Version bump.

Package-Manager: portage-2.2.18/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 e564c5fdaf62..71833f09bf04 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 1.107 2015/07/24 12:22:22 nicolasbock Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/ChangeLog,v 1.108 2015/07/25 13:31:53 nicolasbock Exp $
+
+*lammps-20150724 (25 Jul 2015)
+
+  25 Jul 2015; Nicolas Bock <nicolasbock@gentoo.org> +lammps-20150724.ebuild:
+  Version bump.
 
 *lammps-20150721 (24 Jul 2015)
 *lammps-20150722 (24 Jul 2015)
diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest
index 2b1a7d8d16a8..cbb4892776f0 100644
--- a/sci-physics/lammps/Manifest
+++ b/sci-physics/lammps/Manifest
@@ -10,6 +10,7 @@ DIST lammps-18Apr15.tar.gz 63883297 SHA256 4ce74978da738383a1d808a37481c3c43d4f8
 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-24Jul15.tar.gz 67180142 SHA256 bd183f7b073e1ca86656a8f6ea99195123ce3c7829c872ca45216da4132ff96d SHA512 e285a1f326658bd23f32ecf9409d9f0bf16ed635656bbcee0d84da58e1c008363c7815001bcaa5b7701d99b3318a56240b021447e94754607c2ceb178e377122 WHIRLPOOL 003237f8e9a7caec98aa1f8f0c5e03c0cda6d60f20460e32c4eea3c92707e349f4e1a71510f1290b6e6aeac1621951080f904b1bb2224c8eb9e25067206d2b1b
 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 d3bf0c40480bb9d230678c50d64d40e41cb627a03ac7c258920a9e42c3f883cd SHA512 189bcfce8a7ace252f2bb749ee651ab77f3c2572a453752b6925b96a31383d4e08c7d95092635e28b31f88601ad3eba2e33c9316d33928255e408fce6925869e WHIRLPOOL af857a14e98226c6450386d175e8c1a100bc5aa477659460bf12a74557f72ef825d1149a66083c166d4d0ae14cf0080feba8fcaebd6e762abe81bb08e0732364
@@ -21,16 +22,17 @@ EBUILD lammps-20150515.ebuild 6823 SHA256 e6d5270928f726a0ea2cbd8a97594692460ec1
 EBUILD lammps-20150718.ebuild 6832 SHA256 ddae0705ad287713e68ac2aa00c669f042057dfd157c995eeb1e01db4b4debed SHA512 32568996a1e9fe768ce04bc9afa7c07c7f8e50b766bde05a33081920616f7e905dea38c29f9dcddfaeaacdecb9a618b467ffb0d74fe2d57870992f350d121e68 WHIRLPOOL 951bd37fbc68a7701bb0c2bccf1ce089f0ced322aa6bc29f321ad19c6c09acbac48c0cff90e8e3431f6760adc8f78b70189ecfbc6451031417b02ad8c5468b79
 EBUILD lammps-20150721.ebuild 6832 SHA256 78eeb3095cb63556b61ac64dc2fbe5e77cf838d1be40d1243c146a8d25b07551 SHA512 7bc8f7f0bad9c11b38f76a7cd41f70906055d71d10765b89236384317b185d3ca6b9dae3c18bf65f739034daa635ff891a7bd7c3d4ff9aebef8372a9b9feb982 WHIRLPOOL 13a01f97dde4ac69236c22efbb098f478903f1b5e0110b31b3f5334ecd1693d2f851ed5ad7b0e9dc0ee7dc0d4b4c3642272933d31092740d1b56d43a506a903e
 EBUILD lammps-20150722.ebuild 6832 SHA256 36ce99bc1f14ba14d57100b3d6373d0ae70cb11436c4aeb2ea94527301971ba9 SHA512 b483d0e8dcf3210eb79fc59e821dd69121f754372a96233cae50d69261b20a66a24b75b6904b896ea7b0fc6b4feb6486c41e8ae99712cad35cca6cd57646ad33 WHIRLPOOL 0362e81fdcfb5c30ca7a0bb7d5ad5a3e4818172834d524901d7ad89133bf8a69a2e297a2bfe46e6549ed31cce329c84b0d4d98fb5e99a8681c9aae21d67cf9b6
-MISC ChangeLog 18269 SHA256 095136fffb0649178823208908d16008184bb9c62552d647cf4cd398f618d563 SHA512 260d01d63450c4c353ab814cd2c1878ffe3aecc81e2dc9473daeb18bc66ee1c3c59f60ff6d45ccbaf3272c117342db0209b9da02734217ce93d841398bcbc0f3 WHIRLPOOL 708ddd9b3dd131b2503d843736b69b647d3835d1f75aa1459d9de171b4f8a17e05a8ad70c6d3b802a6ed0f7e558441e72c3afc16449ff2fac9ab7d0218c2e6cb
+EBUILD lammps-20150724.ebuild 6832 SHA256 d8ffe370aeb47d05483a6222529101fa811837adf475a0173a1a3322a9a41d13 SHA512 71317226d055e45cc889f1d92ea954d88e8bb0975a423a2725ef79cf06fbbc7c48374bab95d64e6b04686b3b6d095c098c66753bd57cf1ff9d2718c960f01826 WHIRLPOOL 19ed6a15e5c1b00110a00d710c8aa1089e2a1106af9501a1804c86e4976e41bf9949932984f0e71c477c1349fcf09c14de6f3718d4b9cc24a9645ef19e0c419d
+MISC ChangeLog 18396 SHA256 3dc59a197163aae2cdc8404ebd3e62752b097dcfbf32bad211a7f271b875bd68 SHA512 16c7835271fae3f701140dafb36f2d305e6b5026aad3c1a509a2c4c2db06d95584b83abf74e2f7c6f94cfa2e3fe6db4fbdea9f8d34f54a0ac7007a1082bd3adf WHIRLPOOL 195d6e5b64e26ec541118eb9616dc05ab78cbb79b9661683f4e7543436b9f3e4a14e8f8cb55bf5caad10ed01728ac4f3cc76134ed1a187236545791f70798f00
 MISC metadata.xml 1140 SHA256 c1c836b9a61f0d0c881a3c9de63f7dda4bbe55c187c163154a4fce296d0cc7c2 SHA512 ff4ee9b4a49b43c104fc2f5161f1ca6a32aa536cc2025a61ea0cf1d035d40be194d7889cd6048e2120325542ccfaa1cada82b8a1c8c2c11d5d23ca3ead2130cc WHIRLPOOL 35167e15aff5a79526a9d69fbec8405640c06c1cf69017072984a1f139ba2a939b42aab96c9b5be629d84205414623a4b1a9b9536957777234ad4a26f870401f
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diff --git a/sci-physics/lammps/lammps-20150724.ebuild b/sci-physics/lammps/lammps-20150724.ebuild
new file mode 100644
index 000000000000..3c441782e504
--- /dev/null
+++ b/sci-physics/lammps/lammps-20150724.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-20150724.ebuild,v 1.1 2015/07/25 13:31:53 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
+}