[gentoo-commits] repo/gentoo:master commit in: sci-physics/lammps/files/, sci-physics/lammps/

[gentoo-commits] repo/gentoo:master commit in: sci-physics/lammps/files/, sci-physics/lammps/

[Nicolas Bock]

commit:     c22a2eeed5b52985a216896846832d4cc9b198fe
Author:     Nicolas Bock <nicolasbock <AT> gentoo <DOT> org>
AuthorDate: Thu Oct  6 03:57:19 2016 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gentoo <DOT> org>
CommitDate: Thu Oct  6 03:57:45 2016 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c22a2eee

sci-physics/lammps: Version bump

Package-Manager: portage-2.3.0

 sci-physics/lammps/Manifest               |   1 +
 sci-physics/lammps/files/fm_exp.patch     |  11 ++
 sci-physics/lammps/lammps-20160730.ebuild | 221 ++++++++++++++++++++++++++++++
 3 files changed, 233 insertions(+)

diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest
index ed3e70f..4b79771 100644
--- a/sci-physics/lammps/Manifest
+++ b/sci-physics/lammps/Manifest
@@ -10,6 +10,7 @@ DIST lammps-1Mar16.tar.gz 87945422 SHA256 af2bd7ab2a28aa14b8afa3d8703cbaf27d9244
 DIST lammps-20Nov15.tar.gz 90227651 SHA256 7c392c848e73335226b2fef6bb8034b1152f91862d955a3bae00502bf9d8e8fe SHA512 4bff70e45fb30be10a33b4c6c60b73cceddf8d42588b0630b4802f1e61dea3c237c01c3667585ad210ef2cdb811491b1b8495718a90bb57853c58245e29d1fe4 WHIRLPOOL a01f54911a5edb666ef5af5302cf60d61d58d20f2112578e4d7bd16787b2bf59da09e9fe7ffa021fb6a97db40b23301ed77010f48a05e5471742c0e71413b7e1
 DIST lammps-21Mar16.tar.gz 88654277 SHA256 c2f627db22f332995d90521f0e8d8e9865b85b49cde0ed4bcf727bf4b9b12767 SHA512 27e4a3a0c2c17fb9c85716b499ca2b3de8b0a699891afd32c8409117a0fbe27f1bd84ef16288cc5abda87ee8a7b1059960d8caed5aa339f54290aabeff0fdd4d WHIRLPOOL 370f79af4a8e55851aa0c071d02baddaade991a3208fe504f8b92796bbdb9b17b85af898a71177bbc67d885ffdef9280621c9b7f4bc22cdb14808332cb2eccb8
 DIST lammps-22Jan16.tar.gz 85952234 SHA256 46425bf0ae73f716195a29dc9823c2c5989504f85b49a316bc304caaf6e6a674 SHA512 3ceeeaf76621bbc11ea25d5fb321b602b34ffb3893898a704b02e5cd428a36b2017006fdc1f7b1c5f957c33f26ca103a2939538ae7937555e0b25b5852cd48f3 WHIRLPOOL 7f61ea1924eceb190b7cf56ed32db75f6a45c99dbf1522862124f59acd1f79b1a46310d5e31a988011461a55c319677eaec2bf713e9a5cda0411b5d2280aa784
+DIST lammps-30Jul16.tar.gz 94454127 SHA256 41104065bfb433e9c69a88bf4c0d760a02186cbf81ec481332665b28f8503c1f SHA512 2ebcf30502810f8d6be107760bef0b9b4591142511ae410e7b44573fe9988bbbba5e8d5bfd16f74a3875bb1c41dbc6216a1c7e8a9b1d316fdf19a901ac4479d5 WHIRLPOOL e081b9eaed5a439be1c80c844629030af02b4cff6ed57cac3db209981b9d4e7381315c82de5f76fff7f8ead5b6250a1a4207d3f18c97c59e3ece2a716697175e
 DIST lammps-6Nov15.tar.gz 90177074 SHA256 b908d87106e89aa813c3d1a2e89f297ab42471ee463ef950f87f284d62aa24ac SHA512 91f8e33a00b3605dbb78f622a19886c11ca8ef3f4babe74e8d8f90bb176d5689e75d619155f58e6754a2756d20c05b74389e34f024167cba1841b8aade171daf WHIRLPOOL 4541537ea73292648764d6c8a7560f3127b8f911f4dcff0a97735c8e75868dc3aec7c2b32a2928ea446e8cfec87c81c9f86a635d29f3a65f42fd27661725911e
 DIST lammps-7Apr16.tar.gz 88791123 SHA256 f87c11cbbdbbb64a337e0608ae0fde11f77d9b32d081a8095376db9bbecc6d5f SHA512 1045f0337b37a19760718a2b3b48d31608248069a8fb2dc43daf555e44e720db770ff53e2a2db09c3e1f2703bb98894516229382c810ce45cca3647f353a21cd WHIRLPOOL 4ed6e93efff84888f982aec4c55adff6eda94fec5608e473fe821f77ea7a867fa7de23cf54fe28007b61304e41c9d7e42f4994e455bfb67cfadf79dbfc019e0b
 DIST lammps-7Dec15.tar.gz 82168656 SHA256 7fa1bb1089437c0f38f8c6920286e2f8424e6449956b4d570da2954f507af1e7 SHA512 13078e7614402efc310a178506134409b40fb2768c4d7ee1cfa6992b247ef25169288ec99d4314b1a98125037d7c1c954bd114abc6ac41c58f60506358d150e2 WHIRLPOOL f9ba52c0c93ea6950b2ee7e0f5e15ebef6ea50f647d23cb2f9a1caf523d3dfb8d52adbdf8f8840eebd7f79fc59ab294310b7bf7109b27c6b7e9d6e7d2f18b7ee

diff --git a/sci-physics/lammps/files/fm_exp.patch b/sci-physics/lammps/files/fm_exp.patch
new file mode 100644
index 00000000..3b6bd24
--- /dev/null
+++ b/sci-physics/lammps/files/fm_exp.patch
@@ -0,0 +1,11 @@
+--- lammps-30Jul16-original/lib/meam/fm_exp.c	2016-04-18 14:00:58.000000000 +0000
++++ lammps-30Jul16/lib/meam/fm_exp.c	2016-10-06 03:15:55.631053526 +0000
+@@ -112,7 +112,7 @@
+     return epart.f*x;
+ }
+ 
+-double fm_exp_(double *x)
++extern "C" double fm_exp_(double *x)
+ {
+ #if defined(__BYTE_ORDER__)
+ #if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__

diff --git a/sci-physics/lammps/lammps-20160730.ebuild b/sci-physics/lammps/lammps-20160730.ebuild
new file mode 100644
index 00000000..1e484f1
--- /dev/null
+++ b/sci-physics/lammps/lammps-20160730.ebuild
@@ -0,0 +1,221 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python{2_7,3_3,3_4} )
+
+inherit eutils flag-o-matic fortran-2 multilib python-r1
+
+convert_month() {
+	local months=( "" Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec )
+	echo ${months[${1#0}]}
+}
+
+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"
+
+# blas/lapack is needed by the ATC package which is only built with MPI.
+DEPEND="
+	gzip? ( app-arch/gzip )
+	mpi? (
+		virtual/mpi
+	)
+	python? ( ${PYTHON_DEPS} )
+	sci-libs/voro++
+	virtual/blas
+	virtual/lapack
+	"
+RDEPEND="${DEPEND}"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+	"${FILESDIR}/fm_exp.patch"
+)
+
+lmp_emake() {
+	local LAMMPS_INCLUDEFLAGS
+	LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')"
+	LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN=64' '')"
+
+	# 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
+	local packages=( yes-asphere yes-body yes-class2 yes-colloid \
+		yes-coreshell yes-dipole yes-fld yes-granular yes-kspace \
+		yes-manybody yes-mc yes-meam yes-misc \
+		$(usex mpi "yes-user-atc" "") \
+		yes-molecule yes-opt yes-peri yes-poems yes-qeq yes-reax \
+		yes-replica yes-rigid yes-shock yes-snap yes-srd \
+		yes-user-eff yes-user-fep \
+		$(usex mpi "yes-user-lb" "") \
+		yes-user-phonon	yes-user-sph yes-voronoi yes-xtc )
+
+	for p in ${packages[@]}; do
+		lmp_emake -C src ${p}
+	done
+}
+
+lmp_build_packages() {
+	lmp_emake -C lib/meam -j1 -f Makefile.gfortran
+	lmp_emake -C lib/poems -f Makefile.g++
+	lmp_emake -C lib/reax -j1 -f Makefile.gfortran
+	use mpi && lmp_emake -C lib/atc -f Makefile.g++
+}
+
+lmp_clean_packages() {
+	lmp_emake -C lib/meam -f Makefile.gfortran clean
+	lmp_emake -C lib/poems -f Makefile.g++ clean
+	lmp_emake -C lib/reax -f Makefile.gfortran clean
+	use mpi && lmp_emake -C lib/atc -f Makefile.g++ clean
+}
+
+src_prepare() {
+	# Fix inconsistent use of SHFLAGS.
+	sed -i \
+		-e 's:voronoi_SYSINC\s\+=.*$: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) $(FCFLAGS):' \
+		tools/Makefile || die
+
+	eapply "${PATCHES[@]}"
+	eapply_user
+}
+
+src_compile() {
+	# Fix atc...
+	append-cxxflags -I../../src
+
+	# Acticate packages.
+	elog "Activating lammps packages..."
+	lmp_activate_packages
+
+	# STUBS/mpi.c is using '#include <mpi.h>' now instead of '#include
+	# "mpi.h"' which requires an additional '-I.'.
+	append-cxxflags -I.
+
+	# 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
+}