SHA256
1
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forked from pool/votca
Christoph Junghans 2024-06-05 17:01:20 +00:00 committed by Git OBS Bridge
commit 07b2b69f76
7 changed files with 495 additions and 0 deletions

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## 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

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.osc

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1032.patch Normal file
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From 9a29a3a82ea23c5159d43b0f25218601e12085b4 Mon Sep 17 00:00:00 2001
From: Michael Cho <michael@michaelcho.dev>
Date: Thu, 25 Apr 2024 14:14:54 -0400
Subject: [PATCH] Fix build with Boost 1.85.0
Signed-off-by: Michael Cho <michael@michaelcho.dev>
---
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 <boost/algorithm/string.hpp>
-#include <boost/filesystem/convenience.hpp>
#include <boost/lexical_cast.hpp>
// 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 <boost/format.hpp>
+#include <boost/numeric/conversion/cast.hpp>
// VOTCA includes
#include <votca/tools/constants.h>

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<?xml version="1.0" encoding="UTF-8"?>
<constraints>
<hardware>
<memory>
<size unit="G">6</size>
</memory>
<memoryperjob>
<size unit="M">1000</size>
</memoryperjob>
</hardware>
<sandbox>kvm</sandbox>
</constraints>

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version https://git-lfs.github.com/spec/v1
oid sha256:be1f8ad3de2ce86f0c01014aa5358c181f128a847bc4508ba0a4bffd5c82a1cf
size 38976012

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-------------------------------------------------------------------
Mon Jun 3 21:40:05 UTC 2024 - Christoph Junghans <junghans@votca.org>
- Add upstream patch, 1032.patch, to fix build with newer boost
-------------------------------------------------------------------
Wed Jan 31 20:58:32 UTC 2024 - Christoph Junghans <junghans@votca.org>
- Drop python3-espressomd testing dependency, revert once
gh#espressomd/espresso#4856 is fixed.
-------------------------------------------------------------------
Thu Jan 25 14:33:26 UTC 2024 - Christoph Junghans <junghans@votca.org>
- 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 <junghans@votca.org>
- 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 <junghans@votca.org>
- Add 1083.patch to fix build with boost-1.82
-------------------------------------------------------------------
Mon Jan 2 15:23:48 UTC 2023 - Christoph Junghans <junghans@votca.org>
- don't use mpi gromacs on ix86
-------------------------------------------------------------------
Wed Dec 21 22:25:15 UTC 2022 - Christoph Junghans <junghans@votca.org>
- 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 <guillaume.gardet@opensuse.org>
- 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 <stefan.bruens@rwth-aachen.de>
- 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 <junghans@votca.org>
- only use python3-epressomd for testing on x86_64
-------------------------------------------------------------------
Sun Jan 16 01:10:58 UTC 2022 - Christoph Junghans <junghans@votca.org>
- 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 <junghans@votca.org>
- Also obsoletes votca-csg-apps
-------------------------------------------------------------------
Thu Dec 16 03:53:04 UTC 2021 - Christoph Junghans <junghans@votca.org>
- 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 <junghans@votca.org>
- Merge votca-{tools,csg,xtp} into one package

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votca.spec Normal file
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#
# 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