[sci-chemistry/gromacs] GROMACS 5.0 finaly relesed

Package-Manager: portage-2.2.10/cvs/Linux x86_64
Manifest-Sign-Key: 0xF82F92E6

4 files changed, 310 insertions, 23 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 5a60317eab21..05f974061727 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.139 2014/03/26 21:42:49 maekke Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.140 2014/06/30 03:24:04 alexxy Exp $
+
+*gromacs-5.0 (30 Jun 2014)
+
+  30 Jun 2014; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-5.0.ebuild,
+  metadata.xml:
+  [sci-chemistry/gromacs] GROMACS 5.0 finaly relesed
 
   26 Mar 2014; Markus Meier <maekke@gentoo.org> gromacs-4.6.5.ebuild:
   arm stable, bug #496632
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 375342365cb5..db6b7f1bcaae 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -3,18 +3,31 @@ Hash: SHA256
 
 DIST gromacs-4.6.2.tar.gz 10986082 SHA256 7bcccd15f02e7163455e1f342fc13e609e9088735b962d96afe0a79aaad92d4c SHA512 fe5991f66a638edd5af42c226302ccac4968b722df92eaeb8f65536fd5c7eb64cf7f0264bbfaa09998c870e396087f23b91e377d3abcc9a2d9456850b622b371 WHIRLPOOL 6d563046e2f7fc6178b4c94c7bb9a73a19df02a51b53e2556a5141809b6f286cac86c7b04afafab9e6038733c06ee67965a7dbe6db67d44e0363c18c036d3051
 DIST gromacs-4.6.5.tar.gz 10991576 SHA256 a7242f315963a111e87fd28795696b1e818ac97479788356c4f73a04e9cdef09 SHA512 6ebb3ef74cf9ef2a749bdad6ce7c2deca607ef3b04cab3ce0be25ac1e7c69b3716761a66b5214642b82a96571e488d8a7bffda651840e56d95c14ba099cc1e0c WHIRLPOOL e639f0d1256173dafe8ba1231d46596f23a29b5ab97883600673b078e2927492dd473834398cd9fd864eb3d529ef853c2592d0b2c5ebb18ebb25ca171568aa72
+DIST gromacs-5.0.tar.gz 26862408 SHA256 c2c9b5e75e014785641f39fbbde9829ce200f963344b35fa942f041a0dcfeb20 SHA512 4b3cf7cad06ae7e98d8d794a05561874d8e5061e8c9ee91e5f028e7c7d4b42669b74efa3f52e5d864efa86da78d76637e8917edc99cd1cbf7c8dd9c2681e1270 WHIRLPOOL d9020a1c0e3aaf716a98ac1280e4d67e3f8f611cadc94465119711195c58c6bdc962926dfd579b8e13b1c1092539a1aa9768cb442dd7752c6b310a8116b7aaa3
 DIST gromacs-manual-4.6.2.pdf 6208213 SHA256 b95e4681d474caf0596d179a83f3e499b49e8900eb013900027a783a4c16c3d7 SHA512 e61fef9c2f1d978809c47723b48b35eddcfa5e98e573924d4b53d6aa686e893641b44ce07b217b9b3ecb34221f7eab3e7d0d6a8e1ced7f9db1ff478a32864574 WHIRLPOOL cd313c78472614f242e639d40764d3d797f4202bd52f706b4d0f0385b40dd6dac01a1676ec12374a2fb63e4490dc0a9ef39bbbc319d50fa59eaafcc6213df5f1
 DIST gromacs-manual-4.6.5.pdf 5525415 SHA256 0ae0a1f38c236a9b03200f32fc87a70e74adc2a446669973db1e6069e45dedfe SHA512 31174cc17bebf637a5c565fa307aae6cd5a434cceddab005b2ca8dd10a2e1252818b7f2d9e8f9571ef3fcdb904f1043280ea40c1ac38c4a3fd02ab1397ab8c92 WHIRLPOOL a2f49c2f3241ca2d50e678d452bbf57a8d50b282045d0b8afaca4f5fa96b7e92fe77894376244b45f7286de54a91eb87abeaa9170f56c81433c4cfa703352dd8
 DIST regressiontests-4.6.2.tar.gz 43576124 SHA256 6f79d545affa86c027f1e023dee282885b481551e522e441f772112bcd6295ff SHA512 fa78221201c6390d9b4649c848e464051993cb3acff6f7fb07e8e0e68f70f5ba2d917ba7ff9b5d5fd7a0c3a7435c98e2dbc02925e44f8a220ed073e054f510a0 WHIRLPOOL 1316fd0fe98b2b89ee95a2bccfbb5c4a7f0661bc30ceb04c5d1654b60513097e094ebca661b3fc4df32fad774bc6c14bb68841227530f0618d39fadf2e56d358
 DIST regressiontests-4.6.5.tar.gz 44026759 SHA256 50b611970c68eef3d1d3d043a6ca419c681540d73c96f26d6e9d2857fda3fb91 SHA512 817743f531a072b9940dc916daf79a83980eae7411e36cb003cbf7790282ca33375bdf0cb0e764500e5fac3ff09903b44588bc14a6c92bf73c020ea1fbaa7b38 WHIRLPOOL 835584596f630cea28ba76bb0fa5d131f8f781f64dc98292e20249ec8c9f063e329c15781fe473b66fc0b97292e3f68dce6a868094a45c9139c822425e669de7
+DIST regressiontests-5.0.tar.gz 60961669 SHA256 d1c83bc855eec9a210e8f55362fa99e12f715c16a8bf3d62fe232ad94027c824 SHA512 6c5a11ec0ec9b67ecd80cfed1ed726f5bf2a3821624ca43097393fd7ec76c83ae4bfa0af2e69e6be0fe499b57504bb02e1007da39479daf82ca7c0a10342a10e WHIRLPOOL fcd20ad5db82d6b5fdba41da55d4c6e7998028d03b02c16e222ec292a8291f5aeac959993461dbc867a2ec55085e6bf71f7be06afee0389e8d3dacf7eee3b623
 EBUILD gromacs-4.6.2.ebuild 9000 SHA256 508e8217912fa496d26374d0b4f67276f827a2449681a44d76fa883f18dd7b23 SHA512 8326acfa706b7ad0d3b59671ae3e51ebb420809d093e9fc4a5d9a49970c0b4ec8fd2e35162d90c8607826a052295aeeab57cb5ab2480b4488fd8ca6f77f01c93 WHIRLPOOL 388b819a622f1df21371468ec3579b1bc6896165d35d4570fb9c08c823abc80648055a7ba45db4ce1e7d7ac2912390c7c0d176edf95c686d631eca78b7fd1a0c
 EBUILD gromacs-4.6.5.ebuild 9004 SHA256 b6dc5dc03033100defe0ab09e0573a7c83c3042c250a5361ca23d237cb1ebca5 SHA512 4e7b348c4643f8b9d4c7771d53988f5479f389944993b1930714b0a92c59013fd958926b6da85e5f0f61b12301528e58735db028db2f2dc4a5e82324dfb8ccd7 WHIRLPOOL 4f103cfc28bc3cb10f30e4f087fef0edba7eff0d6328299551022bdde481fc8b38dce32387a8e0f6bb64fc2e1dbad19c1dd947a39978c5025aab7f40d68e5c88
-MISC ChangeLog 22554 SHA256 bf71174fa44685bb73200e7e560b8003a61fb053cef4b16dce6c43df746e6605 SHA512 053fe818517168f3593e9eb32cd21d86cdd6367964af863feb4b13a93982405ac2aff32d60b751453a68a84c245f8f2d2a91428af80bb6e44f1926150f0a8be5 WHIRLPOOL 472f45a4bd2e2d9c1194b3fd05b4b275b7981ba9d839f4a4ba13537121ebdf1667e54d9bd24cfa790a58f9e3b9bc45af386b065b42c3c81cb0a3d0949f46aaf5
-MISC metadata.xml 1001 SHA256 562256f5c9d458e3b4026fdd57fd53568c669b5dfb7fd1daa345d75c7a14baa0 SHA512 0d116b18d30bd2ce0a423bedf61334e9a1f92ad90bb7956eefa6ea4a5807a5fa3b8d13bf7cabd088666496766ad5be9b80d8ad05f8b1c2c6a20b46c663e7f590 WHIRLPOOL 0a0f05d0563f9ca00e45f4df20a55734d916477c1d82bc3e884e94d7ce31605f97ddf31e6d9660f26bd0977e2df930c2d3e6b326927f43dbf1523ba7a624a1cd
+EBUILD gromacs-5.0.ebuild 7502 SHA256 60784609fb51f9075b9c28104f5ff81907ca868613465bb70338ed3c7fefba76 SHA512 f624d7d1c512d89532cbf7d7ff13419f07489c787ec7c4e76798dd8f55435518c782407fe2a771a24246230f13e9ac3b14612ea0b43a8e2ae065ae11e161b04a WHIRLPOOL 8cd7733e6d6b2debed3ed96b7c0d081b6420b286f46a03000517866b31a27d88a8e6920a922411f578bccd381fc96c84400b62aa89527430ddafb8cf56b45a29
+MISC ChangeLog 22724 SHA256 1801b48ce62d9adefa7acfca2454d91d7a95dae4ed8eef140efcf164d1bd5ba0 SHA512 d0b633e316d17a49a570349a83946ffb55d6728fe42e0b366262da0397ea2b172df1e2412e3440b86be2e20cde7053f629a592f1955c21daafb7b2f50c1aec4c WHIRLPOOL 1dcf2d5629ca93854a6afa29bc3a1e4fbe0ab254085c71925e8b40a4967a1d8dad8e2362f4b263b382153dec5055925ea439dacc3a3268f137f12c56bcd24a39
+MISC metadata.xml 1444 SHA256 e58e4769cc016220f8423b30f758dee28183f51c61d7ae7ed5611be07ad372e6 SHA512 f44febb5c06bca01bd788766ddf4cba6c44f21e79eb7d9f2e6cc5ba65be2cac4df5f8b4e4ccfc08fc66df181c8ecd2ae858c67e713e33b5ae8bdaecde3dcf974 WHIRLPOOL df5bc1089c4118f86b289e655a6bd69e66ef5232c854e8e79d6edc69feb506ecea064ff7ba088dac2dd656ddf896c3b84626856ce7da6779722b01acb9672052
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diff --git a/sci-chemistry/gromacs/gromacs-5.0.ebuild b/sci-chemistry/gromacs/gromacs-5.0.ebuild
new file mode 100644
index 000000000000..9f495e26b3d0
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-5.0.ebuild
@@ -0,0 +1,262 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.ebuild,v 1.1 2014/06/30 03:24:04 alexxy Exp $
+
+EAPI=5
+
+TEST_PV="5.0"
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
+
+if [[ $PV = *9999* ]]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+		https://gerrit.gromacs.org/gromacs.git
+		git://github.com/gromacs/gromacs.git
+		http://repo.or.cz/r/gromacs.git"
+	EGIT_BRANCH="release-5-0"
+	inherit git-r3
+else
+	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
+fi
+
+ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+# see COPYING for details
+# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
+SLOT="0/${PV}"
+KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+	X? (
+		x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE
+		)
+	blas? ( virtual/blas )
+	boost? ( >=dev-libs/boost-1.55 )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+	fftw? ( sci-libs/fftw:3.0 )
+	lapack? ( virtual/lapack )
+	mkl? ( sci-libs/mkl )
+	mpi? ( virtual/mpi )
+	"
+DEPEND="${CDEPEND}
+	virtual/pkgconfig
+	doc? (
+		app-doc/doxygen
+		dev-texlive/texlive-latex
+		dev-texlive/texlive-latexextra
+		media-gfx/imagemagick
+	)"
+RDEPEND="${CDEPEND}"
+
+REQUIRED_USE="
+	|| ( single-precision double-precision )
+	cuda? ( single-precision )
+	mkl? ( !blas !fftw !lapack )"
+
+DOCS=( AUTHORS README )
+
+if [[ ${PV} != *9999 ]]; then
+	S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
+pkg_pretend() {
+	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
+	use openmp && ! tc-has-openmp && \
+		die "Please switch to an openmp compatible compiler"
+}
+
+src_unpack() {
+	if [[ ${PV} != *9999 ]]; then
+		default
+	else
+		git-r3_src_unpack
+		if use test; then
+			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
+			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
+				git-r3_src_unpack
+		fi
+	fi
+}
+
+src_prepare() {
+	#notes/todos
+	# -on apple: there is framework support
+
+	cmake-utils_src_prepare
+
+	use cuda && cuda_src_prepare
+
+	GMX_DIRS=""
+	use single-precision && GMX_DIRS+=" float"
+	use double-precision && GMX_DIRS+=" double"
+
+	if use test; then
+		for x in ${GMX_DIRS}; do
+			mkdir -p "${WORKDIR}/${P}_${x}" || die
+			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
+		done
+	fi
+
+	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
+}
+
+src_configure() {
+	local mycmakeargs_pre=( ) extra fft_opts=( )
+
+	#go from slowest to fastest acceleration
+	local acce="None"
+	use sse2 && acce="SSE2"
+	use sse4_1 && acce="SSE4.1"
+	use avx_128_fma && acce="AVX_128_FMA"
+	use avx_256 && acce="AVX_256"
+	use avx2_256 && acee="AVX2_256"
+
+	#to create man pages, build tree binaries are executed (bug #398437)
+	[[ ${CHOST} = *-darwin* ]] && \
+		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+	if use fftw; then
+		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+	elif use mkl && has_version "=sci-libs/mkl-10*"; then
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
+			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
+		)
+	elif use mkl; then
+		local bits=$(get_libdir)
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
+			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
+		)
+	else
+		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
+	fi
+
+	mycmakeargs_pre+=(
+		"${fft_opts[@]}"
+		$(cmake-utils_use X GMX_X11)
+		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
+		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
+		$(cmake-utils_use openmp GMX_OPENMP)
+		$(cmake-utils_use offensive GMX_COOL_QUOTES)
+		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
+		$(cmake-utils_use tng GMX_USE_TNG)
+		$(cmake-utils_use doc GMX_BUILD_MANUAL)
+		$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_SIMD="$acce"
+		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
+		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
+		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
+		-DBUILD_TESTING=OFF
+		-DGMX_BUILD_UNITTESTS=OFF
+		${extra}
+	)
+
+	for x in ${GMX_DIRS}; do
+		einfo "Configuring for ${x} precision"
+		local suffix=""
+		#if we build single and double - double is suffixed
+		use double-precision && use single-precision && \
+			[[ ${x} = "double" ]] && suffix="_d"
+		local p
+		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+		local cuda=( "-DGMX_GPU=OFF" )
+		[[ ${x} = "float" ]] && use cuda && \
+			cuda=( -DGMX_GPU=ON )
+		mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_MPI=OFF
+			$(cmake-utils_use threads GMX_THREAD_MPI)
+			"${cuda[@]}"
+			-DGMX_OPENMM=OFF
+			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
+			-DGMX_BINARY_SUFFIX="${suffix}"
+			-DGMX_LIBS_SUFFIX="${suffix}"
+			)
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		use mpi || continue
+		einfo "Configuring for ${x} precision with mpi"
+		mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_THREAD_MPI=OFF
+			-DGMX_MPI=ON ${cuda}
+			-DGMX_OPENMM=OFF
+			-DGMX_BUILD_MDRUN_ONLY=ON
+			-DBUILD_SHARED_LIBS=OFF
+			-DGMX_BUILD_MANUAL=OFF
+			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
+			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
+			)
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		einfo "Compiling for ${x} precision"
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile
+		# generate bash completion
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile completion
+		if use doc; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}"\
+				cmake-utils_src_compile manual
+		fi
+		use mpi || continue
+		einfo "Compiling for ${x} precision with mpi"
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+			cmake-utils_src_compile
+	done
+}
+
+src_test() {
+	for x in ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_make check
+	done
+}
+
+src_install() {
+	for x in ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}" \
+			cmake-utils_src_install
+		if use doc; then
+			newdoc "${WORKDIR}/${P}_${x}"/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+		fi
+		newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs
+		use mpi || continue
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+			cmake-utils_src_install
+	done
+	# drop unneeded stuff
+	rm -f "${ED}"usr/bin/gmx-completion*
+	rm -f "${ED}"usr/bin/g_options*
+	rm -f "${ED}"usr/bin/GMXRC*
+	rm -f "${ED}"usr/$(get_libdir)/libtng*.a
+
+	readme.gentoo_create_doc
+}
+
+pkg_postinst() {
+	einfo
+	einfo  "Please read and cite:"
+	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+	einfo  "http://dx.doi.org/10.1021/ct700301q"
+	einfo
+	readme.gentoo_print_elog
+}
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 880233ecb116..87e0f0a6ab9f 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -1,21 +1,27 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-chemistry</herd>
-	<maintainer>
-		<email>ottxor@gentoo.org</email>
-		<name>Christoph Junghans</name>
-	</maintainer>
-	<use>
-		<flag name="cuda">Enable cuda non-bonded kernels</flag>
-		<flag name="double-precision">More precise calculations at the expense of speed</flag>
-		<flag name="single-precision">Single precision version of gromacs (default)</flag>
-		<!-- acceleration optimization flags -->
-		<flag name="sse4_1">Enable sse4.1 acceleration</flag>
-		<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
-		<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
-		<flag name="offensive">Enable gromacs partly offensive quotes</flag>
-		<flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
-		<flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
-	</use>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>ottxor@gentoo.org</email>
+    <name>Christoph Junghans</name>
+  </maintainer>
+  <use>
+    <flag name="cuda">Enable cuda non-bonded kernels</flag>
+    <flag name="double-precision">More precise calculations at the expense of speed</flag>
+	<flag name="single-precision">Single precision version of gromacs (default)</flag>
+	<flag name="boost">Enable external boost library</flag>
+	<flag name="tng">Enable new trajectory format - tng</flag>
+	<flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag>
+    <!-- acceleration optimization flags -->
+    <flag name="sse4_1">Enable sse4.1 acceleration</flag>
+	<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
+	<flag name="avx_128_fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
+	<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+	<flag name="avx_256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+	<flag name="avx2_256">Enable 256bit avx2 (e.g. Intel Haswell)</flag>
+    <flag name="offensive">Enable gromacs partly offensive quotes</flag>
+    <flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
+    <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
+  </use>
 </pkgmetadata>