Version bump

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xAC91CA52

3 files changed, 283 insertions, 15 deletions

diff --git a/sci-physics/lammps/ChangeLog b/sci-physics/lammps/ChangeLog
index 1883095dd5c3..9338f501ac1a 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 1.105 2015/06/26 12:14:57 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/ChangeLog,v 1.106 2015/07/18 21:59:49 nicolasbock Exp $
+
+*lammps-20150718 (18 Jul 2015)
+
+  18 Jul 2015; Nicolas Bock <nicolasbock@gentoo.org> +lammps-20150718.ebuild:
+  Version bump
 
   26 Jun 2015; Agostino Sarubbo <ago@gentoo.org> lammps-20150515.ebuild:
   Stable for amd64, wrt bug #552468
diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest
index cf48874fe741..1b2444e71447 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-15May15.tar.gz 63835027 SHA256 0233ea98c7d77d31bd0a538bb674c0ee8f000f1d0ee1b8c049072873192aa228 SHA512 a23c16b98117590b15ca7662b878fb2f76ec41399c329c98deb48e28a0ffce293443269513a96c2503389894b598787b19dadc210d4b4dbc6a7432caf633e7d1 WHIRLPOOL 4c4edfd772bbf534e42fc43e1feaf3b8f76e74c58ec1e985e3c29ee0d8e64aa8c501b8e45e078643409c320a1d834b0d5eb699e7d1ec29df06be0126d12492f1
 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-18Jul15.tar.gz 66065642 SHA256 deb6625b7c21cf94fc7ee9aefb2edf55a6c8dc870e919028c9ffa1cd169d57ed SHA512 d26dd0084779e037af35bc26f81cdca5a7617f841860e6eab7d52f6c023d2c001075aad5dc3d656ceb6e92650589acc472fa5c8954fd9ab81ec0b737e377284b WHIRLPOOL 66794b7250cdb077bcbeb2b95a464aecc684f7592d81f3db4a3702195ef1d8404eb4b1f38e6c1dd859a42dd8ca1ebd039cbac4d9fd11be99a376168f2c498cdd
 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
@@ -15,22 +16,17 @@ EBUILD lammps-20150418.ebuild 6832 SHA256 665ac583ecbc456e5e7e1da98e326b4a73d4c3
 EBUILD lammps-20150428.ebuild 6832 SHA256 65b7165907191e4ac8369d4aa8463f8833233061d0dd1c81be6a62334183122d SHA512 3ce45944204b70f5ff9096b3a9ae242c4fb547cdd49b6f08cc3d69c8d67e883b7389c67a5551bc1d5c1aebe74dc44366d274d84cb93889e106df355a6c4a96bd WHIRLPOOL 63c572cc29d3170248c955b5c26457851f4b1abf42ceb539188d552a3a9a32846114f7599bf52fbbe924b9872eb6ad8928562548b9476bbe9997601687539005
 EBUILD lammps-20150430.ebuild 6832 SHA256 e03b59672c49b6b4a2544c2cdc71c9c2318fa56b702961616f7c2e23d69db10a SHA512 b667229ea19ff29130f26e8b9340a49763544b767195fad88d4b6d5bfaa98771888340b073f09ac679ffa1f1b9ea2baf36e13e1860102c324552275894c16690 WHIRLPOOL 4971609fc471fc551cbd4faac905f5ae86444dc8163a211d76cf63c85f89db02ccc8d09543a74635cd6b48dc7731f6d4f31810a584e06fa073f3676b7271b607
 EBUILD lammps-20150515.ebuild 6823 SHA256 e6d5270928f726a0ea2cbd8a97594692460ec120c7b5e551a6710c60684b3257 SHA512 9cde0cbc15b42d2c83fb95a11e66d2be5214edfd486f8ce36e620cb9e2ae4352b0383b8271ac047cc81e04b7e2c8032e7db750764892c8830ccbd1a9a267ed7c WHIRLPOOL 535cef0d8e477d08427275df3a24aea407ab92136615890bca2097cc6eb923c94c92f1341315973a2e7809b0e90567c04bc04a61c440ab5f99d5c24663d0a585
-MISC ChangeLog 17950 SHA256 ddcb6b44d246a9b924f517b0f900356fa003d3f5f410be546331512c6ec8901e SHA512 601b899da29b610209cf41998c66a66723664d9407db5a89a74cdb789a15df32fb1b07f0e285f7a09ac4d5951111277b71e6157598ef2357871f11893f5754cb WHIRLPOOL 086497dcecb136dd76466b8d275104ee622b174142a0c34f24c8d1b50837a9db5985270afd242cadfc1d88cca1e83be57f684dd68cbd9cc17dd197922ed24816
+EBUILD lammps-20150718.ebuild 6832 SHA256 ddae0705ad287713e68ac2aa00c669f042057dfd157c995eeb1e01db4b4debed SHA512 32568996a1e9fe768ce04bc9afa7c07c7f8e50b766bde05a33081920616f7e905dea38c29f9dcddfaeaacdecb9a618b467ffb0d74fe2d57870992f350d121e68 WHIRLPOOL 951bd37fbc68a7701bb0c2bccf1ce089f0ced322aa6bc29f321ad19c6c09acbac48c0cff90e8e3431f6760adc8f78b70189ecfbc6451031417b02ad8c5468b79
+MISC ChangeLog 18084 SHA256 d9eeb45cc2a65245a2258ac597a8232961d97f02f9af07bc8c1a722635dadf83 SHA512 249728c16116cbb819d06d26f2e905d9ebed768b790d073453172d2ac2b923ded4564520d128c6d035d09a3147ca6a7885d59d2f1578c00236344e842f3b16ad WHIRLPOOL d1cc3dc1eaa5f4643307dd376ab016968ced270c4a2422790905be1e7e3aa6a41c1d9deb5a678dfadb7c8c539a628ea02829eee887840b9c2edb6b71d9624778
 MISC metadata.xml 1140 SHA256 c1c836b9a61f0d0c881a3c9de63f7dda4bbe55c187c163154a4fce296d0cc7c2 SHA512 ff4ee9b4a49b43c104fc2f5161f1ca6a32aa536cc2025a61ea0cf1d035d40be194d7889cd6048e2120325542ccfaa1cada82b8a1c8c2c11d5d23ca3ead2130cc WHIRLPOOL 35167e15aff5a79526a9d69fbec8405640c06c1cf69017072984a1f139ba2a939b42aab96c9b5be629d84205414623a4b1a9b9536957777234ad4a26f870401f
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diff --git a/sci-physics/lammps/lammps-20150718.ebuild b/sci-physics/lammps/lammps-20150718.ebuild
new file mode 100644
index 000000000000..3d7dbf7ec51f
--- /dev/null
+++ b/sci-physics/lammps/lammps-20150718.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-20150718.ebuild,v 1.1 2015/07/18 21:59:49 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
+}