From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1SDTBN-0000YL-Hc for garchives@archives.gentoo.org; Fri, 30 Mar 2012 04:11:26 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 28CAFE0ADC; Fri, 30 Mar 2012 04:11:16 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 81495E0AC9 for ; Fri, 30 Mar 2012 04:11:15 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 982491B400D for ; Fri, 30 Mar 2012 04:11:14 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 3377EE5402 for ; Fri, 30 Mar 2012 04:11:13 +0000 (UTC) From: "Honza Macháček" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Honza Macháček" Message-ID: <1333080646.ecf1ca2b0144aee51f42f521b3d8701fb023f020.honza_machacek@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-libs/bigdft/, sci-libs/bigdft/files/, sci-physics/abinit/files/, ... X-VCS-Repository: proj/sci X-VCS-Files: sci-libs/bigdft/ChangeLog sci-libs/bigdft/bigdft-1.2.0.2.ebuild sci-libs/bigdft/bigdft-1.2.0.5.ebuild sci-libs/bigdft/bigdft-1.6_pre0.ebuild sci-libs/bigdft/files/bigdft-1.2.0.2-0001.patch sci-libs/bigdft/files/bigdft-1.2.0.2-0002.patch sci-libs/bigdft/files/bigdft-1.2.0.2-0003.patch sci-libs/bigdft/files/bigdft-1.2.0.2-0004.patch sci-libs/bigdft/files/bigdft-1.2.0.2-testH.patch sci-libs/bigdft/files/bigdft-1.2.0.5-0001.patch sci-libs/bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch sci-libs/bigdft/files/bigdft-1.6-tuto-libxc_dir_include.patch sci-physics/abinit/ChangeLog sci-physics/abinit/abinit-6.10.3.ebuild sci-physics/abinit/abinit-6.12.1.ebuild sci-physics/abinit/abinit-6.12.2.ebuild sci-physics/abinit/abinit-6.6.3.ebuild sci-physics/abinit/abinit-6.8.2.ebuild sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch sci-physics/abinit/files/6.12.1-gui-conf.patch sci-physics/abinit/files/6.6.1-openmp.patch X-VCS-Directories: sci-libs/bigdft/ sci-libs/bigdft/files/ sci-physics/abinit/files/ sci-physics/abinit/ X-VCS-Committer: honza_machacek X-VCS-Committer-Name: Honza Macháček X-VCS-Revision: ecf1ca2b0144aee51f42f521b3d8701fb023f020 X-VCS-Branch: master Date: Fri, 30 Mar 2012 04:11:13 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: e1bd7029-99c0-4480-8654-b4f8341d8a34 X-Archives-Hash: c0ac13e0639d81ff9f179e0a618869d3 commit: ecf1ca2b0144aee51f42f521b3d8701fb023f020 Author: Honza Mach=C3=A1=C4=8Dek centrum cz> AuthorDate: Fri Mar 30 04:10:46 2012 +0000 Commit: Honza Mach=C3=A1=C4=8Dek centrum cz> CommitDate: Fri Mar 30 04:10:46 2012 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3Decf1ca2b sci-libs/bigdft & sci-physics/abinit clean-up after sci-physics/abinit ve= rsion bump to 6.12.2 and tests --- sci-libs/bigdft/ChangeLog | 9 + sci-libs/bigdft/bigdft-1.2.0.2.ebuild | 89 ---- sci-libs/bigdft/bigdft-1.2.0.5.ebuild | 86 ---- sci-libs/bigdft/bigdft-1.6_pre0.ebuild | 125 ----- sci-libs/bigdft/files/bigdft-1.2.0.2-0001.patch | 92 ---- sci-libs/bigdft/files/bigdft-1.2.0.2-0002.patch | 12 - sci-libs/bigdft/files/bigdft-1.2.0.2-0003.patch | 11 - sci-libs/bigdft/files/bigdft-1.2.0.2-0004.patch | 18 - sci-libs/bigdft/files/bigdft-1.2.0.2-testH.patch | 330 ------------- sci-libs/bigdft/files/bigdft-1.2.0.5-0001.patch | 13 - .../bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch | 203 -------- .../files/bigdft-1.6-tuto-libxc_dir_include.patch | 50 -- sci-physics/abinit/ChangeLog | 8 + sci-physics/abinit/abinit-6.10.3.ebuild | 251 ---------- .../{abinit-6.12.1.ebuild =3D> abinit-6.12.2.ebuild} | 7 +- sci-physics/abinit/abinit-6.6.3.ebuild | 196 -------- sci-physics/abinit/abinit-6.8.2.ebuild | 211 -------- sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch | 61 --- sci-physics/abinit/files/6.12.1-gui-conf.patch | 12 - sci-physics/abinit/files/6.6.1-openmp.patch | 509 --------------= ------ 20 files changed, 21 insertions(+), 2272 deletions(-) diff --git a/sci-libs/bigdft/ChangeLog b/sci-libs/bigdft/ChangeLog index 60bf2cd..f378708 100644 --- a/sci-libs/bigdft/ChangeLog +++ b/sci-libs/bigdft/ChangeLog @@ -2,6 +2,15 @@ # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ =20 + 30 Mar 2012; Honza Mach=C3=A1=C4=8Dek + -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) =20 diff --git a/sci-libs/bigdft/bigdft-1.2.0.2.ebuild b/sci-libs/bigdft/bigd= ft-1.2.0.2.ebuild deleted file mode 100644 index 208b45d..0000000 --- a/sci-libs/bigdft/bigdft-1.2.0.2.ebuild +++ /dev/null @@ -1,89 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3D3 - -inherit eutils fortran-2 toolchain-funcs - -DESCRIPTION=3D"A DFT electronic structure code using a wavelet basis set= " -HOMEPAGE=3D"http://inac.cea.fr/L_Sim/BigDFT/" -SRC_URI=3D" - http://inac.cea.fr/L_Sim/BigDFT/${P}.tar.gz - http://inac.cea.fr/L_Sim/BigDFT/${PN}-1.3.2.tar.gz" - -LICENSE=3D"GPL-3" -SLOT=3D"0" -KEYWORDS=3D"~amd64 ~x86" -IUSE=3D"cuda doc mpi test" - -RDEPEND=3D" - =3Dsci-libs/libxc-1*[fortran] - virtual/blas - virtual/fortran - virtual/lapack - mpi? ( virtual/mpi ) - cuda? ( dev-util/nvidia-cuda-sdk )" -DEPEND=3D"${RDEPEND} - dev-util/pkgconfig - >=3Dsys-devel/autoconf-2.59 - doc? ( virtual/latex-base )" - -src_prepare() { - epatch \ - "${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=3D"mpif90" - export CC=3D"mpicc" - else - tc-export FC CC - fi - - econf \ - $(use_enable mpi) \ - --enable-libpoissonsolver \ - --enable-libbigdft \ - --enable-binaries \ - --with-moduledir=3D/usr/$(get_libdir)/finclude \ - --with-ext-linalg=3D"`pkg-config --libs-only-l lapack`" \ - --with-ext-linalg-path=3D"`pkg-config --libs-only-L lapack`" \ - --with-xc-module-path=3D"/usr/lib/finclude" \ - $(use_enable cuda cuda-gpu) \ - $(use_with cuda cuda-path /opt/cuda) \ - $(use_with cuda lib-cutils /opt/cuda/lib) \ - FCFLAGS=3D"${FCFLAGS:- ${FFLAGS:- -O2}}" \ - LD=3D"$(tc-getLD)" -} - -src_compile() { - emake -j1 HAVE_LIBXC=3D1 || die "make failed" - if use doc; then - emake HAVE_LIBXC=3D1 doc || die "make doc failed" - fi -} - -src_test() { - if use test; then - emake check - fi -} - -src_install() { - emake HAVE_LIBXC=3D1 DESTDIR=3D"${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/bigd= ft-1.2.0.5.ebuild deleted file mode 100644 index 161d7de..0000000 --- a/sci-libs/bigdft/bigdft-1.2.0.5.ebuild +++ /dev/null @@ -1,86 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3D3 - -inherit eutils fortran-2 toolchain-funcs - -DESCRIPTION=3D"A DFT electronic structure code using a wavelet basis set= " -HOMEPAGE=3D"http://inac.cea.fr/L_Sim/BigDFT/" -SRC_URI=3D" - http://inac.cea.fr/L_Sim/BigDFT/${P}.tar.gz - http://inac.cea.fr/L_Sim/BigDFT/${PN}-1.3.2.tar.gz" - -LICENSE=3D"GPL-3" -SLOT=3D"0" -KEYWORDS=3D"~amd64 ~x86" -IUSE=3D"cuda doc mpi test" - -RDEPEND=3D" - =3Dsci-libs/libxc-1*[fortran] - virtual/blas - virtual/fortran - virtual/lapack - mpi? ( virtual/mpi ) - cuda? ( dev-util/nvidia-cuda-sdk )" -DEPEND=3D"${RDEPEND} - dev-util/pkgconfig - >=3Dsys-devel/autoconf-2.59 - doc? ( virtual/latex-base )" - -src_prepare() { - epatch \ - "${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=3D"mpif90" - export CC=3D"mpicc" - else - tc-export FC CC - fi - - econf \ - $(use_enable mpi) \ - --enable-libpoissonsolver \ - --enable-libbigdft \ - --enable-binaries \ - --with-moduledir=3D/usr/$(get_libdir)/finclude \ - --with-ext-linalg=3D"`pkg-config --libs-only-l lapack`" \ - --with-ext-linalg-path=3D"`pkg-config --libs-only-L lapack`" \ - --with-xc-module-path=3D"/usr/lib/finclude" \ - $(use_enable cuda cuda-gpu) \ - $(use_with cuda cuda-path /opt/cuda) \ - $(use_with cuda lib-cutils /opt/cuda/lib) \ - FCFLAGS=3D"${FCFLAGS:- ${FFLAGS:- -O2}}" \ - LD=3D"$(tc-getLD)" -} - -src_compile() { - emake -j1 HAVE_ETSF_XC=3D1 || die "make failed" - if use doc; then - emake HAVE_ETSF_XC=3D1 doc || die "make doc failed" - fi -} - -src_test() { - if use test; then - emake check - fi -} - -src_install() { - emake HAVE_ETSF_XC=3D1 DESTDIR=3D"${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/big= dft-1.6_pre0.ebuild deleted file mode 100644 index f15fa23..0000000 --- a/sci-libs/bigdft/bigdft-1.6_pre0.ebuild +++ /dev/null @@ -1,125 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3D"4" - -inherit autotools-utils flag-o-matic fortran-2 toolchain-funcs - -DESCRIPTION=3D"A DFT electronic structure code using a wavelet basis set= " -HOMEPAGE=3D"http://inac.cea.fr/L_Sim/BigDFT/" - -REAL_P=3D"${P/_pre/-tuto.}" -REAL_P=3D"${REAL_P/-tuto.0/-tuto}" -S=3D"${WORKDIR}/${REAL_P}" - -SRC_URI=3D" - http://inac.cea.fr/L_Sim/BigDFT/${REAL_P}.tar.gz - " - -LICENSE=3D"GPL-3" -SLOT=3D"0" -KEYWORDS=3D"~amd64 ~x86" -IUSE=3D"cuda doc etsf_io mpi netcdf opencl test" - -RDEPEND=3D" - =3Dsci-libs/libxc-1*[fortran] - virtual/blas - virtual/fortran - virtual/lapack - mpi? ( virtual/mpi ) - cuda? ( dev-util/nvidia-cuda-sdk ) - opencl? ( - || ( - dev-util/nvidia-cuda-sdk - dev-util/amdstream - ) - ) - etsf_io? ( sci-libs/etsf_io ) - netcdf? ( - sci-libs/netcdf[fortran] - ) - " -DEPEND=3D"${RDEPEND} - dev-util/pkgconfig - >=3Dsys-devel/autoconf-2.59 - doc? ( virtual/latex-base )" - -DOCS=3D( README INSTALL ChangeLog AUTHORS NEWS ) - -FORTRAN_STANDARD=3D90 - -pkg_setup() { - # fortran-2.eclass does not handle mpi wrappers - if use mpi; then - export FC=3D"mpif90" - export F77=3D"mpif77" - export CC=3D"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=3D"/usr/$(get_libdir)/finclude" - local netcdff_libs=3D"-lnetcdff" - filter-flags '-m*' '-O*' "-pipe" - local nvcflags=3D"${CFLAGS}" -# _filter-var nvcflags '-m*' '-O*' "-pipe" - local myeconfargs=3D( - $(use_enable mpi) - --enable-optimised-convolution - --enable-pseudo - --enable-libbigdft - --enable-binaries - --disable-minima-hopping - --with-moduledir=3D"${modules}" - --with-ext-linalg=3D"$(pkg-config --libs-only-l lapack) \ - $(pkg-config --libs-only-l blas)" - --with-ext-linalg-path=3D"$(pkg-config --libs-only-L lapack) \ - $(pkg-config --libs-only-L blas)" - --disable-internal-libxc - --with-libxc-path=3D"/usr" - --with-libxc-include=3D"${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)") - "$(use etsf_io && echo "--with-netcdf-libs=3D$(pkg-config --libs netcd= f) ${netcdff_libs}")" - FCFLAGS=3D"${FCFLAGS:- ${FFLAGS:- -O2}} -I${modules}" - LD=3D"$(tc-getLD)" - CPP=3D"$(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=3D1 -} diff --git a/sci-libs/bigdft/files/bigdft-1.2.0.2-0001.patch b/sci-libs/b= igdft/files/bigdft-1.2.0.2-0001.patch deleted file mode 100644 index 3903527..0000000 --- a/sci-libs/bigdft/files/bigdft-1.2.0.2-0001.patch +++ /dev/null @@ -1,92 +0,0 @@ -diff -urN bigdft-1.2.0.old/src/PSolver/xcenergy.f90 bigdft-1.2.0.new/src= /PSolver/xcenergy.f90 ---- bigdft-1.2.0.old/src/PSolver/xcenergy.f90 2008-12-09 17:41:42.0= 00000000 +0100 -+++ bigdft-1.2.0.new/src/PSolver/xcenergy.f90 2009-11-19 15:19:03.0= 00000000 +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 -=20 - !interface with drivexc - interface -- subroutine drivexc(exc,ixc,npts,nspden,order,rho_updn,vxc,ndvxc,ng= r2,nvxcdgr,& -- dvxc,d2vxc,grho2_updn,vxcgr,exexch) !Optional arguments=20 -+ subroutine drivexc(exc,ixc,npts,nspden,order,rho_updn,vxc,ndvxc,ng= r2,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=3D8),intent(in) :: rho_updn(npts,nspden) -@@ -113,6 +113,8 @@ - real(kind=3D8),intent(out) :: exc(npts),vxc(npts,nspden) - real(kind=3D8),intent(out),optional :: d2vxc(npts),dvxc(npts,ndv= xc) - real(kind=3D8),intent(out),optional :: vxcgr(npts,nvxcdgr) -+ real(kind=3D8),intent(in),optional :: lrho_updn(npts,nspden), ta= u_updn(npts,nspden) -+ real(kind=3D8),intent(out),optional :: vxclrho(npts,nspden),vxct= au(npts,nspden) - end subroutine drivexc - end interface -=20 -@@ -153,7 +155,8 @@ - ! end do -=20 - !Allocations of the exchange-correlation terms, depending on the i= xc value -- call size_dvxc(ixc,ndvxc,ngr2,nspden,nvxcdgr,order) -+ nd2vxc=3D1 -+ call size_dvxc(ixc,ndvxc,ngr2,nd2vxc,nspden,nvxcdgr,order) -=20 - if (ixc >=3D 11 .and. ixc <=3D 16) then - !computation of the gradient -@@ -204,26 +207,26 @@ - if (ixc >=3D 11 .and. ixc <=3D 16) then - if (order**2 <=3D 1 .or. ixc =3D=3D 16) then - if (ixc /=3D 13) then =20 -- 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=3Dgradient,vxcgr=3Ddvxcdgr)=20 - 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=3Dgradient)=20 - end if - else if (order /=3D 3) then - if (ixc /=3D 13) then =20 -- 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=3Ddvxci,grho2_updn=3Dgradient,vxcgr=3Ddvxcdgr)=20 - 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=3Ddvxci,grho2_updn=3Dgradient)=20 - end if - else if (order =3D=3D 3) then - if (ixc /=3D 13) then =20 -- 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=3Ddvxci,d2vxc=3Dd2vxci,grho2_updn=3Dgradient,vxc= gr=3Ddvxcdgr)=20 - 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=3Ddvxci,d2vxc=3Dd2vxci,grho2_updn=3Dgradient)=20 - end if - end if -@@ -259,12 +262,12 @@ - !cases without gradient - else - if (order**2 <=3D1 .or. ixc >=3D 31 .and. ixc<=3D34) 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=3D=3D3 .and. (ixc=3D=3D3 .or. ixc>=3D7 .and. ixc= <=3D10)) 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=3Ddvxci,d2vxc=3Dd2vxci) - 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=3Ddvxci) - end if - end if diff --git a/sci-libs/bigdft/files/bigdft-1.2.0.2-0002.patch b/sci-libs/b= igdft/files/bigdft-1.2.0.2-0002.patch deleted file mode 100644 index 64506dc..0000000 --- a/sci-libs/bigdft/files/bigdft-1.2.0.2-0002.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -urN bigdft-1.2.0.1/src/geometry.f90 ../bigdft-1.2.0.1/src/geometry= .f90 ---- bigdft-1.2.0.1/src/geometry.f90 2008-12-09 17:41:41.000000000 +0100 -+++ bigdft-1.2.0.1/src/geometry.f90 2009-05-26 18:51:18.620210000 +0200 -@@ -45,7 +45,7 @@ - !write the first position - if (iproc.eq.0) call wtposout(ncount_cluster,etot,rxyz,at) - ! Open a log file for conjgrad -- open(unit=3D16,file=3D'conjgrad.prc',access=3D'append') -+ open(unit=3D16,file=3D'conjgrad.prc',position=3D'append') -=20 - if (in%betax <=3D 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/b= igdft/files/bigdft-1.2.0.2-0003.patch deleted file mode 100644 index 385cbf3..0000000 --- a/sci-libs/bigdft/files/bigdft-1.2.0.2-0003.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- bigdft-1.2.0.1.old/src/PSolver/base.f90 2009-06-01 20:40:35.00000000= 0 +0200 -+++ bigdft-1.2.0.1.new/src/PSolver/base.f90 2009-06-01 20:41:31.00000000= 0 +0200 -@@ -31,6 +31,8 @@ - integer, parameter :: mpidtypg=3DMPI_DOUBLE_PRECISION - !integer, parameter :: mpidtypw=3DMPI_REAL,mpidtypd=3DMPI_REAL !in ca= se of single precision -=20 -+ real(kind=3D4), parameter :: memorylimit=3D3.e0 -+ - !flag for GPU computing, if CUDA libraries are present - !the parameter flag is removed to allow each processor to modify it f= ollowing the needs - !in that case if a GPU is present a given MPI processor may or not pe= rform a GPU calculation diff --git a/sci-libs/bigdft/files/bigdft-1.2.0.2-0004.patch b/sci-libs/b= igdft/files/bigdft-1.2.0.2-0004.patch deleted file mode 100644 index 6ae61aa..0000000 --- a/sci-libs/bigdft/files/bigdft-1.2.0.2-0004.patch +++ /dev/null @@ -1,18 +0,0 @@ ---- bigdft-1.2.0.1.old/src/sumrho.f90 2009-07-01 10:49:36.252793679 +020= 0 -+++ bigdft-1.2.0.1.new/src/sumrho.f90 2009-07-01 10:50:08.693028765 +020= 0 -@@ -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%n= 3i*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%n3= i*nspin,& -+ MPI_DOUBLE_PRECISION,MPI_SUM,MPI_COMM_WORLD,ierr) -+#else -+ stop 'rsflag active in sumrho.f90, check MPI2 implementation' -+#endif - end if - call timing(iproc,'Rho_commun ','OF') - call timing(iproc,'Rho_comput ','ON') diff --git a/sci-libs/bigdft/files/bigdft-1.2.0.2-testH.patch b/sci-libs/= bigdft/files/bigdft-1.2.0.2-testH.patch deleted file mode 100644 index b4ef190..0000000 --- a/sci-libs/bigdft/files/bigdft-1.2.0.2-testH.patch +++ /dev/null @@ -1,330 +0,0 @@ -diff -Naur bigdft-1.2.0.2_orig/tests/C/Makefile.am bigdft-1.2.0.2/tests/= C/Makefile.am ---- tests/C/Makefile.am 2008-12-09 16:41:42.000000000 +0000 -+++ tests/C/Makefile.am 2010-04-23 15:44:31.000000000 +0000 -@@ -21,8 +21,5 @@ - cp $(top_srcdir)/tests/inguess.dat . -=20 - 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)/test= s/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 . -=20 - 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)/test= s/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/test= s/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 . -=20 - check: $(PPFILES) inguess.dat=20 -- 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=3D4.e-10 C= a2.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/test= s/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 . -=20 - check: $(PPFILES) inguess.dat=20 -- 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=3D4.e-10 C= a2.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 $(top_srcdir)/utils/PSPfiles/$@ . -=20 - 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 $(top_srcdir)/utils/PSPfiles/$@ . -=20 - 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/test= s/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 $(top_srcdir)/utils/PSPfiles/HGH/$@ . -=20 - check: $(PPFILES)=20 -- 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)/te= sts/Refs/GPU.out.ref | tee fldiff.report -diff -Naur bigdft-1.2.0.2_orig/tests/GPU/Makefile.in bigdft-1.2.0.2/test= s/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 $(top_srcdir)/utils/PSPfiles/HGH/$@ . -=20 - check: $(PPFILES)=20 -- 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)/te= sts/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 $(top_srcdir)/utils/PSPfiles/$@ . -=20 - check: $(PPFILES)=20 -- 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 $(top_srcdir)/utils/PSPfiles/$@ . -=20 - check: $(PPFILES)=20 -- 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/t= ests/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 @@ -=20 -=20 - 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/t= ests/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 $(top_srcdir)/utils/PSPfiles/HGH/$@ . -=20 - 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 $(top_srcdir)/utils/PSPfiles/HGH/$@ . -=20 - check: $(PPFILES)=20 -- 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_srcdi= r)/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 $(top_srcdir)/utils/PSPfiles/HGH/$@ . -=20 - check: $(PPFILES)=20 -- 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_srcdi= r)/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/test= s/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 @@ -=20 -=20 - check: $(PPFILES)=20 -- 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)/te= sts/Refs/Li+.out.ref | tee fldiff.report -diff -Naur bigdft-1.2.0.2_orig/tests/Li+/Makefile.in bigdft-1.2.0.2/test= s/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 $(top_srcdir)/utils/PSPfiles/$@ . -=20 - check: $(PPFILES)=20 -- 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)/te= sts/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/t= ests/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 $(top_srcdir)/utils/PSPfiles/$@ . -=20 - check: $(PPFILES)=20 -- 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/Re= fs/global.mon.ref -diff -Naur bigdft-1.2.0.2_orig/tests/MINHOP/Makefile.in bigdft-1.2.0.2/t= ests/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 $(top_srcdir)/utils/PSPfiles/$@ . -=20 - check: $(PPFILES)=20 -- 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/Re= fs/global.mon.ref -diff -Naur bigdft-1.2.0.2_orig/tests/Mn2/Makefile.am bigdft-1.2.0.2/test= s/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 $(top_srcdir)/utils/PSPfiles/$@ . -=20 - check: $(PPFILES)=20 -- 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_srcdi= r)/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/test= s/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 $(top_srcdir)/utils/PSPfiles/$@ . -=20 - check: $(PPFILES)=20 -- 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_srcdi= r)/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/tes= ts/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 . -=20 - 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)/t= ests/Refs/NaCl.out.ref | tee fldiff.report -diff -Naur bigdft-1.2.0.2_orig/tests/NaCl/Makefile.in bigdft-1.2.0.2/tes= ts/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 . -=20 - 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)/t= ests/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/t= ests/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 $(top_srcdir)/utils/PSPfiles/HGH/$@ . -=20 - 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/t= ests/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 $(top_srcdir)/utils/PSPfiles/HGH/$@ . -=20 - 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=00=00=00=00=10=00=00=C6=9F>I=DC=C0=D3=02=108=00=00jmach=00=00= =00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00= =00=00=00=00=00=00=00=00tuxium1=00=00=00=00=00=00=00=00=00=00=00=00=00=00= =00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00/var/tmp/portage= /sci-libs/bigdft-1.2.0.2-r2/work/bigdft-1.2.0.2/tests/SiH4/Makefile.am=00= 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=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00= =00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00= =00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00=00= =00=00=00=00=00=00=00=00 python $(top_srcdir)/tests/fldiff.py --bigdft Si= H4.out $ python $(top_srcdir)/tests/fldiff.py --bigdft SiH4.out $(top_src= dir)/tests/Refs/SiH4.out.ref | tee fldiff.report=00 $(run_parallel) $(top= _builddir)/src/cluster > SiH4.out=00 cp -f $(top_srcdir)/tests/SiH4/posin= p .=00 cp -f $(top_srcdir)/tests/SiH4/input.dat .=00check: $(PPFILES)=00=00= cp $(top_srcdir)/utils/PSPfiles/HGH-K/$@ .=00$(PPFILES):=00#dependencies= =00=00 fldiff.report $(EXTRA_DIST) $(PPFILES)=00CLEANFILES =3D $(PPFIL= ES) inguess.new i nguess.dat wavefunction* SiH4.out posout* *.prc\=00=00 psppar.Si=00 pspp= ar.H \=00PPFILES =3D \=00=00 posinp =00 input.dat \=00EXTRA_DIST =3D \=00= =00SUBDIRS =3D =00=00## Process this file with automake to produce Makefi= le.in=00bigdft-1.2.0.2/tests/MINHOP/Makefile.in=00bigdft-1.2.0.2/tests/MI= NHOP/Makefile.am=00bigdft-1.2.0.2/tests/GPU/Makefile.in=00bigdft-1.2.0.2/= tests/GPU/Makefile.am=00bigdft-1.2.0.2/tests/Davidson-SiH4/Makefile.in=00= bigdft-1.2.0.2/tests/Davidson-SiH4/Makefile.am=00bigdft-1.2.0.2/tests/SiB= ulk/Makefile.in=00bigdft-1.2.0.2/tests/SiBulk/Makefile.am=00bigdft-1.2.0.= 2/tests/H2O-CP2K/Makefile.in=00bigdft-1.2.0.2/tests/H2O-CP2K/Makefile.am=00= bigdft-1.2.0.2/tests/Mn2/Makefile.in=00bigdft-1.2.0.2/tests/Mn2/Makefile.= am=00bigdft-1.2.0.2/tests/Ca2/Makefile.in=00bigdft-1.2.0.2/tests/Ca2/Make= file.am=00bigdft-1.2.0.2/tests/C/Makefile.in=00bigdft-1.2.0.2/tests/C/Mak= efile.am=00bigdft-1.2.0.2/tests/NaCl/Makefile.in=00bigdft-1.2.0.2/tests/N= aCl/Makefile.am=00gdft-1.2.0.2/tests/SiH4/Makefile.in=00 -\ No newline at end of file -diff -Naur bigdft-1.2.0.2_orig/tests/SiH4/Makefile.am bigdft-1.2.0.2/tes= ts/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 $(top_srcdir)/utils/PSPfiles/HGH-K/$@ . -=20 - 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)/t= ests/Refs/SiH4.out.ref | tee fldiff.report -diff -Naur bigdft-1.2.0.2_orig/tests/SiH4/Makefile.in bigdft-1.2.0.2/tes= ts/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 $(top_srcdir)/utils/PSPfiles/HGH-K/$@ . -=20 - 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)/t= ests/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/b= igdft/files/bigdft-1.2.0.5-0001.patch deleted file mode 100644 index 32f95af..0000000 --- a/sci-libs/bigdft/files/bigdft-1.2.0.5-0001.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- bigdft-1.2.0.5/configure 2011-11-04 15:35:33.000000000 +0100 -+++ bigdft-1.2.0.5-new/configure 2011-11-19 21:06:31.000000000 +0100 -@@ -4736,6 +4736,9 @@ - "mipspro") - capitalize_module=3Dyes - capitalize_module_ext=3D"mod" ;; -+ "open64") -+ capitalize_module=3Dyes -+ capitalize_module_ext=3D"mod" ;; - *) - capitalize_module=3Dno - capitalize_module_ext=3D"mod" ;; - diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch b/sci-= libs/bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch deleted file mode 100644 index 3ddde70..0000000 --- a/sci-libs/bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch +++ /dev/null @@ -1,203 +0,0 @@ -diff -Naur bigdft-1.6-tuto_orig/Makefile.am bigdft-1.6-tuto/Makefile.am ---- Makefile.am 2011-10-18 07:39:52.000000000 +0000 -+++ Makefile.am 2012-03-21 10:08:44.000000000 +0000 -@@ -4,7 +4,10 @@ -=20 - ACLOCAL_AMFLAGS =3D -I config/m4 -=20 --DISTCLEANFILES =3D config.inc -+DISTCLEANFILES =3D config.inc bigdft.pc -+ -+pkgconfigdir =3D $(libdir)/pkgconfig -+pkgconfig_DATA =3D bigdft.pc -=20 - if BUILD_LIBABINIT - libABINIT_dir =3D 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 =3D : - subdir =3D . - DIST_COMMON =3D 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 =3D $(install_sh) -d - CONFIG_HEADER =3D config.h --CONFIG_CLEAN_FILES =3D config/Doxyfile -+CONFIG_CLEAN_FILES =3D bigdft.pc config/Doxyfile - CONFIG_CLEAN_VPATH_FILES =3D - SOURCES =3D - DIST_SOURCES =3D -@@ -59,6 +59,35 @@ - install-pdf-recursive install-ps-recursive install-recursive \ - installcheck-recursive installdirs-recursive pdf-recursive \ - ps-recursive uninstall-recursive -+am__vpath_adj_setup =3D srcdirstrip=3D`echo "$(srcdir)" | sed 's|.|.|g'= `; -+am__vpath_adj =3D case $$p in \ -+ $(srcdir)/*) f=3D`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \ -+ *) f=3D$$p;; \ -+ esac; -+am__strip_dir =3D f=3D`echo $$p | sed -e 's|^.*/||'`; -+am__install_max =3D 40 -+am__nobase_strip_setup =3D \ -+ srcdirstrip=3D`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'` -+am__nobase_strip =3D \ -+ for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||" -+am__nobase_list =3D $(am__nobase_strip_setup); \ -+ for p in $$list; do echo "$$p $$p"; done | \ -+ sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,= ' | \ -+ $(AWK) 'BEGIN { files["."] =3D "" } { files[$$2] =3D files[$$2] " " $= $1; \ -+ if (++n[$$2] =3D=3D $(am__install_max)) \ -+ { print $$2, files[$$2]; n[$$2] =3D 0; files[$$2] =3D "" } } \ -+ END { for (dir in files) print dir, files[dir] }' -+am__base_list =3D \ -+ sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \ -+ sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g' -+am__uninstall_files_from_dir =3D { \ -+ test -z "$$files" \ -+ || { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; }= \ -+ || { echo " ( cd '$$dir' && rm -f" $$files ")"; \ -+ $(am__cd) "$$dir" && rm -f $$files; }; \ -+ } -+am__installdirs =3D "$(DESTDIR)$(pkgconfigdir)" -+DATA =3D $(pkgconfig_DATA) - RECURSIVE_CLEAN_TARGETS =3D mostlyclean-recursive clean-recursive \ - distclean-recursive maintainer-clean-recursive - AM_RECURSIVE_TARGETS =3D $(RECURSIVE_TARGETS:-recursive=3D) \ -@@ -232,7 +261,9 @@ - config/m4 -=20 - ACLOCAL_AMFLAGS =3D -I config/m4 --DISTCLEANFILES =3D config.inc -+DISTCLEANFILES =3D config.inc bigdft.pc -+pkgconfigdir =3D $(libdir)/pkgconfig -+pkgconfig_DATA =3D bigdft.pc - @BUILD_LIBABINIT_FALSE@libABINIT_dir =3D=20 - @BUILD_LIBABINIT_TRUE@libABINIT_dir =3D libABINIT/src - @BUILD_LIBXC_FALSE@libXC_dir =3D=20 -@@ -307,8 +338,28 @@ -=20 - distclean-hdr: - -rm -f config.h stamp-h1 -+bigdft.pc: $(top_builddir)/config.status $(srcdir)/bigdft.pc.in -+ cd $(top_builddir) && $(SHELL) ./config.status $@ - config/Doxyfile: $(top_builddir)/config.status $(top_srcdir)/config/Dox= yfile.in - cd $(top_builddir) && $(SHELL) ./config.status $@ -+install-pkgconfigDATA: $(pkgconfig_DATA) -+ @$(NORMAL_INSTALL) -+ test -z "$(pkgconfigdir)" || $(MKDIR_P) "$(DESTDIR)$(pkgconfigdir)" -+ @list=3D'$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=3D; \ -+ for p in $$list; do \ -+ if test -f "$$p"; then d=3D; else d=3D"$(srcdir)/"; fi; \ -+ echo "$$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: -+ @$(NORMAL_UNINSTALL) -+ @list=3D'$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=3D; \ -+ files=3D`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \ -+ dir=3D'$(DESTDIR)$(pkgconfigdir)'; $(am__uninstall_files_from_dir) -=20 - # 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 @@ -=20 - info-am: -=20 --install-data-am: -+install-data-am: install-pkgconfigDATA -=20 - install-dvi: install-dvi-recursive -=20 -@@ -718,7 +772,7 @@ -=20 - ps-am: -=20 --uninstall-am: -+uninstall-am: uninstall-pkgconfigDATA -=20 - .MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \ - ctags-recursive install-am install-strip tags-recursive -@@ -733,10 +787,10 @@ - install-data-am install-dvi install-dvi-am install-exec \ - install-exec-am install-html install-html-am install-info \ - install-info-am install-man install-pdf install-pdf-am \ -- install-ps install-ps-am install-strip installcheck \ -+ install-pkgconfigDATA install-ps install-ps-am install-strip installch= eck \ - installcheck-am installdirs installdirs-am maintainer-clean \ - maintainer-clean-generic mostlyclean mostlyclean-generic pdf \ -- pdf-am ps ps-am tags tags-recursive uninstall uninstall-am -+ pdf-am ps ps-am tags tags-recursive uninstall uninstall-am uninstall-p= kgconfigDATA -=20 - configure -=20 -diff -Naur bigdft-1.6-tuto_orig/bigdft.pc.in bigdft-1.6-tuto/bigdft.pc.i= n ---- bigdft.pc.in 1970-01-01 00:00:00.000000000 +0000 -+++ bigdft.pc.in 2012-02-01 09:43:59.000000000 +0000 -@@ -0,0 +1,11 @@ -+prefix=3D@prefix@ -+exec_prefix=3D@exec_prefix@ -+libdir=3D@libdir@ -+includedir=3D@includedir@ -+ -+Name: libbigdft -+Description: Library for DFT calculation over wavelets. -+Requires:=20 -+Version: @VERSION@ -+Libs: -L${libdir} -lbigdft -lpoissonsolver @LIBS@ @FCLIBS@ -+Cflags: -I${includedir} -diff -Naur bigdft-1.6-tuto_orig/configure bigdft-1.6-tuto/configure ---- configure 2012-03-21 10:03:26.000000000 +0000 -+++ configure 2012-03-21 11:04:52.000000000 +0000 -@@ -8512,7 +8512,7 @@ - docdir=3D"${docdir}" -=20 -=20 --ac_config_files=3D"$ac_config_files Makefile libABINIT/src/Makefile con= fig/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc = src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src= /CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-= c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile u= tils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile= pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tes= ts/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NE= B/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefi= le tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/D= FT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makef= ile tests/tutorials/Makefile tests/xc/Makefile" -+ac_config_files=3D"$ac_config_files Makefile bigdft.pc libABINIT/src/Ma= kefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/conf= igure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Ma= kefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/con= volutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/= Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/sr= c/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Ma= kefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefil= e tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsC= heb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefi= le tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETS= F_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile" -=20 -=20 - # Call libXC ./configure script recursively. -@@ -9349,6 +9349,7 @@ - "config.h") CONFIG_HEADERS=3D"$CONFIG_HEADERS config.h" ;; - "depfiles") CONFIG_COMMANDS=3D"$CONFIG_COMMANDS depfiles" ;; - "Makefile") CONFIG_FILES=3D"$CONFIG_FILES Makefile" ;; -+ "bigdft.pc") CONFIG_FILES=3D"$CONFIG_FILES bigdft.pc" ;; - "libABINIT/src/Makefile") CONFIG_FILES=3D"$CONFIG_FILES libABINIT/s= rc/Makefile" ;; - "config/Doxyfile") CONFIG_FILES=3D"$CONFIG_FILES config/Doxyfile" ;= ; - "src/Makefile") CONFIG_FILES=3D"$CONFIG_FILES src/Makefile" ;; -diff -Naur bigdft-1.6-tuto_orig/configure.ac bigdft-1.6-tuto/configure.a= c ---- configure.ac 2012-03-21 10:03:02.000000000 +0000 -+++ configure.ac 2012-03-21 10:48:53.000000000 +0000 -@@ -715,6 +715,7 @@ - dnl Give the name of file.in to transform to file - AC_CONFIG_FILES([ - Makefile -+bigdft.pc - libABINIT/src/Makefile - config/Doxyfile - src/Makefile diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto-libxc_dir_include.patc= h b/sci-libs/bigdft/files/bigdft-1.6-tuto-libxc_dir_include.patch deleted file mode 100644 index 16aca5e..0000000 --- a/sci-libs/bigdft/files/bigdft-1.6-tuto-libxc_dir_include.patch +++ /dev/null @@ -1,50 +0,0 @@ ---- configure.ac.orig 2011-11-23 14:02:15.000000000 +0000 -+++ configure.ac 2011-11-23 14:09:19.000000000 +0000 -@@ -564,14 +564,17 @@ - dnl Test the libXC library - ac_internal_libxc=3D"yes" - AC_ARG_ENABLE(internal-libxc, AS_HELP_STRING([--disable-internal-libxc]= , [Do not build and link with internal libXC library (default =3D yes).])= , ac_internal_libxc=3D$enableval, ac_internal_libxc=3D"yes") --AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the p= ath for an external libXC library, lib and module files (default =3D None= ).]), -+AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the p= ath for an external libXC library, lib files (default =3D None).]), - ac_libxc_dir=3D$withval, ac_libxc_dir=3D) -+AC_ARG_WITH(libxc-include, AS_HELP_STRING([--with-libxc-include], [Give= the path for an external libXC library module files (default =3D None).]= ), -+ ac_libxc_dir_include=3D$withval, ac_libxc_dir_include=3D) - ac_use_libxc=3D"no" - ac_build_libxc=3D$ac_internal_libxc - if test "$ac_internal_libxc" =3D "yes" ; then - ac_build_libxc=3D"yes" - ac_use_libxc=3D"yes" - ac_libxc_dir=3D"$top_builddir"/libxc-1.1.0/src -+ ac_libxc_dir_include=3D"$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=3D"$LDFLAGS -L\$(top_builddir)/libxc-1.1.0/src/.libs" -@@ -579,6 +582,9 @@ - else - if test -n "$ac_libxc_dir" ; then - LDFLAGS=3D"$LDFLAGS -L$ac_libxc_dir/lib" -+ if test x"$ac_libxc_dir_include" =3D x ; then -+ ac_libxc_dir_include=3D"$ac_libxc_dir"/include -+ fi - =20 - dnl Test the given implementation of libXC. - ac_libxc_libname=3D"xc" -@@ -587,13 +593,13 @@ - ac_libxc_libname=3D"dft_xc" - AC_CHECK_LIB($ac_libxc_libname, xc_f90_lda_vxc, withlibxc=3Dyes, = withlibxc=3Dno) - fi -- AC_CHECK_FILE($ac_libxc_dir/include/libxc_funcs_m.$capitalize_modul= e_ext, funcs=3D"yes", funcs=3D"no") -- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_lib_m.$capitalize_module= _ext, lib=3D"yes", lib=3D"no") -- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_types_m.$capitalize_modu= le_ext, types=3D"yes", types=3D"no") -+ AC_CHECK_FILE($ac_libxc_dir_include/libxc_funcs_m.$capitalize_modul= e_ext, funcs=3D"yes", funcs=3D"no") -+ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_lib_m.$capitalize_module= _ext, lib=3D"yes", lib=3D"no") -+ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_types_m.$capitalize_modu= le_ext, types=3D"yes", types=3D"no") - if test "$withlibxc" =3D "yes" -a "$funcs" =3D "yes" -a "$lib" =3D = "yes" -a "$types" =3D "yes"; then - ac_use_libxc=3D"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=3D"-l"$ac_libxc_libname - fi - else diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog index 5af1279..4e3f27e 100644 --- a/sci-physics/abinit/ChangeLog +++ b/sci-physics/abinit/ChangeLog @@ -2,6 +2,14 @@ # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ =20 +*abinit-6.12.2 (30 Mar 2012) + + 30 Mar 2012; Honza Mach=C3=A1=C4=8Dek + -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.ebui= ld, + -abinit-6.10.3.ebuild, -abinit-6.12.1.ebuild, +abinit-6.12.2.ebuild: + Version bump, tests, clean-up. + 23 Mar 2012; Honza Mach=C3=A1=C4=8Dek abinit= -6.12.1.ebuild: Fortran setup improvement in 6.12.1 ebuild corrected, gui preparation = corrected. =20 diff --git a/sci-physics/abinit/abinit-6.10.3.ebuild b/sci-physics/abinit= /abinit-6.10.3.ebuild deleted file mode 100644 index f073558..0000000 --- a/sci-physics/abinit/abinit-6.10.3.ebuild +++ /dev/null @@ -1,251 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3D"3" - -inherit autotools eutils fortran-2 multilib toolchain-funcs - -DESCRIPTION=3D"Find total energy, charge density and electronic structur= e using density functional theory" -HOMEPAGE=3D"http://www.abinit.org/" -SRC_URI=3D"http://ftp.abinit.org/${P}.tar.gz" - -LICENSE=3D"GPL-2" -SLOT=3D"0" -KEYWORDS=3D"~amd64 ~x86" -IUSE=3D"cuda -debug +fftw +fftw-threads +fox gsl gui +hdf5 mpi +netcdf p= ython -test +threads -vdwxc" - -RDEPEND=3D">=3Dsci-libs/bigdft-1.2.0.5 - sci-libs/etsf_io - =3Dsci-libs/libxc-1*[fortran] - sci-physics/atompaw[libxc] - fox? ( sci-libs/fox[dom,sax,wcml,wxml] ) - netcdf? ( - sci-libs/netcdf[fortran] - hdf5? ( - sci-libs/netcdf[fortran,hdf5] - ) - ) - hdf5? ( sci-libs/hdf5[fortran] ) - sci-libs/wannier90 - virtual/blas - virtual/lapack - gsl? ( sci-libs/gsl ) - fftw? ( - sci-libs/fftw:3.0 - fftw-threads? ( sci-libs/fftw:3.0[threads] ) - ) - mpi? ( virtual/mpi ) - python? ( dev-python/numpy ) - cuda? ( dev-util/nvidia-cuda-sdk )" -DEPEND=3D"${RDEPEND} - dev-util/pkgconfig - gui? ( >=3Dvirtual/jdk-1.6.0 - app-arch/sharutils - sys-apps/gawk ) - dev-perl/Text-Markdown" - -S=3D${WORKDIR}/${P%[a-z]} - -lat1loc=3D"" - -pkg_setup() { - fortran-2_pkg_setup - # Doesn't compile with gcc-4.0, only >=3D4.1 - if [[ $(tc-getFC) =3D=3D *gfortran ]]; then - if [[ $(gcc-major-version) -eq 4 ]] \ - && [[ $(gcc-minor-version) -lt 1 ]]; then - die "Requires gcc-4.1 or newer" - fi - fi - if use fftw-threads && ! use fftw; then - ewarn "fftw-threads set but fftw not used, ignored" - fi - if use gui; then - lat1loc=3D"$(locale |awk '/LC_CTYPE=3D"(.*)"/{sub("LC_CTYPE=3D\"","");= sub("\" *$", ""); print}')" - if locale charmap |grep -i "\"; then - einfo "Good, locale compatible with the GUI build" - else - ewarn "The locale ${lat1loc} incompatible with the GUI build" - if latloc=3D`locale -a| grep -i "\"`; then - if echo "${latloc}" |grep -q "^fr"; then - lat1loc=3D"$(echo "${latloc}" | grep -im1 "^fr")" - else - lat1loc=3D"$(echo "${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 "${FILESDIR}"/6.0.3-fftw.patch - eautoreconf -} - -src_configure() { - local libs=3D"-L/usr/$(get_libdir)" - local modules=3D"-I/usr/$(get_libdir)/finclude" - local FoX_libs=3D"${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lF= oX_common -lFoX_utils -lFoX_fsys" - local trio_flavor=3D"etsf_io" - use fox && trio_flavor=3D"${trio_flavor}+fox" - use netcdf && trio_flavor=3D"${trio_flavor}+netcdf" - local netcdff_libs=3D"-lnetcdff" - use hdf5 && netcdff_libs=3D"${netcdff_libs} -lhdf5_fortran" - local fft_flavor=3D"fftw3" - local fft_libs=3D"-L/usr/lib" - # The fftw threads support is protected by black magick. - # Anybody removes it, dies. - # New USE flag "fftw-threads" was added to control usage - # of the threaded fftw variant. Since fftw-3.3 has expanded - # the paralel options by MPI and OpenMP support, analogical - # USE flags should be added to select them in future; - # unusable with previous FFTW versions, they are postponed - # for now. - if use fftw-threads; then - fft_flavor=3D"fftw3-threads" - if has_version '>=3Dsci-libs/fftw-3.3'; then - # pkg-config files for fftw-3.3 are broken - # All the parallel stuff is separated - # from the main body of common routines, - # and -lfftw3 must be always included alongside. - # Until version 3.3 this used to be masked by - # .la files. - # Bug 384645 - fft_libs=3D"${fft_libs} $(pkg-config --libs fftw3_threads) $(pkg-conf= ig --libs fftw3)" - else - fft_libs=3D"${fft_libs} $(pkg-config --libs fftw3_threads)" - fi - else - fft_libs=3D"${fft_libs} $(pkg-config --libs fftw3)" - fi - if use mpi; then - MY_FC=3D"mpif90" - MY_CC=3D"mpicc" - MY_CXX=3D"mpic++" - else - MY_FC=3D"$(tc-getFC)" - MY_CC=3D"$(tc-getCC)" - MY_CXX=3D"$(tc-getCXX)" - fi - MARKDOWN=3DMarkdown.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=3Dcuda-single")" \ - "$(use cuda && echo "--with-gpu-prefix=3D/opt/cuda/")" \ - "$(use gsl && echo "--with-math-flavor=3Dgsl")" \ - "$(use gsl && echo "--with-math-incs=3D$(pkg-config --cflags gsl)")" \ - "$(use gsl && echo "--with-math-libs=3D$(pkg-config --libs gsl)")" \ - --with-linalg-flavor=3D"atlas" \ - --with-linalg-libs=3D"$(pkg-config --libs lapack)" \ - --with-trio-flavor=3D"${trio_flavor}" \ - "$(use netcdf && echo "--with-netcdf-incs=3D-I/usr/include")" \ - "$(use netcdf && echo "--with-netcdf-libs=3D$(pkg-config --libs netcdf= ) ${netcdff_libs}")" \ - "$(use fox && echo "--with-fox-incs=3D${modules}")" \ - "$(use fox && echo "--with-fox-libs=3D${FoX_libs}")" \ - --with-etsf-io-incs=3D"${modules}" \ - --with-etsf-io-libs=3D"${libs} -letsf_io -letsf_io_utils -letsf_io_low= _level" \ - --with-dft-flavor=3D"libxc+bigdft+atompaw+wannier90" \ - --with-libxc-incs=3D"${modules}" \ - --with-libxc-libs=3D"${libs} -lxc" \ - --with-bigdft-incs=3D"${modules}" \ - --with-bigdft-libs=3D"${libs} -lpoissonsolver -lbigdft" \ - --with-atompaw-incs=3D"${modules}" \ - --with-atompaw-libs=3D"${libs} -latompaw" \ - --with-wannier90-bins=3D"/usr/bin" \ - --with-wannier90-incs=3D"${modules}" \ - --with-wannier90-libs=3D"${libs} -lwannier $(pkg-config --libs lapack)= " \ - "$(use fftw && echo "--with-fft-flavor=3D${fft_flavor}")" \ - "$(use fftw && echo "--with-fft-incs=3D-I/usr/include")" \ - "$(use fftw && echo "--with-fft-libs=3D${fft_libs}")" \ - --with-timer-flavor=3D"abinit" \ - FC=3D"${MY_FC}" \ - CC=3D"${MY_CC}" \ - CXX=3D"${MY_CXX}" \ - LD=3D"$(tc-getLD)" \ - FCFLAGS=3D"${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include" - - if use gui; then - cd gui - ./bootstrap.sh - econf - fi -} - -src_compile() { - emake || die "make failed" - - if use gui; then - cd gui - LC_CTYPE=3D"${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 $(find . -name report); do - REPORT=3D${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 ${testdir} - fi - done - - elog "The full test results will be installed as summary_of_tests.tar.b= z2." - elog "Also a concise report tests_summary.txt is installed." -} - -src_install() { - emake DESTDIR=3D"${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 faile= d" - fi - - if use gui; then - ( cd gui - emake DESTDIR=3D"${D}" install || die "The GUI install failed" ) - fi - - - dodoc KNOWN_PROBLEMS README || die "Copying doc files failed" -} - -pkg_postinst() { - if use test; then - elog "The full test results will be installed as summary_tests.tar.bz2= ." - elog "Also a concise report tests_summary.txt is installed." - fi -} diff --git a/sci-physics/abinit/abinit-6.12.1.ebuild b/sci-physics/abinit= /abinit-6.12.2.ebuild similarity index 98% rename from sci-physics/abinit/abinit-6.12.1.ebuild rename to sci-physics/abinit/abinit-6.12.2.ebuild index 59f0f98..ddb4355 100644 --- a/sci-physics/abinit/abinit-6.12.1.ebuild +++ b/sci-physics/abinit/abinit-6.12.2.ebuild @@ -253,12 +253,13 @@ src_test() { # again something the autotools-utils function cannot be called to do # now quite a lot of work actually cd tests - emake tests_min || ewarn "Minimal tests failed" + emake tests_acc || ewarn "Accuracy tests failed" emake tests_paw || ewarn "PAW tests failed" emake tests_gw || ewarn "GW tests failed" emake tests_gw_paw || ewarn "GW-PAW tests failed" - emake tests tdft || ewarn "TDFT tests failed" - emake tests_bench || ewarn "Benchmarks failed" + emake tests_bs || ewarn "BSE tests failed" + emake tests_tddft || ewarn "TDDFT tests failed" + emake tests_eph || ewarn "Elphon tests failed" =20 local REPORT for REPORT in $(find . -name report); do diff --git a/sci-physics/abinit/abinit-6.6.3.ebuild b/sci-physics/abinit/= abinit-6.6.3.ebuild deleted file mode 100644 index 3799d05..0000000 --- a/sci-physics/abinit/abinit-6.6.3.ebuild +++ /dev/null @@ -1,196 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3D"3" - -inherit autotools eutils fortran-2 multilib toolchain-funcs - -DESCRIPTION=3D"Find total energy, charge density and electronic structur= e using density functional theory" -HOMEPAGE=3D"http://www.abinit.org/" -SRC_URI=3D"http://ftp.abinit.org/${P}.tar.gz" - -LICENSE=3D"GPL-2" -SLOT=3D"0" -KEYWORDS=3D"~amd64 ~x86" -IUSE=3D"cuda -debug +fftw +fox gsl +hdf5 mpi +netcdf python -test +threa= ds -vdwxc" - -RDEPEND=3D">=3Dsci-libs/bigdft-1.2.0.2 - sci-libs/etsf_io - =3Dsci-libs/libxc-1.0[fortran] - sci-physics/atompaw[libxc] - fox? ( sci-libs/fox[dom,sax,wcml,wxml] ) - netcdf? ( - sci-libs/netcdf[fortran] - hdf5? ( - sci-libs/netcdf[fortran,hdf5] - ) - ) - hdf5? ( sci-libs/hdf5[fortran] ) - sci-libs/wannier90 - virtual/blas - virtual/lapack - gsl? ( sci-libs/gsl ) - fftw? ( - sci-libs/fftw:3.0 - threads? ( sci-libs/fftw:3.0[threads] ) - ) - mpi? ( virtual/mpi ) - python? ( dev-python/numpy ) - cuda? ( dev-util/nvidia-cuda-sdk )" -DEPEND=3D"${RDEPEND} - dev-util/pkgconfig - dev-perl/Text-Markdown" - -S=3D${WORKDIR}/${P%[a-z]} - -pkg_setup() { - fortran-2_pkg_setup - # Doesn't compile with gcc-4.0, only >=3D4.1 - if [[ $(tc-getFC) =3D=3D *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 "${FILESDIR}"/6.0.3-fftw.patch - eautoreconf -} - -src_configure() { - local libs=3D"-L/usr/$(get_libdir)" - local modules=3D"-I/usr/$(get_libdir)/finclude" - local FoX_libs=3D"${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lF= oX_common -lFoX_utils -lFoX_fsys" - local trio_flavor=3D"etsf_io" - use fox && trio_flavor=3D"${trio_flavor}+fox" - use netcdf && trio_flavor=3D"${trio_flavor}+netcdf" - local netcdff_libs=3D"-lnetcdff" - use hdf5 && netcdff_libs=3D"${netcdff_libs} -lhdf5_fortran" - local fft_flavor=3D"fftw3" - local fft_libs=3D"-L/usr/lib" - # Since now, fftw threads support is protected by black magick. - # Anybody removes it again, dies. - # If it does not work FOR YOU, disable the "threads" USE flag - # for the package at YOUR box. If YOU want it disabled selectively - # for fftw use in abinit, you may consider adding a special USE flag - # for that. NEVER REMOVE AN OPTION FOR OTHERS, at least if there is - # anybody it works for. - if use threads; then - fft_libs=3D"${fft_libs} $(pkg-config --libs fftw3_threads)" - fft_flavor=3D"fftw3-threads" - else - fft_libs=3D"${fft_libs} $(pkg-config --libs fftw3)" - fi - if use mpi; then - MY_FC=3D"mpif90" - MY_CC=3D"mpicc" - MY_CXX=3D"mpic++" - else - MY_FC=3D"$(tc-getFC)" - MY_CC=3D"$(tc-getCC)" - MY_CXX=3D"$(tc-getCXX)" - fi - MARKDOWN=3DMarkdown.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=3Dcuda-single")" \ - "$(use cuda && echo "--with-gpu-prefix=3D/opt/cuda/")" \ - "$(use gsl && echo "--with-math-flavor=3Dgsl")" \ - "$(use gsl && echo "--with-math-incs=3D$(pkg-config --cflags gsl)")" \ - "$(use gsl && echo "--with-math-libs=3D$(pkg-config --libs gsl)")" \ - --with-linalg-flavor=3D"atlas" \ - --with-linalg-libs=3D"$(pkg-config --libs lapack)" \ - --with-trio-flavor=3D"${trio_flavor}" \ - "$(use netcdf && echo "--with-netcdf-incs=3D-I/usr/include")" \ - "$(use netcdf && echo "--with-netcdf-libs=3D$(pkg-config --libs netcdf= ) ${netcdff_libs}")" \ - "$(use fox && echo "--with-fox-incs=3D${modules}")" \ - "$(use fox && echo "--with-fox-libs=3D${FoX_libs}")" \ - --with-etsf-io-incs=3D"${modules}" \ - --with-etsf-io-libs=3D"${libs} -letsf_io -letsf_io_utils -letsf_io_low= _level" \ - --with-dft-flavor=3D"libxc+bigdft+atompaw+wannier90" \ - --with-libxc-incs=3D"${modules}" \ - --with-libxc-libs=3D"${libs} -lxc" \ - --with-bigdft-incs=3D"${modules}" \ - --with-bigdft-libs=3D"${libs} -lpoissonsolver -lbigdft" \ - --with-atompaw-incs=3D"${modules}" \ - --with-atompaw-libs=3D"${libs} -latompaw" \ - --with-wannier90-bins=3D"/usr/bin" \ - --with-wannier90-incs=3D"${modules}" \ - --with-wannier90-libs=3D"${libs} -lwannier $(pkg-config --libs lapack)= " \ - "$(use fftw && echo "--with-fft-flavor=3D${fft_flavor}")" \ - "$(use fftw && echo "--with-fft-incs=3D-I/usr/include")" \ - "$(use fftw && echo "--with-fft-libs=3D${fft_libs}")" \ - --with-timer-flavor=3D"abinit" \ - FC=3D"${MY_FC}" \ - CC=3D"${MY_CC}" \ - CXX=3D"${MY_CXX}" \ - LD=3D"$(tc-getLD)" \ - FCFLAGS=3D"${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 $(find . -name report); do - REPORT=3D${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 ${testdir} - fi - done - - elog "The full test results will be installed as summary_of_tests.tar.b= z2." - elog "Also a concise report tests_summary.txt is installed." -} - -src_install() { - emake DESTDIR=3D"${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 faile= d" - fi - - dodoc KNOWN_PROBLEMS README || die "Copying doc files failed" -} - -pkg_postinst() { - if use test; then - elog "The full test results will be installed as summary_tests.tar.bz2= ." - elog "Also a concise report tests_summary.txt is installed." - fi -} diff --git a/sci-physics/abinit/abinit-6.8.2.ebuild b/sci-physics/abinit/= abinit-6.8.2.ebuild deleted file mode 100644 index cdd495f..0000000 --- a/sci-physics/abinit/abinit-6.8.2.ebuild +++ /dev/null @@ -1,211 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3D"3" - -inherit autotools eutils fortran-2 multilib toolchain-funcs - -DESCRIPTION=3D"Find total energy, charge density and electronic structur= e using density functional theory" -HOMEPAGE=3D"http://www.abinit.org/" -SRC_URI=3D"http://ftp.abinit.org/${P}.tar.gz" - -LICENSE=3D"GPL-2" -SLOT=3D"0" -KEYWORDS=3D"~amd64 ~x86" -IUSE=3D"cuda -debug +fftw +fftw-threads +fox gsl +hdf5 mpi +netcdf pytho= n -test +threads -vdwxc" - -RDEPEND=3D">=3Dsci-libs/bigdft-1.2.0.2 - sci-libs/etsf_io - =3Dsci-libs/libxc-1.0[fortran] - sci-physics/atompaw[libxc] - fox? ( sci-libs/fox[dom,sax,wcml,wxml] ) - netcdf? ( - sci-libs/netcdf[fortran] - hdf5? ( - sci-libs/netcdf[fortran,hdf5] - ) - ) - hdf5? ( sci-libs/hdf5[fortran] ) - sci-libs/wannier90 - virtual/blas - virtual/lapack - gsl? ( sci-libs/gsl ) - fftw? ( - sci-libs/fftw:3.0 - fftw-threads? ( sci-libs/fftw:3.0[threads] ) - ) - mpi? ( virtual/mpi ) - python? ( dev-python/numpy ) - cuda? ( dev-util/nvidia-cuda-sdk )" -DEPEND=3D"${RDEPEND} - dev-util/pkgconfig - dev-perl/Text-Markdown" - -S=3D${WORKDIR}/${P%[a-z]} - -pkg_setup() { - fortran-2_pkg_setup - # Doesn't compile with gcc-4.0, only >=3D4.1 - if [[ $(tc-getFC) =3D=3D *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 "${FILESDIR}"/6.0.3-fftw.patch - eautoreconf -} - -src_configure() { - local libs=3D"-L/usr/$(get_libdir)" - local modules=3D"-I/usr/$(get_libdir)/finclude" - local FoX_libs=3D"${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lF= oX_common -lFoX_utils -lFoX_fsys" - local trio_flavor=3D"etsf_io" - use fox && trio_flavor=3D"${trio_flavor}+fox" - use netcdf && trio_flavor=3D"${trio_flavor}+netcdf" - local netcdff_libs=3D"-lnetcdff" - use hdf5 && netcdff_libs=3D"${netcdff_libs} -lhdf5_fortran" - local fft_flavor=3D"fftw3" - local fft_libs=3D"-L/usr/lib" - # The fftw threads support is protected by black magick. - # Anybody removes it, dies. - # New USE flag "fftw-threads" was added to control usage - # of the threaded fftw variant. Since fftw-3.3 has expanded - # the paralel options by MPI and OpenMP support, analogical - # USE flags should be added to select them in future; - # unusable with previous FFTW versions, they are postponed - # for now. - if use fftw-threads; then - fft_flavor=3D"fftw3-threads" - if has_version '>=3Dsci-libs/fftw-3.3'; then - # pkg-config files for fftw-3.3 are broken - # All the parallel stuff is separated - # from the main body of common routines, - # and -lfftw3 must be always included alongside. - # Until version 3.3 this used to be masked by - # .la files. - # Bug 384645 - fft_libs=3D"${fft_libs} $(pkg-config --libs fftw3_threads) $(pkg-conf= ig --libs fftw3)" - else - fft_libs=3D"${fft_libs} $(pkg-config --libs fftw3_threads)" - fi - else - fft_libs=3D"${fft_libs} $(pkg-config --libs fftw3)" - fi - if use mpi; then - MY_FC=3D"mpif90" - MY_CC=3D"mpicc" - MY_CXX=3D"mpic++" - else - MY_FC=3D"$(tc-getFC)" - MY_CC=3D"$(tc-getCC)" - MY_CXX=3D"$(tc-getCXX)" - fi - MARKDOWN=3DMarkdown.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=3Dcuda-single")" \ - "$(use cuda && echo "--with-gpu-prefix=3D/opt/cuda/")" \ - "$(use gsl && echo "--with-math-flavor=3Dgsl")" \ - "$(use gsl && echo "--with-math-incs=3D$(pkg-config --cflags gsl)")" \ - "$(use gsl && echo "--with-math-libs=3D$(pkg-config --libs gsl)")" \ - --with-linalg-flavor=3D"atlas" \ - --with-linalg-libs=3D"$(pkg-config --libs lapack)" \ - --with-trio-flavor=3D"${trio_flavor}" \ - "$(use netcdf && echo "--with-netcdf-incs=3D-I/usr/include")" \ - "$(use netcdf && echo "--with-netcdf-libs=3D$(pkg-config --libs netcdf= ) ${netcdff_libs}")" \ - "$(use fox && echo "--with-fox-incs=3D${modules}")" \ - "$(use fox && echo "--with-fox-libs=3D${FoX_libs}")" \ - --with-etsf-io-incs=3D"${modules}" \ - --with-etsf-io-libs=3D"${libs} -letsf_io -letsf_io_utils -letsf_io_low= _level" \ - --with-dft-flavor=3D"libxc+bigdft+atompaw+wannier90" \ - --with-libxc-incs=3D"${modules}" \ - --with-libxc-libs=3D"${libs} -lxc" \ - --with-bigdft-incs=3D"${modules}" \ - --with-bigdft-libs=3D"${libs} -lpoissonsolver -lbigdft" \ - --with-atompaw-incs=3D"${modules}" \ - --with-atompaw-libs=3D"${libs} -latompaw" \ - --with-wannier90-bins=3D"/usr/bin" \ - --with-wannier90-incs=3D"${modules}" \ - --with-wannier90-libs=3D"${libs} -lwannier $(pkg-config --libs lapack)= " \ - "$(use fftw && echo "--with-fft-flavor=3D${fft_flavor}")" \ - "$(use fftw && echo "--with-fft-incs=3D-I/usr/include")" \ - "$(use fftw && echo "--with-fft-libs=3D${fft_libs}")" \ - --with-timer-flavor=3D"abinit" \ - FC=3D"${MY_FC}" \ - CC=3D"${MY_CC}" \ - CXX=3D"${MY_CXX}" \ - LD=3D"$(tc-getLD)" \ - FCFLAGS=3D"${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 $(find . -name report); do - REPORT=3D${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 ${testdir} - fi - done - - elog "The full test results will be installed as summary_of_tests.tar.b= z2." - elog "Also a concise report tests_summary.txt is installed." -} - -src_install() { - emake DESTDIR=3D"${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 faile= d" - 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-phy= sics/abinit/files/6.12.1-bigDFT-1.6.0.patch deleted file mode 100644 index 857a27a..0000000 --- a/sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch +++ /dev/null @@ -1,61 +0,0 @@ -diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_descr_psp_set.F90 = abinit-6.12.1/src/42_wvl_wrappers/wvl_descr_psp_set.F90 ---- src/42_wvl_wrappers/wvl_descr_psp_set.F90 2012-01-30 20:43:51.000000= 000 +0000 -+++ src/42_wvl_wrappers/wvl_descr_psp_set.F90 2012-03-19 13:06:59.000000= 000 +0000 -@@ -105,7 +105,7 @@ - ! Missing currently read radii_cf. - wvl%atoms%donlcc =3D .false. - ! TODO: add symmetry support -- wvl%atoms%symObj =3D -1 -+ wvl%atoms%sym%symObj =3D -1 - #endif =20 - 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 20:43:50.00000= 0000 +0000 -+++ src/42_wvl_wrappers/wvl_projectors_set.F90 2012-03-19 13:17:37.00000= 0000 +0000 -@@ -122,7 +122,7 @@ - ABI_ALLOCATE(xcart,(3, natom)) - call xredxcart(natom, 1, rprimd, xcart, xred) -=20 -- 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 abini= t-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 +0= 000 -+++ src/42_wvl_wrappers/wvl_wfs_set.F90 2012-03-19 12:58:54.000000000 +0= 000 -@@ -59,7 +59,7 @@ - use defs_wvltypes - #if defined HAVE_DFT_BIGDFT - use BigDFT_API, only: createWavefunctionsDescriptors, orbitals_descri= ptors, & -- & orbitals_communicators, allocate_diis_objects, wvl_timing =3D>= timing -+ & orbitals_communicators, wvl_timing =3D> timing - #endif -=20 - !This section has been created automatically by the script Abilint (TD)= . -@@ -179,9 +179,9 @@ - call wvl_timing(me,'CrtDescriptors','OF') -=20 - ! 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%nspi= nor, & -- & 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%ns= pinor, & -+ ! & wfs%orbs%norbd, wfs%diis, "wvl_init_wfs_type") -=20 - #else - write(message, '(a,a,a,a)' ) ch10,& diff --git a/sci-physics/abinit/files/6.12.1-gui-conf.patch b/sci-physics= /abinit/files/6.12.1-gui-conf.patch deleted file mode 100644 index 95c12b3..0000000 --- a/sci-physics/abinit/files/6.12.1-gui-conf.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Naur abinit-6.12.1_orig/gui/configure abinit-6.12.1/gui/configure ---- gui/configure 2012-01-30 19:42:26.000000000 +0000 -+++ gui/configure 2012-03-16 13:38:54.000000000 +0000 -@@ -3143,7 +3143,7 @@ - test -z "$as_dir" && as_dir=3D. - for ac_exec_ext in '' $ac_executable_extensions; do - if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$a= c_word$ac_exec_ext"; }; then -- ac_cv_prog_UUDECODE=3D"no" -+ ac_cv_prog_UUDECODE=3D"$as_dir/$ac_word$ac_exec_ext" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_ex= ec_ext" >&5 - break 2 - fi diff --git a/sci-physics/abinit/files/6.6.1-openmp.patch b/sci-physics/ab= init/files/6.6.1-openmp.patch deleted file mode 100644 index af43d57..0000000 --- a/sci-physics/abinit/files/6.6.1-openmp.patch +++ /dev/null @@ -1,509 +0,0 @@ -diff -Naur abinit-6.6.1.orig/src/52_fft_mpi_noabirule/accrho.F90 abinit-= 6.6.1/src/52_fft_mpi_noabirule/accrho.F90 ---- src/52_fft_mpi_noabirule/accrho.F90 2011-02-28 05:14:13.000000000 +0= 000 -+++ src/52_fft_mpi_noabirule/accrho.F90 2011-03-01 19:41:35.000000000 +0= 000 -@@ -91,14 +91,14 @@ - integer unused - unused=3D0 - ! *********************************************************************= **** --!$ interface --!$ integer ( kind=3D4 ) function omp_get_num_threads ( ) --!$ end function omp_get_num_threads --!$ end interface --!$ interface --!$ integer ( kind=3D4 ) function omp_get_thread_num ( ) --!$ end function omp_get_thread_num --!$ end interface -+!% interface -+!% integer ( kind=3D4 ) function omp_get_num_threads ( ) -+!% end function omp_get_num_threads -+!% end interface -+!% interface -+!% integer ( kind=3D4 ) function omp_get_thread_num ( ) -+!% end function omp_get_thread_num -+!% end interface -=20 - write(6,*)' accrho : enter ' -=20 -diff -Naur abinit-6.6.1.orig/src/52_fft_mpi_noabirule/applypot.F90 abini= t-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=3D0 -=20 --!$ interface --!$ integer ( kind=3D4 ) function omp_get_num_threads ( ) --!$ end function omp_get_num_threads --!$ end interface --!$ interface --!$ integer ( kind=3D4 ) function omp_get_thread_num ( ) --!$ end function omp_get_thread_num --!$ end interface -+!% interface -+!% integer ( kind=3D4 ) function omp_get_num_threads ( ) -+!% end function omp_get_num_threads -+!% end interface -+!% interface -+!% integer ( kind=3D4 ) function omp_get_thread_num ( ) -+!% end function omp_get_thread_num -+!% end interface -=20 - write(6,*)' applypot : enter ' -=20 -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 +000= 0 -+++ src/52_fft_mpi_noabirule/back.F90 2011-03-01 19:45:45.000000000 +000= 0 -@@ -90,14 +90,14 @@ - #endif - ! *********************************************************************= **** -=20 --!$ interface --!$ integer ( kind=3D4 ) function omp_get_num_threads ( ) --!$ end function omp_get_num_threads --!$ end interface --!$ interface --!$ integer ( kind=3D4 ) function omp_get_thread_num ( ) --!$ end function omp_get_thread_num --!$ end interface -+!% interface -+!% integer ( kind=3D4 ) function omp_get_num_threads ( ) -+!% end function omp_get_num_threads -+!% end interface -+!% interface -+!% integer ( kind=3D4 ) function omp_get_thread_num ( ) -+!% end function omp_get_thread_num -+!% end interface -=20 - !DEBUG - ! write(6,*)' back : enter ' -@@ -121,7 +121,7 @@ -=20 - lock=3D0 - !$omp parallel default(private) & --!$omp shared(ndat,n1,n2,n3,nd1,nd2,nd3,nd2proc,nd3proc,mpi_enreg%me_fft= ,mpi_enreg%nproc_fft,ncache,zr,zf,lock,icplex) -+!$omp shared(ndat,n1,n2,n3,nd1,nd2,nd3,nd2proc,nd3proc,mpi_enreg,ncache= ,zr,zf,lock,icplex) -=20 - iam=3D0 - npr=3D1 -diff -Naur abinit-6.6.1.orig/src/52_fft_mpi_noabirule/forw.F90 abinit-6.= 6.1/src/52_fft_mpi_noabirule/forw.F90 ---- src/52_fft_mpi_noabirule/forw.F90 2011-02-28 05:14:13.000000000 +000= 0 -+++ src/52_fft_mpi_noabirule/forw.F90 2011-03-01 19:46:53.000000000 +000= 0 -@@ -95,14 +95,14 @@ - integer :: old_paral_level - #endif - ! *********************************************************************= **** --!$ interface --!$ integer ( kind=3D4 ) function omp_get_num_threads ( ) --!$ end function omp_get_num_threads --!$ end interface --!$ interface --!$ integer ( kind=3D4 ) function omp_get_thread_num ( ) --!$ end function omp_get_thread_num --!$ end interface -+!% interface -+!% integer ( kind=3D4 ) function omp_get_num_threads ( ) -+!% end function omp_get_num_threads -+!% end interface -+!% interface -+!% integer ( kind=3D4 ) function omp_get_thread_num ( ) -+!% end function omp_get_thread_num -+!% end interface -=20 - !DEBUG - ! write(6,*)' forw : enter ' -@@ -134,7 +134,7 @@ -=20 - lock=3D0 - !$omp parallel default(private) & --!$omp shared(ndat,n1,n2,n3,nd1,nd2,nd3,nd2proc,nd3proc,mpi_enreg%me_fft= ,mpi_enreg%nproc_fft,ncache,zr,zf,lock,icplex) -+!$omp shared(ndat,n1,n2,n3,nd1,nd2,nd3,nd2proc,nd3proc,mpi_enreg,ncache= ,zr,zf,lock,icplex) -=20 - iam=3D0 - npr=3D1 -diff -Naur abinit-6.6.1.orig/src/53_ffts/fftw3_fourwf.F90 abinit-6.6.1/s= rc/53_ffts/fftw3_fourwf.F90 ---- src/53_ffts/fftw3_fourwf.F90 2011-02-28 06:10:13.000000000 +0000 -+++ src/53_ffts/fftw3_fourwf.F90 2011-03-01 21:30:29.000000000 +0000 -@@ -432,8 +432,8 @@ - end do -=20 - cplex=3D0; istwf_k=3D1; option=3D3 --!$ call sg_fftrisc(cplex,dum_denpot,fofgin,dum_fofgin,fofr,gbound,gbo= und,istwf_k,dum_gvec,gvec,& --!$& mgfft,ngfft,npwwfn,npwwfn,ldx,ldy,ldz,option,weight) -+!% call sg_fftrisc(cplex,dum_denpot,fofgin,dum_fofgin,fofr,gbound,gbo= und,istwf_k,dum_gvec,gvec,& -+!%& mgfft,ngfft,npwwfn,npwwfn,ldx,ldy,ldz,option,weight) -=20 - allocate(ftarr(2,ldx,ldy,ldz)) - !This call gives weird results for R-->G, while G-->R is ok!!!! -diff -Naur abinit-6.6.1.orig/src/53_ffts/sphere_fft.F90 abinit-6.6.1/src= /53_ffts/sphere_fft.F90 ---- src/53_ffts/sphere_fft.F90 2011-02-28 06:10:11.000000000 +0000 -+++ src/53_ffts/sphere_fft.F90 2011-03-01 20:35:57.000000000 +0000 -@@ -99,7 +99,7 @@ - !ENDDEBUG -=20 - !Insert cg into cfft with extra 0 s around outside: --!$OMP PARALLEL DO PRIVATE(i1,i2,i3) SHARED(cfft,ndat,n1,n2,n3) -+!!$OMP PARALLEL DO PRIVATE(i1,i2,i3) SHARED(cfft,ndat,n1,n2,n3) - !do i2=3D1,nd2proc*ndat - !do i3=3D1,n3 - !do i1=3D1,n1 -@@ -108,7 +108,7 @@ - !end do - !end do - !end do --!$OMP END PARALLEL DO -+!!$OMP END PARALLEL DO - cfft(:,:,:,:)=3Dzero - !$OMP PARALLEL DO PRIVATE(i1,i2,i3,idat,ipw) SHARED(cfft,cg,kg_k,ndat,n= pw) - !write(6,*)'In sphere fft,i1,i2,i3,ipw,cfft=3Dcg' -@@ -229,7 +229,7 @@ - !ENDDEBUG -=20 - !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=3D1,nd2proc*ndat - !do i3=3D1,n3 - !do i1=3D1,n1 -@@ -238,7 +238,7 @@ - !end do - !end do - !end do --!$OMP END PARALLEL DO -+!!$OMP END PARALLEL DO - cfft(:,:,:,:)=3Dzero - !$OMP PARALLEL DO PRIVATE(i1,i2,i3,idat,ipw) SHARED(cfft,cg,kg_k,ndat,n= pw) - !write(6,*)'In sphere fft,i1,i2,i3,ipw,cfft=3Dcg' -diff -Naur abinit-6.6.1.orig/src/67_common/m_coulombian.F90 abinit-6.6.1= /src/67_common/m_coulombian.F90 ---- src/67_common/m_coulombian.F90 2011-02-28 06:10:19.000000000 +0000 -+++ src/67_common/m_coulombian.F90 2011-03-01 22:22:13.000000000 +0000 -@@ -1950,7 +1950,7 @@ - real(dp) :: F3 - !**********************************************************************= ** -=20 -- !$F3(z)=3Dz*\sin(qpg_para_*z)/\sqrt(rcut^2+z^2)$ -+ !%$F3(z)=3Dz*\sin(qpg_para_*z)/\sqrt(rcut^2+z^2)$ - F3=3Dxx*SIN(qpg_para_*xx)/SQRT(rcut_**2+xx**2) -=20 - end function F3 -@@ -2039,7 +2039,7 @@ - real(dp) :: k0,rho,arg - !**********************************************************************= ** -=20 -- !$K0cos(y)=3DK0(\rho*|qpg_z|)*COS(x.qpg_x+y*qpg_y)$ -+ !%$K0cos(y)=3DK0(\rho*|qpg_z|)*COS(x.qpg_x+y*qpg_y)$ - rho=3DSQRT(xx_**2+yy**2) ; arg=3Dqpg_para_*rho - call CALCK0(arg,k0,1) - K0cos=3Dk0*COS(qpgx_*xx_+qpgy_*yy) -@@ -2065,7 +2065,7 @@ - real(dp) :: quad - !**********************************************************************= ** -=20 -- !$ K0cos_dy(x)=3D\int_{-b/2}^{b/2} K0(|qpg_z|\rho)cos(x.qpg_x+y.qpg_y)= dy$ -+ !%$ K0cos_dy(x)=3D\int_{-b/2}^{b/2} K0(|qpg_z|\rho)cos(x.qpg_x+y.qpg_y= )dy$ - xx_=3Dxx=20 - call quadrature(K0cos,-hb_,+hb_,qopt_,quad,ierr,ntrial_,accuracy_,npts= _) - if (ierr/=3D0) then=20 -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. -=20 -- !$real(dp) :: kpoint(3) -+ !%real(dp) :: kpoint(3) -=20 - real(dp),pointer :: ph3d(:,:,:) SET2NULL - ! ph3d(2,npw,natom) -@@ -146,7 +146,7 @@ - ! ylm(npw,mpsang**2*useylm) - ! Real spherical harmonics for each k+G -=20 -- !$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 -=20 -- !$ 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 b= e used. -@@ -267,8 +267,8 @@ - integer :: itim - ! 2 is time-reversal is used. 1 otherwise. -=20 -- !$integer :: ngfft(18) -- !$integer :: mgfft -+ !%integer :: ngfft(18) -+ !%integer :: mgfft -=20 - 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(n= gfft(1:3)), used to dimension some arrays. -- !$integer :: mpsang -+ !%integer :: mpsang - integer :: natom - integer :: nfft ! Number of FFT points treated by this = processor - integer :: nfftot ! Total number of points in the FFT gri= d -@@ -338,7 +338,7 @@ - integer :: ntypat - integer :: paral_kgb ! Option for kgb parallelism - integer :: usepaw ! 1 if PAW is used, 0 otherwise. -- !$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=3Dsmearing energy for plane wave kinetic energy (Ha) - ! Cutoff for plane wave basis set. -=20 -- !$real(dp) :: pawecutdg=3Dzero -+ !%real(dp) :: pawecutdg=3Dzero - ! Cutoff for plane wave basis set. -=20 - logical :: gamma_centered=3D.TRUE. - ! .TRUE. if ug are given on the Gamma-centered G-sphere. Flag nedded= to preserve the old Implementation. -=20 -- !$real(dp) :: effmass -+ !%real(dp) :: effmass - ! Effective mass for electrons -=20 - !arrays -@@ -2066,8 +2066,8 @@ -=20 - ! Compute (k+G) vectors - nkpg=3D0 -- !$if (choice=3D=3D3.or.choice=3D=3D2.or.choice=3D=3D23) nkpg=3D3*Wfd%n= loalg(5) -- !$if (choice=3D=3D4.or.choice=3D=3D24) nkpg=3D9*Wfd%nloalg(5) -+ !%if (choice=3D=3D3.or.choice=3D=3D2.or.choice=3D=3D23) nkpg=3D3*Wfd%n= loalg(5) -+ !%if (choice=3D=3D4.or.choice=3D=3D24) nkpg=3D9*Wfd%nloalg(5) - allocate(kpg(npw_k,nkpg)); if (nkpg>0) call mkkpg(kg_k,kpg,kpoint,nkpg= ,npw_k) -=20 - matblk =3D Cryst%natom -@@ -5741,9 +5741,9 @@ - ! *********************************************************************= **** -=20 - ! TODO ngfft should be included in pawfgrtab_type=20 -- !$if (ANY(Wfd%ngfft(1:3)/=3DPawfgrtab%ngfft(1:3)) then -- !$ MSG_ERROR("Wfd%ngfft(1:3)/=3DPawfgrtab%ngfft(1:3)") -- !$end if -+ !%if (ANY(Wfd%ngfft(1:3)/=3DPawfgrtab%ngfft(1:3)) then -+ !% MSG_ERROR("Wfd%ngfft(1:3)/=3DPawfgrtab%ngfft(1:3)") -+ !%end if -=20 - call wfd_get_ur(Wfd,band,ik_ibz,spin,ur_ae) -=20 -@@ -6817,7 +6817,7 @@ - do_sym =3D .FALSE.=20 - if (PRESENT(ISkg)) then=20 - do_sym =3D .TRUE. -- !$ TODO do_sym =3D (ISkg%isym/=3D1 .or. ISkg%itim/=3D1) -+ !% TODO do_sym =3D (ISkg%isym/=3D1 .or. ISkg%itim/=3D1) - end if -=20 - if (.not. do_sym) then -diff -Naur abinit-6.6.1.orig/src/69_wfdesc/outkss.F90 abinit-6.6.1/src/6= 9_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 -=20 - use m_io_tools, only : get_unit -- !$use m_numeric_tools, only : bisect -+ !%use m_numeric_tools, only : bisect - use m_gsphere, only : merge_and_sort_kg, table_gbig2kg, get_k= g - use m_io_kss, only : write_kss_wfgk, write_kss_header, k2gam= ma_centered - use m_hamiltonian, only : ddiago_ctl_type, init_ddiago_ctl -@@ -458,7 +458,7 @@ - EXIT - end if - end do --!$ ishm=3Dbisect(shlim,npwkss) -+!% ishm=3Dbisect(shlim,npwkss) -=20 - if (shlim(ishm)/=3Dnpwkss) then - nrst1=3Dshlim(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 -=20 - rdwr=3D4 -- !$call hdr_io_int(Er%fform,Er%Hscr%Hdr,rdwr,unt) -+ !%call hdr_io_int(Er%fform,Er%Hscr%Hdr,rdwr,unt) - end if ! verbose>0 -=20 - end subroutine print_epsilonm1_results=20 -@@ -796,7 +796,7 @@ -=20 - call metric(gmet,gprimd,-1,rmet,Vcp%rprimd,ucvol) -=20 -- !$ if (Er%ID/=3D0) call reset_Epsilonm1(Er) -+ !% if (Er%ID/=3D0) call reset_Epsilonm1(Er) - Er%ID=3Did_required -=20 - write(*,*) 'Er%ID:',Er%ID -@@ -1892,7 +1892,7 @@ - end if -=20 - if (iqibz=3D=3D1) then=20 -- !$vc_sqrt =3D> Vcp%vcqlwl_sqrt(:,iqlwl) ! Use Coulomb term for q-= ->0 -+ !%vc_sqrt =3D> Vcp%vcqlwl_sqrt(:,iqlwl) ! Use Coulomb term for q-= ->0 - vc_sqrt =3D> Vcp%vcqlwl_sqrt(:,1) ! TODO add treatment of non-Ana= lytic behavior - else=20 - vc_sqrt =3D> Vcp%vc_sqrt(:,iqibz) =20 -@@ -1992,7 +1992,7 @@ - end if -=20 - if (iqibz=3D=3D1) then=20 -- !$vc_sqrt =3D> Vcp%vcqlwl_sqrt(:,iqlwl) ! Use Coulomb term for q-= ->0 -+ !%vc_sqrt =3D> Vcp%vcqlwl_sqrt(:,iqlwl) ! Use Coulomb term for q-= ->0 - vc_sqrt =3D> Vcp%vcqlwl_sqrt(:,1) ! TODO add treatment of non-Ana= lytic behavior - else=20 - vc_sqrt =3D> Vcp%vc_sqrt(:,iqibz) =20 -@@ -2212,7 +2212,7 @@ - end do - ! - !if (PRESENT(rhor)) then -- ! !$call mdielf(epsinf,Er%npw,Er%nomega,iq_ibz,Er%qibz(:,iq_ibz),Er= %gvec,Cryst,Vcp,nspden,nfft,ngfft,rhor,epsm1,comm) -+ ! !%call mdielf(epsinf,Er%npw,Er%nomega,iq_ibz,Er%qibz(:,iq_ibz),Er= %gvec,Cryst,Vcp,nspden,nfft,ngfft,rhor,epsm1,comm) - !end if -=20 - end do ! nqibz -@@ -2393,7 +2393,7 @@ - ! - ! Change the body but do not add the corrections due to the head and= the wings. - ! since they can be obtained on the fly from eps_body and the wings = of eps^{-1}. -- !$chi0(2:,2:,iomega) =3D eps_body -+ !%chi0(2:,2:,iomega) =3D eps_body - end do !iomega -=20 - 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 +00= 00 -+++ src/71_bse/exc_iterative_diago.F90 2011-03-01 22:50:45.000000000 +00= 00 -@@ -762,8 +762,8 @@ - open(unit=3Deig_unt,file=3Doeig_fname,form=3D'unformatted') - write(eig_unt) exc_nst - write(eig_unt) CMPLX(exc_energy(1:exc_nst),kind=3Ddpc) -- !$ fform =3D 1002 ! TODO: change setup_bse so that Hdr_bse reflec= ts the parameters of the run. -- !$ call hdr_io_int(fform,Hdr_bse,rdwr2,eig_unt) -+ !% fform =3D 1002 ! TODO: change setup_bse so that Hdr_bse reflec= ts the parameters of the run. -+ !% call hdr_io_int(fform,Hdr_bse,rdwr2,eig_unt) - close(eig_unt)=20 - end if -=20 -@@ -776,15 +776,15 @@ - msg =3D " MPI_IO error opening file: "//TRIM(oeig_fname) - ABI_CHECK_MPI(ierr,msg) -=20 -- !$call xmpio_read_frm(mpi_fh,ehdr_offset,xmpio_at,fmarker,ierr) -- !$write(std_out,*)"fmarker last record ",fmarker -- !$call hdr_mpio_skip(mpi_fh,fform,ehdr_offset)=20 -- !$ehdr_offset =3D 4*xmpio_bsize_frm + xmpio_bsize_int + exc_nst*xmpi= o_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)=20 -+ !%ehdr_offset =3D 4*xmpio_bsize_frm + xmpio_bsize_int + exc_nst*xmpi= o_bsize_dpc -=20 - is_fortran_file=3D.TRUE.; etype=3DMPI_BYTE; old_type=3DMPI_DOUBLE_CO= MPLEX -=20 - ! TODO Need to add option to create file view. -- !$call xmpio_create_coldistr_from_fherm_packed(array_of_sizes,my_col= s,old_type,eig_type,offset_err) -+ !%call xmpio_create_coldistr_from_fherm_packed(array_of_sizes,my_col= s,old_type,eig_type,offset_err) -=20 - if (offset_err/=3D0) then=20 - write(msg,"(3a)")& -diff -Naur abinit-6.6.1.orig/src/77_ddb/eliashberg_1d.F90 abinit-6.6.1/s= rc/77_ddb/eliashberg_1d.F90 ---- src/77_ddb/eliashberg_1d.F90 2011-02-28 06:10:20.000000000 +0000 -+++ src/77_ddb/eliashberg_1d.F90 2011-03-02 04:21:07.000000000 +0000 -@@ -108,10 +108,10 @@ -=20 - ! - !1) use linearized Eliashberg equation to find Tc --!$ \sum_j \mathbf{M}_{ij} \Delta_j =3D \zeta \cdot \Delta_i $ $i,j =3D = 1 .. n_{\mathrm{Matsubara}}$ --!$\zeta =3D 1$ gives T$_c$ $\beta =3D \frac{1}{\mathrm{T}}$ $\omega_i =3D= (2 i + 1) \pi \mathrm{T}$ --!$ \mathbf{M}_{ij} =3D \frac{\pi}{\beta} \frac{\lambda (\omega_i - \ome= ga_j)}{Z (\omega_i)}$ --!$ Z (\omega_i) =3D 1 + \frac{\pi}{\beta \omega_i} \sum_j \lambda(\omeg= a_i - \omega_j) \mathrm{sgn}(\omega_j)$ -+!%$ \sum_j \mathbf{M}_{ij} \Delta_j =3D \zeta \cdot \Delta_i $ $i,j =3D= 1 .. n_{\mathrm{Matsubara}}$ -+!%$\zeta =3D 1$ gives T$_c$ $\beta =3D \frac{1}{\mathrm{T}}$ $\omega_i = =3D (2 i + 1) \pi \mathrm{T}$ -+!%$ \mathbf{M}_{ij} =3D \frac{\pi}{\beta} \frac{\lambda (\omega_i - \om= ega_j)}{Z (\omega_i)}$ -+!%$ Z (\omega_i) =3D 1 + \frac{\pi}{\beta \omega_i} \sum_j \lambda(\ome= ga_i - \omega_j) \mathrm{sgn}(\omega_j)$ - ! -=20 - !initial guess for T$_c$ in Hartree (1Ha =3D3.067e5 K) -diff -Naur abinit-6.6.1.orig/src/77_ddb/m_eph.F90 abinit-6.6.1/src/77_dd= b/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 -=20 -- !$public :: init_fermi_surface -- !$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 -=20 - ! example: - !type(fermi_surface_type),allocatable :: Fsurf(:) -@@ -325,9 +325,9 @@ - ! Bound Methods:=20 - 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. -=20 - interface nullify_gkk - module procedure nullify_gkk_0D -@@ -379,9 +379,9 @@ - ! Bound Methods:=20 - public :: nullify_gkk_handler - public :: destroy_gkk_handler -- !$init_gkk_handler(Gkk,FSurf,Cryst,Cryst,qpt,fname) -- !$get_gammaq -- !$symmetrize_gkk_over_perts -+ !%init_gkk_handler(Gkk,FSurf,Cryst,Cryst,qpt,fname) -+ !%get_gammaq -+ !%symmetrize_gkk_over_perts -=20 - interface nullify_gkk_handler - module procedure nullify_gkk_handler_0D -diff -Naur abinit-6.6.1.orig/src/95_drive/bethe_salpeter.F90 abinit-6.6.= 1/src/95_drive/bethe_salpeter.F90 ---- src/95_drive/bethe_salpeter.F90 2011-02-28 06:10:13.000000000 +0000 -+++ src/95_drive/bethe_salpeter.F90 2011-03-02 04:34:01.000000000 +0000 -@@ -453,7 +453,7 @@ - end do - end if -=20 -- opt_ecut=3Dzero !$; if (gw_uses_wfk_file) opt_ecut=3DDtset%ecutwfn -+ opt_ecut=3Dzero !%; if (gw_uses_wfk_file) opt_ecut=3DDtset%ecutwfn -=20 - 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 @@ -=20 - !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) - ! - !=3D=3D=3D Additional computation for PAW =3D=3D=3D - if (Dtset%usepaw=3D=3D1) then