sci-physics/lammps: Version bump

Package-Manager: portage-2.2.14/cvs/Linux x86_64
Manifest-Sign-Key: 0xAC91CA52

3 files changed, 283 insertions, 9 deletions

diff --git a/sci-physics/lammps/ChangeLog b/sci-physics/lammps/ChangeLog
index 6fd91467b6f9..efa59de7f088 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 1.97 2015/04/19 19:05:51 nicolasbock Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/ChangeLog,v 1.98 2015/04/20 12:02:02 nicolasbock Exp $
+
+*lammps-20150418 (20 Apr 2015)
+
+  20 Apr 2015; Nicolas Bock <nicolasbock@gentoo.org> +lammps-20150418.ebuild:
+  sci-physics/lammps: Version bump
 
 *lammps-20150416 (19 Apr 2015)
 
diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest
index c28a2dcc699d..5259093af520 100644
--- a/sci-physics/lammps/Manifest
+++ b/sci-physics/lammps/Manifest
@@ -8,6 +8,7 @@ DIST lammps-11Apr15.tar.gz 63843170 SHA256 21ceb4154a1439abeb2f0ac50f3058021facf
 DIST lammps-12Mar15.tar.gz 63521532 SHA256 048dc4d5f9f4d26d6f9bfeb4e20bb48cd01d3b064fb0b091309218c0895dbb3e SHA512 2581d795adcde9ef7bd10ebea5cfa1897835849c8aea112b8d45614e2eabb610316c6f7cba94b5324203b08382d31bdb17a3031d4d7f1ef4e951c35a08eda6f3 WHIRLPOOL 7fd33fed676b5b833dd053d79e64d090aa8384b462026147ee9e62313e937abaaef1d95d04c152254b2a1593f8b0baa077e5b68f85cb9f461f7128363a50214e
 DIST lammps-14Mar15.tar.gz 63563980 SHA256 10dba8d347a7ab7a5ba3e4a87f555177cb0ad5cbf4bcee4125cca5e67cb31dfa SHA512 99dd8fece0ec220f324a0c9dc14b80260119c1038afd4312ad85d6672a65164a6cee6625677f8ef337962677b82d4a0c7b2ca361d004dfd9fb0083c5b7eb1737 WHIRLPOOL 1fc20a1d388d575c3313a65d601b2f099464767c1585f601a961269317fcb320bb9b8dda7a7e4122808d8234d120300a379ba4d119c32d2dcc9ad0e5616893b2
 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-18Mar15.tar.gz 63598942 SHA256 6f76b8840af1581c03c8fd4065116d73d0f68264acf8b88ecab785e851b5a7ec SHA512 99d52891985f1bdaa0fea219057a6b76396b1ea61af62d06be6aecfd007e88eff91905df22cbb7255f5c43a2a62a4224c2daf73f3c8a18ba306f960fb2073c64 WHIRLPOOL a1668ae422aa1ac67ff8572b1b096f38b0eeb6a271ad20710ef82b2e4dd46db6538a5080deb4cfa05992033872f157a0dd53193216baf220565ab9167dcc0c8b
 DIST lammps-24Feb15.tar.gz 63487709 SHA256 f8a42d4fcd3c3b6591898cddee2fae6f29ecfd11bf688b2ae81896360181bdef SHA512 42777481fd6551fc14010c256bcd5665a42b52e79026860eca89724edb50df9e4af6566553e51954cf0c9099e4cc9c982e07cb4a99ec31e07fdb225ee5e7e219 WHIRLPOOL 140566ede55929e528c91da1903bda7667028183bf1d4294c441f98877675af206d66fa476167469f5e1f83aee969635a53c6a56d7eac3eb6d646cf5400d6472
 DIST lammps-25Mar15.tar.gz 63800289 SHA256 c39575a93b136108b54c08ebb888a3b32f6d2ae060514c43c7bf7d042415d06f SHA512 2bacc1a1010b008d16354af999bf2bc4dbd225dbaa8f078eeeb7898d19b41bd563c2ecc9a4bdc30d04c9d336aee28d35ae53d30ac20af7127579872f8c272b8e WHIRLPOOL 05aa0fb15236381c2dd3a4216d7f5c54f5b01e55a6c7b57f8ea8ddface3fbb7c707aed6723d9c603b4937b105f68305a2cae25458dd48a5266dbda86d7edabbb
@@ -41,16 +42,17 @@ EBUILD lammps-20150403.ebuild 5639 SHA256 009c0165f643c9ff35da312848abd88081043e
 EBUILD lammps-20150406.ebuild 5639 SHA256 2803a644d843d77f4896d4af5c94e18c72c797ce4783271242da44d1024449b8 SHA512 b6c6ae44df6ee0be857141a0e0da094b8936d8dc03a907c182dcc5834c8d0895d5eef2224266b89580e7d58df4d15035cbb4bac35976edfef2beaa3ca52213fb WHIRLPOOL a4422314ec7109a1f2f983861beb0a1b7d6228f2b5bcece83f73087c890e4ffa1cf06149005724f289332a20ee4088d04e560f6a031c36d6b10068b89d25ae06
 EBUILD lammps-20150411.ebuild 6832 SHA256 6fde6a18fde97b78370934585ad466bfdec116e2d913af6feb3419afb78029e5 SHA512 3b5035bbb06ee6be1b44f36e5e0befd871041ce6bb60a8204108f3c979ec74ae514a2fac43a3ffe4faaf66eba49baa22b35e271d1dc3a956c63ee14748df1b6c WHIRLPOOL a72393012ef64237711199af01c234465eb0217c8e56ea2378d404e3974ed44fa872f403b097c87d9d655ba78f2eecccb53f02da0ea2e2c2309c4d8065dd020c
 EBUILD lammps-20150416.ebuild 6832 SHA256 4bf509ae365810d708bc92620aa04e8a9e4010a178b1c042b80a65d0085e4f4f SHA512 b8371ef0a764c872ecb74395fbe950fb323dd8390e2a9b783a40445581620755bc4255d60b21297153a3bf554b09ac16fa29cc73830346822c061b328dc88c62 WHIRLPOOL 3e25dec55dfb53b823f9a6ffec66d21d4eb3ecb6ab7e4f396914c80bcb1f6c668dad8cbb3e8c7e4a653aa4622269e4a3d1ea1f972b722c80410897d06b56e8cb
-MISC ChangeLog 16561 SHA256 c7871f80776991287d35225d40b8a2c4e74ffcedc868995368e0aa7699230caf SHA512 329f759a963ff80adeb8909e8160a2a50b16626110ebeb16a8066b24664c751329205d66d5ce00f80288a266831a961b89e146c56e01c473136b9509d084dcc6 WHIRLPOOL fe72a28256c655a7208c37ab8928b1ec30da0b70210f51945dcb3ac94b0ed8eb8f23e4efe19ca9e25388972418792c0c6a4a6e38dad56080c52b9f43fda8b8a8
+EBUILD lammps-20150418.ebuild 6832 SHA256 665ac583ecbc456e5e7e1da98e326b4a73d4c3d16f5b03e0de7a3d9694d06f3e SHA512 e1a10023a8719d745f798ae607b379824fcb13df1d49ea6ff5b133288cebc3586bf1a10364ce9a7c0fb34f4b8f410ad3095d0539b13c9896334b072d6ec7577e WHIRLPOOL 9ce0e97de6eefebce313cd8da8ab3890299112fca379d243b68ee94520b5a20efd0ebdc06a59f208965320c156231b4814d13e21be41d41e2f3ac0ab2dddd7bd
+MISC ChangeLog 16707 SHA256 0765ac6941a1b9e18eb86b2caf33d5f8fa6156332f07a9332d9ef3f5fe4c3ba4 SHA512 9e926af3720beaaa487fbddb3714c15e3be5da4bcf65fce7413041677de9fc4727d8e8e86c3ed2fe73773a798e01df7cc3589993fab6f2999ff1726006a8dbfa WHIRLPOOL f8c88c0b5c628d5b24b7751790917fc2fe485e28050ddf08401fb17db584bbc697563b2144d25f43cbcff3889c11d52d4afbd1bfadcbcd5d1b63afc5103d3447
 MISC metadata.xml 1104 SHA256 cd019e3b907b935374e9818167b4a9c406d938cf132b6656a7aed15fb8070d4c SHA512 9fa9919de32eb24c720fecbb449112b997e331b4ecb37aba8cdfcf90bc832e00ff8deef570f8eb92341f8c82b90787d65befa9ebeacb904abb467b8f3e1c5054 WHIRLPOOL 88fbd760afe74c12310ed3417e8c6d242b282bc78fee612b1c0c1dd1532ec9253f7b5134a9fb8f463f9fe469ce1d5fada43b97b348c221c84869907cfc0dd37e
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diff --git a/sci-physics/lammps/lammps-20150418.ebuild b/sci-physics/lammps/lammps-20150418.ebuild
new file mode 100644
index 000000000000..9dd471017d33
--- /dev/null
+++ b/sci-physics/lammps/lammps-20150418.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-20150418.ebuild,v 1.1 2015/04/20 12:02:02 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
+}