debian/0000755000000000000000000000000012256016257007174 5ustar debian/rules0000755000000000000000000000151312255670047010256 0ustar #!/usr/bin/make -f # -*- makefile -*- #export DH_VERBOSE=1 export CC=mpicxx export BOOST_TOP_DIR=/usr/ export BOOST_INC_DIR=/usr/include/mpi export OPENBLAS_TOP_DIR=/usr/lib/openblas-base/ export OPENBLAS_LIB_DIR=/usr/lib/openblas-base export LIBSBASE=-lstdc++ -lm -lpthread -lgomp -L/usr/lib/lapack/ -llapacke -lmpi -lmpi_cxx export OMPI_MCA_orte_rsh_agent=/bin/false COMPILER_FLAGS = -g -Wall -fopenmp ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) COMPILER_FLAGS += -O0 else COMPILER_FLAGS += -O2 endif export CFLAGS=$(COMPILER_FLAGS) %: dh $@ override_dh_auto_clean: (cd src; make -f Makefile_GNU clean) rm -f test/temp.dat override_dh_auto_build: (cd src; make -f Makefile_GNU) ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) override_dh_auto_test: (cd test; ruby Test_Of_MolDS.rb 2>&1 | grep -v Detect.OpenMP.Loop) endif debian/source/0000755000000000000000000000000012111654751010471 5ustar debian/source/format0000644000000000000000000000001412111654751011677 0ustar 3.0 (quilt) debian/watch0000644000000000000000000000131712207721150010216 0ustar version=3 http://de.sourceforge.jp/projects/molds/scm/svn/tags/ .*/tags/([\d.]+)/$ #opts=downloadurlmangle=s#.*?/tags/([\d.]+)/$#http://de.sourceforge.jp/projects/molds/scm/svn/archive/head/tags/$1/?format=tar.gz#g \ # http://de.sourceforge.jp/projects/molds/scm/svn/tags/ .*/tags/([\d.]+)/$ # filenamemangle=s#.*?/tags/([\d.]+)#molds-$1.tar.gz#g # /projects/molds/scm/svn/archive/head/tags/0.2.0/?format=tar.gz # /projects/molds/scm/svn/tree/head/tags/0.2.0/ # http://de.sourceforge.jp/downloads/scmarchive/g/molds/svn/1136aad2-a195-0410-b898-f5ea1d11b9d8/molds-tags_0.1.0-r1361.tar.gz/ # http://de.sourceforge.jp/downloads/scmarchive/g/molds/svn/1136aad2-a195-0410-b898-f5ea1d11b9d8/molds-tags_0.2.0-r1361.tar.gz/ debian/control0000644000000000000000000000250012255702454010574 0ustar Source: molds Section: science Priority: optional Maintainer: Debichem Team Uploaders: Michael Banck Build-Depends: debhelper (>= 7.0.50~), ruby, gawk, libopenblas-dev, liblapacke-dev, libblas-dev, libboost-dev, libboost-mpi-dev, libboost-serialization-dev, libboost-thread-dev, mpi-default-bin, mpi-default-dev Standards-Version: 3.9.2 Homepage: http://en.sourceforge.jp/projects/molds/ Vcs-Browser: http://svn.debian.org/wsvn/debichem/unstable/molds/ Vcs-Svn: svn://svn.debian.org/svn/debichem/unstable/molds/ DM-Upload-Allowed: yes Package: molds Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: Semi-empirical electronic structure and molecular dynamics MolDS is a semi-empirical electronic structure and molecular dynamics package. . Features includes: . * Semi-Empirical methods CNDO2, INDO, ZINDO/S, MNDO, AM1 and PM3 * Excited States via Single Configuration Interaction (CIS) * Dispersion corrections to AM1 (AM1-D) and PM3 (PM3-D) * Pairwise Distance Directed Gaussian (PDDG) correction to PM3 (PM3/PDDG) * Single-Point, geometry optimization, Molecular Dynamics (MD), Monte-Carlo (MC) and Polymer Molecular Dynamics (RPMD) type of calculations . MolDS currently ships parameters for the elements H, C, N, O, and S. debian/molds.examples0000644000000000000000000000003112255636550012047 0ustar test/ch4_*in test/h2*in debian/molds.links0000644000000000000000000000004212255616511011346 0ustar /usr/bin/molds /usr/bin/MolDS.out debian/molds.docs0000644000000000000000000000001712111654751011157 0ustar doc/README.txt debian/molds.install0000644000000000000000000000002312255616352011676 0ustar src/molds /usr/bin debian/patches/0000755000000000000000000000000012255677641010634 5ustar debian/patches/testsuite_output.patch0000644000000000000000000000227712255672061015325 0ustar --- ./test/Test_Of_MolDS.rb.orig 2013-12-23 00:14:19.200570381 +0100 +++ ./test/Test_Of_MolDS.rb 2013-12-23 00:21:52.762932847 +0100 @@ -45,7 +45,7 @@ @@command = "command: " @@mpiCommand = "mpirun -np " @@mpiProcesses = "2" - @@deleteDiff = " | gawk '{if(($2!=\"SCF\")&&($3!=\"iter\")){print $0}}' | gawk '{if(($4!=\"time:\")){print $0}}' | gawk '{if(($3!=\"Elapsed\")){print $0}}' | gawk '{if(($2!=\"Elapsed\")){print $0}}' | gawk '{if(($3!=\"Welcome\")){print $0}}' | gawk '{if(($7!=\"residual\")){print $0}}' | gawk '{if(($3!=\"mode(nmw):\") ){print $0}}' | gawk '{if( !(($3==\"mode(mw):\")&&($4<6)) ){print $0}}'" + @@deleteDiff = " | gawk '{if(($2!=\"SCF\")&&($3!=\"iter\")){print $0}}' | gawk '{if(($4!=\"time:\")){print $0}}' | gawk '{if(($3!=\"Elapsed\")){print $0}}' | gawk '{if(($2!=\"Elapsed\")){print $0}}' | gawk '{if(($3!=\"Welcome\")){print $0}}' | gawk '{if(($7!=\"residual\")){print $0}}' | gawk '{if(($3!=\"mode(nmw):\") ){print $0}}' | gawk '{if( !(($3==\"mode(mw):\")&&($4<6)) ){print $0}}' | gawk '{if(($3!=\"Heap:\")){print $0}}' | egrep -v ^[-+]{3} | egrep ^[-+]" @@printed_section = [] def doesTestOmp(mklNumThreads, ompNumThreads) return unless should_run? debian/patches/makefile_flags.patch0000644000000000000000000001006212255630502014566 0ustar --- ./src/Makefile_GNU.orig 2013-12-22 14:32:11.566642452 +0100 +++ ./src/Makefile_GNU 2013-12-22 14:32:42.286802463 +0100 @@ -17,22 +17,22 @@ #// You should have received a copy of the GNU General Public License // #// along with MolDS. If not, see . // #//************************************************************************// -CC = mpicxx -CFLAGS = -O2 +CC ?= mpicxx +CFLAGS ?= -O2 override CFLAGS += -fopenmp -BOOST_TOP_DIR = /usr/local/boost/ -BOOST_INC_DIR = $(BOOST_TOP_DIR)/include/ -BOOST_LIB_DIR = $(BOOST_TOP_DIR)/lib/ -BOOST_LIBS = -lboost_serialization -lboost_mpi -lboost_thread -OPENBLAS_TOP_DIR = /usr/local/openblas/ -OPENBLAS_INC_DIR = $(OPENBLAS_TOP_DIR)/include/ -OPENBLAS_LIB_DIR = $(OPENBLAS_TOP_DIR)/lib/ -OPENBLAS_LIBS = -lopenblas -LIBSBASE = -lpthread -lgomp -LIBS = $(LIBSBASE) $(BOOST_LIBS) $(OPENBLAS_LIBS) -EXENAME = molds -DEPFILE = obj/objfile.dep -LDFLAGS = -Wl,-rpath=$(BOOST_LIB_DIR) -Wl,-rpath=$(OPENBLAS_LIB_DIR) +BOOST_TOP_DIR ?= /usr/local/boost/ +BOOST_INC_DIR ?= $(BOOST_TOP_DIR)/include/ +BOOST_LIB_DIR ?= $(BOOST_TOP_DIR)/lib/ +BOOST_LIBS ?= -lboost_serialization -lboost_mpi -lboost_thread -lboost_system +OPENBLAS_TOP_DIR ?= /usr/local/openblas/ +OPENBLAS_INC_DIR ?= $(OPENBLAS_TOP_DIR)/include/ +OPENBLAS_LIB_DIR ?= $(OPENBLAS_TOP_DIR)/lib/ +OPENBLAS_LIBS ?= -lopenblas +LIBSBASE ?= -lpthread -lgomp +LIBS ?= $(LIBSBASE) $(BOOST_LIBS) $(OPENBLAS_LIBS) +EXENAME ?= molds +DEPFILE ?= obj/objfile.dep +LDFLAGS ?= -Wl,-rpath=$(BOOST_LIB_DIR) -Wl,-rpath=$(OPENBLAS_LIB_DIR) ALL_CPP_FILES = base/Enums.cpp base/PrintController.cpp base/MolDSException.cpp base/MallocerFreer.cpp mpi/MpiProcess.cpp mpi/AsyncCommunicator.cpp wrappers/Blas.cpp wrappers/Lapack.cpp base/Utilities.cpp base/MathUtilities.cpp base/EularAngle.cpp base/Parameters.cpp base/atoms/Atom.cpp base/atoms/Hatom.cpp base/atoms/Liatom.cpp base/atoms/Catom.cpp base/atoms/Natom.cpp base/atoms/Oatom.cpp base/atoms/Satom.cpp base/atoms/mm/EnvironmentalPointCharge.cpp base/factories/AtomFactory.cpp base/Molecule.cpp base/InputParser.cpp base/GTOExpansionSTO.cpp base/RealSphericalHarmonicsIndex.cpp base/loggers/MOLogger.cpp base/loggers/DensityLogger.cpp base/loggers/HoleDensityLogger.cpp base/loggers/ParticleDensityLogger.cpp cndo/Cndo2.cpp indo/Indo.cpp zindo/ZindoS.cpp mndo/Mndo.cpp am1/Am1.cpp am1/Am1D.cpp pm3/Pm3.cpp pm3/Pm3D.cpp pm3/Pm3Pddg.cpp base/factories/ElectronicStructureFactory.cpp md/MD.cpp mc/MC.cpp rpmd/RPMD.cpp nasco/NASCO.cpp optimization/Optimizer.cpp optimization/ConjugateGradient.cpp optimization/SteepestDescent.cpp optimization/BFGS.cpp optimization/GEDIIS.cpp base/factories/OptimizerFactory.cpp base/MolDS.cpp Main.cpp ALL_HEAD_FILES = config.h base/Enums.h base/Uncopyable.h base/PrintController.h base/MolDSException.h base/containers/ThreadSafeQueue.h base/MallocerFreer.h mpi/MpiInt.h mpi/MpiProcess.h mpi/AsyncCommunicator.h wrappers/Blas.h wrappers/Lapack.h base/Utilities.h base/MathUtilities.h base/EularAngle.h base/Parameters.h base/atoms/Atom.h base/atoms/Hatom.h base/atoms/Liatom.h base/atoms/Catom.h base/atoms/Natom.h base/atoms/Oatom.h base/atoms/Satom.h base/atoms/mm/EnvironmentalPointCharge.h base/factories/AtomFactory.h base/Molecule.h base/InputParser.h base/GTOExpansionSTO.h base/RealSphericalHarmonicsIndex.h base/loggers/MOLogger.h base/loggers/DensityLogger.h base/loggers/HoleDensityLogger.h base/loggers/ParticleDensityLogger.h base/ElectronicStructure.h cndo/Cndo2.h cndo/ReducedOverlapAOsParameters.h indo/Indo.h zindo/ZindoS.h mndo/Mndo.h am1/Am1.h am1/Am1D.h pm3/Pm3.h pm3/Pm3D.h pm3/Pm3Pddg.h base/factories/ElectronicStructureFactory.h md/MD.h mc/MC.h rpmd/RPMD.h nasco/NASCO.h optimization/Optimizer.h optimization/ConjugateGradient.h optimization/SteepestDescent.h optimization/BFGS.h optimization/GEDIIS.h base/factories/OptimizerFactory.h base/MolDS.h debian/patches/series0000644000000000000000000000005412255672103012034 0ustar makefile_flags.patch testsuite_output.patch debian/changelog0000644000000000000000000000517012256006074011045 0ustar molds (0.3.0-3) unstable; urgency=low * debian/control (Build-Depends): Added mpi-default-bin. -- Michael Banck Mon, 23 Dec 2013 11:10:57 +0100 molds (0.3.0-2) unstable; urgency=low * debian/rules (CC): Reintroduced as mpicxx. * debian/rules (override_dh_auto_test): Filter out warnings from OpenBLAS rather than redirecting stderr to /dev/null. * debian/patches/testsuite_output.patch: New patch, removes spurious "Max Heap:" differences from output diffing. -- Michael Banck Mon, 23 Dec 2013 00:24:40 +0100 molds (0.3.0-1) unstable; urgency=low * New upstream release (upstream tarball based on subversion revision 1586). New features include: - Hybrid MPI/OpenMP parallelization. - GEDIIS algorithm added for geometry optimizations - Mulliken population in excited states - Unpaired electron population * debian/patches/makefile_flags.patch: Updated. * debian/control (Build-Depends): Added mpi-default-dev. * debian/rules (CC): Removed. * debian/control (Build-Depends): Added libboost-mpi-dev, libboost-serialization-dev and libboost-thread-dev. * debian/rules (override_dh_auto_build): Do not run depend target explicitly. * debian/rules (LIBS): Renamed to ... * debian/rules (LIBSBASE): ... this. * debian/rules (LIBSBASE): Added -lstdc++, -lm, -lmpi and -lmpi_cxx. * debian/patches/lapacke_rpath.patch: Removed. * debian/molds.install: Updated to renamed filename. * debian/molds.links: New file, ship a compatibility symlink for the renamed MolDS.out executable. * debian/rules (override_dh_auto_clean): Remove test/temp.dat, if present. * debian/rules (OMPI_MCA_orte_rsh_agent): New variable. * debian/patches/makefile_flags.patch: Added -lboost_system to BOOST_LIBS variable. * debian/rules (override_dh_auto_test): Teporarily redirect stderr to /dev/null to avoid very large amounts (> 1 million) of warnings from OpenBLAS (see #684344). * debian/molds.examples: New file, adding some test cases as exapmles. -- Michael Banck Sun, 22 Dec 2013 20:30:51 +0100 molds (0.2.0-1) unstable; urgency=low * New upstream relesae (upstream tarball based on subversion revision 1157). * debian/patches/makefile_flags.patch: Updated. * debian/patches/lapacke_rpath.patch: Updated. * debian/control (Build-Depends): Added libblas-dev. * debian/rules (LIBS): New variable. -- Michael Banck Sat, 29 Dec 2012 19:52:03 +0100 molds (0.0~20120819-1) unstable; urgency=low * Initial release (Closes: #685316). -- Michael Banck Sun, 19 Aug 2012 15:54:52 +0200 debian/compat0000644000000000000000000000000212111654751010367 0ustar 7 debian/molds.lintian-overrides0000644000000000000000000000020512111654751013664 0ustar # Required until liblapacke package is fixed (#685312), unless we want to ship a wrapper script molds: binary-or-shlib-defines-rpath debian/copyright0000644000000000000000000000435012111654751011126 0ustar This work was packaged for Debian by: Michael Banck on Sun, 19 Aug 2012 15:54:52 +0200 It was downloaded from: http://en.sourceforge.jp/projects/molds/ Upstream Author: Mikiya Fujii, Katsuhiko Nishimra Copyright: Copyright (C) 2011-2012 Mikiya Fujii Copyright (C) 2012-2012 Katsuhiko Nishimra License: This program 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 3 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 3 can be found in "/usr/share/common-licenses/GPL-3". src/third_parties/rEnumStr/rEnumStr.h Copyright: Copyright (C) 2004 rage2050 src/third_parties/rEnumStr/rEnumStr.h License: This program 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". The Debian packaging is: Copyright (C) 2012 Michael Banck and is licensed under the same GNU General Public License version 3 license as the upstream source.