* [gentoo-commits] proj/sci:master commit in: sci-physics/atompaw/, sci-libs/bigdft/, sci-libs/bigdft/files/, ...
@ 2013-01-17 14:39 Honza Macháček
0 siblings, 0 replies; only message in thread
From: Honza Macháček @ 2013-01-17 14:39 UTC (permalink / raw
To: gentoo-commits
commit: 1dd1021d6608584b3157e00c529cea7bcc52abd4
Author: Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Thu Jan 17 14:39:36 2013 +0000
Commit: Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Thu Jan 17 14:39:36 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1dd1021d
sci-physics/openmx added, version 3.6. sci-physics/atompaw version bumped to 3.0.1.9. New versions of sci-physics/abinit and sci-libs/bigdft added, but sci-libs/bigdft-1.7_pre12 is a version from the Abinit site, and the bigdft support in sci-physics/abinit-7.0.4 segfaults; on the other hand abinit-7.0.4 supports openmp. GPU support in sci-libs/bigdft-1.7_pre12 and sci-physics/abinit-7.0.4 not yet tested.
---
sci-libs/bigdft/ChangeLog | 11 +-
sci-libs/bigdft/bigdft-1.7_pre12.ebuild | 142 ++++++++
.../bigdft-1.7-dev.12-libxc_dir_include.patch | 50 +++
.../files/bigdft-1.7-dev.12-nolib_mods.patch | 25 ++
.../bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2 | Bin 0 -> 22103 bytes
sci-physics/abinit/ChangeLog | 9 +-
sci-physics/abinit/abinit-7.0.4.ebuild | 341 ++++++++++++++++++++
sci-physics/abinit/files/7.0.4-test_dirs.patch | 12 +
sci-physics/atompaw/ChangeLog | 8 +-
...ompaw-3.0.1.4.ebuild => atompaw-3.0.1.9.ebuild} | 2 +-
sci-physics/openmx/ChangeLog | 9 +
sci-physics/openmx/openmx-3.6.ebuild | 96 ++++++
12 files changed, 701 insertions(+), 4 deletions(-)
diff --git a/sci-libs/bigdft/ChangeLog b/sci-libs/bigdft/ChangeLog
index 1f24f09..82de595 100644
--- a/sci-libs/bigdft/ChangeLog
+++ b/sci-libs/bigdft/ChangeLog
@@ -1,9 +1,18 @@
# ChangeLog for sci-libs/bigdft
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
<<<<<<< HEAD
+*bigdft-1.7_pre12 (17 Jan 2013)
+
+ 17 Jan 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
+ +bigdft-1.7_pre12.ebuild, +files/bigdft-1.7-dev.12-libxc_dir_include.patch,
+ +files/bigdft-1.7-dev.12-nolib_mods.patch,
+ +files/bigdft-1.7-dev.12-tests.tar.bz2:
+ New version 1.7-dev.12 (1.7_pre12) from the Abinit site added; used by
+ sci-physics/abinit-7.0.4 but apparently segfaults it.
+
*bigdft-1.6_pre1-r4 (01 Sep 2012)
01 Sep 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
diff --git a/sci-libs/bigdft/bigdft-1.7_pre12.ebuild b/sci-libs/bigdft/bigdft-1.7_pre12.ebuild
new file mode 100644
index 0000000..de32f98
--- /dev/null
+++ b/sci-libs/bigdft/bigdft-1.7_pre12.ebuild
@@ -0,0 +1,142 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+inherit autotools-utils eutils flag-o-matic fortran-2 toolchain-funcs
+
+REAL_P="${P/_pre/-dev.}"
+
+DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
+HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
+SRC_URI="http://forge.abinit.org/fallbacks/${REAL_P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE="cuda doc etsf_io mpi netcdf openmp opencl test"
+
+RDEPEND="
+ =sci-libs/libxc-1*[fortran]
+ virtual/blas
+ virtual/fortran
+ virtual/lapack
+ dev-libs/libyaml
+ mpi? ( virtual/mpi )
+ cuda? ( dev-util/nvidia-cuda-sdk )
+ opencl? (
+ || (
+ dev-util/nvidia-cuda-sdk
+ dev-util/amdstream
+ )
+ )
+ etsf_io? ( sci-libs/etsf_io )
+ netcdf? ( || (
+ sci-libs/netcdf[fortran]
+ sci-libs/netcdf-fortran
+ )
+ )"
+DEPEND="${RDEPEND}
+ dev-util/pkgconfig
+ >=sys-devel/autoconf-2.59
+ doc? ( virtual/latex-base )
+ app-arch/tar
+ app-arch/bzip2"
+
+S="${WORKDIR}/${REAL_P}"
+
+DOCS=( README INSTALL ChangeLog AUTHORS NEWS )
+
+FORTRAN_STANDARD=90
+
+pkg_setup() {
+ # fortran-2.eclass does not handle mpi wrappers
+ if use mpi; then
+ export FC="mpif90"
+ export F77="mpif77"
+ export CC="mpicc"
+ else
+ tc-export FC F77 CC
+ fi
+
+ fortran-2_pkg_setup
+ if use openmp; then
+ tc-has-openmp || \
+ die "Please select an openmp capable compiler like gcc[openmp]"
+ fi
+}
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/"${REAL_P}"-libxc_dir_include.patch \
+ "${FILESDIR}"/"${REAL_P}"-nolib_mods.patch
+ tar -xjf "${FILESDIR}"/"${REAL_P}"-tests.tar.bz2 -C "${S}"/tests/DFT/postSCF/
+ eautoreconf
+}
+
+src_configure() {
+ local openmp=""
+ use openmp && openmp="-fopenmp"
+ local modules="${EPREFIX}/usr/$(get_libdir)/finclude"
+ local netcdff_libs="-lnetcdff"
+ filter-flags '-m*' '-O*' "-pipe"
+ local nvcflags="${CFLAGS}"
+ _filter-var nvcflags '-m*' '-O*' "-pipe"
+ local myeconfargs=(
+ $(use_enable mpi)
+ --enable-optimised-convolution
+ --enable-pseudo
+ --enable-libbigdft
+ --enable-binaries
+ --disable-minima-hopping
+ --disable-internal-libyaml
+ --enable-internal-libabinit
+ --with-moduledir="${modules}"
+ --with-ext-linalg="$(pkg-config --libs-only-l lapack) \
+ $(pkg-config --libs-only-l blas)"
+ --with-ext-linalg-path="$(pkg-config --libs-only-L lapack) \
+ $(pkg-config --libs-only-L blas)"
+ --enable-libxc
+ --disable-internal-libxc
+ --with-libxc-include="${modules}"
+ $(use_enable cuda cuda-gpu)
+ $(use_with cuda cuda-path /opt/cuda)
+ $(use_with cuda nvcc-flags "${nvcflags}")
+ $(use_enable opencl)
+ $(use_with etsf_io etsf-io)
+ "$(use etsf_io && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")"
+ FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${openmp} -I${modules}"
+ LD="$(tc-getLD)"
+ CPP="$(tc-getCPP)"
+ )
+ autotools-utils_src_configure
+}
+
+src_compile() {
+ #autotools-utils_src_compile() expanded
+ _check_build_dir
+ pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+ emake -j1
+ sed -i -e's%\$(top_builddir)/[^ ]*/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc
+ popd > /dev/null
+
+ #autotools-utils_src_compile
+ use doc && autotools-utils_src_compile doc
+}
+
+src_test() {
+ if use test; then
+ #autotools-utils_src_test() expanded
+ _check_build_dir
+ pushd "${BUILD_DIR}" > /dev/null || die
+ # Run default src_test as defined in ebuild.sh
+ cd tests
+ emake -j1 check
+ popd > /dev/null
+ fi
+}
+
+src_install() {
+ autotools-utils_src_install HAVE_LIBXC=1
+}
diff --git a/sci-libs/bigdft/files/bigdft-1.7-dev.12-libxc_dir_include.patch b/sci-libs/bigdft/files/bigdft-1.7-dev.12-libxc_dir_include.patch
new file mode 100644
index 0000000..9084d08
--- /dev/null
+++ b/sci-libs/bigdft/files/bigdft-1.7-dev.12-libxc_dir_include.patch
@@ -0,0 +1,50 @@
+--- configure.ac.orig 2011-11-23 14:02:15.000000000 +0000
++++ configure.ac 2011-11-23 14:09:19.000000000 +0000
+@@ -743,14 +743,17 @@
+ ac_build_libxc="no"
+ AC_ARG_ENABLE(libxc, AS_HELP_STRING([--without-libxc], [Do not link with libXC library (default = yes).]), ac_use_libxc=$enableval, ac_use_libxc="yes")
+ AC_ARG_ENABLE(internal-libxc, AS_HELP_STRING([--disable-internal-libxc], [Do not build and link with internal libXC library (default = yes).]), ac_internal_libxc=$enableval, ac_internal_libxc="yes")
+-AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib and module files (default = None).]),
++AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib files (default = None).]),
+ ac_libxc_dir=$withval, ac_libxc_dir=)
++AC_ARG_WITH(libxc-include, AS_HELP_STRING([--with-libxc-include], [Give the path for an external libXC library module files (default = None).]),
++ ac_libxc_dir_include=$withval, ac_libxc_dir_include=)
+ if test x"$ac_use_libxc" = x"yes" ; then
+ ac_build_libxc=$ac_internal_libxc
+ if test "$ac_internal_libxc" = "yes" ; then
+ ac_build_libxc="yes"
+ ac_use_libxc="yes"
+ ac_libxc_dir="$top_builddir"/libxc-1.1.0/src
++ ac_libxc_dir_include="$ac_libxc_dir"/include
+ AC_SUBST(LIBXC_DIR, "\$(top_builddir)"/libxc-1.1.0/src)
+ AC_SUBST(LIBXC_INCLUDE, "-I\$(top_builddir)"/libxc-1.1.0/src)
+ LDFLAGS="$LDFLAGS -L\$(top_builddir)/libxc-1.1.0/src/.libs"
+@@ -758,6 +761,9 @@
+ else
+ if test -n "$ac_libxc_dir" ; then
+ LDFLAGS="$LDFLAGS -L$ac_libxc_dir/lib"
++ if test x"$ac_libxc_dir_include" = x ; then
++ ac_libxc_dir_include="$ac_libxc_dir"/include
++ fi
+
+ dnl Test the given implementation of libXC.
+ ac_libxc_libname="xc"
+@@ -766,13 +772,13 @@
+ ac_libxc_libname="dft_xc"
+ AC_CHECK_LIB($ac_libxc_libname, xc_f90_lda_vxc, withlibxc=yes, withlibxc=no)
+ fi
+- AC_CHECK_FILE($ac_libxc_dir/include/libxc_funcs_m.$ax_fc_mod_ext, funcs="yes", funcs="no")
+- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_lib_m.$ax_fc_mod_ext, lib="yes", lib="no")
+- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_types_m.$ax_fc_mod_ext, types="yes", types="no")
++ AC_CHECK_FILE($ac_libxc_dir_include/libxc_funcs_m.$ax_fc_mod_ext, funcs="yes", funcs="no")
++ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_lib_m.$ax_fc_mod_ext, lib="yes", lib="no")
++ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_types_m.$ax_fc_mod_ext, types="yes", types="no")
+ if test "$withlibxc" = "yes" -a "$funcs" = "yes" -a "$lib" = "yes" -a "$types" = "yes"; then
+ ac_use_libxc="yes"
+- AC_SUBST(LIBXC_DIR, $ac_libxc_dir/include)
+- AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir/include)
++ AC_SUBST(LIBXC_DIR, $ac_libxc_dir_include)
++ AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir_include)
+ LIBXC_LIBS="-l"$ac_libxc_libname
+ fi
+ else
diff --git a/sci-libs/bigdft/files/bigdft-1.7-dev.12-nolib_mods.patch b/sci-libs/bigdft/files/bigdft-1.7-dev.12-nolib_mods.patch
new file mode 100644
index 0000000..8137a48
--- /dev/null
+++ b/sci-libs/bigdft/files/bigdft-1.7-dev.12-nolib_mods.patch
@@ -0,0 +1,25 @@
+diff -Naurp bigdft-1.7-dev.12.orig/src/Makefile.am bigdft-1.7-dev.12/src/Makefile.am
+--- bigdft-1.7-dev.12.orig/src/Makefile.am 2012-07-16 07:46:11.000000000 +0000
++++ bigdft-1.7-dev.12/src/Makefile.am 2013-01-09 14:09:58.198905489 +0000
+@@ -45,6 +45,9 @@ EXTRA_DIST = \
+ # -------------
+ if BUILD_LIB_BIGDFT
+ lib_bigdft = libbigdft.a libdft_common.a
++else
++lib_bigdft =
++endif
+ PS_SOURCES = PSolver/Build_Kernel.f90 \
+ PSolver/xcenergy.f90 \
+ PSolver/3Dgradient.f90 \
+@@ -53,11 +56,6 @@ PS_SOURCES = PSolver/Build_Kernel.f90 \
+ PSolver/wofz.f90 \
+ lib/fft/fft3d.f90
+ PS_MODULES = PSolver/Poisson_Solver.f90
+-else
+-lib_bigdft =
+-PS_SOURCES =
+-PS_MODULES =
+-endif
+ if BUILD_BINARIES
+ binaries_sources = bigdft memguess splsad NEB frequencies MDanalysis $(minima_hopping_sources) bart abscalc BigDFT2Wannier WaCo
+ local_binaries = test_forces
diff --git a/sci-libs/bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2 b/sci-libs/bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2
new file mode 100644
index 0000000..d74c561
Binary files /dev/null and b/sci-libs/bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2 differ
diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index a57ab4c..d814a8a 100644
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@ -1,7 +1,14 @@
# ChangeLog for sci-physics/abinit
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*abinit-7.0.4 (17 Jan 2013)
+
+ 17 Jan 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
+ +files/7.0.4-test_dirs.patch, +abinit-7.0.4.ebuild:
+ New version 7.0.4 added; openmp now supported, but on the other hand, bigdft
+ support segfaults
+
*abinit-6.12.3-r2 (19 Jun 2012)
19 Jun 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
diff --git a/sci-physics/abinit/abinit-7.0.4.ebuild b/sci-physics/abinit/abinit-7.0.4.ebuild
new file mode 100644
index 0000000..2218c10
--- /dev/null
+++ b/sci-physics/abinit/abinit-7.0.4.ebuild
@@ -0,0 +1,341 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+inherit autotools-utils eutils flag-o-matic fortran-2 multilib toolchain-funcs
+
+DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory"
+HOMEPAGE="http://www.abinit.org/"
+SRC_URI="http://ftp.abinit.org/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cuda cuda-double -debug +etsf_io +fftw +fftw-threads +fox gsl gui +hdf5 libabinit mpi +netcdf openmp python -test +threads -vdwxc"
+
+RDEPEND="~sci-libs/bigdft-1.7_pre12
+ =sci-libs/libxc-1*[fortran]
+ sci-physics/atompaw[libxc]
+ etsf_io? ( sci-libs/etsf_io )
+ fox? ( >=sci-libs/fox-4.1.2-r1[sax] )
+ netcdf? (
+ || (
+ sci-libs/netcdf[fortran]
+ sci-libs/netcdf-fortran
+ )
+ hdf5? (
+ sci-libs/netcdf[hdf5]
+ )
+ )
+ hdf5? ( sci-libs/hdf5[fortran] )
+ sci-libs/wannier90
+ virtual/blas
+ virtual/lapack
+ gsl? ( sci-libs/gsl )
+ fftw? (
+ sci-libs/fftw:3.0
+ fftw-threads? ( sci-libs/fftw:3.0[threads] )
+ )
+ mpi? ( virtual/mpi )
+ python? ( dev-python/numpy )
+ cuda? ( dev-util/nvidia-cuda-sdk )"
+DEPEND="${RDEPEND}
+ dev-util/pkgconfig
+ gui? ( >=virtual/jdk-1.6.0
+ app-arch/sharutils
+ sys-apps/gawk )
+ dev-perl/Text-Markdown"
+
+S=${WORKDIR}/${P%[a-z]}
+
+lat1loc=""
+
+DOCS=( AUTHORS ChangeLog COPYING INSTALL KNOWN_PROBLEMS NEWS PACKAGING
+ README README.ChangeLog README.GPU README.xlf RELNOTES THANKS )
+
+FORTRAN_STANDARD=90
+
+pkg_setup() {
+ # Doesn't compile with gcc-4.0, only >=4.1
+ if [[ $(tc-getFC) == *gfortran ]]; then
+ if [[ $(gcc-major-version) -eq 4 ]] \
+ && [[ $(gcc-minor-version) -lt 1 ]]; then
+ die "Requires gcc-4.1 or newer"
+ fi
+ fi
+
+ # fortran-2.eclass does not handle mpi wrappers
+ if use mpi; then
+ export FC="mpif90"
+ export F77="mpif77"
+ export CC="mpicc"
+ export CXX="mpic++"
+ else
+ tc-export FC F77 CC CXX
+ fi
+
+ # Preprocesor macross can make some lines really long
+ append-fflags -ffree-line-length-none
+
+ fortran-2_pkg_setup
+ if use openmp; then
+ tc-has-openmp || \
+ die "Please select an openmp capable compiler like gcc[openmp]"
+ fi
+
+ # Sort out some USE options
+ if use fftw-threads && ! use fftw; then
+ ewarn "fftw-threads set but fftw not used, ignored"
+ fi
+ if use cuda-double && ! use cuda; then
+ ewarn "cuda-double set but cuda not used, ignored"
+ fi
+ if use gui; then
+ lat1loc="$(locale |awk '/LC_CTYPE="(.*)"/{sub("LC_CTYPE=\"",""); sub("\" *$", ""); print}')"
+ if locale charmap |grep -i "\<iso885915\?\>"; then
+ einfo "Good, locale compatible with the GUI build"
+ else
+ ewarn "The locale ${lat1loc} incompatible with the GUI build"
+ if latloc=`locale -a| grep -i "\<iso885915\?\>"`; then
+ if echo "${latloc}" |grep -q "^fr"; then
+ lat1loc="$(echo "${latloc}" | grep -im1 "^fr")"
+ else
+ lat1loc="$(echo "${latloc}" | grep -im1 "iso88591")"
+ fi
+ einfo "Will use ${lat1loc} to build the GUI"
+ else
+ ewarn "No ISO-8859-1 nor ISO-8859-15 locale available, the GUI build may crash"
+ fi
+ fi
+ fi
+}
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/6.2.2-change-default-directories.patch \
+ "${FILESDIR}"/6.12.1-autoconf.patch \
+ "${FILESDIR}"/6.12.1-xmalloc.patch \
+ "${FILESDIR}"/7.0.4-test_dirs.patch
+ eautoreconf
+ sed -e"s/\(grep '\^-\)\(\[LloW\]\)'/\1\\\(\2\\\|pthread\\\)'/g" -i configure
+
+}
+
+src_configure() {
+ local openmp=""
+ use openmp && openmp="-fopenmp"
+ local libs=""
+ local modules="-I/usr/$(get_libdir)/finclude $(FoX-config --sax --fcflags)"
+ local FoX_libs="${libs} $(FoX-config --sax --libs)"
+ local trio_flavor=""
+ use etsf_io && trio_flavor="${trio_flavor}+etsf_io"
+ use fox && trio_flavor="${trio_flavor}+fox"
+ use netcdf && trio_flavor="${trio_flavor}+netcdf"
+ test "no${trio_flavor}" = "no" && trio_flavor="none"
+ local netcdff_libs="-lnetcdff"
+ use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran"
+ local fft_flavor="fftw3"
+ local fft_libs=""
+ # The fftw threads support is protected by black magick.
+ # Anybody removes it, dies.
+ # New USE flag "fftw-threads" was added to control usage
+ # of the threaded fftw variant. Since fftw-3.3 has expanded
+ # the paralel options by MPI and OpenMP support, analogical
+ # USE flags should be added to select them in future;
+ # unusable with previous FFTW versions, they are postponed
+ # for now.
+ if use fftw-threads; then
+ fft_flavor="fftw3-threads"
+ if has_version '>=sci-libs/fftw-3.3'; then
+ # pkg-config files for fftw-3.3 are broken
+ # All the parallel stuff is separated
+ # from the main body of common routines,
+ # and -lfftw3 must be always included alongside.
+ # Until version 3.3 this used to be masked by
+ # .la files.
+ # Bug 384645
+ fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads) $(pkg-config --libs fftw3)"
+ else
+ fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads)"
+ fi
+ else
+ fft_libs="${fft_libs} $(pkg-config --libs fftw3)"
+ fi
+ local gpu_flavor="none"
+ if use cuda; then
+ gpu_flavor="cuda-single"
+ if use cuda-double; then
+ gpu_flavor="cuda-double"
+ fi
+ fi
+
+ local myeconfargs=(
+ --enable-clib
+ --enable-exports
+ $(use_enable gui)
+ $(use_enable debug debug enhanced)
+ $(use_enable mpi)
+ $(use_enable mpi mpi-io)
+ $(use_enable openmp)
+ $(use_enable vdwxc)
+ $(use_enable cuda gpu)
+ "$(use cuda && echo "--with-gpu-flavor=${gpu_flavor}")"
+ "$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")"
+ "$(use gsl && echo "--with-math-flavor=gsl")"
+ "$(use gsl && echo "--with-math-incs=$(pkg-config --cflags gsl)")"
+ "$(use gsl && echo "--with-math-libs=$(pkg-config --libs gsl)")"
+ --with-linalg-flavor="atlas"
+ --with-linalg-libs="$(pkg-config --libs lapack)"
+ --with-trio-flavor="${trio_flavor}"
+ "$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")"
+ "$(use netcdf && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")"
+ "$(use fox && echo "--with-fox-incs=${modules}")"
+ "$(use fox && echo "--with-fox-libs=${FoX_libs}")"
+ "$(use etsf_io && echo "--with-etsf-io-incs=${modules}")"
+ "$(use etsf_io && echo "--with-etsf-io-libs=${libs} -letsf_io -letsf_io_utils -letsf_io_low_level")"
+ --with-dft-flavor="libxc+bigdft+atompaw+wannier90"
+ --with-libxc-incs="${modules}"
+ --with-libxc-libs="${libs} -lxc"
+ --with-bigdft-incs="${modules}"
+ --with-bigdft-libs="$(pkg-config --libs bigdft)"
+ --with-atompaw-incs="${modules}"
+ --with-atompaw-libs="${libs} -latompaw"
+ --with-wannier90-bins="/usr/bin"
+ --with-wannier90-incs="${modules}"
+ --with-wannier90-libs="${libs} -lwannier $(pkg-config --libs lapack)"
+ "$(use fftw && echo "--with-fft-flavor=${fft_flavor}")"
+ "$(use fftw && echo "--with-fft-incs=-I/usr/include")"
+ "$(use fftw && echo "--with-fft-libs=${fft_libs}")"
+ --with-timer-flavor="abinit"
+ LD="$(tc-getLD)"
+ FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${openmp} ${modules} -I/usr/include"
+ )
+
+ MARKDOWN=Markdown.pl autotools-utils_src_configure
+
+ if use gui; then
+ # autotools-utils_src_configure() part expanded
+ _check_build_dir
+ pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+ mkdir -p gui
+ cd gui
+ ECONF_SOURCE="${S}"/gui econf UUDECODE="uudecode"
+ fi
+}
+
+src_compile() {
+ autotools-utils_src_compile
+
+ # Apparently libabinit.a is not built by default
+ # Used by BigDFT. Should probably be built separately,
+ # as a package of its own: BigDFT used by Abinit.
+ # Does libabinit.a depend on BigDFT, if used?
+ # Can Abinit use external libabinit.a?
+ use libabinit && autotools-utils_src_compile libabinit.a
+
+ if use gui; then
+ #autotools-utils_src_compile() expanded
+ # _check_build_dir has already been called
+ pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+ # now what the function cannot be called to do
+ cd gui
+ LC_CTYPE="${lat1loc}" emake || die "Making GUI failed"
+ popd > /dev/null
+ fi
+
+ sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc
+}
+
+src_test() {
+ einfo "The tests take quite a while, easily several hours"
+ # autotools-utils_src_test() expanded
+ _check_build_dir
+ pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+ # again something the autotools-utils function cannot be called to do
+ # now quite a lot of work actually
+ cd tests
+ emake tests_acc || ewarn "Accuracy tests failed"
+ emake tests_paw || ewarn "PAW tests failed"
+ emake tests_gw || ewarn "GW tests failed"
+ emake tests_gw_paw || ewarn "GW-PAW tests failed"
+ emake tests_bs || ewarn "BSE tests failed"
+ emake tests_tddft || ewarn "TDDFT tests failed"
+ emake tests_eph || ewarn "Elphon tests failed"
+
+ local REPORT
+ for REPORT in $(find . -name report); do
+ REPORT=${REPORT#*/}
+ elog "Parameters and unusual results for ${REPORT%%/*} tests"
+ echo "Parameters and unusual results for ${REPORT%%/*} tests" >>tests_summary.txt
+ while read line; do
+ elog "${line}"
+ echo "${line}" >>tests_summary.txt
+ done \
+ < <(grep -v -e succeeded -e passed ${REPORT})
+ done
+
+ local testdir
+ find . -name "tmp-test*" -print | \
+ while read testdir; do
+ if [ -e summary_of_tests.tar ]; then
+ tar rvf summary_of_tests.tar ${testdir}
+ else tar cvf summary_of_tests.tar ${testdir}
+ fi
+ done
+ popd > /dev/null
+
+ elog "The full test results will be installed as summary_of_tests.tar.bz2."
+ elog "Also a concise report tests_summary.txt is installed."
+}
+
+src_install() {
+ #autotools-utils_src_install() expanded
+ _check_build_dir
+ pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+ emake DESTDIR="${D}" install || die "make install failed"
+
+ use libabinit && dolib libabinit.a
+
+ if use gui; then
+ pushd gui
+ emake DESTDIR="${D}" install || die "The GUI install failed"
+ popd
+ fi
+
+ if use test; then
+ for dc in tests_summary.txt summary_of_tests.tar; do
+ test -e tests/"${dc}" && dodoc tests/"${dc}" || ewarn "Copying tests results failed"
+ done
+ fi
+
+ popd > /dev/null
+
+ # XXX: support installing them from builddir as well!!!
+ if [[ ${DOCS} ]]; then
+ dodoc "${DOCS[@]}" || die "dodoc failed"
+ else
+ local f
+ # same list as in PMS
+ for f in README* ChangeLog AUTHORS NEWS TODO CHANGES \
+ THANKS BUGS FAQ CREDITS CHANGELOG; do
+ if [[ -s ${f} ]]; then
+ dodoc "${f}" || die "(default) dodoc ${f} failed"
+ fi
+ done
+ fi
+ if [[ ${HTML_DOCS} ]]; then
+ dohtml -r "${HTML_DOCS[@]}" || die "dohtml failed"
+ fi
+
+ # Remove libtool files and unnecessary static libs
+ remove_libtool_files
+}
+
+pkg_postinst() {
+ if use test; then
+ elog "The full test results will be installed as summary_tests.tar.bz2."
+ elog "Also a concise report tests_summary.txt is installed."
+ fi
+}
diff --git a/sci-physics/abinit/files/7.0.4-test_dirs.patch b/sci-physics/abinit/files/7.0.4-test_dirs.patch
new file mode 100644
index 0000000..94915a0
--- /dev/null
+++ b/sci-physics/abinit/files/7.0.4-test_dirs.patch
@@ -0,0 +1,12 @@
+diff -Naurp abinit-7.0.4.orig/tests/Makefile.am abinit-7.0.4/tests/Makefile.am
+--- abinit-7.0.4.orig/tests/Makefile.am 2012-12-08 15:07:26.000000000 +0000
++++ abinit-7.0.4/tests/Makefile.am 2013-01-08 13:58:56.721725346 +0000
+@@ -3607,7 +3607,7 @@ tests_gw_paw: nightly-stamp
+ tests_bs: nightly-stamp
+ rm -fr */tmp-bs*
+ $(MAKE) tests_v67mbpt dirname=bs start=01 stop=01
+- cd v6/tmp-bs* ; mv fldiff.report fldiff_keep.report
++ cd v67mbpt/tmp-bs* ; mv fldiff.report fldiff_keep.report
+ $(MAKE) tests_v67mbpt dirname=bs start=04 stop=04
+ $(MAKE) tests_tutorial dirname=bs start=bs_1 stop=bs_4
+ echo
diff --git a/sci-physics/atompaw/ChangeLog b/sci-physics/atompaw/ChangeLog
index 91aeda8..66ddb4e 100644
--- a/sci-physics/atompaw/ChangeLog
+++ b/sci-physics/atompaw/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for sci-physics/atompaw
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*atompaw-3.0.1.9 (17 Jan 2013)
+
+ 17 Jan 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
+ -atompaw-3.0.1.4.ebuild, +atompaw-3.0.1.9.ebuild:
+ Version bumped to 3.0.1.9
+
22 May 2012; Justin Lecher <jlec@gentoo.org> -atompaw-3.0.1.3.ebuild,
atompaw-3.0.1.4.ebuild, metadata.xml:
Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
diff --git a/sci-physics/atompaw/atompaw-3.0.1.4.ebuild b/sci-physics/atompaw/atompaw-3.0.1.9.ebuild
similarity index 97%
rename from sci-physics/atompaw/atompaw-3.0.1.4.ebuild
rename to sci-physics/atompaw/atompaw-3.0.1.9.ebuild
index c9e0cfc..e385354 100644
--- a/sci-physics/atompaw/atompaw-3.0.1.4.ebuild
+++ b/sci-physics/atompaw/atompaw-3.0.1.9.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
diff --git a/sci-physics/openmx/ChangeLog b/sci-physics/openmx/ChangeLog
new file mode 100644
index 0000000..37b46f6
--- /dev/null
+++ b/sci-physics/openmx/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-physics/openmx
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*openmx-3.6 (17 Jan 2013)
+
+ 17 Jan 2013; Honza Macháček <Hloupy.Honza@centrum.cz> +openmx-3.6.ebuild:
+ Ebuild for OpenMX added
+
diff --git a/sci-physics/openmx/openmx-3.6.ebuild b/sci-physics/openmx/openmx-3.6.ebuild
new file mode 100644
index 0000000..78f65a3
--- /dev/null
+++ b/sci-physics/openmx/openmx-3.6.ebuild
@@ -0,0 +1,96 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="4"
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="Open source package for Material eXplorer using DFT, norm-conserving
+pseudopotentials, and pseudo-atomic localized basis functions."
+HOMEPAGE="http://www.openmx-square.org/"
+SRC_URI="http://www.openmx-square.org/${PN}${PV}.tar.gz
+ http://www.openmx-square.org/bugfixed/11Nov14/patch${PV}.1.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="-debug mpi openmp test"
+S="${WORKDIR}/${PN}${PV}"
+
+RDEPEND="virtual/blas
+ virtual/lapack
+ sci-libs/fftw:3
+ mpi? ( virtual/mpi
+ sci-libs/fftw:3[mpi] )
+ openmp? ( sys-devel/gcc[openmp]
+ sci-libs/fftw:3[openmp] )"
+DEPEND="${RDEPEND}
+ dev-util/pkgconfig"
+
+
+pkg_setup() {
+ if use mpi; then
+ export CC="mpicc"
+ else
+ tc-export CC
+ fi
+
+ if use openmp; then
+ export CC="${CC} -fopenmp"
+ fi
+}
+
+src_prepare() {
+ cd "${WORKDIR}"
+ mv *.out "${PN}${PV}"/work/input_example
+ mv *.[hc] "${PN}${PV}"/source
+}
+
+src_configure() {
+ CFLAGS="${CFLAGS:- -O3 -funroll-loops -ffast-math}"
+ local FFTW_FLAVOUR=fftw3
+ if use openmp; then
+ FFTW_FLAVOUR=fftw3_omp
+ else
+ export CFLAGS="${CFLAGS} -Dnoomp"
+ fi
+ if use mpi; then
+ FFTW_FLAVOUR=fftw3_mpi
+ else
+ export CFLAGS="${CFLAGS} -Dnompi"
+ fi
+ CFLAGS="${CFLAGS} $(pkg-config --cflags lapack)"
+ CFLAGS="${CFLAGS} $(pkg-config --cflags ${FFTW_FLAVOUR})"
+ export CFLAGS
+
+ local MX_LIB="$(pkg-config --static --libs lapack)"
+ local MX_LIB="${MX_LIB} $(pkg-config --static --libs ${FFTW_FLAVOUR})"
+
+ sed -i -e "s%^CC *=.*$%CC = ${CC} ${CFLAGS}%" \
+ -e "s%^LIB *=.*$%LIB = ${MX_LIB}%" \
+ source/makefile
+}
+
+src_compile() {
+ cd source
+ emake || die "make failed"
+}
+
+src_test() {
+ cd work
+ ../source/openmx -runtest
+}
+
+src_install() {
+ insinto /usr/share/${P}
+ doins -r DFT_DATA11
+ cd work
+ insinto /usr/share/${P}/examples
+ doins -r *
+ cd ../source
+ dodir /usr/bin
+ emake DESTDIR="${D}/usr/bin" install
+ dodoc "${S}/${PN}${PV}.pdf"
+ use test && dodoc "${S}"/work/runtest.result
+}
\ No newline at end of file
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