16 files changed, 707 insertions, 6 deletions
diff --git a/sci-libs/bigdft/ChangeLog b/sci-libs/bigdft/ChangeLog
index 1f24f098c..82de595f0 100644
--- a/sci-libs/bigdft/ChangeLog
+++ b/sci-libs/bigdft/ChangeLog
@@ -1,9 +1,18 @@
 # ChangeLog for sci-libs/bigdft
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
 <<<<<<< HEAD
 
+*bigdft-1.7_pre12 (17 Jan 2013)
+
+  17 Jan 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
+  +bigdft-1.7_pre12.ebuild, +files/bigdft-1.7-dev.12-libxc_dir_include.patch,
+  +files/bigdft-1.7-dev.12-nolib_mods.patch,
+  +files/bigdft-1.7-dev.12-tests.tar.bz2:
+  New version 1.7-dev.12 (1.7_pre12) from the Abinit site added; used by
+  sci-physics/abinit-7.0.4 but apparently segfaults it.
+
 *bigdft-1.6_pre1-r4 (01 Sep 2012)
 
   01 Sep 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
diff --git a/sci-libs/bigdft/Manifest b/sci-libs/bigdft/Manifest
index 5f1f645ce..39acfb0cf 100644
--- a/sci-libs/bigdft/Manifest
+++ b/sci-libs/bigdft/Manifest
@@ -1,2 +1,3 @@
 DIST bigdft-1.6-tuto.1.tar.gz 7510733 SHA256 32020c7e58b36fe1f58a47ef02af99bd0da81c6da7d6f15e89b8075494d39d87 SHA512 48684413b0807b5dcee4b97b5b83d9a839c44043801b923c5f0ce7c8a92024cfee64c1065d4d2ffc67cb249cfcd485680b5526aaaedba06e6a88ccc52ba290f2 WHIRLPOOL d6efcc6f9ded331c42e8e3b13a9260e2acd922c4fa0bf303455e33924a930df6aa01abec897c1d190d5016a5bb3781c491e8a17d500e5485717989bddd4f579d
 DIST bigdft-1.6.0.tar.gz 8876759 SHA256 2d3212ef5f1ebc10fe7c627397ac6282ad41e1433ec6e66905f9d39a302913c0 SHA512 facbb78d126885dd04fed6451aa9cd1f5c755055e146cda1d2d4e90e3310fc3066b661635477db96d5b143ffaaa3ebb01107681437fd9965f3c764cf1b034361 WHIRLPOOL 97bc6c28296a92b09139e3a65266daa583011620fad5aed208e0e48627ab1d9c0ef9993d6c4c3cce5696d5c707bcdfb4b8ca7e64379909b3cf073206e32f9572
+DIST bigdft-1.7-dev.12.tar.gz 8904633 SHA256 2f899f287dd508dc616fb798cc9d01d1c79951dc68c277fb0ce19ea0ad690332 SHA512 35efe93edd7e6fb08abe919c59913c173f23e17a50104ad92e510dba5ba35ba8117012249d620896affc8acc05c9d85c6c61a411bc903750db6593456e9e8142 WHIRLPOOL 94a8d6d25fe82f3f1b89d15b4e23293d018bfb66c96fd1061a09e6352fb6811e79a15161bd3ca92e5f544253c8fa9f919d41fe069635ac07f33e21cc70878719
diff --git a/sci-libs/bigdft/bigdft-1.7_pre12.ebuild b/sci-libs/bigdft/bigdft-1.7_pre12.ebuild
new file mode 100644
index 000000000..de32f986b
--- /dev/null
+++ b/sci-libs/bigdft/bigdft-1.7_pre12.ebuild
@@ -0,0 +1,142 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+inherit autotools-utils eutils flag-o-matic fortran-2 toolchain-funcs
+
+REAL_P="${P/_pre/-dev.}"
+
+DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
+HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
+SRC_URI="http://forge.abinit.org/fallbacks/${REAL_P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE="cuda doc etsf_io mpi netcdf openmp opencl test"
+
+RDEPEND="
+	=sci-libs/libxc-1*[fortran]
+	virtual/blas
+	virtual/fortran
+	virtual/lapack
+	dev-libs/libyaml
+	mpi? ( virtual/mpi )
+	cuda? ( dev-util/nvidia-cuda-sdk )
+	opencl? (
+		|| (
+			dev-util/nvidia-cuda-sdk
+			dev-util/amdstream
+			)
+		)
+	etsf_io? ( sci-libs/etsf_io )
+	netcdf? ( || (
+				sci-libs/netcdf[fortran]
+				sci-libs/netcdf-fortran
+				)
+			)"
+DEPEND="${RDEPEND}
+	dev-util/pkgconfig
+	>=sys-devel/autoconf-2.59
+	doc? ( virtual/latex-base )
+	app-arch/tar
+	app-arch/bzip2"
+
+S="${WORKDIR}/${REAL_P}"
+
+DOCS=( README INSTALL ChangeLog AUTHORS NEWS )
+
+FORTRAN_STANDARD=90
+
+pkg_setup() {
+	# fortran-2.eclass does not handle mpi wrappers
+	if use mpi; then
+		export FC="mpif90"
+		export F77="mpif77"
+		export CC="mpicc"
+	else
+		tc-export FC F77 CC
+	fi
+
+	fortran-2_pkg_setup
+	if use openmp; then
+                tc-has-openmp || \
+                        die "Please select an openmp capable compiler like gcc[openmp]"
+        fi
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/"${REAL_P}"-libxc_dir_include.patch \
+		"${FILESDIR}"/"${REAL_P}"-nolib_mods.patch
+	tar -xjf "${FILESDIR}"/"${REAL_P}"-tests.tar.bz2 -C "${S}"/tests/DFT/postSCF/
+	eautoreconf
+}
+
+src_configure() {
+	local openmp=""
+	use openmp && openmp="-fopenmp"
+	local modules="${EPREFIX}/usr/$(get_libdir)/finclude"
+	local netcdff_libs="-lnetcdff"
+	filter-flags '-m*' '-O*' "-pipe"
+	local nvcflags="${CFLAGS}"
+	_filter-var nvcflags '-m*' '-O*' "-pipe"
+	local myeconfargs=(
+		$(use_enable mpi)
+		--enable-optimised-convolution
+		--enable-pseudo
+		--enable-libbigdft
+		--enable-binaries
+		--disable-minima-hopping
+		--disable-internal-libyaml
+		--enable-internal-libabinit
+		--with-moduledir="${modules}"
+		--with-ext-linalg="$(pkg-config --libs-only-l lapack) \
+			$(pkg-config --libs-only-l blas)"
+		--with-ext-linalg-path="$(pkg-config --libs-only-L lapack) \
+			$(pkg-config --libs-only-L blas)"
+		--enable-libxc
+		--disable-internal-libxc
+		--with-libxc-include="${modules}"
+		$(use_enable cuda cuda-gpu)
+		$(use_with cuda cuda-path /opt/cuda)
+		$(use_with cuda nvcc-flags "${nvcflags}")
+		$(use_enable opencl)
+		$(use_with etsf_io etsf-io)
+		"$(use etsf_io && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")"
+		FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${openmp} -I${modules}"
+		LD="$(tc-getLD)"
+		CPP="$(tc-getCPP)"
+		)
+	autotools-utils_src_configure
+}
+
+src_compile() {
+	#autotools-utils_src_compile() expanded
+	_check_build_dir
+	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+	emake -j1
+	sed -i -e's%\$(top_builddir)/[^ ]*/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc
+	popd > /dev/null
+
+	#autotools-utils_src_compile
+	use doc && autotools-utils_src_compile doc
+}
+
+src_test() {
+	if use test; then
+		#autotools-utils_src_test() expanded
+		_check_build_dir
+		pushd "${BUILD_DIR}" > /dev/null || die
+		# Run default src_test as defined in ebuild.sh
+		cd tests
+		emake -j1 check
+		popd > /dev/null
+	fi
+}
+
+src_install() {
+	autotools-utils_src_install HAVE_LIBXC=1
+}
diff --git a/sci-libs/bigdft/files/bigdft-1.7-dev.12-libxc_dir_include.patch b/sci-libs/bigdft/files/bigdft-1.7-dev.12-libxc_dir_include.patch
new file mode 100644
index 000000000..9084d08e5
--- /dev/null
+++ b/sci-libs/bigdft/files/bigdft-1.7-dev.12-libxc_dir_include.patch
@@ -0,0 +1,50 @@
+--- configure.ac.orig	2011-11-23 14:02:15.000000000 +0000
++++ configure.ac	2011-11-23 14:09:19.000000000 +0000
+@@ -743,14 +743,17 @@
+ ac_build_libxc="no"
+ AC_ARG_ENABLE(libxc, AS_HELP_STRING([--without-libxc], [Do not link with libXC library (default = yes).]), ac_use_libxc=$enableval, ac_use_libxc="yes")
+ AC_ARG_ENABLE(internal-libxc, AS_HELP_STRING([--disable-internal-libxc], [Do not build and link with internal libXC library (default = yes).]), ac_internal_libxc=$enableval, ac_internal_libxc="yes")
+-AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib and module files (default = None).]),
++AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib files (default = None).]),
+             ac_libxc_dir=$withval, ac_libxc_dir=)
++AC_ARG_WITH(libxc-include, AS_HELP_STRING([--with-libxc-include], [Give the path for an external libXC library module files (default = None).]),
++            ac_libxc_dir_include=$withval, ac_libxc_dir_include=)
+ if test x"$ac_use_libxc" = x"yes" ; then
+   ac_build_libxc=$ac_internal_libxc
+   if test "$ac_internal_libxc" = "yes" ; then
+     ac_build_libxc="yes"
+     ac_use_libxc="yes"
+     ac_libxc_dir="$top_builddir"/libxc-1.1.0/src
++    ac_libxc_dir_include="$ac_libxc_dir"/include
+     AC_SUBST(LIBXC_DIR, "\$(top_builddir)"/libxc-1.1.0/src)
+     AC_SUBST(LIBXC_INCLUDE, "-I\$(top_builddir)"/libxc-1.1.0/src)
+     LDFLAGS="$LDFLAGS -L\$(top_builddir)/libxc-1.1.0/src/.libs"
+@@ -758,6 +761,9 @@
+   else
+     if test -n "$ac_libxc_dir" ; then
+       LDFLAGS="$LDFLAGS -L$ac_libxc_dir/lib"
++      if test x"$ac_libxc_dir_include" = x ; then
++        ac_libxc_dir_include="$ac_libxc_dir"/include
++      fi
+       
+       dnl Test the given implementation of libXC.
+       ac_libxc_libname="xc"
+@@ -766,13 +772,13 @@
+         ac_libxc_libname="dft_xc"
+         AC_CHECK_LIB($ac_libxc_libname, xc_f90_lda_vxc, withlibxc=yes, withlibxc=no)
+       fi
+-      AC_CHECK_FILE($ac_libxc_dir/include/libxc_funcs_m.$ax_fc_mod_ext, funcs="yes", funcs="no")
+-      AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_lib_m.$ax_fc_mod_ext, lib="yes", lib="no")
+-      AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_types_m.$ax_fc_mod_ext, types="yes", types="no")
++      AC_CHECK_FILE($ac_libxc_dir_include/libxc_funcs_m.$ax_fc_mod_ext, funcs="yes", funcs="no")
++      AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_lib_m.$ax_fc_mod_ext, lib="yes", lib="no")
++      AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_types_m.$ax_fc_mod_ext, types="yes", types="no")
+       if test "$withlibxc" = "yes" -a "$funcs" = "yes" -a "$lib" = "yes" -a "$types" = "yes"; then
+         ac_use_libxc="yes"
+-        AC_SUBST(LIBXC_DIR, $ac_libxc_dir/include)
+-        AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir/include)
++        AC_SUBST(LIBXC_DIR, $ac_libxc_dir_include)
++        AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir_include)
+         LIBXC_LIBS="-l"$ac_libxc_libname
+       fi
+     else
diff --git a/sci-libs/bigdft/files/bigdft-1.7-dev.12-nolib_mods.patch b/sci-libs/bigdft/files/bigdft-1.7-dev.12-nolib_mods.patch
new file mode 100644
index 000000000..8137a48ab
--- /dev/null
+++ b/sci-libs/bigdft/files/bigdft-1.7-dev.12-nolib_mods.patch
@@ -0,0 +1,25 @@
+diff -Naurp bigdft-1.7-dev.12.orig/src/Makefile.am bigdft-1.7-dev.12/src/Makefile.am
+--- bigdft-1.7-dev.12.orig/src/Makefile.am	2012-07-16 07:46:11.000000000 +0000
++++ bigdft-1.7-dev.12/src/Makefile.am	2013-01-09 14:09:58.198905489 +0000
+@@ -45,6 +45,9 @@ EXTRA_DIST = \
+ # -------------
+ if BUILD_LIB_BIGDFT
+ lib_bigdft = libbigdft.a libdft_common.a
++else
++lib_bigdft =
++endif
+ PS_SOURCES = PSolver/Build_Kernel.f90 \
+ 	PSolver/xcenergy.f90 \
+ 	PSolver/3Dgradient.f90 \
+@@ -53,11 +56,6 @@ PS_SOURCES = PSolver/Build_Kernel.f90 \
+ 	PSolver/wofz.f90 \
+ 	lib/fft/fft3d.f90
+ PS_MODULES = PSolver/Poisson_Solver.f90
+-else
+-lib_bigdft =
+-PS_SOURCES =
+-PS_MODULES =
+-endif
+ if BUILD_BINARIES
+ binaries_sources = bigdft memguess splsad NEB frequencies MDanalysis $(minima_hopping_sources) bart abscalc BigDFT2Wannier WaCo
+ local_binaries = test_forces
diff --git a/sci-libs/bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2 b/sci-libs/bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2
new file mode 100644
index 000000000..d74c56176
--- /dev/null
+++ b/sci-libs/bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2
diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index a57ab4c07..d814a8ab8 100644
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for sci-physics/abinit
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*abinit-7.0.4 (17 Jan 2013)
+
+  17 Jan 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
+  +files/7.0.4-test_dirs.patch, +abinit-7.0.4.ebuild:
+  New version 7.0.4 added; openmp now supported, but on the other hand, bigdft
+  support segfaults
+
 *abinit-6.12.3-r2 (19 Jun 2012)
 
   19 Jun 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
diff --git a/sci-physics/abinit/Manifest b/sci-physics/abinit/Manifest
index 6392e02a1..689bd12de 100644
--- a/sci-physics/abinit/Manifest
+++ b/sci-physics/abinit/Manifest
@@ -1 +1,2 @@
-DIST abinit-6.12.3.tar.gz 58483889 RMD160 d2a1009af7eaafa9d4df99aa6e98e35faa644931 SHA1 ab7bca747639902d586155cb5d335595e3b2b1dc SHA256 243a3832e258d12998d9d188141cfedeabdbfee9867c1951d7f27b8230dec5e9 SHA512 a14764c7c031890ea9cb64dd8fb439959fae4b50d59985bd2e9d9c12a06f71f92491c015c64c7273b4089cd57934a699f3d4c3c2f377032cbd655aa887241a65 WHIRLPOOL caa5e8159fac7353ee87663f195419acee57246f1a3015941368ed026c3a15a07cf135dbf57fc8a81f0cdd24c042af1ccc1c63e3e20a73042d3462530bd5b904
+DIST abinit-6.12.3.tar.gz 58483889 SHA256 243a3832e258d12998d9d188141cfedeabdbfee9867c1951d7f27b8230dec5e9 SHA512 a14764c7c031890ea9cb64dd8fb439959fae4b50d59985bd2e9d9c12a06f71f92491c015c64c7273b4089cd57934a699f3d4c3c2f377032cbd655aa887241a65 WHIRLPOOL caa5e8159fac7353ee87663f195419acee57246f1a3015941368ed026c3a15a07cf135dbf57fc8a81f0cdd24c042af1ccc1c63e3e20a73042d3462530bd5b904
+DIST abinit-7.0.4.tar.gz 61715030 SHA256 b3ad895b75b92b3ff05e873d42d0b26f6e6113b9de4579966f7b6d1b49d6004e SHA512 8edfe4019c968e6f912d0678fe331fc8a6ce2848f1b16973336d4181d010a776ed1ea2c5500499dac895d9d773d72165e20524705cf8928f91ede873272b0417 WHIRLPOOL 35da8681a68e435b460a11112e6cf6990fdf141d53d5849be45225d50e803e2bfc65cb05e5e576c704411be5734e47ed2e4ccca1fd1689311bd4febea937f0f8
diff --git a/sci-physics/abinit/abinit-7.0.4.ebuild b/sci-physics/abinit/abinit-7.0.4.ebuild
new file mode 100644
index 000000000..2218c1051
--- /dev/null
+++ b/sci-physics/abinit/abinit-7.0.4.ebuild
@@ -0,0 +1,341 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+inherit autotools-utils eutils flag-o-matic fortran-2 multilib toolchain-funcs
+
+DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory"
+HOMEPAGE="http://www.abinit.org/"
+SRC_URI="http://ftp.abinit.org/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cuda cuda-double -debug +etsf_io +fftw +fftw-threads +fox gsl gui +hdf5 libabinit mpi +netcdf openmp python -test +threads -vdwxc"
+
+RDEPEND="~sci-libs/bigdft-1.7_pre12
+	=sci-libs/libxc-1*[fortran]
+	sci-physics/atompaw[libxc]
+	etsf_io? ( sci-libs/etsf_io )
+	fox? ( >=sci-libs/fox-4.1.2-r1[sax] )
+	netcdf? (
+		|| (
+			sci-libs/netcdf[fortran]
+			sci-libs/netcdf-fortran
+			)
+		hdf5? (
+			  sci-libs/netcdf[hdf5]
+			  )
+		)
+	hdf5? ( sci-libs/hdf5[fortran] )
+	sci-libs/wannier90
+	virtual/blas
+	virtual/lapack
+	gsl? ( sci-libs/gsl )
+	fftw? (
+		sci-libs/fftw:3.0
+		fftw-threads? ( sci-libs/fftw:3.0[threads] )
+		)
+	mpi? ( virtual/mpi )
+	python? ( dev-python/numpy )
+	cuda? ( dev-util/nvidia-cuda-sdk )"
+DEPEND="${RDEPEND}
+	dev-util/pkgconfig
+	gui? ( >=virtual/jdk-1.6.0
+		app-arch/sharutils
+		sys-apps/gawk )
+	dev-perl/Text-Markdown"
+
+S=${WORKDIR}/${P%[a-z]}
+
+lat1loc=""
+
+DOCS=( AUTHORS ChangeLog COPYING INSTALL KNOWN_PROBLEMS NEWS PACKAGING
+	README README.ChangeLog README.GPU README.xlf RELNOTES THANKS )
+
+FORTRAN_STANDARD=90
+
+pkg_setup() {
+	# Doesn't compile with gcc-4.0, only >=4.1
+	if [[ $(tc-getFC) == *gfortran ]]; then
+		if [[ $(gcc-major-version) -eq 4 ]] \
+			&& [[ $(gcc-minor-version) -lt 1  ]]; then
+				die "Requires gcc-4.1 or newer"
+		fi
+	fi
+
+	# fortran-2.eclass does not handle mpi wrappers
+	if use mpi; then
+		export FC="mpif90"
+		export F77="mpif77"
+		export CC="mpicc"
+		export CXX="mpic++"
+	else
+		tc-export FC F77 CC CXX
+	fi
+
+	# Preprocesor macross can make some lines really long
+	append-fflags -ffree-line-length-none
+
+	fortran-2_pkg_setup
+	if use openmp; then
+                tc-has-openmp || \
+                        die "Please select an openmp capable compiler like gcc[openmp]"
+        fi
+
+	# Sort out some USE options
+	if use fftw-threads && ! use fftw; then
+		ewarn "fftw-threads set but fftw not used, ignored"
+	fi
+	if use cuda-double && ! use cuda; then
+		ewarn "cuda-double set but cuda not used, ignored"
+	fi
+	if use gui; then
+		lat1loc="$(locale |awk '/LC_CTYPE="(.*)"/{sub("LC_CTYPE=\"",""); sub("\" *$", ""); print}')"
+		if locale charmap |grep -i "\<iso885915\?\>"; then
+			einfo "Good, locale compatible with the GUI build"
+		else
+			ewarn "The locale ${lat1loc} incompatible with the GUI build"
+			if latloc=`locale -a| grep -i "\<iso885915\?\>"`; then
+				if echo "${latloc}" |grep -q "^fr"; then
+					lat1loc="$(echo "${latloc}" | grep -im1 "^fr")"
+				else
+					lat1loc="$(echo "${latloc}" | grep -im1 "iso88591")"
+				fi
+				einfo "Will use ${lat1loc} to build the GUI"
+			else
+				ewarn "No ISO-8859-1 nor ISO-8859-15 locale available, the GUI build may crash"
+			fi
+		fi
+	fi
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/6.2.2-change-default-directories.patch \
+		"${FILESDIR}"/6.12.1-autoconf.patch \
+		"${FILESDIR}"/6.12.1-xmalloc.patch \
+		"${FILESDIR}"/7.0.4-test_dirs.patch
+	eautoreconf
+	sed -e"s/\(grep '\^-\)\(\[LloW\]\)'/\1\\\(\2\\\|pthread\\\)'/g" -i configure
+
+}
+
+src_configure() {
+	local openmp=""
+	use openmp && openmp="-fopenmp"
+	local libs=""
+	local modules="-I/usr/$(get_libdir)/finclude $(FoX-config --sax --fcflags)"
+	local FoX_libs="${libs} $(FoX-config --sax --libs)"
+	local trio_flavor=""
+	use etsf_io && trio_flavor="${trio_flavor}+etsf_io"
+	use fox && trio_flavor="${trio_flavor}+fox"
+	use netcdf && trio_flavor="${trio_flavor}+netcdf"
+	test "no${trio_flavor}" = "no" && trio_flavor="none"
+	local netcdff_libs="-lnetcdff"
+	use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran"
+	local fft_flavor="fftw3"
+	local fft_libs=""
+	# The fftw threads support is protected by black magick.
+	# Anybody removes it, dies.
+	# New USE flag "fftw-threads" was added to control usage
+	# of the threaded fftw variant. Since fftw-3.3 has expanded
+	# the paralel options by MPI and OpenMP support, analogical
+	# USE flags should be added to select them in future;
+	# unusable with previous FFTW versions, they are postponed
+	# for now.
+	if use fftw-threads; then
+		fft_flavor="fftw3-threads"
+		if has_version '>=sci-libs/fftw-3.3'; then
+			# pkg-config files for fftw-3.3 are broken
+			# All the parallel stuff is separated
+			# from the main body of common routines,
+			# and -lfftw3 must be always included alongside.
+			# Until version 3.3 this used to be masked by
+			# .la files.
+			# Bug 384645
+			fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads) $(pkg-config --libs fftw3)"
+		else
+			fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads)"
+		fi
+	else
+		fft_libs="${fft_libs} $(pkg-config --libs fftw3)"
+	fi
+	local gpu_flavor="none"
+	if use cuda; then
+		gpu_flavor="cuda-single"
+		if use cuda-double; then
+			gpu_flavor="cuda-double"
+		fi
+	fi
+
+	local myeconfargs=(
+		--enable-clib
+		--enable-exports
+		$(use_enable gui)
+		$(use_enable debug debug enhanced)
+		$(use_enable mpi)
+		$(use_enable mpi mpi-io)
+		$(use_enable openmp)
+		$(use_enable vdwxc)
+		$(use_enable cuda gpu)
+		"$(use cuda && echo "--with-gpu-flavor=${gpu_flavor}")"
+		"$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")"
+		"$(use gsl && echo "--with-math-flavor=gsl")"
+		"$(use gsl && echo "--with-math-incs=$(pkg-config --cflags gsl)")"
+		"$(use gsl && echo "--with-math-libs=$(pkg-config --libs gsl)")"
+		--with-linalg-flavor="atlas"
+		--with-linalg-libs="$(pkg-config --libs lapack)"
+		--with-trio-flavor="${trio_flavor}"
+		"$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")"
+		"$(use netcdf && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")"
+		"$(use fox && echo "--with-fox-incs=${modules}")"
+		"$(use fox && echo "--with-fox-libs=${FoX_libs}")"
+		"$(use etsf_io && echo "--with-etsf-io-incs=${modules}")"
+		"$(use etsf_io && echo "--with-etsf-io-libs=${libs} -letsf_io -letsf_io_utils -letsf_io_low_level")"
+		--with-dft-flavor="libxc+bigdft+atompaw+wannier90"
+		--with-libxc-incs="${modules}"
+		--with-libxc-libs="${libs} -lxc"
+		--with-bigdft-incs="${modules}"
+		--with-bigdft-libs="$(pkg-config --libs bigdft)"
+		--with-atompaw-incs="${modules}"
+		--with-atompaw-libs="${libs} -latompaw"
+		--with-wannier90-bins="/usr/bin"
+		--with-wannier90-incs="${modules}"
+		--with-wannier90-libs="${libs} -lwannier $(pkg-config --libs lapack)"
+		"$(use fftw && echo "--with-fft-flavor=${fft_flavor}")"
+		"$(use fftw && echo "--with-fft-incs=-I/usr/include")"
+		"$(use fftw && echo "--with-fft-libs=${fft_libs}")"
+		--with-timer-flavor="abinit"
+		LD="$(tc-getLD)"
+		FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${openmp} ${modules} -I/usr/include"
+		)
+
+	MARKDOWN=Markdown.pl autotools-utils_src_configure
+
+	if use gui; then
+		# autotools-utils_src_configure() part expanded
+		_check_build_dir
+		pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+		mkdir -p gui
+		cd gui
+		ECONF_SOURCE="${S}"/gui econf UUDECODE="uudecode"
+	fi
+}
+
+src_compile() {
+	autotools-utils_src_compile
+
+	# Apparently libabinit.a is not built by default
+	# Used by BigDFT. Should probably be built separately,
+	# as a package of its own: BigDFT used by Abinit.
+	# Does libabinit.a depend on BigDFT, if used?
+	# Can Abinit use external libabinit.a?
+	use libabinit && autotools-utils_src_compile libabinit.a
+
+	if use gui; then
+		#autotools-utils_src_compile() expanded
+		# _check_build_dir has already been called
+		pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+		# now what the function cannot be called to do
+		cd gui
+		LC_CTYPE="${lat1loc}" emake || die "Making GUI failed"
+		popd > /dev/null
+	fi
+
+	sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc
+}
+
+src_test() {
+	einfo "The tests take quite a while, easily several hours"
+	# autotools-utils_src_test() expanded
+	_check_build_dir
+	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+	# again something the autotools-utils function cannot be called to do
+	# now quite a lot of work actually
+	cd tests
+	emake tests_acc || ewarn "Accuracy tests failed"
+	emake tests_paw || ewarn "PAW tests failed"
+	emake tests_gw || ewarn "GW tests failed"
+	emake tests_gw_paw || ewarn "GW-PAW tests failed"
+	emake tests_bs || ewarn "BSE tests failed"
+	emake tests_tddft || ewarn "TDDFT tests failed"
+	emake tests_eph || ewarn "Elphon tests failed"
+
+	local REPORT
+	for REPORT in $(find . -name report); do
+		REPORT=${REPORT#*/}
+		elog "Parameters and unusual results for ${REPORT%%/*} tests"
+		echo "Parameters and unusual results for ${REPORT%%/*} tests" >>tests_summary.txt
+		while read line; do
+			elog "${line}"
+			echo "${line}" >>tests_summary.txt
+		done \
+			< <(grep -v -e succeeded -e passed ${REPORT})
+	done
+
+	local testdir
+	find . -name "tmp-test*" -print | \
+		while read testdir; do
+			if [ -e summary_of_tests.tar ]; then
+				tar rvf summary_of_tests.tar ${testdir}
+			else tar cvf summary_of_tests.tar ${testdir}
+			fi
+		done
+	popd > /dev/null
+
+	elog "The full test results will be installed as summary_of_tests.tar.bz2."
+	elog "Also a concise report tests_summary.txt is installed."
+}
+
+src_install() {
+	#autotools-utils_src_install() expanded
+	_check_build_dir
+	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+	emake DESTDIR="${D}" install || die "make install failed"
+
+	use libabinit && dolib libabinit.a
+
+	if use gui; then
+		pushd gui
+		emake DESTDIR="${D}" install || die "The GUI install failed"
+		popd
+	fi
+
+	if use test; then
+		for dc in tests_summary.txt summary_of_tests.tar; do
+			test -e tests/"${dc}" && dodoc tests/"${dc}" || ewarn "Copying tests results failed"
+		done
+	fi
+
+	popd > /dev/null
+
+	# XXX: support installing them from builddir as well!!!
+	if [[ ${DOCS} ]]; then
+		dodoc "${DOCS[@]}" || die "dodoc failed"
+	else
+		local f
+		# same list as in PMS
+		for f in README* ChangeLog AUTHORS NEWS TODO CHANGES \
+				THANKS BUGS FAQ CREDITS CHANGELOG; do
+			if [[ -s ${f} ]]; then
+				dodoc "${f}" || die "(default) dodoc ${f} failed"
+			fi
+		done
+	fi
+	if [[ ${HTML_DOCS} ]]; then
+		dohtml -r "${HTML_DOCS[@]}" || die "dohtml failed"
+	fi
+
+	# Remove libtool files and unnecessary static libs
+	remove_libtool_files
+}
+
+pkg_postinst() {
+	if use test; then
+		elog "The full test results will be installed as summary_tests.tar.bz2."
+		elog "Also a concise report tests_summary.txt is installed."
+	fi
+}
diff --git a/sci-physics/abinit/files/7.0.4-test_dirs.patch b/sci-physics/abinit/files/7.0.4-test_dirs.patch
new file mode 100644
index 000000000..94915a0e1
--- /dev/null
+++ b/sci-physics/abinit/files/7.0.4-test_dirs.patch
@@ -0,0 +1,12 @@
+diff -Naurp abinit-7.0.4.orig/tests/Makefile.am abinit-7.0.4/tests/Makefile.am
+--- abinit-7.0.4.orig/tests/Makefile.am	2012-12-08 15:07:26.000000000 +0000
++++ abinit-7.0.4/tests/Makefile.am	2013-01-08 13:58:56.721725346 +0000
+@@ -3607,7 +3607,7 @@ tests_gw_paw: nightly-stamp
+ tests_bs: nightly-stamp
+ 	rm -fr */tmp-bs*
+ 	$(MAKE) tests_v67mbpt dirname=bs start=01 stop=01
+-	cd v6/tmp-bs* ; mv fldiff.report fldiff_keep.report
++	cd v67mbpt/tmp-bs* ; mv fldiff.report fldiff_keep.report
+ 	$(MAKE) tests_v67mbpt dirname=bs start=04 stop=04
+ 	$(MAKE) tests_tutorial dirname=bs start=bs_1 stop=bs_4
+ 	echo
diff --git a/sci-physics/atompaw/ChangeLog b/sci-physics/atompaw/ChangeLog
index 91aeda882..66ddb4e1a 100644
--- a/sci-physics/atompaw/ChangeLog
+++ b/sci-physics/atompaw/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-physics/atompaw
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*atompaw-3.0.1.9 (17 Jan 2013)
+
+  17 Jan 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
+  -atompaw-3.0.1.4.ebuild, +atompaw-3.0.1.9.ebuild:
+  Version bumped to 3.0.1.9
+
   22 May 2012; Justin Lecher <jlec@gentoo.org> -atompaw-3.0.1.3.ebuild,
   atompaw-3.0.1.4.ebuild, metadata.xml:
   Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
diff --git a/sci-physics/atompaw/Manifest b/sci-physics/atompaw/Manifest
index 5c355704b..a36521dcf 100644
--- a/sci-physics/atompaw/Manifest
+++ b/sci-physics/atompaw/Manifest
@@ -1,3 +1,3 @@
-DIST atompaw-3.0.1.4.tar.gz 3785477 SHA256 69c303d28c3698e3ec640b8405b3bfe78a61c2e5a1f5abef92be652040b634db SHA512 adb4fb99647214cae48e81102ca46dfd8500adb5c6a97a62feb0ce2fe48a7fb699f3c873a6b8cef6cd4f856095ab6bbd85f2a941ebcd43ef3d212de22352ed17 WHIRLPOOL 9bfcc48f6d917b33360938186fc55f9982aa25df874380706c17cfe0d6a784379504de737ec2a0eb281e3866011130bf63a92958ff8d6b0308306e4ff1198052
+DIST atompaw-3.0.1.9.tar.gz 3809640 SHA256 6acc591ec3f5c5bb4652a40e4d8414619d680e84e370143d4ca36df7d50f0c63 SHA512 0608e289bfd51bfdce618f24c3056b8258ae2273ecc8671f931dd553d8356bd245911f0c2e461a890b4bf3e14f0fa5f3ac2d0c6c60bc19665b56236619ccf1d4 WHIRLPOOL 5a1a37fc1913a5e510d516ea996842e0cc193856298137c05b28e25d5f653b3c9ef34356fe95829164ab20f7d9e5627c3eac273d3be7511a80150d128aa72e0f
 DIST atompaw.pdf 334715 SHA256 10a70f0c31e4a0a06e31b2b922b938742daf8635c87b95f5a48609555d9397ed SHA512 287f521a10b144bf8c6f59f21a025a8b1e0f6a23d576abe347be8fd41f8577dec0febd289618384d6e7796f0f68bfb41672c9d6d7bf1658f245cff20463ffff7 WHIRLPOOL ae9280374777fd61751d60b4944f3d21aceb86d3b6f4879ced1c26200e33d8ebb08b99e81cffd562e43643274f83bd6d4263360d399acee7eefad3f36791606a
 DIST atompawEqns.pdf 198480 SHA256 181af33190b77b630c1fb94882d0cbc5f79281346f93c25ef4d645806f2c1dc6 SHA512 e0b7fcbce906ceda953e000378786d3b679b68a5dd3d1a53b8d41a61e80bfa5a83fa04a6b8945b274ffe351491bffe3bdd801937f1b838f90b21e462fb09b9e9 WHIRLPOOL 9ba9c90df0c368b935fce573a6be30c492819fda4245f10d217bff3576f82b21036aeee837c28e5b694220f2749a6cf7e26b797b2690624dbfbc3bb598cc2bdd
diff --git a/sci-physics/atompaw/atompaw-3.0.1.4.ebuild b/sci-physics/atompaw/atompaw-3.0.1.9.ebuild
index c9e0cfcc3..e38535457 100644
--- a/sci-physics/atompaw/atompaw-3.0.1.4.ebuild
+++ b/sci-physics/atompaw/atompaw-3.0.1.9.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
diff --git a/sci-physics/openmx/ChangeLog b/sci-physics/openmx/ChangeLog
new file mode 100644
index 000000000..37b46f62f
--- /dev/null
+++ b/sci-physics/openmx/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-physics/openmx
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*openmx-3.6 (17 Jan 2013)
+
+  17 Jan 2013; Honza Macháček <Hloupy.Honza@centrum.cz> +openmx-3.6.ebuild:
+  Ebuild for OpenMX added
+
diff --git a/sci-physics/openmx/Manifest b/sci-physics/openmx/Manifest
new file mode 100644
index 000000000..4e0a74a15
--- /dev/null
+++ b/sci-physics/openmx/Manifest
@@ -0,0 +1,2 @@
+DIST openmx3.6.tar.gz 83023744 SHA256 e344914a615d4179e724877207335e44f9d629cd3931b70e135011877355ab71 SHA512 f4d59e839bbd216893149c83d1059aa4dc4fb011d113cb40efbd99db96d558501b371628f0ea064d3091d8ef0d2c8664412b0c3541fa2a7135811e3536cb0018 WHIRLPOOL 54c72309133dbb010218ce138992362e98eb4c345eb3b2897e1d86f3f2469cc95a2024c8547cc3dc0db78befaf620e624640b6a64522c0937bf7158658a28109
+DIST patch3.6.1.tar.gz 202531 SHA256 56cba052a84c73bf332ff3a65787001376f8d50ec50e7e363a67dfb5b417febd SHA512 1f1c2c156c80a21649826cfaeb79a9b2b7d81b46920e713fb0e4489eeceb8cc6a9193c49efb0d4c1a1a69313e21186e10ed4fd97d27e63b555ce1092425c641d WHIRLPOOL 006cb7ec822ef485c03a371b9c3a99c426fc5e6e1249fd17d9f5527f0220f09df1acc049e31a59d6834a3ce44431ae385268954898613a9fe31ff892262a5503
diff --git a/sci-physics/openmx/openmx-3.6.ebuild b/sci-physics/openmx/openmx-3.6.ebuild
new file mode 100644
index 000000000..78f65a3c0
--- /dev/null
+++ b/sci-physics/openmx/openmx-3.6.ebuild
@@ -0,0 +1,96 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="4"
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="Open source package for Material eXplorer using DFT, norm-conserving
+pseudopotentials, and pseudo-atomic localized basis functions."
+HOMEPAGE="http://www.openmx-square.org/"
+SRC_URI="http://www.openmx-square.org/${PN}${PV}.tar.gz
+		http://www.openmx-square.org/bugfixed/11Nov14/patch${PV}.1.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="-debug mpi openmp test"
+S="${WORKDIR}/${PN}${PV}"
+
+RDEPEND="virtual/blas
+		virtual/lapack
+		sci-libs/fftw:3
+		mpi? ( virtual/mpi
+		     sci-libs/fftw:3[mpi] )
+		openmp? ( sys-devel/gcc[openmp]
+		     sci-libs/fftw:3[openmp] )"
+DEPEND="${RDEPEND}
+	dev-util/pkgconfig"
+
+
+pkg_setup() {
+	if use mpi; then
+		export CC="mpicc"
+	else
+		tc-export CC
+	fi
+
+	if use openmp; then
+		export CC="${CC} -fopenmp"
+	fi
+}
+
+src_prepare() {
+	cd "${WORKDIR}"
+	mv *.out "${PN}${PV}"/work/input_example
+	mv *.[hc] "${PN}${PV}"/source
+}
+
+src_configure() {
+	CFLAGS="${CFLAGS:- -O3 -funroll-loops -ffast-math}"
+	local FFTW_FLAVOUR=fftw3
+	if use openmp; then
+	   FFTW_FLAVOUR=fftw3_omp
+	else
+	   export CFLAGS="${CFLAGS} -Dnoomp"
+	fi
+	if use mpi; then
+	   FFTW_FLAVOUR=fftw3_mpi
+	else
+	   export CFLAGS="${CFLAGS} -Dnompi"
+	fi
+	CFLAGS="${CFLAGS} $(pkg-config --cflags lapack)"
+	CFLAGS="${CFLAGS} $(pkg-config --cflags ${FFTW_FLAVOUR})"
+	export CFLAGS
+
+	local MX_LIB="$(pkg-config --static --libs lapack)"
+	local MX_LIB="${MX_LIB} $(pkg-config --static --libs ${FFTW_FLAVOUR})"
+
+	sed -i -e "s%^CC *=.*$%CC  = ${CC} ${CFLAGS}%" \
+	    -e "s%^LIB *=.*$%LIB = ${MX_LIB}%" \
+	    source/makefile
+}
+
+src_compile() {
+	cd source
+	emake || die "make failed"
+}
+
+src_test() {
+	cd work
+	../source/openmx -runtest
+}
+
+src_install() {
+	insinto /usr/share/${P}
+	doins -r DFT_DATA11
+	cd work
+	insinto /usr/share/${P}/examples
+	doins -r *
+	cd ../source
+	dodir /usr/bin
+	emake DESTDIR="${D}/usr/bin" install
+	dodoc "${S}/${PN}${PV}.pdf"
+	use test && dodoc "${S}"/work/runtest.result
+}
+\ No newline at end of file