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

author: Honza Macháček <Hloupy.Honza@centrum.cz> 2012-03-30 06:10:46 +0200
committer: Honza Macháček <Hloupy.Honza@centrum.cz> 2012-03-30 06:10:46 +0200
commit: ecf1ca2b0144aee51f42f521b3d8701fb023f020 (patch)
tree: 25154725319b3a5227ca1f3d4598a682002e3e89
parent: sci-physics/abinit-6.12.1 fortran setup improvement corrected, gui preparatio... (diff)
download: sci-ecf1ca2b0144aee51f42f521b3d8701fb023f020.tar.gz
sci-ecf1ca2b0144aee51f42f521b3d8701fb023f020.tar.bz2
sci-ecf1ca2b0144aee51f42f521b3d8701fb023f020.zip
22 files changed, 22 insertions, 2280 deletions
diff --git a/sci-libs/bigdft/ChangeLog b/sci-libs/bigdft/ChangeLog
index 60bf2cd54..f378708b5 100644
--- a/sci-libs/bigdft/ChangeLog
+++ b/sci-libs/bigdft/ChangeLog
@@ -2,6 +2,15 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Mar 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
+  -bigdft-1.2.0.2.ebuild, -files/bigdft-1.2.0.2-0001.patch,
+  -files/bigdft-1.2.0.2-0002.patch, -files/bigdft-1.2.0.2-0003.patch,
+  -files/bigdft-1.2.0.2-0004.patch, -files/bigdft-1.2.0.2-testH.patch,
+  -bigdft-1.2.0.5.ebuild, -files/bigdft-1.2.0.5-0001.patch,
+  -bigdft-1.6_pre0.ebuild, -files/bigdft-1.6-tuto-bigdft.pc.patch,
+  -files/bigdft-1.6-tuto-libxc_dir_include.patch:
+  Clean-up.
+
 *bigdft-1.6_pre1 (22 Mar 2012)
 *bigdft-1.6_pre0 (22 Mar 2012)
 
diff --git a/sci-libs/bigdft/Manifest b/sci-libs/bigdft/Manifest
index e94f02430..5f1f645ce 100644
--- a/sci-libs/bigdft/Manifest
+++ b/sci-libs/bigdft/Manifest
@@ -1,6 +1,2 @@
-DIST bigdft-1.2.0.2.tar.gz 944219 SHA256 3143e203879a2f8b1f05789336ceed91250960ef0681c1530868011fc16f56df SHA512 4af0077b00e0f28da1ee5a766a8d58d6942bd191ed37b218d2e5ed5c46867e50946bfd1a5b8e2ea7421d476512092c692330fe5bdff8c65213b44637149a5fd4 WHIRLPOOL 4f4bad4d81ddebc20ae0c96ae8d907f2bcce54311b718232d55475ed53a2a252ffedc1d61bec0eb05446fa4074fc5c3799078edbae2a7832cc0321cc443d1c6e
-DIST bigdft-1.2.0.5.tar.gz 959834 SHA256 e0e6e905b21d784265f812619bfe081388e16eb385a8a502404e39a559a32a92 SHA512 52b647c33d2250488d5fbd61e12a833a7565743dd343023c0c07e68543680ca2882de1433c7c49a6a4d61be3c8e5bf509a4c417585f598253883396b496c5782 WHIRLPOOL bb23bbf5c70582446f0faf580b2f40ea8cd6b1a363717338c1b181a3ce40b7c058a2bc9a6996ab6d9c5e7ad0a2f53cd6b47c52ab67ffd20988b1a629226f9dd2
-DIST bigdft-1.3.2.tar.gz 1370869 SHA256 b18234c321bee98450ea0b6a3c249480ecec66d18dadcc32a7ba0d2d019c820d SHA512 8af2830a9fcf3ef9fa2d51eb05c3339b263ceec4cd0af4dd8a3fdd1901a130fa88867820faf4122d158e2f479fe0e82984244d921b38e1393d7263a0c9a5fd69 WHIRLPOOL 5c52ebd2a45446e774040ef0395057d7c7785141dbbc43897f018242bc5767265d900d5381f8cb3e21aaa319dd302d42f336da86fd9cf2f66e9300209757d31c
 DIST bigdft-1.6-tuto.1.tar.gz 7510733 SHA256 32020c7e58b36fe1f58a47ef02af99bd0da81c6da7d6f15e89b8075494d39d87 SHA512 48684413b0807b5dcee4b97b5b83d9a839c44043801b923c5f0ce7c8a92024cfee64c1065d4d2ffc67cb249cfcd485680b5526aaaedba06e6a88ccc52ba290f2 WHIRLPOOL d6efcc6f9ded331c42e8e3b13a9260e2acd922c4fa0bf303455e33924a930df6aa01abec897c1d190d5016a5bb3781c491e8a17d500e5485717989bddd4f579d
-DIST bigdft-1.6-tuto.tar.gz 7504186 SHA256 265dab2f5d12dd26e5932af5c09b28cbc2e473d87e05679b9bd888ec4ccfeaf3 SHA512 9a3d9695c0a27520711dd65887710099f02ddb89b9ff2457265f49a958212e524a0cfa258f9616bd21add292183a1a358611a66efe267a5ff6a26df40486a602 WHIRLPOOL fa0f509f9b94fed792133700a79c94e8e0e76b6630d03a6747e00cac021bc29e36871ae40f4a7d7aca7c88183f778c2334382280c6c25639132dd2c3dc2769f5
 DIST bigdft-1.6.0.tar.gz 8876759 SHA256 2d3212ef5f1ebc10fe7c627397ac6282ad41e1433ec6e66905f9d39a302913c0 SHA512 facbb78d126885dd04fed6451aa9cd1f5c755055e146cda1d2d4e90e3310fc3066b661635477db96d5b143ffaaa3ebb01107681437fd9965f3c764cf1b034361 WHIRLPOOL 97bc6c28296a92b09139e3a65266daa583011620fad5aed208e0e48627ab1d9c0ef9993d6c4c3cce5696d5c707bcdfb4b8ca7e64379909b3cf073206e32f9572
diff --git a/sci-libs/bigdft/bigdft-1.2.0.2.ebuild b/sci-libs/bigdft/bigdft-1.2.0.2.ebuild
deleted file mode 100644
index 208b45dbd..000000000
--- a/sci-libs/bigdft/bigdft-1.2.0.2.ebuild
+++ /dev/null
@@ -1,89 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils fortran-2 toolchain-funcs
-
-DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
-HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
-SRC_URI="
-	http://inac.cea.fr/L_Sim/BigDFT/${P}.tar.gz
-	http://inac.cea.fr/L_Sim/BigDFT/${PN}-1.3.2.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cuda doc mpi test"
-
-RDEPEND="
-	=sci-libs/libxc-1*[fortran]
-	virtual/blas
-	virtual/fortran
-	virtual/lapack
-	mpi? ( virtual/mpi )
-	cuda? ( dev-util/nvidia-cuda-sdk )"
-DEPEND="${RDEPEND}
-	dev-util/pkgconfig
-	>=sys-devel/autoconf-2.59
-	doc? ( virtual/latex-base )"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-0001.patch \
-		"${FILESDIR}"/${P}-0002.patch \
-		"${FILESDIR}"/${P}-0003.patch \
-		"${FILESDIR}"/${P}-0004.patch \
-		"${FILESDIR}"/${P}-testH.patch
-
-	rm -r src/PSolver/ABINIT-common
-	mv ../${PN}-1.3.2/src/PSolver/ABINIT-common src/PSolver/
-	sed -i -e's%@LIBXC_INCLUDE@%-I/usr/lib/finclude%g' \
-		src/PSolver/ABINIT-common/Makefile.*
-	sed -i -e's%config\.inc%config.h%g' \
-		src/PSolver/ABINIT-common/*.F90
-}
-
-src_configure() {
-	# fortran-2.eclass does not handle mpi wrappers
-	if use mpi; then
-		export FC="mpif90"
-		export CC="mpicc"
-	else
-		tc-export FC CC
-	fi
-
-	econf \
-		$(use_enable mpi) \
-		--enable-libpoissonsolver \
-		--enable-libbigdft \
-		--enable-binaries \
-		--with-moduledir=/usr/$(get_libdir)/finclude \
-		--with-ext-linalg="`pkg-config --libs-only-l lapack`" \
-		--with-ext-linalg-path="`pkg-config --libs-only-L lapack`" \
-		--with-xc-module-path="/usr/lib/finclude" \
-		$(use_enable cuda cuda-gpu) \
-		$(use_with cuda cuda-path /opt/cuda) \
-		$(use_with cuda lib-cutils /opt/cuda/lib) \
-		FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}}" \
-		LD="$(tc-getLD)"
-}
-
-src_compile() {
-	emake -j1 HAVE_LIBXC=1 || die "make failed"
-	if use doc; then
-		emake HAVE_LIBXC=1 doc || die "make doc failed"
-	fi
-}
-
-src_test() {
-	if use test; then
-		emake check
-	fi
-}
-
-src_install() {
-	emake HAVE_LIBXC=1 DESTDIR="${D}" install || die "install failed"
-	dodoc README INSTALL ChangeLog AUTHORS NEWS || die "dodoc failed"
-}
diff --git a/sci-libs/bigdft/bigdft-1.2.0.5.ebuild b/sci-libs/bigdft/bigdft-1.2.0.5.ebuild
deleted file mode 100644
index 161d7def0..000000000
--- a/sci-libs/bigdft/bigdft-1.2.0.5.ebuild
+++ /dev/null
@@ -1,86 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils fortran-2 toolchain-funcs
-
-DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
-HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
-SRC_URI="
-	http://inac.cea.fr/L_Sim/BigDFT/${P}.tar.gz
-	http://inac.cea.fr/L_Sim/BigDFT/${PN}-1.3.2.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cuda doc mpi test"
-
-RDEPEND="
-	=sci-libs/libxc-1*[fortran]
-	virtual/blas
-	virtual/fortran
-	virtual/lapack
-	mpi? ( virtual/mpi )
-	cuda? ( dev-util/nvidia-cuda-sdk )"
-DEPEND="${RDEPEND}
-	dev-util/pkgconfig
-	>=sys-devel/autoconf-2.59
-	doc? ( virtual/latex-base )"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-0001.patch \
-		"${FILESDIR}"/${PN}-1.2.0.2-testH.patch
-
-	rm -r src/PSolver/ABINIT-common
-	mv ../${PN}-1.3.2/src/PSolver/ABINIT-common src/PSolver/
-	sed -i -e's%@LIBXC_INCLUDE@%-I/usr/lib/finclude%g' \
-		src/PSolver/ABINIT-common/Makefile.*
-	sed -i -e's%config\.inc%config.h%g' \
-		src/PSolver/ABINIT-common/*.F90
-}
-
-src_configure() {
-	# fortran-2.eclass does not handle mpi wrappers
-	if use mpi; then
-		export FC="mpif90"
-		export CC="mpicc"
-	else
-		tc-export FC CC
-	fi
-
-	econf \
-		$(use_enable mpi) \
-		--enable-libpoissonsolver \
-		--enable-libbigdft \
-		--enable-binaries \
-		--with-moduledir=/usr/$(get_libdir)/finclude \
-		--with-ext-linalg="`pkg-config --libs-only-l lapack`" \
-		--with-ext-linalg-path="`pkg-config --libs-only-L lapack`" \
-		--with-xc-module-path="/usr/lib/finclude" \
-		$(use_enable cuda cuda-gpu) \
-		$(use_with cuda cuda-path /opt/cuda) \
-		$(use_with cuda lib-cutils /opt/cuda/lib) \
-		FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}}" \
-		LD="$(tc-getLD)"
-}
-
-src_compile() {
-	emake -j1 HAVE_ETSF_XC=1 || die "make failed"
-	if use doc; then
-		emake HAVE_ETSF_XC=1 doc || die "make doc failed"
-	fi
-}
-
-src_test() {
-	if use test; then
-		emake check
-	fi
-}
-
-src_install() {
-	emake HAVE_ETSF_XC=1 DESTDIR="${D}" install || die "install failed"
-	dodoc README INSTALL ChangeLog AUTHORS NEWS || die "dodoc failed"
-}
diff --git a/sci-libs/bigdft/bigdft-1.6_pre0.ebuild b/sci-libs/bigdft/bigdft-1.6_pre0.ebuild
deleted file mode 100644
index f15fa237a..000000000
--- a/sci-libs/bigdft/bigdft-1.6_pre0.ebuild
+++ /dev/null
@@ -1,125 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="4"
-
-inherit autotools-utils flag-o-matic fortran-2 toolchain-funcs
-
-DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
-HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
-
-REAL_P="${P/_pre/-tuto.}"
-REAL_P="${REAL_P/-tuto.0/-tuto}"
-S="${WORKDIR}/${REAL_P}"
-
-SRC_URI="
-	http://inac.cea.fr/L_Sim/BigDFT/${REAL_P}.tar.gz
-	"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cuda doc etsf_io mpi netcdf opencl test"
-
-RDEPEND="
-	=sci-libs/libxc-1*[fortran]
-	virtual/blas
-	virtual/fortran
-	virtual/lapack
-	mpi? ( virtual/mpi )
-	cuda? ( dev-util/nvidia-cuda-sdk )
-	opencl? (
-		|| (
-			dev-util/nvidia-cuda-sdk
-			dev-util/amdstream
-			)
-		)
-	etsf_io? ( sci-libs/etsf_io )
-	netcdf? (
-		sci-libs/netcdf[fortran]
-		)
-	"
-DEPEND="${RDEPEND}
-	dev-util/pkgconfig
-	>=sys-devel/autoconf-2.59
-	doc? ( virtual/latex-base )"
-
-DOCS=( README INSTALL ChangeLog AUTHORS NEWS )
-
-FORTRAN_STANDARD=90
-
-pkg_setup() {
-	# fortran-2.eclass does not handle mpi wrappers
-	if use mpi; then
-		export FC="mpif90"
-		export F77="mpif77"
-		export CC="mpicc"
-	else
-		tc-export FC F77 CC
-	fi
-
-	fortran-2_pkg_setup
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/"${REAL_P}"-libxc_dir_include.patch
-	epatch "${FILESDIR}"/"${REAL_P}"-bigdft.pc.patch
-	eautoreconf
-}
-
-src_configure() {
-	local modules="/usr/$(get_libdir)/finclude"
-	local netcdff_libs="-lnetcdff"
-	filter-flags '-m*' '-O*' "-pipe"
-	local nvcflags="${CFLAGS}"
-#	_filter-var nvcflags '-m*' '-O*' "-pipe"
-	local myeconfargs=(
-		$(use_enable mpi)
-		--enable-optimised-convolution
-		--enable-pseudo
-		--enable-libbigdft
-		--enable-binaries
-		--disable-minima-hopping
-		--with-moduledir="${modules}"
-		--with-ext-linalg="$(pkg-config --libs-only-l lapack) \
-			$(pkg-config --libs-only-l blas)"
-		--with-ext-linalg-path="$(pkg-config --libs-only-L lapack) \
-			$(pkg-config --libs-only-L blas)"
-		--disable-internal-libxc
-		--with-libxc-path="/usr"
-		--with-libxc-include="${modules}"
-		$(use_enable cuda cuda-gpu)
-		$(use_with cuda cuda-path /opt/cuda)
-		$(use_with cuda nvcc-flags "${nvcflags}")
-		$(use_enable opencl)
-		$(use_with opencl ocl-path /usr)
-		$(use_with etsf_io etsf-io)
-		$(use_with etsf_io etsf-io-path "/usr")
-		$(use_with etsf_io netcdf-path "$(pkg-config --libs-only-L netcdf)")
-		"$(use etsf_io && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")"
-		FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} -I${modules}"
-		LD="$(tc-getLD)"
-		CPP="$(tc-getCPP)"
-		)
-	autotools-utils_src_configure
-}
-
-src_compile() {
-	#autotools-utils_src_compile() expanded
-	_check_build_dir
-	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
-	emake -j1 || die 'emake failed'
-	sed -i -e's%\$(top_builddir)/src/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc
-	popd > /dev/null
-
-	use doc && autotools-utils_src_compile doc
-}
-
-src_test() {
-	use test && autotools-utils_src_test
-}
-
-src_install() {
-	autotools-utils_src_install HAVE_LIBXC=1
-}
diff --git a/sci-libs/bigdft/files/bigdft-1.2.0.2-0001.patch b/sci-libs/bigdft/files/bigdft-1.2.0.2-0001.patch
deleted file mode 100644
index 390352745..000000000
--- a/sci-libs/bigdft/files/bigdft-1.2.0.2-0001.patch
+++ /dev/null
@@ -1,92 +0,0 @@
-diff -urN bigdft-1.2.0.old/src/PSolver/xcenergy.f90 bigdft-1.2.0.new/src/PSolver/xcenergy.f90
---- bigdft-1.2.0.old/src/PSolver/xcenergy.f90      2008-12-09 17:41:42.000000000 +0100
-+++ bigdft-1.2.0.new/src/PSolver/xcenergy.f90      2009-11-19 15:19:03.000000000 +0100
-@@ -96,16 +96,16 @@
-   real(dp) :: elocal,vlocal,rho,pot,potion,facpotion,sfactor
-   integer :: npts,i_all,order,offset,i_stat,ispden
-   integer :: i1,i2,i3,j1,j2,j3,jp2,jpp2,jppp2
--  integer :: ndvxc,nvxcdgr,ngr2
-+  integer :: ndvxc,nvxcdgr,ngr2,nd2vxc
- 
-   !interface with drivexc
-   interface
--     subroutine drivexc(exc,ixc,npts,nspden,order,rho_updn,vxc,ndvxc,ngr2,nvxcdgr,&
--          dvxc,d2vxc,grho2_updn,vxcgr,exexch)    !Optional arguments 
-+     subroutine drivexc(exc,ixc,npts,nspden,order,rho_updn,vxc,ndvxc,ngr2,nd2vxc,nvxcdgr,&
-+          dvxc,d2vxc,grho2_updn,vxcgr,exexch,lrho_updn,vxclrho,tau_updn,vxctau)!Optional arguments
-        implicit none
-        !Arguments ------------------------------------
-        !scalars
--       integer,intent(in) :: ixc,ndvxc,ngr2,npts,nspden,nvxcdgr,order
-+       integer,intent(in) :: ixc,ndvxc,ngr2,nd2vxc,npts,nspden,nvxcdgr,order
-        integer,intent(in),optional :: exexch
-        !arrays
-        real(kind=8),intent(in) :: rho_updn(npts,nspden)
-@@ -113,6 +113,8 @@
-        real(kind=8),intent(out) :: exc(npts),vxc(npts,nspden)
-        real(kind=8),intent(out),optional :: d2vxc(npts),dvxc(npts,ndvxc)
-        real(kind=8),intent(out),optional :: vxcgr(npts,nvxcdgr)
-+       real(kind=8),intent(in),optional :: lrho_updn(npts,nspden), tau_updn(npts,nspden)
-+       real(kind=8),intent(out),optional :: vxclrho(npts,nspden),vxctau(npts,nspden)
-      end subroutine drivexc
-   end interface
- 
-@@ -153,7 +155,8 @@
- !     end do
- 
-      !Allocations of the exchange-correlation terms, depending on the ixc value
--     call size_dvxc(ixc,ndvxc,ngr2,nspden,nvxcdgr,order)
-+     nd2vxc=1
-+     call size_dvxc(ixc,ndvxc,ngr2,nd2vxc,nspden,nvxcdgr,order)
- 
-      if (ixc >= 11 .and. ixc <= 16) then
-         !computation of the gradient
-@@ -204,26 +207,26 @@
-      if (ixc >= 11 .and. ixc <= 16) then
-       if (order**2 <= 1 .or. ixc == 16) then
-          if (ixc /= 13) then             
--           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr,&
-+           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr,&
-                  &grho2_updn=gradient,vxcgr=dvxcdgr) 
-          else
--           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr,&
-+           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr,&
-                  &grho2_updn=gradient) 
-          end if
-       else if (order /= 3) then
-          if (ixc /= 13) then             
--           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr,&
-+           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr,&
-                  &dvxc=dvxci,grho2_updn=gradient,vxcgr=dvxcdgr) 
-          else
--           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr,&
-+           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr,&
-                  &dvxc=dvxci,grho2_updn=gradient) 
-          end if
-       else if (order == 3) then
-          if (ixc /= 13) then             
--           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr,&
-+           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr,&
-                  &dvxc=dvxci,d2vxc=d2vxci,grho2_updn=gradient,vxcgr=dvxcdgr) 
-          else
--           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr,&
-+           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr,&
-                  &dvxc=dvxci,d2vxc=d2vxci,grho2_updn=gradient) 
-          end if
-       end if
-@@ -259,12 +262,12 @@
-         !cases without gradient
-      else
-         if (order**2 <=1 .or. ixc >= 31 .and. ixc<=34) then
--           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr)
-+           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr)
-         else if (order==3 .and. (ixc==3 .or. ixc>=7 .and. ixc<=10)) then
--           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr,&
-+           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr,&
-                 &dvxc=dvxci,d2vxc=d2vxci)
-         else
--           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nvxcdgr,&
-+           call drivexc(exci,ixc,npts,nspden,order,rhopot(1,1,offset,1),vxci,ndvxc,ngr2,nd2vxc,nvxcdgr,&
-                 &dvxc=dvxci)
-         end if
-      end if
diff --git a/sci-libs/bigdft/files/bigdft-1.2.0.2-0002.patch b/sci-libs/bigdft/files/bigdft-1.2.0.2-0002.patch
deleted file mode 100644
index 64506dc21..000000000
--- a/sci-libs/bigdft/files/bigdft-1.2.0.2-0002.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -urN bigdft-1.2.0.1/src/geometry.f90 ../bigdft-1.2.0.1/src/geometry.f90
---- bigdft-1.2.0.1/src/geometry.f90	2008-12-09 17:41:41.000000000 +0100
-+++ bigdft-1.2.0.1/src/geometry.f90	2009-05-26 18:51:18.620210000 +0200
-@@ -45,7 +45,7 @@
-   !write the first position
-   if (iproc.eq.0) call  wtposout(ncount_cluster,etot,rxyz,at)
-   !    Open a log file for conjgrad
--  open(unit=16,file='conjgrad.prc',access='append')
-+  open(unit=16,file='conjgrad.prc',position='append')
- 
-   if (in%betax <= 0._gp) then
-      call detbetax(nproc,iproc,at,rxyz,rst,in)
diff --git a/sci-libs/bigdft/files/bigdft-1.2.0.2-0003.patch b/sci-libs/bigdft/files/bigdft-1.2.0.2-0003.patch
deleted file mode 100644
index 385cbf318..000000000
--- a/sci-libs/bigdft/files/bigdft-1.2.0.2-0003.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- bigdft-1.2.0.1.old/src/PSolver/base.f90	2009-06-01 20:40:35.000000000 +0200
-+++ bigdft-1.2.0.1.new/src/PSolver/base.f90	2009-06-01 20:41:31.000000000 +0200
-@@ -31,6 +31,8 @@
-   integer, parameter :: mpidtypg=MPI_DOUBLE_PRECISION
-   !integer, parameter :: mpidtypw=MPI_REAL,mpidtypd=MPI_REAL !in case of single precision
- 
-+  real(kind=4), parameter :: memorylimit=3.e0
-+
-   !flag for GPU computing, if CUDA libraries are present
-   !the parameter flag is removed to allow each processor to modify it following the needs
-   !in that case if a GPU is present a given MPI processor may or not perform a GPU calculation
diff --git a/sci-libs/bigdft/files/bigdft-1.2.0.2-0004.patch b/sci-libs/bigdft/files/bigdft-1.2.0.2-0004.patch
deleted file mode 100644
index 6ae61aa09..000000000
--- a/sci-libs/bigdft/files/bigdft-1.2.0.2-0004.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- bigdft-1.2.0.1.old/src/sumrho.f90	2009-07-01 10:49:36.252793679 +0200
-+++ bigdft-1.2.0.1.new/src/sumrho.f90	2009-07-01 10:50:08.693028765 +0200
-@@ -92,9 +92,12 @@
-                MPI_DOUBLE_PRECISION,MPI_SUM,MPI_COMM_WORLD,ierr)
-         end do
-      else
--         call MPI_ALLREDUCE(MPI_IN_PLACE,rho_p,lr%d%n1i*lr%d%n2i*lr%d%n3i*nspin,&
--              MPI_DOUBLE_PRECISION,MPI_SUM,MPI_COMM_WORLD,ierr)
--         !stop 'rsflag active in sumrho.f90, check MPI2 implementation'
-+#ifdef MPI2
-+        call MPI_ALLREDUCE(MPI_IN_PLACE,rho_p,lr%d%n1i*lr%d%n2i*lr%d%n3i*nspin,&
-+             MPI_DOUBLE_PRECISION,MPI_SUM,MPI_COMM_WORLD,ierr)
-+#else
-+        stop 'rsflag active in sumrho.f90, check MPI2 implementation'
-+#endif
-      end if
-      call timing(iproc,'Rho_commun    ','OF')
-      call timing(iproc,'Rho_comput    ','ON')
diff --git a/sci-libs/bigdft/files/bigdft-1.2.0.2-testH.patch b/sci-libs/bigdft/files/bigdft-1.2.0.2-testH.patch
deleted file mode 100644
index b4ef190a8..000000000
--- a/sci-libs/bigdft/files/bigdft-1.2.0.2-testH.patch
+++ /dev/null
@@ -1,330 +0,0 @@
-diff -Naur bigdft-1.2.0.2_orig/tests/C/Makefile.am bigdft-1.2.0.2/tests/C/Makefile.am
---- tests/C/Makefile.am	2008-12-09 16:41:42.000000000 +0000
-+++ tests/C/Makefile.am	2010-04-23 15:44:31.000000000 +0000
-@@ -21,8 +21,5 @@
- 	cp $(top_srcdir)/tests/inguess.dat .
- 
- check: $(PPFILES) inguess.dat
--	cp -f $(top_srcdir)/tests/C/input.dat .
--	cp -f $(top_srcdir)/tests/C/posinp .
--	cp -f $(top_srcdir)/tests/C/occup.dat .
- 	$(run_parallel) $(top_builddir)/src/cluster > C.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft C.out $(top_srcdir)/tests/Refs/C.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/C/Makefile.in bigdft-1.2.0.2/tests/C/Makefile.in
---- tests/C/Makefile.in	2009-06-04 11:52:08.000000000 +0000
-+++ tests/C/Makefile.in	2010-04-23 15:44:40.000000000 +0000
-@@ -488,9 +488,6 @@
- 	cp $(top_srcdir)/tests/inguess.dat .
- 
- check: $(PPFILES) inguess.dat
--	cp -f $(top_srcdir)/tests/C/input.dat .
--	cp -f $(top_srcdir)/tests/C/posinp .
--	cp -f $(top_srcdir)/tests/C/occup.dat .
- 	$(run_parallel) $(top_builddir)/src/cluster > C.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft C.out $(top_srcdir)/tests/Refs/C.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/Ca2/Makefile.am bigdft-1.2.0.2/tests/Ca2/Makefile.am
---- tests/Ca2/Makefile.am	2009-04-27 08:18:06.000000000 +0000
-+++ tests/Ca2/Makefile.am	2010-04-23 15:45:09.000000000 +0000
-@@ -20,7 +20,5 @@
- 	cp $(top_srcdir)/tests/inguess.dat .
- 
- check: $(PPFILES) inguess.dat 
--	cp -f $(top_srcdir)/tests/Ca2/input.dat .
--	cp -f $(top_srcdir)/tests/Ca2/posinp .
- 	$(run_parallel) $(top_builddir)/src/cluster > Ca2.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft --discrepancy=4.e-10 Ca2.out $(top_srcdir)/tests/Refs/Ca2.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/Ca2/Makefile.in bigdft-1.2.0.2/tests/Ca2/Makefile.in
---- tests/Ca2/Makefile.in	2009-06-04 11:52:08.000000000 +0000
-+++ tests/Ca2/Makefile.in	2010-04-23 15:45:17.000000000 +0000
-@@ -487,8 +487,6 @@
- 	cp $(top_srcdir)/tests/inguess.dat .
- 
- check: $(PPFILES) inguess.dat 
--	cp -f $(top_srcdir)/tests/Ca2/input.dat .
--	cp -f $(top_srcdir)/tests/Ca2/posinp .
- 	$(run_parallel) $(top_builddir)/src/cluster > Ca2.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft --discrepancy=4.e-10 Ca2.out $(top_srcdir)/tests/Refs/Ca2.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/Davidson-SiH4/Makefile.am bigdft-1.2.0.2/tests/Davidson-SiH4/Makefile.am
---- tests/Davidson-SiH4/Makefile.am	2008-12-09 16:41:42.000000000 +0000
-+++ tests/Davidson-SiH4/Makefile.am	2010-04-23 15:46:45.000000000 +0000
-@@ -18,7 +18,5 @@
- 	cp $(top_srcdir)/utils/PSPfiles/$@ .
- 
- check: $(PPFILES)
--	cp -f $(top_srcdir)/tests/Davidson-SiH4/input.dat .
--	cp -f $(top_srcdir)/tests/Davidson-SiH4/posinp .
- 	$(run_parallel) $(top_builddir)/src/cluster > Davidson-SiH4.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft Davidson-SiH4.out $(top_srcdir)/tests/Refs/Davidson-SiH4.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/Davidson-SiH4/Makefile.in bigdft-1.2.0.2/tests/Davidson-SiH4/Makefile.in
---- tests/Davidson-SiH4/Makefile.in	2009-06-04 11:52:08.000000000 +0000
-+++ tests/Davidson-SiH4/Makefile.in	2010-04-23 15:46:53.000000000 +0000
-@@ -485,8 +485,6 @@
- 	cp $(top_srcdir)/utils/PSPfiles/$@ .
- 
- check: $(PPFILES)
--	cp -f $(top_srcdir)/tests/Davidson-SiH4/input.dat .
--	cp -f $(top_srcdir)/tests/Davidson-SiH4/posinp .
- 	$(run_parallel) $(top_builddir)/src/cluster > Davidson-SiH4.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft Davidson-SiH4.out $(top_srcdir)/tests/Refs/Davidson-SiH4.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/GPU/Makefile.am bigdft-1.2.0.2/tests/GPU/Makefile.am
---- tests/GPU/Makefile.am	2008-12-09 16:41:42.000000000 +0000
-+++ tests/GPU/Makefile.am	2010-04-23 15:47:06.000000000 +0000
-@@ -18,8 +18,5 @@
- 	cp $(top_srcdir)/utils/PSPfiles/HGH/$@ .
- 
- check: $(PPFILES) 
--	cp -f $(top_srcdir)/tests/GPU/input.dat .
--	cp -f $(top_srcdir)/tests/GPU/posinp .
--	cp -f $(top_srcdir)/tests/GPU/cpu_gpu_aff.config .
- 	$(top_builddir)/src/cluster > GPU.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft GPU.out $(top_srcdir)/tests/Refs/GPU.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/GPU/Makefile.in bigdft-1.2.0.2/tests/GPU/Makefile.in
---- tests/GPU/Makefile.in	2009-06-04 11:52:08.000000000 +0000
-+++ tests/GPU/Makefile.in	2010-04-23 15:47:13.000000000 +0000
-@@ -485,9 +485,6 @@
- 	cp $(top_srcdir)/utils/PSPfiles/HGH/$@ .
- 
- check: $(PPFILES) 
--	cp -f $(top_srcdir)/tests/GPU/input.dat .
--	cp -f $(top_srcdir)/tests/GPU/posinp .
--	cp -f $(top_srcdir)/tests/GPU/cpu_gpu_aff.config .
- 	$(top_builddir)/src/cluster > GPU.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft GPU.out $(top_srcdir)/tests/Refs/GPU.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/H/Makefile.am bigdft-1.2.0.2/tests/H/Makefile.am
---- tests/H/Makefile.am	2010-04-23 15:39:18.000000000 +0000
-+++ tests/H/Makefile.am	2010-04-23 15:38:46.000000000 +0000
-@@ -17,8 +17,6 @@
- 	cp $(top_srcdir)/utils/PSPfiles/$@ .
- 
- check: $(PPFILES) 
--	cp -f $(top_srcdir)/tests/H/input.dat .
--	cp -f $(top_srcdir)/tests/H/posinp .
- 	$(top_builddir)/src/memguess 1 > H.memguess
- 	python $(top_srcdir)/tests/fldiff.py --bigdft H.memguess $(top_srcdir)/tests/Refs/H.memguess.ref | cat
- 	$(run_parallel) $(top_builddir)/src/cluster > H.out
-diff -Naur bigdft-1.2.0.2_orig/tests/H/Makefile.in bigdft-1.2.0.2/tests/H/Makefile.in
---- tests/H/Makefile.in	2010-04-23 15:39:18.000000000 +0000
-+++ tests/H/Makefile.in	2010-04-23 15:38:46.000000000 +0000
-@@ -484,8 +484,6 @@
- 	cp $(top_srcdir)/utils/PSPfiles/$@ .
- 
- check: $(PPFILES) 
--	cp -f $(top_srcdir)/tests/H/input.dat .
--	cp -f $(top_srcdir)/tests/H/posinp .
- 	$(top_builddir)/src/memguess 1 > H.memguess
- 	python $(top_srcdir)/tests/fldiff.py --bigdft H.memguess $(top_srcdir)/tests/Refs/H.memguess.ref | cat
- 	$(run_parallel) $(top_builddir)/src/cluster > H.out
-diff -Naur bigdft-1.2.0.2_orig/tests/H-spin/Makefile.am bigdft-1.2.0.2/tests/H-spin/Makefile.am
---- tests/H-spin/Makefile.am	2010-04-23 15:39:18.000000000 +0000
-+++ tests/H-spin/Makefile.am	2010-04-23 15:38:46.000000000 +0000
-@@ -18,7 +18,5 @@
- 
- 
- check: $(PPFILES) posinp input.dat
--	cp -f $(top_srcdir)/tests/H-spin/input.dat .
--	cp -f $(top_srcdir)/tests/H-spin/posinp .
- 	$(run_parallel) $(top_builddir)/src/cluster > H-spin.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft H-spin.out $(top_srcdir)/tests/Refs/H-spin.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/H-spin/Makefile.in bigdft-1.2.0.2/tests/H-spin/Makefile.in
---- tests/H-spin/Makefile.in	2010-04-23 15:39:18.000000000 +0000
-+++ tests/H-spin/Makefile.in	2010-04-23 15:38:46.000000000 +0000
-@@ -484,8 +484,6 @@
- 	cp $(top_srcdir)/utils/PSPfiles/HGH/$@ .
- 
- check: $(PPFILES) posinp input.dat
--	cp -f $(top_srcdir)/tests/H-spin/input.dat .
--	cp -f $(top_srcdir)/tests/H-spin/posinp .
- 	$(run_parallel) $(top_builddir)/src/cluster > H-spin.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft H-spin.out $(top_srcdir)/tests/Refs/H-spin.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/H2O-CP2K/Makefile.am bigdft-1.2.0.2/tests/H2O-CP2K/Makefile.am
---- tests/H2O-CP2K/Makefile.am	2008-12-09 16:41:42.000000000 +0000
-+++ tests/H2O-CP2K/Makefile.am	2010-04-23 15:45:57.000000000 +0000
-@@ -20,9 +20,5 @@
- 	cp $(top_srcdir)/utils/PSPfiles/HGH/$@ .
- 
- check: $(PPFILES) 
--	cp -f $(top_srcdir)/tests/H2O-CP2K/input.dat .
--	cp -f $(top_srcdir)/tests/H2O-CP2K/posinp .
--	cp -f $(top_srcdir)/tests/H2O-CP2K/gaucoeff.dat .
--	cp -f $(top_srcdir)/tests/H2O-CP2K/gaubasis.dat .
- 	$(run_parallel) $(top_builddir)/src/cluster > H2O-CP2K.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft H2O-CP2K.out $(top_srcdir)/tests/Refs/H2O-CP2K.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/H2O-CP2K/Makefile.in bigdft-1.2.0.2/tests/H2O-CP2K/Makefile.in
---- tests/H2O-CP2K/Makefile.in	2009-06-04 11:52:08.000000000 +0000
-+++ tests/H2O-CP2K/Makefile.in	2010-04-23 15:46:04.000000000 +0000
-@@ -487,10 +487,6 @@
- 	cp $(top_srcdir)/utils/PSPfiles/HGH/$@ .
- 
- check: $(PPFILES) 
--	cp -f $(top_srcdir)/tests/H2O-CP2K/input.dat .
--	cp -f $(top_srcdir)/tests/H2O-CP2K/posinp .
--	cp -f $(top_srcdir)/tests/H2O-CP2K/gaucoeff.dat .
--	cp -f $(top_srcdir)/tests/H2O-CP2K/gaubasis.dat .
- 	$(run_parallel) $(top_builddir)/src/cluster > H2O-CP2K.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft H2O-CP2K.out $(top_srcdir)/tests/Refs/H2O-CP2K.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/Li+/Makefile.am bigdft-1.2.0.2/tests/Li+/Makefile.am
---- tests/Li+/Makefile.am	2008-12-09 16:41:42.000000000 +0000
-+++ tests/Li+/Makefile.am	2010-04-23 15:39:48.000000000 +0000
-@@ -18,7 +18,5 @@
- 
- 
- check: $(PPFILES) 
--	cp -f $(top_srcdir)/tests/Li+/input.dat .
--	cp -f $(top_srcdir)/tests/Li+/posinp .
- 	$(run_parallel) $(top_builddir)/src/cluster > Li+.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft Li+.out $(top_srcdir)/tests/Refs/Li+.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/Li+/Makefile.in bigdft-1.2.0.2/tests/Li+/Makefile.in
---- tests/Li+/Makefile.in	2009-06-04 11:52:08.000000000 +0000
-+++ tests/Li+/Makefile.in	2010-04-23 15:40:16.000000000 +0000
-@@ -484,8 +484,6 @@
- 	cp $(top_srcdir)/utils/PSPfiles/$@ .
- 
- check: $(PPFILES) 
--	cp -f $(top_srcdir)/tests/Li+/input.dat .
--	cp -f $(top_srcdir)/tests/Li+/posinp .
- 	$(run_parallel) $(top_builddir)/src/cluster > Li+.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft Li+.out $(top_srcdir)/tests/Refs/Li+.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/MINHOP/Makefile.am bigdft-1.2.0.2/tests/MINHOP/Makefile.am
---- tests/MINHOP/Makefile.am	2008-12-09 16:41:42.000000000 +0000
-+++ tests/MINHOP/Makefile.am	2010-04-23 15:47:57.000000000 +0000
-@@ -26,13 +26,6 @@
- 	cp $(top_srcdir)/utils/PSPfiles/$@ .
- 
- check: $(PPFILES) 
--	cp -f $(top_srcdir)/tests/MINHOP/CPUlimit .
--	cp -f $(top_srcdir)/tests/MINHOP/earr.dat .
--	cp -f $(top_srcdir)/tests/MINHOP/input.dat .
--	cp -f $(top_srcdir)/tests/MINHOP/mdinput.dat .
--	cp -f $(top_srcdir)/tests/MINHOP/ioput .
--	cp -f $(top_srcdir)/tests/MINHOP/rand.inp .
--	cp -f $(top_srcdir)/tests/MINHOP/poscur.xyz .
- 	rm -f global.mon
- 	$(run_parallel) $(top_builddir)/src/global > MINHOP.out
- 	python $(top_srcdir)/tests/fldiff.py global.mon $(top_srcdir)/tests/Refs/global.mon.ref
-diff -Naur bigdft-1.2.0.2_orig/tests/MINHOP/Makefile.in bigdft-1.2.0.2/tests/MINHOP/Makefile.in
---- tests/MINHOP/Makefile.in	2009-06-04 11:52:08.000000000 +0000
-+++ tests/MINHOP/Makefile.in	2010-04-23 15:47:32.000000000 +0000
-@@ -493,13 +493,6 @@
- 	cp $(top_srcdir)/utils/PSPfiles/$@ .
- 
- check: $(PPFILES) 
--	cp -f $(top_srcdir)/tests/MINHOP/CPUlimit .
--	cp -f $(top_srcdir)/tests/MINHOP/earr.dat .
--	cp -f $(top_srcdir)/tests/MINHOP/input.dat .
--	cp -f $(top_srcdir)/tests/MINHOP/mdinput.dat .
--	cp -f $(top_srcdir)/tests/MINHOP/ioput .
--	cp -f $(top_srcdir)/tests/MINHOP/rand.inp .
--	cp -f $(top_srcdir)/tests/MINHOP/poscur.xyz .
- 	rm -f global.mon
- 	$(run_parallel) $(top_builddir)/src/global > MINHOP.out
- 	python $(top_srcdir)/tests/fldiff.py global.mon $(top_srcdir)/tests/Refs/global.mon.ref
-diff -Naur bigdft-1.2.0.2_orig/tests/Mn2/Makefile.am bigdft-1.2.0.2/tests/Mn2/Makefile.am
---- tests/Mn2/Makefile.am	2008-12-09 16:41:42.000000000 +0000
-+++ tests/Mn2/Makefile.am	2010-04-23 15:45:33.000000000 +0000
-@@ -18,9 +18,6 @@
- 	cp $(top_srcdir)/utils/PSPfiles/$@ .
- 
- check: $(PPFILES) 
--	cp -f $(top_srcdir)/tests/Mn2/input.dat .
--	cp -f $(top_srcdir)/tests/Mn2/posinp .
--	cp -f $(top_srcdir)/tests/Mn2/moments .
- 	$(top_builddir)/src/memguess 1 > Mn2.memguess
- 	python $(top_srcdir)/tests/fldiff.py --bigdft Mn2.memguess $(top_srcdir)/tests/Refs/Mn2.memguess.ref | cat
- 	$(run_parallel) $(top_builddir)/src/cluster > Mn2.out
-diff -Naur bigdft-1.2.0.2_orig/tests/Mn2/Makefile.in bigdft-1.2.0.2/tests/Mn2/Makefile.in
---- tests/Mn2/Makefile.in	2009-06-04 11:52:09.000000000 +0000
-+++ tests/Mn2/Makefile.in	2010-04-23 15:45:40.000000000 +0000
-@@ -485,9 +485,6 @@
- 	cp $(top_srcdir)/utils/PSPfiles/$@ .
- 
- check: $(PPFILES) 
--	cp -f $(top_srcdir)/tests/Mn2/input.dat .
--	cp -f $(top_srcdir)/tests/Mn2/posinp .
--	cp -f $(top_srcdir)/tests/Mn2/moments .
- 	$(top_builddir)/src/memguess 1 > Mn2.memguess
- 	python $(top_srcdir)/tests/fldiff.py --bigdft Mn2.memguess $(top_srcdir)/tests/Refs/Mn2.memguess.ref | cat
- 	$(run_parallel) $(top_builddir)/src/cluster > Mn2.out
-diff -Naur bigdft-1.2.0.2_orig/tests/NaCl/Makefile.am bigdft-1.2.0.2/tests/NaCl/Makefile.am
---- tests/NaCl/Makefile.am	2008-12-09 16:41:42.000000000 +0000
-+++ tests/NaCl/Makefile.am	2010-04-23 15:44:03.000000000 +0000
-@@ -24,7 +24,5 @@
- 	cp $(top_srcdir)/tests/inguess.dat .
- 
- check: $(PPFILES) inguess.dat
--	cp -f $(top_srcdir)/tests/NaCl/input.dat .
--	cp -f $(top_srcdir)/tests/NaCl/posinp .
- 	$(run_parallel) $(top_builddir)/src/cluster > NaCl.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft NaCl.out $(top_srcdir)/tests/Refs/NaCl.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/NaCl/Makefile.in bigdft-1.2.0.2/tests/NaCl/Makefile.in
---- tests/NaCl/Makefile.in	2009-06-04 11:52:09.000000000 +0000
-+++ tests/NaCl/Makefile.in	2010-04-23 15:44:12.000000000 +0000
-@@ -491,8 +491,6 @@
- 	cp $(top_srcdir)/tests/inguess.dat .
- 
- check: $(PPFILES) inguess.dat
--	cp -f $(top_srcdir)/tests/NaCl/input.dat .
--	cp -f $(top_srcdir)/tests/NaCl/posinp .
- 	$(run_parallel) $(top_builddir)/src/cluster > NaCl.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft NaCl.out $(top_srcdir)/tests/Refs/NaCl.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/SiBulk/Makefile.am bigdft-1.2.0.2/tests/SiBulk/Makefile.am
---- tests/SiBulk/Makefile.am	2008-12-09 16:41:42.000000000 +0000
-+++ tests/SiBulk/Makefile.am	2010-04-23 15:46:20.000000000 +0000
-@@ -17,7 +17,5 @@
- 	cp $(top_srcdir)/utils/PSPfiles/HGH/$@ .
- 
- check: $(PPFILES)
--	cp -f $(top_srcdir)/tests/SiBulk/input.dat .
--	cp -f $(top_srcdir)/tests/SiBulk/posinp .
- 	$(run_parallel) $(top_builddir)/src/cluster > SiBulk.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft SiBulk.out $(top_srcdir)/tests/Refs/SiBulk.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/SiBulk/Makefile.in bigdft-1.2.0.2/tests/SiBulk/Makefile.in
---- tests/SiBulk/Makefile.in	2009-06-04 11:52:09.000000000 +0000
-+++ tests/SiBulk/Makefile.in	2010-04-23 15:46:28.000000000 +0000
-@@ -484,8 +484,6 @@
- 	cp $(top_srcdir)/utils/PSPfiles/HGH/$@ .
- 
- check: $(PPFILES)
--	cp -f $(top_srcdir)/tests/SiBulk/input.dat .
--	cp -f $(top_srcdir)/tests/SiBulk/posinp .
- 	$(run_parallel) $(top_builddir)/src/cluster > SiBulk.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft SiBulk.out $(top_srcdir)/tests/Refs/SiBulk.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
-diff -Naur bigdft-1.2.0.2_orig/tests/SiH4/.Makefile.am.swp bigdft-1.2.0.2/tests/SiH4/.Makefile.am.swp
---- tests/SiH4/.Makefile.am.swp	1970-01-01 00:00:00.000000000 +0000
-+++ tests/SiH4/.Makefile.am.swp	2010-04-23 15:42:22.000000000 +0000
-@@ -0,0 +1,3 @@
-+b0VIM 7.2
-+
-+
-\ No newline at end of file
-diff -Naur bigdft-1.2.0.2_orig/tests/SiH4/Makefile.am bigdft-1.2.0.2/tests/SiH4/Makefile.am
---- tests/SiH4/Makefile.am	2008-12-09 16:41:42.000000000 +0000
-+++ tests/SiH4/Makefile.am	2010-04-23 15:43:36.000000000 +0000
-@@ -18,7 +18,5 @@
- 	cp $(top_srcdir)/utils/PSPfiles/HGH-K/$@ .
- 
- check: $(PPFILES)
--	cp -f $(top_srcdir)/tests/SiH4/input.dat .
--	cp -f $(top_srcdir)/tests/SiH4/posinp .
- 	$(run_parallel) $(top_builddir)/src/cluster > SiH4.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft SiH4.out $(top_srcdir)/tests/Refs/SiH4.out.ref | tee fldiff.report
-diff -Naur bigdft-1.2.0.2_orig/tests/SiH4/Makefile.in bigdft-1.2.0.2/tests/SiH4/Makefile.in
---- tests/SiH4/Makefile.in	2009-06-04 11:52:09.000000000 +0000
-+++ tests/SiH4/Makefile.in	2010-04-23 15:43:47.000000000 +0000
-@@ -485,8 +485,6 @@
- 	cp $(top_srcdir)/utils/PSPfiles/HGH-K/$@ .
- 
- check: $(PPFILES)
--	cp -f $(top_srcdir)/tests/SiH4/input.dat .
--	cp -f $(top_srcdir)/tests/SiH4/posinp .
- 	$(run_parallel) $(top_builddir)/src/cluster > SiH4.out
- 	python $(top_srcdir)/tests/fldiff.py --bigdft SiH4.out $(top_srcdir)/tests/Refs/SiH4.out.ref | tee fldiff.report
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/sci-libs/bigdft/files/bigdft-1.2.0.5-0001.patch b/sci-libs/bigdft/files/bigdft-1.2.0.5-0001.patch
deleted file mode 100644
index 32f95af52..000000000
--- a/sci-libs/bigdft/files/bigdft-1.2.0.5-0001.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- bigdft-1.2.0.5/configure	2011-11-04 15:35:33.000000000 +0100
-+++ bigdft-1.2.0.5-new/configure	2011-11-19 21:06:31.000000000 +0100
-@@ -4736,6 +4736,9 @@
-   "mipspro")
-      capitalize_module=yes
-      capitalize_module_ext="mod" ;;
-+  "open64")
-+     capitalize_module=yes
-+     capitalize_module_ext="mod" ;;
-   *)
-      capitalize_module=no
-      capitalize_module_ext="mod" ;;
-
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch
deleted file mode 100644
index 3ddde7014..000000000
--- a/sci-libs/bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch
+++ /dev/null
@@ -1,203 +0,0 @@
-diff -Naur bigdft-1.6-tuto_orig/Makefile.am bigdft-1.6-tuto/Makefile.am
---- Makefile.am	2011-10-18 07:39:52.000000000 +0000
-+++ Makefile.am	2012-03-21 10:08:44.000000000 +0000
-@@ -4,7 +4,10 @@
- 
- ACLOCAL_AMFLAGS = -I config/m4
- 
--DISTCLEANFILES = config.inc
-+DISTCLEANFILES = config.inc bigdft.pc
-+
-+pkgconfigdir = $(libdir)/pkgconfig
-+pkgconfig_DATA = bigdft.pc
- 
- if BUILD_LIBABINIT
- libABINIT_dir = libABINIT/src
-diff -Naur bigdft-1.6-tuto_orig/Makefile.in bigdft-1.6-tuto/Makefile.in
---- Makefile.in	2012-03-21 10:03:28.000000000 +0000
-+++ Makefile.in	2012-03-21 10:20:48.000000000 +0000
-@@ -33,7 +33,7 @@
- POST_UNINSTALL = :
- subdir = .
- DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \
--	$(srcdir)/Makefile.in $(srcdir)/config.h.in \
-+	$(srcdir)/Makefile.in $(srcdir)/bigdft.pc.in $(srcdir)/config.h.in \
- 	$(top_srcdir)/config/Doxyfile.in $(top_srcdir)/configure \
- 	AUTHORS COPYING ChangeLog INSTALL NEWS config/depcomp \
- 	config/install-sh config/missing
-@@ -48,7 +48,7 @@
-  configure.lineno config.status.lineno
- mkinstalldirs = $(install_sh) -d
- CONFIG_HEADER = config.h
--CONFIG_CLEAN_FILES = config/Doxyfile
-+CONFIG_CLEAN_FILES = bigdft.pc config/Doxyfile
- CONFIG_CLEAN_VPATH_FILES =
- SOURCES =
- DIST_SOURCES =
-@@ -59,6 +59,35 @@
- 	install-pdf-recursive install-ps-recursive install-recursive \
- 	installcheck-recursive installdirs-recursive pdf-recursive \
- 	ps-recursive uninstall-recursive
-+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
-+am__vpath_adj = case $$p in \
-+    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
-+    *) f=$$p;; \
-+  esac;
-+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
-+am__install_max = 40
-+am__nobase_strip_setup = \
-+  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
-+am__nobase_strip = \
-+  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
-+am__nobase_list = $(am__nobase_strip_setup); \
-+  for p in $$list; do echo "$$p $$p"; done | \
-+  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
-+  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
-+    if (++n[$$2] == $(am__install_max)) \
-+      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
-+    END { for (dir in files) print dir, files[dir] }'
-+am__base_list = \
-+  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
-+  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
-+am__uninstall_files_from_dir = { \
-+  test -z "$$files" \
-+    || { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; } \
-+    || { echo " ( cd '$$dir' && rm -f" $$files ")"; \
-+         $(am__cd) "$$dir" && rm -f $$files; }; \
-+  }
-+am__installdirs = "$(DESTDIR)$(pkgconfigdir)"
-+DATA = $(pkgconfig_DATA)
- RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
-   distclean-recursive maintainer-clean-recursive
- AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
-@@ -232,7 +261,9 @@
- 	config/m4
- 
- ACLOCAL_AMFLAGS = -I config/m4
--DISTCLEANFILES = config.inc
-+DISTCLEANFILES = config.inc bigdft.pc
-+pkgconfigdir = $(libdir)/pkgconfig
-+pkgconfig_DATA = bigdft.pc
- @BUILD_LIBABINIT_FALSE@libABINIT_dir = 
- @BUILD_LIBABINIT_TRUE@libABINIT_dir = libABINIT/src
- @BUILD_LIBXC_FALSE@libXC_dir = 
-@@ -307,8 +338,28 @@
- 
- distclean-hdr:
- 	-rm -f config.h stamp-h1
-+bigdft.pc: $(top_builddir)/config.status $(srcdir)/bigdft.pc.in
-+	cd $(top_builddir) && $(SHELL) ./config.status $@
- config/Doxyfile: $(top_builddir)/config.status $(top_srcdir)/config/Doxyfile.in
- 	cd $(top_builddir) && $(SHELL) ./config.status $@
-+install-pkgconfigDATA: $(pkgconfig_DATA)
-+	@$(NORMAL_INSTALL)
-+	test -z "$(pkgconfigdir)" || $(MKDIR_P) "$(DESTDIR)$(pkgconfigdir)"
-+	@list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
-+	for p in $$list; do \
-+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
-+	  echo "$$d$$p"; \
-+	done | $(am__base_list) | \
-+	while read files; do \
-+	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(pkgconfigdir)'"; \
-+	  $(INSTALL_DATA) $$files "$(DESTDIR)$(pkgconfigdir)" || exit $$?; \
-+	done
-+
-+uninstall-pkgconfigDATA:
-+	@$(NORMAL_UNINSTALL)
-+	@list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
-+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
-+	dir='$(DESTDIR)$(pkgconfigdir)'; $(am__uninstall_files_from_dir)
- 
- # This directory's subdirectories are mostly independent; you can cd
- # into them and run `make' without going through this Makefile.
-@@ -622,9 +673,12 @@
- 	       exit 1; } >&2
- check-am: all-am
- check: check-recursive
--all-am: Makefile config.h
-+all-am: Makefile $(DATA) config.h
- installdirs: installdirs-recursive
- installdirs-am:
-+	for dir in "$(DESTDIR)$(pkgconfigdir)"; do \
-+	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-+	done
- install: install-recursive
- install-exec: install-exec-recursive
- install-data: install-data-recursive
-@@ -672,7 +726,7 @@
- 
- info-am:
- 
--install-data-am:
-+install-data-am: install-pkgconfigDATA
- 
- install-dvi: install-dvi-recursive
- 
-@@ -718,7 +772,7 @@
- 
- ps-am:
- 
--uninstall-am:
-+uninstall-am: uninstall-pkgconfigDATA
- 
- .MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \
- 	ctags-recursive install-am install-strip tags-recursive
-@@ -733,10 +787,10 @@
- 	install-data-am install-dvi install-dvi-am install-exec \
- 	install-exec-am install-html install-html-am install-info \
- 	install-info-am install-man install-pdf install-pdf-am \
--	install-ps install-ps-am install-strip installcheck \
-+	install-pkgconfigDATA install-ps install-ps-am install-strip installcheck \
- 	installcheck-am installdirs installdirs-am maintainer-clean \
- 	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
--	pdf-am ps ps-am tags tags-recursive uninstall uninstall-am
-+	pdf-am ps ps-am tags tags-recursive uninstall uninstall-am uninstall-pkgconfigDATA
- 
- 	configure
- 
-diff -Naur bigdft-1.6-tuto_orig/bigdft.pc.in bigdft-1.6-tuto/bigdft.pc.in
---- bigdft.pc.in	1970-01-01 00:00:00.000000000 +0000
-+++ bigdft.pc.in	2012-02-01 09:43:59.000000000 +0000
-@@ -0,0 +1,11 @@
-+prefix=@prefix@
-+exec_prefix=@exec_prefix@
-+libdir=@libdir@
-+includedir=@includedir@
-+
-+Name: libbigdft
-+Description: Library for DFT calculation over wavelets.
-+Requires: 
-+Version: @VERSION@
-+Libs: -L${libdir} -lbigdft -lpoissonsolver @LIBS@ @FCLIBS@
-+Cflags: -I${includedir}
-diff -Naur bigdft-1.6-tuto_orig/configure bigdft-1.6-tuto/configure
---- configure	2012-03-21 10:03:26.000000000 +0000
-+++ configure	2012-03-21 11:04:52.000000000 +0000
-@@ -8512,7 +8512,7 @@
- docdir="${docdir}"
- 
- 
--ac_config_files="$ac_config_files Makefile libABINIT/src/Makefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile"
-+ac_config_files="$ac_config_files Makefile bigdft.pc libABINIT/src/Makefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile"
- 
- 
- # Call libXC ./configure script recursively.
-@@ -9349,6 +9349,7 @@
-     "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;;
-     "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
-     "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
-+    "bigdft.pc") CONFIG_FILES="$CONFIG_FILES bigdft.pc" ;;
-     "libABINIT/src/Makefile") CONFIG_FILES="$CONFIG_FILES libABINIT/src/Makefile" ;;
-     "config/Doxyfile") CONFIG_FILES="$CONFIG_FILES config/Doxyfile" ;;
-     "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
-diff -Naur bigdft-1.6-tuto_orig/configure.ac bigdft-1.6-tuto/configure.ac
---- configure.ac	2012-03-21 10:03:02.000000000 +0000
-+++ configure.ac	2012-03-21 10:48:53.000000000 +0000
-@@ -715,6 +715,7 @@
- dnl Give the name of file.in to transform to file
- AC_CONFIG_FILES([
- Makefile
-+bigdft.pc
- libABINIT/src/Makefile
- config/Doxyfile
- src/Makefile
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto-libxc_dir_include.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto-libxc_dir_include.patch
deleted file mode 100644
index 16aca5ef4..000000000
--- a/sci-libs/bigdft/files/bigdft-1.6-tuto-libxc_dir_include.patch
+++ /dev/null
@@ -1,50 +0,0 @@
---- configure.ac.orig	2011-11-23 14:02:15.000000000 +0000
-+++ configure.ac	2011-11-23 14:09:19.000000000 +0000
-@@ -564,14 +564,17 @@
- dnl Test the libXC library
- ac_internal_libxc="yes"
- AC_ARG_ENABLE(internal-libxc, AS_HELP_STRING([--disable-internal-libxc], [Do not build and link with internal libXC library (default = yes).]), ac_internal_libxc=$enableval, ac_internal_libxc="yes")
--AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib and module files (default = None).]),
-+AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib files (default = None).]),
-             ac_libxc_dir=$withval, ac_libxc_dir=)
-+AC_ARG_WITH(libxc-include, AS_HELP_STRING([--with-libxc-include], [Give the path for an external libXC library module files (default = None).]),
-+            ac_libxc_dir_include=$withval, ac_libxc_dir_include=)
- ac_use_libxc="no"
- ac_build_libxc=$ac_internal_libxc
- if test "$ac_internal_libxc" = "yes" ; then
-   ac_build_libxc="yes"
-   ac_use_libxc="yes"
-   ac_libxc_dir="$top_builddir"/libxc-1.1.0/src
-+  ac_libxc_dir_include="$ac_libxc_dir"/include
-   AC_SUBST(LIBXC_DIR, "\$(top_builddir)"/libxc-1.1.0/src)
-   AC_SUBST(LIBXC_INCLUDE, "-I\$(top_builddir)"/libxc-1.1.0/src)
-   LDFLAGS="$LDFLAGS -L\$(top_builddir)/libxc-1.1.0/src/.libs"
-@@ -579,6 +582,9 @@
- else
-   if test -n "$ac_libxc_dir" ; then
-     LDFLAGS="$LDFLAGS -L$ac_libxc_dir/lib"
-+    if test x"$ac_libxc_dir_include" = x ; then
-+      ac_libxc_dir_include="$ac_libxc_dir"/include
-+    fi
-     
-     dnl Test the given implementation of libXC.
-     ac_libxc_libname="xc"
-@@ -587,13 +593,13 @@
-       ac_libxc_libname="dft_xc"
-       AC_CHECK_LIB($ac_libxc_libname, xc_f90_lda_vxc, withlibxc=yes, withlibxc=no)
-     fi
--    AC_CHECK_FILE($ac_libxc_dir/include/libxc_funcs_m.$capitalize_module_ext, funcs="yes", funcs="no")
--    AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_lib_m.$capitalize_module_ext, lib="yes", lib="no")
--    AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_types_m.$capitalize_module_ext, types="yes", types="no")
-+    AC_CHECK_FILE($ac_libxc_dir_include/libxc_funcs_m.$capitalize_module_ext, funcs="yes", funcs="no")
-+    AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_lib_m.$capitalize_module_ext, lib="yes", lib="no")
-+    AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_types_m.$capitalize_module_ext, types="yes", types="no")
-     if test "$withlibxc" = "yes" -a "$funcs" = "yes" -a "$lib" = "yes" -a "$types" = "yes"; then
-       ac_use_libxc="yes"
--      AC_SUBST(LIBXC_DIR, $ac_libxc_dir/include)
--      AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir/include)
-+      AC_SUBST(LIBXC_DIR, $ac_libxc_dir_include)
-+      AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir_include)
-       LIBXC_LIBS="-l"$ac_libxc_libname
-     fi
-   else
diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index 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
author	Honza Macháček <Hloupy.Honza@centrum.cz>	2012-03-30 06:10:46 +0200
committer	Honza Macháček <Hloupy.Honza@centrum.cz>	2012-03-30 06:10:46 +0200
commit	ecf1ca2b0144aee51f42f521b3d8701fb023f020 (patch)
tree	25154725319b3a5227ca1f3d4598a682002e3e89
parent	sci-physics/abinit-6.12.1 fortran setup improvement corrected, gui preparatio... (diff)
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