* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ball/files/, sci-astronomy/mosstack/, sci-physics/abinit/files/, ...
@ 2018-10-27 20:27 Justin Lecher
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From: Justin Lecher @ 2018-10-27 20:27 UTC (permalink / raw
To: gentoo-commits
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 -----
| 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.laine@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>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@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 ${i}/*
- done
- popd > /dev/null
-
- domenu share/applications/*
-
- rm -rf share/{applications,doc,icons,mime} || die
-
- insinto /usr
- doins -r share
-}
diff --git a/sci-biology/atsas/metadata.xml b/sci-biology/atsas/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/atsas/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild b/sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild
deleted file mode 100644
index 0b761d600..000000000
--- a/sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic qmake-utils toolchain-funcs
-
-MY_P="${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>jlec@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 <jlec@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>jlec@gentoo.org</email>
- </maintainer>
- <maintainer type="project">
- <email>sci-chemistry@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-chemistry@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-chemistry@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 ${INSTALL_DIR}
-
- make_desktop_entry kayali kayali kayali.svg
- use doc && dohtml html/*
- dodoc README
-}
diff --git a/sci-mathematics/kayali/metadata.xml b/sci-mathematics/kayali/metadata.xml
deleted file mode 100644
index df0c0137a..000000000
--- a/sci-mathematics/kayali/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-mathematics@gentoo.org</email>
- <name>Gentoo Mathematics Project</name>
- </maintainer>
- <longdescription lang="en">
-kayali is a Qt based Computer Algebra System (CAS) that can also be
-used as an advanced replacement for KDE KCalc. It is essentially a
-front end GUI forMaxima (and is easily extended to other CAS
-back-ends) and Gnuplot.
-</longdescription>
- <upstream>
- <remote-id type="sourceforge">kayali</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-mathematics/mathics/mathics-1.0.ebuild b/sci-mathematics/mathics/mathics-1.0.ebuild
deleted file mode 100644
index 622b488f1..000000000
--- a/sci-mathematics/mathics/mathics-1.0.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="A free lightweight CAS using Wolfram Language"
-HOMEPAGE="https://mathics.github.io/"
-SRC_URI="https://github.com/mathics/Mathics/archive/v${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>sci@gentoo.org</email>
- </maintainer>
- <maintainer type="project">
- <email>sci-physics@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-physics@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>
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