diff options
Diffstat (limited to 'sci-physics')
-rw-r--r-- | sci-physics/lammps/ChangeLog | 9 | ||||
-rw-r--r-- | sci-physics/lammps/Manifest | 20 | ||||
-rw-r--r-- | sci-physics/lammps/lammps-20150721.ebuild | 267 | ||||
-rw-r--r-- | sci-physics/lammps/lammps-20150722.ebuild | 267 |
4 files changed, 554 insertions, 9 deletions
diff --git a/sci-physics/lammps/ChangeLog b/sci-physics/lammps/ChangeLog index 9338f501ac1a..e564c5fdaf62 100644 --- a/sci-physics/lammps/ChangeLog +++ b/sci-physics/lammps/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-physics/lammps # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/ChangeLog,v 1.106 2015/07/18 21:59:49 nicolasbock Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/ChangeLog,v 1.107 2015/07/24 12:22:22 nicolasbock Exp $ + +*lammps-20150721 (24 Jul 2015) +*lammps-20150722 (24 Jul 2015) + + 24 Jul 2015; Nicolas Bock <nicolasbock@gentoo.org> +lammps-20150721.ebuild, + +lammps-20150722.ebuild: + Version bump. *lammps-20150718 (18 Jul 2015) diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest index 1b2444e71447..2b1a7d8d16a8 100644 --- a/sci-physics/lammps/Manifest +++ b/sci-physics/lammps/Manifest @@ -8,6 +8,8 @@ DIST lammps-15May15.tar.gz 63835027 SHA256 0233ea98c7d77d31bd0a538bb674c0ee8f000 DIST lammps-16Apr15.tar.gz 63842472 SHA256 65aecf6f25a055734ef113890a86ecbf7f8478105238c507e5f9bcbeb657bc99 SHA512 95639145db66e76bd27a865849dc0ad15d3920f7ca9f1fb9a426e457376d0c939c57440e89fa6903d1989ca5e5c6c97d8d283928e1dbf33dd94ba88dbb05a252 WHIRLPOOL 422f6814093f22820cfd8fada1d97735c1a8f0388b34e6bad49e361e411b254ea89e6bf7afa8390c0cba1371a6d038fa84cf93583568c5223e42d95210f13515 DIST lammps-18Apr15.tar.gz 63883297 SHA256 4ce74978da738383a1d808a37481c3c43d4f8f44d919770b3f2cdd4fcf03345b SHA512 be088ec59b7fe495fff3cdfcc5ccb52d2705eec20deb5c8694a215943786652c9dc22a81ba48324707495c3f56c0c347af964d1952ae077c8db02258cf31387a WHIRLPOOL c90403147cc4eda5b4f581cd1bd18bcc8f45a73b1d0e51dcd64c52fc636116c9d57337b89b5753c86e1bbf386f8a2391a9813a6e32154a819f3e35cfc816b5e2 DIST lammps-18Jul15.tar.gz 66065642 SHA256 deb6625b7c21cf94fc7ee9aefb2edf55a6c8dc870e919028c9ffa1cd169d57ed SHA512 d26dd0084779e037af35bc26f81cdca5a7617f841860e6eab7d52f6c023d2c001075aad5dc3d656ceb6e92650589acc472fa5c8954fd9ab81ec0b737e377284b WHIRLPOOL 66794b7250cdb077bcbeb2b95a464aecc684f7592d81f3db4a3702195ef1d8404eb4b1f38e6c1dd859a42dd8ca1ebd039cbac4d9fd11be99a376168f2c498cdd +DIST lammps-21Jul15.tar.gz 66715434 SHA256 2e24a7b6131a35ef83cec08f4dc9f7cc5188c59a630ba61f2a8ac3cfbd284ef7 SHA512 cbf39b3559ac60d5ad92299370bf9af76c0bd7fec62dbaa429d5127d561978426d16b03510b815ffeb6b0acdb362523809adf7ac3fbc2fea8cc484010b1ef7bc WHIRLPOOL 41df92b1f5baf52e846032f12c80f813b84fcd1c71f8c7dad5594780da154345d1b1bdea6b68f4c4b71029346d74d4ff3a813f1101437a01be65df7cf6d0d246 +DIST lammps-22Jul15.tar.gz 67275212 SHA256 b75cdf8ead17f20433737c203c8d29c0cc3e157c9b3d175093467873aea0b869 SHA512 f6e5eaf3ca8bcd25a580a4608e0aec0021f2ed5eb23cf9ccd0a707cb8bc320568504ccffc25cccb5acfe2fc3515c58f8afc8936aea63acb3062bdc897a5eb2ee WHIRLPOOL 13c09e1045a0bdabe15e2125ccef0ea622cb12fcce63d8441b7f9843b8f1a3f7aa0c13908a2e215c1fdba8a579a17a5833111b5cf31a2471bf66e781ef281c59 DIST lammps-28Apr15.tar.gz 63883556 SHA256 6e7c32690cf8bb5a4fb147bab6029cc1d03594ec7b3ea3833e7dc89acc596d8a SHA512 414c786e8666cddd31a3200baedc76974371280dc219636914dd7863f03e32e11f637a9c184af78d8d4da22afe4cf734b6a0eb32c78d6f53ee95d796a3e080c0 WHIRLPOOL c57a91f9d5e977d26cdb2076b5bbd2f3b5791396c23b5326f16cc609b9646e80c602a492b312b4e5f78d1d638c4a6b66e9a49b1ced02274ad7202821a2884975 DIST lammps-30Apr15.tar.gz 63892754 SHA256 d4a193fd5aa9417ec9d15a3be1e2b149302aacf3d9321886a806b0f4ca91611e SHA512 889fc315719e6f50f802b72a8a0c6e6d7eedb84b67e8b39ae9ea93feb2d526914639848cbfbcbb6dd8b8718c3b332f617f001c6ef04fe14d0685106fcac821bd WHIRLPOOL a681662a0c37fcb701ced8f2cd4f085dfd0ff250faac2c62abd07b718e3bf12ddbf366f725fbc21bc4547e6ef3ca3042ee84571a1fa0277a4c3d7d273ccaa099 EBUILD lammps-20150210.ebuild 4947 SHA256 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2015/07/24 12:22:22 nicolasbock Exp $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_7,3_3} ) + +inherit eutils flag-o-matic fortran-2 multilib python-r1 + +convert_month() { + case $1 in + 01) echo Jan + ;; + 02) echo Feb + ;; + 03) echo Mar + ;; + 04) echo Apr + ;; + 05) echo May + ;; + 06) echo Jun + ;; + 07) echo Jul + ;; + 08) echo Aug + ;; + 09) echo Sep + ;; + 10) echo Oct + ;; + 11) echo Nov + ;; + 12) echo Dec + ;; + *) echo unknown + ;; + esac +} + +MY_P=${PN}-$((10#${PV:6:2}))$(convert_month ${PV:4:2})${PV:2:2} + +DESCRIPTION="Large-scale Atomic/Molecular Massively Parallel Simulator" +HOMEPAGE="http://lammps.sandia.gov/" +SRC_URI="http://lammps.sandia.gov/tars/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc examples gzip lammps-memalign mpi python static-libs" + +DEPEND=" + mpi? ( + virtual/blas + virtual/lapack + virtual/mpi + ) + gzip? ( app-arch/gzip ) + sci-libs/voro++ + python? ( ${PYTHON_DEPS} ) + " +RDEPEND="${DEPEND}" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +S="${WORKDIR}/${MY_P}" + +lmp_emake() { + local LAMMPS_INCLUDEFLAGS + LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')" + LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN' '')" + + # The lammps makefile uses CC to indicate the C++ compiler. + emake \ + ARCHIVE=$(tc-getAR) \ + CC=$(usex mpi "mpic++" "$(tc-getCXX)") \ + F90=$(usex mpi "mpif90" "$(tc-getFC)") \ + LINK=$(usex mpi "mpic++" "$(tc-getCXX)") \ + CCFLAGS="${CXXFLAGS}" \ + F90FLAGS="${FCFLAGS}" \ + LINKFLAGS="${LDFLAGS}" \ + LMP_INC="${LAMMPS_INCLUDEFLAGS}" \ + MPI_INC=$(usex mpi "" "-I../STUBS") \ + MPI_PATH=$(usex mpi "" "-L../STUBS") \ + MPI_LIB=$(usex mpi "" "-lmpi_stubs") \ + user-atc_SYSLIB="$(usex mpi "$($(tc-getPKG_CONFIG) --libs blas) $($(tc-getPKG_CONFIG) --libs lapack)" '')"\ + "$@" +} + +lmp_activate_packages() { + # Build packages + lmp_emake -C src yes-asphere + lmp_emake -C src yes-body + lmp_emake -C src yes-class2 + lmp_emake -C src yes-colloid + lmp_emake -C src yes-coreshell + lmp_emake -C src yes-dipole + lmp_emake -C src yes-fld + #lmp_emake -C src yes-gpu + lmp_emake -C src yes-granular + # Need OpenKIM external dependency. + #lmp_emake -C src yes-kim + # Need Kokkos external dependency. + #lmp_emake -C src yes-kokkos + lmp_emake -C src yes-kspace + lmp_emake -C src yes-manybody + lmp_emake -C src yes-mc + lmp_emake -C src yes-meam + lmp_emake -C src yes-misc + lmp_emake -C src yes-molecule + #lmp_emake -C src yes-mpiio + lmp_emake -C src yes-opt + lmp_emake -C src yes-peri + lmp_emake -C src yes-poems + lmp_emake -C src yes-qeq + lmp_emake -C src yes-reax + lmp_emake -C src yes-replica + lmp_emake -C src yes-rigid + lmp_emake -C src yes-shock + lmp_emake -C src yes-snap + lmp_emake -C src yes-srd + lmp_emake -C src yes-voronoi + lmp_emake -C src yes-xtc + + if use mpi; then + lmp_emake -C src yes-user-atc + fi + lmp_emake -C src yes-user-eff + lmp_emake -C src yes-user-fep + use mpi && lmp_emake -C src yes-user-lb + lmp_emake -C src yes-user-phonon + lmp_emake -C src yes-user-sph +} + +lmp_build_packages() { + lmp_emake -C lib/meam -j1 -f Makefile.gfortran + lmp_emake -C lib/poems -f Makefile.g++ + lmp_emake -C lib/reax -j1 -f Makefile.gfortran + use mpi && lmp_emake -C lib/atc -f Makefile.g++ +} + +lmp_clean_packages() { + lmp_emake -C lib/meam -f Makefile.gfortran clean + lmp_emake -C lib/poems -f Makefile.g++ clean + lmp_emake -C lib/reax -f Makefile.gfortran clean + use mpi && lmp_emake -C lib/atc -f Makefile.g++ clean +} + +src_prepare() { + # Fix inconsistent use of SHFLAGS. + sed -i \ + -e 's:voronoi_SYSINC\s\+=.*$:voronoi_SYSINC = -I/usr/include/voro++:' \ + -e 's:voronoi_SYSPATH\s\+=.*$:voronoi_SYSPATH =:' \ + lib/voronoi/Makefile.lammps || die + + # Fix missing .so name. + sed -i \ + -e 's:SHLIBFLAGS\s\+=\s\+:SHLIBFLAGS = -Wl,-soname,liblammps.so.0 :' \ + src/MAKE/Makefile.serial || die + + # Fix makefile in tools. + sed -i \ + -e 's:g++:$(CXX) $(CXXFLAGS):' \ + -e 's:gcc:$(CC) $(CCFLAGS):' \ + -e 's:ifort:$(FC) $(FCFLAGS):' \ + tools/Makefile || die + + # Patch python. + epatch "${FILESDIR}/lammps-python3.patch" + epatch "${FILESDIR}/python-shebang.patch" +} + +src_compile() { + # Fix atc... + append-cxxflags -I../../src + + # Acticate packages. + elog "Activating lammps packages..." + lmp_activate_packages + + # Compile stubs for serial version. + use mpi || lmp_emake -C src mpi-stubs + + elog "Building packages..." + lmp_build_packages + + if use static-libs; then + # Build static library. + elog "Building static library..." + lmp_emake -C src mode=lib serial + fi + + # Clean out packages (that's not done by the build system with the clean + # target), so we can rebuild the packages with -fPIC. + elog "Cleaning packages..." + lmp_clean_packages + + # The build system does not rebuild the packages with -fPIC, adding flag + # manually. + append-cxxflags -fPIC + append-fflags -fPIC + + # Compile stubs for serial version. + use mpi || lmp_emake -C src mpi-stubs + + elog "Building packages..." + lmp_build_packages + + # Build shared library. + elog "Building shared library..." + lmp_emake -C src mode=shlib serial + + # Compile main executable. The shared library is always built, and + # mode=shexe is simply a way to re-use the object files built in the + # "shlib" step when linking the executable. The executable is not actually + # using the shared library. If we have built the static library, then we + # link that into the executable. + elog "Linking executable..." + if use static-libs; then + lmp_emake -C src mode=exe serial + else + lmp_emake -C src mode=shexe serial + fi + + # Compile tools. + elog "Building tools..." + lmp_emake -C tools binary2txt chain data2xmovie micelle2d +} + +src_install() { + use static-libs && newlib.a src/liblammps_serial.a liblammps.a + newlib.so src/liblammps_serial.so liblammps.so.0.0.0 + dosym liblammps.so.0.0.0 /usr/$(get_libdir)/liblammps.so + dosym liblammps.so.0.0.0 /usr/$(get_libdir)/liblammps.so.0 + newbin src/lmp_serial lmp + dobin tools/binary2txt + dobin tools/chain + dobin tools/data2xmovie + dobin tools/micelle2d + # Don't forget to add header files of optional packages as they are added + # to this ebuild. There may also be .mod files from Fortran based + # packages. + insinto "/usr/include/${PN}" + doins -r src/*.h lib/meam/*.mod + + local LAMMPS_POTENTIALS="usr/share/${PN}/potentials" + insinto "/${LAMMPS_POTENTIALS}" + doins potentials/* + echo "LAMMPS_POTENTIALS=${EROOT}${LAMMPS_POTENTIALS}" > 99lammps + doenvd 99lammps + + # Install python script. + use python && python_foreach_impl python_domodule python/lammps.py + + if use examples; then + local LAMMPS_EXAMPLES="/usr/share/${PN}/examples" + insinto "${LAMMPS_EXAMPLES}" + doins -r examples/* + fi + + dodoc README + if use doc; then + dodoc doc/Manual.pdf + dohtml -r doc/* + fi +} diff --git a/sci-physics/lammps/lammps-20150722.ebuild b/sci-physics/lammps/lammps-20150722.ebuild new file mode 100644 index 000000000000..d5782fb346ef --- /dev/null +++ b/sci-physics/lammps/lammps-20150722.ebuild @@ -0,0 +1,267 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/lammps-20150722.ebuild,v 1.1 2015/07/24 12:22:22 nicolasbock Exp $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_7,3_3} ) + +inherit eutils flag-o-matic fortran-2 multilib python-r1 + +convert_month() { + case $1 in + 01) echo Jan + ;; + 02) echo Feb + ;; + 03) echo Mar + ;; + 04) echo Apr + ;; + 05) echo May + ;; + 06) echo Jun + ;; + 07) echo Jul + ;; + 08) echo Aug + ;; + 09) echo Sep + ;; + 10) echo Oct + ;; + 11) echo Nov + ;; + 12) echo Dec + ;; + *) echo unknown + ;; + esac +} + +MY_P=${PN}-$((10#${PV:6:2}))$(convert_month ${PV:4:2})${PV:2:2} + +DESCRIPTION="Large-scale Atomic/Molecular Massively Parallel Simulator" +HOMEPAGE="http://lammps.sandia.gov/" +SRC_URI="http://lammps.sandia.gov/tars/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc examples gzip lammps-memalign mpi python static-libs" + +DEPEND=" + mpi? ( + virtual/blas + virtual/lapack + virtual/mpi + ) + gzip? ( app-arch/gzip ) + sci-libs/voro++ + python? ( ${PYTHON_DEPS} ) + " +RDEPEND="${DEPEND}" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +S="${WORKDIR}/${MY_P}" + +lmp_emake() { + local LAMMPS_INCLUDEFLAGS + LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')" + LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN' '')" + + # The lammps makefile uses CC to indicate the C++ compiler. + emake \ + ARCHIVE=$(tc-getAR) \ + CC=$(usex mpi "mpic++" "$(tc-getCXX)") \ + F90=$(usex mpi "mpif90" "$(tc-getFC)") \ + LINK=$(usex mpi "mpic++" "$(tc-getCXX)") \ + CCFLAGS="${CXXFLAGS}" \ + F90FLAGS="${FCFLAGS}" \ + LINKFLAGS="${LDFLAGS}" \ + LMP_INC="${LAMMPS_INCLUDEFLAGS}" \ + MPI_INC=$(usex mpi "" "-I../STUBS") \ + MPI_PATH=$(usex mpi "" "-L../STUBS") \ + MPI_LIB=$(usex mpi "" "-lmpi_stubs") \ + user-atc_SYSLIB="$(usex mpi "$($(tc-getPKG_CONFIG) --libs blas) $($(tc-getPKG_CONFIG) --libs lapack)" '')"\ + "$@" +} + +lmp_activate_packages() { + # Build packages + lmp_emake -C src yes-asphere + lmp_emake -C src yes-body + lmp_emake -C src yes-class2 + lmp_emake -C src yes-colloid + lmp_emake -C src yes-coreshell + lmp_emake -C src yes-dipole + lmp_emake -C src yes-fld + #lmp_emake -C src yes-gpu + lmp_emake -C src yes-granular + # Need OpenKIM external dependency. + #lmp_emake -C src yes-kim + # Need Kokkos external dependency. + #lmp_emake -C src yes-kokkos + lmp_emake -C src yes-kspace + lmp_emake -C src yes-manybody + lmp_emake -C src yes-mc + lmp_emake -C src yes-meam + lmp_emake -C src yes-misc + lmp_emake -C src yes-molecule + #lmp_emake -C src yes-mpiio + lmp_emake -C src yes-opt + lmp_emake -C src yes-peri + lmp_emake -C src yes-poems + lmp_emake -C src yes-qeq + lmp_emake -C src yes-reax + lmp_emake -C src yes-replica + lmp_emake -C src yes-rigid + lmp_emake -C src yes-shock + lmp_emake -C src yes-snap + lmp_emake -C src yes-srd + lmp_emake -C src yes-voronoi + lmp_emake -C src yes-xtc + + if use mpi; then + lmp_emake -C src yes-user-atc + fi + lmp_emake -C src yes-user-eff + lmp_emake -C src yes-user-fep + use mpi && lmp_emake -C src yes-user-lb + lmp_emake -C src yes-user-phonon + lmp_emake -C src yes-user-sph +} + +lmp_build_packages() { + lmp_emake -C lib/meam -j1 -f Makefile.gfortran + lmp_emake -C lib/poems -f Makefile.g++ + lmp_emake -C lib/reax -j1 -f Makefile.gfortran + use mpi && lmp_emake -C lib/atc -f Makefile.g++ +} + +lmp_clean_packages() { + lmp_emake -C lib/meam -f Makefile.gfortran clean + lmp_emake -C lib/poems -f Makefile.g++ clean + lmp_emake -C lib/reax -f Makefile.gfortran clean + use mpi && lmp_emake -C lib/atc -f Makefile.g++ clean +} + +src_prepare() { + # Fix inconsistent use of SHFLAGS. + sed -i \ + -e 's:voronoi_SYSINC\s\+=.*$:voronoi_SYSINC = -I/usr/include/voro++:' \ + -e 's:voronoi_SYSPATH\s\+=.*$:voronoi_SYSPATH =:' \ + lib/voronoi/Makefile.lammps || die + + # Fix missing .so name. + sed -i \ + -e 's:SHLIBFLAGS\s\+=\s\+:SHLIBFLAGS = -Wl,-soname,liblammps.so.0 :' \ + src/MAKE/Makefile.serial || die + + # Fix makefile in tools. + sed -i \ + -e 's:g++:$(CXX) $(CXXFLAGS):' \ + -e 's:gcc:$(CC) $(CCFLAGS):' \ + -e 's:ifort:$(FC) $(FCFLAGS):' \ + tools/Makefile || die + + # Patch python. + epatch "${FILESDIR}/lammps-python3.patch" + epatch "${FILESDIR}/python-shebang.patch" +} + +src_compile() { + # Fix atc... + append-cxxflags -I../../src + + # Acticate packages. + elog "Activating lammps packages..." + lmp_activate_packages + + # Compile stubs for serial version. + use mpi || lmp_emake -C src mpi-stubs + + elog "Building packages..." + lmp_build_packages + + if use static-libs; then + # Build static library. + elog "Building static library..." + lmp_emake -C src mode=lib serial + fi + + # Clean out packages (that's not done by the build system with the clean + # target), so we can rebuild the packages with -fPIC. + elog "Cleaning packages..." + lmp_clean_packages + + # The build system does not rebuild the packages with -fPIC, adding flag + # manually. + append-cxxflags -fPIC + append-fflags -fPIC + + # Compile stubs for serial version. + use mpi || lmp_emake -C src mpi-stubs + + elog "Building packages..." + lmp_build_packages + + # Build shared library. + elog "Building shared library..." + lmp_emake -C src mode=shlib serial + + # Compile main executable. The shared library is always built, and + # mode=shexe is simply a way to re-use the object files built in the + # "shlib" step when linking the executable. The executable is not actually + # using the shared library. If we have built the static library, then we + # link that into the executable. + elog "Linking executable..." + if use static-libs; then + lmp_emake -C src mode=exe serial + else + lmp_emake -C src mode=shexe serial + fi + + # Compile tools. + elog "Building tools..." + lmp_emake -C tools binary2txt chain data2xmovie micelle2d +} + +src_install() { + use static-libs && newlib.a src/liblammps_serial.a liblammps.a + newlib.so src/liblammps_serial.so liblammps.so.0.0.0 + dosym liblammps.so.0.0.0 /usr/$(get_libdir)/liblammps.so + dosym liblammps.so.0.0.0 /usr/$(get_libdir)/liblammps.so.0 + newbin src/lmp_serial lmp + dobin tools/binary2txt + dobin tools/chain + dobin tools/data2xmovie + dobin tools/micelle2d + # Don't forget to add header files of optional packages as they are added + # to this ebuild. There may also be .mod files from Fortran based + # packages. + insinto "/usr/include/${PN}" + doins -r src/*.h lib/meam/*.mod + + local LAMMPS_POTENTIALS="usr/share/${PN}/potentials" + insinto "/${LAMMPS_POTENTIALS}" + doins potentials/* + echo "LAMMPS_POTENTIALS=${EROOT}${LAMMPS_POTENTIALS}" > 99lammps + doenvd 99lammps + + # Install python script. + use python && python_foreach_impl python_domodule python/lammps.py + + if use examples; then + local LAMMPS_EXAMPLES="/usr/share/${PN}/examples" + insinto "${LAMMPS_EXAMPLES}" + doins -r examples/* + fi + + dodoc README + if use doc; then + dodoc doc/Manual.pdf + dohtml -r doc/* + fi +} |