commit: b4d1c8facd85152c22f79dccf3bff550afb64ab2 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Sat Oct 27 20:27:08 2018 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Sat Oct 27 20:27:08 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b4d1c8fa
Drop obsolete packages Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> sci-astronomy/mosstack/metadata.xml | 23 -- sci-astronomy/mosstack/mosstack-0.6.1-r1.ebuild | 33 -- sci-astronomy/mosstack/mosstack-0.6.1.ebuild | 33 -- sci-biology/Gambit/Gambit-0.4.145.ebuild | 37 -- sci-biology/Gambit/metadata.xml | 12 - sci-biology/atsas/atsas-2.8.3.ebuild | 75 ---- sci-biology/atsas/metadata.xml | 8 - sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild | 78 ----- .../NMRdyn/files/NMRdyn-3.2.5-redefinition.patch | 19 - sci-chemistry/NMRdyn/metadata.xml | 11 - sci-chemistry/ball/ball-9999.ebuild | 75 ---- sci-chemistry/ball/files/ball-9999-multilib.patch | 39 --- sci-chemistry/ball/metadata.xml | 35 -- sci-chemistry/cnsface/cnsface-0.0.12.ebuild | 26 -- sci-chemistry/cnsface/files/0.0.12-binary.patch | 13 - sci-chemistry/cnsface/metadata.xml | 11 - sci-chemistry/phenix-bin/metadata.xml | 8 - .../phenix-bin/phenix-bin-1.10.2155.ebuild | 117 ------- .../kayali/files/kayali-0.2-calcwindow.patch | 11 - sci-mathematics/kayali/kayali-0.3.2.ebuild | 62 ---- sci-mathematics/kayali/metadata.xml | 17 - sci-mathematics/mathics/mathics-1.0.ebuild | 28 -- sci-mathematics/mathics/metadata.xml | 24 -- sci-physics/abinit/abinit-7.10.4.ebuild | 389 -------------------- sci-physics/abinit/abinit-7.4.2-r1.ebuild | 352 ------------------- sci-physics/abinit/abinit-7.6.4-r1.ebuild | 390 --------------------- sci-physics/abinit/files/6.12.1-autoconf.patch | 21 -- sci-physics/abinit/files/6.12.1-xmalloc.patch | 48 --- sci-physics/abinit/files/6.12.3-gui-makefiles.tbz | Bin 14600 -> 0 bytes .../files/6.2.2-change-default-directories.patch | 21 -- sci-physics/abinit/files/7.0.4-test_dirs.patch | 12 - .../abinit/files/7.10.4-libabinit_options.patch | 82 ----- sci-physics/abinit/files/7.10.4-syntax.patch | 12 - .../abinit/files/7.4.2-cuda_link_stdc++.patch | 21 -- .../abinit/files/7.4.2-levmar_diag_scaling.patch | 21 -- sci-physics/abinit/files/7.4.2-syntax.patch | 21 -- .../abinit/files/7.6.3-libabinit_options.patch | 80 ----- sci-physics/abinit/files/7.6.4-cuda_header.patch | 11 - .../abinit/files/7.6.4-libxc_versions.patch | 40 --- sci-physics/abinit/metadata.xml | 60 ---- 40 files changed, 2376 deletions(-) diff --git a/sci-astronomy/mosstack/metadata.xml b/sci-astronomy/mosstack/metadata.xml deleted file mode 100644 index 2cc9b1528..000000000 --- a/sci-astronomy/mosstack/metadata.xml +++ /dev/null @@ -1,23 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>mikko.la...@gmail.com</email> - <name>Mikko Laine</name> - </maintainer> - <longdescription> -An open source stacking software for astronomical images taken with a DSLR -camera. Mosstack can calibrate, debayer, register, align and stack photos -taken with modern DSLR's from Canon. It has a command line user interface -inspired by AstroSurf IRIS and a graphical user interface written with PyQt4 -</longdescription> - <use> - <flag name="opencl">Enables OpenCL support and pulls in pyopencl. This makes -some operations much faster but requires specific hardware and drivers.</flag> - <flag name="qt4">Pulls in PyQt4. Program works on command line interface -without it but for GUI the library is required.</flag> - </use> - <upstream> - <remote-id type="bitbucket">mikko_laine/mosstack</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-astronomy/mosstack/mosstack-0.6.1-r1.ebuild b/sci-astronomy/mosstack/mosstack-0.6.1-r1.ebuild deleted file mode 100644 index 3901240b1..000000000 --- a/sci-astronomy/mosstack/mosstack-0.6.1-r1.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python3_4 ) - -inherit distutils-r1 - -DESCRIPTION="Stacking software for astronomical images" -HOMEPAGE="https://sites.google.com/site/mosstack"; -SRC_URI="http://bitbucket.org/mikko_laine/mosstack/downloads/${P}.tar.gz"; - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -IUSE="opencl qt4" - -DEPEND=">=dev-python/numpy-1.8.0[${PYTHON_USEDEP}] - dev-python/cython[${PYTHON_USEDEP}]" - -RDEPEND=">=dev-python/pillow-2.3.0[${PYTHON_USEDEP}] - sci-libs/scikits_image[${PYTHON_USEDEP}] - >media-gfx/imagemagick-6.8.0.0 - sci-astronomy/sextractor - media-gfx/dcraw - media-libs/exiftool - dev-python/astropy[${PYTHON_USEDEP}] - opencl? ( >=dev-python/pyopencl-2013.1[${PYTHON_USEDEP}] ) - qt4? ( dev-python/PyQt4[${PYTHON_USEDEP}] )" - -DOCS=( CHANGES.txt README.txt ) diff --git a/sci-astronomy/mosstack/mosstack-0.6.1.ebuild b/sci-astronomy/mosstack/mosstack-0.6.1.ebuild deleted file mode 100644 index 92c5bc817..000000000 --- a/sci-astronomy/mosstack/mosstack-0.6.1.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python3_4 ) - -inherit distutils-r1 - -DESCRIPTION="Stacking software for astronomical images" -HOMEPAGE="https://sites.google.com/site/mosstack"; -SRC_URI="http://bitbucket.org/mikko_laine/pyastrostack/downloads/${P}.tar.gz"; - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -IUSE="opencl qt4" - -DEPEND=">=dev-python/numpy-1.8.0[${PYTHON_USEDEP}] - dev-python/cython[${PYTHON_USEDEP}]" - -RDEPEND=">=dev-python/pillow-2.3.0[${PYTHON_USEDEP}] - sci-libs/scikits_image[${PYTHON_USEDEP}] - >media-gfx/imagemagick-6.8.0.0 - sci-astronomy/sextractor - media-gfx/dcraw - media-libs/exiftool - dev-python/astropy[${PYTHON_USEDEP}] - opencl? ( >=dev-python/pyopencl-2013.1[${PYTHON_USEDEP}] ) - qt4? ( dev-python/PyQt4[${PYTHON_USEDEP}] )" - -DOCS=( CHANGES.txt README.txt ) diff --git a/sci-biology/Gambit/Gambit-0.4.145.ebuild b/sci-biology/Gambit/Gambit-0.4.145.ebuild deleted file mode 100644 index 13fdad6d4..000000000 --- a/sci-biology/Gambit/Gambit-0.4.145.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit qmake-utils - -DESCRIPTION="Genomic alignments from BAM files" -HOMEPAGE="http://code.google.com/p/gambit-viewer/"; -SRC_URI=" - http://gambit-viewer.googlecode.com/files/Gambit_v0.4.145_src.tar.gz - doc? ( http://gambit-viewer.googlecode.com/files/GambitDocumentation_v0.4.145.pdf ) -" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="doc" - -DEPEND=" - dev-qt/qtcore:4 - dev-qt/qtgui:4" -RDEPEND="${DEPEND} - sci-biology/samtools" - -S="${WORKDIR}"/Gambit - -src_configure() { - $(qt4_get_bindir)/lupdate ${PN}.pro || die - $(qt4_get_bindir)/lrelease ${PN}.pro || die - eqmake4 ${PN}.pro -} - -src_install() { - dobin ${PN} - use doc && dodoc "${DISTDIR}"/GambitDocumentation_v0.4.145.pdf -} diff --git a/sci-biology/Gambit/metadata.xml b/sci-biology/Gambit/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/Gambit/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>mmokr...@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/atsas/atsas-2.8.3.ebuild b/sci-biology/atsas/atsas-2.8.3.ebuild deleted file mode 100644 index c9b4b802d..000000000 --- a/sci-biology/atsas/atsas-2.8.3.ebuild +++ /dev/null @@ -1,75 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit python-r1 - -DESCRIPTION="Biological Small Angle Scattering" -HOMEPAGE="http://www.embl-hamburg.de/biosaxs"; -#SRC_URI="ATSAS-${PV}-1.sl5.x86_64.tar.gz" -#SRC_URI="ATSAS-${PV}-1.el6.x86_64.tar.gz" -SRC_URI="ATSAS-${PV}-1_amd64.tar.gz" - -SLOT="0" -LICENSE="atsas" -KEYWORDS="~amd64 ~amd64-linux" -IUSE="examples" - -RDEPEND=" - dev-libs/libxml2:2 - dev-qt/qtcore:4 - dev-qt/qtgui:4 - media-libs/tiff:0 - sci-libs/cbflib - x11-libs/qwt:5 -" -DEPEND="dev-util/patchelf" - -RESTRICT="fetch strip" - -S="${WORKDIR}"/${P^^}-1 - -QA_PREBUILT="opt/.* usr/.*" - -pkg_nofetch() { - elog "Please visit http://www.embl-hamburg.de/biosaxs/atsas-online/download.php"; - elog "and download the ${A} for Ubuntu 16.04" - elog "and place it in ${DISTDIR}" -} - -src_install() { - local i - for i in bin/*; do - patchelf \ - --set-rpath "$(gcc-config -L):${EPREFIX}/opt/${PN}/:${EPREFIX}/usr/lib/qt4/" \ - ${i} || die - done - exeinto /opt/bin - doexe bin/* - - insinto /opt/${PN} - doins lib/*/atsas/{libqwt*.so*,libsaxsdocument*.so*,libsaxsplot*.so*} - - python_foreach_impl python_domodule lib/*/atsas/python*/dist-packages/* - - rm share/doc/${P}/LICENSE.txt || die - if use examples; then - cp -rf share/doc/${P}/* share/${PN}/ || die - fi - - pushd share/icons/hicolor/ > /dev/null - for i in *; do - doicon -s ${i} -t hicolor ${i}/* - done - popd > /dev/null - - domenu share/applications/* - - rm -rf share/{applications,doc,icons,mime} || die - - insinto /usr - doins -r share -} diff --git a/sci-biology/atsas/metadata.xml b/sci-biology/atsas/metadata.xml deleted file mode 100644 index 8417d1580..000000000 --- a/sci-biology/atsas/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild b/sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild deleted file mode 100644 index 0b761d600..000000000 --- a/sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild +++ /dev/null @@ -1,78 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils flag-o-matic qmake-utils toolchain-funcs - -MY_P="${PN}_${PV}" - -DESCRIPTION="NMR relaxation studies of protein association" -HOMEPAGE="http://sourceforge.net/projects/nmrdyn/"; -SRC_URI="${MY_P}.tar.gz" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+qt4" - -RDEPEND=" - sci-libs/gsl - qt4? ( - dev-qt/qtcore:4 - dev-qt/qtgui:4 - ) -" -DEPEND="${RDEPEND} - virtual/pkgconfig -" - -RESTRICT="mirror fetch" - -S="${WORKDIR}"/${MY_P} - -pkg_nofetch() { - elog "Please contact the authors and get ${A}" -} - -src_prepare() { - epatch "${FILESDIR}"/${P}-redefinition.patch - append-cppflags "$($(tc-getPKG_CONFIG) --cflags gsl)" - if use qt4; then - cd src/NMRdynGUI || die - cat >> NMRdynGUI.pro <<- EOF - INCLUDEPATH += "${S}"/src/algorithm/src - LIBS += $($(tc-getPKG_CONFIG) --libs gsl) - MOC_DIR = moc/ - OBJECTS += ../objects/*.o - EOF - fi -} - -src_configure() { - if use qt4; then - cd src/NMRdynGUI || die - eqmake4 NMRdynGUI.pro - fi -} - -src_compile() { - emake \ - -C src/algorithm \ - CXX="$(tc-getCXX)" \ - CPPFLAGS="${CPPFLAGS}" \ - CXXFLAGS="${CXXFLAGS}" \ - LDFLAGS="${LDFLAGS}" \ - LIBS="$($(tc-getPKG_CONFIG) --libs gsl)" - - if use qt4; then - cd src/NMRdynGUI || die - default - fi -} - -src_install() { - dobin ${PN} r1r2 - use qt4 && dobin src/NMRdynGUI/${PN}GUI - dodoc HISTORY README_LINUX.txt NMRdynManual.doc README_gridsearch.txt -} diff --git a/sci-chemistry/NMRdyn/files/NMRdyn-3.2.5-redefinition.patch b/sci-chemistry/NMRdyn/files/NMRdyn-3.2.5-redefinition.patch deleted file mode 100644 index f943dd836..000000000 --- a/sci-chemistry/NMRdyn/files/NMRdyn-3.2.5-redefinition.patch +++ /dev/null @@ -1,19 +0,0 @@ - src/NMRdynGUI/src/BatchWizard.cpp | 4 ++-- - 1 file changed, 2 insertions(+), 2 deletions(-) - -diff --git a/src/NMRdynGUI/src/BatchWizard.cpp b/src/NMRdynGUI/src/BatchWizard.cpp -index 653d8e6..e4a8c73 100755 ---- a/src/NMRdynGUI/src/BatchWizard.cpp -+++ b/src/NMRdynGUI/src/BatchWizard.cpp -@@ -159,9 +159,9 @@ bool - BatchInputPage::isComplete () - { - int n = workBook->count (); -- for (int i = 0; i < n; i++) -+ for (int k = 0; k < n; k++) - { -- WorkSheet *worksheet = workBook->getWorkSheet (i); -+ WorkSheet *worksheet = workBook->getWorkSheet (k); - int nRows = worksheet->rowCount(); - int nCols = worksheet->columnCount(); - int i, j; diff --git a/sci-chemistry/NMRdyn/metadata.xml b/sci-chemistry/NMRdyn/metadata.xml deleted file mode 100644 index 5670afe1a..000000000 --- a/sci-chemistry/NMRdyn/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>j...@gentoo.org</email> - <name>Justin Lecher</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">nmrdyn</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/ball/ball-9999.ebuild b/sci-chemistry/ball/ball-9999.ebuild deleted file mode 100644 index 02f96c76f..000000000 --- a/sci-chemistry/ball/ball-9999.ebuild +++ /dev/null @@ -1,75 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils git-r3 python-single-r1 - -DESCRIPTION="Biochemical Algorithms Library" -HOMEPAGE="http://www.ball-project.org/"; -SRC_URI="" -EGIT_REPO_URI="http://bitbucket.org/ball/ball.git"; - -SLOT="0" -LICENSE="LGPL-2 GPL-3" -KEYWORDS="" -IUSE="cuda mpi +python sql test +threads +webkit" - -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" - -RDEPEND=" - dev-cpp/eigen:3 - dev-libs/boost - dev-qt/qtcore:4 - dev-qt/qtgui:4 - dev-qt/qtopengl:4 - dev-qt/qttest:4 - dev-qt/qtwebkit:4 - media-libs/glew:0= - sci-libs/fftw:3.0[threads?] - sci-libs/gsl - sci-libs/libsvm - sci-mathematics/lpsolve - virtual/opengl - x11-libs/libX11 - cuda? ( dev-util/nvidia-cuda-toolkit ) - mpi? ( virtual/mpi ) - python? ( ${PYTHON_DEPS} ) - sql? ( dev-qt/qtsql:4 ) - webkit? ( dev-qt/qtwebkit:4 )" -DEPEND="${RDEPEND} - dev-python/sip - sys-devel/bison - virtual/yacc" - -PATCHES=( - "${FILESDIR}"/${P}-multilib.patch - ) - -pkg_setup() { - use python && python-single-r1_pkg_setup -} - -src_configure() { - local mycmakeargs=( - $(cmake-utils_use_use threads FFTW_THREADS) - $(cmake-utils_use cuda MT_ENABLE_CUDA) - $(cmake-utils_use mpi MT_ENABLE_MPI) - $(cmake-utils_use sql BALL_HAS_QTSQL) - $(cmake-utils_use_use webkit USE_QTWEBKIT) - $(cmake-utils_use python BALL_PYTHON_SUPPORT) - ) - cmake-utils_src_configure - local i - for i in "${S}"/data/*; do - ln -sf "${i}" "${BUILD_DIR}"/source/TEST/ || die - ln -sf "${i}" "${S}"/source/TEST/ || die - done -} - -src_compile() { - cmake-utils_src_compile - use test && cmake-utils_src_make build_tests -} diff --git a/sci-chemistry/ball/files/ball-9999-multilib.patch b/sci-chemistry/ball/files/ball-9999-multilib.patch deleted file mode 100644 index 317c4029c..000000000 --- a/sci-chemistry/ball/files/ball-9999-multilib.patch +++ /dev/null @@ -1,39 +0,0 @@ -From 5b8f4e58b4e54bcdfa6f287e01f91d9dfd4e5a14 Mon Sep 17 00:00:00 2001 -From: Justin Lecher <j...@gentoo.org> -Date: Sun, 25 Mar 2012 14:12:21 +0200 -Subject: [PATCH] Correct path for multilib installation. - -Libraries should go into lib64 not lib on native 64bit. Therefore we can use the LIBDIR detected by cmake. ---- - CMakeLists.txt | 8 ++++---- - 1 files changed, 4 insertions(+), 4 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 940ebf4..7eb3db4 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -426,8 +426,8 @@ SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/bin") - ## These variables are used in all install-targets - IF (NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin") - SET(BALL_RUNTIME_INSTALL_DIRECTORY "bin") -- SET(BALL_LIBRARY_INSTALL_DIRECTORY "lib") -- SET(BALL_ARCHIVE_INSTALL_DIRECTORY "lib") -+ SET(BALL_LIBRARY_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) -+ SET(BALL_ARCHIVE_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) - SET(BALL_HEADER_INSTALL_DIRECTORY ".") - SET(BALL_DATA_INSTALL_DIRECTORY "share/BALL") - SET(BALL_DOCUMENTATION_INSTALL_DIRECTORY "share/BALL/doc") -@@ -435,8 +435,8 @@ IF (NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin") - SET(BALL_PYTHON_INSTALL_DIRECTORY "bin") - SET(BALL_PLUGIN_INSTALL_DIRECTORY "bin") - ELSE() -- SET(BALL_PYTHON_INSTALL_DIRECTORY "lib") -- SET(BALL_PLUGIN_INSTALL_DIRECTORY "lib") -+ SET(BALL_PYTHON_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) -+ SET(BALL_PLUGIN_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) - ENDIF() - ELSE() - SET(BALL_BUNDLE_INSTALL_DIRECTORY "Applications") --- -1.7.8.5 - diff --git a/sci-chemistry/ball/metadata.xml b/sci-chemistry/ball/metadata.xml deleted file mode 100644 index c2980f0b6..000000000 --- a/sci-chemistry/ball/metadata.xml +++ /dev/null @@ -1,35 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>j...@gentoo.org</email> - </maintainer> - <maintainer type="project"> - <email>sci-chemis...@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <longdescription> -Rapid Software Prototyping can significantly reduce development times in the -field of Computational Molecular Biology and Molecular Modeling. -BALL (Biochemical Algorithms Library) is an application framework in C++ that -has been specifically designed for this purpose. It provides an extensive set -of data structures as well as classes for Molecular Mechanics, advanced -solvation methods, comparison and analysis of protein structures, file -import/export, and visualization . - -BALL has been carefully designed to be robust, easy to use, and open to -extensions. Especially its extensibility which results from an object-oriented -and generic programming approach distinguishes it from other software packages. -BALL is well suited to serve as a public repository for reliable data -structures and algorithms. - -Based on BALL we have developed a stand-alone tool for molecular visualization, -BALLView . BALLView makes the broad functionality available through an -integrated user-friendly GUI. -</longdescription> - <use> - <flag name="sql">Include SQL database support</flag> - <flag name="cuda">Include cuda support</flag> - <flag name="webkit">Uses <pkg>dev-qt/qt-webkit</pkg> for drawing</flag> - </use> -</pkgmetadata> diff --git a/sci-chemistry/cnsface/cnsface-0.0.12.ebuild b/sci-chemistry/cnsface/cnsface-0.0.12.ebuild deleted file mode 100644 index 56fb26bab..000000000 --- a/sci-chemistry/cnsface/cnsface-0.0.12.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit distutils-r1 - -DESCRIPTION="GUI for the Crystallography and NMR System" -HOMEPAGE="http://cnsface.sourceforge.net"; -SRC_URI="mirror://sourceforge/project/cnsface/cnsface/Altoona/${P}-altoona.tar.gz" - -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -LICENSE="GPL-2" -IUSE="" - -RDEPEND=" - dev-python/wxpython:2.8[${PYTHON_USEDEP}] - sci-chemistry/cns" -DEPEND="${RDEPEND}" - -S="${WORKDIR}"/${P}-altoona - -PATCHES=( "${FILESDIR}"/${PV}-binary.patch ) diff --git a/sci-chemistry/cnsface/files/0.0.12-binary.patch b/sci-chemistry/cnsface/files/0.0.12-binary.patch deleted file mode 100644 index 4d403a0e1..000000000 --- a/sci-chemistry/cnsface/files/0.0.12-binary.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/setup.py b/setup.py -index 3933d32..8cf0653 100755 ---- a/setup.py -+++ b/setup.py -@@ -54,7 +54,7 @@ setup(name='cnsface', - package_dir={'cnsface':'src'}, - packages=['cnsface'], - requires=['wx'], -- scripts=['scripts/cnsi', 'scripts/convert2mtz'], -+ scripts=['scripts/cnsi'], - license='GNU General Public License (GPL)', - platforms=['OS Independent'], - data_files=data_files diff --git a/sci-chemistry/cnsface/metadata.xml b/sci-chemistry/cnsface/metadata.xml deleted file mode 100644 index 4e146a4b1..000000000 --- a/sci-chemistry/cnsface/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemis...@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">cnsface</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/phenix-bin/metadata.xml b/sci-chemistry/phenix-bin/metadata.xml deleted file mode 100644 index da36ecbfc..000000000 --- a/sci-chemistry/phenix-bin/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemis...@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/phenix-bin/phenix-bin-1.10.2155.ebuild b/sci-chemistry/phenix-bin/phenix-bin-1.10.2155.ebuild deleted file mode 100644 index 9ca302dd8..000000000 --- a/sci-chemistry/phenix-bin/phenix-bin-1.10.2155.ebuild +++ /dev/null @@ -1,117 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -WX_GTK_VER=2.8 - -inherit multilib python-single-r1 versionator wxwidgets - -MY_PV="$(replace_version_separator 2 -)" -MY_P="phenix-installer-${MY_PV}" - -DESCRIPTION="Python-based Hierarchical ENvironment for Integrated Xtallography" -HOMEPAGE="http://phenix-online.org/"; -SRC_URI="${MY_P}-intel-linux-2.6-x86_64-centos6.tar.gz" - -SLOT="0" -LICENSE="phenix" -KEYWORDS="~amd64 ~amd64-linux" -IUSE="" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - app-arch/bzip2 - dev-db/sqlite:3 - dev-libs/atk - dev-libs/boost - dev-libs/expat - dev-libs/glib:2 - dev-libs/openssl - media-gfx/nvidia-cg-toolkit - media-libs/fontconfig - media-libs/freetype - media-libs/libpng:1.2 - sys-libs/db:4.7 - sys-libs/gdbm - sys-libs/ncurses:5/5[tinfo] - sys-libs/readline - virtual/glu - x11-libs/cairo - x11-libs/gdk-pixbuf:2 - x11-libs/gtk+:2 - x11-libs/pango - x11-libs/pixman - x11-libs/libSM - x11-libs/libX11 - x11-libs/libXcursor - x11-libs/libXext - x11-libs/libXfixes - x11-libs/libXft - x11-libs/libXinerama - x11-libs/libXi - x11-libs/libXmu - x11-libs/libXrandr - x11-libs/libXrender - x11-libs/libXxf86vm - x11-libs/wxGTK:${WX_GTK_VER}[X] - sys-libs/zlib - virtual/jpeg:62" -DEPEND="${PYTHON_DEPS}" - -RESTRICT="fetch" - -QA_PREBUILT="opt/phenix-${MY_PV}/.*" - -S="${WORKDIR}"/${MY_P}-intel-linux-2.6-x86_64-centos6 - -pkg_nofetch() { - elog "Please visit" - elog "http://www.phenix-online.org/phenix_request/index.cgi"; - elog "and request a download password. With that done," - elog "visit http://www.phenix-online.org/download/phenix/release"; - elog "and download version \"Kernel 2.6 (64-bit; Fedora 12)\" (${A})" - elog "into ${DISTDIR}" -} - -src_prepare() { - cat > "${S}/bin/machine_type" <<-EOF - #!${EPREFIX}/bin/sh - echo intel-linux-2.6-x86_64 - exit 0 - EOF -} - -src_compile() { - LD_LIBRARY_PATH="${EPREFIX}/usr/$(get_libdir)" ./install --prefix="${S}/foo" || die -} - -src_install() { - find "${S}/foo" -type f -name "*.pyc" -delete || die - sed \ - -e "s:${S}/foo:${EPREFIX}/opt:g" \ - -i \ - foo/phenix-${MY_PV}/build/*_env \ - foo/phenix-${MY_PV}/build/*sh \ - foo/phenix-${MY_PV}/build/bin/* \ - foo/phenix-${MY_PV}/base/etc/{gtk*,pango}/* \ - foo/phenix-${MY_PV}/phenix_env* \ - || die - dodir /opt - mv "${S}/foo/phenix-${MY_PV}" "${ED}/opt/" || die - - cat >> phenix <<- EOF - #!${EPREFIX}/bin/bash - - source "${EPREFIX}/opt/phenix-${MY_PV}/phenix_env.sh" - export LD_LIBRARY_PATH="${EPREFIX}/usr/$(get_libdir)" - exec phenix - EOF - dobin phenix - - python_fix_shebang "${ED}"/opt - python_optimize "${ED}"/opt -} diff --git a/sci-mathematics/kayali/files/kayali-0.2-calcwindow.patch b/sci-mathematics/kayali/files/kayali-0.2-calcwindow.patch deleted file mode 100644 index f1c694732..000000000 --- a/sci-mathematics/kayali/files/kayali-0.2-calcwindow.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- kayali/calcwindow.py 2006-06-02 17:42:16.000000000 +0200 -+++ kayali/calcwindow.py 2006-06-02 17:42:27.000000000 +0200 -@@ -661,7 +661,7 @@ - - self.frmInputEdit = QFrame(self.centralWidget(),"frmInputEdit") - self.frmInputEdit.setGeometry(QRect(2,3,661,30)) -- self.frmInputEdit.setSizePolicy(QSizePolicy(7,5,0,0,self.frmInputEdit.sizePolicy().hasHeightForWidth())) -+ #self.frmInputEdit.setSizePolicy(QSizePolicy(7,5,0,0,self.frmInputEdit.sizePolicy().hasHeightForWidth())) - self.frmInputEdit.setMinimumSize(QSize(0,30)) - self.frmInputEdit.setFrameShape(QFrame.NoFrame) - self.frmInputEdit.setFrameShadow(QFrame.Plain) diff --git a/sci-mathematics/kayali/kayali-0.3.2.ebuild b/sci-mathematics/kayali/kayali-0.3.2.ebuild deleted file mode 100644 index 6e71ffa05..000000000 --- a/sci-mathematics/kayali/kayali-0.3.2.ebuild +++ /dev/null @@ -1,62 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils python-single-r1 - -DESCRIPTION="Qt front-end for Computer Algebra System mainly maxima" -HOMEPAGE="http://kayali.sourceforge.net/"; -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="doc" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND="${PYTHON_DEPS}" -RDEPEND="${DEPEND} - sci-mathematics/maxima - >=dev-python/PyQt4-4.1[${PYTHON_USEDEP}] - media-gfx/imagemagick - >=dev-python/reportlab-2.0[${PYTHON_USEDEP}] - >=sci-visualization/gnuplot-4.0" - -# is a GUI, testing done simply by launching application -# and follow one of the demo -RESTRICT="test" - -S=${WORKDIR}/${PN} - -pkg_setup() { - python-single-r1_pkg_setup -} - -src_compile() { - einfo "Nothing to compile" -} - -src_install() { - local INSTALL_DIR="${EPREFIX}"/usr/share/${PN} - - cat >> "${T}"/kayali <<- EOF - #!${EPREFIX}/bin/sh - cd ${INSTALL_DIR} - exec ${EPYTHON} -OOt kayali.py $@ - EOF - - dobin "${T}"/kayali - insinto ${INSTALL_DIR} - doins *.py *.txt *.in* maximab.bat maxima.g - doins -r engines icons pdf qt4gui *uic - - python_optimize ${INSTALL_DIR} - - make_desktop_entry kayali kayali kayali.svg - use doc && dohtml html/* - dodoc README -} diff --git a/sci-mathematics/kayali/metadata.xml b/sci-mathematics/kayali/metadata.xml deleted file mode 100644 index df0c0137a..000000000 --- a/sci-mathematics/kayali/metadata.xml +++ /dev/null @@ -1,17 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>sci-mathemat...@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <longdescription lang="en"> -kayali is a Qt based Computer Algebra System (CAS) that can also be -used as an advanced replacement for KDE KCalc. It is essentially a -front end GUI forMaxima (and is easily extended to other CAS -back-ends) and Gnuplot. -</longdescription> - <upstream> - <remote-id type="sourceforge">kayali</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-mathematics/mathics/mathics-1.0.ebuild b/sci-mathematics/mathics/mathics-1.0.ebuild deleted file mode 100644 index 622b488f1..000000000 --- a/sci-mathematics/mathics/mathics-1.0.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python{2_7,3_4,3_5} ) - -inherit distutils-r1 - -DESCRIPTION="A free lightweight CAS using Wolfram Language" -HOMEPAGE="https://mathics.github.io/"; -SRC_URI="https://github.com/mathics/Mathics/archive/v${PV}.tar.gz -> ${P}.tar.gz" -S="${WORKDIR}/Mathics-${PV}" - -LICENSE="GPL-3" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - ~dev-python/sympy-1.0[${PYTHON_USEDEP}] - =dev-python/django-1.8*[${PYTHON_USEDEP}] - >=dev-python/mpmath-0.19[${PYTHON_USEDEP}] - dev-python/python-dateutil[${PYTHON_USEDEP}] - dev-python/colorama[${PYTHON_USEDEP}] - >=dev-python/six-1.10[${PYTHON_USEDEP}] -" -DEPEND="$RDEPEND" diff --git a/sci-mathematics/mathics/metadata.xml b/sci-mathematics/mathics/metadata.xml deleted file mode 100644 index b7bcd8c15..000000000 --- a/sci-mathematics/mathics/metadata.xml +++ /dev/null @@ -1,24 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>s...@gentoo.org</email> - </maintainer> - <maintainer type="project"> - <email>sci-phys...@gentoo.org</email> - <name>Gentoo Physics Project</name> - </maintainer> - <longdescription lang="en"> -Mathics—to be pronounced like “Mathematics” without the “emat”—is a general-purpose computer algebra system (CAS). -It is meant to be a free, light-weight alternative to Mathematica®. It is free both as in “free beer” and as in “freedom”. -There are various online mirrors running Mathics but it is also possible to run Mathics locally. A list of mirrors -can be found at the Mathics homepage, http://mathics.github.io. - -The programming language of Mathics is meant to resemble Wolfram's famous Mathematica® as much as possible. -However, Mathics is in no way affiliated or supported by Wolfram. Mathics will probably never have the power to -compete with Mathematica® in industrial applications; yet, it might be an interesting alternative for educational purposes. -</longdescription> - <upstream> - <remote-id type="github">mathics/Mathics</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-physics/abinit/abinit-7.10.4.ebuild b/sci-physics/abinit/abinit-7.10.4.ebuild deleted file mode 100644 index 00fefcbb9..000000000 --- a/sci-physics/abinit/abinit-7.10.4.ebuild +++ /dev/null @@ -1,389 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools-utils eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs - -DESCRIPTION="Total energy, charge density and electronic structure using DFT" -HOMEPAGE="http://www.abinit.org/"; -SRC_URI="http://ftp.abinit.org/${P}.tar.gz"; - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="atompaw bigdft cuda cuda-double -debug +etsf_io +fftw fftw-mpi +fftw-threads +fox gsl +hdf5 levmar -libabinit libxc -lotf mpi +netcdf openmp python scalapack scripts -test +threads wannier" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" -#" scalapack? ( !bigdft )" - -RDEPEND="virtual/blas - virtual/lapack - ${PYTHON_DEPS} - dev-python/numpy - atompaw? ( >=sci-physics/atompaw-4.0.0.10[libxc?] ) - bigdft? ( >=sci-physics/bigdft-1.7.0.93[scalapack?] - <sci-physics/bigdft-1.7.5 ) - cuda? ( dev-util/nvidia-cuda-sdk ) - etsf_io? ( >=sci-libs/etsf_io-1.0.4 ) - fftw? ( - sci-libs/fftw:3.0 - fftw-threads? ( - openmp? ( sci-libs/fftw:3.0[openmp] ) - !openmp? ( sci-libs/fftw:3.0[threads] ) - ) - fftw-mpi? ( - sci-libs/fftw:3.0[mpi] - openmp? ( sci-libs/fftw:3.0[openmp] ) - !openmp? ( sci-libs/fftw:3.0[threads] ) - ) - ) - fox? ( >=sci-libs/fox-4.1.2-r2[sax] ) - gsl? ( sci-libs/gsl ) - hdf5? ( sci-libs/hdf5[fortran] ) - levmar? ( sci-libs/levmar ) - libxc? ( >=sci-libs/libxc-2.0.3[fortran] - <sci-libs/libxc-2.2 ) - netcdf? ( - sci-libs/netcdf[hdf5?] - || ( - sci-libs/netcdf[fortran] - sci-libs/netcdf-fortran - ) - ) - mpi? ( virtual/mpi ) - scalapack? ( virtual/scalapack ) - scripts? ( dev-python/PyQt4 ) - wannier? ( >=sci-libs/wannier90-1.2-r1 )" -DEPEND="${RDEPEND} - virtual/pkgconfig - dev-perl/Text-Markdown" - -S=${WORKDIR}/${P%[a-z]} - -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 - - # This should be correct: - # It is gcc-centric because toolchain-funcs.eclass is gcc-centric. - # Should a bug be filed against toolchain-funcs.eclass? - # if use openmp; then - # tc-has-openmp || \ - # die "Please select an openmp capable compiler like gcc[openmp]" - # fi - # - # This is completely wrong: - # If other compilers than Gnu Compiler Collection can be used by portage, - # their support of OpenMP should be properly tested. This code limits the test - # to gcc, and blindly supposes that other compilers do support OpenMP. - # if use openmp && [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp; then - # die "Please select an openmp capable compiler like gcc[openmp]" - # fi - # - # Luckily Abinit is a fortran package. - # fortran-2.eclass has its own test for OpenMP support, - # more general than toolchain-funcs.eclass - # The test itself proceeds inside fortran-2_pkg_setup - if use openmp; then FORTRAN_NEED_OPENMP=1; fi - - fortran-2_pkg_setup - - if use openmp; then - # based on _fortran-has-openmp() of fortran-2.eclass - local code=ebuild-openmp-flags - local ret - local openmp - - pushd "${T}" - cat <<- EOF > "${code}.c" - # include <omp.h> - main () { - int nthreads; - nthreads=omp_get_num_threads(); - } - EOF - - for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do - ${CC} ${openmp} "${code}.c" -o "${code}.o" &>> "${T}"/_c_compile_test.log - ret=$? - (( ${ret} )) || break - done - - rm -f "${code}.*" - popd - - if (( ${ret} )); then - die "Please switch to an openmp compatible C compiler" - else - export CC="${CC} ${openmp}" - export CXX="${CXX} ${openmp}" - fi - - pushd "${T}" - cat <<- EOF > "${code}.f" - 1 call omp_get_num_threads - 2 end - EOF - - for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do - ${FC} ${openmp} "${code}.f" -o "${code}.o" &>> "${T}"/_f_compile_test.log - ret=$? - (( ${ret} )) || break - done - - rm -f "${code}.*" - popd - - if (( ${ret} )); then - die "Please switch to an openmp compatible fortran compiler." - else - export FC="${FC} ${openmp}" - export F77="${F77} ${openmp}" - fi - fi - - # Sort out some USE options - if use fftw-threads && ! use fftw; then - ewarn "fftw-threads set but fftw not used, ignored." - fi - if use fftw-mpi; then - if ! use fftw; then - ewarn "fftw-mpi set but fftw not used, ignored." - elif ! use mpi; then - ewarn "fftw-mpi set but mpi not used, ignored." - elif ! use fftw-threads; then - ewarn "fftw-mpi set but fftw-threads not. Will use a threaded fftw nevertheless, required with MPI." - fi - fi - if use cuda-double && ! use cuda; then - ewarn "cuda-double set but cuda not used, ignored" - fi - - python-single-r1_pkg_setup - -} - -src_prepare() { - epatch \ - "${FILESDIR}"/6.2.2-change-default-directories.patch \ - "${FILESDIR}"/6.12.1-autoconf.patch \ - "${FILESDIR}"/6.12.1-xmalloc.patch \ - "${FILESDIR}"/7.10.4-libabinit_options.patch \ - "${FILESDIR}"/7.4.2-levmar_diag_scaling.patch \ - "${FILESDIR}"/7.4.2-cuda_link_stdc++.patch \ - "${FILESDIR}"/7.6.4-cuda_header.patch \ - "${FILESDIR}"/7.10.4-syntax.patch - eautoreconf - sed -e"s/\(grep '\^-\)\(\[LloW\]\)'/\1\\\(\2\\\|pthread\\\)'/g" -i configure || ewarn "sed on configure failed" - python_fix_shebang "${S}" -} - -src_configure() { - local modules="$(FoX-config --sax --fcflags)" - local FoX_libs="$(FoX-config --sax --libs)" - - local trio_flavor="" - use etsf_io && trio_flavor="${trio_flavor}+etsf_io" - use fox && trio_flavor="${trio_flavor}+fox" - use netcdf && trio_flavor="${trio_flavor}+netcdf" - test "no${trio_flavor}" = "no" && trio_flavor="none" - - local netcdff_libs="-lnetcdff" - use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran" - -# local linalg_flavor="atlas" - local linalg_flavor="custom" - local mylapack="lapack" - use scalapack && mylapack="scalapack" && linalg_flavor="${linalg_flavor}+scalapack" - - local dft_flavor="" - use atompaw && dft_flavor="${dft_flavor}+atompaw" - use bigdft && dft_flavor="${dft_flavor}+bigdft" - use libxc && dft_flavor="${dft_flavor}+libxc" - use wannier && dft_flavor="${dft_flavor}+wannier90" - test "no${dft_flavor}" = "no" && dft_flavor="none" - - local fft_flavor="fftw3" - local fft_libs="" - # The fftw threads support is protected by black magick. - # Anybody removes it, dies. - # New USE flag "fftw-threads" was added to control usage - # of the threaded fftw variant. Since fftw-3.3 has expanded - # the paralel options by MPI and OpenMP support, analogical - # USE flags should be added to select them in future; - # unusable with previous FFTW versions, they are postponed - # for now. - if use mpi && use fftw-mpi; then - fft_flavor="fftw3-mpi" - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_mpi)" - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_mpi)" - if use openmp; then - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_omp)" - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_omp)" - else - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_threads)" - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_threads)" - fi - elif use fftw-threads; then - fft_flavor="fftw3-threads" - if use openmp; then - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_omp)" - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_omp)" - else - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_threads)" - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_threads)" - fi - else - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3)" - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f)" - 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 debug debug enhanced) - $(use_enable mpi) - $(use_enable mpi mpi-io) - $(use_enable openmp) - $(use_enable lotf) - $(use_enable cuda gpu) - "$(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=$($(tc-getPKG_CONFIG) --cflags gsl)")" - "$(use gsl && echo "--with-math-libs=$($(tc-getPKG_CONFIG) --libs gsl)")" - "$(use levmar && echo "--with-algo-flavor=levmar")" - "$(use levmar && echo "--with-algo-libs=-llevmar")" - --with-linalg-flavor="${linalg_flavor}" - --with-linalg-libs="$($(tc-getPKG_CONFIG) --libs "${mylapack}")" - --with-trio-flavor="${trio_flavor}" - "$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")" - "$(use netcdf && echo "--with-netcdf-libs=$($(tc-getPKG_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=-letsf_io -letsf_io_utils -letsf_io_low_level")" - --with-dft-flavor="${dft_flavor}" - "$(use atompaw && echo "--with-atompaw-incs=${modules}")" - "$(use atompaw && echo "--with-atompaw-libs=-latompaw")" - "$(use bigdft && echo "--with-bigdft-incs=${modules}")" - "$(use bigdft && echo "--with-bigdft-libs=$($(tc-getPKG_CONFIG) --libs bigdft)")" - "$(use libxc && echo "--with-libxc-incs=${modules}")" - "$(use libxc && echo "--with-libxc-libs=$($(tc-getPKG_CONFIG) --libs libxc)")" - "$(use wannier && echo "--with-wannier90-bins=/usr/bin")" - "$(use wannier && echo "--with-wannier90-incs=${modules}")" - "$(use wannier && echo "--with-wannier90-libs=-lwannier $($(tc-getPKG_CONFIG) --libs blas 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}} ${modules} -I/usr/include" - ) - - MARKDOWN=Markdown.pl autotools-utils_src_configure -} - -src_compile() { - autotools-utils_src_compile - - # Apparently libabinit.a is not built by default - # Used by BigDFT. Should probably be built separately, - # as a package of its own: BigDFT used by Abinit. - # Does libabinit.a depend on BigDFT, if used? - # Can Abinit use external libabinit.a? - use libabinit && autotools-utils_src_compile libabinit.a - - sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc || ewarn "sed on config.pc failed" -} - -src_test() { - einfo "The complete tests take quite a while, easily several hours or even days." - # autotools-utils_src_test expanded and modified - _check_build_dir - pushd "${BUILD_DIR}" > /dev/null || die - - einfo "Running the internal tests." - emake tests_in || ewarn 'The internal tests failed.' - - einfo "Running the thorough tests. Be patient, please." - "${S}"/tests/runtests.py || ewarn "The package has not passed the thorough tests." - - popd > /dev/null || die -} - -src_install() { - #autotools-utils_src_install() expanded - _check_build_dir - pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null - default - - use libabinit && dolib libabinit.a - - if use test; then - for dc in results.tar.gz results.txt suite_report.html; do - test -e Test_suite/"${dc}" && dodoc Test_suite/"${dc}" || ewarn "Copying tests results ${dc} failed" - done - fi - - popd > /dev/null - - # XXX: support installing them from builddir as well!!! - if [[ ${DOCS} ]]; then - dodoc "${DOCS[@]}" - 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}" || ewarn "(default) dodoc ${f} failed" - fi - done - fi - if [[ ${HTML_DOCS} ]]; then - dohtml -r "${HTML_DOCS[@]}" || ewarn "dohtml failed" - fi - - if use scripts; then - insinto /usr/share/"${P}" - doins -r scripts - fi - - # Remove libtool files and unnecessary static libs - prune_libtool_files -} diff --git a/sci-physics/abinit/abinit-7.4.2-r1.ebuild b/sci-physics/abinit/abinit-7.4.2-r1.ebuild deleted file mode 100644 index 456fbd271..000000000 --- a/sci-physics/abinit/abinit-7.4.2-r1.ebuild +++ /dev/null @@ -1,352 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools-utils eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs - -DESCRIPTION="Total energy, charge density and electronic structure using DFT" -HOMEPAGE="http://www.abinit.org/"; -SRC_URI="http://ftp.abinit.org/${P}.tar.gz"; - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="atompaw bigdft cuda cuda-double -debug +etsf_io +fftw +fftw-threads +fox gsl +hdf5 levmar -libabinit libxc -lotf mpi +netcdf openmp python scripts -test +threads -vdwxc wannier" - -REQUIRED_USE="scripts? ( ${PYTHON_REQUIRED_USE} ) - test? ( ${PYTHON_REQUIRED_USE} )" - -RDEPEND="virtual/blas - virtual/lapack - atompaw? ( >=sci-physics/atompaw-3.0.1.9-r1[libxc?] ) - bigdft? ( ~sci-libs/bigdft-abi-1.0.4 ) - cuda? ( dev-util/nvidia-cuda-sdk ) - etsf_io? ( >=sci-libs/etsf_io-1.0.3-r2 ) - fftw? ( - sci-libs/fftw:3.0 - fftw-threads? ( sci-libs/fftw:3.0[threads] ) - ) - fox? ( >=sci-libs/fox-4.1.2-r2[sax] ) - gsl? ( sci-libs/gsl ) - hdf5? ( sci-libs/hdf5[fortran] ) - levmar? ( sci-libs/levmar ) - libxc? ( >=sci-libs/libxc-2.0[fortran] - <sci-libs/libxc-2.2 ) - netcdf? ( - sci-libs/netcdf[hdf5?] - || ( - sci-libs/netcdf[fortran] - sci-libs/netcdf-fortran - ) - ) - mpi? ( virtual/mpi ) - python? ( ${PYTHON_DEPS} - dev-python/numpy ) - scripts? ( ${PYTHON_DEPS} - dev-python/numpy - dev-python/PyQt4 ) - wannier? ( >=sci-libs/wannier90-1.2-r1 )" -DEPEND="${RDEPEND} - virtual/pkgconfig - dev-perl/Text-Markdown - test? ( ${PYTHON_DEPS} )" - -S=${WORKDIR}/${P%[a-z]} - -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 - - # This should be correct: - # It is gcc-centric because toolchain-funcs.eclass is gcc-centric. - # Should a bug be filed against toolchain-funcs.eclass? - # if use openmp; then - # tc-has-openmp || \ - # die "Please select an openmp capable compiler like gcc[openmp]" - # fi - # - # This is completely wrong: - # If other compilers than Gnu Compiler Collection can be used by portage, - # their support of OpenMP should be properly tested. This code limits the test - # to gcc, and blindly supposes that other compilers do support OpenMP. - # if use openmp && [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp; then - # die "Please select an openmp capable compiler like gcc[openmp]" - # fi - # - # Luckily Abinit is a fortran package. - # fortran-2.eclass has its own test for OpenMP support, - # more general than toolchain-funcs.eclass - # The test itself proceeds inside fortran-2_pkg_setup - if use openmp; then FORTRAN_NEED_OPENMP=1; fi - - fortran-2_pkg_setup - - if use openmp; then - # based on _fortran-has-openmp() of fortran-2.eclass - local code=ebuild-openmp-flags - local ret - local openmp - - pushd "${T}" - cat <<- EOF > "${code}.c" - # include <omp.h> - main () { - int nthreads; - nthreads=omp_get_num_threads(); - } - EOF - - for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do - ${CC} ${openmp} "${code}.c" -o "${code}.o" &>> "${T}"/_c_compile_test.log - ret=$? - (( ${ret} )) || break - done - - rm -f "${code}.*" - popd - - if (( ${ret} )); then - die "Please switch to an openmp compatible C compiler" - else - export CC="${CC} ${openmp}" - fi - - pushd "${T}" - cat <<- EOF > "${code}.f" - 1 call omp_get_num_threads - 2 end - EOF - - for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do - ${FC} ${openmp} "${code}.f" -o "${code}.o" &>> "${T}"/_f_compile_test.log - ret=$? - (( ${ret} )) || break - done - - rm -f "${code}.*" - popd - - if (( ${ret} )); then - die "Please switch to an openmp compatible fortran compiler" - else - export FC="${FC} ${openmp}" - fi - fi - - # Sort out some USE options - if use fftw-threads && ! use fftw; then - ewarn "fftw-threads set but fftw not used, ignored" - fi - if use cuda-double && ! use cuda; then - ewarn "cuda-double set but cuda not used, ignored" - fi - - if use scripts || use test; then - python-single-r1_pkg_setup - fi - -} - -src_prepare() { - epatch \ - "${FILESDIR}"/6.2.2-change-default-directories.patch \ - "${FILESDIR}"/6.12.1-autoconf.patch \ - "${FILESDIR}"/6.12.1-xmalloc.patch \ - "${FILESDIR}"/7.4.2-levmar_diag_scaling.patch \ - "${FILESDIR}"/7.4.2-syntax.patch \ - "${FILESDIR}"/7.4.2-cuda_link_stdc++.patch \ - "${FILESDIR}"/7.6.4-cuda_header.patch \ - "${FILESDIR}"/7.6.4-libxc_versions.patch - eautoreconf - sed -e"s/\(grep '\^-\)\(\[LloW\]\)'/\1\\\(\2\\\|pthread\\\)'/g" -i configure || die - use test && python_fix_shebang "${S}"/tests -} - -src_configure() { - local modules="$(FoX-config --sax --fcflags)" - local FoX_libs="$(FoX-config --sax --libs)" - - local trio_flavor="" - use etsf_io && trio_flavor="${trio_flavor}+etsf_io" - use fox && trio_flavor="${trio_flavor}+fox" - use netcdf && trio_flavor="${trio_flavor}+netcdf" - test "no${trio_flavor}" = "no" && trio_flavor="none" - - local netcdff_libs="-lnetcdff" - use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran" - - local dft_flavor="" - use atompaw && dft_flavor="${dft_flavor}+atompaw" - use bigdft && dft_flavor="${dft_flavor}+bigdft" - use libxc && dft_flavor="${dft_flavor}+libxc" - use wannier && dft_flavor="${dft_flavor}+wannier90" - test "no${dft_flavor}" = "no" && dft_flavor="none" - - local fft_flavor="fftw3" - local fft_libs="" - # The fftw threads support is protected by black magick. - # Anybody removes it, dies. - # New USE flag "fftw-threads" was added to control usage - # of the threaded fftw variant. Since fftw-3.3 has expanded - # the paralel options by MPI and OpenMP support, analogical - # USE flags should be added to select them in future; - # unusable with previous FFTW versions, they are postponed - # for now. - if use fftw-threads; then - fft_flavor="fftw3-threads" - fft_libs="${fft_libs} $($(tc-getPKG_CONFIG) --libs fftw3_threads)" - fft_libs="${fft_libs} $($(tc-getPKG_CONFIG) --libs fftw3f_threads)" - else - fft_libs="${fft_libs} $($(tc-getPKG_CONFIG) --libs fftw3)" - fft_libs="${fft_libs} $($(tc-getPKG_CONFIG) --libs fftw3f)" - 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 - --enable-pkg-check - $(use_enable debug debug enhanced) - $(use_enable mpi) - $(use_enable mpi mpi-io) - $(use_enable openmp) - $(use_enable vdwxc) - $(use_enable lotf) - $(use_enable cuda gpu) - "$(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=$($(tc-getPKG_CONFIG) --cflags gsl)")" - "$(use gsl && echo "--with-math-libs=$($(tc-getPKG_CONFIG) --libs gsl)")" - "$(use levmar && echo "--with-algo-flavor=levmar")" - "$(use levmar && echo "--with-algo-libs=-llevmar")" - --with-linalg-flavor="atlas" - --with-linalg-libs="$($(tc-getPKG_CONFIG) --libs lapack)" - --with-trio-flavor="${trio_flavor}" - "$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")" - "$(use netcdf && echo "--with-netcdf-libs=$($(tc-getPKG_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=-letsf_io -letsf_io_utils -letsf_io_low_level")" - --with-dft-flavor="${dft_flavor}" - "$(use atompaw && echo "--with-atompaw-incs=${modules}")" - "$(use atompaw && echo "--with-atompaw-libs=-latompaw")" - "$(use bigdft && echo "--with-bigdft-incs=${modules}")" - "$(use bigdft && echo "--with-bigdft-libs=$($(tc-getPKG_CONFIG) --libs bigdft)")" - "$(use libxc && echo "--with-libxc-incs=${modules}")" - "$(use libxc && echo "--with-libxc-libs=$($(tc-getPKG_CONFIG) --libs libxc)")" - "$(use wannier && echo "--with-wannier90-bins=/usr/bin")" - "$(use wannier && echo "--with-wannier90-incs=${modules}")" - "$(use wannier && echo "--with-wannier90-libs=-lwannier $($(tc-getPKG_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}} ${modules} -I/usr/include" - ) - - MARKDOWN=Markdown.pl autotools-utils_src_configure -} - -src_compile() { - autotools-utils_src_compile - - # Apparently libabinit.a is not built by default - # Used by BigDFT. Should probably be built separately, - # as a package of its own: BigDFT used by Abinit. - # Does libabinit.a depend on BigDFT, if used? - # Can Abinit use external libabinit.a? - use libabinit && autotools-utils_src_compile libabinit.a - - sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc || die -} - -src_test() { - einfo "The tests take quite a while, easily several hours or even days" - - autotools-utils_src_test -} - -src_install() { - #autotools-utils_src_install() expanded - _check_build_dir - pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null - default - - use libabinit && dolib libabinit.a - - if use test; then - for dc in results.tar.gz results.txt suite_report.html; do - test -e tests/"${dc}" && dodoc tests/"${dc}" || ewarn "Copying tests results ${dc} failed" - done - fi - - popd > /dev/null - - # XXX: support installing them from builddir as well!!! - if [[ ${DOCS} ]]; then - dodoc "${DOCS[@]}" - 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}" - fi - done - fi - if [[ ${HTML_DOCS} ]]; then - dohtml -r "${HTML_DOCS[@]}" - fi - - if use scripts; then - insinto /usr/share/"${P}" - doins -r scripts - fi - - # Remove libtool files and unnecessary static libs - prune_libtool_files -} - -pkg_postinst() { - if use test; then - elog "The full test results will be installed as summary_tests.tar.bz2." - elog "Also a concise report tests_summary.txt is installed." - fi -} diff --git a/sci-physics/abinit/abinit-7.6.4-r1.ebuild b/sci-physics/abinit/abinit-7.6.4-r1.ebuild deleted file mode 100644 index f12148beb..000000000 --- a/sci-physics/abinit/abinit-7.6.4-r1.ebuild +++ /dev/null @@ -1,390 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools-utils eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs - -DESCRIPTION="Total energy, charge density and electronic structure using DFT" -HOMEPAGE="http://www.abinit.org/"; -SRC_URI="http://ftp.abinit.org/${P}.tar.gz"; - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="atompaw bigdft cuda cuda-double -debug +etsf_io +fftw fftw-mpi +fftw-threads +fox gsl +hdf5 levmar -libabinit libxc -lotf mpi +netcdf openmp python scalapack scripts -test +threads wannier" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" -#" scalapack? ( !bigdft )" - -RDEPEND="virtual/blas - virtual/lapack - ${PYTHON_DEPS} - dev-python/numpy - atompaw? ( >=sci-physics/atompaw-3.0.1.9-r1[libxc?] ) - bigdft? ( ~sci-libs/bigdft-abi-1.0.4[scalapack?] ) - cuda? ( dev-util/nvidia-cuda-sdk ) - etsf_io? ( >=sci-libs/etsf_io-1.0.3-r2 ) - fftw? ( - sci-libs/fftw:3.0 - fftw-threads? ( - openmp? ( sci-libs/fftw:3.0[openmp] ) - !openmp? ( sci-libs/fftw:3.0[threads] ) - ) - fftw-mpi? ( - sci-libs/fftw:3.0[mpi] - openmp? ( sci-libs/fftw:3.0[openmp] ) - !openmp? ( sci-libs/fftw:3.0[threads] ) - ) - ) - fox? ( >=sci-libs/fox-4.1.2-r2[sax] ) - gsl? ( sci-libs/gsl ) - hdf5? ( sci-libs/hdf5[fortran] ) - levmar? ( sci-libs/levmar ) - libxc? ( >=sci-libs/libxc-2.0[fortran] - <sci-libs/libxc-2.2 ) - netcdf? ( - sci-libs/netcdf[hdf5?] - || ( - sci-libs/netcdf[fortran] - sci-libs/netcdf-fortran - ) - ) - mpi? ( virtual/mpi ) - scalapack? ( virtual/scalapack ) - scripts? ( dev-python/PyQt4 ) - wannier? ( >=sci-libs/wannier90-1.2-r1 )" -DEPEND="${RDEPEND} - virtual/pkgconfig - dev-perl/Text-Markdown" - -S=${WORKDIR}/${P%[a-z]} - -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 - - # This should be correct: - # It is gcc-centric because toolchain-funcs.eclass is gcc-centric. - # Should a bug be filed against toolchain-funcs.eclass? - # if use openmp; then - # tc-has-openmp || \ - # die "Please select an openmp capable compiler like gcc[openmp]" - # fi - # - # This is completely wrong: - # If other compilers than Gnu Compiler Collection can be used by portage, - # their support of OpenMP should be properly tested. This code limits the test - # to gcc, and blindly supposes that other compilers do support OpenMP. - # if use openmp && [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp; then - # die "Please select an openmp capable compiler like gcc[openmp]" - # fi - # - # Luckily Abinit is a fortran package. - # fortran-2.eclass has its own test for OpenMP support, - # more general than toolchain-funcs.eclass - # The test itself proceeds inside fortran-2_pkg_setup - if use openmp; then FORTRAN_NEED_OPENMP=1; fi - - fortran-2_pkg_setup - - if use openmp; then - # based on _fortran-has-openmp() of fortran-2.eclass - local code=ebuild-openmp-flags - local ret - local openmp - - pushd "${T}" - cat <<- EOF > "${code}.c" - # include <omp.h> - main () { - int nthreads; - nthreads=omp_get_num_threads(); - } - EOF - - for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do - ${CC} ${openmp} "${code}.c" -o "${code}.o" &>> "${T}"/_c_compile_test.log - ret=$? - (( ${ret} )) || break - done - - rm -f "${code}.*" - popd - - if (( ${ret} )); then - die "Please switch to an openmp compatible C compiler" - else - export CC="${CC} ${openmp}" - export CXX="${CXX} ${openmp}" - fi - - pushd "${T}" - cat <<- EOF > "${code}.f" - 1 call omp_get_num_threads - 2 end - EOF - - for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do - ${FC} ${openmp} "${code}.f" -o "${code}.o" &>> "${T}"/_f_compile_test.log - ret=$? - (( ${ret} )) || break - done - - rm -f "${code}.*" - popd - - if (( ${ret} )); then - die "Please switch to an openmp compatible fortran compiler." - else - export FC="${FC} ${openmp}" - export F77="${F77} ${openmp}" - fi - fi - - # Sort out some USE options - if use fftw-threads && ! use fftw; then - ewarn "fftw-threads set but fftw not used, ignored." - fi - if use fftw-mpi; then - if ! use fftw; then - ewarn "fftw-mpi set but fftw not used, ignored." - elif ! use mpi; then - ewarn "fftw-mpi set but mpi not used, ignored." - elif ! use fftw-threads; then - ewarn "fftw-mpi set but fftw-threads not. Will use a threaded fftw nevertheless, required with MPI." - fi - fi - if use cuda-double && ! use cuda; then - ewarn "cuda-double set but cuda not used, ignored" - fi - - python-single-r1_pkg_setup - -} - -src_prepare() { - epatch \ - "${FILESDIR}"/6.2.2-change-default-directories.patch \ - "${FILESDIR}"/6.12.1-autoconf.patch \ - "${FILESDIR}"/6.12.1-xmalloc.patch \ - "${FILESDIR}"/7.6.3-libabinit_options.patch \ - "${FILESDIR}"/7.4.2-levmar_diag_scaling.patch \ - "${FILESDIR}"/7.4.2-syntax.patch \ - "${FILESDIR}"/7.4.2-cuda_link_stdc++.patch \ - "${FILESDIR}"/7.6.4-cuda_header.patch \ - "${FILESDIR}"/7.6.4-libxc_versions.patch - eautoreconf - sed -e"s/\(grep '\^-\)\(\[LloW\]\)'/\1\\\(\2\\\|pthread\\\)'/g" -i configure || die - python_fix_shebang "${S}" -} - -src_configure() { - local modules="$(FoX-config --sax --fcflags)" - local FoX_libs="$(FoX-config --sax --libs)" - - local trio_flavor="" - use etsf_io && trio_flavor="${trio_flavor}+etsf_io" - use fox && trio_flavor="${trio_flavor}+fox" - use netcdf && trio_flavor="${trio_flavor}+netcdf" - test "no${trio_flavor}" = "no" && trio_flavor="none" - - local netcdff_libs="-lnetcdff" - use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran" - -# local linalg_flavor="atlas" - local linalg_flavor="custom" - local mylapack="lapack" - use scalapack && mylapack="scalapack" && linalg_flavor="${linalg_flavor}+scalapack" - - local dft_flavor="" - use atompaw && dft_flavor="${dft_flavor}+atompaw" - use bigdft && dft_flavor="${dft_flavor}+bigdft" - use libxc && dft_flavor="${dft_flavor}+libxc" - use wannier && dft_flavor="${dft_flavor}+wannier90" - test "no${dft_flavor}" = "no" && dft_flavor="none" - - local fft_flavor="fftw3" - local fft_libs="" - # The fftw threads support is protected by black magick. - # Anybody removes it, dies. - # New USE flag "fftw-threads" was added to control usage - # of the threaded fftw variant. Since fftw-3.3 has expanded - # the paralel options by MPI and OpenMP support, analogical - # USE flags should be added to select them in future; - # unusable with previous FFTW versions, they are postponed - # for now. - if use mpi && use fftw-mpi; then - fft_flavor="fftw3-mpi" - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_mpi)" - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_mpi)" - if use openmp; then - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_omp)" - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_omp)" - else - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_threads)" - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_threads)" - fi - elif use fftw-threads; then - fft_flavor="fftw3-threads" - if use openmp; then - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_omp)" - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_omp)" - else - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_threads)" - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_threads)" - fi - else - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3)" - fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f)" - 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 - --enable-pkg-check - $(use_enable debug debug enhanced) - $(use_enable mpi) - $(use_enable mpi mpi-io) - $(use_enable openmp) - $(use_enable lotf) - $(use_enable cuda gpu) - "$(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=$($(tc-getPKG_CONFIG) --cflags gsl)")" - "$(use gsl && echo "--with-math-libs=$($(tc-getPKG_CONFIG) --libs gsl)")" - "$(use levmar && echo "--with-algo-flavor=levmar")" - "$(use levmar && echo "--with-algo-libs=-llevmar")" - --with-linalg-flavor="${linalg_flavor}" - --with-linalg-libs="$($(tc-getPKG_CONFIG) --libs "${mylapack}")" - --with-trio-flavor="${trio_flavor}" - "$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")" - "$(use netcdf && echo "--with-netcdf-libs=$($(tc-getPKG_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=-letsf_io -letsf_io_utils -letsf_io_low_level")" - --with-dft-flavor="${dft_flavor}" - "$(use atompaw && echo "--with-atompaw-incs=${modules}")" - "$(use atompaw && echo "--with-atompaw-libs=-latompaw")" - "$(use bigdft && echo "--with-bigdft-incs=${modules}")" - "$(use bigdft && echo "--with-bigdft-libs=$($(tc-getPKG_CONFIG) --libs bigdft)")" - "$(use libxc && echo "--with-libxc-incs=${modules}")" - "$(use libxc && echo "--with-libxc-libs=$($(tc-getPKG_CONFIG) --libs libxc)")" - "$(use wannier && echo "--with-wannier90-bins=/usr/bin")" - "$(use wannier && echo "--with-wannier90-incs=${modules}")" - "$(use wannier && echo "--with-wannier90-libs=-lwannier $($(tc-getPKG_CONFIG) --libs blas 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}} ${modules} -I/usr/include" - ) - - MARKDOWN=Markdown.pl autotools-utils_src_configure -} - -src_compile() { - autotools-utils_src_compile - - # Apparently libabinit.a is not built by default - # Used by BigDFT. Should probably be built separately, - # as a package of its own: BigDFT used by Abinit. - # Does libabinit.a depend on BigDFT, if used? - # Can Abinit use external libabinit.a? - use libabinit && autotools-utils_src_compile libabinit.a - - sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc || die -} - -src_test() { - einfo "The complete tests take quite a while, easily several hours or even days." - # autotools-utils_src_test expanded and modified - _check_build_dir - pushd "${BUILD_DIR}" > /dev/null || die - - einfo "Running the internal tests." - emake tests_in - - einfo "Running the thorough tests. Be patient, please." - "${S}"/tests/runtests.py || ewarn "The package has not passed the thorough tests." - - popd > /dev/null || die -} - -src_install() { - #autotools-utils_src_install() expanded - _check_build_dir - pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null - default - - use libabinit && dolib libabinit.a - - if use test; then - for dc in results.tar.gz results.txt suite_report.html; do - test -e Test_suite/"${dc}" && dodoc Test_suite/"${dc}" || ewarn "Copying tests results ${dc} failed" - done - fi - - popd > /dev/null - - # XXX: support installing them from builddir as well!!! - if [[ ${DOCS} ]]; then - dodoc "${DOCS[@]}" - 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}" - fi - done - fi - if [[ ${HTML_DOCS} ]]; then - dohtml -r "${HTML_DOCS[@]}" - fi - - if use scripts; then - insinto /usr/share/"${P}" - doins -r scripts - fi - - # Remove libtool files and unnecessary static libs - prune_libtool_files -} diff --git a/sci-physics/abinit/files/6.12.1-autoconf.patch b/sci-physics/abinit/files/6.12.1-autoconf.patch deleted file mode 100644 index 7e0169f63..000000000 --- a/sci-physics/abinit/files/6.12.1-autoconf.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff -Naur old/fallbacks/configure.ac new/fallbacks/configure.ac ---- old/fallbacks/configure.ac 2012-01-30 19:40:41.000000000 +0000 -+++ new/fallbacks/configure.ac 2012-02-13 08:16:08.000000000 +0000 -@@ -114,6 +114,17 @@ - - # ---------------------------------------------------------------------------- # - -+AM_CONDITIONAL([DO_BUILD_FOX],[test "${enable_fox}" = "yes"]) -+AM_CONDITIONAL([DO_BUILD_LIBXC],[test "${enable_libxc}" = "yes"]) -+AM_CONDITIONAL([DO_BUILD_LINALG],[test "${enable_linalg}" = "yes"]) -+AM_CONDITIONAL([DO_BUILD_NETCDF],[test "${enable_netcdf}" = "yes"]) -+AM_CONDITIONAL([DO_BUILD_ETSF_IO],[test "${enable_etsf_io}" = "yes"]) -+AM_CONDITIONAL([DO_BUILD_ATOMPAW],[test "${enable_atompaw}" = "yes"]) -+AM_CONDITIONAL([DO_BUILD_WANNIER90],[test "${enable_wannier90}" = "yes"]) -+AM_CONDITIONAL([DO_BUILD_BIGDFT],[test "${enable_bigdft}" = "yes"]) -+ -+# ---------------------------------------------------------------------------- # -+ - # - # Downloading support - # diff --git a/sci-physics/abinit/files/6.12.1-xmalloc.patch b/sci-physics/abinit/files/6.12.1-xmalloc.patch deleted file mode 100644 index 0c8d98eea..000000000 --- a/sci-physics/abinit/files/6.12.1-xmalloc.patch +++ /dev/null @@ -1,48 +0,0 @@ -diff -Naur abinit-6.12.1_orig/src/02_clib/fsi_posix.c abinit-6.12.1/src/02_clib/fsi_posix.c ---- src/02_clib/fsi_posix.c 2012-01-30 19:40:41.000000000 +0000 -+++ src/02_clib/fsi_posix.c 2012-03-22 08:21:46.000000000 +0000 -@@ -19,7 +19,7 @@ - */ - - #include "abi_clib.h" --#include "xmalloc.h" -+/* #include "xmalloc.h" */ - #include "string_f.h" - - /* Create a directory */ -diff -Naur abinit-6.12.1_orig/src/02_clib/intrinsics.c abinit-6.12.1/src/02_clib/intrinsics.c ---- src/02_clib/intrinsics.c 2012-01-30 19:40:41.000000000 +0000 -+++ src/02_clib/intrinsics.c 2012-03-22 08:20:26.000000000 +0000 -@@ -18,7 +18,7 @@ - */ - - #include "abi_clib.h" --#include "xmalloc.h" -+/* #include "xmalloc.h" */ - #include "string_f.h" - - /* -diff -Naur abinit-6.12.1_orig/src/02_clib/progress_bar.c abinit-6.12.1/src/02_clib/progress_bar.c ---- src/02_clib/progress_bar.c 2012-01-30 19:40:41.000000000 +0000 -+++ src/02_clib/progress_bar.c 2012-03-22 08:21:06.000000000 +0000 -@@ -20,7 +20,7 @@ - */ - - #include "abi_clib.h" --#include "xmalloc.h" -+/* #include "xmalloc.h" */ - - #include <sys/time.h> - #include <sys/ioctl.h> -diff -Naur abinit-6.12.1_orig/src/02_clib/xmalloc.c abinit-6.12.1/src/02_clib/xmalloc.c ---- src/02_clib/xmalloc.c 2012-01-30 19:40:41.000000000 +0000 -+++ src/02_clib/xmalloc.c 2012-03-22 08:22:09.000000000 +0000 -@@ -19,7 +19,7 @@ - */ - - #include "abi_clib.h" --#include "xmalloc.h" -+/* #include "xmalloc.h" */ - - static void - memory_error_and_abort (const char *fname) diff --git a/sci-physics/abinit/files/6.12.3-gui-makefiles.tbz b/sci-physics/abinit/files/6.12.3-gui-makefiles.tbz deleted file mode 100644 index d324544e9..000000000 Binary files a/sci-physics/abinit/files/6.12.3-gui-makefiles.tbz and /dev/null differ diff --git a/sci-physics/abinit/files/6.2.2-change-default-directories.patch b/sci-physics/abinit/files/6.2.2-change-default-directories.patch deleted file mode 100644 index d6e3ce6aa..000000000 --- a/sci-physics/abinit/files/6.2.2-change-default-directories.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff -urN abinit-6.2.2.orig/config/m4/conf-init.m4 abinit-6.2.2/config/m4/conf-init.m4 ---- abinit-6.2.2.orig/config/m4/conf-init.m4 2010-08-07 06:31:29.000000000 -0700 -+++ abinit-6.2.2/config/m4/conf-init.m4 2010-08-10 15:36:05.000000000 -0700 -@@ -337,7 +337,7 @@ - abinit_bindir="${abinit_prefix}/bin" - abinit_chkdir="${abinit_prefix}/share/abinit/tests" - abinit_datdir="${abinit_prefix}/share/abinit" -- abinit_docdir="${abinit_prefix}/doc/abinit" -+ abinit_docdir="${abinit_prefix}/share/doc/abinit-${ABINIT_VERSION_BASE}" - abinit_incdir="${abinit_prefix}/include" - abinit_libdir="${abinit_prefix}/lib" - abinit_mandir="${abinit_prefix}/share/man" -@@ -394,7 +394,7 @@ - fi - ABINIT_VERSION_BUILD=`date '+%Y%m%d'` - -- ABINIT_VERSION_BASE="${ABINIT_VERSION_MAJOR}.${ABINIT_VERSION_MINOR}" -+ ABINIT_VERSION_BASE="${ABINIT_VERSION_MAJOR}.${ABINIT_VERSION_MINOR}.${ABINIT_VERSION_MICRO}" - - dnl Make numbers available to source files - AC_DEFINE_UNQUOTED(ABINIT_VERSION,"${ABINIT_VERSION}", diff --git a/sci-physics/abinit/files/7.0.4-test_dirs.patch b/sci-physics/abinit/files/7.0.4-test_dirs.patch deleted file mode 100644 index 94915a0e1..000000000 --- a/sci-physics/abinit/files/7.0.4-test_dirs.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Naurp abinit-7.0.4.orig/tests/Makefile.am abinit-7.0.4/tests/Makefile.am ---- abinit-7.0.4.orig/tests/Makefile.am 2012-12-08 15:07:26.000000000 +0000 -+++ abinit-7.0.4/tests/Makefile.am 2013-01-08 13:58:56.721725346 +0000 -@@ -3607,7 +3607,7 @@ tests_gw_paw: nightly-stamp - tests_bs: nightly-stamp - rm -fr */tmp-bs* - $(MAKE) tests_v67mbpt dirname=bs start=01 stop=01 -- cd v6/tmp-bs* ; mv fldiff.report fldiff_keep.report -+ cd v67mbpt/tmp-bs* ; mv fldiff.report fldiff_keep.report - $(MAKE) tests_v67mbpt dirname=bs start=04 stop=04 - $(MAKE) tests_tutorial dirname=bs start=bs_1 stop=bs_4 - echo diff --git a/sci-physics/abinit/files/7.10.4-libabinit_options.patch b/sci-physics/abinit/files/7.10.4-libabinit_options.patch deleted file mode 100644 index 09c61419a..000000000 --- a/sci-physics/abinit/files/7.10.4-libabinit_options.patch +++ /dev/null @@ -1,82 +0,0 @@ -diff -Naurp abinit-7.10.4.orig/Makefile.am abinit-7.10.4/Makefile.am ---- abinit-7.10.4.orig/Makefile.am 2015-03-12 06:28:38.000000000 +0100 -+++ abinit-7.10.4/Makefile.am 2015-04-07 12:14:39.816276230 +0200 -@@ -2878,7 +2878,9 @@ libabinit.a: - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/11_qespresso_ext/lib11_qespresso_ext.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/12_hide_mpi/lib12_hide_mpi.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/14_hidewrite/lib14_hidewrite.a -+if DO_BUILD_15_GPU_TOOLBOX - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a -+endif - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/16_hideleave/lib16_hideleave.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/18_timing/lib18_timing.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/21_psiesta_noabirule/lib21_psiesta_noabirule.a -@@ -2898,7 +2900,9 @@ libabinit.a: - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/51_manage_mpi/lib51_manage_mpi.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a -+if DO_BUILD_52_MANAGE_CUDA - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a -+endif - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_ffts/lib53_ffts.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_spacepar/lib53_spacepar.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/54_abiutil/lib54_abiutil.a -@@ -2917,15 +2921,19 @@ libabinit.a: - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/62_wvl_wfs/lib62_wvl_wfs.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/63_bader/lib63_bader.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/64_atompaw/lib64_atompaw.a -+if DO_BUILD_65_LOTF_BASE - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_lotf_base/lib65_lotf_base.a -+endif - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_nonlocal/lib65_nonlocal.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_psp/lib65_psp.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_fock/lib66_fock.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_paw/lib66_paw.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_wfs/lib66_wfs.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/67_common/lib67_common.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_dmft/lib68_dmft.a -+if DO_BUILD_68_LOTF - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_lotf/lib68_lotf.a -+endif - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_recursion/lib68_recursion.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_rsprc/lib68_rsprc.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/69_wfdesc/lib69_wfdesc.a -diff -Naurp abinit-7.10.4.orig/Makefile.in abinit-7.10.4/Makefile.in ---- abinit-7.10.4.orig/Makefile.in 2015-03-12 06:28:51.000000000 +0100 -+++ abinit-7.10.4/Makefile.in 2015-04-07 12:14:39.816276230 +0200 -@@ -3803,7 +3803,7 @@ libabinit.a: - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/11_qespresso_ext/lib11_qespresso_ext.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/12_hide_mpi/lib12_hide_mpi.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/14_hidewrite/lib14_hidewrite.a -- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a -+@DO_BUILD_15_GPU_TOOLBOX_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/16_hideleave/lib16_hideleave.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/18_timing/lib18_timing.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/21_psiesta_noabirule/lib21_psiesta_noabirule.a -@@ -3823,7 +3823,7 @@ libabinit.a: - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/51_manage_mpi/lib51_manage_mpi.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a -- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a -+@DO_BUILD_52_MANAGE_CUDA_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_ffts/lib53_ffts.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_spacepar/lib53_spacepar.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/54_abiutil/lib54_abiutil.a -@@ -3842,15 +3842,15 @@ libabinit.a: - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/62_wvl_wfs/lib62_wvl_wfs.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/63_bader/lib63_bader.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/64_atompaw/lib64_atompaw.a -- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_lotf_base/lib65_lotf_base.a -+@DO_BUILD_65_LOTF_BASE_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_lotf_base/lib65_lotf_base.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_nonlocal/lib65_nonlocal.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_psp/lib65_psp.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_fock/lib66_fock.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_paw/lib66_paw.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_wfs/lib66_wfs.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/67_common/lib67_common.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_dmft/lib68_dmft.a -- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_lotf/lib68_lotf.a -+@DO_BUILD_68_LOTF_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_lotf/lib68_lotf.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_recursion/lib68_recursion.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_rsprc/lib68_rsprc.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/69_wfdesc/lib69_wfdesc.a diff --git a/sci-physics/abinit/files/7.10.4-syntax.patch b/sci-physics/abinit/files/7.10.4-syntax.patch deleted file mode 100644 index bfb915e71..000000000 --- a/sci-physics/abinit/files/7.10.4-syntax.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Naurp abinit-7.10.4.orig/src/98_main/mrgscr.F90 abinit-7.10.4/src/98_main/mrgscr.F90 ---- abinit-7.10.4.orig/src/98_main/mrgscr.F90 2015-03-12 06:24:36.000000000 +0100 -+++ abinit-7.10.4/src/98_main/mrgscr.F90 2015-04-07 13:00:01.166355853 +0200 -@@ -2312,7 +2312,7 @@ program mrgscr - - !!OMP *** OPENMP SECTION *** Added by MS - !$OMP PARALLEL SHARED(Hscr_file,epsm1,nfreqre,epsm1_pole, & --!$OMP is_scr,npoles,std_out,iqibz,one) & -+!$OMP is_scr,npoles,std_out,iqibz) & - !$OMP PRIVATE(ig1,ig2,refval,imfval,phase) - !!OMP write(std_out,'(a,i0)') ' Entering openmp loop. Number of threads: ',omp_get_num_threads() - ABI_MALLOC(refval,(Hscr_file(1)%nomega)) diff --git a/sci-physics/abinit/files/7.4.2-cuda_link_stdc++.patch b/sci-physics/abinit/files/7.4.2-cuda_link_stdc++.patch deleted file mode 100644 index 225d0392f..000000000 --- a/sci-physics/abinit/files/7.4.2-cuda_link_stdc++.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff -Naur abinit-7.4.2.orig/src/98_main/Makefile.am abinit-7.4.2/src/98_main/Makefile.am ---- src/98_main/Makefile.am 2013-09-08 07:27:21.000000000 +0000 -+++ src/98_main/Makefile.am 2013-10-10 12:20:26.678606398 +0000 -@@ -37,7 +37,7 @@ - LIB_12_HIDE_MPI = $(top_builddir)/src/12_hide_mpi/lib12_hide_mpi.a - LIB_14_HIDEWRITE = $(top_builddir)/src/14_hidewrite/lib14_hidewrite.a - if DO_BUILD_15_GPU_TOOLBOX -- LIB_15_GPU_TOOLBOX = $(top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a -+ LIB_15_GPU_TOOLBOX = $(top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a -lstdc++ - else - LIB_15_GPU_TOOLBOX = - endif -@@ -59,7 +59,7 @@ - LIB_51_MANAGE_MPI = $(top_builddir)/src/51_manage_mpi/lib51_manage_mpi.a - LIB_52_FFT_MPI_NOABIRULE = $(top_builddir)/src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a - if DO_BUILD_52_MANAGE_CUDA -- LIB_52_MANAGE_CUDA = $(top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a -+ LIB_52_MANAGE_CUDA = $(top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a -lstdc++ - else - LIB_52_MANAGE_CUDA = - endif diff --git a/sci-physics/abinit/files/7.4.2-levmar_diag_scaling.patch b/sci-physics/abinit/files/7.4.2-levmar_diag_scaling.patch deleted file mode 100644 index 346146616..000000000 --- a/sci-physics/abinit/files/7.4.2-levmar_diag_scaling.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff -Naurp abinit-7.4.2.orig/src/02_clib/calling_levmar.c abinit-7.4.2/src/02_clib/calling_levmar.c ---- abinit-7.4.2.orig/src/02_clib/calling_levmar.c 2013-09-08 07:24:13.000000000 +0000 -+++ abinit-7.4.2/src/02_clib/calling_levmar.c 2013-09-16 14:59:06.574702521 +0000 -@@ -149,7 +149,7 @@ double opts[LM_OPTS_SZ], info[LM_INFO_SZ - // if (coeffs[i+2]>-1E-16){ - /* invoke the optimisation function with box boundaries*/ - ret=dlevmar_bc_dif(dim_screening, coeffs, yvals, c_ncoeffs, c_nvals, \ -- lower_bounds, upper_bounds, 3000, opts, info, NULL, NULL, \ -+ lower_bounds, upper_bounds, NULL, 3000, opts, info, NULL, NULL, \ - (void *)&adata); // Box boundary conditions without Jacobian - //} - //} -@@ -219,7 +219,7 @@ double opts[LM_OPTS_SZ], info[LM_INFO_SZ - // if (coeffs[i+2]>-1E-16){ - /* invoke the optimisation function with box boundaries*/ - ret=dlevmar_bc_dif(dre_and_im_screening, coeffs, yvals, c_ncoeffs, c_nvals, \ -- lower_bounds, upper_bounds, 1000, opts, info, NULL, NULL, \ -+ lower_bounds, upper_bounds, NULL, 1000, opts, info, NULL, NULL, \ - (void *)&adata); // Box boundary conditions without Jacobian - //} - //} diff --git a/sci-physics/abinit/files/7.4.2-syntax.patch b/sci-physics/abinit/files/7.4.2-syntax.patch deleted file mode 100644 index 87026d926..000000000 --- a/sci-physics/abinit/files/7.4.2-syntax.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff -Naurp abinit-7.4.2.orig/src/98_main/mrgscr.F90 abinit-7.4.2/src/98_main/mrgscr.F90 ---- abinit-7.4.2.orig/src/98_main/mrgscr.F90 2013-09-08 07:24:13.000000000 +0000 -+++ abinit-7.4.2/src/98_main/mrgscr.F90 2013-09-17 10:32:55.212877871 +0000 -@@ -2309,7 +2309,7 @@ program mrgscr - - case(2) ! Fit everything - -- if (is_scr/=.true.) then -+ if (is_scr.neqv..true.) then - write(std_out,'(2(a))') ch10,& - & ' Complete fits can only be done for _SCR file for now. Exiting ...' - goto 100 -@@ -2387,7 +2387,7 @@ program mrgscr - - !!OMP *** OPENMP SECTION *** Added by MS - !$OMP PARALLEL SHARED(Hscr_file,epsm1,nfreqre,epsm1_pole, & --!$OMP is_scr,npoles,std_out,iqibz,one) & -+!$OMP is_scr,npoles,std_out,iqibz) & - !$OMP PRIVATE(ig1,ig2,refval,imfval,phase) - !!OMP write(std_out,'(a,i0)') ' Entering openmp loop. Number of threads: ',omp_get_num_threads() - ABI_MALLOC(refval,(Hscr_file(1)%nomega)) diff --git a/sci-physics/abinit/files/7.6.3-libabinit_options.patch b/sci-physics/abinit/files/7.6.3-libabinit_options.patch deleted file mode 100644 index d97d2daef..000000000 --- a/sci-physics/abinit/files/7.6.3-libabinit_options.patch +++ /dev/null @@ -1,80 +0,0 @@ -diff -Naurp abinit-7.6.3.orig/Makefile.am abinit-7.6.3/Makefile.am ---- abinit-7.6.3.orig/Makefile.am 2014-04-06 20:33:21.000000000 +0000 -+++ abinit-7.6.3/Makefile.am 2014-05-02 10:33:49.836301391 +0000 -@@ -1622,7 +1622,9 @@ libabinit.a: - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/11_qespresso_ext/lib11_qespresso_ext.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/12_hide_mpi/lib12_hide_mpi.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/14_hidewrite/lib14_hidewrite.a -+if DO_BUILD_15_GPU_TOOLBOX - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a -+endif - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/16_hideleave/lib16_hideleave.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/18_timing/lib18_timing.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/21_psiesta_noabirule/lib21_psiesta_noabirule.a -@@ -1642,7 +1644,9 @@ libabinit.a: - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/51_manage_mpi/lib51_manage_mpi.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a -+if DO_BUILD_52_MANAGE_CUDA - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a -+endif - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_abiutil/lib53_abiutil.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_ffts/lib53_ffts.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_spacepar/lib53_spacepar.a -@@ -1661,14 +1665,18 @@ libabinit.a: - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/62_wvl_wfs/lib62_wvl_wfs.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/63_bader/lib63_bader.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/64_atompaw/lib64_atompaw.a -+if DO_BUILD_65_LOTF_BASE - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_lotf_base/lib65_lotf_base.a -+endif - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_nonlocal/lib65_nonlocal.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_psp/lib65_psp.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_paw/lib66_paw.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_wfs/lib66_wfs.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/67_common/lib67_common.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_dmft/lib68_dmft.a -+if DO_BUILD_68_LOTF - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_lotf/lib68_lotf.a -+endif - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_recursion/lib68_recursion.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_rsprc/lib68_rsprc.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/69_wfdesc/lib69_wfdesc.a -diff -Naurp abinit-7.6.3.orig/Makefile.in abinit-7.6.3/Makefile.in ---- abinit-7.6.3.orig/Makefile.in 2014-04-06 20:33:32.000000000 +0000 -+++ abinit-7.6.3/Makefile.in 2014-05-02 11:25:34.961648440 +0000 -@@ -2746,7 +2746,7 @@ libabinit.a: - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/11_qespresso_ext/lib11_qespresso_ext.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/12_hide_mpi/lib12_hide_mpi.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/14_hidewrite/lib14_hidewrite.a -- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a -+@DO_BUILD_15_GPU_TOOLBOX_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/16_hideleave/lib16_hideleave.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/18_timing/lib18_timing.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/21_psiesta_noabirule/lib21_psiesta_noabirule.a -@@ -2766,7 +2766,7 @@ libabinit.a: - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/51_manage_mpi/lib51_manage_mpi.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a -- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a -+@DO_BUILD_52_MANAGE_CUDA_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_abiutil/lib53_abiutil.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_ffts/lib53_ffts.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_spacepar/lib53_spacepar.a -@@ -2785,14 +2785,14 @@ libabinit.a: - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/62_wvl_wfs/lib62_wvl_wfs.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/63_bader/lib63_bader.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/64_atompaw/lib64_atompaw.a -- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_lotf_base/lib65_lotf_base.a -+@DO_BUILD_65_LOTF_BASE_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_lotf_base/lib65_lotf_base.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_nonlocal/lib65_nonlocal.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_psp/lib65_psp.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_paw/lib66_paw.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_wfs/lib66_wfs.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/67_common/lib67_common.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_dmft/lib68_dmft.a -- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_lotf/lib68_lotf.a -+@DO_BUILD_68_LOTF_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_lotf/lib68_lotf.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_recursion/lib68_recursion.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_rsprc/lib68_rsprc.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/69_wfdesc/lib69_wfdesc.a diff --git a/sci-physics/abinit/files/7.6.4-cuda_header.patch b/sci-physics/abinit/files/7.6.4-cuda_header.patch deleted file mode 100644 index cc7481686..000000000 --- a/sci-physics/abinit/files/7.6.4-cuda_header.patch +++ /dev/null @@ -1,11 +0,0 @@ -diff -Naurp abinit-7.6.4.orig/src/incs/cuda_header.h abinit-7.6.4/src/incs/cuda_header.h ---- abinit-7.6.4.orig/src/incs/cuda_header.h 2014-05-03 14:18:46.000000000 +0000 -+++ abinit-7.6.4/src/incs/cuda_header.h 2014-12-04 13:21:36.000000000 +0000 -@@ -17,6 +17,7 @@ - //#include <cutil.h> - #include <stdlib.h> - #include <unistd.h> -+#include <stdio.h> - #include <cufft.h> - #include <cuda_runtime.h> - #include <cuda.h> diff --git a/sci-physics/abinit/files/7.6.4-libxc_versions.patch b/sci-physics/abinit/files/7.6.4-libxc_versions.patch deleted file mode 100644 index 4f45db7b4..000000000 --- a/sci-physics/abinit/files/7.6.4-libxc_versions.patch +++ /dev/null @@ -1,40 +0,0 @@ -diff -Naurp abinit-7.6.4.orig/config/m4/conn-dft.m4 abinit-7.6.4/config/m4/conn-dft.m4 ---- abinit-7.6.4.orig/config/m4/conn-dft.m4 2014-05-03 14:18:46.000000000 +0000 -+++ abinit-7.6.4/config/m4/conn-dft.m4 2014-12-10 14:08:19.786380878 +0000 -@@ -135,7 +135,7 @@ AC_DEFUN([_ABI_DFT_CHECK_BIGDFT],[ - - - --# _ABI_DFT_CHECK_LIBXC(API_MAJOR, API_MINOR) -+# _ABI_DFT_CHECK_LIBXC(API_MIN_MAJOR, API_MIN_MINOR, API_MAX_MAJOR, API_MAX_MINOR) - # ------------------------------------------ - # - # Check whether the LibXC library is working. -@@ -203,7 +203,7 @@ AC_DEFUN([_ABI_DFT_CHECK_LIBXC],[ - dnl Check that we have the correct LibXC version - if test "${abi_dft_libxc_has_incs}" = "yes" -a \ - "${abi_dft_libxc_has_libs}" = "yes"; then -- AC_MSG_CHECKING([whether this is LibXC version $1.$2]) -+ AC_MSG_CHECKING([whether this is LibXC version from $1.$2 to $3.$4]) - AC_LANG_PUSH([C]) - AC_RUN_IFELSE([AC_LANG_PROGRAM( - [[ -@@ -212,7 +212,8 @@ AC_DEFUN([_ABI_DFT_CHECK_LIBXC],[ - [[ - int major = -1, minor = -1; - xc_version(&major, &minor); -- if ( (major != $1) || (minor != $2) ) { -+ if ( (major < $1) || (major == $1) && (minor < $2) || -+ (major == $3) && (minor > $4) || (major > $3) ) { - return 1; } - ]])], [abi_dft_libxc_version="yes"], [abi_dft_libxc_version="no"]) - AC_LANG_POP([C]) -@@ -518,7 +519,7 @@ AC_DEFUN([ABI_CONNECT_DFT],[ - ;; - - libxc) -- _ABI_DFT_CHECK_LIBXC(2,0) -+ _ABI_DFT_CHECK_LIBXC(2,0,2,1) - if test "${abi_dft_libxc_serial}" = "yes" -o \ - "${enable_fallbacks}" = "yes"; then - AC_DEFINE([HAVE_DFT_LIBXC],1, diff --git a/sci-physics/abinit/metadata.xml b/sci-physics/abinit/metadata.xml deleted file mode 100644 index d694831d1..000000000 --- a/sci-physics/abinit/metadata.xml +++ /dev/null @@ -1,60 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>sci-phys...@gentoo.org</email> - <name>Gentoo Physics Project</name> - </maintainer> - <longdescription lang="en"> -ABINIT is a package whose main program allows one to find the total energy, -charge density and electronic structure of systems made of electrons and nuclei -(molecules and periodic solids) within Density Functional Theory (DFT), using -pseudopotentials and a planewave basis. ABINIT also includes options to optimize -the geometry according to the DFT forces and stresses, or to perform molecular -dynamics simulations using these forces, or to generate dynamical matrices, -Born effective charges, and dielectric tensors. Excited states can be computed -within the Time-Dependent Density Functional Theory (for molecules), or within -Many-Body Perturbation Theory (the GW approximation). In addition to the main -ABINIT code, different utility programs are provided. -</longdescription> - <use> - <flag name="atompaw">Enable support for atompaw, a Projector Augmented Waves atomic data generator</flag> - <flag name="bigdft">Enable support for BigDFT, DFT package using wavelet basis set</flag> - <flag name="cuda">Enable support for nVidia CUDA</flag> - <flag name="cuda-double"> -Enable support for double precision nVidia CUDA -</flag> - <flag name="etsf_io"> -Enable support for reading and writing the European Theoretical -Spectroscopy facility (ETSF) file format. -</flag> - <flag name="fftw-threads"> -Use the threaded (openMP or pthreads) version of <pkg>sci-libs/fftw</pkg> -</flag> - <flag name="fftw-mpi"> -Use the MPI version of <pkg>sci-libs/fftw</pkg> (always with either openMP or pthreads too) -</flag> - <flag name="fox">Enable support for FoX Fortran XML library</flag> - <flag name="levmar"> -Enable support for <pkg>sci-libs/levmar</pkg>, -the Levenberg-Marquardt least-squares optimisation -</flag> - <flag name="libabinit"> -Build the libabinit used by <pkg>sci-libs/bigdft</pkg> -(usage not tested yet, circular dependency not resolved) -</flag> - <flag name="libxc">Enable support for libxc, an exchange-correlation potentials library</flag> - <flag name="lotf">Activate the Learn on The Fly method (LOTF) for Molecular Dynamics</flag> - <flag name="scalapack"> -Use ScaLAPACK, a subset of LAPACK routines redesigned for heterogenous computing -</flag> - <flag name="scripts">Install helper scripts, mostly Python</flag> - <flag name="vdwxc"> -Activate van der Waals exchange-correlation correction. Since 7.4.0 -no longer optional -</flag> - <flag name="wannier"> -Enable support for wannier90, a maximally localized Wannier functions (MLWFs) calculator -</flag> - </use> -</pkgmetadata>
