From c22a2eeed5b52985a216896846832d4cc9b198fe Mon Sep 17 00:00:00 2001 From: Nicolas Bock Date: Wed, 5 Oct 2016 21:57:19 -0600 Subject: sci-physics/lammps: Version bump Package-Manager: portage-2.3.0 --- sci-physics/lammps/Manifest | 1 + sci-physics/lammps/files/fm_exp.patch | 11 ++ sci-physics/lammps/lammps-20160730.ebuild | 221 ++++++++++++++++++++++++++++++ 3 files changed, 233 insertions(+) create mode 100644 sci-physics/lammps/files/fm_exp.patch create mode 100644 sci-physics/lammps/lammps-20160730.ebuild (limited to 'sci-physics/lammps') diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest index ed3e70f64ba..4b797717b77 100644 --- a/sci-physics/lammps/Manifest +++ b/sci-physics/lammps/Manifest @@ -10,6 +10,7 @@ DIST lammps-1Mar16.tar.gz 87945422 SHA256 af2bd7ab2a28aa14b8afa3d8703cbaf27d9244 DIST lammps-20Nov15.tar.gz 90227651 SHA256 7c392c848e73335226b2fef6bb8034b1152f91862d955a3bae00502bf9d8e8fe SHA512 4bff70e45fb30be10a33b4c6c60b73cceddf8d42588b0630b4802f1e61dea3c237c01c3667585ad210ef2cdb811491b1b8495718a90bb57853c58245e29d1fe4 WHIRLPOOL a01f54911a5edb666ef5af5302cf60d61d58d20f2112578e4d7bd16787b2bf59da09e9fe7ffa021fb6a97db40b23301ed77010f48a05e5471742c0e71413b7e1 DIST lammps-21Mar16.tar.gz 88654277 SHA256 c2f627db22f332995d90521f0e8d8e9865b85b49cde0ed4bcf727bf4b9b12767 SHA512 27e4a3a0c2c17fb9c85716b499ca2b3de8b0a699891afd32c8409117a0fbe27f1bd84ef16288cc5abda87ee8a7b1059960d8caed5aa339f54290aabeff0fdd4d WHIRLPOOL 370f79af4a8e55851aa0c071d02baddaade991a3208fe504f8b92796bbdb9b17b85af898a71177bbc67d885ffdef9280621c9b7f4bc22cdb14808332cb2eccb8 DIST lammps-22Jan16.tar.gz 85952234 SHA256 46425bf0ae73f716195a29dc9823c2c5989504f85b49a316bc304caaf6e6a674 SHA512 3ceeeaf76621bbc11ea25d5fb321b602b34ffb3893898a704b02e5cd428a36b2017006fdc1f7b1c5f957c33f26ca103a2939538ae7937555e0b25b5852cd48f3 WHIRLPOOL 7f61ea1924eceb190b7cf56ed32db75f6a45c99dbf1522862124f59acd1f79b1a46310d5e31a988011461a55c319677eaec2bf713e9a5cda0411b5d2280aa784 +DIST lammps-30Jul16.tar.gz 94454127 SHA256 41104065bfb433e9c69a88bf4c0d760a02186cbf81ec481332665b28f8503c1f SHA512 2ebcf30502810f8d6be107760bef0b9b4591142511ae410e7b44573fe9988bbbba5e8d5bfd16f74a3875bb1c41dbc6216a1c7e8a9b1d316fdf19a901ac4479d5 WHIRLPOOL e081b9eaed5a439be1c80c844629030af02b4cff6ed57cac3db209981b9d4e7381315c82de5f76fff7f8ead5b6250a1a4207d3f18c97c59e3ece2a716697175e DIST lammps-6Nov15.tar.gz 90177074 SHA256 b908d87106e89aa813c3d1a2e89f297ab42471ee463ef950f87f284d62aa24ac SHA512 91f8e33a00b3605dbb78f622a19886c11ca8ef3f4babe74e8d8f90bb176d5689e75d619155f58e6754a2756d20c05b74389e34f024167cba1841b8aade171daf WHIRLPOOL 4541537ea73292648764d6c8a7560f3127b8f911f4dcff0a97735c8e75868dc3aec7c2b32a2928ea446e8cfec87c81c9f86a635d29f3a65f42fd27661725911e DIST lammps-7Apr16.tar.gz 88791123 SHA256 f87c11cbbdbbb64a337e0608ae0fde11f77d9b32d081a8095376db9bbecc6d5f SHA512 1045f0337b37a19760718a2b3b48d31608248069a8fb2dc43daf555e44e720db770ff53e2a2db09c3e1f2703bb98894516229382c810ce45cca3647f353a21cd WHIRLPOOL 4ed6e93efff84888f982aec4c55adff6eda94fec5608e473fe821f77ea7a867fa7de23cf54fe28007b61304e41c9d7e42f4994e455bfb67cfadf79dbfc019e0b DIST lammps-7Dec15.tar.gz 82168656 SHA256 7fa1bb1089437c0f38f8c6920286e2f8424e6449956b4d570da2954f507af1e7 SHA512 13078e7614402efc310a178506134409b40fb2768c4d7ee1cfa6992b247ef25169288ec99d4314b1a98125037d7c1c954bd114abc6ac41c58f60506358d150e2 WHIRLPOOL f9ba52c0c93ea6950b2ee7e0f5e15ebef6ea50f647d23cb2f9a1caf523d3dfb8d52adbdf8f8840eebd7f79fc59ab294310b7bf7109b27c6b7e9d6e7d2f18b7ee diff --git a/sci-physics/lammps/files/fm_exp.patch b/sci-physics/lammps/files/fm_exp.patch new file mode 100644 index 00000000000..3b6bd24028d --- /dev/null +++ b/sci-physics/lammps/files/fm_exp.patch @@ -0,0 +1,11 @@ +--- lammps-30Jul16-original/lib/meam/fm_exp.c 2016-04-18 14:00:58.000000000 +0000 ++++ lammps-30Jul16/lib/meam/fm_exp.c 2016-10-06 03:15:55.631053526 +0000 +@@ -112,7 +112,7 @@ + return epart.f*x; + } + +-double fm_exp_(double *x) ++extern "C" double fm_exp_(double *x) + { + #if defined(__BYTE_ORDER__) + #if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__ diff --git a/sci-physics/lammps/lammps-20160730.ebuild b/sci-physics/lammps/lammps-20160730.ebuild new file mode 100644 index 00000000000..1e484f126fa --- /dev/null +++ b/sci-physics/lammps/lammps-20160730.ebuild @@ -0,0 +1,221 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) + +inherit eutils flag-o-matic fortran-2 multilib python-r1 + +convert_month() { + local months=( "" Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec ) + echo ${months[${1#0}]} +} + +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" + +# blas/lapack is needed by the ATC package which is only built with MPI. +DEPEND=" + gzip? ( app-arch/gzip ) + mpi? ( + virtual/mpi + ) + python? ( ${PYTHON_DEPS} ) + sci-libs/voro++ + virtual/blas + virtual/lapack + " +RDEPEND="${DEPEND}" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +S="${WORKDIR}/${MY_P}" + +PATCHES=( + "${FILESDIR}/fm_exp.patch" +) + +lmp_emake() { + local LAMMPS_INCLUDEFLAGS + LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')" + LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN=64' '')" + + # 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 + local packages=( yes-asphere yes-body yes-class2 yes-colloid \ + yes-coreshell yes-dipole yes-fld yes-granular yes-kspace \ + yes-manybody yes-mc yes-meam yes-misc \ + $(usex mpi "yes-user-atc" "") \ + yes-molecule yes-opt yes-peri yes-poems yes-qeq yes-reax \ + yes-replica yes-rigid yes-shock yes-snap yes-srd \ + yes-user-eff yes-user-fep \ + $(usex mpi "yes-user-lb" "") \ + yes-user-phonon yes-user-sph yes-voronoi yes-xtc ) + + for p in ${packages[@]}; do + lmp_emake -C src ${p} + done +} + +lmp_build_packages() { + lmp_emake -C lib/meam -j1 -f Makefile.gfortran + lmp_emake -C lib/poems -f Makefile.g++ + lmp_emake -C lib/reax -j1 -f Makefile.gfortran + use mpi && lmp_emake -C lib/atc -f Makefile.g++ +} + +lmp_clean_packages() { + lmp_emake -C lib/meam -f Makefile.gfortran clean + lmp_emake -C lib/poems -f Makefile.g++ clean + lmp_emake -C lib/reax -f Makefile.gfortran clean + use mpi && lmp_emake -C lib/atc -f Makefile.g++ clean +} + +src_prepare() { + # Fix inconsistent use of SHFLAGS. + sed -i \ + -e 's:voronoi_SYSINC\s\+=.*$: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) $(FCFLAGS):' \ + tools/Makefile || die + + eapply "${PATCHES[@]}" + eapply_user +} + +src_compile() { + # Fix atc... + append-cxxflags -I../../src + + # Acticate packages. + elog "Activating lammps packages..." + lmp_activate_packages + + # STUBS/mpi.c is using '#include ' now instead of '#include + # "mpi.h"' which requires an additional '-I.'. + append-cxxflags -I. + + # 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 +} -- cgit v1.2.1