# 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 1.52 2010/07/04 16:48:12 alexxy Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.53 2010/07/05 10:41:17 alexxy Exp $
*gromacs-4.0.7-r4 (04 Jul 2010)
04 Jul 2010; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.0.7-r4.ebuild:
Fix bug #326331. thanks to Christoph Junghans
+ 05 Jul 2010; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-3.3.1-r1.ebuild,
+ -gromacs-3.3.3.ebuild:
+ Gromacs 3.x moved to sci overlay since its unmaintained and no longer
+ supported
+
*gromacs-4.0.7-r3 (27 Jun 2010)
27 Jun 2010; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-4.0.7.ebuild,
AUX gromacs-4.0.9999-docdir.patch 1352 RMD160 336ab23b4b65430caf3205650a8787e8e33d2137 SHA1 77e0cc966c4d755f603b2d0ab9a075c0ee6b7361 SHA256 8ead457b06f7f943455a95494be4648e539934699d29e955d2e05ac02f1ca4ef
DIST ffamber_v4.0-doc.tar.gz 7915520 RMD160 aeadb18bd88bcd9e6fc45af22af15c51e32c66a3 SHA1 8d4969fa7eec660b41f769874be9698980b49ed0 SHA256 0b3395570dfe9bf808a297fcb120e1f525f38a91791fbafe6e444d542d7754aa
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-4.0.4.tar.gz 8443779 RMD160 f90327814170c26a43d99fe7587357a46989fdec SHA1 9466f3ab95d60c0aba8916b1fcc70129cb4e4d72 SHA256 8aefd03cd3269e85c84427f05ceea6d3e16874cd4a90bf3f6fec2b2be24c426f
DIST gromacs-4.0.5.tar.gz 8465397 RMD160 4c2344629307f3a3daa11b986153d65883a44783 SHA1 9969aae6f77e2216add22a7b29805c4de8df649f SHA256 436b7a2a1ba3637eb07e30d676d78962008373a28fd17a3d889fa5816ca30339
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-3.3.1-r1.ebuild 5894 RMD160 1df038d8f1a05cbd4add20be5da6c9a98b45d87c SHA1 284f694ab47286f24c3d46a0bce2fe9e6bca42ff SHA256 9bce1076f25f9ae2be763ecea1860a4a18ec17328d098212412921627a767db4
-EBUILD gromacs-3.3.3.ebuild 6363 RMD160 02cc3ab83e9897408f971355a453b731006edce3 SHA1 eb3790b6d7bcf32ec81bd1e64987b93536c0e573 SHA256 42f87016396ca4fb7b71cdcba9e0d110e3311e2d4acabca2bbdb3c073b4c428f
EBUILD gromacs-4.0.4.ebuild 6918 RMD160 d31ffadfe240147555b227c36456d81c35f5f5dc SHA1 52b59952c4fb4861ed6bbe2f48ba4c3443b07cd4 SHA256 078f3942a1b5bf671326be97dacb22f37783c082c154bf193e28e18c4e314d3e
EBUILD gromacs-4.0.5.ebuild 6762 RMD160 c9945b966f14d1aa3fab96928a8c1269f2d0b4fb SHA1 535119ceb458903fd294f21959df4338eafd475d SHA256 dc76914d616ac4f750e9073601f1fc9cd30ab6f7b15a01152b95ef625a755c3b
EBUILD gromacs-4.0.7-r3.ebuild 9489 RMD160 7f125dc953d744dab91e8b8c34b5d1406fea91b1 SHA1 b14ce5def015cda74fbf7dadd9642a9599f7caeb SHA256 38f44e6c07fdf539a4253d63ec2ccdd604f679016545f6b7ade5d7e7a80ee068
EBUILD gromacs-4.0.7-r4.ebuild 9958 RMD160 669cce5d221ade95b881e573c5753b8b9e36bc7c SHA1 9356ac31bfc1e5317a68f0529dbd8b15fc0c9092 SHA256 6d947ea2171b648e3435d00768d7a6d503e08c03b09cb6fca38f0674c2897972
-MISC ChangeLog 10467 RMD160 34044c78c4da83657f6395d3c6b8268a2db8b7f9 SHA1 a79d24e14f3dc28c477842c47e8d7bdc7b2beebc SHA256 0a8fb5fb978b9a0745092e47a524a4b12c01b1148f659f88611a4f8074280e79
+MISC ChangeLog 10654 RMD160 dfb593bf7d2b20a155fdf5784abeb97291408f9a SHA1 33216a8ebe6a83d5a173a448f121c730a169aea5 SHA256 6aff7aa1c64ff3b8f81839bca329d432e86830ef2d67ab04cd2181423d09c0a5
MISC metadata.xml 643 RMD160 e9ffc42d792f15f3d4438a0de225277ec4814041 SHA1 c83fd4a32d896b7a2586667bc684d46f9daf8693 SHA256 177885ec674e8630a9c9451a0e0a35fc83615b39b387a67002e27f1b0d6b19b2
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+++ /dev/null
-# 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-3.3.1-r1.ebuild,v 1.14 2010/06/24 13:08:43 jlec Exp $
-
-inherit eutils fortran multilib
-
-IUSE="3dnow X altivec double-precision mpi sse sse2"
-
-# mopac7 qm/mm is broken until we can get files from
-# http://md.chem.rug.nl/~groenhof/qmmm.html
-# or somewhere else...
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
-HOMEPAGE="http://www.gromacs.org/"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="alpha amd64 ppc64 sparc x86"
-
-DEPEND=">=sci-libs/fftw-3.0.1
- mpi? ( virtual/mpi )
- >=sys-devel/binutils-2.12
- app-shells/tcsh
- X? ( x11-libs/libX11
- x11-libs/libXt
- x11-libs/libXp
- x11-libs/libXext
- x11-proto/xproto
- x11-libs/openmotif )"
-
-RDEPEND="${DEPEND}
- !sci-mathematics/num-utils"
-
-src_unpack() {
-
- unpack ${A}
- cd "${S}"
-# Fix typos in a couple of files.
- sed -e "s:_nb_kerne010_x86_64_sse2:_nb_kernel010_x86_64_sse2:" \
- -i src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/nb_kernel010_x86_64_sse2.intel_syntax.s \
- -i src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/nb_kernel010_x86_64_sse2.s \
- || die "Failed to fix sse2 typo."
-
- 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"
-
-# Rename disco manpage to fix bug #210083
- sed "s:disco.1:g_disco.1:" \
- -i "${S}"/man/man1/Makefile.am \
- || die "sed failed to rename disco"
-
- mv "${S}"/man/man1/disco.1 "${S}"/man/man1/g_disco.1
-
- cd "${WORKDIR}" && mv ${P} ${P}-single ;
-
- use double-precision && cp -prP ${P}-single ${P}-double ;
-
- if use mpi ; then
- cp -prP ${P}-single ${P}-single-mpi
- use double-precision && cp -prP ${P}-double ${P}-double-mpi
- fi
-}
-
-src_compile() {
- # static should work but something's broken.
- # gcc spec file may be screwed up.
- # Static linking should try -lgcc instead of -lgcc_s.
- # For more info:
- # http://lists.debian.org/debian-gcc/2002/debian-gcc-200201/msg00150.html
-
- # We will compile single precision by default, and suffix double-precision with _d.
- # Sparc is the only arch I can test on that needs to use fortran.
- local myconf ;
-
- case "${ARCH}" in
-
- x86)
- myconf="$myconf $(use_enable sse ia32-sse)"
- myconf="$myconf $(use_enable sse2 ia32-sse)"
- myconf="$myconf $(use_enable 3dnow ia32-3dnow)"
-
- # If you don't enable at least one of the above, you must use g77, not gfortran.
- if ! use sse && ! use sse2 && ! use 3dnow ; then
-
- if ! has_version "=sys-devel/gcc-3*" ; then
- die "If you must run gromacs without sse (not recommended) gfortran will not work."
- else myconf="$myconf --enable-fortran" && fortran_pkg_setup
-
- fi
- fi
- ;;
-
- amd64)
- myconf="$myconf --enable-x86-64-sse"
- ;;
-
- ppc)
- if use altivec ; then
- myconf="$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."
- fi
- myconf="$myconf --enable-fortran" && fortran_pkg_setup
- fi
- ;;
-
- ppc64)
- if use altivec ; then
- myconf="$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."
- fi
- 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
- ;;
-
- ia64)
- myconf="$myconf --enable-ia64-asm"
- ;;
-
- alpha)
- myconf="$myconf --enable-axp-asm --disable-fortran"
- ;;
-
- esac
-
- myconf="--enable-shared \
- --datadir=/usr/share \
- --bindir=/usr/bin \
- --libdir=/usr/$(get_libdir) \
- --with-fft=fftw3 \
- $(use_with X x) \
- ${myconf}"
-
- # $(use_with mopac7 qmmm-mopac) \
-
- cd "${WORKDIR}"/${P}-single
- econf ${myconf} --enable-float || die "configure single-precision failed"
-
- emake || die "emake single failed"
-
- if use mpi ; then
- cd "${WORKDIR}"/${P}-single-mpi
- econf ${myconf} --enable-float --enable-mpi --program-suffix=_mpi \
- || die "failed to configure single-mpi mdrun"
- emake mdrun || die "failed to make single-precision mpi mdrun" ;
- fi
-
- if use double-precision ; then
- cd "${WORKDIR}"/${P}-double
-
- econf ${myconf} --enable-double --program-suffix=_d \
- || die "configure double-precision failed"
-
- emake || die "emake double failed"
-
- if use mpi ; then
- cd "${WORKDIR}"/${P}-double-mpi
- econf ${myconf} --enable-double --enable-mpi --program-suffix=_mpi_d \
- || die "failed to configure double-mpi mdrun" ;
-
- emake mdrun \
- || die "failed to make double-precision mpi mdrun" ;
- fi
- fi
-
-}
-
-src_install () {
- cd "${WORKDIR}"/${P}-single ;
- emake DESTDIR="${D}" install || die "installing single failed"
-
- if use mpi ; then
- cd "${WORKDIR}"/${P}-single-mpi
- emake DESTDIR="${D}" install-mdrun \
- || die "installing mdrun_mpi failed"
- fi
-
- if use double-precision ; then
- cd "${WORKDIR}"/${P}-double && emake DESTDIR="${D}" install \
- || die "installing double failed"
-
- if use mpi ; then
- cd "${WORKDIR}"/${P}-double-mpi
- emake DESTDIR="${D}" install-mdrun \
- || die "installing mdrun_mpi_d failed"
- fi
-
- fi
-
- dodoc AUTHORS INSTALL README
-
- # Move html and leave examples and templates under /usr/share/gromacs.
- mv "${D}"/usr/share/"${PN}"/html "${D}"/usr/share/doc/"${PF}"/
-}
+++ /dev/null
-# 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-3.3.3.ebuild,v 1.3 2010/06/24 13:08:43 jlec 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}
- !sci-mathematics/num-utils"
-
-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"
-
- # Rename disco manpage to fix bug #210083.
- sed "s:disco.1:g_disco.1:" \
- -i "${S}"/man/man1/Makefile.am \
- || die "sed failed to rename disco"
-
- mv "${S}"/man/man1/disco.1 "${S}"/man/man1/g_disco.1
-
- eautoreconf
-
- cd "${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}"/
-}
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