Version bump. This version includes the NEO code.

(Portage version: 2.1.2_rc3-r2)

4 files changed, 448 insertions, 1 deletions

diff --git a/sci-chemistry/gamess/ChangeLog b/sci-chemistry/gamess/ChangeLog
index 9fa212fc1b2f..c3598029d25e 100644
--- a/sci-chemistry/gamess/ChangeLog
+++ b/sci-chemistry/gamess/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/gamess
 # Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/ChangeLog,v 1.17 2006/09/26 14:43:09 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/ChangeLog,v 1.18 2006/12/14 14:52:07 markusle Exp $
+
+*gamess-20060907.4 (14 Dec 2006)
+
+  14 Dec 2006; Markus Dittrich <markusle@gentoo.org>
+  +files/gamess-20060907.4.gentoo.patch, +gamess-20060907.4.ebuild:
+  Version bump. This version includes the NEO code.
 
 *gamess-20060222.5 (26 Sep 2006)
 
diff --git a/sci-chemistry/gamess/files/digest-gamess-20060907.4 b/sci-chemistry/gamess/files/digest-gamess-20060907.4
new file mode 100644
index 000000000000..f59129bd8b3f
--- /dev/null
+++ b/sci-chemistry/gamess/files/digest-gamess-20060907.4
@@ -0,0 +1,3 @@
+MD5 1f31f0c02dd8f87cdeec37e9ebfd9d48 gamess-20060907.4.tar.gz 7864905
+RMD160 6e01ab4aabc41980fff74b512ef3b952a5e3f0c8 gamess-20060907.4.tar.gz 7864905
+SHA256 8361f50e18ce5301e42375f820d8c41297ca1639fe02441c0a376b19d5e61ea9 gamess-20060907.4.tar.gz 7864905
diff --git a/sci-chemistry/gamess/files/gamess-20060907.4.gentoo.patch b/sci-chemistry/gamess/files/gamess-20060907.4.gentoo.patch
new file mode 100644
index 000000000000..746f778de006
--- /dev/null
+++ b/sci-chemistry/gamess/files/gamess-20060907.4.gentoo.patch
@@ -0,0 +1,221 @@
+diff -Naur gamess/comp gamess-new/comp
+--- gamess/comp	2006-11-06 10:17:54.000000000 -0500
++++ gamess-new/comp	2006-12-13 18:06:06.000000000 -0500
+@@ -11,8 +11,8 @@
+ #      linux-ia64,linux-pc,mac32,macG5,necsx,sgi32,sgi64,sun32,sun64
+ #  2. Choose your GAMESS directory tree.
+ #
+-set TARGET=ibm64
+-chdir /u1/mike/gamess
++set TARGET=linux-pc
++#chdir /u1/mike/gamess
+ #
+ #    ---- and now the script begins...
+ #
+@@ -300,6 +300,7 @@
+ if ($MODULE == neomp2)  set NEOCMP=true
+ if ($MODULE == neosym)  set NEOCMP=true
+ if ($MODULE == neotrn)  set NEOCMP=true
++if ($MODULE == neopos)  set NEOCMP=true
+ if ($NEOCMP == true && $ACTONLY != true) set SRCDIR=qmnuc/neo
+ #
+ #   ----- Does this module need to be activated? -----
+@@ -701,7 +702,7 @@
+    switch ($FORTRAN)
+ 
+    case gfortran:
+-      set OPT='-O2'
++      set gentoo-OPT = '-O2'
+       if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
+       if (($MODULE == qeigen) || ($MODULE == int2c)) then
+          mv $MODULE.f $MODULE.junk
+@@ -1148,7 +1149,7 @@
+ #   The only thing you need to change is the next line.
+ #   Note: you must make the analogous choice in compddi and lked, as well.
+ #
+-    set FORTRAN=g77       # choose from g77, gfortran, ifort, pgf77, f2c
++    set FORTRAN=gentoo-g77       # choose from g77, gfortran, ifort, pgf77, f2c
+ #
+     switch ($FORTRAN)
+ #
+@@ -1167,7 +1168,7 @@
+ #   Pentium II fractionally).  None of these optimizations are used below.
+ #
+    case g77:
+-   set OPT = '-O2'
++   set gentoo-OPT = '-O2'
+    if ($MODULE == ormas1) set OPT='-O2 -fno-move-all-movables' # RH9, g77 3.3
+    if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
+ #
+@@ -1203,7 +1204,7 @@
+ #      -std=legacy  suppresses warnings about use of f77 constructs.
+ #
+    case gfortran:
+-   set OPT='-O2'
++   set gentoo-OPT = '-O2'  
+    if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
+    if (($MODULE == qeigen) || ($MODULE == int2c)) then
+       mv $MODULE.f $MODULE.junk
+@@ -1230,7 +1231,7 @@
+ #    but that may cause certain ifort versions to fail on some files.
+ #
+    case ifort:
+-   set OPT = '-O3'
++   set gentoo-OPT = '-O2'
+    if ($MODULE == delocl) set OPT='-O0'  # from Cheol
+    if ($MODULE == zheev)  set OPT='-O0'
+    set echo
+diff -Naur gamess/compall gamess-new/compall
+--- gamess/compall	2006-11-19 18:02:49.000000000 -0500
++++ gamess-new/compall	2006-12-13 09:13:42.000000000 -0500
+@@ -12,8 +12,8 @@
+ #      linux-ia64,linux-pc,mac32,macG5,necsx,sgi32,sgi64,sun32,sun64
+ #  2. Choose your GAMESS directory tree.
+ #
+-set TARGET=ibm64
+-chdir /u1/mike/gamess
++set TARGET=linux-pc
++#chdir /u1/mike/gamess
+ #
+ #  ----- and now the script begins...
+ #
+diff -Naur gamess/ddi/compddi gamess-new/ddi/compddi
+--- gamess/ddi/compddi	2006-08-30 09:34:15.000000000 -0400
++++ gamess-new/ddi/compddi	2006-12-13 09:14:23.000000000 -0500
+@@ -14,7 +14,7 @@
+ #      fuji-pp32,fuji-pp64,hpux32,hpux64,ibm32,ibm64,ibm64-sp,ibm-bg,
+ #      linux-ia64,linux-pc,mac32,macG5,necsx,sgi32,sgi64,sun32,sun64
+ #
+-         set TARGET = ibm64
++         set TARGET = linux-pc
+ 
+ #  2. Choose DDI communication layer, the only legal values are
+ #                   sockets,mixed,mpi,shmem,lapi
+@@ -488,9 +488,9 @@
+ #
+   if($TARGET == linux-pc) then
+ 
+-     set FORTRAN=g77       # choose from g77, gfortran, ifort, pgf77, f2c
++     set FORTRAN=gentoo-g77       # choose from g77, gfortran, ifort, pgf77, f2c
+ 
+-     set CC = 'gcc'
++     set gentoo-CC = 'gcc'
+      set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./include"
+ 
+      switch ($FORTRAN)
+diff -Naur gamess/ddi/tools/ddikick/ddikick.c gamess-new/ddi/tools/ddikick/ddikick.c
+--- gamess/ddi/tools/ddikick/ddikick.c	2006-06-05 03:15:09.000000000 -0400
++++ gamess-new/ddi/tools/ddikick/ddikick.c	2006-12-13 09:13:42.000000000 -0500
+@@ -105,7 +105,7 @@
+           remoteshell = argv[++i];
+        } else {
+           if((remoteshell = getenv("DDI_RSH")) == NULL) {
+-              remoteshell = (char *) strdup("rsh");
++              remoteshell = (char *) strdup("ssh");
+           }
+        }
+ 
+diff -Naur gamess/lked gamess-new/lked
+--- gamess/lked	2006-11-19 18:02:58.000000000 -0500
++++ gamess-new/lked	2006-12-13 09:13:42.000000000 -0500
+@@ -14,8 +14,8 @@
+ #       linux-ia64,linux-pc,mac32,macG5,necsx,sgi32,sgi64,sun32,sun64
+ #  2. Choose your GAMESS directory tree.
+ #
+-set TARGET=ibm64
+-chdir /u1/mike/gamess
++set TARGET=linux-pc
++#chdir /u1/mike/gamess
+ #
+ #    ---- and now the script begins...
+ #
+@@ -330,22 +330,22 @@
+ #
+ if ($TARGET == linux-pc) then
+ #
+-   set FORTRAN=g77       # choose from g77, gfortran, ifort, pgf77, f2c
++   set FORTRAN=gentoo-g77       # choose from g77, gfortran, ifort, pgf77, f2c
+ #
+    switch ($FORTRAN)
+      case g77:
+         set LDR='g77'
+-        set LDOPTS=' '  # add '-Wl,-M' to see load map
++        set gentoo-LDOPTS=' '  # add '-Wl,-M' to see load map
+         set LIBRARIES=' '
+         breaksw
+      case gfortran:
+         set LDR='gfortran'
+-        set LDOPTS=' '
++        set gentoo-LDOPTS=' '
+         set LIBRARIES=' '
+         breaksw
+      case ifort:
+         set LDR='ifort'
+-        set LDOPTS=' '  # add '-Wl,-M' to see load map
++        set gentoo-LDOPTS=' '  # add '-Wl,-M' to see load map
+         set LIBRARIES='-Vaxlib'
+         breaksw
+      case pgf77:
+diff -Naur gamess/runall gamess-new/runall
+--- gamess/runall	2006-11-06 10:04:51.000000000 -0500
++++ gamess-new/runall	2006-12-13 09:13:42.000000000 -0500
+@@ -10,7 +10,7 @@
+ #  Edit this file to set the base path to GAMESS, and execute it to be
+ #  sure all the jobs TERMINATED NORMALLY, and got correct numbers too.
+ #
+-chdir /u1/mike/gamess
++#chdir /u1/mike/gamess
+ set VERNO=00
+ #
+ foreach NUM ( 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 \
+diff -Naur gamess/rungms gamess-new/rungms
+--- gamess/rungms	2006-11-19 18:09:11.000000000 -0500
++++ gamess-new/rungms	2006-12-13 09:13:42.000000000 -0500
+@@ -54,7 +54,7 @@
+ #       of using LoadLeveler via a "llgms" front end in ~/gamess/misc.
+ #
+ set TARGET=sockets
+-set SCR=/scr/$USER
++set SCR=`pwd`
+ #
+ set JOB=$1      # name of the input file xxx.inp, give only the xxx part
+ set VERNO=$2    # revision number of the executable created by 'lked' step
+@@ -114,14 +114,14 @@
+ #
+ set echo
+ #                        ASCII input files (see explanation above)
+-setenv ERICFMT ~mike/gamess/ericfmt.dat
+-setenv MCPPATH ~mike/gamess/mcpdata
++setenv ERICFMT /usr/share/gamess/ericfmt/ericfmt.dat
++setenv MCPPATH /usr/share/gamess/mcpdata
+ setenv  EXTBAS /dev/null
+ setenv  NUCBAS /dev/null
+ #
+-setenv IRCDATA ~$USER/scr/$JOB.irc
++setenv IRCDATA $SCR/$JOB.irc
+ setenv   INPUT $SCR/$JOB.F05
+-setenv   PUNCH ~$USER/scr/$JOB.dat
++setenv   PUNCH $SCR/$JOB.dat
+ setenv  AOINTS $SCR/$JOB.F08
+ setenv  MOINTS $SCR/$JOB.F09
+ setenv DICTNRY $SCR/$JOB.F10
+@@ -151,8 +151,8 @@
+ setenv  SOINTY $SCR/$JOB.F32
+ setenv  SOINTZ $SCR/$JOB.F33
+ setenv  SORESC $SCR/$JOB.F34
+-setenv   SIMEN ~$USER/scr/$JOB.simen
+-setenv  SIMCOR ~$USER/scr/$JOB.simcor
++setenv   SIMEN $SCR/$JOB.simen
++setenv  SIMCOR $SCR/$JOB.simcor
+ setenv GCILIST $SCR/$JOB.F37
+ setenv HESSIAN $SCR/$JOB.F38
+ setenv SOCCDAT $SCR/$JOB.F40
+@@ -332,7 +332,7 @@
+    if ($os == HP-UX)   set GMSPATH=/zr/mike/gamess
+    if ($os == IRIX)    set GMSPATH=/home/hbar4/people/schmidt/gamess
+    if ($os == IRIX64)  set GMSPATH=/home/hbar4/people/schmidt/gamess
+-   if ($os == Linux)   set GMSPATH=/cu/mike/gamess
++   if ($os == Linux)   set GMSPATH=/usr/bin
+    if ($os == OSF1)    set GMSPATH=/au/mike/gamess
+    if ($os == SunOS)   set GMSPATH=/hf/mike/gamess
+ #       special compilation for my old Sun (uname also replies SunOS)
diff --git a/sci-chemistry/gamess/gamess-20060907.4.ebuild b/sci-chemistry/gamess/gamess-20060907.4.ebuild
new file mode 100644
index 000000000000..b9302483f147
--- /dev/null
+++ b/sci-chemistry/gamess/gamess-20060907.4.ebuild
@@ -0,0 +1,217 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/gamess-20060907.4.ebuild,v 1.1 2006/12/14 14:52:07 markusle Exp $
+
+inherit eutils toolchain-funcs fortran flag-o-matic
+
+DESCRIPTION="A powerful quantum chemistry package"
+LICENSE="gamess"
+HOMEPAGE="http://www.msg.ameslab.gov/GAMESS/GAMESS.html"
+SRC_URI="${P}.tar.gz"
+
+SLOT="0"
+KEYWORDS="~ppc ~x86"
+IUSE="hardened blas"
+
+RESTRICT="fetch"
+
+DEPEND="app-shells/tcsh
+	hardened? ( sys-apps/paxctl )
+	blas? ( virtual/blas )"
+
+RDEPEND="app-shells/tcsh
+	net-misc/openssh"
+
+S="${WORKDIR}/${PN}"
+
+GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html"
+GAMESS_VERSION="7 SEP 2006 (R4)"
+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}/${P}.tar.gz"
+	echo
+}
+
+pkg_setup() {
+	fortran_pkg_setup
+
+	# blas and ifc don't go together
+	if use blas && [[ "${FORTRANC}" = "ifc" ]]; then
+		echo
+		ewarn "${PN} can not be compiled with USE=blas and ifc."
+		ewarn "Linking against GAMESS' internal blas instead."
+		echo
+	fi
+}
+
+src_unpack() {
+	unpack ${A}
+
+	# apply LINUX-arch patches to gamess makesfiles
+	epatch "${FILESDIR}"/${P}.gentoo.patch
+
+	# for hardened-gcc let't turn off ssp, since it breakes
+	# a few routines
+	cd "${S}"
+	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"
+
+	# 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
+
+	# use proper blas 
+	if ! use blas || [[ "${FORTRANC}" = "ifc" ]]; then
+		sed -e "s|/usr/lib/libblas.a|/usr/lib/dontuselibblas.a|" \
+			-i lked || die "Failed to adjust blas in lked"
+	fi
+
+	# fix up GAMESS' linker script;
+	sed -e "s/gentoo-g77/${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 ${PN}.00.x 2> /dev/null || \
+			die "paxctl failed on actvte.x"
+	fi
+}
+
+src_install() {
+	cd "${S}"
+
+	# 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/${PN}/mcpdata
+	doins mcpdata/* || die "Failed installing mcpdata"
+
+	# install the tests the user should run, and
+	# fix up the runscript; also grab a copy of rungms
+	# so the user is ready to run the tests
+	insinto /usr/share/${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
+}