[sci-chemistry/gromacs] version bump

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

3 files changed, 280 insertions, 4 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index fcaa17381..f31731e2e 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-4.5.2 (30 Oct 2010)
+
+  30 Oct 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  +gromacs-4.5.2.ebuild:
+  Version bump
+
   25 Oct 2010; Christoph Junghans <kleiner_otti@gmx.de>
   gromacs-4.5.9999.ebuild, gromacs-9999.ebuild, metadata.xml:
   added natural vmd support (bug #340651#c8)
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 0185236d4..537e3e3a6 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -6,18 +6,20 @@ AUX gromacs-4.0.7_upstream2010-09-15.patch.gz 22500 RMD160 d5341f506f50db4fe9772
 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-4.0.7.tar.gz 8404518 RMD160 4fa8e5c90f549ef627a98a907a166676692a4c4b SHA1 8519bef2fa989fb487d54612b0a2d0228f228b30 SHA256 048f8ece2829f01d99f7e04e1d6e8f88d3a32273192274f2e9fcf71f41f212c1
+DIST gromacs-4.5.2.tar.gz 10336521 RMD160 7e523c431a99909906feeadbfa106af717fa6fef SHA1 cae9ffb635767db9816461f6b076c2a0e0bed780 SHA256 369f94c3c16d1c68cd96ebf2671f0941546e14c23f9f7ee99bcf93dd84008d71
 DIST gromacs-manual-4.0.pdf 2135100 RMD160 b963642f8e1433f11328c3d0c4b1645c9de506da SHA1 8ae951ee15b2a7dc626331fce36511bc8766144c SHA256 646f810477eee2d710de6019c52056550413d0ba77baf9680195c835ddafe80a
 DIST gromacs-manual-4.5.pdf 2445884 RMD160 65548f56a71697128ab44cae59d5b7997c86fbdb SHA1 1a6ff8fb56873eccfa03b104770a136e0befe298 SHA256 028cb5b150185157a7d93849c0c1f8e442c41c942932ffbf0530ef1774e66449
 EBUILD gromacs-4.0.7-r5.ebuild 9480 RMD160 f172dac014fc931dc23d14c0466019b858d81637 SHA1 687eaa885b6b88f38f2607d98f40f689ecfe747c SHA256 e84d65116bfbfd437e457b901b98d176de5cc69fa6a3d5fc3b3bb43a31bb42f1
 EBUILD gromacs-4.0.9999.ebuild 9367 RMD160 fa9e3db1d2a292a21d7cf15bf14fc9f7475ea0cc SHA1 a6feb465752a155160701b3a6832c796aaf1049f SHA256 608ef3c08895702eaaa45e1a9a186037b76b0ea0c5c117fa3782bdb02a8d3664
+EBUILD gromacs-4.5.2.ebuild 7829 RMD160 827009ef0e2770cd970062caab50a38c11576693 SHA1 08bda9d29453118d9af620605e0a1d12014d53fb SHA256 7efbe881e7cad0aef2249f4266f60b8e5ea77141f638e92fe520123993fb1575
 EBUILD gromacs-4.5.9999.ebuild 7868 RMD160 5bbdd449ba56b9c43fa4ca569ad133e6ba82c85f SHA1 8b8191f30311aa629347bce93cb30ec85838a682 SHA256 1fd4fac901ac56c8d036621132eac5b8941f5e635103d5b1870b5687d7fc5a5b
 EBUILD gromacs-9999.ebuild 8165 RMD160 e7f1bbed099d11ac3a2f02b7097000fbe76a2aec SHA1 2ce763e1b5620447cf2d46bb176b2390f51fd61d SHA256 5a5388dce2ab5c4709ab7d0f1e3be1a2175357aca4ac8e3f00cc955e70c7e05e
-MISC ChangeLog 6465 RMD160 19063a834db23e48794a850bb1697c1bf1d664dc SHA1 403b5b621eb2d4a682b28b35820dac66c50176ee SHA256 7895371d8caf446ce3950e8603ea92500a5637245c15d98f803bf50fe6083f46
+MISC ChangeLog 6592 RMD160 2497d95f6fa4d7218eb13d67e7c01ea26b665ad4 SHA1 2b9f315ba2d360d88a3e3c977e23e849672c1dbc SHA256 528ea819e7ad56418840c32456ffc54b3b3495e6ea7fced739e74c763a638f7b
 MISC metadata.xml 643 RMD160 e9ffc42d792f15f3d4438a0de225277ec4814041 SHA1 c83fd4a32d896b7a2586667bc684d46f9daf8693 SHA256 177885ec674e8630a9c9451a0e0a35fc83615b39b387a67002e27f1b0d6b19b2
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.16 (GNU/Linux)
 
-iEUEARECAAYFAkzF+HUACgkQy0OE/ans1/nF2wCXYsMrzyRbEm6Uh36E1VsnL3sD
-ggCeJ9jCtyNeJrN4P77wwCbpDafIe7Q=
-=dHsK
+iEYEARECAAYFAkzMkR8ACgkQy0OE/ans1/kFlgCfZZH29yj7mMAOZGzswOwkcBaI
+iNQAoIVR52T443hL6J0tRTxMV9h8hFOj
+=ONBX
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/gromacs/gromacs-4.5.2.ebuild b/sci-chemistry/gromacs/gromacs-4.5.2.ebuild
new file mode 100644
index 000000000..86cf031ed
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.5.2.ebuild
@@ -0,0 +1,268 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="3"
+
+LIBTOOLIZE="true"
+TEST_PV="4.0.4"
+MANUAL_PV="4.5"
+
+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
+		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-${MANUAL_PV}.pdf )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
+mpi +single-precision static static-libs test +threads +xml zsh-completion"
+
+DEPEND="app-shells/tcsh
+	X? ( x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE )
+	dmalloc? ( dev-libs/dmalloc )
+	blas? ( virtual/blas )
+	fftw? ( sci-libs/fftw:3.0 )
+	gsl? ( sci-libs/gsl )
+	lapack? ( virtual/lapack )
+	mpi? ( virtual/mpi )
+	xml? ( dev-libs/libxml2 )"
+
+RDEPEND="${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 mpi && use threads; then
+		elog "mdrun uses only threads OR mpi, and gromacs favours the"
+		elog "use of mpi over threads, so a mpi-version of mdrun will"
+		elog "be compiled. If you want to run mdrun on shared memory"
+		elog "machines only, you can safely disable mpi"
+	fi
+
+	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_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="${myconf} --disable-bluegene"
+
+	#we have pkg-config files
+	myconf="${myconf} --disable-la-files"
+
+	#from gromacs configure
+	if ! use fftw; then
+		ewarn "WARNING: The built-in FFTPACK routines are slow."
+		ewarn "Are you sure you don\'t want to use FFTW?"
+		ewarn "It is free and much faster..."
+	fi
+
+	if [[ $(gcc-version) == "4.1" ]]; then
+		eerror "gcc 4.1 is not supported by gromacs"
+		eerror "please run test suite"
+		die
+	fi
+
+	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
+
+	#fortran will gone in gromacs 4.1 anyway
+	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
+	if use fkernels; then
+		use threads && die "You cannot compile fortran kernel with threads"
+		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
+		ewarn "I hope, you know what are you doing..."
+		myconf="${myconf} --enable-fortran"
+	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) \
+			$(use_enable threads) \
+			${myconf}"
+
+	#if we build single and double - double is suffixed
+	if ( use double-precision && use single-precision ); then
+		suffixdouble="_d"
+	else
+		suffixdouble=""
+	fi
+
+	if use double-precision ; then
+		#from gromacs manual
+		elog
+		elog "For most simulations single precision is accurate enough. In some"
+		elog "cases double precision is required to get reasonable results:"
+		elog
+		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
+		elog " and the calculation and diagonalization of the Hessian "
+		elog "-calculation of the constraint force between two large groups of	atoms"
+		elog "-energy conservation: this can only be done without temperature coupling and"
+		elog " without cutoffs"
+		elog
+	fi
+
+	if use mpi ; then
+		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
+		elog "we configure/compile gromacs twice (with and without mpi) and only"
+		elog "install mdrun with mpi support. In addtion you will get libgmx and"
+		elog "libmd with and without mpi support."
+	fi
+
+	myconfdouble="${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 ${x} failed"
+	done
+
+	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${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*
+
+	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.*
+
+	# Fix typos in a couple of files.
+	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
+		|| die "Failed to fixup demo script."
+
+	cd "${S}"
+	dodoc AUTHORS INSTALL* README*
+	if use doc; then
+		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/"
+}
+
+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 $(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
+}