sci-physics/lammps: Adding new version.

Also added a patch necessary to build this version. The patch has been
reported to upstream (on their mailing list), and will be dropped once
upstream adopts the fix.

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

4 files changed, 245 insertions, 15 deletions

diff --git a/sci-physics/lammps/ChangeLog b/sci-physics/lammps/ChangeLog
index 7d586c0e33ce..ab0f8a5ef729 100644
--- a/sci-physics/lammps/ChangeLog
+++ b/sci-physics/lammps/ChangeLog
@@ -1,6 +1,14 @@
 # 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 1.70 2015/02/19 09:05:37 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/ChangeLog,v 1.71 2015/02/19 18:32:04 nicolasbock Exp $
+
+*lammps-20150213 (19 Feb 2015)
+
+  19 Feb 2015; Nicolas Bock <nicolasbock@gentoo.org> +files/chunk.patch,
+  +lammps-20150213.ebuild:
+  sci-physics/lammps: Adding new version.  Also added a patch necessary to build
+  this version. The patch has been reported to upstream (on their mailing list),
+  and will be dropped once upstream adopts the fix.
 
   19 Feb 2015; Agostino Sarubbo <ago@gentoo.org> lammps-20141030.ebuild:
   Stable for amd64, wrt bug #534042
diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest
index 3626d87539de..dc88522abf77 100644
--- a/sci-physics/lammps/Manifest
+++ b/sci-physics/lammps/Manifest
@@ -1,9 +1,11 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA256
 
+AUX chunk.patch 608 SHA256 1e8eae1e25b0975c949efda91fb97899ca4bedc99f40dbb23eaabb86b6b4e035 SHA512 a45a78cdaff4aca1a352f8f302fe0706eb7c119fb33d284e256d41cf2fa7d5c1d3f38ccc7f7b6e0678956eaf212de4ef5db787a77762b71b0a511dfba7fb014a WHIRLPOOL ff6d3648bbd9255cc9969d531572d74aea3d51ee4afb65c0e295c2a4918f7f1f615bacca242c9f01a6b8a5d5005da80a47d41d1aa7c97e6836bcc33f67cd96db
 DIST lammps-10Feb15.tar.gz 62912048 SHA256 59373e9b5592f7b697a144bbce1fb742726e03536b7bb355dac7a9e013ddf9b8 SHA512 a7804377a23f03f338bdaf443439dffcdc52293b4c45e6369b340a1107510fed0b8a198e3b5afcff2e04e109985b52ee62e7b28276697bae37ac6f783d1ab9f2 WHIRLPOOL 09f29cadf8b072d388abe45ec219341d2a14a6c9cc9e4010a0f7945e930e9984738f7837748d117ab95ca76ce0c8d9160fe88dcec17e8d21b81f385dec8f7005
 DIST lammps-10Jan15.tar.gz 62757375 SHA256 b3cbc1e2efb64b5431744940a8d78a0737824c46bfa18c2f0cc6565d67394421 SHA512 40d273049c9c22cb9828d4f51c29dd1044efad24a78e989f4c0da443ebd8f84d15dc18197ecc41cfc3a3f70ce5b59aeb82bb84dafa014a62b991b6d9b674f4fe WHIRLPOOL 946ab5f4d0701abbaadee94ad5493d6c39bad6ed866ae29176ffa8f16b3508a7cb0a8deefddd987aaf95ae2f74b768cadeddc54b4c053eb12dfde2b9fa597fb8
 DIST lammps-11Jul14.tar.gz 64634749 SHA256 05a9af6fae3f27e41ee776fb3c306a07c2f80b953770fa1ccbd36bbbb6991283 SHA512 6951d9af5d1f77f3160ba13ed70bb1ff71d1f8da0716b784b3e3cf010eb8b9ee68ac49befe4602771bbb4a473fd531f07568d922e0bbff97d4193f9e8c0ea793 WHIRLPOOL f1b814171e81898f7138b6116d4bddedfdccc0a956d11184fb64c82722905a28a97420c19b65edef488915ce956479b0ba255767b45f2f70c53e5674ee6e3744
+DIST lammps-13Feb15.tar.gz 62974524 SHA256 6be39873ff30eaaf467ac201d7f9b06b7fb175c5fcc4687dc38b7e8ab8ac0544 SHA512 20a0e7ba4905cf3e1f57df9bb9ddba298c8ee03e823d920ffa526a6ee318e4c9a5d3319bd79a46441a895c5b03ba0d296a2921f38f5795014f544ec58b3be629 WHIRLPOOL 22e9534dc84a9ce5cc2f5ca0ff693a05cc8afa1f307cac71d739c7504e56a11121acda62cc1d141f2e8f556a4c35bddeeac09cd429cddde531dec115925f4b00
 DIST lammps-14Jun14.tar.gz 64597109 SHA256 cf7d492862c7bbb1865631b8abce34ea8b5edac17a573c8924c4f9b885fccac3 SHA512 fb0d5d58c1abd402d0aa311156f023af9579793b6606f5c449f5bf0b298dc77a0c68198dc2898d9d8f0f84b24bd84fec3d60b1549d60446152b9e18d5f217608 WHIRLPOOL 7336cb8f57aa856ae7b8ca77bbdfb78df9c2a4fd229f58884c302e88dd75aa53c567c22fbdc8c87af032df264dbdd222d23143b23ba5a84dd8e94f5a7a260838
 DIST lammps-15Aug14.tar.gz 65114807 SHA256 de4ad0c90c43c234fb5c4efa179122acdecb5dba6834ec6e42fa7a237ae767c0 SHA512 af61d517ae707ce53f670ec924bb8a55b6e1c2ed67c5343e84696116c2f9d0f716ac5841618600b466462b68fb24e0129e41febbeddd87c68d7672547de3fa9e WHIRLPOOL 0658cdcda382693278b1dc029a59e5fbdda0c4bae43183799486c8c1d85989e509ed7eee9574a862d2fbcb7f533cb718a5f08a23dd4371c41c96296dd7ecc586
 DIST lammps-17Dec14.tar.gz 61474385 SHA256 5631dec2c446d47a1781b774ee9a41306156190991e8c3f0dfc8905b7070012d SHA512 765c2be9d62c39c498d04ca1faa6f1aca07ea03e298828f1ecd311da16c30553d4663aa4bb57898bff55a941e432ceb35ed9df3458c93cb1906de8aa8bc508e4 WHIRLPOOL 5023d5f2813dfda4be8a154e31f379e2f410cc7fe2a6d98ef084f0776303e3c367d8781759fdb05106ab026e0b3484221658c121d98939a3d9ccd68e39719abe
@@ -64,22 +66,13 @@ EBUILD lammps-20150202.ebuild 4955 SHA256 4d6eea969d29fbaf070992b394a8458a21adb9
 EBUILD lammps-20150203.ebuild 4955 SHA256 72d5ca060ed141d4e489b581ab4e044f93f264e24176fc7f5ba8ba9ca421d856 SHA512 f22e84ae026112034ffd64e8868c5278c54e6e789f399a89fa1ca7703c709fa711a1cbfb8ab1ec238a5c5e1cfabe011956943959eb759bfad38a7276496100d5 WHIRLPOOL ac576ee84099d4523cf64feaf047074f43763fa61de1bf9f7975b0da4ffbe753298e20086d8f47e6329853e4b3580f8aa15e8147fc5b29c32144109b4bfa6aee
 EBUILD lammps-20150206.ebuild 4955 SHA256 b48ee96f619f7f722f52d32e1f4f3946c6dd900acf65d0ffed04c8833e24311c SHA512 d1e697d8deb2f5c221dc954e7a2460438ed2d91e407b54c48015995834f27c74fec45e3dcf0cb7bdbae045da91a8e87ede81f6ba635ee82b68edd507348ed08f WHIRLPOOL d0319a19ed1f3de463ba1933d10d7f8da4f47ae5e6173c5100acb5077e6474c4e6d0929ce653af75507a976d75f7e7c2172f3601a7bbea7f19e604321393c229
 EBUILD lammps-20150210.ebuild 4955 SHA256 e96f80d5747310782ae7b9c3eb1637b48b7a8761ab517d9556cd3d1b757dd68b SHA512 0517c6f3d4dce7d74a9f78994f0b54c656d5f9d8bb002b379fb2b6a853e4de867a35d86cce3673a9c6ea6b5f7da30b930cf03f9e183f670e0defa81ad682ad9f WHIRLPOOL f5d5e38ad96b7203667c484066458b84022369e895c741d8b78051e58d9e49a4fa654b9941ba99c1339d18f420a06918c8298bc61bb3f07358338ac1a05186eb
-MISC ChangeLog 11804 SHA256 015ddffd5566c713c9c6b85b1e38fb4fb81636fc2f01ae181740396443b8398f SHA512 2fc1f4b3e8d896114df8e30118d11e59cfe490d81c00dd37f87b402b7a3fb93934d38f8c7a31c998c76cda757ee6123c8cd07c1253a0b6f428f362bc26a6dc1c WHIRLPOOL e3aae89394aa632bae84492b5d84e99b87ab95f878627baa818385b4c15c008243877fb3581ed7ea55c29fae05f21efdf2d6ebc8a9c3825c74035da4926b6bec
+EBUILD lammps-20150213.ebuild 4990 SHA256 de8be7d28c403ff19e860be9949460d277490074de49fd082179d6eebb6681e0 SHA512 6e6a22b4588e7b99bf2a86d01860e74b7a2a9bd199b3e0ece4ccefd48af47c8219a0df1b88c7118988b5bda8449162d8d61ddb317ae7398a9844e57531c6353f WHIRLPOOL 3688c33df07c798c0940d14f1a213b030872cc4a010809049e875dcbfc64c17783e58abe72729da9fdf103a649ca175508f25d491b3344a15f284adb48b5244b
+MISC ChangeLog 12159 SHA256 4c1d09f32e95253f5bab99c382e066ceb00d80cc6454a7e23f99a2ce568eb205 SHA512 b4103592709746ba2a34051cce3a2c0765fed215b6c4abfe3351e528ebc0eec702faa4f84169ed6a02e9dde5a300cb6bee258869b30ac3a88f21c97b29f619e3 WHIRLPOOL ad9300b4927226e3d06b6eb4b785e142c822db25ec00db252a3662cd92c8975880d40b74eaa0c738fb5de78f578313fba6ad5cf7fe5c231b07a4ca9cefb725aa
 MISC metadata.xml 1271 SHA256 2de96e89797d150bffc7933de76da6d8bd24619c475e71286c5fb05637d97f0a SHA512 ce273d9f6f947f976ad008187dce9e5efe62f20a521ac7c0eb23550ef8cdcc2a1e61084e55466c84c77cd8d98eb39cac857057bd82ab9c9537d9cdb1c66d19d1 WHIRLPOOL 8177b79250dc0ad4759c0790111671457a91f9bac4bf21e0bbef3001abb558dfa70dcac45bcfef388c7377c1595854f9729d5881b64d4f699d6664407fc8696c
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diff --git a/sci-physics/lammps/files/chunk.patch b/sci-physics/lammps/files/chunk.patch
new file mode 100644
index 000000000000..22c3811f4a82
--- /dev/null
+++ b/sci-physics/lammps/files/chunk.patch
@@ -0,0 +1,21 @@
+--- lammps-13Feb15/src/fix_ave_chunk.cpp	2015-02-13 09:53:48.000000000 -0700
++++ lammps-13Feb15-new/src/fix_ave_chunk.cpp	2015-02-19 09:16:22.000000000 -0700
+@@ -11,6 +11,9 @@
+    See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+ 
++#include <unistd.h>
++#include <sys/types.h>
++
+ #include "string.h"
+ #include "fix_ave_chunk.h"
+ #include "atom.h"
+@@ -930,7 +933,7 @@
+ 
+     fflush(fp);
+     if (overwrite) {
+-      long fileend = ftell(fp);
++      off_t fileend = ftell(fp);
+       ftruncate(fileno(fp),fileend);
+     }
+   }
diff --git a/sci-physics/lammps/lammps-20150213.ebuild b/sci-physics/lammps/lammps-20150213.ebuild
new file mode 100644
index 000000000000..4cdcc4bdc9d2
--- /dev/null
+++ b/sci-physics/lammps/lammps-20150213.ebuild
@@ -0,0 +1,208 @@
+# 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-20150213.ebuild,v 1.1 2015/02/19 18:32:04 nicolasbock Exp $
+
+EAPI=5
+
+inherit eutils flag-o-matic fortran-2 multilib
+
+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/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc examples gzip lammps-memalign mpi static-libs"
+
+DEPEND="
+	mpi? (
+		virtual/blas
+		virtual/lapack
+		virtual/mpi
+	)
+	sci-libs/voro++
+	"
+RDEPEND="${DEPEND}"
+
+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) $(FCFLAGS):' \
+		tools/Makefile || die
+
+	epatch "${FILESDIR}/chunk.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 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-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-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
+
+	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 mpi; then
+		emake -C src yes-user-atc
+		lmp_emake -C lib/atc -f Makefile.g++
+	fi
+
+	if use static-libs; then
+		# Build static library.
+		lmp_emake -C src makelib
+		lmp_emake -C src -f Makefile.lib serial
+	fi
+
+	# Build shared library.
+	lmp_emake -C src makeshlib
+	lmp_emake -C src -f Makefile.shlib serial
+
+	# Compile main executable.
+	lmp_emake -C src serial
+
+	# Compile tools.
+	emake -C tools binary2txt chain micelle2d data2xmovie
+}
+
+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
+	# 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}${LAMMPS_POTENTIALS}" > 99lammps
+	doenvd 99lammps
+
+	if use examples; then
+		local LAMMPS_EXAMPLES="/usr/share/${PN}/examples"
+		insinto "${LAMMPS_EXAMPLES}"
+		doins -r examples/*
+	fi
+
+	dodoc README
+	if use doc; then
+		dodoc doc/Manual.pdf
+		dohtml -r doc/*
+	fi
+}