Latest version, thanks to Alexxy for the prod :)

Package-Manager: portage-2.1.6.4/cvs/Linux 2.6.28-gentoo x86_64

3 files changed, 221 insertions, 3 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index c80de98090db..cd3021e4fb93 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/gromacs
-# Copyright 2002-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.31 2008/10/12 18:55:36 je_fro Exp $
+# 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 $
+
+*gromacs-4.0.2 (04 Jan 2009)
+
+  04 Jan 2009; Jeff Gardner <je_fro@gentoo.org> +gromacs-4.0.2.ebuild:
+  Latest version, thanks to Alexxy for the prod :)
 
 *gromacs-4.0 (12 Oct 2008)
 
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 26119dcec31d..95734ab4e608 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,8 +1,10 @@
 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.tar.gz 8388265 RMD160 3156220f6b98ec4c04c264c8f798c616ce668a07 SHA1 5c8f0c3bfa2950bb936b4bfc5e9241028ffb8f1d SHA256 88b15d93200534539019754acc462a08572973025d9e147fce3c60529a0ffc16
 EBUILD gromacs-3.3.1-r1.ebuild 5844 RMD160 88dbfeb37cbb7b1611ff006954b354b0eccdcbdb SHA1 ed92d4b319673dfa8c9be145ab28aa92ac4a09b2 SHA256 99e30e2d720bb226c4dcafa52208efb3a0be120c1e8b00c84cdba41b1e0fb2a7
 EBUILD gromacs-3.3.3.ebuild 6316 RMD160 ebd5a70d2706697d2f37ac2f62e6e2dc4bb3961b SHA1 341fc4684db0b9d2f6491e5d85ddd574106d96fd SHA256 3ea05929c90c653cf716254dd4cca85efd28fb1c1d726cda88b47a18586cf2a8
+EBUILD gromacs-4.0.2.ebuild 6099 RMD160 7b216dc2efc16d7290b396b4fc807915a26937c8 SHA1 9c27eba0c69e34bf6be413ba00ccd2fd5b5b3b5f SHA256 d4180b5cc1b8a001601d66b5f17a5d21e43c2a6a0bd3cdfb5171c588a33c6b46
 EBUILD gromacs-4.0.ebuild 6097 RMD160 5143dec1c3bdf5a7dc59243761d3621eb77671e7 SHA1 30f7e6bbed16488a740cd9bd78e2759077ab719b SHA256 9de782cd113c791d0886b47edd8ba861eb866cfcb5a2f1aa6336cf08ca6a4d84
-MISC ChangeLog 7240 RMD160 2f2481b9633c4b63f22a8d5f33f4317a10408b03 SHA1 9dd73250f065bc2a8eac677682d8b8a252da92ae SHA256 37e364685959991e06a0e00b658da88b23f1430f0c7dfcf63c40f7473a9ca834
+MISC ChangeLog 7393 RMD160 e8d15bd9e3db43774837d9d4bd0715a37c421b5a SHA1 c33dbc027db6164f4e196ff11f0556c7d52f490a SHA256 abb3a497764c06cf42b566ddb0a168c0d8814d1298a78394a200638dee4eb3fe
 MISC metadata.xml 347 RMD160 23f2ef9d3b27d90f479c8242f6166e6afcbf4d45 SHA1 46bf8a3fb4b6a4e5c1ca55da0d6db9e1a6148ace SHA256 50d65907b09d524e42754b66da9f8596a6c4e941499922348cb75b774e9a543b
diff --git a/sci-chemistry/gromacs/gromacs-4.0.2.ebuild b/sci-chemistry/gromacs/gromacs-4.0.2.ebuild
new file mode 100644
index 000000000000..e461d2dd5f8b
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.0.2.ebuild
@@ -0,0 +1,211 @@
+# 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 $
+
+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 )"
+
+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}"/
+}