sci-physics/lammps: Version bump.

Package-Manager: portage-2.2.18/cvs/Linux x86_64

3 files changed, 276 insertions, 16 deletions

diff --git a/sci-physics/lammps/ChangeLog b/sci-physics/lammps/ChangeLog
index 961193893ae5..bac2b2851796 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 1.102 2015/05/03 02:52:39 nicolasbock Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/ChangeLog,v 1.103 2015/05/18 22:49:06 nicolasbock Exp $
+
+*lammps-20150515 (18 May 2015)
+
+  18 May 2015; Nicolas Bock <nicolasbock@gentoo.org> +lammps-20150515.ebuild:
+  sci-physics/lammps: Version bump.
 
 *lammps-20150430 (03 May 2015)
 
diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest
index ae97e07133fc..64390e5a6d0e 100644
--- a/sci-physics/lammps/Manifest
+++ b/sci-physics/lammps/Manifest
@@ -1,9 +1,7 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
-
 AUX lammps-python3.patch 509 SHA256 85ab3e1d1cc123af8d63400ec1b83f52f50325aa6990ae9f2f032d6753f8553f SHA512 e88b7e036c3ea86c032a7e8dde771073c08ed96c0a3da240a824fd7f424553ef4d5db2ba6c4fcfcb9f0ec4550a073e7370a163165352911ee4f1d64f91094056 WHIRLPOOL bb73c0b001b39266d4586ff7c409789599b8e64785609037b96e6bbcb89ac100fa4171230fc8e6b28017d898b591c8c0188aace223caaaa728477865a2e97699
 AUX python-shebang.patch 393 SHA256 77ffe7208de583b53f0ec4e688d647218135fa0cafbe374b56c6f4ceec3229e1 SHA512 fd4663ac2ce6949e59509ab03a7eda4471e38350440fe6c64c9fe5321941a5951074578148d0da335292a4e19c6c0b13d3e97c174123eb1d9662bbd63247b5e7 WHIRLPOOL bd792c3cfe7bb85b436ba11e2574c6bfd21364566236c89ca7330206f781d474117daa9cf44c9a4ba902349c673aaefeffb84e45b2afc2553359dcf270370370
 DIST lammps-10Feb15.tar.gz 62912048 SHA256 59373e9b5592f7b697a144bbce1fb742726e03536b7bb355dac7a9e013ddf9b8 SHA512 a7804377a23f03f338bdaf443439dffcdc52293b4c45e6369b340a1107510fed0b8a198e3b5afcff2e04e109985b52ee62e7b28276697bae37ac6f783d1ab9f2 WHIRLPOOL 09f29cadf8b072d388abe45ec219341d2a14a6c9cc9e4010a0f7945e930e9984738f7837748d117ab95ca76ce0c8d9160fe88dcec17e8d21b81f385dec8f7005
+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-28Apr15.tar.gz 63883556 SHA256 6e7c32690cf8bb5a4fb147bab6029cc1d03594ec7b3ea3833e7dc89acc596d8a SHA512 414c786e8666cddd31a3200baedc76974371280dc219636914dd7863f03e32e11f637a9c184af78d8d4da22afe4cf734b6a0eb32c78d6f53ee95d796a3e080c0 WHIRLPOOL c57a91f9d5e977d26cdb2076b5bbd2f3b5791396c23b5326f16cc609b9646e80c602a492b312b4e5f78d1d638c4a6b66e9a49b1ced02274ad7202821a2884975
@@ -13,16 +11,6 @@ EBUILD lammps-20150416.ebuild 6832 SHA256 4bf509ae365810d708bc92620aa04e8a9e4010
 EBUILD lammps-20150418.ebuild 6832 SHA256 665ac583ecbc456e5e7e1da98e326b4a73d4c3d16f5b03e0de7a3d9694d06f3e SHA512 e1a10023a8719d745f798ae607b379824fcb13df1d49ea6ff5b133288cebc3586bf1a10364ce9a7c0fb34f4b8f410ad3095d0539b13c9896334b072d6ec7577e WHIRLPOOL 9ce0e97de6eefebce313cd8da8ab3890299112fca379d243b68ee94520b5a20efd0ebdc06a59f208965320c156231b4814d13e21be41d41e2f3ac0ab2dddd7bd
 EBUILD lammps-20150428.ebuild 6832 SHA256 65b7165907191e4ac8369d4aa8463f8833233061d0dd1c81be6a62334183122d SHA512 3ce45944204b70f5ff9096b3a9ae242c4fb547cdd49b6f08cc3d69c8d67e883b7389c67a5551bc1d5c1aebe74dc44366d274d84cb93889e106df355a6c4a96bd WHIRLPOOL 63c572cc29d3170248c955b5c26457851f4b1abf42ceb539188d552a3a9a32846114f7599bf52fbbe924b9872eb6ad8928562548b9476bbe9997601687539005
 EBUILD lammps-20150430.ebuild 6832 SHA256 e03b59672c49b6b4a2544c2cdc71c9c2318fa56b702961616f7c2e23d69db10a SHA512 b667229ea19ff29130f26e8b9340a49763544b767195fad88d4b6d5bfaa98771888340b073f09ac679ffa1f1b9ea2baf36e13e1860102c324552275894c16690 WHIRLPOOL 4971609fc471fc551cbd4faac905f5ae86444dc8163a211d76cf63c85f89db02ccc8d09543a74635cd6b48dc7731f6d4f31810a584e06fa073f3676b7271b607
-MISC ChangeLog 17610 SHA256 44eb3cf8ed9d8191c96fc213bf5f66a1e685057ae9ca85c7ddaafd6789e3cf96 SHA512 60fddcc589c71735c51ba1229360e2ee95fe48cf5829e4793b4b6abee22d91e86a4bb4f533cadfda498e45a768890946787041ced2aae719bfe08dc424f4b490 WHIRLPOOL 3747cd2fe7a460c14ce48b60fad4d4dce20ab5f330a2caa33aa0f03b01bb245dc7546fcdbafe64d5870cc63f524753194aa2443f5ad7af95885de1fdc0d8e96f
+EBUILD lammps-20150515.ebuild 6832 SHA256 b263735098416332d6606f75c31694fb146a8010d1343203e2c4a57544d3aef6 SHA512 916095631710f429ddea335fd94273b9a3c4d7db9ba5f94087c94979786bc14617fdfb1ec928fe27af52115642b90b51370567289f6130b2d8d2a73b803c0507 WHIRLPOOL 2dd8ff76c5f52ec0b740b1329f99832947b49187865f49183d69e010d92f4a298533fe53bfe54f106c8f6589ada85cff2da83ed710219ab9bfb7daa770b9bfd6
+MISC ChangeLog 17757 SHA256 20d9aa31e51bd7341148c55a050e459c41a30e9030be8b19a74efb4479b3964e SHA512 8da9cda17df483c1f870ca95c08ec1c52404f8a0cc1c42ca6ebb7137c6502a03b9137c6290d06116109026cb83dfd14f810f45c78191fdf599993132a9e378c9 WHIRLPOOL 73c598b3770298b1b8a745fec07d74b1ad663ae72d9d472a158538bc24c3df930ee7c028956b0fba2907298d96aa3dda024739163416214611dbf92c64fe06e7
 MISC metadata.xml 1113 SHA256 7fffeb01fabbbd836129f6765f5f2e6ca92d86eab5f713fae5ce248697e3ff6f SHA512 a7d91b1d8856bc987b7baac7a540d9cf62e82912b7b88e760a57b7c3b342a078f6e901712876b5fa5da262aecb11fcd1786ee671993a3ae2ec55386a9058be9b WHIRLPOOL 8bf5f029ab656e2b7006d5a4458df54df3731922624f81cd6fa84f718a96d1014f261558c5bf92dec176ebd7c884b3538d24d68264f01683ab798eb3aa8cd7b4
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2
-
-iQEcBAEBCAAGBQJVRY18AAoJEF1ww0n44d9NX+0H/1YllrO5B4t4CilGPPYcHxqk
-Q5Qo/MboGmTJh6UlEbbhXTuMJEyITMLr6N0Z9K3WpWiWgygQE37FeMZLIQo/15kO
-6v9/BOsZJt4bJ9TYYIho7VWULU7lwpcC17YDRskxQLW3NOeXhxnob0wwOvi4/Nlk
-2DmB110zcjx4ACeXiWQLIXdeI9MkOlAD37PJ5MbIf/OodffJinnFOIzgcJ5J1Fi1
-m3XDN3jjLc7XZPFPwi5X/D5Qy3Az83NEc10Qsg/CEs+8gwMmr4c8Q2xxxuWFL1i+
-51d2o3ZklpOpmoI2hj8Mpu4WLHfYXO3FQIccgriQNieEBDRdQxRYCVIEhBdLj3s=
-=ADye
------END PGP SIGNATURE-----
diff --git a/sci-physics/lammps/lammps-20150515.ebuild b/sci-physics/lammps/lammps-20150515.ebuild
new file mode 100644
index 000000000000..4631fbeb4184
--- /dev/null
+++ b/sci-physics/lammps/lammps-20150515.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-20150515.ebuild,v 1.1 2015/05/18 22:49:06 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
+}