sci-libs/bigdft & sci-physics/abinit clean-up after sci-physics/abinit version bump to 6.12.2 and tests

9 files changed, 13 insertions, 1247 deletions

diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index 5af127920..4e3f27e1c 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 Macháček <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 Macháček <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/Manifest b/sci-physics/abinit/Manifest
index e35fffeac..5fe0a3651 100644
--- a/sci-physics/abinit/Manifest
+++ b/sci-physics/abinit/Manifest
@@ -1,4 +1 @@
-DIST abinit-6.10.3.tar.gz 69158203 SHA256 185c45c7c9caf5f735d841fa85b2dfc612eee81b76f905a9988b5f0994be6fb5 SHA512 010fee8f0740cc05208f1abe52f5aae25077d5792331a98466ecc13f27605776e19a17bdeab2c7cf09eb233109ae7f14d55afecd89113a91a0d67494f2c5abb2 WHIRLPOOL be7f127116a6f59ea4cbd84f01e3371b5959275bae0957e654eea9dadeef278ad0081f8600476e716865ef32b5aea536ccb09f12f5934f95aaf8eeccb06bc5d6
-DIST abinit-6.12.1.tar.gz 58474634 SHA256 1b0f0fe5a6f8ce97b3da7ea7640f16c36902c7a5bc08651abd139eb7e13222b6 SHA512 59d757400539d0eb385fd37c9a6e2824bd3a2a6378a6c8f39a2f336cf3f842120538a014633561a5c16b9debf4ec054d51beaec2952629e0a88ab283dc2db431 WHIRLPOOL 9c02b1184fabe96405fe05ecd9c40d48f104d92d55ed2900dc3755758aca12cb4dd64e6fea3e3f949bcbb8a615ecd359a76bc9752969e585189865cd75c14c1d
-DIST abinit-6.6.3.tar.gz 41161321 SHA256 fad84d3e774e3b4ba16f2a2924e60b8ba42ab21fefd89d8ce4848f9a9e03f774 SHA512 834bd017a81444a75335d13579c37efe1d58b571a0b2a673f8dfb60342cd10fb849e6a2e92042be59445835e1ad3a484149faa260280e4e6db9b284ed03c208a WHIRLPOOL 302cf85a65e4c07ee716379844d1435503ee042fb987f3c43e5fc4e60ffe32ec0498f8d31dcc7a61043bfcedf56b87eadca11657156fb6d912f6c4627aa60bbf
-DIST abinit-6.8.2.tar.gz 43565001 SHA256 7a0e8ebfce50ae18e5c4f25f9bfd534623a41985082efead918a3878464a181c SHA512 97287a7527f1088435c95697b90a27eaf6cb5b8921e2d4e702279552f9d8669735242d5bfa62b944a7da418286a317131c352952ac0fac58540de4e8ded56385 WHIRLPOOL 27b11310695179e2a8794dbb7b0a3e041477cf9bec1ddc3468f6c54e3549806cef66c348dbb34839d3dfb0633191b5a9531f4e415d2c0a1d776ddf9dddff3756
+DIST abinit-6.12.2.tar.gz 58469873 SHA256 a2b415ddb3809cd1ef670e666fce5b14e6148ebc381dc035de837daac7b6e22e SHA512 0be2bcd0905968cf9b7b7e22d476d514532e9204f267d0acb880f35e925cdb8d5884aec6933b89514cbd3d1532095367355dba65f87b7b5f715b397407f267d9 WHIRLPOOL 7c24266ea1592cd05a29f8536ca8c41a79eb6186a55b7a0df04fbd4d7e45b0d04786106dba99a519c4bb1c7a7ecb5bfdcf54c18eddcc519747a86e7f1d5a5a01
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 f07355891..000000000
--- 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
index 59f0f98b8..ddb435514 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 3799d0578..000000000
--- 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 cdd495fd1..000000000
--- 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 857a27abc..000000000
--- 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 95c12b354..000000000
--- 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$ac_exec_ext" >&5
-     break 2
-   fi
diff --git a/sci-physics/abinit/files/6.6.1-openmp.patch b/sci-physics/abinit/files/6.6.1-openmp.patch
deleted file mode 100644
index af43d5792..000000000
--- a/sci-physics/abinit/files/6.6.1-openmp.patch
+++ /dev/null
@@ -1,509 +0,0 @@
-diff -Naur abinit-6.6.1.orig/src/52_fft_mpi_noabirule/accrho.F90 abinit-6.6.1/src/52_fft_mpi_noabirule/accrho.F90
---- src/52_fft_mpi_noabirule/accrho.F90	2011-02-28 05:14:13.000000000 +0000
-+++ src/52_fft_mpi_noabirule/accrho.F90	2011-03-01 19:41:35.000000000 +0000
-@@ -91,14 +91,14 @@
-         integer unused
-         unused=0
- ! *************************************************************************
--!$      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