From bee40efbb1cb9218b50949f8ad2dd9599e1a15f9 Mon Sep 17 00:00:00 2001 From: Nicolas Bock Date: Sun, 19 Apr 2015 19:06:02 +0000 Subject: [PATCH] sci-physics/lammps: Version bump Package-Manager: portage-2.2.14/cvs/Linux x86_64 Manifest-Sign-Key: 0xAC91CA52 --- sci-physics/lammps/ChangeLog | 7 +- sci-physics/lammps/Manifest | 18 +- sci-physics/lammps/lammps-20150416.ebuild | 267 ++++++++++++++++++++++ 3 files changed, 283 insertions(+), 9 deletions(-) create mode 100644 sci-physics/lammps/lammps-20150416.ebuild diff --git a/sci-physics/lammps/ChangeLog b/sci-physics/lammps/ChangeLog index eead4af97607..6fd91467b6f9 100644 --- a/sci-physics/lammps/ChangeLog +++ b/sci-physics/lammps/ChangeLog @@ -1,6 +1,11 @@ # 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 1.96 2015/04/15 22:00:36 nicolasbock Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/ChangeLog,v 1.97 2015/04/19 19:05:51 nicolasbock Exp $ + +*lammps-20150416 (19 Apr 2015) + + 19 Apr 2015; Nicolas Bock +lammps-20150416.ebuild: + sci-physics/lammps: Version bump 15 Apr 2015; Nicolas Bock -files/chunk.patch: sci-physics/lammps: Removing obsolete patch. diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest index 3911b3ac6d1c..c28a2dcc699d 100644 --- a/sci-physics/lammps/Manifest +++ b/sci-physics/lammps/Manifest @@ -7,6 +7,7 @@ DIST lammps-10Feb15.tar.gz 62912048 SHA256 59373e9b5592f7b697a144bbce1fb742726e0 DIST lammps-11Apr15.tar.gz 63843170 SHA256 21ceb4154a1439abeb2f0ac50f3058021facf0636b280e596b75a3f1a5fae46b SHA512 e9bf8c0612784fae73982e2da2d6034a0ca8d9da69930b9dd953897432e108bcae86d7307591a3e491cac4b5e34e3a148767e5e0e2e89f2b52e37fe272b9bdee WHIRLPOOL f275d4b3c5cd532e3cadd729f8b8cc1d65bb62f1616d121d59f004564238b55724dff37bc311c8ca789a0d1febe94ca7d89a72ec62cc4d65f678493d6afa1600 DIST lammps-12Mar15.tar.gz 63521532 SHA256 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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 +} -- 2.26.2