* [gentoo-commits] proj/sci:master commit in: sci-libs/bigdft/, sci-libs/bigdft/files/, sci-physics/abinit/files/, ...
@ 2012-03-22 12:39 Honza Macháček
0 siblings, 0 replies; 2+ messages in thread
From: Honza Macháček @ 2012-03-22 12:39 UTC (permalink / raw
To: gentoo-commits
commit: de11633feb6440593669f655eb088de809b7067f
Author: Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Thu Mar 22 12:39:20 2012 +0000
Commit: Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Thu Mar 22 12:39:20 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=de11633f
sci-libs/bigdft-1.6.0 corrected, sci-physics/abinit-6.12.1 added and moved to autotools-utils, sci-libs/bigdft-1.6_pre1 it depends on added. Old versions of bigdft needed by old versions of abinit ressurected.
---
sci-libs/bigdft/ChangeLog | 15 +
sci-libs/bigdft/bigdft-1.2.0.2.ebuild | 89 ++++++
.../{bigdft-1.6.0.ebuild => bigdft-1.2.0.5.ebuild} | 77 +++---
sci-libs/bigdft/bigdft-1.6.0.ebuild | 100 ++++--
sci-libs/bigdft/bigdft-1.6_pre0.ebuild | 125 ++++++++
sci-libs/bigdft/bigdft-1.6_pre1.ebuild | 128 ++++++++
.../bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch | 203 ++++++++++++
.../files/bigdft-1.6-tuto-libxc_dir_include.patch | 50 +++
.../bigdft/files/bigdft-1.6-tuto.1-bigdft.pc.patch | 203 ++++++++++++
.../bigdft-1.6-tuto.1-libxc_dir_include.patch | 50 +++
.../files/bigdft-1.6.0-libxc_dir_include.patch | 50 +++
sci-physics/abinit/ChangeLog | 15 +-
sci-physics/abinit/abinit-6.10.1.ebuild | 211 ------------
sci-physics/abinit/abinit-6.12.1.ebuild | 334 ++++++++++++++++++++
sci-physics/abinit/files/6.12.1-autoconf.patch | 21 ++
sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch | 61 ++++
sci-physics/abinit/files/6.12.1-gui-conf.patch | 12 +
.../abinit/files/6.12.1-libabinit_options.patch | 57 ++++
sci-physics/abinit/files/6.12.1-xmalloc.patch | 48 +++
sci-physics/abinit/metadata.xml | 5 +
20 files changed, 1575 insertions(+), 279 deletions(-)
diff --git a/sci-libs/bigdft/ChangeLog b/sci-libs/bigdft/ChangeLog
index ec29389..60bf2cd 100644
--- a/sci-libs/bigdft/ChangeLog
+++ b/sci-libs/bigdft/ChangeLog
@@ -2,6 +2,21 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*bigdft-1.6_pre1 (22 Mar 2012)
+*bigdft-1.6_pre0 (22 Mar 2012)
+
+ 22 Mar 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
+ +bigdft-1.2.0.2.ebuild, +bigdft-1.2.0.5.ebuild, +bigdft-1.6_pre0.ebuild,
+ +bigdft-1.6_pre1.ebuild, bigdft-1.6.0.ebuild,
+ +files/bigdft-1.6.0-libxc_dir_include.patch,
+ +files/bigdft-1.6-tuto.1-bigdft.pc.patch,
+ +files/bigdft-1.6-tuto.1-libxc_dir_include.patch,
+ +files/bigdft-1.6-tuto-bigdft.pc.patch,
+ +files/bigdft-1.6-tuto-libxc_dir_include.patch:
+ Old versions used by old versions of abinit ressurected. May be removed
+ forever if nobody complains about the latest abinit. 1.6.0 corrected,
+ 1.6_pre0 and 1.6_pre1 added; 1.6_pre1 is used by sci-physics/abinit-6.12.1.
+
*bigdft-1.6.0 (18 Feb 2012)
18 Feb 2012; Justin Lecher <jlec@gentoo.org> -bigdft-1.2.0.2.ebuild,
diff --git a/sci-libs/bigdft/bigdft-1.2.0.2.ebuild b/sci-libs/bigdft/bigdft-1.2.0.2.ebuild
new file mode 100644
index 0000000..208b45d
--- /dev/null
+++ b/sci-libs/bigdft/bigdft-1.2.0.2.ebuild
@@ -0,0 +1,89 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit eutils fortran-2 toolchain-funcs
+
+DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
+HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
+SRC_URI="
+ http://inac.cea.fr/L_Sim/BigDFT/${P}.tar.gz
+ http://inac.cea.fr/L_Sim/BigDFT/${PN}-1.3.2.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cuda doc mpi test"
+
+RDEPEND="
+ =sci-libs/libxc-1*[fortran]
+ virtual/blas
+ virtual/fortran
+ virtual/lapack
+ mpi? ( virtual/mpi )
+ cuda? ( dev-util/nvidia-cuda-sdk )"
+DEPEND="${RDEPEND}
+ dev-util/pkgconfig
+ >=sys-devel/autoconf-2.59
+ doc? ( virtual/latex-base )"
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-0001.patch \
+ "${FILESDIR}"/${P}-0002.patch \
+ "${FILESDIR}"/${P}-0003.patch \
+ "${FILESDIR}"/${P}-0004.patch \
+ "${FILESDIR}"/${P}-testH.patch
+
+ rm -r src/PSolver/ABINIT-common
+ mv ../${PN}-1.3.2/src/PSolver/ABINIT-common src/PSolver/
+ sed -i -e's%@LIBXC_INCLUDE@%-I/usr/lib/finclude%g' \
+ src/PSolver/ABINIT-common/Makefile.*
+ sed -i -e's%config\.inc%config.h%g' \
+ src/PSolver/ABINIT-common/*.F90
+}
+
+src_configure() {
+ # fortran-2.eclass does not handle mpi wrappers
+ if use mpi; then
+ export FC="mpif90"
+ export CC="mpicc"
+ else
+ tc-export FC CC
+ fi
+
+ econf \
+ $(use_enable mpi) \
+ --enable-libpoissonsolver \
+ --enable-libbigdft \
+ --enable-binaries \
+ --with-moduledir=/usr/$(get_libdir)/finclude \
+ --with-ext-linalg="`pkg-config --libs-only-l lapack`" \
+ --with-ext-linalg-path="`pkg-config --libs-only-L lapack`" \
+ --with-xc-module-path="/usr/lib/finclude" \
+ $(use_enable cuda cuda-gpu) \
+ $(use_with cuda cuda-path /opt/cuda) \
+ $(use_with cuda lib-cutils /opt/cuda/lib) \
+ FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}}" \
+ LD="$(tc-getLD)"
+}
+
+src_compile() {
+ emake -j1 HAVE_LIBXC=1 || die "make failed"
+ if use doc; then
+ emake HAVE_LIBXC=1 doc || die "make doc failed"
+ fi
+}
+
+src_test() {
+ if use test; then
+ emake check
+ fi
+}
+
+src_install() {
+ emake HAVE_LIBXC=1 DESTDIR="${D}" install || die "install failed"
+ dodoc README INSTALL ChangeLog AUTHORS NEWS || die "dodoc failed"
+}
diff --git a/sci-libs/bigdft/bigdft-1.6.0.ebuild b/sci-libs/bigdft/bigdft-1.2.0.5.ebuild
similarity index 51%
copy from sci-libs/bigdft/bigdft-1.6.0.ebuild
copy to sci-libs/bigdft/bigdft-1.2.0.5.ebuild
index 2def6c6..161d7de 100644
--- a/sci-libs/bigdft/bigdft-1.6.0.ebuild
+++ b/sci-libs/bigdft/bigdft-1.2.0.5.ebuild
@@ -4,9 +4,7 @@
EAPI=3
-FORTRAN_STANDARD=90
-
-inherit autotools-utils eutils fortran-2 toolchain-funcs
+inherit eutils fortran-2 toolchain-funcs
DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
@@ -17,14 +15,13 @@ SRC_URI="
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="cuda doc mpi static-libs test"
+IUSE="cuda doc mpi test"
RDEPEND="
- sci-libs/libxc[fortran]
+ =sci-libs/libxc-1*[fortran]
virtual/blas
virtual/fortran
virtual/lapack
- virtual/opencl
mpi? ( virtual/mpi )
cuda? ( dev-util/nvidia-cuda-sdk )"
DEPEND="${RDEPEND}
@@ -32,7 +29,20 @@ DEPEND="${RDEPEND}
>=sys-devel/autoconf-2.59
doc? ( virtual/latex-base )"
-pkg_setup() {
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-0001.patch \
+ "${FILESDIR}"/${PN}-1.2.0.2-testH.patch
+
+ rm -r src/PSolver/ABINIT-common
+ mv ../${PN}-1.3.2/src/PSolver/ABINIT-common src/PSolver/
+ sed -i -e's%@LIBXC_INCLUDE@%-I/usr/lib/finclude%g' \
+ src/PSolver/ABINIT-common/Makefile.*
+ sed -i -e's%config\.inc%config.h%g' \
+ src/PSolver/ABINIT-common/*.F90
+}
+
+src_configure() {
# fortran-2.eclass does not handle mpi wrappers
if use mpi; then
export FC="mpif90"
@@ -40,41 +50,34 @@ pkg_setup() {
else
tc-export FC CC
fi
- fortran-2_pkg_setup
-}
-
-src_prepare() {
- mv ../${PN}-1.3.2/src/PSolver/ABINIT-common src/PSolver/ || die
- sed -i -e's%@LIBXC_INCLUDE@%-I/usr/lib/finclude%g' \
- src/PSolver/ABINIT-common/Makefile.* || die
- sed -i -e's%config\.inc%config.h%g' \
- src/PSolver/ABINIT-common/*.F90 || die
- autotools-utils_src_prepare
-}
-
-src_configure() {
- local myeconfargs=(
- --enable-libpoissonsolver
- --enable-libbigdft
- --enable-binaries
- --with-moduledir=/usr/$(get_libdir)/finclude
- --with-ext-linalg="$(pkg-config --libs-only-l lapack)"
- --with-ext-linalg-path="$(pkg-config --libs-only-L lapack)"
- --with-xc-module-path="/usr/lib/finclude"
- $(use_enable mpi)
- $(use_enable cuda cuda-gpu)
- $(use_with cuda cuda-path /opt/cuda)
- $(use_with cuda lib-cutils /opt/cuda/lib)
- FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}}"
+ econf \
+ $(use_enable mpi) \
+ --enable-libpoissonsolver \
+ --enable-libbigdft \
+ --enable-binaries \
+ --with-moduledir=/usr/$(get_libdir)/finclude \
+ --with-ext-linalg="`pkg-config --libs-only-l lapack`" \
+ --with-ext-linalg-path="`pkg-config --libs-only-L lapack`" \
+ --with-xc-module-path="/usr/lib/finclude" \
+ $(use_enable cuda cuda-gpu) \
+ $(use_with cuda cuda-path /opt/cuda) \
+ $(use_with cuda lib-cutils /opt/cuda/lib) \
+ FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}}" \
LD="$(tc-getLD)"
- )
- autotools-utils_src_configure
}
src_compile() {
- autotools-utils_src_compile HAVE_ETSF_XC=1
- use doc && autotools-utils_src_compile HAVE_ETSF_XC=1 doc
+ emake -j1 HAVE_ETSF_XC=1 || die "make failed"
+ if use doc; then
+ emake HAVE_ETSF_XC=1 doc || die "make doc failed"
+ fi
+}
+
+src_test() {
+ if use test; then
+ emake check
+ fi
}
src_install() {
diff --git a/sci-libs/bigdft/bigdft-1.6.0.ebuild b/sci-libs/bigdft/bigdft-1.6.0.ebuild
index 2def6c6..66ea41f 100644
--- a/sci-libs/bigdft/bigdft-1.6.0.ebuild
+++ b/sci-libs/bigdft/bigdft-1.6.0.ebuild
@@ -2,82 +2,122 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
+EAPI="4"
-FORTRAN_STANDARD=90
-
-inherit autotools-utils eutils fortran-2 toolchain-funcs
+inherit autotools-utils flag-o-matic fortran-2 toolchain-funcs
DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
+
+REAL_P="${P/_pre0/-tuto}"
+S="${WORKDIR}/${REAL_P}"
+
SRC_URI="
- http://inac.cea.fr/L_Sim/BigDFT/${P}.tar.gz
- http://inac.cea.fr/L_Sim/BigDFT/${PN}-1.3.2.tar.gz"
+ http://inac.cea.fr/L_Sim/BigDFT/${REAL_P}.tar.gz
+ "
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="cuda doc mpi static-libs test"
+IUSE="cuda doc etsf_io mpi netcdf opencl test"
RDEPEND="
- sci-libs/libxc[fortran]
+ =sci-libs/libxc-1*[fortran]
virtual/blas
virtual/fortran
virtual/lapack
- virtual/opencl
mpi? ( virtual/mpi )
- cuda? ( dev-util/nvidia-cuda-sdk )"
+ 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]
+ )
+ "
DEPEND="${RDEPEND}
dev-util/pkgconfig
>=sys-devel/autoconf-2.59
doc? ( virtual/latex-base )"
+DOCS=( README INSTALL ChangeLog AUTHORS NEWS )
+
+FORTRAN_STANDARD=90
+
pkg_setup() {
# fortran-2.eclass does not handle mpi wrappers
if use mpi; then
export FC="mpif90"
+ export F77="mpif77"
export CC="mpicc"
else
- tc-export FC CC
+ tc-export FC F77 CC
fi
+
fortran-2_pkg_setup
}
src_prepare() {
- mv ../${PN}-1.3.2/src/PSolver/ABINIT-common src/PSolver/ || die
- sed -i -e's%@LIBXC_INCLUDE@%-I/usr/lib/finclude%g' \
- src/PSolver/ABINIT-common/Makefile.* || die
- sed -i -e's%config\.inc%config.h%g' \
- src/PSolver/ABINIT-common/*.F90 || die
- autotools-utils_src_prepare
+ epatch "${FILESDIR}"/"${REAL_P}"-libxc_dir_include.patch
+ eautoreconf
}
src_configure() {
-
+ local modules="/usr/$(get_libdir)/finclude"
+ local netcdff_libs="-lnetcdff"
+ filter-flags '-m*' '-O*' "-pipe"
+ local nvcflags="${CFLAGS}"
+# _filter-var nvcflags '-m*' '-O*' "-pipe"
local myeconfargs=(
- --enable-libpoissonsolver
+ $(use_enable mpi)
+ --enable-optimised-convolution
+ --enable-pseudo
--enable-libbigdft
--enable-binaries
- --with-moduledir=/usr/$(get_libdir)/finclude
- --with-ext-linalg="$(pkg-config --libs-only-l lapack)"
- --with-ext-linalg-path="$(pkg-config --libs-only-L lapack)"
- --with-xc-module-path="/usr/lib/finclude"
- $(use_enable mpi)
+ --disable-minima-hopping
+ --with-moduledir="${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) \
+ $(pkg-config --libs-only-L blas)"
+ --disable-internal-libxc
+ --with-libxc-path="/usr"
+ --with-libxc-include="${modules}"
$(use_enable cuda cuda-gpu)
$(use_with cuda cuda-path /opt/cuda)
- $(use_with cuda lib-cutils /opt/cuda/lib)
- FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}}"
+ $(use_with cuda nvcc-flags "${nvcflags}")
+ $(use_enable opencl)
+ $(use_with opencl ocl-path /usr)
+ $(use_with etsf_io etsf-io)
+ $(use_with etsf_io etsf-io-path "/usr")
+ $(use_with etsf_io netcdf-path "$(pkg-config --libs-only-L netcdf)")
+ "$(use etsf_io && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")"
+ FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} -I${modules}"
LD="$(tc-getLD)"
+ CPP="$(tc-getCPP)"
)
autotools-utils_src_configure
}
src_compile() {
- autotools-utils_src_compile HAVE_ETSF_XC=1
- use doc && autotools-utils_src_compile HAVE_ETSF_XC=1 doc
+ #autotools-utils_src_compile() expanded
+ _check_build_dir
+ pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+ emake -j1 || die 'emake failed'
+ sed -i -e's%\$(top_builddir)/src/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc
+ popd > /dev/null
+
+ use doc && autotools-utils_src_compile doc
+}
+
+src_test() {
+ use test && autotools-utils_src_test
}
src_install() {
- emake HAVE_ETSF_XC=1 DESTDIR="${D}" install || die "install failed"
- dodoc README INSTALL ChangeLog AUTHORS NEWS || die "dodoc failed"
+ autotools-utils_src_install HAVE_LIBXC=1
}
diff --git a/sci-libs/bigdft/bigdft-1.6_pre0.ebuild b/sci-libs/bigdft/bigdft-1.6_pre0.ebuild
new file mode 100644
index 0000000..f15fa23
--- /dev/null
+++ b/sci-libs/bigdft/bigdft-1.6_pre0.ebuild
@@ -0,0 +1,125 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="4"
+
+inherit autotools-utils flag-o-matic fortran-2 toolchain-funcs
+
+DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
+HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
+
+REAL_P="${P/_pre/-tuto.}"
+REAL_P="${REAL_P/-tuto.0/-tuto}"
+S="${WORKDIR}/${REAL_P}"
+
+SRC_URI="
+ http://inac.cea.fr/L_Sim/BigDFT/${REAL_P}.tar.gz
+ "
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cuda doc etsf_io mpi netcdf opencl test"
+
+RDEPEND="
+ =sci-libs/libxc-1*[fortran]
+ virtual/blas
+ virtual/fortran
+ virtual/lapack
+ mpi? ( virtual/mpi )
+ cuda? ( dev-util/nvidia-cuda-sdk )
+ opencl? (
+ || (
+ dev-util/nvidia-cuda-sdk
+ dev-util/amdstream
+ )
+ )
+ etsf_io? ( sci-libs/etsf_io )
+ netcdf? (
+ sci-libs/netcdf[fortran]
+ )
+ "
+DEPEND="${RDEPEND}
+ dev-util/pkgconfig
+ >=sys-devel/autoconf-2.59
+ doc? ( virtual/latex-base )"
+
+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
+}
+
+src_prepare() {
+ epatch "${FILESDIR}"/"${REAL_P}"-libxc_dir_include.patch
+ epatch "${FILESDIR}"/"${REAL_P}"-bigdft.pc.patch
+ eautoreconf
+}
+
+src_configure() {
+ local modules="/usr/$(get_libdir)/finclude"
+ local netcdff_libs="-lnetcdff"
+ filter-flags '-m*' '-O*' "-pipe"
+ local nvcflags="${CFLAGS}"
+# _filter-var nvcflags '-m*' '-O*' "-pipe"
+ local myeconfargs=(
+ $(use_enable mpi)
+ --enable-optimised-convolution
+ --enable-pseudo
+ --enable-libbigdft
+ --enable-binaries
+ --disable-minima-hopping
+ --with-moduledir="${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) \
+ $(pkg-config --libs-only-L blas)"
+ --disable-internal-libxc
+ --with-libxc-path="/usr"
+ --with-libxc-include="${modules}"
+ $(use_enable cuda cuda-gpu)
+ $(use_with cuda cuda-path /opt/cuda)
+ $(use_with cuda nvcc-flags "${nvcflags}")
+ $(use_enable opencl)
+ $(use_with opencl ocl-path /usr)
+ $(use_with etsf_io etsf-io)
+ $(use_with etsf_io etsf-io-path "/usr")
+ $(use_with etsf_io netcdf-path "$(pkg-config --libs-only-L netcdf)")
+ "$(use etsf_io && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")"
+ FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} -I${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 || die 'emake failed'
+ sed -i -e's%\$(top_builddir)/src/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc
+ popd > /dev/null
+
+ use doc && autotools-utils_src_compile doc
+}
+
+src_test() {
+ use test && autotools-utils_src_test
+}
+
+src_install() {
+ autotools-utils_src_install HAVE_LIBXC=1
+}
diff --git a/sci-libs/bigdft/bigdft-1.6_pre1.ebuild b/sci-libs/bigdft/bigdft-1.6_pre1.ebuild
new file mode 100644
index 0000000..21cff15
--- /dev/null
+++ b/sci-libs/bigdft/bigdft-1.6_pre1.ebuild
@@ -0,0 +1,128 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="4"
+
+inherit autotools-utils flag-o-matic fortran-2 toolchain-funcs
+
+DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
+HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
+
+REAL_P="${P/_pre/-tuto.}"
+REAL_P="${REAL_P/-tuto.0/-tuto}"
+S="${WORKDIR}/${REAL_P}"
+
+SRC_URI="
+ http://inac.cea.fr/L_Sim/BigDFT/${REAL_P}.tar.gz
+ "
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cuda doc etsf_io mpi netcdf opencl test"
+
+RDEPEND="
+ =sci-libs/libxc-1*[fortran]
+ virtual/blas
+ virtual/fortran
+ virtual/lapack
+ mpi? ( virtual/mpi )
+ cuda? ( dev-util/nvidia-cuda-sdk )
+ opencl? (
+ || (
+ dev-util/nvidia-cuda-sdk
+ dev-util/amdstream
+ )
+ )
+ etsf_io? ( sci-libs/etsf_io )
+ netcdf? (
+ sci-libs/netcdf[fortran]
+ )
+ "
+DEPEND="${RDEPEND}
+ dev-util/pkgconfig
+ >=sys-devel/autoconf-2.59
+ doc? ( virtual/latex-base )"
+
+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
+}
+
+src_prepare() {
+ epatch "${FILESDIR}"/"${REAL_P}"-libxc_dir_include.patch
+ epatch "${FILESDIR}"/"${REAL_P}"-bigdft.pc.patch
+ sed -i -e's/capitalize_module_ext/ax_fc_mod_ext/g' "${S}"/configure
+ sed -i -e's/capitalize_module_ext/ax_fc_mod_ext/g' "${S}"/configure.ac
+ eautoreconf
+}
+
+src_configure() {
+ local modules="/usr/$(get_libdir)/finclude"
+ local netcdff_libs="-lnetcdff"
+ filter-flags '-m*' '-O*' "-pipe"
+ local nvcflags="${CFLAGS}"
+# _filter-var nvcflags '-m*' '-O*' "-pipe"
+ local myeconfargs=(
+ $(use_enable mpi)
+ --enable-optimised-convolution
+ --enable-pseudo
+ --enable-libbigdft
+ --enable-binaries
+ --disable-minima-hopping
+ --with-moduledir="${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) \
+ $(pkg-config --libs-only-L blas)"
+ --enable-libxc
+ --disable-internal-libxc
+ --with-libxc-path="/usr"
+ --with-libxc-include="${modules}"
+ $(use_enable cuda cuda-gpu)
+ $(use_with cuda cuda-path /opt/cuda)
+ $(use_with cuda nvcc-flags "${nvcflags}")
+ $(use_enable opencl)
+ $(use_with opencl ocl-path /usr)
+ $(use_with etsf_io etsf-io)
+ $(use_with etsf_io etsf-io-path "/usr")
+ $(use_with etsf_io netcdf-path "$(pkg-config --libs-only-L netcdf)")
+ "$(use etsf_io && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")"
+ FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} -I${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 || die 'emake failed'
+ sed -i -e's%\$(top_builddir)/src/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc
+ popd > /dev/null
+
+ use doc && autotools-utils_src_compile doc
+}
+
+src_test() {
+ use test && autotools-utils_src_test
+}
+
+src_install() {
+ autotools-utils_src_install HAVE_LIBXC=1
+}
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch
new file mode 100644
index 0000000..3ddde70
--- /dev/null
+++ b/sci-libs/bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch
@@ -0,0 +1,203 @@
+diff -Naur bigdft-1.6-tuto_orig/Makefile.am bigdft-1.6-tuto/Makefile.am
+--- Makefile.am 2011-10-18 07:39:52.000000000 +0000
++++ Makefile.am 2012-03-21 10:08:44.000000000 +0000
+@@ -4,7 +4,10 @@
+
+ ACLOCAL_AMFLAGS = -I config/m4
+
+-DISTCLEANFILES = config.inc
++DISTCLEANFILES = config.inc bigdft.pc
++
++pkgconfigdir = $(libdir)/pkgconfig
++pkgconfig_DATA = bigdft.pc
+
+ if BUILD_LIBABINIT
+ libABINIT_dir = libABINIT/src
+diff -Naur bigdft-1.6-tuto_orig/Makefile.in bigdft-1.6-tuto/Makefile.in
+--- Makefile.in 2012-03-21 10:03:28.000000000 +0000
++++ Makefile.in 2012-03-21 10:20:48.000000000 +0000
+@@ -33,7 +33,7 @@
+ POST_UNINSTALL = :
+ subdir = .
+ DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \
+- $(srcdir)/Makefile.in $(srcdir)/config.h.in \
++ $(srcdir)/Makefile.in $(srcdir)/bigdft.pc.in $(srcdir)/config.h.in \
+ $(top_srcdir)/config/Doxyfile.in $(top_srcdir)/configure \
+ AUTHORS COPYING ChangeLog INSTALL NEWS config/depcomp \
+ config/install-sh config/missing
+@@ -48,7 +48,7 @@
+ configure.lineno config.status.lineno
+ mkinstalldirs = $(install_sh) -d
+ CONFIG_HEADER = config.h
+-CONFIG_CLEAN_FILES = config/Doxyfile
++CONFIG_CLEAN_FILES = bigdft.pc config/Doxyfile
+ CONFIG_CLEAN_VPATH_FILES =
+ SOURCES =
+ DIST_SOURCES =
+@@ -59,6 +59,35 @@
+ install-pdf-recursive install-ps-recursive install-recursive \
+ installcheck-recursive installdirs-recursive pdf-recursive \
+ ps-recursive uninstall-recursive
++am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
++am__vpath_adj = case $$p in \
++ $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
++ *) f=$$p;; \
++ esac;
++am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
++am__install_max = 40
++am__nobase_strip_setup = \
++ srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
++am__nobase_strip = \
++ for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
++am__nobase_list = $(am__nobase_strip_setup); \
++ for p in $$list; do echo "$$p $$p"; done | \
++ sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
++ $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
++ if (++n[$$2] == $(am__install_max)) \
++ { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
++ END { for (dir in files) print dir, files[dir] }'
++am__base_list = \
++ sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
++ sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
++am__uninstall_files_from_dir = { \
++ test -z "$$files" \
++ || { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; } \
++ || { echo " ( cd '$$dir' && rm -f" $$files ")"; \
++ $(am__cd) "$$dir" && rm -f $$files; }; \
++ }
++am__installdirs = "$(DESTDIR)$(pkgconfigdir)"
++DATA = $(pkgconfig_DATA)
+ RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
+ distclean-recursive maintainer-clean-recursive
+ AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
+@@ -232,7 +261,9 @@
+ config/m4
+
+ ACLOCAL_AMFLAGS = -I config/m4
+-DISTCLEANFILES = config.inc
++DISTCLEANFILES = config.inc bigdft.pc
++pkgconfigdir = $(libdir)/pkgconfig
++pkgconfig_DATA = bigdft.pc
+ @BUILD_LIBABINIT_FALSE@libABINIT_dir =
+ @BUILD_LIBABINIT_TRUE@libABINIT_dir = libABINIT/src
+ @BUILD_LIBXC_FALSE@libXC_dir =
+@@ -307,8 +338,28 @@
+
+ distclean-hdr:
+ -rm -f config.h stamp-h1
++bigdft.pc: $(top_builddir)/config.status $(srcdir)/bigdft.pc.in
++ cd $(top_builddir) && $(SHELL) ./config.status $@
+ config/Doxyfile: $(top_builddir)/config.status $(top_srcdir)/config/Doxyfile.in
+ cd $(top_builddir) && $(SHELL) ./config.status $@
++install-pkgconfigDATA: $(pkgconfig_DATA)
++ @$(NORMAL_INSTALL)
++ test -z "$(pkgconfigdir)" || $(MKDIR_P) "$(DESTDIR)$(pkgconfigdir)"
++ @list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
++ for p in $$list; do \
++ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
++ echo "$$d$$p"; \
++ done | $(am__base_list) | \
++ while read files; do \
++ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(pkgconfigdir)'"; \
++ $(INSTALL_DATA) $$files "$(DESTDIR)$(pkgconfigdir)" || exit $$?; \
++ done
++
++uninstall-pkgconfigDATA:
++ @$(NORMAL_UNINSTALL)
++ @list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
++ files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
++ dir='$(DESTDIR)$(pkgconfigdir)'; $(am__uninstall_files_from_dir)
+
+ # This directory's subdirectories are mostly independent; you can cd
+ # into them and run `make' without going through this Makefile.
+@@ -622,9 +673,12 @@
+ exit 1; } >&2
+ check-am: all-am
+ check: check-recursive
+-all-am: Makefile config.h
++all-am: Makefile $(DATA) config.h
+ installdirs: installdirs-recursive
+ installdirs-am:
++ for dir in "$(DESTDIR)$(pkgconfigdir)"; do \
++ test -z "$$dir" || $(MKDIR_P) "$$dir"; \
++ done
+ install: install-recursive
+ install-exec: install-exec-recursive
+ install-data: install-data-recursive
+@@ -672,7 +726,7 @@
+
+ info-am:
+
+-install-data-am:
++install-data-am: install-pkgconfigDATA
+
+ install-dvi: install-dvi-recursive
+
+@@ -718,7 +772,7 @@
+
+ ps-am:
+
+-uninstall-am:
++uninstall-am: uninstall-pkgconfigDATA
+
+ .MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \
+ ctags-recursive install-am install-strip tags-recursive
+@@ -733,10 +787,10 @@
+ install-data-am install-dvi install-dvi-am install-exec \
+ install-exec-am install-html install-html-am install-info \
+ install-info-am install-man install-pdf install-pdf-am \
+- install-ps install-ps-am install-strip installcheck \
++ install-pkgconfigDATA install-ps install-ps-am install-strip installcheck \
+ installcheck-am installdirs installdirs-am maintainer-clean \
+ maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
+- pdf-am ps ps-am tags tags-recursive uninstall uninstall-am
++ pdf-am ps ps-am tags tags-recursive uninstall uninstall-am uninstall-pkgconfigDATA
+
+ configure
+
+diff -Naur bigdft-1.6-tuto_orig/bigdft.pc.in bigdft-1.6-tuto/bigdft.pc.in
+--- bigdft.pc.in 1970-01-01 00:00:00.000000000 +0000
++++ bigdft.pc.in 2012-02-01 09:43:59.000000000 +0000
+@@ -0,0 +1,11 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++includedir=@includedir@
++
++Name: libbigdft
++Description: Library for DFT calculation over wavelets.
++Requires:
++Version: @VERSION@
++Libs: -L${libdir} -lbigdft -lpoissonsolver @LIBS@ @FCLIBS@
++Cflags: -I${includedir}
+diff -Naur bigdft-1.6-tuto_orig/configure bigdft-1.6-tuto/configure
+--- configure 2012-03-21 10:03:26.000000000 +0000
++++ configure 2012-03-21 11:04:52.000000000 +0000
+@@ -8512,7 +8512,7 @@
+ docdir="${docdir}"
+
+
+-ac_config_files="$ac_config_files Makefile libABINIT/src/Makefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile"
++ac_config_files="$ac_config_files Makefile bigdft.pc libABINIT/src/Makefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile"
+
+
+ # Call libXC ./configure script recursively.
+@@ -9349,6 +9349,7 @@
+ "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;;
+ "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+ "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
++ "bigdft.pc") CONFIG_FILES="$CONFIG_FILES bigdft.pc" ;;
+ "libABINIT/src/Makefile") CONFIG_FILES="$CONFIG_FILES libABINIT/src/Makefile" ;;
+ "config/Doxyfile") CONFIG_FILES="$CONFIG_FILES config/Doxyfile" ;;
+ "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
+diff -Naur bigdft-1.6-tuto_orig/configure.ac bigdft-1.6-tuto/configure.ac
+--- configure.ac 2012-03-21 10:03:02.000000000 +0000
++++ configure.ac 2012-03-21 10:48:53.000000000 +0000
+@@ -715,6 +715,7 @@
+ dnl Give the name of file.in to transform to file
+ AC_CONFIG_FILES([
+ Makefile
++bigdft.pc
+ libABINIT/src/Makefile
+ config/Doxyfile
+ src/Makefile
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto-libxc_dir_include.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto-libxc_dir_include.patch
new file mode 100644
index 0000000..16aca5e
--- /dev/null
+++ b/sci-libs/bigdft/files/bigdft-1.6-tuto-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
+@@ -564,14 +564,17 @@
+ dnl Test the libXC library
+ ac_internal_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=)
+ ac_use_libxc="no"
+ 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"
+@@ -579,6 +582,9 @@
+ 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"
+@@ -587,13 +593,13 @@
+ 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.$capitalize_module_ext, funcs="yes", funcs="no")
+- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_lib_m.$capitalize_module_ext, lib="yes", lib="no")
+- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_types_m.$capitalize_module_ext, types="yes", types="no")
++ AC_CHECK_FILE($ac_libxc_dir_include/libxc_funcs_m.$capitalize_module_ext, funcs="yes", funcs="no")
++ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_lib_m.$capitalize_module_ext, lib="yes", lib="no")
++ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_types_m.$capitalize_module_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-1.6-tuto.1-bigdft.pc.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc.patch
new file mode 100644
index 0000000..3ddde70
--- /dev/null
+++ b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc.patch
@@ -0,0 +1,203 @@
+diff -Naur bigdft-1.6-tuto_orig/Makefile.am bigdft-1.6-tuto/Makefile.am
+--- Makefile.am 2011-10-18 07:39:52.000000000 +0000
++++ Makefile.am 2012-03-21 10:08:44.000000000 +0000
+@@ -4,7 +4,10 @@
+
+ ACLOCAL_AMFLAGS = -I config/m4
+
+-DISTCLEANFILES = config.inc
++DISTCLEANFILES = config.inc bigdft.pc
++
++pkgconfigdir = $(libdir)/pkgconfig
++pkgconfig_DATA = bigdft.pc
+
+ if BUILD_LIBABINIT
+ libABINIT_dir = libABINIT/src
+diff -Naur bigdft-1.6-tuto_orig/Makefile.in bigdft-1.6-tuto/Makefile.in
+--- Makefile.in 2012-03-21 10:03:28.000000000 +0000
++++ Makefile.in 2012-03-21 10:20:48.000000000 +0000
+@@ -33,7 +33,7 @@
+ POST_UNINSTALL = :
+ subdir = .
+ DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \
+- $(srcdir)/Makefile.in $(srcdir)/config.h.in \
++ $(srcdir)/Makefile.in $(srcdir)/bigdft.pc.in $(srcdir)/config.h.in \
+ $(top_srcdir)/config/Doxyfile.in $(top_srcdir)/configure \
+ AUTHORS COPYING ChangeLog INSTALL NEWS config/depcomp \
+ config/install-sh config/missing
+@@ -48,7 +48,7 @@
+ configure.lineno config.status.lineno
+ mkinstalldirs = $(install_sh) -d
+ CONFIG_HEADER = config.h
+-CONFIG_CLEAN_FILES = config/Doxyfile
++CONFIG_CLEAN_FILES = bigdft.pc config/Doxyfile
+ CONFIG_CLEAN_VPATH_FILES =
+ SOURCES =
+ DIST_SOURCES =
+@@ -59,6 +59,35 @@
+ install-pdf-recursive install-ps-recursive install-recursive \
+ installcheck-recursive installdirs-recursive pdf-recursive \
+ ps-recursive uninstall-recursive
++am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
++am__vpath_adj = case $$p in \
++ $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
++ *) f=$$p;; \
++ esac;
++am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
++am__install_max = 40
++am__nobase_strip_setup = \
++ srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
++am__nobase_strip = \
++ for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
++am__nobase_list = $(am__nobase_strip_setup); \
++ for p in $$list; do echo "$$p $$p"; done | \
++ sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
++ $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
++ if (++n[$$2] == $(am__install_max)) \
++ { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
++ END { for (dir in files) print dir, files[dir] }'
++am__base_list = \
++ sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
++ sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
++am__uninstall_files_from_dir = { \
++ test -z "$$files" \
++ || { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; } \
++ || { echo " ( cd '$$dir' && rm -f" $$files ")"; \
++ $(am__cd) "$$dir" && rm -f $$files; }; \
++ }
++am__installdirs = "$(DESTDIR)$(pkgconfigdir)"
++DATA = $(pkgconfig_DATA)
+ RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
+ distclean-recursive maintainer-clean-recursive
+ AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
+@@ -232,7 +261,9 @@
+ config/m4
+
+ ACLOCAL_AMFLAGS = -I config/m4
+-DISTCLEANFILES = config.inc
++DISTCLEANFILES = config.inc bigdft.pc
++pkgconfigdir = $(libdir)/pkgconfig
++pkgconfig_DATA = bigdft.pc
+ @BUILD_LIBABINIT_FALSE@libABINIT_dir =
+ @BUILD_LIBABINIT_TRUE@libABINIT_dir = libABINIT/src
+ @BUILD_LIBXC_FALSE@libXC_dir =
+@@ -307,8 +338,28 @@
+
+ distclean-hdr:
+ -rm -f config.h stamp-h1
++bigdft.pc: $(top_builddir)/config.status $(srcdir)/bigdft.pc.in
++ cd $(top_builddir) && $(SHELL) ./config.status $@
+ config/Doxyfile: $(top_builddir)/config.status $(top_srcdir)/config/Doxyfile.in
+ cd $(top_builddir) && $(SHELL) ./config.status $@
++install-pkgconfigDATA: $(pkgconfig_DATA)
++ @$(NORMAL_INSTALL)
++ test -z "$(pkgconfigdir)" || $(MKDIR_P) "$(DESTDIR)$(pkgconfigdir)"
++ @list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
++ for p in $$list; do \
++ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
++ echo "$$d$$p"; \
++ done | $(am__base_list) | \
++ while read files; do \
++ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(pkgconfigdir)'"; \
++ $(INSTALL_DATA) $$files "$(DESTDIR)$(pkgconfigdir)" || exit $$?; \
++ done
++
++uninstall-pkgconfigDATA:
++ @$(NORMAL_UNINSTALL)
++ @list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
++ files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
++ dir='$(DESTDIR)$(pkgconfigdir)'; $(am__uninstall_files_from_dir)
+
+ # This directory's subdirectories are mostly independent; you can cd
+ # into them and run `make' without going through this Makefile.
+@@ -622,9 +673,12 @@
+ exit 1; } >&2
+ check-am: all-am
+ check: check-recursive
+-all-am: Makefile config.h
++all-am: Makefile $(DATA) config.h
+ installdirs: installdirs-recursive
+ installdirs-am:
++ for dir in "$(DESTDIR)$(pkgconfigdir)"; do \
++ test -z "$$dir" || $(MKDIR_P) "$$dir"; \
++ done
+ install: install-recursive
+ install-exec: install-exec-recursive
+ install-data: install-data-recursive
+@@ -672,7 +726,7 @@
+
+ info-am:
+
+-install-data-am:
++install-data-am: install-pkgconfigDATA
+
+ install-dvi: install-dvi-recursive
+
+@@ -718,7 +772,7 @@
+
+ ps-am:
+
+-uninstall-am:
++uninstall-am: uninstall-pkgconfigDATA
+
+ .MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \
+ ctags-recursive install-am install-strip tags-recursive
+@@ -733,10 +787,10 @@
+ install-data-am install-dvi install-dvi-am install-exec \
+ install-exec-am install-html install-html-am install-info \
+ install-info-am install-man install-pdf install-pdf-am \
+- install-ps install-ps-am install-strip installcheck \
++ install-pkgconfigDATA install-ps install-ps-am install-strip installcheck \
+ installcheck-am installdirs installdirs-am maintainer-clean \
+ maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
+- pdf-am ps ps-am tags tags-recursive uninstall uninstall-am
++ pdf-am ps ps-am tags tags-recursive uninstall uninstall-am uninstall-pkgconfigDATA
+
+ configure
+
+diff -Naur bigdft-1.6-tuto_orig/bigdft.pc.in bigdft-1.6-tuto/bigdft.pc.in
+--- bigdft.pc.in 1970-01-01 00:00:00.000000000 +0000
++++ bigdft.pc.in 2012-02-01 09:43:59.000000000 +0000
+@@ -0,0 +1,11 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++includedir=@includedir@
++
++Name: libbigdft
++Description: Library for DFT calculation over wavelets.
++Requires:
++Version: @VERSION@
++Libs: -L${libdir} -lbigdft -lpoissonsolver @LIBS@ @FCLIBS@
++Cflags: -I${includedir}
+diff -Naur bigdft-1.6-tuto_orig/configure bigdft-1.6-tuto/configure
+--- configure 2012-03-21 10:03:26.000000000 +0000
++++ configure 2012-03-21 11:04:52.000000000 +0000
+@@ -8512,7 +8512,7 @@
+ docdir="${docdir}"
+
+
+-ac_config_files="$ac_config_files Makefile libABINIT/src/Makefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile"
++ac_config_files="$ac_config_files Makefile bigdft.pc libABINIT/src/Makefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile"
+
+
+ # Call libXC ./configure script recursively.
+@@ -9349,6 +9349,7 @@
+ "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;;
+ "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+ "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
++ "bigdft.pc") CONFIG_FILES="$CONFIG_FILES bigdft.pc" ;;
+ "libABINIT/src/Makefile") CONFIG_FILES="$CONFIG_FILES libABINIT/src/Makefile" ;;
+ "config/Doxyfile") CONFIG_FILES="$CONFIG_FILES config/Doxyfile" ;;
+ "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
+diff -Naur bigdft-1.6-tuto_orig/configure.ac bigdft-1.6-tuto/configure.ac
+--- configure.ac 2012-03-21 10:03:02.000000000 +0000
++++ configure.ac 2012-03-21 10:48:53.000000000 +0000
+@@ -715,6 +715,7 @@
+ dnl Give the name of file.in to transform to file
+ AC_CONFIG_FILES([
+ Makefile
++bigdft.pc
+ libABINIT/src/Makefile
+ config/Doxyfile
+ src/Makefile
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-libxc_dir_include.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-libxc_dir_include.patch
new file mode 100644
index 0000000..6d0f604
--- /dev/null
+++ b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-libxc_dir_include.patch
@@ -0,0 +1,50 @@
+--- configure.ac.orig 2011-11-23 14:02:15.000000000 +0000
++++ configure.ac 2011-11-23 14:09:19.000000000 +0000
+@@ -551,14 +551,17 @@
+ ac_build_libxc="no"
+ AC_ARG_ENABLE(libxc, AS_HELP_STRING([--disable-libxc], [Do not link with libXC library (default = yes).]), ac_use_libxc=$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="$LDFLAGS -L\$(top_builddir)/libxc-1.1.0/src/.libs"
+@@ -566,6 +569,9 @@
+ else
+ if test -n "$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"
+@@ -574,13 +580,13 @@
+ 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.$capitalize_module_ext, funcs="yes", funcs="no")
+- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_lib_m.$capitalize_module_ext, lib="yes", lib="no")
+- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_types_m.$capitalize_module_ext, types="yes", types="no")
++ AC_CHECK_FILE($ac_libxc_dir_include/libxc_funcs_m.$capitalize_module_ext, funcs="yes", funcs="no")
++ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_lib_m.$capitalize_module_ext, lib="yes", lib="no")
++ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_types_m.$capitalize_module_ext, types="yes", types="no")
+ if test "$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"$ac_libxc_libname
+ fi
+ else
diff --git a/sci-libs/bigdft/files/bigdft-1.6.0-libxc_dir_include.patch b/sci-libs/bigdft/files/bigdft-1.6.0-libxc_dir_include.patch
new file mode 100644
index 0000000..7179fcb
--- /dev/null
+++ b/sci-libs/bigdft/files/bigdft-1.6.0-libxc_dir_include.patch
@@ -0,0 +1,50 @@
+--- configure.ac.orig 2011-11-23 14:02:15.000000000 +0000
++++ configure.ac 2011-11-23 14:09:19.000000000 +0000
+@@ -604,14 +604,17 @@
+ ac_build_libxc="no"
+ AC_ARG_WITH(libxc, AS_HELP_STRING([--without-libxc], [Do not link with libXC library (default = yes).]), ac_use_libxc=$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="$LDFLAGS -L\$(top_builddir)/libxc-1.1.0/src/.libs"
+@@ -619,6 +622,9 @@
+ else
+ if test -n "$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"
+@@ -587,13 +593,13 @@
+ 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-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index b6b8822..2a5c1ee 100644
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@ -1,7 +1,20 @@
# ChangeLog for sci-physics/abinit
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*abinit-6.12.1 (22 Mar 2012)
+
+ 22 Mar 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
+ +files/6.12.1-autoconf.patch, -abinit-6.10.1.ebuild,
+ +files/6.12.1-gui-conf.patch, +abinit-6.12.1.ebuild,
+ +files/6.12.1-libabinit_options.patch, +files/6.12.1-xmalloc.patch,
+ +files/6.12.1-bigDFT-1.6.0.patch, metadata.xml:
+ 6.12.1 added, moved towards autotools-utils. Uses sci-libs/bigdft-1.6_pre1,
+ patching to use the latest 1.6.0 still not done. Libraries installed,
+ pkg-config file corrected; libabinit made an option, but for now would
+ conflict with sci-libs/bigdft. TO DO: Make sci-libs/bigdft compile against
+ libabinit of sci-physics/abinit, solve the resulting circular dependency.
+
*abinit-6.10.3 (14 Dec 2011)
14 Dec 2011; Honza Macháček <Hloupy.Honza@centrum.cz> -abinit-6.8.1.ebuild,
diff --git a/sci-physics/abinit/abinit-6.10.1.ebuild b/sci-physics/abinit/abinit-6.10.1.ebuild
deleted file mode 100644
index cdd495f..0000000
--- a/sci-physics/abinit/abinit-6.10.1.ebuild
+++ /dev/null
@@ -1,211 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="3"
-
-inherit autotools eutils 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/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cuda -debug +fftw +fftw-threads +fox gsl +hdf5 mpi +netcdf python -test +threads -vdwxc"
-
-RDEPEND=">=sci-libs/bigdft-1.2.0.2
- sci-libs/etsf_io
- =sci-libs/libxc-1.0[fortran]
- sci-physics/atompaw[libxc]
- fox? ( sci-libs/fox[dom,sax,wcml,wxml] )
- netcdf? (
- sci-libs/netcdf[fortran]
- hdf5? (
- sci-libs/netcdf[fortran,hdf5]
- )
- )
- hdf5? ( sci-libs/hdf5[fortran] )
- sci-libs/wannier90
- virtual/blas
- virtual/lapack
- gsl? ( sci-libs/gsl )
- fftw? (
- sci-libs/fftw:3.0
- fftw-threads? ( sci-libs/fftw:3.0[threads] )
- )
- mpi? ( virtual/mpi )
- python? ( dev-python/numpy )
- cuda? ( dev-util/nvidia-cuda-sdk )"
-DEPEND="${RDEPEND}
- dev-util/pkgconfig
- dev-perl/Text-Markdown"
-
-S=${WORKDIR}/${P%[a-z]}
-
-pkg_setup() {
- fortran-2_pkg_setup
- # Doesn't compile with gcc-4.0, only >=4.1
- if [[ $(tc-getFC) == *gfortran ]]; then
- if [[ $(gcc-major-version) -eq 4 ]] \
- && [[ $(gcc-minor-version) -lt 1 ]]; then
- die "Requires gcc-4.1 or newer"
- fi
- fi
- if use fftw-threads && ! use fftw; then
- ewarn "fftw-threads set but fftw not used, ignored"
- fi
-}
-
-src_prepare() {
- epatch "${FILESDIR}"/6.2.2-change-default-directories.patch
- epatch "${FILESDIR}"/6.0.3-fftw.patch
- eautoreconf
-}
-
-src_configure() {
- local libs="-L/usr/$(get_libdir)"
- local modules="-I/usr/$(get_libdir)/finclude"
- local FoX_libs="${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lFoX_common -lFoX_utils -lFoX_fsys"
- local trio_flavor="etsf_io"
- use fox && trio_flavor="${trio_flavor}+fox"
- use netcdf && trio_flavor="${trio_flavor}+netcdf"
- local netcdff_libs="-lnetcdff"
- use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran"
- local fft_flavor="fftw3"
- local fft_libs="-L/usr/lib"
- # The fftw threads support is protected by black magick.
- # Anybody removes it, dies.
- # New USE flag "fftw-threads" was added to control usage
- # of the threaded fftw variant. Since fftw-3.3 has expanded
- # the paralel options by MPI and OpenMP support, analogical
- # USE flags should be added to select them in future;
- # unusable with previous FFTW versions, they are postponed
- # for now.
- if use fftw-threads; then
- fft_flavor="fftw3-threads"
- if has_version '>=sci-libs/fftw-3.3'; then
- # pkg-config files for fftw-3.3 are broken
- # All the parallel stuff is separated
- # from the main body of common routines,
- # and -lfftw3 must be always included alongside.
- # Until version 3.3 this used to be masked by
- # .la files.
- # Bug 384645
- fft_libs="${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} $(pkg-config --libs fftw3)"
- fi
- if use mpi; then
- MY_FC="mpif90"
- MY_CC="mpicc"
- MY_CXX="mpic++"
- else
- MY_FC="$(tc-getFC)"
- MY_CC="$(tc-getCC)"
- MY_CXX="$(tc-getCXX)"
- fi
- MARKDOWN=Markdown.pl econf \
- $(use_enable debug debug enhanced) \
- $(use_enable mpi) \
- $(use_enable mpi mpi-io) \
- --disable-smp \
- $(use_enable vdwxc) \
- $(use_enable cuda gpu) \
- "$(use cuda && echo "--with-gpu-flavor=cuda-single")" \
- "$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")" \
- "$(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=${FoX_libs}")" \
- --with-etsf-io-incs="${modules}" \
- --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="${libs} -lpoissonsolver -lbigdft" \
- --with-atompaw-incs="${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" \
- FC="${MY_FC}" \
- CC="${MY_CC}" \
- CXX="${MY_CXX}" \
- LD="$(tc-getLD)" \
- FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include"
-}
-
-src_compile() {
- emake || die
-}
-
-src_test() {
- einfo "The tests take quite a while, on the order of 1-2 hours"
- einfo "on an Intel Penryn (2.5 GHz)."
- cd "${S}"/tests
- emake tests_min || ewarn "Minimal 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 tdft || ewarn "TDFT tests failed"
- emake tests_bench || ewarn "Benchmarks 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 ${testdir}
- fi
- done
-
- elog "The full test results will be installed as summary_of_tests.tar.bz2."
- elog "Also a concise report tests_summary.txt is installed."
-}
-
-src_install() {
- emake DESTDIR="${D}" install || die "make install failed"
-
- if use test; then
- dodoc tests/tests_summary.txt || ewarn "Copying tests summary failed"
- dodoc tests/summary_tests.tar || ewarn "Copying tests results failed"
- dodoc tests/summary_of_tests.tar || ewarn "Copying tests results failed"
- fi
-
- dodoc KNOWN_PROBLEMS README || die "Copying doc files failed"
-}
-
-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/abinit-6.12.1.ebuild b/sci-physics/abinit/abinit-6.12.1.ebuild
new file mode 100644
index 0000000..00e1fa2
--- /dev/null
+++ b/sci-physics/abinit/abinit-6.12.1.ebuild
@@ -0,0 +1,334 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="4"
+
+inherit autotools-utils 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/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cuda cuda-double -debug +etsf_io +fftw +fftw-threads +fox gsl gui +hdf5 libabinit mpi +netcdf python -test +threads -vdwxc"
+
+RDEPEND="=sci-libs/bigdft-1.6_pre1
+ sci-libs/etsf_io
+ =sci-libs/libxc-1*[fortran]
+ sci-physics/atompaw[libxc]
+ etsf_io? ( sci-libs/etsf_io )
+ fox? ( sci-libs/fox[dom,sax,wcml,wxml] )
+ netcdf? (
+ sci-libs/netcdf[fortran]
+ hdf5? (
+ sci-libs/netcdf[fortran,hdf5]
+ )
+ )
+ hdf5? ( sci-libs/hdf5[fortran] )
+ sci-libs/wannier90
+ virtual/blas
+ virtual/lapack
+ gsl? ( sci-libs/gsl )
+ fftw? (
+ sci-libs/fftw:3.0
+ fftw-threads? ( sci-libs/fftw:3.0[threads] )
+ )
+ mpi? ( virtual/mpi )
+ python? ( dev-python/numpy )
+ cuda? ( dev-util/nvidia-cuda-sdk )"
+DEPEND="${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() {
+ # 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
+ fortran-2_pkg_setup
+
+ # Doesn't compile with gcc-4.0, only >=4.1
+ if [[ $(tc-getFC) == *gfortran ]]; then
+ if [[ $(gcc-major-version) -eq 4 ]] \
+ && [[ $(gcc-minor-version) -lt 1 ]]; then
+ die "Requires gcc-4.1 or newer"
+ fi
+ fi
+
+ # Sort out some USE options
+ if use fftw-threads && ! use fftw; then
+ ewarn "fftw-threads set but fftw not used, ignored"
+ fi
+ if use cuda-double && ! use cuda; then
+ ewarn "cuda-double set but cuda not used, ignored"
+ fi
+ if use gui; then
+ lat1loc="$(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
+ epatch "${FILESDIR}"/6.0.3-fftw.patch
+ epatch "${FILESDIR}"/6.12.1-autoconf.patch
+ epatch "${FILESDIR}"/6.12.1-xmalloc.patch
+ epatch "${FILESDIR}"/6.12.1-libabinit_options.patch
+ eautoreconf
+
+ if use gui; then
+ epatch "${FILESDIR}"/6.12.1-gui-conf.patch
+# pushd "${S}"/gui
+ pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+ "${S}"/gui/autogen.sh
+ popd
+ fi
+}
+
+src_configure() {
+ local libs="-L/usr/$(get_libdir)"
+ local modules="-I/usr/$(get_libdir)/finclude"
+ local FoX_libs="${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lFoX_common -lFoX_utils -lFoX_fsys"
+ local trio_flavor=""
+ use etsf_io && trio_flavor="${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="-L/usr/lib"
+ # 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)
+ --disable-smp
+ $(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}} ${modules} -I/usr/include"
+ )
+
+ MARKDOWN=Markdown.pl autotools-utils_src_configure
+
+ if use gui; then
+ # autotools-utils_src_configure() part expanded
+ _check_build_dir
+ pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+ mkdir -p gui
+ cd gui
+ ECONF_SOURCE="${S}"/gui econf
+ fi
+}
+
+src_compile() {
+ autotools-utils_src_compile
+
+ # Apparently libabinit.a is not built by default
+ # Used by BigDFT. Should probably be built separately,
+ # as a package of its own: BigDFT used by Abinit.
+ # Does libabinit.a depend on BigDFT, if used?
+ # Can Abinit use external libabinit.a?
+ use libabinit && autotools-utils_src_compile libabinit.a
+
+ if use gui; then
+ #autotools-utils_src_compile() expanded
+ # _check_build_dir has already been called
+ pushd "${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_min || ewarn "Minimal 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 tdft || ewarn "TDFT tests failed"
+ emake tests_bench || ewarn "Benchmarks 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_tests.tar 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/6.12.1-autoconf.patch b/sci-physics/abinit/files/6.12.1-autoconf.patch
new file mode 100644
index 0000000..7e0169f
--- /dev/null
+++ b/sci-physics/abinit/files/6.12.1-autoconf.patch
@@ -0,0 +1,21 @@
+diff -Naur old/fallbacks/configure.ac new/fallbacks/configure.ac
+--- old/fallbacks/configure.ac 2012-01-30 19:40:41.000000000 +0000
++++ new/fallbacks/configure.ac 2012-02-13 08:16:08.000000000 +0000
+@@ -114,6 +114,17 @@
+
+ # ---------------------------------------------------------------------------- #
+
++AM_CONDITIONAL([DO_BUILD_FOX],[test "${enable_fox}" = "yes"])
++AM_CONDITIONAL([DO_BUILD_LIBXC],[test "${enable_libxc}" = "yes"])
++AM_CONDITIONAL([DO_BUILD_LINALG],[test "${enable_linalg}" = "yes"])
++AM_CONDITIONAL([DO_BUILD_NETCDF],[test "${enable_netcdf}" = "yes"])
++AM_CONDITIONAL([DO_BUILD_ETSF_IO],[test "${enable_etsf_io}" = "yes"])
++AM_CONDITIONAL([DO_BUILD_ATOMPAW],[test "${enable_atompaw}" = "yes"])
++AM_CONDITIONAL([DO_BUILD_WANNIER90],[test "${enable_wannier90}" = "yes"])
++AM_CONDITIONAL([DO_BUILD_BIGDFT],[test "${enable_bigdft}" = "yes"])
++
++# ---------------------------------------------------------------------------- #
++
+ #
+ # Downloading support
+ #
diff --git a/sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch b/sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch
new file mode 100644
index 0000000..857a27a
--- /dev/null
+++ b/sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch
@@ -0,0 +1,61 @@
+diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_descr_psp_set.F90 abinit-6.12.1/src/42_wvl_wrappers/wvl_descr_psp_set.F90
+--- src/42_wvl_wrappers/wvl_descr_psp_set.F90 2012-01-30 20:43:51.000000000 +0000
++++ src/42_wvl_wrappers/wvl_descr_psp_set.F90 2012-03-19 13:06:59.000000000 +0000
+@@ -105,7 +105,7 @@
+ ! Missing currently read radii_cf.
+ wvl%atoms%donlcc = .false.
+ ! TODO: add symmetry support
+- wvl%atoms%symObj = -1
++ wvl%atoms%sym%symObj = -1
+ #endif
+ end subroutine wvl_descr_psp_set
+ !!***
+diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_projectors_set.F90 abinit-6.12.1/src/42_wvl_wrappers/wvl_projectors_set.F90
+--- src/42_wvl_wrappers/wvl_projectors_set.F90 2012-01-30 20:43:50.000000000 +0000
++++ src/42_wvl_wrappers/wvl_projectors_set.F90 2012-03-19 13:17:37.000000000 +0000
+@@ -122,7 +122,7 @@
+ ABI_ALLOCATE(xcart,(3, natom))
+ call xredxcart(natom, 1, rprimd, xcart, xred)
+
+- call createProjectorsArrays(me, wfs%Glr%d%n1, wfs%Glr%d%n2, wfs%Glr%d%n3, &
++ call createProjectorsArrays(me, wfs%Glr, &
+ & xcart, wvl%atoms, wfs%orbs, psps%gth_params%radii_cf, &
+ & wvl_frmult, wvl_frmult, wvl%h(1), wvl%h(2), wvl%h(3), proj%keys, proj%proj)
+ write(message, '(a,a,a,a,I0)' ) ch10,&
+diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_wfs_free.F90 abinit-6.12.1/src/42_wvl_wrappers/wvl_wfs_free.F90
+--- src/42_wvl_wrappers/wvl_wfs_free.F90 2012-01-30 20:43:50.000000000 +0000
++++ src/42_wvl_wrappers/wvl_wfs_free.F90 2012-03-19 13:01:03.000000000 +0000
+@@ -68,7 +68,7 @@
+ #if defined HAVE_DFT_BIGDFT
+ call deallocate_lr(wfs%Glr, sub)
+ call deallocate_orbs(wfs%orbs, sub)
+- call deallocate_diis_objects(wfs%diis, sub)
++ ! call deallocate_diis_objects(wfs%diis, sub)
+ call deallocate_comms(wfs%comms, sub)
+ if (associated(wfs%orbs%eval)) then
+ ABI_DEALLOCATE(wfs%orbs%eval)
+diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_wfs_set.F90 abinit-6.12.1/src/42_wvl_wrappers/wvl_wfs_set.F90
+--- src/42_wvl_wrappers/wvl_wfs_set.F90 2012-01-30 20:43:55.000000000 +0000
++++ src/42_wvl_wrappers/wvl_wfs_set.F90 2012-03-19 12:58:54.000000000 +0000
+@@ -59,7 +59,7 @@
+ use defs_wvltypes
+ #if defined HAVE_DFT_BIGDFT
+ use BigDFT_API, only: createWavefunctionsDescriptors, orbitals_descriptors, &
+- & orbitals_communicators, allocate_diis_objects, wvl_timing => timing
++ & orbitals_communicators, wvl_timing => timing
+ #endif
+
+ !This section has been created automatically by the script Abilint (TD).
+@@ -179,9 +179,9 @@
+ call wvl_timing(me,'CrtDescriptors','OF')
+
+ ! allocate arrays necessary for DIIS convergence acceleration
+- call allocate_diis_objects(nwfshist,1._dp,&
+- & sum(wfs%comms%ncntt(0:nproc-1)), wfs%orbs%nkptsp, wfs%orbs%nspinor, &
+- & wfs%orbs%norbd, wfs%diis, "wvl_init_wfs_type")
++ ! call allocate_diis_objects(nwfshist,1._dp,&
++ ! & sum(wfs%comms%ncntt(0:nproc-1)), wfs%orbs%nkptsp, wfs%orbs%nspinor, &
++ ! & wfs%orbs%norbd, wfs%diis, "wvl_init_wfs_type")
+
+ #else
+ write(message, '(a,a,a,a)' ) ch10,&
diff --git a/sci-physics/abinit/files/6.12.1-gui-conf.patch b/sci-physics/abinit/files/6.12.1-gui-conf.patch
new file mode 100644
index 0000000..95c12b3
--- /dev/null
+++ b/sci-physics/abinit/files/6.12.1-gui-conf.patch
@@ -0,0 +1,12 @@
+diff -Naur abinit-6.12.1_orig/gui/configure abinit-6.12.1/gui/configure
+--- gui/configure 2012-01-30 19:42:26.000000000 +0000
++++ gui/configure 2012-03-16 13:38:54.000000000 +0000
+@@ -3143,7 +3143,7 @@
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+- ac_cv_prog_UUDECODE="no"
++ ac_cv_prog_UUDECODE="$as_dir/$ac_word$ac_exec_ext"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
diff --git a/sci-physics/abinit/files/6.12.1-libabinit_options.patch b/sci-physics/abinit/files/6.12.1-libabinit_options.patch
new file mode 100644
index 0000000..ad28a81
--- /dev/null
+++ b/sci-physics/abinit/files/6.12.1-libabinit_options.patch
@@ -0,0 +1,57 @@
+diff -Naur abinit-6.12.1_orig/Makefile.am abinit-6.12.1/Makefile.am
+--- Makefile.am 2012-01-30 19:42:26.000000000 +0000
++++ Makefile.am 2012-03-22 10:32:50.000000000 +0000
+@@ -1279,12 +1279,16 @@
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/12_hide_mpi/lib12_hide_mpi.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/13_memory_mpi/lib13_memory_mpi.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/14_hidewrite/lib14_hidewrite.a
++if DO_BUILD_15_GPU_TOOLBOX
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a
++endif
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/16_hideleave/lib16_hideleave.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/18_timing/lib18_timing.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/27_toolbox_oop/lib27_toolbox_oop.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/28_numeric_noabirule/lib28_numeric_noabirule.a
++if DO_BUILD_32_CONTRACT
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/32_contract/lib32_contract.a
++endif
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/32_util/lib32_util.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/42_geometry/lib42_geometry.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/42_nlstrain/lib42_nlstrain.a
+@@ -1298,7 +1302,9 @@
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/51_manage_mpi/lib51_manage_mpi.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a
++if DO_BUILD_52_MANAGE_CUDA
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a
++endif
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_abiutil/lib53_abiutil.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_ffts/lib53_ffts.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_spacepar/lib53_spacepar.a
+diff -Naur abinit-6.12.1_orig/Makefile.in abinit-6.12.1/Makefile.in
+--- Makefile.in 2012-03-22 09:23:51.000000000 +0000
++++ Makefile.in 2012-03-22 10:33:22.000000000 +0000
+@@ -2638,12 +2638,12 @@
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/12_hide_mpi/lib12_hide_mpi.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/13_memory_mpi/lib13_memory_mpi.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/14_hidewrite/lib14_hidewrite.a
+- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a
++@DO_BUILD_15_GPU_TOOLBOX_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/16_hideleave/lib16_hideleave.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/18_timing/lib18_timing.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/27_toolbox_oop/lib27_toolbox_oop.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/28_numeric_noabirule/lib28_numeric_noabirule.a
+- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/32_contract/lib32_contract.a
++@DO_BUILD_32_CONTRACT_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/32_contract/lib32_contract.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/32_util/lib32_util.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/42_geometry/lib42_geometry.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/42_nlstrain/lib42_nlstrain.a
+@@ -2657,7 +2657,7 @@
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/51_manage_mpi/lib51_manage_mpi.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a
+- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a
++@DO_BUILD_52_MANAGE_CUDA_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_abiutil/lib53_abiutil.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_ffts/lib53_ffts.a
+ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_spacepar/lib53_spacepar.a
diff --git a/sci-physics/abinit/files/6.12.1-xmalloc.patch b/sci-physics/abinit/files/6.12.1-xmalloc.patch
new file mode 100644
index 0000000..0c8d98e
--- /dev/null
+++ b/sci-physics/abinit/files/6.12.1-xmalloc.patch
@@ -0,0 +1,48 @@
+diff -Naur abinit-6.12.1_orig/src/02_clib/fsi_posix.c abinit-6.12.1/src/02_clib/fsi_posix.c
+--- src/02_clib/fsi_posix.c 2012-01-30 19:40:41.000000000 +0000
++++ src/02_clib/fsi_posix.c 2012-03-22 08:21:46.000000000 +0000
+@@ -19,7 +19,7 @@
+ */
+
+ #include "abi_clib.h"
+-#include "xmalloc.h"
++/* #include "xmalloc.h" */
+ #include "string_f.h"
+
+ /* Create a directory */
+diff -Naur abinit-6.12.1_orig/src/02_clib/intrinsics.c abinit-6.12.1/src/02_clib/intrinsics.c
+--- src/02_clib/intrinsics.c 2012-01-30 19:40:41.000000000 +0000
++++ src/02_clib/intrinsics.c 2012-03-22 08:20:26.000000000 +0000
+@@ -18,7 +18,7 @@
+ */
+
+ #include "abi_clib.h"
+-#include "xmalloc.h"
++/* #include "xmalloc.h" */
+ #include "string_f.h"
+
+ /*
+diff -Naur abinit-6.12.1_orig/src/02_clib/progress_bar.c abinit-6.12.1/src/02_clib/progress_bar.c
+--- src/02_clib/progress_bar.c 2012-01-30 19:40:41.000000000 +0000
++++ src/02_clib/progress_bar.c 2012-03-22 08:21:06.000000000 +0000
+@@ -20,7 +20,7 @@
+ */
+
+ #include "abi_clib.h"
+-#include "xmalloc.h"
++/* #include "xmalloc.h" */
+
+ #include <sys/time.h>
+ #include <sys/ioctl.h>
+diff -Naur abinit-6.12.1_orig/src/02_clib/xmalloc.c abinit-6.12.1/src/02_clib/xmalloc.c
+--- src/02_clib/xmalloc.c 2012-01-30 19:40:41.000000000 +0000
++++ src/02_clib/xmalloc.c 2012-03-22 08:22:09.000000000 +0000
+@@ -19,7 +19,7 @@
+ */
+
+ #include "abi_clib.h"
+-#include "xmalloc.h"
++/* #include "xmalloc.h" */
+
+ static void
+ memory_error_and_abort (const char *fname)
diff --git a/sci-physics/abinit/metadata.xml b/sci-physics/abinit/metadata.xml
index c14bc68..0a34647 100644
--- a/sci-physics/abinit/metadata.xml
+++ b/sci-physics/abinit/metadata.xml
@@ -11,6 +11,11 @@ ABINIT is a package whose main program allows one to find the total energy, char
</flag>
</use>
<use>
+ <flag name="cuda-double">
+ Enable support for double precision nVidia CUDA
+ </flag>
+</use>
+<use>
<flag name="fftw-threads">
Use the threaded version of sci-libs/fftw
</flag>
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/bigdft/, sci-libs/bigdft/files/, sci-physics/abinit/files/, ...
@ 2012-03-30 4:11 Honza Macháček
0 siblings, 0 replies; 2+ messages in thread
From: Honza Macháček @ 2012-03-30 4:11 UTC (permalink / raw
To: gentoo-commits
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1: Type: text/plain; charset=UTF-8, Size: 113082 bytes --]
commit: ecf1ca2b0144aee51f42f521b3d8701fb023f020
Author: Honza MacháÄek <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Fri Mar 30 04:10:46 2012 +0000
Commit: Honza MacháÄek <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Fri Mar 30 04:10:46 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ecf1ca2b
sci-libs/bigdft & sci-physics/abinit clean-up after sci-physics/abinit version bump to 6.12.2 and tests
---
sci-libs/bigdft/ChangeLog | 9 +
sci-libs/bigdft/bigdft-1.2.0.2.ebuild | 89 ----
sci-libs/bigdft/bigdft-1.2.0.5.ebuild | 86 ----
sci-libs/bigdft/bigdft-1.6_pre0.ebuild | 125 -----
sci-libs/bigdft/files/bigdft-1.2.0.2-0001.patch | 92 ----
sci-libs/bigdft/files/bigdft-1.2.0.2-0002.patch | 12 -
sci-libs/bigdft/files/bigdft-1.2.0.2-0003.patch | 11 -
sci-libs/bigdft/files/bigdft-1.2.0.2-0004.patch | 18 -
sci-libs/bigdft/files/bigdft-1.2.0.2-testH.patch | 330 -------------
sci-libs/bigdft/files/bigdft-1.2.0.5-0001.patch | 13 -
.../bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch | 203 --------
.../files/bigdft-1.6-tuto-libxc_dir_include.patch | 50 --
sci-physics/abinit/ChangeLog | 8 +
sci-physics/abinit/abinit-6.10.3.ebuild | 251 ----------
.../{abinit-6.12.1.ebuild => abinit-6.12.2.ebuild} | 7 +-
sci-physics/abinit/abinit-6.6.3.ebuild | 196 --------
sci-physics/abinit/abinit-6.8.2.ebuild | 211 --------
sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch | 61 ---
sci-physics/abinit/files/6.12.1-gui-conf.patch | 12 -
sci-physics/abinit/files/6.6.1-openmp.patch | 509 --------------------
20 files changed, 21 insertions(+), 2272 deletions(-)
diff --git a/sci-libs/bigdft/ChangeLog b/sci-libs/bigdft/ChangeLog
index 60bf2cd..f378708 100644
--- a/sci-libs/bigdft/ChangeLog
+++ b/sci-libs/bigdft/ChangeLog
@@ -2,6 +2,15 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 30 Mar 2012; Honza MacháÄek <Hloupy.Honza@centrum.cz>
+ -bigdft-1.2.0.2.ebuild, -files/bigdft-1.2.0.2-0001.patch,
+ -files/bigdft-1.2.0.2-0002.patch, -files/bigdft-1.2.0.2-0003.patch,
+ -files/bigdft-1.2.0.2-0004.patch, -files/bigdft-1.2.0.2-testH.patch,
+ -bigdft-1.2.0.5.ebuild, -files/bigdft-1.2.0.5-0001.patch,
+ -bigdft-1.6_pre0.ebuild, -files/bigdft-1.6-tuto-bigdft.pc.patch,
+ -files/bigdft-1.6-tuto-libxc_dir_include.patch:
+ Clean-up.
+
*bigdft-1.6_pre1 (22 Mar 2012)
*bigdft-1.6_pre0 (22 Mar 2012)
diff --git a/sci-libs/bigdft/bigdft-1.2.0.2.ebuild b/sci-libs/bigdft/bigdft-1.2.0.2.ebuild
deleted file mode 100644
index 208b45d..0000000
--- a/sci-libs/bigdft/bigdft-1.2.0.2.ebuild
+++ /dev/null
@@ -1,89 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils fortran-2 toolchain-funcs
-
-DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
-HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
-SRC_URI="
- http://inac.cea.fr/L_Sim/BigDFT/${P}.tar.gz
- http://inac.cea.fr/L_Sim/BigDFT/${PN}-1.3.2.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cuda doc mpi test"
-
-RDEPEND="
- =sci-libs/libxc-1*[fortran]
- virtual/blas
- virtual/fortran
- virtual/lapack
- mpi? ( virtual/mpi )
- cuda? ( dev-util/nvidia-cuda-sdk )"
-DEPEND="${RDEPEND}
- dev-util/pkgconfig
- >=sys-devel/autoconf-2.59
- doc? ( virtual/latex-base )"
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/${P}-0001.patch \
- "${FILESDIR}"/${P}-0002.patch \
- "${FILESDIR}"/${P}-0003.patch \
- "${FILESDIR}"/${P}-0004.patch \
- "${FILESDIR}"/${P}-testH.patch
-
- rm -r src/PSolver/ABINIT-common
- mv ../${PN}-1.3.2/src/PSolver/ABINIT-common src/PSolver/
- sed -i -e's%@LIBXC_INCLUDE@%-I/usr/lib/finclude%g' \
- src/PSolver/ABINIT-common/Makefile.*
- sed -i -e's%config\.inc%config.h%g' \
- src/PSolver/ABINIT-common/*.F90
-}
-
-src_configure() {
- # fortran-2.eclass does not handle mpi wrappers
- if use mpi; then
- export FC="mpif90"
- export CC="mpicc"
- else
- tc-export FC CC
- fi
-
- econf \
- $(use_enable mpi) \
- --enable-libpoissonsolver \
- --enable-libbigdft \
- --enable-binaries \
- --with-moduledir=/usr/$(get_libdir)/finclude \
- --with-ext-linalg="`pkg-config --libs-only-l lapack`" \
- --with-ext-linalg-path="`pkg-config --libs-only-L lapack`" \
- --with-xc-module-path="/usr/lib/finclude" \
- $(use_enable cuda cuda-gpu) \
- $(use_with cuda cuda-path /opt/cuda) \
- $(use_with cuda lib-cutils /opt/cuda/lib) \
- FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}}" \
- LD="$(tc-getLD)"
-}
-
-src_compile() {
- emake -j1 HAVE_LIBXC=1 || die "make failed"
- if use doc; then
- emake HAVE_LIBXC=1 doc || die "make doc failed"
- fi
-}
-
-src_test() {
- if use test; then
- emake check
- fi
-}
-
-src_install() {
- emake HAVE_LIBXC=1 DESTDIR="${D}" install || die "install failed"
- dodoc README INSTALL ChangeLog AUTHORS NEWS || die "dodoc failed"
-}
diff --git a/sci-libs/bigdft/bigdft-1.2.0.5.ebuild b/sci-libs/bigdft/bigdft-1.2.0.5.ebuild
deleted file mode 100644
index 161d7de..0000000
--- a/sci-libs/bigdft/bigdft-1.2.0.5.ebuild
+++ /dev/null
@@ -1,86 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils fortran-2 toolchain-funcs
-
-DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
-HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
-SRC_URI="
- http://inac.cea.fr/L_Sim/BigDFT/${P}.tar.gz
- http://inac.cea.fr/L_Sim/BigDFT/${PN}-1.3.2.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cuda doc mpi test"
-
-RDEPEND="
- =sci-libs/libxc-1*[fortran]
- virtual/blas
- virtual/fortran
- virtual/lapack
- mpi? ( virtual/mpi )
- cuda? ( dev-util/nvidia-cuda-sdk )"
-DEPEND="${RDEPEND}
- dev-util/pkgconfig
- >=sys-devel/autoconf-2.59
- doc? ( virtual/latex-base )"
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/${P}-0001.patch \
- "${FILESDIR}"/${PN}-1.2.0.2-testH.patch
-
- rm -r src/PSolver/ABINIT-common
- mv ../${PN}-1.3.2/src/PSolver/ABINIT-common src/PSolver/
- sed -i -e's%@LIBXC_INCLUDE@%-I/usr/lib/finclude%g' \
- src/PSolver/ABINIT-common/Makefile.*
- sed -i -e's%config\.inc%config.h%g' \
- src/PSolver/ABINIT-common/*.F90
-}
-
-src_configure() {
- # fortran-2.eclass does not handle mpi wrappers
- if use mpi; then
- export FC="mpif90"
- export CC="mpicc"
- else
- tc-export FC CC
- fi
-
- econf \
- $(use_enable mpi) \
- --enable-libpoissonsolver \
- --enable-libbigdft \
- --enable-binaries \
- --with-moduledir=/usr/$(get_libdir)/finclude \
- --with-ext-linalg="`pkg-config --libs-only-l lapack`" \
- --with-ext-linalg-path="`pkg-config --libs-only-L lapack`" \
- --with-xc-module-path="/usr/lib/finclude" \
- $(use_enable cuda cuda-gpu) \
- $(use_with cuda cuda-path /opt/cuda) \
- $(use_with cuda lib-cutils /opt/cuda/lib) \
- FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}}" \
- LD="$(tc-getLD)"
-}
-
-src_compile() {
- emake -j1 HAVE_ETSF_XC=1 || die "make failed"
- if use doc; then
- emake HAVE_ETSF_XC=1 doc || die "make doc failed"
- fi
-}
-
-src_test() {
- if use test; then
- emake check
- fi
-}
-
-src_install() {
- emake HAVE_ETSF_XC=1 DESTDIR="${D}" install || die "install failed"
- dodoc README INSTALL ChangeLog AUTHORS NEWS || die "dodoc failed"
-}
diff --git a/sci-libs/bigdft/bigdft-1.6_pre0.ebuild b/sci-libs/bigdft/bigdft-1.6_pre0.ebuild
deleted file mode 100644
index f15fa23..0000000
--- a/sci-libs/bigdft/bigdft-1.6_pre0.ebuild
+++ /dev/null
@@ -1,125 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="4"
-
-inherit autotools-utils flag-o-matic fortran-2 toolchain-funcs
-
-DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
-HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
-
-REAL_P="${P/_pre/-tuto.}"
-REAL_P="${REAL_P/-tuto.0/-tuto}"
-S="${WORKDIR}/${REAL_P}"
-
-SRC_URI="
- http://inac.cea.fr/L_Sim/BigDFT/${REAL_P}.tar.gz
- "
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cuda doc etsf_io mpi netcdf opencl test"
-
-RDEPEND="
- =sci-libs/libxc-1*[fortran]
- virtual/blas
- virtual/fortran
- virtual/lapack
- mpi? ( virtual/mpi )
- cuda? ( dev-util/nvidia-cuda-sdk )
- opencl? (
- || (
- dev-util/nvidia-cuda-sdk
- dev-util/amdstream
- )
- )
- etsf_io? ( sci-libs/etsf_io )
- netcdf? (
- sci-libs/netcdf[fortran]
- )
- "
-DEPEND="${RDEPEND}
- dev-util/pkgconfig
- >=sys-devel/autoconf-2.59
- doc? ( virtual/latex-base )"
-
-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
-}
-
-src_prepare() {
- epatch "${FILESDIR}"/"${REAL_P}"-libxc_dir_include.patch
- epatch "${FILESDIR}"/"${REAL_P}"-bigdft.pc.patch
- eautoreconf
-}
-
-src_configure() {
- local modules="/usr/$(get_libdir)/finclude"
- local netcdff_libs="-lnetcdff"
- filter-flags '-m*' '-O*' "-pipe"
- local nvcflags="${CFLAGS}"
-# _filter-var nvcflags '-m*' '-O*' "-pipe"
- local myeconfargs=(
- $(use_enable mpi)
- --enable-optimised-convolution
- --enable-pseudo
- --enable-libbigdft
- --enable-binaries
- --disable-minima-hopping
- --with-moduledir="${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) \
- $(pkg-config --libs-only-L blas)"
- --disable-internal-libxc
- --with-libxc-path="/usr"
- --with-libxc-include="${modules}"
- $(use_enable cuda cuda-gpu)
- $(use_with cuda cuda-path /opt/cuda)
- $(use_with cuda nvcc-flags "${nvcflags}")
- $(use_enable opencl)
- $(use_with opencl ocl-path /usr)
- $(use_with etsf_io etsf-io)
- $(use_with etsf_io etsf-io-path "/usr")
- $(use_with etsf_io netcdf-path "$(pkg-config --libs-only-L netcdf)")
- "$(use etsf_io && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")"
- FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} -I${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 || die 'emake failed'
- sed -i -e's%\$(top_builddir)/src/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc
- popd > /dev/null
-
- use doc && autotools-utils_src_compile doc
-}
-
-src_test() {
- use test && autotools-utils_src_test
-}
-
-src_install() {
- autotools-utils_src_install HAVE_LIBXC=1
-}
diff --git a/sci-libs/bigdft/files/bigdft-1.2.0.2-0001.patch b/sci-libs/bigdft/files/bigdft-1.2.0.2-0001.patch
deleted file mode 100644
index 3903527..0000000
--- a/sci-libs/bigdft/files/bigdft-1.2.0.2-0001.patch
+++ /dev/null
@@ -1,92 +0,0 @@
-diff -urN bigdft-1.2.0.old/src/PSolver/xcenergy.f90 bigdft-1.2.0.new/src/PSolver/xcenergy.f90
---- bigdft-1.2.0.old/src/PSolver/xcenergy.f90 2008-12-09 17:41:42.000000000 +0100
-+++ bigdft-1.2.0.new/src/PSolver/xcenergy.f90 2009-11-19 15:19:03.000000000 +0100
-@@ -96,16 +96,16 @@
- real(dp) :: elocal,vlocal,rho,pot,potion,facpotion,sfactor
- integer :: npts,i_all,order,offset,i_stat,ispden
- integer :: i1,i2,i3,j1,j2,j3,jp2,jpp2,jppp2
-- integer :: ndvxc,nvxcdgr,ngr2
-+ integer :: ndvxc,nvxcdgr,ngr2,nd2vxc
-
- !interface with drivexc
- interface
-- subroutine drivexc(exc,ixc,npts,nspden,order,rho_updn,vxc,ndvxc,ngr2,nvxcdgr,&
-- dvxc,d2vxc,grho2_updn,vxcgr,exexch) !Optional arguments
-+ subroutine drivexc(exc,ixc,npts,nspden,order,rho_updn,vxc,ndvxc,ngr2,nd2vxc,nvxcdgr,&
-+ dvxc,d2vxc,grho2_updn,vxcgr,exexch,lrho_updn,vxclrho,tau_updn,vxctau)!Optional arguments
- implicit none
- !Arguments ------------------------------------
- !scalars
-- integer,intent(in) :: ixc,ndvxc,ngr2,npts,nspden,nvxcdgr,order
-+ integer,intent(in) :: ixc,ndvxc,ngr2,nd2vxc,npts,nspden,nvxcdgr,order
- integer,intent(in),optional :: exexch
- !arrays
- real(kind=8),intent(in) :: rho_updn(npts,nspden)
-@@ -113,6 +113,8 @@
- real(kind=8),intent(out) :: exc(npts),vxc(npts,nspden)
- real(kind=8),intent(out),optional :: d2vxc(npts),dvxc(npts,ndvxc)
- real(kind=8),intent(out),optional :: vxcgr(npts,nvxcdgr)
-+ real(kind=8),intent(in),optional :: lrho_updn(npts,nspden), tau_updn(npts,nspden)
-+ real(kind=8),intent(out),optional :: vxclrho(npts,nspden),vxctau(npts,nspden)
- end subroutine drivexc
- end interface
-
-@@ -153,7 +155,8 @@
- ! end do
-
- !Allocations of the exchange-correlation terms, depending on the ixc value
-- call size_dvxc(ixc,ndvxc,ngr2,nspden,nvxcdgr,order)
-+ nd2vxc=1
-+ call size_dvxc(ixc,ndvxc,ngr2,nd2vxc,nspden,nvxcdgr,order)
-
- if (ixc >= 11 .and. ixc <= 16) then
- !computation of the gradient
-@@ -204,26 +207,26 @@
- if (ixc >= 11 .and. ixc <= 16) then
- if (order**2 <= 1 .or. ixc == 16) then
- if (ixc /= 13) then
-- call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr,&
-+ call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr,&
- &grho2_updn=gradient,vxcgr=dvxcdgr)
- else
-- call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr,&
-+ call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr,&
- &grho2_updn=gradient)
- end if
- else if (order /= 3) then
- if (ixc /= 13) then
-- call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr,&
-+ call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr,&
- &dvxc=dvxci,grho2_updn=gradient,vxcgr=dvxcdgr)
- else
-- call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr,&
-+ call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr,&
- &dvxc=dvxci,grho2_updn=gradient)
- end if
- else if (order == 3) then
- if (ixc /= 13) then
-- call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr,&
-+ call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr,&
- &dvxc=dvxci,d2vxc=d2vxci,grho2_updn=gradient,vxcgr=dvxcdgr)
- else
-- call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr,&
-+ call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr,&
- &dvxc=dvxci,d2vxc=d2vxci,grho2_updn=gradient)
- end if
- end if
-@@ -259,12 +262,12 @@
- !cases without gradient
- else
- if (order**2 <=1 .or. ixc >= 31 .and. ixc<=34) then
-- call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr)
-+ call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr)
- else if (order==3 .and. (ixc==3 .or. ixc>=7 .and. ixc<=10)) then
-- call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr,&
-+ call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr,&
- &dvxc=dvxci,d2vxc=d2vxci)
- else
-- call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr,&
-+ call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr,&
- &dvxc=dvxci)
- end if
- end if
diff --git a/sci-libs/bigdft/files/bigdft-1.2.0.2-0002.patch b/sci-libs/bigdft/files/bigdft-1.2.0.2-0002.patch
deleted file mode 100644
index 64506dc..0000000
--- a/sci-libs/bigdft/files/bigdft-1.2.0.2-0002.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -urN bigdft-1.2.0.1/src/geometry.f90 ../bigdft-1.2.0.1/src/geometry.f90
---- bigdft-1.2.0.1/src/geometry.f90 2008-12-09 17:41:41.000000000 +0100
-+++ bigdft-1.2.0.1/src/geometry.f90 2009-05-26 18:51:18.620210000 +0200
-@@ -45,7 +45,7 @@
- !write the first position
- if (iproc.eq.0) call wtposout(ncount_cluster,etot,rxyz,at)
- ! Open a log file for conjgrad
-- open(unit=16,file='conjgrad.prc',access='append')
-+ open(unit=16,file='conjgrad.prc',position='append')
-
- if (in%betax <= 0._gp) then
- call detbetax(nproc,iproc,at,rxyz,rst,in)
diff --git a/sci-libs/bigdft/files/bigdft-1.2.0.2-0003.patch b/sci-libs/bigdft/files/bigdft-1.2.0.2-0003.patch
deleted file mode 100644
index 385cbf3..0000000
--- a/sci-libs/bigdft/files/bigdft-1.2.0.2-0003.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- bigdft-1.2.0.1.old/src/PSolver/base.f90 2009-06-01 20:40:35.000000000 +0200
-+++ bigdft-1.2.0.1.new/src/PSolver/base.f90 2009-06-01 20:41:31.000000000 +0200
-@@ -31,6 +31,8 @@
- integer, parameter :: mpidtypg=MPI_DOUBLE_PRECISION
- !integer, parameter :: mpidtypw=MPI_REAL,mpidtypd=MPI_REAL !in case of single precision
-
-+ real(kind=4), parameter :: memorylimit=3.e0
-+
- !flag for GPU computing, if CUDA libraries are present
- !the parameter flag is removed to allow each processor to modify it following the needs
- !in that case if a GPU is present a given MPI processor may or not perform a GPU calculation
diff --git a/sci-libs/bigdft/files/bigdft-1.2.0.2-0004.patch b/sci-libs/bigdft/files/bigdft-1.2.0.2-0004.patch
deleted file mode 100644
index 6ae61aa..0000000
--- a/sci-libs/bigdft/files/bigdft-1.2.0.2-0004.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- bigdft-1.2.0.1.old/src/sumrho.f90 2009-07-01 10:49:36.252793679 +0200
-+++ bigdft-1.2.0.1.new/src/sumrho.f90 2009-07-01 10:50:08.693028765 +0200
-@@ -92,9 +92,12 @@
- MPI_DOUBLE_PRECISION,MPI_SUM,MPI_COMM_WORLD,ierr)
- end do
- else
-- call MPI_ALLREDUCE(MPI_IN_PLACE,rho_p,lr%d%n1i*lr%d%n2i*lr%d%n3i*nspin,&
-- MPI_DOUBLE_PRECISION,MPI_SUM,MPI_COMM_WORLD,ierr)
-- !stop 'rsflag active in sumrho.f90, check MPI2 implementation'
-+#ifdef MPI2
-+ call MPI_ALLREDUCE(MPI_IN_PLACE,rho_p,lr%d%n1i*lr%d%n2i*lr%d%n3i*nspin,&
-+ MPI_DOUBLE_PRECISION,MPI_SUM,MPI_COMM_WORLD,ierr)
-+#else
-+ stop 'rsflag active in sumrho.f90, check MPI2 implementation'
-+#endif
- end if
- call timing(iproc,'Rho_commun ','OF')
- call timing(iproc,'Rho_comput ','ON')
diff --git a/sci-libs/bigdft/files/bigdft-1.2.0.2-testH.patch b/sci-libs/bigdft/files/bigdft-1.2.0.2-testH.patch
deleted file mode 100644
index b4ef190..0000000
--- a/sci-libs/bigdft/files/bigdft-1.2.0.2-testH.patch
+++ /dev/null
@@ -1,330 +0,0 @@
-diff -Naur bigdft-1.2.0.2_orig/tests/C/Makefile.am bigdft-1.2.0.2/tests/C/Makefile.am
---- tests/C/Makefile.am 2008-12-09 16:41:42.000000000 +0000
-+++ tests/C/Makefile.am 2010-04-23 15:44:31.000000000 +0000
-@@ -21,8 +21,5 @@
- cp $(top_srcdir)/tests/inguess.dat .
-
- check: $(PPFILES) inguess.dat
-- cp -f $(top_srcdir)/tests/C/input.dat .
-- cp -f $(top_srcdir)/tests/C/posinp .
-- cp -f $(top_srcdir)/tests/C/occup.dat .
- $(run_parallel) $(top_builddir)/src/cluster > C.out
- python $(top_srcdir)/tests/fldiff.py --bigdft C.out $(top_srcdir)/tests/Refs/C.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/C/Makefile.in bigdft-1.2.0.2/tests/C/Makefile.in
---- tests/C/Makefile.in 2009-06-04 11:52:08.000000000 +0000
-+++ tests/C/Makefile.in 2010-04-23 15:44:40.000000000 +0000
-@@ -488,9 +488,6 @@
- cp $(top_srcdir)/tests/inguess.dat .
-
- check: $(PPFILES) inguess.dat
-- cp -f $(top_srcdir)/tests/C/input.dat .
-- cp -f $(top_srcdir)/tests/C/posinp .
-- cp -f $(top_srcdir)/tests/C/occup.dat .
- $(run_parallel) $(top_builddir)/src/cluster > C.out
- python $(top_srcdir)/tests/fldiff.py --bigdft C.out $(top_srcdir)/tests/Refs/C.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/Ca2/Makefile.am bigdft-1.2.0.2/tests/Ca2/Makefile.am
---- tests/Ca2/Makefile.am 2009-04-27 08:18:06.000000000 +0000
-+++ tests/Ca2/Makefile.am 2010-04-23 15:45:09.000000000 +0000
-@@ -20,7 +20,5 @@
- cp $(top_srcdir)/tests/inguess.dat .
-
- check: $(PPFILES) inguess.dat
-- cp -f $(top_srcdir)/tests/Ca2/input.dat .
-- cp -f $(top_srcdir)/tests/Ca2/posinp .
- $(run_parallel) $(top_builddir)/src/cluster > Ca2.out
- python $(top_srcdir)/tests/fldiff.py --bigdft --discrepancy=4.e-10 Ca2.out $(top_srcdir)/tests/Refs/Ca2.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/Ca2/Makefile.in bigdft-1.2.0.2/tests/Ca2/Makefile.in
---- tests/Ca2/Makefile.in 2009-06-04 11:52:08.000000000 +0000
-+++ tests/Ca2/Makefile.in 2010-04-23 15:45:17.000000000 +0000
-@@ -487,8 +487,6 @@
- cp $(top_srcdir)/tests/inguess.dat .
-
- check: $(PPFILES) inguess.dat
-- cp -f $(top_srcdir)/tests/Ca2/input.dat .
-- cp -f $(top_srcdir)/tests/Ca2/posinp .
- $(run_parallel) $(top_builddir)/src/cluster > Ca2.out
- python $(top_srcdir)/tests/fldiff.py --bigdft --discrepancy=4.e-10 Ca2.out $(top_srcdir)/tests/Refs/Ca2.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/Davidson-SiH4/Makefile.am bigdft-1.2.0.2/tests/Davidson-SiH4/Makefile.am
---- tests/Davidson-SiH4/Makefile.am 2008-12-09 16:41:42.000000000 +0000
-+++ tests/Davidson-SiH4/Makefile.am 2010-04-23 15:46:45.000000000 +0000
-@@ -18,7 +18,5 @@
- cp $(top_srcdir)/utils/PSPfiles/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/Davidson-SiH4/input.dat .
-- cp -f $(top_srcdir)/tests/Davidson-SiH4/posinp .
- $(run_parallel) $(top_builddir)/src/cluster > Davidson-SiH4.out
- python $(top_srcdir)/tests/fldiff.py --bigdft Davidson-SiH4.out $(top_srcdir)/tests/Refs/Davidson-SiH4.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/Davidson-SiH4/Makefile.in bigdft-1.2.0.2/tests/Davidson-SiH4/Makefile.in
---- tests/Davidson-SiH4/Makefile.in 2009-06-04 11:52:08.000000000 +0000
-+++ tests/Davidson-SiH4/Makefile.in 2010-04-23 15:46:53.000000000 +0000
-@@ -485,8 +485,6 @@
- cp $(top_srcdir)/utils/PSPfiles/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/Davidson-SiH4/input.dat .
-- cp -f $(top_srcdir)/tests/Davidson-SiH4/posinp .
- $(run_parallel) $(top_builddir)/src/cluster > Davidson-SiH4.out
- python $(top_srcdir)/tests/fldiff.py --bigdft Davidson-SiH4.out $(top_srcdir)/tests/Refs/Davidson-SiH4.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/GPU/Makefile.am bigdft-1.2.0.2/tests/GPU/Makefile.am
---- tests/GPU/Makefile.am 2008-12-09 16:41:42.000000000 +0000
-+++ tests/GPU/Makefile.am 2010-04-23 15:47:06.000000000 +0000
-@@ -18,8 +18,5 @@
- cp $(top_srcdir)/utils/PSPfiles/HGH/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/GPU/input.dat .
-- cp -f $(top_srcdir)/tests/GPU/posinp .
-- cp -f $(top_srcdir)/tests/GPU/cpu_gpu_aff.config .
- $(top_builddir)/src/cluster > GPU.out
- python $(top_srcdir)/tests/fldiff.py --bigdft GPU.out $(top_srcdir)/tests/Refs/GPU.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/GPU/Makefile.in bigdft-1.2.0.2/tests/GPU/Makefile.in
---- tests/GPU/Makefile.in 2009-06-04 11:52:08.000000000 +0000
-+++ tests/GPU/Makefile.in 2010-04-23 15:47:13.000000000 +0000
-@@ -485,9 +485,6 @@
- cp $(top_srcdir)/utils/PSPfiles/HGH/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/GPU/input.dat .
-- cp -f $(top_srcdir)/tests/GPU/posinp .
-- cp -f $(top_srcdir)/tests/GPU/cpu_gpu_aff.config .
- $(top_builddir)/src/cluster > GPU.out
- python $(top_srcdir)/tests/fldiff.py --bigdft GPU.out $(top_srcdir)/tests/Refs/GPU.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/H/Makefile.am bigdft-1.2.0.2/tests/H/Makefile.am
---- tests/H/Makefile.am 2010-04-23 15:39:18.000000000 +0000
-+++ tests/H/Makefile.am 2010-04-23 15:38:46.000000000 +0000
-@@ -17,8 +17,6 @@
- cp $(top_srcdir)/utils/PSPfiles/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/H/input.dat .
-- cp -f $(top_srcdir)/tests/H/posinp .
- $(top_builddir)/src/memguess 1 > H.memguess
- python $(top_srcdir)/tests/fldiff.py --bigdft H.memguess $(top_srcdir)/tests/Refs/H.memguess.ref | cat
- $(run_parallel) $(top_builddir)/src/cluster > H.out
-diff -Naur bigdft-1.2.0.2_orig/tests/H/Makefile.in bigdft-1.2.0.2/tests/H/Makefile.in
---- tests/H/Makefile.in 2010-04-23 15:39:18.000000000 +0000
-+++ tests/H/Makefile.in 2010-04-23 15:38:46.000000000 +0000
-@@ -484,8 +484,6 @@
- cp $(top_srcdir)/utils/PSPfiles/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/H/input.dat .
-- cp -f $(top_srcdir)/tests/H/posinp .
- $(top_builddir)/src/memguess 1 > H.memguess
- python $(top_srcdir)/tests/fldiff.py --bigdft H.memguess $(top_srcdir)/tests/Refs/H.memguess.ref | cat
- $(run_parallel) $(top_builddir)/src/cluster > H.out
-diff -Naur bigdft-1.2.0.2_orig/tests/H-spin/Makefile.am bigdft-1.2.0.2/tests/H-spin/Makefile.am
---- tests/H-spin/Makefile.am 2010-04-23 15:39:18.000000000 +0000
-+++ tests/H-spin/Makefile.am 2010-04-23 15:38:46.000000000 +0000
-@@ -18,7 +18,5 @@
-
-
- check: $(PPFILES) posinp input.dat
-- cp -f $(top_srcdir)/tests/H-spin/input.dat .
-- cp -f $(top_srcdir)/tests/H-spin/posinp .
- $(run_parallel) $(top_builddir)/src/cluster > H-spin.out
- python $(top_srcdir)/tests/fldiff.py --bigdft H-spin.out $(top_srcdir)/tests/Refs/H-spin.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/H-spin/Makefile.in bigdft-1.2.0.2/tests/H-spin/Makefile.in
---- tests/H-spin/Makefile.in 2010-04-23 15:39:18.000000000 +0000
-+++ tests/H-spin/Makefile.in 2010-04-23 15:38:46.000000000 +0000
-@@ -484,8 +484,6 @@
- cp $(top_srcdir)/utils/PSPfiles/HGH/$@ .
-
- check: $(PPFILES) posinp input.dat
-- cp -f $(top_srcdir)/tests/H-spin/input.dat .
-- cp -f $(top_srcdir)/tests/H-spin/posinp .
- $(run_parallel) $(top_builddir)/src/cluster > H-spin.out
- python $(top_srcdir)/tests/fldiff.py --bigdft H-spin.out $(top_srcdir)/tests/Refs/H-spin.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/H2O-CP2K/Makefile.am bigdft-1.2.0.2/tests/H2O-CP2K/Makefile.am
---- tests/H2O-CP2K/Makefile.am 2008-12-09 16:41:42.000000000 +0000
-+++ tests/H2O-CP2K/Makefile.am 2010-04-23 15:45:57.000000000 +0000
-@@ -20,9 +20,5 @@
- cp $(top_srcdir)/utils/PSPfiles/HGH/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/H2O-CP2K/input.dat .
-- cp -f $(top_srcdir)/tests/H2O-CP2K/posinp .
-- cp -f $(top_srcdir)/tests/H2O-CP2K/gaucoeff.dat .
-- cp -f $(top_srcdir)/tests/H2O-CP2K/gaubasis.dat .
- $(run_parallel) $(top_builddir)/src/cluster > H2O-CP2K.out
- python $(top_srcdir)/tests/fldiff.py --bigdft H2O-CP2K.out $(top_srcdir)/tests/Refs/H2O-CP2K.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/H2O-CP2K/Makefile.in bigdft-1.2.0.2/tests/H2O-CP2K/Makefile.in
---- tests/H2O-CP2K/Makefile.in 2009-06-04 11:52:08.000000000 +0000
-+++ tests/H2O-CP2K/Makefile.in 2010-04-23 15:46:04.000000000 +0000
-@@ -487,10 +487,6 @@
- cp $(top_srcdir)/utils/PSPfiles/HGH/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/H2O-CP2K/input.dat .
-- cp -f $(top_srcdir)/tests/H2O-CP2K/posinp .
-- cp -f $(top_srcdir)/tests/H2O-CP2K/gaucoeff.dat .
-- cp -f $(top_srcdir)/tests/H2O-CP2K/gaubasis.dat .
- $(run_parallel) $(top_builddir)/src/cluster > H2O-CP2K.out
- python $(top_srcdir)/tests/fldiff.py --bigdft H2O-CP2K.out $(top_srcdir)/tests/Refs/H2O-CP2K.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/Li+/Makefile.am bigdft-1.2.0.2/tests/Li+/Makefile.am
---- tests/Li+/Makefile.am 2008-12-09 16:41:42.000000000 +0000
-+++ tests/Li+/Makefile.am 2010-04-23 15:39:48.000000000 +0000
-@@ -18,7 +18,5 @@
-
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/Li+/input.dat .
-- cp -f $(top_srcdir)/tests/Li+/posinp .
- $(run_parallel) $(top_builddir)/src/cluster > Li+.out
- python $(top_srcdir)/tests/fldiff.py --bigdft Li+.out $(top_srcdir)/tests/Refs/Li+.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/Li+/Makefile.in bigdft-1.2.0.2/tests/Li+/Makefile.in
---- tests/Li+/Makefile.in 2009-06-04 11:52:08.000000000 +0000
-+++ tests/Li+/Makefile.in 2010-04-23 15:40:16.000000000 +0000
-@@ -484,8 +484,6 @@
- cp $(top_srcdir)/utils/PSPfiles/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/Li+/input.dat .
-- cp -f $(top_srcdir)/tests/Li+/posinp .
- $(run_parallel) $(top_builddir)/src/cluster > Li+.out
- python $(top_srcdir)/tests/fldiff.py --bigdft Li+.out $(top_srcdir)/tests/Refs/Li+.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/MINHOP/Makefile.am bigdft-1.2.0.2/tests/MINHOP/Makefile.am
---- tests/MINHOP/Makefile.am 2008-12-09 16:41:42.000000000 +0000
-+++ tests/MINHOP/Makefile.am 2010-04-23 15:47:57.000000000 +0000
-@@ -26,13 +26,6 @@
- cp $(top_srcdir)/utils/PSPfiles/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/MINHOP/CPUlimit .
-- cp -f $(top_srcdir)/tests/MINHOP/earr.dat .
-- cp -f $(top_srcdir)/tests/MINHOP/input.dat .
-- cp -f $(top_srcdir)/tests/MINHOP/mdinput.dat .
-- cp -f $(top_srcdir)/tests/MINHOP/ioput .
-- cp -f $(top_srcdir)/tests/MINHOP/rand.inp .
-- cp -f $(top_srcdir)/tests/MINHOP/poscur.xyz .
- rm -f global.mon
- $(run_parallel) $(top_builddir)/src/global > MINHOP.out
- python $(top_srcdir)/tests/fldiff.py global.mon $(top_srcdir)/tests/Refs/global.mon.ref
-diff -Naur bigdft-1.2.0.2_orig/tests/MINHOP/Makefile.in bigdft-1.2.0.2/tests/MINHOP/Makefile.in
---- tests/MINHOP/Makefile.in 2009-06-04 11:52:08.000000000 +0000
-+++ tests/MINHOP/Makefile.in 2010-04-23 15:47:32.000000000 +0000
-@@ -493,13 +493,6 @@
- cp $(top_srcdir)/utils/PSPfiles/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/MINHOP/CPUlimit .
-- cp -f $(top_srcdir)/tests/MINHOP/earr.dat .
-- cp -f $(top_srcdir)/tests/MINHOP/input.dat .
-- cp -f $(top_srcdir)/tests/MINHOP/mdinput.dat .
-- cp -f $(top_srcdir)/tests/MINHOP/ioput .
-- cp -f $(top_srcdir)/tests/MINHOP/rand.inp .
-- cp -f $(top_srcdir)/tests/MINHOP/poscur.xyz .
- rm -f global.mon
- $(run_parallel) $(top_builddir)/src/global > MINHOP.out
- python $(top_srcdir)/tests/fldiff.py global.mon $(top_srcdir)/tests/Refs/global.mon.ref
-diff -Naur bigdft-1.2.0.2_orig/tests/Mn2/Makefile.am bigdft-1.2.0.2/tests/Mn2/Makefile.am
---- tests/Mn2/Makefile.am 2008-12-09 16:41:42.000000000 +0000
-+++ tests/Mn2/Makefile.am 2010-04-23 15:45:33.000000000 +0000
-@@ -18,9 +18,6 @@
- cp $(top_srcdir)/utils/PSPfiles/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/Mn2/input.dat .
-- cp -f $(top_srcdir)/tests/Mn2/posinp .
-- cp -f $(top_srcdir)/tests/Mn2/moments .
- $(top_builddir)/src/memguess 1 > Mn2.memguess
- python $(top_srcdir)/tests/fldiff.py --bigdft Mn2.memguess $(top_srcdir)/tests/Refs/Mn2.memguess.ref | cat
- $(run_parallel) $(top_builddir)/src/cluster > Mn2.out
-diff -Naur bigdft-1.2.0.2_orig/tests/Mn2/Makefile.in bigdft-1.2.0.2/tests/Mn2/Makefile.in
---- tests/Mn2/Makefile.in 2009-06-04 11:52:09.000000000 +0000
-+++ tests/Mn2/Makefile.in 2010-04-23 15:45:40.000000000 +0000
-@@ -485,9 +485,6 @@
- cp $(top_srcdir)/utils/PSPfiles/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/Mn2/input.dat .
-- cp -f $(top_srcdir)/tests/Mn2/posinp .
-- cp -f $(top_srcdir)/tests/Mn2/moments .
- $(top_builddir)/src/memguess 1 > Mn2.memguess
- python $(top_srcdir)/tests/fldiff.py --bigdft Mn2.memguess $(top_srcdir)/tests/Refs/Mn2.memguess.ref | cat
- $(run_parallel) $(top_builddir)/src/cluster > Mn2.out
-diff -Naur bigdft-1.2.0.2_orig/tests/NaCl/Makefile.am bigdft-1.2.0.2/tests/NaCl/Makefile.am
---- tests/NaCl/Makefile.am 2008-12-09 16:41:42.000000000 +0000
-+++ tests/NaCl/Makefile.am 2010-04-23 15:44:03.000000000 +0000
-@@ -24,7 +24,5 @@
- cp $(top_srcdir)/tests/inguess.dat .
-
- check: $(PPFILES) inguess.dat
-- cp -f $(top_srcdir)/tests/NaCl/input.dat .
-- cp -f $(top_srcdir)/tests/NaCl/posinp .
- $(run_parallel) $(top_builddir)/src/cluster > NaCl.out
- python $(top_srcdir)/tests/fldiff.py --bigdft NaCl.out $(top_srcdir)/tests/Refs/NaCl.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/NaCl/Makefile.in bigdft-1.2.0.2/tests/NaCl/Makefile.in
---- tests/NaCl/Makefile.in 2009-06-04 11:52:09.000000000 +0000
-+++ tests/NaCl/Makefile.in 2010-04-23 15:44:12.000000000 +0000
-@@ -491,8 +491,6 @@
- cp $(top_srcdir)/tests/inguess.dat .
-
- check: $(PPFILES) inguess.dat
-- cp -f $(top_srcdir)/tests/NaCl/input.dat .
-- cp -f $(top_srcdir)/tests/NaCl/posinp .
- $(run_parallel) $(top_builddir)/src/cluster > NaCl.out
- python $(top_srcdir)/tests/fldiff.py --bigdft NaCl.out $(top_srcdir)/tests/Refs/NaCl.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/SiBulk/Makefile.am bigdft-1.2.0.2/tests/SiBulk/Makefile.am
---- tests/SiBulk/Makefile.am 2008-12-09 16:41:42.000000000 +0000
-+++ tests/SiBulk/Makefile.am 2010-04-23 15:46:20.000000000 +0000
-@@ -17,7 +17,5 @@
- cp $(top_srcdir)/utils/PSPfiles/HGH/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/SiBulk/input.dat .
-- cp -f $(top_srcdir)/tests/SiBulk/posinp .
- $(run_parallel) $(top_builddir)/src/cluster > SiBulk.out
- python $(top_srcdir)/tests/fldiff.py --bigdft SiBulk.out $(top_srcdir)/tests/Refs/SiBulk.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/SiBulk/Makefile.in bigdft-1.2.0.2/tests/SiBulk/Makefile.in
---- tests/SiBulk/Makefile.in 2009-06-04 11:52:09.000000000 +0000
-+++ tests/SiBulk/Makefile.in 2010-04-23 15:46:28.000000000 +0000
-@@ -484,8 +484,6 @@
- cp $(top_srcdir)/utils/PSPfiles/HGH/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/SiBulk/input.dat .
-- cp -f $(top_srcdir)/tests/SiBulk/posinp .
- $(run_parallel) $(top_builddir)/src/cluster > SiBulk.out
- python $(top_srcdir)/tests/fldiff.py --bigdft SiBulk.out $(top_srcdir)/tests/Refs/SiBulk.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/SiH4/.Makefile.am.swp bigdft-1.2.0.2/tests/SiH4/.Makefile.am.swp
---- tests/SiH4/.Makefile.am.swp 1970-01-01 00:00:00.000000000 +0000
-+++ tests/SiH4/.Makefile.am.swp 2010-04-23 15:42:22.000000000 +0000
-@@ -0,0 +1,3 @@
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nguess.dat wavefunction* SiH4.out posout* *.prc\\0\0 psppar.Si\0 psppar.H \\0PPFILES = \\0\0 posinp \0 input.dat \\0EXTRA_DIST = \\0\0SUBDIRS = \0\0## Process this file with automake to produce Makefile.in\0bigdft-1.2.0.2/tests/MINHOP/Makefile.in\0bigdft-1.2.0.2/tests/MINHOP/Makefile.am\0bigdft-1.2.0.2/tests/GPU/Makefile.in\0bigdft-1.2.0.2/tests/GPU/Makefile.am\0bigdft-1.2.0.2/tests/Davidson-SiH4/Makefile.in\0bigdft-1.2.0.2/tests/Davidson-SiH4/Makefile.am\0bigdft-1.2.0.2/tests/SiBulk/Makefile.in\0bigdft-1.2.0.2/tests/SiBulk/Makefile.am\0bigdft-1.2.0.2/tests/H2O-CP2K/Makefile.in\0bigdft-1.2.0.2/tests/H2O-CP2K/Makefile.am\0bigdft-1.2.0.2/tests/Mn2/Makefile.in\0bigdft-1.2.0.2/tests/Mn2/Makefile.am\0bigdft-1.2.0.2/tests/Ca2/Makefile.in\0bigdft-1.2.0.2/tests/Ca2/Makefile.am\0bigdft-1.2.0.2/tests/C/Makefile.in\0bigdft-1.2.0.2/tests/C/Makefile.am\0bigdft-1.2.0.2/tests/NaCl/Makefile.in\0bigdft-1.2.0.2/tests/NaCl/Makefile.am\0gdft-1.2.0.2/tests/SiH4/Makefile.in\0
-\ No newline at end of file
-diff -Naur bigdft-1.2.0.2_orig/tests/SiH4/Makefile.am bigdft-1.2.0.2/tests/SiH4/Makefile.am
---- tests/SiH4/Makefile.am 2008-12-09 16:41:42.000000000 +0000
-+++ tests/SiH4/Makefile.am 2010-04-23 15:43:36.000000000 +0000
-@@ -18,7 +18,5 @@
- cp $(top_srcdir)/utils/PSPfiles/HGH-K/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/SiH4/input.dat .
-- cp -f $(top_srcdir)/tests/SiH4/posinp .
- $(run_parallel) $(top_builddir)/src/cluster > SiH4.out
- python $(top_srcdir)/tests/fldiff.py --bigdft SiH4.out $(top_srcdir)/tests/Refs/SiH4.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/SiH4/Makefile.in bigdft-1.2.0.2/tests/SiH4/Makefile.in
---- tests/SiH4/Makefile.in 2009-06-04 11:52:09.000000000 +0000
-+++ tests/SiH4/Makefile.in 2010-04-23 15:43:47.000000000 +0000
-@@ -485,8 +485,6 @@
- cp $(top_srcdir)/utils/PSPfiles/HGH-K/$@ .
-
- check: $(PPFILES)
-- cp -f $(top_srcdir)/tests/SiH4/input.dat .
-- cp -f $(top_srcdir)/tests/SiH4/posinp .
- $(run_parallel) $(top_builddir)/src/cluster > SiH4.out
- python $(top_srcdir)/tests/fldiff.py --bigdft SiH4.out $(top_srcdir)/tests/Refs/SiH4.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/sci-libs/bigdft/files/bigdft-1.2.0.5-0001.patch b/sci-libs/bigdft/files/bigdft-1.2.0.5-0001.patch
deleted file mode 100644
index 32f95af..0000000
--- a/sci-libs/bigdft/files/bigdft-1.2.0.5-0001.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- bigdft-1.2.0.5/configure 2011-11-04 15:35:33.000000000 +0100
-+++ bigdft-1.2.0.5-new/configure 2011-11-19 21:06:31.000000000 +0100
-@@ -4736,6 +4736,9 @@
- "mipspro")
- capitalize_module=yes
- capitalize_module_ext="mod" ;;
-+ "open64")
-+ capitalize_module=yes
-+ capitalize_module_ext="mod" ;;
- *)
- capitalize_module=no
- capitalize_module_ext="mod" ;;
-
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch
deleted file mode 100644
index 3ddde70..0000000
--- a/sci-libs/bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch
+++ /dev/null
@@ -1,203 +0,0 @@
-diff -Naur bigdft-1.6-tuto_orig/Makefile.am bigdft-1.6-tuto/Makefile.am
---- Makefile.am 2011-10-18 07:39:52.000000000 +0000
-+++ Makefile.am 2012-03-21 10:08:44.000000000 +0000
-@@ -4,7 +4,10 @@
-
- ACLOCAL_AMFLAGS = -I config/m4
-
--DISTCLEANFILES = config.inc
-+DISTCLEANFILES = config.inc bigdft.pc
-+
-+pkgconfigdir = $(libdir)/pkgconfig
-+pkgconfig_DATA = bigdft.pc
-
- if BUILD_LIBABINIT
- libABINIT_dir = libABINIT/src
-diff -Naur bigdft-1.6-tuto_orig/Makefile.in bigdft-1.6-tuto/Makefile.in
---- Makefile.in 2012-03-21 10:03:28.000000000 +0000
-+++ Makefile.in 2012-03-21 10:20:48.000000000 +0000
-@@ -33,7 +33,7 @@
- POST_UNINSTALL = :
- subdir = .
- DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \
-- $(srcdir)/Makefile.in $(srcdir)/config.h.in \
-+ $(srcdir)/Makefile.in $(srcdir)/bigdft.pc.in $(srcdir)/config.h.in \
- $(top_srcdir)/config/Doxyfile.in $(top_srcdir)/configure \
- AUTHORS COPYING ChangeLog INSTALL NEWS config/depcomp \
- config/install-sh config/missing
-@@ -48,7 +48,7 @@
- configure.lineno config.status.lineno
- mkinstalldirs = $(install_sh) -d
- CONFIG_HEADER = config.h
--CONFIG_CLEAN_FILES = config/Doxyfile
-+CONFIG_CLEAN_FILES = bigdft.pc config/Doxyfile
- CONFIG_CLEAN_VPATH_FILES =
- SOURCES =
- DIST_SOURCES =
-@@ -59,6 +59,35 @@
- install-pdf-recursive install-ps-recursive install-recursive \
- installcheck-recursive installdirs-recursive pdf-recursive \
- ps-recursive uninstall-recursive
-+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
-+am__vpath_adj = case $$p in \
-+ $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
-+ *) f=$$p;; \
-+ esac;
-+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
-+am__install_max = 40
-+am__nobase_strip_setup = \
-+ srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
-+am__nobase_strip = \
-+ for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
-+am__nobase_list = $(am__nobase_strip_setup); \
-+ for p in $$list; do echo "$$p $$p"; done | \
-+ sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
-+ $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
-+ if (++n[$$2] == $(am__install_max)) \
-+ { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
-+ END { for (dir in files) print dir, files[dir] }'
-+am__base_list = \
-+ sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
-+ sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
-+am__uninstall_files_from_dir = { \
-+ test -z "$$files" \
-+ || { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; } \
-+ || { echo " ( cd '$$dir' && rm -f" $$files ")"; \
-+ $(am__cd) "$$dir" && rm -f $$files; }; \
-+ }
-+am__installdirs = "$(DESTDIR)$(pkgconfigdir)"
-+DATA = $(pkgconfig_DATA)
- RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
- distclean-recursive maintainer-clean-recursive
- AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
-@@ -232,7 +261,9 @@
- config/m4
-
- ACLOCAL_AMFLAGS = -I config/m4
--DISTCLEANFILES = config.inc
-+DISTCLEANFILES = config.inc bigdft.pc
-+pkgconfigdir = $(libdir)/pkgconfig
-+pkgconfig_DATA = bigdft.pc
- @BUILD_LIBABINIT_FALSE@libABINIT_dir =
- @BUILD_LIBABINIT_TRUE@libABINIT_dir = libABINIT/src
- @BUILD_LIBXC_FALSE@libXC_dir =
-@@ -307,8 +338,28 @@
-
- distclean-hdr:
- -rm -f config.h stamp-h1
-+bigdft.pc: $(top_builddir)/config.status $(srcdir)/bigdft.pc.in
-+ cd $(top_builddir) && $(SHELL) ./config.status $@
- config/Doxyfile: $(top_builddir)/config.status $(top_srcdir)/config/Doxyfile.in
- cd $(top_builddir) && $(SHELL) ./config.status $@
-+install-pkgconfigDATA: $(pkgconfig_DATA)
-+ @$(NORMAL_INSTALL)
-+ test -z "$(pkgconfigdir)" || $(MKDIR_P) "$(DESTDIR)$(pkgconfigdir)"
-+ @list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
-+ for p in $$list; do \
-+ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
-+ echo "$$d$$p"; \
-+ done | $(am__base_list) | \
-+ while read files; do \
-+ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(pkgconfigdir)'"; \
-+ $(INSTALL_DATA) $$files "$(DESTDIR)$(pkgconfigdir)" || exit $$?; \
-+ done
-+
-+uninstall-pkgconfigDATA:
-+ @$(NORMAL_UNINSTALL)
-+ @list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
-+ files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
-+ dir='$(DESTDIR)$(pkgconfigdir)'; $(am__uninstall_files_from_dir)
-
- # This directory's subdirectories are mostly independent; you can cd
- # into them and run `make' without going through this Makefile.
-@@ -622,9 +673,12 @@
- exit 1; } >&2
- check-am: all-am
- check: check-recursive
--all-am: Makefile config.h
-+all-am: Makefile $(DATA) config.h
- installdirs: installdirs-recursive
- installdirs-am:
-+ for dir in "$(DESTDIR)$(pkgconfigdir)"; do \
-+ test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-+ done
- install: install-recursive
- install-exec: install-exec-recursive
- install-data: install-data-recursive
-@@ -672,7 +726,7 @@
-
- info-am:
-
--install-data-am:
-+install-data-am: install-pkgconfigDATA
-
- install-dvi: install-dvi-recursive
-
-@@ -718,7 +772,7 @@
-
- ps-am:
-
--uninstall-am:
-+uninstall-am: uninstall-pkgconfigDATA
-
- .MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \
- ctags-recursive install-am install-strip tags-recursive
-@@ -733,10 +787,10 @@
- install-data-am install-dvi install-dvi-am install-exec \
- install-exec-am install-html install-html-am install-info \
- install-info-am install-man install-pdf install-pdf-am \
-- install-ps install-ps-am install-strip installcheck \
-+ install-pkgconfigDATA install-ps install-ps-am install-strip installcheck \
- installcheck-am installdirs installdirs-am maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
-- pdf-am ps ps-am tags tags-recursive uninstall uninstall-am
-+ pdf-am ps ps-am tags tags-recursive uninstall uninstall-am uninstall-pkgconfigDATA
-
- configure
-
-diff -Naur bigdft-1.6-tuto_orig/bigdft.pc.in bigdft-1.6-tuto/bigdft.pc.in
---- bigdft.pc.in 1970-01-01 00:00:00.000000000 +0000
-+++ bigdft.pc.in 2012-02-01 09:43:59.000000000 +0000
-@@ -0,0 +1,11 @@
-+prefix=@prefix@
-+exec_prefix=@exec_prefix@
-+libdir=@libdir@
-+includedir=@includedir@
-+
-+Name: libbigdft
-+Description: Library for DFT calculation over wavelets.
-+Requires:
-+Version: @VERSION@
-+Libs: -L${libdir} -lbigdft -lpoissonsolver @LIBS@ @FCLIBS@
-+Cflags: -I${includedir}
-diff -Naur bigdft-1.6-tuto_orig/configure bigdft-1.6-tuto/configure
---- configure 2012-03-21 10:03:26.000000000 +0000
-+++ configure 2012-03-21 11:04:52.000000000 +0000
-@@ -8512,7 +8512,7 @@
- docdir="${docdir}"
-
-
--ac_config_files="$ac_config_files Makefile libABINIT/src/Makefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile"
-+ac_config_files="$ac_config_files Makefile bigdft.pc libABINIT/src/Makefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile"
-
-
- # Call libXC ./configure script recursively.
-@@ -9349,6 +9349,7 @@
- "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;;
- "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
- "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
-+ "bigdft.pc") CONFIG_FILES="$CONFIG_FILES bigdft.pc" ;;
- "libABINIT/src/Makefile") CONFIG_FILES="$CONFIG_FILES libABINIT/src/Makefile" ;;
- "config/Doxyfile") CONFIG_FILES="$CONFIG_FILES config/Doxyfile" ;;
- "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
-diff -Naur bigdft-1.6-tuto_orig/configure.ac bigdft-1.6-tuto/configure.ac
---- configure.ac 2012-03-21 10:03:02.000000000 +0000
-+++ configure.ac 2012-03-21 10:48:53.000000000 +0000
-@@ -715,6 +715,7 @@
- dnl Give the name of file.in to transform to file
- AC_CONFIG_FILES([
- Makefile
-+bigdft.pc
- libABINIT/src/Makefile
- config/Doxyfile
- src/Makefile
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto-libxc_dir_include.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto-libxc_dir_include.patch
deleted file mode 100644
index 16aca5e..0000000
--- a/sci-libs/bigdft/files/bigdft-1.6-tuto-libxc_dir_include.patch
+++ /dev/null
@@ -1,50 +0,0 @@
---- configure.ac.orig 2011-11-23 14:02:15.000000000 +0000
-+++ configure.ac 2011-11-23 14:09:19.000000000 +0000
-@@ -564,14 +564,17 @@
- dnl Test the libXC library
- ac_internal_libxc="yes"
- AC_ARG_ENABLE(internal-libxc, AS_HELP_STRING([--disable-internal-libxc], [Do not build and link with internal libXC library (default = yes).]), ac_internal_libxc=$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=)
- ac_use_libxc="no"
- 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="$LDFLAGS -L\$(top_builddir)/libxc-1.1.0/src/.libs"
-@@ -579,6 +582,9 @@
- else
- if test -n "$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"
-@@ -587,13 +593,13 @@
- 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.$capitalize_module_ext, funcs="yes", funcs="no")
-- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_lib_m.$capitalize_module_ext, lib="yes", lib="no")
-- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_types_m.$capitalize_module_ext, types="yes", types="no")
-+ AC_CHECK_FILE($ac_libxc_dir_include/libxc_funcs_m.$capitalize_module_ext, funcs="yes", funcs="no")
-+ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_lib_m.$capitalize_module_ext, lib="yes", lib="no")
-+ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_types_m.$capitalize_module_ext, types="yes", types="no")
- if test "$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-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index 5af1279..4e3f27e 100644
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@ -2,6 +2,14 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*abinit-6.12.2 (30 Mar 2012)
+
+ 30 Mar 2012; Honza MacháÄek <Hloupy.Honza@centrum.cz>
+ -files/6.12.1-bigDFT-1.6.0.patch, -files/6.6.1-openmp.patch,
+ -files/6.12.1-gui-conf.patch, -abinit-6.6.3.ebuild, -abinit-6.8.2.ebuild,
+ -abinit-6.10.3.ebuild, -abinit-6.12.1.ebuild, +abinit-6.12.2.ebuild:
+ Version bump, tests, clean-up.
+
23 Mar 2012; Honza MacháÄek <Hloupy.Honza@centrum.cz> abinit-6.12.1.ebuild:
Fortran setup improvement in 6.12.1 ebuild corrected, gui preparation corrected.
diff --git a/sci-physics/abinit/abinit-6.10.3.ebuild b/sci-physics/abinit/abinit-6.10.3.ebuild
deleted file mode 100644
index f073558..0000000
--- a/sci-physics/abinit/abinit-6.10.3.ebuild
+++ /dev/null
@@ -1,251 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="3"
-
-inherit autotools eutils 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/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cuda -debug +fftw +fftw-threads +fox gsl gui +hdf5 mpi +netcdf python -test +threads -vdwxc"
-
-RDEPEND=">=sci-libs/bigdft-1.2.0.5
- sci-libs/etsf_io
- =sci-libs/libxc-1*[fortran]
- sci-physics/atompaw[libxc]
- fox? ( sci-libs/fox[dom,sax,wcml,wxml] )
- netcdf? (
- sci-libs/netcdf[fortran]
- hdf5? (
- sci-libs/netcdf[fortran,hdf5]
- )
- )
- hdf5? ( sci-libs/hdf5[fortran] )
- sci-libs/wannier90
- virtual/blas
- virtual/lapack
- gsl? ( sci-libs/gsl )
- fftw? (
- sci-libs/fftw:3.0
- fftw-threads? ( sci-libs/fftw:3.0[threads] )
- )
- mpi? ( virtual/mpi )
- python? ( dev-python/numpy )
- cuda? ( dev-util/nvidia-cuda-sdk )"
-DEPEND="${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=""
-
-pkg_setup() {
- fortran-2_pkg_setup
- # Doesn't compile with gcc-4.0, only >=4.1
- if [[ $(tc-getFC) == *gfortran ]]; then
- if [[ $(gcc-major-version) -eq 4 ]] \
- && [[ $(gcc-minor-version) -lt 1 ]]; then
- die "Requires gcc-4.1 or newer"
- fi
- fi
- if use fftw-threads && ! use fftw; then
- ewarn "fftw-threads set but fftw not used, ignored"
- fi
- if use gui; then
- lat1loc="$(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
- epatch "${FILESDIR}"/6.0.3-fftw.patch
- eautoreconf
-}
-
-src_configure() {
- local libs="-L/usr/$(get_libdir)"
- local modules="-I/usr/$(get_libdir)/finclude"
- local FoX_libs="${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lFoX_common -lFoX_utils -lFoX_fsys"
- local trio_flavor="etsf_io"
- use fox && trio_flavor="${trio_flavor}+fox"
- use netcdf && trio_flavor="${trio_flavor}+netcdf"
- local netcdff_libs="-lnetcdff"
- use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran"
- local fft_flavor="fftw3"
- local fft_libs="-L/usr/lib"
- # The fftw threads support is protected by black magick.
- # Anybody removes it, dies.
- # New USE flag "fftw-threads" was added to control usage
- # of the threaded fftw variant. Since fftw-3.3 has expanded
- # the paralel options by MPI and OpenMP support, analogical
- # USE flags should be added to select them in future;
- # unusable with previous FFTW versions, they are postponed
- # for now.
- if use fftw-threads; then
- fft_flavor="fftw3-threads"
- if has_version '>=sci-libs/fftw-3.3'; then
- # pkg-config files for fftw-3.3 are broken
- # All the parallel stuff is separated
- # from the main body of common routines,
- # and -lfftw3 must be always included alongside.
- # Until version 3.3 this used to be masked by
- # .la files.
- # Bug 384645
- fft_libs="${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} $(pkg-config --libs fftw3)"
- fi
- if use mpi; then
- MY_FC="mpif90"
- MY_CC="mpicc"
- MY_CXX="mpic++"
- else
- MY_FC="$(tc-getFC)"
- MY_CC="$(tc-getCC)"
- MY_CXX="$(tc-getCXX)"
- fi
- MARKDOWN=Markdown.pl econf \
- $(use_enable debug debug enhanced) \
- $(use_enable mpi) \
- $(use_enable mpi mpi-io) \
- --disable-smp \
- $(use_enable vdwxc) \
- $(use_enable cuda gpu) \
- "$(use cuda && echo "--with-gpu-flavor=cuda-single")" \
- "$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")" \
- "$(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=${FoX_libs}")" \
- --with-etsf-io-incs="${modules}" \
- --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="${libs} -lpoissonsolver -lbigdft" \
- --with-atompaw-incs="${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" \
- FC="${MY_FC}" \
- CC="${MY_CC}" \
- CXX="${MY_CXX}" \
- LD="$(tc-getLD)" \
- FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include"
-
- if use gui; then
- cd gui
- ./bootstrap.sh
- econf
- fi
-}
-
-src_compile() {
- emake || die "make failed"
-
- if use gui; then
- cd gui
- LC_CTYPE="${lat1loc}" emake || die "Making GUI failed"
- fi
-}
-
-src_test() {
- einfo "The tests take quite a while, on the order of 1-2 hours"
- einfo "on an Intel Penryn (2.5 GHz)."
- cd "${S}"/tests
- emake tests_min || ewarn "Minimal 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 tdft || ewarn "TDFT tests failed"
- emake tests_bench || ewarn "Benchmarks 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 ${testdir}
- fi
- done
-
- elog "The full test results will be installed as summary_of_tests.tar.bz2."
- elog "Also a concise report tests_summary.txt is installed."
-}
-
-src_install() {
- emake DESTDIR="${D}" install || die "make install failed"
-
- if use test; then
- dodoc tests/tests_summary.txt || ewarn "Copying tests summary failed"
- dodoc tests/summary_tests.tar || ewarn "Copying tests results failed"
- dodoc tests/summary_of_tests.tar || ewarn "Copying tests results failed"
- fi
-
- if use gui; then
- ( cd gui
- emake DESTDIR="${D}" install || die "The GUI install failed" )
- fi
-
-
- dodoc KNOWN_PROBLEMS README || die "Copying doc files failed"
-}
-
-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/abinit-6.12.1.ebuild b/sci-physics/abinit/abinit-6.12.2.ebuild
similarity index 98%
rename from sci-physics/abinit/abinit-6.12.1.ebuild
rename to sci-physics/abinit/abinit-6.12.2.ebuild
index 59f0f98..ddb4355 100644
--- a/sci-physics/abinit/abinit-6.12.1.ebuild
+++ b/sci-physics/abinit/abinit-6.12.2.ebuild
@@ -253,12 +253,13 @@ src_test() {
# again something the autotools-utils function cannot be called to do
# now quite a lot of work actually
cd tests
- emake tests_min || ewarn "Minimal tests failed"
+ 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 tdft || ewarn "TDFT tests failed"
- emake tests_bench || ewarn "Benchmarks 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
diff --git a/sci-physics/abinit/abinit-6.6.3.ebuild b/sci-physics/abinit/abinit-6.6.3.ebuild
deleted file mode 100644
index 3799d05..0000000
--- a/sci-physics/abinit/abinit-6.6.3.ebuild
+++ /dev/null
@@ -1,196 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="3"
-
-inherit autotools eutils 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/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cuda -debug +fftw +fox gsl +hdf5 mpi +netcdf python -test +threads -vdwxc"
-
-RDEPEND=">=sci-libs/bigdft-1.2.0.2
- sci-libs/etsf_io
- =sci-libs/libxc-1.0[fortran]
- sci-physics/atompaw[libxc]
- fox? ( sci-libs/fox[dom,sax,wcml,wxml] )
- netcdf? (
- sci-libs/netcdf[fortran]
- hdf5? (
- sci-libs/netcdf[fortran,hdf5]
- )
- )
- hdf5? ( sci-libs/hdf5[fortran] )
- sci-libs/wannier90
- virtual/blas
- virtual/lapack
- gsl? ( sci-libs/gsl )
- fftw? (
- sci-libs/fftw:3.0
- threads? ( sci-libs/fftw:3.0[threads] )
- )
- mpi? ( virtual/mpi )
- python? ( dev-python/numpy )
- cuda? ( dev-util/nvidia-cuda-sdk )"
-DEPEND="${RDEPEND}
- dev-util/pkgconfig
- dev-perl/Text-Markdown"
-
-S=${WORKDIR}/${P%[a-z]}
-
-pkg_setup() {
- fortran-2_pkg_setup
- # Doesn't compile with gcc-4.0, only >=4.1
- if [[ $(tc-getFC) == *gfortran ]]; then
- if [[ $(gcc-major-version) -eq 4 ]] \
- && [[ $(gcc-minor-version) -lt 1 ]]; then
- die "Requires gcc-4.1 or newer"
- fi
- fi
-}
-
-src_prepare() {
- epatch "${FILESDIR}"/6.2.2-change-default-directories.patch
- epatch "${FILESDIR}"/6.0.3-fftw.patch
- eautoreconf
-}
-
-src_configure() {
- local libs="-L/usr/$(get_libdir)"
- local modules="-I/usr/$(get_libdir)/finclude"
- local FoX_libs="${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lFoX_common -lFoX_utils -lFoX_fsys"
- local trio_flavor="etsf_io"
- use fox && trio_flavor="${trio_flavor}+fox"
- use netcdf && trio_flavor="${trio_flavor}+netcdf"
- local netcdff_libs="-lnetcdff"
- use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran"
- local fft_flavor="fftw3"
- local fft_libs="-L/usr/lib"
- # Since now, fftw threads support is protected by black magick.
- # Anybody removes it again, dies.
- # If it does not work FOR YOU, disable the "threads" USE flag
- # for the package at YOUR box. If YOU want it disabled selectively
- # for fftw use in abinit, you may consider adding a special USE flag
- # for that. NEVER REMOVE AN OPTION FOR OTHERS, at least if there is
- # anybody it works for.
- if use threads; then
- fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads)"
- fft_flavor="fftw3-threads"
- else
- fft_libs="${fft_libs} $(pkg-config --libs fftw3)"
- fi
- if use mpi; then
- MY_FC="mpif90"
- MY_CC="mpicc"
- MY_CXX="mpic++"
- else
- MY_FC="$(tc-getFC)"
- MY_CC="$(tc-getCC)"
- MY_CXX="$(tc-getCXX)"
- fi
- MARKDOWN=Markdown.pl econf \
- $(use_enable debug debug enhanced) \
- $(use_enable mpi) \
- $(use_enable mpi mpi-io) \
- --disable-smp \
- $(use_enable vdwxc) \
- $(use_enable cuda gpu) \
- "$(use cuda && echo "--with-gpu-flavor=cuda-single")" \
- "$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")" \
- "$(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=${FoX_libs}")" \
- --with-etsf-io-incs="${modules}" \
- --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="${libs} -lpoissonsolver -lbigdft" \
- --with-atompaw-incs="${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" \
- FC="${MY_FC}" \
- CC="${MY_CC}" \
- CXX="${MY_CXX}" \
- LD="$(tc-getLD)" \
- FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include"
-}
-
-src_compile() {
- emake || die
-}
-
-src_test() {
- einfo "The tests take quite a while, on the order of 1-2 hours"
- einfo "on an Intel Penryn (2.5 GHz)."
- cd "${S}"/tests
- emake tests_min || ewarn "Minimal 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 tdft || ewarn "TDFT tests failed"
- emake tests_bench || ewarn "Benchmarks 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 ${testdir}
- fi
- done
-
- elog "The full test results will be installed as summary_of_tests.tar.bz2."
- elog "Also a concise report tests_summary.txt is installed."
-}
-
-src_install() {
- emake DESTDIR="${D}" install || die "make install failed"
-
- if use test; then
- dodoc tests/tests_summary.txt || ewarn "Copying tests summary failed"
- dodoc tests/summary_tests.tar || ewarn "Copying tests results failed"
- dodoc tests/summary_of_tests.tar || ewarn "Copying tests results failed"
- fi
-
- dodoc KNOWN_PROBLEMS README || die "Copying doc files failed"
-}
-
-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/abinit-6.8.2.ebuild b/sci-physics/abinit/abinit-6.8.2.ebuild
deleted file mode 100644
index cdd495f..0000000
--- a/sci-physics/abinit/abinit-6.8.2.ebuild
+++ /dev/null
@@ -1,211 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="3"
-
-inherit autotools eutils 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/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cuda -debug +fftw +fftw-threads +fox gsl +hdf5 mpi +netcdf python -test +threads -vdwxc"
-
-RDEPEND=">=sci-libs/bigdft-1.2.0.2
- sci-libs/etsf_io
- =sci-libs/libxc-1.0[fortran]
- sci-physics/atompaw[libxc]
- fox? ( sci-libs/fox[dom,sax,wcml,wxml] )
- netcdf? (
- sci-libs/netcdf[fortran]
- hdf5? (
- sci-libs/netcdf[fortran,hdf5]
- )
- )
- hdf5? ( sci-libs/hdf5[fortran] )
- sci-libs/wannier90
- virtual/blas
- virtual/lapack
- gsl? ( sci-libs/gsl )
- fftw? (
- sci-libs/fftw:3.0
- fftw-threads? ( sci-libs/fftw:3.0[threads] )
- )
- mpi? ( virtual/mpi )
- python? ( dev-python/numpy )
- cuda? ( dev-util/nvidia-cuda-sdk )"
-DEPEND="${RDEPEND}
- dev-util/pkgconfig
- dev-perl/Text-Markdown"
-
-S=${WORKDIR}/${P%[a-z]}
-
-pkg_setup() {
- fortran-2_pkg_setup
- # Doesn't compile with gcc-4.0, only >=4.1
- if [[ $(tc-getFC) == *gfortran ]]; then
- if [[ $(gcc-major-version) -eq 4 ]] \
- && [[ $(gcc-minor-version) -lt 1 ]]; then
- die "Requires gcc-4.1 or newer"
- fi
- fi
- if use fftw-threads && ! use fftw; then
- ewarn "fftw-threads set but fftw not used, ignored"
- fi
-}
-
-src_prepare() {
- epatch "${FILESDIR}"/6.2.2-change-default-directories.patch
- epatch "${FILESDIR}"/6.0.3-fftw.patch
- eautoreconf
-}
-
-src_configure() {
- local libs="-L/usr/$(get_libdir)"
- local modules="-I/usr/$(get_libdir)/finclude"
- local FoX_libs="${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lFoX_common -lFoX_utils -lFoX_fsys"
- local trio_flavor="etsf_io"
- use fox && trio_flavor="${trio_flavor}+fox"
- use netcdf && trio_flavor="${trio_flavor}+netcdf"
- local netcdff_libs="-lnetcdff"
- use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran"
- local fft_flavor="fftw3"
- local fft_libs="-L/usr/lib"
- # The fftw threads support is protected by black magick.
- # Anybody removes it, dies.
- # New USE flag "fftw-threads" was added to control usage
- # of the threaded fftw variant. Since fftw-3.3 has expanded
- # the paralel options by MPI and OpenMP support, analogical
- # USE flags should be added to select them in future;
- # unusable with previous FFTW versions, they are postponed
- # for now.
- if use fftw-threads; then
- fft_flavor="fftw3-threads"
- if has_version '>=sci-libs/fftw-3.3'; then
- # pkg-config files for fftw-3.3 are broken
- # All the parallel stuff is separated
- # from the main body of common routines,
- # and -lfftw3 must be always included alongside.
- # Until version 3.3 this used to be masked by
- # .la files.
- # Bug 384645
- fft_libs="${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} $(pkg-config --libs fftw3)"
- fi
- if use mpi; then
- MY_FC="mpif90"
- MY_CC="mpicc"
- MY_CXX="mpic++"
- else
- MY_FC="$(tc-getFC)"
- MY_CC="$(tc-getCC)"
- MY_CXX="$(tc-getCXX)"
- fi
- MARKDOWN=Markdown.pl econf \
- $(use_enable debug debug enhanced) \
- $(use_enable mpi) \
- $(use_enable mpi mpi-io) \
- --disable-smp \
- $(use_enable vdwxc) \
- $(use_enable cuda gpu) \
- "$(use cuda && echo "--with-gpu-flavor=cuda-single")" \
- "$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")" \
- "$(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=${FoX_libs}")" \
- --with-etsf-io-incs="${modules}" \
- --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="${libs} -lpoissonsolver -lbigdft" \
- --with-atompaw-incs="${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" \
- FC="${MY_FC}" \
- CC="${MY_CC}" \
- CXX="${MY_CXX}" \
- LD="$(tc-getLD)" \
- FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include"
-}
-
-src_compile() {
- emake || die
-}
-
-src_test() {
- einfo "The tests take quite a while, on the order of 1-2 hours"
- einfo "on an Intel Penryn (2.5 GHz)."
- cd "${S}"/tests
- emake tests_min || ewarn "Minimal 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 tdft || ewarn "TDFT tests failed"
- emake tests_bench || ewarn "Benchmarks 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 ${testdir}
- fi
- done
-
- elog "The full test results will be installed as summary_of_tests.tar.bz2."
- elog "Also a concise report tests_summary.txt is installed."
-}
-
-src_install() {
- emake DESTDIR="${D}" install || die "make install failed"
-
- if use test; then
- dodoc tests/tests_summary.txt || ewarn "Copying tests summary failed"
- dodoc tests/summary_tests.tar || ewarn "Copying tests results failed"
- dodoc tests/summary_of_tests.tar || ewarn "Copying tests results failed"
- fi
-
- dodoc KNOWN_PROBLEMS README || die "Copying doc files failed"
-}
-
-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/6.12.1-bigDFT-1.6.0.patch b/sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch
deleted file mode 100644
index 857a27a..0000000
--- a/sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_descr_psp_set.F90 abinit-6.12.1/src/42_wvl_wrappers/wvl_descr_psp_set.F90
---- src/42_wvl_wrappers/wvl_descr_psp_set.F90 2012-01-30 20:43:51.000000000 +0000
-+++ src/42_wvl_wrappers/wvl_descr_psp_set.F90 2012-03-19 13:06:59.000000000 +0000
-@@ -105,7 +105,7 @@
- ! Missing currently read radii_cf.
- wvl%atoms%donlcc = .false.
- ! TODO: add symmetry support
-- wvl%atoms%symObj = -1
-+ wvl%atoms%sym%symObj = -1
- #endif
- end subroutine wvl_descr_psp_set
- !!***
-diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_projectors_set.F90 abinit-6.12.1/src/42_wvl_wrappers/wvl_projectors_set.F90
---- src/42_wvl_wrappers/wvl_projectors_set.F90 2012-01-30 20:43:50.000000000 +0000
-+++ src/42_wvl_wrappers/wvl_projectors_set.F90 2012-03-19 13:17:37.000000000 +0000
-@@ -122,7 +122,7 @@
- ABI_ALLOCATE(xcart,(3, natom))
- call xredxcart(natom, 1, rprimd, xcart, xred)
-
-- call createProjectorsArrays(me, wfs%Glr%d%n1, wfs%Glr%d%n2, wfs%Glr%d%n3, &
-+ call createProjectorsArrays(me, wfs%Glr, &
- & xcart, wvl%atoms, wfs%orbs, psps%gth_params%radii_cf, &
- & wvl_frmult, wvl_frmult, wvl%h(1), wvl%h(2), wvl%h(3), proj%keys, proj%proj)
- write(message, '(a,a,a,a,I0)' ) ch10,&
-diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_wfs_free.F90 abinit-6.12.1/src/42_wvl_wrappers/wvl_wfs_free.F90
---- src/42_wvl_wrappers/wvl_wfs_free.F90 2012-01-30 20:43:50.000000000 +0000
-+++ src/42_wvl_wrappers/wvl_wfs_free.F90 2012-03-19 13:01:03.000000000 +0000
-@@ -68,7 +68,7 @@
- #if defined HAVE_DFT_BIGDFT
- call deallocate_lr(wfs%Glr, sub)
- call deallocate_orbs(wfs%orbs, sub)
-- call deallocate_diis_objects(wfs%diis, sub)
-+ ! call deallocate_diis_objects(wfs%diis, sub)
- call deallocate_comms(wfs%comms, sub)
- if (associated(wfs%orbs%eval)) then
- ABI_DEALLOCATE(wfs%orbs%eval)
-diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_wfs_set.F90 abinit-6.12.1/src/42_wvl_wrappers/wvl_wfs_set.F90
---- src/42_wvl_wrappers/wvl_wfs_set.F90 2012-01-30 20:43:55.000000000 +0000
-+++ src/42_wvl_wrappers/wvl_wfs_set.F90 2012-03-19 12:58:54.000000000 +0000
-@@ -59,7 +59,7 @@
- use defs_wvltypes
- #if defined HAVE_DFT_BIGDFT
- use BigDFT_API, only: createWavefunctionsDescriptors, orbitals_descriptors, &
-- & orbitals_communicators, allocate_diis_objects, wvl_timing => timing
-+ & orbitals_communicators, wvl_timing => timing
- #endif
-
- !This section has been created automatically by the script Abilint (TD).
-@@ -179,9 +179,9 @@
- call wvl_timing(me,'CrtDescriptors','OF')
-
- ! allocate arrays necessary for DIIS convergence acceleration
-- call allocate_diis_objects(nwfshist,1._dp,&
-- & sum(wfs%comms%ncntt(0:nproc-1)), wfs%orbs%nkptsp, wfs%orbs%nspinor, &
-- & wfs%orbs%norbd, wfs%diis, "wvl_init_wfs_type")
-+ ! call allocate_diis_objects(nwfshist,1._dp,&
-+ ! & sum(wfs%comms%ncntt(0:nproc-1)), wfs%orbs%nkptsp, wfs%orbs%nspinor, &
-+ ! & wfs%orbs%norbd, wfs%diis, "wvl_init_wfs_type")
-
- #else
- write(message, '(a,a,a,a)' ) ch10,&
diff --git a/sci-physics/abinit/files/6.12.1-gui-conf.patch b/sci-physics/abinit/files/6.12.1-gui-conf.patch
deleted file mode 100644
index 95c12b3..0000000
--- a/sci-physics/abinit/files/6.12.1-gui-conf.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur abinit-6.12.1_orig/gui/configure abinit-6.12.1/gui/configure
---- gui/configure 2012-01-30 19:42:26.000000000 +0000
-+++ gui/configure 2012-03-16 13:38:54.000000000 +0000
-@@ -3143,7 +3143,7 @@
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
-- ac_cv_prog_UUDECODE="no"
-+ ac_cv_prog_UUDECODE="$as_dir/$ac_word$ac_exec_ext"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
diff --git a/sci-physics/abinit/files/6.6.1-openmp.patch b/sci-physics/abinit/files/6.6.1-openmp.patch
deleted file mode 100644
index af43d57..0000000
--- a/sci-physics/abinit/files/6.6.1-openmp.patch
+++ /dev/null
@@ -1,509 +0,0 @@
-diff -Naur abinit-6.6.1.orig/src/52_fft_mpi_noabirule/accrho.F90 abinit-6.6.1/src/52_fft_mpi_noabirule/accrho.F90
---- src/52_fft_mpi_noabirule/accrho.F90 2011-02-28 05:14:13.000000000 +0000
-+++ src/52_fft_mpi_noabirule/accrho.F90 2011-03-01 19:41:35.000000000 +0000
-@@ -91,14 +91,14 @@
- integer unused
- unused=0
- ! *************************************************************************
--!$ interface
--!$ integer ( kind=4 ) function omp_get_num_threads ( )
--!$ end function omp_get_num_threads
--!$ end interface
--!$ interface
--!$ integer ( kind=4 ) function omp_get_thread_num ( )
--!$ end function omp_get_thread_num
--!$ end interface
-+!% interface
-+!% integer ( kind=4 ) function omp_get_num_threads ( )
-+!% end function omp_get_num_threads
-+!% end interface
-+!% interface
-+!% integer ( kind=4 ) function omp_get_thread_num ( )
-+!% end function omp_get_thread_num
-+!% end interface
-
- write(6,*)' accrho : enter '
-
-diff -Naur abinit-6.6.1.orig/src/52_fft_mpi_noabirule/applypot.F90 abinit-6.6.1/src/52_fft_mpi_noabirule/applypot.F90
---- src/52_fft_mpi_noabirule/applypot.F90 2011-02-28 05:14:13.000000000 +0000
-+++ src/52_fft_mpi_noabirule/applypot.F90 2011-03-01 19:43:37.000000000 +0000
-@@ -91,14 +91,14 @@
- integer unused
- unused=0
-
--!$ interface
--!$ integer ( kind=4 ) function omp_get_num_threads ( )
--!$ end function omp_get_num_threads
--!$ end interface
--!$ interface
--!$ integer ( kind=4 ) function omp_get_thread_num ( )
--!$ end function omp_get_thread_num
--!$ end interface
-+!% interface
-+!% integer ( kind=4 ) function omp_get_num_threads ( )
-+!% end function omp_get_num_threads
-+!% end interface
-+!% interface
-+!% integer ( kind=4 ) function omp_get_thread_num ( )
-+!% end function omp_get_thread_num
-+!% end interface
-
- write(6,*)' applypot : enter '
-
-diff -Naur abinit-6.6.1.orig/src/52_fft_mpi_noabirule/back.F90 abinit-6.6.1/src/52_fft_mpi_noabirule/back.F90
---- src/52_fft_mpi_noabirule/back.F90 2011-02-28 05:14:13.000000000 +0000
-+++ src/52_fft_mpi_noabirule/back.F90 2011-03-01 19:45:45.000000000 +0000
-@@ -90,14 +90,14 @@
- #endif
- ! *************************************************************************
-
--!$ interface
--!$ integer ( kind=4 ) function omp_get_num_threads ( )
--!$ end function omp_get_num_threads
--!$ end interface
--!$ interface
--!$ integer ( kind=4 ) function omp_get_thread_num ( )
--!$ end function omp_get_thread_num
--!$ end interface
-+!% interface
-+!% integer ( kind=4 ) function omp_get_num_threads ( )
-+!% end function omp_get_num_threads
-+!% end interface
-+!% interface
-+!% integer ( kind=4 ) function omp_get_thread_num ( )
-+!% end function omp_get_thread_num
-+!% end interface
-
- !DEBUG
- ! write(6,*)' back : enter '
-@@ -121,7 +121,7 @@
-
- lock=0
- !$omp parallel default(private) &
--!$omp shared(ndat,n1,n2,n3,nd1,nd2,nd3,nd2proc,nd3proc,mpi_enreg%me_fft,mpi_enreg%nproc_fft,ncache,zr,zf,lock,icplex)
-+!$omp shared(ndat,n1,n2,n3,nd1,nd2,nd3,nd2proc,nd3proc,mpi_enreg,ncache,zr,zf,lock,icplex)
-
- iam=0
- npr=1
-diff -Naur abinit-6.6.1.orig/src/52_fft_mpi_noabirule/forw.F90 abinit-6.6.1/src/52_fft_mpi_noabirule/forw.F90
---- src/52_fft_mpi_noabirule/forw.F90 2011-02-28 05:14:13.000000000 +0000
-+++ src/52_fft_mpi_noabirule/forw.F90 2011-03-01 19:46:53.000000000 +0000
-@@ -95,14 +95,14 @@
- integer :: old_paral_level
- #endif
- ! *************************************************************************
--!$ interface
--!$ integer ( kind=4 ) function omp_get_num_threads ( )
--!$ end function omp_get_num_threads
--!$ end interface
--!$ interface
--!$ integer ( kind=4 ) function omp_get_thread_num ( )
--!$ end function omp_get_thread_num
--!$ end interface
-+!% interface
-+!% integer ( kind=4 ) function omp_get_num_threads ( )
-+!% end function omp_get_num_threads
-+!% end interface
-+!% interface
-+!% integer ( kind=4 ) function omp_get_thread_num ( )
-+!% end function omp_get_thread_num
-+!% end interface
-
- !DEBUG
- ! write(6,*)' forw : enter '
-@@ -134,7 +134,7 @@
-
- lock=0
- !$omp parallel default(private) &
--!$omp shared(ndat,n1,n2,n3,nd1,nd2,nd3,nd2proc,nd3proc,mpi_enreg%me_fft,mpi_enreg%nproc_fft,ncache,zr,zf,lock,icplex)
-+!$omp shared(ndat,n1,n2,n3,nd1,nd2,nd3,nd2proc,nd3proc,mpi_enreg,ncache,zr,zf,lock,icplex)
-
- iam=0
- npr=1
-diff -Naur abinit-6.6.1.orig/src/53_ffts/fftw3_fourwf.F90 abinit-6.6.1/src/53_ffts/fftw3_fourwf.F90
---- src/53_ffts/fftw3_fourwf.F90 2011-02-28 06:10:13.000000000 +0000
-+++ src/53_ffts/fftw3_fourwf.F90 2011-03-01 21:30:29.000000000 +0000
-@@ -432,8 +432,8 @@
- end do
-
- cplex=0; istwf_k=1; option=3
--!$ call sg_fftrisc(cplex,dum_denpot,fofgin,dum_fofgin,fofr,gbound,gbound,istwf_k,dum_gvec,gvec,&
--!$& mgfft,ngfft,npwwfn,npwwfn,ldx,ldy,ldz,option,weight)
-+!% call sg_fftrisc(cplex,dum_denpot,fofgin,dum_fofgin,fofr,gbound,gbound,istwf_k,dum_gvec,gvec,&
-+!%& mgfft,ngfft,npwwfn,npwwfn,ldx,ldy,ldz,option,weight)
-
- allocate(ftarr(2,ldx,ldy,ldz))
- !This call gives weird results for R-->G, while G-->R is ok!!!!
-diff -Naur abinit-6.6.1.orig/src/53_ffts/sphere_fft.F90 abinit-6.6.1/src/53_ffts/sphere_fft.F90
---- src/53_ffts/sphere_fft.F90 2011-02-28 06:10:11.000000000 +0000
-+++ src/53_ffts/sphere_fft.F90 2011-03-01 20:35:57.000000000 +0000
-@@ -99,7 +99,7 @@
- !ENDDEBUG
-
- !Insert cg into cfft with extra 0 s around outside:
--!$OMP PARALLEL DO PRIVATE(i1,i2,i3) SHARED(cfft,ndat,n1,n2,n3)
-+!!$OMP PARALLEL DO PRIVATE(i1,i2,i3) SHARED(cfft,ndat,n1,n2,n3)
- !do i2=1,nd2proc*ndat
- !do i3=1,n3
- !do i1=1,n1
-@@ -108,7 +108,7 @@
- !end do
- !end do
- !end do
--!$OMP END PARALLEL DO
-+!!$OMP END PARALLEL DO
- cfft(:,:,:,:)=zero
- !$OMP PARALLEL DO PRIVATE(i1,i2,i3,idat,ipw) SHARED(cfft,cg,kg_k,ndat,npw)
- !write(6,*)'In sphere fft,i1,i2,i3,ipw,cfft=cg'
-@@ -229,7 +229,7 @@
- !ENDDEBUG
-
- !Insert cg into cfft with extra 0 s around outside:
--!$OMP PARALLEL DO PRIVATE(i1,i2,i3) SHARED(cfft,ndat,n1,n2,n3)
-+!!$OMP PARALLEL DO PRIVATE(i1,i2,i3) SHARED(cfft,ndat,n1,n2,n3)
- !do i2=1,nd2proc*ndat
- !do i3=1,n3
- !do i1=1,n1
-@@ -238,7 +238,7 @@
- !end do
- !end do
- !end do
--!$OMP END PARALLEL DO
-+!!$OMP END PARALLEL DO
- cfft(:,:,:,:)=zero
- !$OMP PARALLEL DO PRIVATE(i1,i2,i3,idat,ipw) SHARED(cfft,cg,kg_k,ndat,npw)
- !write(6,*)'In sphere fft,i1,i2,i3,ipw,cfft=cg'
-diff -Naur abinit-6.6.1.orig/src/67_common/m_coulombian.F90 abinit-6.6.1/src/67_common/m_coulombian.F90
---- src/67_common/m_coulombian.F90 2011-02-28 06:10:19.000000000 +0000
-+++ src/67_common/m_coulombian.F90 2011-03-01 22:22:13.000000000 +0000
-@@ -1950,7 +1950,7 @@
- real(dp) :: F3
- !************************************************************************
-
-- !$F3(z)=z*\sin(qpg_para_*z)/\sqrt(rcut^2+z^2)$
-+ !%$F3(z)=z*\sin(qpg_para_*z)/\sqrt(rcut^2+z^2)$
- F3=xx*SIN(qpg_para_*xx)/SQRT(rcut_**2+xx**2)
-
- end function F3
-@@ -2039,7 +2039,7 @@
- real(dp) :: k0,rho,arg
- !************************************************************************
-
-- !$K0cos(y)=K0(\rho*|qpg_z|)*COS(x.qpg_x+y*qpg_y)$
-+ !%$K0cos(y)=K0(\rho*|qpg_z|)*COS(x.qpg_x+y*qpg_y)$
- rho=SQRT(xx_**2+yy**2) ; arg=qpg_para_*rho
- call CALCK0(arg,k0,1)
- K0cos=k0*COS(qpgx_*xx_+qpgy_*yy)
-@@ -2065,7 +2065,7 @@
- real(dp) :: quad
- !************************************************************************
-
-- !$ K0cos_dy(x)=\int_{-b/2}^{b/2} K0(|qpg_z|\rho)cos(x.qpg_x+y.qpg_y)dy$
-+ !%$ K0cos_dy(x)=\int_{-b/2}^{b/2} K0(|qpg_z|\rho)cos(x.qpg_x+y.qpg_y)dy$
- xx_=xx
- call quadrature(K0cos,-hb_,+hb_,qopt_,quad,ierr,ntrial_,accuracy_,npts_)
- if (ierr/=0) then
-diff -Naur abinit-6.6.1.orig/src/69_wfdesc/m_wfs.F90 abinit-6.6.1/src/69_wfdesc/m_wfs.F90
---- src/69_wfdesc/m_wfs.F90 2011-02-28 06:10:19.000000000 +0000
-+++ src/69_wfdesc/m_wfs.F90 2011-03-01 22:32:16.000000000 +0000
-@@ -126,7 +126,7 @@
- ! The boundary of the basis sphere of G vectors at a given k point.
- ! for use in improved zero padding of ffts in 3 dimensions.
-
-- !$real(dp) :: kpoint(3)
-+ !%real(dp) :: kpoint(3)
-
- real(dp),pointer :: ph3d(:,:,:) SET2NULL
- ! ph3d(2,npw,natom)
-@@ -146,7 +146,7 @@
- ! ylm(npw,mpsang**2*useylm)
- ! Real spherical harmonics for each k+G
-
-- !$real(dp),pointer :: kinpw(:)
-+ !%real(dp),pointer :: kinpw(:)
- ! kinpw(npw_k)
- ! compute elements of kinetic energy operator in reciprocal space.
- ! (1/2*effmass) (2 Pi)**2 (k+G)**2:
-@@ -186,7 +186,7 @@
- !integer :: nspinor
- !integer :: natom
-
-- !$ integer :: cplex
-+ !% integer :: cplex
- ! 1 for real wavefunctions u(r)
- ! 2 for complex wavefunctions u(r).
- ! At gamma we always have real u(r) provided that time-reversal can be used.
-@@ -267,8 +267,8 @@
- integer :: itim
- ! 2 is time-reversal is used. 1 otherwise.
-
-- !$integer :: ngfft(18)
-- !$integer :: mgfft
-+ !%integer :: ngfft(18)
-+ !%integer :: mgfft
-
- real(dp) :: ecut
- ! Cutoff energy.
-@@ -326,7 +326,7 @@
- integer :: lmnmax
- integer :: mband ! MAX(nband)
- integer :: mgfft ! Maximum size of 1D FFTs i.e. MAXVAL(ngfft(1:3)), used to dimension some arrays.
-- !$integer :: mpsang
-+ !%integer :: mpsang
- integer :: natom
- integer :: nfft ! Number of FFT points treated by this processor
- integer :: nfftot ! Total number of points in the FFT grid
-@@ -338,7 +338,7 @@
- integer :: ntypat
- integer :: paral_kgb ! Option for kgb parallelism
- integer :: usepaw ! 1 if PAW is used, 0 otherwise.
-- !$integer :: usepawu ! 1 if PAW+U is used, 0 otherwise.
-+ !%integer :: usepawu ! 1 if PAW+U is used, 0 otherwise.
- integer :: prtvol ! Verbosity level.
- integer :: pawprtvol ! Verbosity level for PAW.
- integer :: usewvl ! 1 if BigDFT is used, 0 otherwise.
-@@ -362,13 +362,13 @@
- ! ecutsm=smearing energy for plane wave kinetic energy (Ha)
- ! Cutoff for plane wave basis set.
-
-- !$real(dp) :: pawecutdg=zero
-+ !%real(dp) :: pawecutdg=zero
- ! Cutoff for plane wave basis set.
-
- logical :: gamma_centered=.TRUE.
- ! .TRUE. if ug are given on the Gamma-centered G-sphere. Flag nedded to preserve the old Implementation.
-
-- !$real(dp) :: effmass
-+ !%real(dp) :: effmass
- ! Effective mass for electrons
-
- !arrays
-@@ -2066,8 +2066,8 @@
-
- ! Compute (k+G) vectors
- nkpg=0
-- !$if (choice==3.or.choice==2.or.choice==23) nkpg=3*Wfd%nloalg(5)
-- !$if (choice==4.or.choice==24) nkpg=9*Wfd%nloalg(5)
-+ !%if (choice==3.or.choice==2.or.choice==23) nkpg=3*Wfd%nloalg(5)
-+ !%if (choice==4.or.choice==24) nkpg=9*Wfd%nloalg(5)
- allocate(kpg(npw_k,nkpg)); if (nkpg>0) call mkkpg(kg_k,kpg,kpoint,nkpg,npw_k)
-
- matblk = Cryst%natom
-@@ -5741,9 +5741,9 @@
- ! *************************************************************************
-
- ! TODO ngfft should be included in pawfgrtab_type
-- !$if (ANY(Wfd%ngfft(1:3)/=Pawfgrtab%ngfft(1:3)) then
-- !$ MSG_ERROR("Wfd%ngfft(1:3)/=Pawfgrtab%ngfft(1:3)")
-- !$end if
-+ !%if (ANY(Wfd%ngfft(1:3)/=Pawfgrtab%ngfft(1:3)) then
-+ !% MSG_ERROR("Wfd%ngfft(1:3)/=Pawfgrtab%ngfft(1:3)")
-+ !%end if
-
- call wfd_get_ur(Wfd,band,ik_ibz,spin,ur_ae)
-
-@@ -6817,7 +6817,7 @@
- do_sym = .FALSE.
- if (PRESENT(ISkg)) then
- do_sym = .TRUE.
-- !$ TODO do_sym = (ISkg%isym/=1 .or. ISkg%itim/=1)
-+ !% TODO do_sym = (ISkg%isym/=1 .or. ISkg%itim/=1)
- end if
-
- if (.not. do_sym) then
-diff -Naur abinit-6.6.1.orig/src/69_wfdesc/outkss.F90 abinit-6.6.1/src/69_wfdesc/outkss.F90
---- src/69_wfdesc/outkss.F90 2011-02-28 05:14:13.000000000 +0000
-+++ src/69_wfdesc/outkss.F90 2011-03-01 22:42:00.000000000 +0000
-@@ -131,7 +131,7 @@
- #endif
-
- use m_io_tools, only : get_unit
-- !$use m_numeric_tools, only : bisect
-+ !%use m_numeric_tools, only : bisect
- use m_gsphere, only : merge_and_sort_kg, table_gbig2kg, get_kg
- use m_io_kss, only : write_kss_wfgk, write_kss_header, k2gamma_centered
- use m_hamiltonian, only : ddiago_ctl_type, init_ddiago_ctl
-@@ -458,7 +458,7 @@
- EXIT
- end if
- end do
--!$ ishm=bisect(shlim,npwkss)
-+!% ishm=bisect(shlim,npwkss)
-
- if (shlim(ishm)/=npwkss) then
- nrst1=shlim(ishm)
-diff -Naur abinit-6.6.1.orig/src/70_gw/m_screening.F90 abinit-6.6.1/src/70_gw/m_screening.F90
---- src/70_gw/m_screening.F90 2011-02-28 06:10:19.000000000 +0000
-+++ src/70_gw/m_screening.F90 2011-03-02 05:05:33.000000000 +0000
-@@ -439,7 +439,7 @@
- end do
-
- rdwr=4
-- !$call hdr_io_int(Er%fform,Er%Hscr%Hdr,rdwr,unt)
-+ !%call hdr_io_int(Er%fform,Er%Hscr%Hdr,rdwr,unt)
- end if ! verbose>0
-
- end subroutine print_epsilonm1_results
-@@ -796,7 +796,7 @@
-
- call metric(gmet,gprimd,-1,rmet,Vcp%rprimd,ucvol)
-
-- !$ if (Er%ID/=0) call reset_Epsilonm1(Er)
-+ !% if (Er%ID/=0) call reset_Epsilonm1(Er)
- Er%ID=id_required
-
- write(*,*) 'Er%ID:',Er%ID
-@@ -1892,7 +1892,7 @@
- end if
-
- if (iqibz==1) then
-- !$vc_sqrt => Vcp%vcqlwl_sqrt(:,iqlwl) ! Use Coulomb term for q-->0
-+ !%vc_sqrt => Vcp%vcqlwl_sqrt(:,iqlwl) ! Use Coulomb term for q-->0
- vc_sqrt => Vcp%vcqlwl_sqrt(:,1) ! TODO add treatment of non-Analytic behavior
- else
- vc_sqrt => Vcp%vc_sqrt(:,iqibz)
-@@ -1992,7 +1992,7 @@
- end if
-
- if (iqibz==1) then
-- !$vc_sqrt => Vcp%vcqlwl_sqrt(:,iqlwl) ! Use Coulomb term for q-->0
-+ !%vc_sqrt => Vcp%vcqlwl_sqrt(:,iqlwl) ! Use Coulomb term for q-->0
- vc_sqrt => Vcp%vcqlwl_sqrt(:,1) ! TODO add treatment of non-Analytic behavior
- else
- vc_sqrt => Vcp%vc_sqrt(:,iqibz)
-@@ -2212,7 +2212,7 @@
- end do
- !
- !if (PRESENT(rhor)) then
-- ! !$call mdielf(epsinf,Er%npw,Er%nomega,iq_ibz,Er%qibz(:,iq_ibz),Er%gvec,Cryst,Vcp,nspden,nfft,ngfft,rhor,epsm1,comm)
-+ ! !%call mdielf(epsinf,Er%npw,Er%nomega,iq_ibz,Er%qibz(:,iq_ibz),Er%gvec,Cryst,Vcp,nspden,nfft,ngfft,rhor,epsm1,comm)
- !end if
-
- end do ! nqibz
-@@ -2393,7 +2393,7 @@
- !
- ! Change the body but do not add the corrections due to the head and the wings.
- ! since they can be obtained on the fly from eps_body and the wings of eps^{-1}.
-- !$chi0(2:,2:,iomega) = eps_body
-+ !%chi0(2:,2:,iomega) = eps_body
- end do !iomega
-
- deallocate(modg_inv,cvec)
-diff -Naur abinit-6.6.1.orig/src/71_bse/exc_iterative_diago.F90 abinit-6.6.1/src/71_bse/exc_iterative_diago.F90
---- src/71_bse/exc_iterative_diago.F90 2011-02-28 06:10:19.000000000 +0000
-+++ src/71_bse/exc_iterative_diago.F90 2011-03-01 22:50:45.000000000 +0000
-@@ -762,8 +762,8 @@
- open(unit=eig_unt,file=oeig_fname,form='unformatted')
- write(eig_unt) exc_nst
- write(eig_unt) CMPLX(exc_energy(1:exc_nst),kind=dpc)
-- !$ fform = 1002 ! TODO: change setup_bse so that Hdr_bse reflects the parameters of the run.
-- !$ call hdr_io_int(fform,Hdr_bse,rdwr2,eig_unt)
-+ !% fform = 1002 ! TODO: change setup_bse so that Hdr_bse reflects the parameters of the run.
-+ !% call hdr_io_int(fform,Hdr_bse,rdwr2,eig_unt)
- close(eig_unt)
- end if
-
-@@ -776,15 +776,15 @@
- msg = " MPI_IO error opening file: "//TRIM(oeig_fname)
- ABI_CHECK_MPI(ierr,msg)
-
-- !$call xmpio_read_frm(mpi_fh,ehdr_offset,xmpio_at,fmarker,ierr)
-- !$write(std_out,*)"fmarker last record ",fmarker
-- !$call hdr_mpio_skip(mpi_fh,fform,ehdr_offset)
-- !$ehdr_offset = 4*xmpio_bsize_frm + xmpio_bsize_int + exc_nst*xmpio_bsize_dpc
-+ !%call xmpio_read_frm(mpi_fh,ehdr_offset,xmpio_at,fmarker,ierr)
-+ !%write(std_out,*)"fmarker last record ",fmarker
-+ !%call hdr_mpio_skip(mpi_fh,fform,ehdr_offset)
-+ !%ehdr_offset = 4*xmpio_bsize_frm + xmpio_bsize_int + exc_nst*xmpio_bsize_dpc
-
- is_fortran_file=.TRUE.; etype=MPI_BYTE; old_type=MPI_DOUBLE_COMPLEX
-
- ! TODO Need to add option to create file view.
-- !$call xmpio_create_coldistr_from_fherm_packed(array_of_sizes,my_cols,old_type,eig_type,offset_err)
-+ !%call xmpio_create_coldistr_from_fherm_packed(array_of_sizes,my_cols,old_type,eig_type,offset_err)
-
- if (offset_err/=0) then
- write(msg,"(3a)")&
-diff -Naur abinit-6.6.1.orig/src/77_ddb/eliashberg_1d.F90 abinit-6.6.1/src/77_ddb/eliashberg_1d.F90
---- src/77_ddb/eliashberg_1d.F90 2011-02-28 06:10:20.000000000 +0000
-+++ src/77_ddb/eliashberg_1d.F90 2011-03-02 04:21:07.000000000 +0000
-@@ -108,10 +108,10 @@
-
- !
- !1) use linearized Eliashberg equation to find Tc
--!$ \sum_j \mathbf{M}_{ij} \Delta_j = \zeta \cdot \Delta_i $ $i,j = 1 .. n_{\mathrm{Matsubara}}$
--!$\zeta = 1$ gives T$_c$ $\beta = \frac{1}{\mathrm{T}}$ $\omega_i = (2 i + 1) \pi \mathrm{T}$
--!$ \mathbf{M}_{ij} = \frac{\pi}{\beta} \frac{\lambda (\omega_i - \omega_j)}{Z (\omega_i)}$
--!$ Z (\omega_i) = 1 + \frac{\pi}{\beta \omega_i} \sum_j \lambda(\omega_i - \omega_j) \mathrm{sgn}(\omega_j)$
-+!%$ \sum_j \mathbf{M}_{ij} \Delta_j = \zeta \cdot \Delta_i $ $i,j = 1 .. n_{\mathrm{Matsubara}}$
-+!%$\zeta = 1$ gives T$_c$ $\beta = \frac{1}{\mathrm{T}}$ $\omega_i = (2 i + 1) \pi \mathrm{T}$
-+!%$ \mathbf{M}_{ij} = \frac{\pi}{\beta} \frac{\lambda (\omega_i - \omega_j)}{Z (\omega_i)}$
-+!%$ Z (\omega_i) = 1 + \frac{\pi}{\beta \omega_i} \sum_j \lambda(\omega_i - \omega_j) \mathrm{sgn}(\omega_j)$
- !
-
- !initial guess for T$_c$ in Hartree (1Ha =3.067e5 K)
-diff -Naur abinit-6.6.1.orig/src/77_ddb/m_eph.F90 abinit-6.6.1/src/77_ddb/m_eph.F90
---- src/77_ddb/m_eph.F90 2011-02-28 05:14:13.000000000 +0000
-+++ src/77_ddb/m_eph.F90 2011-03-01 23:17:18.000000000 +0000
-@@ -233,10 +233,10 @@
- public :: nullify_fermi_surface
- public :: destroy_fermi_surface
-
-- !$public :: init_fermi_surface
-- !$public :: wannier_interpolate_fermi_surface
-- !$public :: get_fs_ibz
-- !$public :: bxsf_write_fermi_surface
-+ !%public :: init_fermi_surface
-+ !%public :: wannier_interpolate_fermi_surface
-+ !%public :: get_fs_ibz
-+ !%public :: bxsf_write_fermi_surface
-
- ! example:
- !type(fermi_surface_type),allocatable :: Fsurf(:)
-@@ -325,9 +325,9 @@
- ! Bound Methods:
- public :: nullify_gkk
- public :: destroy_gkk
-- !$ init_gkk
-- !$ read_gkk_from_file
-- !$ get_gkk_full_fsbz ! complete gkk on the full FS BZ.
-+ !% init_gkk
-+ !% read_gkk_from_file
-+ !% get_gkk_full_fsbz ! complete gkk on the full FS BZ.
-
- interface nullify_gkk
- module procedure nullify_gkk_0D
-@@ -379,9 +379,9 @@
- ! Bound Methods:
- public :: nullify_gkk_handler
- public :: destroy_gkk_handler
-- !$init_gkk_handler(Gkk,FSurf,Cryst,Cryst,qpt,fname)
-- !$get_gammaq
-- !$symmetrize_gkk_over_perts
-+ !%init_gkk_handler(Gkk,FSurf,Cryst,Cryst,qpt,fname)
-+ !%get_gammaq
-+ !%symmetrize_gkk_over_perts
-
- interface nullify_gkk_handler
- module procedure nullify_gkk_handler_0D
-diff -Naur abinit-6.6.1.orig/src/95_drive/bethe_salpeter.F90 abinit-6.6.1/src/95_drive/bethe_salpeter.F90
---- src/95_drive/bethe_salpeter.F90 2011-02-28 06:10:13.000000000 +0000
-+++ src/95_drive/bethe_salpeter.F90 2011-03-02 04:34:01.000000000 +0000
-@@ -453,7 +453,7 @@
- end do
- end if
-
-- opt_ecut=zero !$; if (gw_uses_wfk_file) opt_ecut=Dtset%ecutwfn
-+ opt_ecut=zero !%; if (gw_uses_wfk_file) opt_ecut=Dtset%ecutwfn
-
- call wfd_init(Wfd,Cryst,Pawtab,Psps,keep_ur,Dtset%paral_kgb,BSp%npwwfn,mband,nband,Kmesh%nibz,Dtset%nsppol,bks_mask,&
- & Dtset%nspden,Dtset%nspinor,Dtset%ecutsm,Dtset%dilatmx,Hdr_kss%istwfk,Kmesh%ibz,ngfft_osc,&
-@@ -513,7 +513,7 @@
-
- !TODO this has to be done in a better way, moreover wont work for PAW
- !Check Vcp!
--!$ call cutoff_density(ngfftf,Dtset%nspden,Dtset%nsppol,Vcp,ks_rhor,MPI_enreg_seq)
-+!% call cutoff_density(ngfftf,Dtset%nspden,Dtset%nsppol,Vcp,ks_rhor,MPI_enreg_seq)
- !
- !=== Additional computation for PAW ===
- if (Dtset%usepaw==1) then
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