commit 07b2b69f7638ffc36fa7f44d2f4854582318df9dc3df26b1b7173ef93b0e083a Author: Christoph Junghans Date: Wed Jun 5 17:01:20 2024 +0000 OBS-URL: https://build.opensuse.org/package/show/science/votca?expand=0&rev=26 diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..9b03811 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,23 @@ +## Default LFS +*.7z filter=lfs diff=lfs merge=lfs -text +*.bsp filter=lfs diff=lfs merge=lfs -text +*.bz2 filter=lfs diff=lfs merge=lfs -text +*.gem filter=lfs diff=lfs merge=lfs -text +*.gz filter=lfs diff=lfs merge=lfs -text +*.jar filter=lfs diff=lfs merge=lfs -text +*.lz filter=lfs diff=lfs merge=lfs -text +*.lzma filter=lfs diff=lfs merge=lfs -text +*.obscpio filter=lfs diff=lfs merge=lfs -text +*.oxt filter=lfs diff=lfs merge=lfs -text +*.pdf filter=lfs diff=lfs merge=lfs -text +*.png filter=lfs diff=lfs merge=lfs -text +*.rpm filter=lfs diff=lfs merge=lfs -text +*.tbz filter=lfs diff=lfs merge=lfs -text +*.tbz2 filter=lfs diff=lfs merge=lfs -text +*.tgz filter=lfs diff=lfs merge=lfs -text +*.ttf filter=lfs diff=lfs merge=lfs -text +*.txz filter=lfs diff=lfs merge=lfs -text +*.whl filter=lfs diff=lfs merge=lfs -text +*.xz filter=lfs diff=lfs merge=lfs -text +*.zip filter=lfs diff=lfs merge=lfs -text +*.zst filter=lfs diff=lfs merge=lfs -text diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..57affb6 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +.osc diff --git a/1032.patch b/1032.patch new file mode 100644 index 0000000..f8b53fc --- /dev/null +++ b/1032.patch @@ -0,0 +1,35 @@ +From 9a29a3a82ea23c5159d43b0f25218601e12085b4 Mon Sep 17 00:00:00 2001 +From: Michael Cho +Date: Thu, 25 Apr 2024 14:14:54 -0400 +Subject: [PATCH] Fix build with Boost 1.85.0 + +Signed-off-by: Michael Cho +--- + csg/src/libcsg/modules/io/pdbreader.cc | 1 - + xtp/src/libxtp/calculators/kmcmultiple.cc | 1 + + 2 files changed, 1 insertion(+), 1 deletion(-) + +diff --git a/csg/src/libcsg/modules/io/pdbreader.cc b/csg/src/libcsg/modules/io/pdbreader.cc +index 14b259ee8b..3686806e9d 100644 +--- a/csg/src/libcsg/modules/io/pdbreader.cc ++++ b/csg/src/libcsg/modules/io/pdbreader.cc +@@ -22,7 +22,6 @@ + + // Third party includes + #include +-#include + #include + + // VOTCA includes +diff --git a/xtp/src/libxtp/calculators/kmcmultiple.cc b/xtp/src/libxtp/calculators/kmcmultiple.cc +index 1627950277..fa515e78eb 100644 +--- a/xtp/src/libxtp/calculators/kmcmultiple.cc ++++ b/xtp/src/libxtp/calculators/kmcmultiple.cc +@@ -20,6 +20,7 @@ + + // Third party includes + #include ++#include + + // VOTCA includes + #include diff --git a/_constraints b/_constraints new file mode 100644 index 0000000..0075fab --- /dev/null +++ b/_constraints @@ -0,0 +1,12 @@ + + + + + 6 + + + 1000 + + + kvm + diff --git a/votca-2024.tar.gz b/votca-2024.tar.gz new file mode 100644 index 0000000..dc83fc0 --- /dev/null +++ b/votca-2024.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:be1f8ad3de2ce86f0c01014aa5358c181f128a847bc4508ba0a4bffd5c82a1cf +size 38976012 diff --git a/votca.changes b/votca.changes new file mode 100644 index 0000000..ad24d84 --- /dev/null +++ b/votca.changes @@ -0,0 +1,178 @@ +------------------------------------------------------------------- +Mon Jun 3 21:40:05 UTC 2024 - Christoph Junghans + +- Add upstream patch, 1032.patch, to fix build with newer boost + +------------------------------------------------------------------- +Wed Jan 31 20:58:32 UTC 2024 - Christoph Junghans + +- Drop python3-espressomd testing dependency, revert once + gh#espressomd/espresso#4856 is fixed. + +------------------------------------------------------------------- +Thu Jan 25 14:33:26 UTC 2024 - Christoph Junghans + +- Dropped 1093.patch, merged upstream + - fix links in README and doc ([gh#votca/votca#1091]) + - fix python shebang to python3 ([gh#votca/votca#1093]) + - Clean-up CI ([gh#votca/votca#1092], [gh#votca/votca#1095]) + - remove reference to old webpage ([gh#votca/votca#1094]) + - fix doc generation without pyxtp ([gh#votca/votca#1097]) + - Do not run gmx tests without libgromacs ([gh#votca/votca#1099]) + - KS-QMMM for single-particle states ([gh#votca/votca#1100]) + - Spin-orbitals from ORCA in QMMM ([gh#votca/votca#1101]) + - better unit test for DFT embedding ([gh#votca/votca#1102]) +- Update to 2024 + +------------------------------------------------------------------- +Thu Nov 16 04:24:41 UTC 2023 - Christoph Junghans + +- Drop 1083.patch - merged upstream +- Add 1093.patch from upstream to fix python shebang +- Update to 2023 + - fix pyxtp option restart ([gh#votca/votca#1074]) + - fix Changelog check ([gh#votca/votca#1070]) + - add python bindings for xtp ([gh#votca/votca#1061]) + - replaced pointers in MD2QM mapping ([gh#votca/votca#1075]) + - fixed typo in esp2multipole option ([gh#votca/votca#1076]) + - update MKL detection to MKL config ([gh#votca/votca#1053]) + - remove geometry optimization ([gh#votca/votca#1077]) + - remove all references to old pdf manual ([gh#votca/votca#1081]) + - replaced deprecated boost::progress headers ([gh#votca/votca#1083]) + - drop intel classic builds from CI ([gh#votca/votca#1085]) + - disable some libint2 warning and CI clean up ([gh#votca/votca#1088]) + - fix population analysis for embedded DFT ([gh#votca/votca#1089]) + - fix pyxtp xtp-tutorials ([gh#votca/votca#1090]) + - add note on gmx build for install ([gh#votca/votca#1052]) + - fix typos in esp2multipole options ([gh#votca/votca#1054]) + - Used sharedable lock in xtp ([gh#votca/votca#1057]) + - Make votca tests compile without OpenMP ([gh#votca/votca#1065]) + - increase tolerance for diabatization test ([gh#votca/votca#1039], + [gh#votca/votca#1043]) + - removed boost::filesystem ([gh#votca/votca#1041]) + - clean up C++ defines ([gh#votca/votca#1044]) + - drop gmx-2022 builds from CI ([gh#votca/votca#1046]) + - update ccaching in CI ([gh#votca/votca#1048], [gh#votca/votca#1050]) + - add support for gmx-2023 api ([gh#votca/votca#1059]) + - updated formatting ([gh#votca/votca#1062]) + - remove stable branch workflow ([gh#votca/votca#1066]) + - Refactor changelog actions ([gh#votca/votca#1068]) + - fix CI build with icpx ([gh#votca/votca#1018]) + - implemented projection-based DFT embedding ([gh#votca/votca#964]) + - Added LMO energy output and cube file generation ([gh#votca/votca#970]) + - fix typos in csg-tutorials xml files ([gh#votca/votca#980]) + - unitary optimization for localization of orbitals ([gh#votca/votca#971]) + - separate option for density max convergence tolerance in qmmm + ([gh#votca/votca#987]) + - Correct ECP charges added in Orca Molden reader ([gh#votca/votca#990]) + - Implemented truncated basis for embedded DFT ([gh#votca/votca#991]) + - Implemented ER diabatization for BSE ([gh#votca/votca#988]) + - update esp++ spce tutorial to py3 ([gh#votca/votca#997]) + - Truncated GW-in-DFT embedded in static/polar MM implemeted + ([gh#votca/votca#1003]) + - reducing XTP tutorial size ([gh#votca/votca#1020], [gh#votca/votca#1025]) + - Clean up 3body Stillinger-Weber implement, docs and tutorial + ([gh#votca/votca#1012]) + - fixed options handling in xtp_autogen_mapping ([gh#votca/votca#1024]) + - Major CMake refactor ([gh#votca/votca#950], [gh#votca/votca#1022]) + - Fix all doxygen warnings ([gh#votca/votca#1026]) + - basis and auxbasis are written to QMMM checkpoint file + ([gh#votca/votca#1030]) + - iterations_max can now be zero ([gh#votca/votca#1033]) + - add an XML check to csg_inverse ([gh#votca/votca#1031]) + - fix propane/imc and add propane/imc-ibiintra to csg-tutorials + ([gh#votca/votca#821]) + +------------------------------------------------------------------- +Mon Nov 13 23:26:43 UTC 2023 - Christoph Junghans + +- Add 1083.patch to fix build with boost-1.82 + +------------------------------------------------------------------- +Mon Jan 2 15:23:48 UTC 2023 - Christoph Junghans + +- don't use mpi gromacs on ix86 + +------------------------------------------------------------------- +Wed Dec 21 22:25:15 UTC 2022 - Christoph Junghans + +- Update to 2022.1 + - fix PROJECT_VERSION in subdirs ([gh#votca/votca#951]) + - make csg_resample and csg_stat spacing consistent + ([gh#votca/votca#956]) + - fix build on FreeBSD ([gh#votca/votca#959]) + - update CI container names ([gh#votca/votca#961]) + - Fix gw quadrature scheme ([gh#votca/votca#967]) + - update install guide for spack ([gh#votca/votca#972], + [gh#votca/votca#974]) + - drop gmx-2021 builds from CI ([gh#votca/votca#976]) + - update syntax for cmake 3.23 ([gh#votca/votca#978]) + - fix CI build on Ubuntu ([gh#votca/votca#981]) + - fix CI builds with icpx ([gh#votca/votca#984], + [gh#votca/votca#1004]) + - fix CI builds with ESPResSo 4.2.0 ([gh#votca/votca#993]) + - fix localization issue ([gh#votca/votca#998], + [gh#votca/votca#1000]) + - update github actions to new versions ([gh#votca/votca#1007], + [gh#votca/votca#1013]) + +------------------------------------------------------------------- +Thu Dec 15 11:49:02 UTC 2022 - Guillaume GARDET + +- Disable gromacs on 32-bit arm since it is missing +- Do not requires libint when xtp is disabled + +------------------------------------------------------------------- +Wed Dec 7 06:21:38 UTC 2022 - Stefan Brüns + +- Adjust constraints to avoid rejecting too many workers, enable + parallel builds with limit_build. +- Clean up specfile, remove obsolete __DATE__ mangling. + +------------------------------------------------------------------- +Fri Jul 29 05:23:54 UTC 2022 - Christoph Junghans + +- only use python3-epressomd for testing on x86_64 + +------------------------------------------------------------------- +Sun Jan 16 01:10:58 UTC 2022 - Christoph Junghans + +- Update to 2022 + - fix some icpc warnings ([gh#votca/votca#934]) + - only check for pytest if testing is enabled + ([gh#votca/votca#930]) + - exclude some builds from CI ([gh#votca/votca#940], + [gh#votca/votca#942], [gh#votca/votca#944], + [gh#votca/votca#945]) + - update interface documentation ([gh#votca/votca#939]) + - update install guide for binary packages + ([gh#votca/votca#936]) + - fixed sigma plot options passing ([gh#votca/votca#943]) + +------------------------------------------------------------------- +Sun Dec 19 22:37:10 UTC 2021 - Christoph Junghans + +- Also obsoletes votca-csg-apps + +------------------------------------------------------------------- +Thu Dec 16 03:53:04 UTC 2021 - Christoph Junghans + +- Update to 2022-rc.2 + - fix iqm merge orbitals command ([gh#votca/votca#907]) + - fix bug in basisset serialization that caused wrong Vxc values + in GW ([gh#votca/votca#910]) + - update performance compilation info ([gh#votca/votca#911]) + - license for monorepo and all license files rst -> plain text + ([gh#votca/votca#912], [gh#votca/votca#913]) + - use python3 in xtp-tutorials ([gh#votca/votca#917]) + - bump required boost version to 1.71 ([gh#votca/votca#915], + [gh#votca/votca#916]) + - clean up NOTICE files ([gh#votca/votca#919]) + - rm PYTHON_INSTDIR from VOTCARC ([gh#votca/votca#924]) + - update citation in xtp README ([gh#votca/votca#925]) + - fix install permission of tutorials ([gh#votca/votca#926])- + +------------------------------------------------------------------- +Mon Dec 6 11:27:23 UTC 2021 - Christoph Junghans + +- Merge votca-{tools,csg,xtp} into one package diff --git a/votca.spec b/votca.spec new file mode 100644 index 0000000..0e4ff73 --- /dev/null +++ b/votca.spec @@ -0,0 +1,243 @@ +# +# spec file for package votca +# +# Copyright (c) 2022 SUSE LLC +# Copyright (c) 2021-2022 Christoph Junghans +# +# All modifications and additions to the file contributed by third parties +# remain the property of their copyright owners, unless otherwise agreed +# upon. The license for this file, and modifications and additions to the +# file, is the same license as for the pristine package itself (unless the +# license for the pristine package is not an Open Source License, in which +# case the license is the MIT License). An "Open Source License" is a +# license that conforms to the Open Source Definition (Version 1.9) +# published by the Open Source Initiative. + +# Please submit bugfixes or comments via https://bugs.opensuse.org/ +# + +%global with_xtp 1 +# libint2 used by xtp is broken on 32-bit archs +# https://github.com/evaleev/libint/issues/196 +# https://github.com/votca/xtp/issues/652 +%ifarch %ix86 %arm +%global with_xtp 0 +%endif + +Name: votca +Version: 2024 +Release: 0 +%define uversion %{version} +%define sover 2024 +Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications +License: Apache-2.0 +Group: Productivity/Scientific/Chemistry +URL: https://www.votca.org +Source0: https://github.com/votca/votca/archive/v%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz +# PATCH-FIX-UPSTREAM 1032.patch -- fix build with newer boost votca/votca#1032 +Patch0: 1032.patch + +BuildRequires: cmake >= 3.13 +BuildRequires: eigen3-devel +BuildRequires: fdupes +BuildRequires: fftw3-devel +BuildRequires: gcc-c++ +BuildRequires: gnuplot +# gromacs is not available on 32-bit arm +%ifnarch %{arm} +BuildRequires: gromacs-devel +# mpi gromacs is not available on 32-bit intel +# used for testing only +%ifnarch %ix86 +BuildRequires: gromacs-openmpi +%endif +%endif +BuildRequires: hdf5-devel +BuildRequires: lammps +BuildRequires: libboost_filesystem-devel >= 1.71.0 +BuildRequires: libboost_program_options-devel >= 1.71.0 +BuildRequires: libboost_regex-devel >= 1.71.0 +BuildRequires: libboost_serialization-devel >= 1.71.0 +BuildRequires: libboost_system-devel >= 1.71.0 +BuildRequires: libboost_test-devel >= 1.71.0 +BuildRequires: libboost_timer-devel >= 1.71.0 +BuildRequires: libecpint-devel +BuildRequires: libexpat-devel +%if %{with_xtp} +BuildRequires: libint-devel +%endif +BuildRequires: libxc-devel +BuildRequires: memory-constraints +BuildRequires: openmpi-macros-devel +BuildRequires: pkg-config +BuildRequires: procps +BuildRequires: psmisc +BuildRequires: python3-cma +# only needed for testing +BuildRequires: python3-lxml +BuildRequires: python3-pytest +# for hdf5 +BuildRequires: zlib-devel + +Obsoletes: votca-tools <= 2022~rc1 +Provides: votca-tools = %version-%release +Obsoletes: votca-csg <= 2022~rc1 +Provides: votca-csg = %version-%release +Obsoletes: votca-csg-apps <= 2022~rc1 +Provides: votca-csg-apps = %version-%release +Obsoletes: votca-xtp <= 2022~rc1 +Provides: votca-xtp = %version-%release + +%global votca_desc \ +VOTCA is a software package which focuses on the analysis of molecular \ +dynamics data, the development of systematic coarse-graining techniques as \ +well as methods used for simulating microscopic charge (and exciton) transport \ +in disordered semiconductors. + +%description +%{votca_desc} + +%package -n libvotca%sover +Summary: VOTCA tools library +Group: System/Libraries +Obsoletes: libvotca_tools2022 <= 2022~rc1 +Provides: libvotca_tools2022 = %version-%release +Obsoletes: libvotca_csg2022 <= 2022~rc1 +Provides: libvotca_csg2022 = %version-%release +Obsoletes: libvotca_xtp2022 <= 2022~rc1 +Provides: libvotca_xtp2022 = %version-%release + +%description -n libvotca%sover +%{votca_desc} + +This package contains the librares of VOTCA package. + +%package devel +Summary: Development headers and libraries for votca +Group: Development/Libraries/C and C++ +Requires: %{name} = %{version} +Requires: eigen3-devel +Requires: fftw3-devel +Requires: libexpat-devel +Requires: libvotca%sover = %{version} +Obsoletes: votca-tools-devel <= 2022~rc1 +Provides: votca-tools-devel = %version-%release +Obsoletes: votca-csg-devel <= 2022~rc1 +Provides: votca-csg-devel = %version-%release +Obsoletes: votca-xtp-devel <= 2022~rc1 +Provides: votca-xtp-devel = %version-%release + +%description devel +%{votca_desc} + +This package contains development headers and libraries for votca. + +%package common +Summary: Architecture-independent data files for VOTCA +Group: Productivity/Scientific/Chemistry +BuildArch: noarch +Requires: /usr/bin/awk +Requires: bash +Requires: perl +Obsoletes: votca-csg-common <= 2022~rc1 +Provides: votca-csg-common = %version-%release +Obsoletes: votca-xtp-common <= 2022~rc1 +Provides: votca-xtp-common = %version-%release + +%description common +%{votca_desc} + +This package contains the architecture-independent data files for VOTCA. + +%package tutorials +Summary: Tutorial documentation for VOTCA Coarse Graining Engine +Group: Productivity/Scientific/Chemistry +BuildArch: noarch +Requires: /bin/bash +Obsoletes: votca-csg-tutorials <= 2022~rc1 +Provides: votca-csg-tutorials = %version-%release + +%description tutorials +%{votca_desc} + +This package contains the tutorial documentation and sample data. + +%package bash +Summary: Bash completion for votca +Group: System/Shells +Requires: %{name} = %{version} +Requires: bash-completion +BuildArch: noarch +Obsoletes: votca-csg-bash <= 2022~rc1 +Provides: votca-csg-bash = %version-%release + +%description bash +%{votca_desc} + +This package contains the bash completion support for votca. + +%prep +%autosetup -p1 -n %{name}-%{uversion} + +%build +%setup_openmpi + +# save some memory +%limit_build -m 2400 +%{cmake} -DINSTALL_RC_FILES=OFF -DCMAKE_SKIP_RPATH=OFF -DENABLE_TESTING=ON -DENABLE_REGRESSION_TESTING=ON \ + -DINJECT_MARCH_NATIVE=OFF -DBUILD_CSGAPPS=ON \ + -DBUILD_XTP=%{with_xtp} \ + .. +%cmake_build + +%install +%cmake_install +sed -i '1s@env @@' \ + %{buildroot}/%{_datadir}/votca/scripts/inverse/{iie,cma_processor,table_smooth_at_cut_off}.py \ + %{buildroot}/%{_datadir}/votca/csg-tutorials/LJ1-LJ2/imc/svd.py \ + %{buildroot}/%{_datadir}/votca/csg-tutorials/spce/ibi*/spce.py + +%if %{with_xtp} +sed -i '1s@env @@' %{buildroot}/%{_bindir}/xtp_* %{buildroot}/%{_datadir}/votca/xtp/benchmark/xtp_benchmark +%endif + +# Move bash completion file to correct location +mkdir -p %{buildroot}%{_datadir}/bash_completion.d +cp %{__builddir}/csg/scripts/csg-completion.bash %{buildroot}%{_datadir}/bash_completion.d/votca + +%fdupes %{buildroot}%{_prefix} + +%check +%setup_openmpi +%ctest + +%files +%{_bindir}/{votca,csg,xtp}_* +%{_mandir}/man1/* +%{_mandir}/man7/* + +%post -n libvotca%sover -p /sbin/ldconfig +%postun -n libvotca%sover -p /sbin/ldconfig + +%files -n libvotca%sover +%doc NOTICE.rst README.rst CHANGELOG.rst +%license LICENSE +%{_libdir}/libvotca_*.so.%{sover} + +%files devel +%{_includedir}/votca/ +%{_libdir}/libvotca_*.so +%{_libdir}/cmake/VOTCA_* + +%files tutorials +%{_datadir}/votca/{csg,xtp}-tutorials + +%files common +%{_datadir}/votca +%exclude %{_datadir}/votca/{csg,xtp}-tutorials + +%files bash +%dir %{_datadir}/bash_completion.d +%{_datadir}/bash_completion.d/votca + +%changelog