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authorHonza Macháček <Hloupy.Honza@centrum.cz>2013-05-30 15:21:59 +0200
committerHonza Macháček <Hloupy.Honza@centrum.cz>2013-05-30 15:21:59 +0200
commitbaefa0bf89ac382b08e24e32646c176a475b4add (patch)
tree107fc41fa5489651259655138afca2c01d5d25cb /sci-chemistry/nwchem
parentMoved to tree (diff)
downloadsci-baefa0bf89ac382b08e24e32646c176a475b4add.tar.gz
sci-baefa0bf89ac382b08e24e32646c176a475b4add.tar.bz2
sci-baefa0bf89ac382b08e24e32646c176a475b4add.zip
sci-chemistry/freeon improved, the ebuild of the latest snapshot added. sci-chemistry/nwchem bumped to 6.3, building docs allowed.
Diffstat (limited to 'sci-chemistry/nwchem')
-rw-r--r--sci-chemistry/nwchem/ChangeLog6
-rw-r--r--sci-chemistry/nwchem/Manifest1
-rw-r--r--sci-chemistry/nwchem/files/nwchem-6.3-html_doc.patch82
-rw-r--r--sci-chemistry/nwchem/nwchem-6.3.ebuild146
4 files changed, 235 insertions, 0 deletions
diff --git a/sci-chemistry/nwchem/ChangeLog b/sci-chemistry/nwchem/ChangeLog
index b6b85fcc2..687c7c722 100644
--- a/sci-chemistry/nwchem/ChangeLog
+++ b/sci-chemistry/nwchem/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*nwchem-6.3 (30 May 2013)
+
+ 30 May 2013; Honza Macháček <Hloupy.Honza@centrum.cz> +nwchem-6.3.ebuild,
+ +files/nwchem-6.3-html_doc.patch:
+ Version bumped to 6.3, adding the doc option attempted.
+
14 Mar 2013; François Bissey <francois.bissey@canterbury.ac.nz>
nwchem-6.1.1.ebuild:
Improving mpi linking. It will now work with openmpi as well.
diff --git a/sci-chemistry/nwchem/Manifest b/sci-chemistry/nwchem/Manifest
index c26a0a29d..56aeb6eca 100644
--- a/sci-chemistry/nwchem/Manifest
+++ b/sci-chemistry/nwchem/Manifest
@@ -1 +1,2 @@
DIST Nwchem-6.1.1-src.2012-06-27.tar.gz 77838112 SHA256 153a975e18fa88afbacfa2c7d4384e31bc25c43bd5c99c2f4074006a8e035dab SHA512 b2cc796f6fd0e37385a9b8c0a5dbc3c219849938b52809a616cb5c3fa5a3a54a7c61be215cf8975d1287d09ecfae1bedd41e69e445e61adb5a7aac505802170d WHIRLPOOL d6107522fadca8597d0fdff758169a2c25adb8da0ccfbad9a9f408708d0060922fef443f9c92ccd97b3772c70ba9fe90a1ec7c059de536e6a294719080c9bfaf
+DIST Nwchem-6.3-src.2013-05-17.tar.gz 112227871 SHA256 c8049adb14f198d3ee40e38ed6e00dd4d59ef7cf992c4d45f392172df217f378 SHA512 05cb37aae41746c56ab715a47830bdf336cfe469b5f1b492be369c620d300039529ea30ed75f885fc06a5d3a45a64297341555ea71ef5b56efcca14798dcf8d3 WHIRLPOOL 40d46a7bf7b99455219325a03fe72b426f60c058110aa3c17308b57be962210100b58bac6e2e99cfc60b4d7cf87f7e8c5fd712d3c815b260790ff58d59380f36
diff --git a/sci-chemistry/nwchem/files/nwchem-6.3-html_doc.patch b/sci-chemistry/nwchem/files/nwchem-6.3-html_doc.patch
new file mode 100644
index 000000000..fa0e8fad3
--- /dev/null
+++ b/sci-chemistry/nwchem/files/nwchem-6.3-html_doc.patch
@@ -0,0 +1,82 @@
+diff -Naurp old/doc/update_www new/doc/update_www
+--- doc/update_www 2013-05-18 00:40:51.000000000 +0000
++++ doc/update_www 2013-05-22 12:15:27.543414281 +0000
+@@ -16,7 +16,8 @@ set document = $argv[1]
+ echo Updating WWW pages for $document.tex
+ #............... public
+ #foreach WWWDIR (/msrc/www/pub/docs/nwchem/doc)
+-foreach WWWDIR (/msrc/emslweb/docs/nwchem/doc)
++#foreach WWWDIR (/msrc/emslweb/docs/nwchem/doc)
++foreach WWWDIR ("${NWCHEM_TOP}"/html)
+ #
+ # Now copy the revised source into the EMSL public WWW tree
+ echo "update_www: Public pages .. "
+diff -Naurp old/user/geometry.tex new/user/geometry.tex
+--- user/geometry.tex 2013-05-18 00:40:51.000000000 +0000
++++ user/geometry.tex 2013-05-23 13:00:44.234316049 +0000
+@@ -472,11 +472,11 @@ and angles.
+ \ifx\pdfoutput\undefined
+ \includegraphics[angle=270,width=6in]{zmat1.eps}
+ \else
+-\includegraphics[angle=0,width=6in]{zmat1.pdf}
++\includegraphics[angle=0,width=6in,bburx=509,bbury=201]{zmat1.pdf}
+ \fi
+ \end{latexonly}
+ \begin{htmlonly}
+-\psfig{figure=zmat1.eps,angle=270,width=6in}
++\epsfig{figure=zmat1.eps,angle=270,width=6in}
+ \end{htmlonly}
+ \caption{\label{fig:zmat1} Relationships between the centers, bond angle
+ and dihedral angle in Z-matrix input.}
+@@ -488,11 +488,11 @@ and dihedral angle in Z-matrix input.}
+ \ifx\pdfoutput\undefined
+ \includegraphics[angle=270,width=6in]{zmat2.eps}
+ \else
+-\includegraphics[angle=270,width=6in]{zmat2.pdf}
++\includegraphics[angle=270,width=6in,bburx=266,bbury=485]{zmat2.pdf}
+ \fi
+ \end{latexonly}
+ \begin{htmlonly}
+-\psfig{figure=zmat2.eps,angle=270,width=6in}
++\epsfig{figure=zmat2.eps,angle=270,width=6in}
+ \end{htmlonly}
+
+ \caption{\label{fig:zmat2} Relationships between the centers and two
+@@ -505,11 +505,11 @@ and dihedral angle in Z-matrix input.}
+ \ifx\pdfoutput\undefined
+ \includegraphics[angle=270,width=6in]{zmat3.eps}
+ \else
+-\includegraphics[angle=270,width=6in]{zmat3.pdf}
++\includegraphics[angle=270,width=6in,bburx=266,bbury=482]{zmat3.pdf}
+ \fi
+ \end{latexonly}
+ \begin{htmlonly}
+-\psfig{figure=zmat3.eps,angle=270,width=6in}
++\epsfig{figure=zmat3.eps,angle=270,width=6in}
+ \end{htmlonly}
+ \caption{\label{fig:zmat3} Relationships between the centers and two
+ bond angles in Z-matrix input with optional parameter specified as $-1$.}
+diff -Naurp old/user/titlepage.tex new/user/titlepage.tex
+--- user/titlepage.tex 2013-05-18 00:40:51.000000000 +0000
++++ user/titlepage.tex 2013-05-23 13:01:07.304152791 +0000
+@@ -19,7 +19,7 @@
+ {\bf\Large \nwchemmonth \ \nwchemyear}\\[1.0in]
+
+
+-%\psfig{figure=zsm.major.ps,height=4in,width=4in}
++%\epsfig{figure=zsm.major.ps,height=4in,width=4in}
+
+
+ \end{centering}
+diff -Naurp old/user/user.tex new/user/user.tex
+--- user/user.tex 2013-05-18 00:40:51.000000000 +0000
++++ user/user.tex 2013-05-23 13:00:04.961296411 +0000
+@@ -2,7 +2,7 @@
+ \input{top}
+ \usepackage[dvips]{graphicx}
+ \begin{htmlonly}
+-\usepackage{psfig}
++\usepackage{epsfig}
+ \end{htmlonly}
+
+
diff --git a/sci-chemistry/nwchem/nwchem-6.3.ebuild b/sci-chemistry/nwchem/nwchem-6.3.ebuild
new file mode 100644
index 000000000..380de67bb
--- /dev/null
+++ b/sci-chemistry/nwchem/nwchem-6.3.ebuild
@@ -0,0 +1,146 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+inherit eutils fortran-2 multilib python-single-r1 toolchain-funcs
+
+DATE="2013-05-17"
+
+DESCRIPTION="NWChem: Delivering High-Performance Computational Chemistry to Science"
+HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page"
+SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV}-src.${DATE}.tar.gz"
+
+LICENSE="ECL-2.0"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="mpi doc examples nwchem-tests python"
+
+RDEPEND="sys-fs/sysfsutils
+ python? ( ${PYTHON_DEPS} )"
+DEPEND="${RDEPEND}
+ virtual/fortran
+ app-shells/tcsh
+ mpi? ( virtual/mpi[fortran] )
+ doc? ( dev-texlive/texlive-latex
+ dev-tex/latex2html )"
+
+S="${WORKDIR}/${P}-src.${DATE}"
+
+pkg_setup() {
+ fortran-2_pkg_setup
+ use python && python-single-r1_pkg_setup
+}
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/nwchem-6.1.1-makefile.patch \
+ "${FILESDIR}"/nwchem-6.1.1-nwchemrc.patch \
+ "${FILESDIR}"/nwchem-6.1.1-adjust-dir-length.patch
+ use python && epatch "${FILESDIR}"/nwchem-6.1.1-python_makefile.patch
+ use doc && epatch "${FILESDIR}"/nwchem-6.3-html_doc.patch
+
+ sed \
+ -e "s:DBASIS_LIBRARY=\"'\$(SRCDIR)'\":DBASIS_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
+ -i src/basis/MakeFile src/basis/GNUmakefile || die
+ sed \
+ -e "s:DNWPW_LIBRARY=\"'\$(SRCDIR)'\":DNWPW_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
+ -i src/nwpw/libraryps/GNUmakefile || die
+ sed \
+ -e "s:-DCOMPILATION_DIR=\"'\$(TOPDIR)'\":-DCOMPILATION_DIR=\"''\":g" \
+ -i src/GNUmakefile src/MakeFile || die
+
+ if [[ $(tc-getFC) == *-*-*-*-gfortran ]]; then
+ sed \
+ -e "s:ifneq (\$(FC),gfortran):ifneq (\$(FC),$(tc-getFC)):g" \
+ -e "s:ifeq (\$(FC),gfortran):ifeq (\$(FC),$(tc-getFC)):g" \
+ -i src/config/makefile.h || die
+ fi
+}
+
+src_compile() {
+ export USE_SUBGROUPS=yes
+ if use mpi ; then
+ export MSG_COMMS=MPI
+ export USE_MPI=yes
+ export MPI_LOC=/usr
+ export MPI_INCLUDE=$MPI_LOC/include
+ export MPI_LIB=$MPI_LOC/$(get_libdir)
+ export LIBMPI="$(mpif90 -showme:link)"
+ fi
+ if [ "$ARCH" = "amd64" ]; then
+ export NWCHEM_TARGET=LINUX64
+ elif [ "$ARCH" = "ia64" ]; then
+ export NWCHEM_TARGET=LINUX64
+ elif [ "$ARCH" = "x86" ]; then
+ export NWCHEM_TARGET=LINUX
+ elif [ "$ARCH" = "ppc" ]; then
+ export NWCHEM_TARGET=LINUX
+ else
+ die "Unknown architecture"
+ fi
+ if use python ; then
+ if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ]; then
+ export USE_PYTHON64=yes
+ fi
+ export PYTHONHOME=/usr
+ export PYTHONVERSION=$(eselect python show|awk -Fpython '{ print $2 }')
+ export PYTHONPATH="./:${S}/contrib/python/"
+ export NWCHEM_MODULES="all python"
+ else
+ export NWCHEM_MODULES="all"
+ fi
+
+ cd src
+ emake \
+ DIAG=PAR \
+ FC=$(tc-getFC) \
+ CC=$(tc-getCC) \
+ CXX=$(tc-getCXX) \
+ NWCHEM_TOP="${S}" \
+ NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem"
+
+ if use doc; then
+ cd "${S}"/doc
+ emake \
+ DIAG=PAR \
+ NWCHEM_TOP="${S}" \
+ pdf html
+ fi
+}
+
+src_install() {
+ dobin bin/${NWCHEM_TARGET}/nwchem
+
+ insinto /usr/share/NWChem/basis/
+ doins -r src/basis/libraries src/data
+ insinto /usr/share/NWChem/nwpw
+ doins -r src/nwpw/libraryps
+
+ insinto /etc
+ doins nwchemrc
+
+ use examples && \
+ insinto /usr/share/NWChem/ && \
+ doins -r examples
+
+ use nwchem-tests && \
+ insinto /usr/share/NWChem && \
+ doins -r QA/tests
+
+ use doc && \
+ insinto /usr/share/doc/"${P}" && \
+ doins -r doc/nwahtml && \
+ doins -r html
+
+}
+
+pkg_postinst() {
+ echo
+ elog "The user will need to link \$HOME/.nwchemrc to /etc/nwchemrc"
+ elog "or copy it in order to tell NWChem the right position of the"
+ elog "basis library and other necessary data."
+ echo
+}