[gentoo-commits] proj/sci:master commit in: sci-physics/atompaw/, sci-physics/atompaw/files/, sci-physics/abinit/

[gentoo-commits] proj/sci:master commit in: sci-physics/atompaw/, sci-physics/atompaw/files/, sci-physics/abinit/

[Honza Macháček]

commit:     6944874e42492f433a5413c583dfe6e7abf618e1
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Wed Nov  9 10:55:57 2011 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Wed Nov  9 10:55:57 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6944874e

sci-physics/abinit bumped to 6.10.2, sci-physics/atompaw to 3.0.1.3

---
 sci-physics/abinit/ChangeLog                   |    7 +
 sci-physics/abinit/abinit-6.10.1.ebuild        |  211 ++++++++++++++++++++++++
 sci-physics/atompaw/ChangeLog                  |   12 ++
 sci-physics/atompaw/atompaw-3.0.1-r1.ebuild    |   68 ++++++++
 sci-physics/atompaw/atompaw-3.0.1.3.ebuild     |   68 ++++++++
 sci-physics/atompaw/files/3.0.1-longplot.patch |   12 ++
 6 files changed, 378 insertions(+), 0 deletions(-)

diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index 88370a1..5fb986c 100644
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*abinit-6.10.1 (09 Nov 2011)
+
+  09 Nov 2011; Honza Macháček <Hloupy.Honza@centrum.cz>
+  +abinit-6.10.1.ebuild:
+  Version bump to 6.10.1, sci-physics/atompaw ebuild updated as well, update of
+  bigDFT and other issues still to be done
+
 *abinit-6.8.2 (27 Sep 2011)
 
   27 Sep 2011; Honza Macháček <Hloupy.Honza@centrum.cz> +abinit-6.8.2.ebuild,

diff --git a/sci-physics/abinit/abinit-6.10.1.ebuild b/sci-physics/abinit/abinit-6.10.1.ebuild
new file mode 100644
index 0000000..cdd495f
--- /dev/null
+++ b/sci-physics/abinit/abinit-6.10.1.ebuild
@@ -0,0 +1,211 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="3"
+
+inherit autotools eutils fortran-2 multilib toolchain-funcs
+
+DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory"
+HOMEPAGE="http://www.abinit.org/"
+SRC_URI="http://ftp.abinit.org/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cuda -debug +fftw +fftw-threads +fox gsl +hdf5 mpi +netcdf python -test +threads -vdwxc"
+
+RDEPEND=">=sci-libs/bigdft-1.2.0.2
+	sci-libs/etsf_io
+	=sci-libs/libxc-1.0[fortran]
+	sci-physics/atompaw[libxc]
+	fox? ( sci-libs/fox[dom,sax,wcml,wxml] )
+	netcdf? (
+		sci-libs/netcdf[fortran]
+		hdf5? (
+		      sci-libs/netcdf[fortran,hdf5]
+		      )
+		)
+	hdf5? ( sci-libs/hdf5[fortran] )
+	sci-libs/wannier90
+	virtual/blas
+	virtual/lapack
+	gsl? ( sci-libs/gsl )
+	fftw? (
+		sci-libs/fftw:3.0
+		fftw-threads? ( sci-libs/fftw:3.0[threads] )
+		)
+	mpi? ( virtual/mpi )
+	python? ( dev-python/numpy )
+	cuda? ( dev-util/nvidia-cuda-sdk )"
+DEPEND="${RDEPEND}
+	dev-util/pkgconfig
+	dev-perl/Text-Markdown"
+
+S=${WORKDIR}/${P%[a-z]}
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	# Doesn't compile with gcc-4.0, only >=4.1
+	if [[ $(tc-getFC) == *gfortran ]]; then
+		if [[ $(gcc-major-version) -eq 4 ]] \
+			&& [[ $(gcc-minor-version) -lt 1  ]]; then
+				die "Requires gcc-4.1 or newer"
+		fi
+	fi
+	if use fftw-threads && ! use fftw; then
+		ewarn "fftw-threads set but fftw not used, ignored"
+	fi
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/6.2.2-change-default-directories.patch
+	epatch "${FILESDIR}"/6.0.3-fftw.patch
+	eautoreconf
+}
+
+src_configure() {
+	local libs="-L/usr/$(get_libdir)"
+	local modules="-I/usr/$(get_libdir)/finclude"
+	local FoX_libs="${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lFoX_common -lFoX_utils -lFoX_fsys"
+	local trio_flavor="etsf_io"
+	use fox && trio_flavor="${trio_flavor}+fox"
+	use netcdf && trio_flavor="${trio_flavor}+netcdf"
+	local netcdff_libs="-lnetcdff"
+	use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran"
+	local fft_flavor="fftw3"
+	local fft_libs="-L/usr/lib"
+	# The fftw threads support is protected by black magick.
+	# Anybody removes it, dies.
+	# New USE flag "fftw-threads" was added to control usage
+	# of the threaded fftw variant. Since fftw-3.3 has expanded
+	# the paralel options by MPI and OpenMP support, analogical
+	# USE flags should be added to select them in future;
+	# unusable with previous FFTW versions, they are postponed
+	# for now.
+	if use fftw-threads; then
+		fft_flavor="fftw3-threads"
+		if has_version '>=sci-libs/fftw-3.3'; then
+			# pkg-config files for fftw-3.3 are broken
+			# All the parallel stuff is separated
+			# from the main body of common routines,
+			# and -lfftw3 must be always included alongside.
+			# Until version 3.3 this used to be masked by
+			# .la files.
+			# Bug 384645
+			fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads) $(pkg-config --libs fftw3)"
+		else
+			fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads)"
+		fi
+	else
+		fft_libs="${fft_libs} $(pkg-config --libs fftw3)"
+	fi
+	if use mpi; then
+		MY_FC="mpif90"
+		MY_CC="mpicc"
+		MY_CXX="mpic++"
+	else
+		MY_FC="$(tc-getFC)"
+		MY_CC="$(tc-getCC)"
+		MY_CXX="$(tc-getCXX)"
+	fi
+	MARKDOWN=Markdown.pl econf \
+		$(use_enable debug debug enhanced) \
+		$(use_enable mpi) \
+		$(use_enable mpi mpi-io) \
+		--disable-smp \
+		$(use_enable vdwxc) \
+		$(use_enable cuda gpu) \
+		"$(use cuda && echo "--with-gpu-flavor=cuda-single")" \
+		"$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")" \
+		"$(use gsl && echo "--with-math-flavor=gsl")" \
+		"$(use gsl && echo "--with-math-incs=$(pkg-config --cflags gsl)")" \
+		"$(use gsl && echo "--with-math-libs=$(pkg-config --libs gsl)")" \
+		--with-linalg-flavor="atlas" \
+		--with-linalg-libs="$(pkg-config --libs lapack)" \
+		--with-trio-flavor="${trio_flavor}" \
+		"$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")" \
+		"$(use netcdf && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")" \
+		"$(use fox && echo "--with-fox-incs=${modules}")" \
+		"$(use fox && echo "--with-fox-libs=${FoX_libs}")" \
+		--with-etsf-io-incs="${modules}" \
+		--with-etsf-io-libs="${libs} -letsf_io -letsf_io_utils -letsf_io_low_level" \
+		--with-dft-flavor="libxc+bigdft+atompaw+wannier90" \
+		--with-libxc-incs="${modules}" \
+		--with-libxc-libs="${libs} -lxc" \
+		--with-bigdft-incs="${modules}" \
+		--with-bigdft-libs="${libs} -lpoissonsolver -lbigdft" \
+		--with-atompaw-incs="${modules}" \
+		--with-atompaw-libs="${libs} -latompaw" \
+		--with-wannier90-bins="/usr/bin" \
+		--with-wannier90-incs="${modules}" \
+		--with-wannier90-libs="${libs} -lwannier $(pkg-config --libs lapack)" \
+		"$(use fftw && echo "--with-fft-flavor=${fft_flavor}")" \
+		"$(use fftw && echo "--with-fft-incs=-I/usr/include")" \
+		"$(use fftw && echo "--with-fft-libs=${fft_libs}")" \
+		--with-timer-flavor="abinit" \
+		FC="${MY_FC}" \
+		CC="${MY_CC}" \
+		CXX="${MY_CXX}" \
+		LD="$(tc-getLD)" \
+		FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include"
+}
+
+src_compile() {
+	emake || die
+}
+
+src_test() {
+	einfo "The tests take quite a while, on the order of 1-2 hours"
+	einfo "on an Intel Penryn (2.5 GHz)."
+	cd "${S}"/tests
+	emake tests_min || ewarn "Minimal tests failed"
+	emake tests_paw || ewarn "PAW tests failed"
+	emake tests_gw || ewarn "GW tests failed"
+	emake tests_gw_paw || ewarn "GW-PAW tests failed"
+	emake tests tdft || ewarn "TDFT tests failed"
+	emake tests_bench || ewarn "Benchmarks failed"
+
+	local REPORT
+	for REPORT in $(find . -name report); do
+		REPORT=${REPORT#*/}
+		elog "Parameters and unusual results for ${REPORT%%/*} tests"
+		echo "Parameters and unusual results for ${REPORT%%/*} tests" >>tests_summary.txt
+		while read line; do
+			elog "${line}"
+			echo "${line}" >>tests_summary.txt
+		done \
+			< <(grep -v -e succeeded -e passed ${REPORT})
+	done
+
+	local testdir
+	find . -name "tmp-test*" -print | \
+		while read testdir; do
+			if [ -e summary_of_tests.tar ]; then
+				tar rvf summary_of_tests.tar ${testdir}
+			else tar cvf summary_of_tests.tar ${testdir}
+			fi
+		done
+
+	elog "The full test results will be installed as summary_of_tests.tar.bz2."
+	elog "Also a concise report tests_summary.txt is installed."
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die "make install failed"
+
+	if use test; then
+		dodoc tests/tests_summary.txt || ewarn "Copying tests summary failed"
+		dodoc tests/summary_tests.tar || ewarn "Copying tests results failed"
+		dodoc tests/summary_of_tests.tar || ewarn "Copying tests results failed"
+	fi
+
+	dodoc KNOWN_PROBLEMS README || die "Copying doc files failed"
+}
+
+pkg_postinst() {
+	if use test; then
+		elog "The full test results will be installed as summary_tests.tar.bz2."
+		elog "Also a concise report tests_summary.txt is installed."
+	fi
+}

diff --git a/sci-physics/atompaw/ChangeLog b/sci-physics/atompaw/ChangeLog
index ebf5c93..4687ce8 100644
--- a/sci-physics/atompaw/ChangeLog
+++ b/sci-physics/atompaw/ChangeLog
@@ -2,6 +2,18 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*atompaw-3.0.1.3 (09 Nov 2011)
+
+  09 Nov 2011; Honza Macháček <Hloupy.Honza@centrum.cz>
+  +atompaw-3.0.1.3.ebuild:
+  Version bump to 3.0.1.3
+
+*atompaw-3.0.1-r1 (09 Nov 2011)
+
+  09 Nov 2011; Honza Macháček <Hloupy.Honza@centrum.cz>
+  +files/3.0.1-longplot.patch, +atompaw-3.0.1-r1.ebuild:
+  A small patch added to produce longer plots
+
   21 Jun 2011; Justin Lecher <jlec@gentoo.org> atompaw-3.0.1.ebuild,
   +metadata.xml:
   Added fortran-2.eclass support

diff --git a/sci-physics/atompaw/atompaw-3.0.1-r1.ebuild b/sci-physics/atompaw/atompaw-3.0.1-r1.ebuild
new file mode 100644
index 0000000..1b26df1
--- /dev/null
+++ b/sci-physics/atompaw/atompaw-3.0.1-r1.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit eutils fortran-2 multilib toolchain-funcs
+
+DESCRIPTION="PAW atomic data generator"
+HOMEPAGE="http://www.wfu.edu/~natalie/papers/pwpaw/man.html"
+SRC_URI="http://www.wfu.edu/~natalie/papers/pwpaw/${P}.tar.gz
+	doc? ( http://www.wfu.edu/~natalie/papers/pwpaw/atompaw.pdf
+		http://www.wfu.edu/~natalie/papers/pwpaw/atompaw-usersguide.pdf
+		http://www.wfu.edu/~natalie/papers/pwpaw/notes/atompaw/atompawEqns.pdf )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc libxc"
+
+RDEPEND="virtual/lapack
+	virtual/blas
+	libxc? ( sci-libs/libxc[fortran] )"
+DEPEND="${RDEPEND}
+	dev-util/pkgconfig"
+
+src_unpack() {
+	unpack ${P}.tar.gz
+	if use doc; then
+		cp "${DISTDIR}"/atompaw.pdf "${S}"/
+		cp "${DISTDIR}"/atompaw-usersguide.pdf "${S}"/
+		cp "${DISTDIR}"/atompawEqns.pdf "${S}"/
+	fi
+}
+
+src_prepare() {
+	cd ${S}
+	epatch ${FILESDIR}/3.0.1-longplot.patch	      
+}
+
+src_configure() {
+	local modules="-I/usr/$(get_libdir)/finclude"
+	econf $(use_enable libxc) \
+	--with-linalg-flavor=atlas \
+	--with-linalg-libs="$(pkg-config --libs lapack)" \
+	--with-libxc-incs="${modules}" \
+	--with-libxc-libs="${libs} -lxc" \
+	FC="$(tc-getFC)" FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}}" \
+	CC="$(tc-getCC)" LDFLAGS="${LDFLAGS:- ${CFLAGS:- -O2}}"
+}
+
+src_compile() {
+	emake -j1 || die "Make failed"
+}
+
+src_test() {
+	emake check || die "Test failed"
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die "make install failed"
+
+	dodoc README || die "dodoc failed"
+
+	if use doc; then
+		dodoc atompaw.pdf atompaw-usersguide.pdf atompawEqns.pdf || die "PDF doc failed"
+	fi
+}

diff --git a/sci-physics/atompaw/atompaw-3.0.1.3.ebuild b/sci-physics/atompaw/atompaw-3.0.1.3.ebuild
new file mode 100644
index 0000000..1b26df1
--- /dev/null
+++ b/sci-physics/atompaw/atompaw-3.0.1.3.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit eutils fortran-2 multilib toolchain-funcs
+
+DESCRIPTION="PAW atomic data generator"
+HOMEPAGE="http://www.wfu.edu/~natalie/papers/pwpaw/man.html"
+SRC_URI="http://www.wfu.edu/~natalie/papers/pwpaw/${P}.tar.gz
+	doc? ( http://www.wfu.edu/~natalie/papers/pwpaw/atompaw.pdf
+		http://www.wfu.edu/~natalie/papers/pwpaw/atompaw-usersguide.pdf
+		http://www.wfu.edu/~natalie/papers/pwpaw/notes/atompaw/atompawEqns.pdf )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc libxc"
+
+RDEPEND="virtual/lapack
+	virtual/blas
+	libxc? ( sci-libs/libxc[fortran] )"
+DEPEND="${RDEPEND}
+	dev-util/pkgconfig"
+
+src_unpack() {
+	unpack ${P}.tar.gz
+	if use doc; then
+		cp "${DISTDIR}"/atompaw.pdf "${S}"/
+		cp "${DISTDIR}"/atompaw-usersguide.pdf "${S}"/
+		cp "${DISTDIR}"/atompawEqns.pdf "${S}"/
+	fi
+}
+
+src_prepare() {
+	cd ${S}
+	epatch ${FILESDIR}/3.0.1-longplot.patch	      
+}
+
+src_configure() {
+	local modules="-I/usr/$(get_libdir)/finclude"
+	econf $(use_enable libxc) \
+	--with-linalg-flavor=atlas \
+	--with-linalg-libs="$(pkg-config --libs lapack)" \
+	--with-libxc-incs="${modules}" \
+	--with-libxc-libs="${libs} -lxc" \
+	FC="$(tc-getFC)" FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}}" \
+	CC="$(tc-getCC)" LDFLAGS="${LDFLAGS:- ${CFLAGS:- -O2}}"
+}
+
+src_compile() {
+	emake -j1 || die "Make failed"
+}
+
+src_test() {
+	emake check || die "Test failed"
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die "make install failed"
+
+	dodoc README || die "dodoc failed"
+
+	if use doc; then
+		dodoc atompaw.pdf atompaw-usersguide.pdf atompawEqns.pdf || die "PDF doc failed"
+	fi
+}

diff --git a/sci-physics/atompaw/files/3.0.1-longplot.patch b/sci-physics/atompaw/files/3.0.1-longplot.patch
new file mode 100644
index 0000000..7e316bc
--- /dev/null
+++ b/sci-physics/atompaw/files/3.0.1-longplot.patch
@@ -0,0 +1,12 @@
+diff -Naur atompaw-3.0.1-orig/src/atompaw_prog.f90 atompaw-3.0.1/src/atompaw_prog.f90
+--- src/atompaw_prog.f90	2011-01-29 22:53:52.000000000 +0000
++++ src/atompaw_prog.f90	2011-06-03 12:12:36.000000000 +0000
+@@ -485,7 +485,7 @@
+      CALL mkname(io,flnm)
+      OPEN(ifout,file='wfn'//TRIM(flnm),form='formatted')
+      WRITE(ifout,*) '# l=',PAW%l(io),'basis function with energy  ',PAW%eig(io)
+-       DO i=1,irc+50
++       DO i=1,n
+           WRITE(ifout,'(1p,5e12.4)') r(i),PAW%ophi(i,io),PAW%otphi(i,io),PAW%otp(i,io)
+        ENDDO
+        CLOSE(ifout)