From ecf1ca2b0144aee51f42f521b3d8701fb023f020 Mon Sep 17 00:00:00 2001 From: Honza Macháček Date: Fri, 30 Mar 2012 06:10:46 +0200 Subject: sci-libs/bigdft & sci-physics/abinit clean-up after sci-physics/abinit version bump to 6.12.2 and tests --- sci-physics/abinit/ChangeLog | 8 + sci-physics/abinit/Manifest | 5 +- sci-physics/abinit/abinit-6.10.3.ebuild | 251 ---------- sci-physics/abinit/abinit-6.12.1.ebuild | 337 -------------- sci-physics/abinit/abinit-6.12.2.ebuild | 338 ++++++++++++++ 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 --------------------- 10 files changed, 347 insertions(+), 1581 deletions(-) delete mode 100644 sci-physics/abinit/abinit-6.10.3.ebuild delete mode 100644 sci-physics/abinit/abinit-6.12.1.ebuild create mode 100644 sci-physics/abinit/abinit-6.12.2.ebuild delete mode 100644 sci-physics/abinit/abinit-6.6.3.ebuild delete mode 100644 sci-physics/abinit/abinit-6.8.2.ebuild delete mode 100644 sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch delete mode 100644 sci-physics/abinit/files/6.12.1-gui-conf.patch delete mode 100644 sci-physics/abinit/files/6.6.1-openmp.patch (limited to 'sci-physics') diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog index 5af127920..4e3f27e1c 100644 --- a/sci-physics/abinit/ChangeLog +++ b/sci-physics/abinit/ChangeLog @@ -2,6 +2,14 @@ # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*abinit-6.12.2 (30 Mar 2012) + + 30 Mar 2012; Honza Macháček + -files/6.12.1-bigDFT-1.6.0.patch, -files/6.6.1-openmp.patch, + -files/6.12.1-gui-conf.patch, -abinit-6.6.3.ebuild, -abinit-6.8.2.ebuild, + -abinit-6.10.3.ebuild, -abinit-6.12.1.ebuild, +abinit-6.12.2.ebuild: + Version bump, tests, clean-up. + 23 Mar 2012; Honza Macháček abinit-6.12.1.ebuild: Fortran setup improvement in 6.12.1 ebuild corrected, gui preparation corrected. diff --git a/sci-physics/abinit/Manifest b/sci-physics/abinit/Manifest index e35fffeac..5fe0a3651 100644 --- a/sci-physics/abinit/Manifest +++ b/sci-physics/abinit/Manifest @@ -1,4 +1 @@ -DIST abinit-6.10.3.tar.gz 69158203 SHA256 185c45c7c9caf5f735d841fa85b2dfc612eee81b76f905a9988b5f0994be6fb5 SHA512 010fee8f0740cc05208f1abe52f5aae25077d5792331a98466ecc13f27605776e19a17bdeab2c7cf09eb233109ae7f14d55afecd89113a91a0d67494f2c5abb2 WHIRLPOOL be7f127116a6f59ea4cbd84f01e3371b5959275bae0957e654eea9dadeef278ad0081f8600476e716865ef32b5aea536ccb09f12f5934f95aaf8eeccb06bc5d6 -DIST abinit-6.12.1.tar.gz 58474634 SHA256 1b0f0fe5a6f8ce97b3da7ea7640f16c36902c7a5bc08651abd139eb7e13222b6 SHA512 59d757400539d0eb385fd37c9a6e2824bd3a2a6378a6c8f39a2f336cf3f842120538a014633561a5c16b9debf4ec054d51beaec2952629e0a88ab283dc2db431 WHIRLPOOL 9c02b1184fabe96405fe05ecd9c40d48f104d92d55ed2900dc3755758aca12cb4dd64e6fea3e3f949bcbb8a615ecd359a76bc9752969e585189865cd75c14c1d -DIST abinit-6.6.3.tar.gz 41161321 SHA256 fad84d3e774e3b4ba16f2a2924e60b8ba42ab21fefd89d8ce4848f9a9e03f774 SHA512 834bd017a81444a75335d13579c37efe1d58b571a0b2a673f8dfb60342cd10fb849e6a2e92042be59445835e1ad3a484149faa260280e4e6db9b284ed03c208a WHIRLPOOL 302cf85a65e4c07ee716379844d1435503ee042fb987f3c43e5fc4e60ffe32ec0498f8d31dcc7a61043bfcedf56b87eadca11657156fb6d912f6c4627aa60bbf -DIST abinit-6.8.2.tar.gz 43565001 SHA256 7a0e8ebfce50ae18e5c4f25f9bfd534623a41985082efead918a3878464a181c SHA512 97287a7527f1088435c95697b90a27eaf6cb5b8921e2d4e702279552f9d8669735242d5bfa62b944a7da418286a317131c352952ac0fac58540de4e8ded56385 WHIRLPOOL 27b11310695179e2a8794dbb7b0a3e041477cf9bec1ddc3468f6c54e3549806cef66c348dbb34839d3dfb0633191b5a9531f4e415d2c0a1d776ddf9dddff3756 +DIST abinit-6.12.2.tar.gz 58469873 SHA256 a2b415ddb3809cd1ef670e666fce5b14e6148ebc381dc035de837daac7b6e22e SHA512 0be2bcd0905968cf9b7b7e22d476d514532e9204f267d0acb880f35e925cdb8d5884aec6933b89514cbd3d1532095367355dba65f87b7b5f715b397407f267d9 WHIRLPOOL 7c24266ea1592cd05a29f8536ca8c41a79eb6186a55b7a0df04fbd4d7e45b0d04786106dba99a519c4bb1c7a7ecb5bfdcf54c18eddcc519747a86e7f1d5a5a01 diff --git a/sci-physics/abinit/abinit-6.10.3.ebuild b/sci-physics/abinit/abinit-6.10.3.ebuild deleted file mode 100644 index f07355891..000000000 --- a/sci-physics/abinit/abinit-6.10.3.ebuild +++ /dev/null @@ -1,251 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="3" - -inherit autotools eutils fortran-2 multilib toolchain-funcs - -DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory" -HOMEPAGE="http://www.abinit.org/" -SRC_URI="http://ftp.abinit.org/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="cuda -debug +fftw +fftw-threads +fox gsl gui +hdf5 mpi +netcdf python -test +threads -vdwxc" - -RDEPEND=">=sci-libs/bigdft-1.2.0.5 - sci-libs/etsf_io - =sci-libs/libxc-1*[fortran] - sci-physics/atompaw[libxc] - fox? ( sci-libs/fox[dom,sax,wcml,wxml] ) - netcdf? ( - sci-libs/netcdf[fortran] - hdf5? ( - sci-libs/netcdf[fortran,hdf5] - ) - ) - hdf5? ( sci-libs/hdf5[fortran] ) - sci-libs/wannier90 - virtual/blas - virtual/lapack - gsl? ( sci-libs/gsl ) - fftw? ( - sci-libs/fftw:3.0 - fftw-threads? ( sci-libs/fftw:3.0[threads] ) - ) - mpi? ( virtual/mpi ) - python? ( dev-python/numpy ) - cuda? ( dev-util/nvidia-cuda-sdk )" -DEPEND="${RDEPEND} - dev-util/pkgconfig - gui? ( >=virtual/jdk-1.6.0 - app-arch/sharutils - sys-apps/gawk ) - dev-perl/Text-Markdown" - -S=${WORKDIR}/${P%[a-z]} - -lat1loc="" - -pkg_setup() { - fortran-2_pkg_setup - # Doesn't compile with gcc-4.0, only >=4.1 - if [[ $(tc-getFC) == *gfortran ]]; then - if [[ $(gcc-major-version) -eq 4 ]] \ - && [[ $(gcc-minor-version) -lt 1 ]]; then - die "Requires gcc-4.1 or newer" - fi - fi - if use fftw-threads && ! use fftw; then - ewarn "fftw-threads set but fftw not used, ignored" - fi - if use gui; then - lat1loc="$(locale |awk '/LC_CTYPE="(.*)"/{sub("LC_CTYPE=\"",""); sub("\" *$", ""); print}')" - if locale charmap |grep -i "\"; then - einfo "Good, locale compatible with the GUI build" - else - ewarn "The locale ${lat1loc} incompatible with the GUI build" - if latloc=`locale -a| grep -i "\"`; then - if echo "${latloc}" |grep -q "^fr"; then - lat1loc="$(echo "${latloc}" | grep -im1 "^fr")" - else - lat1loc="$(echo "${latloc}" | grep -im1 "iso88591")" - fi - einfo "Will use ${lat1loc} to build the GUI" - else - ewarn "No ISO-8859-1 nor ISO-8859-15 locale available, the GUI build may crash" - fi - fi - fi -} - -src_prepare() { - epatch "${FILESDIR}"/6.2.2-change-default-directories.patch - epatch "${FILESDIR}"/6.0.3-fftw.patch - eautoreconf -} - -src_configure() { - local libs="-L/usr/$(get_libdir)" - local modules="-I/usr/$(get_libdir)/finclude" - local FoX_libs="${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lFoX_common -lFoX_utils -lFoX_fsys" - local trio_flavor="etsf_io" - use fox && trio_flavor="${trio_flavor}+fox" - use netcdf && trio_flavor="${trio_flavor}+netcdf" - local netcdff_libs="-lnetcdff" - use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran" - local fft_flavor="fftw3" - local fft_libs="-L/usr/lib" - # The fftw threads support is protected by black magick. - # Anybody removes it, dies. - # New USE flag "fftw-threads" was added to control usage - # of the threaded fftw variant. Since fftw-3.3 has expanded - # the paralel options by MPI and OpenMP support, analogical - # USE flags should be added to select them in future; - # unusable with previous FFTW versions, they are postponed - # for now. - if use fftw-threads; then - fft_flavor="fftw3-threads" - if has_version '>=sci-libs/fftw-3.3'; then - # pkg-config files for fftw-3.3 are broken - # All the parallel stuff is separated - # from the main body of common routines, - # and -lfftw3 must be always included alongside. - # Until version 3.3 this used to be masked by - # .la files. - # Bug 384645 - fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads) $(pkg-config --libs fftw3)" - else - fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads)" - fi - else - fft_libs="${fft_libs} $(pkg-config --libs fftw3)" - fi - if use mpi; then - MY_FC="mpif90" - MY_CC="mpicc" - MY_CXX="mpic++" - else - MY_FC="$(tc-getFC)" - MY_CC="$(tc-getCC)" - MY_CXX="$(tc-getCXX)" - fi - MARKDOWN=Markdown.pl econf \ - $(use_enable debug debug enhanced) \ - $(use_enable mpi) \ - $(use_enable mpi mpi-io) \ - --disable-smp \ - $(use_enable vdwxc) \ - $(use_enable cuda gpu) \ - "$(use cuda && echo "--with-gpu-flavor=cuda-single")" \ - "$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")" \ - "$(use gsl && echo "--with-math-flavor=gsl")" \ - "$(use gsl && echo "--with-math-incs=$(pkg-config --cflags gsl)")" \ - "$(use gsl && echo "--with-math-libs=$(pkg-config --libs gsl)")" \ - --with-linalg-flavor="atlas" \ - --with-linalg-libs="$(pkg-config --libs lapack)" \ - --with-trio-flavor="${trio_flavor}" \ - "$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")" \ - "$(use netcdf && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")" \ - "$(use fox && echo "--with-fox-incs=${modules}")" \ - "$(use fox && echo "--with-fox-libs=${FoX_libs}")" \ - --with-etsf-io-incs="${modules}" \ - --with-etsf-io-libs="${libs} -letsf_io -letsf_io_utils -letsf_io_low_level" \ - --with-dft-flavor="libxc+bigdft+atompaw+wannier90" \ - --with-libxc-incs="${modules}" \ - --with-libxc-libs="${libs} -lxc" \ - --with-bigdft-incs="${modules}" \ - --with-bigdft-libs="${libs} -lpoissonsolver -lbigdft" \ - --with-atompaw-incs="${modules}" \ - --with-atompaw-libs="${libs} -latompaw" \ - --with-wannier90-bins="/usr/bin" \ - --with-wannier90-incs="${modules}" \ - --with-wannier90-libs="${libs} -lwannier $(pkg-config --libs lapack)" \ - "$(use fftw && echo "--with-fft-flavor=${fft_flavor}")" \ - "$(use fftw && echo "--with-fft-incs=-I/usr/include")" \ - "$(use fftw && echo "--with-fft-libs=${fft_libs}")" \ - --with-timer-flavor="abinit" \ - FC="${MY_FC}" \ - CC="${MY_CC}" \ - CXX="${MY_CXX}" \ - LD="$(tc-getLD)" \ - FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include" - - if use gui; then - cd gui - ./bootstrap.sh - econf - fi -} - -src_compile() { - emake || die "make failed" - - if use gui; then - cd gui - LC_CTYPE="${lat1loc}" emake || die "Making GUI failed" - fi -} - -src_test() { - einfo "The tests take quite a while, on the order of 1-2 hours" - einfo "on an Intel Penryn (2.5 GHz)." - cd "${S}"/tests - emake tests_min || ewarn "Minimal tests failed" - emake tests_paw || ewarn "PAW tests failed" - emake tests_gw || ewarn "GW tests failed" - emake tests_gw_paw || ewarn "GW-PAW tests failed" - emake tests tdft || ewarn "TDFT tests failed" - emake tests_bench || ewarn "Benchmarks failed" - - local REPORT - for REPORT in $(find . -name report); do - REPORT=${REPORT#*/} - elog "Parameters and unusual results for ${REPORT%%/*} tests" - echo "Parameters and unusual results for ${REPORT%%/*} tests" >>tests_summary.txt - while read line; do - elog "${line}" - echo "${line}" >>tests_summary.txt - done \ - < <(grep -v -e succeeded -e passed ${REPORT}) - done - - local testdir - find . -name "tmp-test*" -print | \ - while read testdir; do - if [ -e summary_of_tests.tar ]; then - tar rvf summary_of_tests.tar ${testdir} - else tar cvf summary_of_tests.tar ${testdir} - fi - done - - elog "The full test results will be installed as summary_of_tests.tar.bz2." - elog "Also a concise report tests_summary.txt is installed." -} - -src_install() { - emake DESTDIR="${D}" install || die "make install failed" - - if use test; then - dodoc tests/tests_summary.txt || ewarn "Copying tests summary failed" - dodoc tests/summary_tests.tar || ewarn "Copying tests results failed" - dodoc tests/summary_of_tests.tar || ewarn "Copying tests results failed" - fi - - if use gui; then - ( cd gui - emake DESTDIR="${D}" install || die "The GUI install failed" ) - fi - - - dodoc KNOWN_PROBLEMS README || die "Copying doc files failed" -} - -pkg_postinst() { - if use test; then - elog "The full test results will be installed as summary_tests.tar.bz2." - elog "Also a concise report tests_summary.txt is installed." - fi -} diff --git a/sci-physics/abinit/abinit-6.12.1.ebuild b/sci-physics/abinit/abinit-6.12.1.ebuild deleted file mode 100644 index 59f0f98b8..000000000 --- a/sci-physics/abinit/abinit-6.12.1.ebuild +++ /dev/null @@ -1,337 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="4" - -inherit autotools-utils flag-o-matic fortran-2 multilib toolchain-funcs - -DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory" -HOMEPAGE="http://www.abinit.org/" -SRC_URI="http://ftp.abinit.org/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="cuda cuda-double -debug +etsf_io +fftw +fftw-threads +fox gsl gui +hdf5 libabinit mpi +netcdf python -test +threads -vdwxc" - -RDEPEND="=sci-libs/bigdft-1.6_pre1 - sci-libs/etsf_io - =sci-libs/libxc-1*[fortran] - sci-physics/atompaw[libxc] - etsf_io? ( sci-libs/etsf_io ) - fox? ( sci-libs/fox[dom,sax,wcml,wxml] ) - netcdf? ( - sci-libs/netcdf[fortran] - hdf5? ( - sci-libs/netcdf[fortran,hdf5] - ) - ) - hdf5? ( sci-libs/hdf5[fortran] ) - sci-libs/wannier90 - virtual/blas - virtual/lapack - gsl? ( sci-libs/gsl ) - fftw? ( - sci-libs/fftw:3.0 - fftw-threads? ( sci-libs/fftw:3.0[threads] ) - ) - mpi? ( virtual/mpi ) - python? ( dev-python/numpy ) - cuda? ( dev-util/nvidia-cuda-sdk )" -DEPEND="${RDEPEND} - dev-util/pkgconfig - gui? ( >=virtual/jdk-1.6.0 - app-arch/sharutils - sys-apps/gawk ) - dev-perl/Text-Markdown" - -S=${WORKDIR}/${P%[a-z]} - -lat1loc="" - -DOCS=( AUTHORS ChangeLog COPYING INSTALL KNOWN_PROBLEMS NEWS PACKAGING - README README.ChangeLog README.GPU README.xlf RELNOTES THANKS ) - -FORTRAN_STANDARD=90 - -pkg_setup() { - # Doesn't compile with gcc-4.0, only >=4.1 - if [[ $(tc-getFC) == *gfortran ]]; then - if [[ $(gcc-major-version) -eq 4 ]] \ - && [[ $(gcc-minor-version) -lt 1 ]]; then - die "Requires gcc-4.1 or newer" - fi - fi - - # fortran-2.eclass does not handle mpi wrappers - if use mpi; then - export FC="mpif90" - export F77="mpif77" - export CC="mpicc" - export CXX="mpic++" - else - tc-export FC F77 CC CXX - fi - - # Preprocesor macross can make some lines really long - append-fflags -ffree-line-length-none - - fortran-2_pkg_setup - - # Sort out some USE options - if use fftw-threads && ! use fftw; then - ewarn "fftw-threads set but fftw not used, ignored" - fi - if use cuda-double && ! use cuda; then - ewarn "cuda-double set but cuda not used, ignored" - fi - if use gui; then - lat1loc="$(locale |awk '/LC_CTYPE="(.*)"/{sub("LC_CTYPE=\"",""); sub("\" *$", ""); print}')" - if locale charmap |grep -i "\"; then - einfo "Good, locale compatible with the GUI build" - else - ewarn "The locale ${lat1loc} incompatible with the GUI build" - if latloc=`locale -a| grep -i "\"`; then - if echo "${latloc}" |grep -q "^fr"; then - lat1loc="$(echo "${latloc}" | grep -im1 "^fr")" - else - lat1loc="$(echo "${latloc}" | grep -im1 "iso88591")" - fi - einfo "Will use ${lat1loc} to build the GUI" - else - ewarn "No ISO-8859-1 nor ISO-8859-15 locale available, the GUI build may crash" - fi - fi - fi -} - -src_prepare() { - epatch "${FILESDIR}"/6.2.2-change-default-directories.patch - epatch "${FILESDIR}"/6.0.3-fftw.patch - epatch "${FILESDIR}"/6.12.1-autoconf.patch - epatch "${FILESDIR}"/6.12.1-xmalloc.patch - epatch "${FILESDIR}"/6.12.1-libabinit_options.patch - eautoreconf - - if use gui; then - epatch "${FILESDIR}"/6.12.1-gui-conf.patch - pushd "${S}"/gui > /dev/null - ./autogen.sh - popd - fi -} - -src_configure() { - local libs="-L/usr/$(get_libdir)" - local modules="-I/usr/$(get_libdir)/finclude" - local FoX_libs="${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lFoX_common -lFoX_utils -lFoX_fsys" - local trio_flavor="" - use etsf_io && trio_flavor="${trio_flavor}+etsf_io" - use fox && trio_flavor="${trio_flavor}+fox" - use netcdf && trio_flavor="${trio_flavor}+netcdf" - test "no${trio_flavor}" = "no" && trio_flavor="none" - local netcdff_libs="-lnetcdff" - use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran" - local fft_flavor="fftw3" - local fft_libs="-L/usr/lib" - # The fftw threads support is protected by black magick. - # Anybody removes it, dies. - # New USE flag "fftw-threads" was added to control usage - # of the threaded fftw variant. Since fftw-3.3 has expanded - # the paralel options by MPI and OpenMP support, analogical - # USE flags should be added to select them in future; - # unusable with previous FFTW versions, they are postponed - # for now. - if use fftw-threads; then - fft_flavor="fftw3-threads" - if has_version '>=sci-libs/fftw-3.3'; then - # pkg-config files for fftw-3.3 are broken - # All the parallel stuff is separated - # from the main body of common routines, - # and -lfftw3 must be always included alongside. - # Until version 3.3 this used to be masked by - # .la files. - # Bug 384645 - fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads) $(pkg-config --libs fftw3)" - else - fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads)" - fi - else - fft_libs="${fft_libs} $(pkg-config --libs fftw3)" - fi - local gpu_flavor="none" - if use cuda; then - gpu_flavor="cuda-single" - if use cuda-double; then - gpu_flavor="cuda-double" - fi - fi - - local myeconfargs=( - --enable-clib - --enable-exports - $(use_enable gui) - $(use_enable debug debug enhanced) - $(use_enable mpi) - $(use_enable mpi mpi-io) - --disable-smp - $(use_enable vdwxc) - $(use_enable cuda gpu) - "$(use cuda && echo "--with-gpu-flavor=${gpu_flavor}")" - "$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")" - "$(use gsl && echo "--with-math-flavor=gsl")" - "$(use gsl && echo "--with-math-incs=$(pkg-config --cflags gsl)")" - "$(use gsl && echo "--with-math-libs=$(pkg-config --libs gsl)")" - --with-linalg-flavor="atlas" - --with-linalg-libs="$(pkg-config --libs lapack)" - --with-trio-flavor="${trio_flavor}" - "$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")" - "$(use netcdf && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")" - "$(use fox && echo "--with-fox-incs=${modules}")" - "$(use fox && echo "--with-fox-libs=${FoX_libs}")" - "$(use etsf_io && echo "--with-etsf-io-incs=${modules}")" - "$(use etsf_io && echo "--with-etsf-io-libs=${libs} -letsf_io -letsf_io_utils -letsf_io_low_level")" - --with-dft-flavor="libxc+bigdft+atompaw+wannier90" - --with-libxc-incs="${modules}" - --with-libxc-libs="${libs} -lxc" - --with-bigdft-incs="${modules}" - --with-bigdft-libs="$(pkg-config --libs bigdft)" - --with-atompaw-incs="${modules}" - --with-atompaw-libs="${libs} -latompaw" - --with-wannier90-bins="/usr/bin" - --with-wannier90-incs="${modules}" - --with-wannier90-libs="${libs} -lwannier $(pkg-config --libs lapack)" - "$(use fftw && echo "--with-fft-flavor=${fft_flavor}")" - "$(use fftw && echo "--with-fft-incs=-I/usr/include")" - "$(use fftw && echo "--with-fft-libs=${fft_libs}")" - --with-timer-flavor="abinit" - LD="$(tc-getLD)" - FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include" - ) - - MARKDOWN=Markdown.pl autotools-utils_src_configure - - if use gui; then - # autotools-utils_src_configure() part expanded - _check_build_dir - pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null - mkdir -p gui - cd gui - ECONF_SOURCE="${S}"/gui econf - fi -} - -src_compile() { - autotools-utils_src_compile - - # Apparently libabinit.a is not built by default - # Used by BigDFT. Should probably be built separately, - # as a package of its own: BigDFT used by Abinit. - # Does libabinit.a depend on BigDFT, if used? - # Can Abinit use external libabinit.a? - use libabinit && autotools-utils_src_compile libabinit.a - - if use gui; then - #autotools-utils_src_compile() expanded - # _check_build_dir has already been called - pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null - # now what the function cannot be called to do - cd gui - LC_CTYPE="${lat1loc}" emake || die "Making GUI failed" - popd > /dev/null - fi - - sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc -} - -src_test() { - einfo "The tests take quite a while, easily several hours" - # autotools-utils_src_test() expanded - _check_build_dir - pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null - # again something the autotools-utils function cannot be called to do - # now quite a lot of work actually - cd tests - emake tests_min || ewarn "Minimal tests failed" - emake tests_paw || ewarn "PAW tests failed" - emake tests_gw || ewarn "GW tests failed" - emake tests_gw_paw || ewarn "GW-PAW tests failed" - emake tests tdft || ewarn "TDFT tests failed" - emake tests_bench || ewarn "Benchmarks failed" - - local REPORT - for REPORT in $(find . -name report); do - REPORT=${REPORT#*/} - elog "Parameters and unusual results for ${REPORT%%/*} tests" - echo "Parameters and unusual results for ${REPORT%%/*} tests" >>tests_summary.txt - while read line; do - elog "${line}" - echo "${line}" >>tests_summary.txt - done \ - < <(grep -v -e succeeded -e passed ${REPORT}) - done - - local testdir - find . -name "tmp-test*" -print | \ - while read testdir; do - if [ -e summary_of_tests.tar ]; then - tar rvf summary_of_tests.tar ${testdir} - else tar cvf summary_of_tests.tar ${testdir} - fi - done - popd > /dev/null - - elog "The full test results will be installed as summary_of_tests.tar.bz2." - elog "Also a concise report tests_summary.txt is installed." -} - -src_install() { - #autotools-utils_src_install() expanded - _check_build_dir - pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null - emake DESTDIR="${D}" install || die "make install failed" - - use libabinit && dolib libabinit.a - - if use gui; then - pushd gui - emake DESTDIR="${D}" install || die "The GUI install failed" - popd - fi - - if use test; then - for dc in tests_summary.txt summary_tests.tar summary_of_tests.tar; do - test -e tests/"${dc}" && dodoc tests/"${dc}" || ewarn "Copying tests results failed" - done - fi - - popd > /dev/null - - # XXX: support installing them from builddir as well!!! - if [[ ${DOCS} ]]; then - dodoc "${DOCS[@]}" || die "dodoc failed" - else - local f - # same list as in PMS - for f in README* ChangeLog AUTHORS NEWS TODO CHANGES \ - THANKS BUGS FAQ CREDITS CHANGELOG; do - if [[ -s ${f} ]]; then - dodoc "${f}" || die "(default) dodoc ${f} failed" - fi - done - fi - if [[ ${HTML_DOCS} ]]; then - dohtml -r "${HTML_DOCS[@]}" || die "dohtml failed" - fi - - # Remove libtool files and unnecessary static libs - remove_libtool_files -} - -pkg_postinst() { - if use test; then - elog "The full test results will be installed as summary_tests.tar.bz2." - elog "Also a concise report tests_summary.txt is installed." - fi -} diff --git a/sci-physics/abinit/abinit-6.12.2.ebuild b/sci-physics/abinit/abinit-6.12.2.ebuild new file mode 100644 index 000000000..ddb435514 --- /dev/null +++ b/sci-physics/abinit/abinit-6.12.2.ebuild @@ -0,0 +1,338 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="4" + +inherit autotools-utils flag-o-matic fortran-2 multilib toolchain-funcs + +DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory" +HOMEPAGE="http://www.abinit.org/" +SRC_URI="http://ftp.abinit.org/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="cuda cuda-double -debug +etsf_io +fftw +fftw-threads +fox gsl gui +hdf5 libabinit mpi +netcdf python -test +threads -vdwxc" + +RDEPEND="=sci-libs/bigdft-1.6_pre1 + sci-libs/etsf_io + =sci-libs/libxc-1*[fortran] + sci-physics/atompaw[libxc] + etsf_io? ( sci-libs/etsf_io ) + fox? ( sci-libs/fox[dom,sax,wcml,wxml] ) + netcdf? ( + sci-libs/netcdf[fortran] + hdf5? ( + sci-libs/netcdf[fortran,hdf5] + ) + ) + hdf5? ( sci-libs/hdf5[fortran] ) + sci-libs/wannier90 + virtual/blas + virtual/lapack + gsl? ( sci-libs/gsl ) + fftw? ( + sci-libs/fftw:3.0 + fftw-threads? ( sci-libs/fftw:3.0[threads] ) + ) + mpi? ( virtual/mpi ) + python? ( dev-python/numpy ) + cuda? ( dev-util/nvidia-cuda-sdk )" +DEPEND="${RDEPEND} + dev-util/pkgconfig + gui? ( >=virtual/jdk-1.6.0 + app-arch/sharutils + sys-apps/gawk ) + dev-perl/Text-Markdown" + +S=${WORKDIR}/${P%[a-z]} + +lat1loc="" + +DOCS=( AUTHORS ChangeLog COPYING INSTALL KNOWN_PROBLEMS NEWS PACKAGING + README README.ChangeLog README.GPU README.xlf RELNOTES THANKS ) + +FORTRAN_STANDARD=90 + +pkg_setup() { + # Doesn't compile with gcc-4.0, only >=4.1 + if [[ $(tc-getFC) == *gfortran ]]; then + if [[ $(gcc-major-version) -eq 4 ]] \ + && [[ $(gcc-minor-version) -lt 1 ]]; then + die "Requires gcc-4.1 or newer" + fi + fi + + # fortran-2.eclass does not handle mpi wrappers + if use mpi; then + export FC="mpif90" + export F77="mpif77" + export CC="mpicc" + export CXX="mpic++" + else + tc-export FC F77 CC CXX + fi + + # Preprocesor macross can make some lines really long + append-fflags -ffree-line-length-none + + fortran-2_pkg_setup + + # Sort out some USE options + if use fftw-threads && ! use fftw; then + ewarn "fftw-threads set but fftw not used, ignored" + fi + if use cuda-double && ! use cuda; then + ewarn "cuda-double set but cuda not used, ignored" + fi + if use gui; then + lat1loc="$(locale |awk '/LC_CTYPE="(.*)"/{sub("LC_CTYPE=\"",""); sub("\" *$", ""); print}')" + if locale charmap |grep -i "\"; then + einfo "Good, locale compatible with the GUI build" + else + ewarn "The locale ${lat1loc} incompatible with the GUI build" + if latloc=`locale -a| grep -i "\"`; then + if echo "${latloc}" |grep -q "^fr"; then + lat1loc="$(echo "${latloc}" | grep -im1 "^fr")" + else + lat1loc="$(echo "${latloc}" | grep -im1 "iso88591")" + fi + einfo "Will use ${lat1loc} to build the GUI" + else + ewarn "No ISO-8859-1 nor ISO-8859-15 locale available, the GUI build may crash" + fi + fi + fi +} + +src_prepare() { + epatch "${FILESDIR}"/6.2.2-change-default-directories.patch + epatch "${FILESDIR}"/6.0.3-fftw.patch + epatch "${FILESDIR}"/6.12.1-autoconf.patch + epatch "${FILESDIR}"/6.12.1-xmalloc.patch + epatch "${FILESDIR}"/6.12.1-libabinit_options.patch + eautoreconf + + if use gui; then + epatch "${FILESDIR}"/6.12.1-gui-conf.patch + pushd "${S}"/gui > /dev/null + ./autogen.sh + popd + fi +} + +src_configure() { + local libs="-L/usr/$(get_libdir)" + local modules="-I/usr/$(get_libdir)/finclude" + local FoX_libs="${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lFoX_common -lFoX_utils -lFoX_fsys" + local trio_flavor="" + use etsf_io && trio_flavor="${trio_flavor}+etsf_io" + use fox && trio_flavor="${trio_flavor}+fox" + use netcdf && trio_flavor="${trio_flavor}+netcdf" + test "no${trio_flavor}" = "no" && trio_flavor="none" + local netcdff_libs="-lnetcdff" + use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran" + local fft_flavor="fftw3" + local fft_libs="-L/usr/lib" + # The fftw threads support is protected by black magick. + # Anybody removes it, dies. + # New USE flag "fftw-threads" was added to control usage + # of the threaded fftw variant. Since fftw-3.3 has expanded + # the paralel options by MPI and OpenMP support, analogical + # USE flags should be added to select them in future; + # unusable with previous FFTW versions, they are postponed + # for now. + if use fftw-threads; then + fft_flavor="fftw3-threads" + if has_version '>=sci-libs/fftw-3.3'; then + # pkg-config files for fftw-3.3 are broken + # All the parallel stuff is separated + # from the main body of common routines, + # and -lfftw3 must be always included alongside. + # Until version 3.3 this used to be masked by + # .la files. + # Bug 384645 + fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads) $(pkg-config --libs fftw3)" + else + fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads)" + fi + else + fft_libs="${fft_libs} $(pkg-config --libs fftw3)" + fi + local gpu_flavor="none" + if use cuda; then + gpu_flavor="cuda-single" + if use cuda-double; then + gpu_flavor="cuda-double" + fi + fi + + local myeconfargs=( + --enable-clib + --enable-exports + $(use_enable gui) + $(use_enable debug debug enhanced) + $(use_enable mpi) + $(use_enable mpi mpi-io) + --disable-smp + $(use_enable vdwxc) + $(use_enable cuda gpu) + "$(use cuda && echo "--with-gpu-flavor=${gpu_flavor}")" + "$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")" + "$(use gsl && echo "--with-math-flavor=gsl")" + "$(use gsl && echo "--with-math-incs=$(pkg-config --cflags gsl)")" + "$(use gsl && echo "--with-math-libs=$(pkg-config --libs gsl)")" + --with-linalg-flavor="atlas" + --with-linalg-libs="$(pkg-config --libs lapack)" + --with-trio-flavor="${trio_flavor}" + "$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")" + "$(use netcdf && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")" + "$(use fox && echo "--with-fox-incs=${modules}")" + "$(use fox && echo "--with-fox-libs=${FoX_libs}")" + "$(use etsf_io && echo "--with-etsf-io-incs=${modules}")" + "$(use etsf_io && echo "--with-etsf-io-libs=${libs} -letsf_io -letsf_io_utils -letsf_io_low_level")" + --with-dft-flavor="libxc+bigdft+atompaw+wannier90" + --with-libxc-incs="${modules}" + --with-libxc-libs="${libs} -lxc" + --with-bigdft-incs="${modules}" + --with-bigdft-libs="$(pkg-config --libs bigdft)" + --with-atompaw-incs="${modules}" + --with-atompaw-libs="${libs} -latompaw" + --with-wannier90-bins="/usr/bin" + --with-wannier90-incs="${modules}" + --with-wannier90-libs="${libs} -lwannier $(pkg-config --libs lapack)" + "$(use fftw && echo "--with-fft-flavor=${fft_flavor}")" + "$(use fftw && echo "--with-fft-incs=-I/usr/include")" + "$(use fftw && echo "--with-fft-libs=${fft_libs}")" + --with-timer-flavor="abinit" + LD="$(tc-getLD)" + FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include" + ) + + MARKDOWN=Markdown.pl autotools-utils_src_configure + + if use gui; then + # autotools-utils_src_configure() part expanded + _check_build_dir + pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null + mkdir -p gui + cd gui + ECONF_SOURCE="${S}"/gui econf + fi +} + +src_compile() { + autotools-utils_src_compile + + # Apparently libabinit.a is not built by default + # Used by BigDFT. Should probably be built separately, + # as a package of its own: BigDFT used by Abinit. + # Does libabinit.a depend on BigDFT, if used? + # Can Abinit use external libabinit.a? + use libabinit && autotools-utils_src_compile libabinit.a + + if use gui; then + #autotools-utils_src_compile() expanded + # _check_build_dir has already been called + pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null + # now what the function cannot be called to do + cd gui + LC_CTYPE="${lat1loc}" emake || die "Making GUI failed" + popd > /dev/null + fi + + sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc +} + +src_test() { + einfo "The tests take quite a while, easily several hours" + # autotools-utils_src_test() expanded + _check_build_dir + pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null + # again something the autotools-utils function cannot be called to do + # now quite a lot of work actually + cd tests + emake tests_acc || ewarn "Accuracy tests failed" + emake tests_paw || ewarn "PAW tests failed" + emake tests_gw || ewarn "GW tests failed" + emake tests_gw_paw || ewarn "GW-PAW tests failed" + emake tests_bs || ewarn "BSE tests failed" + emake tests_tddft || ewarn "TDDFT tests failed" + emake tests_eph || ewarn "Elphon tests failed" + + local REPORT + for REPORT in $(find . -name report); do + REPORT=${REPORT#*/} + elog "Parameters and unusual results for ${REPORT%%/*} tests" + echo "Parameters and unusual results for ${REPORT%%/*} tests" >>tests_summary.txt + while read line; do + elog "${line}" + echo "${line}" >>tests_summary.txt + done \ + < <(grep -v -e succeeded -e passed ${REPORT}) + done + + local testdir + find . -name "tmp-test*" -print | \ + while read testdir; do + if [ -e summary_of_tests.tar ]; then + tar rvf summary_of_tests.tar ${testdir} + else tar cvf summary_of_tests.tar ${testdir} + fi + done + popd > /dev/null + + elog "The full test results will be installed as summary_of_tests.tar.bz2." + elog "Also a concise report tests_summary.txt is installed." +} + +src_install() { + #autotools-utils_src_install() expanded + _check_build_dir + pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null + emake DESTDIR="${D}" install || die "make install failed" + + use libabinit && dolib libabinit.a + + if use gui; then + pushd gui + emake DESTDIR="${D}" install || die "The GUI install failed" + popd + fi + + if use test; then + for dc in tests_summary.txt summary_tests.tar summary_of_tests.tar; do + test -e tests/"${dc}" && dodoc tests/"${dc}" || ewarn "Copying tests results failed" + done + fi + + popd > /dev/null + + # XXX: support installing them from builddir as well!!! + if [[ ${DOCS} ]]; then + dodoc "${DOCS[@]}" || die "dodoc failed" + else + local f + # same list as in PMS + for f in README* ChangeLog AUTHORS NEWS TODO CHANGES \ + THANKS BUGS FAQ CREDITS CHANGELOG; do + if [[ -s ${f} ]]; then + dodoc "${f}" || die "(default) dodoc ${f} failed" + fi + done + fi + if [[ ${HTML_DOCS} ]]; then + dohtml -r "${HTML_DOCS[@]}" || die "dohtml failed" + fi + + # Remove libtool files and unnecessary static libs + remove_libtool_files +} + +pkg_postinst() { + if use test; then + elog "The full test results will be installed as summary_tests.tar.bz2." + elog "Also a concise report tests_summary.txt is installed." + fi +} diff --git a/sci-physics/abinit/abinit-6.6.3.ebuild b/sci-physics/abinit/abinit-6.6.3.ebuild deleted file mode 100644 index 3799d0578..000000000 --- a/sci-physics/abinit/abinit-6.6.3.ebuild +++ /dev/null @@ -1,196 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="3" - -inherit autotools eutils fortran-2 multilib toolchain-funcs - -DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory" -HOMEPAGE="http://www.abinit.org/" -SRC_URI="http://ftp.abinit.org/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="cuda -debug +fftw +fox gsl +hdf5 mpi +netcdf python -test +threads -vdwxc" - -RDEPEND=">=sci-libs/bigdft-1.2.0.2 - sci-libs/etsf_io - =sci-libs/libxc-1.0[fortran] - sci-physics/atompaw[libxc] - fox? ( sci-libs/fox[dom,sax,wcml,wxml] ) - netcdf? ( - sci-libs/netcdf[fortran] - hdf5? ( - sci-libs/netcdf[fortran,hdf5] - ) - ) - hdf5? ( sci-libs/hdf5[fortran] ) - sci-libs/wannier90 - virtual/blas - virtual/lapack - gsl? ( sci-libs/gsl ) - fftw? ( - sci-libs/fftw:3.0 - threads? ( sci-libs/fftw:3.0[threads] ) - ) - mpi? ( virtual/mpi ) - python? ( dev-python/numpy ) - cuda? ( dev-util/nvidia-cuda-sdk )" -DEPEND="${RDEPEND} - dev-util/pkgconfig - dev-perl/Text-Markdown" - -S=${WORKDIR}/${P%[a-z]} - -pkg_setup() { - fortran-2_pkg_setup - # Doesn't compile with gcc-4.0, only >=4.1 - if [[ $(tc-getFC) == *gfortran ]]; then - if [[ $(gcc-major-version) -eq 4 ]] \ - && [[ $(gcc-minor-version) -lt 1 ]]; then - die "Requires gcc-4.1 or newer" - fi - fi -} - -src_prepare() { - epatch "${FILESDIR}"/6.2.2-change-default-directories.patch - epatch "${FILESDIR}"/6.0.3-fftw.patch - eautoreconf -} - -src_configure() { - local libs="-L/usr/$(get_libdir)" - local modules="-I/usr/$(get_libdir)/finclude" - local FoX_libs="${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lFoX_common -lFoX_utils -lFoX_fsys" - local trio_flavor="etsf_io" - use fox && trio_flavor="${trio_flavor}+fox" - use netcdf && trio_flavor="${trio_flavor}+netcdf" - local netcdff_libs="-lnetcdff" - use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran" - local fft_flavor="fftw3" - local fft_libs="-L/usr/lib" - # Since now, fftw threads support is protected by black magick. - # Anybody removes it again, dies. - # If it does not work FOR YOU, disable the "threads" USE flag - # for the package at YOUR box. If YOU want it disabled selectively - # for fftw use in abinit, you may consider adding a special USE flag - # for that. NEVER REMOVE AN OPTION FOR OTHERS, at least if there is - # anybody it works for. - if use threads; then - fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads)" - fft_flavor="fftw3-threads" - else - fft_libs="${fft_libs} $(pkg-config --libs fftw3)" - fi - if use mpi; then - MY_FC="mpif90" - MY_CC="mpicc" - MY_CXX="mpic++" - else - MY_FC="$(tc-getFC)" - MY_CC="$(tc-getCC)" - MY_CXX="$(tc-getCXX)" - fi - MARKDOWN=Markdown.pl econf \ - $(use_enable debug debug enhanced) \ - $(use_enable mpi) \ - $(use_enable mpi mpi-io) \ - --disable-smp \ - $(use_enable vdwxc) \ - $(use_enable cuda gpu) \ - "$(use cuda && echo "--with-gpu-flavor=cuda-single")" \ - "$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")" \ - "$(use gsl && echo "--with-math-flavor=gsl")" \ - "$(use gsl && echo "--with-math-incs=$(pkg-config --cflags gsl)")" \ - "$(use gsl && echo "--with-math-libs=$(pkg-config --libs gsl)")" \ - --with-linalg-flavor="atlas" \ - --with-linalg-libs="$(pkg-config --libs lapack)" \ - --with-trio-flavor="${trio_flavor}" \ - "$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")" \ - "$(use netcdf && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")" \ - "$(use fox && echo "--with-fox-incs=${modules}")" \ - "$(use fox && echo "--with-fox-libs=${FoX_libs}")" \ - --with-etsf-io-incs="${modules}" \ - --with-etsf-io-libs="${libs} -letsf_io -letsf_io_utils -letsf_io_low_level" \ - --with-dft-flavor="libxc+bigdft+atompaw+wannier90" \ - --with-libxc-incs="${modules}" \ - --with-libxc-libs="${libs} -lxc" \ - --with-bigdft-incs="${modules}" \ - --with-bigdft-libs="${libs} -lpoissonsolver -lbigdft" \ - --with-atompaw-incs="${modules}" \ - --with-atompaw-libs="${libs} -latompaw" \ - --with-wannier90-bins="/usr/bin" \ - --with-wannier90-incs="${modules}" \ - --with-wannier90-libs="${libs} -lwannier $(pkg-config --libs lapack)" \ - "$(use fftw && echo "--with-fft-flavor=${fft_flavor}")" \ - "$(use fftw && echo "--with-fft-incs=-I/usr/include")" \ - "$(use fftw && echo "--with-fft-libs=${fft_libs}")" \ - --with-timer-flavor="abinit" \ - FC="${MY_FC}" \ - CC="${MY_CC}" \ - CXX="${MY_CXX}" \ - LD="$(tc-getLD)" \ - FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include" -} - -src_compile() { - emake || die -} - -src_test() { - einfo "The tests take quite a while, on the order of 1-2 hours" - einfo "on an Intel Penryn (2.5 GHz)." - cd "${S}"/tests - emake tests_min || ewarn "Minimal tests failed" - emake tests_paw || ewarn "PAW tests failed" - emake tests_gw || ewarn "GW tests failed" - emake tests_gw_paw || ewarn "GW-PAW tests failed" - emake tests tdft || ewarn "TDFT tests failed" - emake tests_bench || ewarn "Benchmarks failed" - - local REPORT - for REPORT in $(find . -name report); do - REPORT=${REPORT#*/} - elog "Parameters and unusual results for ${REPORT%%/*} tests" - echo "Parameters and unusual results for ${REPORT%%/*} tests" >>tests_summary.txt - while read line; do - elog "${line}" - echo "${line}" >>tests_summary.txt - done \ - < <(grep -v -e succeeded -e passed ${REPORT}) - done - - local testdir - find . -name "tmp-test*" -print | \ - while read testdir; do - if [ -e summary_of_tests.tar ]; then - tar rvf summary_of_tests.tar ${testdir} - else tar cvf summary_of_tests.tar ${testdir} - fi - done - - elog "The full test results will be installed as summary_of_tests.tar.bz2." - elog "Also a concise report tests_summary.txt is installed." -} - -src_install() { - emake DESTDIR="${D}" install || die "make install failed" - - if use test; then - dodoc tests/tests_summary.txt || ewarn "Copying tests summary failed" - dodoc tests/summary_tests.tar || ewarn "Copying tests results failed" - dodoc tests/summary_of_tests.tar || ewarn "Copying tests results failed" - fi - - dodoc KNOWN_PROBLEMS README || die "Copying doc files failed" -} - -pkg_postinst() { - if use test; then - elog "The full test results will be installed as summary_tests.tar.bz2." - elog "Also a concise report tests_summary.txt is installed." - fi -} diff --git a/sci-physics/abinit/abinit-6.8.2.ebuild b/sci-physics/abinit/abinit-6.8.2.ebuild deleted file mode 100644 index cdd495fd1..000000000 --- a/sci-physics/abinit/abinit-6.8.2.ebuild +++ /dev/null @@ -1,211 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="3" - -inherit autotools eutils fortran-2 multilib toolchain-funcs - -DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory" -HOMEPAGE="http://www.abinit.org/" -SRC_URI="http://ftp.abinit.org/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="cuda -debug +fftw +fftw-threads +fox gsl +hdf5 mpi +netcdf python -test +threads -vdwxc" - -RDEPEND=">=sci-libs/bigdft-1.2.0.2 - sci-libs/etsf_io - =sci-libs/libxc-1.0[fortran] - sci-physics/atompaw[libxc] - fox? ( sci-libs/fox[dom,sax,wcml,wxml] ) - netcdf? ( - sci-libs/netcdf[fortran] - hdf5? ( - sci-libs/netcdf[fortran,hdf5] - ) - ) - hdf5? ( sci-libs/hdf5[fortran] ) - sci-libs/wannier90 - virtual/blas - virtual/lapack - gsl? ( sci-libs/gsl ) - fftw? ( - sci-libs/fftw:3.0 - fftw-threads? ( sci-libs/fftw:3.0[threads] ) - ) - mpi? ( virtual/mpi ) - python? ( dev-python/numpy ) - cuda? ( dev-util/nvidia-cuda-sdk )" -DEPEND="${RDEPEND} - dev-util/pkgconfig - dev-perl/Text-Markdown" - -S=${WORKDIR}/${P%[a-z]} - -pkg_setup() { - fortran-2_pkg_setup - # Doesn't compile with gcc-4.0, only >=4.1 - if [[ $(tc-getFC) == *gfortran ]]; then - if [[ $(gcc-major-version) -eq 4 ]] \ - && [[ $(gcc-minor-version) -lt 1 ]]; then - die "Requires gcc-4.1 or newer" - fi - fi - if use fftw-threads && ! use fftw; then - ewarn "fftw-threads set but fftw not used, ignored" - fi -} - -src_prepare() { - epatch "${FILESDIR}"/6.2.2-change-default-directories.patch - epatch "${FILESDIR}"/6.0.3-fftw.patch - eautoreconf -} - -src_configure() { - local libs="-L/usr/$(get_libdir)" - local modules="-I/usr/$(get_libdir)/finclude" - local FoX_libs="${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lFoX_common -lFoX_utils -lFoX_fsys" - local trio_flavor="etsf_io" - use fox && trio_flavor="${trio_flavor}+fox" - use netcdf && trio_flavor="${trio_flavor}+netcdf" - local netcdff_libs="-lnetcdff" - use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran" - local fft_flavor="fftw3" - local fft_libs="-L/usr/lib" - # The fftw threads support is protected by black magick. - # Anybody removes it, dies. - # New USE flag "fftw-threads" was added to control usage - # of the threaded fftw variant. Since fftw-3.3 has expanded - # the paralel options by MPI and OpenMP support, analogical - # USE flags should be added to select them in future; - # unusable with previous FFTW versions, they are postponed - # for now. - if use fftw-threads; then - fft_flavor="fftw3-threads" - if has_version '>=sci-libs/fftw-3.3'; then - # pkg-config files for fftw-3.3 are broken - # All the parallel stuff is separated - # from the main body of common routines, - # and -lfftw3 must be always included alongside. - # Until version 3.3 this used to be masked by - # .la files. - # Bug 384645 - fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads) $(pkg-config --libs fftw3)" - else - fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads)" - fi - else - fft_libs="${fft_libs} $(pkg-config --libs fftw3)" - fi - if use mpi; then - MY_FC="mpif90" - MY_CC="mpicc" - MY_CXX="mpic++" - else - MY_FC="$(tc-getFC)" - MY_CC="$(tc-getCC)" - MY_CXX="$(tc-getCXX)" - fi - MARKDOWN=Markdown.pl econf \ - $(use_enable debug debug enhanced) \ - $(use_enable mpi) \ - $(use_enable mpi mpi-io) \ - --disable-smp \ - $(use_enable vdwxc) \ - $(use_enable cuda gpu) \ - "$(use cuda && echo "--with-gpu-flavor=cuda-single")" \ - "$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")" \ - "$(use gsl && echo "--with-math-flavor=gsl")" \ - "$(use gsl && echo "--with-math-incs=$(pkg-config --cflags gsl)")" \ - "$(use gsl && echo "--with-math-libs=$(pkg-config --libs gsl)")" \ - --with-linalg-flavor="atlas" \ - --with-linalg-libs="$(pkg-config --libs lapack)" \ - --with-trio-flavor="${trio_flavor}" \ - "$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")" \ - "$(use netcdf && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")" \ - "$(use fox && echo "--with-fox-incs=${modules}")" \ - "$(use fox && echo "--with-fox-libs=${FoX_libs}")" \ - --with-etsf-io-incs="${modules}" \ - --with-etsf-io-libs="${libs} -letsf_io -letsf_io_utils -letsf_io_low_level" \ - --with-dft-flavor="libxc+bigdft+atompaw+wannier90" \ - --with-libxc-incs="${modules}" \ - --with-libxc-libs="${libs} -lxc" \ - --with-bigdft-incs="${modules}" \ - --with-bigdft-libs="${libs} -lpoissonsolver -lbigdft" \ - --with-atompaw-incs="${modules}" \ - --with-atompaw-libs="${libs} -latompaw" \ - --with-wannier90-bins="/usr/bin" \ - --with-wannier90-incs="${modules}" \ - --with-wannier90-libs="${libs} -lwannier $(pkg-config --libs lapack)" \ - "$(use fftw && echo "--with-fft-flavor=${fft_flavor}")" \ - "$(use fftw && echo "--with-fft-incs=-I/usr/include")" \ - "$(use fftw && echo "--with-fft-libs=${fft_libs}")" \ - --with-timer-flavor="abinit" \ - FC="${MY_FC}" \ - CC="${MY_CC}" \ - CXX="${MY_CXX}" \ - LD="$(tc-getLD)" \ - FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include" -} - -src_compile() { - emake || die -} - -src_test() { - einfo "The tests take quite a while, on the order of 1-2 hours" - einfo "on an Intel Penryn (2.5 GHz)." - cd "${S}"/tests - emake tests_min || ewarn "Minimal tests failed" - emake tests_paw || ewarn "PAW tests failed" - emake tests_gw || ewarn "GW tests failed" - emake tests_gw_paw || ewarn "GW-PAW tests failed" - emake tests tdft || ewarn "TDFT tests failed" - emake tests_bench || ewarn "Benchmarks failed" - - local REPORT - for REPORT in $(find . -name report); do - REPORT=${REPORT#*/} - elog "Parameters and unusual results for ${REPORT%%/*} tests" - echo "Parameters and unusual results for ${REPORT%%/*} tests" >>tests_summary.txt - while read line; do - elog "${line}" - echo "${line}" >>tests_summary.txt - done \ - < <(grep -v -e succeeded -e passed ${REPORT}) - done - - local testdir - find . -name "tmp-test*" -print | \ - while read testdir; do - if [ -e summary_of_tests.tar ]; then - tar rvf summary_of_tests.tar ${testdir} - else tar cvf summary_of_tests.tar ${testdir} - fi - done - - elog "The full test results will be installed as summary_of_tests.tar.bz2." - elog "Also a concise report tests_summary.txt is installed." -} - -src_install() { - emake DESTDIR="${D}" install || die "make install failed" - - if use test; then - dodoc tests/tests_summary.txt || ewarn "Copying tests summary failed" - dodoc tests/summary_tests.tar || ewarn "Copying tests results failed" - dodoc tests/summary_of_tests.tar || ewarn "Copying tests results failed" - fi - - dodoc KNOWN_PROBLEMS README || die "Copying doc files failed" -} - -pkg_postinst() { - if use test; then - elog "The full test results will be installed as summary_tests.tar.bz2." - elog "Also a concise report tests_summary.txt is installed." - fi -} diff --git a/sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch b/sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch deleted file mode 100644 index 857a27abc..000000000 --- a/sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch +++ /dev/null @@ -1,61 +0,0 @@ -diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_descr_psp_set.F90 abinit-6.12.1/src/42_wvl_wrappers/wvl_descr_psp_set.F90 ---- src/42_wvl_wrappers/wvl_descr_psp_set.F90 2012-01-30 20:43:51.000000000 +0000 -+++ src/42_wvl_wrappers/wvl_descr_psp_set.F90 2012-03-19 13:06:59.000000000 +0000 -@@ -105,7 +105,7 @@ - ! Missing currently read radii_cf. - wvl%atoms%donlcc = .false. - ! TODO: add symmetry support -- wvl%atoms%symObj = -1 -+ wvl%atoms%sym%symObj = -1 - #endif - end subroutine wvl_descr_psp_set - !!*** -diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_projectors_set.F90 abinit-6.12.1/src/42_wvl_wrappers/wvl_projectors_set.F90 ---- src/42_wvl_wrappers/wvl_projectors_set.F90 2012-01-30 20:43:50.000000000 +0000 -+++ src/42_wvl_wrappers/wvl_projectors_set.F90 2012-03-19 13:17:37.000000000 +0000 -@@ -122,7 +122,7 @@ - ABI_ALLOCATE(xcart,(3, natom)) - call xredxcart(natom, 1, rprimd, xcart, xred) - -- call createProjectorsArrays(me, wfs%Glr%d%n1, wfs%Glr%d%n2, wfs%Glr%d%n3, & -+ call createProjectorsArrays(me, wfs%Glr, & - & xcart, wvl%atoms, wfs%orbs, psps%gth_params%radii_cf, & - & wvl_frmult, wvl_frmult, wvl%h(1), wvl%h(2), wvl%h(3), proj%keys, proj%proj) - write(message, '(a,a,a,a,I0)' ) ch10,& -diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_wfs_free.F90 abinit-6.12.1/src/42_wvl_wrappers/wvl_wfs_free.F90 ---- src/42_wvl_wrappers/wvl_wfs_free.F90 2012-01-30 20:43:50.000000000 +0000 -+++ src/42_wvl_wrappers/wvl_wfs_free.F90 2012-03-19 13:01:03.000000000 +0000 -@@ -68,7 +68,7 @@ - #if defined HAVE_DFT_BIGDFT - call deallocate_lr(wfs%Glr, sub) - call deallocate_orbs(wfs%orbs, sub) -- call deallocate_diis_objects(wfs%diis, sub) -+ ! call deallocate_diis_objects(wfs%diis, sub) - call deallocate_comms(wfs%comms, sub) - if (associated(wfs%orbs%eval)) then - ABI_DEALLOCATE(wfs%orbs%eval) -diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_wfs_set.F90 abinit-6.12.1/src/42_wvl_wrappers/wvl_wfs_set.F90 ---- src/42_wvl_wrappers/wvl_wfs_set.F90 2012-01-30 20:43:55.000000000 +0000 -+++ src/42_wvl_wrappers/wvl_wfs_set.F90 2012-03-19 12:58:54.000000000 +0000 -@@ -59,7 +59,7 @@ - use defs_wvltypes - #if defined HAVE_DFT_BIGDFT - use BigDFT_API, only: createWavefunctionsDescriptors, orbitals_descriptors, & -- & orbitals_communicators, allocate_diis_objects, wvl_timing => timing -+ & orbitals_communicators, wvl_timing => timing - #endif - - !This section has been created automatically by the script Abilint (TD). -@@ -179,9 +179,9 @@ - call wvl_timing(me,'CrtDescriptors','OF') - - ! allocate arrays necessary for DIIS convergence acceleration -- call allocate_diis_objects(nwfshist,1._dp,& -- & sum(wfs%comms%ncntt(0:nproc-1)), wfs%orbs%nkptsp, wfs%orbs%nspinor, & -- & wfs%orbs%norbd, wfs%diis, "wvl_init_wfs_type") -+ ! call allocate_diis_objects(nwfshist,1._dp,& -+ ! & sum(wfs%comms%ncntt(0:nproc-1)), wfs%orbs%nkptsp, wfs%orbs%nspinor, & -+ ! & wfs%orbs%norbd, wfs%diis, "wvl_init_wfs_type") - - #else - write(message, '(a,a,a,a)' ) ch10,& diff --git a/sci-physics/abinit/files/6.12.1-gui-conf.patch b/sci-physics/abinit/files/6.12.1-gui-conf.patch deleted file mode 100644 index 95c12b354..000000000 --- a/sci-physics/abinit/files/6.12.1-gui-conf.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Naur abinit-6.12.1_orig/gui/configure abinit-6.12.1/gui/configure ---- gui/configure 2012-01-30 19:42:26.000000000 +0000 -+++ gui/configure 2012-03-16 13:38:54.000000000 +0000 -@@ -3143,7 +3143,7 @@ - test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -- ac_cv_prog_UUDECODE="no" -+ ac_cv_prog_UUDECODE="$as_dir/$ac_word$ac_exec_ext" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 - break 2 - fi diff --git a/sci-physics/abinit/files/6.6.1-openmp.patch b/sci-physics/abinit/files/6.6.1-openmp.patch deleted file mode 100644 index af43d5792..000000000 --- a/sci-physics/abinit/files/6.6.1-openmp.patch +++ /dev/null @@ -1,509 +0,0 @@ -diff -Naur abinit-6.6.1.orig/src/52_fft_mpi_noabirule/accrho.F90 abinit-6.6.1/src/52_fft_mpi_noabirule/accrho.F90 ---- src/52_fft_mpi_noabirule/accrho.F90 2011-02-28 05:14:13.000000000 +0000 -+++ src/52_fft_mpi_noabirule/accrho.F90 2011-03-01 19:41:35.000000000 +0000 -@@ -91,14 +91,14 @@ - integer unused - unused=0 - ! ************************************************************************* --!$ interface --!$ integer ( kind=4 ) function omp_get_num_threads ( ) --!$ end function omp_get_num_threads --!$ end interface --!$ interface --!$ integer ( kind=4 ) function omp_get_thread_num ( ) --!$ end function omp_get_thread_num --!$ end interface -+!% interface -+!% integer ( kind=4 ) function omp_get_num_threads ( ) -+!% end function omp_get_num_threads -+!% end interface -+!% interface -+!% integer ( kind=4 ) function omp_get_thread_num ( ) -+!% end function omp_get_thread_num -+!% end interface - - write(6,*)' accrho : enter ' - -diff -Naur abinit-6.6.1.orig/src/52_fft_mpi_noabirule/applypot.F90 abinit-6.6.1/src/52_fft_mpi_noabirule/applypot.F90 ---- src/52_fft_mpi_noabirule/applypot.F90 2011-02-28 05:14:13.000000000 +0000 -+++ src/52_fft_mpi_noabirule/applypot.F90 2011-03-01 19:43:37.000000000 +0000 -@@ -91,14 +91,14 @@ - integer unused - unused=0 - --!$ interface --!$ integer ( kind=4 ) function omp_get_num_threads ( ) --!$ end function omp_get_num_threads --!$ end interface --!$ interface --!$ integer ( kind=4 ) function omp_get_thread_num ( ) --!$ end function omp_get_thread_num --!$ end interface -+!% interface -+!% integer ( kind=4 ) function omp_get_num_threads ( ) -+!% end function omp_get_num_threads -+!% end interface -+!% interface -+!% integer ( kind=4 ) function omp_get_thread_num ( ) -+!% end function omp_get_thread_num -+!% end interface - - write(6,*)' applypot : enter ' - -diff -Naur abinit-6.6.1.orig/src/52_fft_mpi_noabirule/back.F90 abinit-6.6.1/src/52_fft_mpi_noabirule/back.F90 ---- src/52_fft_mpi_noabirule/back.F90 2011-02-28 05:14:13.000000000 +0000 -+++ src/52_fft_mpi_noabirule/back.F90 2011-03-01 19:45:45.000000000 +0000 -@@ -90,14 +90,14 @@ - #endif - ! ************************************************************************* - --!$ interface --!$ integer ( kind=4 ) function omp_get_num_threads ( ) --!$ end function omp_get_num_threads --!$ end interface --!$ interface --!$ integer ( kind=4 ) function omp_get_thread_num ( ) --!$ end function omp_get_thread_num --!$ end interface -+!% interface -+!% integer ( kind=4 ) function omp_get_num_threads ( ) -+!% end function omp_get_num_threads -+!% end interface -+!% interface -+!% integer ( kind=4 ) function omp_get_thread_num ( ) -+!% end function omp_get_thread_num -+!% end interface - - !DEBUG - ! write(6,*)' back : enter ' -@@ -121,7 +121,7 @@ - - lock=0 - !$omp parallel default(private) & --!$omp shared(ndat,n1,n2,n3,nd1,nd2,nd3,nd2proc,nd3proc,mpi_enreg%me_fft,mpi_enreg%nproc_fft,ncache,zr,zf,lock,icplex) -+!$omp shared(ndat,n1,n2,n3,nd1,nd2,nd3,nd2proc,nd3proc,mpi_enreg,ncache,zr,zf,lock,icplex) - - iam=0 - npr=1 -diff -Naur abinit-6.6.1.orig/src/52_fft_mpi_noabirule/forw.F90 abinit-6.6.1/src/52_fft_mpi_noabirule/forw.F90 ---- src/52_fft_mpi_noabirule/forw.F90 2011-02-28 05:14:13.000000000 +0000 -+++ src/52_fft_mpi_noabirule/forw.F90 2011-03-01 19:46:53.000000000 +0000 -@@ -95,14 +95,14 @@ - integer :: old_paral_level - #endif - ! ************************************************************************* --!$ interface --!$ integer ( kind=4 ) function omp_get_num_threads ( ) --!$ end function omp_get_num_threads --!$ end interface --!$ interface --!$ integer ( kind=4 ) function omp_get_thread_num ( ) --!$ end function omp_get_thread_num --!$ end interface -+!% interface -+!% integer ( kind=4 ) function omp_get_num_threads ( ) -+!% end function omp_get_num_threads -+!% end interface -+!% interface -+!% integer ( kind=4 ) function omp_get_thread_num ( ) -+!% end function omp_get_thread_num -+!% end interface - - !DEBUG - ! write(6,*)' forw : enter ' -@@ -134,7 +134,7 @@ - - lock=0 - !$omp parallel default(private) & --!$omp shared(ndat,n1,n2,n3,nd1,nd2,nd3,nd2proc,nd3proc,mpi_enreg%me_fft,mpi_enreg%nproc_fft,ncache,zr,zf,lock,icplex) -+!$omp shared(ndat,n1,n2,n3,nd1,nd2,nd3,nd2proc,nd3proc,mpi_enreg,ncache,zr,zf,lock,icplex) - - iam=0 - npr=1 -diff -Naur abinit-6.6.1.orig/src/53_ffts/fftw3_fourwf.F90 abinit-6.6.1/src/53_ffts/fftw3_fourwf.F90 ---- src/53_ffts/fftw3_fourwf.F90 2011-02-28 06:10:13.000000000 +0000 -+++ src/53_ffts/fftw3_fourwf.F90 2011-03-01 21:30:29.000000000 +0000 -@@ -432,8 +432,8 @@ - end do - - cplex=0; istwf_k=1; option=3 --!$ call sg_fftrisc(cplex,dum_denpot,fofgin,dum_fofgin,fofr,gbound,gbound,istwf_k,dum_gvec,gvec,& --!$& mgfft,ngfft,npwwfn,npwwfn,ldx,ldy,ldz,option,weight) -+!% call sg_fftrisc(cplex,dum_denpot,fofgin,dum_fofgin,fofr,gbound,gbound,istwf_k,dum_gvec,gvec,& -+!%& mgfft,ngfft,npwwfn,npwwfn,ldx,ldy,ldz,option,weight) - - allocate(ftarr(2,ldx,ldy,ldz)) - !This call gives weird results for R-->G, while G-->R is ok!!!! -diff -Naur abinit-6.6.1.orig/src/53_ffts/sphere_fft.F90 abinit-6.6.1/src/53_ffts/sphere_fft.F90 ---- src/53_ffts/sphere_fft.F90 2011-02-28 06:10:11.000000000 +0000 -+++ src/53_ffts/sphere_fft.F90 2011-03-01 20:35:57.000000000 +0000 -@@ -99,7 +99,7 @@ - !ENDDEBUG - - !Insert cg into cfft with extra 0 s around outside: --!$OMP PARALLEL DO PRIVATE(i1,i2,i3) SHARED(cfft,ndat,n1,n2,n3) -+!!$OMP PARALLEL DO PRIVATE(i1,i2,i3) SHARED(cfft,ndat,n1,n2,n3) - !do i2=1,nd2proc*ndat - !do i3=1,n3 - !do i1=1,n1 -@@ -108,7 +108,7 @@ - !end do - !end do - !end do --!$OMP END PARALLEL DO -+!!$OMP END PARALLEL DO - cfft(:,:,:,:)=zero - !$OMP PARALLEL DO PRIVATE(i1,i2,i3,idat,ipw) SHARED(cfft,cg,kg_k,ndat,npw) - !write(6,*)'In sphere fft,i1,i2,i3,ipw,cfft=cg' -@@ -229,7 +229,7 @@ - !ENDDEBUG - - !Insert cg into cfft with extra 0 s around outside: --!$OMP PARALLEL DO PRIVATE(i1,i2,i3) SHARED(cfft,ndat,n1,n2,n3) -+!!$OMP PARALLEL DO PRIVATE(i1,i2,i3) SHARED(cfft,ndat,n1,n2,n3) - !do i2=1,nd2proc*ndat - !do i3=1,n3 - !do i1=1,n1 -@@ -238,7 +238,7 @@ - !end do - !end do - !end do --!$OMP END PARALLEL DO -+!!$OMP END PARALLEL DO - cfft(:,:,:,:)=zero - !$OMP PARALLEL DO PRIVATE(i1,i2,i3,idat,ipw) SHARED(cfft,cg,kg_k,ndat,npw) - !write(6,*)'In sphere fft,i1,i2,i3,ipw,cfft=cg' -diff -Naur abinit-6.6.1.orig/src/67_common/m_coulombian.F90 abinit-6.6.1/src/67_common/m_coulombian.F90 ---- src/67_common/m_coulombian.F90 2011-02-28 06:10:19.000000000 +0000 -+++ src/67_common/m_coulombian.F90 2011-03-01 22:22:13.000000000 +0000 -@@ -1950,7 +1950,7 @@ - real(dp) :: F3 - !************************************************************************ - -- !$F3(z)=z*\sin(qpg_para_*z)/\sqrt(rcut^2+z^2)$ -+ !%$F3(z)=z*\sin(qpg_para_*z)/\sqrt(rcut^2+z^2)$ - F3=xx*SIN(qpg_para_*xx)/SQRT(rcut_**2+xx**2) - - end function F3 -@@ -2039,7 +2039,7 @@ - real(dp) :: k0,rho,arg - !************************************************************************ - -- !$K0cos(y)=K0(\rho*|qpg_z|)*COS(x.qpg_x+y*qpg_y)$ -+ !%$K0cos(y)=K0(\rho*|qpg_z|)*COS(x.qpg_x+y*qpg_y)$ - rho=SQRT(xx_**2+yy**2) ; arg=qpg_para_*rho - call CALCK0(arg,k0,1) - K0cos=k0*COS(qpgx_*xx_+qpgy_*yy) -@@ -2065,7 +2065,7 @@ - real(dp) :: quad - !************************************************************************ - -- !$ K0cos_dy(x)=\int_{-b/2}^{b/2} K0(|qpg_z|\rho)cos(x.qpg_x+y.qpg_y)dy$ -+ !%$ K0cos_dy(x)=\int_{-b/2}^{b/2} K0(|qpg_z|\rho)cos(x.qpg_x+y.qpg_y)dy$ - xx_=xx - call quadrature(K0cos,-hb_,+hb_,qopt_,quad,ierr,ntrial_,accuracy_,npts_) - if (ierr/=0) then -diff -Naur abinit-6.6.1.orig/src/69_wfdesc/m_wfs.F90 abinit-6.6.1/src/69_wfdesc/m_wfs.F90 ---- src/69_wfdesc/m_wfs.F90 2011-02-28 06:10:19.000000000 +0000 -+++ src/69_wfdesc/m_wfs.F90 2011-03-01 22:32:16.000000000 +0000 -@@ -126,7 +126,7 @@ - ! The boundary of the basis sphere of G vectors at a given k point. - ! for use in improved zero padding of ffts in 3 dimensions. - -- !$real(dp) :: kpoint(3) -+ !%real(dp) :: kpoint(3) - - real(dp),pointer :: ph3d(:,:,:) SET2NULL - ! ph3d(2,npw,natom) -@@ -146,7 +146,7 @@ - ! ylm(npw,mpsang**2*useylm) - ! Real spherical harmonics for each k+G - -- !$real(dp),pointer :: kinpw(:) -+ !%real(dp),pointer :: kinpw(:) - ! kinpw(npw_k) - ! compute elements of kinetic energy operator in reciprocal space. - ! (1/2*effmass) (2 Pi)**2 (k+G)**2: -@@ -186,7 +186,7 @@ - !integer :: nspinor - !integer :: natom - -- !$ integer :: cplex -+ !% integer :: cplex - ! 1 for real wavefunctions u(r) - ! 2 for complex wavefunctions u(r). - ! At gamma we always have real u(r) provided that time-reversal can be used. -@@ -267,8 +267,8 @@ - integer :: itim - ! 2 is time-reversal is used. 1 otherwise. - -- !$integer :: ngfft(18) -- !$integer :: mgfft -+ !%integer :: ngfft(18) -+ !%integer :: mgfft - - real(dp) :: ecut - ! Cutoff energy. -@@ -326,7 +326,7 @@ - integer :: lmnmax - integer :: mband ! MAX(nband) - integer :: mgfft ! Maximum size of 1D FFTs i.e. MAXVAL(ngfft(1:3)), used to dimension some arrays. -- !$integer :: mpsang -+ !%integer :: mpsang - integer :: natom - integer :: nfft ! Number of FFT points treated by this processor - integer :: nfftot ! Total number of points in the FFT grid -@@ -338,7 +338,7 @@ - integer :: ntypat - integer :: paral_kgb ! Option for kgb parallelism - integer :: usepaw ! 1 if PAW is used, 0 otherwise. -- !$integer :: usepawu ! 1 if PAW+U is used, 0 otherwise. -+ !%integer :: usepawu ! 1 if PAW+U is used, 0 otherwise. - integer :: prtvol ! Verbosity level. - integer :: pawprtvol ! Verbosity level for PAW. - integer :: usewvl ! 1 if BigDFT is used, 0 otherwise. -@@ -362,13 +362,13 @@ - ! ecutsm=smearing energy for plane wave kinetic energy (Ha) - ! Cutoff for plane wave basis set. - -- !$real(dp) :: pawecutdg=zero -+ !%real(dp) :: pawecutdg=zero - ! Cutoff for plane wave basis set. - - logical :: gamma_centered=.TRUE. - ! .TRUE. if ug are given on the Gamma-centered G-sphere. Flag nedded to preserve the old Implementation. - -- !$real(dp) :: effmass -+ !%real(dp) :: effmass - ! Effective mass for electrons - - !arrays -@@ -2066,8 +2066,8 @@ - - ! Compute (k+G) vectors - nkpg=0 -- !$if (choice==3.or.choice==2.or.choice==23) nkpg=3*Wfd%nloalg(5) -- !$if (choice==4.or.choice==24) nkpg=9*Wfd%nloalg(5) -+ !%if (choice==3.or.choice==2.or.choice==23) nkpg=3*Wfd%nloalg(5) -+ !%if (choice==4.or.choice==24) nkpg=9*Wfd%nloalg(5) - allocate(kpg(npw_k,nkpg)); if (nkpg>0) call mkkpg(kg_k,kpg,kpoint,nkpg,npw_k) - - matblk = Cryst%natom -@@ -5741,9 +5741,9 @@ - ! ************************************************************************* - - ! TODO ngfft should be included in pawfgrtab_type -- !$if (ANY(Wfd%ngfft(1:3)/=Pawfgrtab%ngfft(1:3)) then -- !$ MSG_ERROR("Wfd%ngfft(1:3)/=Pawfgrtab%ngfft(1:3)") -- !$end if -+ !%if (ANY(Wfd%ngfft(1:3)/=Pawfgrtab%ngfft(1:3)) then -+ !% MSG_ERROR("Wfd%ngfft(1:3)/=Pawfgrtab%ngfft(1:3)") -+ !%end if - - call wfd_get_ur(Wfd,band,ik_ibz,spin,ur_ae) - -@@ -6817,7 +6817,7 @@ - do_sym = .FALSE. - if (PRESENT(ISkg)) then - do_sym = .TRUE. -- !$ TODO do_sym = (ISkg%isym/=1 .or. ISkg%itim/=1) -+ !% TODO do_sym = (ISkg%isym/=1 .or. ISkg%itim/=1) - end if - - if (.not. do_sym) then -diff -Naur abinit-6.6.1.orig/src/69_wfdesc/outkss.F90 abinit-6.6.1/src/69_wfdesc/outkss.F90 ---- src/69_wfdesc/outkss.F90 2011-02-28 05:14:13.000000000 +0000 -+++ src/69_wfdesc/outkss.F90 2011-03-01 22:42:00.000000000 +0000 -@@ -131,7 +131,7 @@ - #endif - - use m_io_tools, only : get_unit -- !$use m_numeric_tools, only : bisect -+ !%use m_numeric_tools, only : bisect - use m_gsphere, only : merge_and_sort_kg, table_gbig2kg, get_kg - use m_io_kss, only : write_kss_wfgk, write_kss_header, k2gamma_centered - use m_hamiltonian, only : ddiago_ctl_type, init_ddiago_ctl -@@ -458,7 +458,7 @@ - EXIT - end if - end do --!$ ishm=bisect(shlim,npwkss) -+!% ishm=bisect(shlim,npwkss) - - if (shlim(ishm)/=npwkss) then - nrst1=shlim(ishm) -diff -Naur abinit-6.6.1.orig/src/70_gw/m_screening.F90 abinit-6.6.1/src/70_gw/m_screening.F90 ---- src/70_gw/m_screening.F90 2011-02-28 06:10:19.000000000 +0000 -+++ src/70_gw/m_screening.F90 2011-03-02 05:05:33.000000000 +0000 -@@ -439,7 +439,7 @@ - end do - - rdwr=4 -- !$call hdr_io_int(Er%fform,Er%Hscr%Hdr,rdwr,unt) -+ !%call hdr_io_int(Er%fform,Er%Hscr%Hdr,rdwr,unt) - end if ! verbose>0 - - end subroutine print_epsilonm1_results -@@ -796,7 +796,7 @@ - - call metric(gmet,gprimd,-1,rmet,Vcp%rprimd,ucvol) - -- !$ if (Er%ID/=0) call reset_Epsilonm1(Er) -+ !% if (Er%ID/=0) call reset_Epsilonm1(Er) - Er%ID=id_required - - write(*,*) 'Er%ID:',Er%ID -@@ -1892,7 +1892,7 @@ - end if - - if (iqibz==1) then -- !$vc_sqrt => Vcp%vcqlwl_sqrt(:,iqlwl) ! Use Coulomb term for q-->0 -+ !%vc_sqrt => Vcp%vcqlwl_sqrt(:,iqlwl) ! Use Coulomb term for q-->0 - vc_sqrt => Vcp%vcqlwl_sqrt(:,1) ! TODO add treatment of non-Analytic behavior - else - vc_sqrt => Vcp%vc_sqrt(:,iqibz) -@@ -1992,7 +1992,7 @@ - end if - - if (iqibz==1) then -- !$vc_sqrt => Vcp%vcqlwl_sqrt(:,iqlwl) ! Use Coulomb term for q-->0 -+ !%vc_sqrt => Vcp%vcqlwl_sqrt(:,iqlwl) ! Use Coulomb term for q-->0 - vc_sqrt => Vcp%vcqlwl_sqrt(:,1) ! TODO add treatment of non-Analytic behavior - else - vc_sqrt => Vcp%vc_sqrt(:,iqibz) -@@ -2212,7 +2212,7 @@ - end do - ! - !if (PRESENT(rhor)) then -- ! !$call mdielf(epsinf,Er%npw,Er%nomega,iq_ibz,Er%qibz(:,iq_ibz),Er%gvec,Cryst,Vcp,nspden,nfft,ngfft,rhor,epsm1,comm) -+ ! !%call mdielf(epsinf,Er%npw,Er%nomega,iq_ibz,Er%qibz(:,iq_ibz),Er%gvec,Cryst,Vcp,nspden,nfft,ngfft,rhor,epsm1,comm) - !end if - - end do ! nqibz -@@ -2393,7 +2393,7 @@ - ! - ! Change the body but do not add the corrections due to the head and the wings. - ! since they can be obtained on the fly from eps_body and the wings of eps^{-1}. -- !$chi0(2:,2:,iomega) = eps_body -+ !%chi0(2:,2:,iomega) = eps_body - end do !iomega - - deallocate(modg_inv,cvec) -diff -Naur abinit-6.6.1.orig/src/71_bse/exc_iterative_diago.F90 abinit-6.6.1/src/71_bse/exc_iterative_diago.F90 ---- src/71_bse/exc_iterative_diago.F90 2011-02-28 06:10:19.000000000 +0000 -+++ src/71_bse/exc_iterative_diago.F90 2011-03-01 22:50:45.000000000 +0000 -@@ -762,8 +762,8 @@ - open(unit=eig_unt,file=oeig_fname,form='unformatted') - write(eig_unt) exc_nst - write(eig_unt) CMPLX(exc_energy(1:exc_nst),kind=dpc) -- !$ fform = 1002 ! TODO: change setup_bse so that Hdr_bse reflects the parameters of the run. -- !$ call hdr_io_int(fform,Hdr_bse,rdwr2,eig_unt) -+ !% fform = 1002 ! TODO: change setup_bse so that Hdr_bse reflects the parameters of the run. -+ !% call hdr_io_int(fform,Hdr_bse,rdwr2,eig_unt) - close(eig_unt) - end if - -@@ -776,15 +776,15 @@ - msg = " MPI_IO error opening file: "//TRIM(oeig_fname) - ABI_CHECK_MPI(ierr,msg) - -- !$call xmpio_read_frm(mpi_fh,ehdr_offset,xmpio_at,fmarker,ierr) -- !$write(std_out,*)"fmarker last record ",fmarker -- !$call hdr_mpio_skip(mpi_fh,fform,ehdr_offset) -- !$ehdr_offset = 4*xmpio_bsize_frm + xmpio_bsize_int + exc_nst*xmpio_bsize_dpc -+ !%call xmpio_read_frm(mpi_fh,ehdr_offset,xmpio_at,fmarker,ierr) -+ !%write(std_out,*)"fmarker last record ",fmarker -+ !%call hdr_mpio_skip(mpi_fh,fform,ehdr_offset) -+ !%ehdr_offset = 4*xmpio_bsize_frm + xmpio_bsize_int + exc_nst*xmpio_bsize_dpc - - is_fortran_file=.TRUE.; etype=MPI_BYTE; old_type=MPI_DOUBLE_COMPLEX - - ! TODO Need to add option to create file view. -- !$call xmpio_create_coldistr_from_fherm_packed(array_of_sizes,my_cols,old_type,eig_type,offset_err) -+ !%call xmpio_create_coldistr_from_fherm_packed(array_of_sizes,my_cols,old_type,eig_type,offset_err) - - if (offset_err/=0) then - write(msg,"(3a)")& -diff -Naur abinit-6.6.1.orig/src/77_ddb/eliashberg_1d.F90 abinit-6.6.1/src/77_ddb/eliashberg_1d.F90 ---- src/77_ddb/eliashberg_1d.F90 2011-02-28 06:10:20.000000000 +0000 -+++ src/77_ddb/eliashberg_1d.F90 2011-03-02 04:21:07.000000000 +0000 -@@ -108,10 +108,10 @@ - - ! - !1) use linearized Eliashberg equation to find Tc --!$ \sum_j \mathbf{M}_{ij} \Delta_j = \zeta \cdot \Delta_i $ $i,j = 1 .. n_{\mathrm{Matsubara}}$ --!$\zeta = 1$ gives T$_c$ $\beta = \frac{1}{\mathrm{T}}$ $\omega_i = (2 i + 1) \pi \mathrm{T}$ --!$ \mathbf{M}_{ij} = \frac{\pi}{\beta} \frac{\lambda (\omega_i - \omega_j)}{Z (\omega_i)}$ --!$ Z (\omega_i) = 1 + \frac{\pi}{\beta \omega_i} \sum_j \lambda(\omega_i - \omega_j) \mathrm{sgn}(\omega_j)$ -+!%$ \sum_j \mathbf{M}_{ij} \Delta_j = \zeta \cdot \Delta_i $ $i,j = 1 .. n_{\mathrm{Matsubara}}$ -+!%$\zeta = 1$ gives T$_c$ $\beta = \frac{1}{\mathrm{T}}$ $\omega_i = (2 i + 1) \pi \mathrm{T}$ -+!%$ \mathbf{M}_{ij} = \frac{\pi}{\beta} \frac{\lambda (\omega_i - \omega_j)}{Z (\omega_i)}$ -+!%$ Z (\omega_i) = 1 + \frac{\pi}{\beta \omega_i} \sum_j \lambda(\omega_i - \omega_j) \mathrm{sgn}(\omega_j)$ - ! - - !initial guess for T$_c$ in Hartree (1Ha =3.067e5 K) -diff -Naur abinit-6.6.1.orig/src/77_ddb/m_eph.F90 abinit-6.6.1/src/77_ddb/m_eph.F90 ---- src/77_ddb/m_eph.F90 2011-02-28 05:14:13.000000000 +0000 -+++ src/77_ddb/m_eph.F90 2011-03-01 23:17:18.000000000 +0000 -@@ -233,10 +233,10 @@ - public :: nullify_fermi_surface - public :: destroy_fermi_surface - -- !$public :: init_fermi_surface -- !$public :: wannier_interpolate_fermi_surface -- !$public :: get_fs_ibz -- !$public :: bxsf_write_fermi_surface -+ !%public :: init_fermi_surface -+ !%public :: wannier_interpolate_fermi_surface -+ !%public :: get_fs_ibz -+ !%public :: bxsf_write_fermi_surface - - ! example: - !type(fermi_surface_type),allocatable :: Fsurf(:) -@@ -325,9 +325,9 @@ - ! Bound Methods: - public :: nullify_gkk - public :: destroy_gkk -- !$ init_gkk -- !$ read_gkk_from_file -- !$ get_gkk_full_fsbz ! complete gkk on the full FS BZ. -+ !% init_gkk -+ !% read_gkk_from_file -+ !% get_gkk_full_fsbz ! complete gkk on the full FS BZ. - - interface nullify_gkk - module procedure nullify_gkk_0D -@@ -379,9 +379,9 @@ - ! Bound Methods: - public :: nullify_gkk_handler - public :: destroy_gkk_handler -- !$init_gkk_handler(Gkk,FSurf,Cryst,Cryst,qpt,fname) -- !$get_gammaq -- !$symmetrize_gkk_over_perts -+ !%init_gkk_handler(Gkk,FSurf,Cryst,Cryst,qpt,fname) -+ !%get_gammaq -+ !%symmetrize_gkk_over_perts - - interface nullify_gkk_handler - module procedure nullify_gkk_handler_0D -diff -Naur abinit-6.6.1.orig/src/95_drive/bethe_salpeter.F90 abinit-6.6.1/src/95_drive/bethe_salpeter.F90 ---- src/95_drive/bethe_salpeter.F90 2011-02-28 06:10:13.000000000 +0000 -+++ src/95_drive/bethe_salpeter.F90 2011-03-02 04:34:01.000000000 +0000 -@@ -453,7 +453,7 @@ - end do - end if - -- opt_ecut=zero !$; if (gw_uses_wfk_file) opt_ecut=Dtset%ecutwfn -+ opt_ecut=zero !%; if (gw_uses_wfk_file) opt_ecut=Dtset%ecutwfn - - call wfd_init(Wfd,Cryst,Pawtab,Psps,keep_ur,Dtset%paral_kgb,BSp%npwwfn,mband,nband,Kmesh%nibz,Dtset%nsppol,bks_mask,& - & Dtset%nspden,Dtset%nspinor,Dtset%ecutsm,Dtset%dilatmx,Hdr_kss%istwfk,Kmesh%ibz,ngfft_osc,& -@@ -513,7 +513,7 @@ - - !TODO this has to be done in a better way, moreover wont work for PAW - !Check Vcp! --!$ call cutoff_density(ngfftf,Dtset%nspden,Dtset%nsppol,Vcp,ks_rhor,MPI_enreg_seq) -+!% call cutoff_density(ngfftf,Dtset%nspden,Dtset%nsppol,Vcp,ks_rhor,MPI_enreg_seq) - ! - !=== Additional computation for PAW === - if (Dtset%usepaw==1) then -- cgit v1.2.3-65-gdbad