--- gromacs-4.0.3.ebuild	2009-04-18 18:43:48.000000000 +0200
+++ gromacs-4.0.4.ebuild	2009-04-18 17:01:30.000000000 +0200
@@ -1,35 +1,29 @@
 # 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 1.2 2009/03/08 19:50:46 maekke Exp $
+# $Header: $
 
 EAPI="1"
 
 LIBTOOLIZE="true"
 
-inherit autotools eutils flag-o-matic fortran multilib
+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"
+SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
+		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${PV}.tgz )
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
 
 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"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
+IUSE="X blas dmalloc doc -double-precision fftw fkernels gsl lapack mpi +single-precision static test +xml zsh-completion"
 
-# 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 )
+DEPEND="app-shells/tcsh
+	X? ( x11-libs/libX11 )
+	dmalloc? ( dev-libs/dmalloc )
 	blas? ( virtual/blas )
+	fftw? ( >=sci-libs/fftw-3.0.1 )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
 	mpi? ( virtual/mpi )
@@ -37,10 +31,7 @@
 
 RDEPEND="${DEPEND}"
 
-FORTRAN="g77 gfortran ifc"
-
 src_unpack() {
-
 	unpack ${A}
 	cd "${S}"
 	# Fix typos in a couple of files.
@@ -64,6 +55,8 @@
 	-i src/tools/Makefile.am \
 	|| die "sed tools/Makefile.am failed"
 
+	use fkernels && epatch "${FILESDIR}/${P}-configure-gfortran.patch"
+
 	eautoreconf
 
 	cd "${WORKDIR}"
@@ -75,74 +68,37 @@
 }
 
 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 ;
+	local suffix_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="${myconf} --enable-fortran" && fortran_pkg_setup
-			fi
-			;;
-	esac
+	#leave all assembly options enabled mdrun is smart enough to deside itself
+	#there so no gentoo on bluegene!
+	myconf="${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 [[ $(gcc-version) == "4.1" ]]; then
+		ewarn "gcc 4.1 is not supported by gromacs"
+		ewarn "please run test suite"
+	fi
+
+	#fortran will gone in gromacs 4.1 anyway
+	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
+	if use fkernels; then
+		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
+		ewarn "I hope, you know what are you doing..."
+		FORTRAN="g77 gfortran ifc"
+		myconf="${myconf} --enable-fortran" && fortran_pkg_setup
+	else
+		myconf="${myconf} --disable-fortran"
+	fi
 
 	# if we need external blas
 	if use blas; then
@@ -159,7 +115,8 @@
 	myconf="--datadir=/usr/share \
 			--bindir=/usr/bin \
 			--libdir=/usr/$(get_libdir) \
-			--with-fft=fftw3 \
+			$(use_with dmalloc) \
+			$(use_with fftw fft fftw3) \
 			$(use_with gsl) \
 			$(use_enable mpi) \
 			$(use_with X x) \
@@ -167,35 +124,58 @@
 			$(use_enable static all-static) \
 			${myconf}"
 
+	#if we build both double is suffixed
 	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"
+		suffix_d="_d"	
+	else
+		suffix_d=""
+	fi
 
-	elif use double-precision ; then
+	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
 		einfo "Building Double Precison Gromacs"
 		cd "${WORKDIR}"/"${P}"-double
-		myconf_d="${myconf} --enable-double --disable-float --program-suffix=''"
+		myconf_d="${myconf} --enable-double --program-suffix='${suffix_d}'"
 		econf ${myconf_d} || die "Double Precision econf failed"
 		emake || die "Double Precision emake failed"
+	fi
 
-	elif use single-precision ; then
+	if use single-precision ; then
 		einfo "Building Single Precison Gromacs"
 		cd "${WORKDIR}"/"${P}"-single
-		myconf_s="${myconf} --enable-float --disable-double --program-suffix=''"
+		myconf_s="${myconf} --enable-float --program-suffix=''"
 		econf ${myconf_s} || die "configure failed"
 		emake || die "Single Precision emake failed"
 	fi
 }
 
+src_test() {
+	if use single-precision ; then
+		export PATH="${WORKDIR}/${P}-single/src/kernel:${WORKDIR}/${P}-single/src/tools:$PATH"
+		cd "${WORKDIR}/gmxtest"
+		#test is broken, only do simple tests
+		./gmxtest.pl simple || die "Single Precision test failed"
+	fi
+
+	if use double-precision ; then
+		export PATH="${WORKDIR}/${P}-double/src/kernel:${WORKDIR}/${P}-double/src/tools:$PATH"
+		cd "${WORKDIR}/gmxtest"
+		use single-precision && ./gmxtest.pl clean
+		#test is broken, only do simple tests
+		./gmxtest.pl -double simple || die "Double Precision test failed"	
+	fi
+}
+
 src_install() {
 	if use single-precision ; then
 		einfo "Installing Single Precision"
@@ -208,8 +188,36 @@
 		cd "${WORKDIR}"/"${P}"-double
 		emake DESTDIR="${D}" install || die "Installing Double Precision failed"
 	fi
+	
+	sed -n -e '/^GMXBIN/,/^GMXDATA/p' ${D}/usr/bin/GMXRC.bash > "${T}/80gromacs"
+	doenvd "${T}/80gromacs"
+	rm -f ${D}/usr/bin/GMXRC*
+	
+	dobashcompletion ${D}/usr/bin/completion.bash ${PN}
+	if use zsh-completion ; then
+		insinto /usr/share/zsh/site-functions
+		newins ${D}/usr/bin/completion.zsh _${PN}
+	fi
+	rm -r ${D}/usr/bin/completion.*
 
 	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}"/
+	if use doc; then
+		# Move html and leave examples and templates under /usr/share/gromacs.
+		mv "${D}"/usr/share/"${PN}"/html "${D}"/usr/share/doc/"${PF}"/
+		dodoc "${DISTDIR}"/manual-4.0.pdf
+	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
 }