[gentoo-commits] repo/gentoo:master commit in: sci-physics/lammps/

[Nicolas Bock]

commit:     6b87c500700e9c2ff4c39f41b804b36bfe5d1e65
Author:     Nicolas Bock <nicolasbock <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 24 12:30:52 2015 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gentoo <DOT> org>
CommitDate: Mon Aug 31 14:37:53 2015 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6b87c500

sci-physics/lammps: Version bump.

 sci-physics/lammps/Manifest               |   1 +
 sci-physics/lammps/lammps-20150821.ebuild | 267 ++++++++++++++++++++++++++++++
 2 files changed, 268 insertions(+)

diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest
index 7ef6a63..17bb0ea 100644
--- a/sci-physics/lammps/Manifest
+++ b/sci-physics/lammps/Manifest
@@ -5,6 +5,7 @@ DIST lammps-16Apr15.tar.gz 63842472 SHA256 65aecf6f25a055734ef113890a86ecbf7f847
 DIST lammps-18Apr15.tar.gz 63883297 SHA256 4ce74978da738383a1d808a37481c3c43d4f8f44d919770b3f2cdd4fcf03345b SHA512 be088ec59b7fe495fff3cdfcc5ccb52d2705eec20deb5c8694a215943786652c9dc22a81ba48324707495c3f56c0c347af964d1952ae077c8db02258cf31387a WHIRLPOOL c90403147cc4eda5b4f581cd1bd18bcc8f45a73b1d0e51dcd64c52fc636116c9d57337b89b5753c86e1bbf386f8a2391a9813a6e32154a819f3e35cfc816b5e2
 DIST lammps-18Aug15.tar.gz 87893731 SHA256 513237934cda7c1e026f4983096fd53cb510fadee12c55b13b4735086155245a SHA512 5816509f5b988dbe74c9f40a9faa42b3bcf260388dfe70703a1544517acd3f868d3bc398fb4c2fa7713d24409075d44ad80b8e91a25a28db783c2605aff30977 WHIRLPOOL 7022f3aabadffdfa2ef4c8219589e46fba2572d9ed4b52591f6516a61d4895b39d637d88535ba83881db5d48661e34ca6ff2f22a6819dbec015af979721a0f53
 DIST lammps-18Jul15.tar.gz 66065642 SHA256 deb6625b7c21cf94fc7ee9aefb2edf55a6c8dc870e919028c9ffa1cd169d57ed SHA512 d26dd0084779e037af35bc26f81cdca5a7617f841860e6eab7d52f6c023d2c001075aad5dc3d656ceb6e92650589acc472fa5c8954fd9ab81ec0b737e377284b WHIRLPOOL 66794b7250cdb077bcbeb2b95a464aecc684f7592d81f3db4a3702195ef1d8404eb4b1f38e6c1dd859a42dd8ca1ebd039cbac4d9fd11be99a376168f2c498cdd
+DIST lammps-21Aug15.tar.gz 87096749 SHA256 46f68e7b61e50ab3e790c53cadd82fde7c7aa58aa73e8a3257f24facff2ed0a4 SHA512 b1dd90890c43a6cf55a57a61279dcc4c10fdedb4ad90f225a06c0e93eb139d30f2d56baa233c081b38adeeb0a8419a0315ccc4b0fa15c3ffbf7db626ca261e9d WHIRLPOOL a1d7d4ab30f9ecca3fd64216e729fef6fa1b3f7a6698b9eaf104bcbfa03a66862cd8c5882e94f73e841064d94bf030aaf569ebb457d89fbd345b391f9cee6822
 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-24Jul15.tar.gz 67180142 SHA256 bd183f7b073e1ca86656a8f6ea99195123ce3c7829c872ca45216da4132ff96d SHA512 e285a1f326658bd23f32ecf9409d9f0bf16ed635656bbcee0d84da58e1c008363c7815001bcaa5b7701d99b3318a56240b021447e94754607c2ceb178e377122 WHIRLPOOL 003237f8e9a7caec98aa1f8f0c5e03c0cda6d60f20460e32c4eea3c92707e349f4e1a71510f1290b6e6aeac1621951080f904b1bb2224c8eb9e25067206d2b1b

diff --git a/sci-physics/lammps/lammps-20150821.ebuild b/sci-physics/lammps/lammps-20150821.ebuild
new file mode 100644
index 0000000..1a244c8
--- /dev/null
+++ b/sci-physics/lammps/lammps-20150821.ebuild
@@ -0,0 +1,267 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN=64' '')"
+
+	# The lammps makefile uses CC to indicate the C++ compiler.
+	emake \
+		ARCHIVE=$(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)" '')"\
+		"$@"
+}
+
+lmp_activate_packages() {
+	# Build packages
+	lmp_emake -C src yes-asphere
+	lmp_emake -C src yes-body
+	lmp_emake -C src yes-class2
+	lmp_emake -C src yes-colloid
+	lmp_emake -C src yes-coreshell
+	lmp_emake -C src yes-dipole
+	lmp_emake -C src yes-fld
+	#lmp_emake -C src yes-gpu
+	lmp_emake -C src yes-granular
+	# Need OpenKIM external dependency.
+	#lmp_emake -C src yes-kim
+	# Need Kokkos external dependency.
+	#lmp_emake -C src yes-kokkos
+	lmp_emake -C src yes-kspace
+	lmp_emake -C src yes-manybody
+	lmp_emake -C src yes-mc
+	lmp_emake -C src yes-meam
+	lmp_emake -C src yes-misc
+	lmp_emake -C src yes-molecule
+	#lmp_emake -C src yes-mpiio
+	lmp_emake -C src yes-opt
+	lmp_emake -C src yes-peri
+	lmp_emake -C src yes-poems
+	lmp_emake -C src yes-qeq
+	lmp_emake -C src yes-reax
+	lmp_emake -C src yes-replica
+	lmp_emake -C src yes-rigid
+	lmp_emake -C src yes-shock
+	lmp_emake -C src yes-snap
+	lmp_emake -C src yes-srd
+	lmp_emake -C src yes-voronoi
+	lmp_emake -C src yes-xtc
+
+	if use mpi; then
+		lmp_emake -C src yes-user-atc
+	fi
+	lmp_emake -C src yes-user-eff
+	lmp_emake -C src yes-user-fep
+	use mpi && lmp_emake -C src yes-user-lb
+	lmp_emake -C src yes-user-phonon
+	lmp_emake -C src yes-user-sph
+}
+
+lmp_build_packages() {
+	lmp_emake -C lib/meam -j1 -f Makefile.gfortran
+	lmp_emake -C lib/poems -f Makefile.g++
+	lmp_emake -C lib/reax -j1 -f Makefile.gfortran
+	use mpi && lmp_emake -C lib/atc -f Makefile.g++
+}
+
+lmp_clean_packages() {
+	lmp_emake -C lib/meam -f Makefile.gfortran clean
+	lmp_emake -C lib/poems -f Makefile.g++ clean
+	lmp_emake -C lib/reax -f Makefile.gfortran clean
+	use mpi && lmp_emake -C lib/atc -f Makefile.g++ clean
+}
+
+src_prepare() {
+	# Fix inconsistent use of SHFLAGS.
+	sed -i \
+		-e 's:voronoi_SYSINC\s\+=.*$: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
+}