Latest release

Package-Manager: portage-2.1.6.7/cvs/Linux x86_64

6 files changed, 234 insertions, 8 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index cd3021e4fb93..d8ee96fe7c02 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,9 @@
 # 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 1.32 2009/01/04 01:04:00 je_fro Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.33 2009/01/22 04:14:36 je_fro Exp $
+
+  22 Jan 2009; Jeff Gardner <je_fro@gentoo.org> +gromacs-4.0.3.ebuild:
+  Latest version.
 
 *gromacs-4.0.2 (04 Jan 2009)
 
diff --git a/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild b/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild
index eb87ac057572..dd4793856e7d 100644
--- a/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2008 Gentoo Foundation
+# 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-3.3.1-r1.ebuild,v 1.12 2008/06/27 10:25:34 ulm Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild,v 1.13 2009/01/22 04:14:36 je_fro Exp $
 
 inherit eutils fortran multilib
 
@@ -29,6 +29,8 @@ DEPEND=">=sci-libs/fftw-3.0.1
 		x11-proto/xproto
 		x11-libs/openmotif )"
 
+RDEPEND="${DEPEND}"
+
 src_unpack() {
 
 	unpack ${A}
diff --git a/sci-chemistry/gromacs/gromacs-3.3.3.ebuild b/sci-chemistry/gromacs/gromacs-3.3.3.ebuild
index dd1f16940227..ee1358a7cdc9 100644
--- a/sci-chemistry/gromacs/gromacs-3.3.3.ebuild
+++ b/sci-chemistry/gromacs/gromacs-3.3.3.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2008 Gentoo Foundation
+# 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-3.3.3.ebuild,v 1.1 2008/10/06 02:08:34 je_fro Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.3.ebuild,v 1.2 2009/01/22 04:14:36 je_fro Exp $
 EAPI="1"
 LIBTOOLIZE="true"
 inherit autotools eutils flag-o-matic fortran multilib
@@ -32,6 +32,8 @@ DEPEND=">=sci-libs/fftw-3.0.1
 	mpi? ( virtual/mpi )
 	xml? ( dev-libs/libxml2 )"
 
+RDEPEND="${DEPEND}"
+
 FORTRAN="g77 gfortran ifc"
 
 src_unpack() {
diff --git a/sci-chemistry/gromacs/gromacs-4.0.2.ebuild b/sci-chemistry/gromacs/gromacs-4.0.2.ebuild
index e461d2dd5f8b..716b0ac319bb 100644
--- a/sci-chemistry/gromacs/gromacs-4.0.2.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.0.2.ebuild
@@ -1,6 +1,6 @@
 # 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 1.1 2009/01/04 01:04:00 je_fro Exp $
+# $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"
 
@@ -33,6 +33,8 @@ DEPEND=">=sci-libs/fftw-3.0.1
 	mpi? ( virtual/mpi )
 	xml? ( dev-libs/libxml2 )"
 
+RDEPEND="${DEPEND}"
+
 FORTRAN="g77 gfortran ifc"
 
 src_unpack() {
diff --git a/sci-chemistry/gromacs/gromacs-4.0.3.ebuild b/sci-chemistry/gromacs/gromacs-4.0.3.ebuild
new file mode 100644
index 000000000000..9fa851b10a6f
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.0.3.ebuild
@@ -0,0 +1,215 @@
+# 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-4.0.3.ebuild,v 1.1 2009/01/22 04:14:36 je_fro Exp $
+
+EAPI="1"
+
+LIBTOOLIZE="true"
+
+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.ebuild b/sci-chemistry/gromacs/gromacs-4.0.ebuild
index 23f55c56ddd7..fe25d85dc9e7 100644
--- a/sci-chemistry/gromacs/gromacs-4.0.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.0.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2008 Gentoo Foundation
+# 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 1.1 2008/10/12 18:55:36 je_fro Exp $
+# $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"
 
@@ -33,6 +33,8 @@ DEPEND=">=sci-libs/fftw-3.0.1
 	mpi? ( virtual/mpi )
 	xml? ( dev-libs/libxml2 )"
 
+RDEPEND="${DEPEND}"
+
 FORTRAN="g77 gfortran ifc"
 
 src_unpack() {