sci-physics/lammps: adding new version.

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

4 files changed, 254 insertions, 2 deletions

diff --git a/sci-physics/lammps/ChangeLog b/sci-physics/lammps/ChangeLog
index 64bb0ff55d5b..06fb48df915a 100644
--- a/sci-physics/lammps/ChangeLog
+++ b/sci-physics/lammps/ChangeLog
@@ -1,6 +1,12 @@
 # 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 1.87 2015/03/23 19:06:04 nicolasbock Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/ChangeLog,v 1.88 2015/04/11 04:52:50 nicolasbock Exp $
+
+*lammps-20150325 (11 Apr 2015)
+
+  11 Apr 2015; Nicolas Bock <nicolasbock@gentoo.org>
+  +files/python-shebang.patch, +lammps-20150325.ebuild:
+  sci-physics/lammps: adding new version.
 
 *lammps-20150318 (23 Mar 2015)
 
diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest
index f3d6177ee693..e6c90593f8d7 100644
--- a/sci-physics/lammps/Manifest
+++ b/sci-physics/lammps/Manifest
@@ -1,4 +1,8 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA256
+
 AUX chunk.patch 608 SHA256 1e8eae1e25b0975c949efda91fb97899ca4bedc99f40dbb23eaabb86b6b4e035 SHA512 a45a78cdaff4aca1a352f8f302fe0706eb7c119fb33d284e256d41cf2fa7d5c1d3f38ccc7f7b6e0678956eaf212de4ef5db787a77762b71b0a511dfba7fb014a WHIRLPOOL ff6d3648bbd9255cc9969d531572d74aea3d51ee4afb65c0e295c2a4918f7f1f615bacca242c9f01a6b8a5d5005da80a47d41d1aa7c97e6836bcc33f67cd96db
+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-12Mar15.tar.gz 63521532 SHA256 048dc4d5f9f4d26d6f9bfeb4e20bb48cd01d3b064fb0b091309218c0895dbb3e SHA512 2581d795adcde9ef7bd10ebea5cfa1897835849c8aea112b8d45614e2eabb610316c6f7cba94b5324203b08382d31bdb17a3031d4d7f1ef4e951c35a08eda6f3 WHIRLPOOL 7fd33fed676b5b833dd053d79e64d090aa8384b462026147ee9e62313e937abaaef1d95d04c152254b2a1593f8b0baa077e5b68f85cb9f461f7128363a50214e
 DIST lammps-13Feb15.tar.gz 62974524 SHA256 6be39873ff30eaaf467ac201d7f9b06b7fb175c5fcc4687dc38b7e8ab8ac0544 SHA512 20a0e7ba4905cf3e1f57df9bb9ddba298c8ee03e823d920ffa526a6ee318e4c9a5d3319bd79a46441a895c5b03ba0d296a2921f38f5795014f544ec58b3be629 WHIRLPOOL 22e9534dc84a9ce5cc2f5ca0ff693a05cc8afa1f307cac71d739c7504e56a11121acda62cc1d141f2e8f556a4c35bddeeac09cd429cddde531dec115925f4b00
@@ -8,6 +12,7 @@ DIST lammps-18Mar15.tar.gz 63598942 SHA256 6f76b8840af1581c03c8fd4065116d73d0f68
 DIST lammps-19Feb15.tar.gz 63160551 SHA256 970ea081e424f631c56a93e0bbd8cf37b67f8b3d707b0c6a84e5d942100a3848 SHA512 f8947dce3143ba3bfaa20e71cde35e519f0074c2654c71037cff5e1b1fc68214431e92529235d8ca61d65c4f1c70945df76b6a97f4e291bd9fe15bbb477112f5 WHIRLPOOL 7bc761796bdad741a5f82416262ace5c45a71b2c765f975586d970e7584c43ac0488051381cf6860491af4b0d702ba1223872825af10365635b2c40785a55591
 DIST lammps-1Feb15.tar.gz 62801871 SHA256 4bae0a1bb8e56db0e657e5df068fd7caf62117624227d82400e39a5e171280d6 SHA512 85b59dfe5f24d30625171711555cc95587f2944ff6bba1914c223dfd422975319e8725a45b9bd2743fbf2e770d3af7ef26dc4b283c1514c429c67e9cab9d6eeb WHIRLPOOL ed1e5626314540e0ee6df0c537af93e5b81a00ee9994a6ccaa9a9ff852d9eefb34d5d5918faf4f605d95beb5758ec46c27a8aea3345392e85c9eb1198380b2ec
 DIST lammps-24Feb15.tar.gz 63487709 SHA256 f8a42d4fcd3c3b6591898cddee2fae6f29ecfd11bf688b2ae81896360181bdef SHA512 42777481fd6551fc14010c256bcd5665a42b52e79026860eca89724edb50df9e4af6566553e51954cf0c9099e4cc9c982e07cb4a99ec31e07fdb225ee5e7e219 WHIRLPOOL 140566ede55929e528c91da1903bda7667028183bf1d4294c441f98877675af206d66fa476167469f5e1f83aee969635a53c6a56d7eac3eb6d646cf5400d6472
+DIST lammps-25Mar15.tar.gz 63800289 SHA256 c39575a93b136108b54c08ebb888a3b32f6d2ae060514c43c7bf7d042415d06f SHA512 2bacc1a1010b008d16354af999bf2bc4dbd225dbaa8f078eeeb7898d19b41bd563c2ecc9a4bdc30d04c9d336aee28d35ae53d30ac20af7127579872f8c272b8e WHIRLPOOL 05aa0fb15236381c2dd3a4216d7f5c54f5b01e55a6c7b57f8ea8ddface3fbb7c707aed6723d9c603b4937b105f68305a2cae25458dd48a5266dbda86d7edabbb
 DIST lammps-28Jun14.tar.gz 64598325 SHA256 3dc8f415f076c5b1563e25c06ddf360a7234c0b3428c561764a13618f80fb233 SHA512 568a00249dd88d0ad94714d2b388855376d020a34b546f9f54142b761e95515c1fce44bbbc9db2538a5a9b8335b8ac9e2905b875e954da18831087a3021df0e2 WHIRLPOOL 9d283de197c6e7216c60ed3f34bcd0a55baab925ab4d025717f1bee8a7e8b668c67bf008a9a9a807361c8f5ade36e362afdf7ac9ef6c3ed6d856389591483354
 DIST lammps-2Feb15.tar.gz 62843740 SHA256 34a385dde4e6c4436feaad9d188401a1616ba4fc41b4ff802a2af7cdc66a33ec SHA512 b8fc645ced67571857f89793113fe98eab5c9d44990de4ca9bd46ad3c88e1041986f1f71bc0cd9d5a917a27ba44ebee2e8f3eb0c68df7f9d4f11a2bb73b3d748 WHIRLPOOL ecfaa4f26b55597553b20e38824c1628a071508edb123813c57cc8c0660505a3aaa9012aab6adabdb7be0a7a180284430f773086669b020c226125848cd8aadf
 DIST lammps-30Oct14.tar.gz 59386701 SHA256 b99522370cb2ea3e55c63f401b2bafb0c98f6b28b9af76fb8339e9bd4a3ae205 SHA512 9b9952ec098c17abd9af085d546869a60ba421a380abcd0be3c425e3c1495394417bfee8d8097c99f54131e286a325d736e766e1ae7239bf45ca44c737611c2c WHIRLPOOL b8ad0078b883455cd7e8f06c0ad8f43eefe7d1c158af58baa42ad179154f09f68077d8fb31c22abccedf06daa344e4abb7f3edcc16d9e69e9d2c458f4fda1085
@@ -35,5 +40,17 @@ EBUILD lammps-20150306.ebuild 5179 SHA256 f828047af1693586ddbd41a395bcaf9c27ce08
 EBUILD lammps-20150312.ebuild 5082 SHA256 ecb723ccda7e15bb6eaccf1dec08e94efb363c6b41eca548ded1045eded6870d SHA512 8fb321ab448d94894c95cd1f7ee7948718522b044820e5cb1cbe31f640e9ea7a439f61cc5fa1b1757732c135c7b763d240d3cf35937843a94691c8e70aa42c79 WHIRLPOOL 634b04b5d56cf979e8f96be491a31185b0593cb87e2f1229f2427c7fd3d127589a0ea6a531bdee5dcf34e154684a2fdc355d3fd50640651c9eaf10bf059b14dd
 EBUILD lammps-20150314.ebuild 5082 SHA256 938cbfeab4bb3e6bd198df79eb358e3e52992d3e5ff8c348deb446ef1f414e51 SHA512 fe8183f44a1f4790a77bc4e1692b943841166d3161018d2987103ca61229237c97e0d04bbf1ed728d19883736257e20e3b08daa1af147d17378b0100a1fe049c WHIRLPOOL 6fddbe1bf5b3f4e649d1edee3097cc2d9a907a787700b29ed23549c34aa4a27bd4dd99eeebc7a22d3f42d933f161e95f7affdae7d4674b3b5a544463322ba04c
 EBUILD lammps-20150318.ebuild 5232 SHA256 1acae503e112f81106dd3dd1f34444ce16df2d5f3be82bb51b6a191f77b180d6 SHA512 ed671dca82ef845981134e9ae901474b97cb9746a5250de0a122d4d10eb5048ff46b55028acd1c3c638ac389a26d280c64ee6f7d5c6257cfa913839c403a7ad1 WHIRLPOOL 896a4c719303ed4b7013838ff2218fdd8cdd5af9c3b07d44f6d8616061ccab86cecd753c3c6b332a27c4cba2607a1d935b7e4a8add20e066e717f1f09b81bd82
-MISC ChangeLog 14917 SHA256 e40dc2d2a90f5d817f2e52a098eef2eb75ea2852c374ecd2bb09439bb78b1965 SHA512 e0787d58d57edeb6a9472e1f3f659a43095bba766b053a428deab92c096bf056078b34ffc482a625edf34f597d181949cd3b6aa8d0790fcbd2497bcb78ed1bf2 WHIRLPOOL 442325e78462c14c8c0a2e35cfe926092ee7abb824fa52de64d256f8d8e5d75e532c4b533b3a04b2a70b61232d3e942f36c66e6614062804bb25d8feb4783b75
+EBUILD lammps-20150325.ebuild 5521 SHA256 503e9f3ec4f532b4eff9a0b6f2866ee603dd96cff49283fe168aa351dd9e86bf SHA512 bb235f0b1c503a9c8017b874b43adecb0b722be2b3f566238ebc7e0e8982c211ffa52c7436e8f56de28357e86692812fbae8f4306ce30745676e81fce8da052b WHIRLPOOL 1d2347b66cb42b612f0d76d8f44b9f1a85c9cf9bcc69a3259414ce786c93216cf07a419902125eb5af9820d161c1a3f49cec3be21886cb97655f577556b13563
+MISC ChangeLog 15101 SHA256 a1e8ce7adfaa7a173e2d87d4c38aff309ca4352af81d9dfcf8b34615c81ba50d SHA512 5fade29b60e6954ab8d6177348eb0f997fd20b1bf31308e7b8c9651924b25a2ec82bb4bf4e96cab6b6fc5345b6ef0c171ec6b195004d3bec3688b09d87953661 WHIRLPOOL ad87d78886199a4aae1942dfb596102da85d7bd12fe217535e9821c2c0feafe4ae5af60420f6b2bd2df1682aabd928d2b6efc4b5e81201bfc6771c7c82e5fdbe
 MISC metadata.xml 1104 SHA256 cd019e3b907b935374e9818167b4a9c406d938cf132b6656a7aed15fb8070d4c SHA512 9fa9919de32eb24c720fecbb449112b997e331b4ecb37aba8cdfcf90bc832e00ff8deef570f8eb92341f8c82b90787d65befa9ebeacb904abb467b8f3e1c5054 WHIRLPOOL 88fbd760afe74c12310ed3417e8c6d242b282bc78fee612b1c0c1dd1532ec9253f7b5134a9fb8f463f9fe469ce1d5fada43b97b348c221c84869907cfc0dd37e
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diff --git a/sci-physics/lammps/files/python-shebang.patch b/sci-physics/lammps/files/python-shebang.patch
new file mode 100644
index 000000000000..7dd45797d4ad
--- /dev/null
+++ b/sci-physics/lammps/files/python-shebang.patch
@@ -0,0 +1,7 @@
+--- lammps-25Mar15/python/lammps.py	2015-03-13 16:06:20.000000000 -0600
++++ lammps-25Mar15-new/python/lammps.py	2015-04-10 15:31:14.000000000 -0600
+@@ -1,3 +1,4 @@
++#!/usr/bin/env python
+ # ----------------------------------------------------------------------
+ #   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ #   http://lammps.sandia.gov, Sandia National Laboratories
diff --git a/sci-physics/lammps/lammps-20150325.ebuild b/sci-physics/lammps/lammps-20150325.ebuild
new file mode 100644
index 000000000000..c5d3c1e72db1
--- /dev/null
+++ b/sci-physics/lammps/lammps-20150325.ebuild
@@ -0,0 +1,222 @@
+# 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-20150325.ebuild,v 1.1 2015/04/11 04:52:50 nicolasbock Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+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
+	)
+	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)" '')"\
+		"$@"
+}
+
+src_prepare() {
+	# Fix inconsistent use of SHFLAGS.
+	sed -i \
+		-e 's:voronoi_SYSINC\s\+=.*$: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) $(FCFLAGS):' \
+		tools/Makefile || die
+
+	# Add a python shebang.
+	epatch "${FILESDIR}/python-shebang.patch"
+}
+
+src_compile() {
+	# Prepare compiler flags.
+	append-cxxflags -fPIC -I../../src
+	append-fflags -fPIC
+
+	# Compile stubs for serial version.
+	use mpi || lmp_emake -C src mpi-stubs
+
+	# Build packages
+	emake -C src yes-asphere
+	emake -C src yes-body
+	emake -C src yes-class2
+	emake -C src yes-colloid
+	emake -C src yes-coreshell
+	emake -C src yes-dipole
+	emake -C src yes-fld
+	#emake -C src yes-gpu
+	emake -C src yes-granular
+	# Need OpenKIM external dependency.
+	#emake -C src yes-kim
+	# Need Kokkos external dependency.
+	#emake -C src yes-kokkos
+	emake -C src yes-kspace
+	emake -C src yes-manybody
+	emake -C src yes-mc
+	lmp_emake -C src yes-meam
+	lmp_emake -j1 -C lib/meam -f Makefile.gfortran
+	emake -C src yes-misc
+	emake -C src yes-molecule
+	#emake -C src yes-mpiio
+	emake -C src yes-opt
+	emake -C src yes-peri
+	emake -C src yes-poems
+	lmp_emake -C lib/poems -f Makefile.g++
+	emake -C src yes-qeq
+	emake -C src yes-reax
+	lmp_emake -j1 -C lib/reax -f Makefile.gfortran
+	emake -C src yes-replica
+	emake -C src yes-rigid
+	emake -C src yes-shock
+	emake -C src yes-snap
+	emake -C src yes-srd
+	emake -C src yes-voronoi
+	emake -C src yes-xtc
+
+	if use mpi; then
+		emake -C src yes-user-atc
+		lmp_emake -C lib/atc -f Makefile.g++
+	fi
+	emake -C src yes-user-eff
+	emake -C src yes-user-fep
+	use mpi && emake -C src yes-user-lb
+	emake -C src yes-user-phonon
+	emake -C src yes-user-sph
+
+	if use static-libs; then
+		# Build static library.
+		lmp_emake -C src mode=lib serial
+	fi
+
+	# Build 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.
+	lmp_emake -C src mode=shexe serial
+
+	# Compile tools.
+	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}${LAMMPS_POTENTIALS}" > 99lammps
+	doenvd 99lammps
+
+	# Install python script.
+	use python && python_foreach_impl python_doscript python/lammps.py
+
+	if use examples; then
+		local LAMMPS_EXAMPLES="/usr/share/${PN}/examples"
+		insinto "${LAMMPS_EXAMPLES}"
+		doins -r examples/*
+	fi
+
+	dodoc README
+	if use doc; then
+		dodoc doc/Manual.pdf
+		dohtml -r doc/*
+	fi
+}