9 files changed, 9 insertions, 1194 deletions
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 1e995663e89b..cd6a6ac56be9 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.134 2013/12/05 18:10:06 alexxy Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.135 2013/12/31 23:35:05 ottxor Exp $
+
+  31 Dec 2013; Christoph Junghans <ottxor@gentoo.org>
+  -files/gromacs-4.5.5-cmake-cpp-asm.patch,
+  -files/gromacs-4.5.5-enable-see.patch,
+  -files/gromacs-4.5.7-cmake-cpp-asm.patch, -gromacs-4.5.5-r1.ebuild,
+  -gromacs-4.5.7.ebuild, -gromacs-4.6.3.ebuild, -gromacs-4.6.4.ebuild,
+  metadata.xml:
+  clean up
 
 *gromacs-4.6.5 (05 Dec 2013)
 
diff --git a/sci-chemistry/gromacs/files/gromacs-4.5.5-cmake-cpp-asm.patch b/sci-chemistry/gromacs/files/gromacs-4.5.5-cmake-cpp-asm.patch
deleted file mode 100644
index 71b7a2ff7b4a..000000000000
--- a/sci-chemistry/gromacs/files/gromacs-4.5.5-cmake-cpp-asm.patch
+++ /dev/null
@@ -1,46 +0,0 @@
-diff --git a/cmake/CMakeASM-ATTInformation.cmake b/cmake/CMakeASM-ATTInformation.cmake
-new file mode 100644
-index 0000000..05e9457
---- /dev/null
-+++ b/cmake/CMakeASM-ATTInformation.cmake
-@@ -0,0 +1,13 @@
-+
-+# This a modified version of CMakeASMInformation.cmake coming with cmake 2.8.6, which
-+# supports .S files
-+
-+# support for AT&T syntax assemblers, e.g. GNU as
-+
-+SET(ASM_DIALECT "-ATT")
-+SET(CMAKE_ASM${ASM_DIALECT}_SOURCE_FILE_EXTENSIONS S;s;asm)
-+
-+SET(CMAKE_ASM${ASM_DIALECT}_COMPILE_OBJECT "<CMAKE_ASM${ASM_DIALECT}_COMPILER> <FLAGS> -o <OBJECT> <SOURCE>")
-+
-+INCLUDE(CMakeASMInformation)
-+SET(ASM_DIALECT)
-diff --git a/src/gmxlib/CMakeLists.txt b/src/gmxlib/CMakeLists.txt
-index 021ed19..c3e7b79 100644
---- a/src/gmxlib/CMakeLists.txt
-+++ b/src/gmxlib/CMakeLists.txt
-@@ -47,18 +47,18 @@ endif()
- if(GMX_IA32_ASM)
-   file(GLOB GMX_SSEKERNEL_C_SRC   nonbonded/nb_kernel_ia32_${SSETYPE}/*.c)
-   if(GMX_ASM_USEASM-NASM)
--    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*intel_syntax*.s)    
-+    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*intel_syntax*.S)    
-   else()
--    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*${SSETYPE}.s nonbonded/nb_kernel_ia32_${SSETYPE}/*asm.s)
-+    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*${SSETYPE}.S nonbonded/nb_kernel_ia32_${SSETYPE}/*asm.S)
-   endif()
- endif(GMX_IA32_ASM)
- 
- if(GMX_X86_64_ASM)
-   file(GLOB GMX_SSEKERNEL_C_SRC   nonbonded/nb_kernel_x86_64_${SSETYPE}/*.c)
-   if(GMX_ASM_USEASM-NASM)
--    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*intel_syntax*.s)
-+    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*intel_syntax*.S)
-   else()
--    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*${SSETYPE}.s nonbonded/nb_kernel_x86_64_${SSETYPE}/*asm.s)
-+    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*${SSETYPE}.S nonbonded/nb_kernel_x86_64_${SSETYPE}/*asm.S)
-   endif()
- endif(GMX_X86_64_ASM)
- 
diff --git a/sci-chemistry/gromacs/files/gromacs-4.5.5-enable-see.patch b/sci-chemistry/gromacs/files/gromacs-4.5.5-enable-see.patch
deleted file mode 100644
index e00bb8f91447..000000000000
--- a/sci-chemistry/gromacs/files/gromacs-4.5.5-enable-see.patch
+++ /dev/null
@@ -1,48 +0,0 @@
-See https://gerrit.gromacs.org/376
-
-From 3d2c02960f9f791fc7d95549b686c8b23651613b Mon Sep 17 00:00:00 2001
-From: Christoph Junghans <junghans@votca.org>
-Date: Mon, 19 Dec 2011 11:23:25 -0700
-Subject: [PATCH] Set GMX_*_ASM true if GMX_ACCELERATION != auto
-
-In case GMX_ACCELERATION was set to SSE manually (like in Gentoo Linux)
-GMX_*_ASM would never be set (false), so sse kernel will not be build.
-
-Change-Id: Icf04707c6174a0182fe4472536b568e1d2d91166
----
- CMakeLists.txt |   12 ++++++------
- 1 files changed, 6 insertions(+), 6 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 25f22b7..b56aad1 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -542,12 +542,6 @@ if (${GMX_ACCELERATION} STREQUAL "auto" AND NOT GMX_OPENMM)
- 
-     set(GMX_ACCELERATION "SSE" CACHE STRING "Accelerated kernels. Pick one of: auto, none, SSE, BlueGene, Power6, ia64, altivec, fortran" FORCE)
-     
--    if (GMX_64_BIT)
--      set(GMX_X86_64_ASM ON CACHE BOOL "Add SSE assembly files for x86_64" FORCE)
--    else (GMX_64_BIT)
--      set(GMX_IA32_ASM ON CACHE BOOL "Add SSE assembly files for i386" FORCE)
--    endif (GMX_64_BIT)
--
-     # Determine the assembler/compiler to use
-   else()
-     set(GMX_ACCELERATION "none" CACHE STRING "Accelerated kernels. Pick one of: auto, none, SSE, BlueGene, Power6, ia64, altivec, fortran" FORCE)
-@@ -566,6 +560,12 @@ string(TOUPPER ${GMX_ACCELERATION} ${GMX_ACCELERATION})
- if(${GMX_ACCELERATION} STREQUAL "NONE")
-   # nothing to do
- elseif(${GMX_ACCELERATION} STREQUAL "SSE")
-+    
-+    if (GMX_64_BIT)
-+      set(GMX_X86_64_ASM ON CACHE BOOL "Add SSE assembly files for x86_64" FORCE)
-+    else (GMX_64_BIT)
-+      set(GMX_IA32_ASM ON CACHE BOOL "Add SSE assembly files for i386" FORCE)
-+    endif (GMX_64_BIT)
- 
-     if(CMAKE_GENERATOR MATCHES "Visual Studio")
-       option(GMX_ASM_USEASM-NASM "Use Nasm for assembly instead of compiler (necessary on windows)" ON)
--- 
-1.7.8
-
diff --git a/sci-chemistry/gromacs/files/gromacs-4.5.7-cmake-cpp-asm.patch b/sci-chemistry/gromacs/files/gromacs-4.5.7-cmake-cpp-asm.patch
deleted file mode 100644
index f39921f69846..000000000000
--- a/sci-chemistry/gromacs/files/gromacs-4.5.7-cmake-cpp-asm.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-diff -Naur gromacs-4.5.7.orig/cmake/CMakeASM-ATTInformation.cmake gromacs-4.5.7/cmake/CMakeASM-ATTInformation.cmake
---- gromacs-4.5.7.orig/cmake/CMakeASM-ATTInformation.cmake	1969-12-31 17:00:00.000000000 -0700
-+++ gromacs-4.5.7/cmake/CMakeASM-ATTInformation.cmake	2013-05-03 10:47:52.779868731 -0600
-@@ -0,0 +1,13 @@
-+
-+# This a modified version of CMakeASMInformation.cmake coming with cmake 2.8.6, which
-+# supports .S files
-+
-+# support for AT&T syntax assemblers, e.g. GNU as
-+
-+SET(ASM_DIALECT "-ATT")
-+SET(CMAKE_ASM${ASM_DIALECT}_SOURCE_FILE_EXTENSIONS S;s;asm)
-+
-+SET(CMAKE_ASM${ASM_DIALECT}_COMPILE_OBJECT "<CMAKE_ASM${ASM_DIALECT}_COMPILER> <FLAGS> -o <OBJECT> <SOURCE>")
-+
-+INCLUDE(CMakeASMInformation)
-+SET(ASM_DIALECT)
-diff -Naur gromacs-4.5.7.orig/src/gmxlib/CMakeLists.txt gromacs-4.5.7/src/gmxlib/CMakeLists.txt
---- gromacs-4.5.7.orig/src/gmxlib/CMakeLists.txt	2013-05-03 10:46:29.029305075 -0600
-+++ gromacs-4.5.7/src/gmxlib/CMakeLists.txt	2013-05-03 10:50:34.630582295 -0600
-@@ -47,18 +47,18 @@
- if(GMX_IA32_ASM)
-   file(GLOB GMX_SSEKERNEL_C_SRC   nonbonded/nb_kernel_ia32_${SSETYPE}/*.c)
-   if(GMX_ASM_USEASM_NASM)
--    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*intel_syntax*.s)    
-+    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*intel_syntax*.S)    
-   else()
--    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*${SSETYPE}.s nonbonded/nb_kernel_ia32_${SSETYPE}/*asm.s)
-+    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*${SSETYPE}.S nonbonded/nb_kernel_ia32_${SSETYPE}/*asm.S)
-   endif()
- endif(GMX_IA32_ASM)
- 
- if(GMX_X86_64_ASM)
-   file(GLOB GMX_SSEKERNEL_C_SRC   nonbonded/nb_kernel_x86_64_${SSETYPE}/*.c)
-   if(GMX_ASM_USEASM_NASM)
--    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*intel_syntax*.s)
-+    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*intel_syntax*.S)
-   else()
--    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*${SSETYPE}.s nonbonded/nb_kernel_x86_64_${SSETYPE}/*asm.s)
-+    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*${SSETYPE}.S nonbonded/nb_kernel_x86_64_${SSETYPE}/*asm.S)
-   endif()
- endif(GMX_X86_64_ASM)
- 
diff --git a/sci-chemistry/gromacs/gromacs-4.5.5-r1.ebuild b/sci-chemistry/gromacs/gromacs-4.5.5-r1.ebuild
deleted file mode 100644
index 96690e3f1925..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.5.5-r1.ebuild
+++ /dev/null
@@ -1,247 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.5-r1.ebuild,v 1.11 2012/12/08 22:15:02 ottxor Exp $
-
-EAPI="4"
-
-TEST_PV="4.0.4"
-MANUAL_PV="4.5.4"
-
-#to find external blas/lapack
-CMAKE_MIN_VERSION="2.8.5-r2"
-
-FORTRAN_NEEDED=fkernels
-
-inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
-
-if [ "${PV%9999}" != "${PV}" ]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
-	EGIT_BRANCH="release-4-5-patches"
-	inherit git-2
-else
-	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
-fi
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="${SRC_URI}
-		sse2? ( http://dev.gentoo.org/~alexxy/gromacs/0001-Make-stack-non-executable-for-GAS-assembly.patch.gz )
-		sse2? ( http://dev.gentoo.org/~alexxy/gromacs/0002-Make-stack-non-executable-for-ATT-assembly.patch.gz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )
-		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 ppc64 x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
-mpi +single-precision sse2 test +threads xml zsh-completion"
-REQUIRED_USE="fkernels? ( !threads )"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2:2 )"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig"
-RDEPEND="${CDEPEND}
-	app-shells/tcsh"
-
-RESTRICT="test"
-
-src_prepare() {
-	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
-	epatch_user
-
-	if use mpi && use threads; then
-		elog "mdrun uses only threads OR mpi, and gromacs favours the"
-		elog "use of mpi over threads, so a mpi-version of mdrun will"
-		elog "be compiled. If you want to run mdrun on shared memory"
-		elog "machines only, you can safely disable mpi"
-	fi
-
-	if use sse2; then
-		# Add patches for non-exec stack - qa issue
-		epatch "${WORKDIR}/0001-Make-stack-non-executable-for-GAS-assembly.patch"
-		epatch "${WORKDIR}/0002-Make-stack-non-executable-for-ATT-assembly.patch"
-		#alexxy patches, renamve kernel from .s to .S
-		epatch "${FILESDIR}/${P}-cmake-cpp-asm.patch"
-
-		epatch "${FILESDIR}/${P}-enable-see.patch"
-	fi
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-	#if neither single-precision nor double-precision is enabled
-	#build at least default (single)
-	[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
-
-	for x in ${GMX_DIRS}; do
-		mkdir -p "${WORKDIR}/${P}_${x}" || die
-		use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
-	done
-}
-
-src_configure() {
-	local mycmakeargs_pre=( )
-	#from gromacs configure
-	if use fftw; then
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
-	else
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
-	fi
-
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
-
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-	fi
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
-	#go from slowest to fasterest acceleration
-	local acce="none"
-	use fkernels && acce="fortran"
-	use altivec && acce="altivec"
-	use ia64 && acce="ia64"
-	use sse2 && acce="sse"
-
-	mycmakeargs_pre+=(
-		$(cmake-utils_use X GMX_X11)
-		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use gsl GMX_GSL)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use threads GMX_THREADS)
-		$(cmake-utils_use xml GMX_XML)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_ACCELERATION="$acce"
-		-DGMXLIB="$(get_libdir)"
-	)
-
-	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"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-			-DGMX_BINARY_SUFFIX="${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[@]} ${p} -DGMX_MPI=ON
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" 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
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile mdrun
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		local oldpath="${PATH}"
-		export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
-		cd "${WORKDIR}/${P}_${x}"
-		emake -j1 tests || die "${x} Precision test failed"
-		export PATH="${oldpath}"
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		use mpi || continue
-		#cmake-utils_src_install does not support args
-		#using cmake-utils_src_compile instead
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_make install-mdrun DESTDIR="${D}"
-	done
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
-
-	doenvd "${T}/80gromacs"
-	rm -f "${ED}"/usr/bin/GMXRC*
-
-	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${ED}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -f "${ED}"/usr/bin/completion.*
-
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL* README*
-	if use doc; then
-		newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
-		dohtml -r "${ED}usr/share/gromacs/html/"
-	fi
-	rm -rf "${ED}usr/share/gromacs/html/"
-}
-
-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
-	einfo  $(g_luck)
-	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
-	einfo
-	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
diff --git a/sci-chemistry/gromacs/gromacs-4.5.7.ebuild b/sci-chemistry/gromacs/gromacs-4.5.7.ebuild
deleted file mode 100644
index b5ed0854530f..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.5.7.ebuild
+++ /dev/null
@@ -1,242 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.7.ebuild,v 1.2 2013/05/05 17:31:09 ottxor Exp $
-
-EAPI="4"
-
-TEST_PV="4.0.4"
-MANUAL_PV="4.5.6"
-
-FORTRAN_NEEDED=fkernels
-
-inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
-
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
-
-if [ "${PV%9999}" != "${PV}" ]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-4-5-patches"
-	inherit git-2
-else
-	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-		sse2? ( http://dev.gentoo.org/~alexxy/gromacs/0001-Make-stack-non-executable-for-GAS-assembly.patch.gz )
-		sse2? ( http://dev.gentoo.org/~alexxy/gromacs/0002-Make-stack-non-executable-for-ATT-assembly.patch.gz )"
-fi
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
-mpi +single-precision sse2 test +threads xml zsh-completion"
-REQUIRED_USE="fkernels? ( !threads )"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2:2 )"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig"
-RDEPEND="${CDEPEND}
-	app-shells/tcsh"
-
-RESTRICT="test"
-
-src_prepare() {
-	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
-	epatch_user
-
-	if use mpi && use threads; then
-		elog "mdrun uses only threads OR mpi, and gromacs favours the"
-		elog "use of mpi over threads, so a mpi-version of mdrun will"
-		elog "be compiled. If you want to run mdrun on shared memory"
-		elog "machines only, you can safely disable mpi"
-	fi
-
-	if [[ ${PV} != *9999 ]] && use sse2; then
-		# Add patches for non-exec stack - qa issue
-		epatch "${WORKDIR}/0001-Make-stack-non-executable-for-GAS-assembly.patch"
-		epatch "${WORKDIR}/0002-Make-stack-non-executable-for-ATT-assembly.patch"
-		#alexxy patches, renamve kernel from .s to .S
-		epatch "${FILESDIR}/${P}-cmake-cpp-asm.patch"
-	fi
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-	#if neither single-precision nor double-precision is enabled
-	#build at least default (single)
-	[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
-
-	for x in ${GMX_DIRS}; do
-		mkdir -p "${WORKDIR}/${P}_${x}" || die
-		use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
-	done
-}
-
-src_configure() {
-	local mycmakeargs_pre=( )
-	#from gromacs configure
-	if use fftw; then
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
-	else
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
-	fi
-
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
-
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-	fi
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
-	#go from slowest to fasterest acceleration
-	local acce="none"
-	use fkernels && acce="fortran"
-	use altivec && acce="altivec"
-	use ia64 && acce="ia64"
-	use sse2 && acce="sse"
-
-	mycmakeargs_pre+=(
-		$(cmake-utils_use X GMX_X11)
-		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use gsl GMX_GSL)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use threads GMX_THREADS)
-		$(cmake-utils_use xml GMX_XML)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_ACCELERATION="$acce"
-		-DGMXLIB="$(get_libdir)"
-	)
-
-	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"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-			-DGMX_BINARY_SUFFIX="${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[@]} ${p} -DGMX_MPI=ON
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" 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
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile mdrun
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		local oldpath="${PATH}"
-		export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
-		cd "${WORKDIR}/${P}_${x}"
-		emake -j1 tests || die "${x} Precision test failed"
-		export PATH="${oldpath}"
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		use mpi || continue
-		#cmake-utils_src_install does not support args
-		#using cmake-utils_src_compile instead
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_make install-mdrun DESTDIR="${D}"
-	done
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
-
-	doenvd "${T}/80gromacs"
-	rm -f "${ED}"/usr/bin/GMXRC*
-
-	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${ED}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -f "${ED}"/usr/bin/completion.*
-
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL* README*
-	if use doc; then
-		newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
-		dohtml -r "${ED}usr/share/gromacs/html/"
-	fi
-	rm -rf "${ED}usr/share/gromacs/html/"
-}
-
-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
-	einfo  $(g_luck)
-	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
-	einfo
-	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
diff --git a/sci-chemistry/gromacs/gromacs-4.6.3.ebuild b/sci-chemistry/gromacs/gromacs-4.6.3.ebuild
deleted file mode 100644
index 57ec9f1b3a93..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.6.3.ebuild
+++ /dev/null
@@ -1,283 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.3.ebuild,v 1.1 2013/07/05 23:49:14 ottxor Exp $
-
-EAPI=5
-
-TEST_PV="4.6.2"
-MANUAL_PV="4.6.2"
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		git://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-4-6"
-	inherit git-2
-	LIVE_DEPEND="doc? (
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-		sys-apps/coreutils
-	)"
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
-		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
-	LIVE_DEPEND=""
-fi
-
-ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
-
-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 cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	openmm? (
-		>=dev-util/nvidia-cuda-toolkit-4.2.9-r1
-		sci-libs/openmm[cuda,opencl]
-	)"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	${LIVE_DEPEND}"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	openmm? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ )
-
-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 [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-2_src_unpack
-		if use doc; then
-			EGIT_REPO_URI="git://git.gromacs.org/manual.git" \
-			EGIT_BRANCH="release-4-6" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
-			EGIT_SOURCEDIR="${WORKDIR}/manual"\
-				git-2_src_unpack
-		fi
-		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-2_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 avx128fma && acce="AVX_128_FMA"
-	use avx256 && acce="AVX_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 gsl GMX_GSL)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use openmp GMX_OPENMP)
-		$(cmake-utils_use offensive GMX_COOL_QUOTES)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_ACCELERATION="$acce"
-		-DGMXLIB="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_PREFIX_LIBMD=ON
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=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
-		if [[ ${x} = float ]] && use openmm; then
-			einfo "Configuring for openmm build"
-			mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-				-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
-				-DOpenMM_PLUGIN_DIR="${EPREFIX}/usr/$(get_libdir)/plugins"
-				-DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" )
-			BUILD_DIR="${WORKDIR}/${P}_openmm" \
-				OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure
-		fi
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${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
-		if [[ ${x} = float ]] && use openmm; then
-			einfo "Compiling for openmm build"
-			BUILD_DIR="${WORKDIR}/${P}_openmm"\
-				cmake-utils_src_compile mdrun
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile mdrun
-	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 [[ ${x} = float ]] && use openmm; then
-			BUILD_DIR="${WORKDIR}/${P}_openmm" \
-				DESTDIR="${D}" cmake-utils_src_make install-mdrun
-		fi
-		#manual can only be build after gromacs was installed once in image
-		if use doc && [[ $PV = *9999*  && ! -d ${WORKDIR}/manual_build ]]; then
-			mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )
-			BUILD_DIR="${WORKDIR}"/manual_build \
-				CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure
-			[[ ${CHOST} = *-darwin* ]] && \
-				export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)"
-			BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
-			[[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)"
-			newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			DESTDIR="${D}" cmake-utils_src_make install-mdrun
-	done
-
-	use doc && [[ $PV != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
-	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${ED}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -f "${ED}"usr/bin/completion.*
-	rm -rf "${ED}"usr/share/gromacs/html
-	rm -f "${ED}"usr/bin/g_options*
-	rm -f "${ED}"usr/bin/GMXRC*
-
-	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"
-	if use offensive; then
-		einfo
-		einfo  $(g_luck)
-		einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
-	fi
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-4.6.4.ebuild b/sci-chemistry/gromacs/gromacs-4.6.4.ebuild
deleted file mode 100644
index 8ade0a377274..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.6.4.ebuild
+++ /dev/null
@@ -1,283 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.4.ebuild,v 1.1 2013/11/13 18:17:42 ottxor Exp $
-
-EAPI=5
-
-TEST_PV="4.6.4"
-MANUAL_PV="4.6.4"
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		git://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-4-6"
-	inherit git-2
-	LIVE_DEPEND="doc? (
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-		sys-apps/coreutils
-	)"
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
-		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
-	LIVE_DEPEND=""
-fi
-
-ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
-
-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 cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	openmm? (
-		>=dev-util/nvidia-cuda-toolkit-4.2.9-r1
-		sci-libs/openmm[cuda,opencl]
-	)"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	${LIVE_DEPEND}"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	openmm? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ )
-
-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 [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-2_src_unpack
-		if use doc; then
-			EGIT_REPO_URI="git://git.gromacs.org/manual.git" \
-			EGIT_BRANCH="release-4-6" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
-			EGIT_SOURCEDIR="${WORKDIR}/manual"\
-				git-2_src_unpack
-		fi
-		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-2_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 avx128fma && acce="AVX_128_FMA"
-	use avx256 && acce="AVX_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 gsl GMX_GSL)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use openmp GMX_OPENMP)
-		$(cmake-utils_use offensive GMX_COOL_QUOTES)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_ACCELERATION="$acce"
-		-DGMXLIB="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_PREFIX_LIBMD=ON
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=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
-		if [[ ${x} = float ]] && use openmm; then
-			einfo "Configuring for openmm build"
-			mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-				-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
-				-DOpenMM_PLUGIN_DIR="${EPREFIX}/usr/$(get_libdir)/plugins"
-				-DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" )
-			BUILD_DIR="${WORKDIR}/${P}_openmm" \
-				OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure
-		fi
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${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
-		if [[ ${x} = float ]] && use openmm; then
-			einfo "Compiling for openmm build"
-			BUILD_DIR="${WORKDIR}/${P}_openmm"\
-				cmake-utils_src_compile mdrun
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile mdrun
-	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 [[ ${x} = float ]] && use openmm; then
-			BUILD_DIR="${WORKDIR}/${P}_openmm" \
-				DESTDIR="${D}" cmake-utils_src_make install-mdrun
-		fi
-		#manual can only be build after gromacs was installed once in image
-		if use doc && [[ $PV = *9999*  && ! -d ${WORKDIR}/manual_build ]]; then
-			mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )
-			BUILD_DIR="${WORKDIR}"/manual_build \
-				CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure
-			[[ ${CHOST} = *-darwin* ]] && \
-				export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)"
-			BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
-			[[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)"
-			newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			DESTDIR="${D}" cmake-utils_src_make install-mdrun
-	done
-
-	use doc && [[ $PV != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
-	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${ED}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -f "${ED}"usr/bin/completion.*
-	rm -rf "${ED}"usr/share/gromacs/html
-	rm -f "${ED}"usr/bin/g_options*
-	rm -f "${ED}"usr/bin/GMXRC*
-
-	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"
-	if use offensive; then
-		einfo
-		einfo  $(g_luck)
-		einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
-	fi
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 8a88d53da511..880233ecb116 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -11,7 +11,6 @@
 		<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="fkernels">Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
 		<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>