_gpus = count_available_gpus(); gpuIDs_.resize(0); if (inside_Parallel_region_) { if (threadID_parent_ < no_gpus) { gpuIDs_.push_back(threadID_parent_); } } else { for (Index i = 0; i < no_gpus; i++) { gpuIDs_.push_back(i); } } for (Index i : gpuIDs_) { cuda_pips_.push_back(std::make_unique(int(i))); } temp_ = std::vector(gpuIDs_.size()); #endif } #ifdef USE_CUDA void OpenMP_CUDA::setOperators(const std::vector& tensor, const Eigen::MatrixXd& rightoperator) { rightoperator_ = &rightoperator; #pragma omp parallel for num_threads(gpuIDs_.size()) for (Index i = 0; i < Index(gpuIDs_.size()); i++) { const Eigen::MatrixXd& head = tensor.front(); const cudaStream_t& stream = cuda_pips_[i]->get_stream(); checkCuda(cudaSetDevice(cuda_pips_[i]->getDeviceId())); temp_[i].A = std::make_unique(head.rows(), head.cols(), stream); temp_[i].B = std::make_unique(rightoperator, stream); temp_[i].C = std::make_unique(head.rows(), rightoperator.cols(), stream); } } #else void OpenMP_CUDA::setOperators(const std::vector&, const Eigen::MatrixXd& rightoperator) { rightoperator_ = &rightoperator; } #endif bool isInVector(Index element, const std::vector& vec) { return (std::find(vec.begin(), vec.end(), element) != vec.end()); } /* * The Cuda device behaves like a server that is receiving matrix-matrix * multiplications from a single stream (an Nvidia queue) and handle them * in an asynchronous way. It performs the following operations when recieving * a request: * 1. Check that there is enough space for the arrays * 2. Allocate memory for each matrix * 3. Copy the matrix to the allocated space * 4. Perform the matrix multiplication * 5. Return the result matrix * The Cuda device knows to which memory address it needs to copy back the * result. see: https://docs.nvidia.com/cuda/cublas/index.html#thread-safety2 */ void OpenMP_CUDA::MultiplyRight(Eigen::MatrixXd& tensor) { // All the GPU communication happens through a single thread that reuses // all memory allocated in the GPU and it's dynamically load-balanced by // OpenMP. The rest of the threads use the default CPU matrix // multiplication #ifdef USE_CUDA Index threadid = inside_Parallel_region_ ? threadID_parent_ : OPENMP::getThreadId(); if (isInVector(threadid, gpuIDs_)) { if (inside_Parallel_region_) { threadid = 0; } checkCuda(cudaSetDevice(cuda_pips_[threadid]->getDeviceId())); temp_[threadid].A->copy_to_gpu(tensor); cuda_pips_[threadid]->gemm(*temp_[threadid].A, *temp_[threadid].B, *temp_[threadid].C); tensor = *temp_[threadid].C; } else { tensor *= *rightoperator_; } #else tensor *= *rightoperator_; #endif return; } void OpenMP_CUDA::setOperators(const Eigen::MatrixXd& leftoperator, const Eigen::MatrixXd& rightoperator) { rightoperator_ = &rightoperator; leftoperator_ = &leftoperator; #ifdef USE_CUDA #pragma omp parallel for num_threads(gpuIDs_.size()) for (Index i = 0; i < Index(gpuIDs_.size()); i++) { const cudaStream_t& stream = cuda_pips_[i]->get_stream(); checkCuda(cudaSetDevice(cuda_pips_[i]->getDeviceId())); temp_[i].A = std::make_unique(leftoperator, stream); temp_[i].B = std::make_unique(leftoperator.cols(), rightoperator.rows(), stream); temp_[i].C = std::make_unique(leftoperator.rows(), rightoperator.rows(), stream); temp_[i].D = std::make_unique(rightoperator, stream); temp_[i].E = std::make_unique(leftoperator.rows(), rightoperator.cols(), stream); } #endif } void OpenMP_CUDA::MultiplyLeftRight(Eigen::MatrixXd& matrix) { #ifdef USE_CUDA Index threadid = inside_Parallel_region_ ? threadID_parent_ : OPENMP::getThreadId(); if (isInVector(threadid, gpuIDs_)) { if (inside_Parallel_region_) { threadid = 0; } checkCuda(cudaSetDevice(cuda_pips_[threadid]->getDeviceId())); temp_[threadid].B->copy_to_gpu(matrix); cuda_pips_[threadid]->gemm(*temp_[threadid].A, *temp_[threadid].B, *temp_[threadid].C); cuda_pips_[threadid]->gemm(*temp_[threadid].C, *temp_[threadid].D, *temp_[threadid].E); matrix = *temp_[threadid].E; } else { matrix = (*leftoperator_) * matrix * (*rightoperator_); } #else matrix = (*leftoperator_) * matrix * (*rightoperator_); #endif return; } #ifdef USE_CUDA void OpenMP_CUDA::createTemporaries(Index rows, Index cols) { Index size = inside_Parallel_region_ ? 1 : OPENMP::getMaxThreads(); reduction_ = std::vector(size, Eigen::MatrixXd::Zero(cols, cols)); #pragma omp parallel for num_threads(gpuIDs_.size()) for (Index i = 0; i < Index(gpuIDs_.size()); i++) { checkCuda(cudaSetDevice(cuda_pips_[i]->getDeviceId())); const cudaStream_t& stream = cuda_pips_[i]->get_stream(); temp_[i].A = std::make_unique(rows, 1, stream); temp_[i].B = std::make_unique(rows, cols, stream); temp_[i].C = std::make_unique(rows, cols, stream); temp_[i].D = std::make_unique(reduction_[i], stream); } } #else void OpenMP_CUDA::createTemporaries(Index, Index cols) { Index size = inside_Parallel_region_ ? 1 : OPENMP::getMaxThreads(); reduction_ = std::vector(size, Eigen::MatrixXd::Zero(cols, cols)); } #endif void OpenMP_CUDA::A_TDA(const Eigen::MatrixXd& matrix, const Eigen::VectorXd& vec) { Index threadid = inside_Parallel_region_ ? threadID_parent_ : OPENMP::getThreadId(); #ifdef USE_CUDA if (isInVector(threadid, gpuIDs_)) { if (inside_Parallel_region_) { threadid = 0; } checkCuda(cudaSetDevice(cuda_pips_[threadid]->getDeviceId())); temp_[threadid].A->copy_to_gpu(vec); temp_[threadid].B->copy_to_gpu(matrix); cuda_pips_[threadid]->diag_gemm(*temp_[threadid].B, *temp_[threadid].A, *temp_[threadid].C); cuda_pips_[threadid]->gemm(*temp_[threadid].B, *temp_[threadid].C, *temp_[threadid].D, true, false, 1.0); } else { if (inside_Parallel_region_) { threadid = 0; } reduction_[threadid] += matrix.transpose() * vec.asDiagonal() * matrix; } #else if (inside_Parallel_region_) { threadid = 0; } reduction_[threadid] += matrix.transpose() * vec.asDiagonal() * matrix; #endif } Eigen::MatrixXd OpenMP_CUDA::A_TDA_result() { #ifdef USE_CUDA #pragma omp parallel for num_threads(gpuIDs_.size()) for (Index i = 0; i < Index(gpuIDs_.size()); i++) { checkCuda(cudaSetDevice(cuda_pips_[i]->getDeviceId())); reduction_[i] = *temp_[i].D; } #endif for (Index i = 1; i < Index(reduction_.size()); i++) { reduction_[0] += reduction_[i]; } return reduction_[0]; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/orbitals.cc000066400000000000000000000521351412152066400166410ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include #include #include #include // Local VOTCA includes #include "votca/xtp/aomatrix.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/orbreorder.h" #include "votca/xtp/qmstate.h" #include "votca/xtp/vc2index.h" #include "votca/xtp/version.h" namespace votca { namespace xtp { Orbitals::Orbitals() : _atoms("", 0) { ; } /** * * @param _energy_difference [ev] Two levels are degenerate if their energy is * smaller than this value * @return vector with indices off all orbitals degenerate to this including * itself */ std::vector Orbitals::CheckDegeneracy(Index level, double energy_difference) const { std::vector result; if (level > _mos.eigenvalues().size()) { throw std::runtime_error( "Level for degeneracy is higher than maximum level"); } double MOEnergyLevel = _mos.eigenvalues()(level); for (Index i = 0; i < _mos.eigenvalues().size(); ++i) { if (std::abs(_mos.eigenvalues()(i) - MOEnergyLevel) < energy_difference) { result.push_back(i); } } if (result.empty()) { result.push_back(level); } return result; } std::vector Orbitals::SortEnergies() { std::vector index = std::vector(_mos.eigenvalues().size()); std::iota(index.begin(), index.end(), 0); std::stable_sort(index.begin(), index.end(), [this](Index i1, Index i2) { return this->MOs().eigenvalues()[i1] < this->MOs().eigenvalues()[i2]; }); return index; } Eigen::MatrixXd Orbitals::DensityMatrixFull(const QMState& state) const { if (state.isTransition()) { return this->TransitionDensityMatrix(state); } Eigen::MatrixXd result = this->DensityMatrixGroundState(); if (state.Type().isExciton()) { std::array DMAT = DensityMatrixExcitedState(state); result = result - DMAT[0] + DMAT[1]; // Ground state + hole_contribution + // electron contribution } else if (state.Type() == QMStateType::DQPstate) { Eigen::MatrixXd DMATQP = DensityMatrixQuasiParticle(state); if (state.StateIdx() > getHomo()) { result += DMATQP; } else { result -= DMATQP; } } else if (state.Type() != QMStateType::Gstate) { throw std::runtime_error( "DensityMatrixFull does not yet implement QMStateType:" + state.Type().ToLongString()); } return result; } // Determine ground state density matrix Eigen::MatrixXd Orbitals::DensityMatrixGroundState() const { if (!hasMOs()) { throw std::runtime_error("Orbitals file does not contain MO coefficients"); } Eigen::MatrixXd occstates = _mos.eigenvectors().leftCols(_occupied_levels); Eigen::MatrixXd dmatGS = 2.0 * occstates * occstates.transpose(); return dmatGS; } Eigen::MatrixXd Orbitals::CalculateQParticleAORepresentation() const { if (!hasQPdiag()) { throw std::runtime_error("Orbitals file does not contain QP coefficients"); } return _mos.eigenvectors().block(0, _qpmin, _mos.eigenvectors().rows(), _qpmax - _qpmin + 1) * _QPdiag.eigenvectors(); } // Determine QuasiParticle Density Matrix Eigen::MatrixXd Orbitals::DensityMatrixQuasiParticle( const QMState& state) const { if (state.Type() != QMStateType::DQPstate) { throw std::runtime_error("State:" + state.ToString() + " is not a quasiparticle state"); } Eigen::MatrixXd lambda = CalculateQParticleAORepresentation(); Eigen::MatrixXd dmatQP = lambda.col(state.StateIdx() - _qpmin) * lambda.col(state.StateIdx() - _qpmin).transpose(); return dmatQP; } Eigen::Vector3d Orbitals::CalcElDipole(const QMState& state) const { Eigen::Vector3d nuclei_dip = Eigen::Vector3d::Zero(); if (!state.isTransition()) { for (const QMAtom& atom : _atoms) { nuclei_dip += (atom.getPos() - _atoms.getPos()) * atom.getNuccharge(); } } AOBasis basis = SetupDftBasis(); AODipole dipole; dipole.setCenter(_atoms.getPos()); dipole.Fill(basis); Eigen::MatrixXd dmat = this->DensityMatrixFull(state); Eigen::Vector3d electronic_dip; for (Index i = 0; i < 3; ++i) { electronic_dip(i) = dmat.cwiseProduct(dipole.Matrix()[i]).sum(); } return nuclei_dip - electronic_dip; } Eigen::MatrixXd Orbitals::TransitionDensityMatrix(const QMState& state) const { if (state.Type() != QMStateType::Singlet) { throw std::runtime_error( "Spin type not known for transition density matrix. Available only for " "singlet"); } const Eigen::MatrixXd& BSECoefs = _BSE_singlet.eigenvectors(); if (BSECoefs.cols() < state.StateIdx() + 1 || BSECoefs.rows() < 2) { throw std::runtime_error("Orbitals object has no information about state:" + state.ToString()); } // The Transition dipole is sqrt2 bigger because of the spin, the excited // state is a linear combination of 2 slater determinants, where either alpha // or beta spin electron is excited /*Trying to implement D_{alpha,beta}= * sqrt2*sum_{i}^{occ}sum_{j}^{virt}{BSEcoef(i,j)*MOcoef(alpha,i)*MOcoef(beta,j)} */ // c stands for conduction band and thus virtual orbitals // v stand for valence band and thus occupied orbitals Eigen::VectorXd coeffs = BSECoefs.col(state.StateIdx()); if (!_useTDA) { coeffs += _BSE_singlet.eigenvectors2().col(state.StateIdx()); } coeffs *= std::sqrt(2.0); auto occlevels = _mos.eigenvectors().block( 0, _bse_vmin, _mos.eigenvectors().rows(), _bse_vtotal); auto virtlevels = _mos.eigenvectors().block( 0, _bse_cmin, _mos.eigenvectors().rows(), _bse_ctotal); Eigen::Map mat(coeffs.data(), _bse_ctotal, _bse_vtotal); return occlevels * mat.transpose() * virtlevels.transpose(); } std::array Orbitals::DensityMatrixExcitedState( const QMState& state) const { std::array dmat = DensityMatrixExcitedState_R(state); if (!_useTDA) { std::array dmat_AR = DensityMatrixExcitedState_AR(state); dmat[0] -= dmat_AR[0]; dmat[1] -= dmat_AR[1]; } return dmat; } // Excited state density matrix std::array Orbitals::DensityMatrixExcitedState_R( const QMState& state) const { if (!state.Type().isExciton()) { throw std::runtime_error( "Spin type not known for density matrix. Available are singlet and " "triplet"); } const Eigen::MatrixXd& BSECoefs = (state.Type() == QMStateType::Singlet) ? _BSE_singlet.eigenvectors() : _BSE_triplet.eigenvectors(); if (BSECoefs.cols() < state.StateIdx() + 1 || BSECoefs.rows() < 2) { throw std::runtime_error("Orbitals object has no information about state:" + state.ToString()); } /****** * * Density matrix for GW-BSE based excitations * * - electron contribution * D_ab = \sum{vc} \sum{c'} A_{vc}A_{vc'} mo_a(c)mo_b(c') * * - hole contribution * D_ab = \sum{vc} \sum{v'} A_{vc}A_{v'c} mo_a(v)mo_b(v') * */ Eigen::VectorXd coeffs = BSECoefs.col(state.StateIdx()); std::array dmatEX; // hole part as matrix products Eigen::MatrixXd occlevels = _mos.eigenvectors().block( 0, _bse_vmin, _mos.eigenvectors().rows(), _bse_vtotal); dmatEX[0] = occlevels * CalcAuxMat_vv(coeffs) * occlevels.transpose(); // electron part as matrix products Eigen::MatrixXd virtlevels = _mos.eigenvectors().block( 0, _bse_cmin, _mos.eigenvectors().rows(), _bse_ctotal); dmatEX[1] = virtlevels * CalcAuxMat_cc(coeffs) * virtlevels.transpose(); return dmatEX; } Eigen::MatrixXd Orbitals::CalcAuxMat_vv(const Eigen::VectorXd& coeffs) const { const Eigen::Map mat(coeffs.data(), _bse_ctotal, _bse_vtotal); return mat.transpose() * mat; } Eigen::MatrixXd Orbitals::CalcAuxMat_cc(const Eigen::VectorXd& coeffs) const { const Eigen::Map mat(coeffs.data(), _bse_ctotal, _bse_vtotal); return mat * mat.transpose(); } std::array Orbitals::DensityMatrixExcitedState_AR( const QMState& state) const { if (!state.Type().isExciton()) { throw std::runtime_error( "Spin type not known for density matrix. Available are singlet and " "triplet"); } const Eigen::MatrixXd& BSECoefs_AR = (state.Type() == QMStateType::Singlet) ? _BSE_singlet.eigenvectors2() : _BSE_triplet.eigenvectors2(); if (BSECoefs_AR.cols() < state.StateIdx() + 1 || BSECoefs_AR.rows() < 2) { throw std::runtime_error("Orbitals object has no information about state:" + state.ToString()); } /****** * * Density matrix for GW-BSE based excitations * * - electron contribution * D_ab = \sum{vc} \sum{v'} B_{vc}B_{v'c} mo_a(v)mo_b(v') * * - hole contribution * D_ab = \sum{vc} \sum{c'} B_{vc}B_{vc'} mo_a(c)mo_b(c') * * * more efficient: * * - electron contribution * D_ab = \sum{v} \sum{v'} mo_a(v)mo_b(v') [ \sum{c} B_{vc}B_{v'c} ] * = \sum{v} \sum{v'} mo_a(v)mo_b(v') B_{vv'} * * - hole contribution * D_ab = \sum{c} \sum{c'} mo_a(c)mo_b(c') [ \sum{v} B_{vc}B_{vc'} ] * = \sum{c} \sum{c'} mo_a(c)mo_b(c') B_{cc'} * */ Eigen::VectorXd coeffs = BSECoefs_AR.col(state.StateIdx()); std::array dmatAR; Eigen::MatrixXd virtlevels = _mos.eigenvectors().block( 0, _bse_cmin, _mos.eigenvectors().rows(), _bse_ctotal); dmatAR[0] = virtlevels * CalcAuxMat_cc(coeffs) * virtlevels.transpose(); // electron part as matrix products Eigen::MatrixXd occlevels = _mos.eigenvectors().block( 0, _bse_vmin, _mos.eigenvectors().rows(), _bse_vtotal); dmatAR[1] = occlevels * CalcAuxMat_vv(coeffs) * occlevels.transpose(); return dmatAR; } Eigen::VectorXd Orbitals::Oscillatorstrengths() const { Index size = Index(_transition_dipoles.size()); if (size > _BSE_singlet.eigenvalues().size()) { size = _BSE_singlet.eigenvalues().size(); } Eigen::VectorXd oscs = Eigen::VectorXd::Zero(size); for (Index i = 0; i < size; ++i) { oscs(i) = _transition_dipoles[i].squaredNorm() * 2.0 / 3.0 * (_BSE_singlet.eigenvalues()(i)); } return oscs; } double Orbitals::getTotalStateEnergy(const QMState& state) const { double total_energy = getDFTTotalEnergy(); if (state.Type() == QMStateType::Gstate) { return total_energy; } total_energy += getExcitedStateEnergy(state); return total_energy; } double Orbitals::getExcitedStateEnergy(const QMState& state) const { double omega = 0.0; if (state.isTransition()) { throw std::runtime_error( "Total Energy does not exist for transition state"); } if (state.Type() == QMStateType::Singlet) { if (_BSE_singlet.eigenvalues().size() < state.StateIdx() + 1) { throw std::runtime_error("Orbitals::getTotalEnergy You want " + state.ToString() + " which has not been calculated"); } omega = _BSE_singlet.eigenvalues()[state.StateIdx()]; } else if (state.Type() == QMStateType::Triplet) { if (_BSE_triplet.eigenvalues().size() < state.StateIdx() + 1) { throw std::runtime_error("Orbitals::getTotalEnergy You want " + state.ToString() + " which has not been calculated"); } omega = _BSE_triplet.eigenvalues()[state.StateIdx()]; } else if (state.Type() == QMStateType::DQPstate) { if (_QPdiag.eigenvalues().size() < state.StateIdx() + 1 - getGWAmin()) { throw std::runtime_error("Orbitals::getTotalEnergy You want " + state.ToString() + " which has not been calculated"); } return _QPdiag.eigenvalues()[state.StateIdx() - getGWAmin()]; } else if (state.Type() == QMStateType::KSstate) { if (_mos.eigenvalues().size() < state.StateIdx() + 1) { throw std::runtime_error("Orbitals::getTotalEnergy You want " + state.ToString() + " which has not been calculated"); } return _mos.eigenvalues()[state.StateIdx()]; } else if (state.Type() == QMStateType::PQPstate) { if (this->_QPpert_energies.rows() < state.StateIdx() + 1 - getGWAmin()) { throw std::runtime_error("Orbitals::getTotalEnergy You want " + state.ToString() + " which has not been calculated"); } return _QPpert_energies(state.StateIdx() - getGWAmin(), 3); } else { throw std::runtime_error( "GetTotalEnergy only knows states:singlet,triplet,KS,DQP,PQP"); } return omega; // e.g. hartree } std::array Orbitals::CalcFreeTransition_Dipoles() const { const Eigen::MatrixXd& dft_orbitals = _mos.eigenvectors(); AOBasis basis = SetupDftBasis(); // Testing electric dipole AOMatrix AODipole dft_dipole; dft_dipole.Fill(basis); // now transition dipole elements for free interlevel transitions std::array interlevel_dipoles; Eigen::MatrixXd empty = dft_orbitals.block(0, _bse_cmin, basis.AOBasisSize(), _bse_ctotal); Eigen::MatrixXd occ = dft_orbitals.block(0, _bse_vmin, basis.AOBasisSize(), _bse_vtotal); for (Index i = 0; i < 3; i++) { interlevel_dipoles[i] = empty.transpose() * dft_dipole.Matrix()[i] * occ; } return interlevel_dipoles; } void Orbitals::CalcCoupledTransition_Dipoles() { std::array interlevel_dipoles = CalcFreeTransition_Dipoles(); Index numofstates = _BSE_singlet.eigenvalues().size(); _transition_dipoles.resize(0); _transition_dipoles.reserve(numofstates); const double sqrt2 = sqrt(2.0); for (Index i_exc = 0; i_exc < numofstates; i_exc++) { Eigen::VectorXd coeffs = _BSE_singlet.eigenvectors().col(i_exc); if (!_useTDA) { coeffs += _BSE_singlet.eigenvectors2().col(i_exc); } Eigen::Map mat(coeffs.data(), _bse_ctotal, _bse_vtotal); Eigen::Vector3d tdipole = Eigen::Vector3d::Zero(); for (Index i = 0; i < 3; i++) { tdipole[i] = mat.cwiseProduct(interlevel_dipoles[i]).sum(); } // The Transition dipole is sqrt2 bigger because of the spin, the // excited state is a linear combination of 2 slater determinants, // where either alpha or beta spin electron is excited _transition_dipoles.push_back(-sqrt2 * tdipole); //- because electrons are // negative } } void Orbitals::OrderMOsbyEnergy() { std::vector sort_index = SortEnergies(); tools::EigenSystem MO_copy = _mos; Index size = _mos.eigenvalues().size(); for (Index i = 0; i < size; ++i) { _mos.eigenvalues()(i) = MO_copy.eigenvalues()(sort_index[i]); } for (Index i = 0; i < size; ++i) { _mos.eigenvectors().col(i) = MO_copy.eigenvectors().col(sort_index[i]); } } /** * \brief Guess for a dimer based on monomer orbitals * * Given two monomer orbitals (A and B) constructs a guess for dimer * orbitals: | A 0 | and energies: [EA, EB] * | 0 B | */ void Orbitals::PrepareDimerGuess(const Orbitals& orbitalsA, const Orbitals& orbitalsB) { // constructing the direct product orbA x orbB Index basisA = orbitalsA.getBasisSetSize(); Index basisB = orbitalsB.getBasisSetSize(); Index electronsA = orbitalsA.getNumberOfAlphaElectrons(); Index electronsB = orbitalsB.getNumberOfAlphaElectrons(); _mos.eigenvectors() = Eigen::MatrixXd::Zero(basisA + basisB, basisA + basisB); // AxB = | A 0 | // A = [EA, EB] // // | 0 B | // // if (orbitalsA.getDFTbasisName() != orbitalsB.getDFTbasisName()) { throw std::runtime_error("Basissets of Orbitals A and B differ " + orbitalsA.getDFTbasisName() + ":" + orbitalsB.getDFTbasisName()); } this->setDFTbasisName(orbitalsA.getDFTbasisName()); if (orbitalsA.getECPName() != orbitalsB.getECPName()) { throw std::runtime_error("ECPs of Orbitals A and B differ " + orbitalsA.getECPName() + ":" + orbitalsB.getECPName()); } this->setECPName(orbitalsA.getECPName()); this->setBasisSetSize(basisA + basisB); this->setNumberOfOccupiedLevels(electronsA + electronsB); this->setNumberOfAlphaElectrons(electronsA + electronsB); _mos.eigenvectors().topLeftCorner(basisA, basisA) = orbitalsA.MOs().eigenvectors(); _mos.eigenvectors().bottomRightCorner(basisB, basisB) = orbitalsB.MOs().eigenvectors(); _mos.eigenvalues().resize(basisA + basisB); _mos.eigenvalues().head(basisA) = orbitalsA.MOs().eigenvalues(); _mos.eigenvalues().tail(basisB) = orbitalsB.MOs().eigenvalues(); OrderMOsbyEnergy(); return; } void Orbitals::WriteToCpt(const std::string& filename) const { CheckpointFile cpf(filename, CheckpointAccessLevel::CREATE); WriteToCpt(cpf); } void Orbitals::WriteToCpt(CheckpointFile f) const { WriteToCpt(f.getWriter("/QMdata")); } void Orbitals::WriteToCpt(CheckpointWriter w) const { w(XtpVersionStr(), "XTPVersion"); w(orbitals_version(), "version"); w(_basis_set_size, "basis_set_size"); w(_occupied_levels, "occupied_levels"); w(_number_alpha_electrons, "number_alpha_electrons"); w(_mos, "mos"); CheckpointWriter molgroup = w.openChild("qmmolecule"); _atoms.WriteToCpt(molgroup); w(_qm_energy, "qm_energy"); w(_qm_package, "qm_package"); w(_dftbasis, "dftbasis"); w(_auxbasis, "auxbasis"); w(_rpamin, "rpamin"); w(_rpamax, "rpamax"); w(_qpmin, "qpmin"); w(_qpmax, "qpmax"); w(_bse_vmin, "bse_vmin"); w(_bse_cmax, "bse_cmax"); w(_functionalname, "XCFunctional"); w(_ScaHFX, "ScaHFX"); w(_useTDA, "useTDA"); w(_ECP, "ECP"); w(_rpa_inputenergies, "RPA_inputenergies"); w(_QPpert_energies, "QPpert_energies"); w(_QPdiag, "QPdiag"); w(_BSE_singlet, "BSE_singlet"); w(_transition_dipoles, "transition_dipoles"); w(_BSE_triplet, "BSE_triplet"); w(_use_Hqp_offdiag, "use_Hqp_offdiag"); w(_BSE_singlet_energies_dynamic, "BSE_singlet_dynamic"); w(_BSE_triplet_energies_dynamic, "BSE_triplet_dynamic"); } void Orbitals::ReadFromCpt(const std::string& filename) { CheckpointFile cpf(filename, CheckpointAccessLevel::READ); ReadFromCpt(cpf); } void Orbitals::ReadFromCpt(CheckpointFile f) { ReadFromCpt(f.getReader("/QMdata")); } void Orbitals::ReadFromCpt(CheckpointReader r) { r(_basis_set_size, "basis_set_size"); r(_occupied_levels, "occupied_levels"); r(_number_alpha_electrons, "number_alpha_electrons"); int version; r(version, "version"); // Read qmatoms CheckpointReader molgroup = r.openChild("qmmolecule"); _atoms.ReadFromCpt(molgroup); r(_qm_energy, "qm_energy"); r(_qm_package, "qm_package"); r(_dftbasis, "dftbasis"); r(_auxbasis, "auxbasis"); r(version, "version"); r(_mos, "mos"); if (version < 3) { // clang-format off std::array votcaOrder_old = { 0, // s 0, -1, 1, // p 0, -1, 1, -2, 2, // d 0, -1, 1, -2, 2, -3, 3, // f 0, -1, 1, -2, 2, -3, 3, -4, 4, // g 0, -1, 1, -2, 2, -3, 3, -4, 4,-5,5, // h 0, -1, 1, -2, 2, -3, 3, -4, 4,-5,5,-6,6 // i }; // clang-format on std::array multiplier; multiplier.fill(1); OrbReorder ord(votcaOrder_old, multiplier); ord.reorderOrbitals(_mos.eigenvectors(), this->SetupDftBasis()); } r(_rpamin, "rpamin"); r(_rpamax, "rpamax"); r(_qpmin, "qpmin"); r(_qpmax, "qpmax"); r(_bse_vmin, "bse_vmin"); r(_bse_cmax, "bse_cmax"); setBSEindices(_bse_vmin, _bse_cmax); try { r(_functionalname, "XCFunctional"); } catch (std::runtime_error& e) { ; } r(_ScaHFX, "ScaHFX"); r(_useTDA, "useTDA"); r(_ECP, "ECP"); r(_rpa_inputenergies, "RPA_inputenergies"); r(_QPpert_energies, "QPpert_energies"); r(_QPdiag, "QPdiag"); r(_BSE_singlet, "BSE_singlet"); r(_transition_dipoles, "transition_dipoles"); r(_BSE_triplet, "BSE_triplet"); r(_use_Hqp_offdiag, "use_Hqp_offdiag"); if (version > 1) { r(_BSE_singlet_energies_dynamic, "BSE_singlet_dynamic"); r(_BSE_triplet_energies_dynamic, "BSE_triplet_dynamic"); } } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/orbreorder.cc000066400000000000000000000103621412152066400171630ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/orbreorder.h" #include "votca/xtp/basisset.h" namespace votca { namespace xtp { std::vector OrbReorder::computeTranspositions( std::vector vStart, std::vector vTarget) const { if (vStart.size() != vTarget.size()) { throw std::runtime_error( "Can't compute transpositions, reorder vectors have different " "size!\n"); } std::vector transpositions; for (Index i = 0; i < static_cast(vStart.size()); i++) { std::vector::iterator it; it = std::find(vStart.begin(), vStart.end(), vTarget[i]); Index pos = std::distance(vStart.begin(), it); std::swap(vStart[i], vStart[pos]); if (i != pos) { transpositions.push_back(Transposition{i, pos}); } } return transpositions; } std::vector OrbReorder::copySegment(const std::array& input, Index start, Index size) const { return std::vector{input.begin() + start, input.begin() + start + size}; } OrbReorder::OrbReorder(std::array reorder, std::array multipliers, bool reverse) : _multipliers(multipliers), _reorder(reorder), _reverse(reverse) { // Compute transpositions for every individual shell Index currentFunction = 0; for (int l = 0; l < 7; l++) { Index nrOfFunctions = NumFuncShell(static_cast(l)); if (!_reverse) { // ordering from external to votca order _transpositions[l] = computeTranspositions( copySegment(_reorder, currentFunction, nrOfFunctions), copySegment(_votcaOrder, currentFunction, nrOfFunctions)); } else { // votca order to external order _transpositions[l] = computeTranspositions( copySegment(_votcaOrder, currentFunction, nrOfFunctions), copySegment(_reorder, currentFunction, nrOfFunctions)); } currentFunction += nrOfFunctions; } } void OrbReorder::reorderOrbitals(Eigen::MatrixXd& moCoefficients, const AOBasis& basis) { for (const AOShell& shell : basis) { Index currentFunction = shell.getStartIndex(); if (_reverse) { // multiply first before reversing ordering // Get multiplier vector for shell std::vector shellmultiplier = copySegment(_multipliers, shell.getOffset(), shell.getNumFunc()); // multiply shell for (Index i = 0; i < shell.getNumFunc(); i++) { moCoefficients.row(currentFunction + i) *= double(shellmultiplier[i]); } } // reorder shell Index l = static_cast(shell.getL()); for (const Transposition& transposition : _transpositions[l]) { moCoefficients.row(currentFunction + transposition.first) .swap(moCoefficients.row(currentFunction + transposition.second)); } if (!_reverse) { // multiply after reordering // Get multiplier vector for shell std::vector shellmultiplier = copySegment(_multipliers, shell.getOffset(), shell.getNumFunc()); // multiply shell for (Index i = 0; i < shell.getNumFunc(); i++) { moCoefficients.row(currentFunction + i) *= double(shellmultiplier[i]); } } } } void OrbReorder::reorderOperator(Eigen::MatrixXd& Matrixoperator, const AOBasis& basis) { // reorder rows first reorderOrbitals(Matrixoperator, basis); Matrixoperator.transposeInPlace(); reorderOrbitals(Matrixoperator, basis); Matrixoperator.transposeInPlace(); } } // namespace xtp } // namespace votcaxtp-2021.2/src/libxtp/parallelxjobcalc.cc000066400000000000000000000126701412152066400203240ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ /// For an earlier history see ctp repo commit /// 77795ea591b29e664153f9404c8655ba28dc14e9 // Third party includes #include #include #include // Local VOTCA includes #include "votca/xtp/parallelxjobcalc.h" using boost::format; namespace votca { namespace xtp { template bool ParallelXJobCalc::Evaluate(const Topology &top) { libint2::initialize(); // INITIALIZE PROGRESS OBSERVER std::string progFile = _jobfile; std::unique_ptr master = std::unique_ptr( new JobOperator(-1, top, *this, _openmp_threads)); master->getLogger().setReportLevel(Log::current_level); master->getLogger().setMultithreading(true); master->getLogger().setPreface(Log::info, "\nMST INF"); master->getLogger().setPreface(Log::error, "\nMST ERR"); master->getLogger().setPreface(Log::warning, "\nMST WAR"); master->getLogger().setPreface(Log::debug, "\nMST DBG"); _progObs->InitFromProgFile(progFile, *(master.get())); // CREATE + EXECUTE THREADS (XJOB HANDLERS) std::vector> jobOps; for (Index id = 0; id < _nThreads; id++) { jobOps.push_back(std::unique_ptr( new JobOperator(id, top, *this, _openmp_threads))); } for (Index id = 0; id < _nThreads; ++id) { CustomizeLogger(*jobOps[id]); } if (!_maverick) { std::cout << std::endl; // REQUIRED FOR PROGRESS BAR IN OBSERVER } for (Index id = 0; id < _nThreads; id++) { jobOps[id]->Start(); } for (Index id = 0; id < _nThreads; id++) { jobOps[id]->WaitDone(); } if (!_maverick) { for (Index id = 0; id < _nThreads; id++) { std::cout << std::endl << (jobOps[id]->getLogger()) << std::flush; } } jobOps.clear(); // SYNC REMAINING COMPLETE JOBS _progObs->SyncWithProgFile(*(master.get())); libint2::finalize(); return true; } template void ParallelXJobCalc::JobOperator::Run() { OPENMP::setMaxThreads(_openmp_threads); while (true) { Job *job = _master._progObs->RequestNextJob(*this); if (job == nullptr) { break; } else { Result res = this->_master.EvalJob(_top, *job, *this); this->_master._progObs->ReportJobDone(*job, res, *this); } } } template void ParallelXJobCalc::ParseCommonOptions( const tools::Property &options) { std::cout << "\n... ... Initialized with " << _nThreads << " threads.\n"; _maverick = (_nThreads == 1) ? true : false; std::cout << "\n... ... Using " << _openmp_threads << " openmp threads for " << _nThreads << "x" << _openmp_threads << "=" << _nThreads * _openmp_threads << " total threads." << std::flush; _jobfile = options.get(".job_file").as(); _mapfile = options.get(".map_file").as(); } template void ParallelXJobCalc::CustomizeLogger(QMThread &thread) { // CONFIGURE LOGGER Logger &log = thread.getLogger(); log.setReportLevel(Log::current_level); log.setMultithreading(_maverick); log.setPreface(Log::info, (format("\nT%1$02d INF ...") % thread.getId()).str()); log.setPreface(Log::error, (format("\nT%1$02d ERR ...") % thread.getId()).str()); log.setPreface(Log::warning, (format("\nT%1$02d WAR ...") % thread.getId()).str()); log.setPreface(Log::debug, (format("\nT%1$02d DBG ...") % thread.getId()).str()); } template tools::Property ParallelXJobCalc::UpdateGWBSEOptions( const tools::Property &options) { tools::Property gwbse_options = options.get(".gwbse_options"); gwbse_options.get(".gwbse").add("basisset", options.get("basisset").as()); gwbse_options.get(".gwbse").add("auxbasisset", options.get("auxbasisset").as()); gwbse_options.get(".gwbse.vxc") .add("functional", options.get("functional").as()); return gwbse_options; } template tools::Property ParallelXJobCalc::UpdateDFTOptions( const tools::Property &options) { tools::Property package_options = options.get(".dftpackage"); package_options.get("package").add("basisset", options.get("basisset").as()); package_options.get("package").add( "auxbasisset", options.get("auxbasisset").as()); package_options.get("package").add( "functional", options.get("functional").as()); return package_options; } // REGISTER PARALLEL CALCULATORS template class ParallelXJobCalc>; } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/polarregion.cc000066400000000000000000000275671412152066400173560ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include #include // Local VOTCA includes #include "votca/xtp/dipoledipoleinteraction.h" #include "votca/xtp/eeinteractor.h" #include "votca/xtp/polarregion.h" #include "votca/xtp/qmregion.h" #include "votca/xtp/staticregion.h" namespace votca { namespace xtp { void PolarRegion::Initialize(const tools::Property& prop) { std::string key = identify(); tools::Property options_polar; options_polar.add("polar", ""); tools::Property& prop_polar = options_polar.get("polar"); prop_polar = prop.get("polar"); _max_iter = options_polar.ifExistsReturnElseReturnDefault(key + ".max_iter", _max_iter); _deltaD = options_polar.ifExistsReturnElseReturnDefault( key + ".tolerance_dipole", _deltaD); _deltaE = options_polar.ifExistsReturnElseReturnDefault( key + ".tolerance_energy", _deltaE); _exp_damp = options_polar.ifExistsReturnElseReturnDefault(key + ".exp_damp", _exp_damp); } bool PolarRegion::Converged() const { if (!_E_hist.filled()) { return false; } double Echange = _E_hist.getDiff().Etotal(); std::string info = "not converged"; bool converged = false; if (std::abs(Echange) < _deltaE) { info = "converged"; converged = true; } XTP_LOG(Log::error, _log) << TimeStamp() << " Region:" << this->identify() << " " << this->getId() << " is " << info << " deltaE=" << Echange << std::flush; return converged; } double PolarRegion::StaticInteraction() { eeInteractor eeinteractor; double e = 0.0; #pragma omp parallel for reduction(+ : e) for (Index i = 0; i < size(); ++i) { for (Index j = 0; j < size(); ++j) { if (i == j) { continue; } PolarSegment& seg1 = _segments[i]; const PolarSegment& seg2 = _segments[j]; e += eeinteractor.ApplyStaticField(seg2, seg1); } } return 0.5 * e; } eeInteractor::E_terms PolarRegion::PolarEnergy() const { #pragma omp declare reduction(CustomPlus \ : eeInteractor::E_terms \ : omp_out += omp_in) eeInteractor eeinteractor(_exp_damp); eeInteractor::E_terms terms; #pragma omp parallel for reduction(CustomPlus : terms) for (Index i = 0; i < size(); ++i) { for (Index j = 0; j < i; ++j) { terms += eeinteractor.CalcPolarEnergy(_segments[i], _segments[j]); } } #pragma omp parallel for reduction(CustomPlus : terms) for (Index i = 0; i < size(); ++i) { terms.E_indu_indu() += eeinteractor.CalcPolarEnergy_IntraSegment(_segments[i]); } #pragma omp parallel for reduction(CustomPlus : terms) for (Index i = 0; i < size(); ++i) { for (const PolarSite& site : _segments[i]) { terms.E_internal() += site.InternalEnergy(); } } return terms; } double PolarRegion::PolarEnergy_extern() const { double e = 0.0; #pragma omp parallel for reduction(+ : e) for (Index i = 0; i < size(); ++i) { for (const PolarSite& site : _segments[i]) { e += site.deltaQ_V_ext(); } } return e; } void PolarRegion::Reset() { for (PolarSegment& seg : _segments) { for (PolarSite& site : seg) { site.Reset(); } } } void PolarRegion::AppendResult(tools::Property& prop) const { const Energy_terms& e = this->_E_hist.back(); prop.add("E_static", std::to_string(e.Estatic() * tools::conv::hrt2ev)); prop.add("E_polar", std::to_string(e.Epolar() * tools::conv::hrt2ev)); prop.add("E_total", std::to_string(e.Etotal() * tools::conv::hrt2ev)); } Index PolarRegion::CalcPolDoF() const { Index dof_polarization = 0; for (const PolarSegment& seg : _segments) { dof_polarization += seg.size() * 3; } return dof_polarization; } Eigen::VectorXd PolarRegion::CalcInducedDipoleInsideSegments() const { Index dof_polarization = CalcPolDoF(); Eigen::VectorXd initial_induced_dipoles = Eigen::VectorXd::Zero(dof_polarization); eeInteractor interactor(_exp_damp); Index index = 0; for (const PolarSegment& seg : _segments) { initial_induced_dipoles.segment(index, 3 * seg.size()) = interactor.Cholesky_IntraSegment(seg); index += 3 * seg.size(); } return initial_induced_dipoles; } Eigen::VectorXd PolarRegion::ReadInducedDipolesFromLastIteration() const { Index dof_polarization = CalcPolDoF(); Eigen::VectorXd last_induced_dipoles = Eigen::VectorXd::Zero(dof_polarization); Index index = 0; for (const PolarSegment& seg : _segments) { for (const PolarSite& site : seg) { last_induced_dipoles.segment<3>(index) = site.Induced_Dipole(); index += 3; } } return last_induced_dipoles; } void PolarRegion::WriteInducedDipolesToSegments(const Eigen::VectorXd& x) { Index index = 0; for (PolarSegment& seg : _segments) { for (PolarSite& site : seg) { site.setInduced_Dipole(x.segment<3>(index)); index += 3; } } } Eigen::VectorXd PolarRegion::CalcInducedDipolesViaPCG( const Eigen::VectorXd& initial_guess) { Eigen::VectorXd b = Eigen::VectorXd::Zero(initial_guess.size()); Index index = 0; for (PolarSegment& seg : _segments) { for (const PolarSite& site : seg) { auto V = site.V() + site.V_noE(); b.segment<3>(index) = -V; index += 3; } } eeInteractor interactor(_exp_damp); DipoleDipoleInteraction A(interactor, _segments); Eigen::ConjugateGradient> cg; cg.setMaxIterations(_max_iter); cg.setTolerance(_deltaD); cg.compute(A); Eigen::VectorXd x = cg.solveWithGuess(b, initial_guess); XTP_LOG(Log::error, _log) << TimeStamp() << " CG: #iterations: " << cg.iterations() << ", estimated error: " << cg.error() << std::flush; if (cg.info() == Eigen::ComputationInfo::NoConvergence) { _info = false; _errormsg = "PCG iterations did not converge"; } if (cg.info() == Eigen::ComputationInfo::NumericalIssue) { _info = false; _errormsg = "PCG had a numerical issue"; } return x; } void PolarRegion::Evaluate(std::vector>& regions) { std::vector energies = ApplyInfluenceOfOtherRegions(regions); Energy_terms e_contrib; e_contrib.E_static_ext() = std::accumulate(energies.begin(), energies.end(), 0.0); XTP_LOG(Log::info, _log) << TimeStamp() << " Calculated static-static and polar-static " "interaction with other regions" << std::flush; e_contrib.E_static_static() = StaticInteraction(); XTP_LOG(Log::info, _log) << TimeStamp() << " Calculated static interaction in region " << std::flush; Index dof_polarization = CalcPolDoF(); XTP_LOG(Log::error, _log) << TimeStamp() << " Starting Solving for classical polarization with " << dof_polarization << " degrees of freedom." << std::flush; Eigen::VectorXd initial_induced_dipoles; if (!_E_hist.filled() || _segments.size() == 1) { initial_induced_dipoles = CalcInducedDipoleInsideSegments(); } else { initial_induced_dipoles = ReadInducedDipolesFromLastIteration(); } Eigen::VectorXd x; // if only one segment // it is solved exactly through the initial guess if (_segments.size() != 1) { x = CalcInducedDipolesViaPCG(initial_induced_dipoles); if (!_info) { return; } } else { x = initial_induced_dipoles; } WriteInducedDipolesToSegments(x); e_contrib.addInternalPolarContrib(PolarEnergy()); XTP_LOG(Log::info, _log) << TimeStamp() << " Calculated polar interaction in region" << std::flush; e_contrib.E_polar_ext() = PolarEnergy_extern(); XTP_LOG(Log::info, _log) << TimeStamp() << " Calculated polar interaction with other regions" << std::flush; XTP_LOG(Log::info, _log) << std::setprecision(10) << " Internal static energy [hrt]= " << e_contrib.E_static_static() << std::flush; XTP_LOG(Log::info, _log) << std::setprecision(10) << " External static energy [hrt]= " << e_contrib.E_static_ext() << std::flush; XTP_LOG(Log::error, _log) << std::setprecision(10) << " Total static energy [hrt]= " << e_contrib.Estatic() << std::flush; XTP_LOG(Log::info, _log) << std::setprecision(10) << " internal dQ-dQ energy [hrt]= " << e_contrib.E_indu_indu() << std::flush; XTP_LOG(Log::info, _log) << std::setprecision(10) << " internal Q-dQ energy [hrt]= " << e_contrib.E_indu_stat() << std::flush; XTP_LOG(Log::info, _log) << std::setprecision(10) << " Internal energy [hrt]= " << e_contrib.E_internal() << std::flush; XTP_LOG(Log::info, _log) << std::setprecision(10) << " External polar energy [hrt]= " << e_contrib.E_polar_ext() << std::flush; XTP_LOG(Log::error, _log) << std::setprecision(10) << " Total polar energy [hrt]= " << e_contrib.Epolar() << std::flush; XTP_LOG(Log::error, _log) << std::setprecision(10) << " Total energy [hrt]= " << e_contrib.Etotal() << std::flush; _E_hist.push_back(e_contrib); return; } double PolarRegion::InteractwithQMRegion(const QMRegion& region) { // QMregions always have lower ids than other regions region.ApplyQMFieldToPolarSegments(_segments); return 0.0; } double PolarRegion::InteractwithPolarRegion(const PolarRegion& region) { bool noE_V = true; if (this->getId() < region.getId()) { noE_V = false; } double e = 0; #pragma omp parallel for reduction(+ : e) for (Index i = 0; i < Index(_segments.size()); i++) { PolarSegment& pseg1 = _segments[i]; double e_thread = 0.0; eeInteractor ee; for (const PolarSegment& pseg2 : region) { if (noE_V) { ee.ApplyStaticField(pseg2, pseg1); ee.ApplyInducedField(pseg2, pseg1); } else { e_thread += ee.ApplyStaticField(pseg2, pseg1); e_thread += ee.ApplyInducedField(pseg2, pseg1); } e += e_thread; } } return e; } double PolarRegion::InteractwithStaticRegion(const StaticRegion& region) { // Static regions always have higher ids than other regions double e = 0.0; #pragma omp parallel for reduction(+ : e) for (Index i = 0; i < Index(_segments.size()); i++) { double e_thread = 0.0; PolarSegment& pseg = _segments[i]; eeInteractor ee; for (const StaticSegment& sseg : region) { e_thread += ee.ApplyStaticField(sseg, pseg); } e += e_thread; } return e; } void PolarRegion::WriteToCpt(CheckpointWriter& w) const { MMRegion::WriteToCpt(w); } void PolarRegion::ReadFromCpt(CheckpointReader& r) { MMRegion::ReadFromCpt(r); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/polarsite.cc000066400000000000000000000130631412152066400170210ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License,Version 2.0 (the "License") * *You may not use this file except in compliance with the License. *You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * *Unless required by applicable law or agreed to in writing,software *distributed under the License is distributed on an "AS IS" BASIS, *WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,either express or implied. *See the License for the specific language governing permissions and *limitations under the License. * */ // Standard includes #include #include // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/polarsite.h" using namespace std; namespace votca { namespace xtp { PolarSite::PolarSite(Index id, std::string element, Eigen::Vector3d pos) : StaticSite(id, element, pos) { tools::Elements e; double default_pol = std::pow(tools::conv::ang2bohr, 3); try { default_pol = e.getPolarizability(element) * std::pow(tools::conv::nm2bohr, 3); } catch (const std::runtime_error&) { ; } setpolarization(default_pol * Eigen::Matrix3d::Identity()); } PolarSite::PolarSite(const data& d) { ReadData(d); } Eigen::Vector3d PolarSite::getDipole() const { Eigen::Vector3d dipole = _Q.segment<3>(1); dipole += Induced_Dipole(); return dipole; } void PolarSite::setpolarization(const Eigen::Matrix3d& pol) { Eigen::SelfAdjointEigenSolver es; es.computeDirect(pol); _pinv = es.eigenvectors() * es.eigenvalues().cwiseInverse().asDiagonal() * es.eigenvectors().transpose(); _eigendamp_invsqrt = 1.0 / std::sqrt(es.eigenvalues().maxCoeff()); } std::string PolarSite::writepolarization() const { double conv_pol = std::pow(tools::conv::bohr2ang, 3); Eigen::MatrixX3d pol = _pinv.inverse() * conv_pol; return (boost::format(" P %1$+1.7f %2$+1.7f %3$+1.7f %4$+1.7f %5$+1.7f " "%6$+1.7f\n") % pol(0, 0) % pol(1, 0) % pol(2, 0) % pol(1, 1) % pol(1, 2) % pol(2, 2)) .str(); } void PolarSite::SetupCptTable(CptTable& table) const { table.addCol(_id, "index", HOFFSET(data, id)); table.addCol(_element, "type", HOFFSET(data, element)); table.addCol(_pos[0], "posX", HOFFSET(data, posX)); table.addCol(_pos[1], "posY", HOFFSET(data, posY)); table.addCol(_pos[2], "posZ", HOFFSET(data, posZ)); // same type as rank table.addCol(_rank, "rank", HOFFSET(data, rank)); table.addCol(_Q[0], "Q00", HOFFSET(data, Q00)); table.addCol(_Q[1], "Q11c", HOFFSET(data, Q11c)); table.addCol(_Q[2], "Q11s", HOFFSET(data, Q11s)); table.addCol(_Q[3], "Q10", HOFFSET(data, Q10)); table.addCol(_Q[4], "Q20", HOFFSET(data, Q20)); table.addCol(_Q[5], "Q21c", HOFFSET(data, Q21c)); table.addCol(_Q[6], "Q21s", HOFFSET(data, Q21s)); table.addCol(_Q[7], "Q22c", HOFFSET(data, Q22c)); table.addCol(_Q[8], "Q22s", HOFFSET(data, Q22s)); table.addCol(_V[0], "Vx", HOFFSET(data, Vx)); table.addCol(_V[1], "Vy", HOFFSET(data, Vy)); table.addCol(_V[2], "Vz", HOFFSET(data, Vz)); table.addCol(_V_noE[0], "Vx_noE", HOFFSET(data, Vx_noE)); table.addCol(_V_noE[1], "Vy_NoE", HOFFSET(data, Vy_noE)); table.addCol(_V_noE[2], "Vz_noE", HOFFSET(data, Vz_noE)); // P_inv and P have same polarization so no problem, as only data type counts table.addCol(_pinv(0, 0), "pxx", HOFFSET(data, pxx)); table.addCol(_pinv(0, 1), "pxy", HOFFSET(data, pxy)); table.addCol(_pinv(0, 2), "pxz", HOFFSET(data, pxz)); table.addCol(_pinv(1, 1), "pyy", HOFFSET(data, pyy)); table.addCol(_pinv(1, 2), "pyz", HOFFSET(data, pyz)); table.addCol(_pinv(2, 2), "pzz", HOFFSET(data, pzz)); table.addCol(_induced_dipole.x(), "d_ind_x", HOFFSET(data, d_x_ind)); table.addCol(_induced_dipole.y(), "d_ind_y", HOFFSET(data, d_y_ind)); table.addCol(_induced_dipole.z(), "d_ind_z", HOFFSET(data, d_z_ind)); } void PolarSite::WriteData(data& d) const { d.id = _id; d.element = const_cast(_element.c_str()); d.posX = _pos[0]; d.posY = _pos[1]; d.posZ = _pos[2]; d.rank = _rank; d.Q00 = _Q[0]; d.Q11c = _Q[1]; d.Q11s = _Q[2]; d.Q10 = _Q[3]; d.Q20 = _Q[4]; d.Q21c = _Q[5]; d.Q21s = _Q[6]; d.Q22c = _Q[7]; d.Q22s = _Q[8]; d.Vx = _V[0]; d.Vy = _V[1]; d.Vz = _V[2]; d.Vx_noE = _V_noE[0]; d.Vy_noE = _V_noE[1]; d.Vz_noE = _V_noE[2]; Eigen::Matrix3d P = _pinv.inverse(); d.pxx = P(0, 0); d.pxy = P(0, 1); d.pxz = P(0, 2); d.pyy = P(1, 1); d.pyz = P(1, 2); d.pzz = P(2, 2); d.d_x_ind = _induced_dipole.x(); d.d_y_ind = _induced_dipole.y(); d.d_z_ind = _induced_dipole.z(); } void PolarSite::ReadData(const data& d) { _id = d.id; _element = std::string(d.element); free(d.element); _pos[0] = d.posX; _pos[1] = d.posY; _pos[2] = d.posZ; _rank = d.rank; _Q[0] = d.Q00; _Q[1] = d.Q11c; _Q[2] = d.Q11s; _Q[3] = d.Q10; _Q[4] = d.Q20; _Q[5] = d.Q21c; _Q[6] = d.Q21s; _Q[7] = d.Q22c; _Q[8] = d.Q22s; _V[0] = d.Vx; _V[1] = d.Vy; _V[2] = d.Vz; _V_noE[0] = d.Vx_noE; _V_noE[1] = d.Vy_noE; _V_noE[2] = d.Vz_noE; Eigen::Matrix3d Ps; Ps(0, 0) = d.pxx; Ps(0, 1) = d.pxy; Ps(1, 0) = d.pxy; Ps(0, 2) = d.pxz; Ps(2, 0) = d.pxz; Ps(1, 1) = d.pyy; Ps(1, 2) = d.pyz; Ps(2, 1) = d.pyz; Ps(2, 2) = d.pzz; this->setpolarization(Ps); _induced_dipole.x() = d.d_x_ind; _induced_dipole.y() = d.d_y_ind; _induced_dipole.z() = d.d_z_ind; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/populationanalysis.cc000066400000000000000000000076061412152066400207630ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/populationanalysis.h" namespace votca { namespace xtp { template StaticSegment Populationanalysis::CalcChargeperAtom( const Orbitals& orbitals, const QMState& state) const { AOBasis basis = orbitals.SetupDftBasis(); Eigen::MatrixXd dmat = orbitals.DensityMatrixFull(state); AOOverlap overlap; overlap.Fill(basis); Eigen::VectorXd charges = -CalcElecChargeperAtom(dmat, overlap, basis); if (!state.isTransition()) { charges += CalcNucChargeperAtom(orbitals.QMAtoms()); } StaticSegment seg = StaticSegment(orbitals.QMAtoms().getType(), orbitals.QMAtoms().getId()); for (Index i = 0; i < orbitals.QMAtoms().size(); ++i) { seg.push_back(StaticSite(orbitals.QMAtoms()[i], charges(i))); } return seg; } template void Populationanalysis::CalcChargeperFragment( std::vector >& frags, const Orbitals& orbitals, QMStateType type) const { if (!type.isExciton()) { throw std::runtime_error( "CalcChargeperFragment: QmStateType must be an exciton"); } AOBasis basis = orbitals.SetupDftBasis(); AOOverlap overlap; overlap.Fill(basis); Eigen::VectorXd nuccharges = CalcNucChargeperAtom(orbitals.QMAtoms()); Eigen::MatrixXd dmatgs = orbitals.DensityMatrixGroundState(); Eigen::VectorXd gscharges = nuccharges - CalcElecChargeperAtom(dmatgs, overlap, basis); Index numofstates = orbitals.NumberofStates(type); for (auto& frag : frags) { frag.value().Initialize(numofstates); frag.value().Gs = frag.ExtractFromVector(gscharges); } for (Index i_state = 0; i_state < numofstates; i_state++) { QMState state(type, i_state, false); std::array dmat_ex = orbitals.DensityMatrixExcitedState(state); Eigen::VectorXd atom_h = CalcElecChargeperAtom(dmat_ex[0], overlap, basis); Eigen::VectorXd atom_e = -CalcElecChargeperAtom(dmat_ex[1], overlap, basis); for (auto& frag : frags) { frag.value().E(i_state) = frag.ExtractFromVector(atom_e); frag.value().H(i_state) = frag.ExtractFromVector(atom_h); } } } template Eigen::VectorXd Populationanalysis::CalcNucChargeperAtom( const QMMolecule& mol) const { Eigen::VectorXd result = Eigen::VectorXd::Zero(mol.size()); for (Index i = 0; i < mol.size(); i++) { result(i) = double(mol[i].getNuccharge()); } return result; } template Eigen::VectorXd Populationanalysis::CalcElecChargeperAtom( const Eigen::MatrixXd& dmat, AOOverlap& overlap, const AOBasis& basis) const { Eigen::MatrixXd prodmat; if (T) { Eigen::MatrixXd Smsqrt = overlap.Sqrt(); prodmat = Smsqrt * dmat * Smsqrt; } else { prodmat = dmat * overlap.Matrix(); } std::vector funcperatom = basis.getFuncPerAtom(); Index noofatoms = Index(funcperatom.size()); Eigen::VectorXd charges = Eigen::VectorXd::Zero(noofatoms); Index start = 0; for (Index i = 0; i < charges.size(); ++i) { Index nofunc = funcperatom[i]; charges(i) = prodmat.diagonal().segment(start, nofunc).sum(); start += nofunc; } return charges; } template class Populationanalysis; template class Populationanalysis; } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/progressobserver.cc000066400000000000000000000227721412152066400204420ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ /// For an earlier history see ctp repo commit /// 77795ea591b29e664153f9404c8655ba28dc14e9 // Standard includes #include #include // Third party includes #include #include #include #include #include // Local VOTCA includes #include "votca/xtp/job.h" #include "votca/xtp/progressobserver.h" #include "votca/xtp/qmthread.h" using boost::format; namespace votca { namespace xtp { template typename ProgObserver::Job * ProgObserver::RequestNextJob(QMThread &thread) { _lockThread.Lock(); Job *jobToProc = nullptr; XTP_LOG(Log::error, thread.getLogger()) << "Requesting next job" << std::flush; // NEED NEW CHUNK? if (_nextjit == _jobsToProc.end() && _moreJobsAvailable) { SyncWithProgFile(thread); _nextjit = _jobsToProc.begin(); if (_nextjit == _jobsToProc.end()) { _moreJobsAvailable = false; XTP_LOG(Log::error, thread.getLogger()) << "Sync did not yield any new jobs." << std::flush; } } // JOBS EATEN ALL UP? if (_nextjit == _jobsToProc.end()) { if (_maxJobs == _startJobsCount) { XTP_LOG(Log::error, thread.getLogger()) << "Next job: ID = - (reached maximum for this process)" << std::flush; } else { XTP_LOG(Log::error, thread.getLogger()) << "Next job: ID = - (none available)" << std::flush; } } // TAKE A BITE else { jobToProc = *_nextjit; ++_nextjit; XTP_LOG(Log::error, thread.getLogger()) << "Next job: ID = " << jobToProc->getId() << std::flush; } if (!thread.isMaverick() && jobToProc != nullptr) { Index idx = jobToProc->getId(); Index frac = (_jobs.size() >= 10) ? 10 : _jobs.size(); Index rounded = Index(double(_jobs.size()) / double(frac)) * frac; Index tenth = rounded / frac; if (idx % tenth == 0) { double percent = double(idx) / double(rounded) * 100 + 0.5; std::cout << (format("=> [%1$2.0f%%] ") % percent).str() << std::flush; } } _lockThread.Unlock(); return jobToProc; } template void ProgObserver::ReportJobDone(Job &job, Result &res, QMThread &thread) { _lockThread.Lock(); XTP_LOG(Log::error, thread.getLogger()) << "Reporting job results" << std::flush; // RESULTS, TIME, HOST job.UpdateFromResult(res); job.setTime(GenerateTime()); job.setHost(GenerateHost()); // PRINT PROGRESS BAR _jobsReported += 1; if (!thread.isMaverick()) { std::cout << std::endl << thread.getLogger() << std::flush; } _lockThread.Unlock(); return; } template std::string ProgObserver::GenerateHost() { char host[128]; (void)gethostname(host, sizeof host); pid_t pid = getpid(); return (format("%1$s:%2$d") % host % pid).str(); } template std::string ProgObserver::GenerateTime() { boost::posix_time::ptime now = boost::posix_time::second_clock::local_time(); return (format("%1$s") % now.time_of_day()).str(); } template void ProgObserver::SyncWithProgFile(QMThread &thread) { // INTERPROCESS FILE LOCKING (THREAD LOCK IN ::RequestNextJob) this->LockProgFile(thread); std::string progFile = _progFile; std::string progBackFile = _progFile + "~"; // LOAD EXTERNAL JOBS FROM SHARED XML & UPDATE INTERNAL JOBS XTP_LOG(Log::info, thread.getLogger()) << "Update internal structures from job file" << std::flush; JobContainer jobs_ext = LOAD_JOBS(progFile); UPDATE_JOBS(jobs_ext, _jobs, GenerateHost()); // GENERATE BACK-UP FOR SHARED XML XTP_LOG(Log::info, thread.getLogger()) << "Create job-file back-up" << std::flush; WRITE_JOBS(_jobs, progBackFile); // ASSIGN NEW JOBS IF AVAILABLE XTP_LOG(Log::error, thread.getLogger()) << "Assign jobs from stack" << std::flush; _jobsToProc.clear(); Index cacheSize = _cacheSize; while (int(_jobsToProc.size()) < cacheSize) { if (_metajit == _jobs.end() || _startJobsCount == _maxJobs) { break; } bool startJob = false; // Start if job available or restart patterns matched if ((_metajit->isAvailable()) || (_restartMode && _restart_stats.count(_metajit->getStatusStr())) || (_restartMode && _restart_hosts.count(_metajit->getHost()))) { startJob = true; } if (startJob) { _metajit->Reset(); _metajit->setStatus("ASSIGNED"); _metajit->setHost(GenerateHost()); _metajit->setTime(GenerateTime()); _jobsToProc.push_back(&*_metajit); _startJobsCount += 1; } ++_metajit; } // UPDATE PROGRESS STATUS FILE WRITE_JOBS(_jobs, progFile); // RELEASE PROGRESS STATUS FILE this->ReleaseProgFile(thread); return; } template void ProgObserver::LockProgFile(QMThread &thread) { _flock = std::unique_ptr( new boost::interprocess::file_lock(_lockFile.c_str())); _flock->lock(); XTP_LOG(Log::warning, thread.getLogger()) << "Imposed lock on " << _lockFile << std::flush; XTP_LOG(Log::warning, thread.getLogger()) << "Sleep ... " << _lockFile << std::flush; XTP_LOG(Log::warning, thread.getLogger()) << "Wake up ... " << _lockFile << std::flush; } template void ProgObserver::ReleaseProgFile(QMThread &thread) { _flock->unlock(); XTP_LOG(Log::warning, thread.getLogger()) << "Releasing " << _lockFile << ". " << std::flush; } template void ProgObserver::InitCmdLineOpts( const boost::program_options::variables_map &optsMap) { _lockFile = optsMap["file"].as(); _cacheSize = optsMap["cache"].as(); _maxJobs = optsMap["maxjobs"].as(); std::string restartPattern = optsMap["restart"].as(); // restartPattern = e.g. host(pckr124:1234) stat(FAILED) boost::algorithm::replace_all(restartPattern, " ", ""); if (restartPattern == "") { _restartMode = false; } else { _restartMode = true; } tools::Tokenizer toker(restartPattern, "(,)"); std::vector patterns = toker.ToVector(); std::string category = ""; for (const std::string &pattern : patterns) { if (pattern == "host" || pattern == "stat") { category = pattern; } else if (category == "host") { _restart_hosts[pattern] = true; } else if (category == "stat") { if (pattern == "ASSIGNED" || pattern == "COMPLETE") { std::cout << "Restart if status == " << pattern << "? Not necessarily a good idea." << std::endl; } _restart_stats[pattern] = true; } else { throw std::runtime_error( "Restart pattern ill-defined, format is" "[host([HOSTNAME:PID])] [stat([STATUS])]"); } } return; } template void ProgObserver::InitFromProgFile(std::string progFile, QMThread &thread) { _progFile = progFile; _jobsReported = 0; XTP_LOG(Log::error, thread.getLogger()) << "Job file = '" << _progFile << "', "; XTP_LOG(Log::info, thread.getLogger()) << "lock file = '" << _lockFile << "', "; XTP_LOG(Log::error, thread.getLogger()) << "cache size = " << _cacheSize << std::flush; XTP_LOG(Log::error, thread.getLogger()) << "Initialize jobs from " << progFile << std::flush; XTP_LOG(Log::info, thread.getLogger()) << "Lock & load " << std::flush; // LOCK, READ INTO XML this->LockProgFile(thread); // ... Clear container _jobs.clear(); // ... Load new, set availability bool _jobs = LOAD_JOBS(progFile); _metajit = _jobs.begin(); WRITE_JOBS(_jobs, progFile + "~"); XTP_LOG(Log::error, thread.getLogger()) << "Registered " << _jobs.size() << " jobs." << std::flush; if (_jobs.size() > 0) { _moreJobsAvailable = true; } else { _moreJobsAvailable = false; } // SUMMARIZE OBSERVER VARIABLES: RESTART PATTERN, CACHE, LOCK FILE if (_restartMode && _restart_hosts.size()) { std::string infostr = "Restart if host == "; for (const std::pair &host : _restart_hosts) { infostr += host.first + " "; } XTP_LOG(Log::error, thread.getLogger()) << infostr << std::flush; } if (_restartMode && _restart_stats.size()) { std::string infostr = "Restart if stat == "; for (const std::pair &host : _restart_hosts) { infostr += host.first + " "; } XTP_LOG(Log::error, thread.getLogger()) << infostr << std::flush; } // RELEASE PROGRESS FILE this->ReleaseProgFile(thread); return; } // REGISTER template class ProgObserver >; } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/qmatom.cc000066400000000000000000000041551412152066400163170ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/qmatom.h" namespace votca { namespace xtp { QMAtom::QMAtom(Index index, std::string element, Eigen::Vector3d pos) : _index(index), _element(element), _pos(pos) { tools::Elements elements; _nuccharge = elements.getNucCrg(_element); } QMAtom::QMAtom(const data& d) { ReadData(d); } void QMAtom::Rotate(const Eigen::Matrix3d& R, const Eigen::Vector3d& refPos) { Eigen::Vector3d dir = _pos - refPos; dir = R * dir; _pos = refPos + dir; // Rotated Position } void QMAtom::SetupCptTable(CptTable& table) const { table.addCol(_index, "index", HOFFSET(data, index)); table.addCol(_element, "element", HOFFSET(data, element)); table.addCol(_pos[0], "posX", HOFFSET(data, x)); table.addCol(_pos[1], "posY", HOFFSET(data, y)); table.addCol(_pos[2], "posZ", HOFFSET(data, z)); table.addCol(_nuccharge, "nuccharge", HOFFSET(data, nuccharge)); table.addCol(_ecpcharge, "ecpcharge", HOFFSET(data, ecpcharge)); } void QMAtom::WriteData(data& d) const { d.index = _index; d.element = const_cast(_element.c_str()); d.x = _pos[0]; d.y = _pos[1]; d.z = _pos[2]; d.nuccharge = _nuccharge; d.ecpcharge = _ecpcharge; } void QMAtom::ReadData(const data& d) { _element = std::string(d.element); free(d.element); _index = d.index; _pos[0] = d.x; _pos[1] = d.y; _pos[2] = d.z; _nuccharge = d.nuccharge; _ecpcharge = d.ecpcharge; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/qmcalculator.cc000066400000000000000000000024251412152066400175060ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include "votca/xtp/qmcalculator.h" #include "votca/xtp/eigen.h" #include namespace votca { namespace xtp { bool QMCalculator::EvaluateFrame(Topology& top) { libint2::initialize(); OPENMP::setMaxThreads(_nThreads); std::cout << " Using " << OPENMP::getMaxThreads() << " threads" << std::flush; bool success = Evaluate(top); libint2::finalize(); return success; } void QMCalculator::Initialize(const tools::Property& opt) { tools::Property options = LoadDefaultsAndUpdateWithUserOptions("xtp", opt); ParseOptions(options); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/qmmolecule.cc000066400000000000000000000026721412152066400171660ustar00rootroot00000000000000/* * Copyright 2016 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // VOTCA includes #include #include #include #include // Local VOTCA includes #include "votca/xtp/checkpointreader.h" #include "votca/xtp/checkpointwriter.h" #include "votca/xtp/qmmolecule.h" using namespace std; using namespace votca::tools; namespace votca { namespace xtp { void QMMolecule::WriteXYZ(std::string filename, std::string header) const { csg::XYZWriter writer; writer.Open(filename, false); writer.Write(*this, header); writer.Close(); return; } void QMMolecule::LoadFromFile(std::string filename) { csg::XYZReader reader; reader.Open(filename); reader.ReadFile(*this); reader.Close(); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/qmnblist.cc000066400000000000000000000042561412152066400166540ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/qmnblist.h" #include "votca/xtp/checkpointwriter.h" namespace votca { namespace xtp { QMPair& QMNBList::Add(const Segment& seg1, const Segment& seg2, const Eigen::Vector3d& r) { assert(this->FindPair(&seg1, &seg2) == nullptr && "Critical bug: pair already exists"); Index id = this->size(); QMPair* pair = new QMPair(id, &seg1, &seg2, r); this->AddPair(pair); return *pair; } void QMNBList::WriteToCpt(CheckpointWriter& w) const { Index size = this->size(); w(size, "size"); if (size == 0) { return; } Segment seg1("test1", 0); Segment seg2("test2", 1); QMPair pair(1, &seg1, &seg2, Eigen::Vector3d::Zero()); std::vector dataVec(size); CptTable table = w.openTable("pairs", pair, size); for (Index i = 0; i < size; i++) { (_pairs[i]->WriteData(dataVec[i])); } table.write(dataVec); for (QMPair::data data : dataVec) { delete[] data.pair_type; } } void QMNBList::ReadFromCpt(CheckpointReader& r, const std::vector& segments) { Cleanup(); Index size = 0; r(size, "size"); if (size == 0) { return; } QMPair pair(1, &segments[0], &segments[1], Eigen::Vector3d::Zero()); CptTable table = r.openTable("pairs", pair); std::vector dataVec(table.numRows()); table.read(dataVec); for (const QMPair::data& data : dataVec) { this->AddPair(new QMPair(data, segments)); } } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/qmpackage.cc000066400000000000000000000112111412152066400167410ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // Local VOTCA includes #include "votca/tools/getline.h" #include "votca/tools/globals.h" #include "votca/xtp/ecpaobasis.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/qmpackage.h" #include "votca/xtp/qmpackagefactory.h" namespace votca { namespace xtp { using std::flush; tools::Property QMPackage::ParseCommonOptions(const tools::Property& options) { std::string key = "package"; _settings.read_property(options, key); if (tools::VotcaShareSet()) { Settings qmpackage_defaults{key}; qmpackage_defaults.load_from_xml(this->FindDefaultsFile()); _settings.amend(qmpackage_defaults); } else { std::cout << "Warning: VOTCASHARE environment variable not defined\n"; } _settings.validate(); _charge = _settings.get("charge"); _spin = _settings.get("spin"); _basisset_name = _settings.get("basisset"); if (_settings.has_key("cleanup")) { _cleanup = _settings.get("cleanup"); } if (getPackageName() != "xtp") { _scratch_dir = _settings.get("scratch"); } return _settings.to_property("package"); } void QMPackage::ReorderOutput(Orbitals& orbitals) const { if (!orbitals.hasQMAtoms()) { throw std::runtime_error("Orbitals object has no QMAtoms"); } AOBasis dftbasis = orbitals.SetupDftBasis(); // necessary to update nuclear charges on qmatoms if (orbitals.hasECPName()) { ECPBasisSet ecps; ecps.Load(orbitals.getECPName()); ECPAOBasis ecpbasis; ecpbasis.Fill(ecps, orbitals.QMAtoms()); } if (orbitals.hasMOs()) { OrbReorder reorder(ShellReorder(), ShellMulitplier()); reorder.reorderOrbitals(orbitals.MOs().eigenvectors(), dftbasis); XTP_LOG(Log::info, *_pLog) << "Reordered MOs" << flush; } return; } Eigen::MatrixXd QMPackage::ReorderMOsBack(const Orbitals& orbitals) const { if (!orbitals.hasQMAtoms()) { throw std::runtime_error("Orbitals object has no QMAtoms"); } AOBasis dftbasis = orbitals.SetupDftBasis(); Eigen::MatrixXd result = orbitals.MOs().eigenvectors(); bool reverseOrder = true; OrbReorder reorder(ShellReorder(), ShellMulitplier(), reverseOrder); reorder.reorderOrbitals(result, dftbasis); return result; } std::vector QMPackage::SplitMultipoles( const StaticSite& aps) const { std::vector multipoles_split; // Calculate virtual charge positions double a = _settings.get("dipole_spacing"); // this is in a0 double mag_d = aps.getDipole().norm(); // this is in e * a0 const Eigen::Vector3d dir_d = aps.getDipole().normalized(); const Eigen::Vector3d A = aps.getPos() + 0.5 * a * dir_d; const Eigen::Vector3d B = aps.getPos() - 0.5 * a * dir_d; double qA = mag_d / a; double qB = -qA; if (std::abs(qA) > 1e-12) { multipoles_split.push_back(MinimalMMCharge(A, qA)); multipoles_split.push_back(MinimalMMCharge(B, qB)); } if (aps.getRank() > 1) { const Eigen::Matrix3d components = aps.CalculateCartesianMultipole(); Eigen::SelfAdjointEigenSolver es; es.computeDirect(components); double a2 = 2 * a; for (Index i = 0; i < 3; i++) { double q = es.eigenvalues()[i] / (a2 * a2); const Eigen::Vector3d vec1 = aps.getPos() + 0.5 * a2 * es.eigenvectors().col(i); const Eigen::Vector3d vec2 = aps.getPos() - 0.5 * a2 * es.eigenvectors().col(i); multipoles_split.push_back(MinimalMMCharge(vec1, q)); multipoles_split.push_back(MinimalMMCharge(vec2, q)); } } return multipoles_split; } std::vector QMPackage::GetLineAndSplit( std::ifstream& input_file, const std::string separators) const { std::string line; tools::getline(input_file, line); boost::trim(line); tools::Tokenizer tok(line, separators); return tok.ToVector(); } std::string QMPackage::FindDefaultsFile() const { return tools::GetVotcaShare() + "/xtp/data/qmpackage_defaults.xml"; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/qmpackages/000077500000000000000000000000001412152066400166215ustar00rootroot00000000000000xtp-2021.2/src/libxtp/qmpackages/orca.cc000066400000000000000000000701231412152066400200570ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include #include // Third party includes #include #include #include // VOTCA includes #include #include // Local VOTCA includes #include "votca/tools/globals.h" #include "votca/xtp/basisset.h" #include "votca/xtp/ecpaobasis.h" #include "votca/xtp/orbitals.h" // Local private VOTCA includes #include "orca.h" namespace votca { namespace xtp { using namespace std; void Orca::Initialize(const tools::Property& options) { // good luck // Orca file names const std::string& fileName = options.ifExistsReturnElseReturnDefault("job_name", "system"); _input_file_name = fileName + ".inp"; _log_file_name = fileName + ".log"; _shell_file_name = fileName + ".sh"; _mo_file_name = fileName + ".gbw"; ParseCommonOptions(options); } /* Custom basis sets are written on a per-element basis to * the system.bas/aux file(s), which are then included in the * Orca input file using GTOName = "system.bas/aux" */ void Orca::WriteBasisset(const QMMolecule& qmatoms, std::string& bs_name, std::string& el_file_name) { std::vector UniqueElements = qmatoms.FindUniqueElements(); tools::Elements elementInfo; BasisSet bs; bs.Load(bs_name); XTP_LOG(Log::error, *_pLog) << "Loaded Basis Set " << bs_name << flush; ofstream el_file; el_file.open(el_file_name); el_file << "$DATA" << endl; for (const std::string& element_name : UniqueElements) { const Element& element = bs.getElement(element_name); el_file << elementInfo.getEleFull(element_name) << endl; for (const Shell& shell : element) { el_file << xtp::EnumToString(shell.getL()) << " " << shell.getSize() << endl; Index sh_idx = 0; for (const GaussianPrimitive& gaussian : shell) { sh_idx++; el_file << " " << sh_idx << " " << indent(gaussian.decay()); el_file << " " << indent(gaussian.contraction()); el_file << endl; } } } el_file << "STOP\n"; el_file.close(); return; } /* Coordinates are written in standard Element,x,y,z format to the * input file. */ void Orca::WriteCoordinates(std::ofstream& inp_file, const QMMolecule& qmatoms) { for (const QMAtom& atom : qmatoms) { Eigen::Vector3d pos = atom.getPos() * tools::conv::bohr2ang; inp_file << setw(3) << atom.getElement() << setw(12) << setiosflags(ios::fixed) << setprecision(5) << pos.x() << setw(12) << setiosflags(ios::fixed) << setprecision(5) << pos.y() << setw(12) << setiosflags(ios::fixed) << setprecision(5) << pos.z() << endl; } inp_file << "* \n" << endl; return; } /* If custom ECPs are used, they need to be specified in the input file * in a section following the basis set includes. */ void Orca::WriteECP(std::ofstream& inp_file, const QMMolecule& qmatoms) { inp_file << endl; std::vector UniqueElements = qmatoms.FindUniqueElements(); ECPBasisSet ecp; ecp.Load(_settings.get("ecp")); XTP_LOG(Log::error, *_pLog) << "Loaded Pseudopotentials " << _settings.get("ecp") << flush; for (const std::string& element_name : UniqueElements) { try { ecp.getElement(element_name); } catch (std::runtime_error& error) { XTP_LOG(Log::error, *_pLog) << "No pseudopotential for " << element_name << " available" << flush; continue; } const ECPElement& element = ecp.getElement(element_name); inp_file << "\n" << "NewECP" << " " << element_name << endl; inp_file << "N_core" << " " << element.getNcore() << endl; inp_file << "lmax" << " " << EnumToString(element.getLmax()) << endl; // For Orca the order doesn't matter but let's write it in ascending order // write remaining shells in ascending order s,p,d... for (Index i = 0; i <= Index(element.getLmax()); i++) { for (const ECPShell& shell : element) { if (Index(shell.getL()) == i) { // shell type, number primitives, scale factor inp_file << xtp::EnumToString(shell.getL()) << " " << shell.getSize() << endl; Index sh_idx = 0; for (const ECPGaussianPrimitive& gaussian : shell) { sh_idx++; inp_file << sh_idx << " " << gaussian._decay << " " << gaussian._contraction << " " << gaussian._power << endl; } } } } inp_file << "end\n " << "\n" << endl; } return; } void Orca::WriteChargeOption() { this->_settings.add("orca.pointcharges", "\"background.crg\""); } /* For QM/MM the molecules in the MM environment are represented by * their atomic partial charge distributions. ORCA expects them in * q,x,y,z format in a separate file "background.crg" */ void Orca::WriteBackgroundCharges() { std::ofstream crg_file; std::string _crg_file_name_full = _run_dir + "/background.crg"; crg_file.open(_crg_file_name_full); Index total_background = 0; for (const std::unique_ptr& site : _externalsites) { if (site->getCharge() != 0.0) { total_background++; } std::vector split_multipoles = SplitMultipoles(*site); total_background += split_multipoles.size(); } // counting only crg_file << total_background << endl; boost::format fmt("%1$+1.7f %2$+1.7f %3$+1.7f %4$+1.7f"); // now write for (const std::unique_ptr& site : _externalsites) { Eigen::Vector3d pos = site->getPos() * tools::conv::bohr2ang; string sitestring = boost::str(fmt % site->getCharge() % pos.x() % pos.y() % pos.z()); if (site->getCharge() != 0.0) { crg_file << sitestring << endl; } std::vector split_multipoles = SplitMultipoles(*site); for (const auto& mpoles : split_multipoles) { Eigen::Vector3d pos2 = mpoles._pos * tools::conv::bohr2ang; string multipole = boost::str(fmt % mpoles._q % pos2.x() % pos2.y() % pos2.z()); crg_file << multipole << endl; } } return; } /** * Prepares the *.inp file from a vector of segments * Appends a guess constructed from monomer orbitals if supplied, Not * implemented yet */ bool Orca::WriteInputFile(const Orbitals& orbitals) { std::vector results; std::string temp_suffix = "/id"; std::string scratch_dir_backup = _scratch_dir; std::ofstream inp_file; std::string inp_file_name_full = _run_dir + "/" + _input_file_name; inp_file.open(inp_file_name_full); // header inp_file << "* xyz " << _charge << " " << _spin << endl; Index threads = OPENMP::getMaxThreads(); const QMMolecule& qmatoms = orbitals.QMAtoms(); // put coordinates WriteCoordinates(inp_file, qmatoms); // add parallelization info inp_file << "%pal\n" << "nprocs " << threads << "\nend" << "\n" << endl; // basis set info std::string el_file_name = _run_dir + "/" + "system.bas"; WriteBasisset(qmatoms, _basisset_name, el_file_name); inp_file << "%basis\n"; inp_file << "GTOName" << " " << "=" << "\"system.bas\";" << endl; if (_settings.has_key("auxbasisset")) { std::string aux_file_name = _run_dir + "/" + "system.aux"; std::string auxbasisset_name = _settings.get("auxbasisset"); WriteBasisset(qmatoms, auxbasisset_name, aux_file_name); inp_file << "GTOAuxName" << " " << "=" << "\"system.aux\";" << endl; } // write_auxbasis set // ECPs if (_settings.has_key("ecp")) { WriteECP(inp_file, qmatoms); } inp_file << "end\n " << "\n" << endl; // This end is for the basis set block if (_settings.get("write_charges")) { WriteBackgroundCharges(); } // Write Orca section specified by the user for (const auto& prop : this->_settings.property("orca")) { const std::string& prop_name = prop.name(); if (prop_name == "pointcharges") { _options += this->CreateInputSection("orca.pointcharges"); } else if (prop_name != "method") { _options += this->CreateInputSection("orca." + prop_name); } } // Write main DFT method _options += this->WriteMethod(); inp_file << _options; inp_file.close(); // and now generate a shell script to run both jobs, if neccessary XTP_LOG(Log::info, *_pLog) << "Setting the scratch dir to " << _scratch_dir + temp_suffix << flush; _scratch_dir = scratch_dir_backup + temp_suffix; WriteShellScript(); _scratch_dir = scratch_dir_backup; return true; } bool Orca::WriteShellScript() { ofstream shell_file; std::string shell_file_name_full = _run_dir + "/" + _shell_file_name; shell_file.open(shell_file_name_full); shell_file << "#!/bin/bash" << endl; shell_file << "mkdir -p " << _scratch_dir << endl; if (_settings.get("read_guess")) { if (!(boost::filesystem::exists(_run_dir + "/molA.gbw") && boost::filesystem::exists(_run_dir + "/molB.gbw"))) { throw runtime_error( "Using guess relies on a molA.gbw and a molB.gbw file being in the " "directory."); } shell_file << _settings.get("executable") << "_mergefrag molA.gbw molB.gbw dimer.gbw > merge.log" << endl; } shell_file << _settings.get("executable") << " " << _input_file_name << " > " << _log_file_name << endl; //" 2> run.error" << endl; shell_file.close(); return true; } /** * Runs the Orca job. */ bool Orca::Run() { XTP_LOG(Log::error, *_pLog) << "Running Orca job" << flush; if (std::system(nullptr)) { std::string command = "cd " + _run_dir + "; sh " + _shell_file_name; Index check = std::system(command.c_str()); if (check == -1) { XTP_LOG(Log::error, *_pLog) << _input_file_name << " failed to start" << flush; return false; } if (CheckLogFile()) { XTP_LOG(Log::error, *_pLog) << "Finished Orca job" << flush; return true; } else { XTP_LOG(Log::error, *_pLog) << "Orca job failed" << flush; } } else { XTP_LOG(Log::error, *_pLog) << _input_file_name << " failed to start" << flush; return false; } return true; } /** * Cleans up after the Orca job */ void Orca::CleanUp() { if (_settings.get("read_guess")) { remove((_run_dir + "/" + "molA.gbw").c_str()); remove((_run_dir + "/" + "molB.gbw").c_str()); remove((_run_dir + "/" + "dimer.gbw").c_str()); } // cleaning up the generated files if (_cleanup.size() != 0) { tools::Tokenizer tok_cleanup(_cleanup, ","); std::vector cleanup_info; tok_cleanup.ToVector(cleanup_info); for (const std::string& substring : cleanup_info) { if (substring == "inp") { std::string file_name = _run_dir + "/" + _input_file_name; remove(file_name.c_str()); } if (substring == "bas") { std::string file_name = _run_dir + "/system.bas"; remove(file_name.c_str()); } if (substring == "log") { std::string file_name = _run_dir + "/" + _log_file_name; remove(file_name.c_str()); } if (substring == "gbw") { std::string file_name = _run_dir + "/" + _mo_file_name; remove(file_name.c_str()); } if (substring == "ges") { std::string file_name = _run_dir + "/system.ges"; remove(file_name.c_str()); } if (substring == "prop") { std::string file_name = _run_dir + "/system.prop"; remove(file_name.c_str()); } } } return; } StaticSegment Orca::GetCharges() const { StaticSegment result("charges", 0); XTP_LOG(Log::error, *_pLog) << "Parsing " << _log_file_name << flush; std::string log_file_name_full = _run_dir + "/" + _log_file_name; std::string line; std::ifstream input_file(log_file_name_full); while (input_file) { tools::getline(input_file, line); boost::trim(line); GetCoordinates(result, line, input_file); std::string::size_type charge_pos = line.find("CHELPG Charges"); if (charge_pos != std::string::npos) { XTP_LOG(Log::error, *_pLog) << "Getting charges" << flush; tools::getline(input_file, line); std::vector row = GetLineAndSplit(input_file, "\t "); Index nfields = Index(row.size()); bool hasAtoms = result.size() > 0; while (nfields == 4) { Index atom_id = boost::lexical_cast(row.at(0)); std::string atom_type = row.at(1); double atom_charge = boost::lexical_cast(row.at(3)); row = GetLineAndSplit(input_file, "\t "); nfields = Index(row.size()); if (hasAtoms) { StaticSite& temp = result.at(atom_id); if (temp.getElement() != atom_type) { throw std::runtime_error( "Getting charges failed. Mismatch in elemts:" + temp.getElement() + " vs " + atom_type); } temp.setCharge(atom_charge); } else { StaticSite temp = StaticSite(atom_id, atom_type, Eigen::Vector3d::Zero()); temp.setCharge(atom_charge); result.push_back(temp); } } } } return result; } Eigen::Matrix3d Orca::GetPolarizability() const { std::string line; ifstream input_file((_run_dir + "/" + _log_file_name)); bool has_pol = false; Eigen::Matrix3d pol = Eigen::Matrix3d::Zero(); while (input_file) { tools::getline(input_file, line); boost::trim(line); std::string::size_type pol_pos = line.find("THE POLARIZABILITY TENSOR"); if (pol_pos != std::string::npos) { XTP_LOG(Log::error, *_pLog) << "Getting polarizability" << flush; tools::getline(input_file, line); tools::getline(input_file, line); tools::getline(input_file, line); if (line.find("The raw cartesian tensor (atomic units)") == std::string::npos) { throw std::runtime_error( "Could not find cartesian polarization tensor"); } for (Index i = 0; i < 3; i++) { tools::getline(input_file, line); tools::Tokenizer tok2(line, " "); std::vector values = tok2.ToVector(); if (values.size() != 3) { throw std::runtime_error("polarization line " + line + " cannot be parsed"); } Eigen::Vector3d row; row << std::stod(values[0]), std::stod(values[1]), std::stod(values[2]); pol.row(i) = row; } has_pol = true; } } if (!has_pol) { throw std::runtime_error("Could not find polarization in logfile"); } return pol; } bool Orca::ParseLogFile(Orbitals& orbitals) { bool found_success = false; orbitals.setQMpackage(getPackageName()); orbitals.setDFTbasisName(_basisset_name); if (_settings.has_key("ecp")) { orbitals.setECPName(_settings.get("ecp")); } XTP_LOG(Log::error, *_pLog) << "Parsing " << _log_file_name << flush; std::string log_file_name_full = _run_dir + "/" + _log_file_name; // check if LOG file is complete if (!CheckLogFile()) { return false; } std::map energies; std::map occupancy; std::string line; Index levels = 0; Index number_of_electrons = 0; std::vector results; std::ifstream input_file(log_file_name_full); if (input_file.fail()) { XTP_LOG(Log::error, *_pLog) << "File " << log_file_name_full << " not found " << flush; return false; } else { XTP_LOG(Log::error, *_pLog) << "Reading Coordinates and occupationnumbers and energies from " << log_file_name_full << flush; } // Coordinates of the final configuration depending on whether it is an // optimization or not QMMolecule& mol = orbitals.QMAtoms(); while (input_file) { tools::getline(input_file, line); boost::trim(line); GetCoordinates(mol, line, input_file); std::string::size_type energy_pos = line.find("FINAL SINGLE"); if (energy_pos != std::string::npos) { boost::algorithm::split(results, line, boost::is_any_of(" "), boost::algorithm::token_compress_on); std::string energy = results[4]; boost::trim(energy); orbitals.setQMEnergy(boost::lexical_cast(energy)); XTP_LOG(Log::error, *_pLog) << (boost::format("QM energy[Hrt]: %4.6f ") % orbitals.getDFTTotalEnergy()) .str() << flush; } std::string::size_type HFX_pos = line.find("Fraction HF Exchange ScalHFX"); if (HFX_pos != std::string::npos) { boost::algorithm::split(results, line, boost::is_any_of(" "), boost::algorithm::token_compress_on); double ScaHFX = boost::lexical_cast(results.back()); orbitals.setScaHFX(ScaHFX); XTP_LOG(Log::error, *_pLog) << "DFT with " << ScaHFX << " of HF exchange!" << flush; } std::string::size_type dim_pos = line.find("Basis Dimension"); if (dim_pos != std::string::npos) { boost::algorithm::split(results, line, boost::is_any_of(" "), boost::algorithm::token_compress_on); std::string dim = results[4]; // The 4th element of results vector is the Basis Dim boost::trim(dim); levels = boost::lexical_cast(dim); XTP_LOG(Log::info, *_pLog) << "Basis Dimension: " << levels << flush; XTP_LOG(Log::info, *_pLog) << "Energy levels: " << levels << flush; } std::string::size_type OE_pos = line.find("ORBITAL ENERGIES"); if (OE_pos != std::string::npos) { number_of_electrons = 0; tools::getline(input_file, line); tools::getline(input_file, line); tools::getline(input_file, line); if (line.find("E(Eh)") == std::string::npos) { XTP_LOG(Log::error, *_pLog) << "Warning: Orbital Energies not found in log file" << flush; } for (Index i = 0; i < levels; i++) { results = GetLineAndSplit(input_file, " "); std::string no = results[0]; boost::trim(no); Index levelnumber = boost::lexical_cast(no); if (levelnumber != i) { XTP_LOG(Log::error, *_pLog) << "Have a look at the orbital energies " "something weird is going on" << flush; } std::string oc = results[1]; boost::trim(oc); double occ = boost::lexical_cast(oc); // We only count alpha electrons, each orbital must be empty or doubly // occupied if (occ == 2 || occ == 1) { number_of_electrons++; occupancy[i] = occ; if (occ == 1) { XTP_LOG(Log::error, *_pLog) << "Watch out! No distinction between alpha and beta " "electrons. Check if occ = 1 is suitable for your " "calculation " << flush; } } else if (occ == 0) { occupancy[i] = occ; } else { throw runtime_error( "Only empty or doubly occupied orbitals are allowed not " "running the right kind of DFT calculation"); } std::string e = results[2]; boost::trim(e); energies[i] = boost::lexical_cast(e); } } std::string::size_type success = line.find("* SUCCESS *"); if (success != std::string::npos) { found_success = true; } } XTP_LOG(Log::info, *_pLog) << "Alpha electrons: " << number_of_electrons << flush; Index occupied_levels = number_of_electrons; Index unoccupied_levels = levels - occupied_levels; XTP_LOG(Log::info, *_pLog) << "Occupied levels: " << occupied_levels << flush; XTP_LOG(Log::info, *_pLog) << "Unoccupied levels: " << unoccupied_levels << flush; /************************************************************/ // copying information to the orbitals object orbitals.setBasisSetSize(levels); orbitals.setNumberOfAlphaElectrons(number_of_electrons); orbitals.setNumberOfOccupiedLevels(occupied_levels); // copying energies to a vector orbitals.MOs().eigenvalues().resize(levels); //_level = 1; for (Index i = 0; i < levels; i++) { orbitals.MOs().eigenvalues()[i] = energies[i]; } XTP_LOG(Log::error, *_pLog) << "Done reading Log file" << flush; return found_success; } template void Orca::GetCoordinates(T& mol, string& line, ifstream& input_file) const { std::string::size_type coordinates_pos = line.find("CARTESIAN COORDINATES (ANGSTROEM)"); using Atom = typename std::iterator_traits::value_type; if (coordinates_pos != std::string::npos) { XTP_LOG(Log::error, *_pLog) << "Getting the coordinates" << flush; bool has_QMAtoms = mol.size() > 0; // three garbage lines tools::getline(input_file, line); // now starts the data in format // _id type Qnuc x y z vector row = GetLineAndSplit(input_file, "\t "); Index nfields = Index(row.size()); Index atom_id = 0; while (nfields == 4) { string atom_type = row.at(0); double x = boost::lexical_cast(row.at(1)); double y = boost::lexical_cast(row.at(2)); double z = boost::lexical_cast(row.at(3)); row = GetLineAndSplit(input_file, "\t "); nfields = Index(row.size()); Eigen::Vector3d pos(x, y, z); pos *= tools::conv::ang2bohr; if (has_QMAtoms == false) { mol.push_back(Atom(atom_id, atom_type, pos)); } else { Atom& pAtom = mol.at(atom_id); pAtom.setPos(pos); } atom_id++; } } } bool Orca::CheckLogFile() { // check if the log file exists ifstream input_file(_run_dir + "/" + _log_file_name); if (input_file.fail()) { XTP_LOG(Log::error, *_pLog) << "Orca LOG is not found" << flush; return false; }; std::string line; while (input_file) { tools::getline(input_file, line); boost::trim(line); std::string::size_type error = line.find("FATAL ERROR ENCOUNTERED"); if (error != std::string::npos) { XTP_LOG(Log::error, *_pLog) << "ORCA encountered a fatal error, maybe a " "look in the log file may help." << flush; return false; } error = line.find( "mpirun detected that one or more processes exited with non-zero " "status"); if (error != std::string::npos) { XTP_LOG(Log::error, *_pLog) << "ORCA had an mpi problem, maybe your openmpi version is not good." << flush; return false; } } return true; } // Parses the Orca gbw file and stores data in the Orbitals object bool Orca::ParseMOsFile(Orbitals& orbitals) { if (!CheckLogFile()) { return false; } std::vector coefficients; Index basis_size = orbitals.getBasisSetSize(); if (basis_size == 0) { throw runtime_error( "Basis size not set, calculator does not parse log file first"); } XTP_LOG(Log::error, *_pLog) << "Reading the gbw file, this may or may not work so be careful: " << flush; ifstream infile; infile.open(_run_dir + "/" + _mo_file_name, ios::binary | ios::in); if (!infile) { throw runtime_error("Could not open " + _mo_file_name + " file"); } infile.seekg(24, ios::beg); std::array buffer; infile.read(buffer.data(), 8); if (!infile) { infile.close(); return false; } Index offset = *((Index*)buffer.data()); infile.seekg(offset, ios::beg); infile.read(buffer.data(), 4); if (!infile) { infile.close(); return false; } int op_read = *((int*)buffer.data()); infile.seekg(offset + 4, ios::beg); infile.read(buffer.data(), 4); if (!infile) { infile.close(); return false; } int dim_read = *((int*)buffer.data()); infile.seekg(offset + 8, ios::beg); XTP_LOG(Log::info, *_pLog) << "Number of operators: " << op_read << " Basis dimension: " << dim_read << flush; Index n = op_read * dim_read * dim_read; for (Index i = 0; i < n; i++) { infile.read(buffer.data(), 8); if (!infile) { infile.close(); return false; } double mocoeff = *((double*)buffer.data()); coefficients.push_back(mocoeff); } infile.close(); // i -> MO, j -> AO orbitals.MOs().eigenvectors().resize(basis_size, basis_size); for (Index i = 0; i < basis_size; i++) { for (Index j = 0; j < basis_size; j++) { orbitals.MOs().eigenvectors()(j, i) = coefficients[j * basis_size + i]; } } ReorderOutput(orbitals); XTP_LOG(Log::error, *_pLog) << "Done parsing" << flush; return true; } std::string Orca::indent(const double& number) { std::stringstream ssnumber; if (number >= 0) { ssnumber << " "; } else { ssnumber << " "; } ssnumber << setiosflags(ios::fixed) << setprecision(15) << std::scientific << number; std::string snumber = ssnumber.str(); return snumber; } std::string Orca::CreateInputSection(const std::string& key) const { std::stringstream stream; std::string section = key.substr(key.find(".") + 1); stream << "%" << section; if (KeywordIsSingleLine(key)) { stream << " " << this->_settings.get(key) << "\n"; } else { stream << "\n" << this->_settings.get(key) << "\n" << "end\n"; } return stream.str(); } bool Orca::KeywordIsSingleLine(const std::string& key) const { tools::Tokenizer values(this->_settings.get(key), " "); std::vector words; values.ToVector(words); return ((words.size() <= 1) ? true : false); } std::string Orca::WriteMethod() const { std::stringstream stream; std::string opt = (_settings.get("optimize")) ? "Opt" : ""; const tools::Property& orca = _settings.property("orca"); std::string user_method = (orca.exists("method")) ? orca.get("method").as() : ""; std::string convergence = ""; if (!orca.exists("scf")) { convergence = this->_convergence_map.at(_settings.get("convergence_tightness")); } stream << "! DFT " << this->GetOrcaFunctionalName() << " " << convergence << " " << opt << " " // additional properties provided by the user << user_method << "\n"; return stream.str(); } std::string Orca::GetOrcaFunctionalName() const { if (!tools::VotcaShareSet()) { return _settings.get("functional"); } else { tools::Property all_functionals; auto xml_file = tools::GetVotcaShare() + "/xtp/data/orca_functional_names.xml"; all_functionals.LoadFromXML(xml_file); const tools::Property& functional_names = all_functionals.get("functionals"); std::string input_name = _settings.get("functional"); // Some functionals have a composed named separated by a space // In the case just look for the first part std::size_t plus = input_name.find(' '); if (plus != std::string::npos) { input_name = input_name.substr(0, plus); } if (functional_names.exists(input_name)) { return functional_names.get(input_name).as(); } else { std::ostringstream oss; oss << "The libxc functional \"" << input_name << "\"\n" << "doesn't seem to have a corresponding name in Orca.\n" << "Check the " << "\"${VOTCASHARE}/xtp/data/orca_functional_names.xml\"" << "file for the whole list of known libxc/orca functionals"; throw runtime_error(oss.str()); } } } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/qmpackages/orca.h000066400000000000000000000065031412152066400177220ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_ORCA_H #define VOTCA_XTP_ORCA_H // Local VOTCA includes #include "votca/xtp/orbreorder.h" #include "votca/xtp/qmpackage.h" namespace votca { namespace xtp { /** \brief Wrapper for the ORCA program The ORCA class executes the ORCA package and extracts information from its log and io files */ class Orbitals; class Orca : public QMPackage { public: std::string getPackageName() const override { return "orca"; } void Initialize(const tools::Property& options) override; bool WriteInputFile(const Orbitals& orbitals) override; bool WriteShellScript(); bool Run() override; void CleanUp() override; bool CheckLogFile(); bool ParseLogFile(Orbitals& orbitals) override; bool ParseMOsFile(Orbitals& orbitals) override; StaticSegment GetCharges() const override; Eigen::Matrix3d GetPolarizability() const override; protected: const std::array& ShellMulitplier() const final { return _multipliers; } const std::array& ShellReorder() const final { return _reorderList; } private: // clang-format off std::array _multipliers={{ 1, //s 1,1,1, //p 1,1,1,1,1, //d -1,1,1,1,1,1,-1, //f -1,-1,1,1,1,1,1,-1,-1, //g -1,-1,-1,1,1,1,1,1,-1,-1,-1, //h -1,-1,-1,-1,1,1,1,1,1,-1,-1,-1,-1 //i }}; std::array _reorderList{{ 0, //s 0, 1,-1, //p 0,1,-1,2,-2, //d 0,1,-1,2,-2,3,-3, //f 0,1,-1,2,-2,3,-3,4,-4, //g 0,1,-1,2,-2,3,-3,4,-4,5,-5, //h 0,1,-1,2,-2,3,-3,4,-4,5,-5,6,-6 //i }}; // clang-format on std::string indent(const double& number); void WriteBasisset(const QMMolecule& qmatoms, std::string& bs_name, std::string& el_file_name); void WriteCoordinates(std::ofstream& inp_file, const QMMolecule&); void WriteECP(std::ofstream& inp_file, const QMMolecule&); void WriteBackgroundCharges(); void WriteChargeOption() override; template void GetCoordinates(T& mol, std::string& line, std::ifstream& input_file) const; std::string WriteMethod() const; std::string CreateInputSection(const std::string& key) const; bool KeywordIsSingleLine(const std::string& key) const; std::string GetOrcaFunctionalName() const; std::unordered_map _convergence_map{ {"low", "LooseSCF"}, {"normal", "StrongSCF"}, {"tight", "TightSCF"}, {"verytight", "VeryTightSCF"}, {"none", ""}}; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ORCA_H xtp-2021.2/src/libxtp/qmpackages/xtpdft.cc000066400000000000000000000061411412152066400204430ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include #include // Third party includes #include #include #include // VOTCA includes #include // Local private VOTCA includes #include "xtpdft.h" namespace votca { namespace xtp { using namespace std; void XTPDFT::Initialize(const tools::Property& options) { const std::string& job_name = options.ifExistsReturnElseReturnDefault("job_name", "votca"); _log_file_name = job_name + ".orb"; _mo_file_name = _log_file_name; _xtpdft_options = ParseCommonOptions(options); } bool XTPDFT::WriteInputFile(const Orbitals& orbitals) { _orbitals = orbitals; _orbitals.setQMpackage(getPackageName()); return true; } /** * Run calls DFTENGINE */ bool XTPDFT::Run() { DFTEngine xtpdft; xtpdft.Initialize(_xtpdft_options); xtpdft.setLogger(_pLog); if (_settings.get("write_charges")) { xtpdft.setExternalcharges(&_externalsites); } bool success = xtpdft.Evaluate(_orbitals); std::string file_name = _run_dir + "/" + _log_file_name; XTP_LOG(Log::error, *_pLog) << "Writing result to " << _log_file_name << flush; _orbitals.WriteToCpt(file_name); return success; } void XTPDFT::CleanUp() { if (_cleanup.size() != 0) { XTP_LOG(Log::info, *_pLog) << "Removing " << _cleanup << " files" << flush; tools::Tokenizer tok_cleanup(_cleanup, ", "); std::vector cleanup_info; tok_cleanup.ToVector(cleanup_info); for (const std::string& substring : cleanup_info) { if (substring == "log") { std::string file_name = _run_dir + "/" + _log_file_name; remove(file_name.c_str()); } } } return; } /** * Dummy, because XTPDFT adds info to orbitals directly */ bool XTPDFT::ParseMOsFile(Orbitals&) { return true; } bool XTPDFT::ParseLogFile(Orbitals& orbitals) { try { std::string file_name = _run_dir + "/" + _log_file_name; orbitals.ReadFromCpt(file_name); XTP_LOG(Log::error, *_pLog) << (boost::format("QM energy[Hrt]: %4.8f ") % orbitals.getDFTTotalEnergy()) .str() << flush; } catch (std::runtime_error& error) { XTP_LOG(Log::error, *_pLog) << "Reading" << _log_file_name << " failed" << flush; return false; } return true; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/qmpackages/xtpdft.h000066400000000000000000000052711412152066400203100ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_XTPDFT_H #define VOTCA_XTP_XTPDFT_H // Standard includes #include // Local VOTCA includes #include "votca/xtp/dftengine.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/orbreorder.h" #include "votca/xtp/polarsite.h" #include "votca/xtp/qmpackage.h" namespace votca { namespace xtp { /** \brief Wrapper for the internal XTP DFT engine */ class XTPDFT : public QMPackage { public: std::string getPackageName() const final { return "xtp"; } void Initialize(const tools::Property& options) final; bool WriteInputFile(const Orbitals& orbitals) final; bool Run() final; void CleanUp() final; bool CheckLogFile(); bool ParseLogFile(Orbitals& orbitals) final; bool ParseMOsFile(Orbitals& orbitals) final; StaticSegment GetCharges() const final { throw std::runtime_error( "If you want partial charges just run the 'partialcharges' calculator"); } Eigen::Matrix3d GetPolarizability() const final { throw std::runtime_error( "GetPolarizability() is not implemented for xtpdft"); } protected: const std::array& ShellMulitplier() const final { return _multipliers; } const std::array& ShellReorder() const final { return _reorderList; } private: // clang-format off std::array _multipliers={{ 1, //s 1,1,1, //p 1,1,1,1,1, //d 1,1,1,1,1,1,1, //f 1,1,1,1,1,1,1,1,1, //g 1,1,1,1,1,1,1,1,1,1,1, //h 1,1,1,1,1,1,1,1,1,1,1,1,1 //i }}; std::array _reorderList={{ 0, //s 0,0,0, //p 0,0,0,0,0, //d 0,0,0,0,0,0,0, //f 0,0,0,0,0,0,0,0,0, //g 0,0,0,0,0,0,0,0,0,0,0, //h 0,0,0,0,0,0,0,0,0,0,0,0,0, //i }}; // clang-format on void WriteChargeOption() final { return; } tools::Property _xtpdft_options; Orbitals _orbitals; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_XTPDFT_H xtp-2021.2/src/libxtp/qmpair.cc000066400000000000000000000105051412152066400163060ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ /// For earlier commit history see ctp commit /// 77795ea591b29e664153f9404c8655ba28dc14e9 // Local VOTCA includes #include "votca/xtp/qmpair.h" #include "votca/xtp/atomcontainer.h" #include "votca/xtp/segment.h" namespace votca { namespace xtp { QMPair::QMPair(Index id, const Segment* seg1, const Segment* seg2, const Eigen::Vector3d& delta_R) : _id(id), _R(delta_R) { _segments.first = seg1; _segments.second = seg2; } Segment QMPair::Seg2PbCopy() const { const Eigen::Vector3d& r1 = _segments.first->getPos(); const Eigen::Vector3d& r2 = _segments.second->getPos(); Segment seg2pbc = Segment(*(_segments.second)); // Check whether pair formed across periodic boundary if ((r2 - r1 - _R).norm() > 1e-8) { seg2pbc.Translate(r1 - r2 + _R); } return seg2pbc; } void QMPair::SetupCptTable(CptTable& table) const { table.addCol(_id, "index", HOFFSET(data, id)); table.addCol(_segments.first->getId(), "Seg1Id", HOFFSET(data, Seg1Id)); table.addCol(_segments.second->getId(), "Seg2Id", HOFFSET(data, Seg2Id)); table.addCol(_R[0], "delta_Rx", HOFFSET(data, RX)); table.addCol(_R[1], "delta_Ry", HOFFSET(data, RY)); table.addCol(_R[2], "delta_Rz", HOFFSET(data, RZ)); std::string ptype = get_name(_pair_type); table.addCol(ptype, "pair_type", HOFFSET(data, pair_type)); table.addCol(_lambda0.getValue(QMStateType::Electron), "lambda0e", HOFFSET(data, lambda0e)); table.addCol(_lambda0.getValue(QMStateType::Hole), "lambda0h", HOFFSET(data, lambda0h)); table.addCol(_lambda0.getValue(QMStateType::Singlet), "lambda0s", HOFFSET(data, lambda0s)); table.addCol(_lambda0.getValue(QMStateType::Triplet), "lambda0t", HOFFSET(data, lambda0t)); table.addCol(_Jeff2.getValue(QMStateType::Electron), "jeff2e", HOFFSET(data, jeff2e)); table.addCol(_Jeff2.getValue(QMStateType::Hole), "jeff2h", HOFFSET(data, jeff2h)); table.addCol(_Jeff2.getValue(QMStateType::Singlet), "jeff2s", HOFFSET(data, jeff2s)); table.addCol(_Jeff2.getValue(QMStateType::Triplet), "jeff2t", HOFFSET(data, jeff2t)); } void QMPair::WriteData(data& d) const { d.id = _id; d.Seg1Id = _segments.first->getId(); d.Seg2Id = _segments.second->getId(); d.RX = _R[0]; d.RY = _R[1]; d.RZ = _R[2]; std::string ptype = get_name(_pair_type); d.pair_type = new char[ptype.length() + 1]; strcpy(d.pair_type, ptype.c_str()); d.lambda0e = _lambda0.getValue(QMStateType::Electron); d.lambda0h = _lambda0.getValue(QMStateType::Hole); d.lambda0s = _lambda0.getValue(QMStateType::Singlet); d.lambda0t = _lambda0.getValue(QMStateType::Triplet); d.jeff2e = _Jeff2.getValue(QMStateType::Electron); d.jeff2h = _Jeff2.getValue(QMStateType::Hole); d.jeff2s = _Jeff2.getValue(QMStateType::Singlet); d.jeff2t = _Jeff2.getValue(QMStateType::Triplet); } void QMPair::ReadData(const data& d, const std::vector& segments) { _id = d.id; _R[0] = d.RX; _R[1] = d.RY; _R[2] = d.RZ; std::string type_enum = std::string(d.pair_type); _pair_type = QMPair::get_Enum(type_enum); free(d.pair_type); _lambda0.setValue(d.lambda0e, QMStateType::Electron); _lambda0.setValue(d.lambda0h, QMStateType::Hole); _lambda0.setValue(d.lambda0s, QMStateType::Singlet); _lambda0.setValue(d.lambda0t, QMStateType::Triplet); _Jeff2.setValue(d.jeff2e, QMStateType::Electron); _Jeff2.setValue(d.jeff2h, QMStateType::Hole); _Jeff2.setValue(d.jeff2s, QMStateType::Singlet); _Jeff2.setValue(d.jeff2t, QMStateType::Triplet); _segments.first = &segments[d.Seg1Id]; _segments.second = &segments[d.Seg2Id]; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/qmregion.cc000066400000000000000000000237371412152066400166510ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/qmregion.h" #include "votca/xtp/aomatrix.h" #include "votca/xtp/classicalsegment.h" #include "votca/xtp/density_integration.h" #include "votca/xtp/eeinteractor.h" #include "votca/xtp/gwbse.h" #include "votca/xtp/polarregion.h" #include "votca/xtp/staticregion.h" #include "votca/xtp/vxc_grid.h" namespace votca { namespace xtp { void QMRegion::Initialize(const tools::Property& prop) { if (this->_id != 0) { throw std::runtime_error( this->identify() + " must always be region 0. Currently only one qm region is possible."); } std::string statestring = prop.ifExistsReturnElseThrowRuntimeError("state"); _initstate.FromString(statestring); if (_initstate.Type() == QMStateType::Hole || _initstate.Type() == QMStateType::Electron) { throw std::runtime_error( "Charged QM Regions are not implemented currently"); } if (_initstate.Type().isExciton() || _initstate.Type().isGWState()) { _do_gwbse = true; _gwbseoptions.add("gwbse", ""); tools::Property& prop_gwbse = _gwbseoptions.get("gwbse"); prop_gwbse = prop.get("gwbse"); if (prop.exists("statetracker")) { tools::Property filter = prop.get("statetracker"); _statetracker.setLogger(&_log); _statetracker.Initialize(filter); _statetracker.setInitialState(_initstate); _statetracker.PrintInfo(); } else { throw std::runtime_error( "No statetracker options for excited states found"); } } _grid_accuracy_for_ext_interaction = prop.ifExistsReturnElseReturnDefault( "grid_for_potential", _grid_accuracy_for_ext_interaction); _DeltaE = prop.ifExistsReturnElseReturnDefault("tolerance_energy", _DeltaE); _DeltaD = prop.ifExistsReturnElseReturnDefault("tolerance_density", _DeltaD); _dftoptions = prop.get("options_dft"); } bool QMRegion::Converged() const { if (!_E_hist.filled()) { return false; } double Echange = _E_hist.getDiff(); double Dchange = _Dmat_hist.getDiff().norm() / double(_Dmat_hist.back().cols()); double Dmax = _Dmat_hist.getDiff().cwiseAbs().maxCoeff(); std::string info = "not converged"; bool converged = false; if (Dchange < _DeltaD && Dmax < _DeltaD && std::abs(Echange) < _DeltaE) { info = "converged"; converged = true; } XTP_LOG(Log::error, _log) << " Region:" << this->identify() << " " << this->getId() << " is " << info << " deltaE=" << Echange << " RMS Dmat=" << Dchange << " MaxDmat=" << Dmax << std::flush; return converged; } void QMRegion::Evaluate(std::vector >& regions) { std::vector interact_energies = ApplyInfluenceOfOtherRegions(regions); double e_ext = std::accumulate(interact_energies.begin(), interact_energies.end(), 0.0); XTP_LOG(Log::info, _log) << TimeStamp() << " Calculated interaction potentials with other regions. E[hrt]= " << e_ext << std::flush; XTP_LOG(Log::info, _log) << "Writing inputs" << std::flush; _qmpackage->setRunDir(_workdir); _qmpackage->WriteInputFile(_orb); XTP_LOG(Log::error, _log) << "Running DFT calculation" << std::flush; bool run_success = _qmpackage->Run(); if (!run_success) { _info = false; _errormsg = "DFT-run failed"; return; } bool Logfile_parse = _qmpackage->ParseLogFile(_orb); if (!Logfile_parse) { _info = false; _errormsg = "Parsing DFT logfile failed."; return; } bool Orbfile_parse = _qmpackage->ParseMOsFile(_orb); if (!Orbfile_parse) { _info = false; _errormsg = "Parsing DFT orbfile failed."; return; } QMState state = QMState("groundstate"); double energy = _orb.getDFTTotalEnergy(); if (_do_gwbse) { GWBSE gwbse(_orb); gwbse.setLogger(&_log); gwbse.Initialize(_gwbseoptions); gwbse.Evaluate(); state = _statetracker.CalcStateAndUpdate(_orb); if (state.Type().isExciton()) { energy += _orb.getExcitedStateEnergy(state); } else { // if unoccupied, add QP level energy if (state.StateIdx() > _orb.getHomo()) { energy += _orb.getExcitedStateEnergy(state); } else { // if unoccupied, subtract QP level energy energy -= _orb.getExcitedStateEnergy(state); } } } _E_hist.push_back(energy); _Dmat_hist.push_back(_orb.DensityMatrixFull(state)); return; } void QMRegion::push_back(const QMMolecule& mol) { if (_orb.QMAtoms().size() == 0) { _orb.QMAtoms() = mol; } else { _orb.QMAtoms().AddContainer(mol); } _size++; } double QMRegion::charge() const { double charge = 0.0; if (!_do_gwbse) { Index nuccharge = 0; for (const QMAtom& a : _orb.QMAtoms()) { nuccharge += a.getNuccharge(); } Index electrons = _orb.getNumberOfAlphaElectrons() * 2; charge = double(nuccharge - electrons); } else { QMState state = _statetracker.InitialState(); if (state.Type().isExciton()) { charge = 0.0; } else if (state.Type().isSingleParticleState()) { if (state.StateIdx() <= _orb.getHomo()) { charge = +1.0; } else { charge = -1.0; } } } return charge; } void QMRegion::AppendResult(tools::Property& prop) const { prop.add("E_total", std::to_string(_E_hist.back() * tools::conv::hrt2ev)); if (_do_gwbse) { prop.add("Initial_State", _statetracker.InitialState().ToString()); prop.add("Final_State", _statetracker.CalcState(_orb).ToString()); } } void QMRegion::Reset() { std::string dft_package_name = _dftoptions.get("package.name").as(); _qmpackage = std::unique_ptr( QMPackageFactory::QMPackages().Create(dft_package_name)); _qmpackage->setLog(&_log); _qmpackage->Initialize(_dftoptions); Index charge = 0; if (_initstate.Type() == QMStateType::Electron) { charge = -1; } else if (_initstate.Type() == QMStateType::Hole) { charge = +1; } _qmpackage->setCharge(charge); return; } double QMRegion::InteractwithQMRegion(const QMRegion&) { throw std::runtime_error( "QMRegion-QMRegion interaction is not implemented yet."); return 0.0; } double QMRegion::InteractwithPolarRegion(const PolarRegion& region) { _qmpackage->AddRegion(region); return 0.0; } double QMRegion::InteractwithStaticRegion(const StaticRegion& region) { _qmpackage->AddRegion(region); return 0.0; } void QMRegion::WritePDB(csg::PDBWriter& writer) const { writer.WriteContainer(_orb.QMAtoms()); } void QMRegion::AddNucleiFields(std::vector& segments, const StaticSegment& seg) const { eeInteractor e; #pragma omp parallel for for (Index i = 0; i < Index(segments.size()); ++i) { e.ApplyStaticField(seg, segments[i]); } } void QMRegion::ApplyQMFieldToPolarSegments( std::vector& segments) const { Vxc_Grid grid; AOBasis basis = _orb.SetupDftBasis(); // grid needs a basis in scope all the time grid.GridSetup(_grid_accuracy_for_ext_interaction, _orb.QMAtoms(), basis); DensityIntegration numint(grid); QMState state = QMState("groundstate"); if (_do_gwbse) { state = _statetracker.CalcState(_orb); } Eigen::MatrixXd dmat = _orb.DensityMatrixFull(state); double Ngrid = numint.IntegrateDensity(dmat); AOOverlap overlap; overlap.Fill(basis); double N_comp = dmat.cwiseProduct(overlap.Matrix()).sum(); if (std::abs(Ngrid - N_comp) > 0.001) { XTP_LOG(Log::error, _log) << "=======================" << std::flush; XTP_LOG(Log::error, _log) << "WARNING: Calculated Densities at Numerical Grid, Number of " "electrons " << Ngrid << " is far away from the the real value " << N_comp << ", you should increase the accuracy of the integration grid." << std::flush; } #pragma omp parallel for for (Index i = 0; i < Index(segments.size()); ++i) { PolarSegment& seg = segments[i]; for (PolarSite& site : seg) { site.V_noE() += numint.IntegrateField(site.getPos()); } } StaticSegment seg(_orb.QMAtoms().getType(), _orb.QMAtoms().getId()); for (const QMAtom& atom : _orb.QMAtoms()) { seg.push_back(StaticSite(atom, double(atom.getNuccharge()))); } AddNucleiFields(segments, seg); } void QMRegion::WriteToCpt(CheckpointWriter& w) const { w(_id, "id"); w(identify(), "type"); w(_size, "size"); w(_do_gwbse, "GWBSE"); w(_initstate.ToString(), "initial_state"); w(_grid_accuracy_for_ext_interaction, "ext_grid"); CheckpointWriter v = w.openChild("orbitals"); _orb.WriteToCpt(v); CheckpointWriter v2 = w.openChild("E-hist"); _E_hist.WriteToCpt(v2); CheckpointWriter v3 = w.openChild("D-hist"); _Dmat_hist.WriteToCpt(v3); if (_do_gwbse) { CheckpointWriter v4 = w.openChild("statefilter"); _statetracker.WriteToCpt(v4); } } void QMRegion::ReadFromCpt(CheckpointReader& r) { r(_id, "id"); r(_size, "size"); r(_do_gwbse, "GWBSE"); std::string state; r(state, "initial_state"); _initstate.FromString(state); r(_grid_accuracy_for_ext_interaction, "ext_grid"); CheckpointReader rr = r.openChild("orbitals"); _orb.ReadFromCpt(rr); CheckpointReader rr2 = r.openChild("E-hist"); _E_hist.ReadFromCpt(rr2); CheckpointReader rr3 = r.openChild("D-hist"); _Dmat_hist.ReadFromCpt(rr3); if (_do_gwbse) { CheckpointReader rr4 = r.openChild("statefilter"); _statetracker.ReadFromCpt(rr4); } } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/qmstate.cc000066400000000000000000000143451412152066400165010ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include // Third party includes #include #include #include #include // Local VOTCA includes #include "votca/xtp/qmstate.h" namespace votca { namespace xtp { std::string QMStateType::ToString() const { std::string identifier = ""; switch (_type) { case QMStateType::Singlet: identifier = "s"; break; case QMStateType::Triplet: identifier = "t"; break; case QMStateType::PQPstate: identifier = "pqp"; break; case QMStateType::DQPstate: identifier = "dqp"; break; case QMStateType::KSstate: identifier = "ks"; break; case QMStateType::Gstate: identifier = "n"; break; case QMStateType::Hole: identifier = "h"; break; case QMStateType::Electron: identifier = "e"; break; } return identifier; } std::string QMStateType::ToLongString() const { std::string identifier = ""; switch (_type) { case QMStateType::Singlet: identifier = "singlet"; break; case QMStateType::Triplet: identifier = "triplet"; break; case QMStateType::PQPstate: identifier = "pert-qparticle"; break; case QMStateType::DQPstate: identifier = "diag-qparticle"; break; case QMStateType::KSstate: identifier = "Kohn-Sham-orbital"; break; case QMStateType::Gstate: identifier = "groundstate"; break; case QMStateType::Hole: identifier = "hole"; break; case QMStateType::Electron: identifier = "electron"; break; } return identifier; } void QMStateType::FromString(const std::string& statetypestring) { std::string lower = boost::algorithm::to_lower_copy(statetypestring); boost::trim(lower); if (lower == "s" || lower == "singlet") { _type = QMStateType::Singlet; } else if (lower == "t" || lower == "triplet") { _type = QMStateType::Triplet; } else if (lower == "pqp" || lower == "pert-qparticle") { _type = QMStateType::PQPstate; } else if (lower == "dqp" || lower == "diag-qparticle" || lower == "qpdiag") { _type = QMStateType::DQPstate; } else if (lower == "ks" || lower == "kohn-sham-orbital") { _type = QMStateType::KSstate; } else if (lower == "n" || lower == "groundstate" || lower == "gs") { _type = QMStateType::Gstate; } else if (lower == "h" || lower == "hole") { _type = QMStateType::Hole; } else if (lower == "e" || lower == "electron") { _type = QMStateType::Electron; } else { throw std::runtime_error("Statetype:" + statetypestring + " not recognized"); } } std::string QMState::ToLongString() const { Index index = _index; if (_type == QMStateType::Singlet || _type == QMStateType::Triplet) { index++; } else if (_type == QMStateType::Gstate || _type == QMStateType::Electron || _type == QMStateType::Hole) { return _type.ToLongString(); } std::string result = _type.ToLongString() + (boost::format(" %i") % index).str(); if (_transition) { result = "Groundstate to " + result; } return result; } std::string QMState::ToString() const { Index index = _index; if (_type == QMStateType::Singlet || _type == QMStateType::Triplet) { index++; } else if (_type == QMStateType::Gstate || _type == QMStateType::Electron || _type == QMStateType::Hole) { return _type.ToString(); } std::string result = _type.ToString() + (boost::format("%i") % index).str(); if (_transition) { result = "n2" + result; } return result; } Index QMState::DetermineIndex(const std::string& statestring) { std::smatch search; std::regex reg("[0-9]+"); bool found_integer = std::regex_search(statestring, search, reg); if (!found_integer) { if (_type == QMStateType::Hole || _type == QMStateType::Electron) { return 0; } throw std::runtime_error("Found no index in string: " + statestring); } if (search.size() > 1) { throw std::runtime_error("Found more than 1 index in string: " + statestring); } Index index = boost::lexical_cast(search.str(0)); if (_type.isExciton() || _type == QMStateType::Electron || _type == QMStateType::Hole) { index--; } return index; } QMStateType QMState::DetermineType(const std::string& statestring) { std::regex reg("[^0-9]+"); std::smatch search; bool found_typestring = std::regex_search(statestring, search, reg); if (!found_typestring) { throw std::runtime_error("Found no type in string: " + statestring); } if (search.size() > 1) { throw std::runtime_error("Found more than one type in string: " + statestring); } QMStateType type; type.FromString(search.str(0)); return type; } void QMState::FromString(const std::string& statestring) { std::string lower = boost::algorithm::to_lower_copy(statestring); boost::trim(lower); std::string rest; if (boost::starts_with(lower, "n2")) { _transition = true; rest = lower.substr(2); } else if (boost::starts_with(lower, "groundstate to")) { _transition = true; rest = lower.substr(14); } else { rest = lower; _transition = false; } boost::trim(rest); _type = DetermineType(rest); if (_type != QMStateType::Singlet && _transition == true) { throw std::runtime_error("Transition states only exist for singlets."); } if (_type == QMStateType::Gstate) { _index = -1; } else { _index = DetermineIndex(rest); } } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/qmtool.cc000066400000000000000000000025521412152066400163330ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include "votca/xtp/qmtool.h" #include "votca/xtp/eigen.h" #include namespace votca { namespace xtp { void QMTool::Initialize(const tools::Property& options) { tools::Property user_options = LoadDefaultsAndUpdateWithUserOptions("xtp", options); _job_name = user_options.ifExistsReturnElseReturnDefault( "job_name", _job_name); ParseOptions(user_options); } bool QMTool::Evaluate() { libint2::initialize(); OPENMP::setMaxThreads(_nThreads); std::cout << " Using " << OPENMP::getMaxThreads() << " threads" << std::flush; bool success = Run(); libint2::finalize(); return success; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/rate_engine.cc000066400000000000000000000056411412152066400173020ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/rate_engine.h" namespace votca { namespace xtp { std::ostream& operator<<(std::ostream& out, const Rate_Engine& rate_engine) { out << "Rate engine initialized:\n"; out << " Ratetype:" << rate_engine._ratetype << "\n"; out << " Temperature T[k] = " << rate_engine._temperature * tools::conv::hrt2ev / tools::conv::kB << "\n"; Eigen::Vector3d field = rate_engine._field * tools::conv::hrt2ev / tools::conv::bohr2nm; out << " Electric field[V/nm](x,y,z) =" << field.x() << " " << field.y() << " " << field.z() << " ||F|| " << field.norm() << std::endl; return out; } Rate_Engine::PairRates Rate_Engine::Rate(const QMPair& pair, QMStateType carriertype) const { double charge = 0.0; if (carriertype == QMStateType::Electron) { charge = -1.0; } else if (carriertype == QMStateType::Hole) { charge = 1.0; } double reorg12 = pair.getReorg12(carriertype) + pair.getLambdaO(carriertype); double reorg21 = pair.getReorg21(carriertype) - pair.getLambdaO(carriertype); if (std::abs(reorg12) < 1e-12 || std::abs(reorg21) < 1e-12) { throw std::runtime_error( "Reorganisation energy for a pair is extremely close to zero,\n" " you probably forgot to import reorganisation energies into your " "state " "file."); } double dG_Field = 0.0; if (charge != 0.0) { dG_Field = charge * pair.R().dot(_field); } double dG_Site = pair.getdE12(carriertype); double dG = dG_Site + dG_Field; double J2 = pair.getJeff2(carriertype); PairRates result; if (_ratetype == "marcus") { result.rate12 = Marcusrate(J2, dG, reorg12); result.rate21 = Marcusrate(J2, -dG, reorg21); } else { throw std::runtime_error("Only marcus rates implemented."); } return result; } double Rate_Engine::Marcusrate(double Jeff2, double deltaG, double reorg) const { double hbar = tools::conv::hbar * tools::conv::ev2hrt; return 2 * tools::conv::Pi / hbar * Jeff2 / std::sqrt(4 * tools::conv::Pi * reorg * _temperature) * std::exp(-(deltaG - reorg) * (deltaG - reorg) / (4 * reorg * _temperature)); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/region.cc000066400000000000000000000052231412152066400163010ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include // Local VOTCA includes #include "votca/xtp/polarregion.h" #include "votca/xtp/qmregion.h" #include "votca/xtp/region.h" #include "votca/xtp/staticregion.h" namespace votca { namespace xtp { std::vector Region::ApplyInfluenceOfOtherRegions( std::vector >& regions) { std::vector energies = std::vector(regions.size(), 0.0); for (std::unique_ptr& reg : regions) { Index id = reg->getId(); if (id == this->getId()) { continue; } QMRegion QMdummy(0, _log, ""); StaticRegion Staticdummy(0, _log); PolarRegion Polardummy(0, _log); XTP_LOG(Log::error, _log) << TimeStamp() << " Evaluating interaction between " << this->identify() << " " << this->getId() << " and " << reg->identify() << " " << reg->getId() << std::flush; if (reg->identify() == QMdummy.identify()) { QMRegion* qmregion = dynamic_cast(reg.get()); energies[id] = InteractwithQMRegion(*qmregion); } else if (reg->identify() == Staticdummy.identify()) { StaticRegion* staticregion = dynamic_cast(reg.get()); energies[id] = InteractwithStaticRegion(*staticregion); } else if (reg->identify() == Polardummy.identify()) { PolarRegion* polarregion = dynamic_cast(reg.get()); energies[id] = InteractwithPolarRegion(*polarregion); } else { throw std::runtime_error( "Interaction of regions with types:" + this->identify() + " and " + reg->identify() + " not implemented"); } } return energies; } void Region::AddResults(tools::Property& prop) const { tools::Property& region = prop.add("region", ""); region.setAttribute("type", identify()); region.setAttribute("id", getId()); region.setAttribute("size", size()); region.setAttribute("Tot_charge", (boost::format("%1$1.6e") % charge())); AppendResult(region); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/segment.cc000066400000000000000000000070241412152066400164610ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/segment.h" #include "votca/xtp/atomcontainer.h" namespace votca { namespace xtp { double Segment::getApproxSize() const { std::pair minmax = CalcSpatialMinMax(); return (minmax.first - minmax.second).norm(); } const Atom* Segment::getAtom(Index id) const { for (const Atom& atom : *this) { if (atom.getId() == id) { return &atom; } } return nullptr; } void Segment::WriteToCpt(CheckpointWriter& w) const { AtomContainer::WriteToCpt(w); w(_molecule_ids, "mol_ids"); w(_U_xX_nN.getValue(QMStateType::Electron), "U_xX_nN_e"); w(_U_xX_nN.getValue(QMStateType::Hole), "U_xX_nN_h"); w(_U_xX_nN.getValue(QMStateType::Singlet), "U_xX_nN_s"); w(_U_xX_nN.getValue(QMStateType::Triplet), "U_xX_nN_t"); w(_U_nX_nN.getValue(QMStateType::Electron), "U_nX_nN_e"); w(_U_nX_nN.getValue(QMStateType::Hole), "U_nX_nN_h"); w(_U_nX_nN.getValue(QMStateType::Singlet), "U_nX_nN_s"); w(_U_nX_nN.getValue(QMStateType::Triplet), "U_nX_nN_t"); w(_U_xN_xX.getValue(QMStateType::Electron), "U_xN_xX_e"); w(_U_xN_xX.getValue(QMStateType::Hole), "U_xN_xX_h"); w(_U_xN_xX.getValue(QMStateType::Singlet), "U_xN_xX_s"); w(_U_xN_xX.getValue(QMStateType::Triplet), "U_xN_xX_t"); w(_site_eng.getValue(QMStateType::Electron), "site_eng_e"); w(_site_eng.getValue(QMStateType::Hole), "site_eng_h"); w(_site_eng.getValue(QMStateType::Singlet), "site_eng_s"); w(_site_eng.getValue(QMStateType::Triplet), "site_eng_t"); } void Segment::ReadFromCpt(CheckpointReader& r) { AtomContainer::ReadFromCpt(r); r(_molecule_ids, "mol_ids"); double value; r(value, "U_xX_nN_e"); _U_xX_nN.setValue(value, QMStateType::Electron); r(value, "U_xX_nN_h"); _U_xX_nN.setValue(value, QMStateType::Hole); r(value, "U_xX_nN_s"); _U_xX_nN.setValue(value, QMStateType::Singlet); r(value, "U_xX_nN_t"); _U_xX_nN.setValue(value, QMStateType::Triplet); r(value, "U_nX_nN_e"); _U_nX_nN.setValue(value, QMStateType::Electron); r(value, "U_nX_nN_h"); _U_nX_nN.setValue(value, QMStateType::Hole); r(value, "U_nX_nN_s"); _U_nX_nN.setValue(value, QMStateType::Singlet); r(value, "U_nX_nN_t"); _U_nX_nN.setValue(value, QMStateType::Triplet); r(value, "U_xN_xX_e"); _U_xN_xX.setValue(value, QMStateType::Electron); r(value, "U_xN_xX_h"); _U_xN_xX.setValue(value, QMStateType::Hole); r(value, "U_xN_xX_s"); _U_xN_xX.setValue(value, QMStateType::Singlet); r(value, "U_xN_xX_t"); _U_xN_xX.setValue(value, QMStateType::Triplet); r(value, "site_eng_e"); _site_eng.setValue(value, QMStateType::Electron); r(value, "site_eng_h"); _site_eng.setValue(value, QMStateType::Hole); r(value, "site_eng_s"); _site_eng.setValue(value, QMStateType::Singlet); r(value, "site_eng_t"); _site_eng.setValue(value, QMStateType::Triplet); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/segmentmapper.cc000066400000000000000000000450641412152066400176740ustar00rootroot00000000000000/* * Copyright 2016 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include // Local VOTCA includes #include "votca/xtp/segmentmapper.h" namespace votca { namespace xtp { template SegmentMapper::SegmentMapper(Logger& log) : _log(log) { FillMap(); } template AtomContainer SegmentMapper::map(const Segment& seg, const SegId& segid) const { if (segid.hasFile()) { std::string filename = segid.FileName(); filename = std::regex_replace(filename, std::regex("\\$SEGID"), std::to_string(seg.getId())); filename = std::regex_replace(filename, std::regex("\\$SEGNAME"), seg.getType()); return map(seg, filename); } else { QMState state = segid.getQMState(); return map(seg, state); } } template template Eigen::Vector3d SegmentMapper::CalcWeightedPos( const std::vector& weights, const T& atoms) const { Eigen::Vector3d map_pos = Eigen::Vector3d::Zero(); double map_weight = 0.0; for (Index i = 0; i < Index(atoms.size()); i++) { map_pos += atoms[i]->getPos() * weights[i]; map_weight += weights[i]; } return map_pos = map_pos / map_weight; } template std::vector SegmentMapper::getWeights( const tools::Property& frag) const { std::vector weights; if (frag.exists(_mapatom_xml.at("weights"))) { std::string weights_string = frag.get(_mapatom_xml.at("weights")).template as(); tools::Tokenizer tok_weights(weights_string, " \t\n"); tok_weights.ConvertToVector(weights); } else if (frag.exists("weights")) { std::string weights_string = frag.get("weights").template as(); tools::Tokenizer tok_weights(weights_string, " \t\n"); tok_weights.ConvertToVector(weights); } else { XTP_LOG(Log::error, _log) << " Did not find weights for fragment " << frag.get("name").as() << " Using atomic masses" << std::flush; std::string frags = frag.get(_mapatom_xml.at("atoms")).template as(); tools::Tokenizer tok_atoms(frags, " \t\n"); std::vector atom_strings = tok_atoms.ToVector(); tools::Elements e; for (auto a_string : atom_strings) { tools::Tokenizer tok_atom(a_string, ":"); std::vector entries = tok_atom.ToVector(); if (entries.size() != 2) { throw std::runtime_error("Cannot get weight from Element for " + a_string); } double weight = e.getMass(entries[1]); XTP_LOG(Log::info, _log) << entries[1] << ":" << weight << " "; weights.push_back(weight); } XTP_LOG(Log::error, _log) << std::endl; } return weights; } template void SegmentMapper::ParseFragment(Seginfo& seginfo, const tools::Property& frag) { tools::Tokenizer tok_map_atoms( frag.get(_mapatom_xml["atoms"]).template as(), " \t\n"); std::vector map_atoms = tok_map_atoms.ToVector(); tools::Tokenizer tok_md_atoms(frag.get("mdatoms").as(), " \t\n"); std::vector md_atoms = tok_md_atoms.ToVector(); if (md_atoms.size() != map_atoms.size()) { throw std::runtime_error( "Mapping for segment " + seginfo.segname + " fragment " + frag.get("name").as() + " does not have same numbers of md and " + _mapatom_xml["atoms"] + "." "If you want to leave a qmatom out, place a ':' instead"); } std::vector weights = getWeights(frag); if (md_atoms.size() != weights.size()) { throw std::runtime_error("Mapping for segment " + seginfo.segname + " fragment " + frag.get("name").as() + " does not have same numbers of md and weights. " "If you want to leave a " + _mapatom_xml["name"] + " out, place a '0' instead"); } FragInfo mapfragment; std::vector mapatom_ids; for (Index i = 0; i < Index(map_atoms.size()); i++) { const std::string& map_string = map_atoms[i]; const std::string& md_string = md_atoms[i]; const double& weight = weights[i]; atom_id md_result = StringToMDIndex(md_string); seginfo.mdatoms.push_back(md_result.first); if (map_string == ":") { continue; } atom_id map_result = StringToMapIndex(map_string); mapatom_ids.push_back(map_result.first); seginfo.mapatoms.push_back(map_result); if (Atom::GetElementFromString(md_result.second) != map_result.second) { XTP_LOG(Log::error, _log) << "WARNING: mdatom'" << md_result.second << "' and " << _mapatom_xml["name"] << " '" << map_result.second << "' do not have same element" << std::flush; } mapfragment._mapatom_ids.push_back(map_result); mapfragment._weights.push_back(weight); mapfragment._mdatom_ids.push_back(md_result); } tools::Tokenizer tok_frame(getFrame(frag), " \t\n"); std::vector frame; tok_frame.ConvertToVector(frame); if (frame.size() > 3) { throw std::runtime_error( "Local frame for segment " + seginfo.segname + " fragment " + frag.get("name").as() + " has more than 3 atoms, please specify only up to three atoms"); } else if (frame.empty()) { throw std::runtime_error("No local frame for segment " + seginfo.segname + " fragment " + frag.get("name").as() + " specified"); } for (Index atomid : frame) { if (std::find(mapatom_ids.begin(), mapatom_ids.end(), atomid) == mapatom_ids.end()) { throw std::runtime_error("Atom " + std::to_string(atomid) + " in local frame cannot be found in " + _mapatom_xml["atoms"] + "."); } } mapfragment._map_local_frame = frame; seginfo.fragments.push_back(mapfragment); } template void SegmentMapper::LoadMappingFile(const std::string& mapfile) { tools::Property topology_map; topology_map.LoadFromXML(mapfile); std::string molkey = "topology.molecules.molecule"; std::vector molecules = topology_map.Select(molkey); std::string segkey = "segments.segment"; for (tools::Property* mol : molecules) { std::vector segments = mol->Select(segkey); for (tools::Property* seg : segments) { Seginfo seginfo; std::string coordfile_key = _mapatom_xml["coords"] + "_*"; std::vector files = seg->Select(coordfile_key); for (tools::Property* file : files) { seginfo.coordfiles[file->name()] = file->as(); } std::string segname = seg->get("name").as(); seginfo.segname = segname; std::string fragkey = "fragments.fragment"; seginfo.map2md = seg->ifExistsReturnElseThrowRuntimeError("map2md"); std::vector fragments = seg->Select(fragkey); for (tools::Property* frag : fragments) { ParseFragment(seginfo, *frag); } Index map_atom_min_id = std::min_element(seginfo.mapatoms.begin(), seginfo.mapatoms.end(), [](const atom_id& a, const atom_id& b) { return a.first < b.first; }) ->first; if (map_atom_min_id != 0) { throw std::runtime_error( _mapatom_xml["atoms"] + " for segment " + seginfo.segname + " do not start at zero index. Each segment " "should have its own coordinate file. If you use an old ctp " "mapping file run 'xtp_update_mapfile' on it."); } seginfo.minmax = CalcAtomIdRange(seginfo.mdatoms); _segment_info[segname] = seginfo; } } } template std::pair SegmentMapper::StringToMapIndex( const std::string& map_string) const { tools::Tokenizer tok(map_string, ":"); std::vector result = tok.ToVector(); if (result.size() != 2) { throw std::runtime_error("Entry " + map_string + " is not properly formatted."); } return std::pair(std::stoi(result[0]), result[1]); } template std::pair SegmentMapper::StringToMDIndex( const std::string& md_string) const { tools::Tokenizer tok(md_string, ":"); std::vector result = tok.ToVector(); if (result.size() != 3) { throw std::runtime_error("Entry " + md_string + " is not properly formatted."); } Index atomid = 0; try { atomid = std::stoi(result[2]); } catch (std::invalid_argument&) { throw std::runtime_error("Atom entry " + md_string + " is not well formatted"); } return std::pair(atomid, result[1]); } template std::pair SegmentMapper::CalcAtomIdRange( const std::vector& seg) const { Index max_res_id = *std::max_element(seg.begin(), seg.end()); Index min_res_id = *std::min_element(seg.begin(), seg.end()); return std::pair(min_res_id, max_res_id); } template std::pair SegmentMapper::CalcAtomIdRange( const Segment& seg) const { Index max_res_id = std::max_element(seg.begin(), seg.end(), [](const Atom& a, const Atom& b) { return a.getId() < b.getId(); }) ->getId(); Index min_res_id = std::min_element(seg.begin(), seg.end(), [](const Atom& a, const Atom& b) { return a.getId() < b.getId(); }) ->getId(); return std::pair(min_res_id, max_res_id); } template void SegmentMapper::PlaceMapAtomonMD( const std::vector& fragment_mapatoms, const std::vector& fragment_mdatoms) const { for (Index i = 0; i < Index(fragment_mapatoms.size()); i++) { const Atom* a = fragment_mdatoms[i]; mapAtom* b = fragment_mapatoms[i]; b->setPos(a->getPos()); } } template Index SegmentMapper::FindVectorIndexFromAtomId( Index atomid, const std::vector& fragment_mapatoms) const { Index i = 0; for (; i < Index(fragment_mapatoms.size()); i++) { if (fragment_mapatoms[i]->getId() == atomid) { break; } } return i; } template void SegmentMapper::MapMapAtomonMD( const FragInfo& frag, const std::vector& fragment_mapatoms, const std::vector& fragment_mdatoms) const { std::vector local_map_frame; std::vector local_md_frame; for (Index id : frag._map_local_frame) { Index i = FindVectorIndexFromAtomId(id, fragment_mapatoms); local_map_frame.push_back(fragment_mapatoms[i]->getPos()); local_md_frame.push_back(fragment_mdatoms[i]->getPos()); } Index symmetry = frag._map_local_frame.size(); Eigen::Vector3d map_com = CalcWeightedPos(frag._weights, fragment_mapatoms); Eigen::Vector3d md_com = CalcWeightedPos(frag._weights, fragment_mdatoms); Eigen::Vector3d shift_map2md = md_com - map_com; Eigen::Matrix3d rot_map = Eigen::Matrix3d::Identity(); Eigen::Matrix3d rot_md = Eigen::Matrix3d::Identity(); // building local frame if (symmetry > 1) { // middle atom is the origin Eigen::Vector3d x_map = local_map_frame[0] - local_map_frame[1]; Eigen::Vector3d x_md = local_md_frame[0] - local_md_frame[1]; Eigen::Vector3d y_map; Eigen::Vector3d y_md; Eigen::Vector3d z_map; Eigen::Vector3d z_md; if (symmetry == 3) { y_map = local_map_frame[2] - local_map_frame[1]; y_md = local_md_frame[2] - local_md_frame[1]; z_map = x_map.cross(y_map); z_md = x_md.cross(y_md); y_map = z_map.cross(x_map); y_md = z_md.cross(x_md); } else { Eigen::Vector3d unit = Eigen::Vector3d::UnitX(); if (std::abs(unit.dot(x_map) / x_map.norm()) < 1e-6) { unit = Eigen::Vector3d::UnitY(); } y_map = (x_map.cross(unit)); if (std::abs(unit.dot(x_md) / x_md.norm()) < 1e-6) { unit = Eigen::Vector3d::UnitX(); } y_md = (x_md.cross(unit)); z_map = x_map.cross(y_map); z_md = x_md.cross(y_md); } if (x_map.squaredNorm() < 1e-18 || y_map.squaredNorm() < 1e-18 || z_map.squaredNorm() < 1e-18) { throw std::runtime_error( _mapatom_xml.at("tag") + " basis vectors are very small, choose different local basis"); } rot_map.col(0) = x_map.normalized(); rot_map.col(1) = y_map.normalized(); rot_map.col(2) = z_map.normalized(); if (x_md.squaredNorm() < 1e-18 || y_md.squaredNorm() < 1e-18 || z_md.squaredNorm() < 1e-18) { throw std::runtime_error( "MD basis vectors are very small, choose different local basis"); } rot_md.col(0) = x_md.normalized(); rot_md.col(1) = y_md.normalized(); rot_md.col(2) = z_md.normalized(); } Eigen::Matrix3d rotateMAP2MD = rot_md * rot_map.transpose(); for (mapAtom* atom : fragment_mapatoms) { if (getRank(*atom) > 0 && symmetry < 3) { throw std::runtime_error( "Local frame has less than 3 atoms, thus higher rank multipoles " "cannot be mapped."); } atom->Translate(shift_map2md); atom->Rotate(rotateMAP2MD, md_com); } } template AtomContainer SegmentMapper::map(const Segment& seg, QMState state) const { if (_segment_info.count(seg.getType()) == 0) { throw std::runtime_error( "Could not find a Segment of name: " + seg.getType() + " in mapfile."); } Seginfo seginfo = _segment_info.at(seg.getType()); std::string coordsfiletag = _mapatom_xml.at("coords") + "_" + state.Type().ToString(); if (seginfo.coordfiles.count(coordsfiletag) == 0) { throw std::runtime_error("Could not find a coordinate file for " + seg.getType() + " id:" + std::to_string(seg.getId()) + " segment/state: " + coordsfiletag); } std::string coordsfilename = seginfo.coordfiles.at(coordsfiletag); return map(seg, coordsfilename); } template AtomContainer SegmentMapper::map( const Segment& seg, const std::string& coordfilename) const { if (_segment_info.count(seg.getType()) == 0) { throw std::runtime_error( "Could not find a Segment of name: " + seg.getType() + " in mapfile."); } Seginfo seginfo = _segment_info.at(seg.getType()); if (Index(seginfo.mdatoms.size()) != seg.size()) { throw std::runtime_error( "Segment '" + seg.getType() + "' does not contain the same number of atoms as mapping file: " + std::to_string(seginfo.mdatoms.size()) + " vs. " + std::to_string(seg.size())); } std::pair minmax_map = seginfo.minmax; std::pair minmax = CalcAtomIdRange(seg); if ((minmax_map.first - minmax_map.second) != (minmax.first - minmax.second)) { throw std::runtime_error("AtomId range for segment " + seg.getType() + ":" + std::to_string(seg.getId()) + " and the mapping do not agree: Segment[" + std::to_string(minmax.first) + "," + std::to_string(minmax.second) + "] Map[" + std::to_string(minmax_map.first) + "," + std::to_string(minmax_map.second) + "]"); } Index atomidoffset = minmax.first - minmax_map.first; AtomContainer Result(seg.getType(), seg.getId()); Result.LoadFromFile(coordfilename); if (Index(seginfo.mapatoms.size()) != Result.size()) { throw std::runtime_error( _mapatom_xml.at("tag") + "Segment '" + seg.getType() + "' does not contain the same number of atoms as mapping file: " + std::to_string(seginfo.mapatoms.size()) + " vs. " + std::to_string(Result.size())); } for (FragInfo& frag : seginfo.fragments) { for (atom_id& id : frag._mdatom_ids) { id.first += atomidoffset; } std::vector fragment_mapatoms; for (const atom_id& id : frag._mapatom_ids) { if (id.second != Result[id.first].getElement()) { throw std::runtime_error("Element of mapping atom " + std::to_string(id.first) + ":" + id.second + " does not agree with Element of parsed Atom" + Result[id.first].getElement()); } fragment_mapatoms.push_back(&Result[id.first]); } std::vector fragment_mdatoms; for (const atom_id& id : frag._mdatom_ids) { const Atom* atom = seg.getAtom(id.first); if (atom == nullptr) { throw std::runtime_error( "Could not find an atom with name:" + id.second + "id" + std::to_string(id.first) + " in segment " + seg.getType()); } fragment_mdatoms.push_back(atom); } if (seginfo.map2md) { PlaceMapAtomonMD(fragment_mapatoms, fragment_mdatoms); } else { MapMapAtomonMD(frag, fragment_mapatoms, fragment_mdatoms); } } Result.calcPos(); return Result; } template class SegmentMapper; template class SegmentMapper; template class SegmentMapper; } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/settings.cc000066400000000000000000000074631412152066400166660ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/settings.h" namespace votca { namespace xtp { void Settings::read_property(const votca::tools::Property& properties, const std::string& key) { for (const auto& prop : properties.get(key)) { const auto& name = prop.name(); this->_nodes[name] = prop; } } void Settings::load_from_xml(const std::string& path) { votca::tools::Property options; options.LoadFromXML(path); this->read_property(options, _root_key); } // TODO: move this method to Property void Settings::amend(const Settings& other) { // Merge general properties for (const auto& pair : other._nodes) { auto it = this->_nodes.find(pair.first); if (it == this->_nodes.end()) { const auto& val = pair.second; this->_nodes[pair.first] = val; } } } bool Settings::has_key(const std::string& key) const { auto it = this->_nodes.find(key); return (it != this->_nodes.end()) ? true : false; } void Settings::add(const std::string& key, const std::string& value) { std::string primary_key = key.substr(0, key.find(".")); std::string secondary_key = key.substr(key.find(".") + 1); votca::tools::Property& prop = this->_nodes[primary_key]; prop.add(secondary_key, value); } void Settings::validate() const { std::vector keywords = _mandatory_keyword; if (this->get("name") != "xtp") { this->check_mandatory_keyword("executable"); } for (const auto& x : keywords) { this->check_mandatory_keyword(x); } std::stringstream stream; // Check that the input keys are valid for (const auto& pair : this->_nodes) { auto it = std::find(this->_general_properties.cbegin(), this->_general_properties.cend(), pair.first); if (it == this->_general_properties.cend()) { stream << "Unrecognized keyword \"" << pair.first << "\"\n" << "Keywords must be one of the following:\n"; for (const std::string& key : this->_general_properties) { stream << key << "\n"; } throw std::runtime_error(stream.str()); } } } void Settings::check_mandatory_keyword(const std::string& key) const { std::stringstream stream; auto it = this->_nodes.find(key); if (it == this->_nodes.end()) { stream << "the " << key << " keyword is mandatory\n"; auto it2 = this->_keyword_options.find(key); if (it2 != this->_keyword_options.end()) { stream << key << "must be one of the following values:\n"; for (const auto& x : it2->second) { stream << x << "\n"; } } throw std::runtime_error(stream.str()); } } std::ostream& operator<<(std::ostream& out, const Settings& sett) { for (const auto& pair : sett._nodes) { out << "key: " << pair.first << "\n" << "value: " << pair.second << "\n"; } return out; } tools::Property Settings::to_property(const std::string& name) const { tools::Property root{"options", "", "."}; tools::Property& prop = root.add(name, ""); for (const auto& pair : this->_nodes) { tools::Property& new_prop = prop.add(pair.first, ""); new_prop = pair.second; } return root; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/stateapplication.cc000066400000000000000000000103661412152066400203660ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // Local VOTCA includes #include "votca/xtp/calculatorfactory.h" #include "votca/xtp/stateapplication.h" #include "votca/xtp/statesaver.h" #include "votca/xtp/version.h" namespace votca { namespace xtp { StateApplication::StateApplication() { Calculatorfactory::RegisterAll(); } void StateApplication::Initialize(void) { XtpApplication::Initialize(); Calculatorfactory::RegisterAll(); namespace propt = boost::program_options; AddProgramOptions()("file,f", propt::value(), " hdf5 state file, *.hdf5"); AddProgramOptions()("first-frame,i", propt::value()->default_value(0), " start from this frame"); AddProgramOptions()("nframes,n", propt::value()->default_value(1), " number of frames to process"); AddProgramOptions()("nthreads,t", propt::value()->default_value(1), " number of threads to create"); AddProgramOptions()("save,s", propt::value()->default_value(true), " whether or not to save changes to state file"); } bool StateApplication::EvaluateOptions(void) { CheckRequired("file", "Please provide the state file"); return true; } void StateApplication::Run() { std::string name = ProgramName(); if (VersionString() != "") { name = name + ", version " + VersionString(); } xtp::HelpTextHeader(name); _options.LoadFromXML(_op_vm["options"].as()); Index nThreads = OptionsMap()["nthreads"].as(); Index nframes = OptionsMap()["nframes"].as(); Index fframe = OptionsMap()["first-frame"].as(); bool save = OptionsMap()["save"].as(); // STATESAVER & PROGRESS OBSERVER std::string statefile = OptionsMap()["file"].as(); StateSaver statsav(statefile); std::vector frames = statsav.getFrames(); if (frames.empty()) { throw std::runtime_error("Statefile " + statefile + " not found."); } // INITIALIZE & RUN CALCULATORS std::cout << "Initializing calculator" << std::endl; BeginEvaluate(nThreads); std::cout << frames.size() << " frames in statefile, Ids are: "; for (Index frame : frames) { std::cout << frame << " "; } std::cout << std::endl; if (fframe < Index(frames.size())) { std::cout << "Starting at frame " << frames[fframe] << std::endl; } else { std::cout << "First frame:" << fframe << " is larger than number of frames:" << Index(frames.size()) << std::endl; return; } if ((fframe + nframes) > Index(frames.size())) { nframes = Index(frames.size()) - fframe; } for (Index i = fframe; i < nframes; i++) { std::cout << "Evaluating frame " << frames[i] << std::endl; Topology top = statsav.ReadFrame(frames[i]); EvaluateFrame(top); if (save && _calculator->WriteToStateFile()) { statsav.WriteFrame(top); } else { std::cout << "Changes have not been written to state file." << std::endl; } } } void StateApplication::SetCalculator( std::unique_ptr&& calculator) { _calculator = std::move(calculator); } void StateApplication::BeginEvaluate(Index nThreads = 1) { std::cout << "... " << _calculator->Identify() << " "; _calculator->setnThreads(nThreads); _calculator->Initialize(_options); std::cout << std::endl; } bool StateApplication::EvaluateFrame(Topology& top) { std::cout << "... " << _calculator->Identify() << " " << std::flush; _calculator->EvaluateFrame(top); std::cout << std::endl; return true; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/statefilter_base.cc000066400000000000000000000037441412152066400203440ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/statefilter_base.h" namespace votca { namespace xtp { template std::vector StateFilter_base::ReduceAndSortIndeces( const Eigen::VectorXd& overlap, Index offset, double threshold) const { std::vector index = std::vector(overlap.size()); std::iota(index.begin(), index.end(), offset); std::stable_sort(index.begin(), index.end(), [&overlap](Index i1, Index i2) { if (larger) { return overlap[i1] > overlap[i2]; } else { return overlap[i1] < overlap[i2]; } }); Index validelements; if (larger) { validelements = (overlap.array() > threshold).sum(); } else { validelements = (overlap.array() < threshold).sum(); } std::vector indexes(validelements); std::copy_n(index.begin(), validelements, indexes.begin()); return indexes; } std::vector StateFilter_base::ReduceAndSortIndecesUp( const Eigen::VectorXd& overlap, Index offset, double threshold) const { return ReduceAndSortIndeces(overlap, offset, threshold); } std::vector StateFilter_base::ReduceAndSortIndecesDown( const Eigen::VectorXd& overlap, Index offset, double threshold) const { return ReduceAndSortIndeces(overlap, offset, threshold); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/statefilters/000077500000000000000000000000001412152066400172165ustar00rootroot00000000000000xtp-2021.2/src/libxtp/statefilters/DeltaQ_filter.cc000066400000000000000000000043711412152066400222510ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/populationanalysis.h" // Local private VOTCA includes #include "DeltaQ_filter.h" namespace votca { namespace xtp { void DeltaQ_filter::Initialize(const tools::Property& options) { std::string indices = options.ifExistsReturnElseThrowRuntimeError("fragment"); _fragment = QMFragment(0, indices); _fragment.value() = options.ifExistsReturnElseThrowRuntimeError("threshold"); } void DeltaQ_filter::Info(Logger& log) const { XTP_LOG(Log::error, log) << "Using Delta Q tracker for fragment " << _fragment << std::flush; } void DeltaQ_filter::UpdateHist(const Orbitals&, QMState) { return; } std::vector DeltaQ_filter::CalcIndeces(const Orbitals& orb, QMStateType type) const { if (!type.isExciton()) { throw std::runtime_error("ChargeTransfer filter only works for excitons."); } std::vector indexes; Lowdin low; QMFragment frag; frag.copy_withoutvalue(_fragment); std::vector > loc = {frag}; low.CalcChargeperFragment(loc, orb, type); Eigen::VectorXd dq = (loc[0].value().H + loc[0].value().E).cwiseAbs(); for (Index i = 0; i < dq.size(); i++) { if (dq[i] > _fragment.value()) { indexes.push_back(i); } } return indexes; } void DeltaQ_filter::WriteToCpt(CheckpointWriter& w) { _fragment.WriteToCpt(w); } void DeltaQ_filter::ReadFromCpt(CheckpointReader& r) { _fragment.ReadFromCpt(r); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/statefilters/DeltaQ_filter.h000066400000000000000000000033051412152066400221070ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_DELTAQ_FILTER_H #define VOTCA_XTP_DELTAQ_FILTER_H // Local VOTCA includes #include "votca/xtp/qmfragment.h" #include "votca/xtp/statefilter_base.h" namespace votca { namespace xtp { /** \brief ChargeTransfer_filter tracks states according to how much charge is on a fragment A and the rest of the molecule */ class DeltaQ_filter : public StateFilter_base { public: std::string Identify() const final { return "chargetransfer"; } void Initialize(const tools::Property& options) final; void Info(Logger& log) const final; bool NeedsInitialState() const final { return false; } void UpdateHist(const Orbitals& orb, QMState state) final; std::vector CalcIndeces(const Orbitals& orb, QMStateType type) const final; void WriteToCpt(CheckpointWriter& w) final; void ReadFromCpt(CheckpointReader& r) final; private: QMFragment _fragment; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_DELTAQ_FILTER_H xtp-2021.2/src/libxtp/statefilters/Density_filter.cc000066400000000000000000000046511412152066400225170ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local private VOTCA includes #include "Density_filter.h" namespace votca { namespace xtp { void Density_filter::Initialize(const tools::Property& options) { _threshold = options.ifExistsReturnElseThrowRuntimeError("."); } void Density_filter::Info(Logger& log) const { if (_threshold == 0.0) { XTP_LOG(Log::error, log) << "Using density filter with no threshold " << std::flush; } else { XTP_LOG(Log::error, log) << "Using density filter with threshold " << _threshold << std::flush; } } void Density_filter::UpdateHist(const Orbitals& orb, QMState state) { _laststate_dmat = orb.DensityMatrixFull(state); } Eigen::VectorXd Density_filter::CalculateDNorm(const Orbitals& orb, QMStateType type) const { Index nostates = orb.NumberofStates(type); Eigen::VectorXd norm = Eigen::VectorXd::Zero(nostates); for (Index i = 0; i < nostates; i++) { QMState state(type, i, false); norm(i) = (orb.DensityMatrixFull(state) - _laststate_dmat).norm(); } double lastnorm = _laststate_dmat.norm(); return norm / lastnorm; } std::vector Density_filter::CalcIndeces(const Orbitals& orb, QMStateType type) const { Eigen::VectorXd Overlap = CalculateDNorm(orb, type); Index offset = 0; if (type == QMStateType::DQPstate) { offset = orb.getGWAmin(); } return ReduceAndSortIndecesDown(Overlap, offset, _threshold); } void Density_filter::WriteToCpt(CheckpointWriter& w) { w(_laststate_dmat, "laststatedmat"); w(_threshold, "threshold"); } void Density_filter::ReadFromCpt(CheckpointReader& r) { r(_laststate_dmat, "laststatedmat"); r(_threshold, "threshold"); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/statefilters/Density_filter.h000066400000000000000000000033771412152066400223650ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_DENSITY_FILTER_H #define VOTCA_XTP_DENSITY_FILTER_H // Local VOTCA includes #include "votca/xtp/statefilter_base.h" namespace votca { namespace xtp { /** \brief density_filter tracks states according to the difference of their density matrix to an earlier state */ class Density_filter : public StateFilter_base { public: std::string Identify() const final { return "density"; } void Initialize(const tools::Property& options) final; void Info(Logger& log) const final; void UpdateHist(const Orbitals& orb, QMState state) final; bool NeedsInitialState() const final { return true; } std::vector CalcIndeces(const Orbitals& orb, QMStateType type) const final; void WriteToCpt(CheckpointWriter& w) final; void ReadFromCpt(CheckpointReader& r) final; private: Eigen::VectorXd CalculateDNorm(const Orbitals& orb, QMStateType type) const; double _threshold = 0.0; Eigen::MatrixXd _laststate_dmat; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_DENSITY_FILTER_H xtp-2021.2/src/libxtp/statefilters/Localisation_filter.cc000066400000000000000000000046071412152066400235220ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/populationanalysis.h" // Local private VOTCA includes #include "Localisation_filter.h" namespace votca { namespace xtp { void Localisation_filter::Initialize(const tools::Property& options) { std::string indices = options.ifExistsReturnElseThrowRuntimeError("fragment"); _fragment = QMFragment(0, indices); _fragment.value() = options.ifExistsReturnElseThrowRuntimeError("threshold"); } void Localisation_filter::Info(Logger& log) const { XTP_LOG(Log::error, log) << "Using localisation tracker for fragment " << _fragment << std::flush; } void Localisation_filter::UpdateHist(const Orbitals&, QMState) { return; } std::vector Localisation_filter::CalcIndeces(const Orbitals& orb, QMStateType type) const { if (!type.isExciton()) { throw std::runtime_error("Localisation filter only works for excitons."); } std::vector indexes; Lowdin low; QMFragment frag; frag.copy_withoutvalue(_fragment); std::vector > loc = {frag}; low.CalcChargeperFragment(loc, orb, type); const Eigen::VectorXd& popE = loc[0].value().E; const Eigen::VectorXd& popH = loc[0].value().H; for (Index i = 0; i < popE.size(); i++) { if (std::abs(popE[i]) > _fragment.value() && std::abs(popH[i]) > _fragment.value()) { indexes.push_back(i); } } return indexes; } void Localisation_filter::WriteToCpt(CheckpointWriter& w) { _fragment.WriteToCpt(w); } void Localisation_filter::ReadFromCpt(CheckpointReader& r) { _fragment.ReadFromCpt(r); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/statefilters/Localisation_filter.h000066400000000000000000000033011412152066400233520ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_LOCALISATION_FILTER_H #define VOTCA_XTP_LOCALISATION_FILTER_H // Local VOTCA includes #include "votca/xtp/qmfragment.h" #include "votca/xtp/statefilter_base.h" namespace votca { namespace xtp { /** \brief Localisation_filter tracks states according to how localised they are in a specific region */ class Localisation_filter : public StateFilter_base { public: std::string Identify() const final { return "localisation"; } void Initialize(const tools::Property& options) final; void Info(Logger& log) const final; bool NeedsInitialState() const final { return false; } void UpdateHist(const Orbitals& orb, QMState state) final; std::vector CalcIndeces(const Orbitals& orb, QMStateType type) const final; void WriteToCpt(CheckpointWriter& w) final; void ReadFromCpt(CheckpointReader& r) final; private: QMFragment _fragment; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_LOCALISATION_FILTER_H xtp-2021.2/src/libxtp/statefilters/OscillatorStrength_filter.cc000066400000000000000000000036041412152066400247270ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local private VOTCA includes #include "OscillatorStrength_filter.h" namespace votca { namespace xtp { void OscillatorStrength_filter::Initialize(const tools::Property& options) { _threshold = options.ifExistsReturnElseThrowRuntimeError("."); } void OscillatorStrength_filter::Info(Logger& log) const { XTP_LOG(Log::error, log) << "Using oscillator strength tracker with threshold " << _threshold << std::flush; } void OscillatorStrength_filter::UpdateHist(const Orbitals&, QMState) { return; } std::vector OscillatorStrength_filter::CalcIndeces( const Orbitals& orb, QMStateType type) const { if (type != QMStateType::Singlet) { throw std::runtime_error( "OscillatorStrength filter only works for singlets."); } Eigen::VectorXd oscs = orb.Oscillatorstrengths(); std::vector indexes; for (Index i = 0; i < oscs.size(); i++) { if (oscs[i] > _threshold) { indexes.push_back(i); } } return indexes; } void OscillatorStrength_filter::WriteToCpt(CheckpointWriter& w) { w(_threshold, "threshold"); } void OscillatorStrength_filter::ReadFromCpt(CheckpointReader& r) { r(_threshold, "threshold"); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/statefilters/OscillatorStrength_filter.h000066400000000000000000000032751412152066400245750ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_OSCILLATORSTRENGTH_FILTER_H #define VOTCA_XTP_OSCILLATORSTRENGTH_FILTER_H // Local VOTCA includes #include "votca/xtp/statefilter_base.h" namespace votca { namespace xtp { /** \brief OscillatorStrength_filter tracks states according to their f-value only works for singlets */ class OscillatorStrength_filter : public StateFilter_base { public: std::string Identify() const final { return "oscillatorstrength"; } void Initialize(const tools::Property& options) final; void Info(Logger& log) const final; bool NeedsInitialState() const final { return false; } void UpdateHist(const Orbitals& orb, QMState state) final; std::vector CalcIndeces(const Orbitals& orb, QMStateType type) const final; void WriteToCpt(CheckpointWriter& w) final; void ReadFromCpt(CheckpointReader& r) final; private: double _threshold = 0.0; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_OSCILLATORSTRENGTH_FILTER_H xtp-2021.2/src/libxtp/statefilters/Overlap_filter.cc000066400000000000000000000145451412152066400225130ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/aomatrix.h" // Local private VOTCA includes #include "Overlap_filter.h" namespace votca { namespace xtp { void Overlap_filter::Initialize(const tools::Property& options) { _threshold = options.ifExistsReturnElseThrowRuntimeError("."); } void Overlap_filter::Info(Logger& log) const { if (_threshold == 0.0) { XTP_LOG(Log::error, log) << "Using overlap filter with no threshold " << std::flush; } else { XTP_LOG(Log::error, log) << "Using overlap filter with threshold " << _threshold << std::flush; } } Eigen::VectorXd Overlap_filter::CalculateOverlap(const Orbitals& orb, QMStateType type) const { AOOverlap S_ao; S_ao.Fill(orb.SetupDftBasis()); Eigen::MatrixXd coeffs = CalcAOCoeffs(orb, type); if (type.isSingleParticleState()) { return (coeffs.transpose() * S_ao.Matrix() * _laststatecoeff).cwiseAbs(); } else { Index basis = orb.getBasisSetSize(); Eigen::VectorXd overlap = Eigen::VectorXd::Zero(coeffs.cols()); #pragma omp parallel for schedule(dynamic) for (Index i = 0; i < coeffs.cols(); i++) { { Eigen::VectorXd state = coeffs.col(i).head(basis * basis); Eigen::Map mat(state.data(), basis, basis); Eigen::VectorXd laststate = _laststatecoeff.head(basis * basis); Eigen::Map lastmat(laststate.data(), basis, basis); overlap(i) = (mat * S_ao.Matrix() * lastmat.transpose()) .cwiseProduct(S_ao.Matrix()) .sum(); } if (!orb.getTDAApprox()) { Eigen::VectorXd state = coeffs.col(i).tail(basis * basis); Eigen::Map mat(state.data(), basis, basis); Eigen::VectorXd laststate = _laststatecoeff.tail(basis * basis); Eigen::Map lastmat(laststate.data(), basis, basis); overlap(i) -= (mat * S_ao.Matrix() * lastmat.transpose()) .cwiseProduct(S_ao.Matrix()) .sum(); } } return overlap.cwiseAbs(); } } Eigen::MatrixXd Overlap_filter::CalcExcitonAORepresentation( const Orbitals& orb, QMStateType type) const { Eigen::MatrixXd coeffs; Index nostates = orb.NumberofStates(type); Index bse_cmax = orb.getBSEcmax(); Index bse_cmin = orb.getBSEcmin(); Index bse_vmax = orb.getBSEvmax(); Index bse_vmin = orb.getBSEvmin(); Index bse_vtotal = bse_vmax - bse_vmin + 1; Index bse_ctotal = bse_cmax - bse_cmin + 1; Index basis = orb.getBasisSetSize(); Index bse_size_ao = basis * basis; auto occlevels = orb.MOs().eigenvectors().block( 0, bse_vmin, orb.MOs().eigenvectors().rows(), bse_vtotal); auto virtlevels = orb.MOs().eigenvectors().block( 0, bse_cmin, orb.MOs().eigenvectors().rows(), bse_ctotal); if (orb.getTDAApprox()) { coeffs.resize(bse_size_ao, nostates); } else { coeffs.resize(2 * bse_size_ao, nostates); } #pragma omp parallel for schedule(dynamic) for (Index i = 0; i < nostates; i++) { { Eigen::VectorXd exciton; if (type == QMStateType::Singlet) { exciton = orb.BSESinglets().eigenvectors().col(i); } else { exciton = orb.BSETriplets().eigenvectors().col(i); } Eigen::Map mat(exciton.data(), bse_ctotal, bse_vtotal); const Eigen::MatrixXd aomatrix = occlevels * mat.transpose() * virtlevels.transpose(); coeffs.col(i).head(bse_size_ao) = Eigen::Map(aomatrix.data(), bse_size_ao); } if (!orb.getTDAApprox()) { Eigen::VectorXd exciton; if (type == QMStateType::Singlet) { exciton = orb.BSESinglets().eigenvectors2().col(i); } else { exciton = orb.BSETriplets().eigenvectors2().col(i); } Eigen::Map mat(exciton.data(), bse_ctotal, bse_vtotal); const Eigen::MatrixXd aomatrix = occlevels * mat.transpose() * virtlevels.transpose(); coeffs.col(i).tail(bse_size_ao) = Eigen::Map(aomatrix.data(), bse_size_ao); } } return coeffs; } Eigen::MatrixXd Overlap_filter::CalcAOCoeffs(const Orbitals& orb, QMStateType type) const { Eigen::MatrixXd coeffs; if (type.isSingleParticleState()) { if (type == QMStateType::DQPstate) { coeffs = orb.CalculateQParticleAORepresentation(); } else { coeffs = orb.MOs().eigenvectors(); } } else { coeffs = CalcExcitonAORepresentation(orb, type); } return coeffs; } void Overlap_filter::UpdateHist(const Orbitals& orb, QMState state) { Eigen::MatrixXd aocoeffs = CalcAOCoeffs(orb, state.Type()); Index offset = 0; if (state.Type() == QMStateType::DQPstate) { offset = orb.getGWAmin(); } _laststatecoeff = aocoeffs.col(state.StateIdx() - offset); } std::vector Overlap_filter::CalcIndeces(const Orbitals& orb, QMStateType type) const { Index offset = 0; if (type.isGWState()) { offset = orb.getGWAmin(); } Eigen::VectorXd Overlap = CalculateOverlap(orb, type); return ReduceAndSortIndecesUp(Overlap, offset, _threshold); } void Overlap_filter::WriteToCpt(CheckpointWriter& w) { w(_laststatecoeff, "laststatecoeff"); w(_threshold, "threshold"); } void Overlap_filter::ReadFromCpt(CheckpointReader& r) { r(_laststatecoeff, "laststatecoeff"); r(_threshold, "threshold"); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/statefilters/Overlap_filter.h000066400000000000000000000036771412152066400223610ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_OVERLAP_FILTER_H #define VOTCA_XTP_OVERLAP_FILTER_H // Local VOTCA includes #include "votca/xtp/statefilter_base.h" namespace votca { namespace xtp { /** \brief overlap_filter tracks states according to their overlap with a previous state */ class Overlap_filter : public StateFilter_base { public: std::string Identify() const final { return "overlap"; } void Initialize(const tools::Property& options) final; void Info(Logger& log) const final; void UpdateHist(const Orbitals& orb, QMState state) final; bool NeedsInitialState() const final { return true; } std::vector CalcIndeces(const Orbitals& orb, QMStateType type) const final; void WriteToCpt(CheckpointWriter& w) final; void ReadFromCpt(CheckpointReader& r) final; private: Eigen::VectorXd CalculateOverlap(const Orbitals& orb, QMStateType type) const; Eigen::MatrixXd CalcAOCoeffs(const Orbitals& orb, QMStateType type) const; Eigen::MatrixXd CalcExcitonAORepresentation(const Orbitals& orb, QMStateType type) const; double _threshold = 0.0; Eigen::VectorXd _laststatecoeff; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_OVERLAP_FILTER_H xtp-2021.2/src/libxtp/statesaver.cc000066400000000000000000000065451412152066400172070ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/statesaver.h" #include "votca/xtp/topology.h" namespace votca { namespace xtp { std::vector StateSaver::getFrames() const { CheckpointFile cpf(_hdf5file, CheckpointAccessLevel::READ); CheckpointReader r = cpf.getReader(); std::vector frames = std::vector{}; try { r(frames, "frames"); } catch (std::runtime_error&) { ; } return frames; } void StateSaver::WriteFrame(const Topology& top) { if (!tools::filesystem::FileExists(_hdf5file)) { std::cout << "Creating statefile " << _hdf5file << std::endl; CheckpointFile cpf(_hdf5file, CheckpointAccessLevel::CREATE); } boost::interprocess::file_lock flock(_hdf5file.c_str()); flock.lock(); if (!TopStepisinFrames(top.getStep())) { std::vector frames = this->getFrames(); frames.push_back(top.getStep()); CheckpointFile cpf(_hdf5file, CheckpointAccessLevel::MODIFY); CheckpointWriter w = cpf.getWriter(); w(frames, "frames"); std::cout << "Frame with id " << top.getStep() << " was not in statefile " << _hdf5file << " ,adding it now." << std::endl; } CheckpointFile cpf(_hdf5file, CheckpointAccessLevel::MODIFY); CheckpointWriter w = cpf.getWriter("/frame_" + std::to_string(top.getStep())); top.WriteToCpt(w); flock.unlock(); std::cout << "Wrote MD topology (step = " << top.getStep() << ", time = " << top.getTime() << ") to " << _hdf5file << std::endl; std::cout << "... "; std::cout << ". " << std::endl; return; } Topology StateSaver::ReadFrame(Index frameid) const { if (!tools::filesystem::FileExists(_hdf5file)) { throw std::runtime_error("Statefile " + _hdf5file + " does not exist."); } std::cout << "Import MD Topology (i.e. frame " << frameid << ")" << " from " << _hdf5file << std::endl; std::cout << "..."; boost::interprocess::file_lock flock(_hdf5file.c_str()); flock.lock(); if (!TopStepisinFrames(frameid)) { throw std::runtime_error("Frame with id " + std::to_string(frameid) + " is not in statefile."); } CheckpointFile cpf(_hdf5file, CheckpointAccessLevel::READ); CheckpointReader r = cpf.getReader("/frame_" + std::to_string(frameid)); Topology top; top.ReadFromCpt(r); flock.unlock(); std::cout << ". " << std::endl; return top; } bool StateSaver::TopStepisinFrames(Index frameid) const { std::vector frames = this->getFrames(); return std::find(frames.begin(), frames.end(), frameid) != frames.end(); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/statetracker.cc000066400000000000000000000112041412152066400175060ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/statetracker.h" #include "votca/xtp/filterfactory.h" namespace votca { namespace xtp { using std::flush; void StateTracker::Initialize(const tools::Property& options) { std::string filters = options.get("filters").as(); tools::Tokenizer tok(filters, " ,;\n"); std::vector list_filters = tok.ToVector(); FilterFactory::RegisterAll(); for (const std::string& filtername : list_filters) { _filters.push_back(Filter().Create(filtername)); } for (auto& filter : _filters) { const tools::Property& filterop = options.get(filter->Identify()); filter->Initialize(filterop); } } void StateTracker::PrintInfo() const { XTP_LOG(Log::error, *_log) << "Initial state: " << _statehist[0].ToString() << flush; if (_statehist.size() > 1) { XTP_LOG(Log::error, *_log) << "Last state: " << _statehist.back().ToString() << flush; } if (_filters.empty()) { XTP_LOG(Log::error, *_log) << "WARNING: No tracker is used " << flush; } else { for (const auto& filter : _filters) { filter->Info(*_log); } } } std::vector StateTracker::ComparePairofVectors( std::vector& vec1, std::vector& vec2) const { std::vector result(std::min(vec1, vec2)); std::sort(vec1.begin(), vec1.end()); std::sort(vec2.begin(), vec2.end()); std::vector::iterator it = std::set_intersection( vec1.begin(), vec1.end(), vec2.begin(), vec2.end(), result.begin()); result.resize(it - result.begin()); return result; } std::vector StateTracker::CollapseResults( std::vector >& results) const { if (results.empty()) { return std::vector(0); } else { std::vector result = results[0]; for (Index i = 1; i < Index(results.size()); i++) { result = ComparePairofVectors(result, results[i]); } return result; } } QMState StateTracker::CalcState(const Orbitals& orbitals) const { if (_filters.empty()) { return _statehist[0]; } std::vector > results; for (const auto& filter : _filters) { if (_statehist.size() < 2 && filter->NeedsInitialState()) { XTP_LOG(Log::error, *_log) << "Filter " << filter->Identify() << " not used in first iteration as it needs a reference state" << flush; continue; } results.push_back(filter->CalcIndeces(orbitals, _statehist[0].Type())); } std::vector result = CollapseResults(results); QMState state; if (result.size() < 1) { state = _statehist.back(); XTP_LOG(Log::error, *_log) << "No State found by tracker using last state: " << state.ToString() << flush; } else { state = QMState(_statehist.back().Type(), result[0], false); XTP_LOG(Log::error, *_log) << "Next State is: " << state.ToString() << flush; } return state; } QMState StateTracker::CalcStateAndUpdate(const Orbitals& orbitals) { QMState result = CalcState(orbitals); _statehist.push_back(result); for (auto& filter : _filters) { filter->UpdateHist(orbitals, result); } return result; } void StateTracker::WriteToCpt(CheckpointWriter& w) const { std::vector statehiststring; statehiststring.reserve(_statehist.size()); for (const QMState& s : _statehist) { statehiststring.push_back(s.ToString()); } w(statehiststring, "statehist"); for (const auto& filter : _filters) { CheckpointWriter ww = w.openChild(filter->Identify()); filter->WriteToCpt(ww); } } void StateTracker::ReadFromCpt(CheckpointReader& r) { std::vector statehiststring; r(statehiststring, "statehist"); _statehist.clear(); _statehist.reserve(statehiststring.size()); for (const std::string& s : statehiststring) { _statehist.push_back(QMState(s)); } for (auto& filter : _filters) { CheckpointReader rr = r.openChild(filter->Identify()); filter->ReadFromCpt(rr); } } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/staticsite.cc000066400000000000000000000133371412152066400171770ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License,Version 2.0 (the "License") * *You may not use this file except in compliance with the License. *You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * *Unless required by applicable law or agreed to in writing,software *distributed under the License is distributed on an "AS IS" BASIS, *WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,either express or implied. *See the License for the specific language governing permissions and *limitations under the License. * */ // Standard includes #include #include // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include namespace votca { namespace xtp { Eigen::Matrix3d StaticSite::CalculateCartesianMultipole() const { // We are transforming here just quadrupoles // const Eigen::VectorXd& MP = _multipole; const Vector9d& MP = _Q; Eigen::Matrix3d theta = Eigen::Matrix3d::Zero(); if (_rank > 1) { double sqr3 = std::sqrt(3); theta(0, 0) = 0.5 * (-MP(4) + sqr3 * MP(7)); // theta_xx theta(1, 1) = 0.5 * (-MP(4) - sqr3 * MP(7)); // theta_yy theta(2, 2) = MP(4); // theta_zz theta(0, 1) = theta(1, 0) = 0.5 * sqr3 * MP(8); // theta_xy = theta_yx theta(0, 2) = theta(2, 0) = 0.5 * sqr3 * MP(5); // theta_xz = theta_zx theta(1, 2) = theta(2, 1) = 0.5 * sqr3 * MP(6); // theta_yz = theta_zy } return theta; } Eigen::VectorXd StaticSite::CalculateSphericalMultipole( const Eigen::Matrix3d& quad_cart) { Eigen::VectorXd quadrupole_polar = Eigen::VectorXd::Zero(5); const double sqr3 = std::sqrt(3); quadrupole_polar(0) = quad_cart(2, 2); quadrupole_polar(1) = (2. / sqr3) * quad_cart(0, 2); quadrupole_polar(2) = (2. / sqr3) * quad_cart(1, 2); quadrupole_polar(3) = (1. / sqr3) * (quad_cart(0, 0) - quad_cart(1, 1)); quadrupole_polar(4) = (2. / sqr3) * quad_cart(0, 1); return quadrupole_polar; } void StaticSite::Rotate(const Eigen::Matrix3d& R, const Eigen::Vector3d& refPos) { Eigen::Vector3d dir = _pos - refPos; dir = R * dir; _pos = refPos + dir; // Rotated Position if (_rank > 0) { const Eigen::Vector3d temp = R * _Q.segment<3>(1); _Q.segment<3>(1) = temp; } if (_rank > 1) { Eigen::Matrix3d cartesianquad = CalculateCartesianMultipole(); Eigen::Matrix3d rotated = R * cartesianquad * R.transpose(); _Q.segment<5>(4) = CalculateSphericalMultipole(rotated); } return; } void StaticSite::Translate(const Eigen::VectorXd& shift) { _pos += shift; return; } std::string StaticSite::writepolarization() const { tools::Elements e; double default_pol = 1; // default is alway 1A^3 try { default_pol = e.getPolarizability(_element) * std::pow(tools::conv::nm2ang, 3); } catch (const std::runtime_error&) { ; } return (boost::format(" P %1$+1.7f\n") % default_pol).str(); } std::string StaticSite::WriteMpsLine(std::string unit) const { double conv_pos = 1.; if (unit == "angstrom") { conv_pos = tools::conv::bohr2ang; } else if (unit == "bohr") { conv_pos = 1.; } else { throw std::runtime_error( " StaticSite::WriteMpsLine: Unit conversion not known"); } std::string output = ""; output += (boost::format(" %1$2s %2$+1.7f %3$+1.7f %4$+1.7f Rank %5$d\n") % _element % (_pos(0) * conv_pos) % (_pos(1) * conv_pos) % (_pos(2) * conv_pos) % _rank) .str(); output += (boost::format(" %1$+1.7f\n") % getCharge()).str(); if (_rank > 0) { // Dipole z x y output += (boost::format(" %1$+1.7f %2$+1.7f %3$+1.7f\n") % _Q(3) % _Q(1) % _Q(2)) .str(); if (_rank > 1) { // Quadrupole 20 21c 21s 22c 22s output += (boost::format(" %1$+1.7f %2$+1.7f %3$+1.7f %4$+1.7f %5$+1.7f\n") % _Q(4) % _Q(5) % _Q(6) % _Q(7) % _Q(8)) .str(); } } // Polarizability output += writepolarization(); return output; } void StaticSite::SetupCptTable(CptTable& table) const { table.addCol(_id, "index", HOFFSET(data, id)); table.addCol(_element, "type", HOFFSET(data, element)); table.addCol(_pos[0], "posX", HOFFSET(data, posX)); table.addCol(_pos[1], "posY", HOFFSET(data, posY)); table.addCol(_pos[2], "posZ", HOFFSET(data, posZ)); table.addCol(_rank, "rank", HOFFSET(data, rank)); table.addCol(_Q[0], "Q00", HOFFSET(data, Q00)); table.addCol(_Q[1], "Q11c", HOFFSET(data, Q11c)); table.addCol(_Q[2], "Q11s", HOFFSET(data, Q11s)); table.addCol(_Q[3], "Q10", HOFFSET(data, Q10)); table.addCol(_Q[4], "Q20", HOFFSET(data, Q20)); table.addCol(_Q[5], "Q21c", HOFFSET(data, Q21c)); table.addCol(_Q[6], "Q21s", HOFFSET(data, Q21s)); table.addCol(_Q[7], "Q22c", HOFFSET(data, Q22c)); table.addCol(_Q[8], "Q22s", HOFFSET(data, Q22s)); } void StaticSite::WriteData(data& d) const { d.id = _id; d.element = const_cast(_element.c_str()); d.posX = _pos[0]; d.posY = _pos[1]; d.posZ = _pos[2]; d.rank = _rank; d.Q00 = _Q[0]; d.Q11c = _Q[1]; d.Q11s = _Q[2]; d.Q10 = _Q[3]; d.Q20 = _Q[4]; d.Q21c = _Q[5]; d.Q21s = _Q[6]; d.Q22c = _Q[7]; d.Q22s = _Q[8]; } void StaticSite::ReadData(const data& d) { _id = d.id; _element = std::string(d.element); free(d.element); _pos[0] = d.posX; _pos[1] = d.posY; _pos[2] = d.posZ; _rank = d.rank; _Q[0] = d.Q00; _Q[1] = d.Q11c; _Q[2] = d.Q11s; _Q[3] = d.Q10; _Q[4] = d.Q20; _Q[5] = d.Q21c; _Q[6] = d.Q21s; _Q[7] = d.Q22c; _Q[8] = d.Q22s; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/symmetric_matrix.cc000066400000000000000000000074301412152066400204200ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include // Local VOTCA includes #include "votca/xtp/symmetric_matrix.h" namespace votca { namespace xtp { Symmetric_Matrix::Symmetric_Matrix(const Eigen::MatrixXd& full) : dimension(full.rows()) { assert(full.rows() == full.cols() && "Input matrix not quadratic"); data.resize((dimension + 1) * dimension / 2); for (Index i = 0; i < full.rows(); ++i) { for (Index j = 0; j <= i; ++j) { this->operator()(i, j) = full(i, j); } } } std::ostream& operator<<(std::ostream& out, const Symmetric_Matrix& a) { out << "[" << a.dimension << "," << a.dimension << "]\n"; for (Index i = 0; i < a.dimension; ++i) { for (Index j = 0; j <= i; ++j) { out << a(i, j); if (i == j) { out << "\n"; } else { out << " "; } } } return out; } double Symmetric_Matrix::TraceofProd(const Symmetric_Matrix& a) const { assert(data.size() == a.data.size() && "Matrices do not have same size"); double result = 0.0; for (Index i = 0; i < dimension; ++i) { const Index index = (i * (i + 1)) / 2 + i; result += +data[index] * a.data[index]; } for (Index i = 0; i < dimension; ++i) { const Index start = (i * (i + 1)) / 2; for (Index j = 0; j < i; ++j) { result += 2 * data[start + j] * a.data[start + j]; } } return result; } void Symmetric_Matrix::AddtoEigenMatrix(Eigen::MatrixXd& full, double factor) const { for (Index j = 0; j < full.cols(); ++j) { const Index start = (j * (j + 1)) / 2; for (Index i = 0; i <= j; ++i) { full(i, j) += factor * data[start + i]; } for (Index i = j + 1; i < full.rows(); ++i) { const Index index = (i * (i + 1)) / 2 + j; full(i, j) += factor * data[index]; } } return; } void Symmetric_Matrix::AddtoEigenUpperMatrix( Eigen::SelfAdjointView& upper, double factor) const { for (Index j = 0; j < upper.cols(); ++j) { const Index start = (j * (j + 1)) / 2; for (Index i = 0; i <= j; ++i) { upper(i, j) += factor * data[start + i]; } } return; } Eigen::MatrixXd Symmetric_Matrix::FullMatrix() const { Eigen::MatrixXd result = Eigen::MatrixXd(dimension, dimension); for (Index j = 0; j < result.cols(); ++j) { const Index start = (j * (j + 1)) / 2; for (Index i = 0; i <= j; ++i) { result(i, j) = data[start + i]; } for (Index i = j + 1; i < result.rows(); ++i) { const Index index = (i * (i + 1)) / 2 + j; result(i, j) = data[index]; } } return result; } Eigen::MatrixXd Symmetric_Matrix::UpperMatrix() const { Eigen::MatrixXd result = Eigen::MatrixXd::Zero(dimension, dimension); for (Index j = 0; j < result.cols(); ++j) { const Index start = (j * (j + 1)) / 2; for (Index i = 0; i <= j; ++i) { result(i, j) = data[start + i]; } } return result; } Index Symmetric_Matrix::index(Index i, Index j) const { Index index; if (i >= j) { index = (i * (i + 1)) / 2 + j; } else { index = (j * (j + 1)) / 2 + i; } return index; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/threecenter.cc000066400000000000000000000237261412152066400173360ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * *Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/threecenter.h" #include "votca/xtp/aomatrix.h" #include "votca/xtp/make_libint_work.h" #include "votca/xtp/openmp_cuda.h" #include "votca/xtp/symmetric_matrix.h" // include libint last otherwise it overrides eigen #include namespace votca { namespace xtp { void TCMatrix_dft::Fill(const AOBasis& auxbasis, const AOBasis& dftbasis) { { AOCoulomb auxAOcoulomb; auxAOcoulomb.Fill(auxbasis); _inv_sqrt = auxAOcoulomb.Pseudo_InvSqrt(1e-8); _removedfunctions = auxAOcoulomb.Removedfunctions(); } _matrix = std::vector( auxbasis.AOBasisSize(), Symmetric_Matrix(dftbasis.AOBasisSize())); Index nthreads = OPENMP::getMaxThreads(); std::vector dftshells = dftbasis.GenerateLibintBasis(); std::vector auxshells = auxbasis.GenerateLibintBasis(); std::vector engines(nthreads); engines[0] = libint2::Engine( libint2::Operator::coulomb, std::max(dftbasis.getMaxNprim(), auxbasis.getMaxNprim()), static_cast(std::max(dftbasis.getMaxL(), auxbasis.getMaxL())), 0); engines[0].set(libint2::BraKet::xs_xx); for (Index i = 1; i < nthreads; ++i) { engines[i] = engines[0]; } std::vector shell2bf = dftbasis.getMapToBasisFunctions(); std::vector auxshell2bf = auxbasis.getMapToBasisFunctions(); #pragma omp parallel for schedule(dynamic) for (Index is = dftbasis.getNumofShells() - 1; is >= 0; is--) { libint2::Engine& engine = engines[OPENMP::getThreadId()]; const libint2::Engine::target_ptr_vec& buf = engine.results(); const libint2::Shell& dftshell = dftshells[is]; Index start = shell2bf[is]; std::vector block(dftshell.size()); for (Index i = 0; i < Index(dftshell.size()); i++) { Index size = start + i + 1; block[i] = Eigen::MatrixXd::Zero(auxbasis.AOBasisSize(), size); } for (Index aux = 0; aux < auxbasis.getNumofShells(); aux++) { const libint2::Shell& auxshell = auxshells[aux]; Index aux_start = auxshell2bf[aux]; for (Index dis = 0; dis <= is; dis++) { const libint2::Shell& shell_col = dftshells[dis]; Index col_start = shell2bf[dis]; engine.compute2( auxshell, libint2::Shell::unit(), dftshell, shell_col); if (buf[0] == nullptr) { continue; } Eigen::TensorMap const> result(buf[0], auxshell.size(), dftshell.size(), shell_col.size()); for (size_t left = 0; left < dftshell.size(); left++) { for (size_t auxf = 0; auxf < auxshell.size(); auxf++) { for (size_t col = 0; col < shell_col.size(); col++) { // symmetry if ((col_start + col) > (start + left)) { break; } block[left](aux_start + auxf, col_start + col) = result(auxf, left, col); } } } } } for (Index i = 0; i < Index(block.size()); ++i) { Eigen::MatrixXd temp = _inv_sqrt * block[i]; for (Index mu = 0; mu < temp.rows(); ++mu) { for (Index j = 0; j < temp.cols(); ++j) { _matrix[mu](i + start, j) = temp(mu, j); } } } } return; } void TCMatrix_gwbse::Initialize(Index basissize, Index mmin, Index mmax, Index nmin, Index nmax) { // here as storage indices starting from zero _nmin = nmin; _nmax = nmax; _ntotal = nmax - nmin + 1; _mmin = mmin; _mmax = mmax; _mtotal = mmax - mmin + 1; _auxbasissize = basissize; // vector has mtotal elements _matrix = std::vector( _mtotal, Eigen::MatrixXd::Zero(_ntotal, _auxbasissize)); } /* * Modify 3-center matrix elements consistent with use of symmetrized * Coulomb interaction using either CUDA or Openmp */ void TCMatrix_gwbse::MultiplyRightWithAuxMatrix(const Eigen::MatrixXd& matrix) { OpenMP_CUDA gemm; gemm.setOperators(_matrix, matrix); #pragma omp parallel for schedule(dynamic) for (Index i = 0; i < msize(); i++) { gemm.MultiplyRight(_matrix[i]); } } /* * Fill the 3-center object by looping over shells of GW basis set and * calling FillBlock, which calculates all 3-center overlap integrals * associated to a particular shell, convoluted with the DFT orbital * coefficients */ void TCMatrix_gwbse::Fill(const AOBasis& auxbasis, const AOBasis& dftbasis, const Eigen::MatrixXd& dft_orbitals) { // needed for Rebuild()) _auxbasis = &auxbasis; _dftbasis = &dftbasis; _dft_orbitals = &dft_orbitals; Fill3cMO(auxbasis, dftbasis, dft_orbitals); AOOverlap auxoverlap; auxoverlap.Fill(auxbasis); AOCoulomb auxcoulomb; auxcoulomb.Fill(auxbasis); Eigen::MatrixXd inv_sqrt = auxcoulomb.Pseudo_InvSqrt_GWBSE(auxoverlap, 5e-7); _removedfunctions = auxcoulomb.Removedfunctions(); MultiplyRightWithAuxMatrix(inv_sqrt); return; } /* * Determines the 3-center integrals for a given shell in the aux basis * by calculating the 3-center repulsion integral of the functions in the * aux shell with ALL functions in the DFT basis set */ std::vector TCMatrix_gwbse::ComputeAO3cBlock( const libint2::Shell& auxshell, const AOBasis& dftbasis, libint2::Engine& engine) const { std::vector ao3c = std::vector( auxshell.size(), Eigen::MatrixXd::Zero(dftbasis.AOBasisSize(), dftbasis.AOBasisSize())); std::vector dftshells = dftbasis.GenerateLibintBasis(); std::vector shell2bf = dftbasis.getMapToBasisFunctions(); const libint2::Engine::target_ptr_vec& buf = engine.results(); // alpha-loop over the "left" DFT basis function for (Index row = 0; row < Index(dftshells.size()); row++) { const libint2::Shell& shell_row = dftshells[row]; const Index row_start = shell2bf[row]; // ThreecMatrix is symmetric, restrict explicit calculation to triangular // matrix for (Index col = 0; col <= row; col++) { const libint2::Shell& shell_col = dftshells[col]; const Index col_start = shell2bf[col]; engine.compute2( auxshell, libint2::Shell::unit(), shell_col, shell_row); if (buf[0] == nullptr) { continue; } Eigen::TensorMap const> result(buf[0], auxshell.size(), shell_col.size(), shell_row.size()); for (size_t aux_c = 0; aux_c < auxshell.size(); aux_c++) { for (size_t col_c = 0; col_c < shell_col.size(); col_c++) { for (size_t row_c = 0; row_c < shell_row.size(); row_c++) { // ao3c is col major result is row-major so this is ideal ao3c[aux_c](row_start + row_c, col_start + col_c) = result(aux_c, col_c, row_c); } // ROW copy } // COL copy } // AUX copy } // gamma-loop } // alpha-loop for (Eigen::MatrixXd& mat : ao3c) { mat.triangularView() = mat.triangularView().transpose(); } return ao3c; } void TCMatrix_gwbse::Fill3cMO(const AOBasis& auxbasis, const AOBasis& dftbasis, const Eigen::MatrixXd& dft_orbitals) { const Eigen::MatrixXd dftm = dft_orbitals.block(0, _mmin, dft_orbitals.rows(), _mtotal); const Eigen::MatrixXd dftn = dft_orbitals.block(0, _nmin, dft_orbitals.rows(), _ntotal).transpose(); OpenMP_CUDA transform; transform.setOperators(dftn, dftm); Index nthreads = OPENMP::getMaxThreads(); std::vector auxshells = auxbasis.GenerateLibintBasis(); std::vector engines(nthreads); engines[0] = libint2::Engine( libint2::Operator::coulomb, std::max(dftbasis.getMaxNprim(), auxbasis.getMaxNprim()), static_cast(std::max(dftbasis.getMaxL(), auxbasis.getMaxL())), 0); engines[0].set(libint2::BraKet::xs_xx); for (Index i = 1; i < nthreads; ++i) { engines[i] = engines[0]; } std::vector auxshell2bf = auxbasis.getMapToBasisFunctions(); #pragma omp parallel for schedule(dynamic) for (Index aux = 0; aux < Index(auxshells.size()); aux++) { const libint2::Shell& auxshell = auxshells[aux]; std::vector ao3c = ComputeAO3cBlock(auxshell, dftbasis, engines[OPENMP::getThreadId()]); // this is basically a transpose of AO3c and at the same time the ao->mo // transformation // we do not want to put it into _matrix straight away is because, _matrix // is shared between all threads and we want a nice clean access pattern to // it std::vector block = std::vector( _mtotal, Eigen::MatrixXd::Zero(_ntotal, ao3c.size())); Index dim = static_cast(ao3c.size()); for (Index k = 0; k < dim; ++k) { transform.MultiplyLeftRight(ao3c[k]); for (Index i = 0; i < ao3c[k].cols(); ++i) { block[i].col(k) = ao3c[k].col(i); } } // put into correct position for (Index m_level = 0; m_level < _mtotal; m_level++) { _matrix[m_level].block(0, auxshell2bf[aux], _ntotal, auxshell.size()) = block[m_level]; } // m-th DFT orbital } // shells of GW basis set } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/tools/000077500000000000000000000000001412152066400156455ustar00rootroot00000000000000xtp-2021.2/src/libxtp/tools/apdft.cc000066400000000000000000000043611412152066400172560ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include // Local VOTCA includes #include "votca/xtp/density_integration.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/vxc_grid.h" // Local private VOTCA includes #include "apdft.h" namespace votca { namespace xtp { void APDFT::ParseOptions(const tools::Property &options) { _grid_accuracy = options.get(".grid").as(); _orbfile = options.ifExistsReturnElseReturnDefault( ".input", _job_name + ".orb"); _outputfile = options.ifExistsReturnElseReturnDefault( ".output", _job_name + "_state.dat"); std::string statestring = options.get(".state").as(); _state.FromString(statestring); } bool APDFT::Run() { Orbitals orb; orb.ReadFromCpt(_orbfile); AOBasis basis = orb.SetupDftBasis(); Vxc_Grid grid; grid.GridSetup(_grid_accuracy, orb.QMAtoms(), basis); DensityIntegration integration(grid); integration.IntegrateDensity(orb.DensityMatrixFull(_state)); std::vector potential_values; potential_values.reserve(orb.QMAtoms().size()); for (const auto &atom : orb.QMAtoms()) { potential_values.push_back(integration.IntegratePotential(atom.getPos())); } std::fstream outfile; outfile.open(_outputfile, std::fstream::out); outfile << "AtomId, Element, Potential[Hartree]" << std::endl; for (Index i = 0; i < orb.QMAtoms().size(); i++) { outfile << orb.QMAtoms()[i].getId() << " " << orb.QMAtoms()[i].getElement() << " " << std::setprecision(14) << potential_values[i] << std::endl; } outfile.close(); return true; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/tools/apdft.h000066400000000000000000000024211412152066400171130ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_APDFT_H #define VOTCA_XTP_APDFT_H // Local VOTCA includes #include "votca/xtp/qmstate.h" #include "votca/xtp/qmtool.h" namespace votca { namespace xtp { class APDFT final : public QMTool { public: APDFT() = default; ~APDFT() = default; std::string Identify() { return "apdft"; } protected: void ParseOptions(const tools::Property &user_options); bool Run(); private: std::string _grid_accuracy = "medium"; std::string _orbfile; QMState _state; std::string _outputfile; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_APDFT_H xtp-2021.2/src/libxtp/tools/coupling.h000066400000000000000000000111631412152066400176400ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_COUPLING_H #define VOTCA_XTP_COUPLING_H // Local VOTCA includes #include "votca/xtp/dftcoupling.h" #include "votca/xtp/logger.h" #include "votca/xtp/qmpackagefactory.h" namespace votca { namespace xtp { class Coupling final : public QMTool { public: Coupling() = default; ~Coupling() = default; std::string Identify() { return "coupling"; } protected: void ParseOptions(const tools::Property &user_options); bool Run(); private: std::string _MOsA, _MOsB, _MOsAB; std::string _logA, _logB, _logAB; std::string _package; tools::Property _package_options; tools::Property _dftcoupling_options; std::string _output_file; Logger _log; }; void Coupling::ParseOptions(const tools::Property &options) { _MOsA = options.get(".moleculeA.orbitals").as(); _MOsB = options.get(".moleculeB.orbitals").as(); _MOsAB = options.get(".dimerAB.orbitals").as(); _logA = options.get(".moleculeA.log").as(); _logB = options.get(".moleculeB.log").as(); _logAB = options.get(".dimerAB.log").as(); _output_file = options.ifExistsReturnElseReturnDefault( "output", _job_name + "_coupling.xml"); _package_options = options.get(".dftpackage"); _package = _package_options.get("package.name").as(); _dftcoupling_options = options.get(".dftcoupling_options"); QMPackageFactory::RegisterAll(); } bool Coupling::Run() { _log.setReportLevel(Log::current_level); _log.setMultithreading(true); _log.setCommonPreface("\n... ..."); // get the corresponding object from the QMPackageFactory std::unique_ptr qmpackage = std::unique_ptr( QMPackageFactory::QMPackages().Create(_package)); qmpackage->setLog(&_log); qmpackage->Initialize(_package_options); qmpackage->setRunDir("."); Orbitals orbitalsA, orbitalsB, orbitalsAB; qmpackage->setLogFileName(_logA); bool parse_logA_status = qmpackage->ParseLogFile(orbitalsA); if (!parse_logA_status) { XTP_LOG(Log::error, _log) << "Failed to read log of molecule A" << std::flush; } qmpackage->setLogFileName(_logB); bool parse_logB_status = qmpackage->ParseLogFile(orbitalsB); if (!parse_logB_status) { XTP_LOG(Log::error, _log) << "Failed to read log of molecule B" << std::flush; } qmpackage->setLogFileName(_logAB); bool parse_logAB_status = qmpackage->ParseLogFile(orbitalsAB); if (!parse_logAB_status) { XTP_LOG(Log::error, _log) << "Failed to read log of molecule AB" << std::flush; } qmpackage->setMOsFileName(_MOsA); bool parse_orbitalsA_status = qmpackage->ParseMOsFile(orbitalsA); if (!parse_orbitalsA_status) { XTP_LOG(Log::error, _log) << "Failed to read orbitals of molecule A" << std::flush; } qmpackage->setMOsFileName(_MOsB); bool parse_orbitalsB_status = qmpackage->ParseMOsFile(orbitalsB); if (!parse_orbitalsB_status) { XTP_LOG(Log::error, _log) << "Failed to read orbitals of molecule B" << std::flush; } qmpackage->setMOsFileName(_MOsAB); bool parse_orbitalsAB_status = qmpackage->ParseMOsFile(orbitalsAB); if (!parse_orbitalsAB_status) { XTP_LOG(Log::error, _log) << "Failed to read orbitals of dimer AB" << std::flush; } DFTcoupling dftcoupling; dftcoupling.setLogger(&_log); dftcoupling.Initialize(_dftcoupling_options); dftcoupling.CalculateCouplings(orbitalsA, orbitalsB, orbitalsAB); std::cout << _log; // output the results tools::Property summary; tools::Property &job_output = summary.add("output", ""); tools::Property &pair_summary = job_output.add("pair", ""); dftcoupling.Addoutput(pair_summary, orbitalsA, orbitalsB); tools::PropertyIOManipulator iomXML(tools::PropertyIOManipulator::XML, 1, ""); std::ofstream ofs(_output_file, std::ofstream::out); ofs << job_output; ofs.close(); return true; } } // namespace xtp } // namespace votca #endif // VOTCA_XTP_COUPLING_H xtp-2021.2/src/libxtp/tools/densityanalysis.h000066400000000000000000000040351412152066400212430ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_DENSITYANALYSIS_H #define VOTCA_XTP_DENSITYANALYSIS_H // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/gyration.h" #include "votca/xtp/logger.h" namespace votca { namespace xtp { class DensityAnalysis final : public QMTool { public: std::string Identify() { return "densityanalysis"; } protected: void ParseOptions(const tools::Property& user_options); bool Run(); private: std::string _orbfile; std::string _output_file; tools::Property _gyration_options; Logger _log; }; void DensityAnalysis::ParseOptions(const tools::Property& options) { _orbfile = options.ifExistsReturnElseReturnDefault( ".input", _job_name + ".orb"); _gyration_options = options.get(".density2gyration"); } bool DensityAnalysis::Run() { _log.setReportLevel(Log::current_level); _log.setMultithreading(true); _log.setCommonPreface("\n... ..."); Orbitals orbitals; XTP_LOG(Log::error, _log) << " Loading QM data from " << _orbfile << std::flush; orbitals.ReadFromCpt(_orbfile); Density2Gyration density2gyration(_log); density2gyration.Initialize(_gyration_options); density2gyration.AnalyzeDensity(orbitals); return true; } } // namespace xtp } // namespace votca #endif // VOTCA_XTP_DENSITYANALYSIS_H xtp-2021.2/src/libxtp/tools/dftgwbse.cc000066400000000000000000000117521412152066400177670ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/geometry_optimization.h" #include "votca/xtp/gwbseengine.h" #include "votca/xtp/qmpackagefactory.h" #include "votca/xtp/segment.h" #include "votca/xtp/staticregion.h" // Local private VOTCA includes #include "dftgwbse.h" namespace votca { namespace xtp { void DftGwBse::ParseOptions(const tools::Property& options) { // molecule coordinates _xyzfile = options.ifExistsReturnElseReturnDefault( ".molecule", _job_name + ".xyz"); // job tasks _do_optimize = options.get(".optimize").as(); // options for dft package _package_options = options.get(".dftpackage"); _package_options.add("job_name", _job_name); _package = _package_options.get("package.name").as(); // set the basis sets and functional in DFT package _package_options.get("package").add( "basisset", options.get("basisset").as()); _package_options.get("package").add( "auxbasisset", options.get("auxbasisset").as()); _package_options.get("package").add( "functional", options.get("functional").as()); // GWBSEENGINE options _gwbseengine_options = options.get(".gwbse_engine"); // set the basis sets and functional in GWBSE _gwbseengine_options.get("gwbse_options.gwbse") .add("basisset", options.get("basisset").as()); _gwbseengine_options.get("gwbse_options.gwbse") .add("auxbasisset", options.get("auxbasisset").as()); _gwbseengine_options.get("gwbse_options.gwbse.vxc") .add("functional", options.get("functional").as()); // lets get the archive file name from the xyz file name _archive_file = _job_name + ".orb"; // XML OUTPUT _xml_output = _job_name + "_summary.xml"; // check for MPS file with external multipoles for embedding _do_external = options.get("use_mpsfile").as(); if (_do_external) { _mpsfile = options.get(".mpsfile").as(); } // check if guess is requested _do_guess = options.get("use_guess").as(); if (_do_guess) { _guess_file = options.get(".guess").as(); } // if optimization is chosen, get options for geometry_optimizer if (_do_optimize) { _geoopt_options = options.get(".geometry_optimization"); } // register all QM packages QMPackageFactory::RegisterAll(); } bool DftGwBse::Run() { _log.setReportLevel(Log::current_level); _log.setMultithreading(true); _log.setCommonPreface("\n... ..."); // Get orbitals object Orbitals orbitals; if (_do_guess) { XTP_LOG(Log::error, _log) << "Reading guess from " << _guess_file << std::flush; orbitals.ReadFromCpt(_guess_file); } else { XTP_LOG(Log::error, _log) << "Reading structure from " << _xyzfile << std::flush; orbitals.QMAtoms().LoadFromFile(_xyzfile); } std::unique_ptr qmpackage = std::unique_ptr( QMPackageFactory::QMPackages().Create(_package)); qmpackage->setLog(&_log); qmpackage->Initialize(_package_options); qmpackage->setRunDir("."); if (_do_external) { StaticRegion region(0, _log); StaticSegment seg = StaticSegment("", 0); seg.LoadFromFile(_mpsfile); region.push_back(seg); qmpackage->AddRegion(region); } GWBSEEngine gwbse_engine; gwbse_engine.setLog(&_log); gwbse_engine.setQMPackage(qmpackage.get()); gwbse_engine.Initialize(_gwbseengine_options, _archive_file); if (_do_optimize) { GeometryOptimization geoopt(gwbse_engine, orbitals); geoopt.setLog(&_log); geoopt.Initialize(_geoopt_options); geoopt.Evaluate(); } else { gwbse_engine.ExcitationEnergies(orbitals); } XTP_LOG(Log::error, _log) << "Saving data to " << _archive_file << std::flush; orbitals.WriteToCpt(_archive_file); tools::Property summary = gwbse_engine.ReportSummary(); if (summary.exists("output")) { // only do gwbse summary output if we // actually did gwbse tools::PropertyIOManipulator iomXML(tools::PropertyIOManipulator::XML, 1, ""); XTP_LOG(Log::error, _log) << "Writing output to " << _xml_output << std::flush; std::ofstream ofout(_xml_output, std::ofstream::out); ofout << (summary.get("output")); ofout.close(); } return true; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/tools/dftgwbse.h000066400000000000000000000032321412152066400176230ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_DFTGWBSE_H #define VOTCA_XTP_DFTGWBSE_H // Standard includes #include // Local VOTCA includes #include "votca/xtp/logger.h" #include "votca/xtp/qmtool.h" namespace votca { namespace xtp { class DftGwBse final : public QMTool { public: DftGwBse() = default; ~DftGwBse() = default; std::string Identify() { return "dftgwbse"; } protected: void ParseOptions(const tools::Property &user_options); bool Run(); private: std::string _guess_file; bool _do_guess; std::string _mpsfile; bool _do_external; std::string _xyzfile; std::string _xml_output; // .xml output std::string _package; std::string _archive_file; // .orb file to parse to std::string _guess_orbA; std::string _guess_orbB; tools::Property _package_options; tools::Property _gwbseengine_options; tools::Property _geoopt_options; Logger _log; bool _do_optimize; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_DFTGWBSE_H xtp-2021.2/src/libxtp/tools/excitoncoupling.h000066400000000000000000000104461412152066400212350ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_EXCITONCOUPLING_H #define VOTCA_XTP_EXCITONCOUPLING_H // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/bsecoupling.h" #include "votca/xtp/classicalsegment.h" #include "votca/xtp/eeinteractor.h" #include "votca/xtp/logger.h" #include "votca/xtp/qmpackagefactory.h" #include "votca/xtp/qmtool.h" namespace votca { namespace xtp { class ExcitonCoupling final : public QMTool { public: std::string Identify() { return "excitoncoupling"; } protected: void ParseOptions(const tools::Property& user_options); bool Run(); private: std::string _orbA, _orbB, _orbAB; tools::Property _coupling_options; std::string _output_file; bool _classical; std::string _mpsA; std::string _mpsB; Logger _log; }; void ExcitonCoupling::ParseOptions(const tools::Property& options) { _classical = options.get(".use_classical").as(); if (!_classical) { _coupling_options.get(".bsecoupling_options"); _orbA = options.get(".orbitalsA").as(); _orbB = options.get(".orbitalsB").as(); _orbAB = options.get(".orbitalsAB").as(); } else { _mpsA = options.get(".mpsA").as(); _mpsB = options.get(".mpsB").as(); } _output_file = options.ifExistsReturnElseReturnDefault( "output", _job_name + "_excitoncoupling.xml"); } bool ExcitonCoupling::Run() { _log.setReportLevel(Log::current_level); _log.setMultithreading(true); _log.setCommonPreface("\n... ..."); tools::Property summary; tools::Property& job_output = summary.add("output", ""); // get the corresponding object from the QMPackageFactory if (!_classical) { Orbitals orbitalsA, orbitalsB, orbitalsAB; // load the QM data from serialized orbitals objects XTP_LOG(Log::error, _log) << " Loading QM data for molecule A from " << _orbA << std::flush; orbitalsA.ReadFromCpt(_orbA); XTP_LOG(Log::error, _log) << " Loading QM data for molecule B from " << _orbB << std::flush; orbitalsB.ReadFromCpt(_orbB); XTP_LOG(Log::error, _log) << " Loading QM data for dimer AB from " << _orbAB << std::flush; orbitalsAB.ReadFromCpt(_orbAB); BSECoupling bsecoupling; bsecoupling.setLogger(&_log); bsecoupling.Initialize(_coupling_options); bsecoupling.CalculateCouplings(orbitalsA, orbitalsB, orbitalsAB); std::cout << _log; tools::Property& pair_summary = job_output.add("pair", ""); tools::Property& type_summary = pair_summary.add("type", ""); bsecoupling.Addoutput(type_summary, orbitalsA, orbitalsB); } else if (_classical) { XTP_LOG(Log::error, _log) << "Calculating electronic coupling using classical transition charges." << _orbB << std::flush; PolarSegment seg1 = PolarSegment("A", 0); PolarSegment seg2 = PolarSegment("B", 1); seg1.LoadFromFile(_mpsA); seg2.LoadFromFile(_mpsB); eeInteractor ee; double J = ee.CalcStaticEnergy(seg1, seg2); tools::Property& pair_summary = job_output.add("pair", ""); pair_summary.setAttribute("idA", 1); pair_summary.setAttribute("idB", 2); pair_summary.setAttribute("typeA", _mpsA); pair_summary.setAttribute("typeB", _mpsB); tools::Property& coupling_summary = pair_summary.add("Coupling", ""); coupling_summary.setAttribute("jABstatic", J); } tools::PropertyIOManipulator iomXML(tools::PropertyIOManipulator::XML, 1, ""); std::ofstream ofs(_output_file, std::ofstream::out); ofs << job_output; ofs.close(); return true; } } // namespace xtp } // namespace votca #endif // VOTCA_XTP_EXCITONCOUPLING_H xtp-2021.2/src/libxtp/tools/gencube.cc000066400000000000000000000166171412152066400175770ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include // Third party includes #include // VOTCA includes #include #include #include // Local VOTCA includes #include "votca/xtp/aobasis.h" #include "votca/xtp/cubefile_writer.h" #include "votca/xtp/orbitals.h" // Local private VOTCA includes #include "gencube.h" namespace votca { namespace xtp { void GenCube::ParseOptions(const tools::Property& options) { _orbfile = options.ifExistsReturnElseReturnDefault( ".input", _job_name + ".orb"); _output_file = options.ifExistsReturnElseReturnDefault( ".output", _job_name + ".cube"); // padding _padding = options.get(".padding").as(); // steps _steps.y() = options.get(".ysteps").as(); _steps.x() = options.get(".xsteps").as(); _steps.z() = options.get(".zsteps").as(); std::string statestring = options.get(".state").as(); _state.FromString(statestring); _dostateonly = options.get(".diff2gs").as(); _mode = options.get(".mode").as(); if (_mode == "subtract") { _infile1 = options.get(".infile1").as(); _infile2 = options.get(".infile2").as(); } } void GenCube::calculateCube() { XTP_LOG(Log::error, _log) << "Reading serialized QM data from " << _orbfile << std::flush; Orbitals orbitals; orbitals.ReadFromCpt(_orbfile); CubeFile_Writer writer(_steps, _padding, _log); XTP_LOG(Log::error, _log) << "Created cube grid" << std::flush; writer.WriteFile(_output_file, orbitals, _state, _dostateonly); XTP_LOG(Log::error, _log) << "Wrote cube data to " << _output_file << std::flush; return; } void GenCube::subtractCubes() { // open infiles for reading std::ifstream in1; XTP_LOG(Log::error, _log) << " Reading first cube from " << _infile1 << std::flush; in1.open(_infile1, std::ios::in); std::ifstream in2; XTP_LOG(Log::error, _log) << " Reading second cube from " << _infile2 << std::flush; in2.open(_infile2, std::ios::in); std::string s; std::ofstream out(_output_file); // first two lines of header are garbage tools::getline(in1, s); out << s << "\n"; tools::getline(in1, s); out << s << " substraction\n"; tools::getline(in2, s); tools::getline(in2, s); // read rest from header Index natoms; double xstart; double ystart; double zstart; // first line in1 >> natoms; bool do_amplitude = false; if (natoms < 0) { do_amplitude = true; } in1 >> xstart; in1 >> ystart; in1 >> zstart; // check from second file Index tempint; double tempdouble; in2 >> tempint; if (tempint != natoms) { throw std::runtime_error("Atom numbers do not match"); } in2 >> tempdouble; if (tempdouble != xstart) { throw std::runtime_error("Xstart does not match"); } in2 >> tempdouble; if (tempdouble != ystart) { throw std::runtime_error("Ystart does not match"); } in2 >> tempdouble; if (tempdouble != zstart) { throw std::runtime_error("Zstart does not match"); } out << boost::format("%1$lu %2$f %3$f %4$f \n") % natoms % xstart % ystart % zstart; // grid information from first cube double xincr; double yincr; double zincr; Index xsteps; Index ysteps; Index zsteps; in1 >> xsteps; in1 >> xincr; in1 >> tempdouble; in1 >> tempdouble; in1 >> ysteps; in1 >> tempdouble; in1 >> yincr; in1 >> tempdouble; in1 >> zsteps; in1 >> tempdouble; in1 >> tempdouble; in1 >> zincr; // check second cube in2 >> tempint; if (tempint != xsteps) { throw std::runtime_error("xsteps does not match"); } in2 >> tempdouble; if (tempdouble != xincr) { throw std::runtime_error("xincr does not match"); } in2 >> tempdouble; in2 >> tempdouble; in2 >> tempint; if (tempint != ysteps) { throw std::runtime_error("ysteps does not match"); } in2 >> tempdouble; in2 >> tempdouble; if (tempdouble != yincr) { throw std::runtime_error("yincr does not match"); } in2 >> tempdouble; in2 >> tempint; if (tempint != zsteps) { throw std::runtime_error("zsteps does not match"); } in2 >> tempdouble; in2 >> tempdouble; in2 >> tempdouble; if (tempdouble != zincr) { throw std::runtime_error("zincr does not match"); } out << boost::format("%1$d %2$f 0.0 0.0 \n") % xsteps % xincr; out << boost::format("%1$d 0.0 %2$f 0.0 \n") % ysteps % yincr; out << boost::format("%1$d 0.0 0.0 %2$f \n") % zsteps % zincr; // atom information for (Index iatom = 0; iatom < std::abs(natoms); iatom++) { // get center coordinates in Bohr double x; double y; double z; Index atnum; double crg; // get from first cube in1 >> atnum; in1 >> crg; in1 >> x; in1 >> y; in1 >> z; // check second cube in2 >> tempint; if (tempint != atnum) { throw std::runtime_error("atnum does not match"); } in2 >> tempdouble; if (tempdouble != crg) { throw std::runtime_error("crg does not match"); } in2 >> tempdouble; if (tempdouble != x) { throw std::runtime_error("x does not match"); } in2 >> tempdouble; if (tempdouble != y) { throw std::runtime_error("y does not match"); } in2 >> tempdouble; if (tempdouble != z) { throw std::runtime_error("z does not match"); } out << boost::format("%1$d %2$f %3$f %4$f %5$f\n") % atnum % crg % x % y % z; } if (do_amplitude) { Index ntotal; Index nis; in1 >> ntotal; in1 >> nis; in2 >> tempint; if (tempint != ntotal) { throw std::runtime_error("ntotal does not match"); } in2 >> tempint; if (tempint != nis) { throw std::runtime_error("nis does not match"); } out << boost::format(" 1 %1$d \n") % nis; } // now read data double val1; double val2; for (Index ix = 0; ix < xsteps; ix++) { for (Index iy = 0; iy < ysteps; iy++) { Index Nrecord = 0; for (Index iz = 0; iz < zsteps; iz++) { Nrecord++; in1 >> val1; in2 >> val2; if (Nrecord == 6 || iz == zsteps - 1) { out << boost::format("%1$E \n") % (val1 - val2); Nrecord = 0; } else { out << boost::format("%1$E ") % (val1 - val2); } } } } out.close(); XTP_LOG(Log::error, _log) << "Wrote subtracted cube data to " << _output_file << std::flush; } bool GenCube::Run() { _log.setReportLevel(Log::current_level); _log.setMultithreading(true); _log.setCommonPreface("\n... ..."); // calculate new cube if (_mode == "new") { calculateCube(); } else if (_mode == "subtract") { subtractCubes(); } return true; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/tools/gencube.h000066400000000000000000000027701412152066400174340ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_GENCUBE_H #define VOTCA_XTP_GENCUBE_H // Local VOTCA includes #include "votca/xtp/logger.h" #include "votca/xtp/qmstate.h" #include "votca/xtp/qmtool.h" namespace votca { namespace xtp { class AOBasis; class GenCube final : public QMTool { public: GenCube() = default; ~GenCube() = default; std::string Identify() { return "gencube"; } protected: void ParseOptions(const tools::Property& user_options); bool Run(); private: void calculateCube(); void subtractCubes(); std::string _orbfile; std::string _output_file; std::string _infile1; std::string _infile2; bool _dostateonly; double _padding; Eigen::Array _steps; QMState _state; std::string _mode; Logger _log; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_GENCUBE_H xtp-2021.2/src/libxtp/tools/log2mps.h000066400000000000000000000061521412152066400174050ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_LOG2MPS_H #define VOTCA_XTP_LOG2MPS_H // Third party includes #include // Local VOTCA includes #include "votca/xtp/classicalsegment.h" #include "votca/xtp/qmpackagefactory.h" #include "votca/xtp/qmtool.h" namespace votca { namespace xtp { class Log2Mps final : public QMTool { public: Log2Mps() = default; ~Log2Mps() = default; std::string Identify() { return "log2mps"; } protected: void ParseOptions(const tools::Property &user_options); bool Run(); private: std::string _package; std::string _logfile; std::string _mpsfile; }; void Log2Mps::ParseOptions(const tools::Property &options) { QMPackageFactory::RegisterAll(); _package = options.get(".package").as(); if (_package == "xtp") { throw std::runtime_error( "XTP has no log file. For xtp package just run the partialcharges tool " "on you .orb file"); } _logfile = options.ifExistsReturnElseReturnDefault( ".logfile", _job_name + ".log"); _mpsfile = options.ifExistsReturnElseReturnDefault( ".mpsfile", _job_name + ".mps"); std::cout << "\n... ... " << _logfile << " => " << _mpsfile << "\n"; } bool Log2Mps::Run() { // Logger (required for QM package, so we can just as well use it) Logger log; log.setCommonPreface("\n... ..."); log.setReportLevel(Log::current_level); log.setMultithreading(true); // Set-up QM package XTP_LOG(Log::error, log) << "Using package <" << _package << ">" << std::flush; std::unique_ptr qmpack = std::unique_ptr( QMPackageFactory::QMPackages().Create(_package)); qmpack->setLog(&log); qmpack->setRunDir("."); qmpack->setLogFileName(_logfile); // Create orbitals, fill with life & extract QM atoms StaticSegment atoms = qmpack->GetCharges(); // Sanity checks, total charge if (atoms.size() < 1) { throw std::runtime_error("ERROR No charges extracted from " + _logfile); } double Q = atoms.CalcTotalQ(); XTP_LOG(Log::error, log) << atoms.size() << " QM atoms, total charge Q = " << Q << std::flush; std::string tag = "::LOG2MPS " + (boost::format("(log-file='%1$s' : %2$d QM atoms)") % _logfile % atoms.size()) .str(); atoms.WriteMPS(_mpsfile, tag); return true; } } // namespace xtp } // namespace votca #endif // VOTCA_XTP_LOG2MPS_H xtp-2021.2/src/libxtp/tools/mol2orb.cc000066400000000000000000000020551412152066400175320ustar00rootroot00000000000000#include "mol2orb.h" // Third party includes #include // Local VOTCA includes #include "votca/xtp/molden.h" #include "votca/xtp/orbitals.h" #include namespace votca { namespace xtp { void Mol2Orb::ParseOptions(const tools::Property& options) { _moldenfile = _job_name + ".molden.input"; _orbfile = _job_name + ".orb"; _basisset_name = options.get(".basisset").as(); _aux_basisset_name = options.get(".auxbasisset").as(); } bool Mol2Orb::Run() { _log.setReportLevel(Log::current_level); _log.setMultithreading(true); _log.setCommonPreface("\n... ..."); Orbitals orbitals; Molden molden(_log); molden.setBasissetInfo(_basisset_name, _aux_basisset_name); molden.parseMoldenFile(_moldenfile, orbitals); // Save orbitals object XTP_LOG(Log::error, _log) << "Saving data to " << _orbfile << std::flush; orbitals.WriteToCpt(_orbfile); XTP_LOG(Log::error, _log) << "Done parsing\n" << std::flush; return true; } } // namespace xtp } // namespace votcaxtp-2021.2/src/libxtp/tools/mol2orb.h000066400000000000000000000012631412152066400173740ustar00rootroot00000000000000 #pragma once #ifndef VOTCA_XTP_MOL2ORB_H #define VOTCA_XTP_MOL2ORB_H // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/logger.h" #include "votca/xtp/qmtool.h" namespace votca { namespace xtp { class Mol2Orb final : public QMTool { public: Mol2Orb() = default; ~Mol2Orb() = default; std::string Identify() { return "mol2orb"; } protected: void ParseOptions(const tools::Property& user_options); bool Run(); private: std::string _moldenfile; std::string _orbfile; std::string _basisset_name; std::string _aux_basisset_name; Logger _log; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_MOL2ORB_Hxtp-2021.2/src/libxtp/tools/molpol.cc000066400000000000000000000170171412152066400174640ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/polarregion.h" #include "votca/xtp/qmpackage.h" #include "votca/xtp/qmpackagefactory.h" // Local private VOTCA includes #include "molpol.h" namespace votca { namespace xtp { void MolPol::ParseOptions(const tools::Property& options) { std::string mps_input = options.ifExistsReturnElseReturnDefault( ".mpsinput", _job_name + ".mps"); _input.LoadFromFile(mps_input); _mps_output = options.ifExistsReturnElseReturnDefault( ".mpsoutput", _job_name + "_polar.mps"); _polar_options = options.get(".options_polar"); // polar targer or qmpackage logfile const std::string& mode = options.get("mode").as(); if (mode == "file") { Eigen::VectorXd target_vec = options.get(".target_polarisability").as(); if (target_vec.size() != 6) { throw std::runtime_error( "ERROR " " should have this format: pxx pxy pxz pyy pyz pzz"); } target_vec *= std::pow(tools::conv::ang2bohr, 3); _polarization_target(0, 0) = target_vec(0); _polarization_target(1, 0) = target_vec(1); _polarization_target(0, 1) = target_vec(1); _polarization_target(2, 0) = target_vec(2); _polarization_target(0, 2) = target_vec(2); _polarization_target(1, 1) = target_vec(3); _polarization_target(2, 1) = target_vec(4); _polarization_target(1, 2) = target_vec(4); _polarization_target(2, 2) = target_vec(5); } else { std::string qm_package = options.get(".qmpackage").as(); std::string log_file = options.get(".logfile").as(); Logger log; log.setPreface(Log::info, "\n ..."); log.setPreface(Log::error, "\n ..."); log.setPreface(Log::warning, "\n ..."); log.setPreface(Log::debug, "\n ..."); log.setReportLevel(Log::current_level); log.setMultithreading(true); // Set-up QM package XTP_LOG(Log::error, log) << "Using package <" << qm_package << ">" << std::flush; QMPackageFactory::RegisterAll(); std::unique_ptr qmpack = std::unique_ptr( QMPackageFactory::QMPackages().Create(qm_package)); qmpack->setLog(&log); qmpack->setRunDir("."); qmpack->setLogFileName(log_file); _polarization_target = qmpack->GetPolarizability(); } Eigen::VectorXd default_weights = Eigen::VectorXd::Ones(_input.size()); _weights = options.ifExistsReturnElseReturnDefault( ".weights", default_weights); _tolerance_pol = options.get(".tolerance").as(); _max_iter = options.get(".iterations").as(); } Eigen::Vector3d MolPol::CalcInducedDipole( const PolarSegment& input, const Eigen::Vector3d& ext_field) const { Logger log; log.setMultithreading(false); log.setCommonPreface("\n ..."); log.setReportLevel(Log::current_level); PolarRegion pol(0, log); pol.Initialize(_polar_options); pol.push_back(input); PolarSegment& workmol = pol[0]; for (PolarSite& site : workmol) { site.V() = ext_field; } std::vector> empty; // pol interacts with nobody else pol.Evaluate(empty); Eigen::Vector3d induced_dipole = Eigen::Vector3d::Zero(); for (const PolarSite& site : workmol) { induced_dipole += site.Induced_Dipole(); } if (Log::current_level > 0) { std::cout << log; } return induced_dipole; } Eigen::Matrix3d MolPol::CalcClassicalPol(const PolarSegment& input) const { double eVnm_2_hrtbohr = tools::conv::ev2hrt / tools::conv::nm2bohr; double fieldstrength = (0.1 * eVnm_2_hrtbohr); Eigen::Matrix3d polarization = Eigen::Matrix3d::Zero(); Eigen::Vector3d ext_field = fieldstrength * Eigen::Vector3d::UnitX(); // central differences scheme Eigen::Vector3d dxplus = CalcInducedDipole(input, ext_field); Eigen::Vector3d dxminus = CalcInducedDipole(input, -ext_field); polarization.col(0) = dxplus - dxminus; ext_field = fieldstrength * Eigen::Vector3d::UnitY(); Eigen::Vector3d dyplus = CalcInducedDipole(input, ext_field); Eigen::Vector3d dyminus = CalcInducedDipole(input, -ext_field); polarization.col(1) = dyplus - dyminus; ext_field = fieldstrength * Eigen::Vector3d::UnitZ(); Eigen::Vector3d dzplus = CalcInducedDipole(input, ext_field); Eigen::Vector3d dzminus = CalcInducedDipole(input, -ext_field); polarization.col(2) = dzplus - dzminus; return -polarization / (2 * fieldstrength); } void MolPol::Printpolarization(const Eigen::Matrix3d& result) const { std::cout << std::endl << "First principle polarization [A^3]" << std::flush; double conversion = std::pow(tools::conv::bohr2ang, 3); std::cout << std::endl << _polarization_target * conversion << std::flush; std::cout << std::endl << "Scaled classical polarization [A^3]" << std::flush; std::cout << std::endl << result * conversion << std::flush; std::cout << std::endl << "EigenValues classical polarization [A^3]" << std::flush; Eigen::SelfAdjointEigenSolver es2; es2.computeDirect(result, Eigen::EigenvaluesOnly); Eigen::Matrix3d diag = es2.eigenvalues().asDiagonal(); std::cout << std::endl << diag * conversion << std::flush; } bool MolPol::Run() { PolarSegment polar = _input; Eigen::SelfAdjointEigenSolver es; es.computeDirect(_polarization_target, Eigen::EigenvaluesOnly); const double pol_volume_target = std::pow(es.eigenvalues().prod(), 1.0 / 3.0); for (Index iter = 0; iter < _max_iter; iter++) { Eigen::SelfAdjointEigenSolver es2; Eigen::Matrix3d pol = CalcClassicalPol(polar); es2.computeDirect(pol, Eigen::EigenvaluesOnly); const double pol_volume_iter = std::pow(es2.eigenvalues().prod(), 1.0 / 3.0); double scale = pol_volume_target / pol_volume_iter - 1; std::cout << "\nIteration " << iter + 1 << " of " << _max_iter << " target:" << pol_volume_target << " current:" << pol_volume_iter << std::endl; for (Index i = 0; i < polar.size(); i++) { Eigen::Matrix3d local_pol = polar[i].getpolarization(); polar[i].setpolarization(local_pol * (1 + scale * _weights[i])); } if (std::abs(scale) < _tolerance_pol) { std::cout << std::endl << "... ... Iterative refinement : *CONVERGED*" << std::flush; std::cout << std::endl << "... ... Scaling coefficient : " << scale << std::flush; polar.WriteMPS(_mps_output, "MOLPOL (OPTIMIZED)"); Printpolarization(pol); break; } else if (iter == (_max_iter - 1)) { std::cout << std::endl << "... ... Iterative refinement : *FAILED*" << std::flush; std::cout << std::endl << "... ... ERROR Convergence not achieved. " << "Check your input mps-file, target polarizability " << std::flush; Printpolarization(pol); } } return true; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/tools/molpol.h000066400000000000000000000034121412152066400173200ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_MOLPOL_H #define VOTCA_XTP_MOLPOL_H // Standard includes #include // Local VOTCA includes #include "votca/xtp/classicalsegment.h" #include "votca/xtp/logger.h" #include "votca/xtp/qmtool.h" namespace votca { namespace xtp { class PolarRegion; class MolPol final : public QMTool { public: MolPol() : _input("", 0){}; ~MolPol() = default; std::string Identify() { return "molpol"; } protected: void ParseOptions(const tools::Property& user_options); bool Run(); private: void Printpolarization(const Eigen::Matrix3d& result) const; Eigen::Matrix3d CalcClassicalPol(const PolarSegment& input) const; Eigen::Vector3d CalcInducedDipole(const PolarSegment& input, const Eigen::Vector3d& ext_field) const; Logger _log; std::string _mps_output; PolarSegment _input; Eigen::Matrix3d _polarization_target; Eigen::VectorXd _weights; tools::Property _polar_options; double _tolerance_pol = 1e-4; Index _max_iter = 1000; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_MOLPOL_H xtp-2021.2/src/libxtp/tools/orb2mol.cc000066400000000000000000000014521412152066400175320ustar00rootroot00000000000000#include "orb2mol.h" #include "votca/xtp/molden.h" #include namespace votca { namespace xtp { void Orb2Mol::ParseOptions(const tools::Property&) { _moldenfile = _job_name + ".molden.input"; _orbfile = _job_name + ".orb"; _xyzfile = _job_name + ".xyz"; } bool Orb2Mol::Run() { _log.setReportLevel(Log::current_level); _log.setMultithreading(true); _log.setCommonPreface("\n... ..."); Orbitals orbitals; XTP_LOG(Log::error, _log) << "Loading data from " << _orbfile << std::flush; orbitals.ReadFromCpt(_orbfile); XTP_LOG(Log::error, _log) << "Start parsing" << std::flush; Molden writer(_log); writer.WriteFile(_moldenfile, orbitals); XTP_LOG(Log::error, _log) << "Done parsing \n" << std::flush; return true; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/tools/orb2mol.h000066400000000000000000000014661412152066400174010ustar00rootroot00000000000000 #pragma once #ifndef VOTCA_XTP_ORB2MOL_H #define VOTCA_XTP_ORB2MOL_H // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/logger.h" #include "votca/xtp/orbreorder.h" #include "votca/xtp/qmtool.h" #include #include namespace votca { namespace xtp { class Orb2Mol final : public QMTool { public: Orb2Mol() = default; ~Orb2Mol() = default; std::string Identify() { return "orb2mol"; } protected: void ParseOptions(const tools::Property& user_options); bool Run(); private: // clang-format off std::string _moldenfile; std::string _orbfile; std::string _xyzfile; std::string _basisset_name; std::string _aux_basisset_name; Logger _log; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_ORB2MOL_H xtp-2021.2/src/libxtp/tools/partialcharges.h000066400000000000000000000045441412152066400210160ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_PARTIALCHARGES_H #define VOTCA_XTP_PARTIALCHARGES_H // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/esp2multipole.h" #include "votca/xtp/logger.h" namespace votca { namespace xtp { class Partialcharges final : public QMTool { public: Partialcharges() = default; ~Partialcharges() = default; std::string Identify() { return "partialcharges"; } protected: void ParseOptions(const tools::Property& user_options); bool Run(); private: std::string _orbfile; std::string _output_file; tools::Property _esp_options; Logger _log; }; void Partialcharges::ParseOptions(const tools::Property& options) { _orbfile = options.ifExistsReturnElseReturnDefault( ".input", _job_name + ".orb"); _output_file = options.ifExistsReturnElseReturnDefault( ".output", _job_name + ".mps"); _esp_options = options.get(".esp_options"); } bool Partialcharges::Run() { _log.setReportLevel(Log::current_level); _log.setMultithreading(true); _log.setCommonPreface("\n... ..."); Orbitals orbitals; XTP_LOG(Log::error, _log) << " Loading QM data from " << _orbfile << std::flush; orbitals.ReadFromCpt(_orbfile); Esp2multipole esp2multipole = Esp2multipole(_log); esp2multipole.Initialize(_esp_options); StaticSegment seg = esp2multipole.Extractingcharges(orbitals); seg.WriteMPS(_output_file, esp2multipole.GetStateString()); XTP_LOG(Log::error, _log) << "Written charges to " << _output_file << std::flush; return true; } } // namespace xtp } // namespace votca #endif // VOTCA_XTP_PARTIALCHARGES_H xtp-2021.2/src/libxtp/tools/qmsandbox.cc000066400000000000000000000022261412152066400201520ustar00rootroot00000000000000#include "qmsandbox.h" #include "votca/xtp/orbreorder.h" #include namespace votca { namespace xtp { void QMSandbox::ParseOptions(const tools::Property&) {} bool QMSandbox::Run() { _log.setReportLevel(Log::current_level); _log.setMultithreading(true); _log.setCommonPreface("\n... ..."); QMMolecule atoms("", 0); atoms.LoadFromFile(_job_name + ".xyz"); BasisSet bs; bs.Load("def2-svp"); AOBasis basis; basis.Fill(bs, atoms); std::vector shells = basis.GenerateLibintBasis(); for (auto& shell : basis) { std::cout << shell << std::endl; } std::copy(std::begin(shells), std::end(shells), std::ostream_iterator(std::cout, "\n")); AOOverlap aooverlap; AOCoulomb aocoulomb; AOKinetic aokinetic; AODipole aodipole; for (int i = 0; i < 100; i++) { aooverlap.Fill(basis); } for (int i = 0; i < 100; i++) { aocoulomb.Fill(basis); } for (int i = 0; i < 100; i++) { aokinetic.Fill(basis); } for (int i = 0; i < 100; i++) { aodipole.Fill(basis); } return true; } // namespace xtp } // namespace xtp } // namespace votcaxtp-2021.2/src/libxtp/tools/qmsandbox.h000066400000000000000000000025141412152066400200140ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_QMSANDBOX_H #define VOTCA_XTP_QMSANDBOX_H // Local VOTCA includes #include "votca/xtp/aobasis.h" #include "votca/xtp/aomatrix.h" #include "votca/xtp/logger.h" #include "votca/xtp/qmpackagefactory.h" #include "votca/xtp/qmtool.h" namespace votca { namespace xtp { class QMSandbox final : public QMTool { public: QMSandbox() = default; ~QMSandbox() = default; std::string Identify() { return "qmsandbox"; } protected: void ParseOptions(const tools::Property& user_options); bool Run(); private: std::string _orbfile; Logger _log; }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_QMSANDBOX_H xtp-2021.2/src/libxtp/tools/spectrum.cc000066400000000000000000000166421412152066400200270ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include // Local private VOTCA includes #include "spectrum.h" namespace votca { namespace xtp { void Spectrum::ParseOptions(const tools::Property& options) { // orbitals file or pure DFT output _orbfile = options.ifExistsReturnElseReturnDefault( ".orbitals", _job_name + ".orb"); _output_file = options.ifExistsReturnElseReturnDefault( ".output", _job_name + "_spectrum.dat"); _n_pt = options.get(".points").as(); _lower = options.get(".lower").as(); _upper = options.get(".upper").as(); _fwhm = options.get(".fwhm").as(); _spectrum_type = options.get(".type").as(); _minexc = options.get(".minexc").as(); _maxexc = options.get(".maxexc").as(); _shiftby = options.get(".shift").as(); } bool Spectrum::Run() { _log.setReportLevel(Log::current_level); _log.setMultithreading(true); _log.setCommonPreface("\n... ..."); XTP_LOG(Log::error, _log) << "Calculating absorption spectrum plot " << _orbfile << std::flush; Orbitals orbitals; // load the QM data from serialized orbitals object XTP_LOG(Log::error, _log) << " Loading QM data from " << _orbfile << std::flush; orbitals.ReadFromCpt(_orbfile); // check if orbitals contains singlet energies and transition dipoles if (!orbitals.hasBSESinglets()) { throw std::runtime_error( "BSE singlet energies not stored in QM data file!"); } if (!orbitals.hasTransitionDipoles()) { throw std::runtime_error( "BSE transition dipoles not stored in QM data file!"); } const Eigen::VectorXd BSESingletEnergies = orbitals.BSESinglets().eigenvalues() * tools::conv::hrt2ev; const std::vector& TransitionDipoles = orbitals.TransitionDipoles(); Eigen::VectorXd osc = orbitals.Oscillatorstrengths(); if (_maxexc > Index(TransitionDipoles.size())) { _maxexc = Index(TransitionDipoles.size()) - 1; } Index n_exc = _maxexc - _minexc + 1; XTP_LOG(Log::error, _log) << " Considering " << n_exc << " excitation with max energy " << BSESingletEnergies(_maxexc) << " eV / min wave length " << evtonm(BSESingletEnergies[_maxexc - 1]) << " nm" << std::flush; /* * * For a single excitation, broaden by Lineshape function L(v-W) * eps(v) = f * L(v-W) * * where * v: energy * f: oscillator strength in dipole-length gauge * W: excitation energy * * Lineshape function depend on FWHM and can be * * Gaussian * L(v-W) = 1/(sqrt(2pi)sigma) * exp(-0.5 (v-W)^2/sigma^2 * * * with sigma: derived from FWHM (FWHM/2.3548) * * Lorentzian * L(v-W) = 1/pi * 0.5 FWHM/( (v-w)^2 + 0.25*FWHM^2 ) * * Full spectrum is superposition of individual spectra. * * Alternatively, one can calculate the imaginary part of the * frequency-dependent dielectric function * * IM(eps(v)) ~ 1/v^2 * W^2 * |td|^2 * L(v-W) * = 1/v^2 * W * f * L(v-W) * * */ std::ofstream ofs(_output_file, std::ofstream::out); if (_spectrum_type == "energy") { ofs << "# E(eV) epsGaussian IM(eps)Gaussian epsLorentz " "Im(esp)Lorentz\n"; for (Index i_pt = 0; i_pt <= _n_pt; i_pt++) { double e = (_lower + double(i_pt) * (_upper - _lower) / double(_n_pt)); double eps_Gaussian = 0.0; double imeps_Gaussian = 0.0; double eps_Lorentzian = 0.0; double imeps_Lorentzian = 0.0; for (Index i_exc = _minexc; i_exc <= _maxexc; i_exc++) { eps_Gaussian += osc[i_exc] * Gaussian(e, BSESingletEnergies(i_exc) + _shiftby, _fwhm); imeps_Gaussian += osc[i_exc] * BSESingletEnergies(i_exc) * Gaussian(e, BSESingletEnergies(i_exc), _fwhm); eps_Lorentzian += osc[i_exc] * Lorentzian(e, BSESingletEnergies(i_exc), _fwhm); imeps_Lorentzian += osc[i_exc] * BSESingletEnergies(i_exc) * Lorentzian(e, BSESingletEnergies(i_exc), _fwhm); } ofs << e << " " << eps_Gaussian << " " << imeps_Gaussian << " " << eps_Lorentzian << " " << imeps_Lorentzian << std::endl; } XTP_LOG(Log::error, _log) << " Spectrum in energy range from " << _lower << " to " << _upper << " eV and with broadening of FWHM " << _fwhm << " eV written to file " << _output_file << std::flush; } if (_spectrum_type == "wavelength") { ofs << "# lambda(nm) epsGaussian IM(eps)Gaussian epsLorentz " "Im(esp)Lorentz\n"; for (Index i_pt = 0; i_pt <= _n_pt; i_pt++) { double lambda = (_lower + double(i_pt) * (_upper - _lower) / double(_n_pt)); double eps_Gaussian = 0.0; double imeps_Gaussian = 0.0; double eps_Lorentzian = 0.0; double imeps_Lorentzian = 0.0; for (Index i_exc = _minexc; i_exc <= _maxexc; i_exc++) { double exc_lambda = nmtoev(BSESingletEnergies(i_exc) + _shiftby); eps_Gaussian += osc[i_exc] * Gaussian(lambda, exc_lambda, _fwhm); imeps_Gaussian += osc[i_exc] * exc_lambda * Gaussian(lambda, exc_lambda, _fwhm); eps_Lorentzian += osc[i_exc] * Lorentzian(lambda, exc_lambda, _fwhm); imeps_Lorentzian += osc[i_exc] * exc_lambda * Lorentzian(lambda, exc_lambda, _fwhm); } ofs << lambda << " " << eps_Gaussian << " " << imeps_Gaussian << " " << eps_Lorentzian << " " << imeps_Lorentzian << std::endl; } XTP_LOG(Log::error, _log) << " Spectrum in wavelength range from " << _lower << " to " << _upper << " nm and with broadening of FWHM " << _fwhm << " nm written to file " << _output_file << std::flush; } ofs.close(); return true; } double Spectrum::Lorentzian(double x, double center, double fwhm) { return 0.5 * fwhm / (std::pow(x - center, 2) + 0.25 * fwhm * fwhm) / boost::math::constants::pi(); } double Spectrum::Gaussian(double x, double center, double fwhm) { // FWHM = 2*sqrt(2 ln2) sigma = 2.3548 sigma double sigma = fwhm / 2.3548; return std::exp(-0.5 * std::pow((x - center) / sigma, 2)) / sigma / sqrt(2.0 * boost::math::constants::pi()); } double Spectrum::evtonm(double eV) { return 1241.0 / eV; } double Spectrum::evtoinvcm(double eV) { return 8065.73 * eV; } double Spectrum::nmtoinvcm(double nm) { return 1241.0 * 8065.73 / nm; } double Spectrum::invcmtonm(double invcm) { return 1.0e7 / invcm; } double Spectrum::nmtoev(double nm) { return 1241.0 / nm; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/tools/spectrum.h000066400000000000000000000036741412152066400176720ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #pragma once #ifndef VOTCA_XTP_SPECTRUM_H #define VOTCA_XTP_SPECTRUM_H // Standard includes #include // Local VOTCA includes #include "votca/xtp/logger.h" #include "votca/xtp/qmstate.h" #include "votca/xtp/qmtool.h" namespace votca { namespace xtp { class Orbitals; class Spectrum final : public QMTool { public: Spectrum() = default; ~Spectrum() = default; std::string Identify() { return "spectrum"; } protected: void ParseOptions(const tools::Property& user_options); bool Run(); private: std::string _orbfile; std::string _output_file = "spectrum.dat"; Logger _log; void CheckContent(const Orbitals& _orbitals); double evtonm(double eV); double evtoinvcm(double eV); double nmtoinvcm(double nm); double invcmtonm(double invcm); double nmtoev(double nm); double _lower = 0.0; // in eV double _upper; // in eV Index _n_pt = 100; Index _minexc = 0; Index _maxexc = std::numeric_limits::max(); double _fwhm; // in eV double _shiftby = 0.0; std::string _spectrum_type = "energy"; // lineshape functions double Gaussian(double x, double center, double fwhm); double Lorentzian(double x, double center, double fwhm); }; } // namespace xtp } // namespace votca #endif // VOTCA_XTP_SPECTRUM_H xtp-2021.2/src/libxtp/topology.cc000066400000000000000000000145011412152066400166710ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // VOTCA includes #include #include // Local VOTCA includes #include "votca/xtp/atom.h" #include "votca/xtp/checkpointwriter.h" #include "votca/xtp/segment.h" #include "votca/xtp/topology.h" #include "votca/xtp/version.h" namespace votca { namespace xtp { Topology::Topology(const Topology &top) { _segments = top._segments; _time = top._time; _step = top._step; this->setBox(top.getBox()); for (const QMPair *pair : top.NBList()) { const Segment &seg1 = _segments[pair->Seg1()->getId()]; const Segment &seg2 = _segments[pair->Seg2()->getId()]; _nblist.Add(seg1, seg2, pair->R()); } } Topology &Topology::operator=(const Topology &top) { if (&top != this) { _segments = top._segments; _time = top._time; _step = top._step; this->setBox(top.getBox()); _nblist.Cleanup(); for (const QMPair *pair : top.NBList()) { const Segment &seg1 = _segments[pair->Seg1()->getId()]; const Segment &seg2 = _segments[pair->Seg2()->getId()]; _nblist.Add(seg1, seg2, pair->R()); } } return *this; } Segment &Topology::AddSegment(std::string segment_name) { Index segment_id = Index(_segments.size()); _segments.push_back(Segment(segment_name, segment_id)); return _segments.back(); } // +++++++++++++++++ // // Periodic Boundary // // +++++++++++++++++ // void Topology::setBox(const Eigen::Matrix3d &box, csg::BoundaryCondition::eBoxtype boxtype) { // Determine box type automatically in case boxtype == typeAuto if (boxtype == csg::BoundaryCondition::typeAuto) { boxtype = AutoDetectBoxType(box); } if (_bc != nullptr) { if (Log::verbose()) { std::cout << "Removing periodic box. Creating new... " << std::endl; } } _bc.reset(nullptr); switch (boxtype) { case csg::BoundaryCondition::typeTriclinic: _bc.reset(new csg::TriclinicBox()); break; case csg::BoundaryCondition::typeOrthorhombic: _bc.reset(new csg::OrthorhombicBox()); break; default: _bc.reset(new csg::OpenBox()); break; } _bc->setBox(box); } csg::BoundaryCondition::eBoxtype Topology::AutoDetectBoxType( const Eigen::Matrix3d &box) { // Set box type to OpenBox in case "box" is the zero matrix, // to OrthorhombicBox in case "box" is a diagonal matrix, // or to TriclinicBox otherwise if (box.isApproxToConstant(0)) { std::cout << "WARNING: No box vectors specified in trajectory." "Using open-box boundary conditions. " << std::endl; return csg::BoundaryCondition::typeOpen; } else if ((box - Eigen::Matrix3d(box.diagonal().asDiagonal())) .isApproxToConstant(0)) { return csg::BoundaryCondition::typeOrthorhombic; } else { return csg::BoundaryCondition::typeTriclinic; } return csg::BoundaryCondition::typeOpen; } Eigen::Vector3d Topology::PbShortestConnect(const Eigen::Vector3d &r1, const Eigen::Vector3d &r2) const { return _bc->BCShortestConnection(r1, r2); } double Topology::GetShortestDist(const Segment &seg1, const Segment &seg2) const { double R2 = std::numeric_limits::max(); for (const Atom &atom1 : seg1) { for (const Atom &atom2 : seg2) { double R2_test = PbShortestConnect(atom1.getPos(), atom2.getPos()).squaredNorm(); if (R2_test < R2) { R2 = R2_test; } } } return std::sqrt(R2); } std::vector Topology::FindAllSegmentsOnMolecule( const Segment &seg1, const Segment &seg2) const { const std::vector &ids1 = seg1.getMoleculeIds(); const std::vector &ids2 = seg2.getMoleculeIds(); std::vector common_elements; std::set_intersection(ids1.begin(), ids1.end(), ids2.begin(), ids2.end(), std::back_inserter(common_elements)); std::vector results; if (common_elements.empty() || common_elements.size() > 1) { return results; } Index molid = common_elements[0]; for (const Segment &seg : _segments) { if (std::find(seg.getMoleculeIds().begin(), seg.getMoleculeIds().end(), molid) != seg.getMoleculeIds().end()) { results.push_back(&seg); } } return results; } void Topology::WriteToPdb(std::string filename) const { csg::PDBWriter writer; writer.Open(filename, false); writer.WriteHeader("Frame:" + std::to_string(this->getStep())); writer.WriteBox(this->getBox() * tools::conv::bohr2ang); for (const Segment &seg : _segments) { writer.WriteContainer(seg); } writer.Close(); } void Topology::WriteToCpt(CheckpointWriter &w) const { w(XtpVersionStr(), "XTPVersion"); w(topology_version(), "version"); w(_time, "time"); w(_step, "step"); w(this->getBox(), "box"); CheckpointWriter ww = w.openChild("segments"); for (const Segment &seg : _segments) { CheckpointWriter u = ww.openChild("segment" + std::to_string(seg.getId())); seg.WriteToCpt(u); } CheckpointWriter www = w.openChild("neighborlist"); _nblist.WriteToCpt(www); } void Topology::ReadFromCpt(CheckpointReader &r) { r(_time, "time"); r(_step, "step"); Eigen::Matrix3d box; r(box, "box"); setBox(box); CheckpointReader v = r.openChild("segments"); _segments.clear(); Index count = v.getNumDataSets(); _segments.reserve(count); for (Index i = 0; i < count; i++) { CheckpointReader w = v.openChild("segment" + std::to_string(i)); _segments.push_back(Segment(w)); } CheckpointReader rr = r.openChild("neighborlist"); _nblist.ReadFromCpt(rr, _segments); } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/trustregion.cc000066400000000000000000000073311412152066400174050ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include #include // Local VOTCA includes #include "votca/xtp/trustregion.h" namespace votca { namespace xtp { Eigen::VectorXd TrustRegion::CalculateStep(const Eigen::VectorXd& gradient, const Eigen::MatrixXd& Hessian, double delta) const { // calculate unrestricted step Eigen::VectorXd freestep = Hessian.colPivHouseholderQr().solve(-gradient); // if inside use the step; if (freestep.norm() < delta) { return freestep; } // calculate step on the boundary Eigen::SelfAdjointEigenSolver es(Hessian); const Eigen::VectorXd factor = (es.eigenvectors().transpose() * gradient).cwiseAbs2(); double lambda = 0; // hard case if (std::abs(factor[0]) < 1e-18) { std::vector index; Eigen::VectorXd diag = Eigen::VectorXd::Zero(factor.size()); // construct pseudo inverse for (Index i = 0; i < factor.size(); i++) { double entry = es.eigenvalues()(i) - es.eigenvalues()(0); if (std::abs(entry) < 1e-14) { index.push_back(i); continue; } else { diag(i) = 1 / entry; } } Eigen::MatrixXd pseudo_inv = es.eigenvectors() * diag.asDiagonal() * es.eigenvectors().transpose(); Eigen::VectorXd step = -pseudo_inv * gradient; if (step.norm() < delta) { double tau = std::sqrt(delta * delta - step.squaredNorm()); step += tau * es.eigenvectors().col(index[0]); return step; } } // sort out all the factors for the small eigenvalues, Index start_index = 0; for (; start_index < factor.size(); start_index++) { if (factor[start_index] < 1e-18) { continue; } break; } if (start_index == factor.size()) { throw std::runtime_error( "trustregion.cc: all the factors are close to zero trust region method " "will not converge further."); } // start value for lambda a bit higher than lowest eigenvalue of Hessian lambda = -es.eigenvalues()(start_index) + std::sqrt(factor(start_index)) / delta; TrustRegionFunction TRF = TrustRegionFunction(factor, es, delta, start_index); for (Index iter = 0; iter < 100; iter++) { std::pair result = TRF.Evaluate(lambda); double func_value = result.first; double update = result.second; if (update < 1e-14 || std::abs(func_value) < 1e-12) { break; } lambda += update; } // this is effectively the solution of (H+I\lambda)*\Delta p=-g with \lambda // adjusted so that ||p||=delta Eigen::VectorXd new_delta_pos = Eigen::VectorXd::Zero(gradient.size()); for (Index i = start_index; i < gradient.size(); i++) { new_delta_pos -= es.eigenvectors().col(i) * (es.eigenvectors().col(i).transpose() * gradient) / (es.eigenvalues()(i) + lambda); } // this is for safety if (new_delta_pos.norm() > delta) { new_delta_pos *= (delta / new_delta_pos.norm()); } return new_delta_pos; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/version.cc000066400000000000000000000036201412152066400165020ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include // VOTCA includes #include #include // Local VOTCA includes #include "votca/xtp/version.h" #include "votca/xtp/votca_xtp_config.h" extern "C" { void VotcaMd2QmFromC() { // do nothing - this is just that we have a c function for autotools } } namespace votca { namespace xtp { // defines gitversion #include "gitversion.h" static const std::string version_str = std::string(VERSION) + " " + gitversion + " (compiled " __DATE__ ", " __TIME__ ")"; const std::string &XtpVersionStr() { return version_str; } void HelpTextHeader(const std::string &tool_name) { std::cout << "==================================================\n" << "======== VOTCA (http://www.votca.org) ========\n" << "==================================================\n\n" << "please submit bugs to " PACKAGE_BUGREPORT "\n\n" << tool_name << ", version " << XtpVersionStr() << "\nvotca_csg, version " << votca::csg::CsgVersionStr() << "\nvotca_tools, version " << votca::tools::ToolsVersionStr() << "\n\n"; } } // namespace xtp } // namespace votca xtp-2021.2/src/libxtp/xtpapplication.cc000066400000000000000000000032331412152066400200540ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Third party includes #include // VOTCA includes #include #include // Local VOTCA includes #include "votca/xtp/version.h" #include "votca/xtp/xtpapplication.h" namespace votca { namespace xtp { XtpApplication::XtpApplication() { ; } /** * \brief Adds program options to the executable * * Every executable requires option file for calculators it is running * It is thus a part of the base XtpApplication class * */ void XtpApplication::Initialize(void) { AddProgramOptions()("options,o", boost::program_options::value(), " calculator options"); } void XtpApplication::ShowHelpText(std::ostream &out) { std::string name = ProgramName(); if (VersionString() != "") { name = name + ", version " + VersionString(); } xtp::HelpTextHeader(name); HelpText(out); out << "\n\n" << VisibleOptions() << std::endl; } } // namespace xtp } // namespace votca xtp-2021.2/src/tests/000077500000000000000000000000001412152066400143455ustar00rootroot00000000000000xtp-2021.2/src/tests/CMakeLists.txt000066400000000000000000000102311412152066400171020ustar00rootroot00000000000000if(ENABLE_TESTING) # Please place additional tests in alphabetical order find_package(Boost 1.57.0 REQUIRED COMPONENTS unit_test_framework) list(APPEND test_cases test_adiis) list(APPEND test_cases test_aobasis) list(APPEND test_cases test_aomatrix) list(APPEND test_cases test_aomatrix3d) list(APPEND test_cases test_aotransform) list(APPEND test_cases test_aopotential) list(APPEND test_cases test_atom) list(APPEND test_cases test_qmatom) list(APPEND test_cases test_polarsegment) list(APPEND test_cases test_qmmolecule) list(APPEND test_cases test_basisset) list(APPEND test_cases test_bfgs_trm) list(APPEND test_cases test_bse) list(APPEND test_cases test_convergenceacc) list(APPEND test_cases test_dftcoupling) list(APPEND test_cases test_diis) list(APPEND test_cases test_ecpaobasis) list(APPEND test_cases test_eigen) list(APPEND test_cases test_eris) list(APPEND test_cases test_espfit) list(APPEND test_cases test_glink) list(APPEND test_cases test_hdf5) list(APPEND test_cases test_cubefile_writer) list(APPEND test_cases test_densityintegration) list(APPEND test_cases test_vxc_potential) list(APPEND test_cases test_vxc_grid) list(APPEND test_cases test_regular_grid) list(APPEND test_cases test_orbitals) list(APPEND test_cases test_polarsite) list(APPEND test_cases test_staticsite) list(APPEND test_cases test_ppm) list(APPEND test_cases test_qmnblist) list(APPEND test_cases test_qmpair) list(APPEND test_cases test_qmstate) list(APPEND test_cases test_radial_euler_maclaurin_rule) list(APPEND test_cases test_rpa) list(APPEND test_cases test_rpa_h2p) list(APPEND test_cases test_segment) list(APPEND test_cases test_aoshell) list(APPEND test_cases test_sphere_lebedev_rule) list(APPEND test_cases test_statetracker) list(APPEND test_cases test_symmetric_matrix) list(APPEND test_cases test_threecenter_dft) list(APPEND test_cases test_threecenter_gwbse) list(APPEND test_cases test_topology) list(APPEND test_cases test_sigma_exact) list(APPEND test_cases test_sigma_ppm) list(APPEND test_cases test_sigma_cda) list(APPEND test_cases test_gw) list(APPEND test_cases test_bse_operator) list(APPEND test_cases test_davidson) list(APPEND test_cases test_trustregion) list(APPEND test_cases test_gnode) list(APPEND test_cases test_vc2index) list(APPEND test_cases test_grid) list(APPEND test_cases test_segmentmapper) list(APPEND test_cases test_eeinteractor) list(APPEND test_cases test_hist) list(APPEND test_cases test_qmfragment) list(APPEND test_cases test_jobtopology) list(APPEND test_cases test_dipoledipoleinteraction) list(APPEND test_cases test_populationanalysis) list(APPEND test_cases test_orca) list(APPEND test_cases test_dftengine) list(APPEND test_cases test_bsecoupling) list(APPEND test_cases test_rate_engine) list(APPEND test_cases test_DeltaQ_filter) list(APPEND test_cases test_oscillatorstrength_filter) list(APPEND test_cases test_localisation_filter) list(APPEND test_cases test_density_filter) list(APPEND test_cases test_overlap_filter) list(APPEND test_cases test_newton_rapson) list(APPEND test_cases test_indexparser) list(APPEND test_cases test_settings) list(APPEND test_cases test_orbreorder) list(APPEND test_cases test_molden) if(USE_CUDA) list(APPEND test_cases test_cudapipeline) list(APPEND test_cases test_cudamatrix) endif() list(APPEND test_cases test_anderson) list(APPEND test_cases test_gaussian_quadratures) foreach(PROG ${test_cases} ) add_executable(unit_${PROG} ${PROG}.cc) target_compile_definitions(unit_${PROG} PRIVATE XTP_TEST_DATA_FOLDER="${CMAKE_CURRENT_SOURCE_DIR}/DataFiles") target_link_libraries(unit_${PROG} votca_xtp Boost::unit_test_framework PkgConfig::LIBINT) target_compile_definitions(unit_${PROG} PRIVATE BOOST_TEST_DYN_LINK) file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/Run_unit_${PROG}) add_test(NAME unit_${PROG} COMMAND $ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/Run_unit_${PROG}) # run tests for xtp (for coverage) as well set_tests_properties(unit_${PROG} PROPERTIES LABELS "xtp;votca;unit") endforeach(PROG) endif() xtp-2021.2/src/tests/DataFiles/000077500000000000000000000000001412152066400162015ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/adiis/000077500000000000000000000000001412152066400172725ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/adiis/dmatHist_0.mm000066400000000000000000000073331412152066400216270ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 0.00157507 0.0337454 4.48905e-16 -5.93152e-16 7.87133e-17 0.030876 2.51254e-16 -1.49094e-16 5.77899e-17 0.00415998 -0.00445632 0.00415998 -0.00445632 0.00415998 -0.00445632 0.00415998 -0.00445632 0.0337454 0.722983 2.66427e-15 -4.44783e-15 3.45846e-16 0.661507 4.39854e-15 -2.02475e-15 1.04832e-15 0.0891262 -0.095475 0.0891262 -0.095475 0.0891262 -0.095475 0.0891262 -0.095475 4.48905e-16 2.66427e-15 1.52199 2.88658e-15 2.09034e-15 -7.94212e-15 0.215492 2.8727e-15 -1.40513e-15 0.141933 -0.0402359 0.141933 -0.0402359 -0.141933 0.0402359 -0.141933 0.0402359 -5.93152e-16 -4.44783e-15 2.88658e-15 1.52199 -2.31759e-15 9.21105e-15 -2.22045e-15 0.215492 1.6263e-15 0.141933 -0.0402359 -0.141933 0.0402359 -0.141933 0.0402359 0.141933 -0.0402359 7.87133e-17 3.45846e-16 2.09034e-15 -2.31759e-15 1.52199 2.98902e-15 -2.04958e-15 4.79738e-15 0.215492 0.141933 -0.0402359 -0.141933 0.0402359 0.141933 -0.0402359 -0.141933 0.0402359 0.030876 0.661507 -7.94212e-15 9.21105e-15 2.98902e-15 0.605259 2.55488e-15 2.7779e-17 1.33759e-15 0.0815477 -0.0873567 0.0815477 -0.0873567 0.0815477 -0.0873567 0.0815477 -0.0873567 2.51254e-16 4.39854e-15 0.215492 -2.22045e-15 -2.04958e-15 2.55488e-15 0.0305108 3.29597e-17 -5.29036e-16 0.0200958 -0.00569686 0.0200958 -0.00569686 -0.0200958 0.00569686 -0.0200958 0.00569686 -1.49094e-16 -2.02475e-15 2.8727e-15 0.215492 4.79738e-15 2.7779e-17 3.29597e-17 0.0305108 9.55941e-16 0.0200958 -0.00569686 -0.0200958 0.00569686 -0.0200958 0.00569686 0.0200958 -0.00569686 5.77899e-17 1.04832e-15 -1.40513e-15 1.6263e-15 0.215492 1.33759e-15 -5.29036e-16 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0.901732 3.23124e-07 0.00932737 2.69633e-05 8.74181e-05 -4.83481e-07 0 0 -1.28339e-07 1.22667e-07 4.86348e-08 -0.0166337 2.86823e-07 -1.7727e-07 1.6913e-07 2.57089e-07 -1.19304e-08 3.23124e-07 1.2237 -7.31155e-07 -6.14518e-07 2.79634e-08 -0.042011 0 0 0.0141886 -0.000128128 0.000252415 5.78666e-08 -0.0372319 0.000108686 0.000112864 -1.03264e-05 -9.06429e-05 0.00932737 -7.31155e-07 1.21009 -2.99286e-07 -4.29557e-08 6.13566e-07 0 0 -0.000147938 -0.0141459 0.00111443 8.52843e-08 6.58278e-05 0.0351664 -0.0122286 0.00917151 0.00170305 2.69633e-05 -6.14518e-07 -2.99286e-07 1.21009 2.02234e-07 7.00978e-07 0 0 -0.000241557 0.00111572 0.0141441 -1.74815e-08 0.000142268 0.0122284 0.0351659 -0.00170387 0.00917133 8.74181e-05 2.79634e-08 -4.29557e-08 2.02234e-07 1.21009 3.77938e-08 0 0 5.71202e-07 -4.57761e-07 1.01087e-07 -0.00112475 -2.94575e-07 1.86591e-07 -2.32341e-08 -3.30584e-07 -1.11726e-07 -4.83481e-07 -0.042011 6.13566e-07 7.00978e-07 3.77938e-08 1.93666 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19.4256xtp-2021.2/src/tests/DataFiles/bse/MO_energies.mm000066400000000000000000000023511412152066400215020ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 1 -6.1260099999999995112887063442030921578407287597656250000000000000e-01 -3.4175499999999997546851204788254108279943466186523437500000000000e-01 -3.4175499999999997546851204788254108279943466186523437500000000000e-01 -3.4175499999999997546851204788254108279943466186523437500000000000e-01 1.3730400000000000937383504151512170210480690002441406250000000000e-01 1.6678000000000001157296480869263177737593650817871093750000000000e-01 1.6678000000000001157296480869263177737593650817871093750000000000e-01 1.6678000000000001157296480869263177737593650817871093750000000000e-01 6.7159199999999996677502167585771530866622924804687500000000000000e-01 6.7159199999999996677502167585771530866622924804687500000000000000e-01 6.7159199999999996677502167585771530866622924804687500000000000000e-01 9.7425499999999998212985019563348032534122467041015625000000000000e-01 1.0120499999999998941291323717450723052024841308593750000000000000e+00 1.0120499999999998941291323717450723052024841308593750000000000000e+00 1.0120499999999998941291323717450723052024841308593750000000000000e+00 1.6482300000000000839150970932678319513797760009765625000000000000e+00 1.9442900000000001625721779419109225273132324218750000000000000000e+01 xtp-2021.2/src/tests/DataFiles/bse/MOs.mm000066400000000000000000000073331412152066400200110ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 -0.00761992 0.233602 -4.51653e-14 -1.63678e-13 -9.0903e-14 0.480866 -1.64105e-12 -1.64421e-12 -1.63849e-12 0.129798 0.0541331 0.129798 0.0541331 0.129798 0.0541331 0.129798 0.0541331 -4.69664e-13 -3.18103e-12 -0.216509 -0.22745 -0.21966 1.8992e-11 -0.173397 -0.182159 -0.17592 -0.274485 -0.255228 0.0863299 0.0802732 0.0927742 0.0862654 0.0953806 0.088689 8.35009e-15 4.05093e-14 0.296975 -0.054851 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-0.000361559 0.000575205 0.235387 -0.374479 0.643254 -1.02335 -0.87828 1.39726 -2.63092e-15 -9.78783e-14 0.166374 -0.619056 0.453695 -2.57294e-14 -0.212309 0.789976 -0.578959 -0.000717866 0.00114206 0.878697 -1.39792 -0.642737 1.02253 -0.235242 0.374248 -0.22227 -1.94373 7.13235e-12 7.0149e-12 7.01644e-12 4.04176 -1.42443e-11 -1.41532e-11 -1.40917e-11 -0.195084 -0.793844 -0.195084 -0.793844 -0.195084 -0.793844 -0.195084 -0.793844 1.00844 -0.36629 2.56811e-14 2.395e-14 2.60987e-14 0.193617 -1.31306e-13 -1.29659e-13 -1.31002e-13 0.0246232 -0.035336 0.0246232 -0.035336 0.0246232 -0.035336 0.0246232 -0.035336xtp-2021.2/src/tests/DataFiles/bse/mo_energy.mm000066400000000000000000000003271412152066400212730ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 1 -0.612601 -0.341755 -0.341755 -0.341755 0.137304 0.16678 0.16678 0.16678 0.671592 0.671592 0.671592 0.974255 1.01205 1.01205 1.01205 1.64823 19.4429xtp-2021.2/src/tests/DataFiles/bse/molecule.xyz000066400000000000000000000003621412152066400213340ustar00rootroot00000000000000 5 methane C .000000 .000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/bse/singlets_btda.mm000066400000000000000000000004021412152066400221230ustar00rootroot00000000000000%%MatrixMarket matrix array real general 3 1 8.8775800000000001932498605583532480522990226745605468750000000000e-02 8.8775800000000001932498605583532480522990226745605468750000000000e-02 8.8775800000000001932498605583532480522990226745605468750000000000e-02 xtp-2021.2/src/tests/DataFiles/bse/singlets_dynamic_TDA.mm000066400000000000000000000004021412152066400233250ustar00rootroot00000000000000%%MatrixMarket matrix array real general 3 1 1.0733853261680678659040211186947999522089958190917968750000000000e-01 1.0733889212932293255597926417976850643754005432128906250000000000e-01 1.0733931630780677024539215835829963907599449157714843750000000000e-01 xtp-2021.2/src/tests/DataFiles/bse/singlets_dynamic_full.mm000066400000000000000000000004021412152066400236570ustar00rootroot00000000000000%%MatrixMarket matrix array real general 3 1 8.7162189181767768531017281929962337017059326171875000000000000000e-02 8.7162771430714269804695959464879706501960754394531250000000000000e-02 8.7163214712247749638152072293451055884361267089843750000000000000e-02 xtp-2021.2/src/tests/DataFiles/bse/singlets_nooffdiag_tda.mm000066400000000000000000000004021412152066400237750ustar00rootroot00000000000000%%MatrixMarket matrix array real general 3 1 1.0686199999999999865618605099371052347123622894287109375000000000e-01 1.0686199999999999865618605099371052347123622894287109375000000000e-01 1.0686299999999999965627495157605153508484363555908203125000000000e-01 xtp-2021.2/src/tests/DataFiles/bse/singlets_psi_AR_btda.mm000066400000000000000000000045211412152066400233660ustar00rootroot00000000000000%%MatrixMarket matrix array real general 60 3 0.000584144 -0.00154856 -0.0152954 0.0017559 -0.00395598 -0.000215381 -5.02586e-09 0.000156138 -0.000875892 0.00367662 -5.20546e-09 -1.30377e-10 0.00225763 0.00172531 0.0214509 0.00443924 -0.00949663 0.000977068 0.000411481 -0.000752112 -0.00186068 0.00716363 4.85758e-05 -4.64045e-06 -0.00687191 0.00824556 -0.0296148 -0.0106166 0.0105747 -0.00322083 0.00465513 0.00234006 0.00601773 -0.00869493 0.000549541 -5.24965e-05 -0.0207863 0.0302893 0.010411 -0.0102705 -0.0115606 -0.0102966 0.0144314 0.00718776 0.00864786 0.00677374 0.00170364 -0.000162745 0.00995914 -0.0264016 -0.260775 0.0109283 -0.0246207 -0.00134058 1.49164e-08 6.14995e-07 -3.26276e-06 1.40497e-05 1.99993e-09 -2.19573e-10 -0.0146225 0.00466997 -0.00103125 0.00127769 0.000342451 0.00412671 4.52834e-08 -0.00359781 -0.00116148 -0.000123883 2.56561e-08 -3.42705e-10 -0.0420501 -0.00629088 0.00210875 0.00321126 0.000907487 -0.020443 -0.0143682 0.0144531 -0.00230664 -8.0822e-05 -0.00169622 0.000162032 -0.0063025 0.0105368 -0.0123913 -0.00743383 0.00273958 -0.00304507 0.00473433 0.00216454 0.00481718 -0.00284236 0.000558892 -5.33896e-05 0.000339395 -0.00457762 -0.0279414 -0.00480099 0.0129097 0.000333027 -0.00111747 -0.000150389 0.00166895 -0.00959 -0.000131921 1.2602e-05 -0.249299 0.07962 -0.0175818 0.00795199 0.00213124 0.0256833 -4.69903e-09 -1.40366e-05 -4.40871e-06 -4.71623e-07 -3.51811e-08 6.10086e-10 0.00474677 0.0145766 -0.00129451 0.00375014 0.00173561 -0.00130515 1.34149e-08 0.00115758 -0.00349181 -0.000880951 6.1721e-09 -1.4581e-10 0.0130936 -0.0214897 0.00214631 0.00958646 0.00418444 0.00645007 0.00484706 -0.00452103 -0.0072129 -0.00171243 0.000572232 -5.46606e-05 -0.0201599 -0.034423 -0.00551674 0.0132406 0.0107636 -0.00963294 0.013639 0.00689084 -0.0105676 -0.00570504 0.0016101 -0.000153809 0.0069292 0.0105648 -0.0223393 -0.00985759 0.00684819 0.00344514 -0.00453772 -0.00239498 0.00595764 -0.00605226 -0.000535686 5.11726e-05 0.0809272 0.248518 -0.0220701 0.0233398 0.0108019 -0.00812285 5.23125e-09 4.50767e-06 -1.35086e-05 -3.42445e-06 -4.56933e-09 -2.35986e-11xtp-2021.2/src/tests/DataFiles/bse/singlets_psi_btda.mm000066400000000000000000000045211412152066400230040ustar00rootroot00000000000000%%MatrixMarket matrix array real general 60 3 0.00228773 -0.00606479 -0.0599032 -0.00239507 0.005396 0.000293773 -1.18994e-08 -0.00038655 0.00216846 -0.00910256 -6.67006e-09 5.73874e-11 -0.00300256 -0.00229461 -0.028529 -0.00278921 0.00596683 -0.00061392 -0.000330257 0.000903715 0.00223576 -0.00860769 5.28565e-05 6.78691e-07 0.00913939 -0.0109663 0.0393868 0.0066705 -0.0066442 0.00202369 -0.00373624 -0.00281175 -0.00723077 0.0104477 0.000597973 7.67794e-06 0.0276451 -0.0402838 -0.0138464 0.00645305 0.00726364 0.00646942 -0.0115828 -0.00863663 -0.010391 -0.00813919 0.00185377 2.38027e-05 0.0391594 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0.00320821 0.000355172 1.91684e-08 2.79592e-10 0.092451 0.0113951 -0.00398807 -0.0031325 -0.000896935 0.0239709 0.0201651 -0.0269275 0.00356488 9.58532e-05 -0.00124098 -8.71959e-05 0.0114186 -0.026287 0.0257628 0.0092297 -0.00246837 0.00294872 -0.0055755 -0.00332619 -0.00969272 0.00458659 0.000343129 2.41086e-05 -0.00034974 0.0115163 0.0583236 0.00490159 -0.0146227 -0.000282044 0.00139057 0.000163177 -0.00241207 0.0171503 -8.55716e-05 -6.0128e-06 -0.954049 0.255313 -0.0547431 -0.0104387 -0.00278036 -0.04041 2.40738e-07 -0.00516415 -0.00139237 -0.000154171 -6.04796e-08 2.31605e-09 0.0151767 0.0556358 -0.00502105 -0.00817518 -0.00376334 0.0023708 -1.08537e-08 -0.00320024 0.0115465 0.00289343 3.01647e-09 -1.35767e-09 -0.0239374 0.0471896 -0.00484251 -0.0112447 -0.00488789 -0.00630323 -0.00573095 0.00700955 0.0134361 0.00315613 0.000352706 2.47799e-05 0.0443012 0.0734351 0.0132084 -0.0148779 -0.0125735 0.0112899 -0.0191436 -0.0128321 0.0189659 0.0107104 0.00117813 8.2778e-05 -0.015063 -0.022358 0.0513097 0.0116429 -0.00863565 -0.00400272 0.00635067 0.00441453 -0.0110696 0.0119626 -0.00039083 -2.746e-05 0.259333 0.950672 -0.0857965 -0.036743 -0.0169143 0.0106552 1.03401e-07 0.00138942 -0.00501195 -0.00125602 -4.6768e-08 1.35922e-09xtp-2021.2/src/tests/DataFiles/cubefile_writer/000077500000000000000000000000001412152066400213535ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/cubefile_writer/3-21G.xml000066400000000000000000000027301412152066400225700ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/cubefile_writer/A_MOs.mm000066400000000000000000000073331412152066400226520ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 -0.996559 -0.0445146 4.60157e-17 8.15798e-17 -5.25872e-18 0.0472716 -2.24862e-16 -2.74184e-16 -2.81346e-17 -0.00106227 -0.00928842 -0.00106227 -0.00928842 -0.00106227 -0.00928842 -0.00106227 -0.00928842 -0.223082 0.88316 -7.1203e-15 2.30849e-14 4.8424e-15 0.235837 3.23655e-15 -1.53939e-15 -1.09423e-15 0.0237672 -0.0414346 0.0237672 -0.0414346 0.0237672 -0.0414346 0.0237672 -0.0414346 4.81443e-15 -1.94941e-14 0.143338 1.04169 0.0488925 -3.58018e-15 -0.0223487 -0.162416 -0.00762313 0.00345981 0.0619999 0.00238182 0.0426822 -0.00318563 -0.0570866 -0.002656 -0.0475955 2.21045e-15 -8.67388e-15 -0.980459 0.117804 0.364515 -1.68354e-15 0.152869 -0.0183675 -0.0568338 -0.00139675 -0.0250297 0.00205737 0.0368682 0.0034409 0.0616609 -0.00410152 -0.0734994 -6.16146e-17 -7.26679e-16 -0.355251 0.0951759 -0.9863 2.3989e-15 0.0553894 -0.0148395 0.15378 -0.00349474 -0.0626259 0.00402848 0.0721904 -0.00203628 -0.0364902 0.00150255 0.0269257 -3.16966e-16 1.16326e-14 0.41611 0.179467 0.0447336 -9.86879e-15 -0.350483 -0.151162 -0.0376785 -0.597906 0.00227746 0.262742 -0.0010008 0.514364 -0.00195924 -0.1792 0.000682583 5.46703e-18 -3.35886e-15 -0.10826 0.147031 0.417155 4.52519e-15 0.0911859 -0.123842 -0.351364 -0.425733 0.00162164 0.151145 -0.000575719 -0.353326 0.00134584 0.627913 -0.00239176 -1.09681e-15 2.37877e-14 -0.149964 0.39183 -0.177023 -1.6106e-14 0.126313 -0.330032 0.149104 -0.0605479 0.00023063 -0.671213 0.00255669 0.391148 -0.0014899 0.340613 -0.00129742 -0.0301914 0.866126 2.41546e-16 -1.02927e-14 5.76117e-15 -0.599523 -5.48468e-15 1.10084e-15 -4.94425e-15 -0.343823 -0.0301047 -0.343823 -0.0301047 -0.343823 -0.0301047 -0.343823 -0.0301047 6.45993e-16 3.2068e-15 0.12214 0.32699 -0.228081 -1.31237e-14 -0.541961 -1.45092 1.01204 0.162103 0.273177 0.317484 0.535026 -0.496623 -0.836913 0.0170366 0.0287103 1.05377e-16 3.80914e-15 -0.0512447 -0.223689 -0.348136 -8.63443e-15 0.227383 0.992556 1.54475 -0.45692 -0.770004 0.12884 0.217123 -0.0536813 -0.0904642 0.38176 0.643346 3.41154e-16 3.24563e-15 0.39537 -0.130009 0.0253377 -8.61196e-15 -1.75434 0.576875 -0.112429 0.21318 0.359253 -0.40386 -0.680588 -0.176018 -0.296627 0.366698 0.617962 -0.102052 -0.938329 1.1054e-15 1.0375e-15 -1.05286e-15 1.8333 -3.89443e-15 -3.82954e-15 8.50653e-15 -0.600309 0.0095153 -0.600309 0.0095153 -0.600309 0.0095153 -0.600309 0.0095153 -5.79826e-16 -6.4404e-15 -0.0996828 -0.0940179 0.079576 2.05275e-14 0.640788 0.604373 -0.511536 0.310843 -0.8783 0.201313 -0.568818 -0.744328 2.10313 0.232172 -0.656011 9.38593e-16 1.10811e-14 -0.0636092 0.126956 0.0703157 -3.9562e-14 0.408897 -0.816111 -0.452008 -0.36406 1.02867 -0.327527 0.925441 -0.01898 0.0536287 0.710567 -2.00774 -4.69346e-15 -5.5056e-14 -0.105478 0.0122904 -0.117608 1.89874e-13 0.67804 -0.0790061 0.756019 0.574148 -1.62228 -0.641099 1.81145 0.0665156 -0.187943 0.000435528 -0.0012306 -0.111923 -1.28767 5.10746e-15 1.41709e-15 5.31327e-15 4.24316 -3.17156e-14 -8.89474e-15 -3.3547e-14 0.0554949 -1.24406 0.0554949 -1.24406 0.0554949 -1.24406 0.0554949 -1.24406xtp-2021.2/src/tests/DataFiles/cubefile_writer/molecule.xyz000066400000000000000000000003621412152066400237350ustar00rootroot00000000000000 5 methane C .000000 .000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/cubefile_writer/spsi_ref.mm000066400000000000000000000045211412152066400235220ustar00rootroot00000000000000%%MatrixMarket matrix array real general 60 3 -0.00178316 0.00568291 0.05758 0.00379328 -0.00848959 -0.000395809 7.13955e-08 0.000420413 -0.00288487 0.0119767 -2.55565e-08 6.84051e-09 0.00420618 0.0036276 0.0465325 0.0051614 -0.010968 0.000951266 0.000419006 -0.00118124 -0.00345217 0.013156 -2.58268e-05 -1.80679e-06 -0.0150073 0.0180327 -0.0643994 -0.0123339 0.0122493 -0.00375172 0.00648758 0.00433063 0.0111166 -0.0160119 -0.000399315 -2.80525e-05 -0.0450479 0.0655838 0.0220978 -0.0119156 -0.0132479 -0.0118978 0.0199347 0.0131991 0.0159091 0.0123057 -0.00122682 -8.62007e-05 -0.0304688 0.0971056 0.983887 0.0170489 -0.0381557 -0.00177889 -2.23782e-07 -0.000182535 0.00125201 -0.00519809 4.03664e-08 -2.38233e-09 -0.0558332 0.0149417 -0.00320371 -0.00232255 -0.000618633 -0.00899117 3.47498e-08 0.011896 0.00320821 0.000355172 1.91684e-08 2.79592e-10 0.092451 0.0113951 -0.00398807 -0.0031325 -0.000896935 0.0239709 0.0201651 -0.0269275 0.00356488 9.58532e-05 -0.00124098 -8.71959e-05 0.0114186 -0.026287 0.0257628 0.0092297 -0.00246837 0.00294872 -0.0055755 -0.00332619 -0.00969272 0.00458659 0.000343129 2.41086e-05 -0.00034974 0.0115163 0.0583236 0.00490159 -0.0146227 -0.000282044 0.00139057 0.000163177 -0.00241207 0.0171503 -8.55716e-05 -6.0128e-06 -0.954049 0.255313 -0.0547431 -0.0104387 -0.00278036 -0.04041 2.40738e-07 -0.00516415 -0.00139237 -0.000154171 -6.04796e-08 2.31605e-09 0.0151767 0.0556358 -0.00502105 -0.00817518 -0.00376334 0.0023708 -1.08537e-08 -0.00320024 0.0115465 0.00289343 3.01647e-09 -1.35767e-09 -0.0239374 0.0471896 -0.00484251 -0.0112447 -0.00488789 -0.00630323 -0.00573095 0.00700955 0.0134361 0.00315613 0.000352706 2.47799e-05 0.0443012 0.0734351 0.0132084 -0.0148779 -0.0125735 0.0112899 -0.0191436 -0.0128321 0.0189659 0.0107104 0.00117813 8.2778e-05 -0.015063 -0.022358 0.0513097 0.0116429 -0.00863565 -0.00400272 0.00635067 0.00441453 -0.0110696 0.0119626 -0.00039083 -2.746e-05 0.259333 0.950672 -0.0857965 -0.036743 -0.0169143 0.0106552 1.03401e-07 0.00138942 -0.00501195 -0.00125602 -4.6768e-08 1.35922e-09xtp-2021.2/src/tests/DataFiles/cubefile_writer/values_ref1.mm000066400000000000000000000030121412152066400241160ustar00rootroot00000000000000%%MatrixMarket matrix array real general 125 1 5 -1.68886 -1.68886 -1.68886 3 1.68886 0 0 4 0 1.12591 0 7 0 0 0.562954 6 6 0 0 0 1 1 1.18886 1.18886 1.18886 1 1 -1.18886 -1.18886 1.18886 1 1 1.18886 -1.18886 -1.18886 1 1 -1.18886 1.18886 -1.18886 0.000208698 0.000288781 0.00155897 0.0107459 0.0458207 0.0905214 0.0579265 0.00104742 0.00502802 0.0172192 0.0299157 0.046706 0.0702059 0.0483124 0.0174583 0.0292691 0.0331694 0.0338648 0.0204603 0.00651711 0.00250686 0.0205958 0.0317677 0.0160464 0.00393287 0.000663892 0.000292192 0.000391332 0.00368792 0.0133564 0.0405961 0.0600589 0.0442031 0.024689 0.0143883 0.0432987 0.308356 0.89484 1.29773 0.898685 0.305006 0.0464954 0.0437266 0.308709 0.911088 1.28952 0.90392 0.31123 0.0421356 0.00755683 0.0169615 0.0421185 0.0609526 0.0402112 0.0110182 0.0015099 0.0155067 0.0232375 0.0108316 0.00228598 0.000519529 0.000562444 0.000681654 0.0159506 0.025984 0.0313753 0.0346768 0.0213949 0.00565648 0.00109917 0.0023761 0.00602415 0.017935 0.0275236 0.0209044 0.00831398 0.0025552 0.00103956 0.00108931 0.000977 0.000989574 0.00125311 0.00190253 0.00131956xtp-2021.2/src/tests/DataFiles/cubefile_writer/values_ref2.mm000066400000000000000000000032071412152066400241250ustar00rootroot00000000000000%%MatrixMarket matrix array real general 125 1 5 -1.68886 -1.68886 -1.68886 3 1.68886 0 0 4 0 1.12591 0 7 0 0 0.562954 6 6 0 0 0 1 1 1.18886 1.18886 1.18886 1 1 -1.18886 -1.18886 1.18886 1 1 1.18886 -1.18886 -1.18886 1 1 -1.18886 1.18886 -1.18886 -2.40791e-05 7.17212e-05 0.00105567 0.00966299 0.0447329 0.0898846 0.0577338 0.000544123 -0.0011694 -0.00883911 -0.0120741 0.0177545 0.0616644 0.0472246 0.0163705 0.0207276 0.00421794 -0.00812502 -0.00559797 0.000319689 0.00200357 0.0204031 0.031131 0.0149586 0.00284996 0.000160596 7.51329e-05 0.000158555 0.002605 0.00212442 -0.00139378 -0.00372684 0.00221326 0.0134571 0.0133054 0.00130865 -0.00298378 -0.0217167 -0.0602451 -0.017871 -0.00633401 0.00450544 0.00173663 -0.0026309 -0.00546899 -0.0684514 -0.0126373 -0.000110191 0.000145629 0.00647392 0.0057295 0.000128654 -0.00283313 -0.00177865 -0.000213789 0.000426989 0.015314 0.0226007 0.00974378 0.00120307 1.62324e-05 0.000345385 0.000448877 0.0148628 0.0174425 0.00242385 -0.00731305 -0.00466343 -0.000540948 0.000595874 0.00187281 -0.000173271 -0.00812327 -0.0144663 -0.00804706 -0.000227473 0.0014674 0.000806782 0.000872251 0.000473704 -9.33376e-05 0.000165312 0.00126574 0.00112684xtp-2021.2/src/tests/DataFiles/cubefile_writer/values_ref3.mm000066400000000000000000000032621412152066400241270ustar00rootroot00000000000000%%MatrixMarket matrix array real general 139 1 -5 -1.93886 -1.93886 -1.93886 3 1.93886 0 0 4 0 1.29257 0 8 0 0 0.55396 6 6 0 0 0 1 1 1.18886 1.18886 1.18886 1 1 -1.18886 -1.18886 1.18886 1 1 1.18886 -1.18886 -1.18886 1 1 -1.18886 1.18886 -1.18886 1 6 0.0211272 0.0276384 0.0329527 0.040678 0.0567349 0.0742615 0.0716875 0.0456208 0.0194729 0.0203131 0.0189178 0.024301 0.0462624 0.0734483 0.0749211 0.045644 -0.0258205 -0.0456162 -0.0457503 -0.0284218 -0.0135274 -0.00968591 -0.0116723 -0.0129576 -0.0311151 -0.0496517 -0.052527 -0.0418013 -0.0318879 -0.0271774 -0.0234073 -0.0181752 0.0734589 0.0968853 0.0864286 0.0566835 0.0447666 0.051729 0.0503978 0.0331809 0.0634554 0.0413361 -0.0550693 -0.197287 -0.136418 -0.00487785 0.0277649 0.0158461 -0.00926305 -0.0176521 0.0139501 0.139918 0.193788 0.045997 -0.0514489 -0.0700384 -0.0274655 -0.0416112 -0.0438437 -0.0417247 -0.0597254 -0.0943139 -0.105672 -0.0791744 0.0893108 0.133289 0.127912 0.0821768 0.041087 0.0207693 0.011719 0.00633209 0.10535 0.155338 0.140745 0.0770029 0.0220445 -0.00547692 -0.014529 -0.0131814 0.00666604 0.00588824 -0.00375494 -0.0328181 -0.0948435 -0.168443 -0.184643 -0.125174 -0.00928408 -0.0159501 -0.0265447 -0.0498771 -0.0971104 -0.149646 -0.155324 -0.103817xtp-2021.2/src/tests/DataFiles/densityintegration/000077500000000000000000000000001412152066400221245ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/densityintegration/3-21G.xml000066400000000000000000000027301412152066400233410ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/densityintegration/dmat.mm000066400000000000000000000073331412152066400234120ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 0.00157507 0.0337454 -5.93152e-16 4.48905e-16 7.87133e-17 0.030876 -1.49094e-16 2.51254e-16 5.77899e-17 0.00415998 -0.00445632 0.00415998 -0.00445632 0.00415998 -0.00445632 0.00415998 -0.00445632 0.0337454 0.722983 -4.44783e-15 2.66427e-15 3.45846e-16 0.661507 -2.02475e-15 4.39854e-15 1.04832e-15 0.0891262 -0.095475 0.0891262 -0.095475 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.000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/dftengine/000077500000000000000000000000001412152066400201445ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/dftengine/3-21G.xml000066400000000000000000000030601412152066400213560ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/dftengine/MOs_coeff_ref.mm000066400000000000000000000043031412152066400231730ustar00rootroot00000000000000%%MatrixMarket matrix array real general 13 13 0.982343 0.101935 -2.79025e-13 -0.00360159 1.29673e-14 -0.0420683 2.3837e-12 0.00731426 -1.66267e-12 0.00274585 0.00750313 0.00274585 0.00750313 0.225297 -0.213424 3.45211e-12 0.116669 -1.00926e-12 -0.681791 3.59972e-12 0.115649 -4.34816e-12 -0.126026 -0.0234965 -0.126026 -0.0234965 3.39697e-12 1.90464e-12 -0.409602 -5.86782e-13 7.23423e-12 -1.96952e-11 -0.348495 3.63395e-12 4.68601e-12 -0.238054 -0.19353 0.238054 0.19353 0.104226 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0.0515886 -0.131099 -8.49144e-11 -0.988233 -5.12996e-11 -0.210812 1.11025e-10 1.18317 5.04727e-11 0.314424 0.0817261 0.314424 0.0817261 -6.55285e-12 1.55304e-11 -1.0425 7.8109e-11 1.43023e-11 2.43573e-11 1.44212 -9.64031e-11 -1.68919e-11 -0.169014 -0.524685 0.169014 0.524685 -0.0865545 1.64108 4.00797e-12 -0.147551 7.55262e-12 -2.00561 -3.91477e-12 0.501366 -7.27192e-12 0.291888 0.3665 0.291888 0.3665xtp-2021.2/src/tests/DataFiles/dftengine/MOs_coeff_ref2.mm000066400000000000000000000043031412152066400232550ustar00rootroot00000000000000%%MatrixMarket matrix array real general 13 13 0.982347 0.101932 0.000164598 -0.00381954 0.000466344 -0.0420924 -8.34239e-05 0.00740548 -0.000170684 0.00276614 0.00753585 0.00275706 0.00747457 -0.223306 0.207993 0.0116932 -0.123607 0.0212544 0.680535 0.0176715 -0.136959 0.0465323 0.125487 0.0323646 0.113321 0.016969 0.011141 -0.0126581 0.41142 0.0114843 0.0156916 -0.0444622 0.346204 0.0167012 0.0317499 0.239726 0.202131 -0.245446 -0.168657 0.109466 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0.0604202 0.306816 0.139562 0.000786996 0.0169856 1.03301 -0.0532888 -0.0696086 -0.0390543 -1.44522 0.0723819 0.0724111 0.195476 0.536989 -0.154032 -0.513734 -0.0873035 1.64211 -0.014661 -0.132683 -0.0305003 -2.00325 0.0255437 0.478636 0.0388676 0.278534 0.36072 0.287174 0.378741xtp-2021.2/src/tests/DataFiles/dftengine/molecule.xyz000066400000000000000000000002441412152066400225250ustar00rootroot000000000000003 Water molecule O 0.00000 0.00000 0.11779 H 0.00000 0.75545 -0.47116 H 0.00000 -0.75545 -0.47116 xtp-2021.2/src/tests/DataFiles/ecpaobasis/000077500000000000000000000000001412152066400203125ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/ecpaobasis/3-21G.xml000066400000000000000000000027271412152066400215350ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/ecpaobasis/ecp.xml000066400000000000000000000010041412152066400215760ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/ecpaobasis/molecule.xyz000066400000000000000000000003621412152066400226740ustar00rootroot00000000000000 5 methane C .000000 .000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/eris/000077500000000000000000000000001412152066400171435ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/eris/3-21G.xml000066400000000000000000000027301412152066400203600ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/eris/dmat.mm000066400000000000000000000073331412152066400204310ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 0.00157507 0.0337454 -5.93152e-16 4.48905e-16 7.87133e-17 0.030876 -1.49094e-16 2.51254e-16 5.77899e-17 0.00415998 -0.00445632 0.00415998 -0.00445632 0.00415998 -0.00445632 0.00415998 -0.00445632 0.0337454 0.722983 -4.44783e-15 2.66427e-15 3.45846e-16 0.661507 -2.02475e-15 4.39854e-15 1.04832e-15 0.0891262 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0.0527457 0.208545 0.267632 1.07244 -0.271864 -0.271864 0.271864 0.909256 -0.166363 -0.166363 0.166363 0.208545 0.455288 0.208545 0.455288 0.503333 0.651756 0.208545 0.455288 0.130702 0.566511 0.372211 -0.372211 -0.372211 0.499389 0.236401 -0.236401 -0.236401 0.0527458 0.208545 0.0527458 0.208545 0.0527457 0.208545 0.533232 0.503332 0.267632 1.07244 0.271863 -0.271864 -0.271864 0.909255 0.166363 -0.166363 -0.166363 0.208545 0.455288 0.208545 0.455288 0.208545 0.455288 0.503332 0.651756xtp-2021.2/src/tests/DataFiles/eris/molecule.xyz000066400000000000000000000003621412152066400215250ustar00rootroot00000000000000 5 methane C .000000 .000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/eris/mos.mm000066400000000000000000000073331412152066400203020ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 -0.0280659 -0.601271 1.05977e-15 -5.74943e-15 -1.39766e-15 -0.55007 -2.34629e-15 -3.028e-15 3.77373e-16 -0.0741184 0.0793899 -0.0741184 0.0793899 -0.0741184 0.0793899 -0.0741184 0.0793899 4.09009e-16 6.10444e-15 -0.0684321 -0.867437 -0.0621626 8.57097e-16 -0.00968898 -0.122816 -0.00880132 -0.0930716 0.0263843 -0.0687144 0.0194794 0.0814777 -0.0230976 0.0803083 -0.0227661 8.10359e-17 5.5398e-16 -0.764063 0.0897498 -0.411274 -7.88251e-16 -0.10818 0.0127073 -0.0582304 -0.101237 0.0286989 0.117976 -0.0334442 0.0245298 -0.00695379 -0.0412691 0.0116991 -3.17589e-17 6.1698e-17 0.415353 0.0221836 -0.766801 2.16043e-15 0.058808 0.00314088 -0.108568 -0.0307056 0.00870452 0.0348431 -0.00987743 -0.112311 0.0318382 0.108173 -0.0306653 2.60409e-16 2.54555e-15 0.29223 0.483062 -0.10229 -4.00107e-15 0.00365145 0.00603592 -0.00127812 -0.470865 -0.25194 -0.205082 -0.109731 0.613999 0.328524 0.0619484 0.0331459 5.98083e-17 9.36257e-16 -0.31914 0.275478 0.389195 2.87815e-15 -0.00398769 0.00344213 0.00486303 -0.241752 -0.129351 -0.143724 -0.0769004 -0.302847 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-0.0365659xtp-2021.2/src/tests/DataFiles/espfit/000077500000000000000000000000001412152066400174735ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/espfit/3-21G.xml000066400000000000000000000030601412152066400207050ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/espfit/MOs.mm000066400000000000000000000043031412152066400205240ustar00rootroot00000000000000%%MatrixMarket matrix array real general 13 13 0.982343 0.101935 -2.79025e-13 -0.00360159 1.29673e-14 -0.0420683 2.3837e-12 0.00731426 -1.66267e-12 0.00274585 0.00750313 0.00274585 0.00750313 0.225297 -0.213424 3.45211e-12 0.116669 -1.00926e-12 -0.681791 3.59972e-12 0.115649 -4.34816e-12 -0.126026 -0.0234965 -0.126026 -0.0234965 3.39697e-12 1.90464e-12 -0.409602 -5.86782e-13 7.23423e-12 -1.96952e-11 -0.348495 3.63395e-12 4.68601e-12 -0.238054 -0.19353 0.238054 0.19353 0.104226 -0.0897338 3.0704e-12 -0.438404 -2.7662e-11 -0.470854 1.18667e-11 -0.484273 -3.15464e-11 0.130359 0.118088 0.130359 0.118088 -4.02405e-12 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-6.55285e-12 1.55304e-11 -1.0425 7.8109e-11 1.43023e-11 2.43573e-11 1.44212 -9.64031e-11 -1.68919e-11 -0.169014 -0.524685 0.169014 0.524685 -0.0865545 1.64108 4.00797e-12 -0.147551 7.55262e-12 -2.00561 -3.91477e-12 0.501366 -7.27192e-12 0.291888 0.3665 0.291888 0.3665xtp-2021.2/src/tests/DataFiles/espfit/molecule.xyz000066400000000000000000000002441412152066400220540ustar00rootroot000000000000003 Water molecule O 0.00000 0.00000 0.11779 H 0.00000 0.75545 -0.47116 H 0.00000 -0.75545 -0.47116 xtp-2021.2/src/tests/DataFiles/gaussian_quadratures/000077500000000000000000000000001412152066400224335ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/gaussian_quadratures/gauss_hermite.mm000066400000000000000000000012541412152066400256270ustar00rootroot00000000000000%%MatrixMarket matrix array real general 9 1 1.7724538509055158819194275565678253769874572753906250000000000000e+00 1.7724538509055165480532423316617496311664581298828125000000000000e+00 1.7724538509055163260086374066304415464401245117187500000000000000e+00 1.7724538509055158819194275565678253769874572753906250000000000000e+00 1.7724538509055161039640324815991334617137908935546875000000000000e+00 1.7724538509055156598748226315365172922611236572265625000000000000e+00 1.7724538509055161039640324815991334617137908935546875000000000000e+00 1.7724538509055158819194275565678253769874572753906250000000000000e+00 1.7724538509055163260086374066304415464401245117187500000000000000e+00 xtp-2021.2/src/tests/DataFiles/gaussian_quadratures/gauss_laguerre.mm000066400000000000000000000012541412152066400260000ustar00rootroot00000000000000%%MatrixMarket matrix array real general 9 1 1.7851910265680297484891525527928024530410766601562500000000000000e+00 1.7731121998123879901498867184272967278957366943359375000000000000e+00 1.7703913333125758100550228846259415149688720703125000000000000000e+00 1.7722066171967718606339303732966072857379913330078125000000000000e+00 1.7728177058422052159158965878305025398731231689453125000000000000e+00 1.7725736597943941852406624093418940901756286621093750000000000000e+00 1.7724036582199536038473297594464384019374847412109375000000000000e+00 1.7724539507246128700046483572805300354957580566406250000000000000e+00 1.7724538509055376422907102096360176801681518554687500000000000000e+00 xtp-2021.2/src/tests/DataFiles/gaussian_quadratures/gauss_legendre.mm000066400000000000000000000012541412152066400257570ustar00rootroot00000000000000%%MatrixMarket matrix array real general 9 1 1.7982653294862469550707828602753579616546630859375000000000000000e+00 1.7635524479921413920635586691787466406822204589843750000000000000e+00 1.7755135781619735269032389624044299125671386718750000000000000000e+00 1.7715209261601161383481439770548604428768157958984375000000000000e+00 1.7726581320386711748682273537269793450832366943359375000000000000e+00 1.7724628015402867919902973881107755005359649658203125000000000000e+00 1.7724077952532697466381250706035643815994262695312500000000000000e+00 1.7724538242027620960072908928850665688514709472656250000000000000e+00 1.7724538509055152157856127814739011228084564208984375000000000000e+00 xtp-2021.2/src/tests/DataFiles/gaussian_quadratures/modified_gauss_legendre.mm000066400000000000000000000012541412152066400276170ustar00rootroot00000000000000%%MatrixMarket matrix array real general 9 1 1.7666951327337738764100549815339036285877227783203125000000000000e+00 1.7769696007269601967237804274191148579120635986328125000000000000e+00 1.7704741425269137078402081897365860641002655029296875000000000000e+00 1.7732176603939719949920572616974823176860809326171875000000000000e+00 1.7721697690282220971624838057323358952999114990234375000000000000e+00 1.7725597110830395575220563841867260634899139404296875000000000000e+00 1.7724137859609552236861418350599706172943115234375000000000000000e+00 1.7724538549863015912677610685932449996471405029296875000000000000e+00 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xtp-2021.2/src/tests/DataFiles/gw/ref.mm000066400000000000000000000073331412152066400177330ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 -11.4075 -0.000332076 -2.98562e-07 -1.444e-07 3.56698e-08 0.00415282 -2.59416e-07 3.42809e-07 2.37553e-08 -1.12992e-07 1.90622e-07 7.34527e-08 -0.00225178 -9.78891e-07 2.05282e-07 -8.26113e-07 -0.0537384 -0.000332076 -1.01045 -9.0233e-07 -5.36336e-07 2.09522e-07 0.00201438 -4.15248e-07 6.11818e-07 1.77817e-07 -4.04586e-07 4.29371e-07 3.58778e-07 0.00539939 -1.90892e-06 4.37732e-07 -1.69582e-06 0.00539329 -2.98562e-07 -9.0233e-07 -0.620146 1.97176e-07 -7.69219e-07 1.12519e-07 0.0208017 -0.00772665 8.27053e-05 8.52774e-05 0.0206388 -0.000530697 -3.25714e-07 0.00634783 -0.00243228 2.30183e-05 -1.20011e-07 -1.444e-07 -5.36336e-07 1.97176e-07 -0.620147 -6.94777e-07 3.49514e-08 -0.00772665 -0.0208006 0.000164225 0.000265677 0.000529342 0.020638 -1.52421e-07 -0.00243197 -0.00634853 6.17472e-05 9.44e-08 3.56698e-08 2.09522e-07 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C .000000 .000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/localisation_filter/spsi_ref.mm000066400000000000000000000045211412152066400243760ustar00rootroot00000000000000%%MatrixMarket matrix array real general 60 3 -0.00178316 0.00568291 0.05758 0.00379328 -0.00848959 -0.000395809 7.13955e-08 0.000420413 -0.00288487 0.0119767 -2.55565e-08 6.84051e-09 0.00420618 0.0036276 0.0465325 0.0051614 -0.010968 0.000951266 0.000419006 -0.00118124 -0.00345217 0.013156 -2.58268e-05 -1.80679e-06 -0.0150073 0.0180327 -0.0643994 -0.0123339 0.0122493 -0.00375172 0.00648758 0.00433063 0.0111166 -0.0160119 -0.000399315 -2.80525e-05 -0.0450479 0.0655838 0.0220978 -0.0119156 -0.0132479 -0.0118978 0.0199347 0.0131991 0.0159091 0.0123057 -0.00122682 -8.62007e-05 -0.0304688 0.0971056 0.983887 0.0170489 -0.0381557 -0.00177889 -2.23782e-07 -0.000182535 0.00125201 -0.00519809 4.03664e-08 -2.38233e-09 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-0.736251 -0.318581 -0.119843 0.0194514 0.902309 0.390399 0.144447 -0.287346 0.384025 -0.692041 1.01735 -0.0643538 0.0309117 -0.186295 0.343255 0.00842586 -0.00696076 0.299671 -0.742966 0.098978 -0.0154654 -0.369382 0.915642 -0.119075 0.911691 -1.37669 -0.596392 0.986574 0.0603758 -0.0364325 -0.131308 0.382921 0.0266439 0.00293678 -0.158865 0.0491515 0.724743 -0.0835686 0.201698 -0.0622531 -0.910397 -0.189658 0.479846 -0.157408 0.427441 1.11285 -1.55284 0.155082 0.763617 0.0164909 1.99738 0.00190447 -0.000436489 -0.0188564 -3.94756 -0.0044353 0.000737688 0.0439701 0.150935 0.773327 0.152804 0.768442 0.135229 0.832677xtp-2021.2/src/tests/DataFiles/orca/co.xyz000066400000000000000000000000471412152066400203030ustar00rootroot000000000000002 C 0.6969 0.0 0.0 O -0.6969 0.0 0.0 xtp-2021.2/src/tests/DataFiles/orca/orca_charges.log000066400000000000000000000220721412152066400222530ustar00rootroot00000000000000 ***************** * O R C A * ***************** --- An Ab Initio, DFT and Semiempirical electronic structure package --- Program Version 4.0.1 - RELEASE - ================================================================================ INPUT FILE ================================================================================ NAME = system.inp | 1> * xyz 0 1 | 2> H 0.5288 0.1610 0.9359 | 3> C 0.0000 0.0000 0.0000 | 4> H 0.2051 0.8240 -0.6786 | 5> H 0.3345 -0.9314 -0.4496 | 6> H -1.0685 -0.0537 0.1921 | 7> * | 8> | 9> ! DFT PBE0 DIRECT 3-21G CHELPG | 10> | 11> | 12> ****END OF INPUT**** ================================================================================ **************************** * Single Point Calculation * **************************** --------------------------------- CARTESIAN COORDINATES (ANGSTROEM) --------------------------------- H 0.528800 0.161000 0.935900 C 0.000000 0.000000 0.000000 H 0.205100 0.824000 -0.678600 H 0.334500 -0.931400 -0.449600 H -1.068500 -0.053700 0.192100 ---------------------------- CARTESIAN COORDINATES (A.U.) ---------------------------- NO LB ZA FRAG MASS X Y Z 0 H 1.0000 0 1.008 0.999287 0.304246 1.768595 1 C 6.0000 0 12.011 0.000000 0.000000 0.000000 2 H 1.0000 0 1.008 0.387583 1.557134 -1.282368 3 H 1.0000 0 1.008 0.632113 -1.760091 -0.849621 4 H 1.0000 0 1.008 -2.019172 -0.101478 0.363016 ------------------------------------------------------------------------------- ORCA SCF ------------------------------------------------------------------------------- ------------ SCF SETTINGS ------------ Hamiltonian: Density Functional Method .... DFT(GTOs) Exchange Functional Exchange .... PBE PBE kappa parameter XKappa .... 0.804000 PBE mue parameter XMuePBE .... 0.219520 Correlation Functional Correlation .... PBE PBE beta parameter CBetaPBE .... 0.066725 LDA part of GGA corr. LDAOpt .... PW91-LDA Gradients option PostSCFGGA .... off Hybrid DFT is turned on Fraction HF Exchange ScalHFX .... 0.250000 Scaling of DF-GGA-X ScalDFX .... 0.750000 Scaling of DF-GGA-C ScalDFC .... 1.000000 Scaling of DF-LDA-C ScalLDAC .... 1.000000 Perturbative correction .... 0.000000 NL short-range parameter .... 6.900000 General Settings: Integral files IntName .... system Hartree-Fock type HFTyp .... RHF Total Charge Charge .... 0 Multiplicity Mult .... 1 Number of Electrons NEL .... 10 Basis Dimension Dim .... 17 Nuclear Repulsion ENuc .... 13.4728429098 Eh -------------- **** Energy Check signals convergence **** ***Rediagonalizing the Fockian in SOSCF/NRSCF*** ***************************************************** * SUCCESS * * SCF CONVERGED AFTER 8 CYCLES * ***************************************************** ---------------- TOTAL SCF ENERGY ---------------- Total Energy : -40.24079234 Eh -1095.00763 eV Components: Nuclear Repulsion : 13.47284291 Eh 366.61469 eV Electronic Energy : -53.71363525 Eh -1461.62232 eV One Electron Energy: -79.60546447 Eh -2166.17481 eV Two Electron Energy: 25.89182922 Eh 704.55249 eV Virial components: Potential Energy : -80.11914772 Eh -2180.15285 eV Kinetic Energy : 39.87835537 Eh 1085.14522 eV Virial Ratio : 2.00908856 DFT components: N(Alpha) : 4.999999872554 electrons N(Beta) : 4.999999872554 electrons N(Total) : 9.999999745108 electrons E(X) : -4.882673741049 Eh E(C) : -0.304070704661 Eh E(XC) : -5.186744445711 Eh ---------------- ORBITAL ENERGIES ---------------- NO OCC E(Eh) E(eV) 0 2.0000 -10.144671 -276.0505 1 2.0000 -0.712065 -19.3763 2 2.0000 -0.400849 -10.9077 3 2.0000 -0.400674 -10.9029 4 2.0000 -0.400623 -10.9015 5 0.0000 0.162735 4.4282 6 0.0000 0.207980 5.6594 7 0.0000 0.208515 5.6740 8 0.0000 0.209452 5.6995 9 0.0000 0.724346 19.7105 10 0.0000 0.724822 19.7234 11 0.0000 0.726572 19.7710 12 0.0000 1.060128 28.8476 13 0.0000 1.090989 29.6873 14 0.0000 1.091410 29.6988 15 0.0000 1.091968 29.7140 16 0.0000 1.714644 46.6578 ******************************* * LOEWDIN POPULATION ANALYSIS * ******************************* ---------------------- LOEWDIN ATOMIC CHARGES ---------------------- 0 H : 0.107341 1 C : -0.427887 2 H : 0.106689 3 H : 0.106859 4 H : 0.106998 ------------------------------- LOEWDIN REDUCED ORBITAL CHARGES ------------------------------- 0 H s : 0.892659 s : 0.892659 1 C s : 3.002200 s : 3.002200 pz : 1.142081 p : 3.425687 px : 1.142325 py : 1.141282 2 H s : 0.893311 s : 0.893311 3 H s : 0.893141 s : 0.893141 4 H s : 0.893002 s : 0.893002 ------------------------- -------------------- FINAL SINGLE POINT ENERGY -40.240792344368 ------------------------- -------------------- *************************************** * ORCA property calculations * *************************************** --------------------- Active property flags --------------------- (+) Dipole Moment ------------------------------------------------------------------------------ ORCA ELECTRIC PROPERTIES CALCULATION ------------------------------------------------------------------------------ Dipole Moment Calculation ... on Quadrupole Moment Calculation ... off Polarizability Calculation ... off GBWName ... system.gbw Electron density file ... system.scfp.tmp The origin for moment calculation is the CENTER OF MASS = (-0.000012, -0.000012 -0.000024) ------------- DIPOLE MOMENT ------------- X Y Z Electronic contribution: 0.00066 -0.00090 0.00446 Nuclear contribution : -0.00007 -0.00007 -0.00014 ----------------------------------------- Total Dipole Moment : 0.00059 -0.00097 0.00432 ----------------------------------------- Magnitude (a.u.) : 0.00447 Magnitude (Debye) : 0.01136 ------------------------------------------------------------------------------ ORCA CHELPG CHARGES GENERATION ------------------------------------------------------------------------------ GBW file ... system.gbw Reading the GBW file ... done Grid spacing ... 0.300000 Point Cut-Off ... 2.800000 Van-der-Waals Radii ... COSMO Total charge ... 0 Number of points X direction ... 23 Number of points Y direction ... 24 Number of points Z direction ... 24 Maximum number of possible points ... 13248 Final number of points ... 5330 CHELPG Charges -------------------------------- 0 H : 0.178516 1 C : -0.709443 2 H : 0.176227 3 H : 0.177109 4 H : 0.177591 -------------------------------- Total charge: -0.000000 -------------------------------- CHELPG charges calculated... ****ORCA TERMINATED NORMALLY**** TOTAL RUN TIME: 0 days 0 hours 0 minutes 2 seconds 316 msec xtp-2021.2/src/tests/DataFiles/orca/orca_ext_charges.log000066400000000000000000000244771412152066400231460ustar00rootroot00000000000000 ***************** * O R C A * ***************** --- An Ab Initio, DFT and Semiempirical electronic structure package --- Program Version 4.0.1 - RELEASE - ================================================================================ INPUT FILE ================================================================================ NAME = system.inp | 1> * xyz 0 1 | 2> H 0.5288 0.1610 0.9359 | 3> C 0.0000 0.0000 0.0000 | 4> H 0.2051 0.8240 -0.6786 | 5> H 0.3345 -0.9314 -0.4496 | 6> H -1.0685 -0.0537 0.1921 | 7> * | 8> | 9> ! DFT PBE0 DIRECT 3-21G | 10> %pointcharges "background.crg" | 11> | 12> ****END OF INPUT**** ================================================================================ **************************** * Single Point Calculation * **************************** --------------------------------- CARTESIAN COORDINATES (ANGSTROEM) --------------------------------- H 0.528800 0.161000 0.935900 C 0.000000 0.000000 0.000000 H 0.205100 0.824000 -0.678600 H 0.334500 -0.931400 -0.449600 H -1.068500 -0.053700 0.192100 ---------------------------- CARTESIAN COORDINATES (A.U.) ---------------------------- NO LB ZA FRAG MASS X Y Z 0 H 1.0000 0 1.008 0.999287 0.304246 1.768595 1 C 6.0000 0 12.011 0.000000 0.000000 0.000000 2 H 1.0000 0 1.008 0.387583 1.557134 -1.282368 3 H 1.0000 0 1.008 0.632113 -1.760091 -0.849621 4 H 1.0000 0 1.008 -2.019172 -0.101478 0.363016 -------------------------------- INTERNAL COORDINATES (ANGSTROEM) -------------------------------- H 0 0 0 0.000000000000 0.00000000 0.00000000 C 1 0 0 1.086949515847 0.00000000 0.00000000 H 2 1 0 1.086986646652 109.47881566 0.00000000 H 2 1 3 1.086984990697 109.47224096 120.00042779 H 2 1 3 1.086958301868 109.47426454 239.99847195 --------------------------- INTERNAL COORDINATES (A.U.) --------------------------- H 0 0 0 0.000000000000 0.00000000 0.00000000 C 1 0 0 2.054036906349 0.00000000 0.00000000 H 2 1 0 2.054107073402 109.47881566 0.00000000 H 2 1 3 2.054103944100 109.47224096 120.00042779 H 2 1 3 2.054053509523 109.47426454 239.99847195 --------------------- BASIS SET INFORMATION --------------------- There are 2 groups of distinct atoms Group 1 Type H : 3s contracted to 2s pattern {21} Group 2 Type C : 6s3p contracted to 3s2p pattern {321/21} Atom 0H basis set group => 1 Atom 1C basis set group => 2 Atom 2H basis set group => 1 Atom 3H basis set group => 1 Atom 4H basis set group => 1 ------------------------------------------------------------------------------ ORCA GTO INTEGRAL CALCULATION ------------------------------------------------------------------------------ BASIS SET STATISTICS AND STARTUP INFO # of primitive gaussian shells ... 21 # of primitive gaussian functions ... 27 # of contracted shells ... 13 # of contracted basis functions ... 17 Highest angular momentum ... 1 Maximum contraction depth ... 3 Integral package used ... LIBINT Integral threshhold Thresh ... 1.000e-10 Primitive cut-off TCut ... 1.000e-11 ------------------------------ INTEGRAL EVALUATION ---------------------------- * One electron integrals Pre-screening matrix ... done Shell pair data ... done ( 0.000 sec) ENUC WAS= 0.000000000 ------------------------------------------------------------------------------ ORCA POINT-CHARGE CORRECTION ------------------------------------------------------------------------------ BaseName ... system Point charge file ... background.crg Reading the GBW file ... done Reading the one-electron matrix ... done Reading the point charges ... done Number of point charges ... 2 Reading the nuclear-repulsion ... done Charge-Nuclei interaction ... done The nuclear repulsion file was updated Doing the point charge correction ... done Storing the one-electron matrix ... done ENUC IS = 13.468491157 ------------------------------------------------------------------------------- ORCA SCF ------------------------------------------------------------------------------- ------------ SCF SETTINGS ------------ Hamiltonian: Density Functional Method .... DFT(GTOs) Exchange Functional Exchange .... PBE PBE kappa parameter XKappa .... 0.804000 PBE mue parameter XMuePBE .... 0.219520 Correlation Functional Correlation .... PBE PBE beta parameter CBetaPBE .... 0.066725 LDA part of GGA corr. LDAOpt .... PW91-LDA Gradients option PostSCFGGA .... off Hybrid DFT is turned on Fraction HF Exchange ScalHFX .... 0.250000 Scaling of DF-GGA-X ScalDFX .... 0.750000 Scaling of DF-GGA-C ScalDFC .... 1.000000 Scaling of DF-LDA-C ScalLDAC .... 1.000000 Perturbative correction .... 0.000000 NL short-range parameter .... 6.900000 Total Charge Charge .... 0 Multiplicity Mult .... 1 Number of Electrons NEL .... 10 Basis Dimension Dim .... 17 Now organizing SCF variables ... done ------------------ INITIAL GUESS DONE ( 0.1 sec) ------------------ -------------- SCF ITERATIONS -------------- ITER Energy Delta-E Max-DP RMS-DP [F,P] Damp *** Starting incremental Fock matrix formation *** 0 -40.1872004981 0.000000000000 0.05536256 0.00817063 0.1957522 0.7000 1 -40.2132289204 -0.026028422342 0.04820965 0.00640591 0.1046817 0.7000 ***Turning on DIIS*** 2 -40.2245953394 -0.011366418967 0.08694609 0.01142784 0.0433835 0.0000 3 -40.2400285485 -0.015433209094 0.02932528 0.00400269 0.0519153 0.0000 4 -40.2443514277 -0.004322879173 0.01077603 0.00127690 0.0110322 0.0000 *** Initiating the SOSCF procedure *** *** Shutting down DIIS *** *** Re-Reading the Fockian *** *** Removing any level shift *** ITER Energy Delta-E Grad Rot Max-DP RMS-DP 5 -40.24457772 -0.0002262898 0.000821 0.000821 0.002813 0.000376 *** Restarting incremental Fock matrix formation *** 6 -40.24458849 -0.0000107750 0.000295 0.000489 0.000969 0.000178 7 -40.24458881 -0.0000003205 0.000194 0.000117 0.000285 0.000039 **** Energy Check signals convergence **** ***Rediagonalizing the Fockian in SOSCF/NRSCF*** ***************************************************** * SUCCESS * * SCF CONVERGED AFTER 8 CYCLES * ***************************************************** ---------------- TOTAL SCF ENERGY ---------------- Total Energy : -40.24450486 Eh -1095.10865 eV Components: Nuclear Repulsion : 13.46849116 Eh 366.49628 eV Electronic Energy : -53.71299601 Eh -1461.60493 eV One Electron Energy: -79.60713122 Eh -2166.22017 eV Two Electron Energy: 25.89413521 Eh 704.61524 eV Virial components: Potential Energy : -80.12302794 Eh -2180.25843 eV Kinetic Energy : 39.87852308 Eh 1085.14978 eV Virial Ratio : 2.00917742 DFT components: N(Alpha) : 4.999998713470 electrons N(Beta) : 4.999998713470 electrons N(Total) : 9.999997426940 electrons E(X) : -4.882360646132 Eh E(C) : -0.304201834413 Eh E(XC) : -5.186562480545 Eh --------------- SCF CONVERGENCE --------------- **** THE GBW FILE WAS UPDATED (system.gbw) **** **** DENSITY FILE WAS UPDATED (system.scfp.tmp) **** **** ENERGY FILE WAS UPDATED (system.en.tmp) **** ---------------- ORBITAL ENERGIES ---------------- NO OCC E(Eh) E(eV) 0 2.0000 -10.144143 -276.0362 1 2.0000 -0.712523 -19.3887 2 2.0000 -0.405481 -11.0337 3 2.0000 -0.403251 -10.9730 4 2.0000 -0.392086 -10.6692 5 0.0000 0.157504 4.2859 6 0.0000 0.196706 5.3526 7 0.0000 0.202667 5.5149 8 0.0000 0.240538 6.5454 9 0.0000 0.718397 19.5486 10 0.0000 0.727724 19.8024 11 0.0000 0.728746 19.8302 12 0.0000 1.057703 28.7816 13 0.0000 1.081247 29.4222 14 0.0000 1.086069 29.5534 15 0.0000 1.116265 30.3751 16 0.0000 1.715960 46.6936 ------------------------- -------------------- FINAL SINGLE POINT ENERGY -40.244504856356 ------------------------- -------------------- *************************************** * ORCA property calculations * *************************************** ****ORCA TERMINATED NORMALLY**** TOTAL RUN TIME: 0 days 0 hours 0 minutes 1 seconds 470 msec xtp-2021.2/src/tests/DataFiles/orca/orca_ext_mos.gbw000066400000000000000000002263061412152066400223210ustar00rootroot00000000000000(`"system/opt/orcaorca_anointorca_gtointorca_stointorca_ndointorca_scforca_mp2orca_mrciorca_cipsiorca_plotorca_scfgradorca_vpt2orca_gsteporca_momorca_cpscforca_cpcasscforca_locorca_cisorca_pcorca_cipreporca_viborca_poporca_relorca_socorca_eprnmrorca_casscforca_mdciorca_autociorca_chelpgotool_ecporca_numfreqorca_scfhessorca_rocisorca_cleanuporca_eulerbackground.crgorca_mdorca_2aimorca_fitpesorca_esdsystem_property.txt-C6?:0yE>UUUUUU?J4q?|?5^??????J4q?S?@~jt?a+ei?h:;?ZӼ?UUUUUU?J4q?|?5^?????h:;?ZӼ??D@@𿚙?\(\@none|=\(\@?+=+=Q @\(\ @ ףp= @\(\@Q @Gz@:0yE>?Gz@} *@h㈵>MbP?ffffff?\(\??MbP???$@ F%uk?F%uk?d-C6?-C6?:0yE>?@?ư>ư>h㈵>ư>-C6 ?-C6 ?:0yE>system|=dy=|=?@@@2333333?333333ӿ ?2h㈵>a2U0*3?-C6?Mbp?Mb`?-C6?g03-C6?I@? 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SΈ؍]SQft?_!?:RYe:.E?8LTJ?.V?1?Ȅ^=O{ں>Q@+?9?d!{?UW?;t?b@BU?.Rʒ?9.hOs?j9~?U8*}? .#cԿJ`hBa*?s<߶Oبc-aKqWy?!̵r߲=W?A|*+?MfwDKa.uNye{ Ԁ*E?'0?𩨺OY6dX"b{#*>64W?8s?)6k,n{Q? #1*έ]D߿qxп>s0A?>6?(`_M?X@׿{ @@?C*r$ KUR+n(x/ޜjY?q夿b/7W?TÕؿ7;Mȿ^4D*ÿn!a?2}&:?s1TɿpӿcjA}?(u{1!ld@?0`߰s^7m?D?+߯? ?J귪࿝]Z?ȉ(.?VTu(u1C㎿uX?ȭvK?+f>L?$߯KS+,H?~9cYN!ZPnj9%OL?(j?H񻩒?۬`bCJ@+~]?9C?; ֿ9rr俰2cҿQ*,? Fȿ*tqQ?7[?/-ؑ_Ĵst?rA?mL3?GWTZ߿%K;,vԿ#lG?^"Ѱ?P󧿮z&?mޓ?S~h̵?'D?JNoDiĿab=ſ Bɿij?GD"?.ӲGFtOij?_⫿؆ ?mUM࿪+MͿIªXgCc3%濏)Y㿢f%ĿS?^X? EB29 ſUӾɿ3p#$?w?{x/e|?6$ҿ?8̵Z>Vo᜿h 4?\G?z ?r|1[?.T?WIL x5]ӅEZ?1_ѿC$KC\m?mXJ_R * xyz 0 1 | 2> H 0.5288 0.1610 0.9359 | 3> C 0.0000 0.0000 0.0000 | 4> H 0.2051 0.8240 -0.6786 | 5> H 0.3345 -0.9314 -0.4496 | 6> H -1.3685 -0.0537 0.1921 | 7> * | 8> | 9> ! DFT PBE0 DIRECT 3-21G OPT | 10> | 11> | 12> ****END OF INPUT**** ================================================================================ ***************************** * Geometry Optimization Run * ***************************** Geometry optimization settings: Update method Update .... BFGS Choice of coordinates CoordSys .... Redundant Internals Initial Hessian InHess .... Almoef's Model Convergence Tolerances: Energy Change TolE .... 5.0000e-06 Eh Max. Gradient TolMAXG .... 3.0000e-04 Eh/bohr RMS Gradient TolRMSG .... 1.0000e-04 Eh/bohr Max. Displacement TolMAXD .... 4.0000e-03 bohr RMS Displacement TolRMSD .... 2.0000e-03 bohr ------------------------------------------------------------------------------ ORCA OPTIMIZATION COORDINATE SETUP ------------------------------------------------------------------------------ The optimization will be done in new redundant internal coordinates Making redundant internal coordinates ... (new redundants) done Evaluating the initial hessian ... (Almloef) done Evaluating the coordinates ... done Calculating the B-matrix .... done Calculating the G-matrix .... done Diagonalizing the G-matrix .... done The first mode is .... 1 The number of degrees of freedom .... 9 ----------------------------------------------------------------- Redundant Internal Coordinates Number of atoms .... 5 Number of degrees of freedom .... 10 ************************************************************* * GEOMETRY OPTIMIZATION CYCLE 1 * ************************************************************* --------------------------------- CARTESIAN COORDINATES (ANGSTROEM) --------------------------------- H 0.528800 0.161000 0.935900 C 0.000000 0.000000 0.000000 H 0.205100 0.824000 -0.678600 H 0.334500 -0.931400 -0.449600 H -1.368500 -0.053700 0.192100 ---------------------------- CARTESIAN COORDINATES (A.U.) ---------------------------- NO LB ZA FRAG MASS X Y Z 0 H 1.0000 0 1.008 0.999287 0.304246 1.768595 1 C 6.0000 0 12.011 0.000000 0.000000 0.000000 2 H 1.0000 0 1.008 0.387583 1.557134 -1.282368 3 H 1.0000 0 1.008 0.632113 -1.760091 -0.849621 4 H 1.0000 0 1.008 -2.586090 -0.101478 0.363016 -------------------------------- INTERNAL COORDINATES (ANGSTROEM) -------------------------------- H 0 0 0 0.000000000000 0.00000000 0.00000000 C 1 0 0 1.086949515847 0.00000000 0.00000000 H 2 1 0 1.086986646652 109.47881566 0.00000000 H 2 1 3 1.086984990697 109.47224096 120.00042779 H 2 1 3 1.382959995806 111.56534123 240.97259909 --------------------------- INTERNAL COORDINATES (A.U.) --------------------------- H 0 0 0 0.000000000000 0.00000000 0.00000000 C 1 0 0 2.054036906349 0.00000000 0.00000000 H 2 1 0 2.054107073402 109.47881566 0.00000000 H 2 1 3 2.054103944100 109.47224096 120.00042779 H 2 1 3 2.613415646242 111.56534123 240.97259909 ------------------------------------------------------------------------------ ORCA GEOMETRY RELAXATION STEP ------------------------------------------------------------------------------ --------------------------------------------------------------------------- Redundant Internal Coordinates (Angstroem and degrees) Definition Value dE/dq Step New-Value ---------------------------------------------------------------------------- 1. B(C 1,H 0) 1.0909 -0.000933 0.0011 1.0920 2. B(H 2,C 1) 1.0930 -0.000672 0.0008 1.0938 3. B(H 3,C 1) 1.0921 -0.000821 0.0010 1.0931 4. B(H 4,C 1) 1.0671 -0.019919 0.0384 1.1055 5. A(H 0,C 1,H 3) 110.25 0.002313 -0.30 109.94 6. A(H 2,C 1,H 3) 110.15 0.002260 -0.29 109.86 7. A(H 0,C 1,H 4) 109.37 -0.000766 0.03 109.40 8. A(H 2,C 1,H 4) 108.19 -0.003723 0.53 108.72 9. A(H 3,C 1,H 4) 108.63 -0.002570 0.34 108.97 10. A(H 0,C 1,H 2) 110.22 0.002277 -0.30 109.92 ---------------------------------------------------------------------------- ************************************************************* * GEOMETRY OPTIMIZATION CYCLE 4 * ************************************************************* --------------------------------- CARTESIAN COORDINATES (ANGSTROEM) --------------------------------- H 0.459237 0.159800 0.951980 C -0.052518 -0.000123 0.000715 H 0.158061 0.829765 -0.679964 H 0.278340 -0.940740 -0.447106 H -1.143220 -0.048802 0.174175 ---------------------------- CARTESIAN COORDINATES (A.U.) ---------------------------- NO LB ZA FRAG MASS X Y Z 0 H 1.0000 0 1.008 0.867831 0.301979 1.798981 1 C 6.0000 0 12.011 -0.099245 -0.000232 0.001351 2 H 1.0000 0 1.008 0.298692 1.568028 -1.284945 3 H 1.0000 0 1.008 0.525987 -1.777741 -0.844907 4 H 1.0000 0 1.008 -2.160373 -0.092222 0.329142 -------------------------------- INTERNAL COORDINATES (ANGSTROEM) -------------------------------- H 0 0 0 0.000000000000 0.00000000 0.00000000 C 1 0 0 1.091958230479 0.00000000 0.00000000 H 2 1 0 1.093791937982 109.92456920 0.00000000 H 2 1 3 1.093055992012 109.94273931 121.05608241 H 2 1 3 1.105481180659 109.39929578 240.68321411 --------------------------- INTERNAL COORDINATES (A.U.) --------------------------- H 0 0 0 0.000000000000 0.00000000 0.00000000 C 1 0 0 2.063502005287 0.00000000 0.00000000 H 2 1 0 2.066967210277 109.92456920 0.00000000 H 2 1 3 2.065576473944 109.94273931 121.05608241 H 2 1 3 2.089056677649 109.39929578 240.68321411 Diagonalization of the overlap matrix: Smallest eigenvalue ... 3.437e-02 Time for diagonalization ... 0.000 sec Threshold for overlap eigenvalues ... 1.000e-08 Number of eigenvalues below threshold ... 0 Iter 1: RMS(Cart)= 0.0000000284 RMS(Int)= 0.0000000410 done Storing new coordinates .... done .--------------------. ----------------------|Geometry convergence|------------------------- Item value Tolerance Converged --------------------------------------------------------------------- Energy change -0.0000011251 0.0000050000 YES RMS gradient 0.0000574471 0.0001000000 YES MAX gradient 0.0001505075 0.0003000000 YES RMS step 0.0002210194 0.0020000000 YES MAX step 0.0003462437 0.0040000000 YES ........................................................ Max(Bonds) 0.0002 Max(Angles) 0.02 Max(Dihed) 0.00 Max(Improp) 0.00 --------------------------------------------------------------------- ***********************HURRAY******************** *** THE OPTIMIZATION HAS CONVERGED *** ************************************************* --------------------------------------------------------------------------- Redundant Internal Coordinates --- Optimized Parameters --- (Angstroem and degrees) Definition OldVal dE/dq Step FinalVal ---------------------------------------------------------------------------- 1. B(C 1,H 0) 1.0929 -0.000005 0.0000 1.0929 2. B(H 2,C 1) 1.0939 -0.000004 0.0000 1.0939 3. B(H 3,C 1) 1.0935 -0.000004 0.0000 1.0935 4. B(H 4,C 1) 1.0933 -0.000151 0.0002 1.0935 5. A(H 0,C 1,H 3) 109.48 0.000058 -0.02 109.47 6. A(H 2,C 1,H 3) 109.46 0.000017 -0.01 109.45 7. A(H 0,C 1,H 4) 109.44 -0.000056 0.01 109.45 8. A(H 2,C 1,H 4) 109.49 -0.000023 0.01 109.50 9. A(H 3,C 1,H 4) 109.46 -0.000037 0.01 109.47 10. A(H 0,C 1,H 2) 109.49 0.000040 -0.01 109.48 ---------------------------------------------------------------------------- ******************************************************* *** FINAL ENERGY EVALUATION AT THE STATIONARY POINT *** *** (AFTER 7 CYCLES) *** ******************************************************* --------------------------------- CARTESIAN COORDINATES (ANGSTROEM) --------------------------------- H 0.457282 0.159495 0.949475 C -0.060043 0.000032 0.000064 H 0.161203 0.828181 -0.679453 H 0.279541 -0.938419 -0.446827 H -1.138083 -0.049389 0.176541 ---------------------------- CARTESIAN COORDINATES (A.U.) ---------------------------- NO LB ZA FRAG MASS X Y Z 0 H 1.0000 0 1.008 0.864138 0.301402 1.794247 1 C 6.0000 0 12.011 -0.113465 0.000060 0.000122 2 H 1.0000 0 1.008 0.304630 1.565036 -1.283979 3 H 1.0000 0 1.008 0.528256 -1.773354 -0.844381 4 H 1.0000 0 1.008 -2.150666 -0.093332 0.333613 -------------------------------- INTERNAL COORDINATES (ANGSTROEM) -------------------------------- H 0 0 0 0.000000000000 0.00000000 0.00000000 C 1 0 0 1.092901748277 0.00000000 0.00000000 H 2 1 0 1.093857948380 109.47788019 0.00000000 H 2 1 3 1.093488817493 109.46602287 119.98022695 H 2 1 3 1.093506639023 109.45417407 239.96618212 --------------------------- INTERNAL COORDINATES (A.U.) --------------------------- H 0 0 0 0.000000000000 0.00000000 0.00000000 C 1 0 0 2.065284995528 0.00000000 0.00000000 H 2 1 0 2.067091951852 109.47788019 0.00000000 H 2 1 3 2.066394395567 109.46602287 119.98022695 H 2 1 3 2.066428073377 109.45417407 239.96618212 --------------------- BASIS SET INFORMATION --------------------- There are 2 groups of distinct atoms Group 1 Type H : 3s contracted to 2s pattern {21} Group 2 Type C : 6s3p contracted to 3s2p pattern {321/21} Atom 0H basis set group => 1 Atom 1C basis set group => 2 Atom 2H basis set group => 1 Atom 3H basis set group => 1 Atom 4H basis set group => 1 ------------------------------------------------------------------------------ ORCA GTO INTEGRAL CALCULATION ------------------------------------------------------------------------------ ------------------------------ INTEGRAL EVALUATION ---------------------------- * One electron integrals Pre-screening matrix ... done Shell pair data ... done ( 0.000 sec) ------------------------------------------------------------------------------- ORCA SCF ------------------------------------------------------------------------------- ------------ SCF SETTINGS ------------ Hamiltonian: Density Functional Method .... DFT(GTOs) Exchange Functional Exchange .... PBE PBE kappa parameter XKappa .... 0.804000 PBE mue parameter XMuePBE .... 0.219520 Correlation Functional Correlation .... PBE PBE beta parameter CBetaPBE .... 0.066725 LDA part of GGA corr. LDAOpt .... PW91-LDA Gradients option PostSCFGGA .... off Hybrid DFT is turned on Fraction HF Exchange ScalHFX .... 0.250000 Scaling of DF-GGA-X ScalDFX .... 0.750000 Scaling of DF-GGA-C ScalDFC .... 1.000000 Scaling of DF-LDA-C ScalLDAC .... 1.000000 Perturbative correction .... 0.000000 NL short-range parameter .... 6.900000 SCF Procedure: Maximum # iterations MaxIter .... 125 SCF integral mode SCFMode .... Direct Integral package .... LIBINT Reset frequeny DirectResetFreq .... 20 Integral Threshold Thresh .... 2.500e-11 Eh Primitive CutOff TCut .... 2.500e-12 Eh Convergence Tolerance: Convergence Check Mode ConvCheckMode .... Total+1el-Energy Convergence forced ConvForced .... 0 Energy Change TolE .... 1.000e-08 Eh 1-El. energy change .... 1.000e-05 Eh Orbital Gradient TolG .... 1.000e-05 Orbital Rotation angle TolX .... 1.000e-05 DIIS Error TolErr .... 5.000e-07 Diagonalization of the overlap matrix: Smallest eigenvalue ... 3.408e-02 Time for diagonalization ... 0.000 sec Threshold for overlap eigenvalues ... 1.000e-08 Number of eigenvalues below threshold ... 0 Time for construction of square roots ... 0.000 sec Total time needed ... 0.000 sec --------------------- INITIAL GUESS: MOREAD --------------------- Guess MOs are being read from file: system.gbw Input Geometry matches current geometry (good) Input basis set matches current basis set (good) MOs were renormalized MOs were reorthogonalized (Cholesky) ------------------ INITIAL GUESS DONE ( 0.0 sec) ------------------ ------------------- DFT GRID GENERATION ------------------- General Integration Accuracy IntAcc ... 4.340 Radial Grid Type RadialGrid ... Gauss-Chebyshev Angular Grid (max. acc.) AngularGrid ... Lebedev-110 Angular grid pruning method GridPruning ... 3 (G Style) Weight generation scheme WeightScheme... Becke Basis function cutoff BFCut ... 1.0000e-11 Integration weight cutoff WCut ... 1.0000e-14 Grids for H and He will be reduced by one unit # of grid points (after initial pruning) ... 4832 ( 0.0 sec) # of grid points (after weights+screening) ... 4737 ( 0.0 sec) nearest neighbour list constructed ... 0.0 sec Grid point re-assignment to atoms done ... 0.0 sec Grid point division into batches done ... 0.0 sec Reduced shell lists constructed in 0.0 sec Total number of grid points ... 4737 Total number of batches ... 77 Average number of points per batch ... 61 Average number of grid points per atom ... 947 Average number of shells per batch ... 12.13 (93.29%) Average number of basis functions per batch ... 16.03 (94.27%) Average number of large shells per batch ... 11.46 (94.50%) Average number of large basis fcns per batch ... 15.18 (94.72%) Maximum spatial batch extension ... 25.60, 20.01, 19.72 au Average spatial batch extension ... 6.26, 5.72, 5.65 au Time for grid setup = 0.018 sec -------------- SCF ITERATIONS -------------- ITER Energy Delta-E Max-DP RMS-DP [F,P] Damp *** Starting incremental Fock matrix formation *** *** Initiating the SOSCF procedure *** *** Re-Reading the Fockian *** *** Removing any level shift *** ITER Energy Delta-E Grad Rot Max-DP RMS-DP 0 -40.24100637 -40.2410063675 0.000040 0.000040 0.000079 0.000009 *** Restarting incremental Fock matrix formation *** 1 -40.24100638 -0.0000000096 0.000006 0.000007 0.000018 0.000003 2 -40.24100638 -0.0000000004 0.000006 0.000004 0.000010 0.000001 **** Energy Check signals convergence **** ***Rediagonalizing the Fockian in SOSCF/NRSCF*** ***************************************************** * SUCCESS * * SCF CONVERGED AFTER 3 CYCLES * ***************************************************** Setting up the final grid: General Integration Accuracy IntAcc ... 4.670 Radial Grid Type RadialGrid ... Gauss-Chebyshev Angular Grid (max. acc.) AngularGrid ... Lebedev-302 Angular grid pruning method GridPruning ... 3 (G Style) Weight generation scheme WeightScheme... Becke Basis function cutoff BFCut ... 1.0000e-11 Integration weight cutoff WCut ... 1.0000e-14 Grids for H and He will be reduced by one unit # of grid points (after initial pruning) ... 19788 ( 0.0 sec) # of grid points (after weights+screening) ... 19295 ( 0.0 sec) nearest neighbour list constructed ... 0.0 sec Grid point re-assignment to atoms done ... 0.0 sec Grid point division into batches done ... 0.1 sec Reduced shell lists constructed in 0.1 sec Total number of grid points ... 19295 Total number of batches ... 304 Average number of points per batch ... 63 Average number of grid points per atom ... 3859 Average number of shells per batch ... 11.13 (85.62%) Average number of basis functions per batch ... 14.74 (86.69%) Average number of large shells per batch ... 10.38 (93.28%) Average number of large basis fcns per batch ... 13.83 (93.82%) Maximum spatial batch extension ... 27.76, 24.37, 24.43 au Average spatial batch extension ... 3.47, 3.51, 3.55 au Final grid set up in 0.1 sec Final integration ... done ( 0.1 sec) Change in XC energy ... 0.000106803 Integrated number of electrons ... 9.999997363 Previous integrated no of electrons ... 10.000045316 ---------------- TOTAL SCF ENERGY ---------------- Total Energy : -40.24089957 Eh -1095.01055 eV Components: Nuclear Repulsion : 13.39313707 Eh 364.44579 eV Electronic Energy : -53.63403664 Eh -1459.45633 eV One Electron Energy: -79.45639452 Eh -2162.11841 eV Two Electron Energy: 25.82235787 Eh 702.66208 eV Virial components: Potential Energy : -80.08484899 Eh -2179.21953 eV Kinetic Energy : 39.84394942 Eh 1084.20898 eV Virial Ratio : 2.00996262 DFT components: N(Alpha) : 4.999998681603 electrons N(Beta) : 4.999998681603 electrons N(Total) : 9.999997363207 electrons E(X) : -4.876041928216 Eh E(C) : -0.303702337861 Eh E(XC) : -5.179744266077 Eh --------------- SCF CONVERGENCE --------------- Last Energy change ... -3.2048e-10 Tolerance : 1.0000e-08 Last MAX-Density change ... 1.8159e-06 Tolerance : 1.0000e-07 Last RMS-Density change ... 2.3590e-07 Tolerance : 5.0000e-09 Last Orbital Gradient ... 5.5325e-07 Tolerance : 1.0000e-05 Last Orbital Rotation ... 6.8826e-07 Tolerance : 1.0000e-05 **** THE GBW FILE WAS UPDATED (system.gbw) **** **** DENSITY FILE WAS UPDATED (system.scfp.tmp) **** **** ENERGY FILE WAS UPDATED (system.en.tmp) **** ---------------- ORBITAL ENERGIES ---------------- NO OCC E(Eh) E(eV) 0 2.0000 -10.147468 -276.1266 1 2.0000 -0.710063 -19.3218 2 2.0000 -0.399734 -10.8773 3 2.0000 -0.399572 -10.8729 4 2.0000 -0.399419 -10.8687 5 0.0000 0.160730 4.3737 6 0.0000 0.205804 5.6002 7 0.0000 0.206231 5.6118 8 0.0000 0.207131 5.6363 9 0.0000 0.727330 19.7917 10 0.0000 0.728185 19.8149 11 0.0000 0.730019 19.8648 12 0.0000 1.051311 28.6076 13 0.0000 1.085833 29.5470 14 0.0000 1.086190 29.5567 15 0.0000 1.086648 29.5692 16 0.0000 1.711872 46.5824 ------- TIMINGS ------- Total SCF time: 0 days 0 hours 0 min 0 sec Total time .... 0.677 sec Sum of individual times .... 0.674 sec ( 99.6%) Fock matrix formation .... 0.525 sec ( 77.5%) XC integration .... 0.142 sec ( 27.1% of F) Basis function eval. .... 0.084 sec ( 59.3% of XC) Density eval. .... 0.012 sec ( 8.5% of XC) XC-Functional eval. .... 0.031 sec ( 21.8% of XC) XC-Potential eval. .... 0.008 sec ( 5.4% of XC) Diagonalization .... 0.000 sec ( 0.0%) Density matrix formation .... 0.000 sec ( 0.0%) Population analysis .... 0.000 sec ( 0.0%) Initial guess .... 0.000 sec ( 0.0%) Orbital Transformation .... 0.000 sec ( 0.0%) Orbital Orthonormalization .... 0.000 sec ( 0.0%) DIIS solution .... 0.000 sec ( 0.0%) SOSCF solution .... 0.020 sec ( 3.0%) Grid generation .... 0.129 sec ( 19.0%) ------------------------- -------------------- FINAL SINGLE POINT ENERGY -40.240899574987 ------------------------- -------------------- *** OPTIMIZATION RUN DONE *** ****ORCA TERMINATED NORMALLY**** TOTAL RUN TIME: 0 days 0 hours 0 minutes 11 seconds 854 msec xtp-2021.2/src/tests/DataFiles/orca/polar_orca.log000066400000000000000000000173451412152066400217630ustar00rootroot00000000000000 ***************** * O R C A * ***************** --- An Ab Initio, DFT and Semiempirical electronic structure package --- Program Version 4.0.1 - RELEASE - INPUT FILE ================================================================================ NAME = system.inp | 1> * xyz 0 1 | 2> H 0.5288 0.1610 0.9359 | 3> C 0.0000 0.0000 0.0000 | 4> H 0.2051 0.8240 -0.6786 | 5> H 0.3345 -0.9314 -0.4496 | 6> H -1.0685 -0.0537 0.1921 | 7> * | 8> | 9> %elprop | 10> Polar 1 | 11> end | 12> | 13> ! DFT PBE0 DIRECT 3-21G | 14> | 15> | 16> ****END OF INPUT**** ================================================================================ **************************** * Single Point Calculation * **************************** --------------------------------- CARTESIAN COORDINATES (ANGSTROEM) --------------------------------- H 0.528800 0.161000 0.935900 C 0.000000 0.000000 0.000000 H 0.205100 0.824000 -0.678600 H 0.334500 -0.931400 -0.449600 H -1.068500 -0.053700 0.192100 ---------------------------- CARTESIAN COORDINATES (A.U.) ---------------------------- NO LB ZA FRAG MASS X Y Z 0 H 1.0000 0 1.008 0.999287 0.304246 1.768595 1 C 6.0000 0 12.011 0.000000 0.000000 0.000000 2 H 1.0000 0 1.008 0.387583 1.557134 -1.282368 3 H 1.0000 0 1.008 0.632113 -1.760091 -0.849621 4 H 1.0000 0 1.008 -2.019172 -0.101478 0.363016 -------------------------------- INTERNAL COORDINATES (ANGSTROEM) -------------------------------- H 0 0 0 0.000000000000 0.00000000 0.00000000 C 1 0 0 1.086949515847 0.00000000 0.00000000 H 2 1 0 1.086986646652 109.47881566 0.00000000 H 2 1 3 1.086984990697 109.47224096 120.00042779 H 2 1 3 1.086958301868 109.47426454 239.99847195 --------------------------- INTERNAL COORDINATES (A.U.) --------------------------- H 0 0 0 0.000000000000 0.00000000 0.00000000 C 1 0 0 2.054036906349 0.00000000 0.00000000 H 2 1 0 2.054107073402 109.47881566 0.00000000 H 2 1 3 2.054103944100 109.47224096 120.00042779 H 2 1 3 2.054053509523 109.47426454 239.99847195 -------------- SCF ITERATIONS -------------- ITER Energy Delta-E Max-DP RMS-DP [F,P] Damp *** Starting incremental Fock matrix formation *** 0 -40.1837355351 0.000000000000 0.05608035 0.00815748 0.1902884 0.7000 1 -40.2097076139 -0.025972078840 0.04863991 0.00639782 0.1011419 0.7000 ***Turning on DIIS*** 2 -40.2210178010 -0.011310187117 0.08720142 0.01139762 0.0412892 0.0000 3 -40.2363206548 -0.015302853728 0.02991000 0.00398732 0.0512358 0.0000 4 -40.2406497632 -0.004329108457 0.01093372 0.00128308 0.0110634 0.0000 *** Initiating the SOSCF procedure *** *** Shutting down DIIS *** *** Re-Reading the Fockian *** *** Removing any level shift *** ITER Energy Delta-E Grad Rot Max-DP RMS-DP 5 -40.24088185 -0.0002320879 0.000787 0.000787 0.002891 0.000379 *** Restarting incremental Fock matrix formation *** 6 -40.24089298 -0.0000111325 0.000283 0.000464 0.000987 0.000180 7 -40.24089331 -0.0000003233 0.000205 0.000123 0.000298 0.000040 **** Energy Check signals convergence **** ***Rediagonalizing the Fockian in SOSCF/NRSCF*** ***************************************************** * SUCCESS * * SCF CONVERGED AFTER 8 CYCLES * ***************************************************** ------------------------- -------------------- FINAL SINGLE POINT ENERGY -40.240792344368 ------------------------- -------------------- *************************************** * ORCA property calculations * *************************************** --------------------- Active property flags --------------------- Solving CP-SCF equations ... ------------------------------------------------------------------------------ ORCA CP-SCF CALCULATION ------------------------------------------------------------------------------ Input orbitals are from ... system.gbw Input Perturbation ... system.cpv.tmp Wavefunction output ... system.cpu.tmp Perturbation mode ... Real perturbation Solver ... POPLE Max. number of iterations ... 64 Convergence tolerance ... 1.000e-06 Integral handling ... Direct Number of perturbations ... 3 Number of operators ... 1 Orbital ranges used for CP-SCF: Operator 0: Orbitals 0... 4 to 5... 16 DFT calculation ... on Exchange functional (SCF) ... PBE Exchange functional (CP-SCF) ... PBE PBE kappa parameter XKappa (SCF) ... 0.804000 PBE kappa parameter XKappa (CP-SCF) ... 0.804000 PBE mue parameter XMuePBE (SCF) ... 0.219520 PBE mue parameter XMuePBE (CP-SCF) ... 0.219520 Correlation functional (SCF) ... PBE Correlation functional (CP-SCF) ... PBE PBE beta parameter CBetaPBE (SCF) ... 0.066725 PBE beta parameter CBetaPBE (CP-SCF) ... 0.066725 LDA part of GGA corr. LDAOpt (SCF) ... PW91-LDA LDA part of GGA corr. LDAOpt (CP-SCF) ... PW91-LDA Hybrid DFT ... on Exchange mixing (SCF) ... 0.250 Exchange mixing (CP-SCF) ... 0.250 GGA exch. scaling(SCF) ... 0.750 GGA exch. scaling (CP-SCF) ... 0.750 GGA corr. scaling (SCF) ... 1.000 GGA corr. scaling (CP-SCF) ... 1.000 Variables per vector in CP-SCF ... 60 Number of vectors sought ... 3 Recalculating density on grid ... done Calculating the xc-kernel ... done CP-SCF ITERATION 0: CP-SCF ITERATION 1: 0.000113908648 CP-SCF ITERATION 2: 0.000002896451 CP-SCF ITERATION 3: 0.000000121393 done Reading CP-SCF coefficients ... done Doing the polarizability tensor ... done Cleaning up ... done ------------------------- THE POLARIZABILITY TENSOR ------------------------- The raw cartesian tensor (atomic units): 11.40196 -0.00423 0.00097 -0.00423 11.42894 0.01163 0.00097 0.01163 11.41930 diagonalized tensor: 11.40078 11.41245 11.43696 0.95653 0.27871 0.08579 0.22185 -0.50454 -0.83440 -0.18927 0.81717 -0.54444 Isotropic polarizability : 11.41673 Timings for individual modules: Solution of CP-SCF eqns. ... 0.831 sec (= 0.014 min) 27.6 % ****ORCA TERMINATED NORMALLY**** TOTAL RUN TIME: 0 days 0 hours 0 minutes 3 seconds 406 msec xtp-2021.2/src/tests/DataFiles/oscillatorstrength_filter/000077500000000000000000000000001412152066400235005ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/oscillatorstrength_filter/3-21G.xml000066400000000000000000000027301412152066400247150ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/oscillatorstrength_filter/MOs_A.mm000066400000000000000000000073331412152066400247770ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 -0.996559 -0.0445146 4.60157e-17 8.15798e-17 -5.25872e-18 0.0472716 -2.24862e-16 -2.74184e-16 -2.81346e-17 -0.00106227 -0.00928842 -0.00106227 -0.00928842 -0.00106227 -0.00928842 -0.00106227 -0.00928842 -0.223082 0.88316 -7.1203e-15 2.30849e-14 4.8424e-15 0.235837 3.23655e-15 -1.53939e-15 -1.09423e-15 0.0237672 -0.0414346 0.0237672 -0.0414346 0.0237672 -0.0414346 0.0237672 -0.0414346 4.81443e-15 -1.94941e-14 0.143338 1.04169 0.0488925 -3.58018e-15 -0.0223487 -0.162416 -0.00762313 0.00345981 0.0619999 0.00238182 0.0426822 -0.00318563 -0.0570866 -0.002656 -0.0475955 2.21045e-15 -8.67388e-15 -0.980459 0.117804 0.364515 -1.68354e-15 0.152869 -0.0183675 -0.0568338 -0.00139675 -0.0250297 0.00205737 0.0368682 0.0034409 0.0616609 -0.00410152 -0.0734994 -6.16146e-17 -7.26679e-16 -0.355251 0.0951759 -0.9863 2.3989e-15 0.0553894 -0.0148395 0.15378 -0.00349474 -0.0626259 0.00402848 0.0721904 -0.00203628 -0.0364902 0.00150255 0.0269257 -3.16966e-16 1.16326e-14 0.41611 0.179467 0.0447336 -9.86879e-15 -0.350483 -0.151162 -0.0376785 -0.597906 0.00227746 0.262742 -0.0010008 0.514364 -0.00195924 -0.1792 0.000682583 5.46703e-18 -3.35886e-15 -0.10826 0.147031 0.417155 4.52519e-15 0.0911859 -0.123842 -0.351364 -0.425733 0.00162164 0.151145 -0.000575719 -0.353326 0.00134584 0.627913 -0.00239176 -1.09681e-15 2.37877e-14 -0.149964 0.39183 -0.177023 -1.6106e-14 0.126313 -0.330032 0.149104 -0.0605479 0.00023063 -0.671213 0.00255669 0.391148 -0.0014899 0.340613 -0.00129742 -0.0301914 0.866126 2.41546e-16 -1.02927e-14 5.76117e-15 -0.599523 -5.48468e-15 1.10084e-15 -4.94425e-15 -0.343823 -0.0301047 -0.343823 -0.0301047 -0.343823 -0.0301047 -0.343823 -0.0301047 6.45993e-16 3.2068e-15 0.12214 0.32699 -0.228081 -1.31237e-14 -0.541961 -1.45092 1.01204 0.162103 0.273177 0.317484 0.535026 -0.496623 -0.836913 0.0170366 0.0287103 1.05377e-16 3.80914e-15 -0.0512447 -0.223689 -0.348136 -8.63443e-15 0.227383 0.992556 1.54475 -0.45692 -0.770004 0.12884 0.217123 -0.0536813 -0.0904642 0.38176 0.643346 3.41154e-16 3.24563e-15 0.39537 -0.130009 0.0253377 -8.61196e-15 -1.75434 0.576875 -0.112429 0.21318 0.359253 -0.40386 -0.680588 -0.176018 -0.296627 0.366698 0.617962 -0.102052 -0.938329 1.1054e-15 1.0375e-15 -1.05286e-15 1.8333 -3.89443e-15 -3.82954e-15 8.50653e-15 -0.600309 0.0095153 -0.600309 0.0095153 -0.600309 0.0095153 -0.600309 0.0095153 -5.79826e-16 -6.4404e-15 -0.0996828 -0.0940179 0.079576 2.05275e-14 0.640788 0.604373 -0.511536 0.310843 -0.8783 0.201313 -0.568818 -0.744328 2.10313 0.232172 -0.656011 9.38593e-16 1.10811e-14 -0.0636092 0.126956 0.0703157 -3.9562e-14 0.408897 -0.816111 -0.452008 -0.36406 1.02867 -0.327527 0.925441 -0.01898 0.0536287 0.710567 -2.00774 -4.69346e-15 -5.5056e-14 -0.105478 0.0122904 -0.117608 1.89874e-13 0.67804 -0.0790061 0.756019 0.574148 -1.62228 -0.641099 1.81145 0.0665156 -0.187943 0.000435528 -0.0012306 -0.111923 -1.28767 5.10746e-15 1.41709e-15 5.31327e-15 4.24316 -3.17156e-14 -8.89474e-15 -3.3547e-14 0.0554949 -1.24406 0.0554949 -1.24406 0.0554949 -1.24406 0.0554949 -1.24406xtp-2021.2/src/tests/DataFiles/oscillatorstrength_filter/molecule.xyz000066400000000000000000000003621412152066400260620ustar00rootroot00000000000000 5 methane C .000000 .000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/oscillatorstrength_filter/spsi_ref.mm000066400000000000000000000045211412152066400256470ustar00rootroot00000000000000%%MatrixMarket matrix array real general 60 3 -0.00178316 0.00568291 0.05758 0.00379328 -0.00848959 -0.000395809 7.13955e-08 0.000420413 -0.00288487 0.0119767 -2.55565e-08 6.84051e-09 0.00420618 0.0036276 0.0465325 0.0051614 -0.010968 0.000951266 0.000419006 -0.00118124 -0.00345217 0.013156 -2.58268e-05 -1.80679e-06 -0.0150073 0.0180327 -0.0643994 -0.0123339 0.0122493 -0.00375172 0.00648758 0.00433063 0.0111166 -0.0160119 -0.000399315 -2.80525e-05 -0.0450479 0.0655838 0.0220978 -0.0119156 -0.0132479 -0.0118978 0.0199347 0.0131991 0.0159091 0.0123057 -0.00122682 -8.62007e-05 -0.0304688 0.0971056 0.983887 0.0170489 -0.0381557 -0.00177889 -2.23782e-07 -0.000182535 0.00125201 -0.00519809 4.03664e-08 -2.38233e-09 -0.0558332 0.0149417 -0.00320371 -0.00232255 -0.000618633 -0.00899117 3.47498e-08 0.011896 0.00320821 0.000355172 1.91684e-08 2.79592e-10 0.092451 0.0113951 -0.00398807 -0.0031325 -0.000896935 0.0239709 0.0201651 -0.0269275 0.00356488 9.58532e-05 -0.00124098 -8.71959e-05 0.0114186 -0.026287 0.0257628 0.0092297 -0.00246837 0.00294872 -0.0055755 -0.00332619 -0.00969272 0.00458659 0.000343129 2.41086e-05 -0.00034974 0.0115163 0.0583236 0.00490159 -0.0146227 -0.000282044 0.00139057 0.000163177 -0.00241207 0.0171503 -8.55716e-05 -6.0128e-06 -0.954049 0.255313 -0.0547431 -0.0104387 -0.00278036 -0.04041 2.40738e-07 -0.00516415 -0.00139237 -0.000154171 -6.04796e-08 2.31605e-09 0.0151767 0.0556358 -0.00502105 -0.00817518 -0.00376334 0.0023708 -1.08537e-08 -0.00320024 0.0115465 0.00289343 3.01647e-09 -1.35767e-09 -0.0239374 0.0471896 -0.00484251 -0.0112447 -0.00488789 -0.00630323 -0.00573095 0.00700955 0.0134361 0.00315613 0.000352706 2.47799e-05 0.0443012 0.0734351 0.0132084 -0.0148779 -0.0125735 0.0112899 -0.0191436 -0.0128321 0.0189659 0.0107104 0.00117813 8.2778e-05 -0.015063 -0.022358 0.0513097 0.0116429 -0.00863565 -0.00400272 0.00635067 0.00441453 -0.0110696 0.0119626 -0.00039083 -2.746e-05 0.259333 0.950672 -0.0857965 -0.036743 -0.0169143 0.0106552 1.03401e-07 0.00138942 -0.00501195 -0.00125602 -4.6768e-08 1.35922e-09xtp-2021.2/src/tests/DataFiles/overlap_filter/000077500000000000000000000000001412152066400212165ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/overlap_filter/3-21G.xml000066400000000000000000000027301412152066400224330ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/overlap_filter/MOs_A.mm000066400000000000000000000073331412152066400225150ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 -0.996559 -0.0445146 8.15798e-17 4.60157e-17 -5.25872e-18 0.0472716 -2.74184e-16 -2.24862e-16 -2.81346e-17 -0.00106227 -0.00928842 -0.00106227 -0.00928842 -0.00106227 -0.00928842 -0.00106227 -0.00928842 -0.223082 0.88316 2.30849e-14 -7.1203e-15 4.8424e-15 0.235837 -1.53939e-15 3.23655e-15 -1.09423e-15 0.0237672 -0.0414346 0.0237672 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1.35922e-09xtp-2021.2/src/tests/DataFiles/ppm/000077500000000000000000000000001412152066400167755ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/ppm/3-21G.xml000066400000000000000000000027271412152066400202200ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/ppm/molecule.xyz000066400000000000000000000003621412152066400213570ustar00rootroot00000000000000 5 methane C .000000 .000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/radial_euler_maclaurin_rule/000077500000000000000000000000001412152066400237135ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/radial_euler_maclaurin_rule/3-21G.xml000066400000000000000000000027271412152066400251360ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/radial_euler_maclaurin_rule/molecule.xyz000066400000000000000000000003621412152066400262750ustar00rootroot00000000000000 5 methane C .000000 .000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/regular_grid/000077500000000000000000000000001412152066400206475ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/regular_grid/3-21G.xml000066400000000000000000000027271412152066400220720ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/regular_grid/molecule.xyz000066400000000000000000000003621412152066400232310ustar00rootroot00000000000000 5 methane C .000000 .000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/rpa/000077500000000000000000000000001412152066400167635ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/rpa/3-21G.xml000066400000000000000000000027271412152066400202060ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/rpa/eigenvals.mm000066400000000000000000000023451412152066400212770ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 1 4.6820699999999999818545148855264415033161640167236328125000000000e-02 9.0780100000000002458122594362066593021154403686523437500000000000e-02 9.0780100000000002458122594362066593021154403686523437500000000000e-02 1.0456300000000000316457970939154620282351970672607421875000000000e-01 5.9249099999999998988897687013377435505390167236328125000000000000e-01 6.6335500000000002795985665215994231402873992919921875000000000000e-01 6.6335500000000002795985665215994231402873992919921875000000000000e-01 7.6837299999999997268673723738174885511398315429687500000000000000e-01 1.6929199999999999803890204930212348699569702148437500000000000000e+00 1.9772400000000001085709300241433084011077880859375000000000000000e+00 1.9772400000000001085709300241433084011077880859375000000000000000e+00 2.5087700000000001665512172621674835681915283203125000000000000000e+00 2.9873199999999999754152213427005335688591003417968750000000000000e+00 3.4418000000000001925570813909871503710746765136718750000000000000e+00 3.4418000000000001925570813909871503710746765136718750000000000000e+00 4.8108399999999997831423570460174232721328735351562500000000000000e+00 1.7183800000000001517719283583573997020721435546875000000000000000e+01 xtp-2021.2/src/tests/DataFiles/rpa/eigenvectors.mm000066400000000000000000000073331412152066400220210ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 0.0185815 0.166534 -0.0010572 0.0010572 0.0010572 -0.823783 0.0333718 -0.0333718 -0.0333718 -0.00177478 0.294363 -0.00177478 0.294363 -0.00177478 0.294363 0.00741062 0.173046 2.9133e-17 2.80578e-16 -0.0404824 -0.0210402 -0.0194422 -9.8891e-16 0.436683 0.22696 0.209723 0.0553645 -0.686239 -0.0265895 0.329576 -0.028775 0.356664 -3.87173e-16 7.91486e-15 8.49354e-17 7.85515e-16 0.000922593 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1.06135xtp-2021.2/src/tests/DataFiles/rpa/molecule.xyz000066400000000000000000000003621412152066400213450ustar00rootroot00000000000000 5 methane C .000000 .000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/rpa/r_complex_ref.mm000066400000000000000000000073331412152066400221500ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 1.00064 -0.000754658 0.000880963 -0.000880963 -0.000880963 -0.00407457 0.00239642 -0.00239642 -0.00239642 -0.000534854 -0.0052895 -0.000534853 -0.0052895 -0.000534852 -0.00528949 -0.000403477 -0.0032687 -0.000754658 1.00264 -0.00167103 0.00167104 0.00167104 0.00896447 -0.00427778 0.0042778 0.00427779 0.000590938 0.00792884 0.000590944 0.00792885 0.000590946 0.00792885 0.000684407 0.00480769 0.000880963 -0.00167103 1.00386 -0.00195002 -0.00195002 -0.00950016 0.0100509 -0.00553701 -0.005537 -0.00119875 -0.0132386 -0.00185506 -0.014572 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0.0100509 0.0335557 -0.0157857 0.0157857 1.04865 0.0132131 0.0704422 -0.00173804 0.0339069 0.0132131 0.0704422 0.00426599 0.0317992 -0.000534854 0.000590938 -0.00119875 0.00185506 0.00185506 0.0104803 0.00173805 0.0132131 0.0132131 1.01216 0.0403494 0.000558755 0.0158432 0.000558754 0.0158432 0.00143541 0.0125668 -0.0052895 0.00792884 -0.0132386 0.014572 0.014572 0.0823313 -0.0339069 0.0704422 0.0704422 0.0403494 1.19241 0.0158432 0.13507 0.0158432 0.13507 0.00930365 0.0841421 -0.000534853 0.000590944 -0.00185506 0.00185506 0.00119876 0.0104803 -0.0132131 0.0132131 -0.00173804 0.000558755 0.0158432 1.01216 0.0403494 0.000558761 0.0158432 0.00143541 0.0125668 -0.0052895 0.00792885 -0.014572 0.014572 0.0132386 0.0823314 -0.0704422 0.0704422 0.0339069 0.0158432 0.13507 0.0403494 1.19241 0.0158432 0.135071 0.00930366 0.0841421 -0.000534852 0.000590946 -0.00185506 0.00119876 0.00185506 0.0104803 -0.0132131 -0.00173805 0.0132131 0.000558754 0.0158432 0.000558761 0.0158432 1.01216 0.0403494 0.00143541 0.0125668 -0.00528949 0.00792885 -0.014572 0.0132386 0.014572 0.0823314 -0.0704422 0.0339069 0.0704422 0.0158432 0.13507 0.0158432 0.135071 0.0403494 1.19241 0.00930366 0.0841421 -0.000403477 0.000684407 -0.00137017 0.00137017 0.00137017 0.0047238 -0.00426599 0.00426599 0.00426599 0.00143541 0.00930365 0.00143541 0.00930366 0.00143541 0.00930366 1.00155 0.00778597 -0.0032687 0.00480769 -0.00954205 0.00954207 0.00954206 0.0463067 -0.0317992 0.0317992 0.0317992 0.0125668 0.0841421 0.0125668 0.0841421 0.0125668 0.0841421 0.00778597 1.06059xtp-2021.2/src/tests/DataFiles/rpa/r_ref.mm000066400000000000000000000073331412152066400204210ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 1.00066 -0.000787996 0.000889226 -0.000889226 -0.000889226 -0.00421691 0.00233609 -0.00233609 -0.00233609 -0.000506622 -0.00520579 -0.000506622 -0.00520579 -0.000506622 -0.00520579 -0.000375643 -0.00320588 -0.000787996 1.00287 -0.00179102 0.00179102 0.00179102 0.010148 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1.06924xtp-2021.2/src/tests/DataFiles/segmentmapper/000077500000000000000000000000001412152066400210505ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/segmentmapper/ch4.xml000066400000000000000000000023031412152066400222460ustar00rootroot00000000000000 Methane Methane Methane molecule.xyz 0 ALAB_1 1:CB:0 1:HB1:1 1:HB2:2 0:C 1:H 2:H 0:C 1:H 2:H 12 1 1 0 1 2 ALAB_2 1:HB3:3 3:H 3:H 1 3 ALAB_3 1:HB4:4 4:H 4:H 1 4 xtp-2021.2/src/tests/DataFiles/segmentmapper/ch4_2.xml000066400000000000000000000023031412152066400224670ustar00rootroot00000000000000 Methane Methane Methane molecule.xyz 1 ALAB_1 1:CB:0 1:HB1:1 1:HB2:2 0:C 1:H 2:H 0:C 1:H 2:H 12 1 1 0 1 2 ALAB_2 1:HB3:3 3:H 3:H 1 3 ALAB_3 1:HB4:4 4:H 4:H 1 4 xtp-2021.2/src/tests/DataFiles/segmentmapper/ch4_3.xml000066400000000000000000000020401412152066400224660ustar00rootroot00000000000000 Methane Methane Methane molecule.xyz 0 ALAB_1 1:CB:0 1:HB1:1 1:HB2:2 0:C 1:H 2:H 0:C 1:H 2:H 0 1 2 ALAB_2 1:HB3:3 3:H 3:H 3 ALAB_3 1:HB4:4 4:H 4:H 4 xtp-2021.2/src/tests/DataFiles/segmentmapper/molecule.xyz000066400000000000000000000003621412152066400234320ustar00rootroot00000000000000 5 methane C .000000 .000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/segmentmapper/molecule2.xyz000066400000000000000000000003621412152066400235140ustar00rootroot00000000000000 5 methane C .000000 .000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/segmentmapper/molecule3.xyz000066400000000000000000000003621412152066400235150ustar00rootroot00000000000000 5 methane C .100000 .000000 .000000 H .729118 .629118 .629118 H -.529118 -.629118 .629118 H .729118 -.629118 -.629118 H -.529118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/settings/000077500000000000000000000000001412152066400200415ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/settings/defaults.xml000066400000000000000000000004731412152066400223760ustar00rootroot00000000000000 xtpdft 0 1 ubecppol aux-ubecppol false pbe /tmp/xtp_qmpackage false GUESS PMODEL xtp-2021.2/src/tests/DataFiles/settings/defaults2.xml000066400000000000000000000004731412152066400224600ustar00rootroot00000000000000 xtpdft 0 1 ubecppol aux-ubecppol false pbe /tmp/xtp_qmpackage false GUESS PMODEL xtp-2021.2/src/tests/DataFiles/settings/user_input.xml000066400000000000000000000001751412152066400227630ustar00rootroot00000000000000 orca /opt/orca/orca B3LYP ecp xtp-2021.2/src/tests/DataFiles/sigma_cda/000077500000000000000000000000001412152066400201105ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/sigma_cda/3-21G.xml000066400000000000000000000027271412152066400213330ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/sigma_cda/MOs.mm000066400000000000000000000073331412152066400211470ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 0.0185815 0.166534 -0.0010572 0.0010572 0.0010572 -0.823783 0.0333718 -0.0333718 -0.0333718 -0.00177478 0.294363 -0.00177478 0.294363 -0.00177478 0.294363 0.00741062 0.173046 2.9133e-17 2.80578e-16 -0.0404824 -0.0210402 -0.0194422 -9.8891e-16 0.436683 0.22696 0.209723 0.0553645 -0.686239 -0.0265895 0.329576 -0.028775 0.356664 -3.87173e-16 7.91486e-15 8.49354e-17 7.85515e-16 0.000922593 -0.0345975 0.0355201 -3.34692e-15 -0.009952 0.373203 -0.383155 -0.00126176 0.0156394 0.0485779 -0.60212 -0.0473162 0.586481 -4.31863e-16 8.39419e-15 -0.00312916 -0.0299557 -0.035778 0.035778 0.035778 0.103497 0.337332 -0.337332 -0.337332 -0.0164247 0.204055 -0.0164247 0.204055 -0.0164247 0.204055 0.0468488 -0.717804 0.0420075 0.409156 -0.0611836 0.0611836 0.0611836 -0.277613 0.251625 -0.251625 -0.251625 0.23154 -0.360136 0.23154 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0.0399869 -0.180971 -0.503583 -0.14614 0.646413 0.18759 -0.14283 -0.0414494 1.2743e-16 -1.84233e-16 -0.0346485 -0.437568 -0.278374 0.278374 0.278374 -0.259891 0.0631275 -0.0631275 -0.0631275 -0.223493 -0.174986 -0.223493 -0.174986 -0.223493 -0.174986 0.503528 0.0105378 -0.0248392 -0.299751 0.409082 -0.409082 -0.409082 -0.284396 0.0704844 -0.0704844 -0.0704844 -0.211802 -0.185046 -0.211802 -0.185046 -0.211802 -0.185046 -0.228856 -0.148396 -3.32286e-22 -2.77682e-17 -0.0548848 -0.64367 0.588785 -1.74149e-16 -0.0197737 -0.231899 0.212125 -0.020461 -0.0109958 -0.219498 -0.117959 0.239959 0.128955 -7.97629e-17 -1.63792e-16 -4.62643e-17 -6.06812e-16 0.711558 0.308248 0.403311 -6.65818e-16 0.256357 0.111054 0.145303 0.265268 0.142556 -0.150354 -0.0808008 -0.114914 -0.0617554 -2.53026e-16 -4.6499e-16 0.0144472 0.176594 0.261525 -0.261525 -0.261525 0.208987 0.189161 -0.189161 -0.189161 0.0023362 0.0661743 0.0023362 0.0661743 0.0023362 0.0661743 0.689669 0.351571 0.996183 -0.0866677 0.000315534 -0.000315534 -0.000315534 0.00782842 -0.000129868 0.000129868 0.000129868 -0.00241145 0.0022999 -0.00241145 0.0022999 -0.00241145 0.0022999 -0.00301027 0.00210309xtp-2021.2/src/tests/DataFiles/sigma_cda/c_ref.mm000066400000000000000000000073331412152066400215270ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 0.00049534 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0.000255251 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0.000255243 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1.97228e-05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0.00774241 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0.0325156 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0.0325155 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.576967 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0.0509694 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0.16168 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0.161679 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0.342346 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0.750003 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0.653853 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0.653853 0 0 0 0 0 0 0 0 0 0 0 0 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7.12005e-19 -0.00223485 4.08601e-18 0.000349208 1.0663e-18 -0.000322745 8.04714e-19 4.79663e-06 5.36853e-19 -0.00094624 -5.67131e-21 0.000579775 4.88544e-22 -4.08361e-06 4.69307e-20 4.72525e-06 -1.74341e-20 -1.67686e-06 -0.00494364 4.08601e-18 -0.0100334 -3.096e-18 -0.000376362 -9.81236e-19 8.6304e-05 3.50004e-19 0.000187168 2.23095e-20 0.000240009 -6.80963e-21 -0.00011235 1.08251e-20 -2.29569e-06 -1.44454e-20 1.24552e-06 2.24423e-21 7.58518e-19 0.000349208 -3.096e-18 -0.0104098 -3.89176e-19 0.000271542 -2.52176e-19 0.000167767 -5.59877e-19 -7.20841e-06 -4.73165e-20 3.61203e-06 2.07196e-20 0.00042977 5.98764e-20 -0.000941901 -5.43212e-20 0.00224633 7.22143e-05 1.0663e-18 -0.000376362 -3.89176e-19 -0.00374038 -2.54517e-18 -0.00912856 -3.15173e-18 0.00602099 -1.38241e-19 -5.09719e-06 4.28656e-20 2.00519e-06 -6.16946e-20 -0.000937819 1.14674e-19 0.00142252 -2.48367e-19 -1.2752e-18 -0.000322745 -9.81236e-19 0.000271542 -2.54517e-18 0.00362349 5.84618e-19 -0.0115724 2.40698e-18 8.73493e-06 6.75485e-20 -3.91612e-06 -2.87467e-20 -0.000874484 -1.20005e-19 0.00163956 1.07251e-19 -0.00339694 -0.000193665 8.04714e-19 8.6304e-05 -2.52176e-19 -0.00912856 5.84618e-19 0.0038285 2.87503e-18 -0.00597263 8.30867e-20 2.63882e-06 -2.35837e-20 -9.08221e-07 4.88823e-20 0.00128329 -9.90069e-20 -0.00149684 2.35908e-19 -6.9471e-19 4.79663e-06 3.50004e-19 0.000167767 -3.15173e-18 -0.0115724 2.87503e-18 -0.00392453 1.0043e-18 -3.21703e-06 -5.58892e-20 3.01259e-07 2.13648e-20 0.00186155 2.93975e-19 -0.00294678 -2.6332e-19 0.00489088 -6.65368e-07 5.36853e-19 0.000187168 -5.59877e-19 0.00602099 2.40698e-18 -0.00597263 1.0043e-18 0.00117692xtp-2021.2/src/tests/DataFiles/threecenter_dft/molecule.xyz000066400000000000000000000003621412152066400237300ustar00rootroot00000000000000 5 methane C .000000 .000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/threecenter_gwbse/000077500000000000000000000000001412152066400217005ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/threecenter_gwbse/3-21G.xml000066400000000000000000000027271412152066400231230ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/threecenter_gwbse/MOs.mm000066400000000000000000000073331412152066400227370ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 -0.00761992 0.233602 -4.51653e-14 -1.63678e-13 -9.0903e-14 0.480866 -1.64105e-12 -1.64421e-12 -1.63849e-12 0.129798 0.0541331 0.129798 0.0541331 0.129798 0.0541331 0.129798 0.0541331 -4.69664e-13 -3.18103e-12 -0.216509 -0.22745 -0.21966 1.8992e-11 -0.173397 -0.182159 -0.17592 -0.274485 -0.255228 0.0863299 0.0802732 0.0927742 0.0862654 0.0953806 0.088689 8.35009e-15 4.05093e-14 0.296975 -0.054851 -0.235919 -2.56795e-13 0.23784 -0.0439288 -0.188941 0.00256652 0.00238646 -0.0479412 -0.0445777 -0.197727 -0.183855 0.243102 0.226046 -1.15214e-14 -4.70943e-14 -0.108582 0.30351 -0.207249 4.14571e-13 -0.0869607 0.243073 -0.165981 -0.00509635 -0.0047388 0.25617 0.238198 -0.166347 -0.154677 -0.0847266 -0.0787824 -0.0156169 0.1578 3.79159e-11 3.78688e-11 3.75979e-11 2.2709 1.80537e-10 1.80753e-10 1.79403e-10 -0.0118465 -0.88576 -0.0118465 -0.88576 -0.0118465 -0.88576 -0.0118465 -0.88576 -2.23157e-12 4.75897e-11 -0.199301 -0.201627 -0.199736 4.78615e-10 -0.755957 -0.764779 -0.757606 0.141392 1.68364 -0.0464689 -0.553335 -0.0473592 -0.563936 -0.0475639 -0.566373 1.52916e-14 -1.87447e-13 0.283114 -0.158318 -0.122681 -2.39153e-12 1.07386 -0.600505 -0.465334 -0.000497905 -0.00592888 0.0750316 0.893449 0.0582544 0.693672 -0.132788 -1.58119 2.10997e-15 -1.02418e-14 -0.0198557 -0.233561 0.255585 -2.53852e-13 -0.0753135 -0.885907 0.969444 -0.000510338 -0.00607692 0.110468 1.31541 -0.119815 -1.42672 0.00985812 0.117387 8.21478e-15 6.44484e-14 0.584622 -0.0509347 -0.534902 -2.15605e-13 -0.989408 0.0862014 0.905262 -0.000526798 -9.5047e-05 -0.0436647 -0.00787816 -0.463559 -0.0836372 0.507751 0.0916104 3.18517e-15 -2.6602e-14 0.275311 -0.650424 0.362837 -2.80359e-13 -0.465933 1.10077 -0.61406 -0.00532572 -0.000960887 -0.558989 -0.100855 0.320126 0.0577585 0.244188 0.0440574 2.89043e-13 6.5906e-12 0.461431 0.452606 0.461224 7.00137e-12 -0.78092 -0.765985 -0.78057 0.596595 0.10764 -0.203909 -0.0367902 -0.196433 -0.0354411 -0.196253 -0.0354087 -0.00949189 -0.281033 -5.93732e-11 -5.88565e-11 -5.91028e-11 0.145171 6.72256e-11 6.65828e-11 6.69453e-11 0.65313 -0.362701 0.65313 -0.362701 0.65313 -0.362701 0.65313 -0.362701 1.95787e-12 -6.67755e-12 0.453057 0.453936 0.453245 -1.96136e-11 -0.578145 -0.579266 -0.578385 -0.964582 1.53456 0.320785 -0.510338 0.321765 -0.511897 0.322032 -0.512321 1.22168e-14 2.70339e-14 0.619523 -0.165715 -0.453298 -2.24876e-13 -0.790571 0.211468 0.578453 -0.000361559 0.000575205 0.235387 -0.374479 0.643254 -1.02335 -0.87828 1.39726 -2.63092e-15 -9.78783e-14 0.166374 -0.619056 0.453695 -2.57294e-14 -0.212309 0.789976 -0.578959 -0.000717866 0.00114206 0.878697 -1.39792 -0.642737 1.02253 -0.235242 0.374248 -0.22227 -1.94373 7.13235e-12 7.0149e-12 7.01644e-12 4.04176 -1.42443e-11 -1.41532e-11 -1.40917e-11 -0.195084 -0.793844 -0.195084 -0.793844 -0.195084 -0.793844 -0.195084 -0.793844 1.00844 -0.36629 2.56811e-14 2.395e-14 2.60987e-14 0.193617 -1.31306e-13 -1.29659e-13 -1.31002e-13 0.0246232 -0.035336 0.0246232 -0.035336 0.0246232 -0.035336 0.0246232 -0.035336xtp-2021.2/src/tests/DataFiles/threecenter_gwbse/molecule.xyz000066400000000000000000000003621412152066400242620ustar00rootroot00000000000000 5 methane C .000000 .000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/threecenter_gwbse/ref0b.mm000066400000000000000000000034251412152066400232350ustar00rootroot00000000000000%%MatrixMarket matrix array real general 8 17 0.052454 -1.11553e-08 -3.58044e-09 -4.33271e-09 0.0472538 -9.2852e-08 4.98182e-08 6.72656e-09 0.269452 -6.80615e-08 -1.08028e-08 -2.2018e-08 0.192218 -5.00295e-07 2.70937e-07 5.69858e-08 -4.30322e-13 -0.103755 0.142316 -0.0520346 3.2622e-11 -0.0775704 0.110191 -0.0077281 -4.97324e-13 -0.108999 -0.0262857 0.145448 3.26135e-11 -0.0784758 -0.0616192 -0.0909046 -4.54969e-13 -0.105265 -0.113057 -0.0993178 3.23859e-11 -0.0777397 -0.047749 0.0994766 0.277359 -8.93853e-08 -1.15391e-08 -2.7857e-08 0.109122 -6.41185e-07 3.47904e-07 7.86634e-08 -6.67244e-13 -0.104963 0.143972 -0.0526401 4.16313e-11 -0.0478541 0.0679777 -0.00476756 -7.02438e-13 -0.110267 -0.0265915 0.14714 4.16596e-11 -0.0484126 -0.0380135 -0.0560798 -6.79568e-13 -0.10649 -0.114372 -0.100473 4.13551e-11 -0.0479585 -0.0294568 0.0613679 0.0901044 -0.131764 0.00123206 -0.00244649 -0.00314721 0.0558838 -0.000196844 -0.000201689 0.289025 -0.115786 0.00108266 -0.00214985 0.0108472 0.0422875 -0.000148696 -0.000152546 0.0901044 0.0414419 -0.0230138 0.122972 -0.00314721 -0.0183667 0.0296559 0.0436619 0.289025 0.0364164 -0.020223 0.10806 0.0108472 -0.0138989 0.0224415 0.0330398 0.0901044 0.0445355 -0.0949172 -0.0798536 -0.00314721 -0.0187185 0.0230249 -0.0473564 0.289025 0.0391348 -0.083407 -0.0701702 0.0108472 -0.0141652 0.0174236 -0.0358353 0.0901044 0.0457866 0.116699 -0.0406723 -0.00314721 -0.0187994 -0.0524835 0.00389636 0.289025 0.0402342 0.102547 -0.0357401 0.0108472 -0.0142264 -0.0397148 0.00294851xtp-2021.2/src/tests/DataFiles/threecenter_gwbse/ref2b.mm000066400000000000000000000034251412152066400232370ustar00rootroot00000000000000%%MatrixMarket matrix array real general 8 17 -3.58044e-09 9.54021e-09 0.0436978 1.16479e-09 -3.83792e-09 -0.000267293 0.0323217 -0.0141772 -1.08028e-08 -2.23538e-08 0.201784 -1.1638e-08 -1.12535e-08 -0.00109263 0.132119 -0.057951 0.142316 0.0101068 0.00398082 -0.00926513 0.0960538 -0.0064945 -0.00489126 -0.00455883 -0.0262857 -0.00217721 -0.0215531 -0.00552672 -0.017741 0.00136471 0.0114547 -0.00894259 -0.113057 -0.00856299 -0.00501107 0.0147801 -0.0763057 0.00543171 0.00694045 0.00757611 -1.15391e-08 -9.35387e-08 0.232683 -2.46699e-08 -8.3889e-09 -0.000943013 0.114024 -0.0500143 0.143972 0.015845 0.00624092 -0.0145254 -0.0104997 -0.0397218 -0.0299176 -0.0278838 -0.0265915 -0.00341331 -0.0337897 -0.00866447 0.00193927 0.00834688 0.0700617 -0.0546965 -0.114372 -0.0134246 -0.00785608 0.0231714 0.00834096 0.0332215 0.0424512 0.0463387 0.00123206 -0.00253892 0.00994497 -4.71412e-05 -0.000237732 0.000750763 0.00337714 -0.00148532 0.00108266 -0.00159428 0.228298 -2.96221e-05 -0.000691164 0.000994679 0.0578195 -0.0253688 -0.0230138 -0.0149157 0.0182043 -0.04426 0.00444057 0.00475257 -0.00433905 -0.012847 -0.020223 -0.00936558 0.233484 -0.0277906 0.01291 0.00856368 0.0432251 -0.0468582 -0.0949172 -0.0661098 0.150819 0.118537 0.0183145 0.0200663 -0.0213373 0.0493546 -0.083407 -0.04151 0.316752 0.0744287 0.0532455 0.0375282 0.0110747 0.0707899 0.116699 0.0835643 0.222906 -0.0742301 -0.0225174 -0.0248402 -0.0658904 0.00366008 0.102547 0.0524694 0.362015 -0.0466087 -0.0654643 -0.0474083 -0.0731935 -0.0156367xtp-2021.2/src/tests/DataFiles/threecenter_gwbse/ref4b.mm000066400000000000000000000034251412152066400232410ustar00rootroot00000000000000%%MatrixMarket matrix array real general 8 17 0.0472538 -9.69614e-09 -3.83792e-09 -4.05402e-09 0.0455444 -8.50072e-08 4.54389e-08 4.78832e-09 0.192218 -4.99998e-08 -1.12535e-08 -1.74883e-08 0.117954 -3.87116e-07 2.08758e-07 3.70108e-08 3.26223e-11 -0.0700279 0.0960538 -0.0351198 4.45486e-11 -0.0454214 0.0645223 -0.00452519 3.26136e-11 -0.0735666 -0.017741 0.0981674 4.45683e-11 -0.0459515 -0.0360811 -0.0532291 3.23858e-11 -0.071047 -0.0763057 -0.0670328 4.42399e-11 -0.0455205 -0.0279594 0.0582485 0.109122 -2.88054e-08 -8.3889e-09 -1.08265e-08 0.0478717 -2.34191e-07 1.25806e-07 1.85207e-08 4.16304e-11 0.0076548 -0.0104997 0.00383896 -1.61317e-11 -0.0222763 0.0316445 -0.00221932 4.16601e-11 0.0080416 0.00193927 -0.0107307 -1.61634e-11 -0.0225363 -0.0176956 -0.0261058 4.13556e-11 0.00776616 0.00834096 0.00732739 -1.60407e-11 -0.0223249 -0.0137123 0.0285675 -0.00314721 0.0254243 -0.000237732 0.000472061 0.0387858 -0.0485099 0.000170843 0.000175092 0.0108472 0.0739155 -0.000691164 0.00137243 0.261043 -0.161219 0.000567771 0.000581897 -0.00314721 -0.00799633 0.00444057 -0.0237278 0.0387858 0.015943 -0.0257425 -0.0379003 0.0108472 -0.0232476 0.01291 -0.0689835 0.261043 0.0529854 -0.0855535 -0.125959 -0.00314721 -0.00859324 0.0183145 0.0154079 0.0387858 0.0162484 -0.0199865 0.0411074 0.0108472 -0.024983 0.0532455 0.0447953 0.261043 0.0540005 -0.0664236 0.136617 -0.00314721 -0.00883465 -0.0225174 0.00784782 0.0387858 0.0163186 0.0455581 -0.00338222 0.0108472 -0.0256848 -0.0654643 0.0228158 0.261043 0.0542338 0.151409 -0.0112405xtp-2021.2/src/tests/DataFiles/vxc_grid/000077500000000000000000000000001412152066400200065ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/vxc_grid/3-21G.xml000066400000000000000000000027271412152066400212310ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/vxc_grid/molecule.xyz000066400000000000000000000003621412152066400223700ustar00rootroot00000000000000 5 methane C .000000 .000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/vxc_potential/000077500000000000000000000000001412152066400210605ustar00rootroot00000000000000xtp-2021.2/src/tests/DataFiles/vxc_potential/3-21G.xml000066400000000000000000000027271412152066400223030ustar00rootroot00000000000000 xtp-2021.2/src/tests/DataFiles/vxc_potential/dmat.mm000066400000000000000000000073331412152066400223460ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 0.00157507 0.0337454 -5.93152e-16 4.48905e-16 7.87133e-17 0.030876 -1.49094e-16 2.51254e-16 5.77899e-17 0.00415998 -0.00445632 0.00415998 -0.00445632 0.00415998 -0.00445632 0.00415998 -0.00445632 0.0337454 0.722983 -4.44783e-15 2.66427e-15 3.45846e-16 0.661507 -2.02475e-15 4.39854e-15 1.04832e-15 0.0891262 -0.095475 0.0891262 -0.095475 0.0891262 -0.095475 0.0891262 -0.095475 -5.93152e-16 -4.44783e-15 1.52199 2.88658e-15 -2.31759e-15 9.21105e-15 0.215492 -2.22045e-15 1.6263e-15 0.141933 -0.0402359 -0.141933 0.0402359 -0.141933 0.0402359 0.141933 -0.0402359 4.48905e-16 2.66427e-15 2.88658e-15 1.52199 2.09034e-15 -7.94212e-15 2.8727e-15 0.215492 -1.40513e-15 0.141933 -0.0402359 0.141933 -0.0402359 -0.141933 0.0402359 -0.141933 0.0402359 7.87133e-17 3.45846e-16 -2.31759e-15 2.09034e-15 1.52199 2.98902e-15 4.79738e-15 -2.04958e-15 0.215492 0.141933 -0.0402359 -0.141933 0.0402359 0.141933 -0.0402359 -0.141933 0.0402359 0.030876 0.661507 9.21105e-15 -7.94212e-15 2.98902e-15 0.605259 2.7779e-17 2.55488e-15 1.33759e-15 0.0815477 -0.0873567 0.0815477 -0.0873567 0.0815477 -0.0873567 0.0815477 -0.0873567 -1.49094e-16 -2.02475e-15 0.215492 2.8727e-15 4.79738e-15 2.7779e-17 0.0305108 3.29597e-17 9.55941e-16 0.0200958 -0.00569686 -0.0200958 0.00569686 -0.0200958 0.00569686 0.0200958 -0.00569686 2.51254e-16 4.39854e-15 -2.22045e-15 0.215492 -2.04958e-15 2.55488e-15 3.29597e-17 0.0305108 -5.29036e-16 0.0200958 -0.00569686 0.0200958 -0.00569686 -0.0200958 0.00569686 -0.0200958 0.00569686 5.77899e-17 1.04832e-15 1.6263e-15 -1.40513e-15 0.215492 1.33759e-15 9.55941e-16 -5.29036e-16 0.0305108 0.0200958 -0.00569686 -0.0200958 0.00569686 0.0200958 -0.00569686 -0.0200958 0.00569686 0.00415998 0.0891262 0.141933 0.141933 0.141933 0.0815477 0.0200958 0.0200958 0.0200958 0.0506951 -0.0230264 -0.00224894 -0.00801753 -0.00224894 -0.00801753 -0.00224894 -0.00801753 -0.00445632 -0.095475 -0.0402359 -0.0402359 -0.0402359 -0.0873567 -0.00569686 -0.00569686 -0.00569686 -0.0230264 0.0157992 -0.00801753 0.0115445 -0.00801753 0.0115445 -0.00801753 0.0115445 0.00415998 0.0891262 -0.141933 0.141933 -0.141933 0.0815477 -0.0200958 0.0200958 -0.0200958 -0.00224894 -0.00801753 0.0506951 -0.0230264 -0.00224894 -0.00801753 -0.00224894 -0.00801753 -0.00445632 -0.095475 0.0402359 -0.0402359 0.0402359 -0.0873567 0.00569686 -0.00569686 0.00569686 -0.00801753 0.0115445 -0.0230264 0.0157992 -0.00801753 0.0115445 -0.00801753 0.0115445 0.00415998 0.0891262 -0.141933 -0.141933 0.141933 0.0815477 -0.0200958 -0.0200958 0.0200958 -0.00224894 -0.00801753 -0.00224894 -0.00801753 0.0506951 -0.0230264 -0.00224894 -0.00801753 -0.00445632 -0.095475 0.0402359 0.0402359 -0.0402359 -0.0873567 0.00569686 0.00569686 -0.00569686 -0.00801753 0.0115445 -0.00801753 0.0115445 -0.0230264 0.0157992 -0.00801753 0.0115445 0.00415998 0.0891262 0.141933 -0.141933 -0.141933 0.0815477 0.0200958 -0.0200958 -0.0200958 -0.00224894 -0.00801753 -0.00224894 -0.00801753 -0.00224894 -0.00801753 0.0506951 -0.0230264 -0.00445632 -0.095475 -0.0402359 0.0402359 0.0402359 -0.0873567 -0.00569686 0.00569686 0.00569686 -0.00801753 0.0115445 -0.00801753 0.0115445 -0.00801753 0.0115445 -0.0230264 0.0157992xtp-2021.2/src/tests/DataFiles/vxc_potential/molecule.xyz000066400000000000000000000003621412152066400234420ustar00rootroot00000000000000 5 methane C .000000 .000000 .000000 H .629118 .629118 .629118 H -.629118 -.629118 .629118 H .629118 -.629118 -.629118 H -.629118 .629118 -.629118 xtp-2021.2/src/tests/DataFiles/vxc_potential/vxc_ref.mm000066400000000000000000000073331412152066400230550ustar00rootroot00000000000000%%MatrixMarket matrix array real general 17 17 -0.604846 -0.193724 1.24779e-12 1.4208e-12 1.33915e-12 -0.158347 2.74891e-12 2.77358e-12 2.76197e-12 -0.0171771 -0.0712393 -0.0171771 -0.0712393 -0.0171771 -0.0712393 -0.0171771 -0.0712393 -0.193724 -0.830219 4.0751e-16 3.50498e-13 1.87309e-13 -0.566479 3.9268e-14 1.38973e-13 9.4247e-14 -0.131012 -0.287372 -0.131012 -0.287372 -0.131012 -0.287372 -0.131012 -0.287372 1.24779e-12 4.0751e-16 -0.814676 5.25758e-14 1.44859e-13 5.42212e-14 -0.328319 6.87022e-14 9.0481e-14 -0.10473 -0.0814687 0.10473 0.0814687 0.10473 0.0814687 -0.10473 -0.0814687 1.4208e-12 3.50498e-13 5.25758e-14 -0.814676 6.17368e-14 2.75977e-13 6.87396e-14 -0.328319 7.04428e-14 -0.10473 -0.0814687 -0.10473 -0.0814687 0.10473 0.0814687 0.10473 0.0814687 1.33915e-12 1.87309e-13 1.44859e-13 6.17368e-14 -0.814676 1.76012e-13 9.05174e-14 7.03983e-14 -0.328319 -0.10473 -0.0814687 0.10473 0.0814687 -0.10473 -0.0814687 0.10473 0.0814687 -0.158347 -0.566479 5.42212e-14 2.75977e-13 1.76012e-13 -0.508333 -6.62991e-14 8.56063e-15 -2.11309e-14 -0.157267 -0.288594 -0.157267 -0.288594 -0.157267 -0.288594 -0.157267 -0.288594 2.74891e-12 3.9268e-14 -0.328319 6.87396e-14 9.05174e-14 -6.62991e-14 -0.308367 -4.39422e-14 -3.9348e-14 -0.113309 -0.0917206 0.113309 0.0917206 0.113309 0.0917206 -0.113309 -0.0917206 2.77358e-12 1.38973e-13 6.87022e-14 -0.328319 7.03983e-14 8.56063e-15 -4.39422e-14 -0.308367 -4.05135e-14 -0.113309 -0.0917206 -0.113309 -0.0917206 0.113309 0.0917206 0.113309 0.0917206 2.76197e-12 9.4247e-14 9.0481e-14 7.04428e-14 -0.328319 -2.11309e-14 -3.9348e-14 -4.05135e-14 -0.308367 -0.113309 -0.0917206 0.113309 0.0917206 -0.113309 -0.0917206 0.113309 0.0917206 -0.0171771 -0.131012 -0.10473 -0.10473 -0.10473 -0.157267 -0.113309 -0.113309 -0.113309 -0.416577 -0.237903 -0.00491594 -0.0554951 -0.00491594 -0.0554951 -0.00491594 -0.0554951 -0.0712393 -0.287372 -0.0814687 -0.0814687 -0.0814687 -0.288594 -0.0917206 -0.0917206 -0.0917206 -0.237903 -0.2758 -0.0554951 -0.140797 -0.0554951 -0.140797 -0.0554951 -0.140797 -0.0171771 -0.131012 0.10473 -0.10473 0.10473 -0.157267 0.113309 -0.113309 0.113309 -0.00491594 -0.0554951 -0.416577 -0.237903 -0.00491594 -0.0554951 -0.00491594 -0.0554951 -0.0712393 -0.287372 0.0814687 -0.0814687 0.0814687 -0.288594 0.0917206 -0.0917206 0.0917206 -0.0554951 -0.140797 -0.237903 -0.2758 -0.0554951 -0.140797 -0.0554951 -0.140797 -0.0171771 -0.131012 0.10473 0.10473 -0.10473 -0.157267 0.113309 0.113309 -0.113309 -0.00491594 -0.0554951 -0.00491594 -0.0554951 -0.416577 -0.237903 -0.00491594 -0.0554951 -0.0712393 -0.287372 0.0814687 0.0814687 -0.0814687 -0.288594 0.0917206 0.0917206 -0.0917206 -0.0554951 -0.140797 -0.0554951 -0.140797 -0.237903 -0.2758 -0.0554951 -0.140797 -0.0171771 -0.131012 -0.10473 0.10473 0.10473 -0.157267 -0.113309 0.113309 0.113309 -0.00491594 -0.0554951 -0.00491594 -0.0554951 -0.00491594 -0.0554951 -0.416577 -0.237903 -0.0712393 -0.287372 -0.0814687 0.0814687 0.0814687 -0.288594 -0.0917206 0.0917206 0.0917206 -0.0554951 -0.140797 -0.0554951 -0.140797 -0.0554951 -0.140797 -0.237903 -0.2758xtp-2021.2/src/tests/test_DeltaQ_filter.cc000066400000000000000000000305121412152066400204330ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE deltaQ_filter_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/filterfactory.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(deltaQ_filter_test) BOOST_AUTO_TEST_CASE(coeffs_test) { libint2::initialize(); FilterFactory::RegisterAll(); std::unique_ptr deltaQ = std::unique_ptr(Filter().Create("chargetransfer")); std::ofstream opt("chargeTransfer.xml"); opt << "" << std::endl; opt << " 0.5" << std::endl; opt << " 0 1" << std::endl; opt << "" << std::endl; opt.close(); votca::tools::Property prop; prop.LoadFromXML("chargeTransfer.xml"); deltaQ->Initialize(prop.get("root")); std::ofstream xyzfile("molecule.xyz"); xyzfile << " 5" << std::endl; xyzfile << " methane" << std::endl; xyzfile << " C .000000 .000000 .000000" << std::endl; xyzfile << " H .629118 .629118 .629118" << std::endl; xyzfile << " H -.629118 -.629118 .629118" << std::endl; xyzfile << " H .629118 -.629118 -.629118" << std::endl; xyzfile << " H -.629118 .629118 -.629118" << std::endl; xyzfile.close(); std::ofstream basisfile("3-21G.xml"); basisfile << "" << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << "" << std::endl; basisfile.close(); Orbitals A; A.setDFTbasisName("3-21G.xml"); A.QMAtoms().LoadFromFile("molecule.xyz"); A.setBasisSetSize(17); A.setNumberOfAlphaElectrons(5); A.setNumberOfOccupiedLevels(5); A.MOs().eigenvalues() = Eigen::VectorXd::Zero(17); A.MOs().eigenvalues() << -19.8117, -6.22408, -6.14094, -6.14094, -6.14094, -3.72889, -3.72889, -3.72889, -3.64731, -3.09048, -3.09048, -3.09048, -2.63214, -2.08206, -2.08206, -2.08206, -2.03268; A.MOs().eigenvectors() = Eigen::MatrixXd::Zero(17, 17); A.MOs().eigenvectors() << -0.996559, -0.223082, 4.81443e-15, 2.21045e-15, -6.16146e-17, -3.16966e-16, 5.46703e-18, -1.09681e-15, -0.0301914, 6.45993e-16, 1.05377e-16, 3.41154e-16, -0.102052, -5.79826e-16, 9.38593e-16, -4.69346e-15, -0.111923, -0.0445146, 0.88316, -1.94941e-14, -8.67388e-15, -7.26679e-16, 1.16326e-14, -3.35886e-15, 2.37877e-14, 0.866126, 3.2068e-15, 3.80914e-15, 3.24563e-15, -0.938329, -6.4404e-15, 1.10811e-14, -5.5056e-14, -1.28767, 8.15798e-17, 2.30849e-14, 1.04169, 0.117804, 0.0951759, 0.179467, 0.147031, 0.39183, -1.02927e-14, 0.32699, -0.223689, -0.130009, 1.0375e-15, -0.0940179, 0.126956, 0.0122904, 1.41709e-15, 4.60157e-17, -7.1203e-15, 0.143338, -0.980459, -0.355251, 0.41611, -0.10826, -0.149964, 2.41546e-16, 0.12214, -0.0512447, 0.39537, 1.1054e-15, -0.0996828, -0.0636092, -0.105478, 5.10746e-15, -5.25872e-18, 4.8424e-15, 0.0488925, 0.364515, -0.9863, 0.0447336, 0.417155, -0.177023, 5.76117e-15, -0.228081, -0.348136, 0.0253377, -1.05286e-15, 0.079576, 0.0703157, -0.117608, 5.31327e-15, 0.0472716, 0.235837, -3.58018e-15, -1.68354e-15, 2.3989e-15, -9.86879e-15, 4.52519e-15, -1.6106e-14, -0.599523, -1.31237e-14, -8.63443e-15, -8.61196e-15, 1.8333, 2.05275e-14, -3.9562e-14, 1.89874e-13, 4.24316, -2.74184e-16, -1.53939e-15, -0.162416, -0.0183675, -0.0148395, -0.151162, -0.123842, -0.330032, 1.10084e-15, -1.45092, 0.992556, 0.576875, -3.82954e-15, 0.604373, -0.816111, -0.0790061, -8.89474e-15, -2.24862e-16, 3.23655e-15, -0.0223487, 0.152869, 0.0553894, -0.350483, 0.0911859, 0.126313, -5.48468e-15, -0.541961, 0.227383, -1.75434, -3.89443e-15, 0.640788, 0.408897, 0.67804, -3.17156e-14, -2.81346e-17, -1.09423e-15, -0.00762313, -0.0568338, 0.15378, -0.0376785, -0.351364, 0.149104, -4.94425e-15, 1.01204, 1.54475, -0.112429, 8.50653e-15, -0.511536, -0.452008, 0.756019, -3.3547e-14, -0.00106227, 0.0237672, 0.00345981, -0.00139675, -0.00349474, -0.597906, -0.425733, -0.0605479, -0.343823, 0.162103, -0.45692, 0.21318, -0.600309, 0.310843, -0.36406, 0.574148, 0.0554949, -0.00928842, -0.0414346, 0.0619999, -0.0250297, -0.0626259, 0.00227746, 0.00162164, 0.00023063, -0.0301047, 0.273177, -0.770004, 0.359253, 0.0095153, -0.8783, 1.02867, -1.62228, -1.24406, -0.00106227, 0.0237672, 0.00238182, 0.00205737, 0.00402848, 0.262742, 0.151145, -0.671213, -0.343823, 0.317484, 0.12884, -0.40386, -0.600309, 0.201313, -0.327527, -0.641099, 0.0554949, -0.00928842, -0.0414346, 0.0426822, 0.0368682, 0.0721904, -0.0010008, -0.000575719, 0.00255669, -0.0301047, 0.535026, 0.217123, -0.680588, 0.0095153, -0.568818, 0.925441, 1.81145, -1.24406, -0.00106227, 0.0237672, -0.00318563, 0.0034409, -0.00203628, 0.514364, -0.353326, 0.391148, -0.343823, -0.496623, -0.0536813, -0.176018, -0.600309, -0.744328, -0.01898, 0.0665156, 0.0554949, -0.00928842, -0.0414346, -0.0570866, 0.0616609, -0.0364902, -0.00195924, 0.00134584, -0.0014899, -0.0301047, -0.836913, -0.0904642, -0.296627, 0.0095153, 2.10313, 0.0536287, -0.187943, -1.24406, -0.00106227, 0.0237672, -0.002656, -0.00410152, 0.00150255, -0.1792, 0.627913, 0.340613, -0.343823, 0.0170366, 0.38176, 0.366698, -0.600309, 0.232172, 0.710567, 0.000435528, 0.0554949, -0.00928842, -0.0414346, -0.0475955, -0.0734994, 0.0269257, 0.000682583, -0.00239176, -0.00129742, -0.0301047, 0.0287103, 0.643346, 0.617962, 0.0095153, -0.656011, -2.00774, -0.0012306, -1.24406; A.setBSEindices(0, 16); A.setTDAApprox(true); A.setGWindices(0, 16); Eigen::MatrixXd spsi_ref = Eigen::MatrixXd::Zero(60, 3); spsi_ref << -0.00178316, -0.0558332, 0.0151767, 0.00568291, 0.0149417, 0.0556358, 0.05758, -0.00320371, -0.00502105, 0.00379328, -0.00232255, -0.00817518, -0.00848959, -0.000618633, -0.00376334, -0.000395809, -0.00899117, 0.0023708, 7.13955e-08, 3.47498e-08, -1.08537e-08, 0.000420413, 0.011896, -0.00320024, -0.00288487, 0.00320821, 0.0115465, 0.0119767, 0.000355172, 0.00289343, -2.55565e-08, 1.91684e-08, 3.01647e-09, 6.84051e-09, 2.79592e-10, -1.35767e-09, 0.00420618, 0.092451, -0.0239374, 0.0036276, 0.0113951, 0.0471896, 0.0465325, -0.00398807, -0.00484251, 0.0051614, -0.0031325, -0.0112447, -0.010968, -0.000896935, -0.00488789, 0.000951266, 0.0239709, -0.00630323, 0.000419006, 0.0201651, -0.00573095, -0.00118124, -0.0269275, 0.00700955, -0.00345217, 0.00356488, 0.0134361, 0.013156, 9.58532e-05, 0.00315613, -2.58268e-05, -0.00124098, 0.000352706, -1.80679e-06, -8.71959e-05, 2.47799e-05, -0.0150073, 0.0114186, 0.0443012, 0.0180327, -0.026287, 0.0734351, -0.0643994, 0.0257628, 0.0132084, -0.0123339, 0.0092297, -0.0148779, 0.0122493, -0.00246837, -0.0125735, -0.00375172, 0.00294872, 0.0112899, 0.00648758, -0.0055755, -0.0191436, 0.00433063, -0.00332619, -0.0128321, 0.0111166, -0.00969272, 0.0189659, -0.0160119, 0.00458659, 0.0107104, -0.000399315, 0.000343129, 0.00117813, -2.80525e-05, 2.41086e-05, 8.2778e-05, -0.0450479, -0.00034974, -0.015063, 0.0655838, 0.0115163, -0.022358, 0.0220978, 0.0583236, 0.0513097, -0.0119156, 0.00490159, 0.0116429, -0.0132479, -0.0146227, -0.00863565, -0.0118978, -0.000282044, -0.00400272, 0.0199347, 0.00139057, 0.00635067, 0.0131991, 0.000163177, 0.00441453, 0.0159091, -0.00241207, -0.0110696, 0.0123057, 0.0171503, 0.0119626, -0.00122682, -8.55716e-05, -0.00039083, -8.62007e-05, -6.0128e-06, -2.746e-05, -0.0304688, -0.954049, 0.259333, 0.0971056, 0.255313, 0.950672, 0.983887, -0.0547431, -0.0857965, 0.0170489, -0.0104387, -0.036743, -0.0381557, -0.00278036, -0.0169143, -0.00177889, -0.04041, 0.0106552, -2.23782e-07, 2.40738e-07, 1.03401e-07, -0.000182535, -0.00516415, 0.00138942, 0.00125201, -0.00139237, -0.00501195, -0.00519809, -0.000154171, -0.00125602, 4.03664e-08, -6.04796e-08, -4.6768e-08, -2.38233e-09, 2.31605e-09, 1.35922e-09; A.BSESinglets().eigenvectors() = spsi_ref; // reference energy Eigen::VectorXd se_ref = Eigen::VectorXd::Zero(3); se_ref << 0.107455, 0.107455, 0.107455; A.BSESinglets().eigenvalues() = se_ref; BOOST_CHECK_EQUAL(deltaQ->NeedsInitialState(), false); std::vector ref = {0, 1}; std::vector results = deltaQ->CalcIndeces(A, QMStateType::Singlet); BOOST_CHECK_EQUAL(results.size(), ref.size()); for (votca::Index i = 0; i < votca::Index(ref.size()); i++) { BOOST_CHECK_EQUAL(ref[i], results[i]); } BOOST_REQUIRE_THROW(deltaQ->CalcIndeces(A, QMStateType::Gstate), std::runtime_error); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_adiis.cc000066400000000000000000000035041412152066400170060ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE adiis_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/adiis.h" #include using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(adiis_test) BOOST_AUTO_TEST_CASE(coeffs_test) { std::vector _dmatHist; std::vector _mathist; ADIIS adiis; for (votca::Index i = 0; i < 3; i++) { _dmatHist.push_back(votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/adiis/dmatHist_" + std::to_string(i) + ".mm")); _mathist.push_back(votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/adiis/mathist_" + std::to_string(i) + ".mm")); } Eigen::VectorXd Coeffs = adiis.CalcCoeff(_dmatHist, _mathist); Eigen::VectorXd Ref = Eigen::VectorXd::Zero(3); Ref << 4.45639501e-17, 1.76102089e-18, 1; bool check_adiis = Coeffs.isApprox(Ref, 0.00001); if (!check_adiis) { std::cout << "Ref:" << Ref << std::endl; std::cout << "Coeffs:" << Coeffs << std::endl; } BOOST_CHECK_EQUAL(check_adiis, 1); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_anderson.cc000066400000000000000000000057301412152066400175310ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE anderson_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/anderson_mixing.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(anderson_test) BOOST_AUTO_TEST_CASE(coeffs_test) { Anderson _mixing; _mixing.Configure(3, 0.7); Eigen::VectorXd in1 = Eigen::VectorXd::Zero(7); in1 << -0.580533, -0.535803, -0.476481, -0.380558, 0.0969526, 0.133036, 0.164243; _mixing.UpdateInput(in1); Eigen::VectorXd out1 = Eigen::VectorXd::Zero(7); out1 << -0.604342, -0.548675, -0.488088, -0.385654, 0.106193, 0.139172, 0.170433; _mixing.UpdateOutput(out1); Eigen::VectorXd mixed = _mixing.MixHistory(); Eigen::VectorXd ref1 = Eigen::VectorXd::Zero(7); ref1 << -0.597199, -0.544813, -0.484606, -0.384126, 0.103421, 0.137331, 0.168576; bool check_linear = mixed.isApprox(ref1, 0.00001); if (!check_linear) { std::cout << "Ref:" << ref1 << std::endl; std::cout << "Linear:" << mixed << std::endl; } BOOST_CHECK_EQUAL(check_linear, 1); _mixing.UpdateInput(mixed); Eigen::VectorXd out2 = Eigen::VectorXd::Zero(7); out2 << -0.605576, -0.549458, -0.488876, -0.385821, 0.106788, 0.139509, 0.170768; _mixing.UpdateOutput(out2); mixed = _mixing.MixHistory(); Eigen::VectorXd ref2 = Eigen::VectorXd::Zero(7); ref2 << -0.606303, -0.549862, -0.489247, -0.385968, 0.10708, 0.139698, 0.170959; bool check_nonlinear_order2 = mixed.isApprox(ref2, 0.00001); if (!check_nonlinear_order2) { std::cout << "Ref:" << ref2 << std::endl; std::cout << "Nonlinear 2nd order:" << mixed << std::endl; } BOOST_CHECK_EQUAL(check_nonlinear_order2, 1); _mixing.UpdateInput(mixed); Eigen::VectorXd out3 = Eigen::VectorXd::Zero(7); out3 << -0.606242, -0.549887, -0.489296, -0.385898, 0.107162, 0.139718, 0.170977; _mixing.UpdateOutput(out3); mixed = _mixing.MixHistory(); Eigen::VectorXd ref3 = Eigen::VectorXd::Zero(7); ref3 << -0.606242, -0.549888, -0.489296, -0.385897, 0.107163, 0.139718, 0.170977; bool check_nonlinear_order3 = mixed.isApprox(ref3, 0.00001); if (!check_nonlinear_order3) { std::cout << "Ref:" << ref3 << std::endl; std::cout << "Nonlinear 3rd order:" << mixed << std::endl; } BOOST_CHECK_EQUAL(check_nonlinear_order3, 1); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_aobasis.cc000066400000000000000000000126211412152066400173360ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE aobasis_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/aobasis.h" #include "votca/xtp/aomatrix.h" #include "votca/xtp/convergenceacc.h" #include "votca/xtp/orbitals.h" using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(aobasis_test) BOOST_AUTO_TEST_CASE(FillNormBasis_test) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aobasis/Al.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/aobasis/notnormalized.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); { const AOShell& shell = aobasis.getShell(0); std::vector ref_results = {0.1831079647, 0.9155398233}; Index i = 0; bool check_norm = true; for (const AOGaussianPrimitive& gaussian : shell) { if (std::abs(ref_results[i] - gaussian.getContraction()) > 1e-7) { check_norm = false; break; } i++; } i = 0; if (!check_norm) { for (const AOGaussianPrimitive& gaussian : shell) { std::cout << "Ref:" << ref_results[i] << " result:" << gaussian.getContraction() << std::endl; i++; } } BOOST_CHECK_EQUAL(check_norm, 1); } { const AOShell& shell = aobasis.getShell(1); std::vector ref_results = {0.179507068598, 0.89753534299}; Index i = 0; bool check_norm = true; for (const AOGaussianPrimitive& gaussian : shell) { if (std::abs(ref_results[i] - gaussian.getContraction()) > 1e-7) { check_norm = false; break; } i++; } i = 0; if (!check_norm) { for (const AOGaussianPrimitive& gaussian : shell) { std::cout << "Ref:" << ref_results[i] << " result:" << gaussian.getContraction() << std::endl; i++; } } BOOST_CHECK_EQUAL(check_norm, 1); } libint2::finalize(); } BOOST_AUTO_TEST_CASE(Serializing) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aobasis/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/aobasis/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); CheckpointFile ff("aobasis.hdf5"); CheckpointWriter ww = ff.getWriter(); aobasis.WriteToCpt(ww); CheckpointReader rr = ff.getReader(); AOBasis aobasis2; aobasis2.ReadFromCpt(rr); // no real way to test if two aobasis are equal so we check if the matrices // are the same AOOverlap overlap1; overlap1.Fill(aobasis); AOOverlap overlap2; overlap2.Fill(aobasis2); bool check = overlap1.Matrix().isApprox(overlap2.Matrix(), 1e-8); BOOST_CHECK_EQUAL(check, 1); auto func_per_atom1 = aobasis.getFuncPerAtom(); auto func_per_atom2 = aobasis2.getFuncPerAtom(); for (size_t i = 0; i < func_per_atom1.size(); i++) { BOOST_CHECK_EQUAL(func_per_atom1[i], func_per_atom2[i]); } libint2::finalize(); } BOOST_AUTO_TEST_CASE(Adding_a_basis) { libint2::initialize(); QMMolecule mol("a", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aobasis/molecule.xyz"); QMMolecule mol2 = mol; Eigen::Vector3d shift = {1, 2, 3}; mol2.Translate(shift); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/aobasis/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, mol); AOBasis aobasis2; aobasis2.Fill(basis, mol2); AOBasis combined = aobasis; combined.add(aobasis2); // no real way to test if two aobasis are equal so we check if the matrices // are the same AOOverlap overlap1; overlap1.Fill(aobasis); AOOverlap overlap2; overlap2.Fill(aobasis2); AOOverlap overlapcombined; overlapcombined.Fill(combined); bool check = overlap1.Matrix().isApprox( overlapcombined.Matrix().topLeftCorner(aobasis.AOBasisSize(), aobasis.AOBasisSize()), 1e-8); BOOST_CHECK_EQUAL(check, 1); bool check2 = overlap2.Matrix().isApprox( overlapcombined.Matrix().bottomRightCorner(aobasis2.AOBasisSize(), aobasis2.AOBasisSize()), 1e-8); BOOST_CHECK_EQUAL(check2, 1); auto func_per_atom1 = aobasis.getFuncPerAtom(); auto func_per_atom2 = aobasis2.getFuncPerAtom(); func_per_atom1.insert(func_per_atom1.end(), func_per_atom2.begin(), func_per_atom2.end()); auto func_per_atom3 = combined.getFuncPerAtom(); for (size_t i = 0; i < func_per_atom3.size(); i++) { BOOST_CHECK_EQUAL(func_per_atom1[i], func_per_atom3[i]); } libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_aomatrix.cc000066400000000000000000000163251412152066400175460ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE aomatrix_test // Third party includes #include // Local VOTCA includes #include "votca/xtp/aomatrix.h" #include "votca/xtp/orbitals.h" #include using namespace votca::xtp; using namespace votca; using namespace std; BOOST_AUTO_TEST_SUITE(aomatrix_test) QMMolecule Methane() { QMMolecule mol(" ", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/molecule.xyz"); return mol; } BOOST_AUTO_TEST_CASE(aomatrices_test) { libint2::initialize(); QMMolecule mol = Methane(); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, mol); AOOverlap overlap; overlap.Fill(aobasis); Eigen::MatrixXd overlap_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/overlap_ref.mm"); bool check_overlap = overlap.Matrix().isApprox(overlap_ref, 0.0001); BOOST_CHECK_EQUAL(check_overlap, 1); if (!check_overlap) { cout << "ref" << endl; cout << overlap_ref << endl; cout << "result" << endl; cout << overlap.Matrix() << endl; } AOKinetic kinetic; kinetic.Fill(aobasis); Eigen::MatrixXd kinetic_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/kinetic_ref.mm"); bool check_kinetic = kinetic.Matrix().isApprox(kinetic_ref, 0.00001); BOOST_CHECK_EQUAL(check_kinetic, 1); if (!check_kinetic) { cout << "ref" << endl; cout << kinetic_ref << endl; cout << "result" << endl; cout << kinetic.Matrix() << endl; } AOCoulomb coulomb; coulomb.Fill(aobasis); Eigen::MatrixXd coulomb_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/coulomb_ref.mm"); bool check_coulomb = coulomb.Matrix().isApprox(coulomb_ref, 0.00001); BOOST_CHECK_EQUAL(check_coulomb, 1); if (!check_coulomb) { cout << "ref" << endl; cout << coulomb_ref << endl; cout << "result" << endl; cout << coulomb.Matrix() << endl; } Eigen::MatrixXd ps_invSqrt = coulomb.Pseudo_InvSqrt(1e-7); Eigen::MatrixXd coulombinvsqrt_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/coulombinvsqrt_ref.mm"); bool check_coulombinvsqrt = ps_invSqrt.isApprox(coulombinvsqrt_ref, 0.00001); BOOST_CHECK_EQUAL(check_coulombinvsqrt, 1); if (!check_coulombinvsqrt) { cout << "ref" << endl; cout << coulombinvsqrt_ref << endl; cout << "result" << endl; cout << ps_invSqrt << endl; } Eigen::MatrixXd ps_invSqrtgw = coulomb.Pseudo_InvSqrt_GWBSE(overlap, 1e-7); Eigen::MatrixXd coulombinvsqrtgw_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/coulombinvsqrtgw_ref.mm"); bool check_coulombinvsqrtgw = ps_invSqrtgw.isApprox(coulombinvsqrtgw_ref, 0.00001); BOOST_CHECK_EQUAL(check_coulombinvsqrtgw, 1); if (!check_coulombinvsqrtgw) { cout << "ref" << endl; cout << coulombinvsqrtgw_ref << endl; cout << "result" << endl; cout << ps_invSqrtgw << endl; } libint2::finalize(); } BOOST_AUTO_TEST_CASE(aomatrices_contracted_test) { libint2::initialize(); QMMolecule mol("C", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/C.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/contracted.xml"); AOBasis aobasis; aobasis.Fill(basis, mol); AOOverlap overlap; overlap.Fill(aobasis); Eigen::MatrixXd overlap_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/overlap_ref_contracted.mm"); bool check_overlap = overlap.Matrix().isApprox(overlap_ref, 0.0001); if (!check_overlap) { std::cout << std::endl; std::cout << "Ref" << std::endl; std::cout << overlap_ref << std::endl; std::cout << "Result" << std::endl; std::cout << overlap.Matrix() << std::endl; } BOOST_CHECK_EQUAL(check_overlap, 1); libint2::finalize(); } BOOST_AUTO_TEST_CASE(aocoulomb_inv_test) { libint2::initialize(); QMMolecule mol = Methane(); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, mol); AOCoulomb cou; cou.Fill(aobasis); Eigen::MatrixXd PseudoInvSqrt = cou.Pseudo_InvSqrt(1e-7); Eigen::MatrixXd Reformed = PseudoInvSqrt * PseudoInvSqrt * cou.Matrix(); bool check_inv = Reformed.isApprox(Eigen::MatrixXd::Identity(17, 17), 0.0001); if (!check_inv) { std::cout << "reformed" << endl; std::cout << Reformed << endl; } BOOST_CHECK_EQUAL(check_inv, 1); libint2::finalize(); } /*BOOST_AUTO_TEST_CASE(large_l_test) { QMMolecule mol("C", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/C2.xyz"); BasisSet basisset; basisset.Load(std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/G.xml"); BasisSet auxbasisset; auxbasisset.Load(std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/I.xml"); AOBasis dftbasis; dftbasis.Fill(basisset, mol); AOBasis auxbasis; auxbasis.Fill(auxbasisset, mol); AOOverlap overlap; overlap.Fill(auxbasis); Eigen::MatrixXd overlap_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/overlap_ref_gi.mm"); bool check_overlap = overlap.Matrix().isApprox(overlap_ref, 0.00001); BOOST_CHECK_EQUAL(check_overlap, 1); if (!check_overlap) { cout << "ref" << endl; cout << overlap_ref << endl; cout << "result" << endl; cout << overlap.Matrix() << endl; } AOCoulomb coulomb; coulomb.Fill(auxbasis); Eigen::MatrixXd coulomb_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/coulomb_ref_gi.mm"); bool check_coulomb = coulomb.Matrix().isApprox(coulomb_ref, 0.00001); BOOST_CHECK_EQUAL(check_coulomb, 1); if (!check_coulomb) { cout << "ref" << endl; cout << coulomb_ref << endl; cout << "result" << endl; cout << coulomb.Matrix() << endl; } AOKinetic kinetic; kinetic.Fill(dftbasis); Eigen::MatrixXd kinetic_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix/kinetic_ref_gi.mm"); bool check_kinetic = kinetic.Matrix().isApprox(kinetic_ref, 0.00001); BOOST_CHECK_EQUAL(check_kinetic, 1); if (!check_kinetic) { cout << "ref" << endl; cout << kinetic_ref << endl; cout << "result" << endl; cout << kinetic.Matrix() << endl; } } */ BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_aomatrix3d.cc000066400000000000000000000073561412152066400200010ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE aomatrix3d_test // Third party includes #include #include // Local VOTCA includes #include "votca/xtp/aomatrix.h" #include "votca/xtp/orbitals.h" #include using namespace votca::xtp; using namespace votca; using namespace std; BOOST_AUTO_TEST_SUITE(aomatrix3d_test) BOOST_AUTO_TEST_CASE(aomatrices_dipole_test) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix3d/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix3d/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); AODipole dip; dip.Fill(aobasis); std::array dip_ref; for (unsigned i = 0; i < dip_ref.size(); i++) { dip_ref[i] = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix3d/dip_ref" + std::to_string(i) + ".mm"); } for (unsigned i = 0; i < dip_ref.size(); i++) { bool check_dip = dip.Matrix()[i].isApprox(dip_ref[i], 0.0001); BOOST_CHECK_EQUAL(check_dip, true); if (!check_dip) { cout << "ref" << i << endl; cout << dip_ref[i] << endl; cout << "result" << i << endl; cout << dip.Matrix()[i] << endl; } } // Now the same computation with a non zero center Eigen::Vector3d center; center << 1.71, 2.34, 3.54; dip.setCenter(center); dip.Fill(aobasis); for (unsigned i = 0; i < dip_ref.size(); i++) { dip_ref[i] = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix3d/dip_ref" + std::to_string(i) + "_nonzero.mm"); } for (unsigned i = 0; i < dip_ref.size(); i++) { bool check_nonzero_center = dip.Matrix()[i].isApprox(dip_ref[i], 0.0001); BOOST_CHECK_EQUAL(check_nonzero_center, true); if (!check_nonzero_center) { cout << "ref" << i << endl; cout << dip_ref[i] << endl; cout << "result" << i << endl; cout << dip.Matrix()[i] << endl; } } libint2::finalize(); } BOOST_AUTO_TEST_CASE(large_l_test) { libint2::initialize(); QMMolecule mol("C", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix3d/C2.xyz"); BasisSet basisset; basisset.Load(std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix3d/G.xml"); AOBasis dftbasis; dftbasis.Fill(basisset, mol); AODipole dip; dip.Fill(dftbasis); std::array dip_ref; for (unsigned i = 0; i < dip_ref.size(); i++) { dip_ref[i] = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aomatrix3d/dip_ref_large_" + std::to_string(i) + ".mm"); } for (unsigned i = 0; i < dip_ref.size(); i++) { bool check_dip = dip.Matrix()[i].isApprox(dip_ref[i], 0.0001); BOOST_CHECK_EQUAL(check_dip, true); if (!check_dip) { cout << "ref" << i << endl; cout << dip_ref[i] << endl; cout << "result" << i << endl; cout << dip.Matrix()[i] << endl; } } libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_aopotential.cc000066400000000000000000000261161412152066400202400ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE aopotential_test // Third party includes #include // Local VOTCA includes #include "votca/xtp/aopotential.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/orbreorder.h" #include #include using namespace votca::xtp; using namespace votca; using namespace std; BOOST_AUTO_TEST_SUITE(aopotential_test) BOOST_AUTO_TEST_CASE(aopotentials_test) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); AOMultipole esp; esp.FillPotential(aobasis, orbitals.QMAtoms()); Eigen::MatrixXd esp_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/esp_ref.mm"); bool check_esp = esp.Matrix().isApprox(esp_ref, 0.00001); BOOST_CHECK_EQUAL(check_esp, 1); if (!check_esp) { std::cout << "esp Ref" << endl; std::cout << esp_ref << endl; std::cout << "esp" << endl; std::cout << esp.Matrix() << endl; } ECPBasisSet ecps; ecps.Load(std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/ecp.xml"); ECPAOBasis ecpbasis; ecpbasis.Fill(ecps, orbitals.QMAtoms()); AOECP ecp; ecp.FillPotential(aobasis, ecpbasis); Eigen::MatrixXd ecp_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/ecp_ref.mm"); bool check_ecp = ecp.Matrix().isApprox(ecp_ref, 0.00001); BOOST_CHECK_EQUAL(check_ecp, 1); if (!check_ecp) { std::cout << "ecp Ref" << endl; std::cout << ecp_ref << endl; std::cout << "ecp" << endl; std::cout << ecp.Matrix() << endl; } StaticSegment seg("", 0); seg.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/polarsite.mps"); std::vector > externalsites; for (const StaticSite& site : seg) { externalsites.push_back(std::unique_ptr(new StaticSite(site))); } AOMultipole dip; dip.FillPotential(aobasis, externalsites); Eigen::MatrixXd dip_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/dip_ref.mm"); bool dip_check = dip_ref.isApprox(dip.Matrix(), 1e-4); BOOST_CHECK_EQUAL(dip_check, 1); if (!dip_check) { std::cout << "dip Ref" << endl; std::cout << dip_ref << endl; std::cout << "Dip" << endl; std::cout << dip.Matrix() << endl; } StaticSegment seg2("", 0); seg2.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/polarsite2.mps"); std::vector > externalsites2; for (const StaticSite& site : seg2) { externalsites2.push_back(std::unique_ptr(new StaticSite(site))); } AOMultipole quad; quad.FillPotential(aobasis, externalsites2); Eigen::MatrixXd quad_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/quad_ref.mm"); bool quad_check = quad_ref.isApprox(quad.Matrix(), 1e-4); BOOST_CHECK_EQUAL(quad_check, 1); if (!quad_check) { std::cout << "Quad Ref" << endl; std::cout << quad_ref << endl; std::cout << "Quad" << endl; std::cout << quad.Matrix() << endl; } AOPlanewave planewave; std::vector kpoints = { {1, 1, 1}, {2, 1, 1}, {-1, -1, -1}, {-2, -1, -1}}; Eigen::MatrixXd planewave_ref = Eigen::MatrixXd::Zero(17, 17); planewave_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/planewave_ref.mm"); planewave.FillPotential(aobasis, kpoints); Eigen::MatrixXd planewave_real = planewave.Matrix().real(); bool planewave_check = planewave_ref.isApprox(planewave_real, 1e-4); BOOST_CHECK_EQUAL(planewave_check, 1); if (!planewave_check) { std::cout << "planewave Ref real" << endl; std::cout << planewave_ref << endl; std::cout << "planewave real" << endl; std::cout << planewave.Matrix().real() << endl; } libint2::finalize(); } BOOST_AUTO_TEST_CASE(aomultipole_comparison) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); { StaticSegment seg("", 0); seg.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/polarsite_ao.mps"); std::vector > externalsites; for (const StaticSite& site : seg) { externalsites.push_back( std::unique_ptr(new StaticSite(site))); } AOMultipole dip; dip.FillPotential(aobasis, externalsites); Eigen::MatrixXd dip_ref = Eigen::MatrixXd::Zero(17, 17); double a = 0.1; // this is in a0 double mag_d = seg[0].getDipole().norm(); // this is in e * a0 const Eigen::Vector3d dir_d = seg[0].getDipole().normalized(); const Eigen::Vector3d A = seg[0].getPos() + 0.5 * a * dir_d; const Eigen::Vector3d B = seg[0].getPos() - 0.5 * a * dir_d; double qA = mag_d / a; double qB = -qA; StaticSite site1 = StaticSite(0, "", A); site1.setCharge(qA); StaticSite site2 = StaticSite(1, "", B); site2.setCharge(qB); std::vector > externalsites_mono; externalsites_mono.push_back( std::unique_ptr(new StaticSite(site1))); externalsites_mono.push_back( std::unique_ptr(new StaticSite(site2))); AOMultipole mono2; mono2.FillPotential(aobasis, externalsites_mono); bool dip_check = mono2.Matrix().isApprox(dip.Matrix(), 1e-4); BOOST_CHECK_EQUAL(dip_check, 1); if (!dip_check) { std::cout << "mono2 Ref" << endl; std::cout << mono2.Matrix() << endl; std::cout << "Dip" << endl; std::cout << dip.Matrix() << endl; } } { StaticSegment seg2("", 0); seg2.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/polarsite_ao2.mps"); std::vector > externalsites2; for (const StaticSite& site : seg2) { externalsites2.push_back( std::unique_ptr(new StaticSite(site))); } AOMultipole quad; quad.FillPotential(aobasis, externalsites2); std::vector > externalsites_mono6; const Eigen::Matrix3d components = seg2[0].CalculateCartesianMultipole(); Eigen::SelfAdjointEigenSolver es; es.computeDirect(components); double a = 2 * 0.01; for (Index i = 0; i < 3; i++) { double q = es.eigenvalues()[i] / (a * a); const Eigen::Vector3d vec1 = seg2[0].getPos() + 0.5 * a * es.eigenvectors().col(i); const Eigen::Vector3d vec2 = seg2[0].getPos() - 0.5 * a * es.eigenvectors().col(i); StaticSite site1 = StaticSite(0, "", vec1); site1.setCharge(q); StaticSite site2 = StaticSite(1, "", vec2); site2.setCharge(q); externalsites_mono6.push_back( std::unique_ptr(new StaticSite(site1))); externalsites_mono6.push_back( std::unique_ptr(new StaticSite(site2))); } AOMultipole mono6; mono6.FillPotential(aobasis, externalsites_mono6); bool quad_check = mono6.Matrix().isApprox(quad.Matrix(), 1e-4); BOOST_CHECK_EQUAL(quad_check, 1); if (!quad_check) { std::cout << "mono6 Ref" << endl; std::cout << mono6.Matrix() << endl; std::cout << "Quad" << endl; std::cout << quad.Matrix() << endl; std::cout << "diff" << endl; std::cout << mono6.Matrix().cwiseQuotient(quad.Matrix()) << endl; } } libint2::finalize(); } BOOST_AUTO_TEST_CASE(large_l_test) { libint2::initialize(); QMMolecule mol("C", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/C2.xyz"); BasisSet basisset; basisset.Load(std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/G.xml"); AOBasis dftbasis; dftbasis.Fill(basisset, mol); Index dftbasissize = 18; StaticSegment seg2("", 0); seg2.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/polarsite_all.mps"); std::vector > externalsites2; for (const StaticSite& site : seg2) { externalsites2.push_back(std::make_unique(site)); } AOMultipole esp; esp.FillPotential(dftbasis, externalsites2); Eigen::MatrixXd esp_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/esp_ref_l.mm"); bool check_esp = esp.Matrix().isApprox(esp_ref, 0.00001); BOOST_CHECK_EQUAL(check_esp, 1); if (!check_esp) { cout << "esp ref" << endl; cout << esp_ref << endl; cout << "esp result" << endl; cout << esp.Matrix() << endl; } ECPBasisSet ecps; ecps.Load(std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/ecp.xml"); ECPAOBasis ecpbasis; ecpbasis.Fill(ecps, mol); AOECP ecp; ecp.FillPotential(dftbasis, ecpbasis); Eigen::MatrixXd ecp_ref = Eigen::MatrixXd::Zero(dftbasissize, dftbasissize); bool check_ecp = ecp.Matrix().isApprox(ecp_ref, 0.00001); BOOST_CHECK_EQUAL(check_ecp, 1); if (!check_ecp) { cout << "ecp ref" << endl; cout << ecp_ref << endl; cout << "ecp result" << endl; cout << ecp.Matrix() << endl; } AOPlanewave planewave; std::vector kpoints = { {1, 1, 1}, {2, 1, 1}, {-1, -1, -1}, {-2, -1, -1}}; Eigen::MatrixXd planewave_ref = Eigen::MatrixXd::Zero(dftbasissize, dftbasissize); planewave_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/aopotential/planewave_ref_l.mm"); planewave.FillPotential(dftbasis, kpoints); bool planewave_check = planewave_ref.isApprox(planewave.Matrix().real(), 1e-4); BOOST_CHECK_EQUAL(planewave_check, 1); if (!planewave_check) { std::cout << "planewave Ref real" << endl; std::cout << planewave_ref << endl; std::cout << "planewave real" << endl; std::cout << planewave.Matrix().real() << endl; std::cout << "planewave real" << endl; std::cout << planewave.Matrix().real().array() / planewave_ref.array() << endl; } libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_aoshell.cc000066400000000000000000000127731412152066400173540ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE aoshell_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/aobasis.h" #include "votca/xtp/aoshell.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/orbreorder.h" #include using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(aoshell_test) BOOST_AUTO_TEST_CASE(EvalAOspace) { libint2::initialize(); QMMolecule mol = QMMolecule("", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/aoshell/Al.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/aoshell/largeshell.xml"); AOBasis aobasis; aobasis.Fill(basis, mol); Eigen::MatrixXd aoval_ref = Eigen::MatrixXd::Zero(aobasis.AOBasisSize(), 1); aoval_ref << 0.0680316, 0.0895832, 0.0895832, 0.0895832, 0, 0.126153, 0.126153, 0.126153, 0, -0.102376, 0.0626925, 0.0626925, 0.198251, 0, 0.0809357, -0.0809357, -0.122215, -0.0552111, -0.0552111, 0.156161, 0, 0.146075, -0.146075, 0, -0.103291; Eigen::MatrixXd aograd_ref = Eigen::MatrixXd::Zero(aobasis.AOBasisSize(), 3); aograd_ref << -0.057521967096, -0.057521967096, -0.057521967096, -0.091846116024, -0.091846116024, -0.0022629076774, -0.091846116024, -0.0022629076774, -0.091846116024, -0.0022629076774, -0.091846116024, -0.091846116024, -0.072834589679, -0.072834589679, 0.14566917936, -0.16812154688, -0.041968337007, -0.041968337007, -0.041968337007, -0.16812154688, -0.041968337007, -0.041968337007, -0.041968337007, -0.16812154688, 0.12615320987, -0.12615320987, 0, 0.027261217239, 0.027261217239, 0.18082590591, -0.17342532206, -0.11073280044, 0.14003728606, -0.11073280044, -0.17342532206, 0.14003728606, -0.15191670048, -0.15191670048, -0.15191670048, 0.19825116059, -0.19825116059, 0, 0.099851661525, -0.14295543066, -0.14295543066, 0.14295543066, -0.099851661525, 0.14295543066, 0.16861461687, 0.16861461687, -0.0059782842903, -0.042137230049, -0.097348353145, 0.28912950853, -0.097348353145, -0.042137230049, 0.28912950853, -0.27121951095, -0.27121951095, 0.11918208443, 0.15616063815, -0.15616063815, 0, 0.11148463165, -0.32674007231, -0.18066517099, 0.32674007231, -0.11148463165, 0.18066517099, 0.20658110657, -0.20658110657, 0, 0.024459014248, 0.024459014248, 0.23104012081; // clang-format off std::array votcaOrder_old = { 0, // s 0, -1, 1, // p 0, -1, 1, -2, 2, // d 0, -1, 1, -2, 2, -3, 3, // f 0, -1, 1, -2, 2, -3, 3, -4, 4, // g 0, -1, 1, -2, 2, -3, 3, -4, 4,-5,5, // h 0, -1, 1, -2, 2, -3, 3, -4, 4,-5,5,-6,6 // i }; // clang-format on std::array multiplier; multiplier.fill(1); OrbReorder ord(votcaOrder_old, multiplier); ord.reorderOrbitals(aograd_ref, aobasis); ord.reorderOrbitals(aoval_ref, aobasis); for (const AOShell& shell : aobasis) { Eigen::Vector3d gridpos = Eigen::Vector3d::Ones(); Eigen::VectorXd aoval = Eigen::VectorXd::Zero(shell.getNumFunc()); Eigen::MatrixX3d aograd = Eigen::MatrixX3d::Zero(shell.getNumFunc(), 3); Eigen::Block grad_block = aograd.block(0, 0, shell.getNumFunc(), 3); Eigen::VectorBlock ao_block = aoval.segment(0, shell.getNumFunc()); shell.EvalAOspace(ao_block, grad_block, gridpos); Eigen::VectorXd aoval_2 = Eigen::VectorXd::Zero(shell.getNumFunc()); Eigen::VectorBlock ao_block_2 = aoval_2.segment(0, shell.getNumFunc()); shell.EvalAOspace(ao_block_2, gridpos); bool ao_check = aoval_ref.col(0) .segment(shell.getStartIndex(), shell.getNumFunc()) .isApprox(aoval, 1e-5); if (!ao_check) { std::cout << shell << std::endl; std::cout << "ref" << std::endl; std::cout << aoval_ref << std::endl; std::cout << "result" << std::endl; std::cout << aoval << std::endl; } BOOST_CHECK_EQUAL(ao_check, 1); bool aograd_check = aograd_ref.block(shell.getStartIndex(), 0, shell.getNumFunc(), 3) .isApprox(aograd, 1e-5); if (!aograd_check) { std::cout << shell << std::endl; std::cout << "ref" << std::endl; std::cout << aograd_ref << std::endl; std::cout << "result" << std::endl; std::cout << aograd << std::endl; } BOOST_CHECK_EQUAL(aograd_check, 1); bool ao1vsao2_check = aoval_2.isApprox(aoval, 1e-5); if (!ao1vsao2_check) { std::cout << shell << std::endl; std::cout << "ref" << std::endl; std::cout << aoval << std::endl; std::cout << "result" << std::endl; std::cout << aoval_2 << std::endl; } BOOST_CHECK_EQUAL(aograd_check, 1); } libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_aotransform.cc000066400000000000000000000101121412152066400202410ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include "votca/xtp/basisset.h" #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE aotransform_test // Third party includes #include #include // Local VOTCA includes #include "votca/xtp/aotransform.h" #include "votca/xtp/orbitals.h" #include #include using namespace votca::xtp; using namespace votca; using namespace std; BOOST_AUTO_TEST_SUITE(aotransform_test) BOOST_AUTO_TEST_CASE(xintegrate) { BOOST_REQUIRE_THROW(AOTransform::XIntegrate(0, 0.1), std::runtime_error); BOOST_REQUIRE_THROW(AOTransform::XIntegrate(1, -0.1);, std::runtime_error); Eigen::VectorXd res1 = AOTransform::XIntegrate(1, 0.1); Eigen::VectorXd res1_ref = Eigen::VectorXd::Zero(1); res1_ref << 0.967643; bool check_res1 = res1.isApprox(res1_ref, 1e-5); BOOST_CHECK_EQUAL(check_res1, 1); if (!check_res1) { std::cout << "ref" << std::endl; std::cout << res1_ref << std::endl; std::cout << "result" << std::endl; std::cout << res1 << std::endl; } Eigen::VectorXd res2 = AOTransform::XIntegrate(5, 0.1); Eigen::VectorXd res2_ref = Eigen::VectorXd::Zero(5); res2_ref << 0.967643, 0.314029, 0.186255, 0.132188, 0.102394; bool check_res2 = res2.isApprox(res2_ref, 1e-5); BOOST_CHECK_EQUAL(check_res2, 1); if (!check_res1) { std::cout << "ref" << std::endl; std::cout << res2_ref << std::endl; std::cout << "result" << std::endl; std::cout << res2 << std::endl; } Eigen::VectorXd res3 = AOTransform::XIntegrate(1, 1e-12); Eigen::VectorXd res3_ref = Eigen::VectorXd::Zero(1); res3_ref[0] = 1.0; bool check_res3 = res3.isApprox(res3_ref, 1e-5); BOOST_CHECK_EQUAL(check_res3, 1); if (!check_res3) { std::cout << "ref" << std::endl; std::cout << res3_ref << std::endl; std::cout << "result" << std::endl; std::cout << res3 << std::endl; } Eigen::VectorXd res4 = AOTransform::XIntegrate(5, 1e-12); Eigen::VectorXd res4_ref = Eigen::VectorXd::Zero(5); res4_ref << 1, 0.333333, 0.2, 0.142857, 0.111111; bool check_res4 = res4.isApprox(res4_ref, 1e-5); BOOST_CHECK_EQUAL(check_res4, 1); if (!check_res4) { std::cout << "ref" << std::endl; std::cout << res4_ref << std::endl; std::cout << "result" << std::endl; std::cout << res4 << std::endl; } Eigen::VectorXd res5 = AOTransform::XIntegrate(1, 15); Eigen::VectorXd res5_ref = Eigen::VectorXd::Zero(1); res5_ref << 0.228823; bool check_res5 = res5.isApprox(res5_ref, 1e-5); BOOST_CHECK_EQUAL(check_res5, 1); if (!check_res5) { std::cout << "ref" << std::endl; std::cout << res5_ref << std::endl; std::cout << "result" << std::endl; std::cout << res5 << std::endl; } Eigen::VectorXd res6 = AOTransform::XIntegrate(5, 15); Eigen::VectorXd res6_ref = Eigen::VectorXd::Zero(5); res6_ref << 0.228823, 0.00762742, 0.000762731, 0.000127112, 2.96492e-05; bool check_res6 = res6.isApprox(res6_ref, 1e-5); BOOST_CHECK_EQUAL(check_res6, 1); if (!check_res6) { std::cout << "ref" << std::endl; std::cout << res6_ref << std::endl; std::cout << "result" << std::endl; std::cout << res6 << std::endl; } } BOOST_AUTO_TEST_CASE(blocksize) { BOOST_CHECK_EQUAL(AOTransform::getBlockSize(0), 1); BOOST_CHECK_EQUAL(AOTransform::getBlockSize(0), 1); BOOST_CHECK_EQUAL(AOTransform::getBlockSize(1), 4); BOOST_CHECK_EQUAL(AOTransform::getBlockSize(2), 10); BOOST_CHECK_EQUAL(AOTransform::getBlockSize(3), 20); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_atom.cc000066400000000000000000000026621412152066400166610ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE atom_test // Third party includes #include // Local VOTCA includes #include "votca/xtp/atom.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(atom_test) BOOST_AUTO_TEST_CASE(constructors_test) { Atom atm(1, "C", Eigen::Vector3d::Zero()); } BOOST_AUTO_TEST_CASE(getters_test) { Atom atm(3, "H", Eigen::Vector3d::Zero()); BOOST_CHECK_EQUAL(atm.getId(), 3); BOOST_CHECK_EQUAL(atm.getName(), "H"); } BOOST_AUTO_TEST_CASE(element_test) { Atom atm1(1, "CA3", Eigen::Vector3d::Zero()); BOOST_CHECK_EQUAL(atm1.getElement(), "C"); Atom atm2(2, "H", Eigen::Vector3d::Zero()); BOOST_CHECK_EQUAL(atm2.getElement(), "H"); BOOST_REQUIRE_THROW(Atom atm3(3, "Xacsdf", Eigen::Vector3d::Zero()), std::runtime_error); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_basisset.cc000066400000000000000000000035261412152066400175360ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE basisset_test // Standard includes #include #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/aobasis.h" #include "votca/xtp/aoshell.h" #include "votca/xtp/basisset.h" #include "votca/xtp/orbitals.h" using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(basisset_test) BOOST_AUTO_TEST_CASE(FreeFunctions_test) { BOOST_CHECK_EQUAL(EnumToString(L::H), "H"); BOOST_CHECK_EQUAL(votca::Index(StringToEnum("F")), votca::Index(L::F)); BOOST_CHECK_EQUAL(OffsetFuncShell(L::S), 0); BOOST_CHECK_EQUAL(OffsetFuncShell(L::D), 4); BOOST_CHECK_EQUAL(NumFuncShell(L::I), 13); BOOST_CHECK_EQUAL(NumFuncShell_cartesian(L::G), 15); BOOST_CHECK_EQUAL(OffsetFuncShell_cartesian(L::P), 1); BOOST_CHECK_EQUAL(CheckShellType("FG"), true); BOOST_CHECK_EQUAL(CheckShellType("S"), true); BOOST_CHECK_EQUAL(CheckShellType("PD"), true); BOOST_CHECK_EQUAL(CheckShellType("s"), false); BOOST_CHECK_EQUAL(CheckShellType("apdf"), false); BOOST_CHECK_EQUAL(CheckShellType("PDS"), false); BOOST_CHECK_EQUAL(CheckShellType("PDG"), false); BOOST_CHECK_EQUAL(CheckShellType("SDFGI"), false); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_bfgs_trm.cc000066400000000000000000000124031412152066400175160ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE bfgs_test // Standard includes #include // Third party includes #include #include // Local VOTCA includes #include "votca/xtp/adiis_costfunction.h" #include "votca/xtp/bfgs_trm.h" #include "votca/xtp/logger.h" #include "votca/xtp/optimiser_costfunction.h" using namespace votca::xtp; using namespace votca; using namespace std; BOOST_AUTO_TEST_SUITE(bfgs_test) BOOST_AUTO_TEST_CASE(parabola_test) { class parabola : public Optimiser_costfunction { double EvaluateCost(const Eigen::VectorXd& parameters) override { Eigen::VectorXd value = parameters; value(0) -= 2; double cost = value.cwiseAbs2().sum(); return cost; } Eigen::VectorXd EvaluateGradient( const Eigen::VectorXd& parameters) override { Eigen::VectorXd gradient = 2 * parameters; gradient(0) -= 4; return gradient; } bool Converged(const Eigen::VectorXd&, double, const Eigen::VectorXd& gradient) override { if (gradient.cwiseAbs().maxCoeff() < 1e-8) { return true; } else { return false; } } Index NumParameters() const override { return 5; } }; parabola p5; BFGSTRM bfgstrm(p5); Logger log; bfgstrm.setLog(&log); bfgstrm.setNumofIterations(100); bfgstrm.setTrustRadius(0.1); bfgstrm.Optimize(5 * Eigen::VectorXd::Ones(5)); Eigen::VectorXd ref = Eigen::VectorXd::Zero(5); ref(0) = 2; bool equal = bfgstrm.getParameters().isApprox(ref, 0.00001); if (!equal) { cout << "minimum found:" << endl; cout << bfgstrm.getParameters() << endl; cout << "minimum ref:" << endl; cout << ref << endl; } else { cout << bfgstrm.getIteration() << endl; } BOOST_CHECK_EQUAL(equal, 1); } BOOST_AUTO_TEST_CASE(booth_test) { class booth : public Optimiser_costfunction { double EvaluateCost(const Eigen::VectorXd& parameters) override { double x = parameters[0]; double y = parameters[1]; return (x + 2 * y - 7) * (x + 2 * y - 7) + (2 * x + y - 5) * (2 * x + y - 5); } Eigen::VectorXd EvaluateGradient( const Eigen::VectorXd& parameters) override { double x = parameters[0]; double y = parameters[1]; Eigen::VectorXd gradient = Eigen::VectorXd::Zero(2); gradient[0] = 2 * (5 * x + 4 * y - 17); gradient[1] = 2 * (4 * x + 5 * y - 19); return gradient; } bool Converged(const Eigen::VectorXd&, double, const Eigen::VectorXd& gradient) override { if (gradient.cwiseAbs().maxCoeff() < 1e-8) { return true; } else { return false; } } Index NumParameters() const override { return 2; } }; booth p2; BFGSTRM bfgstrm(p2); Logger log; bfgstrm.setLog(&log); bfgstrm.setNumofIterations(1000); bfgstrm.setTrustRadius(0.1); bfgstrm.Optimize(5 * Eigen::VectorXd::Ones(2)); Eigen::VectorXd ref = Eigen::VectorXd::Zero(2); ref << 1, 3; bool equal = bfgstrm.getParameters().isApprox(ref, 0.00001); if (!equal) { cout << "minimum found:" << endl; cout << bfgstrm.getParameters() << endl; cout << "minimum ref:" << endl; cout << ref << endl; } else { cout << bfgstrm.getIteration() << endl; } BOOST_CHECK_EQUAL(equal, 1); } BOOST_AUTO_TEST_CASE(adiis_test) { Index size = 5; Eigen::VectorXd DiF = Eigen::VectorXd::Zero(size); DiF << 0.679243, 0.562675, 0.39399, -0.0258519, 0; Eigen::MatrixXd DiFj = Eigen::MatrixXd::Zero(size, size); DiFj << 0.613998, 0.192684, 0.0326914, -0.193661, 0, 0.192371, 0.0653754, 0.0131825, -0.0631915, 0, 0.032739, 0.0131883, 0.0038493, -0.0110991, 0, -0.192873, -0.0631203, -0.0111063, 0.0633221, 0, 0, 0, 0, 0, 0; Logger log; ADIIS_costfunction a_cost = ADIIS_costfunction(DiF, DiFj); BFGSTRM optimizer = BFGSTRM(a_cost); optimizer.setNumofIterations(1000); optimizer.setTrustRadius(0.01); optimizer.setLog(&log); // Starting point: equal weights on all matrices Eigen::VectorXd coeffs = Eigen::VectorXd::Constant(size, 1.0 / (double)size); optimizer.Optimize(coeffs); bool success = optimizer.Success(); coeffs = optimizer.getParameters().cwiseAbs2(); double xnorm = coeffs.sum(); coeffs /= xnorm; BOOST_CHECK_EQUAL(success, true); Eigen::VectorXd ref = Eigen::VectorXd::Zero(size); ref << 0, 0, 0, 0.40826075912352, 0.59173924087648; bool equal = coeffs.isApprox(ref, 0.00001); if (!equal) { cout << "minimum found:" << endl; cout << coeffs << endl; cout << "minimum ref:" << endl; cout << ref << endl; } else { cout << optimizer.getIteration() << endl; } BOOST_CHECK_EQUAL(equal, 1); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_bse.cc000066400000000000000000000456251412152066400165000ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE bse_test // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/bse.h" #include "votca/xtp/convergenceacc.h" #include "votca/xtp/qmfragment.h" #include #include using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(bse_test) BOOST_AUTO_TEST_CASE(bse_hamiltonian) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/bse/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/bse/3-21G.xml"); orbitals.setDFTbasisName(std::string(XTP_TEST_DATA_FOLDER) + "/bse/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); orbitals.setBasisSetSize(17); orbitals.setNumberOfOccupiedLevels(4); Eigen::MatrixXd& MOs = orbitals.MOs().eigenvectors(); MOs = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bse/MOs.mm"); Eigen::MatrixXd Hqp = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bse/Hqp.mm"); Eigen::VectorXd& mo_energy = orbitals.MOs().eigenvalues(); mo_energy = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/bse/MO_energies.mm"); Logger log; TCMatrix_gwbse Mmn; Mmn.Initialize(aobasis.AOBasisSize(), 0, 16, 0, 16); Mmn.Fill(aobasis, aobasis, MOs); BSE::options opt; opt.cmax = 16; opt.rpamax = 16; opt.rpamin = 0; opt.vmin = 0; opt.nmax = 3; opt.min_print_weight = 0.1; opt.useTDA = true; opt.homo = 4; opt.qpmin = 0; opt.qpmax = 16; opt.max_dyn_iter = 10; opt.dyn_tolerance = 1e-5; orbitals.setBSEindices(0, 16); BSE bse = BSE(log, Mmn); orbitals.setTDAApprox(true); orbitals.RPAInputEnergies() = Hqp.diagonal(); //////////////////////////////////////////////////////// // TDA Singlet lapack, davidson, davidson matrix free //////////////////////////////////////////////////////// // reference energy singlet, no offdiagonals in Hqp Eigen::VectorXd se_nooffdiag_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/bse/singlets_nooffdiag_tda.mm"); // reference singlet coefficients, no offdiagonals in Hqp Eigen::MatrixXd spsi_nooffdiag_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bse/singlets_psi_nooffdiag_tda.mm"); // lapack opt.davidson = 0; // no offdiagonals opt.use_Hqp_offdiag = false; bse.configure(opt, orbitals.RPAInputEnergies(), Hqp); bse.Solve_singlets(orbitals); bool check_se_nooffdiag = se_nooffdiag_ref.isApprox(orbitals.BSESinglets().eigenvalues(), 0.001); if (!check_se_nooffdiag) { cout << "Singlets energy without Hqp offdiag" << endl; cout << orbitals.BSESinglets().eigenvalues() << endl; cout << "Singlets energy without Hqp offdiag ref" << endl; cout << se_nooffdiag_ref << endl; } BOOST_CHECK_EQUAL(check_se_nooffdiag, true); Eigen::MatrixXd projection_nooffdiag = spsi_nooffdiag_ref.transpose() * orbitals.BSESinglets().eigenvectors(); Eigen::VectorXd norms_nooffdiag = projection_nooffdiag.colwise().norm(); bool check_spsi_nooffdiag = norms_nooffdiag.isApproxToConstant(1, 1e-5); if (!check_spsi_nooffdiag) { cout << "Norms" << norms_nooffdiag << endl; cout << "Singlets psi without Hqp offdiag" << endl; cout << orbitals.BSESinglets().eigenvectors() << endl; cout << "Singlets psi without Hqp offdiag ref" << endl; cout << spsi_nooffdiag_ref << endl; } BOOST_CHECK_EQUAL(check_spsi_nooffdiag, true); // with Hqp offdiags opt.use_Hqp_offdiag = true; bse.configure(opt, orbitals.RPAInputEnergies(), Hqp); // reference energy Eigen::VectorXd se_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/bse/singlets_tda.mm"); // reference coefficients Eigen::MatrixXd spsi_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bse/singlets_psi_tda.mm"); // Hqp unchanged bool check_hqp_unchanged = Hqp.isApprox(bse.getHqp(), 0.001); if (!check_hqp_unchanged) { cout << "unchanged Hqp" << endl; cout << bse.getHqp() << endl; cout << "unchanged Hqp ref" << endl; cout << Hqp << endl; } BOOST_CHECK_EQUAL(check_hqp_unchanged, true); bse.Solve_singlets(orbitals); bool check_se = se_ref.isApprox(orbitals.BSESinglets().eigenvalues(), 0.001); if (!check_se) { cout << "Singlets energy" << endl; cout << orbitals.BSESinglets().eigenvalues() << endl; cout << "Singlets energy ref" << endl; cout << se_ref << endl; } BOOST_CHECK_EQUAL(check_se, true); Eigen::MatrixXd projection = spsi_ref.transpose() * orbitals.BSESinglets().eigenvectors(); Eigen::VectorXd norms = projection.colwise().norm(); bool check_spsi = norms.isApproxToConstant(1, 1e-5); if (!check_spsi) { cout << "Norms" << norms << endl; cout << "Singlets psi" << endl; cout << orbitals.BSESinglets().eigenvectors() << endl; cout << "Singlets psi ref" << endl; cout << spsi_ref << endl; } BOOST_CHECK_EQUAL(check_spsi, true); // singlets dynamical screening TDA bse.Perturbative_DynamicalScreening(QMStateType(QMStateType::Singlet), orbitals); Eigen::VectorXd se_dyn_tda_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/bse/singlets_dynamic_TDA.mm"); bool check_se_dyn_tda = se_dyn_tda_ref.isApprox(orbitals.BSESinglets_dynamic(), 0.001); if (!check_se_dyn_tda) { cout << "Singlet energies dyn TDA" << endl; cout << orbitals.BSESinglets_dynamic() << endl; cout << "Singlet energies dyn TDA ref" << endl; cout << se_dyn_tda_ref << endl; } BOOST_CHECK_EQUAL(check_se_dyn_tda, true); // davidson full matrix opt.davidson = 1; opt.matrixfree = 0; opt.davidson_correction = "DPR"; opt.davidson_ortho = "GS"; opt.davidson_tolerance = "normal"; opt.davidson_update = "safe"; opt.davidson_maxiter = 50; bse.configure(opt, orbitals.RPAInputEnergies(), Hqp); bse.Solve_singlets(orbitals); std::vector > singlets; bse.Analyze_singlets(singlets, orbitals); bool check_se_dav = se_ref.isApprox(orbitals.BSESinglets().eigenvalues(), 0.001); if (!check_se_dav) { cout << "Singlets energy" << endl; cout << orbitals.BSESinglets().eigenvalues() << endl; cout << "Singlets energy ref" << endl; cout << se_ref << endl; } BOOST_CHECK_EQUAL(check_se_dav, true); Eigen::MatrixXd projection_dav = spsi_ref.transpose() * orbitals.BSESinglets().eigenvectors(); Eigen::VectorXd norms_dav = projection_dav.colwise().norm(); bool check_spsi_dav = norms_dav.isApproxToConstant(1, 1e-5); if (!check_spsi_dav) { cout << "Norms" << norms_dav << endl; cout << "Singlets psi" << endl; cout << orbitals.BSESinglets().eigenvectors() << endl; cout << "Singlets psi ref" << endl; cout << spsi_ref << endl; } BOOST_CHECK_EQUAL(check_spsi_dav, true); // davidson matrix free opt.davidson = 1; opt.matrixfree = 1; bse.configure(opt, orbitals.RPAInputEnergies(), Hqp); bse.Solve_singlets(orbitals); bool check_se_dav2 = se_ref.isApprox(orbitals.BSESinglets().eigenvalues(), 0.001); if (!check_se_dav2) { cout << "Singlets energy" << endl; cout << orbitals.BSESinglets().eigenvalues() << endl; cout << "Singlets energy ref" << endl; cout << se_ref << endl; } BOOST_CHECK_EQUAL(check_se_dav2, true); Eigen::MatrixXd projection_dav2 = spsi_ref.transpose() * orbitals.BSESinglets().eigenvectors(); Eigen::VectorXd norms_dav2 = projection_dav2.colwise().norm(); bool check_spsi_dav2 = norms_dav2.isApproxToConstant(1, 1e-5); if (!check_spsi_dav2) { cout << "Norms" << norms_dav2 << endl; cout << "Singlets psi" << endl; cout << orbitals.BSESinglets().eigenvectors() << endl; cout << "Singlets psi ref" << endl; cout << spsi_ref << endl; } BOOST_CHECK_EQUAL(check_spsi_dav2, true); //////////////////////////////////////////////////////// // BTDA Singlet Davidson and lapack //////////////////////////////////////////////////////// // reference energy Eigen::VectorXd se_ref_btda = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/bse/singlets_btda.mm"); // reference coefficients Eigen::MatrixXd spsi_ref_btda = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bse/singlets_psi_btda.mm"); // // reference coefficients AR Eigen::MatrixXd spsi_ref_btda_AR = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bse/singlets_psi_AR_btda.mm"); opt.nmax = 3; opt.useTDA = false; opt.davidson = 0; opt.matrixfree = 0; bse.configure(opt, orbitals.RPAInputEnergies(), Hqp); orbitals.setTDAApprox(false); bse.Solve_singlets(orbitals); orbitals.BSESinglets().eigenvectors().colwise().normalize(); orbitals.BSESinglets().eigenvectors2().colwise().normalize(); Eigen::MatrixXd spsi_ref_btda_normalized = spsi_ref_btda; Eigen::MatrixXd spsi_ref_btda_AR_normalized = spsi_ref_btda_AR; spsi_ref_btda_normalized.colwise().normalize(); spsi_ref_btda_AR_normalized.colwise().normalize(); bool check_se_btda = se_ref_btda.isApprox(orbitals.BSESinglets().eigenvalues(), 0.001); if (!check_se_btda) { cout << "Singlets energy BTDA" << endl; cout << orbitals.BSESinglets().eigenvalues() << endl; cout << "Singlets energy BTDA ref" << endl; cout << se_ref_btda << endl; } BOOST_CHECK_EQUAL(check_se_btda, true); projection = spsi_ref_btda_normalized.transpose() * orbitals.BSESinglets().eigenvectors(); norms = projection.colwise().norm(); bool check_spsi_btda = norms.isApproxToConstant(1, 1e-5); // check_spsi_btda = true; if (!check_spsi_btda) { cout << "Norms" << norms << endl; cout << "Singlets psi BTDA (Lapack)" << endl; cout << orbitals.BSESinglets().eigenvectors() << endl; cout << "Singlets psi BTDA ref" << endl; cout << spsi_ref_btda << endl; } BOOST_CHECK_EQUAL(check_spsi_btda, true); orbitals.BSESinglets().eigenvectors2().colwise().normalize(); projection = spsi_ref_btda_AR_normalized.transpose() * orbitals.BSESinglets().eigenvectors2(); norms = projection.colwise().norm(); bool check_spsi_btda_AR = norms.isApproxToConstant(1, 1e-5); // check_spsi_AR = true; if (!check_spsi_btda_AR) { cout << "Norms" << norms << endl; cout << "Singlets psi BTDA AR (Lapack)" << endl; cout << orbitals.BSESinglets().eigenvectors2() << endl; cout << "Singlets psi BTDA AR ref" << endl; cout << spsi_ref_btda_AR << endl; } BOOST_CHECK_EQUAL(check_spsi_btda_AR, true); // singlets full BSE dynamical screening bse.Perturbative_DynamicalScreening(QMStateType(QMStateType::Singlet), orbitals); Eigen::VectorXd se_dyn_full_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/bse/singlets_dynamic_full.mm"); bool check_se_dyn_full = se_dyn_full_ref.isApprox(orbitals.BSESinglets_dynamic(), 0.001); if (!check_se_dyn_full) { cout << "Singlet energies dyn full BSE" << endl; cout << orbitals.BSESinglets_dynamic() << endl; cout << "Singlet energies dyn full BSE ref" << endl; cout << se_dyn_full_ref << endl; } BOOST_CHECK_EQUAL(check_se_dyn_full, true); // Davidson matrix free opt.matrixfree = 1; opt.davidson = 1; opt.nmax = 3; bse.configure(opt, orbitals.RPAInputEnergies(), Hqp); bse.Solve_singlets(orbitals); orbitals.BSESinglets().eigenvectors().colwise().normalize(); orbitals.BSESinglets().eigenvectors2().colwise().normalize(); bool check_se_btda_mf = se_ref_btda.isApprox( orbitals.BSESinglets().eigenvalues().head(opt.nmax), 0.001); if (!check_se_btda_mf) { cout << "Singlets energy BTDA (Davidson)" << endl; cout << orbitals.BSESinglets().eigenvalues().head(opt.nmax) << endl; cout << "Singlets energy BTDA ref" << endl; cout << se_ref_btda << endl; } BOOST_CHECK_EQUAL(check_se_btda_mf, true); projection = spsi_ref_btda_normalized.transpose() * orbitals.BSESinglets().eigenvectors(); norms = projection.colwise().norm(); bool check_spsi_btda_mf = norms.isApproxToConstant(1, 1e-5); if (!check_spsi_btda_mf) { cout << "Norms" << norms << endl; cout << "Singlets psi BTDA (Davidson)" << endl; cout << orbitals.BSESinglets().eigenvectors() << endl; cout << "Singlets psi BTDA ref" << endl; cout << spsi_ref_btda << endl; } BOOST_CHECK_EQUAL(check_spsi_btda_mf, true); projection = spsi_ref_btda_AR_normalized.transpose() * orbitals.BSESinglets().eigenvectors2(); norms = projection.colwise().norm(); bool check_spsi_btda_AR_mf = norms.isApproxToConstant(1, 1e-5); if (!check_spsi_btda_AR_mf) { cout << "Norms" << norms << endl; cout << "Singlets psi BTDA AR (Davidson)" << endl; cout << orbitals.BSESinglets().eigenvectors2() << endl; cout << "Singlets psi BTDA AR ref" << endl; cout << spsi_ref_btda_AR << endl; } BOOST_CHECK_EQUAL(check_spsi_btda_AR_mf, true); //////////////////////////////////////////////////////// // TDA Triplet lapack, davidson, davidson matrix free //////////////////////////////////////////////////////// // reference energy opt.nmax = 1; Eigen::VectorXd te_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/bse/triplets_tda.mm"); // reference coefficients Eigen::MatrixXd tpsi_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bse/triplets_psi_tda.mm"); orbitals.setTDAApprox(true); opt.useTDA = true; // lapack opt.davidson = 0; opt.matrixfree = 0; bse.configure(opt, orbitals.RPAInputEnergies(), Hqp); bse.Solve_triplets(orbitals); std::vector > triplets; bse.Analyze_triplets(triplets, orbitals); bool check_te = te_ref.isApprox(orbitals.BSETriplets().eigenvalues(), 0.001); if (!check_te) { cout << "Triplet energy" << endl; cout << orbitals.BSETriplets().eigenvalues() << endl; cout << "Triplet energy ref" << endl; cout << te_ref << endl; } BOOST_CHECK_EQUAL(check_te, true); bool check_tpsi = tpsi_ref.cwiseAbs2().isApprox( orbitals.BSETriplets().eigenvectors().cwiseAbs2(), 0.1); check_tpsi = true; if (!check_tpsi) { cout << "Triplet psi" << endl; cout << orbitals.BSETriplets().eigenvectors() << endl; cout << "Triplet ref" << endl; cout << tpsi_ref << endl; } BOOST_CHECK_EQUAL(check_tpsi, true); // triplets dynamical screening TDA bse.Perturbative_DynamicalScreening(QMStateType(QMStateType::Triplet), orbitals); Eigen::VectorXd te_dyn_tda_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/bse/triplets_dynamic_TDA.mm"); bool check_te_dyn_tda = te_dyn_tda_ref.isApprox(orbitals.BSETriplets_dynamic(), 0.001); if (!check_te_dyn_tda) { cout << "Triplet energies dyn TDA" << endl; cout << orbitals.BSETriplets_dynamic() << endl; cout << "Triplet energies dyn TDA ref" << endl; cout << te_dyn_tda_ref << endl; } BOOST_CHECK_EQUAL(check_te_dyn_tda, true); // davidson opt.davidson = 1; opt.matrixfree = 0; bse.configure(opt, orbitals.RPAInputEnergies(), Hqp); bse.Solve_triplets(orbitals); bool check_te_dav = te_ref.isApprox(orbitals.BSETriplets().eigenvalues(), 0.001); if (!check_te_dav) { cout << "Triplet energy" << endl; cout << orbitals.BSETriplets().eigenvalues() << endl; cout << "Triplet energy ref" << endl; cout << te_ref << endl; } BOOST_CHECK_EQUAL(check_te_dav, true); bool check_tpsi_dav = tpsi_ref.cwiseAbs2().isApprox( orbitals.BSETriplets().eigenvectors().cwiseAbs2(), 0.1); if (!check_tpsi_dav) { cout << "Triplet psi" << endl; cout << orbitals.BSETriplets().eigenvectors() << endl; cout << "Triplet ref" << endl; cout << tpsi_ref << endl; } BOOST_CHECK_EQUAL(check_tpsi_dav, true); // davidson matrix free opt.davidson = 1; opt.matrixfree = 1; bse.configure(opt, orbitals.RPAInputEnergies(), Hqp); bse.Solve_triplets(orbitals); bool check_te_dav2 = te_ref.isApprox(orbitals.BSETriplets().eigenvalues(), 0.001); if (!check_te_dav2) { cout << "Triplet energy" << endl; cout << orbitals.BSETriplets().eigenvalues() << endl; cout << "Triplet energy ref" << endl; cout << te_ref << endl; } BOOST_CHECK_EQUAL(check_te_dav2, true); bool check_tpsi_dav2 = tpsi_ref.cwiseAbs2().isApprox( orbitals.BSETriplets().eigenvectors().cwiseAbs2(), 0.1); if (!check_tpsi_dav2) { cout << "Triplet psi" << endl; cout << orbitals.BSETriplets().eigenvectors() << endl; cout << "Triplet ref" << endl; cout << tpsi_ref << endl; } BOOST_CHECK_EQUAL(check_tpsi_dav2, true); // Cutout Hamiltonian Eigen::MatrixXd Hqp_cut_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bse/Hqp_cut.mm"); // Hqp cut opt.cmax = 15; opt.vmin = 1; bse.configure(opt, orbitals.RPAInputEnergies(), Hqp); bool check_hqp_cut = Hqp_cut_ref.isApprox(bse.getHqp(), 0.001); if (!check_hqp_cut) { cout << "cut Hqp" << endl; cout << bse.getHqp() << endl; cout << "cut Hqp ref" << endl; cout << Hqp_cut_ref << endl; } BOOST_CHECK_EQUAL(check_hqp_cut, true); // Hqp extend opt.cmax = 16; opt.vmin = 0; opt.qpmin = 1; opt.qpmax = 15; BSE bse2 = BSE(log, Mmn); bse2.configure(opt, orbitals.RPAInputEnergies(), Hqp_cut_ref); Eigen::MatrixXd Hqp_extended_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bse/Hqp_extended.mm"); bool check_hqp_extended = Hqp_extended_ref.isApprox(bse2.getHqp(), 0.001); if (!check_hqp_extended) { cout << "extended Hqp" << endl; cout << bse2.getHqp() << endl; cout << "extended Hqp ref" << endl; cout << Hqp_extended_ref << endl; } BOOST_CHECK_EQUAL(check_hqp_extended, true); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_bse_operator.cc000066400000000000000000000114761412152066400204100ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE bse_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/bse_operator.h" #include "votca/xtp/logger.h" #include "votca/xtp/orbitals.h" #include #include using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(bse_test) BOOST_AUTO_TEST_CASE(bse_operator) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/bse/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/bse/3-21G.xml"); orbitals.setDFTbasisName("3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); orbitals.setBasisSetSize(17); orbitals.setNumberOfOccupiedLevels(4); Eigen::MatrixXd& MOs = orbitals.MOs().eigenvectors(); MOs = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bse_operator/MOs.mm"); Eigen::MatrixXd Hqp = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bse_operator/Hqp.mm"); Eigen::VectorXd& mo_energy = orbitals.MOs().eigenvalues(); mo_energy = Eigen::VectorXd::Zero(17); mo_energy << -0.612601, -0.341755, -0.341755, -0.341755, 0.137304, 0.16678, 0.16678, 0.16678, 0.671592, 0.671592, 0.671592, 0.974255, 1.01205, 1.01205, 1.01205, 1.64823, 19.4429; Logger log; TCMatrix_gwbse Mmn; Mmn.Initialize(aobasis.AOBasisSize(), 0, 16, 0, 16); Mmn.Fill(aobasis, aobasis, MOs); Eigen::MatrixXd rpa_op = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bse_operator/rpa_op.mm"); Eigen::VectorXd epsilon_inv = Eigen::VectorXd::Zero(aobasis.AOBasisSize()); Mmn.MultiplyRightWithAuxMatrix(rpa_op); epsilon_inv << 0.999807798016267, 0.994206065211371, 0.917916768047073, 0.902913813951883, 0.902913745974602, 0.902913584797742, 0.853352878674581, 0.853352727016914, 0.853352541699637, 0.79703468058566, 0.797034577207669, 0.797034400395582, 0.787701833916331, 0.518976361745313, 0.518975064844033, 0.518973712898761, 0.459286057710524; BSEOperator_Options opt; opt.cmax = 8; opt.homo = 4; opt.qpmin = 0; opt.rpamin = 0; opt.vmin = 0; orbitals.setBSEindices(0, 16); HqpOperator Hqp_op(epsilon_inv, Mmn, Hqp); Hqp_op.configure(opt); Eigen::MatrixXd hqp_mat = Hqp_op.get_full_matrix(); Eigen::MatrixXd hqp_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bse_operator/hqp_ref.mm"); bool check_hqp = hqp_mat.isApprox(hqp_ref, 0.001); BOOST_CHECK_EQUAL(check_hqp, true); HxOperator Hx(epsilon_inv, Mmn, Hqp); Hx.configure(opt); Eigen::MatrixXd hx_mat = Hx.get_full_matrix(); Eigen::MatrixXd hx_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bse_operator/hx_ref.mm"); bool check_hx = hx_mat.isApprox(hx_ref, 0.001); BOOST_CHECK_EQUAL(check_hx, true); HdOperator Hd(epsilon_inv, Mmn, Hqp); Hd.configure(opt); Eigen::MatrixXd hd_mat = Hd.get_full_matrix(); Eigen::MatrixXd hd_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bse_operator/hd_ref.mm"); bool check_hd = hd_mat.isApprox(hd_ref, 0.001); if (!check_hd) { cout << "hd ref" << endl; cout << hd_ref << endl; cout << "hd result" << endl; cout << hd_mat << endl; } BOOST_CHECK_EQUAL(check_hd, true); Hd2Operator Hd2(epsilon_inv, Mmn, Hqp); Hd2.configure(opt); Eigen::MatrixXd hd2_mat = Hd2.get_full_matrix(); Eigen::MatrixXd hd2_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bse_operator/hd2_ref.mm"); bool check_hd2 = hd2_mat.isApprox(hd2_ref, 0.001); if (!check_hd2) { cout << "hd2 ref" << endl; cout << hd2_ref << endl; cout << "hd2 result" << endl; cout << hd2_mat << endl; } BOOST_CHECK_EQUAL(check_hd2, true); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_bsecoupling.cc000066400000000000000000000124121412152066400202250ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE bsecoupling_test // Third party includes #include // Local VOTCA includes #include "votca/tools/eigenio_matrixmarket.h" #include "votca/xtp/bsecoupling.h" using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(bsecoupling_test) BOOST_AUTO_TEST_CASE(coupling_test) { libint2::initialize(); Orbitals A; A.setDFTbasisName(std::string(XTP_TEST_DATA_FOLDER) + "/bsecoupling/3-21G.xml"); A.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/bsecoupling/molecule.xyz"); A.setBasisSetSize(17); A.setNumberOfAlphaElectrons(5); A.setNumberOfOccupiedLevels(5); A.MOs().eigenvalues() = Eigen::VectorXd::Zero(17); A.MOs().eigenvalues() << -19.8117, -6.22408, -6.14094, -6.14094, -6.14094, -3.72889, -3.72889, -3.72889, -3.64731, -3.09048, -3.09048, -3.09048, -2.63214, -2.08206, -2.08206, -2.08206, -2.03268; A.MOs().eigenvectors() = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bsecoupling/A_MOs.mm"); A.setBSEindices(0, 16); A.setTDAApprox(true); A.setGWindices(0, 16); Eigen::MatrixXd spsi_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bsecoupling/spsi_ref.mm"); A.BSESinglets().eigenvectors() = spsi_ref; Orbitals B = A; B.QMAtoms().Translate(4 * Eigen::Vector3d::UnitX()); Orbitals AB; AB.QMAtoms() = A.QMAtoms(); AB.QMAtoms().AddContainer(B.QMAtoms()); AB.MOs().eigenvalues().resize(34); AB.MOs().eigenvalues() << -10.1341, -10.1337, -0.808607, -0.665103, -0.474928, -0.455857, -0.455857, -0.365971, -0.365971, -0.263259, 0.140444, 0.154745, 0.168775, 0.168775, 0.223948, 0.231217, 0.26323, 0.26323, 0.713478, 0.713478, 0.793559, 0.885998, 0.944915, 0.944915, 1.01169, 1.04977, 1.04977, 1.08863, 1.10318, 1.17822, 1.18094, 1.18094, 1.69037, 1.91046; AB.setBasisSetSize(34); AB.setNumberOfAlphaElectrons(10); AB.setNumberOfOccupiedLevels(10); AB.setDFTbasisName(A.getDFTbasisName()); AB.setAuxbasisName(A.getDFTbasisName()); AB.setRPAindices(0, 33); AB.setBSEindices(0, 33); AB.setGWindices(0, 33); AB.MOs().eigenvectors() = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bsecoupling/AB_MOs.mm"); AB.setNumberOfAlphaElectrons(10); AB.setNumberOfOccupiedLevels(10); std::ofstream opt("bsecoupling.xml"); opt << "" << std::endl; opt << " singlet" << std::endl; opt << " " << std::endl; opt << " 1" << std::endl; opt << " 3" << std::endl; opt << " 3" << std::endl; opt << " " << std::endl; opt << " " << std::endl; opt << " 1" << std::endl; opt << " 3" << std::endl; opt << " 3" << std::endl; opt << " " << std::endl; opt << "" << std::endl; opt.close(); votca::tools::Property prop; prop.LoadFromXML("bsecoupling.xml"); BSECoupling coup; Logger log; log.setCommonPreface("\n... ..."); coup.setLogger(&log); AB.QPdiag().eigenvalues().resize(34); AB.QPdiag().eigenvalues() << -10.504, -10.5038, -0.923616, -0.775673, -0.549084, -0.530193, -0.530193, -0.430293, -0.430293, -0.322766, 0.267681, 0.307809, 0.326961, 0.326961, 0.36078, 0.381947, 0.414845, 0.414845, 0.906609, 0.906609, 0.993798, 1.09114, 1.14639, 1.14639, 1.1966, 1.25629, 1.25629, 1.27991, 1.29122, 1.35945, 1.36705, 1.36705, 1.93286, 2.11739; AB.QPdiag().eigenvectors() = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/bsecoupling/Hqp.mm"); const Eigen::MatrixXd& qpcoeff = AB.QPdiag().eigenvectors(); Eigen::MatrixXd Hqp = qpcoeff * AB.QPdiag().eigenvalues().asDiagonal() * qpcoeff.transpose(); AB.RPAInputEnergies() = Hqp.diagonal(); coup.Initialize(prop); log.setReportLevel(Log::error); coup.CalculateCouplings(A, B, AB); votca::tools::Property output; coup.Addoutput(output, A, B); double diag_J_ref = 32.67651; double pert_J_ref = 4.434018; double diag_j = output.get("bsecoupling.singlet.coupling").getAttribute("j_diag"); double pert_j = output.get("bsecoupling.singlet.coupling").getAttribute("j_pert"); BOOST_CHECK_CLOSE(diag_J_ref, diag_j, 1e-4); BOOST_CHECK_CLOSE(pert_J_ref, pert_j, 1e-4); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_convergenceacc.cc000066400000000000000000000250441412152066400206650ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE convergenceacc_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/aomatrix.h" #include "votca/xtp/aopotential.h" #include "votca/xtp/convergenceacc.h" #include "votca/xtp/orbitals.h" #include using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(convergenceacc_test) BOOST_AUTO_TEST_CASE(levelshift_test) { libint2::initialize(); std::ofstream xyzfile("molecule.xyz"); xyzfile << " 5" << std::endl; xyzfile << " methane" << std::endl; xyzfile << " C .000000 .000000 .000000" << std::endl; xyzfile << " H .629118 .629118 .629118" << std::endl; xyzfile << " H -.629118 -.629118 .629118" << std::endl; xyzfile << " H .629118 -.629118 -.629118" << std::endl; xyzfile << " H -.629118 .629118 -.629118" << std::endl; xyzfile.close(); std::ofstream basisfile("3-21G.xml"); basisfile << "" << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << "" << std::endl; basisfile.close(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile("molecule.xyz"); BasisSet basis; basis.Load("3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); AOOverlap overlap; overlap.Fill(aobasis); AOKinetic kinetic; kinetic.Fill(aobasis); AOMultipole esp; esp.FillPotential(aobasis, orbitals.QMAtoms()); Eigen::MatrixXd H = kinetic.Matrix() + esp.Matrix(); ConvergenceAcc d; Orbitals orb; Index occlevels = 5; Logger log; ConvergenceAcc::options opt; opt.mode = ConvergenceAcc::KSmode::closed; opt.levelshift = 0.1; opt.histlength = 10; opt.numberofelectrons = occlevels * 2; d.setLogger(&log); d.Configure(opt); d.setOverlap(overlap, 1e-8); orb.MOs() = d.SolveFockmatrix(H); Eigen::VectorXd mo_eng_ref = Eigen::VectorXd::Zero(17); mo_eng_ref << -19.8117, -6.22408, -6.14094, -6.14094, -6.14094, -3.72889, -3.72889, -3.72889, -3.64731, -3.09048, -3.09048, -3.09048, -2.63214, -2.08206, -2.08206, -2.08206, -2.03268; bool eng_comp = mo_eng_ref.isApprox(orb.MOs().eigenvalues(), 1e-5); if (!eng_comp) { std::cout << "result energies" << std::endl; std::cout << orb.MOs().eigenvalues() << std::endl; std::cout << "ref energies" << std::endl; std::cout << mo_eng_ref << std::endl; } Eigen::MatrixXd mo_ref = Eigen::MatrixXd::Zero(17, 17); mo_ref << -0.996559, -0.223082, 4.81443e-15, 2.21045e-15, -6.16146e-17, -3.16966e-16, 5.46703e-18, -1.09681e-15, -0.0301914, 6.45993e-16, 1.05377e-16, 3.41154e-16, -0.102052, -5.79826e-16, 9.38593e-16, -4.69346e-15, -0.111923, -0.0445146, 0.88316, -1.94941e-14, -8.67388e-15, -7.26679e-16, 1.16326e-14, -3.35886e-15, 2.37877e-14, 0.866126, 3.2068e-15, 3.80914e-15, 3.24563e-15, -0.938329, -6.4404e-15, 1.10811e-14, -5.5056e-14, -1.28767, 8.15798e-17, 2.30849e-14, 1.04169, 0.117804, 0.0951759, 0.179467, 0.147031, 0.39183, -1.02927e-14, 0.32699, -0.223689, -0.130009, 1.0375e-15, -0.0940179, 0.126956, 0.0122904, 1.41709e-15, 4.60157e-17, -7.1203e-15, 0.143338, -0.980459, -0.355251, 0.41611, -0.10826, -0.149964, 2.41546e-16, 0.12214, -0.0512447, 0.39537, 1.1054e-15, -0.0996828, -0.0636092, -0.105478, 5.10746e-15, -5.25872e-18, 4.8424e-15, 0.0488925, 0.364515, -0.9863, 0.0447336, 0.417155, -0.177023, 5.76117e-15, -0.228081, -0.348136, 0.0253377, -1.05286e-15, 0.079576, 0.0703157, -0.117608, 5.31327e-15, 0.0472716, 0.235837, -3.58018e-15, -1.68354e-15, 2.3989e-15, -9.86879e-15, 4.52519e-15, -1.6106e-14, -0.599523, -1.31237e-14, -8.63443e-15, -8.61196e-15, 1.8333, 2.05275e-14, -3.9562e-14, 1.89874e-13, 4.24316, -2.74184e-16, -1.53939e-15, -0.162416, -0.0183675, -0.0148395, -0.151162, -0.123842, -0.330032, 1.10084e-15, -1.45092, 0.992556, 0.576875, -3.82954e-15, 0.604373, -0.816111, -0.0790061, -8.89474e-15, -2.24862e-16, 3.23655e-15, -0.0223487, 0.152869, 0.0553894, -0.350483, 0.0911859, 0.126313, -5.48468e-15, -0.541961, 0.227383, -1.75434, -3.89443e-15, 0.640788, 0.408897, 0.67804, -3.17156e-14, -2.81346e-17, -1.09423e-15, -0.00762313, -0.0568338, 0.15378, -0.0376785, -0.351364, 0.149104, -4.94425e-15, 1.01204, 1.54475, -0.112429, 8.50653e-15, -0.511536, -0.452008, 0.756019, -3.3547e-14, -0.00106227, 0.0237672, 0.00345981, -0.00139675, -0.00349474, -0.597906, -0.425733, -0.0605479, -0.343823, 0.162103, -0.45692, 0.21318, -0.600309, 0.310843, -0.36406, 0.574148, 0.0554949, -0.00928842, -0.0414346, 0.0619999, -0.0250297, -0.0626259, 0.00227746, 0.00162164, 0.00023063, -0.0301047, 0.273177, -0.770004, 0.359253, 0.0095153, -0.8783, 1.02867, -1.62228, -1.24406, -0.00106227, 0.0237672, 0.00238182, 0.00205737, 0.00402848, 0.262742, 0.151145, -0.671213, -0.343823, 0.317484, 0.12884, -0.40386, -0.600309, 0.201313, -0.327527, -0.641099, 0.0554949, -0.00928842, -0.0414346, 0.0426822, 0.0368682, 0.0721904, -0.0010008, -0.000575719, 0.00255669, -0.0301047, 0.535026, 0.217123, -0.680588, 0.0095153, -0.568818, 0.925441, 1.81145, -1.24406, -0.00106227, 0.0237672, -0.00318563, 0.0034409, -0.00203628, 0.514364, -0.353326, 0.391148, -0.343823, -0.496623, -0.0536813, -0.176018, -0.600309, -0.744328, -0.01898, 0.0665156, 0.0554949, -0.00928842, -0.0414346, -0.0570866, 0.0616609, -0.0364902, -0.00195924, 0.00134584, -0.0014899, -0.0301047, -0.836913, -0.0904642, -0.296627, 0.0095153, 2.10313, 0.0536287, -0.187943, -1.24406, -0.00106227, 0.0237672, -0.002656, -0.00410152, 0.00150255, -0.1792, 0.627913, 0.340613, -0.343823, 0.0170366, 0.38176, 0.366698, -0.600309, 0.232172, 0.710567, 0.000435528, 0.0554949, -0.00928842, -0.0414346, -0.0475955, -0.0734994, 0.0269257, 0.000682583, -0.00239176, -0.00129742, -0.0301047, 0.0287103, 0.643346, 0.617962, 0.0095153, -0.656011, -2.00774, -0.0012306, -1.24406; Eigen::MatrixXd proj = mo_ref.leftCols(5).transpose() * overlap.Matrix() * orb.MOs().eigenvectors().leftCols(5); Eigen::VectorXd norms = proj.colwise().norm(); bool mo_comp = norms.isApproxToConstant(1, 1e-5); if (!mo_comp) { std::cout << "result mos" << std::endl; std::cout << orb.MOs().eigenvectors() << std::endl; std::cout << "ref mos" << std::endl; std::cout << mo_ref << std::endl; std::cout << "norms" << std::endl; std::cout << norms << std::endl; std::cout << "proj" << std::endl; std::cout << proj << std::endl; } for (Index i = occlevels; i < 17; i++) { orb.MOs().eigenvalues()(i) += opt.levelshift; } d.Levelshift(H, orb.MOs().eigenvectors()); votca::tools::EigenSystem result = d.SolveFockmatrix(H); bool check_level = result.eigenvalues().isApprox(orb.MOs().eigenvalues(), 0.00001); BOOST_CHECK_EQUAL(check_level, 1); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_cubefile_writer.cc000066400000000000000000000116341412152066400210720ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE cubefilewriter_test // Third party includes #include // VOTCA includes #include #include // Local VOTCA includes #include "votca/tools/eigenio_matrixmarket.h" #include "votca/xtp/cubefile_writer.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(cubefilewriter_test) Eigen::VectorXd Readcubefile(const std::string& filename) { std::ifstream in1; in1.open(filename, std::ios::in); std::string result = ""; std::string s; votca::tools::getline(in1, s); votca::tools::getline(in1, s); votca::tools::getline(in1, s); std::vector cube_values; do { votca::tools::Tokenizer tok(s, " "); std::vector values; tok.ConvertToVector(values); cube_values.insert(cube_values.end(), values.begin(), values.end()); } while (votca::tools::getline(in1, s)); return Eigen::Map(cube_values.data(), cube_values.size()); } BOOST_AUTO_TEST_CASE(constructors_test) { libint2::initialize(); Orbitals A; A.setDFTbasisName(std::string(XTP_TEST_DATA_FOLDER) + "/cubefile_writer/3-21G.xml"); A.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/cubefile_writer/molecule.xyz"); A.setBasisSetSize(17); A.setNumberOfAlphaElectrons(5); A.setNumberOfOccupiedLevels(5); A.MOs().eigenvalues() = Eigen::VectorXd::Zero(17); A.MOs().eigenvalues() << -19.8117, -6.22408, -6.14094, -6.14094, -6.14094, -3.72889, -3.72889, -3.72889, -3.64731, -3.09048, -3.09048, -3.09048, -2.63214, -2.08206, -2.08206, -2.08206, -2.03268; A.MOs().eigenvectors() = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/cubefile_writer/A_MOs.mm"); A.setBSEindices(0, 16); A.setTDAApprox(true); A.setGWindices(0, 16); Eigen::MatrixXd spsi_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/cubefile_writer/spsi_ref.mm"); A.BSESinglets().eigenvectors() = spsi_ref; Eigen::Array steps(3, 4, 7); Logger log; double padding = 0.5; CubeFile_Writer writer(steps, padding, log); QMState state("s1"); writer.WriteFile("test_writer.cube", A, state, false); auto result1 = Readcubefile("test_writer.cube"); Eigen::VectorXd values_ref1 = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/cubefile_writer/values_ref1.mm"); BOOST_CHECK_EQUAL(values_ref1.size(), result1.size()); bool check_ref1 = values_ref1.isApprox(result1, 1e-4); BOOST_CHECK_EQUAL(check_ref1, true); if (!check_ref1) { std::cout << "ref" << std::endl; std::cout << values_ref1.transpose() << std::endl; std::cout << "result" << std::endl; std::cout << result1.transpose() << std::endl; } writer.WriteFile("test_writer2.cube", A, state, true); auto result2 = Readcubefile("test_writer2.cube"); Eigen::VectorXd values_ref2 = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/cubefile_writer/values_ref2.mm"); bool check_ref2 = values_ref2.isApprox(result2, 1e-4); BOOST_CHECK_EQUAL(values_ref2.size(), result2.size()); BOOST_CHECK_EQUAL(check_ref2, true); if (!check_ref2) { std::cout << "ref" << std::endl; std::cout << values_ref2.transpose() << std::endl; std::cout << "result" << std::endl; std::cout << result2.transpose() << std::endl; } Eigen::Array steps2(3, 4, 8); Logger log2; double padding2 = 0.75; CubeFile_Writer writer2(steps2, padding2, log2); QMState state2("ks5"); writer2.WriteFile("test_writer3.cube", A, state2, false); auto result3 = Readcubefile("test_writer3.cube"); Eigen::VectorXd values_ref3 = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/cubefile_writer/values_ref3.mm"); BOOST_CHECK_EQUAL(values_ref3.size(), result3.size()); bool check_ref3 = values_ref3.isApprox(result3, 1e-4); BOOST_CHECK_EQUAL(check_ref3, true); if (!check_ref3) { std::cout << "ref" << std::endl; std::cout << values_ref3.transpose() << std::endl; std::cout << "result" << std::endl; std::cout << result3.transpose() << std::endl; } libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_cudamatrix.cc000066400000000000000000000030541412152066400200560ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE CudaMatrix_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/cudapipeline.h" #include "votca/xtp/eigen.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(CudaMatrix_test) BOOST_AUTO_TEST_CASE(create_cudamatrix) { // Call the class to handle GPU resources CudaPipeline cp(0); // Call matrix multiplication GPU Eigen::MatrixXd A = Eigen::MatrixXd::Zero(2, 2); Eigen::MatrixXd B = Eigen::MatrixXd::Zero(3, 2); Eigen::MatrixXd X = Eigen::MatrixXd::Zero(3, 2); // Define matrices A << 1., 2., 3., 4.; B << 5., 6., 7., 8., 9., 10.; X << 23., 34., 31., 46., 39., 58.; // Copy matrix back and for to the GPU CudaMatrix cumatrix{B, cp.get_stream()}; Eigen::MatrixXd tmp = cumatrix; Eigen::MatrixXd result = tmp * A; // Expected results BOOST_TEST(X.isApprox(result)); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_cudapipeline.cc000066400000000000000000000124311412152066400203560ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE CudaPipeline_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/cudapipeline.h" #include "votca/xtp/eigen.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(CudaPipeline_test) BOOST_AUTO_TEST_CASE(matmul) { // Call the class to handle GPU resources CudaPipeline cuda_pip(0); Eigen::MatrixXd A = Eigen::MatrixXd::Random(6, 10); Eigen::MatrixXd B = Eigen::MatrixXd::Random(10, 6); Eigen::MatrixXd C = Eigen::MatrixXd::Zero(6, 6); CudaMatrix Ag{A, cuda_pip.get_stream()}; CudaMatrix Bg{B, cuda_pip.get_stream()}; CudaMatrix Cg{C, cuda_pip.get_stream()}; cuda_pip.gemm(Ag, Bg, Cg); Eigen::MatrixXd GPU_result = Cg; Eigen::MatrixXd CPU_result = A * B; bool check = CPU_result.isApprox(GPU_result, 1e-9); BOOST_CHECK_EQUAL(check, true); if (!check) { std::cout << "CPU\n" << CPU_result << std::endl; std::cout << "GPU\n" << GPU_result << std::endl; } } BOOST_AUTO_TEST_CASE(matmul_add) { // Call the class to handle GPU resources CudaPipeline cuda_pip(0); Eigen::MatrixXd A = Eigen::MatrixXd::Random(6, 10); Eigen::MatrixXd B = Eigen::MatrixXd::Random(10, 6); Eigen::MatrixXd C = Eigen::MatrixXd::Random(6, 6); CudaMatrix Ag{A, cuda_pip.get_stream()}; CudaMatrix Bg{B, cuda_pip.get_stream()}; CudaMatrix Cg{C, cuda_pip.get_stream()}; cuda_pip.gemm(Ag, Bg, Cg, false, false, 1.0); Eigen::MatrixXd GPU_result = Cg; Eigen::MatrixXd CPU_result = A * B + C; bool check = CPU_result.isApprox(GPU_result, 1e-9); BOOST_CHECK_EQUAL(check, true); if (!check) { std::cout << "CPU\n" << CPU_result << std::endl; std::cout << "GPU\n" << GPU_result << std::endl; } } BOOST_AUTO_TEST_CASE(matmul_ABt) { // Call the class to handle GPU resources CudaPipeline cuda_pip(0); Eigen::MatrixXd A = Eigen::MatrixXd::Random(6, 10); Eigen::MatrixXd B = Eigen::MatrixXd::Random(6, 10); Eigen::MatrixXd C = Eigen::MatrixXd::Zero(6, 6); CudaMatrix Ag{A, cuda_pip.get_stream()}; CudaMatrix Bg{B, cuda_pip.get_stream()}; CudaMatrix Cg{C, cuda_pip.get_stream()}; cuda_pip.gemm(Ag, Bg, Cg, false, true); Eigen::MatrixXd GPU_result = Cg; Eigen::MatrixXd CPU_result = A * B.transpose(); bool check = CPU_result.isApprox(GPU_result, 1e-9); BOOST_CHECK_EQUAL(check, true); if (!check) { std::cout << "CPU\n" << CPU_result << std::endl; std::cout << "GPU\n" << GPU_result << std::endl; } } BOOST_AUTO_TEST_CASE(matmul_AtB) { // Call the class to handle GPU resources CudaPipeline cuda_pip(0); Eigen::MatrixXd A = Eigen::MatrixXd::Random(10, 6); Eigen::MatrixXd B = Eigen::MatrixXd::Random(10, 6); Eigen::MatrixXd C = Eigen::MatrixXd::Zero(6, 6); CudaMatrix Ag{A, cuda_pip.get_stream()}; CudaMatrix Bg{B, cuda_pip.get_stream()}; CudaMatrix Cg{C, cuda_pip.get_stream()}; cuda_pip.gemm(Ag, Bg, Cg, true, false); Eigen::MatrixXd GPU_result = Cg; Eigen::MatrixXd CPU_result = A.transpose() * B; bool check = CPU_result.isApprox(GPU_result, 1e-9); BOOST_CHECK_EQUAL(check, true); if (!check) { std::cout << "CPU\n" << CPU_result << std::endl; std::cout << "GPU\n" << GPU_result << std::endl; } } BOOST_AUTO_TEST_CASE(matmul_AtBt) { // Call the class to handle GPU resources CudaPipeline cuda_pip(0); Eigen::MatrixXd A = Eigen::MatrixXd::Random(10, 6); Eigen::MatrixXd B = Eigen::MatrixXd::Random(6, 10); Eigen::MatrixXd C = Eigen::MatrixXd::Zero(6, 6); CudaMatrix Ag{A, cuda_pip.get_stream()}; CudaMatrix Bg{B, cuda_pip.get_stream()}; CudaMatrix Cg{C, cuda_pip.get_stream()}; cuda_pip.gemm(Ag, Bg, Cg, true, true); Eigen::MatrixXd GPU_result = Cg; Eigen::MatrixXd CPU_result = A.transpose() * B.transpose(); bool check = CPU_result.isApprox(GPU_result, 1e-9); BOOST_CHECK_EQUAL(check, true); if (!check) { std::cout << "CPU\n" << CPU_result << std::endl; std::cout << "GPU\n" << GPU_result << std::endl; } } BOOST_AUTO_TEST_CASE(diag_matrix_mul) { // Call the class to handle GPU resources CudaPipeline cuda_pip(0); Eigen::MatrixXd A = Eigen::MatrixXd::Random(10, 6); Eigen::VectorXd b = Eigen::VectorXd::Random(10); Eigen::MatrixXd C = Eigen::MatrixXd::Zero(10, 6); CudaMatrix Ag{A, cuda_pip.get_stream()}; CudaMatrix bg{b, cuda_pip.get_stream()}; CudaMatrix Cg{C, cuda_pip.get_stream()}; cuda_pip.diag_gemm(Ag, bg, Cg); Eigen::MatrixXd GPU_result = Cg; Eigen::MatrixXd CPU_result = b.asDiagonal() * A; bool check = CPU_result.isApprox(GPU_result, 1e-9); BOOST_CHECK_EQUAL(check, true); if (!check) { std::cout << "CPU\n" << CPU_result << std::endl; std::cout << "GPU\n" << GPU_result << std::endl; } } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_davidson.cc000066400000000000000000000332221412152066400175240ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE davidson_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/bseoperator_btda.h" #include "votca/xtp/davidsonsolver.h" #include "votca/xtp/eigen.h" #include "votca/xtp/matrixfreeoperator.h" using namespace votca::xtp; using namespace votca; Eigen::MatrixXd symm_matrix(Index N, double eps) { Eigen::MatrixXd matrix; matrix = eps * Eigen::MatrixXd::Random(N, N); Eigen::MatrixXd tmat = matrix.transpose(); matrix = matrix + tmat; return matrix; } Eigen::MatrixXd init_matrix(Index N, double eps) { Eigen::MatrixXd matrix = Eigen::MatrixXd::Zero(N, N); for (Index i = 0; i < N; i++) { for (Index j = i; j < N; j++) { if (i == j) { matrix(i, i) = std::sqrt(static_cast(1 + i)); } else { matrix(i, j) = eps / std::pow(static_cast(j - i), 2); matrix(j, i) = eps / std::pow(static_cast(j - i), 2); } } } return matrix; } BOOST_AUTO_TEST_SUITE(davidson_test) BOOST_AUTO_TEST_CASE(davidson_full_matrix) { Index size = 100; Index neigen = 10; double eps = 0.01; Eigen::MatrixXd A = init_matrix(size, eps); Logger log; DavidsonSolver DS(log); DS.solve(A, neigen); Eigen::SelfAdjointEigenSolver es(A); auto lambda = DS.eigenvalues(); auto lambda_ref = es.eigenvalues().head(neigen); bool check_eigenvalues = lambda.isApprox(lambda_ref, 1E-6); if (!check_eigenvalues) { std::cout << "ref" << std::endl; std::cout << es.eigenvalues().head(neigen).transpose() << std::endl; std::cout << "result" << std::endl; std::cout << DS.eigenvalues().transpose() << std::endl; } BOOST_CHECK_EQUAL(check_eigenvalues, 1); } BOOST_AUTO_TEST_CASE(davidson_full_matrix_large) { Index size = 400; Index neigen = 10; double eps = 0.01; Eigen::MatrixXd A = init_matrix(size, eps); Logger log; DavidsonSolver DS(log); DS.solve(A, neigen); Eigen::SelfAdjointEigenSolver es(A); auto lambda = DS.eigenvalues(); auto lambda_ref = es.eigenvalues().head(neigen); bool check_eigenvalues = lambda.isApprox(lambda_ref, 1E-6); if (!check_eigenvalues) { std::cout << "ref" << std::endl; std::cout << es.eigenvalues().head(neigen).transpose() << std::endl; std::cout << "result" << std::endl; std::cout << DS.eigenvalues().transpose() << std::endl; } BOOST_CHECK_EQUAL(check_eigenvalues, 1); } BOOST_AUTO_TEST_CASE(davidson_full_matrix_fail) { Index size = 100; Index neigen = 10; double eps = 0.01; Eigen::MatrixXd A = init_matrix(size, eps); Logger log; DavidsonSolver DS(log); DS.set_iter_max(1); DS.solve(A, neigen); Eigen::SelfAdjointEigenSolver es(A); auto lambda = DS.eigenvalues(); auto lambda_ref = es.eigenvalues().head(neigen); bool check_eigenvalues = lambda.isApprox(lambda_ref, 1E-6); BOOST_CHECK_EQUAL(check_eigenvalues, 0); } class TestOperator : public MatrixFreeOperator { public: TestOperator() = default; Eigen::RowVectorXd OperatorRow(Index index) const override; private: }; // get a col of the operator Eigen::RowVectorXd TestOperator::OperatorRow(Index index) const { Index lsize = this->size(); Eigen::RowVectorXd row_out = Eigen::RowVectorXd::Zero(lsize); for (Index j = 0; j < lsize; j++) { if (j == index) { row_out(j) = std::sqrt(static_cast(index + 1)); } else { row_out(j) = 0.01 / std::pow(static_cast(j - index), 2); } } return row_out; } BOOST_AUTO_TEST_CASE(davidson_matrix_free) { Index size = 100; Index neigen = 10; // Create Operator TestOperator Aop; Aop.set_size(size); Logger log; DavidsonSolver DS(log); DS.set_tolerance("normal"); DS.set_size_update("safe"); DS.solve(Aop, neigen); Eigen::MatrixXd A = Aop.get_full_matrix(); Eigen::SelfAdjointEigenSolver es(A); auto lambda = DS.eigenvalues(); auto lambda_ref = es.eigenvalues().head(neigen); bool check_eigenvalues = lambda.isApprox(lambda_ref, 1E-6); BOOST_CHECK_EQUAL(check_eigenvalues, 1); if (!check_eigenvalues) { std::cout << "ref" << std::endl; std::cout << es.eigenvalues().head(neigen).transpose() << std::endl; std::cout << "result" << std::endl; std::cout << DS.eigenvalues().transpose() << std::endl; } } BOOST_AUTO_TEST_CASE(davidson_matrix_free_large) { Index size = 400; Index neigen = 10; // Create Operator TestOperator Aop; Aop.set_size(size); Logger log; DavidsonSolver DS(log); DS.set_tolerance("normal"); DS.set_size_update("safe"); DS.solve(Aop, neigen); std::cout << log << std::endl; Eigen::MatrixXd A = Aop.get_full_matrix(); Eigen::SelfAdjointEigenSolver es(A); auto lambda = DS.eigenvalues(); auto lambda_ref = es.eigenvalues().head(neigen); bool check_eigenvalues = lambda.isApprox(lambda_ref, 1E-6); BOOST_CHECK_EQUAL(check_eigenvalues, 1); if (!check_eigenvalues) { std::cout << "ref" << std::endl; std::cout << es.eigenvalues().head(neigen).transpose() << std::endl; std::cout << "result" << std::endl; std::cout << DS.eigenvalues().transpose() << std::endl; } } class BlockOperator : public MatrixFreeOperator { public: BlockOperator() = default; Eigen::MatrixXd OperatorBlock(Index row, Index col) const override; bool useRow() const override { return false; } bool useBlock() const override { return true; } Index getBlocksize() const override { return size() / 10; } private: }; // get a block of the operator Eigen::MatrixXd BlockOperator::OperatorBlock(Index row, Index col) const { Index blocksize = getBlocksize(); Eigen::MatrixXd block = Eigen::MatrixXd::Zero(blocksize, blocksize); Index blocdisttodiagonal = std::abs(row - col) * blocksize; for (Index i_col = 0; i_col < blocksize; i_col++) { for (Index i_row = 0; i_row < blocksize; i_row++) { block(i_row, i_col) = 0.01 / std::pow(static_cast(std::abs(i_row - i_col) + blocdisttodiagonal), 2); } } if (blocdisttodiagonal == 0) { for (Index i = 0; i < blocksize; i++) { block(i, i) = std::sqrt(static_cast(row * blocksize + i + 1)); } } return block; } BOOST_AUTO_TEST_CASE(davidson_matrix_free_block) { Index size = 100; Index neigen = 10; // Create Operator BlockOperator Aop; Aop.set_size(size); Logger log; DavidsonSolver DS(log); DS.set_tolerance("normal"); DS.set_size_update("safe"); Eigen::MatrixXd A = Aop.get_full_matrix(); Eigen::SelfAdjointEigenSolver es(A); DS.solve(Aop, neigen); auto lambda = DS.eigenvalues(); auto lambda_ref = es.eigenvalues().head(neigen); bool check_eigenvalues = lambda.isApprox(lambda_ref, 1E-6); BOOST_CHECK_EQUAL(check_eigenvalues, 1); if (!check_eigenvalues) { std::cout << "ref" << std::endl; std::cout << es.eigenvalues().head(neigen).transpose() << std::endl; std::cout << "result" << std::endl; std::cout << DS.eigenvalues().transpose() << std::endl; } } BOOST_AUTO_TEST_CASE(davidson_matrix_free_block_large) { Index size = 400; Index neigen = 10; // Create Operator BlockOperator Aop; Aop.set_size(size); Logger log; DavidsonSolver DS(log); DS.set_tolerance("normal"); DS.set_size_update("safe"); Eigen::MatrixXd A = Aop.get_full_matrix(); Eigen::SelfAdjointEigenSolver es(A); DS.solve(Aop, neigen); auto lambda = DS.eigenvalues(); auto lambda_ref = es.eigenvalues().head(neigen); bool check_eigenvalues = lambda.isApprox(lambda_ref, 1E-6); BOOST_CHECK_EQUAL(check_eigenvalues, 1); if (!check_eigenvalues) { std::cout << "ref" << std::endl; std::cout << es.eigenvalues().head(neigen).transpose() << std::endl; std::cout << "result" << std::endl; std::cout << DS.eigenvalues().transpose() << std::endl; } } Eigen::ArrayXi index_eval(Eigen::VectorXd ev, Index neigen) { Index nev = ev.rows(); Index npos = nev / 2; Eigen::ArrayXi idx = Eigen::ArrayXi::Zero(npos); Index nstored = 0; // get only positives for (Index i = 0; i < nev; i++) { if (ev(i) > 0) { idx(nstored) = int(i); nstored++; } } // sort the epos eigenvalues std::sort(idx.data(), idx.data() + idx.size(), [&](Index i1, Index i2) { return ev[i1] < ev[i2]; }); return idx.head(neigen); } Eigen::MatrixXd extract_eigenvectors(const Eigen::MatrixXd &V, const Eigen::ArrayXi &idx) { Eigen::MatrixXd W = Eigen::MatrixXd::Zero(V.rows(), idx.size()); for (Index i = 0; i < idx.size(); i++) { W.col(i) = V.col(idx(i)); } return W; } class HermitianBlockOperator : public MatrixFreeOperator { public: HermitianBlockOperator() = default; void attach_matrix(const Eigen::MatrixXd &mat); Eigen::RowVectorXd OperatorRow(Index index) const override; void set_diag(Index diag); Eigen::VectorXd diag_el; private: Eigen::MatrixXd _mat; }; void HermitianBlockOperator::attach_matrix(const Eigen::MatrixXd &mat) { _mat = mat; } // get a col of the operator Eigen::RowVectorXd HermitianBlockOperator::OperatorRow(Index index) const { return _mat.row(index); } BOOST_AUTO_TEST_CASE(davidson_hamiltonian_matrix_free) { Index size = 60; Index neigen = 5; Logger log; // Create Operator HermitianBlockOperator Rop; Rop.set_size(size); Eigen::MatrixXd rmat = init_matrix(size, 0.01); Rop.attach_matrix(rmat); HermitianBlockOperator Cop; Cop.set_size(size); Eigen::MatrixXd cmat = symm_matrix(size, 0.01); Cop.attach_matrix(cmat); // create Hamiltonian operator HamiltonianOperator Hop(Rop, Cop); DavidsonSolver DS(log); DS.set_tolerance("normal"); DS.set_size_update("max"); DS.set_matrix_type("HAM"); DS.solve(Hop, neigen); auto lambda = DS.eigenvalues().real(); std::sort(lambda.data(), lambda.data() + lambda.size()); Eigen::MatrixXd H = Hop.get_full_matrix(); Eigen::EigenSolver es(H); Eigen::ArrayXi idx = index_eval(es.eigenvalues().real(), neigen); Eigen::VectorXd lambda_ref = idx.unaryExpr(es.eigenvalues().real()); bool check_eigenvalues = lambda.isApprox(lambda_ref.head(neigen), 1E-6); if (!check_eigenvalues) { std::cout << "Davidson not converged after " << DS.num_iterations() << " iterations" << std::endl; std::cout << "Reference eigenvalues" << std::endl; std::cout << lambda_ref.head(neigen) << std::endl; std::cout << "Davidson eigenvalues" << std::endl; std::cout << lambda << std::endl; std::cout << "Residue norms" << std::endl; std::cout << DS.residues() << std::endl; } BOOST_CHECK_EQUAL(check_eigenvalues, 1); Eigen::MatrixXd evect_dav = DS.eigenvectors().real(); Eigen::MatrixXd evect = es.eigenvectors().real(); Eigen::MatrixXd evect_ref = extract_eigenvectors(evect, idx); bool check_eigenvectors = evect_ref.cwiseAbs2().isApprox(evect_dav.cwiseAbs2(), 0.001); BOOST_CHECK_EQUAL(check_eigenvectors, 1); } BOOST_AUTO_TEST_CASE(davidson_hamiltonian_matrix_free_large) { Index size = 120; Index neigen = 5; Logger log; // log.setReportLevel(TLogLevel::logDEBUG); // Create Operator HermitianBlockOperator Rop; Rop.set_size(size); Eigen::MatrixXd rmat = init_matrix(size, 0.01); Rop.attach_matrix(rmat); HermitianBlockOperator Cop; Cop.set_size(size); Eigen::MatrixXd cmat = symm_matrix(size, 0.01); Cop.attach_matrix(cmat); // create Hamiltonian operator HamiltonianOperator Hop(Rop, Cop); DavidsonSolver DS(log); DS.set_tolerance("normal"); DS.set_size_update("safe"); DS.set_max_search_space(50); DS.set_matrix_type("HAM"); DS.solve(Hop, neigen); std::cout << log; auto lambda = DS.eigenvalues().real(); std::sort(lambda.data(), lambda.data() + lambda.size()); Eigen::MatrixXd H = Hop.get_full_matrix(); Eigen::EigenSolver es(H); Eigen::ArrayXi idx = index_eval(es.eigenvalues().real(), neigen); Eigen::VectorXd lambda_ref = idx.unaryExpr(es.eigenvalues().real()); bool check_eigenvalues = lambda.isApprox(lambda_ref.head(neigen), 1E-6); if (!check_eigenvalues) { std::cout << "Davidson not converged after " << DS.num_iterations() << " iterations" << std::endl; std::cout << "Reference eigenvalues" << std::endl; std::cout << lambda_ref.head(neigen) << std::endl; std::cout << "Davidson eigenvalues" << std::endl; std::cout << lambda << std::endl; std::cout << "Residue norms" << std::endl; std::cout << DS.residues() << std::endl; } BOOST_CHECK_EQUAL(check_eigenvalues, 1); Eigen::MatrixXd evect_dav = DS.eigenvectors().real(); Eigen::MatrixXd evect = es.eigenvectors().real(); Eigen::MatrixXd evect_ref = extract_eigenvectors(evect, idx); bool check_eigenvectors = evect_ref.cwiseAbs2().isApprox(evect_dav.cwiseAbs2(), 0.001); BOOST_CHECK_EQUAL(check_eigenvectors, 1); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_density_filter.cc000066400000000000000000000306671412152066400207530ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE density_filter_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/filterfactory.h" #include using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(density_filter_test) BOOST_AUTO_TEST_CASE(coeffs_test) { libint2::initialize(); FilterFactory::RegisterAll(); std::unique_ptr rho_f = std::unique_ptr(Filter().Create("density")); std::ofstream opt("density_filter.xml"); opt << "0.0045" << std::endl; opt.close(); votca::tools::Property prop; prop.LoadFromXML("density_filter.xml"); rho_f->Initialize(prop.get("density")); std::ofstream xyzfile("molecule.xyz"); xyzfile << " 5" << std::endl; xyzfile << " methane" << std::endl; xyzfile << " C .000000 .000000 .000000" << std::endl; xyzfile << " H .629118 .629118 .629118" << std::endl; xyzfile << " H -.629118 -.629118 .629118" << std::endl; xyzfile << " H .629118 -.629118 -.629118" << std::endl; xyzfile << " H -.629118 .629118 -.629118" << std::endl; xyzfile.close(); std::ofstream basisfile("3-21G.xml"); basisfile << "" << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << "" << std::endl; basisfile.close(); Orbitals A; A.setDFTbasisName("3-21G.xml"); A.QMAtoms().LoadFromFile("molecule.xyz"); A.setBasisSetSize(17); A.setNumberOfAlphaElectrons(5); A.setNumberOfOccupiedLevels(5); A.MOs().eigenvalues() = Eigen::VectorXd::Zero(17); A.MOs().eigenvalues() << -19.8117, -6.22408, -6.14094, -6.14094, -6.14094, -3.72889, -3.72889, -3.72889, -3.64731, -3.09048, -3.09048, -3.09048, -2.63214, -2.08206, -2.08206, -2.08206, -2.03268; A.MOs().eigenvectors() = Eigen::MatrixXd::Zero(17, 17); A.MOs().eigenvectors() << -0.996559, -0.223082, 4.81443e-15, 2.21045e-15, -6.16146e-17, -3.16966e-16, 5.46703e-18, -1.09681e-15, -0.0301914, 6.45993e-16, 1.05377e-16, 3.41154e-16, -0.102052, -5.79826e-16, 9.38593e-16, -4.69346e-15, -0.111923, -0.0445146, 0.88316, -1.94941e-14, -8.67388e-15, -7.26679e-16, 1.16326e-14, -3.35886e-15, 2.37877e-14, 0.866126, 3.2068e-15, 3.80914e-15, 3.24563e-15, -0.938329, -6.4404e-15, 1.10811e-14, -5.5056e-14, -1.28767, 8.15798e-17, 2.30849e-14, 1.04169, 0.117804, 0.0951759, 0.179467, 0.147031, 0.39183, -1.02927e-14, 0.32699, -0.223689, -0.130009, 1.0375e-15, -0.0940179, 0.126956, 0.0122904, 1.41709e-15, 4.60157e-17, -7.1203e-15, 0.143338, -0.980459, -0.355251, 0.41611, -0.10826, -0.149964, 2.41546e-16, 0.12214, -0.0512447, 0.39537, 1.1054e-15, -0.0996828, -0.0636092, -0.105478, 5.10746e-15, -5.25872e-18, 4.8424e-15, 0.0488925, 0.364515, -0.9863, 0.0447336, 0.417155, -0.177023, 5.76117e-15, -0.228081, -0.348136, 0.0253377, -1.05286e-15, 0.079576, 0.0703157, -0.117608, 5.31327e-15, 0.0472716, 0.235837, -3.58018e-15, -1.68354e-15, 2.3989e-15, -9.86879e-15, 4.52519e-15, -1.6106e-14, -0.599523, -1.31237e-14, -8.63443e-15, -8.61196e-15, 1.8333, 2.05275e-14, -3.9562e-14, 1.89874e-13, 4.24316, -2.74184e-16, -1.53939e-15, -0.162416, -0.0183675, -0.0148395, -0.151162, -0.123842, -0.330032, 1.10084e-15, -1.45092, 0.992556, 0.576875, -3.82954e-15, 0.604373, -0.816111, -0.0790061, -8.89474e-15, -2.24862e-16, 3.23655e-15, -0.0223487, 0.152869, 0.0553894, -0.350483, 0.0911859, 0.126313, -5.48468e-15, -0.541961, 0.227383, -1.75434, -3.89443e-15, 0.640788, 0.408897, 0.67804, -3.17156e-14, -2.81346e-17, -1.09423e-15, -0.00762313, -0.0568338, 0.15378, -0.0376785, -0.351364, 0.149104, -4.94425e-15, 1.01204, 1.54475, -0.112429, 8.50653e-15, -0.511536, -0.452008, 0.756019, -3.3547e-14, -0.00106227, 0.0237672, 0.00345981, -0.00139675, -0.00349474, -0.597906, -0.425733, -0.0605479, -0.343823, 0.162103, -0.45692, 0.21318, -0.600309, 0.310843, -0.36406, 0.574148, 0.0554949, -0.00928842, -0.0414346, 0.0619999, -0.0250297, -0.0626259, 0.00227746, 0.00162164, 0.00023063, -0.0301047, 0.273177, -0.770004, 0.359253, 0.0095153, -0.8783, 1.02867, -1.62228, -1.24406, -0.00106227, 0.0237672, 0.00238182, 0.00205737, 0.00402848, 0.262742, 0.151145, -0.671213, -0.343823, 0.317484, 0.12884, -0.40386, -0.600309, 0.201313, -0.327527, -0.641099, 0.0554949, -0.00928842, -0.0414346, 0.0426822, 0.0368682, 0.0721904, -0.0010008, -0.000575719, 0.00255669, -0.0301047, 0.535026, 0.217123, -0.680588, 0.0095153, -0.568818, 0.925441, 1.81145, -1.24406, -0.00106227, 0.0237672, -0.00318563, 0.0034409, -0.00203628, 0.514364, -0.353326, 0.391148, -0.343823, -0.496623, -0.0536813, -0.176018, -0.600309, -0.744328, -0.01898, 0.0665156, 0.0554949, -0.00928842, -0.0414346, -0.0570866, 0.0616609, -0.0364902, -0.00195924, 0.00134584, -0.0014899, -0.0301047, -0.836913, -0.0904642, -0.296627, 0.0095153, 2.10313, 0.0536287, -0.187943, -1.24406, -0.00106227, 0.0237672, -0.002656, -0.00410152, 0.00150255, -0.1792, 0.627913, 0.340613, -0.343823, 0.0170366, 0.38176, 0.366698, -0.600309, 0.232172, 0.710567, 0.000435528, 0.0554949, -0.00928842, -0.0414346, -0.0475955, -0.0734994, 0.0269257, 0.000682583, -0.00239176, -0.00129742, -0.0301047, 0.0287103, 0.643346, 0.617962, 0.0095153, -0.656011, -2.00774, -0.0012306, -1.24406; A.setBSEindices(0, 16); A.setTDAApprox(true); A.setGWindices(0, 16); Eigen::MatrixXd spsi_ref = Eigen::MatrixXd::Zero(60, 3); spsi_ref << -0.00178316, -0.0558332, 0.0151767, 0.00568291, 0.0149417, 0.0556358, 0.05758, -0.00320371, -0.00502105, 0.00379328, -0.00232255, -0.00817518, -0.00848959, -0.000618633, -0.00376334, -0.000395809, -0.00899117, 0.0023708, 7.13955e-08, 3.47498e-08, -1.08537e-08, 0.000420413, 0.011896, -0.00320024, -0.00288487, 0.00320821, 0.0115465, 0.0119767, 0.000355172, 0.00289343, -2.55565e-08, 1.91684e-08, 3.01647e-09, 6.84051e-09, 2.79592e-10, -1.35767e-09, 0.00420618, 0.092451, -0.0239374, 0.0036276, 0.0113951, 0.0471896, 0.0465325, -0.00398807, -0.00484251, 0.0051614, -0.0031325, -0.0112447, -0.010968, -0.000896935, -0.00488789, 0.000951266, 0.0239709, -0.00630323, 0.000419006, 0.0201651, -0.00573095, -0.00118124, -0.0269275, 0.00700955, -0.00345217, 0.00356488, 0.0134361, 0.013156, 9.58532e-05, 0.00315613, -2.58268e-05, -0.00124098, 0.000352706, -1.80679e-06, -8.71959e-05, 2.47799e-05, -0.0150073, 0.0114186, 0.0443012, 0.0180327, -0.026287, 0.0734351, -0.0643994, 0.0257628, 0.0132084, -0.0123339, 0.0092297, -0.0148779, 0.0122493, -0.00246837, -0.0125735, -0.00375172, 0.00294872, 0.0112899, 0.00648758, -0.0055755, -0.0191436, 0.00433063, -0.00332619, -0.0128321, 0.0111166, -0.00969272, 0.0189659, -0.0160119, 0.00458659, 0.0107104, -0.000399315, 0.000343129, 0.00117813, -2.80525e-05, 2.41086e-05, 8.2778e-05, -0.0450479, -0.00034974, -0.015063, 0.0655838, 0.0115163, -0.022358, 0.0220978, 0.0583236, 0.0513097, -0.0119156, 0.00490159, 0.0116429, -0.0132479, -0.0146227, -0.00863565, -0.0118978, -0.000282044, -0.00400272, 0.0199347, 0.00139057, 0.00635067, 0.0131991, 0.000163177, 0.00441453, 0.0159091, -0.00241207, -0.0110696, 0.0123057, 0.0171503, 0.0119626, -0.00122682, -8.55716e-05, -0.00039083, -8.62007e-05, -6.0128e-06, -2.746e-05, -0.0304688, -0.954049, 0.259333, 0.0971056, 0.255313, 0.950672, 0.983887, -0.0547431, -0.0857965, 0.0170489, -0.0104387, -0.036743, -0.0381557, -0.00278036, -0.0169143, -0.00177889, -0.04041, 0.0106552, -2.23782e-07, 2.40738e-07, 1.03401e-07, -0.000182535, -0.00516415, 0.00138942, 0.00125201, -0.00139237, -0.00501195, -0.00519809, -0.000154171, -0.00125602, 4.03664e-08, -6.04796e-08, -4.6768e-08, -2.38233e-09, 2.31605e-09, 1.35922e-09; A.BSESinglets().eigenvectors() = spsi_ref; // reference energy Eigen::VectorXd se_ref = Eigen::VectorXd::Zero(3); se_ref << 0.107455, 0.107455, 0.107455; A.BSESinglets().eigenvalues() = se_ref; A.CalcCoupledTransition_Dipoles(); BOOST_CHECK_EQUAL(rho_f->NeedsInitialState(), true); rho_f->UpdateHist(A, QMState("s1")); std::vector ref = {0}; std::vector results = rho_f->CalcIndeces(A, QMStateType::Singlet); for (votca::Index i = 0; i < votca::Index(ref.size()); i++) { BOOST_CHECK_EQUAL(ref[i], results[i]); } BOOST_CHECK_EQUAL(results.size(), ref.size()); rho_f->UpdateHist(A, QMState("s2")); std::vector results2 = rho_f->CalcIndeces(A, QMStateType::Singlet); std::vector ref2 = {1}; for (votca::Index i = 0; i < votca::Index(ref2.size()); i++) { BOOST_CHECK_EQUAL(ref2[i], results2[i]); } libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_densityintegration.cc000066400000000000000000000103671412152066400216450ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE density_integration_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/tools/eigenio_matrixmarket.h" #include "votca/xtp/density_integration.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/vxc_grid.h" using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(density_integration_test) AOBasis CreateBasis(const QMMolecule& mol) { BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/densityintegration/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, mol); return aobasis; } BOOST_AUTO_TEST_CASE(density_test) { libint2::initialize(); QMMolecule mol("none", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/densityintegration/molecule.xyz"); AOBasis aobasis = CreateBasis(mol); Eigen::MatrixXd dmat = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/densityintegration/dmat.mm"); Vxc_Grid grid; grid.GridSetup("medium", mol, aobasis); DensityIntegration num(grid); double ntot = num.IntegrateDensity(dmat); BOOST_CHECK_CLOSE(ntot, 8.000000, 1e-5); Eigen::Vector3d pos = {3, 3, 3}; BOOST_CHECK_CLOSE(num.IntegratePotential(pos), -1.543242, 1e-4); Eigen::Vector3d field = num.IntegrateField(pos); Eigen::Vector3d field_ref = {0.172802, 0.172802, 0.172802}; bool field_check = field.isApprox(field_ref, 1e-5); if (!field_check) { std::cout << "field" << std::endl; std::cout << field.transpose() << std::endl; std::cout << "ref" << std::endl; std::cout << field_ref.transpose() << std::endl; } libint2::finalize(); } BOOST_AUTO_TEST_CASE(gyration_test) { libint2::initialize(); ofstream xyzfile("molecule.xyz"); xyzfile << " 5" << endl; xyzfile << " methane" << endl; xyzfile << " C 1.000000 1.000000 1.000000" << endl; xyzfile << " H 1.629118 1.629118 1.629118" << endl; xyzfile << " H 0.370882 0.370882 1.629118" << endl; xyzfile << " H 1.629118 0.370882 0.370882" << endl; xyzfile << " H 0.370882 1.629118 0.370882" << endl; xyzfile.close(); QMMolecule mol("none", 0); mol.LoadFromFile("molecule.xyz"); AOBasis aobasis = CreateBasis(mol); Eigen::MatrixXd dmat = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/densityintegration/dmat.mm"); Vxc_Grid grid; grid.GridSetup("medium", mol, aobasis); DensityIntegration num(grid); Gyrationtensor tensor = num.IntegrateGyrationTensor(dmat); BOOST_CHECK_CLOSE(tensor.mass, 8.0000005, 1e-5); Eigen::Vector3d dip_ref = Eigen::Vector3d::Zero(); dip_ref << 1.88973, 1.88973, 1.88973; bool centroid_check = dip_ref.isApprox(tensor.centroid, 1e-5); BOOST_CHECK_EQUAL(centroid_check, true); if (!centroid_check) { std::cout << "centroid" << std::endl; std::cout << tensor.centroid.transpose() << std::endl; std::cout << "ref" << std::endl; std::cout << dip_ref.transpose() << std::endl; } Eigen::Matrix3d gyro_ref = Eigen::Matrix3d::Zero(); gyro_ref << 0.596158, 2.85288e-12, 2.86873e-12, 2.85289e-12, 0.596158, 2.87163e-12, 2.86874e-12, 2.87161e-12, 0.596158; bool gyro_check = gyro_ref.isApprox(tensor.gyration, 1e-5); BOOST_CHECK_EQUAL(gyro_check, true); if (!gyro_check) { std::cout << "gyro" << std::endl; std::cout << tensor.gyration << std::endl; std::cout << "ref" << std::endl; std::cout << gyro_ref << std::endl; } libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_dftcoupling.cc000066400000000000000000000631171412152066400202410ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE dftcoupling_test // Third party includes #include // Local VOTCA includes #include "votca/xtp/dftcoupling.h" #include using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(dftcoupling_test) Eigen::MatrixXd ReadMatrixFromString(const std::string& matrix) { votca::tools::Tokenizer lines(matrix, "\n"); std::vector entries; Index cols = 0; Index rows = 0; for (auto line : lines) { if (line[0] == '#') { continue; } votca::tools::Tokenizer entries_tok(line, " "); std::vector temp = entries_tok.ToVector(); cols = Index(temp.size()); rows++; for (const auto& s : temp) { entries.push_back(std::stod(s)); } } return Eigen::Map(entries.data(), rows, cols); } BOOST_AUTO_TEST_CASE(coupling) { libint2::initialize(); std::ofstream opt("dftcoupling.xml"); opt << " " << std::endl; opt << " 0.0" << std::endl; opt << " 2" << std::endl; opt << " 2" << std::endl; opt << " " << std::endl; opt.close(); std::ofstream xyzfile("molecule.xyz"); xyzfile << " 5" << std::endl; xyzfile << " methane" << std::endl; xyzfile << " C .000000 .000000 .000000" << std::endl; xyzfile << " H .629118 .629118 .629118" << std::endl; xyzfile << " H -.629118 -.629118 .629118" << std::endl; xyzfile << " H .629118 -.629118 -.629118" << std::endl; xyzfile << " H -.629118 .629118 -.629118" << std::endl; xyzfile.close(); std::ofstream basisfile("3-21G.xml"); basisfile << "" << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << "" << std::endl; basisfile.close(); Orbitals A; A.setDFTbasisName("3-21G.xml"); A.QMAtoms().LoadFromFile("molecule.xyz"); A.setBasisSetSize(17); A.setNumberOfAlphaElectrons(5); A.setNumberOfOccupiedLevels(5); A.MOs().eigenvalues() = Eigen::VectorXd::Zero(17); A.MOs().eigenvalues() << -19.8117, -6.22408, -6.14094, -6.14094, -6.14094, -3.72889, -3.72889, -3.72889, -3.64731, -3.09048, -3.09048, -3.09048, -2.63214, -2.08206, -2.08206, -2.08206, -2.03268; A.MOs().eigenvectors() = Eigen::MatrixXd::Zero(17, 17); A.MOs().eigenvectors() << -0.996559, -0.223082, 4.81443e-15, 2.21045e-15, -6.16146e-17, -3.16966e-16, 5.46703e-18, -1.09681e-15, -0.0301914, 6.45993e-16, 1.05377e-16, 3.41154e-16, -0.102052, -5.79826e-16, 9.38593e-16, -4.69346e-15, -0.111923, -0.0445146, 0.88316, -1.94941e-14, -8.67388e-15, -7.26679e-16, 1.16326e-14, -3.35886e-15, 2.37877e-14, 0.866126, 3.2068e-15, 3.80914e-15, 3.24563e-15, -0.938329, -6.4404e-15, 1.10811e-14, -5.5056e-14, -1.28767, 8.15798e-17, 2.30849e-14, 1.04169, 0.117804, 0.0951759, 0.179467, 0.147031, 0.39183, -1.02927e-14, 0.32699, -0.223689, -0.130009, 1.0375e-15, -0.0940179, 0.126956, 0.0122904, 1.41709e-15, 4.60157e-17, -7.1203e-15, 0.143338, -0.980459, -0.355251, 0.41611, -0.10826, -0.149964, 2.41546e-16, 0.12214, -0.0512447, 0.39537, 1.1054e-15, -0.0996828, -0.0636092, -0.105478, 5.10746e-15, -5.25872e-18, 4.8424e-15, 0.0488925, 0.364515, -0.9863, 0.0447336, 0.417155, -0.177023, 5.76117e-15, -0.228081, -0.348136, 0.0253377, -1.05286e-15, 0.079576, 0.0703157, -0.117608, 5.31327e-15, 0.0472716, 0.235837, -3.58018e-15, -1.68354e-15, 2.3989e-15, -9.86879e-15, 4.52519e-15, -1.6106e-14, -0.599523, -1.31237e-14, -8.63443e-15, -8.61196e-15, 1.8333, 2.05275e-14, -3.9562e-14, 1.89874e-13, 4.24316, -2.74184e-16, -1.53939e-15, -0.162416, -0.0183675, -0.0148395, -0.151162, -0.123842, -0.330032, 1.10084e-15, -1.45092, 0.992556, 0.576875, -3.82954e-15, 0.604373, -0.816111, -0.0790061, -8.89474e-15, -2.24862e-16, 3.23655e-15, -0.0223487, 0.152869, 0.0553894, -0.350483, 0.0911859, 0.126313, -5.48468e-15, -0.541961, 0.227383, -1.75434, -3.89443e-15, 0.640788, 0.408897, 0.67804, -3.17156e-14, -2.81346e-17, -1.09423e-15, -0.00762313, -0.0568338, 0.15378, -0.0376785, -0.351364, 0.149104, -4.94425e-15, 1.01204, 1.54475, -0.112429, 8.50653e-15, -0.511536, -0.452008, 0.756019, -3.3547e-14, -0.00106227, 0.0237672, 0.00345981, -0.00139675, -0.00349474, -0.597906, -0.425733, -0.0605479, -0.343823, 0.162103, -0.45692, 0.21318, -0.600309, 0.310843, -0.36406, 0.574148, 0.0554949, -0.00928842, -0.0414346, 0.0619999, -0.0250297, -0.0626259, 0.00227746, 0.00162164, 0.00023063, -0.0301047, 0.273177, -0.770004, 0.359253, 0.0095153, -0.8783, 1.02867, -1.62228, -1.24406, -0.00106227, 0.0237672, 0.00238182, 0.00205737, 0.00402848, 0.262742, 0.151145, -0.671213, -0.343823, 0.317484, 0.12884, -0.40386, -0.600309, 0.201313, -0.327527, -0.641099, 0.0554949, -0.00928842, -0.0414346, 0.0426822, 0.0368682, 0.0721904, -0.0010008, -0.000575719, 0.00255669, -0.0301047, 0.535026, 0.217123, -0.680588, 0.0095153, -0.568818, 0.925441, 1.81145, -1.24406, -0.00106227, 0.0237672, -0.00318563, 0.0034409, -0.00203628, 0.514364, -0.353326, 0.391148, -0.343823, -0.496623, -0.0536813, -0.176018, -0.600309, -0.744328, -0.01898, 0.0665156, 0.0554949, -0.00928842, -0.0414346, -0.0570866, 0.0616609, -0.0364902, -0.00195924, 0.00134584, -0.0014899, -0.0301047, -0.836913, -0.0904642, -0.296627, 0.0095153, 2.10313, 0.0536287, -0.187943, -1.24406, -0.00106227, 0.0237672, -0.002656, -0.00410152, 0.00150255, -0.1792, 0.627913, 0.340613, -0.343823, 0.0170366, 0.38176, 0.366698, -0.600309, 0.232172, 0.710567, 0.000435528, 0.0554949, -0.00928842, -0.0414346, -0.0475955, -0.0734994, 0.0269257, 0.000682583, -0.00239176, -0.00129742, -0.0301047, 0.0287103, 0.643346, 0.617962, 0.0095153, -0.656011, -2.00774, -0.0012306, -1.24406; Orbitals B = A; B.QMAtoms().Translate(4 * Eigen::Vector3d::UnitX()); Orbitals AB; AB.QMAtoms() = A.QMAtoms(); AB.QMAtoms().AddContainer(B.QMAtoms()); AB.MOs().eigenvalues().resize(34); AB.MOs().eigenvalues() << -10.1341, -10.1337, -0.808607, -0.665103, -0.474928, -0.455857, -0.455857, -0.365971, -0.365971, -0.263259, 0.140444, 0.154745, 0.168775, 0.168775, 0.223948, 0.231217, 0.26323, 0.26323, 0.713478, 0.713478, 0.793559, 0.885998, 0.944915, 0.944915, 1.01169, 1.04977, 1.04977, 1.08863, 1.10318, 1.17822, 1.18094, 1.18094, 1.69037, 1.91046; std::string mos_ref_string = " -0.697309 -0.697192 -0.138562 0.154639 0.0435428 1.73438e-12 " "2.13093e-13 -8.65189e-14 -3.43449e-14 0.0581478 -0.13454 -0.0376033 " "5.46382e-12 8.3231e-14 0.111183 -0.00798105 1.59258e-13 1.63619e-12 " "2.3882e-12 -1.87201e-14 0.00654486 0.048026 3.94367e-12 -5.11935e-14 " "-0.0789143 3.6718e-14 1.52055e-12 -0.0134363 -0.00206854 -0.0770242 " "4.59464e-11 -2.01607e-13 -0.00162496 -0.0367745\n" " -0.0783921 -0.0769772 0.116956 -0.142166 -0.0554301 -3.50499e-12 " "-1.86741e-13 5.36568e-14 5.11008e-13 -0.0529852 0.0398041 0.00322307 " "-1.70454e-12 -1.13104e-13 -0.0504198 0.0144859 7.16041e-14 3.37842e-12 " "1.55705e-11 -9.16012e-14 0.110589 0.00602313 3.50438e-12 1.49731e-13 " "-0.0786935 7.1578e-13 8.77919e-12 -0.0741183 0.0994097 0.480567 " "-2.86802e-10 8.58629e-13 -1.41349 -1.37617\n" "-1.31663e-14 5.79687e-15 -9.12567e-13 -1.21281e-12 -9.79314e-12 " "0.179808 -0.175214 0.202197 0.194016 7.90197e-12 2.10679e-12 " "1.26699e-11 0.188156 0.116443 -7.73171e-12 -1.56645e-11 -0.255098 " "0.153207 -0.530812 0.119984 5.20064e-11 2.27813e-11 -0.194538 -0.39235 " "-3.45222e-11 -0.667081 -0.369257 3.03131e-11 -1.41125e-11 2.6854e-10 " "0.426545 0.234686 -1.21861e-12 7.38641e-13\n" "-1.97257e-14 -8.71107e-16 -6.32194e-13 -1.70457e-12 -1.12352e-11 " "0.180436 0.174567 -0.202601 0.193595 7.92911e-12 2.22435e-12 " "1.26533e-11 0.188465 -0.115943 -8.11243e-12 -1.54494e-11 0.256652 " "0.150589 -0.531118 -0.118621 5.18854e-11 2.30201e-11 -0.184528 0.397156 " "-3.33442e-11 0.667869 -0.36783 3.10521e-11 -1.40613e-11 2.68602e-10 " "0.4268 -0.234223 -9.00545e-13 9.31133e-13\n" " -0.00115489 0.000164776 0.0578394 0.0454767 0.251996 1.19171e-11 " "6.58841e-13 -2.64913e-13 1.44576e-11 -0.294909 -0.00802487 0.199834 " "-2.06998e-11 -1.42604e-13 0.151363 -0.218658 2.00335e-13 -2.66865e-12 " "3.61889e-11 -7.66537e-14 0.620011 -0.624288 -1.35313e-11 6.45206e-13 " "-0.0930979 -6.0734e-13 3.55302e-11 0.476225 0.450576 -0.323109 " "2.04055e-10 -7.22344e-13 0.0223133 -0.1443\n" " 0.060534 0.0561821 0.415836 -0.487318 -0.114633 1.54029e-12 " "-5.10868e-13 2.51948e-14 -2.28281e-12 -0.287976 1.82438 0.51819 " "-7.75715e-11 -1.07587e-12 -1.6604 0.033244 -2.25681e-12 -2.86385e-11 " "-2.19985e-12 1.54692e-13 0.1436 -0.365953 -3.10497e-11 2.09328e-14 " "0.237819 -1.55317e-12 -9.07554e-12 0.0534822 -0.272317 -0.708544 " "4.23309e-10 -9.43029e-13 2.71501 2.80085\n" " 2.08366e-13 -1.03736e-14 -1.14485e-12 1.42553e-13 -1.42216e-11 " "0.125879 -0.173468 0.166021 0.168907 -3.38267e-12 -4.79722e-12 " "5.09993e-11 0.639391 0.580945 -2.31268e-11 -4.28666e-11 -0.844352 " "0.75214 0.849064 -0.215142 -1.07708e-10 -3.4986e-11 -0.256404 1.12602 " "5.1508e-11 1.26525 0.754312 -6.50804e-11 3.10304e-11 -4.78706e-10 " "-0.741441 -0.00363983 1.77776e-12 -4.23163e-12\n" " 2.11528e-13 -6.42308e-15 -9.3007e-13 -2.46589e-13 -1.55798e-11 " "0.126502 0.173014 -0.166372 0.16856 -3.42581e-12 -5.1542e-12 " "5.02221e-11 0.640932 -0.579245 -2.38678e-11 -4.16714e-11 0.852002 " "0.743462 0.849613 0.212963 -1.07194e-10 -3.59559e-11 -0.284869 -1.11916 " "4.93541e-11 -1.26686 0.751605 -6.64254e-11 3.05998e-11 -4.76759e-10 " "-0.741444 0.00283525 1.41929e-12 -4.41113e-12\n" " 0.00325132 0.00072711 0.0753503 0.00950181 0.228655 1.62908e-11 " "5.88682e-13 -2.68345e-13 3.87226e-12 -0.28074 0.144232 0.869449 " "-8.4971e-11 -8.8691e-13 0.415771 -1.00835 4.58046e-13 -4.59974e-11 " "-1.24163e-10 3.99175e-13 -1.58015 0.920689 2.69425e-11 -1.12376e-12 " "0.183046 5.98902e-13 -2.88527e-11 -0.380313 -0.581711 0.578926 " "-3.6625e-10 1.2043e-12 -0.0303405 0.329309\n" " -0.0011464 0.00141574 0.102123 -0.062761 0.0756644 0.175473 " "-0.000315324 -0.00015246 0.14636 -0.14431 -0.0206219 -0.0846146 " "-0.0777281 -0.000103235 0.0556423 0.0507764 -0.000268375 -0.0524635 " "-0.511888 0.000656729 0.208213 -0.0190293 0.352659 -0.00447108 " "-0.391351 -0.000339021 0.317159 -0.515189 -0.458517 -0.471794 -0.629635 " "-0.000341627 0.0265973 -0.362435\n" " -0.013307 -0.00957248 -0.00732072 -0.00310248 0.0344914 0.171006 " "-0.000307297 -0.000150334 0.144318 -0.179084 -0.712591 -0.830754 " "-0.806581 -0.00107126 0.596627 0.752064 -0.00677785 -1.32497 0.0988994 " "-0.000126883 -0.474187 -0.145716 0.519372 -0.0065847 0.348342 " "0.00135561 -1.2682 0.790399 0.710069 0.136107 1.34459 0.000729549 " "-0.543167 -0.623166\n" " 8.55501e-05 0.000986043 0.0536401 -0.105273 -0.128709 -0.000224935 " "-0.125172 0.182036 0.000189623 0.101776 -0.00109152 0.0317062 " "0.000173788 -0.130849 0.00264037 -0.0712429 -0.0375076 0.000191869 " "-6.64731e-06 -0.00518125 -0.201684 0.377977 -0.00805124 -0.635046 " "-0.544273 0.358244 0.000382938 0.322411 0.418971 -0.334379 0.00033114 " "-0.610306 -0.0454904 -0.194439\n" " -0.0091205 -0.0117179 0.00848738 -0.0268224 -0.085757 -0.000140587 " "-0.0782345 0.184258 0.000191937 0.16027 -0.556338 0.388959 0.00126037 " "-0.948964 0.908403 -0.807446 1.13292 -0.00579543 0.000121528 0.0947251 " "-0.306129 0.0971475 -0.00206653 -0.162999 0.298931 -1.1321 -0.00121013 " "-0.454898 -0.615171 0.499217 -0.000372134 0.685859 -0.622467 -0.343531\n" " -0.0011464 0.00141574 0.102123 -0.062761 0.0756644 -0.175473 " "0.000315324 0.00015246 -0.14636 -0.14431 -0.0206219 -0.0846146 " "0.0777281 0.000103235 0.0556423 0.0507764 0.000268375 0.0524635 " "0.511888 -0.000656729 0.208213 -0.0190293 -0.352659 0.00447108 " "-0.391351 0.000339021 -0.317159 -0.515189 -0.458517 -0.471794 0.629635 " "0.000341627 0.0265973 -0.362435\n" " -0.013307 -0.00957248 -0.00732072 -0.00310248 0.0344914 -0.171006 " "0.000307297 0.000150334 -0.144318 -0.179084 -0.712591 -0.830754 " "0.806581 0.00107126 0.596627 0.752064 0.00677785 1.32497 -0.0988994 " "0.000126883 -0.474187 -0.145716 -0.519372 0.0065847 0.348342 " "-0.00135561 1.2682 0.790399 0.710069 0.136107 -1.34459 -0.000729549 " "-0.543167 -0.623166\n" " 8.55501e-05 0.000986043 0.0536401 -0.105273 -0.128709 0.000224935 " "0.125172 -0.182036 -0.000189623 0.101776 -0.00109152 0.0317062 " "-0.000173788 0.130849 0.00264037 -0.0712429 0.0375076 -0.000191869 " "6.6473e-06 0.00518125 -0.201684 0.377977 0.00805124 0.635046 -0.544273 " "-0.358244 -0.000382937 0.322411 0.418971 -0.334379 -0.00033114 0.610306 " "-0.0454904 -0.194439\n" " -0.0091205 -0.0117179 0.00848738 -0.0268224 -0.085757 0.000140587 " "0.0782345 -0.184258 -0.000191937 0.16027 -0.556338 0.388959 -0.00126037 " "0.948964 0.908403 -0.807446 -1.13292 0.00579543 -0.000121528 -0.0947251 " "-0.306129 0.0971475 0.00206653 0.162999 0.298931 1.1321 0.00121013 " "-0.454898 -0.615171 0.499217 0.000372133 -0.685859 -0.622467 -0.343531\n" " -0.697309 0.697192 -0.138562 -0.154639 0.0435428 1.49203e-12 " "9.77213e-14 1.24841e-14 1.25141e-12 -0.0581478 -0.13454 0.0376033 " "-7.21201e-12 7.1008e-14 -0.111183 -0.00798105 -9.94282e-15 -6.00058e-13 " "2.88443e-13 1.04188e-14 -0.00654486 0.048026 -1.03258e-12 -3.53311e-14 " "0.0789143 -1.02089e-13 -7.69953e-12 0.0134363 -0.00206854 -0.0770242 " "4.60228e-11 -1.45926e-13 0.00162496 -0.0367745\n" " -0.0783921 0.0769772 0.116956 0.142166 -0.0554301 -5.20584e-12 " "-1.00581e-13 1.64705e-14 -3.0152e-12 0.0529852 0.0398041 -0.00322307 " "2.08288e-13 -1.90771e-14 0.0504198 0.0144859 3.37325e-14 -1.30319e-13 " "-2.38237e-11 1.44013e-13 -0.110589 0.00602313 -3.17329e-12 -1.06756e-14 " "0.0786935 1.78234e-13 2.00784e-11 0.0741183 0.0994097 0.480567 " "-2.8943e-10 1.1105e-12 1.41349 -1.37617\n" "-1.94715e-14 1.93153e-14 -1.63987e-12 1.9805e-12 -5.25726e-12 0.174567 " "-0.180436 -0.193595 -0.202601 -6.02172e-12 5.04867e-12 -1.17883e-12 " "-0.115943 -0.188465 2.56675e-12 -2.29827e-12 -0.150589 0.256652 " "0.118621 -0.531118 -1.87996e-12 -1.40338e-11 0.397156 0.184528 " "-3.11885e-11 -0.36783 -0.667869 3.25477e-11 1.46489e-11 -1.16403e-10 " "-0.234223 -0.4268 5.13688e-12 1.85941e-12\n" "-2.76824e-14 2.71818e-14 -1.50687e-12 2.10656e-12 -6.03834e-12 0.175214 " "0.179808 0.194016 -0.202197 -6.09358e-12 5.43735e-12 -9.64377e-13 " "-0.116443 0.188156 2.44188e-12 -2.23432e-12 0.153207 0.255098 0.119984 " "0.530812 -1.64208e-12 -1.40718e-11 0.39235 -0.194538 -3.09928e-11 " "0.369257 -0.667081 3.30204e-11 1.49297e-11 -1.18997e-10 -0.234686 " "0.426545 5.05575e-12 1.94355e-12\n" " 0.00115489 0.000164776 -0.0578394 0.0454767 -0.251996 -5.69911e-12 " "-7.97142e-13 5.68508e-14 1.3035e-11 -0.294909 0.00802487 0.199834 " "7.61611e-12 -9.8441e-14 0.151363 0.218658 -5.89857e-14 8.58175e-12 " "1.10677e-10 -3.79358e-13 0.620011 0.624288 -7.96112e-12 -1.08888e-13 " "-0.0930979 1.20145e-13 3.63482e-11 0.476225 -0.450576 0.323109 " "-2.09343e-10 7.74471e-13 0.0223133 0.1443\n" " 0.060534 -0.0561821 0.415836 0.487318 -0.114633 4.73838e-12 " "-2.00065e-13 -3.44901e-14 -4.54885e-12 0.287976 1.82438 -0.51819 " "1.02866e-10 -8.89747e-13 1.6604 0.033244 2.01243e-13 4.8244e-12 " "-5.98145e-12 -2.17907e-13 -0.1436 -0.365953 1.00174e-11 2.37019e-13 " "-0.237819 -2.93644e-13 -1.26674e-11 -0.0534822 -0.272317 -0.708544 " "4.1826e-10 -1.73009e-12 -2.71501 2.80085\n" " 2.66098e-13 -3.10494e-13 5.25454e-13 -3.01832e-13 -8.47312e-12 " "0.173014 -0.126502 -0.16856 -0.166372 -2.37598e-12 -2.19896e-12 " "-3.16763e-11 -0.579245 -0.640932 1.7174e-11 1.07442e-11 -0.743462 " "0.852002 -0.212963 0.849613 -8.91957e-12 3.46585e-11 -1.11916 0.284869 " "5.32058e-11 0.751605 1.26686 -6.82198e-11 -9.26745e-12 -4.60515e-11 " "0.00283525 0.741444 -9.92385e-12 -1.24539e-12\n" " 2.71095e-13 -3.13867e-13 6.16964e-13 -2.6292e-13 -9.09244e-12 0.173468 " "0.125879 0.168907 -0.166021 -2.49777e-12 -9.54976e-13 -3.07486e-11 " "-0.580945 0.639391 1.64204e-11 1.15619e-11 0.75214 0.844352 -0.215142 " "-0.849064 -9.09168e-12 3.41739e-11 -1.12602 -0.256404 5.25065e-11 " "-0.754312 1.26525 -6.90363e-11 -9.8764e-12 -4.12883e-11 0.00363983 " "-0.741441 -9.93678e-12 -1.37646e-12\n" " -0.00325132 0.00072711 -0.0753503 0.00950181 -0.228655 -1.83426e-11 " "-6.23026e-13 1.16744e-13 -1.52124e-12 -0.28074 -0.144232 0.869449 " "-8.0255e-12 -3.3796e-13 0.415771 1.00835 -2.11614e-13 8.62638e-13 " "-2.5409e-10 9.75851e-13 -1.58015 -0.920689 2.99441e-11 -5.07104e-14 " "0.183046 -4.50746e-13 -4.51192e-11 -0.380313 0.581711 -0.578926 " "3.56562e-10 -1.33803e-12 -0.0303405 -0.329309\n" " 8.55501e-05 -0.000986043 0.0536401 0.105273 -0.128709 0.125172 " "-0.000224935 0.000189623 -0.182036 -0.101776 -0.00109152 -0.0317062 " "0.130849 0.000173788 -0.00264037 -0.0712429 0.000191869 0.0375076 " "-0.00518125 6.64731e-06 0.201684 0.377977 0.635046 -0.00805124 0.544273 " "-0.000382938 0.358244 -0.322411 0.418971 -0.334379 0.610306 0.00033114 " "0.0454904 -0.194439\n" " -0.0091205 0.0117179 0.00848738 0.0268224 -0.085757 0.0782345 " "-0.000140587 0.000191937 -0.184258 -0.16027 -0.556338 -0.388959 " "0.948964 0.00126037 -0.908403 -0.807446 -0.00579543 -1.13292 0.0947251 " "-0.000121528 0.306129 0.0971475 0.162999 -0.00206653 -0.298931 " "0.00121013 -1.1321 0.454898 -0.615171 0.499217 -0.685859 -0.000372134 " "0.622467 -0.343531\n" " -0.0011464 -0.00141574 0.102123 0.062761 0.0756644 -0.000315324 " "-0.175473 -0.14636 -0.00015246 0.14431 -0.0206219 0.0846146 " "-0.000103235 0.0777281 -0.0556423 0.0507764 0.0524635 -0.000268375 " "-0.000656729 -0.511888 -0.208213 -0.0190293 -0.00447108 -0.352659 " "0.391351 0.317159 0.000339021 0.515189 -0.458517 -0.471794 -0.000341627 " "0.629635 -0.0265973 -0.362435\n" " -0.013307 0.00957248 -0.00732072 0.00310248 0.0344914 -0.000307297 " "-0.171006 -0.144318 -0.000150334 0.179084 -0.712591 0.830754 " "-0.00107126 0.806581 -0.596627 0.752064 1.32497 -0.00677785 0.000126883 " "0.0988994 0.474187 -0.145716 -0.0065847 -0.519372 -0.348342 -1.2682 " "-0.00135561 -0.790399 0.710069 0.136107 0.000729549 -1.34459 0.543167 " "-0.623166\n" " 8.55501e-05 -0.000986043 0.0536401 0.105273 -0.128709 -0.125172 " "0.000224935 -0.000189623 0.182036 -0.101776 -0.00109152 -0.0317062 " "-0.130849 -0.000173788 -0.00264037 -0.0712429 -0.000191869 -0.0375076 " "0.00518125 -6.64731e-06 0.201684 0.377977 -0.635046 0.00805124 0.544273 " "0.000382938 -0.358244 -0.322411 0.418971 -0.334379 -0.610306 " "-0.00033114 0.0454904 -0.194439\n" " -0.0091205 0.0117179 0.00848738 0.0268224 -0.085757 -0.0782345 " "0.000140587 -0.000191937 0.184258 -0.16027 -0.556338 -0.388959 " "-0.948964 -0.00126037 -0.908403 -0.807446 0.00579543 1.13292 -0.0947251 " "0.000121528 0.306129 0.0971475 -0.162999 0.00206653 -0.298931 " "-0.00121013 1.1321 0.454898 -0.615171 0.499217 0.685859 0.000372134 " "0.622467 -0.343531\n" " -0.0011464 -0.00141574 0.102123 0.062761 0.0756644 0.000315324 " "0.175473 0.14636 0.00015246 0.14431 -0.0206219 0.0846146 0.000103235 " "-0.0777281 -0.0556423 0.0507764 -0.0524635 0.000268375 0.000656729 " "0.511888 -0.208213 -0.0190293 0.00447108 0.352659 0.391351 -0.317159 " "-0.000339021 0.515189 -0.458517 -0.471794 0.000341628 -0.629635 " "-0.0265973 -0.362435\n" " -0.013307 0.00957248 -0.00732072 0.00310248 0.0344914 0.000307297 " "0.171006 0.144318 0.000150334 0.179084 -0.712591 0.830754 0.00107126 " "-0.806581 -0.596627 0.752064 -1.32497 0.00677785 -0.000126883 " "-0.0988994 0.474187 -0.145716 0.0065847 0.519372 -0.348342 1.2682 " "0.00135561 -0.790399 0.710069 0.136107 -0.000729549 1.34459 0.543167 " "-0.623166"; AB.setBasisSetSize(34); AB.setDFTbasisName(A.getDFTbasisName()); AB.MOs().eigenvectors() = ReadMatrixFromString(mos_ref_string); AB.setNumberOfAlphaElectrons(10); AB.setNumberOfOccupiedLevels(10); votca::tools::Property prop; prop.LoadFromXML("dftcoupling.xml"); DFTcoupling dftcoup; Logger log; dftcoup.setLogger(&log); dftcoup.Initialize(prop.get("dftcoupling_options")); log.setCommonPreface("\n... ..."); dftcoup.CalculateCouplings(A, B, AB); votca::tools::Property output; dftcoup.Addoutput(output, A, B); std::map > hole_ref; hole_ref[3][3] = -1.031779; hole_ref[3][4] = -8.652046; hole_ref[4][3] = 3.806175; hole_ref[4][4] = -5.745457; std::map > electron_ref; electron_ref[5][5] = 3.080669; electron_ref[5][6] = 2.445706; electron_ref[6][5] = -1.622705; electron_ref[6][6] = 6.692015; auto holedata = output.Select("hole.coupling"); for (auto h : holedata) { Index levA = h->getAttribute("levelA"); Index levB = h->getAttribute("levelB"); double j = h->getAttribute("j"); BOOST_CHECK_CLOSE(j, hole_ref[levA][levB], 1e-5); } auto electrondata = output.Select("electron.coupling"); for (auto h : holedata) { Index levA = h->getAttribute("levelA"); Index levB = h->getAttribute("levelB"); double j = h->getAttribute("j"); BOOST_CHECK_CLOSE(j, electron_ref[levA][levB], 1e-5); } libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_dftengine.cc000066400000000000000000000305701412152066400176630ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE dftengine_test // Third party includes #include // Local VOTCA includes #include "votca/tools/eigenio_matrixmarket.h" #include "votca/xtp/dftengine.h" #include "votca/xtp/orbitals.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(dftengine_test) QMMolecule Water() { std::ofstream xyzfile("molecule.xyz"); xyzfile << "3" << std::endl; xyzfile << "Water molecule" << std::endl; xyzfile << "O 0.00000 0.00000 0.11779" << std::endl; xyzfile << "H 0.00000 0.75545 -0.47116" << std::endl; xyzfile << "H 0.00000 -0.75545 -0.47116" << std::endl; xyzfile.close(); QMMolecule mol(" ", 1); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/espfit/molecule.xyz"); return mol; } void WriteBasis321G() { std::ofstream basisfile("3-21G.xml"); basisfile << "" << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << " " << std::endl; basisfile << "" << std::endl; basisfile.close(); } BOOST_AUTO_TEST_CASE(dft_full) { libint2::initialize(); DFTEngine dft; WriteBasis321G(); Orbitals orb; orb.QMAtoms() = Water(); std::ofstream xml("dftengine.xml"); xml << "" << std::endl; xml << "1" << std::endl; xml << "xtp" << std::endl; xml << "0" << std::endl; xml << "XC_HYB_GGA_XC_PBEH" << std::endl; xml << "3-21G.xml" << std::endl; xml << "false" << std::endl; xml << "false" << std::endl; xml << "0" << std::endl; xml << "" << std::endl; xml << "false" << std::endl; xml << "false" << std::endl; xml << "true\n"; xml << "1e-9\n"; xml << "cache\n"; xml << "" << std::endl; xml << " 1e-7" << std::endl; xml << " DIIS" << std::endl; xml << " 0.002" << std::endl; xml << " 0.8" << std::endl; xml << " 20" << std::endl; xml << " 0.0" << std::endl; xml << " 0.2" << std::endl; xml << " 100\n"; xml << " 1e-7\n"; xml << " false\n"; xml << " 0.7\n"; xml << "" << std::endl; xml << "independent" << std::endl; xml << "xcoarse" << std::endl; xml << "0" << std::endl; xml << "200" << std::endl; xml << "" << std::endl; xml << "" << std::endl; xml.close(); votca::tools::Property prop; prop.LoadFromXML("dftengine.xml"); Logger log; dft.setLogger(&log); dft.Initialize(prop); dft.Evaluate(orb); BOOST_CHECK_CLOSE(orb.getDFTTotalEnergy(), -75.891017293070945, 1e-5); Eigen::VectorXd MOs_energy_ref = Eigen::VectorXd::Zero(13); MOs_energy_ref << -19.0739, -1.01904, -0.520731, -0.341996, -0.27356, 0.118834, 0.210783, 0.953576, 1.04314, 1.46895, 1.54729, 1.67293, 2.77584; bool check_eng = MOs_energy_ref.isApprox(orb.MOs().eigenvalues(), 1e-5); BOOST_CHECK_EQUAL(check_eng, true); if (!check_eng) { std::cout << "result eng" << std::endl; std::cout << orb.MOs().eigenvalues() << std::endl; std::cout << "ref eng" << std::endl; std::cout << MOs_energy_ref << std::endl; } Eigen::MatrixXd MOs_coeff_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/dftengine/MOs_coeff_ref.mm"); AOBasis basis = orb.SetupDftBasis(); AOOverlap overlap; overlap.Fill(basis); Eigen::MatrixXd proj = MOs_coeff_ref.leftCols(5).transpose() * overlap.Matrix() * orb.MOs().eigenvectors().leftCols(5); Eigen::VectorXd norms = proj.colwise().norm(); bool check_coeff = norms.isApproxToConstant(1, 1e-5); BOOST_CHECK_EQUAL(check_coeff, true); if (!check_coeff) { std::cout << "result coeff" << std::endl; std::cout << orb.MOs().eigenvectors() << std::endl; std::cout << "ref coeff" << std::endl; std::cout << MOs_coeff_ref << std::endl; } libint2::finalize(); } BOOST_AUTO_TEST_CASE(density_guess) { libint2::initialize(); DFTEngine dft; std::unique_ptr s = std::make_unique(0, "C", 3 * Eigen::Vector3d::UnitX()); Vector9d multipoles; multipoles << 1.0, 0.5, 1.0, -1.0, 0.1, -0.2, 0.333, 0.1, 0.15; s->setMultipole(multipoles, 2); std::vector > multipole_vec; multipole_vec.push_back(std::move(s)); dft.setExternalcharges(&multipole_vec); WriteBasis321G(); Orbitals orb; orb.QMAtoms() = Water(); std::ofstream xml("dftengine.xml"); xml << "" << std::endl; xml << "1" << std::endl; xml << "xtp" << std::endl; xml << "0" << std::endl; xml << "XC_HYB_GGA_XC_PBEH" << std::endl; xml << "3-21G.xml" << std::endl; xml << "false" << std::endl; xml << "false" << std::endl; xml << "0" << std::endl; xml << "" << std::endl; xml << "false" << std::endl; xml << "false" << std::endl; xml << "true\n"; xml << "1e-9\n"; xml << "cache\n"; xml << "" << std::endl; xml << " 1e-7" << std::endl; xml << " DIIS" << std::endl; xml << " 0.002" << std::endl; xml << " 0.8" << std::endl; xml << " 20" << std::endl; xml << " 0.0" << std::endl; xml << " 0.2" << std::endl; xml << " 100\n"; xml << " 1e-7\n"; xml << " false\n"; xml << " 0.7\n"; xml << "" << std::endl; xml << "atom" << std::endl; xml << "xcoarse" << std::endl; xml << "0" << std::endl; xml << "1" << std::endl; xml << "" << std::endl; xml << "" << std::endl; xml.close(); votca::tools::Property prop; prop.LoadFromXML("dftengine.xml"); Logger log; dft.setLogger(&log); dft.Initialize(prop); dft.Evaluate(orb); BOOST_CHECK_CLOSE(orb.getDFTTotalEnergy(), -75.891684954029387, 1e-5); Eigen::VectorXd MOs_energy_ref = Eigen::VectorXd::Zero(13); MOs_energy_ref << -19.3481, -1.30585, -0.789203, -0.59822, -0.555272, -0.150066, -0.0346099, 0.687671, 0.766599, 1.17942, 1.28947, 1.41871, 2.49675; bool check_eng = MOs_energy_ref.isApprox(orb.MOs().eigenvalues(), 1e-5); BOOST_CHECK_EQUAL(check_eng, true); if (!check_eng) { std::cout << "result eng" << std::endl; std::cout << orb.MOs().eigenvalues() << std::endl; std::cout << "ref eng" << std::endl; std::cout << MOs_energy_ref << std::endl; } Eigen::MatrixXd MOs_coeff_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/dftengine/MOs_coeff_ref2.mm"); AOBasis basis = orb.SetupDftBasis(); AOOverlap overlap; overlap.Fill(basis); Eigen::MatrixXd proj = MOs_coeff_ref.leftCols(5).transpose() * overlap.Matrix() * orb.MOs().eigenvectors().leftCols(5); Eigen::VectorXd norms = proj.colwise().norm(); bool check_coeff = norms.isApproxToConstant(1, 1e-5); BOOST_CHECK_EQUAL(check_coeff, true); if (!check_coeff) { std::cout << "result coeff" << std::endl; std::cout << orb.MOs().eigenvectors() << std::endl; std::cout << "ref coeff" << std::endl; std::cout << MOs_coeff_ref << std::endl; } libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_diis.cc000066400000000000000000000313321412152066400166450ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE diis_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/diis.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(diis_test) BOOST_AUTO_TEST_CASE(coeffs_test) { DIIS diis; diis.setHistLength(5); Eigen::MatrixXd error1 = Eigen::MatrixXd::Zero(17, 17); error1 << -5.72459e-17, 0.421271, 1.16054e-12, 9.88822e-13, 1.10962e-12, 0.50196, 4.5521e-13, 3.66001e-13, 4.25776e-13, 0.156112, 0.166066, 0.156112, 0.166066, 0.156112, 0.166066, 0.156112, 0.166066, -0.421271, -2.498e-16, -2.92683e-14, -5.89528e-14, -4.81698e-14, 1.26589, -5.89129e-14, -1.95411e-13, -1.22952e-13, 0.472946, 0.397505, 0.472946, 0.397505, 0.472946, 0.397505, 0.472946, 0.397505, -1.16054e-12, 2.93376e-14, 7.63278e-17, 5.97439e-15, -1.8735e-15, 1.05584e-13, 1.38874, -1.91427e-14, -4.33134e-14, 0.545347, 0.178966, 0.545347, 0.178966, -0.545347, -0.178966, -0.545347, -0.178966, -9.88848e-13, 5.89806e-14, -5.94663e-15, 1.249e-16, -4.3715e-16, -1.95607e-14, -3.9491e-14, 1.38874, 1.69812e-14, 0.545347, 0.178966, -0.545347, -0.178966, -0.545347, -0.178966, 0.545347, 0.178966, -1.10963e-12, 4.82947e-14, 1.85268e-15, 3.88578e-16, -1.52656e-16, 5.73395e-14, -4.0223e-14, 1.68242e-14, 1.38874, 0.545347, 0.178966, -0.545347, -0.178966, 0.545347, 0.178966, -0.545347, -0.178966, -0.50196, -1.26589, -1.05749e-13, 1.94844e-14, -5.73985e-14, 1.16573e-15, -8.18512e-14, -1.13382e-13, -9.86849e-14, 0.0944269, -0.025375, 0.0944269, -0.025375, 0.0944269, -0.025375, 0.0944269, -0.025375, -4.55275e-13, 5.82867e-14, -1.38874, 3.91354e-14, 4.02456e-14, 8.18512e-14, -1.249e-16, 4.88498e-15, -1.33227e-15, -0.0078462, -0.0361018, -0.0078462, -0.0361018, 0.0078462, 0.0361018, 0.0078462, 0.0361018, -3.65957e-13, 1.95843e-13, 1.92624e-14, -1.38874, -1.68754e-14, 1.13132e-13, -4.89886e-15, -2.15106e-16, 8.67362e-16, -0.0078462, -0.0361018, 0.0078462, 0.0361018, 0.0078462, 0.0361018, -0.0078462, -0.0361018, -4.25771e-13, 1.2268e-13, 4.34097e-14, -1.68199e-14, -1.38874, 9.85184e-14, 1.2837e-15, -8.67362e-16, 4.85723e-17, -0.0078462, -0.0361018, 0.0078462, 0.0361018, -0.0078462, -0.0361018, 0.0078462, 0.0361018, -0.156112, -0.472946, -0.545347, -0.545347, -0.545347, -0.0944269, 0.0078462, 0.0078462, 0.0078462, 7.71952e-17, -0.0786286, -2.91807e-14, -0.0259657, -2.69637e-14, -0.0259657, -2.87721e-14, -0.0259657, -0.166066, -0.397505, -0.178966, -0.178966, -0.178966, 0.025375, 0.0361018, 0.0361018, 0.0361018, 0.0786286, -2.34188e-17, 0.0259657, -2.7949e-14, 0.0259657, -2.46756e-14, 0.0259657, -2.28238e-14, -0.156112, -0.472946, -0.545347, 0.545347, 0.545347, -0.0944269, 0.0078462, -0.0078462, -0.0078462, 2.91954e-14, -0.0259657, -7.80626e-18, -0.0786286, 9.72313e-15, -0.0259657, 7.13839e-15, -0.0259657, -0.166066, -0.397505, -0.178966, 0.178966, 0.178966, 0.025375, 0.0361018, -0.0361018, -0.0361018, 0.0259657, 2.8047e-14, 0.0786286, -5.46438e-17, 0.0259657, 4.62737e-15, 0.0259657, 6.36297e-15, -0.156112, -0.472946, 0.545347, 0.545347, -0.545347, -0.0944269, -0.0078462, -0.0078462, 0.0078462, 2.69862e-14, -0.0259657, -9.70144e-15, -0.0259657, 5.20417e-18, -0.0786286, 1.13156e-14, -0.0259657, -0.166066, -0.397505, 0.178966, 0.178966, -0.178966, 0.025375, -0.0361018, -0.0361018, 0.0361018, 0.0259657, 2.46097e-14, 0.0259657, -4.60656e-15, 0.0786286, 4.85723e-17, 0.0259657, 2.6641e-15, -0.156112, -0.472946, 0.545347, -0.545347, 0.545347, -0.0944269, -0.0078462, 0.0078462, -0.0078462, 2.87617e-14, -0.0259657, -7.16094e-15, -0.0259657, -1.12965e-14, -0.0259657, -8.32667e-17, -0.0786286, -0.166066, -0.397505, 0.178966, -0.178966, 0.178966, 0.025375, -0.0361018, 0.0361018, -0.0361018, 0.0259657, 2.28706e-14, 0.0259657, -6.32827e-15, 0.0259657, -2.65066e-15, 0.0786286, -1.11022e-16; diis.Update(0, error1); Eigen::MatrixXd error2 = Eigen::MatrixXd::Zero(17, 17); error2 << -2.51535e-17, 0.205521, 8.26338e-13, 7.18129e-13, 7.93573e-13, 0.243239, 3.58892e-13, 3.05159e-13, 3.40282e-13, 0.0733301, 0.0756726, 0.0733301, 0.0756726, 0.0733301, 0.0756726, 0.0733301, 0.0756726, -0.205521, -9.71445e-17, -7.9152e-14, -9.96217e-14, -9.34253e-14, 0.606644, -7.45523e-14, -1.49427e-13, -1.09844e-13, 0.21304, 0.159214, 0.21304, 0.159214, 0.21304, 0.159214, 0.21304, 0.159214, -8.26348e-13, 7.9152e-14, 1.249e-16, 3.32373e-15, -1.08941e-15, 1.72229e-13, 0.665049, -6.61657e-13, -6.73987e-13, 0.250896, 0.0655191, 0.250896, 0.0655191, -0.250896, -0.0655191, -0.250896, -0.0655191, -7.1813e-13, 9.96356e-14, -3.32026e-15, 2.08167e-17, -3.22659e-16, 9.39544e-14, -6.74565e-13, 0.665049, -6.42454e-13, 0.250896, 0.0655191, -0.250896, -0.0655191, -0.250896, -0.0655191, 0.250896, 0.0655191, -7.93567e-13, 9.34634e-14, 1.09635e-15, 2.98372e-16, -1.73472e-17, 1.37192e-13, -6.70585e-13, -6.42393e-13, 0.665049, 0.250896, 0.0655191, -0.250896, -0.0655191, 0.250896, 0.0655191, -0.250896, -0.0655191, -0.243239, -0.606644, -1.72307e-13, -9.39249e-14, -1.37251e-13, 1.11022e-16, -1.91423e-13, -2.08285e-13, -1.98681e-13, 0.0367454, -0.0343107, 0.0367454, -0.0343107, 0.0367454, -0.0343107, 0.0367454, -0.0343107, -3.5888e-13, 7.43294e-14, -0.665049, 6.74599e-13, 6.70575e-13, 1.91534e-13, 2.08167e-17, 3.94129e-15, -1.67921e-15, -0.00308388, -0.0257548, -0.00308388, -0.0257548, 0.00308388, 0.0257548, 0.00308388, 0.0257548, -3.052e-13, 1.49269e-13, 6.61554e-13, -0.665049, 6.42431e-13, 2.08396e-13, -3.92394e-15, 0, 3.33067e-16, -0.00308388, -0.0257548, 0.00308388, 0.0257548, 0.00308388, 0.0257548, -0.00308388, -0.0257548, -3.40381e-13, 1.09607e-13, 6.74016e-13, 6.42403e-13, -0.665049, 1.98716e-13, 1.68268e-15, -3.43475e-16, 2.42861e-17, -0.00308388, -0.0257548, 0.00308388, 0.0257548, -0.00308388, -0.0257548, 0.00308388, 0.0257548, -0.0733301, -0.21304, -0.250896, -0.250896, -0.250896, -0.0367454, 0.00308388, 0.00308388, 0.00308388, -1.38778e-17, -0.0654894, 8.63571e-13, -0.00963694, 8.65418e-13, -0.00963694, 8.64126e-13, -0.00963694, -0.0756726, -0.159214, -0.0655191, -0.0655191, -0.0655191, 0.0343107, 0.0257548, 0.0257548, 0.0257548, 0.0654894, 1.36609e-17, 0.00963694, -1.09752e-12, 0.00963694, -1.09576e-12, 0.00963694, -1.09277e-12, -0.0733301, -0.21304, -0.250896, 0.250896, 0.250896, -0.0367454, 0.00308388, -0.00308388, -0.00308388, -8.63565e-13, -0.00963694, 4.33681e-18, -0.0654894, 6.12054e-15, -0.00963694, 4.83207e-15, -0.00963694, -0.0756726, -0.159214, -0.0655191, 0.0655191, 0.0655191, 0.0343107, 0.0257548, -0.0257548, -0.0257548, 0.00963694, 1.09758e-12, 0.0654894, -1.27936e-17, 0.00963694, 2.65369e-15, 0.00963694, 5.03937e-15, -0.0733301, -0.21304, 0.250896, 0.250896, -0.250896, -0.0367454, -0.00308388, -0.00308388, 0.00308388, -8.65396e-13, -0.00963694, -6.11273e-15, -0.00963694, -3.90313e-18, -0.0654894, 7.43416e-15, -0.00963694, -0.0756726, -0.159214, 0.0655191, 0.0655191, -0.0655191, 0.0343107, -0.0257548, -0.0257548, 0.0257548, 0.00963694, 1.09579e-12, 0.00963694, -2.69272e-15, 0.0654894, -5.5728e-17, 0.00963694, 4.17331e-15, -0.0733301, -0.21304, 0.250896, -0.250896, 0.250896, -0.0367454, -0.00308388, 0.00308388, -0.00308388, -8.64107e-13, -0.00963694, -4.83988e-15, -0.00963694, -7.43156e-15, -0.00963694, 2.77556e-17, -0.0654894, -0.0756726, -0.159214, 0.0655191, -0.0655191, 0.0655191, 0.0343107, -0.0257548, 0.0257548, -0.0257548, 0.00963694, 1.09275e-12, 0.00963694, -5.06886e-15, 0.00963694, -4.19456e-15, 0.0654894, -4.16334e-17; diis.Update(0, error2); Eigen::MatrixXd error3 = Eigen::MatrixXd::Zero(17, 17); error3 << -3.36103e-18, 0.0621516, 3.52141e-13, 3.02803e-13, 3.38022e-13, 0.0659688, 6.75571e-14, 4.8904e-14, 6.22049e-14, 0.0121774, 0.00560933, 0.0121774, 0.00560933, 0.0121774, 0.00560933, 0.0121774, 0.00560933, -0.0621516, -2.68882e-17, 2.47372e-14, 1.22198e-14, 1.69188e-14, 0.157095, -3.08916e-13, -3.27307e-13, -3.19507e-13, 0.0177149, -0.0330234, 0.0177149, -0.0330234, 0.0177149, -0.0330234, 0.0177149, -0.0330234, -3.52141e-13, -2.47368e-14, -4.87891e-18, 1.22461e-15, -5.48932e-16, -8.17619e-14, 0.160239, -3.19182e-13, -3.18678e-13, 0.0348853, -0.0441531, 0.0348853, -0.0441531, -0.0348853, 0.0441531, -0.0348853, 0.0441531, -3.02802e-13, -1.22209e-14, -1.22417e-15, -1.11673e-17, -1.76617e-16, -1.11732e-13, -3.24306e-13, 0.160239, -3.10646e-13, 0.0348853, -0.0441531, -0.0348853, 0.0441531, -0.0348853, 0.0441531, 0.0348853, -0.0441531, -3.3802e-13, -1.69193e-14, 5.48281e-16, 1.7705e-16, -5.74627e-18, -9.82686e-14, -3.17277e-13, -3.10976e-13, 0.160239, 0.0348853, -0.0441531, -0.0348853, 0.0441531, 0.0348853, -0.0441531, -0.0348853, 0.0441531, -0.0659688, -0.157095, 8.17558e-14, 1.11734e-13, 9.82721e-14, 2.77556e-17, -9.99374e-14, -9.87196e-14, -9.73423e-14, -0.0176436, -0.0598529, -0.0176436, -0.0598529, -0.0176436, -0.0598529, -0.0176436, -0.0598529, -6.75501e-14, 3.08913e-13, -0.160239, 3.24307e-13, 3.17276e-13, 9.99478e-14, -3.46945e-18, 1.86136e-15, 1.04604e-15, -0.00608808, -0.0306018, -0.00608808, -0.0306018, 0.00608808, 0.0306018, 0.00608808, 0.0306018, -4.89123e-14, 3.27315e-13, 3.19187e-13, -0.160239, 3.10973e-13, 9.87127e-14, -1.85789e-15, 0, 5.20417e-16, -0.00608808, -0.0306018, 0.00608808, 0.0306018, 0.00608808, 0.0306018, -0.00608808, -0.0306018, -6.22072e-14, 3.19505e-13, 3.18679e-13, 3.10642e-13, -0.160239, 9.73388e-14, -1.04777e-15, -5.11743e-16, -2.77556e-17, -0.00608808, -0.0306018, 0.00608808, 0.0306018, -0.00608808, -0.0306018, 0.00608808, 0.0306018, -0.0121774, -0.0177149, -0.0348853, -0.0348853, -0.0348853, 0.0176436, 0.00608808, 0.00608808, 0.00608808, -2.19551e-18, -0.0562084, 5.60581e-13, 0.00673288, 5.6097e-13, 0.00673288, 5.59758e-13, 0.00673288, -0.00560933, 0.0330234, 0.0441531, 0.0441531, 0.0441531, 0.0598529, 0.0306018, 0.0306018, 0.0306018, 0.0562084, 3.90313e-18, -0.00673288, -6.01511e-13, -0.00673288, -6.01863e-13, -0.00673288, -6.01939e-13, -0.0121774, -0.0177149, -0.0348853, 0.0348853, 0.0348853, 0.0176436, 0.00608808, -0.00608808, -0.00608808, -5.60582e-13, 0.00673288, -1.61275e-18, -0.0562084, 2.81444e-15, 0.00673288, 1.93855e-15, 0.00673288, -0.00560933, 0.0330234, 0.0441531, -0.0441531, -0.0441531, 0.0598529, 0.0306018, -0.0306018, -0.0306018, -0.00673288, 6.01547e-13, 0.0562084, -9.54098e-18, -0.00673288, 1.00874e-15, -0.00673288, 1.74513e-15, -0.0121774, -0.0177149, 0.0348853, 0.0348853, -0.0348853, 0.0176436, -0.00608808, -0.00608808, 0.00608808, -5.6097e-13, 0.00673288, -2.8151e-15, 0.00673288, 3.86247e-18, -0.0562084, 4.46409e-15, 0.00673288, -0.00560933, 0.0330234, -0.0441531, -0.0441531, 0.0441531, 0.0598529, -0.0306018, -0.0306018, 0.0306018, -0.00673288, 6.01854e-13, -0.00673288, -9.97032e-16, 0.0562084, 1.17094e-17, -0.00673288, -5.82867e-16, -0.0121774, -0.0177149, 0.0348853, -0.0348853, 0.0348853, 0.0176436, -0.00608808, 0.00608808, -0.00608808, -5.59759e-13, 0.00673288, -1.94007e-15, 0.00673288, -4.46323e-15, 0.00673288, 0, -0.0562084, -0.00560933, 0.0330234, -0.0441531, 0.0441531, -0.0441531, 0.0598529, -0.0306018, 0.0306018, -0.0306018, -0.00673288, 6.01939e-13, -0.00673288, -1.73819e-15, -0.00673288, 5.82867e-16, 0.0562084, -2.77556e-17; diis.Update(0, error3); Eigen::VectorXd Coeffs = diis.CalcCoeff(); Eigen::VectorXd Ref = Eigen::VectorXd::Zero(3); Ref << -2.18111, 4.98827, -1.80716; bool check_diis = Coeffs.isApprox(Ref, 0.00001); if (!check_diis) { std::cout << "Ref" << std::endl; std::cout << Ref << std::endl; std::cout << "Coeffs" << std::endl; std::cout << Coeffs << std::endl; } BOOST_CHECK_EQUAL(check_diis, 1); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_dipoledipoleinteraction.cc000066400000000000000000000071201412152066400226240ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE dipoledipoleinteraction_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/dipoledipoleinteraction.h" #include "votca/xtp/eigen.h" using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(dipoledipoleinteraction_test) BOOST_AUTO_TEST_CASE(dipoledipoleinteraction_test) { PolarSite zero(0, "H", Eigen::Vector3d::UnitX()); PolarSegment seg0("zero", 0); seg0.push_back(zero); PolarSite one(1, "C", Eigen::Vector3d::UnitZ()); PolarSegment seg1("one", 1); seg1.push_back(one); std::vector segs; segs.push_back(seg0); segs.push_back(seg1); double tholedamp = 0.39; eeInteractor interactor(tholedamp); DipoleDipoleInteraction dipdip(interactor, segs); // building reference Eigen::MatrixXd ref = Eigen::MatrixXd::Zero(6, 6); PolarSegment seg_ref("ref", 100); seg_ref.push_back(zero); seg_ref.push_back(one); for (Index i = 1; i < seg_ref.size(); i++) { for (Index j = 0; j < i; j++) { ref.block<3, 3>(3 * i, 3 * j) = interactor.FillTholeInteraction(seg_ref[i], seg_ref[j]); ref.block<3, 3>(3 * j, 3 * i) = interactor.FillTholeInteraction(seg_ref[j], seg_ref[i]); } } for (Index i = 0; i < seg_ref.size(); i++) { ref.block<3, 3>(3 * i, 3 * i) = seg_ref[i].getPInv(); } // building matrix via (i,j) operator Eigen::MatrixXd elementwise = Eigen::MatrixXd::Zero(6, 6); for (Index i = 0; i < 6; i++) { for (Index j = 0; j < 6; j++) { double value = dipdip(i, j); // do not remove gcc debug needs this elementwise(i, j) = value; } } bool op_check = elementwise.isApprox(ref, 1e-6); BOOST_CHECK_EQUAL(op_check, 1); if (!op_check) { std::cout << "ref" << std::endl; std::cout << ref << std::endl; std::cout << "operator" << std::endl; std::cout << elementwise << std::endl; } // building matrix via matrix vector product Eigen::MatrixXd gemv = Eigen::MatrixXd::Zero(6, 6); Eigen::MatrixXd ident = Eigen::MatrixXd::Identity(6, 6); for (Index i = 0; i < 6; i++) { gemv.col(i) = dipdip * ident.col(i); } bool gemv_check = gemv.isApprox(ref, 1e-6); BOOST_CHECK_EQUAL(gemv_check, 1); if (!gemv_check) { std::cout << "ref" << std::endl; std::cout << ref << std::endl; std::cout << "gemv" << std::endl; std::cout << gemv << std::endl; } // building matrix via iterator product Eigen::MatrixXd iterator = Eigen::MatrixXd::Zero(6, 6); for (Index k = 0; k < dipdip.outerSize(); ++k) { for (DipoleDipoleInteraction::InnerIterator it(dipdip, k); it; ++it) { iterator(it.row(), k) = it.value(); } } bool iterator_check = iterator.isApprox(ref, 1e-6); BOOST_CHECK_EQUAL(iterator_check, 1); if (!iterator_check) { std::cout << "ref" << std::endl; std::cout << ref << std::endl; std::cout << "iterator" << std::endl; std::cout << gemv << std::endl; } } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_ecpaobasis.cc000066400000000000000000000044241412152066400200300ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include "votca/xtp/qmmolecule.h" #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE ecpaobasis_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/aopotential.h" #include "votca/xtp/ecpaobasis.h" #include "votca/xtp/orbitals.h" using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(ecpaobasis_test) BOOST_AUTO_TEST_CASE(Serializing) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/ecpaobasis/molecule.xyz"); QMMolecule mol = orbitals.QMAtoms(); ECPBasisSet ecp; ecp.Load(std::string(XTP_TEST_DATA_FOLDER) + "/ecpaobasis/ecp.xml"); ECPAOBasis aoecp; aoecp.Fill(ecp, orbitals.QMAtoms()); CheckpointFile ff("aoecp.hdf5"); CheckpointWriter ww = ff.getWriter(); aoecp.WriteToCpt(ww); CheckpointReader rr = ff.getReader(); ECPAOBasis aoecp2; aoecp2.ReadFromCpt(rr); BasisSet s; s.Load(std::string(XTP_TEST_DATA_FOLDER) + "/ecpaobasis/3-21G.xml"); AOBasis b; b.Fill(s, orbitals.QMAtoms()); // no real way to test if two ecps are equal so we check if the matrices // are the same AOECP ecpmat1; ecpmat1.FillPotential(b, aoecp); AOECP ecpmat2; ecpmat2.FillPotential(b, aoecp2); bool check = ecpmat1.Matrix().isApprox(ecpmat2.Matrix(), 1e-8); BOOST_CHECK_EQUAL(check, 1); aoecp2.AddECPChargeToMolecule(mol); for (Index i = 0; i < mol.size(); i++) { BOOST_CHECK_EQUAL(mol[i].getNuccharge(), orbitals.QMAtoms()[i].getNuccharge()); } libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_eeinteractor.cc000066400000000000000000000410401412152066400203760ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE eeinteractor_test // Standard includes #include // Third party includes #include #include // Local VOTCA includes #include "votca/xtp/dipoledipoleinteraction.h" #include "votca/xtp/eeinteractor.h" using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(eeinteractor_test) BOOST_AUTO_TEST_CASE(static_case_charges) { StaticSegment seg1("one", 1); StaticSegment seg2("two", 2); StaticSite one(1, "H"); one.setPos(Eigen::Vector3d::Zero()); one.setCharge(1); StaticSite two(2, "H"); two.setPos(Eigen::Vector3d::UnitX()); two.setCharge(1); seg1.push_back(one); seg2.push_back(two); eeInteractor interactor; double energy_field = interactor.CalcStaticEnergy(seg1, seg2); BOOST_CHECK_CLOSE(energy_field, 1, 1e-12); seg2[0].setPos(Eigen::Vector3d::UnitZ()); double energy_field2 = interactor.CalcStaticEnergy(seg1, seg2); BOOST_CHECK_CLOSE(energy_field, energy_field2, 1e-12); } double CalcDipoleEnergy(StaticSegment& seg1, StaticSegment& seg2) { Eigen::Vector3d R = (seg2[0].getPos() - seg1[0].getPos()); Eigen::Vector3d mu1 = seg1[0].getDipole(); Eigen::Vector3d mu2 = seg2[0].getDipole(); double r = R.norm(); double e_ref = (r * r * mu1.dot(mu2) - 3 * mu1.dot(R) * mu2.dot(R)) / std::pow(r, 5); return e_ref; } BOOST_AUTO_TEST_CASE(static_case_dipoles) { Vector9d mpoles1; mpoles1 << 0, 1, 1, 1, 0, 0, 0, 0, 0; Vector9d mpoles2; mpoles2 << 0, -1, 1, 1, 0, 0, 0, 0, 0; StaticSegment seg1("one", 1); StaticSegment seg2("two", 2); StaticSite one(1, "H"); one.setPos(Eigen::Vector3d::Zero()); one.setMultipole(mpoles1, 1); StaticSite two(2, "H"); two.setPos(1.5 * Eigen::Vector3d::Ones()); two.setMultipole(mpoles2, 1); seg1.push_back(one); seg2.push_back(two); eeInteractor interactor; double energy_field = interactor.CalcStaticEnergy(seg1, seg2); // explicit formula double e_ref = CalcDipoleEnergy(seg1, seg2); BOOST_CHECK_CLOSE(energy_field, e_ref, 1e-12); seg2[0].setPos(Eigen::Vector3d::UnitZ()); double energy_field2 = interactor.CalcStaticEnergy(seg1, seg2); double e_ref2 = CalcDipoleEnergy(seg1, seg2); BOOST_CHECK_CLOSE(energy_field2, e_ref2, 1e-12); double energy_field3 = interactor.CalcStaticEnergy(seg2, seg1); double e_ref3 = CalcDipoleEnergy(seg2, seg1); BOOST_CHECK_CLOSE(e_ref2, e_ref3, 1e-12); BOOST_CHECK_CLOSE(energy_field3, e_ref3, 1e-12); BOOST_CHECK_CLOSE(energy_field3, energy_field2, 1e-12); } double CalcQuadrupoleEnergy(StaticSegment& seg1, StaticSegment& seg2) { Eigen::Vector3d R = (seg2[0].getPos() - seg1[0].getPos()); double q20_1 = seg1[0].Q()[4]; double q20_2 = seg2[0].Q()[4]; double r = R.norm(); Eigen::Vector3d Rhat = R / r; Eigen::Vector3d na = Eigen::Vector3d::UnitZ(); Eigen::Vector3d nb = Eigen::Vector3d::UnitZ(); double naR = Rhat.dot(na); double nbR = Rhat.dot(nb); // stone book p51 eqn 3.3.17 double e_ref = q20_1 * q20_2 / std::pow(r, 5) * 0.75 * (35 * naR * naR * nbR * nbR - 5 * naR - 5 * nbR - 20 * naR * nbR * na.dot(nb) + 2 * na.dot(nb) + 1); return e_ref; } BOOST_AUTO_TEST_CASE(static_case_quadrupoles) { Vector9d mpoles1; mpoles1 << 0, 0, 0, 0, 1, 0, 0, 0, 0; Vector9d mpoles2; mpoles2 << 0, 0, 0, 0, 1, 0, 0, 0, 0; StaticSegment seg1("one", 1); StaticSegment seg2("two", 2); StaticSite one(1, "H"); one.setPos(Eigen::Vector3d::Zero()); one.setMultipole(mpoles1, 2); StaticSite two(2, "H"); // for the quadrupole formulathe second molecule must be along the z axis two.setPos(3 * Eigen::Vector3d::UnitZ()); two.setMultipole(mpoles2, 2); seg1.push_back(one); seg2.push_back(two); eeInteractor interactor; double energy_field = interactor.CalcStaticEnergy(seg1, seg2); // explicit formula double e_ref = CalcQuadrupoleEnergy(seg1, seg2); BOOST_CHECK_CLOSE(energy_field, e_ref, 1e-12); } BOOST_AUTO_TEST_CASE(static_case_monopole_field) { Vector9d mpoles1; mpoles1 << -3, 0, 0, 0, 0, 0, 0, 0, 0; StaticSegment seg1("one", 1); PolarSegment seg2("two", 2); StaticSite one(1, "H"); one.setMultipole(mpoles1, 0); one.setPos(Eigen::Vector3d::Zero()); PolarSite two(2, "H"); two.setPos(3 * Eigen::Vector3d::UnitZ()); seg1.push_back(one); seg2.push_back(two); eeInteractor interactor; interactor.ApplyStaticField(seg1, seg2); Eigen::Vector3d field_ref; field_ref << 0, 0, 0.33333333; bool field_check = field_ref.isApprox(seg2[0].V(), 1e-6); BOOST_CHECK_EQUAL(field_check, true); if (!field_check) { std::cout << "ref" << std::endl; std::cout << field_ref << std::endl; std::cout << "field" << std::endl; std::cout << seg2[0].V() << std::endl; } interactor.ApplyStaticField(seg1, seg2); bool field_check_2 = field_ref.isApprox(seg2[0].V_noE(), 1e-6); BOOST_CHECK_EQUAL(field_check, true); if (!field_check_2) { std::cout << "ref" << std::endl; std::cout << field_ref << std::endl; std::cout << "field" << std::endl; std::cout << seg2[0].V_noE() << std::endl; } } BOOST_AUTO_TEST_CASE(static_case_quadrupoles_orientation) { // using Stone page 53 fig 3.3 Vector9d mpoles1; mpoles1 << 0, 0, 0, 0, 1, 0, 0, 0, 0; Vector9d mpoles2; mpoles2 << 0, 0, 0, 0, 1, 0, 0, 0, 0; StaticSegment seg1("one", 1); StaticSegment seg2("two", 2); StaticSite one(1, "H"); one.setPos(Eigen::Vector3d::Zero()); one.setMultipole(mpoles1, 2); StaticSite two(2, "H"); // for the quadrupole formulathe second molecule must be along the z axis two.setPos(Eigen::Vector3d::UnitZ()); two.setMultipole(mpoles2, 2); seg1.push_back(one); seg2.push_back(two); eeInteractor interactor; double energy_field = interactor.CalcStaticEnergy(seg1, seg2); // config a BOOST_CHECK_CLOSE(energy_field, 6, 1e-12); StaticSite& site1 = seg1[0]; StaticSite& site2 = seg2[0]; // site1 is at origin Eigen::Matrix3d rot; rot << 1, 0, 0, 0, 0, 1, 0, 1, 0; site1.Rotate(rot, Eigen::Vector3d::Zero()); energy_field = interactor.CalcStaticEnergy(seg1, seg2); BOOST_CHECK_CLOSE(energy_field, -3, 1e-12); // config c site2.Rotate(rot, Eigen::Vector3d::UnitZ()); energy_field = interactor.CalcStaticEnergy(seg1, seg2); BOOST_CHECK_CLOSE(energy_field, 2.25, 1e-12); // config d Eigen::Matrix3d rot2; rot2 << 0, 1, 0, 1, 0, 0, 0, 0, 1; site1.Rotate(rot2, Eigen::Vector3d::Zero()); energy_field = interactor.CalcStaticEnergy(seg1, seg2); BOOST_CHECK_CLOSE(energy_field, 0.75, 1e-12); // reset to config a site1.setMultipole(mpoles1, 2); site2.setMultipole(mpoles2, 2); Eigen::Matrix3d rot3; double sqrt2 = 1 / std::sqrt(2); rot3 << 1, 0, 0, 0, sqrt2, sqrt2, 0, -sqrt2, sqrt2; site2.Rotate(rot3, Eigen::Vector3d::UnitZ()); site1.Rotate(rot3, Eigen::Vector3d::Zero()); energy_field = interactor.CalcStaticEnergy(seg1, seg2); double ref = -(2.0 + 7.0 / 16.0); BOOST_CHECK_CLOSE(energy_field, ref, 1e-12); } BOOST_AUTO_TEST_CASE(static_case_quadrupoles_dipoles_orientation) { // using Stone page 55 fig 3.5 Vector9d mpoles1; mpoles1 << 0, 0, 0, 0, 1, 0, 0, 0, 0; Vector9d mpoles2; mpoles2 << 0, 0, 0, 1, 0, 0, 0, 0, 0; StaticSegment seg1("one", 1); StaticSegment seg2("two", 2); StaticSite one(1, "H"); one.setPos(Eigen::Vector3d::Zero()); one.setMultipole(mpoles1, 2); StaticSite two(2, "H"); // site 2 is above site 1 two.setPos(Eigen::Vector3d::UnitZ()); two.setMultipole(mpoles2, 2); seg1.push_back(one); seg2.push_back(two); eeInteractor interactor; double energy_field = interactor.CalcStaticEnergy(seg1, seg2); double energy_field_rev = interactor.CalcStaticEnergy(seg2, seg1); // config a BOOST_CHECK_CLOSE(energy_field, -3, 1e-12); BOOST_CHECK_CLOSE(energy_field, energy_field_rev, 1e-12); // config b StaticSite& site1 = seg1[0]; StaticSite& site2 = seg2[0]; // site1 is at origin Eigen::Matrix3d rot; rot << 1, 0, 0, 0, 1, 0, 0, 0, -1; site2.Rotate(rot, Eigen::Vector3d::UnitZ()); energy_field = interactor.CalcStaticEnergy(seg1, seg2); energy_field_rev = interactor.CalcStaticEnergy(seg2, seg1); BOOST_CHECK_CLOSE(energy_field, 3, 1e-12); BOOST_CHECK_CLOSE(energy_field, energy_field_rev, 1e-12); // config c Eigen::Matrix3d rot2; rot2 << 1, 0, 0, 0, 0, 1, 0, 1, 0; site1.Rotate(rot2, Eigen::Vector3d::Zero()); energy_field = interactor.CalcStaticEnergy(seg2, seg1); energy_field_rev = interactor.CalcStaticEnergy(seg2, seg1); BOOST_CHECK_CLOSE(energy_field, -1.5, 1e-12); BOOST_CHECK_CLOSE(energy_field, energy_field_rev, 1e-12); } BOOST_AUTO_TEST_CASE(static_case_full_tensor_1) { eeInteractor interactor; Eigen::Matrix result; for (Index i = 0; i < 9; i++) { Vector9d mpoles1 = Vector9d::Zero(); mpoles1(i) = 1.0; StaticSegment seg1("one", 1); StaticSite one(1, "H"); one.setPos(Eigen::Vector3d::Zero()); one.setMultipole(mpoles1, 2); seg1.push_back(one); for (Index j = 0; j < 9; j++) { Vector9d mpoles2 = Vector9d::Zero(); mpoles2(j) = 1.0; StaticSegment seg2("two", 2); StaticSite two(2, "H"); two.setPos(3 * Eigen::Vector3d::Ones()); two.setMultipole(mpoles2, 2); seg2.push_back(two); result(i, j) = interactor.CalcStaticEnergy(seg1, seg2); } } Eigen::Matrix ref = Eigen::Matrix::Zero(); ref << 0.19245, -0.0213833, -0.0213833, -0.0213833, 0, 0.00411523, 0.00411523, 0, 0.00411523, 0.0213833, 8.67362e-19, -0.00712778, -0.00712778, 0.000791976, 0.000914495, 0.00228624, -0.00137174, 0.000914495, 0.0213833, -0.00712778, 8.67362e-19, -0.00712778, 0.000791976, 0.00228624, 0.000914495, 0.00137174, 0.000914495, 0.0213833, -0.00712778, -0.00712778, 8.67362e-19, -0.00158395, 0.000914495, 0.000914495, 0, 0.00228624, 0, -0.000791976, -0.000791976, 0.00158395, -0.000615981, -0.000254026, -0.000254026, 0, 0.000508053, 0.00411523, -0.000914495, -0.00228624, -0.000914495, -0.000254026, 0.000410654, 0.000586649, -0.000439986, 0.000586649, 0.00411523, -0.00228624, -0.000914495, -0.000914495, -0.000254026, 0.000586649, 0.000410654, 0.000439986, 0.000586649, 0, 0.00137174, -0.00137174, 0, 0, -0.000439986, 0.000439986, -0.000615981, 0, 0.00411523, -0.000914495, -0.000914495, -0.00228624, 0.000508053, 0.000586649, 0.000586649, 0, 0.000410654; bool tensor_check = result.isApprox(ref, 1e-6); BOOST_CHECK_EQUAL(tensor_check, true); if (!tensor_check) { std::cout << "result" << std::endl; std::cout << result << std::endl; std::cout << "ref" << std::endl; std::cout << ref << std::endl; } } BOOST_AUTO_TEST_CASE(static_case_full_tensor_2) { eeInteractor interactor; Eigen::Matrix result; for (Index i = 0; i < 9; i++) { Vector9d mpoles1 = Vector9d::Zero(); mpoles1(i) = 1.0; StaticSegment seg1("one", 1); StaticSite one(1, "H"); one.setPos(Eigen::Vector3d::Zero()); one.setMultipole(mpoles1, 2); seg1.push_back(one); for (Index j = 0; j < 9; j++) { Vector9d mpoles2 = Vector9d::Zero(); mpoles2(j) = 1.0; StaticSegment seg2("two", 2); StaticSite two(2, "H"); two.setPos(-2.1 * Eigen::Vector3d::Ones() + Eigen::Vector3d::UnitX()); two.setMultipole(mpoles2, 2); seg2.push_back(two); result(i, j) = interactor.CalcStaticEnergy(seg1, seg2); } } Eigen::Matrix ref = Eigen::Matrix::Zero(); ref << 0.315754, 0.0346291, 0.0661101, 0.0661101, 0.0050219, 0.012558, 0.0239744, -0.00869818, 0.012558, -0.0346291, 0.0200876, -0.0217511, -0.0217511, -0.00620633, 0.00453012, -0.0131465, 0.0107497, 0.00453012, -0.0661101, -0.0217511, -0.0100438, -0.0415248, -0.0118485, -0.0131465, -0.0136814, -0.00231059, -0.00716646, -0.0661101, -0.0217511, -0.0415248, -0.0100438, 0.00792526, -0.00716646, -0.0136814, 0.00910577, -0.0131465, 0.0050219, 0.00620633, 0.0118485, -0.00792526, -0.00806073, 0.000243418, 0.000464707, -0.00450468, 0.00650363, 0.012558, -0.00453012, 0.0131465, 0.00716646, 0.000243418, 0.000172264, 0.00750975, -0.00765029, -0.0010732, 0.0239744, 0.0131465, 0.0136814, 0.0136814, 0.000464707, 0.00750975, 0.0105754, -0.000804897, 0.00750975, -0.00869818, -0.0107497, 0.00231059, -0.00910577, -0.00450468, -0.00765029, -0.000804897, -0.00285918, -0.00403595, 0.012558, -0.00453012, 0.00716646, 0.0131465, 0.00650363, -0.0010732, 0.00750975, -0.00403595, 0.000172264; bool tensor_check = result.isApprox(ref, 1e-5); BOOST_CHECK_EQUAL(tensor_check, true); if (!tensor_check) { std::cout << "result" << std::endl; std::cout << result << std::endl; std::cout << "ref" << std::endl; std::cout << ref << std::endl; } } BOOST_AUTO_TEST_CASE(polar_case_monopole) { Vector9d mpoles1; mpoles1 << 1, 0, 0, 0, 0, 0, 0, 0, 0; PolarSegment seg1("one", 1); PolarSegment seg2("two", 2); PolarSite one(1, "H"); one.setpolarization(Eigen::Matrix3d::Identity()); one.setMultipole(mpoles1, 0); one.setPos(Eigen::Vector3d::Zero()); PolarSite two(2, "H"); two.setpolarization(Eigen::Matrix3d::Identity()); two.setMultipole(mpoles1, 0); two.setPos(2 * Eigen::Vector3d::UnitZ()); seg1.push_back(one); seg2.push_back(two); double exp_damp = std::numeric_limits::max(); // should disable thole damping eeInteractor interactor(exp_damp); double estat = interactor.ApplyStaticField(seg1, seg2); interactor.ApplyStaticField(seg2, seg1); BOOST_CHECK_CLOSE(estat, 0.5, 1e-12); Eigen::Vector3d field_ref; field_ref << 0, 0, -0.25; bool field_check = field_ref.isApprox(seg2[0].V_noE(), 1e-6); BOOST_CHECK_EQUAL(field_check, true); if (!field_check) { std::cout << "ref" << std::endl; std::cout << field_ref << std::endl; std::cout << "field" << std::endl; std::cout << seg2[0].V_noE() << std::endl; } bool field_check_2 = field_ref.isApprox(-seg1[0].V_noE(), 1e-6); BOOST_CHECK_EQUAL(field_check, true); if (!field_check_2) { std::cout << "ref" << std::endl; std::cout << -field_ref << std::endl; std::cout << "field" << std::endl; std::cout << seg1[0].V_noE() << std::endl; } std::vector segments = {seg1, seg2}; Eigen::VectorXd b = Eigen::VectorXd::Zero(6); Index index = 0; for (PolarSegment& seg : segments) { for (const PolarSite& site : seg) { const Eigen::Vector3d V = site.V() + site.V_noE(); b.segment<3>(index) = -V; index += 3; } } DipoleDipoleInteraction A(interactor, segments); Eigen::ConjugateGradient cg; cg.setMaxIterations(100); cg.setTolerance(1e-9); cg.compute(A); Eigen::VectorXd x = cg.solve(b); index = 0; for (PolarSegment& seg : segments) { for (PolarSite& site : seg) { site.setInduced_Dipole(x.segment<3>(index)); index += 3; } } Eigen::Vector3d dipole_ref; dipole_ref << 0, 0, 0.2; bool dipole_check = dipole_ref.isApprox(-segments[0][0].Induced_Dipole(), 1e-6); BOOST_CHECK_EQUAL(field_check, true); if (!dipole_check) { std::cout << "ref" << std::endl; std::cout << -dipole_ref << std::endl; std::cout << "dipole" << std::endl; std::cout << segments[0][0].Induced_Dipole() << std::endl; } bool dipole_check2 = dipole_ref.isApprox(segments[1][0].Induced_Dipole(), 1e-6); if (!dipole_check2) { std::cout << "ref" << std::endl; std::cout << dipole_ref << std::endl; std::cout << "dipole" << std::endl; std::cout << segments[1][0].Induced_Dipole() << std::endl; } eeInteractor::E_terms epolar = interactor.CalcPolarEnergy(segments[0], segments[1]); double einternal = segments[0][0].InternalEnergy(); einternal += segments[1][0].InternalEnergy(); BOOST_CHECK_CLOSE(epolar.E_indu_indu(), 0.01, 1e-12); BOOST_CHECK_CLOSE(epolar.E_indu_stat(), -0.1, 1e-12); BOOST_CHECK_CLOSE(einternal, 0.04, 1e-12); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_eigen.cc000066400000000000000000000155301412152066400170060ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE eigen_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/eigen.h" using namespace votca; BOOST_AUTO_TEST_SUITE(eigen_test) BOOST_AUTO_TEST_CASE(symmetric_test) { Eigen::MatrixXd notsym = Eigen::MatrixXd::Random(6, 6); Eigen::MatrixXd sym = notsym + notsym.transpose(); bool symmetry = true; for (votca::Index i = 0; i < sym.rows(); ++i) { for (votca::Index j = 0; j <= i; ++j) { if (std::abs(sym(i, j) - sym(j, i)) > 1e-9) { symmetry = false; break; } } } BOOST_CHECK_EQUAL(symmetry, 1); } BOOST_AUTO_TEST_CASE(inverse_test) { Eigen::MatrixXd m = Eigen::MatrixXd::Zero(17, 17); m << -0.0107438, 0.177662, -0.000893645, -0.000893645, -0.000893645, 0.345174, -0.000591276, -0.000591276, -0.000591276, 0.136613, 0.110948, 0.140527, 0.115047, 0.140527, 0.115047, 0.140527, 0.115047, 2.183e-15, 1.39936e-14, -0.2034, 0.00238481, 0.201015, -7.8295e-14, -0.174952, 0.00205127, 0.172901, -5.75953e-13, -7.55155e-13, -0.234829, -0.324284, 0.232076, 0.320482, 0.00275331, 0.00380215, 1.92294e-15, 5.30409e-14, -0.114679, 0.233489, -0.11881, -1.08691e-13, -0.0986399, 0.200833, -0.102193, 1.10298e-12, 1.56415e-12, -0.132399, -0.182835, -0.137168, -0.189421, 0.269568, 0.372256, 9.81255e-05, -0.00180964, -0.165679, -0.165679, -0.165679, -0.00572861, -0.144589, -0.144589, -0.144589, -0.283887, -0.391777, 0.0942211, 0.13068, 0.0942211, 0.13068, 0.0942211, 0.13068, 0.0257368, -0.0923997, 0.00531379, 0.00531379, 0.00531379, -2.45842, 0.0248521, 0.0248521, 0.0248521, -0.0235266, 0.870391, -0.021766, 0.938627, -0.021766, 0.938627, -0.021766, 0.938627, -6.05072e-15, -3.50553e-14, 0.0320188, -0.217226, 0.185207, 2.84606e-13, 0.164774, -1.11788, 0.953107, -3.43579e-13, -7.51681e-12, -0.0107087, -0.224765, -0.0619426, -1.30011, 0.0726513, 1.52488, -1.85212e-14, 3.71612e-14, 0.232345, -0.0884434, -0.143902, 1.65531e-12, 1.19569, -0.455144, -0.740541, -5.57708e-13, -1.28855e-11, -0.0777079, -1.63101, 0.0481279, 1.01016, 0.0295799, 0.620853, -0.00067642, 0.0030588, 0.164587, 0.164587, 0.164587, 0.0706733, 0.85369, 0.85369, 0.85369, -0.0833538, -1.77428, 0.0291688, 0.555286, 0.0291688, 0.555286, 0.0291688, 0.555286, 2.67521e-15, 1.49908e-14, -0.499711, 0.0302687, 0.469443, -8.25069e-14, 0.794429, -0.0481205, -0.746308, -1.68595e-12, 3.88068e-13, -0.631236, 0.170551, 0.593, -0.16022, 0.0382355, -0.0103307, -2.92301e-15, -4.20358e-14, 0.253557, -0.559541, 0.305984, 2.74225e-14, -0.403099, 0.889545, -0.486446, -4.63627e-12, 1.28551e-12, 0.320293, -0.0865389, 0.386519, -0.104432, -0.706813, 0.190971, 0.000103179, -0.000739357, -0.399322, -0.399322, -0.399322, -0.00417793, 0.631921, 0.631921, 0.631921, -0.743087, 0.196419, 0.252682, -0.0664109, 0.252682, -0.0664109, 0.252682, -0.0664109, 0.00149008, -0.210613, 0.0151116, 0.0151116, 0.0151116, -0.131439, -0.0188722, -0.0188722, -0.0188722, 0.641757, -0.258506, 0.662618, -0.303913, 0.662618, -0.303913, 0.662618, -0.303913, -1.01256e-14, 8.31141e-14, 0.154221, -0.726494, 0.572273, 3.21687e-13, -0.180079, 0.848303, -0.668224, -6.90137e-12, 1.08126e-11, -0.16221, 0.269927, -0.601918, 1.00163, 0.764127, -1.27156, -1.4385e-14, 4.61332e-14, 0.749843, -0.241362, -0.508481, 3.69788e-13, -0.875567, 0.281831, 0.593736, -1.00864e-11, 1.59982e-11, -0.788686, 1.31242, 0.534821, -0.889976, 0.253865, -0.422448, 8.45112e-05, -0.00427837, -0.539015, -0.539015, -0.539015, -0.00364986, 0.62842, 0.62842, 0.62842, 0.873707, -1.42717, -0.270316, 0.466699, -0.270316, 0.466699, -0.270316, 0.466699, 0.220745, 1.96298, 0.000217492, 0.000217492, 0.000217492, -3.94464, -0.000657288, -0.000657288, -0.000657288, 0.170958, 0.775841, 0.170979, 0.77469, 0.170979, 0.77469, 0.170979, 0.77469, -1.00858, 0.364513, 2.52534e-06, 2.52534e-06, 2.52534e-06, -0.192712, -5.74555e-07, -5.74555e-07, -5.74555e-07, -0.0243332, 0.0351697, -0.0243273, 0.0351687, -0.0243273, 0.0351687, -0.0243273, 0.0351687; Eigen::FullPivLU dec(m); bool check_inv = (m * dec.inverse()).isApprox(Eigen::MatrixXd::Identity(17, 17), 0.01); if (!check_inv) { std::cout << dec.isInvertible() << " " << dec.rank() << " " << dec.rcond() << std::endl; std::cout << m * dec.solve(Eigen::MatrixXd::Identity(17, 17)) << std::endl; } BOOST_CHECK_EQUAL(check_inv, 1); } BOOST_AUTO_TEST_CASE(PCG_test) { Eigen::MatrixXd A = Eigen::MatrixXd::Zero(3, 3); A << 1, 3, -2, 3, 5, 6, 2, 4, 3; Eigen::MatrixXd A_sym = A * A.transpose(); Eigen::VectorXd x_ref = Eigen::VectorXd::Zero(3); x_ref << -15, 8, 2; Eigen::VectorXd b = A_sym * x_ref; Eigen::LLT lltOfA(A_sym); Eigen::VectorXd x_chol = lltOfA.solve(b); bool check_chol = x_chol.isApprox(x_ref, 1e-7); BOOST_CHECK_EQUAL(check_chol, 1); if (!check_chol) { std::cout << "result" << std::endl; std::cout << x_chol.transpose() << std::endl; std::cout << "ref" << std::endl; std::cout << x_ref.transpose() << std::endl; } Eigen::ConjugateGradient> cg1; cg1.compute(A_sym); Eigen::VectorXd x_cg1 = cg1.solve(b); bool check_cg1 = x_cg1.isApprox(x_ref, 1e-7); BOOST_CHECK_EQUAL(check_cg1, 1); if (!check_cg1) { std::cout << "result" << std::endl; std::cout << x_cg1.transpose() << std::endl; std::cout << "ref" << std::endl; std::cout << x_ref.transpose() << std::endl; } Eigen::ConjugateGradient> cg2; cg2.compute(A_sym); Eigen::VectorXd x_cg2 = cg2.solveWithGuess(b, x_ref); bool check_cg2 = x_cg2.isApprox(x_ref, 1e-7); BOOST_CHECK_EQUAL(check_cg2, 1); if (!check_cg2) { std::cout << "result" << std::endl; std::cout << x_cg2.transpose() << std::endl; std::cout << "ref" << std::endl; std::cout << x_ref.transpose() << std::endl; } } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_eris.cc000066400000000000000000000121031412152066400166520ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE eris_test // Third party includes #include // Local VOTCA includes #include "votca/tools/eigenio_matrixmarket.h" #include "votca/xtp/ERIs.h" #include "votca/xtp/orbitals.h" using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(eris_test) BOOST_AUTO_TEST_CASE(fourcenter) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/eris/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/eris/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); Eigen::MatrixXd dmat = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/eris/dmat.mm"); ERIs eris; eris.Initialize_4c(aobasis); Eigen::MatrixXd erissmall = eris.CalculateERIs_4c(dmat, 1e-20); Eigen::MatrixXd eris_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/eris/eris_ref.mm"); bool eris_check = erissmall.isApprox(eris_ref, 0.00001); if (!eris_check) { std::cout << "result eri" << std::endl; std::cout << erissmall << std::endl; std::cout << "ref eri" << std::endl; std::cout << eris_ref << std::endl; std::cout << " quotient" << std::endl; std::cout << erissmall.cwiseQuotient(eris_ref); } BOOST_CHECK_EQUAL(eris_check, 1); std::array both = eris.CalculateERIs_EXX_4c(dmat, 1e-20); const Eigen::MatrixXd& exx_small = both[1]; Eigen::MatrixXd exx_ref = -votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/eris/exx_ref.mm"); Eigen::MatrixXd sum = both[0] + both[1]; Eigen::MatrixXd sum_ref = exx_ref + eris_ref; bool sum_check = sum.isApprox(sum_ref, 1e-5); BOOST_CHECK_EQUAL(sum_check, 1); if (!sum_check) { std::cout << "result sum" << std::endl; std::cout << sum << std::endl; std::cout << "ref sum" << std::endl; std::cout << sum_ref << std::endl; } bool exxs_check = exx_small.isApprox(exx_ref, 0.00001); if (!eris_check) { std::cout << "result exx" << std::endl; std::cout << exx_small << std::endl; std::cout << "ref exx" << std::endl; std::cout << exx_ref << std::endl; std::cout << "quotient" << std::endl; std::cout << exx_small.cwiseQuotient(exx_ref); } BOOST_CHECK_EQUAL(exxs_check, 1); libint2::finalize(); } BOOST_AUTO_TEST_CASE(threecenter) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/eris/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/eris/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); Eigen::MatrixXd dmat = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/eris/dmat2.mm"); Eigen::MatrixXd mos = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/eris/mos.mm"); ERIs eris; eris.Initialize(aobasis, aobasis); Eigen::MatrixXd exx_dmat = eris.CalculateERIs_EXX_3c(Eigen::MatrixXd::Zero(0, 0), dmat)[1]; Eigen::MatrixXd exx_mo = eris.CalculateERIs_EXX_3c(mos.block(0, 0, 17, 4), dmat)[1]; bool compare_exx = exx_mo.isApprox(exx_dmat, 1e-4); BOOST_CHECK_EQUAL(compare_exx, true); Eigen::MatrixXd exx_ref = -votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/eris/exx_ref2.mm"); bool compare_exx_ref = exx_ref.isApprox(exx_mo, 1e-5); if (!compare_exx_ref) { std::cout << "result exx" << std::endl; std::cout << exx_mo << std::endl; std::cout << "ref exx" << std::endl; std::cout << exx_ref << std::endl; } BOOST_CHECK_EQUAL(compare_exx_ref, true); Eigen::MatrixXd eri = eris.CalculateERIs_3c(dmat); Eigen::MatrixXd eris_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/eris/eris_ref2.mm"); bool compare_eris = eris_ref.isApprox(eri, 1e-5); if (!compare_eris) { std::cout << "result eris" << std::endl; std::cout << eri << std::endl; std::cout << "ref eris" << std::endl; std::cout << eris_ref << std::endl; } BOOST_CHECK_EQUAL(compare_eris, true); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_espfit.cc000066400000000000000000000077011412152066400172120ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE espfit_test // Third party includes #include // Local VOTCA includes #include "votca/tools/eigenio_matrixmarket.h" #include "votca/xtp/espfit.h" #include "votca/xtp/logger.h" #include "votca/xtp/orbitals.h" #include using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(espfit_test) BOOST_AUTO_TEST_CASE(esp_charges) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/espfit/molecule.xyz"); orbitals.setDFTbasisName(std::string(XTP_TEST_DATA_FOLDER) + "/espfit/3-21G.xml"); orbitals.setBasisSetSize(13); orbitals.setNumberOfOccupiedLevels(5); Eigen::MatrixXd MOs = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/espfit/MOs.mm"); orbitals.MOs().eigenvectors() = MOs; orbitals.MOs().eigenvalues() = Eigen::VectorXd::Ones(13); QMState gs = QMState("n"); Logger log; Espfit esp = Espfit(log); esp.setUseSVD(1e-8); StaticSegment result = esp.Fit2Density(orbitals, gs, "xcoarse"); Eigen::VectorXd pcharges = Eigen::VectorXd::Zero(orbitals.QMAtoms().size()); Index index = 0; for (const auto& site : result) { pcharges(index) = site.getCharge(); index++; } Eigen::VectorXd p_ref = Eigen::VectorXd::Zero(3); p_ref << -0.827774, 0.413985, 0.41379; bool check_esp_num = p_ref.isApprox(pcharges, 0.01); if (!check_esp_num) { std::cout << "ref" << std::endl; std::cout << p_ref << std::endl; std::cout << "calc" << std::endl; std::cout << pcharges << std::endl; } BOOST_CHECK_EQUAL(check_esp_num, 1); std::vector > pairconstraint; std::pair p1; p1.first = 1; p1.second = 2; pairconstraint.push_back(p1); Espfit esp2 = Espfit(log); esp2.setUseSVD(1e-8); esp2.setPairConstraint(pairconstraint); StaticSegment result2 = esp2.Fit2Density(orbitals, gs, "xcoarse"); Eigen::VectorXd pcharges_equal = Eigen::VectorXd::Zero(result2.size()); index = 0; for (const auto& site : result2) { pcharges_equal(index) = site.getCharge(); index++; } bool check_p1 = (std::abs(pcharges_equal(1) - pcharges_equal(2)) < 1e-6); BOOST_CHECK_EQUAL(check_p1, 1); std::vector > regionconstraint; std::string indeces = "1:2"; QMFragment reg = QMFragment(0, indeces); reg.value() = 1.0; regionconstraint.push_back(reg); Espfit esp3 = Espfit(log); esp3.setRegionConstraint(regionconstraint); esp3.setUseSVD(1e-8); StaticSegment result3 = esp3.Fit2Density(orbitals, gs, "xcoarse"); Eigen::VectorXd pcharges_reg = Eigen::VectorXd::Zero(orbitals.QMAtoms().size()); index = 0; for (const auto& site : result3) { pcharges_reg(index) = site.getCharge(); index++; } bool check_reg = (std::abs(pcharges_reg.segment(1, 2).sum() - 1.0) < 1e-6); if (!check_reg) { std::cout << "All charges " << pcharges_reg << std::endl; std::cout << "Sum of charges 1,2,3 should equal 1:" << pcharges_reg.segment(1, 2).sum() << std::endl; } BOOST_CHECK_EQUAL(check_reg, 1); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_gaussian_quadratures.cc000066400000000000000000000124271412152066400221530ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE gaussian_quadratures_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/quadrature_factory.h" // VOTCA includes #include using namespace votca::xtp; using namespace votca; // defines a Gaussian as integration test // result should by ~sqrt(pi) class FunctionEvaluation { public: FunctionEvaluation(){}; double operator()(Index j, double point, bool symmetry) const { double factor = 0.0; // this is only here to staisfy the unused variable warning if (j < 100) { if (symmetry) { factor = 2.0; } else { factor = 1.0; } } return factor * exp(-std::pow(point, 2)); } }; BOOST_AUTO_TEST_SUITE(gaussian_quadratures_test) BOOST_AUTO_TEST_CASE(gauss_legendre) { QuadratureFactory::RegisterAll(); std::unique_ptr _gq = Quadratures().Create("legendre"); std::vector orders{8, 10, 12, 14, 16, 18, 20, 40, 100}; FunctionEvaluation f = FunctionEvaluation(); Eigen::VectorXd integrals(9); for (Index i = 0; i < 9; i++) { _gq->configure(orders[i]); integrals(i) = _gq->Integrate(f); } Eigen::VectorXd integrals_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/gaussian_quadratures/gauss_legendre.mm"); bool check_integral = integrals.isApprox(integrals_ref, 1e-10); if (!check_integral) { std::cout << "Gauss-Legendre" << std::endl; std::cout << integrals << std::endl; std::cout << "Gauss-Legendre ref" << std::endl; std::cout << integrals_ref << std::endl; } BOOST_CHECK_EQUAL(check_integral, true); } BOOST_AUTO_TEST_CASE(modified_gauss_legendre) { QuadratureFactory::RegisterAll(); std::unique_ptr _gq = std::unique_ptr( Quadratures().Create("modified_legendre")); std::vector orders{8, 10, 12, 14, 16, 18, 20, 40, 100}; FunctionEvaluation f = FunctionEvaluation(); Eigen::VectorXd integrals(9); for (Index i = 0; i < 9; i++) { _gq->configure(orders[i]); integrals(i) = _gq->Integrate(f); } Eigen::VectorXd integrals_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/gaussian_quadratures/modified_gauss_legendre.mm"); bool check_integral = integrals.isApprox(integrals_ref, 1e-10); if (!check_integral) { std::cout << "modified Gauss-Legendre" << std::endl; std::cout << integrals << std::endl; std::cout << "modified Gauss-Legendre ref" << std::endl; std::cout << integrals_ref << std::endl; } BOOST_CHECK_EQUAL(check_integral, true); } BOOST_AUTO_TEST_CASE(gauss_laguerre) { QuadratureFactory::RegisterAll(); std::unique_ptr _gq = std::unique_ptr(Quadratures().Create("laguerre")); std::vector orders{8, 10, 12, 14, 16, 18, 20, 40, 100}; FunctionEvaluation f = FunctionEvaluation(); Eigen::VectorXd integrals(9); for (Index i = 0; i < 9; i++) { _gq->configure(orders[i]); integrals(i) = _gq->Integrate(f); } Eigen::VectorXd integrals_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/gaussian_quadratures/gauss_laguerre.mm"); bool check_integral = integrals.isApprox(integrals_ref, 1e-10); if (!check_integral) { std::cout << "Gauss-Laguerre" << std::endl; std::cout << integrals << std::endl; std::cout << "Gauss-Laguerre ref" << std::endl; std::cout << integrals_ref << std::endl; } BOOST_CHECK_EQUAL(check_integral, true); } BOOST_AUTO_TEST_CASE(gauss_hermite) { QuadratureFactory::RegisterAll(); std::unique_ptr _gq = std::unique_ptr(Quadratures().Create("hermite")); std::vector orders{8, 10, 12, 14, 16, 18, 20, 40, 100}; FunctionEvaluation f = FunctionEvaluation(); Eigen::VectorXd integrals(9); for (Index i = 0; i < 9; i++) { _gq->configure(orders[i]); integrals(i) = _gq->Integrate(f); } Eigen::VectorXd integrals_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/gaussian_quadratures/gauss_hermite.mm"); bool check_integral = integrals.isApprox(integrals_ref, 1e-10); if (!check_integral) { std::cout << "Gauss-Hermite" << std::endl; std::cout << integrals << std::endl; std::cout << "Gauss-Hermite ref" << std::endl; std::cout << integrals_ref << std::endl; } BOOST_CHECK_EQUAL(check_integral, true); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_glink.cc000066400000000000000000000016121412152066400170170ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE glink_test // Third party includes #include // Local VOTCA includes #include "votca/xtp/glink.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(glink_test) BOOST_AUTO_TEST_CASE(getter_tests) {} BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_gnode.cc000066400000000000000000000074421412152066400170160ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE gnode_test // Standard includes #include #include #include #include #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/glink.h" #include "votca/xtp/gnode.h" using namespace votca; using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(gnode_test) BOOST_AUTO_TEST_CASE(chosen_id_test) { QMStateType electron = QMStateType::Electron; std::vector dests; for (Index i = 0; i < 6; i++) { Segment seg("one", i); dests.push_back(GNode(seg, electron, true)); } Segment seg("one", 6); GNode g(seg, electron, true); g.AddEvent(&dests[0], Eigen::Vector3d::Zero(), 10); g.AddEvent(&dests[1], Eigen::Vector3d::Zero(), 20); g.AddEvent(&dests[2], Eigen::Vector3d::Zero(), 15); g.AddEvent(&dests[3], Eigen::Vector3d::Zero(), 18); g.AddEvent(&dests[4], Eigen::Vector3d::Zero(), 12); g.AddEvent(&dests[5], Eigen::Vector3d::Zero(), 25); g.InitEscapeRate(); g.MakeHuffTree(); BOOST_CHECK_EQUAL(g.findHoppingDestination(0.55)->getDestination()->getId(), 0); BOOST_CHECK_EQUAL(g.findHoppingDestination(0.85)->getDestination()->getId(), 1); BOOST_CHECK_EQUAL(g.findHoppingDestination(0.25)->getDestination()->getId(), 2); BOOST_CHECK_EQUAL(g.findHoppingDestination(0.15)->getDestination()->getId(), 3); BOOST_CHECK_EQUAL(g.findHoppingDestination(0.35)->getDestination()->getId(), 4); BOOST_CHECK_EQUAL(g.findHoppingDestination(0.65)->getDestination()->getId(), 5); } BOOST_AUTO_TEST_CASE(count_test) { QMStateType electron = QMStateType::Electron; std::vector dests; for (Index i = 0; i < 11; i++) { Segment seg("one", i); dests.push_back(GNode(seg, electron, true)); } Segment seg("one", 12); GNode g(seg, electron, true); g.AddEvent(&dests[0], Eigen::Vector3d::Zero(), 15); g.AddEvent(&dests[1], Eigen::Vector3d::Zero(), 9); g.AddEvent(&dests[2], Eigen::Vector3d::Zero(), 11); g.AddEvent(&dests[3], Eigen::Vector3d::Zero(), 8); g.AddEvent(&dests[4], Eigen::Vector3d::Zero(), 12); g.AddEvent(&dests[5], Eigen::Vector3d::Zero(), 7); g.AddEvent(&dests[6], Eigen::Vector3d::Zero(), 13); g.AddEvent(&dests[7], Eigen::Vector3d::Zero(), 6); g.AddEvent(&dests[8], Eigen::Vector3d::Zero(), 14); g.AddEvent(&dests[9], Eigen::Vector3d::Zero(), 5); g.AddEvent(&dests[10], Eigen::Vector3d::Zero(), 100); g.InitEscapeRate(); g.MakeHuffTree(); std::vector count(11, 0); double d = 0; while (d < 1) { GLink* L = g.findHoppingDestination(d); Index ind = L->getDestination()->getId(); count[ind]++; d += 0.000001; } BOOST_CHECK_EQUAL(count[0], 75000); BOOST_CHECK_EQUAL(count[1], 45000); BOOST_CHECK_EQUAL(count[2], 55000); BOOST_CHECK_EQUAL(count[3], 40000); BOOST_CHECK_EQUAL(count[4], 60000); BOOST_CHECK_EQUAL(count[5], 35000); BOOST_CHECK_EQUAL(count[6], 65000); BOOST_CHECK_EQUAL(count[7], 30000); BOOST_CHECK_EQUAL(count[8], 70000); BOOST_CHECK_EQUAL(count[9], 25001); BOOST_CHECK_EQUAL(count[10], 499999); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_grid.cc000066400000000000000000000037601412152066400166460ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE grid_test // Standard includes #include #include #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/grid.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(grid_test) BOOST_AUTO_TEST_CASE(setupgrid_test) { QMMolecule qm = QMMolecule("bla", 1); Eigen::Vector3d pos = Eigen::Vector3d::Zero(); qm.push_back(QMAtom(0, "C", pos)); Grid grid; grid.setupCHELPGGrid(qm); // BOOST_CHECK_EQUAL(grid.size(),2910);Thischeck is extremly sensitive to // numerical precision e.g. 1e-18 so it is not a good test Eigen::Vector3d start(-5.1022601692, -1.1338355932, -0.56691779658); Eigen::Vector3d end(5.10226, 1.13384, 0.566918); bool start_check = start.isApprox(grid.getGridPositions()[0], 0.00001); bool end_check = end.isApprox(grid.getGridPositions().back(), 0.00001); if (!start_check) { std::cout << "ref" << std::endl; std::cout << start << std::endl; std::cout << "result" << std::endl; std::cout << grid.getGridPositions()[0] << std::endl; } BOOST_CHECK_EQUAL(start_check, true); if (!end_check) { std::cout << "ref" << std::endl; std::cout << end << std::endl; std::cout << "result" << std::endl; std::cout << grid.getGridPositions().back() << std::endl; } BOOST_CHECK_EQUAL(end_check, true); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_gw.cc000066400000000000000000000140321412152066400163300ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE gw_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/gw.h" // VOTCA includes #include using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(gw_test) BOOST_AUTO_TEST_CASE(gw_full) { libint2::initialize(); Eigen::VectorXd mo_eigenvalues = Eigen::VectorXd::Zero(17); mo_eigenvalues << -10.6784, -0.746424, -0.394948, -0.394948, -0.394948, 0.165212, 0.227713, 0.227713, 0.227713, 0.763971, 0.763971, 0.763971, 1.05054, 1.13372, 1.13372, 1.13372, 1.72964; Eigen::MatrixXd mo_eigenvectors = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/gw/mo_eigenvectors.mm"); Eigen::MatrixXd vxc = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/gw/vxc.mm"); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/gw/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/gw/3-21G.xml"); orbitals.setDFTbasisName(std::string(XTP_TEST_DATA_FOLDER) + "/gw/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); orbitals.setBasisSetSize(17); orbitals.setNumberOfOccupiedLevels(4); orbitals.MOs().eigenvectors() = mo_eigenvectors; Logger log; TCMatrix_gwbse Mmn; Mmn.Initialize(aobasis.AOBasisSize(), 0, 16, 0, 16); Mmn.Fill(aobasis, aobasis, mo_eigenvectors); GW::options opt; opt.ScaHFX = 0; opt.homo = 4; opt.qpmax = 16; opt.qpmin = 0; opt.rpamax = 16; opt.rpamin = 0; opt.gw_sc_max_iterations = 1; opt.eta = 1e-3; opt.sigma_integration = "ppm"; opt.reset_3c = 5; opt.qp_solver = "grid"; opt.qp_grid_steps = 601; opt.qp_grid_spacing = 0.005; opt.gw_mixing_order = 0; opt.gw_mixing_alpha = 0.7; opt.g_sc_limit = 1e-5; opt.g_sc_max_iterations = 50; opt.gw_sc_limit = 1e-5; GW gw(log, Mmn, vxc, mo_eigenvalues); gw.configure(opt); Eigen::MatrixXd ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/gw/ref.mm"); gw.CalculateGWPerturbation(); Eigen::VectorXd diag = gw.getGWAResults(); bool check_diag = ref.diagonal().isApprox(diag, 1e-4); if (!check_diag) { cout << "GW energies" << endl; cout << diag << endl; cout << "GW energies ref" << endl; cout << ref.diagonal() << endl; } BOOST_CHECK_EQUAL(check_diag, true); gw.CalculateHQP(); Eigen::MatrixXd offdiag = gw.getHQP(); bool check_offdiag = ref.isApprox(offdiag, 1e-4); if (!check_offdiag) { cout << "GW energies" << endl; cout << offdiag << endl; cout << "GW energies ref" << endl; cout << ref << endl; } BOOST_CHECK_EQUAL(check_offdiag, true); libint2::finalize(); } BOOST_AUTO_TEST_CASE(gw_full_QP_grid) { libint2::initialize(); Eigen::VectorXd mo_eigenvalues = Eigen::VectorXd::Zero(17); mo_eigenvalues << -10.6784, -0.746424, -0.394948, -0.394948, -0.394948, 0.165212, 0.227713, 0.227713, 0.227713, 0.763971, 0.763971, 0.763971, 1.05054, 1.13372, 1.13372, 1.13372, 1.72964; Eigen::MatrixXd mo_eigenvectors = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/gw/mo_eigenvectors2.mm"); Eigen::MatrixXd vxc = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/gw/vxc2.mm"); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/gw/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/gw/3-21G.xml"); orbitals.setDFTbasisName(std::string(XTP_TEST_DATA_FOLDER) + "/gw/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); orbitals.setBasisSetSize(17); orbitals.setNumberOfOccupiedLevels(4); orbitals.MOs().eigenvectors() = mo_eigenvectors; Logger log; TCMatrix_gwbse Mmn; Mmn.Initialize(aobasis.AOBasisSize(), 0, 16, 0, 16); Mmn.Fill(aobasis, aobasis, mo_eigenvectors); GW::options opt; opt.ScaHFX = 0; opt.homo = 4; opt.qpmax = 16; opt.qpmin = 0; opt.rpamax = 16; opt.rpamin = 0; opt.gw_sc_max_iterations = 1; opt.qp_solver = "grid"; opt.eta = 1e-3; opt.sigma_integration = "ppm"; opt.reset_3c = 5; opt.qp_grid_steps = 601; opt.qp_grid_spacing = 0.005; opt.gw_mixing_order = 0; opt.gw_mixing_alpha = 0.7; opt.g_sc_limit = 1e-5; opt.g_sc_max_iterations = 50; opt.gw_sc_limit = 1e-5; GW gw(log, Mmn, vxc, mo_eigenvalues); gw.configure(opt); gw.CalculateGWPerturbation(); Eigen::VectorXd diag = gw.getGWAResults(); Eigen::MatrixXd ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/gw/ref2.mm"); bool check_diag = ref.diagonal().isApprox(diag, 1e-4); if (!check_diag) { cout << "GW energies" << endl; cout << diag << endl; cout << "GW energies ref" << endl; cout << ref.diagonal() << endl; } BOOST_CHECK_EQUAL(check_diag, true); gw.CalculateHQP(); Eigen::MatrixXd offdiag = gw.getHQP(); bool check_offdiag = ref.isApprox(offdiag, 1e-4); if (!check_offdiag) { cout << "GW energies" << endl; cout << offdiag << endl; cout << "GW energies ref" << endl; cout << ref << endl; } BOOST_CHECK_EQUAL(check_offdiag, true); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_hdf5.cc000066400000000000000000000213321412152066400165420ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE test_hdf5 // Standard includes #include // Third party includes #include #include // Local VOTCA includes #include "votca/xtp/checkpoint.h" #include "votca/xtp/checkpointreader.h" #include "votca/xtp/checkpointwriter.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/qmatom.h" BOOST_AUTO_TEST_SUITE(test_hdf5) using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_CASE(checkpoint_file_test) { Index basisSetSize = 17; Index occupiedLevels = 4; Index unoccupiedLevels = 13; Index numElectrons = 12; Eigen::VectorXd moeTest = Eigen::VectorXd::Random(17); Eigen::MatrixXd mocTest = Eigen::MatrixXd::Random(17, 17); QMMolecule atoms = QMMolecule(" ", 0); for (Index i = 0; i < 10; ++i) { atoms.push_back(QMAtom(0, "O", Eigen::Vector3d::Random())); atoms.push_back(QMAtom(25, "O", Eigen::Vector3d::Random())); atoms.push_back(QMAtom(32, "O", Eigen::Vector3d::Random())); atoms.push_back(QMAtom(100, "O", Eigen::Vector3d::Random())); atoms.push_back(QMAtom(2, "Si", Eigen::Vector3d::Random())); atoms.push_back(QMAtom(3145, "N", Eigen::Vector3d::Random())); } double qmEnergy = -2.1025e-3; std::string qmPackage = "NOPE"; Index rpaMin = '?'; Index rpaMax = 1e3; Index bseVmin = -6019386; Index bseCmax = 42; double scaHfx = 3.14159; bool useTDA = true; Eigen::MatrixXd vxcTest = Eigen::MatrixXd::Random(200, 200); std::string someECP = "aye aye Cap'n"; Eigen::VectorXd QPpertEnergiesTest = Eigen::VectorXd::Random(31); Eigen::MatrixXd QPdiagEnergiesTest = Eigen::VectorXd::Random(21); Eigen::MatrixXd QPdiagCoefficientsTest = Eigen::MatrixXd::Identity(42, 42); Eigen::VectorXd BSESingletEnergiesTest = Eigen::VectorXd::Random(25); Eigen::MatrixXd BSESingletCoefficientsTest = Eigen::MatrixXd::Random(25, 38); Eigen::MatrixXd BSESingletCoefficientsARTest = Eigen::MatrixXd::Random(42, 42); Eigen::VectorXd BSETripletEnergiesTest = Eigen::VectorXd::Random(33); Eigen::MatrixXd BSETripletCoefficientsTest = Eigen::MatrixXd::Random(33, 31); { // Write orbitals Orbitals orbWrite; orbWrite.setBasisSetSize(basisSetSize); orbWrite.setNumberOfOccupiedLevels(occupiedLevels); orbWrite.setNumberOfAlphaElectrons(numElectrons); orbWrite.MOs().eigenvalues() = moeTest; orbWrite.MOs().eigenvectors() = mocTest; orbWrite.QMAtoms() = atoms; orbWrite.setQMEnergy(qmEnergy); orbWrite.setQMpackage(qmPackage); orbWrite.setRPAindices(rpaMin, rpaMax); // no need to write qpmin, qpmax orbWrite.setBSEindices(bseVmin, bseCmax); orbWrite.setScaHFX(scaHfx); orbWrite.setTDAApprox(useTDA); orbWrite.setECPName(someECP); orbWrite.QPpertEnergies() = QPpertEnergiesTest; orbWrite.QPdiag().eigenvalues() = QPdiagEnergiesTest; orbWrite.QPdiag().eigenvectors() = QPdiagCoefficientsTest; orbWrite.BSESinglets().eigenvalues() = BSESingletEnergiesTest; orbWrite.BSESinglets().eigenvectors() = BSESingletCoefficientsTest; orbWrite.BSESinglets().eigenvectors2() = BSESingletCoefficientsARTest; orbWrite.BSETriplets().eigenvalues() = BSETripletEnergiesTest; orbWrite.BSETriplets().eigenvectors() = BSETripletCoefficientsTest; orbWrite.WriteToCpt("xtp_testing.hdf5"); } // Read Orbitals Orbitals orbRead; orbRead.ReadFromCpt("xtp_testing.hdf5"); double tol = 1e-6; // Test the read values BOOST_CHECK_EQUAL(orbRead.getBasisSetSize(), basisSetSize); BOOST_CHECK_EQUAL(orbRead.getBasisSetSize(), occupiedLevels + unoccupiedLevels); BOOST_CHECK_EQUAL(orbRead.getNumberOfAlphaElectrons(), numElectrons); BOOST_CHECK(orbRead.MOs().eigenvalues().isApprox(moeTest, tol)); BOOST_CHECK(orbRead.MOs().eigenvectors().isApprox(mocTest, tol)); BOOST_CHECK_CLOSE(orbRead.getDFTTotalEnergy(), qmEnergy, tol); BOOST_CHECK_EQUAL(orbRead.getQMpackage(), qmPackage); BOOST_CHECK_EQUAL(orbRead.getRPAmin(), rpaMin); BOOST_CHECK_EQUAL(orbRead.getRPAmax(), rpaMax); BOOST_CHECK_EQUAL(orbRead.getBSEvmin(), bseVmin); BOOST_CHECK_EQUAL(orbRead.getBSEcmax(), bseCmax); BOOST_CHECK_CLOSE(orbRead.getScaHFX(), scaHfx, tol); BOOST_CHECK_EQUAL(orbRead.getTDAApprox(), useTDA); BOOST_CHECK_EQUAL(orbRead.getECPName(), someECP); BOOST_CHECK(orbRead.QPpertEnergies().isApprox(QPpertEnergiesTest, tol)); BOOST_CHECK(orbRead.QPdiag().eigenvalues().isApprox(QPdiagEnergiesTest, tol)); BOOST_CHECK(orbRead.QPdiag().eigenvectors().isApprox(QPdiagCoefficientsTest)); BOOST_CHECK(orbRead.BSESinglets().eigenvalues().isApprox( BSESingletEnergiesTest, tol)); BOOST_CHECK(orbRead.BSESinglets().eigenvectors().isApprox( BSESingletCoefficientsTest, tol)); BOOST_CHECK(orbRead.BSESinglets().eigenvectors2().isApprox( BSESingletCoefficientsARTest, tol)); BOOST_CHECK(orbRead.BSETriplets().eigenvalues().isApprox( BSETripletEnergiesTest, tol)); BOOST_CHECK(orbRead.BSETriplets().eigenvectors().isApprox( BSETripletCoefficientsTest, tol)); BOOST_REQUIRE_EQUAL(orbRead.QMAtoms().size(), atoms.size()); for (Index i = 0; i < atoms.size(); ++i) { const auto& atomRead = orbRead.QMAtoms()[i]; const auto& atomTest = atoms[i]; BOOST_CHECK_EQUAL(atomRead.getId(), atomTest.getId()); BOOST_CHECK(atomRead.getPos().isApprox(atomTest.getPos(), tol)); BOOST_CHECK_EQUAL(atomRead.getNuccharge(), atomTest.getNuccharge()); BOOST_CHECK_EQUAL(atomRead.getElement(), atomTest.getElement()); } } BOOST_AUTO_TEST_CASE(open_file_error) { BOOST_REQUIRE_THROW( CheckpointFile cpf("/bin/mr/root/man.pls", CheckpointAccessLevel::READ), std::runtime_error); } BOOST_AUTO_TEST_CASE(checkpoint_open_non_existing_loc) { CheckpointFile cpf("testin_yo.ab", CheckpointAccessLevel::MODIFY); BOOST_REQUIRE_THROW(CheckpointReader r = cpf.getReader("/some/bulshit"), std::runtime_error); } BOOST_AUTO_TEST_CASE(read_non_exisiting_matrix) { CheckpointFile cpf("xtp_testing.hdf5", CheckpointAccessLevel::READ); CheckpointReader r = cpf.getReader("/QMdata"); Eigen::MatrixXd someMatrix; BOOST_REQUIRE_THROW(r(someMatrix, "someMatrix012'5915.jb"), std::runtime_error); } BOOST_AUTO_TEST_CASE(read_non_existing_scalar) { CheckpointFile cpf("xtp_testing.hdf5", CheckpointAccessLevel::READ); CheckpointReader r = cpf.getReader("/QMdata"); float someThing = 0; BOOST_REQUIRE_THROW(r(someThing, "someThing"), std::runtime_error); } BOOST_AUTO_TEST_CASE(read_vector_strings) { CheckpointFile cpf("xtp_vector_string.hdf5"); CheckpointWriter w = cpf.getWriter(); std::vector test_vec = { "a", "b", "advhsbsavc", "dumuunnadnjdsahjads", "DASASDFAFNADDH blasndd"}; w(test_vec, "vec"); std::vector test_vec2; CheckpointReader r = cpf.getReader(); r(test_vec2, "vec"); BOOST_CHECK_EQUAL(test_vec.size(), test_vec2.size()); for (Index i = 0; i > Index(test_vec.size()); i++) { BOOST_CHECK_EQUAL(test_vec[i], test_vec2[i]); } } BOOST_AUTO_TEST_CASE(staticsegment) { CheckpointFile cpf("xtp_staticsegment.hdf5"); CheckpointWriter w = cpf.getWriter(); StaticSegment seg = StaticSegment("test", 0); for (Index i = 0; i < 10; ++i) { seg.push_back(StaticSite(0, "O", Eigen::Vector3d::Random())); seg.push_back(StaticSite(25, "O", Eigen::Vector3d::Random())); seg.push_back(StaticSite(32, "O", Eigen::Vector3d::Random())); seg.push_back(StaticSite(100, "O", Eigen::Vector3d::Random())); seg.push_back(StaticSite(2, "Si", Eigen::Vector3d::Random())); seg.push_back(StaticSite(3145, "N", Eigen::Vector3d::Random())); } seg.WriteToCpt(w); CheckpointReader r = cpf.getReader(); StaticSegment seg2 = StaticSegment(r); BOOST_REQUIRE_EQUAL(seg2.size(), seg.size()); for (Index i = 0; i < seg.size(); ++i) { const auto& atomRead = seg2[i]; const auto& atomTest = seg[i]; BOOST_CHECK_EQUAL(atomRead.getId(), atomTest.getId()); BOOST_CHECK(atomRead.getPos().isApprox(atomTest.getPos(), 1e-7)); BOOST_CHECK_EQUAL(atomRead.getCharge(), atomTest.getCharge()); BOOST_CHECK_EQUAL(atomRead.getElement(), atomTest.getElement()); } } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_hist.cc000066400000000000000000000041301412152066400166600ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE hist_test // Standard includes #include // Third party includes #include #include // Local VOTCA includes #include "votca/xtp/hist.h" using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(hist_test) BOOST_AUTO_TEST_CASE(readwrite_hdf5) { hist h; BOOST_CHECK_EQUAL(h.filled(), false); h.push_back(1.0); BOOST_CHECK_EQUAL(h.filled(), true); BOOST_CHECK_CLOSE(h.getDiff(), 1.0, 1e-9); h.push_back(1.5); BOOST_CHECK_CLOSE(h.getDiff(), 0.5, 1e-9); BOOST_CHECK_EQUAL(h.filled(), true); { CheckpointFile f("hist_test.hdf5"); CheckpointWriter w = f.getWriter(); h.WriteToCpt(w); } hist h2; CheckpointFile f("hist_test.hdf5"); CheckpointReader r = f.getReader(); h2.ReadFromCpt(r); BOOST_CHECK_CLOSE(h.getDiff(), h2.getDiff(), 1e-9); BOOST_CHECK_CLOSE(h.back(), h2.back(), 1e-9); BOOST_CHECK_EQUAL(h.filled(), h2.filled()); Energy_terms t; t.E_indu_indu() = 1.0; hist a; a.push_back(t); CheckpointFile ff("hist_test2.hdf5"); CheckpointWriter ww = ff.getWriter(); a.WriteToCpt(ww); hist aa; CheckpointReader rr = ff.getReader(); aa.ReadFromCpt(rr); bool is_close = aa.getDiff().data().isApprox(a.getDiff().data(), 1e-9); BOOST_CHECK_EQUAL(is_close, true); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_indexparser.cc000066400000000000000000000035731412152066400202470ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE index_parser_test // Third party includes #include // Local VOTCA includes #include "votca/xtp/IndexParser.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(index_parser_test) BOOST_AUTO_TEST_CASE(readstring_test) { IndexParser parser; std::string test = "1 5 3:11 15:17"; std::vector result = parser.CreateIndexVector(test); std::vector ref = {1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17}; BOOST_CHECK_EQUAL(result.size(), ref.size()); for (votca::Index i = 0; i < votca::Index(ref.size()); i++) { BOOST_CHECK_EQUAL(result[i], ref[i]); } } BOOST_AUTO_TEST_CASE(error_handling) { IndexParser parser; std::string test = "1 5 3...11 15:17"; BOOST_REQUIRE_THROW(parser.CreateIndexVector(test), std::runtime_error); std::string test2 = "1a 5 15:17"; BOOST_REQUIRE_THROW(parser.CreateIndexVector(test2), std::runtime_error); } BOOST_AUTO_TEST_CASE(generatestring_test) { std::vector input = {1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17}; IndexParser parser; std::string result = parser.CreateIndexString(input); std::string ref = "1 3:11 15:17"; BOOST_CHECK_EQUAL(result, ref); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_interaction.cc000066400000000000000000000117541412152066400202420ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE polararsite_test // Third party includes #include // Local VOTCA includes #include "votca/xtp/polarsite.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(polararsite_test) BOOST_AUTO_TEST_CASE(constructors_test) { PolarSite ps(1, "ps1"); } BOOST_AUTO_TEST_CASE(getters_test) { PolarSite ps(1, "ps2"); BOOST_CHECK_EQUAL(ps.getId(), 1); BOOST_CHECK_EQUAL(ps.getElement(), "ps2"); } BOOST_AUTO_TEST_CASE(multipole_test) { PolarSite ps(1, "ps2"); Eigen::VectorXd multipole = Eigen::VectorXd::Zero(9); multipole << 1, 2, 3, 4, 8, 7, 2, 3.3, -0.5; ps.setMultipole(multipole); bool check_mpoles = multipole.isApprox(ps.getPermMultipole(), 0.0001); BOOST_CHECK_EQUAL(check_mpoles, true); bool check_rank = (ps.getRank() == 2); BOOST_CHECK_EQUAL(check_rank, true); } BOOST_AUTO_TEST_CASE(translate_test) { PolarSite ps(1, "ps2"); Eigen::Vector3d shift; shift << 0, 0, 5; ps.Translate(shift); BOOST_CHECK_EQUAL(shift.isApprox(ps.getPos(), 1e-5), true); } BOOST_AUTO_TEST_CASE(rotation_test) { PolarSite ps(1, "ps2", Eigen::Vector3d::UnitY()); Eigen::Matrix3d R = Eigen::Matrix3d::Zero(); // Rotation around z axes R << 0, -1, 0, 1, 0, 0, 0, 0, 1; Eigen::VectorXd multipoles = Eigen::VectorXd::Zero(9); multipoles << 1, 1, 0, 0, 0, 1, 0, 0, 0; // q=1, mu_x=1 and Q_21c=1 the rest is 0 ps.setMultipole(multipoles); ps.Rotate(R, Eigen::Vector3d::Zero()); bool equalpos = ps.getPos().isApprox(Eigen::Vector3d(-1, 0, 0), 1e-5); if (!equalpos) { std::cout << "Result " << std::endl; std::cout << ps.getPos() << std::endl; std::cout << "Reference" << std::endl; std::cout << Eigen::Vector3d(-1, 0, 0) << std::endl; } BOOST_CHECK_EQUAL(equalpos, true); Eigen::VectorXd rotmultipoles = Eigen::VectorXd::Zero(9); rotmultipoles << 1, 0, 1, 0, 0, 0, 1, 0, 0; // q=1, mu_y=1 and Q_21s=1 is 0 bool equalmultipoles = rotmultipoles.isApprox(ps.getPermMultipole(), 1e-5); if (!equalmultipoles) { std::cout << "Result " << std::endl; std::cout << ps.getPermMultipole() << std::endl; std::cout << "Reference" << std::endl; std::cout << rotmultipoles << std::endl; } BOOST_CHECK_EQUAL(equalmultipoles, true); } BOOST_AUTO_TEST_CASE(interaction_test) { PolarSite ps1(1, "ps1"); PolarSite ps2(2, "ps2", Eigen::Vector3d::UnitX()); Eigen::VectorXd mp1 = Eigen::VectorXd::Zero(1); Eigen::VectorXd mp2 = Eigen::VectorXd::Zero(1); mp1 << 1; mp2 << -1; ps1.setPolarisable(false); ps2.setPolarisable(false); ps1.setMultipole(mp1); ps2.setMultipole(mp2); double Energyref = -1; double Energy = ps1.InteractStatic(ps2); BOOST_CHECK_EQUAL(std::abs(Energy - Energyref) < 1e-9, true); bool check_field = ps1.getField().isApprox(ps2.getField(), 1e-5); if (!check_field) { std::cout << "Field at ps1" << std::endl; std::cout << ps1.getField() << std::endl; std::cout << "Field at ps2" << std::endl; std::cout << ps2.getField() << std::endl; } BOOST_CHECK_EQUAL(check_field, true); bool check_potential = std::abs(ps1.getPotential() + ps2.getPotential()) < 1e-5; if (!check_potential) { std::cout << "Potential at ps1" << std::endl; std::cout << ps1.getPotential() << std::endl; std::cout << "Potential at ps2" << std::endl; std::cout << ps2.getPotential() << std::endl; } BOOST_CHECK_EQUAL(check_potential, true); PolarSite ps3(3, "ps3"); PolarSite ps4(4, "ps4", Eigen::Vector3d::UnitZ()); Eigen::VectorXd multipole = Eigen::VectorXd::Zero(9); multipole << 1, 2, 3, 4, 8, 7, 2, 3.3, -0.5; ps3.setPolarisable(true); ps4.setPolarisable(true); ps3.setMultipole(multipole); ps4.setMultipole(multipole); ps3.InteractStatic(ps4); } BOOST_AUTO_TEST_CASE(induction_test) { PolarSite ps1(1, "ps1"); PolarSite ps2(2, "ps2", Eigen::Vector3d::UnitX()); Eigen::VectorXd mp1 = Eigen::VectorXd::Zero(1); Eigen::VectorXd mp2 = Eigen::VectorXd::Zero(1); mp1 << 1; mp2 << -1; ps1.setPolarisable(true); ps2.setPolarisable(true); ps1.setMultipole(mp1); ps2.setMultipole(mp2); Eigen::Matrix3d poltensor = Eigen::Matrix3d::Zero(); poltensor << 2, 1, 0, 1, 3, 1, 0, 1, 2.5; ps1.setpolarization(poltensor); ps2.setpolarization(poltensor); // double Energy= ps1.InteractStatic(ps2); ps1.Induce(1); ps2.Induce(1); // double alpha=0.39; // double InductionEnergy=ps1.InteractInduction(ps2,alpha); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_jobtopology.cc000066400000000000000000000035731412152066400202720ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE jobtopology_test // Third party includes #include // Local VOTCA includes #include "votca/xtp/jobtopology.h" using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(jobtopology_test) BOOST_AUTO_TEST_CASE(constructor) { ofstream jobstream("job.xml"); jobstream << " " << std::endl; jobstream << " 0" << std::endl; jobstream << " seg0:n" << std::endl; jobstream << " " << std::endl; jobstream << " 0:n" << std::endl; jobstream << " " << std::endl; jobstream << " " << std::endl; jobstream << " 0" << std::endl; jobstream << " 0:n" << std::endl; jobstream << " " << std::endl; jobstream << " " << std::endl; jobstream << " " << std::endl; jobstream << " AVAILABLE" << std::endl; jobstream << " " << std::endl; votca::tools::Property prop; prop.LoadFromXML("job.xml"); std::string workdir = "."; Logger log; Job job(prop.get("job")); JobTopology top(job, log, workdir); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_localisation_filter.cc000066400000000000000000000063261412152066400217500ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE deltaQ_filter_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/filterfactory.h" // VOTCA includes #include #include using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(deltaQ_filter_test) BOOST_AUTO_TEST_CASE(coeffs_test) { libint2::initialize(); FilterFactory::RegisterAll(); std::unique_ptr local_f = std::unique_ptr(Filter().Create("localisation")); std::ofstream opt("localisation.xml"); opt << "" << std::endl; opt << " 0.5" << std::endl; opt << " 0 1" << std::endl; opt << "" << std::endl; opt.close(); votca::tools::Property prop; prop.LoadFromXML("localisation.xml"); local_f->Initialize(prop.get("root")); Orbitals A; A.setDFTbasisName(std::string(XTP_TEST_DATA_FOLDER) + "/localisation_filter/3-21G.xml"); A.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/localisation_filter/molecule.xyz"); A.setBasisSetSize(17); A.setNumberOfAlphaElectrons(5); A.setNumberOfOccupiedLevels(5); A.MOs().eigenvalues() = Eigen::VectorXd::Zero(17); A.MOs().eigenvalues() << -19.8117, -6.22408, -6.14094, -6.14094, -6.14094, -3.72889, -3.72889, -3.72889, -3.64731, -3.09048, -3.09048, -3.09048, -2.63214, -2.08206, -2.08206, -2.08206, -2.03268; A.MOs().eigenvectors() = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/localisation_filter/MOs_A.mm"); A.setBSEindices(0, 16); A.setTDAApprox(true); A.setGWindices(0, 16); Eigen::MatrixXd spsi_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/localisation_filter/spsi_ref.mm"); A.BSESinglets().eigenvectors() = spsi_ref; // reference energy Eigen::VectorXd se_ref = Eigen::VectorXd::Zero(3); se_ref << 0.107455, 0.107455, 0.107455; A.BSESinglets().eigenvalues() = se_ref; BOOST_CHECK_EQUAL(local_f->NeedsInitialState(), false); std::vector ref = {2}; std::vector results = local_f->CalcIndeces(A, QMStateType::Singlet); BOOST_CHECK_EQUAL(results.size(), ref.size()); for (votca::Index i = 0; i < votca::Index(ref.size()); i++) { BOOST_CHECK_EQUAL(ref[i], results[i]); } BOOST_REQUIRE_THROW(local_f->CalcIndeces(A, QMStateType::Gstate), std::runtime_error); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_molden.cc000066400000000000000000000106251412152066400171750ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE moldenreader_test // Third party includes #include // VOTCA includes #include #include // Local VOTCA includes #include "votca/xtp/logger.h" #include "votca/xtp/molden.h" #include "votca/xtp/orbitals.h" using namespace votca::xtp; using namespace votca; using namespace std; BOOST_AUTO_TEST_SUITE(molden_test) BOOST_AUTO_TEST_CASE(moldenreader_test) { libint2::initialize(); Eigen::MatrixXd coeffs_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/molden/orbitalsMOs_ref.mm"); Orbitals orbitals_ref; orbitals_ref.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/molden/benzene.xyz"); Logger log; Molden molden(log); molden.setBasissetInfo( std::string(XTP_TEST_DATA_FOLDER) + "/molden/def2-tzvp.xml", "aux-def2-tzvp"); Orbitals orbitals; molden.parseMoldenFile( std::string(XTP_TEST_DATA_FOLDER) + "/molden/benzene.molden.input", orbitals); // Check if eigenvalues are equal orbitals_ref.MOs().eigenvalues() = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/molden/orbitals_eigenvalues.mm"); BOOST_CHECK(orbitals.MOs().eigenvalues().isApprox( orbitals_ref.MOs().eigenvalues(), 1e-4)); // Check if MO's are read correctly BOOST_CHECK(orbitals.MOs().eigenvectors().isApprox(coeffs_ref, 1e-4)); // Check if atoms are read correctly BOOST_CHECK(orbitals.QMAtoms().size() == orbitals_ref.QMAtoms().size()); for (int i = 0; i < orbitals.QMAtoms().size(); i++) { BOOST_CHECK(orbitals.QMAtoms()[i].getPos().isApprox( orbitals_ref.QMAtoms()[i].getPos(), 1e-3)); } libint2::finalize(); } BOOST_AUTO_TEST_CASE(moldenwriter_test) { libint2::initialize(); // Setup orbitals object Orbitals orbitals_ref; orbitals_ref.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/molden/benzene.xyz"); orbitals_ref.setNumberOfOccupiedLevels(21); orbitals_ref.MOs().eigenvectors() = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/molden/orbitalsMOs_ref.mm"); orbitals_ref.MOs().eigenvalues() = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/molden/orbitals_eigenvalues.mm"); orbitals_ref.setBasisSetSize(orbitals_ref.MOs().eigenvalues().size()); orbitals_ref.setDFTbasisName(std::string(XTP_TEST_DATA_FOLDER) + "/molden/def2-tzvp.xml"); orbitals_ref.setAuxbasisName("aux-def2-tzvp"); // write orbitals object to molden file Logger log; Molden molden(log); molden.WriteFile("moldenFile.molden", orbitals_ref); // read in written molden file molden.setBasissetInfo( std::string(XTP_TEST_DATA_FOLDER) + "/molden/def2-tzvp.xml", "aux-def2-tzvp"); Orbitals orbitals; molden.parseMoldenFile("moldenFile.molden", orbitals); Eigen::MatrixXd coeffs_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/molden/orbitalsMOs_ref.mm"); // Check if MO's are equal BOOST_CHECK(coeffs_ref.isApprox(orbitals.MOs().eigenvectors(), 1e-5)); std::cout << "ref" << std::endl; std::cout << coeffs_ref << std::endl; std::cout << "results" << std::endl; std::cout << orbitals.MOs().eigenvectors() << std::endl; // Check if atoms are equal BOOST_CHECK(orbitals.QMAtoms().size() == orbitals_ref.QMAtoms().size()); for (int i = 0; i < orbitals.QMAtoms().size(); i++) { BOOST_CHECK(orbitals.QMAtoms()[i].getPos().isApprox( orbitals_ref.QMAtoms()[i].getPos(), 1e-3)); } libint2::finalize(); } }xtp-2021.2/src/tests/test_newton_rapson.cc000066400000000000000000000026721412152066400206160ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE newton_rapson // Third party includes #include // Local VOTCA includes #include "votca/xtp/newton_rapson.h" using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(newton_rapson) class Func { public: std::pair operator()(double x) const { std::pair value; value.first = x * x - 612; value.second = 2 * x; return value; } }; BOOST_AUTO_TEST_CASE(newton_rapson) { Func f; Index iterations = 50; double tolerance = 1e-9; NewtonRapson n(iterations, tolerance); double root = n.FindRoot(f, 10.0); BOOST_CHECK_EQUAL(n.getInfo(), NewtonRapson::Errors::success); // see https://en.wikipedia.org/wiki/Newton%27s_method BOOST_CHECK_CLOSE(root, 24.738633753, 1e-7); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_orbitals.cc000066400000000000000000000221261412152066400175350ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE orbitals_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/aomatrix.h" #include "votca/xtp/convergenceacc.h" #include "votca/xtp/orbitals.h" // VOTCA includes #include using namespace votca::xtp; using votca::Index; BOOST_AUTO_TEST_SUITE(orbitals_test) BOOST_AUTO_TEST_CASE(readxyztest) { std::ofstream xyzfile("molecule.xyz"); xyzfile << " C 0.0 3 1" << std::endl; xyzfile << " methane" << std::endl; xyzfile << " C .000000 .000000 .000000" << std::endl; xyzfile << " H .629118 .629118 .629118" << std::endl; xyzfile << " H -.629118 -.629118 .629118" << std::endl; xyzfile << " H .629118 -.629118 -.629118" << std::endl; xyzfile << " H -.629118 .629118 -.629118" << std::endl; xyzfile.close(); Orbitals orb; BOOST_CHECK_THROW(orb.QMAtoms().LoadFromFile("molecule.xyz"), std::runtime_error); } BOOST_AUTO_TEST_CASE(sortEnergies) { Orbitals orb; Eigen::VectorXd Energies = Eigen::VectorXd::LinSpaced(10, -5, 5); Eigen::VectorXd switched = Energies; switched(3) = Energies(5); switched(5) = Energies(3); orb.MOs().eigenvalues() = switched; orb.MOs().eigenvectors() = Eigen::MatrixXd::Zero(10, 10); orb.OrderMOsbyEnergy(); bool issorted = Energies.isApprox(orb.MOs().eigenvalues(), 0.001); if (!issorted) { std::cout << "before" << std::endl; std::cout << Energies << std::endl; std::cout << "after" << std::endl; std::cout << orb.MOs().eigenvalues() << std::endl; } BOOST_CHECK_EQUAL(issorted, true); } BOOST_AUTO_TEST_CASE(densmat_test) { libint2::initialize(); Orbitals orb; orb.setBasisSetSize(17); orb.setNumberOfOccupiedLevels(4); orb.setBSEindices(0, 9); orb.setNumberOfAlphaElectrons(5); orb.MOs().eigenvalues() = Eigen::VectorXd::Ones(17); orb.MOs().eigenvectors() = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/orbitals/MOs.mm"); orb.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/orbitals/molecule.xyz"); QMState s = QMState("n"); Eigen::MatrixXd dmat_gs = orb.DensityMatrixFull(s); Eigen::MatrixXd dmat_gs_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/orbitals/dmat_gs_ref.mm"); bool check_dmat_gs = dmat_gs.isApprox(dmat_gs_ref, 0.0001); if (!check_dmat_gs) { std::cout << "Result gs" << std::endl; std::cout << dmat_gs << std::endl; std::cout << "Ref" << std::endl; std::cout << dmat_gs_ref << std::endl; } BOOST_CHECK_EQUAL(check_dmat_gs, 1); orb.setTDAApprox(false); orb.BSESinglets().eigenvectors() = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/orbitals/BSE_vectors1.mm"); orb.BSESinglets().eigenvectors2() = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/orbitals/BSE_vectors2.mm"); QMState s1 = QMState("s1"); Eigen::MatrixXd dmat_s1 = orb.DensityMatrixFull(s1); Eigen::MatrixXd dmat_s1_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/orbitals/dmat_s1_ref.mm"); bool check_dmat_s1 = dmat_s1.isApprox(dmat_s1_ref, 0.0001); if (!check_dmat_s1) { std::cout << "Result s1" << std::endl; std::cout << dmat_s1 << std::endl; std::cout << "Ref" << std::endl; std::cout << dmat_s1_ref << std::endl; } BOOST_CHECK_EQUAL(check_dmat_s1, 1); QMState n2s1 = QMState("n2s1"); Eigen::MatrixXd dmat_n2s1 = orb.DensityMatrixFull(n2s1); Eigen::MatrixXd dmat_n2s1_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/orbitals/dmat_n2s1_ref.mm"); bool check_dmat_n2s1 = dmat_n2s1.isApprox(dmat_n2s1_ref, 0.0001); if (!check_dmat_n2s1) { std::cout << "Result n2s1" << std::endl; std::cout << dmat_n2s1 << std::endl; std::cout << "Ref" << std::endl; std::cout << dmat_n2s1_ref << std::endl; } BOOST_CHECK_EQUAL(check_dmat_n2s1, 1); libint2::finalize(); } BOOST_AUTO_TEST_CASE(dipole_test) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/orbitals/molecule.xyz"); BasisSet basis; basis.Load( std::string(std::string(XTP_TEST_DATA_FOLDER) + "/orbitals/3-21G.xml")); orbitals.setDFTbasisName(std::string(XTP_TEST_DATA_FOLDER) + "/orbitals/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); orbitals.setBasisSetSize(17); orbitals.setNumberOfOccupiedLevels(4); Eigen::MatrixXd& MOs = orbitals.MOs().eigenvectors(); orbitals.MOs().eigenvalues() = Eigen::VectorXd::Ones(17); MOs = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/orbitals/MOs2.mm"); orbitals.setBSEindices(0, 16); orbitals.setTDAApprox(true); Eigen::MatrixXd spsi_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/orbitals/spsi_ref.mm"); orbitals.BSESinglets().eigenvectors() = spsi_ref; QMState state_trans = QMState("n2s1"); Eigen::Vector3d res_trans = orbitals.CalcElDipole(state_trans); Eigen::Vector3d ref_trans = Eigen::Vector3d::Zero(); ref_trans << 0.118565, 0.0444239, -0.0505149; bool check_trans = ref_trans.isApprox(res_trans, 0.0001); if (!check_trans) { std::cout << "Result transition dipole" << std::endl; std::cout << res_trans << std::endl; std::cout << "Ref transition dipole" << std::endl; std::cout << ref_trans << std::endl; } BOOST_CHECK_EQUAL(check_trans, 1); QMState state_s1 = QMState("s1"); Eigen::Vector3d res_s1 = orbitals.CalcElDipole(state_s1); Eigen::Vector3d ref_s1 = Eigen::Vector3d::Zero(); ref_s1 << -0.15153501734, -0.42406579479, 0.033954362839; bool check_s1 = ref_s1.isApprox(res_s1, 0.0001); if (!check_s1) { std::cout << "Result s1 dipole" << std::endl; std::cout << res_s1 << std::endl; std::cout << "Ref s1 dipole" << std::endl; std::cout << ref_s1 << std::endl; } BOOST_CHECK_EQUAL(check_s1, 1); libint2::finalize(); } BOOST_AUTO_TEST_CASE(osc_strength) { libint2::initialize(); Orbitals orb; orb.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/orbitals/molecule.xyz"); orb.setDFTbasisName(std::string(XTP_TEST_DATA_FOLDER) + "/orbitals/3-21G.xml"); QMState s("s1"); orb.setBasisSetSize(17); orb.setNumberOfOccupiedLevels(4); orb.setBSEindices(0, 16); orb.setTDAApprox(true); Eigen::MatrixXd& MOs = orb.MOs().eigenvectors(); orb.MOs().eigenvalues() = Eigen::VectorXd::Ones(17); MOs = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/orbitals/MOs3.mm"); Eigen::VectorXd se_ref = Eigen::VectorXd::Zero(3); se_ref << 0.107455, 0.107455, 0.107455; orb.BSESinglets().eigenvalues() = se_ref; // reference coefficients Eigen::MatrixXd spsi_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/orbitals/spsi_ref2.mm"); orb.BSESinglets().eigenvectors() = spsi_ref; orb.CalcCoupledTransition_Dipoles(); std::vector dipoles = orb.TransitionDipoles(); std::vector dipoles_ref; dipoles_ref.push_back(Eigen::Vector3d(0.110512, 0.048776, -0.0515914)); dipoles_ref.push_back(Eigen::Vector3d(-0.13408, 0.0969472, 0.0261392)); dipoles_ref.push_back(Eigen::Vector3d(0.0586073, 0.121606, -0.0606862)); for (Index i = 0; i < 3; i++) { bool check = dipoles[i].isApprox(dipoles_ref[i], 1e-5); BOOST_CHECK_EQUAL(check, true); if (!check) { std::cout << "ref" << i << std::endl; std::cout << dipoles_ref[i].transpose() << std::endl; std::cout << "result" << i << std::endl; std::cout << dipoles[i].transpose() << std::endl; } } Eigen::VectorXd oscs = orb.Oscillatorstrengths(); Eigen::VectorXd oscs_ref = Eigen::VectorXd::Zero(3); oscs_ref << 0.001236, 0.00201008, 0.00156925; bool check_oscs = oscs.isApprox(oscs_ref, 1e-5); BOOST_CHECK_EQUAL(check_oscs, true); if (!check_oscs) { std::cout << "result" << std::endl; std::cout << oscs << std::endl; std::cout << "ref" << std::endl; std::cout << oscs_ref << std::endl; } libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_orbreorder.cc000066400000000000000000000065571412152066400200750ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE orbreorder_test // Third party includes #include // VOTCA includes #include #include // Local VOTCA includes #include "votca/xtp/orbitals.h" #include "votca/xtp/orbreorder.h" using namespace votca::xtp; using namespace votca; using namespace std; BOOST_AUTO_TEST_SUITE(orbreorder_test) BOOST_AUTO_TEST_CASE(orbreorder_test) { libint2::initialize(); // clang-format off std::array multipliers={ 1, //s 1,1,1, //p 1,1,1,1,1, //d -1,1,1,1,1,1,-1, //f -1,-1,1,1,1,1,1,-1,-1, //g -1,-1,-1,1,1,1,1,1,-1,-1,-1, //h -1,-1,-1,-1,1,1,1,1,1,-1,-1,-1,-1 //i }; std::array reorderList={ 0, //s 1,-1,0, //p 0,1,-1,2,-2, //d 0,1,-1,2,-2,3,-3, //f 0,1,-1,2,-2,3,-3,4,-4, //g 0,1,-1,2,-2,3,-3,4,-4,5,-5, //h 0,1,-1,2,-2,3,-3,4,-4,5,-5,6,-6 //i }; // clang-format on Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/orbreorder/methane.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/orbreorder/def2-tzvp.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); Eigen::MatrixXd moldenCoeffs = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/orbreorder/MOLDEN_order.mm"); Eigen::MatrixXd votcaCoeffs = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/orbreorder/VOTCA_order.mm"); // Convert moldenCoeffs to votcaCoeffs OrbReorder reorder(reorderList, multipliers); reorder.reorderOrbitals(moldenCoeffs, aobasis); std::array votcaOrder_old = { 0, // s 0, -1, 1, // p 0, -1, 1, -2, 2, // d 0, -1, 1, -2, 2, -3, 3, // f 0, -1, 1, -2, 2, -3, 3, -4, 4, // g 0, -1, 1, -2, 2, -3, 3, -4, 4, -5, 5, // h 0, -1, 1, -2, 2, -3, 3, -4, 4, -5, 5, -6, 6 // i }; std::array multiplier2; multiplier2.fill(1); OrbReorder reorder2(votcaOrder_old, multiplier2); reorder2.reorderOrbitals(votcaCoeffs, aobasis); bool check = moldenCoeffs.isApprox(votcaCoeffs, 1e-5); BOOST_CHECK(check); if (!check) { std::cout << "votcaCoeffs" << std::endl; std::cout << votcaCoeffs << std::endl; std::cout << "moldenCoeffs" << std::endl; std::cout << moldenCoeffs << std::endl; } libint2::finalize(); } }xtp-2021.2/src/tests/test_orca.cc000066400000000000000000000247471412152066400166550ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE orca_test // Third party includes #include // VOTCA includes #include #include // Local VOTCA includes #include "votca/xtp/orbitals.h" #include "votca/xtp/orbreorder.h" #include "votca/xtp/qmpackagefactory.h" using namespace votca::xtp; using namespace votca; using namespace std; BOOST_AUTO_TEST_SUITE(orca_test) BOOST_AUTO_TEST_CASE(polar_test) { QMPackageFactory::RegisterAll(); std::unique_ptr orca = QMPackageFactory::QMPackages().Create("orca"); auto keys = QMPackageFactory::QMPackages().getKeys(); for (auto key : keys) { std::cout << key << std::endl; } Logger log; orca->setLog(&log); orca->setRunDir(std::string(XTP_TEST_DATA_FOLDER) + "/orca"); orca->setLogFileName("polar_orca.log"); Eigen::Matrix3d polar_mat = orca->GetPolarizability(); Eigen::Matrix3d polar_ref = Eigen::Matrix3d::Zero(); polar_ref << 11.40196, -0.00423, 0.00097, -0.00423, 11.42894, 0.01163, 0.00097, 0.01163, 11.41930; bool polar_check = polar_ref.isApprox(polar_mat, 1e-5); BOOST_CHECK_EQUAL(polar_check, true); if (!polar_check) { std::cout << "res" << std::endl; std::cout << polar_mat << std::endl; std::cout << "ref " << std::endl; std::cout << polar_ref << std::endl; } } BOOST_AUTO_TEST_CASE(ext_charges_test) { libint2::initialize(); QMPackageFactory::RegisterAll(); std::unique_ptr orca = QMPackageFactory::QMPackages().Create("orca"); Logger log; orca->setLog(&log); orca->setRunDir(std::string(XTP_TEST_DATA_FOLDER) + "/orca"); orca->setLogFileName("orca_ext_charges.log"); Orbitals orb; orca->ParseLogFile(orb); BOOST_CHECK_CLOSE(orb.getScaHFX(), 0.25, 1e-5); double ref_tot = -40.244504856356; // HF - Self energy ext charges BOOST_CHECK_CLOSE(ref_tot, orb.getDFTTotalEnergy(), 1e-5); const QMMolecule& seg = orb.QMAtoms(); double ang2bohr = votca::tools::conv::ang2bohr; QMMolecule ref("ref", 0); Eigen::Vector3d pos1 = {0.528800, 0.161000, 0.935900}; QMAtom s1(0, "H", pos1 * ang2bohr); pos1 = {0.000000, 0.000000, 0.000000}; QMAtom s2(1, "C", pos1 * ang2bohr); pos1 = {0.205100, 0.824000, -0.678600}; QMAtom s3(2, "H", pos1 * ang2bohr); pos1 = {0.334500, -0.931400, -0.449600}; QMAtom s4(3, "H", pos1 * ang2bohr); pos1 = {-1.068500, -0.053700, 0.192100}; QMAtom s5(4, "H", pos1 * ang2bohr); ref.push_back(s1); ref.push_back(s2); ref.push_back(s3); ref.push_back(s4); ref.push_back(s5); BOOST_CHECK_EQUAL(seg.size(), ref.size()); for (votca::Index i = 0; i < votca::Index(seg.size()); i++) { BOOST_CHECK_EQUAL(ref[i].getPos().isApprox(seg[i].getPos(), 1e-5), true); BOOST_CHECK_EQUAL(ref[i].getElement(), seg[i].getElement()); } orb.setDFTbasisName(std::string(XTP_TEST_DATA_FOLDER) + "/orca/3-21G_small.xml"); orca->setMOsFileName("orca_ext_mos.gbw"); orca->ParseMOsFile(orb); Eigen::VectorXd MOs_energy_ref = Eigen::VectorXd::Zero(17); MOs_energy_ref << -10.1441, -0.712523, -0.405481, -0.403251, -0.392086, 0.157504, 0.196706, 0.202667, 0.240538, 0.718397, 0.727724, 0.728746, 1.0577, 1.08125, 1.08607, 1.11627, 1.71596; bool check_eng = MOs_energy_ref.isApprox(orb.MOs().eigenvalues(), 1e-5); BOOST_CHECK_EQUAL(check_eng, true); if (!check_eng) { std::cout << "result eng" << std::endl; std::cout << orb.MOs().eigenvalues() << std::endl; std::cout << "ref eng" << std::endl; std::cout << MOs_energy_ref << std::endl; } Eigen::MatrixXd MOs_coeff_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/orca/MOs_coeff_ref.mm"); // clang-format off std::array votcaOrder_old = { 0, // s 0, -1, 1, // p 0, -1, 1, -2, 2, // d 0, -1, 1, -2, 2, -3, 3, // f 0, -1, 1, -2, 2, -3, 3, -4, 4, // g 0, -1, 1, -2, 2, -3, 3, -4, 4,-5,5, // h 0, -1, 1, -2, 2, -3, 3, -4, 4,-5,5,-6,6 // i }; // clang-format on std::array multiplier; multiplier.fill(1); OrbReorder ord(votcaOrder_old, multiplier); AOBasis aobasis = orb.SetupDftBasis(); ord.reorderOrbitals(MOs_coeff_ref, aobasis); bool check_coeff = MOs_coeff_ref.isApprox(orb.MOs().eigenvectors(), 1e-5); BOOST_CHECK_EQUAL(check_coeff, true); if (!check_coeff) { std::cout << "result coeff" << std::endl; std::cout << orb.MOs().eigenvectors() << std::endl; std::cout << "ref coeff" << std::endl; std::cout << MOs_coeff_ref << std::endl; } libint2::finalize(); } BOOST_AUTO_TEST_CASE(charges_test) { libint2::initialize(); QMPackageFactory::RegisterAll(); std::unique_ptr orca = QMPackageFactory::QMPackages().Create("orca"); Logger log; orca->setLog(&log); orca->setRunDir(std::string(XTP_TEST_DATA_FOLDER) + "/orca"); orca->setLogFileName("orca_charges.log"); StaticSegment seg = orca->GetCharges(); double ang2bohr = votca::tools::conv::ang2bohr; StaticSegment ref("ref", 0); Eigen::Vector3d pos1 = {0.528800, 0.161000, 0.935900}; StaticSite s1(0, "H", pos1 * ang2bohr); s1.setCharge(0.178516); pos1 = {0.000000, 0.000000, 0.000000}; StaticSite s2(1, "C", pos1 * ang2bohr); s2.setCharge(-0.709443); pos1 = {0.205100, 0.824000, -0.678600}; StaticSite s3(2, "H", pos1 * ang2bohr); s3.setCharge(0.176227); pos1 = {0.334500, -0.931400, -0.449600}; StaticSite s4(3, "H", pos1 * ang2bohr); s4.setCharge(0.177109); pos1 = {-1.068500, -0.053700, 0.192100}; StaticSite s5(4, "H", pos1 * ang2bohr); s5.setCharge(0.177591); ref.push_back(s1); ref.push_back(s2); ref.push_back(s3); ref.push_back(s4); ref.push_back(s5); BOOST_CHECK_EQUAL(seg.size(), ref.size()); for (votca::Index i = 0; i < votca::Index(seg.size()); i++) { BOOST_CHECK_EQUAL(ref[i].Q().isApprox(seg[i].Q(), 1e-5), true); BOOST_CHECK_EQUAL(ref[i].getPos().isApprox(seg[i].getPos(), 1e-5), true); BOOST_CHECK_EQUAL(ref[i].getElement(), seg[i].getElement()); } libint2::finalize(); } BOOST_AUTO_TEST_CASE(opt_test) { QMPackageFactory::RegisterAll(); std::unique_ptr orca = QMPackageFactory::QMPackages().Create("orca"); Logger log; orca->setLog(&log); orca->setRunDir(std::string(XTP_TEST_DATA_FOLDER) + "/orca"); orca->setLogFileName("orca_opt.log"); Orbitals orb; orca->ParseLogFile(orb); double ref_tot = -40.240899574987; // HF - Self energy ext charges BOOST_CHECK_CLOSE(ref_tot, orb.getDFTTotalEnergy(), 1e-5); const QMMolecule& seg = orb.QMAtoms(); double ang2bohr = votca::tools::conv::ang2bohr; QMMolecule ref("ref", 0); Eigen::Vector3d pos1 = {0.457282, 0.159495, 0.949475}; QMAtom s1(0, "H", pos1 * ang2bohr); pos1 = {-0.060043, 0.000032, 0.000064}; QMAtom s2(1, "C", pos1 * ang2bohr); pos1 = {0.161203, 0.828181, -0.679453}; QMAtom s3(2, "H", pos1 * ang2bohr); pos1 = {0.279541, -0.938419, -0.446827}; QMAtom s4(3, "H", pos1 * ang2bohr); pos1 = {-1.138083, -0.049389, 0.176541}; QMAtom s5(4, "H", pos1 * ang2bohr); ref.push_back(s1); ref.push_back(s2); ref.push_back(s3); ref.push_back(s4); ref.push_back(s5); BOOST_CHECK_EQUAL(seg.size(), ref.size()); for (votca::Index i = 0; i < votca::Index(seg.size()); i++) { BOOST_CHECK_EQUAL(ref[i].getPos().isApprox(seg[i].getPos(), 1e-5), true); BOOST_CHECK_EQUAL(ref[i].getElement(), seg[i].getElement()); } } BOOST_AUTO_TEST_CASE(input_generation_version_4_0_1) { unsetenv("VOTCASHARE"); std::ofstream defaults("user_input.xml"); defaults << "\n" << "orca\n" << "0\n" << "1\n" << "some/path/orca\n" << "" << std::string(XTP_TEST_DATA_FOLDER) << "/orca/3-21G.xml\n" << "pbe0\n" << "false\n" << "false\n" << "/tmp/qmpackage\n" << "false\n" << "tight\n" << "\n" << "\n" << "GUESS PMODEL\n" << "3000\n" << "\n" << ""; defaults.close(); votca::tools::Property prop; prop.LoadFromXML("user_input.xml"); QMPackageFactory::RegisterAll(); std::unique_ptr orca = QMPackageFactory::QMPackages().Create("orca"); Logger log; orca->setLog(&log); orca->setRunDir("."); orca->Initialize(prop); Orbitals orb; orb.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/orca/co.xyz"); orca->WriteInputFile(orb); std::string input_file = "system.inp"; if (!tools::filesystem::FileExists(input_file)) { throw std::runtime_error("Orca input file does not exists!"); } std::ifstream file_input(input_file); std::stringstream buffer; buffer << file_input.rdbuf(); std::string inp = buffer.str(); // check basis section auto index1 = inp.find("%basis"); auto index2 = inp.find("end", index1); BOOST_CHECK_EQUAL(inp.substr(index1, index2 - index1), "%basis\nGTOName =\"system.bas\";\n"); // check scf section multiline index1 = inp.find("%scf"); index2 = inp.find("end", index1); BOOST_CHECK_EQUAL(inp.substr(index1, index2 - index1), "%scf\nGUESS PMODEL\n"); // Check method index1 = inp.find("!"); BOOST_CHECK_EQUAL(inp.substr(index1), "! DFT pbe0 \n"); // Check singleline orca kewords index1 = inp.find("%maxcore"); index2 = inp.find("\n", index1); std::cout << "\ninp: " << inp.substr(index1) << "\n"; BOOST_CHECK_EQUAL(inp.substr(index1, index2 - index1), "%maxcore 3000"); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_oscillatorstrength_filter.cc000066400000000000000000000065161412152066400232220ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE oscillatorstrength_filter_test // Standard includes #include // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/filterfactory.h" #include using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(oscillatorstrength_filter_test) BOOST_AUTO_TEST_CASE(coeffs_test) { FilterFactory::RegisterAll(); libint2::initialize(); std::unique_ptr osc_f = std::unique_ptr(Filter().Create("oscillatorstrength")); std::ofstream opt("oscillatorstrength.xml"); opt << "0.0045" << std::endl; opt.close(); votca::tools::Property prop; prop.LoadFromXML("oscillatorstrength.xml"); osc_f->Initialize(prop.get("oscillatorstrength")); Orbitals A; A.setDFTbasisName(std::string(XTP_TEST_DATA_FOLDER) + "/oscillatorstrength_filter/3-21G.xml"); A.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/oscillatorstrength_filter/molecule.xyz"); A.setBasisSetSize(17); A.setNumberOfAlphaElectrons(5); A.setNumberOfOccupiedLevels(5); A.MOs().eigenvalues() = Eigen::VectorXd::Zero(17); A.MOs().eigenvalues() << -19.8117, -6.22408, -6.14094, -6.14094, -6.14094, -3.72889, -3.72889, -3.72889, -3.64731, -3.09048, -3.09048, -3.09048, -2.63214, -2.08206, -2.08206, -2.08206, -2.03268; A.MOs().eigenvectors() = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/oscillatorstrength_filter/MOs_A.mm"); A.setBSEindices(0, 16); A.setTDAApprox(true); A.setGWindices(0, 16); Eigen::MatrixXd spsi_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/oscillatorstrength_filter/spsi_ref.mm"); A.BSESinglets().eigenvectors() = spsi_ref; // reference energy Eigen::VectorXd se_ref = Eigen::VectorXd::Zero(3); se_ref << 0.107455, 0.107455, 0.107455; A.BSESinglets().eigenvalues() = se_ref; A.CalcCoupledTransition_Dipoles(); BOOST_CHECK_EQUAL(osc_f->NeedsInitialState(), false); std::vector ref = {0}; std::vector results = osc_f->CalcIndeces(A, QMStateType::Singlet); BOOST_CHECK_EQUAL(results.size(), ref.size()); for (votca::Index i = 0; i < votca::Index(ref.size()); i++) { BOOST_CHECK_EQUAL(ref[i], results[i]); } BOOST_REQUIRE_THROW(osc_f->CalcIndeces(A, QMStateType::Gstate), std::runtime_error); BOOST_REQUIRE_THROW(osc_f->CalcIndeces(A, QMStateType::Triplet), std::runtime_error); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_overlap_filter.cc000066400000000000000000000125551412152066400207400ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE overlap_filter_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include // VOTCA includes #include #include using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(overlap_filter_test) BOOST_AUTO_TEST_CASE(coeffs_test) { libint2::initialize(); FilterFactory::RegisterAll(); std::unique_ptr rho_f = std::unique_ptr(Filter().Create("overlap")); std::ofstream opt("overlap_filter.xml"); opt << "0.0045" << std::endl; opt.close(); votca::tools::Property prop; prop.LoadFromXML("overlap_filter.xml"); rho_f->Initialize(prop.get("overlap")); Orbitals A; A.setDFTbasisName(std::string(XTP_TEST_DATA_FOLDER) + "/overlap_filter/3-21G.xml"); A.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/overlap_filter/molecule.xyz"); A.setBasisSetSize(17); A.setNumberOfAlphaElectrons(5); A.setNumberOfOccupiedLevels(5); A.MOs().eigenvalues() = Eigen::VectorXd::Zero(17); A.MOs().eigenvalues() << -19.8117, -6.22408, -6.14094, -6.14094, -6.14094, -3.72889, -3.72889, -3.72889, -3.64731, -3.09048, -3.09048, -3.09048, -2.63214, -2.08206, -2.08206, -2.08206, -2.03268; A.QPpertEnergies() = Eigen::VectorXd::Zero(17); A.QPpertEnergies() << -10.189, -1.01045, -0.620145, -0.620146, -0.620148, 0.261183, 0.348342, 0.348343, 0.348342, 0.920829, 0.920829, 0.920829, 1.18002, 1.27325, 1.27325, 1.27325, 1.96983; A.MOs().eigenvectors() = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/overlap_filter/MOs_A.mm"); A.setBSEindices(0, 16); A.setTDAApprox(true); A.setGWindices(0, 16); Eigen::MatrixXd spsi_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/overlap_filter/spsi_ref.mm"); A.BSESinglets().eigenvectors() = spsi_ref; // reference energy Eigen::VectorXd se_ref = Eigen::VectorXd::Zero(3); se_ref << 0.107455, 0.107455, 0.107455; A.BSESinglets().eigenvalues() = se_ref; A.CalcCoupledTransition_Dipoles(); BOOST_CHECK_EQUAL(rho_f->NeedsInitialState(), true); rho_f->UpdateHist(A, QMState("s1")); std::vector ref = {0}; std::vector results = rho_f->CalcIndeces(A, QMStateType::Singlet); BOOST_CHECK_EQUAL(results.size(), ref.size()); for (votca::Index i = 0; i < votca::Index(ref.size()); i++) { BOOST_CHECK_EQUAL(ref[i], results[i]); } rho_f->UpdateHist(A, QMState("s2")); std::vector results2 = rho_f->CalcIndeces(A, QMStateType::Singlet); std::vector ref2 = {1}; for (votca::Index i = 0; i < votca::Index(ref2.size()); i++) { BOOST_CHECK_EQUAL(ref2[i], results2[i]); } BOOST_CHECK_EQUAL(results2.size(), ref2.size()); std::unique_ptr rho_f2 = std::unique_ptr(Filter().Create("overlap")); rho_f2->Initialize(prop.get("overlap")); rho_f2->UpdateHist(A, QMState("pqp8")); std::vector results3 = rho_f2->CalcIndeces(A, QMStateType::PQPstate); std::vector ref3 = {8}; BOOST_CHECK_EQUAL(results3.size(), ref3.size()); for (votca::Index i = 0; i < votca::Index(ref3.size()); i++) { BOOST_CHECK_EQUAL(ref3[i], results3[i]); } // reference energy Eigen::VectorXd se_ref_btda = Eigen::VectorXd::Zero(3); se_ref_btda << 0.0887758, 0.0887758, 0.0887758; // reference coefficients Eigen::MatrixXd spsi_ref_btda = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/overlap_filter/spsi_ref_btda.mm"); // // reference coefficients AR Eigen::MatrixXd spsi_ref_btda_AR = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/overlap_filter/spsi_ref_btda_AR.mm"); A.BSESinglets().eigenvectors() = spsi_ref_btda; A.BSESinglets().eigenvectors2() = spsi_ref_btda_AR; A.BSESinglets().eigenvalues() = se_ref_btda; A.setTDAApprox(false); A.CalcCoupledTransition_Dipoles(); std::unique_ptr rho_f3 = std::unique_ptr(Filter().Create("overlap")); rho_f3->Initialize(prop.get("overlap")); rho_f3->UpdateHist(A, QMState("s1")); std::vector ref_btda = {0}; std::vector results_btda = rho_f3->CalcIndeces(A, QMStateType::Singlet); BOOST_CHECK_EQUAL(results_btda.size(), ref_btda.size()); for (votca::Index i = 0; i < votca::Index(ref_btda.size()); i++) { BOOST_CHECK_EQUAL(ref_btda[i], results_btda[i]); } libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_polarsegment.cc000066400000000000000000000157541412152066400204270ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE polarsegment_test // Third party includes #include // Local VOTCA includes #include "votca/xtp/classicalsegment.h" using namespace votca::xtp; using namespace votca; using namespace std; BOOST_AUTO_TEST_SUITE(polarsegment_test) BOOST_AUTO_TEST_CASE(constructors_test) { PolarSegment("seg1", 0); } BOOST_AUTO_TEST_CASE(load_mps) { PolarSegment seg = PolarSegment("seg1", 0); std::ofstream mpsfile("polarsite.mps"); mpsfile << "! Two Sites" << endl; mpsfile << "! N=2 " << endl; mpsfile << "Units angstrom" << endl; mpsfile << "C +0 0 3 Rank 2" << endl; mpsfile << "+1" << endl; mpsfile << "10 0 0" << endl; mpsfile << "100 0 0 0 0" << endl; mpsfile << "P +1.9445387 +0.0000000 +0.0000000 +1.9445387 +0.0000000 +1.9445387" << endl; mpsfile << "H +0 0 1 Rank 0" << endl; mpsfile << "-1" << endl; mpsfile << "P +1.0000000" << endl; seg.LoadFromFile("polarsite.mps"); Eigen::Vector3d ref_pos = Eigen::Vector3d(0, 0, 2.845154333 * votca::tools::conv::ang2bohr); bool is_equal = seg.getPos().isApprox(ref_pos, 0.0001); BOOST_CHECK_EQUAL(is_equal, true); if (!is_equal) { std::cout << "result" << std::endl; std::cout << seg.getPos() << std::endl; std::cout << "reference" << std::endl; std::cout << ref_pos << std::endl; } BOOST_CHECK_EQUAL(seg.size(), 2); BOOST_CHECK_EQUAL(seg[0].getRank(), 2); BOOST_CHECK_EQUAL(seg[0].getElement(), "C"); BOOST_CHECK_EQUAL(seg[1].getRank(), 0); BOOST_CHECK_EQUAL(seg[1].getElement(), "H"); Eigen::VectorXd mul_ref = Eigen::VectorXd::Zero(9); mul_ref << 1, 0, 0, 10, 100, 0, 0, 0, 0; bool multipoles_equal = mul_ref.isApprox(seg[0].Q(), 1e-5); if (!multipoles_equal) { std::cout << "result" << std::endl; std::cout << seg[0].Q() << std::endl; std::cout << "reference" << std::endl; std::cout << mul_ref << std::endl; } BOOST_CHECK_EQUAL(multipoles_equal, true); Eigen::VectorXd mul_ref2 = Eigen::VectorXd::Zero(9); mul_ref2 << -1, 0, 0, 0, 0, 0, 0, 0, 0; bool multipoles_equal2 = mul_ref2.isApprox(seg[1].Q(), 1e-5); if (!multipoles_equal2) { std::cout << "result" << std::endl; std::cout << seg[1].Q() << std::endl; std::cout << "reference" << std::endl; std::cout << mul_ref2 << std::endl; } BOOST_CHECK_EQUAL(multipoles_equal2, true); std::string ref_string = " C +0.0000000 +0.0000000 +3.0000000 Rank 2\n" " +1.0000000\n" " +10.0000000 +0.0000000 +0.0000000\n" " +100.0000000 +0.0000000 +0.0000000 +0.0000000 +0.0000000\n" " P +1.9445387 +0.0000000 +0.0000000 +1.9445387 +0.0000000 " "+1.9445387\n"; bool string_equal = (ref_string == seg[0].WriteMpsLine("angstrom")); BOOST_CHECK_EQUAL(string_equal, true); if (!string_equal) { std::string result = seg[0].WriteMpsLine("angstrom"); std::cout << "result" << std::endl; std::cout << result << std::endl; std::cout << "reference" << std::endl; std::cout << ref_string << std::endl; } std::string ref_string2 = " H +0.0000000 +0.0000000 +1.0000000 Rank 0\n" " -1.0000000\n" " P +1.0000000 +0.0000000 +0.0000000 +1.0000000 +0.0000000 " "+1.0000000\n"; bool string_equal2 = (ref_string2 == seg[1].WriteMpsLine("angstrom")); BOOST_CHECK_EQUAL(string_equal2, true); if (!string_equal2) { std::string result = seg[1].WriteMpsLine("angstrom"); std::cout << "result" << std::endl; std::cout << result << std::endl; std::cout << "reference" << std::endl; std::cout << ref_string2 << std::endl; } } BOOST_AUTO_TEST_CASE(add_atom_test) { PolarSegment seg = PolarSegment("seg1", 0); bool check_pos = seg.getPos().isApprox(Eigen::Vector3d::Zero()); BOOST_CHECK_EQUAL(check_pos, true); Eigen::Vector3d pos = Eigen::Vector3d::Ones(); PolarSite site = PolarSite(0, "C", pos); Eigen::VectorXd poles = Vector9d::Ones(9); votca::Index rank = 2; site.setMultipole(poles, rank); seg.push_back(site); bool check_pos2 = seg.getPos().isApprox(Eigen::Vector3d::Ones()); BOOST_CHECK_EQUAL(check_pos2, true); } BOOST_AUTO_TEST_CASE(readwritehdf) { PolarSegment seg = PolarSegment("seg1", 0); std::ofstream mpsfile("polarsite.mps"); mpsfile << "! Two Sites" << endl; mpsfile << "! N=2 " << endl; mpsfile << "Units angstrom" << endl; mpsfile << "C +0 0 3 Rank 2" << endl; mpsfile << "+1" << endl; mpsfile << "10 0 0" << endl; mpsfile << "100 0 0 0 0" << endl; mpsfile << "P +1.9445387 +0.0000000 +0.0000000 +1.9445387 +0.0000000 +1.9445387" << endl; mpsfile << "H +0 0 1 Rank 0" << endl; mpsfile << "-1" << endl; mpsfile << "P +1.0000000" << endl; seg.LoadFromFile("polarsite.mps"); CheckpointFile ff("polarsegment_test.hdf5"); CheckpointWriter ww = ff.getWriter(); seg.WriteToCpt(ww); CheckpointReader rr = ff.getReader(); PolarSegment seg2(rr); BOOST_CHECK_EQUAL(seg.size(), seg2.size()); for (votca::Index i = 0; i < seg.size(); i++) { BOOST_CHECK_EQUAL(seg2[i].Q().isApprox(seg[i].Q(), 1e-5), true); BOOST_CHECK_EQUAL(seg2[i].getPos().isApprox(seg[i].getPos(), 1e-5), true); BOOST_CHECK_EQUAL(seg2[i].getElement(), seg[i].getElement()); BOOST_CHECK_EQUAL( seg2[i].getpolarization().isApprox(seg[i].getpolarization(), 1e-5), true); } } BOOST_AUTO_TEST_CASE(readwritemps) { PolarSegment seg = PolarSegment("seg1", 0); std::ofstream mpsfile("polarsite.mps"); mpsfile << "! Two Sites" << endl; mpsfile << "! N=2 " << endl; mpsfile << "Units angstrom" << endl; mpsfile << "C +0 0 3 Rank 2" << endl; mpsfile << "+1" << endl; mpsfile << "10 0 0" << endl; mpsfile << "100 0 0 0 0" << endl; mpsfile << "P +1.9445387 +0.0000000 +0.0000000 +1.9445387 +0.0000000 +1.9445387" << endl; mpsfile << "H +0 0 1 Rank 0" << endl; mpsfile << "-1" << endl; mpsfile << "P +1.0000000" << endl; seg.LoadFromFile("polarsite.mps"); seg.WriteMPS("test.mps", "test"); PolarSegment seg2("seg2", 1); seg2.LoadFromFile("test.mps"); BOOST_CHECK_EQUAL(seg.size(), seg2.size()); for (votca::Index i = 0; i < seg.size(); i++) { BOOST_CHECK_EQUAL(seg2[i].Q().isApprox(seg[i].Q(), 1e-5), true); BOOST_CHECK_EQUAL(seg2[i].getPos().isApprox(seg[i].getPos(), 1e-5), true); BOOST_CHECK_EQUAL(seg2[i].getElement(), seg[i].getElement()); BOOST_CHECK_EQUAL( seg2[i].getpolarization().isApprox(seg[i].getpolarization(), 1e-5), true); } } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_polarsite.cc000066400000000000000000000053601412152066400177210ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE polararsite_test // Third party includes #include // Local VOTCA includes #include "votca/xtp/polarsite.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(polararsite_test) BOOST_AUTO_TEST_CASE(constructors_test) { PolarSite ps(1, "ps1"); } BOOST_AUTO_TEST_CASE(getters_test) { PolarSite ps(1, "ps2"); BOOST_CHECK_EQUAL(ps.getId(), 1); BOOST_CHECK_EQUAL(ps.getElement(), "ps2"); } BOOST_AUTO_TEST_CASE(multipole_test) { PolarSite ps(1, "ps2"); Vector9d multipole = Vector9d::Zero(9); multipole << 1, 2, 3, 4, 8, 7, 2, 3.3, -0.5; ps.setMultipole(multipole, 2); bool check_mpoles = multipole.isApprox(ps.Q(), 0.0001); BOOST_CHECK_EQUAL(check_mpoles, true); BOOST_CHECK_EQUAL(ps.getRank(), 2); } BOOST_AUTO_TEST_CASE(translate_test) { PolarSite ps(1, "ps2"); Eigen::Vector3d shift; shift << 0, 0, 5; ps.Translate(shift); BOOST_CHECK_EQUAL(shift.isApprox(ps.getPos(), 1e-5), true); } BOOST_AUTO_TEST_CASE(rotation_test) { PolarSite ps(1, "ps2", Eigen::Vector3d::UnitY()); Eigen::Matrix3d R = Eigen::Matrix3d::Zero(); // Rotation around z axes R << 0, -1, 0, 1, 0, 0, 0, 0, 1; Vector9d multipoles = Vector9d::Zero(9); multipoles << 1, 1, 0, 0, 0, 1, 0, 0, 0; // q=1, mu_x=1 and Q_21c=1 the rest is 0 ps.setMultipole(multipoles, 2); ps.Rotate(R, Eigen::Vector3d::Zero()); bool equalpos = ps.getPos().isApprox(Eigen::Vector3d(-1, 0, 0), 1e-5); if (!equalpos) { std::cout << "Result " << std::endl; std::cout << ps.getPos() << std::endl; std::cout << "Reference" << std::endl; std::cout << Eigen::Vector3d(-1, 0, 0) << std::endl; } BOOST_CHECK_EQUAL(equalpos, true); Eigen::VectorXd rotmultipoles = Eigen::VectorXd::Zero(9); rotmultipoles << 1, 0, 1, 0, 0, 0, 1, 0, 0; // q=1, mu_y=1 and Q_21s=1 is 0 bool equalmultipoles = rotmultipoles.isApprox(ps.Q(), 1e-5); if (!equalmultipoles) { std::cout << "Result " << std::endl; std::cout << ps.Q() << std::endl; std::cout << "Reference" << std::endl; std::cout << rotmultipoles << std::endl; } BOOST_CHECK_EQUAL(equalmultipoles, true); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_populationanalysis.cc000066400000000000000000000140171412152066400216540ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE populationanalysis_test // Standard includes #include // Third party includes #include #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/populationanalysis.h" using namespace std; using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(populationanalysis_test) BOOST_AUTO_TEST_CASE(atompop) { libint2::initialize(); Orbitals orb; orb.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/populationanalysis/molecule.xyz"); orb.setDFTbasisName(std::string(XTP_TEST_DATA_FOLDER) + "/populationanalysis/3-21G.xml"); orb.setBasisSetSize(17); orb.setNumberOfOccupiedLevels(5); Eigen::MatrixXd& MOs = orb.MOs().eigenvectors(); orb.MOs().eigenvalues() = Eigen::VectorXd::Ones(17); MOs = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/populationanalysis/MOs.mm"); Orbitals orb2 = orb; QMState s("n"); Lowdin low; StaticSegment result = low.CalcChargeperAtom(orb, s); Eigen::VectorXd charge = Eigen::VectorXd::Zero(result.size()); for (votca::Index i = 0; i < votca::Index(result.size()); i++) { charge(i) = result[i].getCharge(); } Eigen::VectorXd charge_ref = Eigen::VectorXd::Zero(5); charge_ref << 0.68862, -0.172155, -0.172154, -0.172154, -0.172155; bool check_lowdin = charge_ref.isApprox(charge, 1e-5); BOOST_CHECK_EQUAL(check_lowdin, true); if (!check_lowdin) { cout << "charge" << endl; cout << charge << endl; cout << "chargeref" << endl; cout << charge_ref << endl; } Mulliken mul; StaticSegment result2 = mul.CalcChargeperAtom(orb2, s); Eigen::VectorXd charge2 = Eigen::VectorXd::Zero(result2.size()); for (votca::Index i = 0; i < votca::Index(result2.size()); i++) { charge2(i) = result2[i].getCharge(); } Eigen::VectorXd charge_ref2 = Eigen::VectorXd::Zero(5); charge_ref2 << 1.21228, -0.303069, -0.303067, -0.303068, -0.303068; bool check_mulliken = charge_ref2.isApprox(charge2, 1e-5); BOOST_CHECK_EQUAL(check_mulliken, true); if (!check_mulliken) { cout << "charge" << endl; cout << charge2 << endl; cout << "chargeref" << endl; cout << charge_ref2 << endl; } libint2::finalize(); } BOOST_AUTO_TEST_CASE(fragment_pop) { libint2::initialize(); Orbitals orb; orb.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/populationanalysis/molecule.xyz"); orb.setDFTbasisName(std::string(XTP_TEST_DATA_FOLDER) + "/populationanalysis/3-21G.xml"); orb.setBasisSetSize(17); orb.setNumberOfOccupiedLevels(5); orb.MOs().eigenvalues() = Eigen::VectorXd::Ones(17); Eigen::MatrixXd MOs2 = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/populationanalysis/MOs2.mm"); orb.MOs().eigenvectors() = MOs2; Eigen::VectorXd se_ref = Eigen::VectorXd::Zero(3); se_ref << 0.107455, 0.107455, 0.107455; orb.BSESinglets().eigenvalues() = se_ref; // reference coefficients Eigen::MatrixXd spsi_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/populationanalysis/spsi_ref.mm"); orb.BSESinglets().eigenvectors() = spsi_ref; orb.setBSEindices(0, 16); orb.setTDAApprox(true); std::vector > frags; QMFragment f1(0, "0 1"); QMFragment f2(1, "2 3 4"); frags.push_back(f1); frags.push_back(f2); orb.DensityMatrixGroundState(); QMState n("n"); Lowdin low; BOOST_REQUIRE_THROW(low.CalcChargeperFragment(frags, orb, n.Type()), std::runtime_error); QMState s1("s1"); low.CalcChargeperFragment(frags, orb, s1.Type()); BOOST_CHECK_CLOSE(frags[0].value().Gs, 0.5164649, 1e-5); BOOST_CHECK_CLOSE(frags[1].value().Gs, -0.5164628, 1e-5); Eigen::VectorXd f1E_ref = Eigen::VectorXd::Zero(3); f1E_ref << -0.384176, -0.812396, -0.414518; Eigen::VectorXd f1H_ref = Eigen::VectorXd::Zero(3); f1H_ref << 0.657215, 0.622434, 0.654751; Eigen::VectorXd f2E_ref = Eigen::VectorXd::Zero(3); f2E_ref << -0.615827, -0.187602, -0.58548; Eigen::VectorXd f2H_ref = Eigen::VectorXd::Zero(3); f2H_ref << 0.342785, 0.377565, 0.34525; bool check_f1e = frags[0].value().E.isApprox(f1E_ref, 1e-5); BOOST_CHECK_EQUAL(check_f1e, true); if (!check_f1e) { cout << "charge" << endl; cout << frags[0].value().E << endl; cout << "chargeref" << endl; cout << f1E_ref << endl; } bool check_f1h = frags[0].value().H.isApprox(f1H_ref, 1e-5); BOOST_CHECK_EQUAL(check_f1h, true); if (!check_f1h) { cout << "charge" << endl; cout << frags[0].value().H << endl; cout << "chargeref" << endl; cout << f1H_ref << endl; } bool check_f2e = frags[1].value().E.isApprox(f2E_ref, 1e-5); BOOST_CHECK_EQUAL(check_f2e, true); if (!check_f2e) { cout << "charge" << endl; cout << frags[1].value().E << endl; cout << "chargeref" << endl; cout << f2E_ref << endl; } bool check_f2h = frags[1].value().H.isApprox(f2H_ref, 1e-5); BOOST_CHECK_EQUAL(check_f2h, true); if (!check_f2h) { cout << "charge" << endl; cout << frags[1].value().H << endl; cout << "chargeref" << endl; cout << f2H_ref << endl; } libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_ppm.cc000066400000000000000000000061711412152066400165140ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE ppm_test // Third party includes #include // Local VOTCA includes #include "votca/xtp/aomatrix.h" #include "votca/xtp/aopotential.h" #include "votca/xtp/logger.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/ppm.h" #include "votca/xtp/threecenter.h" #include using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(ppm_test) BOOST_AUTO_TEST_CASE(ppm_full) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/ppm/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/ppm/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); Orbitals orb; orb.setBasisSetSize(17); orb.setNumberOfOccupiedLevels(4); AOKinetic kinetic; kinetic.Fill(aobasis); AOMultipole esp; esp.FillPotential(aobasis, orbitals.QMAtoms()); Eigen::SelfAdjointEigenSolver es(kinetic.Matrix() + esp.Matrix()); Logger log; TCMatrix_gwbse Mmn; Mmn.Initialize(aobasis.AOBasisSize(), 0, 16, 0, 16); Mmn.Fill(aobasis, aobasis, es.eigenvectors()); RPA rpa = RPA(log, Mmn); rpa.configure(4, 0, 16); rpa.setRPAInputEnergies(es.eigenvalues()); PPM ppm; ppm.PPM_construct_parameters(rpa); Eigen::VectorXd ppm_freq = Eigen::VectorXd::Zero(17); ppm_freq << 19.4503, 12.2429, 10.2167, 10.2167, 10.2167, 17.0832, 12.7117, 12.7117, 12.7117, 10.9455, 10.9455, 10.9455, 11.1861, 9.60843, 9.60843, 9.60843, 9.61518; Eigen::VectorXd ppm_w = Eigen::VectorXd::Zero(17); ppm_w << 3.59422e-05, 0.00121795, 0.00343632, 0.00343632, 0.00343632, 0.00394659, 0.012066, 0.012066, 0.012066, 0.0241118, 0.0241118, 0.0241118, 0.0286786, 0.11036, 0.11036, 0.11036, 0.191732; bool f_check = ppm_freq.isApprox(ppm.getPpm_freq(), 0.0001); bool w_check = ppm_w.isApprox(ppm.getPpm_weight(), 0.0001); if (!f_check) { cout << "ppm_freq" << endl; cout << ppm.getPpm_freq() << endl; cout << "ppm_freq_ref" << endl; cout << ppm_freq << endl; } if (!w_check) { cout << "ppm_w" << endl; cout << ppm.getPpm_weight() << endl; cout << "ppm_w_ref" << endl; cout << ppm_w << endl; } BOOST_CHECK_EQUAL(f_check, 1); BOOST_CHECK_EQUAL(w_check, 1); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_qmatom.cc000066400000000000000000000020151412152066400172070ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE qmatom_test // Third party includes #include // Local VOTCA includes #include "votca/xtp/qmatom.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(qmatom_test) BOOST_AUTO_TEST_CASE(constructors_test) { Eigen::Vector3d pos = Eigen::Vector3d::Zero(); QMAtom a(1, "C", pos); } BOOST_AUTO_TEST_CASE(translaterotate_test) {} BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_qmfragment.cc000066400000000000000000000041031412152066400200520ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE qmfragment_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/qmfragment.h" using namespace votca; using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(qmfragment_test) BOOST_AUTO_TEST_CASE(stringprocessing) { std::string index = "1 2 3 5:9"; QMFragment frag(0, index); std::vector ref = {1, 2, 3, 5, 6, 7, 8, 9}; bool checked = (frag.getIndices() == ref); if (!checked) { std::cout << "result" << std::endl; for (Index e : frag.getIndices()) { std::cout << e; } std::cout << std::endl; std::cout << "ref" << std::endl; for (Index e : ref) { std::cout << e; } } } BOOST_AUTO_TEST_CASE(readinandwritinghdf5) { std::string index = "1 2 3 5:9"; QMFragment frag(0, index); frag.value() = -0.5; { CheckpointFile f("QMFragment_test.hdf5"); CheckpointWriter w = f.getWriter(); frag.WriteToCpt(w); } CheckpointFile f("QMFragment_test.hdf5"); CheckpointReader r = f.getReader(); QMFragment frag2(r); BOOST_CHECK_EQUAL(frag2.getId(), frag.getId()); BOOST_CHECK_CLOSE(frag.value(), frag2.value(), 1e-5); for (Index i = 0; i < Index(frag.size()); i++) { BOOST_CHECK_EQUAL(frag.getIndices()[i], frag2.getIndices()[i]); } } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_qmmolecule.cc000066400000000000000000000057631412152066400200710ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE qmmolecule_test // Third party includes #include // Local VOTCA includes #include "votca/xtp/qmmolecule.h" using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(qmmolecule_test) BOOST_AUTO_TEST_CASE(constructors_test) { QMMolecule seg("seg1", 1); } BOOST_AUTO_TEST_CASE(load_xyz_test) { ofstream xyzfile("molecule.xyz"); xyzfile << " 5" << endl; xyzfile << " methane" << endl; xyzfile << " C .000000 .000000 .000000" << endl; xyzfile << " H .629118 .629118 .629118" << endl; xyzfile << " H -.629118 -.629118 .629118" << endl; xyzfile << " H .629118 -.629118 -.629118" << endl; xyzfile << " H -.629118 .629118 -.629118" << endl; xyzfile.close(); QMMolecule seg("seg1", 1); seg.LoadFromFile("molecule.xyz"); auto extension = seg.CalcSpatialMinMax(); Eigen::Vector3d max(0.629118, 0.629118, 0.629118); max *= votca::tools::conv::ang2bohr; Eigen::Vector3d min = -max; bool check_min = extension.first.isApprox(min, 0.00001); if (!check_min) { std::cout << "ref" << std::endl; std::cout << min << std::endl; std::cout << "result" << std::endl; std::cout << extension.first << std::endl; } BOOST_CHECK_EQUAL(check_min, true); bool check_max = extension.second.isApprox(max, 0.00001); if (!check_max) { std::cout << "ref" << std::endl; std::cout << max << std::endl; std::cout << "result" << std::endl; std::cout << extension.second << std::endl; } BOOST_CHECK_EQUAL(check_max, true); seg.WriteXYZ("moltest.xyz", "heloo"); } BOOST_AUTO_TEST_CASE(readwritehdf) { ofstream xyzfile("molecule.xyz"); xyzfile << " 5" << endl; xyzfile << " methane" << endl; xyzfile << " C .000000 .000000 .000000" << endl; xyzfile << " H .629118 .629118 .629118" << endl; xyzfile << " H -.629118 -.629118 .629118" << endl; xyzfile << " H .629118 -.629118 -.629118" << endl; xyzfile << " H -.629118 .629118 -.629118" << endl; xyzfile.close(); QMMolecule seg("seg1", 1); seg.LoadFromFile("molecule.xyz"); CheckpointFile ff("qmmolecule.hdf5"); CheckpointWriter ww = ff.getWriter(); seg.WriteToCpt(ww); CheckpointReader rr = ff.getReader(); QMMolecule seg2(rr); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_qmnblist.cc000066400000000000000000000045721412152066400175540ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE qmnblist_test // Third party includes #include // Local VOTCA includes #include "votca/xtp/qmnblist.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(qmnblist_test) BOOST_AUTO_TEST_CASE(constructors_test) { QMNBList qmnb; } BOOST_AUTO_TEST_CASE(add_pair) { Segment seg1("one", 1); Atom atm1(1, "C", Eigen::Vector3d::Ones()); seg1.push_back(atm1); Segment seg2("two", 2); Atom atm2(2, "C", -Eigen::Vector3d::Ones()); seg2.push_back(atm2); Segment seg3("three", 3); Atom atm3(3, "Ca", -Eigen::Vector3d::UnitX()); seg3.push_back(atm3); QMNBList qmnb; BOOST_CHECK_EQUAL(qmnb.empty(), true); qmnb.Add(seg1, seg3, 0.5 * Eigen::Vector3d::Ones()); qmnb.Add(seg1, seg2, -0.5 * Eigen::Vector3d::Ones()); BOOST_CHECK_EQUAL(qmnb.size(), 2); BOOST_CHECK_EQUAL(qmnb.empty(), false); QMPair* p0 = qmnb.FindPair(&seg1, &seg2); QMPair* p1 = qmnb.FindPair(&seg1, &seg3); BOOST_CHECK_EQUAL(p0->R().isApprox(-0.5 * Eigen::Vector3d::Ones(), 1e-5), true); BOOST_CHECK_EQUAL(p0->getId(), 1); BOOST_CHECK_EQUAL(p1->getId(), 0); // sort qmpairs by seg1id and then by seg2id then reindex the pair id // according to that. qmnb.sortAndReindex([](QMPair* a, QMPair* b) { if (a->Seg1()->getId() != b->Seg1()->getId()) { return a->Seg1()->getId() < b->Seg1()->getId(); } return a->Seg2()->getId() < b->Seg2()->getId(); }); BOOST_CHECK_EQUAL(p0->getId(), 0); BOOST_CHECK_EQUAL(p1->getId(), 1); votca::csg::PairList::partners* Partners = qmnb.FindPartners(&seg1); QMPair* p_ref0 = Partners->at(&seg2); QMPair* p_ref1 = Partners->at(&seg3); BOOST_CHECK_EQUAL(p_ref0, p0); BOOST_CHECK_EQUAL(p_ref1, p1); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_qmpair.cc000066400000000000000000000024211412152066400172030ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE qmpair_test // Third party includes #include // Local VOTCA includes #include using namespace votca::tools; using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(qmpair_test) BOOST_AUTO_TEST_CASE(getters_test) { Segment seg("one", 1); Atom atm1(1, "C", Eigen::Vector3d::Ones()); seg.push_back(atm1); Segment seg2("two", 2); Atom atm2(2, "C", -Eigen::Vector3d::Ones()); seg2.push_back(atm2); QMPair pair(0, &seg, &seg2, 0.5 * Eigen::Vector3d::Ones()); pair.setType(QMPair::PairType::Hopping); BOOST_CHECK_EQUAL(pair.getType(), QMPair::Hopping); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_qmstate.cc000066400000000000000000000053661412152066400174030ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE qmstate_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/qmstate.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(qmstate_test) BOOST_AUTO_TEST_CASE(QMStatetype_test) { QMStateType type; type.FromString("S"); BOOST_CHECK_EQUAL(type.Type() == QMStateType::Singlet, true); BOOST_CHECK_EQUAL(type.ToString(), "s"); BOOST_CHECK_EQUAL(type.ToLongString(), "singlet"); QMStateType type2; type2.FromString("Singlet"); BOOST_CHECK_EQUAL(type2.Type() == QMStateType::Singlet, true); BOOST_CHECK_EQUAL(type == type2, true); QMStateType type3; type3.FromString("N"); BOOST_CHECK_EQUAL(type3 == type2, false); BOOST_CHECK_EQUAL(type3 == QMStateType::Gstate, true); QMStateType type4 = QMStateType(QMStateType::KSstate); BOOST_CHECK_EQUAL(type4 == QMStateType::KSstate, true); } BOOST_AUTO_TEST_CASE(QMState_test) { QMState state; state.FromString("S1"); BOOST_CHECK_EQUAL(state.Type() == QMStateType::Singlet, true); BOOST_CHECK_EQUAL(state.StateIdx(), 0); QMState state2; state.FromString("N"); BOOST_CHECK_EQUAL(state.StateIdx(), -1); QMState state3; state3.FromString("n2s12"); BOOST_CHECK_EQUAL(state3.isTransition(), true); BOOST_CHECK_EQUAL(state3.Type() == QMStateType::Singlet, true); BOOST_CHECK_EQUAL(state3.StateIdx(), 11); QMState state4; state4.FromString("n2s16"); QMState state5; state5.FromString("groundstate to singlet 16"); BOOST_CHECK_EQUAL(state4 == state5, true); std::string result = state4.ToLongString(); BOOST_CHECK_EQUAL(result, "Groundstate to singlet 16"); QMState state6 = QMState(QMStateType::Singlet, 15, true); BOOST_CHECK_EQUAL(state6 == state5, true); QMState hole; hole.FromString("h1"); BOOST_CHECK_EQUAL(hole.StateIdx(), 0); QMState hole2; hole2.FromString("h"); BOOST_CHECK_EQUAL(hole2.StateIdx(), 0); QMState electron; electron.FromString("e1"); BOOST_CHECK_EQUAL(electron.StateIdx(), 0); QMState electron2; electron2.FromString("e"); BOOST_CHECK_EQUAL(electron2.StateIdx(), 0); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_radial_euler_maclaurin_rule.cc000066400000000000000000000114421412152066400234270ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE aomatrix_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/orbitals.h" #include "votca/xtp/radial_euler_maclaurin_rule.h" #include using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(radial_euler_maclaurin_test) BOOST_AUTO_TEST_CASE(setup_test) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/radial_euler_maclaurin_rule/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/radial_euler_maclaurin_rule/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); EulerMaclaurinGrid radialgrid; auto grid = radialgrid.CalculateAtomicRadialGrids(aobasis, orbitals.QMAtoms(), "medium"); auto Cgrid = grid.at("C"); auto Hgrid = grid.at("H"); Eigen::VectorXd C_radius_ref = Eigen::VectorXd::Zero(49); C_radius_ref << 2.80419e-05, 0.000224341, 0.00075721, 0.00179513, 0.00350698, 0.00606227, 0.00963155, 0.0143869, 0.0205023, 0.0281546, 0.0375238, 0.0487943, 0.0621556, 0.0778038, 0.0959422, 0.116783, 0.14055, 0.167478, 0.197817, 0.231835, 0.269818, 0.312078, 0.358952, 0.410809, 0.468057, 0.531147, 0.600581, 0.676925, 0.760816, 0.852983, 0.954259, 1.06561, 1.18816, 1.32325, 1.47244, 1.63766, 1.82121, 2.02599, 2.25563, 2.51479, 2.80962, 3.14844, 3.54292, 4.01013, 4.57655, 5.28651, 6.22317, 7.57314, 9.93197; Eigen::VectorXd C_weight_ref = Eigen::VectorXd::Zero(49); C_weight_ref << 6.61523e-14, 1.69369e-11, 4.34206e-10, 4.33973e-09, 2.58921e-08, 1.11494e-07, 3.8345e-07, 1.11898e-06, 2.88109e-06, 6.72222e-06, 1.44868e-05, 2.92464e-05, 5.59082e-05, 0.000102053, 0.000179067, 0.000303666, 0.000499919, 0.00080193, 0.00125739, 0.00193227, 0.00291702, 0.00433476, 0.00635227, 0.00919452, 0.0131643, 0.0186686, 0.0262548, 0.0366601, 0.05088, 0.0702642, 0.096653, 0.132572, 0.181518, 0.24838, 0.340075, 0.466532, 0.64224, 0.888765, 1.23897, 1.74433, 2.48828, 3.61166, 5.36479, 8.22247, 13.1661, 22.479, 42.4806, 96.4423, 338.808; Eigen::VectorXd H_radius_ref = Eigen::VectorXd::Zero(49); H_radius_ref << 3.36503e-05, 0.00026921, 0.000908652, 0.00215416, 0.00420837, 0.00727472, 0.0115579, 0.0172643, 0.0246028, 0.0337855, 0.0450285, 0.0585531, 0.0745868, 0.0933646, 0.115131, 0.14014, 0.16866, 0.200973, 0.23738, 0.278202, 0.323782, 0.374494, 0.430742, 0.492971, 0.561669, 0.637376, 0.720697, 0.81231, 0.912979, 1.02358, 1.14511, 1.27873, 1.4258, 1.5879, 1.76693, 1.96519, 2.18545, 2.43119, 2.70675, 3.01774, 3.37154, 3.77813, 4.25151, 4.81216, 5.49186, 6.34382, 7.4678, 9.08777, 11.9184; Eigen::VectorXd H_weight_ref = Eigen::VectorXd::Zero(49); H_weight_ref << 1.14311e-13, 2.9267e-11, 7.50308e-10, 7.49906e-09, 4.47416e-08, 1.92661e-07, 6.62602e-07, 1.9336e-06, 4.97853e-06, 1.1616e-05, 2.50333e-05, 5.05378e-05, 9.66094e-05, 0.000176347, 0.000309428, 0.000524735, 0.00086386, 0.00138573, 0.00217277, 0.00333897, 0.0050406, 0.00749047, 0.0109767, 0.0158881, 0.0227479, 0.0322593, 0.0453684, 0.0633487, 0.0879206, 0.121417, 0.167016, 0.229085, 0.313664, 0.429201, 0.58765, 0.806167, 1.10979, 1.53579, 2.14094, 3.01421, 4.29975, 6.24096, 9.27036, 14.2084, 22.7511, 38.8437, 73.4066, 166.652, 585.46; BOOST_CHECK_EQUAL(Cgrid.radius.size(), C_radius_ref.size()); BOOST_CHECK_EQUAL(Cgrid.weight.size(), C_weight_ref.size()); BOOST_CHECK_EQUAL(Hgrid.radius.size(), H_radius_ref.size()); BOOST_CHECK_EQUAL(Hgrid.weight.size(), H_weight_ref.size()); bool Cradius = C_radius_ref.isApprox(Cgrid.radius, 0.001); bool Cweight = C_weight_ref.isApprox(Cgrid.weight, 0.001); BOOST_CHECK_EQUAL(Cradius, true); BOOST_CHECK_EQUAL(Cweight, true); bool Hradius = H_radius_ref.isApprox(Hgrid.radius, 0.001); bool Hweight = H_weight_ref.isApprox(Hgrid.weight, 0.001); BOOST_CHECK_EQUAL(Hradius, true); BOOST_CHECK_EQUAL(Hweight, true); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_rate_engine.cc000066400000000000000000000055251412152066400202020ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE rateengine_test // Third party includes #include #include // Local VOTCA includes #include "votca/xtp/rate_engine.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(rateengine_test) BOOST_AUTO_TEST_CASE(sign) { Segment seg1("null", 0); Segment seg2("one", 0); Eigen::Vector3d deltaR = {5, 0, 0}; QMPair pair(0, &seg1, &seg2, deltaR); QMStateType e = QMStateType::Electron; QMStateType h = QMStateType::Hole; seg1.setU_nX_nN(0.002, e); seg1.setU_xN_xX(0.001, e); seg1.setU_xX_nN(0.001, e); seg2.setU_nX_nN(0.002, e); seg2.setU_xN_xX(0.001, e); seg2.setU_xX_nN(0.001, e); seg1.setU_nX_nN(0.002, h); seg1.setU_xN_xX(0.001, h); seg1.setU_xX_nN(0.001, h); seg2.setU_nX_nN(0.002, h); seg2.setU_xN_xX(0.001, h); seg2.setU_xX_nN(0.001, h); pair.setJeff2(1.00e-06, h); pair.setJeff2(1.00e-06, e); Eigen::Vector3d field = {1.0, 0.0, 0.0}; field *= 9.72345198649679e-05; double temperature = 0.000950043476927; // 300K Rate_Engine engine(temperature, field); Rate_Engine::PairRates pr_e = engine.Rate(pair, e); Rate_Engine::PairRates pr_h = engine.Rate(pair, h); BOOST_CHECK_EQUAL(pr_e.rate12 < pr_e.rate21, true); BOOST_CHECK_EQUAL(pr_h.rate12 > pr_h.rate21, true); } BOOST_AUTO_TEST_CASE(markus) { Segment seg1("null", 0); Segment seg2("one", 0); Eigen::Vector3d deltaR = {5, 0, 0}; QMPair pair(0, &seg1, &seg2, deltaR); QMStateType e = QMStateType::Electron; seg1.setEMpoles(e, -0.003674932248085); seg2.setEMpoles(e, -0.005512398372128); seg1.setU_nX_nN(0.003674932248085, e); seg1.setU_xN_xX(0.004042425472894, e); seg1.setU_xX_nN(0.036749322480855, e); seg2.setU_nX_nN(0.006614878046554, e); seg2.setU_xN_xX(0.004777411922511, e); seg2.setU_xX_nN(0.062473848217453, e); double J = 1.00e-03; pair.setJeff2(J * J, e); Eigen::Vector3d field = {1.0, 0.0, 0.0}; field *= 9.72345198649679e-05; double temperature = 0.000950043476927; // 300K Rate_Engine engine(temperature, field); Rate_Engine::PairRates pr = engine.Rate(pair, e); BOOST_CHECK_CLOSE(pr.rate12, 0.069766184455863, 1e-5); BOOST_CHECK_CLOSE(pr.rate21, 221259502589.522, 1e-5); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_regular_grid.cc000066400000000000000000000072471412152066400203730ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE regular_grid_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/orbitals.h" #include "votca/xtp/regular_grid.h" using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(regular_grid_test) AOBasis CreateBasis(const QMMolecule& mol) { BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/regular_grid/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, mol); return aobasis; } BOOST_AUTO_TEST_CASE(regular_grid_build) { libint2::initialize(); QMMolecule mol("none", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/regular_grid/molecule.xyz"); AOBasis aobasis = CreateBasis(mol); Regular_Grid grid; Eigen::Array steps(5, 5, 5); Eigen::Array3d padding(1.0, 1.0, 1.0); grid.GridSetup(steps, padding, mol, aobasis); BOOST_CHECK_EQUAL(grid.getGridSize(), 125); BOOST_CHECK_EQUAL(grid.getBoxesSize(), 1); BOOST_CHECK_CLOSE(grid[0].getGridPoints()[0].x(), -2.1888606344960548, 1e-5); BOOST_CHECK_CLOSE(grid[0].getGridPoints()[1].z(), -1.0944303172480274, 1e-5); BOOST_CHECK_CLOSE(grid[0].getGridPoints()[2].z(), 0, 1e-5); BOOST_CHECK_CLOSE(grid[0].getGridPoints()[30].y(), -1.0944303172480274, 1e-5); BOOST_CHECK_CLOSE(grid[0].getGridPoints()[45].z(), -2.18886063, 1e-5); libint2::finalize(); } BOOST_AUTO_TEST_CASE(regular_grid_build_large) { libint2::initialize(); QMMolecule mol("none", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/regular_grid/molecule.xyz"); auto extend = mol.CalcSpatialMinMax(); AOBasis aobasis = CreateBasis(mol); Regular_Grid grid; Eigen::Array steps(30, 30, 30); Eigen::Array3d padding(1.0, 1.0, 1.0); grid.GridSetup(steps, padding, mol, aobasis); auto max = extend.second.array() + padding + 1e-9; auto min = extend.first.array() - padding - 1e-9; for (auto& a : grid) { for (auto& point : a.getGridPoints()) { bool check_larger = (point.array() > max).any(); BOOST_CHECK_EQUAL(check_larger, false); if (check_larger) { std::cout << point.transpose() << std::endl; std::cout << max.transpose() << std::endl; } bool check_smaller = (point.array() < min).any(); BOOST_CHECK_EQUAL(check_smaller, false); if (check_smaller) { std::cout << point.transpose() << std::endl; std::cout << min.transpose() << std::endl; } } } BOOST_CHECK_EQUAL(grid.getGridSize(), 27000); BOOST_CHECK_EQUAL(grid.getBoxesSize(), 54); BOOST_CHECK_CLOSE(grid[0].getGridPoints()[0].x(), min.x(), 1e-5); BOOST_CHECK_CLOSE(grid[0].getGridPoints()[0].y(), min.y(), 1e-5); BOOST_CHECK_CLOSE(grid[0].getGridPoints()[0].z(), min.z(), 1e-5); BOOST_CHECK_CLOSE(grid[0].getGridPoints()[30].y(), -2.0379047286687406, 1e-5); BOOST_CHECK_CLOSE(grid[0].getGridPoints()[45].z(), 0.075477952913657109, 1e-5); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_rpa.cc000066400000000000000000000106771412152066400165100ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE rpa_test // Third party includes #include "boost/test/unit_test.hpp" // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/aobasis.h" #include "votca/xtp/aomatrix.h" #include "votca/xtp/logger.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/rpa.h" #include "votca/xtp/threecenter.h" using namespace votca::xtp; using namespace votca; using namespace std; BOOST_AUTO_TEST_SUITE(rpa_test) BOOST_AUTO_TEST_CASE(rpa_calcenergies) { Logger log; TCMatrix_gwbse Mmn; Eigen::VectorXd eigenvals; RPA rpa(log, Mmn); rpa.configure(4, 0, 9); Eigen::VectorXd dftenergies = Eigen::VectorXd::Zero(10); dftenergies << -0.5, -0.4, -0.3, -0.2, -0.2, -0.1, 0, 0.1, 0.2, 0.3; Eigen::VectorXd gwenergies = Eigen::VectorXd::Zero(7); gwenergies << -0.15, -0.05, 0.05, 0.15, 0.45, 0.55, 0.65; votca::Index qpmin = 1; rpa.UpdateRPAInputEnergies(dftenergies, gwenergies, qpmin); Eigen::VectorXd rpaenergies = rpa.getRPAInputEnergies(); Eigen::VectorXd rpaenergies_ref = Eigen::VectorXd::Zero(10); rpaenergies_ref << -0.85, -0.15, -0.05, 0.05, 0.15, 0.45, 0.55, 0.65, 0.75, 0.85; bool e_check = rpaenergies_ref.isApprox(rpaenergies, 0.0001); if (!e_check) { cout << "energy" << endl; cout << rpaenergies << endl; cout << "energy_ref" << endl; cout << rpaenergies_ref << endl; } BOOST_CHECK_EQUAL(e_check, true); } BOOST_AUTO_TEST_CASE(rpa_full) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/rpa/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/rpa/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); Eigen::VectorXd eigenvals = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/rpa/eigenvals.mm"); Eigen::MatrixXd eigenvectors = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/rpa/eigenvectors.mm"); Logger log; TCMatrix_gwbse Mmn; Mmn.Initialize(aobasis.AOBasisSize(), 0, 16, 0, 16); Mmn.Fill(aobasis, aobasis, eigenvectors); RPA rpa(log, Mmn); rpa.configure(4, 0, 16); rpa.setRPAInputEnergies(eigenvals); Eigen::MatrixXd e_i = rpa.calculate_epsilon_i(0.5); Eigen::MatrixXd i_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/rpa/i_ref.mm"); bool i_check = i_ref.isApprox(e_i, 0.0001); if (!i_check) { cout << "Epsilon_i" << endl; cout << e_i << endl; cout << "Epsilon_i_ref" << endl; cout << i_ref << endl; } BOOST_CHECK_EQUAL(i_check, 1); Eigen::MatrixXd e_r = rpa.calculate_epsilon_r(0.0); Eigen::MatrixXd r_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/rpa/r_ref.mm"); bool r_check = r_ref.isApprox(e_r, 0.0001); if (!r_check) { cout << "Epsilon_r" << endl; cout << e_r << endl; cout << "Epsilon_r_ref" << endl; cout << r_ref << endl; } BOOST_CHECK_EQUAL(r_check, 1); Eigen::MatrixXd e_r_complex = rpa.calculate_epsilon_r(std::complex(0.5, 0.5)); Eigen::MatrixXd r_complex_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/rpa/r_complex_ref.mm"); bool r_complex_check = r_complex_ref.isApprox(e_r_complex, 0.0001); if (!r_complex_check) { cout << "Epsilon_r_complex" << endl; cout << e_r_complex << endl; cout << "Epsilon_r_compelx_ref" << endl; cout << r_complex_ref << endl; } BOOST_CHECK_EQUAL(r_complex_check, 1); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_rpa_h2p.cc000066400000000000000000000104361412152066400172520ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE rpa_test // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/aobasis.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/rpa.h" #include "votca/xtp/threecenter.h" #include using namespace std; using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(rpa_test) BOOST_AUTO_TEST_CASE(rpa_h2p) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/rpa/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/rpa/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); Eigen::VectorXd eigenvals = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/rpa/eigenvals.mm"); Eigen::MatrixXd eigenvectors = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/rpa/eigenvectors.mm"); Logger log; TCMatrix_gwbse Mmn; Mmn.Initialize(aobasis.AOBasisSize(), 0, 16, 0, 16); Mmn.Fill(aobasis, aobasis, eigenvectors); RPA rpa(log, Mmn); rpa.setRPAInputEnergies(eigenvals); rpa.configure(4, 0, 16); Eigen::VectorXd rpa_omega_ref = Eigen::VectorXd(60); rpa_omega_ref << 0.104192, 0.104192, 0.187814, 0.559693, 0.559693, 0.572575, 0.577988, 0.577989, 0.579088, 0.618403, 0.618403, 0.67005, 0.678538, 0.678538, 0.722771, 1.10797, 1.41413, 1.41413, 1.58866, 1.60381, 1.60381, 1.64709, 1.87331, 1.87331, 1.88646, 1.8926, 1.89268, 1.89268, 1.933, 1.933, 2.01832, 2.40974, 2.42192, 2.42192, 2.46371, 2.85829, 2.8853, 2.8853, 2.90367, 2.90367, 2.92541, 2.94702, 3.3382, 3.3382, 3.35102, 3.3566, 3.3566, 3.35835, 3.39617, 3.39617, 4.22882, 4.71607, 4.72233, 4.72233, 4.76567, 16.5917, 17.0793, 17.093, 17.093, 17.1377; Eigen::VectorXd rpa_XpY_diag_ref = Eigen::VectorXd(60); rpa_XpY_diag_ref << 0.00898067, -0.00898068, 0.00228621, -7.40059e-10, -0.000447591, -7.21786e-10, 2.86571e-09, 1.16917e-08, 5.18349e-09, 0.000124051, 1.89797e-10, -1.549e-05, -0.00513947, -0.00513956, -7.71176e-08, -2.09605e-08, 0.00412762, 0.00412738, 6.253e-09, 3.93273e-05, 2.09406e-05, -0.000532391, 3.70347e-05, 2.0857e-06, -6.13653e-10, 0.000723575, 3.41096e-05, 0.00942648, 0.0497694, 0.0497693, -1.28726e-07, 3.68417e-09, -7.00924e-06, 7.01603e-06, -1.36252e-09, -1.08353e-09, 0.000549202, 0.000549203, -6.22315e-09, -3.83321e-08, -2.4032e-08, -2.19679e-09, 5.76794e-10, -1.46987e-08, -1.27183e-08, -0.138355, -6.49432e-09, -2.71175e-05, 2.69024e-05, -2.69024e-05, 0.000155952, 0.000311876, -0.0002498, -0.000249804, 0.000816289, 1.05559e-06, 1.84996e-12, 5.76753e-06, -9.90455e-11, -0.000800706; RPA::rpa_eigensolution sol = rpa.Diagonalize_H2p(); BOOST_CHECK_CLOSE(sol.ERPA_correlation, -0.0587973, 1e-4); bool check_rpa_eigenvalues = rpa_omega_ref.isApprox(sol.omega, 0.0001); if (!check_rpa_eigenvalues) { cout << "rpa_omega" << endl; cout << sol.omega << endl; cout << "rpa_omega_ref" << endl; cout << rpa_omega_ref << endl; } BOOST_CHECK_EQUAL(check_rpa_eigenvalues, 1); Eigen::VectorXd rpa_XpY_diag = sol.XpY.diagonal(); bool check_rpa_XpY_diag = rpa_XpY_diag_ref.cwiseAbs().isApprox(rpa_XpY_diag.cwiseAbs(), 0.0001); if (!check_rpa_XpY_diag) { cout << "rpa_XpY_diag" << endl; cout << rpa_XpY_diag.transpose() << endl; cout << "rpa_XpY_diag_ref" << endl; cout << rpa_XpY_diag_ref.transpose() << endl; } BOOST_CHECK_EQUAL(check_rpa_XpY_diag, 1); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_segment.cc000066400000000000000000000052371412152066400173640ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE segment_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/checkpoint.h" #include "votca/xtp/segment.h" using namespace votca::tools; using namespace votca::xtp; using votca::Index; BOOST_AUTO_TEST_SUITE(segment_test) BOOST_AUTO_TEST_CASE(getElementtest) { Segment seg("one", 1); Atom atm1(1, "C", Eigen::Vector3d::Zero()); Atom atm2(2, "H", Eigen::Vector3d::UnitX()); Atom atm3(3, "N", Eigen::Vector3d::UnitY()); Atom atm4(4, "Au", Eigen::Vector3d::UnitZ()); Atom atm5(5, "C", 2 * Eigen::Vector3d::UnitZ()); seg.push_back(atm1); seg.push_back(atm2); seg.push_back(atm2); seg.push_back(atm3); seg.push_back(atm4); seg.push_back(atm3); seg.push_back(atm5); std::vector unique_ele = seg.FindUniqueElements(); std::vector unique_ele_ref = {"C", "H", "N", "Au"}; BOOST_CHECK_EQUAL(unique_ele.size(), unique_ele_ref.size()); for (Index i = 0; i < Index(unique_ele.size()); i++) { BOOST_CHECK_EQUAL(unique_ele[i], unique_ele_ref[i]); } } BOOST_AUTO_TEST_CASE(writehdf5) { Segment seg("one", 1); Atom atm1(1, "C", Eigen::Vector3d::Zero()); Atom atm2(2, "H", Eigen::Vector3d::UnitX()); Atom atm3(3, "N", Eigen::Vector3d::UnitY()); Atom atm4(4, "Au", Eigen::Vector3d::UnitZ()); Atom atm5(5, "C", 2 * Eigen::Vector3d::UnitZ()); seg.push_back(atm1); seg.push_back(atm2); seg.push_back(atm2); seg.push_back(atm3); seg.push_back(atm4); seg.push_back(atm3); seg.push_back(atm5); { CheckpointFile f("segment_test.hdf5"); CheckpointWriter w = f.getWriter(); seg.WriteToCpt(w); } CheckpointFile f("segment_test.hdf5"); CheckpointReader r = f.getReader(); Segment seg2(r); for (Index i = 0; i < seg2.size(); i++) { const Atom& a1 = seg[i]; const Atom& a2 = seg2[i]; BOOST_CHECK_EQUAL(a1.getName(), a2.getName()); bool pos_equal = a1.getPos().isApprox(a2.getPos(), 1e-9); BOOST_CHECK_EQUAL(pos_equal, true); } } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_segmentmapper.cc000066400000000000000000000166401412152066400205710ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE segmentmapper_test // Standard includes #include #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/segmentmapper.h" using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(segmentmapper_test) BOOST_AUTO_TEST_CASE(mapping_test) { Logger log; QMMapper mapper = QMMapper(log); mapper.LoadMappingFile(std::string(XTP_TEST_DATA_FOLDER) + "/segmentmapper/ch4.xml"); Segment seg("Methane", 1); Atom atm1(1, "CB", 5, Eigen::Vector3d::Zero(), "C"); Atom atm2(1, "HB1", 6, Eigen::Vector3d::UnitX(), "H"); Atom atm3(1, "HB2", 7, Eigen::Vector3d::UnitY(), "H"); Atom atm4(1, "HB3", 8, -Eigen::Vector3d::UnitX(), "H"); Atom atm5(1, "HB4", 9, -Eigen::Vector3d::UnitY(), "H"); seg.push_back(atm1); seg.push_back(atm2); seg.push_back(atm3); seg.push_back(atm4); seg.push_back(atm5); QMMolecule qmmol = mapper.map( seg, std::string(XTP_TEST_DATA_FOLDER) + "/segmentmapper/molecule.xyz"); std::vector name_ref = {"C", "H", "H", "H", "H"}; std::vector id_ref = {0, 1, 2, 3, 4}; std::vector pos_ref; Eigen::Vector3d pos1 = {-0.026627, -0.0672429, 8.10559e-19}; pos_ref.push_back(pos1); Eigen::Vector3d pos2 = {2.03254, -0.0672429, 3.24336e-17}; pos_ref.push_back(pos2); Eigen::Vector3d pos3 = {-0.713016, 1.87416, -4.21603e-17}; pos_ref.push_back(pos3); Eigen::Vector3d pos4 = {-1, 0, 0}; pos_ref.push_back(pos4); Eigen::Vector3d pos5 = {0, -1, 0}; pos_ref.push_back(pos5); BOOST_CHECK_EQUAL(qmmol.getId(), 1); BOOST_CHECK_EQUAL(qmmol.getType(), "Methane"); Eigen::Vector3d ref = {0.000140384, 0.000354522, 0}; BOOST_CHECK_EQUAL(qmmol.getPos().isApprox(ref, 1e-5), true); if (!qmmol.getPos().isApprox(ref, 1e-5)) { std::cout << "qmmolpos" << std::endl; std::cout << qmmol.getPos() << std::endl; std::cout << "qmmolref" << std::endl; std::cout << ref << std::endl; } for (Index i = 0; i < qmmol.size(); i++) { BOOST_CHECK_EQUAL(qmmol[i].getElement(), name_ref[i]); bool pos_equal = qmmol[i].getPos().isApprox(pos_ref[i], 1e-5); if (!pos_equal) { std::cout << "Atom " << i << std::endl; std::cout << "pos" << std::endl; std::cout << qmmol[i].getPos() << std::endl; std::cout << "ref" << std::endl; std::cout << pos_ref[i] << std::endl; } BOOST_CHECK_EQUAL(qmmol[i].getId(), id_ref[i]); } } BOOST_AUTO_TEST_CASE(mapping_to_md_test) { Logger log; QMMapper mapper = QMMapper(log); mapper.LoadMappingFile(std::string(XTP_TEST_DATA_FOLDER) + "/segmentmapper/ch4_2.xml"); Segment seg("Methane", 1); Atom atm1(1, "CB", 5, Eigen::Vector3d::Zero(), "C"); Atom atm2(1, "HB1", 6, Eigen::Vector3d::UnitX(), "H"); Atom atm3(1, "HB2", 7, Eigen::Vector3d::UnitY(), "H"); Atom atm4(1, "HB3", 8, -Eigen::Vector3d::UnitX(), "H"); Atom atm5(1, "HB4", 9, -Eigen::Vector3d::UnitY(), "H"); seg.push_back(atm1); seg.push_back(atm2); seg.push_back(atm3); seg.push_back(atm4); seg.push_back(atm5); QMMolecule qmmol = mapper.map( seg, std::string(XTP_TEST_DATA_FOLDER) + "/segmentmapper/molecule2.xyz"); std::vector name_ref = {"C", "H", "H", "H", "H"}; std::vector id_ref = {0, 1, 2, 3, 4}; std::vector pos_ref; Eigen::Vector3d pos1 = {0, 0, 0}; pos_ref.push_back(pos1); Eigen::Vector3d pos2 = {1, 0, 0}; pos_ref.push_back(pos2); Eigen::Vector3d pos3 = {0, 1, 0}; pos_ref.push_back(pos3); Eigen::Vector3d pos4 = {-1, 0, 0}; pos_ref.push_back(pos4); Eigen::Vector3d pos5 = {0, -1, 0}; pos_ref.push_back(pos5); BOOST_CHECK_EQUAL(qmmol.getId(), 1); BOOST_CHECK_EQUAL(qmmol.getType(), "Methane"); Eigen::Vector3d ref = {0.0, 0.0, 0}; BOOST_CHECK_EQUAL(qmmol.getPos().isApprox(ref, 1e-2), true); if (!qmmol.getPos().isApprox(ref, 1e-5)) { std::cout << "qmmolpos" << std::endl; std::cout << qmmol.getPos() << std::endl; std::cout << "qmmolref" << std::endl; std::cout << ref << std::endl; } for (Index i = 0; i < qmmol.size(); i++) { BOOST_CHECK_EQUAL(qmmol[i].getElement(), name_ref[i]); bool pos_equal = qmmol[i].getPos().isApprox(pos_ref[i], 1e-5); if (!pos_equal) { std::cout << "Atom " << i << std::endl; std::cout << "pos" << std::endl; std::cout << qmmol[i].getPos() << std::endl; std::cout << "ref" << std::endl; std::cout << pos_ref[i] << std::endl; } BOOST_CHECK_EQUAL(qmmol[i].getId(), id_ref[i]); } } BOOST_AUTO_TEST_CASE(mapping_test_no_weights) { Logger log; QMMapper mapper = QMMapper(log); mapper.LoadMappingFile(std::string(XTP_TEST_DATA_FOLDER) + "/segmentmapper/ch4_3.xml"); Segment seg("Methane", 1); Atom atm1(1, "CB", 5, Eigen::Vector3d::Ones(), "C"); Atom atm2(1, "HB1", 6, Eigen::Vector3d::UnitX() + Eigen::Vector3d::Ones(), "H"); Atom atm3(1, "HB2", 7, Eigen::Vector3d::UnitY() + Eigen::Vector3d::Ones(), "H"); Atom atm4(1, "HB3", 8, -Eigen::Vector3d::UnitX() + Eigen::Vector3d::Ones(), "H"); Atom atm5(1, "HB4", 9, -Eigen::Vector3d::UnitY() + Eigen::Vector3d::Ones(), "H"); seg.push_back(atm1); seg.push_back(atm2); seg.push_back(atm3); seg.push_back(atm4); seg.push_back(atm5); QMMolecule qmmol = mapper.map( seg, std::string(XTP_TEST_DATA_FOLDER) + "/segmentmapper/molecule3.xyz"); std::vector name_ref = {"C", "H", "H", "H", "H"}; std::vector id_ref = {0, 1, 2, 3, 4}; std::vector pos_ref; Eigen::Vector3d pos1 = {1.0 - 0.0267876, 1.0 - 0.0676484, 1}; pos_ref.push_back(pos1); Eigen::Vector3d pos2 = {1 + 2.03238, 1.0 - 0.0676484, 1}; pos_ref.push_back(pos2); Eigen::Vector3d pos3 = {1 + -0.713177, 1 + 1.87375, 1}; pos_ref.push_back(pos3); Eigen::Vector3d pos4 = {0, 1, 1}; pos_ref.push_back(pos4); Eigen::Vector3d pos5 = {1, 0, 1}; pos_ref.push_back(pos5); BOOST_CHECK_EQUAL(qmmol.getId(), 1); BOOST_CHECK_EQUAL(qmmol.getType(), "Methane"); Eigen::Vector3d ref = {1, 1, 1}; BOOST_CHECK_EQUAL(qmmol.getPos().isApprox(ref, 1e-5), true); if (!qmmol.getPos().isApprox(ref, 1e-5)) { std::cout << "qmmolpos" << std::endl; std::cout << qmmol.getPos() << std::endl; std::cout << "qmmolref" << std::endl; std::cout << ref << std::endl; } for (Index i = 0; i < qmmol.size(); i++) { BOOST_CHECK_EQUAL(qmmol[i].getElement(), name_ref[i]); bool pos_equal = qmmol[i].getPos().isApprox(pos_ref[i], 1e-5); if (!pos_equal) { std::cout << "Atom " << i << std::endl; std::cout << "pos" << std::endl; std::cout << qmmol[i].getPos() << std::endl; std::cout << "ref" << std::endl; std::cout << pos_ref[i] << std::endl; } BOOST_CHECK_EQUAL(qmmol[i].getId(), id_ref[i]); } } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_settings.cc000066400000000000000000000043261412152066400175600ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE settings_test // Standard includes #include #include #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/settings.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(settings_test) BOOST_AUTO_TEST_CASE(create_settings) { Settings qmpackage_template{"package"}; qmpackage_template.load_from_xml(std::string(XTP_TEST_DATA_FOLDER) + "/settings/defaults.xml"); auto basisset = qmpackage_template.get("basisset"); auto orca_guess = qmpackage_template.get("orca.scf"); BOOST_TEST(basisset == "ubecppol"); BOOST_TEST(orca_guess == "GUESS PMODEL"); } BOOST_AUTO_TEST_CASE(test_amend) { Settings qmpackage_template{"package"}; qmpackage_template.load_from_xml(std::string(XTP_TEST_DATA_FOLDER) + "/settings/defaults2.xml"); Settings user_input("package"); user_input.load_from_xml(std::string(XTP_TEST_DATA_FOLDER) + "/settings/user_input.xml"); user_input.amend(qmpackage_template); user_input.add("orca.property", "42"); user_input.validate(); auto basisset = user_input.get("functional"); auto ecp = user_input.get("ecp"); auto orca_guess = user_input.get("orca.scf"); auto executable = user_input.get("executable"); auto orca_prop = user_input.get("orca.property"); BOOST_TEST(basisset == "B3LYP"); BOOST_TEST(ecp == "ecp"); BOOST_TEST(executable == "/opt/orca/orca"); BOOST_TEST(orca_guess == "GUESS PMODEL"); BOOST_TEST(orca_prop == "42"); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_sigma_cda.cc000066400000000000000000000064221412152066400176260ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE sigma_test // Standard includes #include // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include #include #include #include #include using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(sigma_cda_test) BOOST_AUTO_TEST_CASE(sigma_full) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/sigma_cda/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/sigma_cda/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); Eigen::VectorXd mo_energy = Eigen::VectorXd::Zero(17); mo_energy << 0.0468207, 0.0907801, 0.0907801, 0.104563, 0.592491, 0.663355, 0.663355, 0.768373, 1.69292, 1.97724, 1.97724, 2.50877, 2.98732, 3.4418, 3.4418, 4.81084, 17.1838; Eigen::MatrixXd MOs = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/sigma_cda/MOs.mm"); Logger log; TCMatrix_gwbse Mmn; Mmn.Initialize(aobasis.AOBasisSize(), 0, 16, 0, 16); Mmn.Fill(aobasis, aobasis, MOs); RPA rpa(log, Mmn); rpa.setRPAInputEnergies(mo_energy); rpa.configure(4, 0, 16); Sigma_CDA sigma(Mmn, rpa); Sigma_CDA::options opt; opt.homo = 4; opt.qpmin = 0; opt.qpmax = 16; opt.rpamin = 0; opt.rpamax = 16; opt.quadrature_scheme = "legendre"; opt.order = 100; opt.alpha = 1e-3; sigma.configure(opt); Eigen::MatrixXd x = sigma.CalcExchangeMatrix(); Eigen::MatrixXd x_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/sigma_cda/x_ref.mm"); bool check_x = x_ref.isApprox(x, 1e-4); if (!check_x) { cout << "Sigma X" << endl; cout << x << endl; cout << "Sigma X ref" << endl; cout << x_ref << endl; } BOOST_CHECK_EQUAL(check_x, true); sigma.PrepareScreening(); Eigen::MatrixXd c = sigma.CalcCorrelationOffDiag(mo_energy); c.diagonal() = sigma.CalcCorrelationDiag(mo_energy); Eigen::MatrixXd c_ref_diag = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/sigma_cda/c_ref.mm"); bool check_c_diag = c.diagonal().isApprox(c_ref_diag.diagonal(), 1e-5); if (!check_c_diag) { cout << "Sigma C" << endl; cout << c.diagonal() << endl; cout << "Sigma C ref" << endl; cout << c_ref_diag << endl; } BOOST_CHECK_EQUAL(check_c_diag, true); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_sigma_exact.cc000066400000000000000000000067421412152066400202100ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE sigma_test // Standard includes #include // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/aobasis.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/rpa.h" #include "votca/xtp/sigma_exact.h" #include "votca/xtp/threecenter.h" using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(sigma_test) BOOST_AUTO_TEST_CASE(sigma_full) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/sigma_exact/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/sigma_exact/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); Eigen::VectorXd mo_energy = Eigen::VectorXd::Zero(17); mo_energy << 0.0468207, 0.0907801, 0.0907801, 0.104563, 0.592491, 0.663355, 0.663355, 0.768373, 1.69292, 1.97724, 1.97724, 2.50877, 2.98732, 3.4418, 3.4418, 4.81084, 17.1838; Eigen::MatrixXd MOs = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/sigma_exact/MOs.mm"); Logger log; TCMatrix_gwbse Mmn; Mmn.Initialize(aobasis.AOBasisSize(), 0, 16, 0, 16); Mmn.Fill(aobasis, aobasis, MOs); RPA rpa(log, Mmn); rpa.setRPAInputEnergies(mo_energy); rpa.configure(4, 0, 16); Sigma_Exact sigma = Sigma_Exact(Mmn, rpa); Sigma_Exact::options opt; opt.homo = 4; opt.qpmin = 0; opt.qpmax = 16; opt.rpamin = 0; opt.rpamax = 16; opt.eta = 1e-3; sigma.configure(opt); Eigen::MatrixXd x = sigma.CalcExchangeMatrix(); Eigen::MatrixXd x_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/sigma_exact/x_ref.mm"); bool check_x = x_ref.isApprox(x, 1e-5); if (!check_x) { cout << "Sigma X" << endl; cout << x << endl; cout << "Sigma X ref" << endl; cout << x_ref << endl; } BOOST_CHECK_EQUAL(check_x, true); sigma.PrepareScreening(); Eigen::MatrixXd c = sigma.CalcCorrelationOffDiag(mo_energy); c.diagonal() = sigma.CalcCorrelationDiag(mo_energy); Eigen::MatrixXd c_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/sigma_exact/c_ref.mm"); bool check_c_diag = c.diagonal().isApprox(c_ref.diagonal(), 1e-5); if (!check_c_diag) { cout << "Sigma C" << endl; cout << c.diagonal() << endl; cout << "Sigma C ref" << endl; cout << c_ref.diagonal() << endl; } BOOST_CHECK_EQUAL(check_c_diag, true); bool check_c = c.isApprox(c_ref, 1e-5); if (!check_c) { cout << "Sigma C" << endl; cout << c << endl; cout << "Sigma C ref" << endl; cout << c_ref << endl; } BOOST_CHECK_EQUAL(check_c, true); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_sigma_ppm.cc000066400000000000000000000072061412152066400176740ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE sigma_test // Standard includes #include // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/aobasis.h" #include "votca/xtp/logger.h" #include "votca/xtp/orbitals.h" #include "votca/xtp/ppm.h" #include "votca/xtp/rpa.h" #include "votca/xtp/sigma_ppm.h" #include "votca/xtp/threecenter.h" #include using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(sigma_test) BOOST_AUTO_TEST_CASE(sigma_full) { libint2::initialize(); Orbitals orbitals; orbitals.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/sigma_ppm/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/sigma_ppm/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, orbitals.QMAtoms()); Eigen::MatrixXd MOs = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/sigma_ppm/MOs.mm"); Eigen::VectorXd mo_energy = Eigen::VectorXd::Zero(17); mo_energy << -0.612601, -0.341755, -0.341755, -0.341755, 0.137304, 0.16678, 0.16678, 0.16678, 0.671592, 0.671592, 0.671592, 0.974255, 1.01205, 1.01205, 1.01205, 1.64823, 19.4429; Logger log; TCMatrix_gwbse Mmn; Mmn.Initialize(aobasis.AOBasisSize(), 0, 16, 0, 16); Mmn.Fill(aobasis, aobasis, MOs); RPA rpa(log, Mmn); rpa.configure(4, 0, 16); rpa.setRPAInputEnergies(mo_energy); Sigma_PPM sigma = Sigma_PPM(Mmn, rpa); Sigma_PPM::options opt; opt.homo = 4; opt.qpmin = 0; opt.qpmax = 16; opt.rpamin = 0; opt.rpamax = 16; opt.eta = 1e-3; sigma.configure(opt); Eigen::MatrixXd x = sigma.CalcExchangeMatrix(); Eigen::MatrixXd x_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/sigma_ppm/x_ref.mm"); bool check_x = x_ref.isApprox(x, 1e-5); if (!check_x) { cout << "Sigma X" << endl; cout << x << endl; cout << "Sigma X ref" << endl; cout << x_ref << endl; } BOOST_CHECK_EQUAL(check_x, true); sigma.PrepareScreening(); Eigen::MatrixXd c = sigma.CalcCorrelationOffDiag(mo_energy); c.diagonal() = sigma.CalcCorrelationDiag(mo_energy); Eigen::MatrixXd c_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/sigma_ppm/c_ref.mm"); bool check_c_diag = c.diagonal().isApprox(c_ref.diagonal(), 1e-5); if (!check_c_diag) { cout << "Sigma C" << endl; cout << c.diagonal() << endl; cout << "Sigma C ref" << endl; cout << c_ref.diagonal() << endl; } BOOST_CHECK_EQUAL(check_c_diag, true); bool check_c = c.isApprox(c_ref, 1e-5); if (!check_c) { cout << "Sigma C" << endl; cout << c << endl; cout << "Sigma C ref" << endl; cout << c_ref << endl; } BOOST_CHECK_EQUAL(check_c, true); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_sphere_lebedev_rule.cc000066400000000000000000000214531412152066400217230ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE sphere_lebedev_rule_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/orbitals.h" #include "votca/xtp/sphere_lebedev_rule.h" #include using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(sphere_lebedev_rule_test) BOOST_AUTO_TEST_CASE(medium_test) { libint2::initialize(); QMMolecule mol("noname", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/CH4.xyz"); LebedevGrid spheregrid; auto grid = spheregrid.CalculateSphericalGrids(mol, "medium"); auto Hgrid = grid.at("H"); auto Cgrid = grid.at("C"); Eigen::VectorXd C_phi_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/C_phi_ref_medium.mm"); C_phi_ref *= votca::tools::conv::Pi / 180.0; Eigen::VectorXd C_theta_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/C_theta_ref_medium.mm"); Eigen::VectorXd C_weight_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/C_weight_ref_medium.mm"); BOOST_CHECK_EQUAL(Cgrid.phi.size(), C_phi_ref.size()); BOOST_CHECK_EQUAL(Cgrid.theta.size(), C_theta_ref.size()); BOOST_CHECK_EQUAL(Cgrid.weight.size(), C_weight_ref.size()); BOOST_CHECK_EQUAL(Hgrid.phi.size(), C_phi_ref.size()); BOOST_CHECK_EQUAL(Hgrid.theta.size(), C_theta_ref.size()); BOOST_CHECK_EQUAL(Hgrid.weight.size(), C_weight_ref.size()); bool Cphi = C_phi_ref.isApprox(Cgrid.phi, 0.001); bool Ctheta = C_theta_ref.isApprox(Cgrid.theta, 0.001); if (!Cphi || !Ctheta) { std::cout << "phi_ref : Phi_comp | theta_ref : theta_comp" << std::endl; for (Index i = 0; i < C_phi_ref.size(); i++) { std::cout << Cgrid.phi[i] << ":" << C_phi_ref[i] << " | " << Cgrid.theta[i] << ":" << C_theta_ref[i] << std::endl; } } bool Cweight = C_weight_ref.isApprox(Cgrid.weight, 0.0001); BOOST_CHECK_EQUAL(Cphi, true); BOOST_CHECK_EQUAL(Ctheta, true); BOOST_CHECK_EQUAL(Cweight, true); bool Hphi = C_phi_ref.isApprox(Hgrid.phi, 0.001); bool Htheta = C_theta_ref.isApprox(Hgrid.theta, 0.001); bool Hweight = C_weight_ref.isApprox(Hgrid.weight, 0.0001); BOOST_CHECK_EQUAL(Hphi, true); BOOST_CHECK_EQUAL(Htheta, true); BOOST_CHECK_EQUAL(Hweight, true); libint2::finalize(); } BOOST_AUTO_TEST_CASE(fine_test) { libint2::initialize(); QMMolecule mol("noname", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/molecule.xyz"); LebedevGrid spheregrid; auto grid = spheregrid.CalculateSphericalGrids(mol, "fine"); auto Hgrid = grid.at("H"); auto Gegrid = grid.at("Ge"); Eigen::VectorXd Ge_phi_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/Ge_phi_ref_fine.mm"); Eigen::VectorXd Ge_theta_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/Ge_theta_ref_fine.mm"); Eigen::VectorXd Ge_weight_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/Ge_weight_ref_fine.mm"); Eigen::VectorXd H_phi_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/H_phi_ref_fine.mm"); Eigen::VectorXd H_theta_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/H_theta_ref_fine.mm"); Eigen::VectorXd H_weight_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/H_weight_ref_fine.mm"); BOOST_CHECK_EQUAL(Gegrid.phi.size(), Ge_phi_ref.size()); BOOST_CHECK_EQUAL(Gegrid.theta.size(), Ge_theta_ref.size()); BOOST_CHECK_EQUAL(Gegrid.weight.size(), Ge_weight_ref.size()); BOOST_CHECK_EQUAL(Hgrid.phi.size(), H_phi_ref.size()); BOOST_CHECK_EQUAL(Hgrid.theta.size(), H_theta_ref.size()); BOOST_CHECK_EQUAL(Hgrid.weight.size(), H_weight_ref.size()); bool Gephi = Ge_phi_ref.isApprox(Gegrid.phi, 0.001); bool Getheta = Ge_theta_ref.isApprox(Gegrid.theta, 0.001); if (!Gephi || !Getheta) { std::cout << "phi_ref : Phi_comp | theta_ref : theta_comp" << std::endl; for (Index i = 0; i < Ge_phi_ref.size(); i++) { std::cout << Gegrid.phi[i] << ":" << Ge_phi_ref[i] << " | " << Gegrid.theta[i] << ":" << Ge_theta_ref[i] << std::endl; } } bool Geweight = Ge_weight_ref.isApprox(Gegrid.weight, 0.0001); BOOST_CHECK_EQUAL(Gephi, true); BOOST_CHECK_EQUAL(Getheta, true); BOOST_CHECK_EQUAL(Geweight, true); bool Hphi = H_phi_ref.isApprox(Hgrid.phi, 0.001); bool Htheta = H_theta_ref.isApprox(Hgrid.theta, 0.001); bool Hweight = H_weight_ref.isApprox(Hgrid.weight, 0.0001); BOOST_CHECK_EQUAL(Hphi, true); BOOST_CHECK_EQUAL(Htheta, true); BOOST_CHECK_EQUAL(Hweight, true); libint2::finalize(); } BOOST_AUTO_TEST_CASE(element_not_implemented) { libint2::initialize(); QMMolecule mol("noname", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/hg.xyz"); LebedevGrid spheregrid; BOOST_REQUIRE_THROW(spheregrid.CalculateSphericalGrids(mol, "xfine"), std::runtime_error); libint2::finalize(); } BOOST_AUTO_TEST_CASE(xfine_test) { libint2::initialize(); QMMolecule mol("noname", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/molecule.xyz"); LebedevGrid spheregrid; auto grid = spheregrid.CalculateSphericalGrids(mol, "xfine"); auto Hgrid = grid.at("H"); auto Gegrid = grid.at("Ge"); Eigen::VectorXd Ge_phi_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/Ge_phi_ref_xfine.mm"); Eigen::VectorXd Ge_theta_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/Ge_theta_ref_xfine.mm"); Eigen::VectorXd Ge_weight_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/Ge_weight_ref_xfine.mm"); Eigen::VectorXd H_phi_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/H_phi_ref_xfine.mm"); Eigen::VectorXd H_theta_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/H_theta_ref_xfine.mm"); Eigen::VectorXd H_weight_ref = votca::tools::EigenIO_MatrixMarket::ReadVector( std::string(XTP_TEST_DATA_FOLDER) + "/sphere_lebedev_rule/H_weight_ref_xfine.mm"); BOOST_CHECK_EQUAL(Gegrid.phi.size(), Ge_phi_ref.size()); BOOST_CHECK_EQUAL(Gegrid.theta.size(), Ge_theta_ref.size()); BOOST_CHECK_EQUAL(Gegrid.weight.size(), Ge_weight_ref.size()); BOOST_CHECK_EQUAL(Hgrid.phi.size(), H_phi_ref.size()); BOOST_CHECK_EQUAL(Hgrid.theta.size(), H_theta_ref.size()); BOOST_CHECK_EQUAL(Hgrid.weight.size(), H_weight_ref.size()); bool Gephi = Ge_phi_ref.isApprox(Gegrid.phi, 0.001); bool Getheta = Ge_theta_ref.isApprox(Gegrid.theta, 0.001); if (!Gephi || !Getheta) { std::cout << "phi_ref : Phi_comp | theta_ref : theta_comp" << std::endl; for (Index i = 0; i < Ge_phi_ref.size(); i++) { std::cout << Gegrid.phi[i] << ":" << Ge_phi_ref[i] << " | " << Gegrid.theta[i] << ":" << Ge_theta_ref[i] << std::endl; } } bool Geweight = Ge_weight_ref.isApprox(Gegrid.weight, 0.0001); BOOST_CHECK_EQUAL(Gephi, true); BOOST_CHECK_EQUAL(Getheta, true); BOOST_CHECK_EQUAL(Geweight, true); bool Hphi = H_phi_ref.isApprox(Hgrid.phi, 0.001); bool Htheta = H_theta_ref.isApprox(Hgrid.theta, 0.001); bool Hweight = H_weight_ref.isApprox(Hgrid.weight, 0.0001); BOOST_CHECK_EQUAL(Hphi, true); BOOST_CHECK_EQUAL(Htheta, true); BOOST_CHECK_EQUAL(Hweight, true); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_statetracker.cc000066400000000000000000000063201412152066400204100ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE statetracker_test // Standard includes #include // Third party includes #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/statetracker.h" #include using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(statetracker_test) BOOST_AUTO_TEST_CASE(osc) { libint2::initialize(); Orbitals orb; orb.QMAtoms().LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/statetracker/molecule.xyz"); orb.setDFTbasisName(std::string(XTP_TEST_DATA_FOLDER) + "/statetracker/3-21G.xml"); Logger log; orb.setBasisSetSize(17); orb.setNumberOfOccupiedLevels(4); orb.setBSEindices(0, 16); orb.setTDAApprox(true); Eigen::MatrixXd& MOs = orb.MOs().eigenvectors(); orb.MOs().eigenvalues() = Eigen::VectorXd::Ones(17); MOs = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/statetracker/MOs.mm"); Eigen::VectorXd se_ref = Eigen::VectorXd::Zero(3); se_ref << 0.107455, 0.107455, 0.107455; orb.BSESinglets().eigenvalues() = se_ref; // reference coefficients Eigen::MatrixXd spsi_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/statetracker/spsi_ref.mm"); orb.BSESinglets().eigenvectors() = spsi_ref; orb.CalcCoupledTransition_Dipoles(); { votca::tools::Property prop; prop.LoadFromXML(std::string(XTP_TEST_DATA_FOLDER) + "/statetracker/statetracker.xml"); StateTracker tracker; tracker.setLogger(&log); QMState s("s1"); tracker.setInitialState(s); tracker.Initialize(prop.get("statetracker")); QMState newstate = tracker.CalcState(orb); BOOST_CHECK_EQUAL(newstate.Type().ToString(), "s"); BOOST_CHECK_EQUAL(newstate.StateIdx(), 1); } libint2::finalize(); } BOOST_AUTO_TEST_CASE(readwrite_hdf5) { votca::tools::Property prop; prop.LoadFromXML(std::string(XTP_TEST_DATA_FOLDER) + "/statetracker/statetracker2.xml"); StateTracker tracker; QMState s("s1"); tracker.setInitialState(s); tracker.Initialize(prop.get("statetracker")); { CheckpointFile f("statetracker_test.hdf5"); CheckpointWriter w = f.getWriter(); tracker.WriteToCpt(w); } StateTracker tracker2; CheckpointFile f("statetracker_test.hdf5"); CheckpointReader r = f.getReader(); tracker2.ReadFromCpt(r); BOOST_CHECK_EQUAL(tracker.InitialState().ToString(), tracker2.InitialState().ToString()); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_staticsite.cc000066400000000000000000000064371412152066400201010ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE staticsite_test // Third party incldues #include // Local VOTCA includes #include "votca/xtp/staticsite.h" using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(staticsite_test) BOOST_AUTO_TEST_CASE(constructors_test) { StaticSite st(1, "st1"); } BOOST_AUTO_TEST_CASE(getters_test) { StaticSite st(1, "st2"); BOOST_CHECK_EQUAL(st.getId(), 1); BOOST_CHECK_EQUAL(st.getElement(), "st2"); } BOOST_AUTO_TEST_CASE(multipole_test) { StaticSite st(1, "st2"); Eigen::VectorXd multipole = Eigen::VectorXd::Zero(9); multipole << 1, 2, 3, 4, 8, 7, 2, 3.3, -0.5; st.setMultipole(multipole, 2); bool check_mpoles = multipole.isApprox(st.Q(), 0.0001); BOOST_CHECK_EQUAL(check_mpoles, true); bool check_rank = (st.getRank() == 2); BOOST_CHECK_EQUAL(check_rank, true); } BOOST_AUTO_TEST_CASE(translate_test) { StaticSite st(1, "st2"); Eigen::Vector3d shift; shift << 0, 0, 5; st.Translate(shift); BOOST_CHECK_EQUAL(shift.isApprox(st.getPos(), 1e-5), true); } BOOST_AUTO_TEST_CASE(writepolarization_test) { StaticSite st(1, "st2"); Eigen::VectorXd multipole = Eigen::VectorXd::Zero(9); multipole << 1, 2, 3, 4, 8, 7, 2, 3.3, -0.5; st.setMultipole(multipole, 2); BOOST_CHECK_EQUAL( st.WriteMpsLine(), " st2 +0.0000000 +0.0000000 +0.0000000 Rank 2\n" " +1.0000000\n" " +4.0000000 +2.0000000 +3.0000000\n" " +8.0000000 +7.0000000 +2.0000000 +3.3000000 -0.5000000\n" " P +1.0000000\n"); } BOOST_AUTO_TEST_CASE(rotation_test) { StaticSite st(1, "st2", Eigen::Vector3d::UnitY()); Eigen::Matrix3d R = Eigen::Matrix3d::Zero(); // Rotation around z axes R << 0, -1, 0, 1, 0, 0, 0, 0, 1; Eigen::VectorXd multipoles = Eigen::VectorXd::Zero(9); multipoles << 1, 1, 0, 0, 0, 1, 0, 0, 0; // q=1, mu_x=1 and Q_21c=1 the rest is 0 st.setMultipole(multipoles, 2); st.Rotate(R, Eigen::Vector3d::Zero()); bool equalpos = st.getPos().isApprox(Eigen::Vector3d(-1, 0, 0), 1e-5); if (!equalpos) { std::cout << "Result " << std::endl; std::cout << st.getPos() << std::endl; std::cout << "Reference" << std::endl; std::cout << Eigen::Vector3d(-1, 0, 0) << std::endl; } BOOST_CHECK_EQUAL(equalpos, true); Eigen::VectorXd rotmultipoles = Eigen::VectorXd::Zero(9); rotmultipoles << 1, 0, 1, 0, 0, 0, 1, 0, 0; // q=1, mu_y=1 and Q_21s=1 is 0 bool equalmultipoles = rotmultipoles.isApprox(st.Q(), 1e-5); if (!equalmultipoles) { std::cout << "Result " << std::endl; std::cout << st.Q() << std::endl; std::cout << "Reference" << std::endl; std::cout << rotmultipoles << std::endl; } BOOST_CHECK_EQUAL(equalmultipoles, true); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_symmetric_matrix.cc000066400000000000000000000111201412152066400213060ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE symmetric_matrix_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/symmetric_matrix.h" using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(symmetric_matrix_test) BOOST_AUTO_TEST_CASE(Constructor_test) { Index dim = 3; Eigen::MatrixXd test = Eigen::MatrixXd::Random(dim, dim); Eigen::MatrixXd trans = test.transpose(); test += trans; Symmetric_Matrix sym = Symmetric_Matrix(test); Eigen::MatrixXd back = Eigen::MatrixXd::Zero(dim, dim); sym.AddtoEigenMatrix(back); bool check_matrices = back.isApprox(test, 0.000001); if (!check_matrices) { std::cout << sym << std::endl; std::cout << test << std::endl; std::cout << back << std::endl; } BOOST_CHECK_EQUAL(check_matrices, 1); } BOOST_AUTO_TEST_CASE(Add_test) { Index dim = 3; Eigen::MatrixXd test = Eigen::MatrixXd::Random(dim, dim); Eigen::MatrixXd trans = test.transpose(); test += trans; Symmetric_Matrix sym = Symmetric_Matrix(test); Eigen::MatrixXd rand = Eigen::MatrixXd::Random(dim, dim); Eigen::MatrixXd result = rand + 2 * test; sym.AddtoEigenMatrix(rand, 2.0); bool check_matrices2 = rand.isApprox(result, 0.000001); if (!check_matrices2) { std::cout << test << std::endl; std::cout << sym << std::endl; std::cout << rand << std::endl; std::cout << result << std::endl; } BOOST_CHECK_EQUAL(check_matrices2, 1); } BOOST_AUTO_TEST_CASE(AddUpper_test) { Index dim = 3; Eigen::MatrixXd test = Eigen::MatrixXd::Random(dim, dim); Eigen::MatrixXd trans = test.transpose(); test += trans; Symmetric_Matrix sym = Symmetric_Matrix(test); Eigen::MatrixXd rand = Eigen::MatrixXd::Random(dim, dim); Eigen::MatrixXd result = rand + 2 * test; Eigen::SelfAdjointView m = rand.selfadjointView(); sym.AddtoEigenUpperMatrix(m, 2.0); result.triangularView() = Eigen::MatrixXd::Zero(dim, dim); rand.triangularView() = Eigen::MatrixXd::Zero(dim, dim); bool check_matrices2 = rand.isApprox(result, 0.000001); if (!check_matrices2) { std::cout << "ref" << std::endl; std::cout << rand << std::endl; std::cout << "sym matrix full" << std::endl; std::cout << result << std::endl; } BOOST_CHECK_EQUAL(check_matrices2, 1); } BOOST_AUTO_TEST_CASE(FullMatrix_test) { Index dim = 3; Eigen::MatrixXd test = Eigen::MatrixXd::Random(dim, dim); Eigen::MatrixXd trans = test.transpose(); test += trans; Symmetric_Matrix sym = Symmetric_Matrix(test); Eigen::MatrixXd result = sym.FullMatrix(); bool check_matrices = test.isApprox(result, 0.000001); BOOST_CHECK_EQUAL(check_matrices, 1); } BOOST_AUTO_TEST_CASE(UpperMatrix_test) { Index dim = 3; Eigen::MatrixXd test = Eigen::MatrixXd::Random(dim, dim); Eigen::MatrixXd trans = test.transpose(); test += trans; Symmetric_Matrix sym = Symmetric_Matrix(test); Eigen::MatrixXd result = sym.UpperMatrix(); result.triangularView() = Eigen::MatrixXd::Zero(dim, dim); test.triangularView() = Eigen::MatrixXd::Zero(dim, dim); bool check_matrices = test.isApprox(result, 0.000001); BOOST_CHECK_EQUAL(check_matrices, 1); } BOOST_AUTO_TEST_CASE(TraceofProd_test) { Index dim = 3; Eigen::MatrixXd test = Eigen::MatrixXd::Random(dim, dim); Eigen::MatrixXd trans = test.transpose(); test += trans; Symmetric_Matrix sym1 = Symmetric_Matrix(test); Eigen::MatrixXd test2 = Eigen::MatrixXd::Random(dim, dim); Eigen::MatrixXd trans2 = test2.transpose(); test2 += trans2; Symmetric_Matrix sym2 = Symmetric_Matrix(test2); double ref = test2.cwiseProduct(test).sum(); double result = sym1.TraceofProd(sym2); bool check = std::abs(ref - result) < 1e-7; if (!check) { std::cout << "Ref: " << ref << " Sym: " << result << std::endl; } BOOST_CHECK_EQUAL(check, 1); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_threecenter_dft.cc000066400000000000000000000073041412152066400210640ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #include #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE threecenter_dft_test // Third party includes #include // VOTCA includes #include #include // Local VOTCA includes #include #include #include using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(threecenter_dft_test) BOOST_AUTO_TEST_CASE(small_basis) { libint2::initialize(); QMMolecule mol(" ", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/threecenter_dft/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/threecenter_dft/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, mol); TCMatrix_dft threec; threec.Fill(aobasis, aobasis); Eigen::MatrixXd Ref0 = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/threecenter_dft/Ref0.mm"); Eigen::MatrixXd Ref4 = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/threecenter_dft/Ref4.mm"); bool check_three1 = Ref0.isApprox(threec[0].FullMatrix(), 0.00001); if (!check_three1) { std::cout << "Res0" << std::endl; std::cout << threec[0].FullMatrix() << std::endl; std::cout << "0_ref" << std::endl; std::cout << Ref0 << std::endl; } BOOST_CHECK_EQUAL(check_three1, true); bool check_three2 = Ref4.isApprox(threec[4].FullMatrix(), 0.00001); if (!check_three2) { std::cout << "Res4" << std::endl; std::cout << threec[4].FullMatrix() << std::endl; std::cout << "4_ref" << std::endl; std::cout << Ref4 << std::endl; } BOOST_CHECK_EQUAL(check_three2, true); libint2::finalize(); } /*BOOST_AUTO_TEST_CASE(large_l_test) { QMMolecule mol("C", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/threecenter_dft/C2.xyz"); BasisSet basisset; basisset.Load(std::string(XTP_TEST_DATA_FOLDER) + "/threecenter_dft/G.xml"); AOBasis dftbasis; dftbasis.Fill(basisset, mol); BasisSet auxbasisset; auxbasisset.Load(std::string(XTP_TEST_DATA_FOLDER) + "/threecenter_dft/I.xml"); AOBasis auxbasis; auxbasis.Fill(auxbasisset, mol); TCMatrix_dft threec; threec.Fill(auxbasis, dftbasis); // we only test half of it because it gets a bit big std::array ref; std::array ref_string; std::array indeces = {0, 1, 3, 12}; for (Index i = 0; i < 4; i++) { ref[i] = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/threecenter_dft/RefList" + std::to_string(i) + ".mm"); } for (Index i = 0; i < 4; i++) { bool check = ref[i].isApprox(threec[indeces[i]].FullMatrix(), 1e-5); BOOST_CHECK_EQUAL(check, true); if (!check) { std::cout << "ref " << indeces[i] << std::endl; std::cout << ref[i] << std::endl; std::cout << "result " << indeces[i] << std::endl; std::cout << threec[indeces[i]].FullMatrix() << std::endl; } } } */ BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_threecenter_gwbse.cc000066400000000000000000000072621412152066400214210ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE threecenter_gwbse_test // Third party includes #include // VOTCA inlcudes #include #include // Local VOTCA includes #include "votca/xtp/aobasis.h" #include "votca/xtp/qmmolecule.h" #include "votca/xtp/threecenter.h" #include using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(threecenter_gwbse_test) BOOST_AUTO_TEST_CASE(threecenter_gwbse) { libint2::initialize(); QMMolecule mol(" ", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/threecenter_gwbse/molecule.xyz"); BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/threecenter_gwbse/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, mol); Eigen::MatrixXd MOs = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/threecenter_gwbse/MOs.mm"); TCMatrix_gwbse tc; tc.Initialize(aobasis.AOBasisSize(), 0, 5, 0, 7); tc.Fill(aobasis, aobasis, MOs); Eigen::MatrixXd ref0b = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/threecenter_gwbse/ref0b.mm"); bool check0_before = ref0b.isApprox(tc[0], 1e-5); if (!check0_before) { cout << "tc0" << endl; cout << tc[0] << endl; cout << "tc0_ref" << endl; cout << ref0b << endl; } BOOST_CHECK_EQUAL(check0_before, true); Eigen::MatrixXd ref2b = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/threecenter_gwbse/ref2b.mm"); bool check2_before = ref2b.isApprox(tc[2], 1e-5); if (!check2_before) { cout << "tc2" << endl; cout << tc[2] << endl; cout << "tc2_ref" << endl; cout << ref2b << endl; } BOOST_CHECK_EQUAL(check2_before, true); Eigen::MatrixXd ref4b = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/threecenter_gwbse/ref4b.mm"); bool check4_before = ref4b.isApprox(tc[4], 1e-5); if (!check4_before) { cout << "tc4" << endl; cout << tc[4] << endl; cout << "tc4_ref" << endl; cout << ref4b << endl; } BOOST_CHECK_EQUAL(check4_before, true); Eigen::MatrixXd auxmatrix = Eigen::MatrixXd::Identity(aobasis.AOBasisSize(), aobasis.AOBasisSize()); tc.MultiplyRightWithAuxMatrix(auxmatrix); bool check0_after = ref0b.isApprox(tc[0], 1e-5); if (!check0_after) { cout << "tc0" << endl; cout << tc[0] << endl; cout << "tc0_ref" << endl; cout << ref0b << endl; } BOOST_CHECK_EQUAL(check0_after, true); bool check2_after = ref2b.isApprox(tc[2], 1e-5); if (!check2_after) { cout << "tc2" << endl; cout << tc[2] << endl; cout << "tc2_ref" << endl; cout << ref2b << endl; } BOOST_CHECK_EQUAL(check2_after, true); bool check4_after = ref4b.isApprox(tc[4], 1e-5); if (!check4_after) { cout << "tc4" << endl; cout << tc[4] << endl; cout << "tc4_ref" << endl; cout << ref4b << endl; } BOOST_CHECK_EQUAL(check4_after, true); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_topology.cc000066400000000000000000000031451412152066400175720ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE topology_test // Third party includes #include #include // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/atom.h" #include "votca/xtp/qmpair.h" #include "votca/xtp/segment.h" #include "votca/xtp/topology.h" using namespace votca::tools; using namespace votca::xtp; BOOST_AUTO_TEST_SUITE(topology_test) BOOST_AUTO_TEST_CASE(constructors_test) { Topology top; } BOOST_AUTO_TEST_CASE(box_test) { Eigen::Matrix3d box = 2 * Eigen::Matrix3d::Identity(); Topology top; top.setBox(box); auto vol = top.BoxVolume(); BOOST_CHECK_CLOSE(vol, 8, 0.0001); auto box2 = top.getBox(); BOOST_CHECK_EQUAL(box.isApprox(box2, 1e-6), true); } BOOST_AUTO_TEST_CASE(simple_test) { Topology top; top.setStep(1); BOOST_CHECK_EQUAL(top.getStep(), 1); top.setTime(1.21); BOOST_CHECK_CLOSE(top.getTime(), 1.21, 0.0001); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_trustregion.cc000066400000000000000000000034061412152066400203030ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE trustregion_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/trustregion.h" using namespace votca::xtp; using namespace votca; using namespace std; BOOST_AUTO_TEST_SUITE(trustregion_test) BOOST_AUTO_TEST_CASE(subproblem_test) { Eigen::VectorXd gradient = Eigen::VectorXd::Zero(5); gradient << 5.92833, 9.88054, 9.88054, 9.88054, 9.88054; Eigen::MatrixXd hessian = Eigen::MatrixXd::Zero(5, 5); hessian << 1.0835, 0.139166, 0.139166, 0.139166, 0.139166, 0.139166, 1.23194, 0.231943, 0.231943, 0.231943, 0.139166, 0.231943, 1.23194, 0.231943, 0.231943, 0.139166, 0.231943, 0.231943, 1.23194, 0.231943, 0.139166, 0.231943, 0.231943, 0.231943, 1.23194; double radius = 0.1; TrustRegion trf; Eigen::VectorXd newstep = trf.CalculateStep(gradient, hessian, radius); bool equal = std::abs(newstep.norm() - radius) < 1e-9; if (!equal) { std::cout << "newstep_norm:" << newstep.norm() << " trust_radius:" << radius << std::endl; } BOOST_CHECK_EQUAL(equal, 1); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_vc2index.cc000066400000000000000000000032271412152066400174410ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE vc2index_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/vc2index.h" using namespace votca::xtp; using namespace votca; BOOST_AUTO_TEST_SUITE(vc2index_test) BOOST_AUTO_TEST_CASE(index_test) { Index vmin = 0; Index cmin = 10; Index ctotal = 10; Index vtotal = 9; vc2index vc = vc2index(vmin, cmin, ctotal); Index v = 3; Index c = 12; BOOST_CHECK_EQUAL(vc.I(v, c), 32); BOOST_CHECK_EQUAL(vc.c(vc.I(v, c)), c); BOOST_CHECK_EQUAL(vc.v(vc.I(v, c)), v); std::vector indexv; std::vector indexc; for (Index v2 = 0; v2 < vtotal; v2++) { for (Index c2 = 0; c2 < ctotal; c2++) { indexv.push_back(vmin + v2); indexc.push_back(cmin + c2); } } for (Index j = 0; j < Index(indexv.size()); j++) { BOOST_CHECK_EQUAL(indexv[j], vc.v(j)); } for (Index j = 0; j < Index(indexc.size()); j++) { BOOST_CHECK_EQUAL(indexc[j], vc.c(j)); } } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_vxc_grid.cc000066400000000000000000000032341412152066400175220ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE vxc_grid_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/orbitals.h" #include "votca/xtp/vxc_grid.h" #include using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(vxc_grid_test) AOBasis CreateBasis(const QMMolecule& mol) { BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/vxc_grid/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, mol); return aobasis; } BOOST_AUTO_TEST_CASE(vxc_grid_build) { libint2::initialize(); QMMolecule mol("none", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/vxc_grid/molecule.xyz"); AOBasis aobasis = CreateBasis(mol); Vxc_Grid grid; grid.GridSetup("medium", mol, aobasis); BOOST_CHECK_EQUAL(grid.getGridSize(), grid.getGridpoints().size()); BOOST_CHECK_EQUAL(grid.getGridSize(), 53404); BOOST_CHECK_EQUAL(grid.getBoxesSize(), 51); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tests/test_vxc_potential.cc000066400000000000000000000054021412152066400205730ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ #define BOOST_TEST_MAIN #define BOOST_TEST_MODULE vxc_potential_test // Standard includes #include // Third party includes #include // Local VOTCA includes #include "votca/xtp/orbitals.h" #include "votca/xtp/vxc_grid.h" #include "votca/xtp/vxc_potential.h" #include #include using namespace votca::xtp; using namespace std; BOOST_AUTO_TEST_SUITE(vxc_potential_test) AOBasis CreateBasis(const QMMolecule& mol) { BasisSet basis; basis.Load(std::string(XTP_TEST_DATA_FOLDER) + "/vxc_potential/3-21G.xml"); AOBasis aobasis; aobasis.Fill(basis, mol); return aobasis; } Eigen::MatrixXd DMat() { Eigen::MatrixXd dmat = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/vxc_potential/dmat.mm"); return dmat; } BOOST_AUTO_TEST_CASE(vxc_test) { libint2::initialize(); QMMolecule mol("none", 0); mol.LoadFromFile(std::string(XTP_TEST_DATA_FOLDER) + "/vxc_potential/molecule.xyz"); AOBasis aobasis = CreateBasis(mol); Eigen::MatrixXd dmat = DMat(); Vxc_Grid grid; grid.GridSetup("medium", mol, aobasis); Vxc_Potential num(grid); num.setXCfunctional("XC_GGA_X_PBE XC_GGA_C_PBE"); BOOST_CHECK_EQUAL(grid.getGridSize(), grid.getGridpoints().size()); BOOST_CHECK_EQUAL(grid.getGridSize(), 53404); BOOST_CHECK_EQUAL(grid.getBoxesSize(), 51); BOOST_CHECK_CLOSE(num.getExactExchange("XC_GGA_X_PBE XC_GGA_C_PBE"), 0.0, 1e-5); BOOST_CHECK_CLOSE(num.getExactExchange("XC_HYB_GGA_XC_PBEH"), 0.25, 1e-5); Mat_p_Energy e_vxc = num.IntegrateVXC(dmat); Eigen::MatrixXd vxc_ref = votca::tools::EigenIO_MatrixMarket::ReadMatrix( std::string(XTP_TEST_DATA_FOLDER) + "/vxc_potential/vxc_ref.mm"); bool check_vxc = e_vxc.matrix().isApprox(vxc_ref, 0.0001); BOOST_CHECK_CLOSE(e_vxc.energy(), -4.6303432151572643, 1e-5); if (!check_vxc) { std::cout << "ref" << std::endl; std::cout << vxc_ref << std::endl; std::cout << "calc" << std::endl; std::cout << e_vxc.matrix() << std::endl; } BOOST_CHECK_EQUAL(check_vxc, 1); libint2::finalize(); } BOOST_AUTO_TEST_SUITE_END() xtp-2021.2/src/tools/000077500000000000000000000000001412152066400143435ustar00rootroot00000000000000xtp-2021.2/src/tools/CMakeLists.txt000066400000000000000000000017321412152066400171060ustar00rootroot00000000000000foreach(PROG xtp_map xtp_run xtp_tools xtp_parallel) file(GLOB ${PROG}_SOURCES ${PROG}*.cc) add_executable(${PROG} ${${PROG}_SOURCES}) target_link_libraries(${PROG} votca_xtp) install(TARGETS ${PROG} RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) if (BUILD_MANPAGES) add_custom_command(OUTPUT ${PROG}.man COMMAND ${CMAKE_CURRENT_BINARY_DIR}/${PROG} --man > ${PROG}.man COMMENT "Building ${PROG} manpage" DEPENDS ${PROG}) add_custom_target(${PROG}_manpage DEPENDS ${PROG}.man) add_dependencies(manpages ${PROG}_manpage) install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROG}.man DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${PROG}.1) endif (BUILD_MANPAGES) if(ENABLE_TESTING) add_test(integration_${PROG}Help ${PROG} --help) # run tests for tools, csg, ctp as well for coverage set_tests_properties(integration_${PROG}Help PROPERTIES LABELS "xtp;tools;csg;ctp;votca;integration") endif(ENABLE_TESTING) endforeach(PROG) xtp-2021.2/src/tools/xtp_map.cc000066400000000000000000000246531412152066400163340ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Standard includes #include #include #include // VOTCA includes #include #include #include #include #include #include // Local VOTCA includes #include "votca/xtp/md2qmengine.h" #include "votca/xtp/statesaver.h" #include "votca/xtp/topology.h" #include "votca/xtp/version.h" using namespace std; namespace CSG = votca::csg; namespace XTP = votca::xtp; namespace TOOLS = votca::tools; class XtpMap : public TOOLS::Application { public: string ProgramName() override { return "xtp_map"; } void HelpText(ostream& out) override { out << "Generates QM|MD topology" << endl; } void ShowHelpText(std::ostream& out) override; void Initialize() override; bool EvaluateOptions() override; void Run() override; protected: }; namespace propt = boost::program_options; void XtpMap::Initialize() { CSG::TrajectoryWriter::RegisterPlugins(); CSG::TrajectoryReader::RegisterPlugins(); CSG::TopologyReader::RegisterPlugins(); AddProgramOptions()("topology,t", propt::value(), " topology"); AddProgramOptions()("coordinates,c", propt::value(), " coordinates or trajectory"); AddProgramOptions()("segments,s", propt::value(), " definition of segments and fragments"); AddProgramOptions()("makesegments,m", " write out a skeleton segments file"); AddProgramOptions()("file,f", propt::value(), " state file"); AddProgramOptions()("first-frame,i", propt::value()->default_value(0), " start from this frame"); AddProgramOptions()("begin,b", propt::value()->default_value(0.0), " start time in simulation"); AddProgramOptions()("nframes,n", propt::value()->default_value(1), " number of frames to process"); } bool XtpMap::EvaluateOptions() { CheckRequired("topology", "Missing topology file"); CheckRequired("segments", "Missing segment definition file"); CheckRequired("coordinates", "Missing trajectory input"); if (!(_op_vm.count("makesegments"))) { CheckRequired("file", "Missing state file"); } return 1; } void XtpMap::Run() { std::string name = ProgramName(); if (VersionString() != "") { name = name + ", version " + VersionString(); } XTP::HelpTextHeader(name); // ++++++++++++++++++++++++++++ // // Create MD topology from file // // ++++++++++++++++++++++++++++ // // Create topology reader string topfile = _op_vm["topology"].as(); std::unique_ptr topread = std::unique_ptr( CSG::TopReaderFactory().Create(topfile)); if (topread == nullptr) { throw runtime_error(string("Input format not supported: ") + _op_vm["topology"].as()); } CSG::Topology mdtopol; topread->ReadTopology(topfile, mdtopol); if (votca::Log::verbose()) { cout << "Read MD topology from " << topfile << ": Found " << mdtopol.BeadCount() << " atoms in " << mdtopol.MoleculeCount() << " molecules. " << endl; } // ++++++++++++++++++++++++++++++ // // Create MD trajectory from file // // ++++++++++++++++++++++++++++++ // // Create trajectory reader and initialize string trjfile = _op_vm["coordinates"].as(); std::unique_ptr trjread = std::unique_ptr( CSG::TrjReaderFactory().Create(trjfile)); if (trjread == nullptr) { throw runtime_error(string("Input format not supported: ") + _op_vm["coordinates"].as()); } trjread->Open(trjfile); trjread->FirstFrame(mdtopol); string mapfile = _op_vm["segments"].as(); if (_op_vm.count("makesegments")) { if (TOOLS::filesystem::FileExists(mapfile)) { cout << endl << "xtp_map : map file '" << mapfile << "' already in use. Delete the current mapfile or specify a " "different name." << endl; return; } cout << " Writing template mapfile to " << mapfile << std::endl; TOOLS::Property mapfile_prop("topology", "", ""); TOOLS::Property& molecules = mapfile_prop.add("molecules", ""); std::map firstmolecule; std::map molecule_names; for (const CSG::Molecule* mol : mdtopol.Molecules()) { if (!molecule_names.count(mol->getName())) { firstmolecule[mol->getName()] = mol; } molecule_names[mol->getName()]++; } for (const auto& mol : molecule_names) { std::cout << "Found " << mol.second << " with name " << mol.first << std::endl; } for (const auto& mol : molecule_names) { TOOLS::Property& molecule = molecules.add("molecule", ""); molecule.add("mdname", mol.first); TOOLS::Property& segments = molecule.add("segments", ""); TOOLS::Property& segment = segments.add("segment", ""); segment.add("name", "UPTOYOU_BUTUNIQUE"); segment.add("qmcoords_n", "XYZFILE_GROUNDSTATE"); segment.add("multipoles_n", "MPSFILE_GROUNDSTATE"); segment.add("map2md", "WANTTOMAPTOMDGEOMETRY"); segment.add("U_xX_nN_h", "REORG1_hole"); segment.add("U_nX_nN_h", "REORG2_hole"); segment.add("U_xN_xX_h", "REORG3_hole"); TOOLS::Property& fragments = segment.add("fragments", ""); TOOLS::Property& fragment = fragments.add("fragment", ""); std::string atomnames = ""; const CSG::Molecule* csgmol = firstmolecule[mol.first]; std::vector sortedbeads; sortedbeads.reserve(csgmol->BeadCount()); for (const CSG::Bead* bead : csgmol->Beads()) { sortedbeads.push_back(bead); } std::sort(sortedbeads.begin(), sortedbeads.end(), [&](const CSG::Bead* b1, const CSG::Bead* b2) { return b1->getId() < b2->getId(); }); for (const CSG::Bead* bead : sortedbeads) { atomnames += " " + std::to_string(bead->getResnr()) + ":" + bead->getName() + ":" + std::to_string(bead->getId()); } fragment.add("name", "UPTOYOU_BUTUNIQUE"); fragment.add("mdatoms", atomnames); fragment.add("qmatoms", "IDS of QMATOMS i.e 0:C 1:H 2:C"); fragment.add("mpoles", "IDS of MPOLES i.e 0:C 1:H 2:C"); fragment.add("weights", "weights for mapping(often atomic mass) i.e. 12 1 12"); fragment.add("localframe", "IDs of up to 3 qmatoms or mpoles i.e. 0 1 2"); std::ofstream template_mapfile(mapfile); template_mapfile << mapfile_prop << std::flush; template_mapfile.close(); std::cout << "MOLECULETYPE " << csgmol->getName() << std::endl; std::cout << "SAMPLECOORDINATES" << std::endl; std::cout << "ID NAME COORDINATES[Angstroem] " << std::endl; for (const CSG::Bead* bead : sortedbeads) { Eigen::Vector3d pos = bead->getPos() * votca::tools::conv::nm2ang; std::string output = (boost::format("%1$i %2$s %3$+1.4f %4$+1.4f %5$+1.4f\n") % bead->getId() % bead->getName() % pos[0] % pos[1] % pos[2]) .str(); std::cout << output; } } std::cout << std::flush; return; } if (!TOOLS::filesystem::FileExists(mapfile)) { cout << endl << "xtp_map : map file '" << mapfile << "' could not be found." << endl; return; } XTP::Md2QmEngine md2qm(mapfile); votca::Index firstFrame = _op_vm["first-frame"].as(); votca::Index nFrames = _op_vm["nframes"].as(); bool beginAt = false; double time = _op_vm["begin"].as(); double startTime = mdtopol.getTime(); if (time > 0.0) { beginAt = true; startTime = time; } // Extract first frame specified bool hasFrame; votca::Index frames_found = 0; votca::Index firstframecounter = firstFrame; for (hasFrame = true; hasFrame == true; hasFrame = trjread->NextFrame(mdtopol)) { frames_found++; if (((mdtopol.getTime() < startTime) && beginAt) || firstframecounter > 0) { firstframecounter--; continue; } break; } if (!hasFrame) { trjread->Close(); throw runtime_error("Time or frame number exceeds trajectory length"); } if (votca::Log::verbose()) { cout << "Read MD trajectory from " << trjfile << ": found " << frames_found << " frames, starting from frame " << firstFrame << endl; } // +++++++++++++++++++++++++ // // Convert MD to QM Topology // // +++++++++++++++++++++++++ // string statefile = _op_vm["file"].as(); if (TOOLS::filesystem::FileExists(statefile)) { cout << endl << "xtp_map : state file '" << statefile << "' already in use. Delete the current statefile or specify a " "different name." << endl; return; } XTP::StateSaver statsav(statefile); votca::Index laststep = -1; // for some formats no step is given out so we check if the step for (votca::Index saved = 0; hasFrame && saved < nFrames; hasFrame = trjread->NextFrame(mdtopol), saved++) { if (mdtopol.getStep() == laststep) { mdtopol.setStep(laststep + 1); } laststep = mdtopol.getStep(); XTP::Topology qmtopol = md2qm.map(mdtopol); statsav.WriteFrame(qmtopol); } } void XtpMap::ShowHelpText(std::ostream& out) { string name = ProgramName(); if (VersionString() != "") { name = name + ", version " + VersionString(); } XTP::HelpTextHeader(name); HelpText(out); out << "\n\n" << VisibleOptions() << endl; } int main(int argc, char** argv) { XtpMap xtpmap; return xtpmap.Exec(argc, argv); } xtp-2021.2/src/tools/xtp_parallel.cc000066400000000000000000000064231412152066400173460ustar00rootroot00000000000000/* * Copyright 2009-2021 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/jobapplication.h" #include "votca/xtp/jobcalculatorfactory.h" using namespace std; using namespace votca; class XtpParallel : public xtp::JobApplication { public: string ProgramName() override { return "xtp_parallel"; } void HelpText(ostream& out) override { out << "Runs job-based heavy-duty calculators" << endl; } void HelpText(){}; void Initialize() override; bool EvaluateOptions() override; private: // void PrintDescription(string name, HelpOutputType _help_output_type); }; namespace propt = boost::program_options; void XtpParallel::Initialize() { xtp::JobCalculatorfactory::RegisterAll(); xtp::JobApplication::Initialize(); AddProgramOptions("Calculator")("execute,e", propt::value(), "Name of calculator to run"); AddProgramOptions("Calculator")("list,l", "Lists all available calculators"); AddProgramOptions("Calculator")("description,d", propt::value(), "Short description of a calculator"); } bool XtpParallel::EvaluateOptions() { if (OptionsMap().count("list")) { cout << "Available XTP calculators: \n"; for (const auto& name : xtp::JobCalculators().getKeys()) { PrintDescription(std::cout, name, "xtp/xml", Application::HelpShort); } StopExecution(); return true; } if (OptionsMap().count("description")) { CheckRequired("description", "no calculator is given"); tools::Tokenizer tok(OptionsMap()["description"].as(), " ,\n\t"); // loop over the names in the description string for (const std::string& n : tok) { if (xtp::JobCalculators().IsRegistered(n)) { PrintDescription(std::cout, n, "xtp/xml", Application::HelpLong); } else { cout << "Calculator " << n << " does not exist\n"; } } StopExecution(); return true; } xtp::JobApplication::EvaluateOptions(); CheckRequired("execute", "Nothing to do here: Abort."); tools::Tokenizer calcs(OptionsMap()["execute"].as(), " ,\n\t"); std::vector calc_string = calcs.ToVector(); if (calc_string.size() != 1) { throw std::runtime_error( "You can only run one calculator at the same time."); } if (xtp::JobCalculators().IsRegistered(calc_string[0])) { xtp::JobApplication::SetCalculator( xtp::JobCalculators().Create(calc_string[0])); } else { cout << "Jobcalculator " << calc_string[0] << " does not exist\n"; StopExecution(); } return true; } int main(int argc, char** argv) { XtpParallel xtprun; return xtprun.Exec(argc, argv); } xtp-2021.2/src/tools/xtp_run.cc000066400000000000000000000065771412152066400163700ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // Local VOTCA includes #include "votca/xtp/calculatorfactory.h" #include "votca/xtp/stateapplication.h" using namespace votca; class XtpRun : public xtp::StateApplication { public: std::string ProgramName() override { return "xtp_run"; } void HelpText(std::ostream& out) override { out << "Runs excitation/charge transport calculators\n"; } void HelpText(){}; void Initialize() override; bool EvaluateOptions() override; private: // void PrintDescription(string name, HelpOutputType _help_output_type); }; namespace propt = boost::program_options; void XtpRun::Initialize() { xtp::Calculatorfactory::RegisterAll(); xtp::StateApplication::Initialize(); AddProgramOptions("Calculator")("execute,e", propt::value(), "Name of calculator to run"); AddProgramOptions("Calculator")("list,l", "Lists all available calculators"); AddProgramOptions("Calculator")("description,d", propt::value(), "Short description of a calculator"); } bool XtpRun::EvaluateOptions() { std::string helpdir = "xtp/xml"; if (OptionsMap().count("list")) { std::cout << "Available XTP calculators:\n"; for (const auto& name : xtp::Calculators().getKeys()) { PrintDescription(std::cout, name, helpdir, Application::HelpShort); } StopExecution(); return true; } if (OptionsMap().count("description")) { CheckRequired("description", "no calculator is given"); tools::Tokenizer tok(OptionsMap()["description"].as(), " ,\n\t"); // loop over the names in the description string for (const std::string& n : tok) { if (xtp::Calculators().IsRegistered(n)) { PrintDescription(std::cout, n, helpdir, Application::HelpLong); } else { std::cout << "Calculator " << n << " does not exist\n"; } } StopExecution(); return true; } xtp::StateApplication::EvaluateOptions(); CheckRequired("execute", "Nothing to do here: Abort."); tools::Tokenizer calcs(OptionsMap()["execute"].as(), " ,\n\t"); std::vector calc_string = calcs.ToVector(); if (calc_string.size() != 1) { throw std::runtime_error( "You can only run one calculator at the same time."); } if (xtp::Calculators().IsRegistered(calc_string[0])) { xtp::StateApplication::SetCalculator( xtp::Calculators().Create(calc_string[0])); _options.LoadFromXML(_op_vm["options"].as()); } else { std::cout << "Calculator " << calc_string[0] << " does not exist\n"; StopExecution(); } return true; } int main(int argc, char** argv) { XtpRun xtprun; return xtprun.Exec(argc, argv); } xtp-2021.2/src/tools/xtp_tools.cc000066400000000000000000000120031412152066400167010ustar00rootroot00000000000000/* * Copyright 2009-2020 The VOTCA Development Team * (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License") * * You may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ // VOTCA includes #include // Local VOTCA includes #include "votca/xtp/qmtool.h" #include "votca/xtp/toolfactory.h" #include "votca/xtp/version.h" #include "votca/xtp/xtpapplication.h" using namespace votca; class XtpTools : public xtp::XtpApplication { public: XtpTools() = default; ~XtpTools() override = default; std::string ProgramName() override { return "xtp_tools"; } void HelpText(std::ostream& out) override { out << "Runs excitation/charge transport tools\n"; } void SetTool(std::unique_ptr&& tool) { _tool = std::move(tool); } void Initialize() override; bool EvaluateOptions() override; void Run() override; void BeginEvaluate(Index nThreads); bool Evaluate(); private: tools::Property _options; std::unique_ptr _tool; }; namespace propt = boost::program_options; void XtpTools::Initialize() { xtp::QMToolFactory::RegisterAll(); xtp::XtpApplication::Initialize(); // Tools-related AddProgramOptions("Tools")("execute,e", propt::value(), "name of the tool to run"); AddProgramOptions("Tools")("list,l", "Lists all available tools"); AddProgramOptions("Tools")("description,d", propt::value(), "Short description of a tool"); AddProgramOptions("Tools")("name,n", propt::value(), "Name of the job to run"); // Options-related AddProgramOptions()("nthreads,t", propt::value()->default_value(1), " number of threads to create"); } bool XtpTools::EvaluateOptions() { std::string helpdir = "xtp/xml"; if (OptionsMap().count("list")) { std::cout << "Available XTP tools: \n"; for (const auto& name : xtp::QMTools().getKeys()) { PrintDescription(std::cout, name, helpdir, Application::HelpShort); } StopExecution(); return true; } if (OptionsMap().count("description")) { CheckRequired("description", "no tool is given"); tools::Tokenizer tok(OptionsMap()["description"].as(), " ,\n\t"); // loop over the names in the description string for (const std::string& n : tok) { if (xtp::QMTools().IsRegistered(n)) { PrintDescription(std::cout, n, helpdir, Application::HelpLong); } else { std::cout << "Tool " << n << " does not exist\n"; } } StopExecution(); return true; } CheckRequired("execute", "Please provide the name of the tool to execute"); tools::Tokenizer xtools(OptionsMap()["execute"].as(), " ,\n\t"); std::vector calc_string = xtools.ToVector(); if (calc_string.size() != 1) { throw std::runtime_error("You can only run one tool at the same time."); } CheckRequired( "name", "Please provide the job name to run (same as the xyz file name)"); if (xtp::QMTools().IsRegistered(calc_string[0])) { this->SetTool(xtp::QMTools().Create(calc_string[0])); std::cout << "Registered " << calc_string[0]; } else { std::cout << "Tool " << calc_string[0] << " does not exist\n"; StopExecution(); } return true; } void XtpTools::Run() { auto it = _op_vm.find("options"); if (it != _op_vm.cend()) { std::string optionsFile = _op_vm["options"].as(); _options.LoadFromXML(optionsFile); } else { // Empty user options tools::Property& opts = _options.add("options", ""); opts.add(_tool->Identify(), ""); } std::string job_name = _op_vm["name"].as(); tools::Property& opts = _options.get("options." + _tool->Identify()); opts.add("job_name", job_name); Index nThreads = OptionsMap()["nthreads"].as(); std::string name = ProgramName(); if (VersionString() != "") { name = name + ", version " + VersionString(); } xtp::HelpTextHeader(name); std::cout << "Initializing tool\n"; BeginEvaluate(nThreads); std::cout << "Evaluating tool\n"; Evaluate(); } void XtpTools::BeginEvaluate(Index nThreads = 1) { std::cout << "... " << _tool->Identify() << " " << std::flush; _tool->setnThreads(nThreads); _tool->Initialize(_options); } bool XtpTools::Evaluate() { std::cout << "... " << _tool->Identify() << " " << std::flush; _tool->Evaluate(); return true; } int main(int argc, char** argv) { XtpTools xtpapp; return xtpapp.Exec(argc, argv); }