diff options
Diffstat (limited to 'sci-chemistry')
| -rw-r--r-- | sci-chemistry/freeon/ChangeLog | 8 | ||||
| -rw-r--r-- | sci-chemistry/freeon/Manifest | 1 | ||||
| -rw-r--r-- | sci-chemistry/freeon/files/freeon-2012.05.03-no_internal_libs.patch | 50 | ||||
| -rw-r--r-- | sci-chemistry/freeon/files/freeon-9999-no_internal_libs.patch | 47 | ||||
| -rw-r--r-- | sci-chemistry/freeon/freeon-2012.05.03.ebuild | 53 | ||||
| -rw-r--r-- | sci-chemistry/freeon/freeon-9999.ebuild | 9 | ||||
| -rw-r--r-- | sci-chemistry/nwchem/ChangeLog | 6 | ||||
| -rw-r--r-- | sci-chemistry/nwchem/Manifest | 1 | ||||
| -rw-r--r-- | sci-chemistry/nwchem/files/nwchem-6.3-html_doc.patch | 82 | ||||
| -rw-r--r-- | sci-chemistry/nwchem/nwchem-6.3.ebuild | 146 |
10 files changed, 403 insertions, 0 deletions
diff --git a/sci-chemistry/freeon/ChangeLog b/sci-chemistry/freeon/ChangeLog index 25af9d785..4e266dee5 100644 --- a/sci-chemistry/freeon/ChangeLog +++ b/sci-chemistry/freeon/ChangeLog @@ -2,6 +2,14 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*freeon-2012.05.03 (30 May 2013) + + 30 May 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + +freeon-2012.05.03.ebuild, freeon-9999.ebuild, + +files/freeon-2012.05.03-no_internal_libs.patch, + +files/freeon-9999-no_internal_libs.patch: + Internal hdf5 and lapack removed, the ebuild of the latest snapshot added. + 22 Feb 2013; Justin Lecher <jlec@gentoo.org> freeon-9999.ebuild, metadata.xml: Add missing dep on virtual/pkgconfig; bump to eapi=5; use pkg-config to diff --git a/sci-chemistry/freeon/Manifest b/sci-chemistry/freeon/Manifest new file mode 100644 index 000000000..8cf18b96f --- /dev/null +++ b/sci-chemistry/freeon/Manifest @@ -0,0 +1 @@ +DIST freeon-beta-2012-05-03.tar.bz2 15259173 SHA256 48a4657fd99aed25f90fd68e50e515b691b5c09d2b7c8305ddfb35bd1d2ba17c SHA512 30b5d5406df3eb0bd44166e78e16df2013e40b024f0350caefaf08d5c157308896d6ade66a7184f7c8e93c5db6c39c7f3a73340d48b06c5acb6272de525ce18a WHIRLPOOL 55aa72b03b414be40987fab416bf17c3cc4f9b2783501830ffc8c27b987c73fa471878024f04139266c69d9c76f16476737b2241f294ec9b32f828d831b0b7ac diff --git a/sci-chemistry/freeon/files/freeon-2012.05.03-no_internal_libs.patch b/sci-chemistry/freeon/files/freeon-2012.05.03-no_internal_libs.patch new file mode 100644 index 000000000..e37622b0e --- /dev/null +++ b/sci-chemistry/freeon/files/freeon-2012.05.03-no_internal_libs.patch @@ -0,0 +1,50 @@ +diff -Naurp freeon-beta-2012-05-03.orig/Makefile.am freeon-beta-2012-05-03/Makefile.am +--- freeon-beta-2012-05-03.orig/Makefile.am 2012-05-04 03:53:04.000000000 +0000 ++++ freeon-beta-2012-05-03/Makefile.am 2013-05-29 14:42:07.791473885 +0000 +@@ -5,18 +5,9 @@ ACLOCAL_AMFLAGS = -I m4 + CPP = @CPP@ + AM_CPPFLAGS = @AM_CPPFLAGS@ + +-if INTERNAL_LAPACK +-INTERNAL_LAPACK_DIRS = lapack +-endif ++SUBDIRS = Modules FreeON SCFeqs OneE QCTC HiCu TwoE ONX PostProcessing BasisSets tests Validate + +-if INTERNAL_HDF5 +-INTERNAL_HDF5_DIRS = hdf5-1.8.3 +-HDF5_INCLUDES = -I$(srcdir)/hdf5-1.8.3/src -I$(builddir)/hdf5-1.8.3/src +-endif +- +-SUBDIRS = $(INTERNAL_LAPACK_DIRS) $(INTERNAL_HDF5_DIRS) Modules FreeON SCFeqs OneE QCTC HiCu TwoE ONX PostProcessing BasisSets tests Validate +- +-DIST_SUBDIRS = $(SUBDIRS) lapack hdf5-1.8.3 ++DIST_SUBDIRS = $(SUBDIRS) + + EXTRA_DIST = fix_localversion.sh localversion FreeON.bibtex $(top_builddir)/latex/refman.pdf + +--- freeon-beta-2012-05-03.orig/configure.ac 2012-05-04 04:38:47.000000000 +0000 ++++ freeon-beta-2012-05-03/configure.ac 2013-05-29 15:04:02.886109082 +0000 +@@ -855,7 +855,6 @@ AC_MSG_RESULT([${use_internal_hdf5}]) + + AM_CONDITIONAL(INTERNAL_HDF5, [test "${use_internal_hdf5}" = "yes"]) + +-AC_CONFIG_SUBDIRS([hdf5-1.8.3]) + + if test "${use_internal_hdf5}" = "yes"; then + +@@ -1027,15 +1026,6 @@ Makefile + documentation/main_page.h + FreeON/Makefile + Modules/Makefile +-lapack/Makefile +-lapack/install/Makefile +-lapack/blas/Makefile +-lapack/lapack/Makefile +-lapack/blas_testing/Makefile +-lapack/lapack_testing/Makefile +-lapack/lapack_testing/lin/Makefile +-lapack/lapack_testing/eig/Makefile +-lapack/lapack_testing/matgen/Makefile + SCFeqs/Makefile + OneE/Makefile + QCTC/Makefile diff --git a/sci-chemistry/freeon/files/freeon-9999-no_internal_libs.patch b/sci-chemistry/freeon/files/freeon-9999-no_internal_libs.patch new file mode 100644 index 000000000..a908aa7d9 --- /dev/null +++ b/sci-chemistry/freeon/files/freeon-9999-no_internal_libs.patch @@ -0,0 +1,47 @@ +diff -Naurp freeon-9999.orig/Modules/Makefile.am freeon-9999/Modules/Makefile.am +--- freeon-9999.orig/Modules/Makefile.am 2013-05-28 08:09:39.000000000 +0000 ++++ freeon-9999/Modules/Makefile.am 2013-05-29 14:32:24.879721200 +0000 +@@ -1,17 +1,5 @@ + include $(top_srcdir)/make.inc + +-if INTERNAL_LAPACK +-INTERNAL_LAPACK_DIRS = lapack +-endif +- +-if INTERNAL_HDF5 +-INTERNAL_HDF5_DIRS = hdf5-1.8.3 +-HDF5_INCLUDES = -I$(srcdir)/hdf5-1.8.3/src -I$(builddir)/hdf5-1.8.3/src +-endif +- +-DIST_SUBDIRS = lapack hdf5-1.8.3 +-SUBDIRS = $(INTERNAL_HDF5_DIRS) $(INTERNAL_LAPACK_DIRS) +- + if USE_DYNAMIC_LINKING + lib_LTLIBRARIES = libfreeonmodules.la + else +--- freeon-9999.orig/configure.ac 2013-05-29 15:34:16.000000000 +0000 ++++ freeon-9999/configure.ac 2013-05-29 15:36:22.000063299 +0000 +@@ -870,7 +870,6 @@ AM_CONDITIONAL(INTERNAL_HDF5, [test "${u + if test "${use_internal_hdf5}" = "yes"; then + + AC_DEFINE(HAVE_INTERNAL_HDF5, 1, [Use the inernal hdf5 library.]) +- AC_CONFIG_SUBDIRS([Modules/hdf5-1.8.3]) + + else + +@@ -1069,15 +1068,6 @@ config_localversion.h + Makefile + FreeON/Makefile + Modules/Makefile +-Modules/lapack/Makefile +-Modules/lapack/install/Makefile +-Modules/lapack/blas/Makefile +-Modules/lapack/lapack/Makefile +-Modules/lapack/blas_testing/Makefile +-Modules/lapack/lapack_testing/Makefile +-Modules/lapack/lapack_testing/lin/Makefile +-Modules/lapack/lapack_testing/eig/Makefile +-Modules/lapack/lapack_testing/matgen/Makefile + SCFeqs/Makefile + OneE/Makefile + QCTC/Makefile diff --git a/sci-chemistry/freeon/freeon-2012.05.03.ebuild b/sci-chemistry/freeon/freeon-2012.05.03.ebuild new file mode 100644 index 000000000..99805e0dc --- /dev/null +++ b/sci-chemistry/freeon/freeon-2012.05.03.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=1 + +FORTRAN_STANDARD=90 + +inherit autotools-utils fortran-2 + +REAL_PN="${PN}-beta" +REAL_PV="${PV//./-}" + +DESCRIPTION="an experimental suite of programs for linear scaling quantum chemistry." +HOMEPAGE="http://www.freeon.org" +SRC_URI="http://download.savannah.gnu.org/releases/${PN}/${REAL_PN}-${REAL_PV}.tar.bz2" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +RDEPEND=" + sys-libs/zlib + sci-libs/hdf5 + virtual/blas + virtual/lapack" +DEPEND="${DEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${REAL_PN}-${REAL_PV}" + +src_prepare() { + # Get rid of the obsolete internal hdf5 + rm -r "${S}"/hdf5-1.8.3 + # as well as of the internal lapack + rm -r "${S}"/lapack + epatch "${FILESDIR}"/"${P}"-no_internal_libs.patch + eautoreconf +} + +src_configure() { + local myeconfargs=( + --disable-internal-hdf5 + --disable-static-binaries + --disable-internal-lapack + --with-lapacklibs="$($(tc-getPKG_CONFIG) --libs lapack)" + ) + #TODO mv BasisSets from /usr to /usr/share/freeon/ + autotools-utils_src_configure +} diff --git a/sci-chemistry/freeon/freeon-9999.ebuild b/sci-chemistry/freeon/freeon-9999.ebuild index 2fe44e90d..369e063f8 100644 --- a/sci-chemistry/freeon/freeon-9999.ebuild +++ b/sci-chemistry/freeon/freeon-9999.ebuild @@ -30,6 +30,15 @@ RDEPEND=" DEPEND="${DEPEND} virtual/pkgconfig" +src_prepare() { + # Get rid of the obsolete internal hdf5 + rm -r "${S}"/Modules/hdf5-1.8.3 + # as well as of the internal lapack + rm -r "${S}"/Modules/lapack + epatch "${FILESDIR}"/"${P}"-no_internal_libs.patch + eautoreconf +} + src_configure() { local myeconfargs=( --disable-internal-hdf5 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 +} |