Version Bump

Package-Manager: portage-2.1.9.24/cvs/Linux x86_64

6 files changed, 542 insertions, 7 deletions

diff --git a/sci-chemistry/cns/ChangeLog b/sci-chemistry/cns/ChangeLog
index f9a32a5912a6..ddf3bacbbbc6 100644
--- a/sci-chemistry/cns/ChangeLog
+++ b/sci-chemistry/cns/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/cns
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.25 2010/11/16 20:05:49 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.26 2010/11/17 13:10:04 jlec Exp $
+
+*cns-1.3 (17 Nov 2010)
+
+  17 Nov 2010; Justin Lecher <jlec@gentoo.org> +files/1.3-delete.patch,
+  +files/1.3-gentoo.patch, +files/cns_solve_env_sh-1.3, +cns-1.3.ebuild:
+  Version Bump
 
 *cns-1.2.1-r5 (16 Nov 2010)
 
diff --git a/sci-chemistry/cns/Manifest b/sci-chemistry/cns/Manifest
index 6ba9f342d1fd..7da8baa911d8 100644
--- a/sci-chemistry/cns/Manifest
+++ b/sci-chemistry/cns/Manifest
@@ -9,7 +9,10 @@ AUX 1.2.1-aria2.3.patch 658 RMD160 a372156b7a783cb78c81aadae2eca5c64c9630e5 SHA1
 AUX 1.2.1-gentoo.patch 2411 RMD160 a82893524541961a9797fd2bb84982e609fda717 SHA1 7d3168a9cf7622923138022a5683aa65b5d5c34d SHA256 58972606d23d87fdeb08c9e37d9d5c536983e5a1ad4647dedd5b283ef67bc52c
 AUX 1.2.1-ifort.patch 5346 RMD160 106cf7dc7b4e13674fdf34ca0fd9af78effbc84b SHA1 26ccc71740ee2539352009f730b79b2ae20b5047 SHA256 bac35147159fac06fcb3a03a4f09c56224d4ee852b86a771121d98c42f3a9c65
 AUX 1.2.1-parallel.patch 641 RMD160 dffcaf7a4d7c79b9362640b64e677a7fde04ac80 SHA1 5de790cee7acf9ff4a87a61fdc866c330ef6d6f1 SHA256 7cd3312c35d2dbbd2146fdfa977f9866365c4a7be16787b1ba5d9807ff823d31
+AUX 1.3-delete.patch 448 RMD160 17b6ac426c11ae1832e7edf71a954e02434a5a46 SHA1 cd6f63a167dd9392c35d06ffdd31afd086e5c146 SHA256 aa61180b60fd008e3ba445bab5a4a6b0c4634b34fc5655be94ce07dc45abe958
+AUX 1.3-gentoo.patch 2536 RMD160 335c1e6374f3ad9b4340de223ce5e481e96ac875 SHA1 99072abd426614979eb7659a4fb2187bb5ffb3d2 SHA256 0cf8135a5680ebd3df0474d3b04e66c08e8b31547afeed91ceb3108dce8d8864
 AUX cns_solve_env_sh 7070 RMD160 4104b22476a61a80c7adae8a363da1dd4ab4f136 SHA1 30ba978f4862fd94d9fa939cbb7c3eb55ece46cd SHA256 da571cba2a2244e571870b1783fd6cdce1b595e14234cfb43011e9e9eb50151c
+AUX cns_solve_env_sh-1.3 7332 RMD160 eee19d64dc863e434159994282a78d8d576adf62 SHA1 050de938d0c0b4d1e497b03ff196416e416a0da7 SHA256 88127d99380544e502dfe3b3a7788102a7f6b30e7245b26e5e204b8b611bbc1d
 DIST aria2.2.tar.gz 1710084 RMD160 b96a900befd5521649ccce84d4d5b93d30709799 SHA1 faa5ff9e7682026afc334f1c8b3b10259a5e69f9 SHA256 a1695ee11b06a045c4b4bb9f0113d1e48c86e12d4149c0dcb505ca894069d054
 DIST aria2.3.1.tar.gz 1833973 RMD160 f2ee0bfc7e3164b5c34c81abb74256c5d76f53d7 SHA1 b257094bdaf6ba5b64645b8251d9243654e6d0fc SHA256 cc45ed2d66182cf0ee197a7cf3bc7edd8d5043d95cdcd19e1cec9aeb82c2fdbc
 DIST cns_solve_1.1_basic_inputs.tar.gz 5049767 RMD160 eb5686a006d53cf269456eaecd7507842c8a10eb SHA1 255e7c5170168f9e032ef9e84a870eddf176f4ce SHA256 916d86d96159bd945a3b05e26c71af0cc6097234776385630f618fa2641cf3eb
@@ -18,6 +21,7 @@ DIST cns_solve_1.1_test.tar.gz 2852870 RMD160 2f7e7b5ed4e603b2459944a8991829d136
 DIST cns_solve_1.21_all-mp.tar.gz 32748040 RMD160 0da9c1858e858474a8798149b7692b9e097adc9e SHA1 3ba32a6622b55dfff397b6844e8b8a594124a482 SHA256 7ab464e20932eb024ba6378738da77a4a03642d63b0ca9772b612a7cf27baec1
 DIST cns_solve_1.21_all.tar.gz 32739912 RMD160 ab763373923264497d1ccb507cab23b2e1af9826 SHA1 93059805e14f0482cf58755daecc52cf97863215 SHA256 a581c6a0e9e5ffd45f025520959921d7ba91bb5d1e6569f1c81e709bb6f87c81
 DIST cns_solve_1.2_all.tar.gz 30456531 RMD160 45cff57b3f026d730032cfc1c9476880f7cc81ab SHA1 1611ad499746993a9d210e6053e1cdd1553848a7 SHA256 230847d8e00def4b55dda8c50d9148bca11a88ed6bc575e735041c91f8fff064
+DIST cns_solve_1.3_all.tar.gz 61208156 RMD160 430e733e05166330b93977e48b72546c4ddabadd SHA1 b708e3006627642279ae571c31d6ec013adaa4c6 SHA256 de5c0be8ab924f5cbd57b1d651fcfea32a76766b7ff4af69556203191b4e40b6
 EBUILD cns-1.1.ebuild 3598 RMD160 c659528cda734552ca1faa9bc85c371b92d90d46 SHA1 e891a1be5f873e869bce5a6b617bbfd54a7aa71d SHA256 2be38322ddc333590c4d891f675921cabb0e18ef795042c1c4a849beb0793f6b
 EBUILD cns-1.2-r1.ebuild 4467 RMD160 cc3f1a26a8c28c111f25b74572dc4af3bb1d56c9 SHA1 f4da145be4190c1837e3262291f75c9eeaa3ef2d SHA256 ac40399a59987612e7602811cb79fdb4ae0295d23222afb6947ad1b79f5a8238
 EBUILD cns-1.2.1-r1.ebuild 5585 RMD160 d25d66002ffe133c390912e265f81aae860134c9 SHA1 239355135deb0213fe9bb9c85c480e3bce86a887 SHA256 9c91c6093b03f28c7c59cd73aa08c32397867fce5bfc28a6f1b5534a92c73ec4
@@ -27,14 +31,13 @@ EBUILD cns-1.2.1-r4.ebuild 6582 RMD160 544cf18f4dd459c7d2325da7998fef6db0eebaa3
 EBUILD cns-1.2.1-r5.ebuild 6589 RMD160 0faf1a389e72ef6b75a17930ccc814ec6777926c SHA1 bc14809d78f7bcbbea8dbb31ed5a4c57aa25f93c SHA256 fd257513ef87379d509c7f7ed55ab98dbafbc15d297d0c01cc50e5bb02f8686b
 EBUILD cns-1.2.1.ebuild 5620 RMD160 84fae2bc1f0780f77b931ee23a18acdd7353e766 SHA1 4b58160d9a20c103a7f443491ed5e1d5bade2afe SHA256 8504163c5874f0e90582ef37a44800ec2dbf9b112282682c237236e708ed79cf
 EBUILD cns-1.2.ebuild 3497 RMD160 9e097171ebd44f1a7e5dd317beeb6b65aefac2f6 SHA1 3afc4b415d2ef559b717843a05bc6afb8ee651a2 SHA256 1a6094c8bca3797e62c375a2370cc7425e9c1dd1106d20f202681bc5a87da1fc
-MISC ChangeLog 4500 RMD160 4d0cfea2f8c7a9798b000d9bd3ac5a30a8d806e1 SHA1 1aa7a55e53334007978f004beb65140a484b2d20 SHA256 a19abdc674b3431e08e86e9eb3607033c4d3bdf87aa563731bf3709a45c8d062
+EBUILD cns-1.3.ebuild 5763 RMD160 719c446c9efb69ab36e308a8ea1673e22b1c9357 SHA1 e6921f1814aa51b8d6e757700fcba68f7bc2dd4f SHA256 cfa1b1f03c51cb3c0fbe60c7e3f81f2d55be0aed7950e6181b70ce492763efd2
+MISC ChangeLog 4679 RMD160 ce4873d827a347d47ae19a3bf5c51b215cfa2282 SHA1 c990b481eab917d844dba4152e758b47d8edb1ee SHA256 c9d306e158e161e223bdcd6fe26e8fa1399a90577b85e36b8a7343137ee1a291
 MISC metadata.xml 302 RMD160 d60d9cd875115eaba68ad4b504bff76b39a136b0 SHA1 ecdd8feeea2de489927403f1941acfc582c17222 SHA256 a374144760a8ac1f72b1c625c41f98cee3f74511c964133bda119da580664c50
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diff --git a/sci-chemistry/cns/cns-1.3.ebuild b/sci-chemistry/cns/cns-1.3.ebuild
new file mode 100644
index 000000000000..22e5224782de
--- /dev/null
+++ b/sci-chemistry/cns/cns-1.3.ebuild
@@ -0,0 +1,208 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.3.ebuild,v 1.1 2010/11/17 13:10:04 jlec Exp $
+
+EAPI="3"
+
+inherit eutils fortran toolchain-funcs versionator flag-o-matic
+
+MY_PN="${PN}_solve"
+MY_PV="$(delete_version_separator 2)"
+MY_P="${MY_PN}_${MY_PV}"
+
+DESCRIPTION="Crystallography and NMR System"
+HOMEPAGE="http://cns.csb.yale.edu/"
+SRC_URI="${MY_P}_all.tar.gz
+	aria? ( aria2.3.1.tar.gz )"
+
+SLOT="0"
+LICENSE="cns"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="aria openmp"
+
+RDEPEND="app-shells/tcsh"
+DEPEND="${RDEPEND}"
+PDEPEND="aria? ( ~sci-chemistry/aria-2.3.1 )"
+
+RESTRICT="fetch"
+S="${WORKDIR}/${MY_P}"
+
+FORTRAN="gfortran ifc"
+
+pkg_nofetch() {
+	elog "Fill out the form at http://cns.csb.yale.edu/cns_request/"
+	use aria && elog "and http://aria.pasteur.fr/"
+	elog "and place these files:"
+	elog ${A}
+	elog "in ${DISTDIR}."
+}
+
+pkg_setup() {
+	fortran_pkg_setup
+
+	if [[ $(tc-getCC) == *gcc* ]] &&
+		( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] ||
+		! built_with_use sys-devel/gcc openmp )
+	then
+		ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 "
+		ewarn "Switch CC to an OpenMP capable compiler"
+	fi
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-gentoo.patch \
+		"${FILESDIR}"/${PV}-delete.patch
+
+	if use aria; then
+		pushd "${WORKDIR}"/aria* >& /dev/null
+			# Update the cns sources in aria for version 1.2.1
+			epatch "${FILESDIR}"/1.2.1-aria2.3.patch
+
+			# Update the code with aria specific things
+			cp -rf cns/src/* "${S}"/source/
+		popd >& /dev/null
+	fi
+
+	# the code uses Intel-compiler-specific directives
+	if [[ ${FORTRANC} == gfortran ]]; then
+		use openmp && \
+			OMPLIB="-lgomp" && append-flags -fopenmp
+		COMP="gfortran"
+		use amd64 && \
+			append-fflags -fdefault-integer-8
+	else
+		use openmp && OMPLIB="-liomp5" && \
+			append-flags -openmp && append-ldflags -openmp
+		COMP="ifort"
+		use amd64 && append-fflags -i8
+		append-fflags -Vaxlib
+		append-ldflags -Vaxlib
+	fi
+
+	use amd64 && \
+		append-cflags "-DINTEGER='long long int'"
+
+	# Set up location for the build directory
+	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
+	cp "${FILESDIR}"/cns_solve_env_sh-${PV} "${T}"/cns_solve_env_sh || die
+	sed -i \
+		-e "s:_CNSsolve_location_:${S}:g" \
+		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
+		"${S}"/cns_solve_env
+	sed -i \
+		-e "s:_CNSsolve_location_:${S}:g" \
+		-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \
+		"${T}"/cns_solve_env_sh
+
+	ebegin "Fixing shebangs..."
+		find "${S}" -type f \
+			-exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' \; || die
+		find . -name "Makefile*" \
+			-exec \
+				sed \
+					-e "s:^SHELL=/bin/sh:SHELL=${EPREFIX}/bin/sh:g" \
+					-e "s:/bin/ls:ls:g" \
+					-e "s:/bin/rm:rm:g" \
+					-i '{}' \; || die
+	eend
+}
+
+src_compile() {
+	local GLOBALS
+	local MALIGN
+
+	# Set up the compiler to use
+	pushd instlib/machine/unsupported/g77-unix 2>/dev/null
+	ln -s Makefile.header Makefile.header.${FORTRANC} || die
+	popd 2>/dev/null
+
+	# make install really means build, since it's expected to be used in-place
+	# -j1 doesn't mean we do no respect MAKEOPTS!
+	emake -j1 \
+		CC="$(tc-getCC)" \
+		CXX="$(tc-getCXX)" \
+		F77="${FORTRANC}" \
+		LD="${FORTRANC}" \
+		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
+		CXXFLAGS="${CXXFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
+		LDFLAGS="${LDFLAGS}" \
+		F77OPT="${FFLAGS:- -O2} ${MALIGN}" \
+		F77STD="${GLOBALS}" \
+		OMPLIB="${OMPLIB}" \
+		compiler="${COMP}" \
+		install \
+		|| die "emake failed"
+
+}
+
+src_test() {
+	# We need to force on g77 manually, because we can't get aliases working
+	# when we source in a -c
+	einfo "Running tests ..."
+	sh -c \
+		"export CNS_G77=ON; source ${T}/cns_solve_env_sh; make run_tests" \
+		|| die "tests failed"
+	einfo "Displaying test results ..."
+	cat "${S}"/*_g77/test/*.diff-test
+}
+
+src_install() {
+	cat >> "${T}"/66cns <<- EOF
+	CNS_SOLVE="${EPREFIX}/usr"
+	CNS_ROOT="${EPREFIX}/usr"
+	CNS_DATA="${EPREFIX}/usr/share/cns"
+	CNS_DOC="${EPREFIX}/usr/share/doc/cns-1.3"
+	CNS_LIB="${EPREFIX}/usr/share/cns/libraries"
+	CNS_MODULE="${EPREFIX}/usr/share/cns/modules"
+	CNS_TOPPAR="${EPREFIX}/usr/share/cns/libraries/toppar"
+	CNS_CONFDB="${EPREFIX}/usr/share/cns/libraries/confdb"
+	CNS_XTALLIB="${EPREFIX}/usr/share/cns/libraries/xtal"
+	CNS_NMRLIB="${EPREFIX}/usr/share/cns/libraries/nmr"
+	CNS_XRAYLIB="${EPREFIX}/usr/share/cns/libraries/xray"
+	CNS_XTALMODULE="${EPREFIX}/usr/share/cns/modules/xtal"
+	CNS_NMRMODULE="${EPREFIX}/usr/share/cns/modules/nmr"
+	CNS_HELPLIB="${EPREFIX}/usr/share/cns/helplib"
+	EOF
+
+	doenvd "${T}"/66cns || die
+
+	# Don't want to install this
+	rm -f "${S}"/*linux*/utils/Makefile
+
+	sed -i \
+		-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
+		"${S}"/bin/cns_web || die
+
+	newbin "${S}"/*linux*/bin/cns_solve* cns_solve \
+		|| die "install cns_solve failed"
+
+	# Can be run by either cns_solve or cns
+	dosym cns_solve /usr/bin/cns
+
+	dobin \
+		"${S}"/*linux*/utils/* \
+		"${S}"/bin/cns_{edit,header,import_cif,transfer,web} || die "install bin failed"
+
+	insinto /usr/share/cns
+	doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib "${S}"/bin/cns_info || die
+
+	dohtml \
+		-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
+		-f all_cns_info_template,omac,def \
+		-r doc/html/* || die
+	# Conflits with app-text/dos2unix
+	rm -f "${D}"/usr/bin/dos2unix || die
+}
+
+pkg_info() {
+	if use openmp; then
+		elog "Set OMP_NUM_THREADS to the number of threads you want."
+		elog "If you get segfaults on large structures, set the GOMP_STACKSIZE"
+		elog "variable if using gcc (16384 should be good)."
+	fi
+}
+
+pkg_postinst() {
+	pkg_info
+}
diff --git a/sci-chemistry/cns/files/1.3-delete.patch b/sci-chemistry/cns/files/1.3-delete.patch
new file mode 100644
index 000000000000..cbddf4289158
--- /dev/null
+++ b/sci-chemistry/cns/files/1.3-delete.patch
@@ -0,0 +1,13 @@
+diff --git a/utils/cluster_struc.cpp b/utils/cluster_struc.cpp
+index b64467a..5f727db 100644
+--- a/utils/cluster_struc.cpp
++++ b/utils/cluster_struc.cpp
+@@ -173,7 +173,7 @@ int main(int argc, char *argv[]) {
+         for (int i = 0; i < nrstruc; i++) {
+           delete[] neighbor[i];
+         }
+-        delete[] neighbor, neighborcount;
++        delete[] neighbor, delete[] neighborcount;
+         return 5;
+       }
+       if (rmsd < cutoff) {
diff --git a/sci-chemistry/cns/files/1.3-gentoo.patch b/sci-chemistry/cns/files/1.3-gentoo.patch
new file mode 100644
index 000000000000..95961fe6ff0c
--- /dev/null
+++ b/sci-chemistry/cns/files/1.3-gentoo.patch
@@ -0,0 +1,76 @@
+diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto
+index 0d0dd3e..dd4b680 100644
+--- a/instlib/source/Makefile.proto
++++ b/instlib/source/Makefile.proto
+@@ -11,6 +11,8 @@
+ 
+ SHELL=/bin/sh
+ 
++cns_string=`date "+%y%m%d%H%M"`
++
+ # commands
+ RM = /bin/rm
+ 
+@@ -19,32 +21,26 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o
+ 
+ # the default is to make the cns executable
+ cns_solve:
+-	@ make -k printflags       F77BUG="$(debug)" DEBUG="$(debug)"
+-	@ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)"
+-	@ make -k exepurge
++	@ make printflags       F77BUG="$(debug)" DEBUG="$(debug)"
++	@ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)"
++	@ make exepurge
+ 
+ # rule for the fortran routines
+ $(OBJS): 
+-	@ echo "compiling: $(@:.o=.f)"; \
+-	  $(F77) -c $(F77FLAGS) $(@:.o=.f)
++	$(F77) -c $(F77FLAGS) $(@:.o=.f)
+ 
+ # rule for the dynamic memory allocation C routines
+ dmemory.o: dmemory.c
+-	@ echo ; echo "compiling: $?"
+-	@ $(CC) -c $(CCFLAGS) $?
++	$(CC) -c $(CCFLAGS) $?
+ 
+ # rule for the machine specific C routines
+ machine_c.o: machine_c.c
+-	@ echo ; echo "compiling: $?"
+-	@ $(CC) -c $(CCFLAGS) $?
++	$(CC) -c $(CCFLAGS) $?
+ 
+ # rule for the executable itself
+ ../bin/cns_solve: $(DEPENDS) 
+-	@ echo ; echo "linking: cns_solve"; echo
+-	@ cns_string=`date "+%y%m%d%H%M"`; \
+-	  $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \
+-	                                      $(LDFLAGS) \
+-	                                      $(CNS_FFTDIR) $(CNS_FFTLIB); \
++	$(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \
++	                                      $(CNS_FFTDIR) $(CNS_FFTLIB) $(OMPLIB); \
+ 	  if [ -x cns_solve-$$cns_string.exe ]; \
+ 	    then echo "created executable file cns_solve-$$cns_string.exe"; \
+ 	         echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \
+@@ -59,7 +55,7 @@ printflags:
+ 	@ echo; echo "flags:"; \
+ 	  echo " fortran -> [$(F77)] $(F77FLAGS)"; \
+ 	  echo "       c -> [$(CC)] $(CCFLAGS)"; \
+-	  echo "    link -> [$(LD)] $(LDFLAGS) $(CNS_FFTDIR) $(CNS_FFTLIB)"; \
++	  echo "    link -> [$(LD)] $(LDFLAGS) $(CNS_FFTDIR) $(CNS_FFTLIB)  $(OMP_LIB)"; \
+ 	  echo
+ 
+ # regenerate makefiles
+diff --git a/instlib/utils/Makefile b/instlib/utils/Makefile
+index 98de84f..2b0a9ce 100644
+--- a/instlib/utils/Makefile
++++ b/instlib/utils/Makefile
+@@ -28,7 +28,7 @@ utils:
+ 	$(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK)
+ 
+ .cpp:
+-	$(CPP) -o $@ $(CCFLAGS) $(@).cpp $(CCLINK)
++	$(CXX) -o $@ $(CXXFLAGS) $(@).cpp $(CCLINK)
+ 
+ .l:
+ 	lex $(@).l
diff --git a/sci-chemistry/cns/files/cns_solve_env_sh-1.3 b/sci-chemistry/cns/files/cns_solve_env_sh-1.3
new file mode 100644
index 000000000000..12368f87b596
--- /dev/null
+++ b/sci-chemistry/cns/files/cns_solve_env_sh-1.3
@@ -0,0 +1,229 @@
+#!/bin/sh
+#
+# This file sets up the appropriate environmental variables and paths
+# for CNSsolve. In the case of the same machines with different versions
+# of the OS, backward compatibility is assumed - ie. a later version will
+# be setup for a previous version of the OS if nothing else is available.
+#
+#   written by: Paul Adams
+#
+#   copyright Yale University
+#
+# ==========================================================================
+#
+# >>>>>> Important: define the location of the CNSsolve directory <<<<<<
+#
+# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY
+
+	CNS_SOLVE=_CNSsolve_location_
+
+#
+# ==========================================================================
+#
+# full expansion of the CNS_SOLVE variable prior to use.
+#
+export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE
+#
+# ==========================================================================
+#
+# get the machine architecture
+#
+if [ -d $CNS_SOLVE ]; then
+  if [ ! "$CNS_ARCH" ]; then
+    export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch`
+  fi
+else
+  export CNS_ARCH; CNS_ARCH='unknown'
+fi
+#
+# ==========================================================================
+#
+# system variables for OpenMP
+#
+# The default stack sizes are usually insufficient, especially when
+# CNS is compiled using OpenMP. If the stack sizes are too
+# small segfaults may occur. Recommended setting for "stacksize":
+limit stacksize unlimited
+#
+# KMP_STACKSIZE is specific for Intel ifort, icc:
+##setenv KMP_STACKSIZE 256m
+#
+# OMP_STACKSIZE is used by all compilers:
+setenv OMP_STACKSIZE 256m
+#
+# Uncomment the following line and change as appropriate to set the number 
+# of processors (threads) to use. 
+###setenv OMP_NUM_THREADS 4
+#
+# ==========================================================================
+#
+# general environmental variables
+#
+export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries
+export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules
+export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar
+export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb
+export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal
+export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr
+export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray
+export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal
+export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr
+export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib
+#
+# general user aliases
+#
+cns_web () { $CNS_SOLVE/bin/cns_web; }
+cns_header () { $CNS_SOLVE/bin/cns_header; }
+cns_info () { cat $CNS_SOLVE/bin/cns_info; }
+cns_transfer () { $CNS_SOLVE/bin/cns_transfer; }
+if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then
+  cns_edit () { $CNS_SOLVE/bin/cns_edit_local; }
+else
+  cns_edit () { $CNS_SOLVE/bin/cns_edit; }
+fi
+#
+# g77 compilation and use
+#
+g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; }
+g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; }
+#
+# developer aliases
+#
+run_tests () { $CNS_SOLVE/bin/run_tests; }
+run_diffs () { $CNS_SOLVE/bin/run_diffs; }
+maketar () { $CNS_SOLVE/bin/maketar; }
+create_patch () { $CNS_SOLVE/bin/create_patch; }
+#
+#
+# ==========================================================================
+#
+# to do expansions - unset noglob just in case user has it otherwise
+#
+set +f
+#
+# try to set up appropriate path
+#
+# first strip off any trailing information (eg. _g77)
+#
+CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'`
+#
+cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'`
+cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'`
+cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'`
+cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'`
+cns_minor=`echo $cns_major | sed -e 's/\./ /g'`
+#
+# if we are looking for a specific type of setup then limit search
+#
+cns_dirs=""
+if [ ! "$CNS_G77" ]; then
+  if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then
+    cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`"
+  fi
+else
+  CNS_ARCH="${CNS_ARCH}_g77"
+  if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then
+    cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`"
+  fi
+fi
+#
+# first look for an exact match (with os version)
+#
+#
+cns_found=0
+if [ -n "$cns_dirs" ]; then
+  for cns_dir in $cns_dirs ; do
+    cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'`
+    if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
+      if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \
+           $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ]; then
+        cns_archenv=$cns_dir
+        cns_found=1
+      fi
+    fi
+  done
+#
+#
+# now look for an exact match (without os version)
+#
+  if [ $cns_found -eq 0 ]; then
+    for cns_dir in $cns_dirs ; do
+      if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
+        if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \
+             $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then
+          cns_archenv=$cns_dir
+          cns_found=1
+        fi
+      fi
+    done
+  fi
+#
+# now look for a backwards compatible match (with os version major/minor)
+#
+  if [ $cns_found -eq 0 ]; then
+    for cns_dir in $cns_dirs ; do
+      if [ $cns_found -eq 0 ]; then
+        cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'`
+        if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
+          if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then
+	    osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'`
+            if [ $osv_test -eq 1 ]; then
+              cns_archenv=$cns_dir
+	      cns_found=1
+            fi
+          fi
+        fi
+      fi
+    done
+  fi
+#
+# now look for a wildcard match on cpu
+#
+  if [ $cns_found -eq 0 ]; then
+    cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'`
+    cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'`
+    for cns_dir in $cns_dirs ; do
+      if [ $cns_found -eq 0 ]; then
+        cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'`
+        cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'`
+        if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
+          if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \
+               $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then
+  	    cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'`
+            if [ $cpu_test -eq 1 ]; then
+              cns_archenv=$cns_dir
+	      cns_found=1
+            fi
+          fi
+        fi
+      fi
+    done
+  fi
+fi
+#
+# if found set environment
+#
+if [ $cns_found -eq 1 ]; then
+  #
+  # set installation and source directory
+  #
+  export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv
+  export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source
+  #
+  # path for CNSsolve utility programs
+  #
+  if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then
+    export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils`
+  fi
+  #
+  # path for CNSsolve executable if installed
+  #
+  if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then
+    export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin`
+  fi
+fi
+#
+unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor
+unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same
+unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test
+#