sci-chemistry/gromacs: added stable patch + prefix

(Portage version: 2.1.8.3/git/Linux i686)
 (Signed Manifest commit)

4 files changed, 309 insertions, 4 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 48046093e..341f7bbc8 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*gromacs-4.0.7-r3 (22 Jun 2010)
+
+  22 Jun 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  +gromacs-4.0.7-r3.ebuild, +files/gromacs-4.0.7to2010-06-08.patch.gz:
+  added patches from stable branch
+
 *gromacs-4.0.7-r2 (26 Feb 2010)
 
   26 Feb 2010; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.0.7-r2.ebuild:
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 073271aee..d2006acf2 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,6 +1,7 @@
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 Hash: SHA1
 
+AUX gromacs-4.0.7to2010-06-08.patch.gz 11869 RMD160 131579a5f0e03b3193b65013060cb6a2cbbaa1f9 SHA1 8009e50241ab79994fb450f409b0bbf7f39267e5 SHA256 c71f29372492c44f5b14b3ea2fa6ee5fbdad25c98b7ba53d722b9f516a3e7136
 AUX gromacs-4.0.9999-ccache.patch 678 RMD160 043d0e207e04a275fe00a3bd2b28f8dc0dfd4b7f SHA1 08bc5ac8bc0b28f68e1ede994d49616dd920af5d SHA256 ca477d54351c418f1d39dda29373a1426c9403ec0d2f21c28fc7568227d47632
 AUX gromacs-4.0.9999-configure-gfortran.patch 760 RMD160 1700579b0c2dfb8cbb743d795aa9f0f9f467c06b SHA1 e6924d3598b20195fcb6809e64f333def5b0f919 SHA256 1a59dfde8a3db8db729bd19691a5945e02be2725fa66ec0b125ab3b931518761
 AUX gromacs-4.0.9999-docdir.patch 1352 RMD160 336ab23b4b65430caf3205650a8787e8e33d2137 SHA1 77e0cc966c4d755f603b2d0ab9a075c0ee6b7361 SHA256 8ead457b06f7f943455a95494be4648e539934699d29e955d2e05ac02f1ca4ef
@@ -9,14 +10,15 @@ DIST gmxtest-4.0.4.tgz 14845017 RMD160 c7c583415438bdef4c9996da9064254e9460cf16
 DIST gromacs-4.0.7.tar.gz 8404518 RMD160 4fa8e5c90f549ef627a98a907a166676692a4c4b SHA1 8519bef2fa989fb487d54612b0a2d0228f228b30 SHA256 048f8ece2829f01d99f7e04e1d6e8f88d3a32273192274f2e9fcf71f41f212c1
 DIST manual-4.0.pdf 2135100 RMD160 b963642f8e1433f11328c3d0c4b1645c9de506da SHA1 8ae951ee15b2a7dc626331fce36511bc8766144c SHA256 646f810477eee2d710de6019c52056550413d0ba77baf9680195c835ddafe80a
 EBUILD gromacs-4.0.7-r2.ebuild 9140 RMD160 b82dadb42718e908dc185126e509a85e5535b924 SHA1 125a64f4a703ae31e83900d880a16933a3b0f7a4 SHA256 d9e77d56b79382ab1922cef41b679e58a2b9498755791f7d349c69022503d20b
+EBUILD gromacs-4.0.7-r3.ebuild 9467 RMD160 b61e85fdb4cd533ca86079b9cdd37440a978d47c SHA1 3cbf238ac7bb014f7d4925f953ccc50d2d085a39 SHA256 0bb6fe54603d1633ef47797215ac32c167f687a14ba9fe49f32d5bb548fc4960
 EBUILD gromacs-4.0.9999.ebuild 6857 RMD160 727af5d38f52f5db01f6185c7ca0a7c05191be21 SHA1 2d1988574567e9c19af1d5624e51055a6b39d199 SHA256 b2304948a62c4e42c048e7912b24354265901ce6d9e7ac260ee65fa5ed7f56f5
 EBUILD gromacs-9999.ebuild 6447 RMD160 40392fd740056f9a533d2126ab374964d048f496 SHA1 b6bb1fa00d20b8e13455984e5e2ed661eff0f678 SHA256 07c745f4cb7563911a313b572af25eba4f613f3aeb733f8e80dd6b4df7f79a5e
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diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.7to2010-06-08.patch.gz b/sci-chemistry/gromacs/files/gromacs-4.0.7to2010-06-08.patch.gz
new file mode 100644
index 000000000..b3a36d0d1
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-4.0.7to2010-06-08.patch.gz
diff --git a/sci-chemistry/gromacs/gromacs-4.0.7-r3.ebuild b/sci-chemistry/gromacs/gromacs-4.0.7-r3.ebuild
new file mode 100644
index 000000000..68ad9fbea
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.0.7-r3.ebuild
@@ -0,0 +1,297 @@
+# 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-r1.ebuild,v 1.1 2010/01/24 19:39:09 alexxy Exp $
+
+EAPI="3"
+
+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-${TEST_PV}.tgz )
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )
+		ffamber? ( http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+IUSE="X blas dmalloc doc -double-precision ffamber +fftw fkernels +gsl lapack
+mpi +single-precision static static-libs test +xml zsh-completion"
+
+DEPEND="app-shells/tcsh
+	X? ( x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE )
+	dmalloc? ( dev-libs/dmalloc )
+	blas? ( virtual/blas )
+	fftw? ( sci-libs/fftw:3.0 )
+	gsl? ( sci-libs/gsl )
+	lapack? ( virtual/lapack )
+	mpi? ( virtual/mpi )
+	xml? ( dev-libs/libxml2 )"
+
+RDEPEND="${DEPEND}"
+
+RESTRICT="test"
+
+src_prepare() {
+
+	epatch "${FILESDIR}/${P}to2010-06-08.patch.gz"
+	sed -e '/AC_INIT/s/4\.0\.7/&-2010-06-08/' -i configure.ac \
+		|| die "Failed to change version in configure.ac"
+	epatch "${FILESDIR}/${PN}-4.0.9999-docdir.patch"
+	epatch "${FILESDIR}/${PN}-4.0.9999-ccache.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=\"${ED}usr/$( 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=\"${ED}usr/$( 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}-4.0.9999-configure-gfortran.patch"
+
+	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 [[ $(gcc-version) == "4.1" ]]; then
+		eerror "gcc 4.1 is not supported by gromacs"
+		eerror "please run test suite"
+		die
+	fi
+
+	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
+
+	#fortran will gone in gromacs 4.1 anyway
+	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
+	if use fkernels; then
+		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
+		ewarn "I hope, you know what are you doing..."
+		FORTRAN="g77 gfortran ifc"
+		myconf="${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} $(use_with lapack external-lapack)"
+	fi
+
+	# by default its better to have dynamicaly linked binaries
+	if use static; then
+		#gmx build static libs by default
+		myconf="${myconf} $(use_enable static all-static)"
+	else
+		myconf="${myconf} --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 ${!p} --disable-mpi
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		ECONF_SOURCE="${S}" econf ${!p} --enable-mpi
+	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}-${x}"
+		emake DESTDIR="${ED}" install || die "emake install for ${x} failed"
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		emake DESTDIR="${ED}" install-mdrun || die "emake install-mdrun for ${x} failed"
+	done
+
+	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
+	doenvd "${T}/80gromacs"
+	rm -f "${ED}"/usr/bin/GMXRC*
+
+	dobashcompletion "${ED}"/usr/bin/completion.bash ${PN}
+	if use zsh-completion ; then
+		insinto "${EPREFIX}"/usr/share/zsh/site-functions
+		newins "${ED}"/usr/bin/completion.zsh _${PN}
+	fi
+	rm -r "${ED}"/usr/bin/completion.*
+
+	cd "${S}"
+	dodoc AUTHORS INSTALL README
+	use doc && dodoc "${DISTDIR}/manual-4.0.pdf"
+
+	if use ffamber; then
+		use doc && dodoc "${WORKDIR}/ffamber_v4.0/README/pdfs/*.pdf"
+		# prepare vdwradii.dat
+		cat >>"${D}"/usr/share/gromacs/top/vdwradii.dat <<-EOF
+			SOL  MW    0
+			SOL  LP    0
+		EOF
+		# regenerate aminoacids.dat
+		cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
+		"${D}"/usr/share/gromacs/top/aminoacids.dat \
+		| awk '{print $1}' | sort -u | tail -n+4 | wc -l \
+		>> "${D}"/usr/share/gromacs/top/aminoacids.dat.new
+		cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
+		"${D}"/usr/share/gromacs/top/aminoacids.dat \
+		| awk '{print $1}' | sort -u | tail -n+4 \
+		>> "${D}"/usr/share/gromacs/top/aminoacids.dat.new
+		mv -f "${D}"/usr/share/gromacs/top/aminoacids.dat.new \
+		"${D}"/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/${x}/* "${D}"/usr/share/gromacs/top
+		done
+		# copy suplementary files
+		cp "${WORKDIR}"/ffamber_v4.0/*.gro "${D}"/usr/share/gromacs/top
+		cp "${WORKDIR}"/ffamber_v4.0/*.itp "${D}"/usr/share/gromacs/top
+		# actualy add records to FF.dat
+		cat >>"${D}"/usr/share/gromacs/top/FF.dat.new <<-EOF
+			ffamber94   AMBER94 Cornell protein/nucleic forcefield
+			ffamber96   AMBER96 Kollman protein/nucleic forcefield
+			ffamberGS   AMBER-GS Garcia &  Sanbonmatsu forcefield
+			ffamberGSs  AMBER-GSs Nymeyer &  Garcia forcefield
+			ffamber99   AMBER99 Wang protein/nucleic acid forcefield
+			ffamber99p  AMBER99p protein/nucleic forcefield
+			ffamber99sb AMBER99sb Hornak protein/nucleic forcefield
+			ffamber03   AMBER03 Duan protein/nucleic forcefield
+		EOF
+		cat "${D}"/usr/share/gromacs/top/FF.dat \
+			"${D}"/usr/share/gromacs/top/FF.dat.new \
+			| tail -n+2 > "${D}"/usr/share/gromacs/top/FF.dat.new2
+		cat "${D}"/usr/share/gromacs/top/FF.dat.new2 | wc -l > \
+			"${D}"/usr/share/gromacs/top/FF.dat
+		cat "${D}"/usr/share/gromacs/top/FF.dat.new2 >> \
+			"${D}"/usr/share/gromacs/top/FF.dat
+		rm -f "${D}"/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
+}