--- /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-4.0.7-r4.ebuild,v 1.1 2010/07/04 16:48:12 alexxy Exp $
+
+EAPI="3"
+
+LIBTOOLIZE="true"
+TEST_PV="4.0.4"
+
+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-${TEST_PV}.tgz )
+ doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )
+ ffamber? ( http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+IUSE="X blas dmalloc doc -double-precision ffamber +fftw fkernels +gsl lapack
+mpi +single-precision static static-libs test +xml zsh-completion"
+
+DEPEND="app-shells/tcsh
+ X? ( x11-libs/libX11
+ x11-libs/libSM
+ x11-libs/libICE )
+ dmalloc? ( dev-libs/dmalloc )
+ blas? ( virtual/blas )
+ fftw? ( sci-libs/fftw:3.0 )
+ gsl? ( sci-libs/gsl )
+ lapack? ( virtual/lapack )
+ mpi? ( virtual/mpi )
+ xml? ( dev-libs/libxml2 )"
+
+RDEPEND="${DEPEND}"
+
+RESTRICT="test"
+
+QA_EXECSTACK="usr/lib/libgmx.so.*
+ usr/lib/libgmx_d.so.*"
+
+use static && QA_EXECSTACK="$QA_EXECSTACK usr/bin/*"
+
+src_prepare() {
+
+ ( use single-precision || use double-precision ) || \
+ die "Nothing to compile, enable single-precision and/or double-precision"
+
+ if use static; then
+ use X && die "You cannot compile a static version with X support, disable X or static"
+ use xml && die "You cannot compile a static version with xml support
+ (see bug #306479), disable xml or static"
+ fi
+
+ epatch "${FILESDIR}/${P}_upstream2010-06-08.patch.gz"
+ sed -e '/AC_INIT/s/4\.0\.7/&-2010-06-08/' -i configure.ac \
+ || die "Failed to change version in configure.ac"
+ epatch "${FILESDIR}/${PN}-4.0.9999-docdir.patch"
+ # Fix typos in a couple of files.
+ sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
+ || die "Failed to fixup demo script."
+
+ # Fix a sandbox violation that occurs when re-emerging with mpi.
+ sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${ED}usr/$( get_libdir )\" ; \\\\" \
+ -i src/tools/Makefile.am \
+ || die "sed tools/Makefile.am failed"
+
+ sed -e "s:\$\$libdir:\$temp_libdir:" \
+ -i src/tools/Makefile.am \
+ || die "sed tools/Makefile.am failed"
+
+ sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${ED}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
+ 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"
+
+ #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 [[ $(gcc-version) == "4.1" ]]; then
+ eerror "gcc 4.1 is not supported by gromacs"
+ eerror "please run test suite"
+ die
+ fi
+
+ #note for gentoo-PREFIX on apple: use --enable-apple-64bit
+
+ #fortran will gone in gromacs 4.1 anyway
+ #note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
+ if use fkernels; then
+ ewarn "Fortran kernels are usually not faster than C kernels and assembly"
+ ewarn "I hope, you know what are you doing..."
+ FORTRAN="g77 gfortran ifc"
+ myconf="${myconf} --enable-fortran" && fortran_pkg_setup
+ else
+ myconf="${myconf} --disable-fortran"
+ fi
+
+ # if we need external blas
+ if use blas; then
+ export LIBS="${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) \
+ ${myconf}"
+
+ #if we build single and double - double is suffixed
+ if ( use double-precision && use single-precision ); then
+ suffixdouble="_d"
+ else
+ suffixdouble=""
+ fi
+
+ if use double-precision ; then
+ #from gromacs manual
+ elog
+ elog "For most simulations single precision is accurate enough. In some"
+ elog "cases double precision is required to get reasonable results:"
+ elog
+ elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
+ elog " and the calculation and diagonalization of the Hessian "
+ elog "-calculation of the constraint force between two large groups of atoms"
+ elog "-energy conservation: this can only be done without temperature coupling and"
+ elog " without cutoffs"
+ elog
+ fi
+
+ if use mpi ; then
+ elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
+ elog "we configure/compile gromacs twice (with and without mpi) and only"
+ elog "install mdrun with mpi support. In addtion you will get libgmx and"
+ elog "libmd with and without mpi support."
+ fi
+
+ myconfdouble="${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}-${x}"
+ emake DESTDIR="${ED}" install || die "emake install for ${x} failed"
+ use mpi || continue
+ cd "${S}-${x}_mpi"
+ emake DESTDIR="${ED}" install-mdrun || die "emake install-mdrun for ${x} failed"
+ done
+
+ sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
+ doenvd "${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.*
+
+ cd "${S}"
+ dodoc AUTHORS INSTALL README
+ use doc && dodoc "${DISTDIR}/manual-4.0.pdf"
+ if use ffamber; then
+ use doc && dodoc "${WORKDIR}/ffamber_v4.0/README/pdfs/*.pdf"
+ # prepare vdwradii.dat
+ cat >>"${ED}"/usr/share/gromacs/top/vdwradii.dat <<-EOF
+ SOL MW 0
+ SOL LP 0
+ EOF
+ # regenerate aminoacids.dat
+ cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
+ "${ED}"/usr/share/gromacs/top/aminoacids.dat \
+ | awk '{print $1}' | sort -u | tail -n+4 | wc -l \
+ >> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new
+ cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
+ "${ED}"/usr/share/gromacs/top/aminoacids.dat \
+ | awk '{print $1}' | sort -u | tail -n+4 \
+ >> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new
+ mv -f "${ED}"/usr/share/gromacs/top/aminoacids.dat.new \
+ "${ED}"/usr/share/gromacs/top/aminoacids.dat
+ # copy ff files
+ for x in ffamber94 ffamber96 ffamber99 ffamber99p ffamber99sb \
+ ffamberGS ffamberGSs ffamber03 ; do
+ einfo "Adding ${x} to gromacs"
+ cp "${WORKDIR}"/ffamber_v4.0/${x}/* "${ED}"/usr/share/gromacs/top
+ done
+ # copy suplementary files
+ cp "${WORKDIR}"/ffamber_v4.0/*.gro "${ED}"/usr/share/gromacs/top
+ cp "${WORKDIR}"/ffamber_v4.0/*.itp "${ED}"/usr/share/gromacs/top
+ # actualy add records to FF.dat
+ cat >>"${ED}"/usr/share/gromacs/top/FF.dat.new <<-EOF
+ ffamber94 AMBER94 Cornell protein/nucleic forcefield
+ ffamber96 AMBER96 Kollman protein/nucleic forcefield
+ ffamberGS AMBER-GS Garcia & Sanbonmatsu forcefield
+ ffamberGSs AMBER-GSs Nymeyer & Garcia forcefield
+ ffamber99 AMBER99 Wang protein/nucleic acid forcefield
+ ffamber99p AMBER99p protein/nucleic forcefield
+ ffamber99sb AMBER99sb Hornak protein/nucleic forcefield
+ ffamber03 AMBER03 Duan protein/nucleic forcefield
+ EOF
+ cat "${ED}"/usr/share/gromacs/top/FF.dat \
+ "${ED}"/usr/share/gromacs/top/FF.dat.new \
+ | tail -n+2 > "${ED}"/usr/share/gromacs/top/FF.dat.new2
+ cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 | wc -l > \
+ "${ED}"/usr/share/gromacs/top/FF.dat
+ cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 >> \
+ "${ED}"/usr/share/gromacs/top/FF.dat
+ rm -f "${ED}"/usr/share/gromacs/top/FF.dat.new*
+ 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
+}
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