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.

10 files changed, 556 insertions, 216 deletions

diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index b6b882218..2a5c1ee69 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/Manifest b/sci-physics/abinit/Manifest
index 412fab010..e35fffeac 100644
--- a/sci-physics/abinit/Manifest
+++ b/sci-physics/abinit/Manifest
@@ -1,4 +1,4 @@
-DIST abinit-6.10.1.tar.gz 44363678 RMD160 44d4aaeb58fdbc81f376025dbf4c13af91e6aa4d SHA1 2fb55ab80b1a90756dd664086c3263636716ef82 SHA256 a28c76829d4230937c3a4e670cebeaf3b8e3989a532c189dddabdafe26da8c8a
-DIST abinit-6.10.3.tar.gz 69158203 RMD160 5b9c9fea3d488aa5f819037e8ae0acc0a19512ef SHA1 d47b72e226d722eed3eadb30890ad534617328e3 SHA256 185c45c7c9caf5f735d841fa85b2dfc612eee81b76f905a9988b5f0994be6fb5
-DIST abinit-6.6.3.tar.gz 41161321 RMD160 f9169812cfb2dc30f752bf0ab0ffc41250ea0bbb SHA1 02c9fd6abe1b73164b804b6e0b1f829ec9fd286e SHA256 fad84d3e774e3b4ba16f2a2924e60b8ba42ab21fefd89d8ce4848f9a9e03f774
-DIST abinit-6.8.2.tar.gz 43565001 RMD160 151fcd3fa3c8aad204aa01a0877b101b7faf0550 SHA1 2b96bb175e1946c48ee3a72064b08ccc1b8dbdea SHA256 7a0e8ebfce50ae18e5c4f25f9bfd534623a41985082efead918a3878464a181c
+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
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 cdd495fd1..000000000
--- 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 000000000..00e1fa2fb
--- /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 000000000..7e0169f63
--- /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 000000000..857a27abc
--- /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 000000000..95c12b354
--- /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 000000000..ad28a8183
--- /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 000000000..0c8d98eea
--- /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 c14bc6829..0a34647b9 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>