debian/0000755000000000000000000000000012253143076007171 5ustar debian/psi4-data.dirs0000644000000000000000000000006612206735752011652 0ustar /usr/share/doc/psi4/html /usr/share/doc/psi4/examples debian/get-orig-source.sh0000755000000000000000000000153412235476477012564 0ustar #!/bin/sh set -ex UPSTREAM_VERSION=$2 ORIG_TARBALL=$3 REAL_TARBALL=`readlink -f ${ORIG_TARBALL}` WORKING_DIR=`dirname ${ORIG_TARBALL}` ORIG_TARBALL_DFSG=`echo ${ORIG_TARBALL} | sed -e "s/\(${UPSTREAM_VERSION}\)\(\.orig\)/\1+dfsg\2/g"` ORIG_TARBALL_DIR=`echo ${ORIG_TARBALL_DFSG} | sed -e "s/_\(${UPSTREAM_VERSION}\)/-\1/g" -e "s/\.tar\.gz//g"` ORIG_TARBALL_DIR_STRIP=`basename ${ORIG_TARBALL_DIR}` mkdir -p ${ORIG_TARBALL_DIR} tar --directory=${ORIG_TARBALL_DIR} --strip 1 -xzf ${REAL_TARBALL} || exit 1 rm -f ${ORIG_TARBALL} ${REAL_TARBALL} # delete embedded copy of madness rm -rf ${ORIG_TARBALL_DIR}/madness # delete an eps file because the Adobe copyright leaked into it rm -rf ${ORIG_TARBALL_DIR}/doc/progman/svn/svn.eps.in GZIP=-9 tar --remove-files --directory ${WORKING_DIR} -czf ${ORIG_TARBALL_DFSG} ${ORIG_TARBALL_DIR_STRIP} || exit 1 exit 0 debian/psi4.install0000644000000000000000000000001512201766715011440 0ustar usr/bin/psi4 debian/rules0000755000000000000000000000334112253071320010242 0ustar #!/usr/bin/make -f # -*- makefile -*- #export DH_VERBOSE=1 DEB_BUILD_MULTIARCH=$(shell dpkg-architecture -qDEB_BUILD_MULTIARCH) export PSI_SCRATCH=$(CURDIR)/tmp-scratch export SCRATCH=$(CURDIR)/tmp-scratch %: dh $@ --with autotools_dev --parallel override_dh_auto_clean: dh_auto_clean --builddirectory=builddir find $(CURDIR) -name "*.pyc" -delete $(RM) -r tmp-scratch override_dh_auto_configure: dh_auto_configure --builddirectory=builddir -- --docdir=/usr/share/doc/psi4 --with-boost-system --with-boost-libdir=/usr/lib/$(DEB_BUILD_MULTIARCH) override_dh_auto_build: dh_auto_build --builddirectory=builddir (cd builddir/doc; $(MAKE)) override_dh_auto_install-arch: dh_auto_install --builddirectory=builddir $(RM) debian/tmp/usr/share/psi/databases/*.pyc cp samples/example_psi4rc_file debian/psi4/usr/share/doc/psi4/psi4rc.example override_dh_auto_install-indep: for i in tu1-h2o-energy tu2-ch2-energy tu3-h2o-opt tu4-h2o-freq \ tu5-sapt castup1 scf1 scf2 scf3 scf5 scf-guess-read dft1 dfmp2-1 \ cc1 cc2 cc3 cc4 cc8 cc8a cc12 \ cc15 cc16 cc17 cc18 cc19 cc23 cc24 cc28 cc32 cc49 \ fci-dipole cisd-h2o+-0 ci-multi \ cisd-opt-fd rasci-h2o mpn-bh \ mcscf1 sapt1 sad1 \ psimrcc-sp1 mints1 mints2 matrix1 opt1 opt1-fd gibbs omp2-2 \ omp3-1 omp2_5-2 ocepa1 fnocc2 fnocc4 \ mp2_5-grad1 ocepa-grad2 omp2-grad1 \ dcft1 dcft2 dcft3 dcft4 pywrap-db1 pywrap-db2 pywrap-cbs1 pywrap-all pywrap-alias \ pywrap-checkrun-rhf pywrap-freq-e-sowreap; \ do cp samples/$$i/input.dat \ $(CURDIR)/debian/psi4-data/usr/share/doc/psi4/examples/$$i.dat; \ done (cd builddir/doc; $(MAKE) install DESTDIR=$(CURDIR)/debian/psi4-data) ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) override_dh_auto_test: -(cd builddir/tests; $(MAKE) quicktests) endif debian/README.source0000644000000000000000000000070212253125200011334 0ustar psi4 for Debian =============== The PSI4 upstream tarball contains the following embedded source copies, which are not used by the binary Debian packages: * boost/boost_1_53_0.tar.gz: Boot-1.53. Furthermore, several files/directories were stripped off the tarball, see debian/get-orig-source.sh for further details: * madness: Contains unclear copyright and is an embedded source copy. * doc/progman/svn/svn.eps.in: Contains Adobe copyright. debian/source/0000755000000000000000000000000012217410113010456 5ustar debian/source/format0000644000000000000000000000001412204475123011674 0ustar 3.0 (quilt) debian/psi4-data.links0000644000000000000000000000011712203754615012022 0ustar /usr/share/doc/psi4/html/sphinx/index.html /usr/share/doc/psi4/html/index.html debian/watch0000644000000000000000000000026212221606127010216 0ustar version=3 opts=dversionmangle=s/\+dfsg$//,uversionmangle=s#([\d.]+)b(\d+)?#$1~beta$2#g \ http://sf.net/psicode/psi([\db.]+)\.tar\.gz \ debian /bin/sh debian/get-orig-source.sh debian/control0000644000000000000000000001025012207733605010574 0ustar Source: psi4 Section: science Priority: optional Maintainer: Debichem Team Uploaders: Michael Banck Build-Depends: autotools-dev, debhelper (>> 8), dvipng, gfortran, libblas-dev, libboost-filesystem-dev, libboost-python-dev, libboost-regex-dev, libboost-serialization-dev, libboost-system-dev, libboost-thread-dev, liblapack-dev, python-dev, python-numpy, python-sphinx, texlive-latex-extra Standards-Version: 3.9.4 Homepage: http://www.psicode.org/ Vcs-Browser: http://anonscm.debian.org/viewvc/debichem/unstable/psi4/ Vcs-Svn: svn://anonscm.debian.org/debichem/unstable/psi4/ Package: psi4 Architecture: any Depends: psi4-data (= ${source:Version}), ${misc:Depends}, ${shlibs:Depends} Description: Quantum Chemical Program Suite PSI4 is an ab-initio quantum chemistry program. It is especially designed to accurately compute properties of small to medium molecules using highly correlated techniques. PSI4 is the parallelized successor of PSI3 and includes many state-of-the-art theoretical methods. . It can compute energies and gradients for the following methods: * Restricted, unrestricted and general restricted open shell Hartree-Fock (RHF/ROHF) * Restricted, unrestricted and general restricted open shell Densitry-Functional Theory, including density-fitting (DF-DFT) * Density Cumulant Functional Theory (DCFT) * Closed-shell Density-fitted Moeller-Plesset perturbation theory (DF-MP2) * Unrestricted Moeller-Plesset perturbation theory (MP2) * Orbital-Optimized MP2 theory (OMP2) * Third order Moeller-Plesset perturbation theory (MP3) * Orbital-Optimized MP3 theory (OMP3) * Coupled-cluster singles doubles (CCSD) * Coupled-cluster singles doubles with perturbative triples (CCSD(T)) (only for unrestricted (UHF) reference wavefunctions) * Equation-of-motion coupled-cluster singles doubles (EOM-CCSD) . Additionally, it can compute energies for the following methods: * Closed/open shell Moeller-Plesset perturbation theory (MP2) * Spin-component scaled MP2 theory (SCS-MP2) * Fourth order Moeller-Plesset perturbation theory (MP4) * Density-fitted symmetry-adapted perturbation theory (DF-SAPT) * Multireference configuration-interaction (MRCI) * Closed-shell Density-fitted coupled-cluster singles doubles (DF-CCSD) * Closed-shell Density-fitted Coupled-cluster singles doubles with perturbative triples (DF-CCSD(T)) * Second/third-order approximate coupled-cluster singles doubles (CC2/CC3) * Mukherjee Multireference coupled-cluster singles doubles theory (mk-MRCCSD) * Mukherjee Multireference coupled-cluster singles doubles with perturbative triples theory (mk-MRCCSD(T)) * Second order algebraic-diagrammatic construction theory (ADC(2)) * Quadratic configuration interaction singles doubles (QCISD) * Quadratic configuration interaction singles doubles with perturbative triples (QCISD(T)) . Further features include: * Flexible, modular and customizable input format via python * Excited state calculations with the EOM-CC2/CC3, EOM-CCSD, ADC(2), MRCI and mk-MRCC methods * Utilization of molecular point-group symmetry to increase efficiency * Internal coordinate geometry optimizer * Harmonic frequencies calculations (via finite differences) * Potential surface scans * Counterpoise correction * One-electron properties like dipole/quadrupole moments, transition dipole moments, natural orbitals occupations or electrostatic potential * Composite methods like complete basis set extrapolation or G2/G3 Package: psi4-data Architecture: all Depends: ${misc:Depends}, ${shlibs:Depends} Description: Quantum Chemical Program Suite (data files) PSI4 is an ab-initio quantum chemistry program. It is especially designed to accurately compute properties of small to medium molecules using highly correlated techniques. PSI4 is the parallelized successor of PSI3 and includes many state-of-the-art theoretical methods. . This package contains data files and the HTML documentation. debian/psi4.dirs0000644000000000000000000000002412206735760010734 0ustar /usr/share/doc/psi4 debian/psi4-data.install0000644000000000000000000000001612204467134012344 0ustar usr/share/psi debian/upstream0000644000000000000000000000143112217405700010746 0ustar Name: PSI4 Reference: - Author: Justin M. Turney and Andrew C. Simmonett and Robert M. Parrish and Edward G. Hohenstein and Francesco A. Evangelista and Justin T. Fermann and Benjamin J. Mintz and Lori A. Burns and Jeremiah J. Wilke and Micah L. Abrams and Nicholas J. Russ and Matthew L. Leininger and Curtis L. Janssen and Edward T. Seidl and Wesley D. Allen and Henry F. Schaefer and Rollin A. King and Edward F. Valeev and C. David Sherrill and T. Daniel Crawford Title: "PSI4: an open-source ab initio electronic structure program" Journal: WIREs Comput. Mol. Sci. Year: 2012 Volume: 2 Number: 4 Pages: 556-565 URL: http://onlinelibrary.wiley.com/doi/10.1002/wcms.93/abstract eprint: http://onlinelibrary.wiley.com/doi/10.1002/wcms.93/pdf DOI: 10.1002/wcms.93 debian/patches/0000755000000000000000000000000012235512065010616 5ustar debian/patches/psi4rc-changes.patch0000644000000000000000000000145612204472344014460 0ustar --- ./samples/example_psi4rc_file.orig 2013-08-19 21:34:31.652255189 +0200 +++ ./samples/example_psi4rc_file 2013-08-19 21:40:38.286157634 +0200 @@ -1,11 +1,18 @@ import os +# +# Example ~/.psi4rc file +# # Set the default path for all PSI4 data files. Be sure to include the trailing '/' . # Uncomment the final line(s) of one of the options below or construct your own set_default_path +# [0] +# By default, /tmp is used +psi4_io.set_default_path('/tmp/') + # [1] # Sends scratch files for all jobs to one place. Usually safe since pid labeled. # Useful when psi4 is run on box from which it's called (not queued cluster system) -psi4_io.set_default_path('/scratch/parrish/') +#psi4_io.set_default_path('/scratch/parrish/') # [2] # Sends scratch files to directory from which psi4 was called. debian/patches/dfcc-bugfix.patch0000644000000000000000000000423712206763763014041 0ustar # Taken from https://gist.github.com/edeprince3/6023223 diff --git a/theoryfs2/ds/deprince/ccsd.cc b/src/bin/fnocc/ccsd.cc index a66ec02..ef0e662 100644 --- a/theoryfs2/ds/deprince/ccsd.cc +++ b/src/bin/fnocc/ccsd.cc @@ -3015,7 +3015,6 @@ void DFCoupledCluster::T1Fock(){ nrows++; rowsize = nQ_scf / nrows; if (nrows * rowsize < nQ_scf) rowsize++; - if (rowsize == 1) break; } long int lastrowsize = nQ_scf - (nrows - 1L) * rowsize; long int * rowdims = new long int [nrows]; @@ -3075,7 +3074,6 @@ void DFCoupledCluster::T1Fock(){ nrows++; rowsize = nQ_scf / nrows; if (nrows * rowsize < nQ_scf) rowsize++; - if (rowsize == 1) break; } lastrowsize = nQ_scf - (nrows - 1L) * rowsize; rowdims = new long int [nrows]; @@ -3192,7 +3190,6 @@ void DFCoupledCluster::T1Integrals(){ nrows++; rowsize = nQ / nrows; if (nrows * rowsize < nQ) rowsize++; - if (rowsize == 1) break; } long int lastrowsize = nQ - (nrows - 1L) * rowsize; long int * rowdims = new long int [nrows]; @@ -3435,11 +3432,7 @@ void DFCoupledCluster::AllocateMemory() { if (nQmax*v*v>dim) dim = nQmax*v*v; if (nQmax*nso*nso>dim) dim = nQmax*nso*nso; - long int tempvdim = o*o*v*v+o*v; - if ( nQ * o * v > tempvdim) tempvdim = nQ * o * v; - if ( nso * nso > tempvdim) tempvdim = nso * nso; - - double total_memory = dim+tempvdim+(o*(o+1)*v*(v+1)+o*v)+o*o*v*v+2.*o*v+2.*v*v; + double total_memory = dim+(o*o*v*v+o*v)+(o*(o+1)*v*(v+1)+o*v)+o*o*v*v+2.*o*v+2.*v*v; long int max = nvirt*nvirt*nQmax > (nfzv+ndocc+nvirt)*ndocc*nQmax ? nvirt*nvirt*nQmax : (nfzv+ndocc+nvirt)*ndocc*nQmax; double df_memory = nQ*(o*o+o*v)+max; @@ -3497,6 +3490,8 @@ void DFCoupledCluster::AllocateMemory() { integrals = (double*)malloc(dim*sizeof(double)); tempt = (double*)malloc((o*(o+1)*v*(v+1)+o*v)*sizeof(double)); + long int tempvdim = o*o*v*v+o*v; + if ( nQ * o * v > tempvdim) tempvdim = nQ * o * v; tempv = (double*)malloc(tempvdim*sizeof(double)); Abij = (double*)malloc(o*(o+1)/2*v*sizeof(double)); Sbij = (double*)malloc(o*(o+1)/2*v*sizeof(double)); debian/patches/series0000644000000000000000000000005012210161214012013 0ustar psi4rc-changes.patch #dfcc-bugfix.patch debian/TODO0000644000000000000000000000017112207724031007653 0ustar * Fix debian/copyright (or rather get upstream to add a copyright notices) * Enable MPI (apparently requires MADNESS) debian/changelog0000644000000000000000000000120512253142506011036 0ustar psi4 (4.0~beta5+dfsg-2) unstable; urgency=low * debian/rules (DEB_BUILD_MULTIARCH): New variable, populated from dpkg-architecture. * debian/rules (override_dh_auto_configure): Added --with-boost-libdir. * debian/rules (override_dh_auto_install): Split up into override_dh_auto_install-arch and override_dh_auto_install-indep (Closes: #732044). * debian/README.source: New file. -- Michael Banck Sat, 14 Dec 2013 20:00:46 +0100 psi4 (4.0~beta5+dfsg-1) unstable; urgency=low * Initial Upload of psi4, based on psi3 packaging. -- Michael Banck Sun, 03 Nov 2013 17:43:51 +0100 debian/compat0000644000000000000000000000000212202127603010357 0ustar 8 debian/copyright0000644000000000000000000001323412235475345011136 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: psi Source: http://sourceforge.net/projects/psicode/files/psi/ Files: * Copyright: 2013 PSI4 Developers License: GPL-2.0+ Files: boost/boost*.tar.gz Copyright: Boost Developers License: Boost Software License 1.0 Files: src/bin/psimrcc/* Copyright: 2007 Francesco Evangelista and Andrew Simmonett License: GPL-2.0+ Files: lib/python/pyparsing.py Copyright: 2003-20082003-2008 Paul McGuire License: MIT Files: lib/python/pep8.py Copyright: 2006 Johann Rocholl License: MIT Files: lib/python/grendel/util/containers.py Copyright: 2003 Josiah Carlson License: GPL-2.0 Files: doc/sphinxman/source/psi4_sptheme/themes/psi4/static/toggle_sections.js doc/sphinxman/source/psi4_sptheme/themes/psi4/static/toggle_sidebar.js_t doc/sphinxman/source/psi4_sptheme/themes/psi4/static/psi4.css_t Copyright: 2011 Assurance Technologies License: BSD Files: doc/sphinxman/source/psi4_sptheme/themes/psi4/static/jquery.cookie.js Copyright: 2010 Klaus Hartl License: MIT or GPL Files: debian/* Copyright: 2013 Michael Banck License: GPL-2.0+ License: GPL-2.0+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". License: Boost Software License 1.0 Permission is hereby granted, free of charge, to any person or organization obtaining a copy of the software and accompanying documentation covered by this license (the "Software") to use, reproduce, display, distribute, execute, and transmit the Software, and to prepare derivative works of the Software, and to permit third-parties to whom the Software is furnished to do so, all subject to the following: . The copyright notices in the Software and this entire statement, including the above license grant, this restriction and the following disclaimer, must be included in all copies of the Software, in whole or in part, and all derivative works of the Software, unless such copies or derivative works are solely in the form of machine-executable object code generated by a source language processor. . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. License: BSD Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. License: MIT Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.