[sci-chemistry/gromacs] Version bump. Clean up old versions. Thanks to Christoph Junghans

(Portage version: 2.2.0_alpha5_p2/cvs/Linux x86_64)

10 files changed, 337 insertions, 546 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 6c0529d29419..6bdbc599d0e7 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,18 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.61 2010/10/25 08:53:31 ssuominen Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.62 2010/11/25 13:08:58 alexxy Exp $
+
+*gromacs-4.5.3 (25 Nov 2010)
+*gromacs-4.0.7-r5 (25 Nov 2010)
+
+  25 Nov 2010; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-4.0.4.ebuild,
+  -files/gromacs-4.0.4-configure-gfortran.patch,
+  -files/gromacs-4.0.4-sparc-cyclecounter.patch, -gromacs-4.0.5.ebuild,
+  gromacs-4.0.7-r4.ebuild, +gromacs-4.0.7-r5.ebuild,
+  -files/gromacs-4.0.9999-ccache.patch,
+  -files/gromacs-4.0.9999-configure-gfortran.patch, -gromacs-4.5.1.ebuild,
+  +gromacs-4.5.3.ebuild:
+  Version bump. Clean up old versions. Thanks to Christoph Junghans
 
   25 Oct 2010; Samuli Suominen <ssuominen@gentoo.org>
   gromacs-4.0.7-r4.ebuild:
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
deleted file mode 100644
index c330fcaf0cdc..000000000000
--- a/sci-chemistry/gromacs/files/gromacs-4.0.4-configure-gfortran.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-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/files/gromacs-4.0.4-sparc-cyclecounter.patch b/sci-chemistry/gromacs/files/gromacs-4.0.4-sparc-cyclecounter.patch
deleted file mode 100644
index f174aef2769d..000000000000
--- a/sci-chemistry/gromacs/files/gromacs-4.0.4-sparc-cyclecounter.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur gromacs-4.0.4-orig/include/gmx_cyclecounter.h gromacs-4.0.4/include/gmx_cyclecounter.h
---- gromacs-4.0.4-orig/include/gmx_cyclecounter.h	2009-05-09 18:46:02.000000000 +0200
-+++ gromacs-4.0.4/include/gmx_cyclecounter.h	2009-05-09 18:56:50.000000000 +0200
-@@ -408,7 +408,7 @@
- static __inline__ gmx_cycles_t gmx_cycles_read(void)
- { 
-     /* gcc inline assembly on sparc v9 */
--    ticks ret;
-+    unsigned long ret;
-     __asm__("rd %%tick, %0" : "=r" (ret));
-     return ret;  
- }
diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.9999-ccache.patch b/sci-chemistry/gromacs/files/gromacs-4.0.9999-ccache.patch
deleted file mode 100644
index 68b6a1e66e1d..000000000000
--- a/sci-chemistry/gromacs/files/gromacs-4.0.9999-ccache.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-cc is not cache by ccache (bug #302048), work around that
-
-diff --git a/configure.ac b/configure.ac
-index 3100101..db9d0b6 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -288,11 +288,11 @@ AC_DEFINE_UNQUOTED([BUILD_MACHINE],["`uname -srm`"],[Hardware and OS version for
- # normally we use the default compiler, but on alpha/linux we try the compaq ones first
- case "${host_cpu}-${host_os}" in
-   alpha*-linux*)
--    cc_names="ccc cc gcc"
-+    cc_names="ccc gcc"
-     f77_names="fort f77 g77"
-     ;;
-   *) 
--    cc_names="cc icc xlc gcc"
-+    cc_names="icc xlc gcc"
-     f77_names="f77 ifort xlf xlf77 cf77 fl32 g77 fort77 f90 xlf90 pgf77 cf77 fort fort77 pgf90"
-     ;;
- esac
diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.9999-configure-gfortran.patch b/sci-chemistry/gromacs/files/gromacs-4.0.9999-configure-gfortran.patch
deleted file mode 100644
index 1bf19ddf532e..000000000000
--- a/sci-chemistry/gromacs/files/gromacs-4.0.9999-configure-gfortran.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-enable gfortan as fortan compiler
-
-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 gcc"
--    f77_names="fort f77 g77"
-+    f77_names="fort f77 g77 gfortran"
-     ;;
-   *) 
-     cc_names="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-4.0.4.ebuild b/sci-chemistry/gromacs/gromacs-4.0.4.ebuild
deleted file mode 100644
index 7ef25acf118e..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.0.4.ebuild
+++ /dev/null
@@ -1,235 +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-4.0.4.ebuild,v 1.8 2009/09/26 19:49:46 ranger 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() {
-
-	epatch "${FILESDIR}/${P}-sparc-cyclecounter.patch"
-	# 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-4.0.5.ebuild b/sci-chemistry/gromacs/gromacs-4.0.5.ebuild
deleted file mode 100644
index 1106c0e215a7..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.0.5.ebuild
+++ /dev/null
@@ -1,234 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.5.ebuild,v 1.4 2010/01/18 19:16:11 armin76 Exp $
-
-EAPI="2"
-
-LIBTOOLIZE="true"
-TEST_PV="4.0.4"
-
-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-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="alpha amd64 ~ppc64 sparc x86"
-IUSE="X blas dmalloc doc -double-precision +fftw fkernels gsl lapack mpi +single-precision static test +xml zsh-completion"
-
-DEPEND="app-shells/tcsh
-	X? ( x11-libs/libX11 )
-	dmalloc? ( dev-libs/dmalloc )
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2 )"
-
-RDEPEND="${DEPEND}"
-
-RESTRICT="test"
-
-src_prepare() {
-
-	epatch "${FILESDIR}/${PN}-4.0.4-sparc-cyclecounter.patch"
-	# 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 "${FILESDIR}/${PN}-4.0.4-configure-gfortran.patch"
-
-	eautoreconf
-
-	cd "${WORKDIR}"
-
-	use test && mv gmxtest "${P}"
-	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) \
-			--docdir=/usr/share/doc/"${PF}" \
-			$(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 "${WORKDIR}"/"${P}"-single
-		emake -j1 tests || 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}"/"${P}"-double
-		emake -j1 tests || die "Double Precision test failed"
-	fi
-}
-
-src_install() {
-	if use single-precision ; then
-		einfo "Installing Single Precision"
-		cd "${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
-	use doc && dodoc "${DISTDIR}"/manual-4.0.pdf
-}
-
-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-4.0.7-r4.ebuild b/sci-chemistry/gromacs/gromacs-4.0.7-r4.ebuild
index 0225aa53d5c7..b97c49027465 100644
--- a/sci-chemistry/gromacs/gromacs-4.0.7-r4.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.0.7-r4.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.7-r4.ebuild,v 1.8 2010/10/25 08:53:31 ssuominen Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.7-r4.ebuild,v 1.9 2010/11/25 13:08:58 alexxy Exp $
 
 EAPI="3"
 
@@ -14,7 +14,7 @@ HOMEPAGE="http://www.gromacs.org/"
 SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
 		mirror://gentoo/${P}_upstream2010-06-08.patch.gz
 		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf -> gromacs-manual-4.0.pdf )
 		ffamber? ( http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz )"
 
 LICENSE="GPL-2"
diff --git a/sci-chemistry/gromacs/gromacs-4.0.7-r5.ebuild b/sci-chemistry/gromacs/gromacs-4.0.7-r5.ebuild
new file mode 100644
index 000000000000..3576b8b380fd
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.0.7-r5.ebuild
@@ -0,0 +1,309 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.7-r5.ebuild,v 1.1 2010/11/25 13:08:58 alexxy Exp $
+
+EAPI="3"
+
+LIBTOOLIZE="true"
+TEST_PV="4.0.4"
+
+inherit autotools bash-completion eutils fortran multilib toolchain-funcs
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
+		mirror://gentoo/${P}_upstream2010-09-15.patch.bz2
+		mirror://gentoo/${P}_missing_distfiles.patch.bz2
+		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf -> gromacs-manual-4.0.pdf )
+		ffamber? ( http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+IUSE="X blas dmalloc doc -double-precision ffamber +fftw fkernels +gsl lapack
+mpi +single-precision static static-libs test +xml zsh-completion"
+
+DEPEND="app-shells/tcsh
+	X? ( x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE )
+	dmalloc? ( dev-libs/dmalloc )
+	blas? ( virtual/blas )
+	fftw? ( sci-libs/fftw:3.0 )
+	gsl? ( sci-libs/gsl )
+	lapack? ( virtual/lapack )
+	mpi? ( virtual/mpi )
+	xml? ( dev-libs/libxml2 )"
+
+RDEPEND="${DEPEND}"
+
+RESTRICT="test"
+
+QA_EXECSTACK="usr/lib/libgmx.so.*
+	usr/lib/libgmx_d.so.*"
+
+use static && QA_EXECSTACK="$QA_EXECSTACK usr/bin/*"
+
+pkg_setup() {
+	if use fkernels; then
+		FORTRAN="g77 gfortran ifc"
+		fortran_pkg_setup
+	else
+		FORTRANC=""
+	fi
+}
+
+src_prepare() {
+
+	( use single-precision || use double-precision ) || \
+		die "Nothing to compile, enable single-precision and/or double-precision"
+
+	if use static; then
+		use X && die "You cannot compile a static version with X support, disable X or static"
+		use xml && die "You cannot compile a static version with xml support
+		(see bug #306479), disable xml or static"
+	fi
+
+	epatch "${WORKDIR}/${P}_upstream2010-09-15.patch"
+	epatch "${WORKDIR}/${P}_missing_distfiles.patch"
+	sed -e '/AC_INIT/s/4\.0\.7/&-2010-09-15/' -i configure.ac \
+		|| die "Failed to change version in configure.ac"
+
+	# Fix typos in a couple of files.
+	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
+		|| die "Failed to fixup demo script."
+
+	epatch_user
+	eautoreconf
+	GMX_DIRS=""
+	use single-precision && GMX_DIRS+=" single"
+	use double-precision && GMX_DIRS+=" double"
+	for x in ${GMX_DIRS}; do
+		mkdir "${S}-${x}" || die
+		use test && cp -r "${WORKDIR}"/gmxtest "${S}-${x}"
+		use mpi || continue
+		mkdir "${S}-${x}_mpi" || die
+	done
+}
+
+src_configure() {
+	local myconf
+	local myconfsingle
+	local myconfdouble
+	local suffixdouble
+
+	#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 [[ $(gcc-version) == "4.1" ]]; then
+		eerror "gcc 4.1 is not supported by gromacs"
+		eerror "please run test suite"
+		die
+	fi
+
+	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
+
+	#fortran will gone in gromacs 4.1 anyway
+	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
+	if use fkernels; then
+		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
+		ewarn "I hope, you know what are you doing..."
+		myconf="${myconf} --enable-fortran"
+	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} $(use_with lapack external-lapack)"
+	fi
+
+	# by default its better to have dynamicaly linked binaries
+	if use static; then
+		#gmx build static libs by default
+		myconf="${myconf} --disable-shared $(use_enable static all-static)"
+	else
+		myconf="${myconf} --disable-all-static --enable-shared $(use_enable static-libs static)"
+	fi
+
+	myconf="--datadir="${EPREFIX}"/usr/share \
+			--bindir="${EPREFIX}"/usr/bin \
+			--libdir="${EPREFIX}"/usr/$(get_libdir) \
+			--docdir="${EPREFIX}"/usr/share/doc/"${PF}" \
+			$(use_with dmalloc) \
+			$(use_with fftw fft fftw3) \
+			$(use_with gsl) \
+			$(use_with X x) \
+			$(use_with xml) \
+			${myconf}"
+
+	#if we build single and double - double is suffixed
+	if ( use double-precision && use single-precision ); then
+		suffixdouble="_d"
+	else
+		suffixdouble=""
+	fi
+
+	if use double-precision ; then
+		#from gromacs manual
+		elog
+		elog "For most simulations single precision is accurate enough. In some"
+		elog "cases double precision is required to get reasonable results:"
+		elog
+		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
+		elog " and the calculation and diagonalization of the Hessian "
+		elog "-calculation of the constraint force between two large groups of	atoms"
+		elog "-energy conservation: this can only be done without temperature coupling and"
+		elog " without cutoffs"
+		elog
+	fi
+
+	if use mpi ; then
+		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
+		elog "we configure/compile gromacs twice (with and without mpi) and only"
+		elog "install mdrun with mpi support. In addtion you will get libgmx and"
+		elog "libmd with and without mpi support."
+	fi
+
+	myconfdouble="${myconf} --enable-double --program-suffix='${suffixdouble}'"
+	myconfsingle="${myconf} --enable-float --program-suffix=''"
+	for x in ${GMX_DIRS}; do
+		einfo "Configuring for ${x} precision"
+		cd "${S}-${x}"
+		local p=myconf${x}
+		ECONF_SOURCE="${S}" econf ${!p} --disable-mpi CC="$(tc-getCC)" F77="${FORTRANC}"
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		ECONF_SOURCE="${S}" econf ${!p} --enable-mpi CC="$(tc-getCC)" F77="${FORTRANC}"
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		cd "${S}-${x}"
+		einfo "Compiling for ${x} precision"
+		emake || die "emake for ${x} precision failed"
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		emake mdrun || die "emake mdrun for ${x} precision failed"
+	done
+}
+
+src_test() {
+	for x in ${GMX_DIRS}; do
+		local oldpath="${PATH}"
+		export PATH="${S}-${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
+		cd "${S}-${x}"
+		emake -j1 tests || die "${x} Precision test failed"
+		export PATH="${oldpath}"
+	done
+}
+
+src_install() {
+	for x in ${GMX_DIRS}; do
+		cd "${S}-${x}"
+		emake DESTDIR="${D}" install || die "emake install for ${x} failed"
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		emake DESTDIR="${D}" install-mdrun || die "emake install-mdrun for ${x} failed"
+	done
+	#we have pkg-config files
+	rm "${ED}"/usr/$(get_libdir)/*.la
+
+	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
+	doenvd "${T}/80gromacs"
+	rm -f "${ED}"/usr/bin/GMXRC*
+
+	dobashcompletion "${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.*
+
+	cd "${S}"
+	dodoc AUTHORS INSTALL README
+	if use doc; then
+		newdoc "${DISTDIR}/gromacs-manual-4.0.pdf" "manual-4.0.pdf"
+		dohtml -r "${ED}usr/share/gromacs/html/"
+	fi
+	rm -rf "${ED}usr/share/gromacs/html/"
+
+	if use ffamber; then
+		use doc && dodoc "${WORKDIR}/ffamber_v4.0/README/pdfs/*.pdf"
+		# prepare vdwradii.dat
+		cat >>"${ED}"/usr/share/gromacs/top/vdwradii.dat <<-EOF
+			SOL  MW    0
+			SOL  LP    0
+		EOF
+		# regenerate aminoacids.dat
+		cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
+		"${ED}"/usr/share/gromacs/top/aminoacids.dat \
+		| awk '{print $1}' | sort -u | tail -n+4 | wc -l \
+		>> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new
+		cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
+		"${ED}"/usr/share/gromacs/top/aminoacids.dat \
+		| awk '{print $1}' | sort -u | tail -n+4 \
+		>> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new
+		mv -f "${ED}"/usr/share/gromacs/top/aminoacids.dat.new \
+		"${ED}"/usr/share/gromacs/top/aminoacids.dat
+		# copy ff files
+		for x in ffamber94 ffamber96 ffamber99 ffamber99p ffamber99sb \
+				ffamberGS ffamberGSs ffamber03 ; do
+			einfo "Adding ${x} to gromacs"
+			cp "${WORKDIR}"/ffamber_v4.0/${x}/* "${ED}"/usr/share/gromacs/top
+		done
+		# copy suplementary files
+		cp "${WORKDIR}"/ffamber_v4.0/*.gro "${ED}"/usr/share/gromacs/top
+		cp "${WORKDIR}"/ffamber_v4.0/*.itp "${ED}"/usr/share/gromacs/top
+		# actualy add records to FF.dat
+		cat >>"${ED}"/usr/share/gromacs/top/FF.dat.new <<-EOF
+			ffamber94   AMBER94 Cornell protein/nucleic forcefield
+			ffamber96   AMBER96 Kollman protein/nucleic forcefield
+			ffamberGS   AMBER-GS Garcia &  Sanbonmatsu forcefield
+			ffamberGSs  AMBER-GSs Nymeyer &  Garcia forcefield
+			ffamber99   AMBER99 Wang protein/nucleic acid forcefield
+			ffamber99p  AMBER99p protein/nucleic forcefield
+			ffamber99sb AMBER99sb Hornak protein/nucleic forcefield
+			ffamber03   AMBER03 Duan protein/nucleic forcefield
+		EOF
+		cat "${ED}"/usr/share/gromacs/top/FF.dat \
+			"${ED}"/usr/share/gromacs/top/FF.dat.new \
+			| tail -n+2 > "${ED}"/usr/share/gromacs/top/FF.dat.new2
+		cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 | wc -l > \
+			"${ED}"/usr/share/gromacs/top/FF.dat
+		cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 >> \
+			"${ED}"/usr/share/gromacs/top/FF.dat
+		rm -f "${ED}"/usr/share/gromacs/top/FF.dat.new*
+	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-4.5.1.ebuild b/sci-chemistry/gromacs/gromacs-4.5.3.ebuild
index d065c2194dee..ff7e1d3a88ae 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.3.ebuild
@@ -1,12 +1,12 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.1.ebuild,v 1.1 2010/09/14 12:59:31 alexxy Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.3.ebuild,v 1.1 2010/11/25 13:08:58 alexxy Exp $
 
 EAPI="3"
 
 LIBTOOLIZE="true"
 TEST_PV="4.0.4"
-MANUAL_PV="4.5"
+MANUAL_PV="4.5.3"
 
 inherit autotools bash-completion eutils fortran multilib toolchain-funcs
 
@@ -14,8 +14,7 @@ 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-${TEST_PV}.tgz )
-		doc? (
-		http://www.gromacs.org/@api/deki/files/126/=gromacs_manual-${MANUAL_PV}.pdf -> gromacs-${MANUAL_PV}.pdf )"
+		doc? ( http://www.gromacs.org/@api/deki/files/133/=manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
 
 LICENSE="GPL-2"
 SLOT="0"
@@ -93,6 +92,9 @@ src_configure() {
 	#there so no gentoo on bluegene!
 	myconf="${myconf} --disable-bluegene"
 
+	#we have pkg-config files
+	myconf="${myconf} --disable-la-files"
+
 	#from gromacs configure
 	if ! use fftw; then
 		ewarn "WARNING: The built-in FFTPACK routines are slow."
@@ -111,6 +113,7 @@ src_configure() {
 	#fortran will gone in gromacs 4.1 anyway
 	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
 	if use fkernels; then
+		use threads && die "You cannot compile fortran kernel with threads"
 		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
 		ewarn "I hope, you know what are you doing..."
 		myconf="${myconf} --enable-fortran"
@@ -222,6 +225,8 @@ src_install() {
 	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*
 
@@ -237,9 +242,9 @@ src_install() {
 		|| die "Failed to fixup demo script."
 
 	cd "${S}"
-	dodoc AUTHORS INSTALL README
+	dodoc AUTHORS INSTALL* README*
 	if use doc; then
-		dodoc "${DISTDIR}/manual-${MANUAL_PV}.pdf"
+		newdoc "${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/"
@@ -257,4 +262,6 @@ pkg_postinst() {
 	elog $(g_luck)
 	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
 	elog
+	elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
+	elog
 }