[sci-chemistry/gamess] Version bump. Also this version has improved qmmm support

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

3 files changed, 336 insertions, 3 deletions

diff --git a/sci-chemistry/gamess/ChangeLog b/sci-chemistry/gamess/ChangeLog
index 2b92975e1f07..1c838dcd01ae 100644
--- a/sci-chemistry/gamess/ChangeLog
+++ b/sci-chemistry/gamess/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/gamess
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/ChangeLog,v 1.39 2009/11/30 15:13:46 alexxy Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/ChangeLog,v 1.40 2010/05/24 12:38:11 alexxy Exp $
+
+*gamess-20100325.2 (24 May 2010)
+
+  24 May 2010; Alexey Shvetsov <alexxy@gentoo.org>
+  +gamess-20100325.2.ebuild:
+  Version bump with improved qmmm stuff
 
   30 Nov 2009; Alexey Shvetsov <alexxy@gentoo.org>
   gamess-20090112.3-r1.ebuild:
diff --git a/sci-chemistry/gamess/Manifest b/sci-chemistry/gamess/Manifest
index 88cb1555f29e..f0cf39953387 100644
--- a/sci-chemistry/gamess/Manifest
+++ b/sci-chemistry/gamess/Manifest
@@ -1,13 +1,25 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
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 DIST gamess-20090112.1.tar.gz 10823509 RMD160 409aafba9136a441c1524fe30eb1fccdff1f9883 SHA1 4af8dd470700649d32317d8ab57814b010a4403d SHA256 9f7763933479ba8aa730c392af25b8a271152115a0392707786b45871b52f6e0
 DIST gamess-20090112.3.tar.gz 11000803 RMD160 8bb155885d9a1264a894b72004d9662c3c4a0cd4 SHA1 4c0cd9a50d422b2e4462cbef83902b9a34e548a9 SHA256 0502c216c792a1c0fcebd6d3955f0feaeb4f9295b75cf0cb3af04c3516cec0bd
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 DIST tinker.tar.Z 1038267 RMD160 7231bdbe1785e98890037d654e8d3eab8ac066cf SHA1 05de4825fc2e97d3a898f2776a6494aed02da47a SHA256 d3e06eb13c2c35b01bbbc8dc7bc8c3a32337d9b9e26ff754db1ff0a1cc153db8
 EBUILD gamess-20080411.1.ebuild 6449 RMD160 f4ce142a0e539f7d9d6c6b53cb6365b146184296 SHA1 66ed15b13ace9f16e7a1c4898a6177e929938f7f SHA256 851552f6fc1e7f85d1590850c5718c18e7f2748cd0b0361b0a665be746c30d08
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diff --git a/sci-chemistry/gamess/gamess-20100325.2.ebuild b/sci-chemistry/gamess/gamess-20100325.2.ebuild
new file mode 100644
index 000000000000..753db5d445ec
--- /dev/null
+++ b/sci-chemistry/gamess/gamess-20100325.2.ebuild
@@ -0,0 +1,315 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/gamess-20100325.2.ebuild,v 1.1 2010/05/24 12:38:11 alexxy Exp $
+
+EAPI="2"
+
+inherit eutils toolchain-funcs fortran flag-o-matic
+
+DESCRIPTION="A powerful quantum chemistry package"
+LICENSE="gamess"
+HOMEPAGE="http://www.msg.chem.iastate.edu/GAMESS/GAMESS.html"
+SRC_URI="
+		${P}.tar.gz
+		qmmm-tinker? ( tinker.tar.Z )"
+
+SLOT="0"
+# NOTE: PLEASE do not stabilize gamess. It does not make sense
+# since the tarball has fetch restrictions and upstream only
+# provides the latest version. In other words: As soon as a
+# new version comes out the stable version will be useless since
+# users can not get at the tarball any more.
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE="hardened mpi qmmm-tinker"
+
+RESTRICT="fetch"
+
+DEPEND="app-shells/tcsh
+	hardened? ( sys-apps/paxctl )
+	mpi? ( virtual/mpi )
+	virtual/blas"
+
+RDEPEND="${DEPEND}
+	net-misc/openssh"
+
+S="${WORKDIR}/${PN}"
+
+GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html"
+GAMESS_VERSION="12 JAN 2009 (R3)"
+FORTRAN="ifc g77 gfortran"
+
+pkg_nofetch() {
+	echo
+	elog "Please download ${PN}-current.tar.gz from"
+	elog "${GAMESS_DOWNLOAD}."
+	elog "Be sure to select the version ${GAMESS_VERSION} tarball!!"
+	elog "Then move the tarball to"
+	elog "${DISTDIR}/${P}.tar.gz"
+	if use qmmm-tinker ; then
+		elog "Also download http://www.msg.ameslab.gov/GAMESS/tinker.tar.Z"
+		elog "and place tinker.tar.Z to ${DISTDIR}"
+	fi
+	echo
+}
+
+pkg_setup() {
+	fortran_pkg_setup
+
+	# currently amd64 is only supported with gfortran
+	if [[ "${ARCH}" == "amd64" ]] && [[ "${FORTRANC}" != "gfortran" ]];
+		then die "You will need gfortran to compile gamess on amd64"
+	fi
+
+	# note about qmmm-tinker
+	if use qmmm-tinker; then
+		if [ "x$QMMM_GAMESS_MAXMM" == "x" || \
+			"x$QMMM_GAMESS_MAXCLASS" == "x" || \
+			"x$QMMM_GAMESS_MAXCTYP" == "x" || \
+			"x$QMMM_GAMESS_MAXHESS" == "x"  ]; then
+			einfo "By default MM subsistem is restricted to 1000 atoms"
+			einfo "if you want larger MM subsystems then you should set"
+			einfo "QMMM_GAMESS_MAXMM variable to needed value in your make.conf"
+			einfo "By default maximum number of atom classes types and size of"
+			einfo "hessian are restricted to 250, 500 and 1000000 respectively"
+			einfo "If you want larger sizes set:"
+			einfo "QMMM_GAMESS_MAXCLASS"
+			einfo "QMMM_GAMESS_MAXCTYP"
+			einfo "QMMM_GAMESS_MAXHESS"
+			einfo "in your make.conf"
+			ebeep 5
+		fi
+	fi
+
+	#note about mpi
+	if use mpi; then
+		ewarn ""
+		ewarn "You should adjust rungms script for your mpi implentation"
+		ewarn "because deafult one will not work"
+		ewarn ""
+	fi
+}
+
+src_unpack() {
+	unpack ${A}
+
+	if use qmmm-tinker; then
+		mv tinker gamess/ || die "failed to move tinker directory"
+	fi
+}
+
+src_prepare() {
+	# apply LINUX-arch patches to gamess makesfiles
+	epatch "${FILESDIR}"/${PN}-20090112.1.gentoo.patch
+	# select arch
+	# NOTE: please leave lked alone; it should be good as is!!
+	cd "${S}"
+	local active_arch;
+	if [[ "${ARCH}" == "amd64" ]]; then
+		active_arch="linux64";
+	else
+		active_arch="linux32";
+	fi
+	sed -e "s:gentoo-target:${active_arch}:" \
+		-i comp compall ddi/compddi \
+		|| die "Failed to select proper architecure"
+
+	# for hardened-gcc let't turn off ssp, since it breakes
+	# a few routines
+	if use hardened && [[ "${FORTRANC}" = "g77" ]]; then
+		FFLAGS="${FFLAGS} -fno-stack-protector-all"
+	fi
+
+	# Enable mpi stuff
+	if use mpi; then
+		sed -e "s:set COMM = sockets:set COMM = mpi:g" \
+			-i ddi/compddi || die "Enabling mpi build failed"
+		sed -e "s:MPI_INCLUDE_PATH = ' ':MPI_INCLUDE_PATH =	'-I/usr/include ':g" \
+			-i ddi/compddi || die "Enabling mpi build failed"
+		sed -e "s:MSG_LIBRARIES='../ddi/libddi.a -lpthread':MSG_LIBRARIES='../ddi/libddi.a -lmpi -lpthread':g" \
+			-i lked || die "Enabling mpi build failed"
+	fi
+
+	# enable NEO
+	sed -e "s:NEO=false:NEO=true:" -i compall lked || \
+		die "Failed to enable NEO code"
+	# enable GAMESS-qmmm
+	if use qmmm-tinker; then
+		sed -e "s:TINKER=false:TINKER=true:" -i compall lked || \
+			die "Failed to enable TINKER code"
+		if [ "x$QMMM_GAMESS_MAXMM" == "x" ]; then
+			einfo "No QMMM_GAMESS_MAXMM set. Using default value = 1000"
+		else
+			einfo "Setting QMMM_GAMESS_MAXMM to $QMMM_GAMESS_MAXMM"
+			sed -e "s:maxatm=1000:maxatm=$QMMM_GAMESS_MAXMM:g" \
+			 -i tinker/sizes.i \
+			 || die "Setting QMMM_GAMESS_MAXMM failed"
+			sed -e "s:MAXATM=1000:MAXATM=$QMMM_GAMESS_MAXMM:g" \
+			 -i source/inputb.src \
+			 || die "Setting QMMM_GAMESS_MAXMM failed"
+		fi
+		sed -e "s:maxclass=250:maxclass=$QMMM_GAMESS_MAXCLASS:g" \
+			-i tinker/sizes.i \
+			|| die "Setting QMMM_GAMESS_MAXCLASS failed"
+		sed -e "s:maxtyp=500:maxtyp=$QMMM_GAMESS_MAXCTYP:g" \
+			-i tinker/sizes.i \
+			|| die "Setting QMMM_GAMESS_MAXCTYP failed"
+		sed -e "s:maxhess=1000000:maxhess=$QMMM_GAMESS_MAXHESS:g" \
+			-i tinker/sizes.i \
+			|| die "Setting QMMM_GAMESS_MAXHESS failed"
+	fi
+	# greate proper activate sourcefile
+	cp "./tools/actvte.code" "./tools/actvte.f" || \
+		die "Failed to create actvte.f"
+	sed -e "s/^\*UNX/    /" -i "./tools/actvte.f" || \
+		die "Failed to perform UNX substitutions in actvte.f"
+
+	# fix GAMESS' compall script to use proper CC
+	sed -e "s|\$CCOMP -c \$extraflags source/zunix.c|$(tc-getCC) -c \$extraflags source/zunix.c|" \
+		-i compall || die "Failed setting up compall script"
+
+	# insert proper FFLAGS into GAMESS' comp makefile
+	# in case we're using ifc let's strip all the gcc
+	# specific stuff
+	if [[ "${FORTRANC}" == "ifc" ]]; then
+		sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS} -quiet'/" \
+			-e "s/gentoo-g77/${FORTRANC}/" \
+			-i comp || die "Failed setting up comp script"
+	elif ! use x86; then
+		sed -e "s/-malign-double //" \
+			-e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \
+			-e "s/gentoo-g77/${FORTRANC}/" \
+			-i comp || die "Failed setting up comp script"
+	else
+		sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \
+			-e "s/gentoo-g77/${FORTRANC}/" \
+			-i comp || die "Failed setting up comp script"
+	fi
+
+	# fix up GAMESS' linker script;
+	sed -e "s/gentoo-g77/${FORTRANC}/" \
+		-e "s/gentoo-LDOPTS=' '/LDOPTS='${LDFLAGS}'/" \
+		-i lked || die "Failed setting up lked script"
+
+	# fix up GAMESS' ddi TCP/IP socket build
+	sed -e "s/gentoo-CC = 'gcc'/CC = '$(tc-getCC)'/" \
+		-e "s/gentoo-g77/${FORTRANC}/" \
+		-i ddi/compddi || die "Failed setting up compddi script"
+
+	# fix up the checker scripts for gamess tests
+	sed -e "s:set GMSPATH:#set GMSPATH:g" \
+		-e "s:\$GMSPATH/tools/checktst:.:g" \
+		-i tools/checktst/checktst
+}
+
+src_compile() {
+	# build actvte
+	cd "${S}"/tools
+	"${FORTRANC}" -o actvte.x actvte.f || \
+		die "Failed to compile actvte.x"
+
+	# for hardened (PAX) users and ifc we need to turn
+	# MPROTECT off
+	if [[ "${FORTRANC}" == "ifc" ]] && use hardened; then
+		/sbin/paxctl -PemRxS actvte.x 2> /dev/null || \
+			die "paxctl failed on actvte.x"
+	fi
+
+	# build gamess
+	cd "${S}"
+	./compall || die "compall failed"
+
+	# build the ddi TCP/IP socket stuff
+	cd ${S}/"ddi"
+	./compddi || die "compddi failed"
+
+	# finally, link it all together
+	cd "${S}"
+	./lked || die "lked failed"
+
+	# for hardened (PAX) users and ifc we need to turn
+	# MPROTECT off
+	if [[ "${FORTRANC}" == "ifc" ]] && use hardened; then
+		/sbin/paxctl -PemRxS ${PN}.00.x 2> /dev/null || \
+			die "paxctl failed on actvte.x"
+	fi
+}
+
+src_install() {
+	# the executables
+	dobin ${PN}.00.x rungms \
+		|| die "Failed installing binaries"
+	if use !mpi; then
+		dobin ddi/ddikick.x \
+			|| die "Failed installing binaries"
+	fi
+
+	# the docs
+	dodoc *.DOC qmnuc/*.DOC || die "Failed installing docs"
+
+	# install ericftm
+	insinto /usr/share/${PN}/ericfmt
+	doins ericfmt.dat || die "Failed installing ericfmt.dat"
+
+	# install mcpdata
+	insinto /usr/share/${PN}/mcpdata
+	doins mcpdata/* || die "Failed installing mcpdata"
+
+	# install tinker params in case of qmmm
+	if use qmmm-tinker ; then
+			dodoc tinker/simomm.doc || die "Failed installing docs"
+			insinto /usr/share/${PN}
+			doins -r tinker/params || die "Failed to install Tinker params"
+	fi
+
+	# install the tests the user should run, and
+	# fix up the runscript; also grab a copy of rungms
+	# so the user is ready to run the tests
+	insinto /usr/share/${PN}/tests
+	insopts -m0644
+	doins tests/* || die "Failed installing tests"
+	insopts -m0744
+	doins runall || die "Failed installing tests"
+	doins tools/checktst/checktst tools/checktst/chkabs || \
+		die "Failed to install main test checker"
+	doins tools/checktst/exam* || \
+		die "Failed to install individual test files"
+
+	insinto /usr/share/${PN}/neotests
+	insopts -m0644
+	doins -r qmnuc/neotests/* || die "Failed to install NEO tests"
+}
+
+pkg_postinst() {
+	echo
+	einfo "Before you use GAMESS for any serious work you HAVE"
+	einfo "to run the supplied test files located in"
+	einfo "/usr/share/gamess/tests and check them thoroughly."
+	einfo "Otherwise all scientific publications resulting from"
+	einfo "your GAMESS runs should be immediately rejected :)"
+	einfo "To do so copy the content of /usr/share/gamess/tests"
+	einfo "to some temporary location and execute './runall'. "
+	einfo "Then run the checktst script in the same directory to"
+	einfo "validate the tests."
+	einfo "Please consult TEST.DOC and the other docs!"
+
+	if [[ "${FORTRANC}" == "ifc" ]]; then
+		echo
+		ewarn "IMPORTANT NOTE: We STRONGLY recommend to stay away"
+		ewarn "from ifc-9.0 for now and use the ifc-8.1 series of"
+		ewarn "compilers UNLESS you can run through ALL of the "
+		ewarn "test cases (see above) successfully."
+	fi
+
+	echo
+	einfo "If you want to run on more than a single CPU"
+	einfo "you will have to acquaint yourself with the way GAMESS"
+	einfo "does multiprocessor runs and adjust rungms according to"
+	einfo "your target network architecture."
+	echo
+	
+	if use qmmm-tinker; then
+		einfo "You may want to install sci-chemistry/tinker to use addition FF"
+		einfo "parameters for your qmmm calculations"
+		echo
+	fi
+}