Add new gromacs 4.0.4

Package-Manager: portage-2.2_rc30/cvs/Linux x86_64

7 files changed, 271 insertions, 446 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 922f0d06abfb..de215d952daf 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 2002-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.34 2009/03/08 19:50:46 maekke Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.35 2009/04/20 13:39:12 alexxy Exp $
+
+*gromacs-4.0.4 (20 Apr 2009)
+
+  20 Apr 2009; Alexey Shvetsov <alexxy@gentoo.org>
+  +files/gromacs-4.0.4-configure-gfortran.patch, metadata.xml,
+  -gromacs-4.0.ebuild, -gromacs-4.0.2.ebuild, +gromacs-4.0.4.ebuild:
+  Add new gromacs 4.0.4
 
   08 Mar 2009; Markus Meier <maekke@gentoo.org> gromacs-4.0.3.ebuild:
   amd64/x86 stable, bug #260995
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index f6434750b7a3..c12075f01ce0 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,22 +1,13 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
+AUX gromacs-4.0.4-configure-gfortran.patch 731 RMD160 1ccea4fafd6837461114fc36bc31db4f9390fc08 SHA1 0ec79e9ab691cbae5f116adaa3245ef0b123a598 SHA256 5b902eac127bc84e188224fbfe0182ab3fa3b03c200325ada9cd628bb913b479
+DIST gmxtest-4.0.4.tgz 14845017 RMD160 c7c583415438bdef4c9996da9064254e9460cf16 SHA1 998179aa2bfbc4f80514f10ed774762f85c854c3 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361
 DIST gromacs-3.3.1.tar.gz 7992897 RMD160 48e6f9098ac4f5b834f4beb050846c60aea18fff SHA1 8c67ee772cadf93067b3c8bcec65d7b3520df1dc SHA256 3df40151ff5364fab1c4d8692ec247d8245437e954882a803178cbe6b812d81f
 DIST gromacs-3.3.3.tar.gz 8013789 RMD160 c7b495423eb07682e88bd7d5c61e0aa9156a17d1 SHA1 318802e39f3ca3e847261a3b96906266e32deba2 SHA256 b95becbe410b71fe9bc19b91dfeb98b940dbb2d66613c9e1de7f6d21fb7534fa
-DIST gromacs-4.0.2.tar.gz 8413529 RMD160 192d692d15b9d2ef7daa84abc9a2c2441229d60a SHA1 631db66fb29d93d0735f047060a12d700ae9df11 SHA256 36ea84acc546189c698a77192073a20362d8a8c0a75985226758a1d8dfbb979b
 DIST gromacs-4.0.3.tar.gz 8420556 RMD160 e799d3cc813787a6a68a8d5d370818a10224a2a2 SHA1 099f6b793d1b198a7bb6c4fa59beae915aba3d52 SHA256 6fc33ac9e1e9b208e2e8c73cb9e95940ed86969207fedc02bf30119f2ed58572
-DIST gromacs-4.0.tar.gz 8388265 RMD160 3156220f6b98ec4c04c264c8f798c616ce668a07 SHA1 5c8f0c3bfa2950bb936b4bfc5e9241028ffb8f1d SHA256 88b15d93200534539019754acc462a08572973025d9e147fce3c60529a0ffc16
+DIST gromacs-4.0.4.tar.gz 8443779 RMD160 f90327814170c26a43d99fe7587357a46989fdec SHA1 9466f3ab95d60c0aba8916b1fcc70129cb4e4d72 SHA256 8aefd03cd3269e85c84427f05ceea6d3e16874cd4a90bf3f6fec2b2be24c426f
+DIST manual-4.0.pdf 2135100 RMD160 b963642f8e1433f11328c3d0c4b1645c9de506da SHA1 8ae951ee15b2a7dc626331fce36511bc8766144c SHA256 646f810477eee2d710de6019c52056550413d0ba77baf9680195c835ddafe80a
 EBUILD gromacs-3.3.1-r1.ebuild 5868 RMD160 7273c8a595865adc537f6f95baa448fd68f38a2c SHA1 81f0f47eaf50ad6eefd24ed8ef4bd27a7d208a48 SHA256 5abce8ce4d132b019bf31aa2ae0e0a21648505026156f46a25ddbc9e594cfc9c
 EBUILD gromacs-3.3.3.ebuild 6337 RMD160 3c64811596e905462858f7dd7790384b83dcdc8f SHA1 6f7174596c6a68d5bcddd3fc623ea25b174b8c0d SHA256 85a8fad766c16655a023a04a2e93d4f1d782f1e5463cebe12b3d4a31a0c9cee3
-EBUILD gromacs-4.0.2.ebuild 6120 RMD160 873931420e1ddb8d2d8bc14cd42552ded2afc8ba SHA1 12c911300efe5adfe93f75e97f62f4f1717d8fed SHA256 508495bc63b300c3e799b03445eb4eb98949966f4b5a0013a4e0b5614ebc11d1
 EBUILD gromacs-4.0.3.ebuild 6137 RMD160 0101757bf0ec75bf69d318c70bab19caaa29055a SHA1 62438c624a13fa163451b5af83296c424b42b03f SHA256 48019b2af7e448062add15edacb05ecc9a7341f149ab9346cddd2fd2848ae5ef
-EBUILD gromacs-4.0.ebuild 6118 RMD160 14fe7f16afb8cbe6d0bf769350d1a1a66e4f9e9b SHA1 8944953873b70bd5ae855780448a71fc22fa284d SHA256 b4eb4306ec9a34d81b9d75807ff085139a9959b681f28aa329f5cb178cd71a17
-MISC ChangeLog 7586 RMD160 e1a52388f1ba2625bd180ad5363757af655a1491 SHA1 d5614c19f81920c3698a6e4fac3de09ea78dc446 SHA256 60ac6672184292a64c31c256c58cd637e44e1bac331875fc6ce9f5f5b5e44210
-MISC metadata.xml 347 RMD160 23f2ef9d3b27d90f479c8242f6166e6afcbf4d45 SHA1 46bf8a3fb4b6a4e5c1ca55da0d6db9e1a6148ace SHA256 50d65907b09d524e42754b66da9f8596a6c4e941499922348cb75b774e9a543b
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+EBUILD gromacs-4.0.4.ebuild 6870 RMD160 0798b440ad0ae001099b1f97c8507cc9f05dc17e SHA1 efec7532d7a8c680db4cb7946ca5002513372d5b SHA256 4ed36c48be6438c1454c79765ed5e76a5b559cdfec1daa5ab508ac27d8b68759
+MISC ChangeLog 7824 RMD160 cb8026b1c16e083715b660bc4cb5b57b5e33d356 SHA1 a726d23513bb8ab700267e8de4313f0ea8f3e5f3 SHA256 4cf28c4c1813b7e3aff4ae8e478a08b8c80acd1f8e9da8884e958a76a91aeec1
+MISC metadata.xml 573 RMD160 4966393ae1104e5be4480167f6da1c42e94a6df6 SHA1 fcabeba87b97a7340946278a126f9a0d543ef87b SHA256 77d80380160cd95c6d7b4a9e97ca837d773f0a7102670464ad4f02ac7e4e7eb3
diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.4-configure-gfortran.patch b/sci-chemistry/gromacs/files/gromacs-4.0.4-configure-gfortran.patch
new file mode 100644
index 000000000000..c330fcaf0cdc
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-4.0.4-configure-gfortran.patch
@@ -0,0 +1,17 @@
+diff -Naur gromacs-4.0.4-orig/configure.ac gromacs-4.0.4/configure.ac
+--- gromacs-4.0.4-orig/configure.ac	2009-04-09 21:12:31.000000000 +0200
++++ gromacs-4.0.4/configure.ac	2009-04-09 21:13:38.000000000 +0200
+@@ -320,11 +320,11 @@
+ case "${host_cpu}-${host_os}" in
+   alpha*-linux*)
+     cc_names="ccc cc gcc"
+-    f77_names="fort f77 g77"
++    f77_names="fort f77 g77 gfortran"
+     ;;
+   *) 
+     cc_names="cc icc xlc gcc"
+-    f77_names="f77 ifort xlf xlf77 cf77 fl32 g77 fort77 f90 xlf90 pgf77 cf77 fort fort77 pgf90"
++    f77_names="f77 ifort xlf xlf77 cf77 fl32 g77 fort77 f90 xlf90 pgf77 cf77 fort fort77 pgf90 gfortran"
+     ;;
+ esac
+ # the (non-mpi) c compiler, which is also used for programs executed during build stage
diff --git a/sci-chemistry/gromacs/gromacs-4.0.2.ebuild b/sci-chemistry/gromacs/gromacs-4.0.2.ebuild
deleted file mode 100644
index 716b0ac319bb..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.0.2.ebuild
+++ /dev/null
@@ -1,213 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.2.ebuild,v 1.2 2009/01/22 04:14:36 je_fro Exp $
-
-EAPI="1"
-
-inherit autotools eutils flag-o-matic fortran multilib
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
-IUSE="3dnow X altivec blas double-precision gsl lapack mpi +single-precision sse sse2 static xml"
-
-# mopac7 qm/mm is broken until we can get files from
-# http://md.chem.rug.nl/~groenhof/qmmm.html
-# or somewhere else...
-
-DEPEND=">=sci-libs/fftw-3.0.1
-	app-shells/tcsh
-	X? ( x11-libs/libX11
-		x11-libs/libXt
-		x11-libs/libXp
-		x11-libs/libXext
-		x11-proto/xproto
-		x11-libs/openmotif )
-	blas? ( virtual/blas )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2 )"
-
-RDEPEND="${DEPEND}"
-
-FORTRAN="g77 gfortran ifc"
-
-src_unpack() {
-
-	unpack ${A}
-	cd "${S}"
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	# Fix a sandbox violation that occurs when re-emerging with mpi.
-	sed "/libdir=\"\$(libdir)\"/ a\	temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed -e "s:\$\$libdir:\$temp_libdir:" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed -e "s:\$\$libdir:\$\$temp_libdir:" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	eautoreconf
-
-	cd "${WORKDIR}"
-	mv "${P}" "${P}-single"
-	if ( use double-precision ) ; then
-		einfo "Moving sources for Multiprecision Build"
-		cp -prP "${P}-single" "${P}-double"
-	fi
-}
-
-src_compile() {
-
-	# static should work but something's broken.
-	# gcc spec file may be screwed up.
-	# Static linking should try -lgcc instead of -lgcc_s.
-	# For more info:
-	# http://lists.debian.org/debian-gcc/2002/debian-gcc-200201/msg00150.html
-
-	# We will compile single precision by default, and suffix double-precision with _d.
-	# Sparc is the only arch I can test on that needs to use fortran.
-	local myconf ;
-	local myconf_s ;
-	local myconf_d ;
-
-	case "${ARCH}" in
-
-		x86)
-			if ( use sse || use sse2 ) ; then
-				myconf="${myconf} --enable-ia32-sse"
-			fi
-			myconf="$myconf $(use_enable 3dnow ia32-3dnow)"
-
-			if ( ! use sse && ! use sse2 && ! use 3dnow ) ; then
-				if ! has_version "=sys-devel/gcc-3*" ; then
-					die "If you must run gromacs without sse (not recommended) gfortran will not work."
-				else
-					myconf="${myconf} --enable-fortran" && fortran_pkg_setup
-				fi
-			else
-				myconf="${myconf} --disable-fortran"
-			fi
-			;;
-
-		amd64)
-			myconf="$myconf --enable-x86-64-sse --disable-fortran"
-			;;
-
-		ppc*)
-			if use altivec ; then
-				myconf="${myconf} --enable-ppc-altivec --disable-fortran"
-			else
-				if ! has_version "=sys-devel/gcc-3*" ; then
-					die "If you must run gromacs without sse (not recommended) gfortran will not work."
-				else
-					myconf="${myconf} --enable-fortran" && fortran_pkg_setup
-				fi
-			fi
-			;;
-
-		ia64)
-			myconf="$myconf --enable-ia64-asm --disable-fortran"
-			;;
-
-		alpha)
-			if ! has_version "=sys-devel/gcc-3*" ; then
-				die "If you must run gromacs without sse (not recommended) gfortran will not work."
-			else
-				myconf="$myconf --enable-fortran" && fortran_pkg_setup
-			fi
-			;;
-
-		sparc)
-			if ! has_version "=sys-devel/gcc-3*" ; then
-				die "If you must run gromacs without sse (not recommended) gfortran will not work."
-			else
-				myconf="${myconf} --enable-fortran" && fortran_pkg_setup
-			fi
-			;;
-	esac
-
-	# if we need external blas
-	if use blas; then
-		export LIBS="${LIBS} -lblas"
-		myconf="${myconf} $(use_with blas external-blas)"
-	fi
-
-	# if we need external lapack
-	if use lapack; then
-		export LIBS="${LIBS} -llapack"
-		myconf="${myconf} $(use_with lapack external-lapack)"
-	fi
-
-	myconf="--datadir=/usr/share \
-			--bindir=/usr/bin \
-			--libdir=/usr/$(get_libdir) \
-			--with-fft=fftw3 \
-			$(use_with gsl) \
-			$(use_enable mpi) \
-			$(use_with X x) \
-			$(use_with xml) \
-			$(use_enable static all-static) \
-			${myconf}"
-
-	if ( use double-precision && use single-precision ); then
-		einfo "Building Single Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-single
-		myconf_s="${myconf}  --enable-float --disable-double --program-suffix=''"
-		econf ${myconf_s} || die "Single Precision econf failed"
-		emake || die "Single Precision emake failed"
-
-		einfo "Building Double Precision Gromacs"
-		cd "${WORKDIR}"/"${P}"-double
-		myconf_d="${myconf} --enable-double --disable-float --program-suffix=_d"
-		econf ${myconf_d} || die "Double Precision econf failed"
-		emake || die "Double Precision emake failed"
-
-	elif use double-precision ; then
-		einfo "Building Double Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-double
-		myconf_d="${myconf} --enable-double --disable-float --program-suffix=''"
-		econf ${myconf_d} || die "Double Precision econf failed"
-		emake || die "Double Precision emake failed"
-
-	elif use single-precision ; then
-		einfo "Building Single Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-single
-		myconf_s="${myconf} --enable-float --disable-double --program-suffix=''"
-		econf ${myconf_s} || die "configure failed"
-		emake || die "Single Precision emake failed"
-	fi
-}
-
-src_install() {
-	if use single-precision ; then
-		einfo "Installing Single Precision"
-		cd "${WORKDIR}"/"${P}"-single
-		emake DESTDIR="${D}" install || die "Installing Single Precision failed"
-	fi
-
-	if use double-precision ; then
-		einfo "Installing Double Precision"
-		cd "${WORKDIR}"/"${P}"-double
-		emake DESTDIR="${D}" install || die "Installing Double Precision failed"
-	fi
-
-	dodoc AUTHORS INSTALL README
-	# Move html and leave examples and templates under /usr/share/gromacs.
-	mv "${D}"/usr/share/"${PN}"/html "${D}"/usr/share/doc/"${PF}"/
-}
diff --git a/sci-chemistry/gromacs/gromacs-4.0.4.ebuild b/sci-chemistry/gromacs/gromacs-4.0.4.ebuild
new file mode 100644
index 000000000000..e6564e8d90c7
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.0.4.ebuild
@@ -0,0 +1,233 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.4.ebuild,v 1.1 2009/04/20 13:39:12 alexxy Exp $
+
+EAPI="2"
+
+LIBTOOLIZE="true"
+
+inherit autotools bash-completion eutils fortran multilib
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
+		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${PV}.tgz )
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
+IUSE="X blas dmalloc doc -double-precision +fftw fkernels gsl lapack mpi +single-precision static test +xml zsh-completion"
+
+DEPEND="app-shells/tcsh
+	X? ( x11-libs/libX11 )
+	dmalloc? ( dev-libs/dmalloc )
+	blas? ( virtual/blas )
+	fftw? ( sci-libs/fftw:3.0 )
+	gsl? ( sci-libs/gsl )
+	lapack? ( virtual/lapack )
+	mpi? ( virtual/mpi )
+	xml? ( dev-libs/libxml2 )"
+
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	# Fix typos in a couple of files.
+	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
+		|| die "Failed to fixup demo script."
+
+	# Fix a sandbox violation that occurs when re-emerging with mpi.
+	sed "/libdir=\"\$(libdir)\"/ a\	temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	sed -e "s:\$\$libdir:\$temp_libdir:" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	sed -e "s:\$\$libdir:\$\$temp_libdir:" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	use fkernels && epatch "${FILESDIR}/${P}-configure-gfortran.patch"
+
+	eautoreconf
+
+	cd "${WORKDIR}"
+	mv "${P}" "${P}-single"
+	if ( use double-precision ) ; then
+		einfo "Moving sources for Multiprecision Build"
+		cp -prP "${P}-single" "${P}-double"
+	fi
+}
+
+src_configure() {
+	local myconf ;
+	local myconf_s ;
+	local myconf_d ;
+	local suffix_d ;
+
+	#leave all assembly options enabled mdrun is smart enough to deside itself
+	#there so no gentoo on bluegene!
+	myconf="${myconf} --disable-bluegene"
+
+	#from gromacs configure
+	if ! use fftw; then
+		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 [[ $(gcc-version) == "4.1" ]]; then
+		ewarn "gcc 4.1 is not supported by gromacs"
+		ewarn "please run test suite"
+	fi
+
+	#fortran will gone in gromacs 4.1 anyway
+	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
+	if use fkernels; then
+		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
+		ewarn "I hope, you know what are you doing..."
+		FORTRAN="g77 gfortran ifc"
+		myconf="${myconf} --enable-fortran" && fortran_pkg_setup
+	else
+		myconf="${myconf} --disable-fortran"
+	fi
+
+	# if we need external blas
+	if use blas; then
+		export LIBS="${LIBS} -lblas"
+		myconf="${myconf} $(use_with blas external-blas)"
+	fi
+
+	# if we need external lapack
+	if use lapack; then
+		export LIBS="${LIBS} -llapack"
+		myconf="${myconf} $(use_with lapack external-lapack)"
+	fi
+
+	myconf="--datadir=/usr/share \
+			--bindir=/usr/bin \
+			--libdir=/usr/$(get_libdir) \
+			$(use_with dmalloc) \
+			$(use_with fftw fft fftw3) \
+			$(use_with gsl) \
+			$(use_enable mpi) \
+			$(use_with X x) \
+			$(use_with xml) \
+			$(use_enable static all-static) \
+			${myconf}"
+
+	#if we build both double is suffixed
+	if ( use double-precision && use single-precision ); then
+		suffix_d="_d"
+	else
+		suffix_d=""
+	fi
+
+	if use double-precision ; then
+		#from gromacs manual
+		elog
+		elog "For most simulations single precision is accurate enough. In some"
+		elog "cases double precision is required	to get reasonable results:"
+		elog
+		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
+		elog " and the calculation and diagonalization of the Hessian "
+		elog "-calculation of the constraint force between two large groups of	atoms"
+		elog "-energy conservation: this can only be done without temperature coupling and"
+		elog " without cutoffs"
+		elog
+		einfo "Configuring Double Precison Gromacs"
+		cd "${WORKDIR}"/"${P}"-double
+		myconf_d="${myconf} --enable-double --program-suffix='${suffix_d}'"
+		econf ${myconf_d} || die "Double Precision econf failed"
+	fi
+
+	if use single-precision ; then
+		einfo "Configuring Single Precison Gromacs"
+		cd "${WORKDIR}"/"${P}"-single
+		myconf_s="${myconf} --enable-float --program-suffix=''"
+		econf ${myconf_s} || die "configure failed"
+	fi
+}
+
+src_compile() {
+	if use double-precision ; then
+		einfo "Building Double Precison Gromacs"
+		cd "${WORKDIR}"/"${P}"-double
+		emake || die "Double Precision emake failed"
+	fi
+
+	if use single-precision ; then
+		einfo "Building Single Precison Gromacs"
+		cd "${WORKDIR}"/"${P}"-single
+		emake || die "Single Precision emake failed"
+	fi
+}
+
+src_test() {
+	if use single-precision ; then
+		export PATH="${WORKDIR}/${P}-single/src/kernel:${WORKDIR}/${P}-single/src/tools:$PATH"
+		cd "${WORKDIR}/gmxtest"
+		#test is broken, only do simple tests
+		./gmxtest.pl simple || die "Single Precision test failed"
+	fi
+
+	if use double-precision ; then
+		export PATH="${WORKDIR}/${P}-double/src/kernel:${WORKDIR}/${P}-double/src/tools:$PATH"
+		cd "${WORKDIR}/gmxtest"
+		use single-precision && ./gmxtest.pl clean
+		#test is broken, only do simple tests
+		./gmxtest.pl -double simple || die "Double Precision test failed"
+	fi
+}
+
+src_install() {
+	if use single-precision ; then
+		einfo "Installing Single Precision"
+		cd "${WORKDIR}"/"${P}"-single
+		emake DESTDIR="${D}" install || die "Installing Single Precision failed"
+	fi
+
+	if use double-precision ; then
+		einfo "Installing Double Precision"
+		cd "${WORKDIR}"/"${P}"-double
+		emake DESTDIR="${D}" install || die "Installing Double Precision failed"
+	fi
+
+	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${D}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
+	doenvd "${T}/80gromacs"
+	rm -f "${D}"/usr/bin/GMXRC*
+
+	dobashcompletion "${D}"/usr/bin/completion.bash ${PN}
+	if use zsh-completion ; then
+		insinto /usr/share/zsh/site-functions
+		newins "${D}"/usr/bin/completion.zsh _${PN}
+	fi
+	rm -r "${D}"/usr/bin/completion.*
+
+	dodoc AUTHORS INSTALL README
+	if use doc; then
+		# Move html and leave examples and templates under /usr/share/gromacs.
+		mv "${D}"/usr/share/"${PN}"/html "${D}"/usr/share/doc/"${PF}"/
+		dodoc "${DISTDIR}"/manual-4.0.pdf
+	fi
+}
+
+pkg_postinst() {
+	env-update && source /etc/profile
+	elog
+	elog "Please read and cite:"
+	elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 \(2008\). "
+	elog "http://dx.doi.org/10.1021/ct700301q"
+	elog
+	bash-completion_pkg_postinst
+	elog
+	elog $(luck)
+	elog "For more Gromacs cool quotes \(gcq\)  add luck to your .bashrc"
+	elog
+}
diff --git a/sci-chemistry/gromacs/gromacs-4.0.ebuild b/sci-chemistry/gromacs/gromacs-4.0.ebuild
deleted file mode 100644
index fe25d85dc9e7..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.0.ebuild
+++ /dev/null
@@ -1,213 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.ebuild,v 1.2 2009/01/22 04:14:36 je_fro Exp $
-
-EAPI="1"
-
-inherit autotools eutils flag-o-matic fortran multilib
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
-IUSE="3dnow X altivec blas double-precision gsl lapack mpi +single-precision sse sse2 static xml"
-
-# mopac7 qm/mm is broken until we can get files from
-# http://md.chem.rug.nl/~groenhof/qmmm.html
-# or somewhere else...
-
-DEPEND=">=sci-libs/fftw-3.0.1
-	app-shells/tcsh
-	X? ( x11-libs/libX11
-		x11-libs/libXt
-		x11-libs/libXp
-		x11-libs/libXext
-		x11-proto/xproto
-		x11-libs/openmotif )
-	blas? ( virtual/blas )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2 )"
-
-RDEPEND="${DEPEND}"
-
-FORTRAN="g77 gfortran ifc"
-
-src_unpack() {
-
-	unpack ${A}
-	cd "${S}"
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	# Fix a sandbox violation that occurs when re-emerging with mpi.
-	sed "/libdir=\"\$(libdir)\"/ a\	temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed -e "s:\$\$libdir:\$temp_libdir:" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed -e "s:\$\$libdir:\$\$temp_libdir:" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	eautoreconf
-
-	cd "${WORKDIR}"
-	mv "${P}" "${P}-single"
-	if ( use double-precision ) ; then
-		einfo "Moving sources for Multiprecision Build"
-		cp -prP "${P}-single" "${P}-double"
-	fi
-}
-
-src_compile() {
-
-	# static should work but something's broken.
-	# gcc spec file may be screwed up.
-	# Static linking should try -lgcc instead of -lgcc_s.
-	# For more info:
-	# http://lists.debian.org/debian-gcc/2002/debian-gcc-200201/msg00150.html
-
-	# We will compile single precision by default, and suffix double-precision with _d.
-	# Sparc is the only arch I can test on that needs to use fortran.
-	local myconf ;
-	local myconf_s ;
-	local myconf_d ;
-
-	case "${ARCH}" in
-
-		x86)
-			if ( use sse || use sse2 ) ; then
-				myconf="${myconf} --enable-ia32-sse"
-			fi
-			myconf="$myconf $(use_enable 3dnow ia32-3dnow)"
-
-			if ( ! use sse && ! use sse2 && ! use 3dnow ) ; then
-				if ! has_version "=sys-devel/gcc-3*" ; then
-					die "If you must run gromacs without sse (not recommended) gfortran will not work."
-				else
-					myconf="${myconf} --enable-fortran" && fortran_pkg_setup
-				fi
-			else
-				myconf="${myconf} --disable-fortran"
-			fi
-			;;
-
-		amd64)
-			myconf="$myconf --enable-x86-64-sse --disable-fortran"
-			;;
-
-		ppc*)
-			if use altivec ; then
-				myconf="${myconf} --enable-ppc-altivec --disable-fortran"
-			else
-				if ! has_version "=sys-devel/gcc-3*" ; then
-					die "If you must run gromacs without sse (not recommended) gfortran will not work."
-				else
-					myconf="${myconf} --enable-fortran" && fortran_pkg_setup
-				fi
-			fi
-			;;
-
-		ia64)
-			myconf="$myconf --enable-ia64-asm --disable-fortran"
-			;;
-
-		alpha)
-			if ! has_version "=sys-devel/gcc-3*" ; then
-				die "If you must run gromacs without sse (not recommended) gfortran will not work."
-			else
-				myconf="$myconf --enable-fortran" && fortran_pkg_setup
-			fi
-			;;
-
-		sparc)
-			if ! has_version "=sys-devel/gcc-3*" ; then
-				die "If you must run gromacs without sse (not recommended) gfortran will not work."
-			else
-				myconf="${myconf} --enable-fortran" && fortran_pkg_setup
-			fi
-			;;
-	esac
-
-	# if we need external blas
-	if use blas; then
-		export LIBS="${LIBS} -lblas"
-		myconf="${myconf} $(use_with blas external-blas)"
-	fi
-
-	# if we need external lapack
-	if use lapack; then
-		export LIBS="${LIBS} -llapack"
-		myconf="${myconf} $(use_with lapack external-lapack)"
-	fi
-
-	myconf="--datadir=/usr/share \
-			--bindir=/usr/bin \
-			--libdir=/usr/$(get_libdir) \
-			--with-fft=fftw3 \
-			$(use_with gsl) \
-			$(use_enable mpi) \
-			$(use_with X x) \
-			$(use_with xml) \
-			$(use_enable static all-static) \
-			${myconf}"
-
-	if ( use double-precision && use single-precision ); then
-		einfo "Building Single Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-single
-		myconf_s="${myconf}  --enable-float --disable-double --program-suffix=''"
-		econf ${myconf_s} || die "Single Precision econf failed"
-		emake || die "Single Precision emake failed"
-
-		einfo "Building Double Precision Gromacs"
-		cd "${WORKDIR}"/"${P}"-double
-		myconf_d="${myconf} --enable-double --disable-float --program-suffix=_d"
-		econf ${myconf_d} || die "Double Precision econf failed"
-		emake || die "Double Precision emake failed"
-
-	elif use double-precision ; then
-		einfo "Building Double Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-double
-		myconf_d="${myconf} --enable-double --disable-float --program-suffix=''"
-		econf ${myconf_d} || die "Double Precision econf failed"
-		emake || die "Double Precision emake failed"
-
-	elif use single-precision ; then
-		einfo "Building Single Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-single
-		myconf_s="${myconf} --enable-float --disable-double --program-suffix=''"
-		econf ${myconf_s} || die "configure failed"
-		emake || die "Single Precision emake failed"
-	fi
-}
-
-src_install() {
-	if use single-precision ; then
-		einfo "Installing Single Precision"
-		cd "${WORKDIR}"/"${P}"-single
-		emake DESTDIR="${D}" install || die "Installing Single Precision failed"
-	fi
-
-	if use double-precision ; then
-		einfo "Installing Double Precision"
-		cd "${WORKDIR}"/"${P}"-double
-		emake DESTDIR="${D}" install || die "Installing Double Precision failed"
-	fi
-
-	dodoc AUTHORS INSTALL README
-	# Move html and leave examples and templates under /usr/share/gromacs.
-	mv "${D}"/usr/share/"${PN}"/html "${D}"/usr/share/doc/"${PF}"/
-}
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index fff268723f62..5b928e0803af 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -3,8 +3,11 @@
 <pkgmetadata>
 <herd>sci-chemistry</herd>
 <use>
-  <flag name='double-precision'>More precise calculations at the expense of
-    speed</flag>
-  <flag name='single-precision'>Single precision version of gromacs</flag>
+	<flag name='dmalloc'>Enable use of Debug Malloc</flag>
+	<flag name='double-precision'>More precise calculations at the expense of speed</flag>
+	<flag name='fkernels'>Enable building of Fortran Kernels for platforms that
+	dont have assembly loops</flag>
+	<flag name='single-precision'>Single precision version of gromacs</flag>
+	<flag name='zsh-completion'>Enable zsh completion support</flag>
 </use>
 </pkgmetadata>