Add QM/MM support to GAMESS-US

Package-Manager: portage-2.2_rc31/cvs/Linux x86_64

4 files changed, 252 insertions, 7 deletions

diff --git a/sci-chemistry/gamess/ChangeLog b/sci-chemistry/gamess/ChangeLog
index 64b8180bc33c..d2c1c7088d0d 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 1.30 2009/02/20 09:53:10 alexxy Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/ChangeLog,v 1.31 2009/04/22 13:07:57 alexxy Exp $
+
+*gamess-20090112.1-r1 (22 Apr 2009)
+
+  22 Apr 2009; Alexey Shvetsov <alexxy@gentoo.org> metadata.xml,
+  +gamess-20090112.1-r1.ebuild:
+  Add QM/MM support to GAMESS-US
 
 *gamess-20090112.1 (20 Feb 2009)
 
diff --git a/sci-chemistry/gamess/Manifest b/sci-chemistry/gamess/Manifest
index d82aa60c79eb..f5fed9a38300 100644
--- a/sci-chemistry/gamess/Manifest
+++ b/sci-chemistry/gamess/Manifest
@@ -10,17 +10,19 @@ DIST gamess-20070324.3.tar.gz 8219816 RMD160 e9a3ad26a520072322006d7f429ad5172a6
 DIST gamess-20070324.6.tar.gz 8452642 RMD160 b7f850db6d816f9011b646b31bc1c4a8b07983bc SHA1 19ea60d555ea10687e8fc43f9734b3fef5d646e3 SHA256 3c47012c17c544f6c6fe35526232e3d2b4aa61a4c22b7a944fcb72cad3295ae5
 DIST gamess-20080411.1.tar.gz 10301653 RMD160 9742a676cc2da693fff78594cdc0edf0f380a2de SHA1 8e0e01b255ebad8e2fd9b2012248648a11212b5c SHA256 493a99448afc6de15b6f054b702c6e67646e020cfee551aca0ef48a374fc6d05
 DIST gamess-20090112.1.tar.gz 10823509 RMD160 409aafba9136a441c1524fe30eb1fccdff1f9883 SHA1 4af8dd470700649d32317d8ab57814b010a4403d SHA256 9f7763933479ba8aa730c392af25b8a271152115a0392707786b45871b52f6e0
+DIST tinker.tar.Z 1038267 RMD160 7231bdbe1785e98890037d654e8d3eab8ac066cf SHA1 05de4825fc2e97d3a898f2776a6494aed02da47a SHA256 d3e06eb13c2c35b01bbbc8dc7bc8c3a32337d9b9e26ff754db1ff0a1cc153db8
 EBUILD gamess-20070324.1.ebuild 6360 RMD160 5e6cb711089868a160b7e0e7befd392a334af44b SHA1 197ee11d53e9ffc7c19bdffb7a911a856d5edf17 SHA256 fdec395b93f930890c2fdec43c1d3b3f0ddfc91e29d8ef95e8152e8054a507e3
 EBUILD gamess-20070324.3.ebuild 6449 RMD160 00fd64e09e495bcbcc01f5d73218b36ce504b07f SHA1 0ebd365b38d28cd5a7fd83574d6547c1a695dec2 SHA256 2e81527989a11bacf6f72a14cfb7a00bd2cced0a745d8a4253eb6c1a1f1d8c21
 EBUILD gamess-20070324.6.ebuild 6461 RMD160 6f8c07650f96b231a33135f4f17a63b92729028d SHA1 54f2472dbe2a24ecb8f841b9e5a4b65df4c4e1a4 SHA256 09535141a5d14a388775db0da3187f0d9beeb244dda6918b3877cad27c98654f
 EBUILD gamess-20080411.1.ebuild 6449 RMD160 f4ce142a0e539f7d9d6c6b53cb6365b146184296 SHA1 66ed15b13ace9f16e7a1c4898a6177e929938f7f SHA256 851552f6fc1e7f85d1590850c5718c18e7f2748cd0b0361b0a665be746c30d08
+EBUILD gamess-20090112.1-r1.ebuild 7049 RMD160 fc8b60034d3446a0ddc16eaa82a9556291c77ac2 SHA1 ed5f81e1f81c8870213ce94097b865e680470a8a SHA256 4b6a10835d34476052a1b3024649b3f99d4a6396b96960bcba8576f1dc3007cb
 EBUILD gamess-20090112.1.ebuild 6456 RMD160 f26f2ccab0b5c230da6be09efd017555f6a815be SHA1 3ff4edc79c03d71f457101616b2ace00c4b0c066 SHA256 5674413ba5f411e9a5cde75677387c87fdf62d8f0eb65ddbf7b2e136807ffefa
-MISC ChangeLog 7220 RMD160 a941930e169d7a1726f9eeecc396798cf1343774 SHA1 b291e684e702e780ce061da6acd1c364c56aa93c SHA256 77d24aeb6bedb60b3e415a1687bef8aa12b7a9d7804973f568da4847e7f3dc1a
-MISC metadata.xml 359 RMD160 3155769eae83f4d89e87c36947569ce944085a00 SHA1 a6f4d8de76b849b861d3ba094c35cae9d6534f34 SHA256 8df41f26afc6361d3adf1fc38121c3808d9a8bb8262e7e6ed45854a5b6e54d58
+MISC ChangeLog 7388 RMD160 93424efeba70c90c242e1945428097598e8767cc SHA1 568ad9b1203765c7603d15b5e5496ae1108b28fa SHA256 d103edbb37680c68a2784ba7b0cf74ba9f3db72b8ef9657d8e7e48741b2260a3
+MISC metadata.xml 432 RMD160 36785f37503fb3d7ab09a459d5c146ba9f2639c5 SHA1 3e7483cf552e4946b0791b97f40fae541c8ee1aa SHA256 bcc821dc1c54441f16d9b763e7dd172cc8a1f9b51a6e93fa9af5dc2fa56f3e8d
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.10 (GNU/Linux)
+Version: GnuPG v2.0.11 (GNU/Linux)
 
-iEYEARECAAYFAkmefZgACgkQ5BmOA85PVLglqwCeMPtowh32NyFzXFkYHqjFWxtP
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-=wUxE
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diff --git a/sci-chemistry/gamess/gamess-20090112.1-r1.ebuild b/sci-chemistry/gamess/gamess-20090112.1-r1.ebuild
new file mode 100644
index 000000000000..99c6edc9f000
--- /dev/null
+++ b/sci-chemistry/gamess/gamess-20090112.1-r1.ebuild
@@ -0,0 +1,234 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/gamess-20090112.1-r1.ebuild,v 1.1 2009/04/22 13:07:57 alexxy Exp $
+
+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="
+		${P}.tar.gz
+		qmmm-tinker? ( tinker.tar.Z )"
+
+SLOT="0"
+KEYWORDS="~ppc ~x86 ~amd64"
+IUSE="hardened qmmm-tinker"
+
+RESTRICT="fetch"
+
+DEPEND="app-shells/tcsh
+	hardened? ( sys-apps/paxctl )
+	virtual/blas"
+
+RDEPEND="${DEPEND}
+	net-misc/openssh"
+
+S="${WORKDIR}/${PN}"
+
+GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html"
+GAMESS_VERSION="12 JAN 2009 (R1)"
+FORTRAN="ifc g77 gfortran"
+
+pkg_nofetch() {
+	echo
+	einfo "Please download ${PN}-current.tar.gz from"
+	einfo "${GAMESS_DOWNLOAD}."
+	einfo "Be sure to select the version ${GAMESS_VERSION} tarball!!"
+	einfo "Then move the tarball to"
+	einfo "${DISTDIR}/${P}.tar.gz"
+	if use qmmm-tinker ; then
+		einfo "Also download http://www.msg.ameslab.gov/GAMESS/tinker.tar.Z"
+		einfo "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
+}
+
+src_unpack() {
+	unpack ${A}
+	mv tinker gamess/
+	# apply LINUX-arch patches to gamess makesfiles
+	epatch "${FILESDIR}"/${P}.gentoo.patch
+
+	# select arch
+	# NOTE: please leave lked alone; it should be good as is!!
+	cd "${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 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"
+	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 ${PN}.00.x ddi/ddikick.x rungms \
+		|| die "Failed installing binaries"
+
+	# the docs
+	dodoc *.DOC qmnuc/*.DOC || die "Failed installing docs"
+
+	# install ericftm
+	insinto /usr/share/${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
+}
diff --git a/sci-chemistry/gamess/metadata.xml b/sci-chemistry/gamess/metadata.xml
index 9193c15f60d4..1ee128aaacb2 100644
--- a/sci-chemistry/gamess/metadata.xml
+++ b/sci-chemistry/gamess/metadata.xml
@@ -10,4 +10,7 @@
 		<name>Alexey Shvetsov</name>
 	</maintainer>
 	<herd>sci-chemistry</herd>
+	<use>
+		<flag name='qmmm-tinker'>Enable tinker qmmm code</flag>
+	</use>
 </pkgmetadata>