automatic import of lammps

3 files changed, 385 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..bfe5fc0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1,5 @@
+/googletest-1.12.1.tar.gz
+/lammps-patch_19Nov2024.tar.gz
+/opencl-loader-2024.05.09.tar.gz
+/spglib-1.11.2.1.tar.gz
+/yaml-0.2.5.tar.gz
diff --git a/lammps.spec b/lammps.spec
new file mode 100644
index 0000000..ec2f41a
--- /dev/null
+++ b/lammps.spec
@@ -0,0 +1,375 @@
+%global git 0
+%global commit 570c9d190fee556c62e5bd0a9c6797c4dffcc271
+%global shortcommit %(c=%{commit}; echo ${c:0:7})
+
+%global blaslib openblas
+%global blasvar o
+%global cmake_blas_flags -DBLAS_LIBRARIES=%{_libdir}/lib%{blaslib}%{blasvar}.so -DLAPACK_LIBRARIES=%{_libdir}/lib%{blaslib}%{blasvar}.so
+
+Name:           lammps
+%if %{git}
+Version:        20241119^%{shortcommit}
+%else
+Version:        20241119
+%endif
+%global         uversion %(v=%{version}; \
+                  patch=${v##*.}; [[ $v = $patch ]] && patch= \
+                  v=${v%%.*}; \
+                  months=( "" Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec ); \
+                  d=${v:6:2}; \
+                  m=${v:4:2};
+                  y=${v:0:4};
+                  echo $([[ -z $patch ]] && echo patch || echo stable)_${d#0}${months[${m#0}]}${y}$([[ -n $patch ]] && echo _update${patch}))
+Release:        1%{?dist}
+Summary:        Molecular Dynamics Simulator
+# Automatically converted from old format: GPLv2 - review is highly recommended.
+License:        GPL-2.0-only
+Url:            https://www.lammps.org/
+%if %{git}
+Source0:        https://github.com/lammps/lammps/archive/%{commit}/lammps-%{commit}.tar.gz#/%{name}-%{commit}.tar.gz
+%else
+Source0:        https://github.com/lammps/lammps/archive/%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz
+%endif
+Source1:        https://github.com/google/googletest/archive/release-1.12.1.tar.gz#/googletest-1.12.1.tar.gz
+Source2:        https://pyyaml.org/download/libyaml/yaml-0.2.5.tar.gz
+Source3:        https://download.lammps.org/thirdparty/opencl-loader-2024.05.09.tar.gz
+Source4:        https://github.com/spglib/spglib/archive/refs/tags/v1.11.2.1.tar.gz#/spglib-1.11.2.1.tar.gz
+
+# https://fedoraproject.org/wiki/Changes/EncourageI686LeafRemoval
+# mpi is broken on s390x see, bug #2322073
+ExcludeArch: %{ix86} s390x
+
+BuildRequires:  fftw-devel
+BuildRequires:  gcc-c++
+BuildRequires:  gcc-fortran
+BuildRequires:  libpng-devel
+BuildRequires:  libjpeg-devel
+%ifnarch %ix86
+BuildRequires:  openmpi-devel
+BuildRequires:  heffte-openmpi-devel
+BuildRequires:  python3-mpi4py-openmpi
+BuildRequires:  python3-mpi4py-mpich
+%endif
+BuildRequires:  mpich-devel
+BuildRequires:  heffte-mpich-devel
+BuildRequires:  python3-devel
+BuildRequires:  python3-numpy
+BuildRequires:  fftw3-devel
+BuildRequires:  zlib-devel
+BuildRequires:  gsl-devel
+BuildRequires:  voro++-devel
+BuildRequires:  %{blaslib}-devel
+BuildRequires:  hdf5-devel
+BuildRequires:  kim-api-devel
+BuildRequires:  kim-api-examples
+BuildRequires:  cmake3 >= 3.16
+BuildRequires:  ocl-icd-devel
+BuildRequires:  opencl-headers
+BuildRequires:  tbb-devel
+BuildRequires:  readline-devel
+# before F33 there was no kokkos package
+%if 0%{?fedora} >= 33
+%ifnarch i686 armv7hl
+%global         with_kokkos 1
+# kokkos needs a lot of memory
+%global         _smp_mflags -j1
+BuildRequires:  kokkos-devel >= 4.3
+%endif
+%endif
+Requires:       %{name}-data
+
+%global lammps_desc \
+LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale \
+Atomic/Molecular Massively Parallel Simulator.\
+\
+LAMMPS has potentials for soft materials (biomolecules, polymers) and \
+solid-state materials (metals, semiconductors) and coarse-grained or \
+mesoscopic systems. It can be used to model atoms or, more generically, as a \
+parallel particle simulator at the atomic, meso, or continuum scale. \
+\
+LAMMPS runs on single processors or in parallel using message-passing \
+techniques and a spatial-decomposition of the simulation domain. The code is \
+designed to be easy to modify or extend with new functionality.
+
+
+%description
+%{lammps_desc}
+
+%ifnarch %ix86
+%global with_openmpi 1
+%package openmpi
+Summary:        LAMMPS Open MPI binaries and libraries
+Requires:       openmpi
+Requires:       %{name}-data
+
+%description openmpi
+%{lammps_desc}
+
+This package contains LAMMPS Open MPI binaries and libraries
+%endif
+
+%package mpich
+Summary:        LAMMPS MPICH binaries and libraries
+Requires:       mpich
+Requires:       %{name}-data
+
+%description mpich
+%{lammps_desc}
+
+This package contains LAMMPS MPICH binaries and libraries
+
+%package -n python3-%{name}
+Summary:        LAMMPS Python interface
+Requires:       python3
+Requires:       python3-numpy
+Requires:       %{name}%{?_isa} = %{version}-%{release}
+%{?python_provide:%python_provide python3-%{name}}
+
+%description -n python3-%{name}
+%{lammps_desc}
+
+This package contains LAMMPS Python interface
+
+%package headers
+Summary:        Development headers for LAMMPS
+
+%description headers
+%{lammps_desc}
+
+This package contains development headers for LAMMPS.
+
+%package devel
+Summary:        Development libraries for LAMMPS
+Requires:       %{name}%{?_isa} = %{version}-%{release}
+Requires:       %{name}-headers%{?_isa} = %{version}-%{release}
+
+%description devel
+%{lammps_desc}
+
+This package contains development libraries for serial LAMMPS.
+
+%package mpich-devel
+Summary:        Development libraries for MPICH LAMMPS
+Requires:       %{name}-mpich%{?_isa} = %{version}-%{release}
+Requires:       %{name}-headers%{?_isa} = %{version}-%{release}
+
+%description mpich-devel
+%{lammps_desc}
+
+This package contains development headers and libraries for MPICH LAMMPS.
+
+%ifnarch %ix86
+%package openmpi-devel
+Summary:        Development libraries for Open MPI LAMMPS
+Requires:       %{name}-openmpi%{?_isa} = %{version}-%{release}
+Requires:       %{name}-headers%{?_isa} = %{version}-%{release}
+
+%description openmpi-devel
+%{lammps_desc}
+
+This package contains development libraries for Open MPI LAMMPS.
+%endif
+
+%if 0%{?el7}
+%package openmpi3
+Summary:        LAMMPS Open MPI 3 binaries and libraries
+BuildRequires:  openmpi3-devel
+Requires:       openmpi3
+Requires:       %{name}-data
+
+%description openmpi3
+%{lammps_desc}
+
+This package contains LAMMPS Open MPI 3 binaries and libraries
+
+%package openmpi3-devel
+Summary:        Development libraries for Open MPI 3 LAMMPS
+Requires:       %{name}-openmpi3%{?_isa} = %{version}-%{release}
+Requires:       %{name}-headers%{?_isa} = %{version}-%{release}
+
+%description openmpi3-devel
+%{lammps_desc}
+
+This package contains development libraries for Open MPI 3 LAMMPS.
+%endif
+
+%package data
+Summary:        Data files for LAMMPS
+BuildArch:      noarch
+
+%description data
+%{lammps_desc}
+
+This package contains data files for LAMMPS.
+
+%generate_buildrequires
+cd python
+%pyproject_buildrequires
+
+%prep
+%if %{git}
+%setup -q -n %{name}-%{commit}
+%else
+%setup -q -n %{name}-%{uversion}
+%endif
+
+%build
+%global _vpath_srcdir cmake
+%global _vpath_builddir ${mpi:-serial}
+set +e
+. /etc/profile.d/modules.sh
+set -e
+
+
+for mpi in '' mpich %{?with_openmpi:openmpi} ; do
+  test -n "${mpi}" && module load mpi/${mpi}-%{_arch}
+  #python wrapper isn't mpi specific
+  %{cmake3} \
+  -C cmake/presets/all_on.cmake \
+  -C cmake/presets/nolib.cmake \
+  %{cmake_blas_flags} \
+  -DCMAKE_TUNE_FLAGS='' \
+  -DCMAKE_CUSTOM_LINKER="default" \
+  -DPKG_PYTHON=ON \
+  -DPKG_VORONOI=ON \
+  -DPKG_ATC=ON \
+  -DPKG_H5MD=ON \
+  %{?with_kokkos:-DPKG_KOKKOS=ON -DEXTERNAL_KOKKOS=ON} \
+  -DPKG_KIM=ON \
+  -DENABLE_TESTING=ON \
+  -DGTEST_URL=file://%{S:1} \
+  -DYAML_URL=file://%{S:2} \
+  -DOPENCL_LOADER_URL=file://%{S:3} \
+  -DSPGLIB_URL=file://%{S:4} \
+  -DDOWNLOAD_POTENTIALS=OFF \
+  -DPYTHON_INSTDIR=%{python3_sitelib} \
+  -DCMAKE_INSTALL_SYSCONFDIR=/etc \
+  -DPKG_GPU=ON -DGPU_API=OpenCL \
+  -DBUILD_OMP=ON \
+  -DFFT=FFTW3 \
+%ifnarch x86_64 %x86
+  -DPKG_INTEL=OFF \
+%endif
+    -DCMAKE_INSTALL_BINDIR=${MPI_BIN:-%{_bindir}} -DCMAKE_INSTALL_LIBDIR=${MPI_LIB:-%{_libdir}} -DLAMMPS_MACHINE="${MPI_SUFFIX#_}" -DLAMMPS_LIB_SUFFIX="${MPI_SUFFIX#_}" -DCMAKE_INSTALL_MANDIR=${MPI_MAN:-%{_mandir}} \
+    ${mpi:+-DBUILD_MPI=ON -DFFT_USE_HEFFTE=ON -DCMAKE_EXE_LINKER_FLAGS="%{__global_ldflags} -Wl,-rpath -Wl,${MPI_LIB} -Wl,--enable-new-dtags" -DCMAKE_SHARED_LINKER_FLAGS="%{__global_ldflags} -Wl,-rpath -Wl,${MPI_LIB} -Wl,--enable-new-dtags" $(test "$mpi" != openmpi || echo "-DMPIEXEC_PREFLAGS=--oversubscribe") } \
+    $(test -z "${mpi}" && echo -DBUILD_MPI=OFF -DBUILD_LAMMPS_SHELL=ON -DBUILD_TOOLS=ON)
+  %cmake_build
+  test -n "${mpi}" && module unload mpi/${mpi}-%{_arch}
+done
+
+cd python
+%pyproject_wheel
+
+%install
+set +e
+. /etc/profile.d/modules.sh
+set -e
+
+for mpi in '' mpich %{?with_openmpi:openmpi} ; do
+  %cmake_install
+done
+
+cd python
+%pyproject_install
+%pyproject_save_files lammps
+
+%check
+
+%global testargs --label-exclude unstable --exclude-regex '\(SimpleCommands\|Variables\|ComputeGlobal\|MolPairStyle:coul_slater_long\|AtomicPairStyle:meam_spline\|FixTimestep:.*\|.*tip4p.*\)'
+
+%ifnarch %ix86
+%global testargs --label-exclude unstable --exclude-regex '\(SimpleCommands\|Variables\|ComputeGlobal\|MolPairStyle:coul_slater_long\|AtomicPairStyle:meam_spline\|FixTimestep:.*\|.*tip4p.*\|Groups\|AtomicPairStyle:lj_cut_sphere\|AtomicPairStyle:lj_expand_sphere\|AtomicPairStyle:meam_ms\|AtomicPairStyle:pedone\|DihedralStyle:cosine_squared_restricted\|BondStyle:harmonic_restrain\)'
+%endif
+
+%ifarch s390x
+%global testargs --label-exclude unstable --exclude-regex '\(SimpleCommands\|Variables\|ComputeGlobal\|MolPairStyle:coul_slater_long\|AtomicPairStyle:meam_spline\|FixTimestep:.*\|.*tip4p.*\|LibraryMPI\|MPILoadBalancing\|FileOperations\|Groups\|SetProperty\|AtomicPairStyle:lj_cut_sphere\|AtomicPairStyle:lj_expand_sphere\|AtomicPairStyle:meam_ms\|AtomicPairStyle:pedone\|DihedralStyle:cosine_squared_restricted\|BondStyle:harmonic_restrain\|TestPairList\)'
+%endif
+
+set +e
+. /etc/profile.d/modules.sh
+set -e
+
+for mpi in '' mpich %{?with_openmpi:openmpi} ; do
+  old_PYTHONPATH="${PYTHONPATH}"
+  test -n "${mpi}" && module load mpi/${mpi}-%{_arch} && export PYTHONPATH="${MPI_PYTHON3_SITEARCH}:${PYTHONPATH}"
+  %ctest --output-on-failure %{?testargs}
+  test -n "${mpi}" && module unload mpi/${mpi}-%{_arch} && export PYTHONPATH="${old_PYTHONPATH}"
+done
+
+%pyproject_check_import -t
+
+%ldconfig_scriptlets
+
+%files
+%doc README
+%license LICENSE
+%{_bindir}/lmp
+%{_mandir}/man1/lmp.*
+%{_libdir}/liblammps.so.*
+%{_bindir}/msi2lmp
+%{_mandir}/man1/msi2lmp.*
+%{_bindir}/binary2txt
+%{_bindir}/chain.x
+%{_bindir}/micelle2d.x
+%{_bindir}/stl_bin2txt
+%{_bindir}/phana
+
+%files devel
+%{_libdir}/liblammps.so
+%{_libdir}/pkgconfig/liblammps.pc
+%{_libdir}/cmake/LAMMPS
+
+%ifnarch %ix86
+%files openmpi-devel
+%{_libdir}/openmpi*/lib/liblammps_openmpi.so
+%{_libdir}/openmpi*/lib/pkgconfig/liblammps_openmpi.pc
+%{_libdir}/openmpi*/lib/cmake/LAMMPS
+%endif
+
+%files mpich-devel
+%{_libdir}/mpich*/lib/liblammps_mpich.so
+%{_libdir}/mpich*/lib/pkgconfig/liblammps_mpich.pc
+%{_libdir}/mpich*/lib/cmake/LAMMPS
+
+%files -n python3-%{name} -f %{pyproject_files}
+
+%files headers
+%license LICENSE
+%{_includedir}/%{name}/
+
+%ifnarch %ix86
+%files openmpi
+%license LICENSE
+%{_libdir}/openmpi*/bin/lmp_openmpi
+%{_mandir}/openmpi*/man1/lmp_openmpi.*
+%{_libdir}/openmpi*/lib/liblammps_openmpi.so.*
+%endif
+
+%if 0%{?el7}
+%files openmpi3
+%license LICENSE
+%{_libdir}/openmpi3*/bin/lmp_openmpi3
+%{_mandir}/openmpi3*/man1/lmp_openmpi3.*
+%{_libdir}/openmpi3*/lib/liblammps_openmpi3.so.*
+
+%files openmpi3-devel
+%{_libdir}/openmpi3*/lib/liblammps_openmpi3.so
+%{_libdir}/openmpi3*/lib/pkgconfig/liblammps_openmpi3.pc
+%{_libdir}/openmpi3/lib/cmake/LAMMPS
+%endif
+
+%files mpich
+%license LICENSE
+%{_libdir}/mpich*/bin/lmp_mpich
+%{_mandir}/mpich*/man1/lmp_mpich.*
+%{_libdir}/mpich*/lib/liblammps_mpich.so.*
+
+%files data
+%license LICENSE
+%{_datadir}/%{name}
+%config %{_sysconfdir}/profile.d/lammps.*
+
+%changelog
+
+* Tue Dec 12 2024 zhtianyu <zhangtianyu@iscas.ac.cn> - 20241119-1
+- Package init
diff --git a/sources b/sources
new file mode 100644
index 0000000..c35aaf0
--- /dev/null
+++ b/sources
@@ -0,0 +1,5 @@
+e82199374acdfda3f425331028eb4e2a  googletest-1.12.1.tar.gz
+a71f7054175aa4fa376122d2b93b753a  lammps-patch_19Nov2024.tar.gz
+e7796826b21c059224fabe997e0f2075  opencl-loader-2024.05.09.tar.gz
+3089782bc85b5034dd4765a18ee70bc7  spglib-1.11.2.1.tar.gz
+bb15429d8fb787e7d3f1c83ae129a999  yaml-0.2.5.tar.gz