From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1RO5pQ-0006tK-7W for garchives@archives.gentoo.org; Wed, 09 Nov 2011 10:56:24 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 1237B21C043; Wed, 9 Nov 2011 10:56:13 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id B202921C043 for ; Wed, 9 Nov 2011 10:56:13 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 059BC1B404C for ; Wed, 9 Nov 2011 10:56:13 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 4494480042 for ; Wed, 9 Nov 2011 10:56:12 +0000 (UTC) From: "Honza Macháček" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Honza Macháček" Message-ID: <6944874e42492f433a5413c583dfe6e7abf618e1.honza_machacek@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-physics/atompaw/, sci-physics/atompaw/files/, sci-physics/abinit/ X-VCS-Repository: proj/sci X-VCS-Files: sci-physics/abinit/ChangeLog sci-physics/abinit/abinit-6.10.1.ebuild sci-physics/atompaw/ChangeLog sci-physics/atompaw/atompaw-3.0.1-r1.ebuild sci-physics/atompaw/atompaw-3.0.1.3.ebuild sci-physics/atompaw/files/3.0.1-longplot.patch X-VCS-Directories: sci-physics/atompaw/ sci-physics/atompaw/files/ sci-physics/abinit/ X-VCS-Committer: honza_machacek X-VCS-Committer-Name: Honza Macháček X-VCS-Revision: 6944874e42492f433a5413c583dfe6e7abf618e1 Date: Wed, 9 Nov 2011 10:56:12 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: 4eb2e4b5-be8c-4047-9f79-f654fe393f1d X-Archives-Hash: 9d57b7d46a98e8be34e94bc488dde71f commit: 6944874e42492f433a5413c583dfe6e7abf618e1 Author: Honza Mach=C3=A1=C4=8Dek centrum cz> AuthorDate: Wed Nov 9 10:55:57 2011 +0000 Commit: Honza Mach=C3=A1=C4=8Dek centrum cz> CommitDate: Wed Nov 9 10:55:57 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D6944874e 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: $ =20 +*abinit-6.10.1 (09 Nov 2011) + + 09 Nov 2011; Honza Mach=C3=A1=C4=8Dek + +abinit-6.10.1.ebuild: + Version bump to 6.10.1, sci-physics/atompaw ebuild updated as well, up= date of + bigDFT and other issues still to be done + *abinit-6.8.2 (27 Sep 2011) =20 27 Sep 2011; Honza Mach=C3=A1=C4=8Dek +abini= t-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=3D"3" + +inherit autotools eutils fortran-2 multilib toolchain-funcs + +DESCRIPTION=3D"Find total energy, charge density and electronic structur= e using density functional theory" +HOMEPAGE=3D"http://www.abinit.org/" +SRC_URI=3D"http://ftp.abinit.org/${P}.tar.gz" + +LICENSE=3D"GPL-2" +SLOT=3D"0" +KEYWORDS=3D"~amd64 ~x86" +IUSE=3D"cuda -debug +fftw +fftw-threads +fox gsl +hdf5 mpi +netcdf pytho= n -test +threads -vdwxc" + +RDEPEND=3D">=3Dsci-libs/bigdft-1.2.0.2 + sci-libs/etsf_io + =3Dsci-libs/libxc-1.0[fortran] + sci-physics/atompaw[libxc] + fox? ( sci-libs/fox[dom,sax,wcml,wxml] ) + netcdf? ( + sci-libs/netcdf[fortran] + hdf5? ( + sci-libs/netcdf[fortran,hdf5] + ) + ) + hdf5? ( sci-libs/hdf5[fortran] ) + sci-libs/wannier90 + virtual/blas + virtual/lapack + gsl? ( sci-libs/gsl ) + fftw? ( + sci-libs/fftw:3.0 + fftw-threads? ( sci-libs/fftw:3.0[threads] ) + ) + mpi? ( virtual/mpi ) + python? ( dev-python/numpy ) + cuda? ( dev-util/nvidia-cuda-sdk )" +DEPEND=3D"${RDEPEND} + dev-util/pkgconfig + dev-perl/Text-Markdown" + +S=3D${WORKDIR}/${P%[a-z]} + +pkg_setup() { + fortran-2_pkg_setup + # Doesn't compile with gcc-4.0, only >=3D4.1 + if [[ $(tc-getFC) =3D=3D *gfortran ]]; then + if [[ $(gcc-major-version) -eq 4 ]] \ + && [[ $(gcc-minor-version) -lt 1 ]]; then + die "Requires gcc-4.1 or newer" + fi + fi + if use fftw-threads && ! use fftw; then + ewarn "fftw-threads set but fftw not used, ignored" + fi +} + +src_prepare() { + epatch "${FILESDIR}"/6.2.2-change-default-directories.patch + epatch "${FILESDIR}"/6.0.3-fftw.patch + eautoreconf +} + +src_configure() { + local libs=3D"-L/usr/$(get_libdir)" + local modules=3D"-I/usr/$(get_libdir)/finclude" + local FoX_libs=3D"${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lF= oX_common -lFoX_utils -lFoX_fsys" + local trio_flavor=3D"etsf_io" + use fox && trio_flavor=3D"${trio_flavor}+fox" + use netcdf && trio_flavor=3D"${trio_flavor}+netcdf" + local netcdff_libs=3D"-lnetcdff" + use hdf5 && netcdff_libs=3D"${netcdff_libs} -lhdf5_fortran" + local fft_flavor=3D"fftw3" + local fft_libs=3D"-L/usr/lib" + # The fftw threads support is protected by black magick. + # Anybody removes it, dies. + # New USE flag "fftw-threads" was added to control usage + # of the threaded fftw variant. Since fftw-3.3 has expanded + # the paralel options by MPI and OpenMP support, analogical + # USE flags should be added to select them in future; + # unusable with previous FFTW versions, they are postponed + # for now. + if use fftw-threads; then + fft_flavor=3D"fftw3-threads" + if has_version '>=3Dsci-libs/fftw-3.3'; then + # pkg-config files for fftw-3.3 are broken + # All the parallel stuff is separated + # from the main body of common routines, + # and -lfftw3 must be always included alongside. + # Until version 3.3 this used to be masked by + # .la files. + # Bug 384645 + fft_libs=3D"${fft_libs} $(pkg-config --libs fftw3_threads) $(pkg-conf= ig --libs fftw3)" + else + fft_libs=3D"${fft_libs} $(pkg-config --libs fftw3_threads)" + fi + else + fft_libs=3D"${fft_libs} $(pkg-config --libs fftw3)" + fi + if use mpi; then + MY_FC=3D"mpif90" + MY_CC=3D"mpicc" + MY_CXX=3D"mpic++" + else + MY_FC=3D"$(tc-getFC)" + MY_CC=3D"$(tc-getCC)" + MY_CXX=3D"$(tc-getCXX)" + fi + MARKDOWN=3DMarkdown.pl econf \ + $(use_enable debug debug enhanced) \ + $(use_enable mpi) \ + $(use_enable mpi mpi-io) \ + --disable-smp \ + $(use_enable vdwxc) \ + $(use_enable cuda gpu) \ + "$(use cuda && echo "--with-gpu-flavor=3Dcuda-single")" \ + "$(use cuda && echo "--with-gpu-prefix=3D/opt/cuda/")" \ + "$(use gsl && echo "--with-math-flavor=3Dgsl")" \ + "$(use gsl && echo "--with-math-incs=3D$(pkg-config --cflags gsl)")" \ + "$(use gsl && echo "--with-math-libs=3D$(pkg-config --libs gsl)")" \ + --with-linalg-flavor=3D"atlas" \ + --with-linalg-libs=3D"$(pkg-config --libs lapack)" \ + --with-trio-flavor=3D"${trio_flavor}" \ + "$(use netcdf && echo "--with-netcdf-incs=3D-I/usr/include")" \ + "$(use netcdf && echo "--with-netcdf-libs=3D$(pkg-config --libs netcdf= ) ${netcdff_libs}")" \ + "$(use fox && echo "--with-fox-incs=3D${modules}")" \ + "$(use fox && echo "--with-fox-libs=3D${FoX_libs}")" \ + --with-etsf-io-incs=3D"${modules}" \ + --with-etsf-io-libs=3D"${libs} -letsf_io -letsf_io_utils -letsf_io_low= _level" \ + --with-dft-flavor=3D"libxc+bigdft+atompaw+wannier90" \ + --with-libxc-incs=3D"${modules}" \ + --with-libxc-libs=3D"${libs} -lxc" \ + --with-bigdft-incs=3D"${modules}" \ + --with-bigdft-libs=3D"${libs} -lpoissonsolver -lbigdft" \ + --with-atompaw-incs=3D"${modules}" \ + --with-atompaw-libs=3D"${libs} -latompaw" \ + --with-wannier90-bins=3D"/usr/bin" \ + --with-wannier90-incs=3D"${modules}" \ + --with-wannier90-libs=3D"${libs} -lwannier $(pkg-config --libs lapack)= " \ + "$(use fftw && echo "--with-fft-flavor=3D${fft_flavor}")" \ + "$(use fftw && echo "--with-fft-incs=3D-I/usr/include")" \ + "$(use fftw && echo "--with-fft-libs=3D${fft_libs}")" \ + --with-timer-flavor=3D"abinit" \ + FC=3D"${MY_FC}" \ + CC=3D"${MY_CC}" \ + CXX=3D"${MY_CXX}" \ + LD=3D"$(tc-getLD)" \ + FCFLAGS=3D"${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include" +} + +src_compile() { + emake || die +} + +src_test() { + einfo "The tests take quite a while, on the order of 1-2 hours" + einfo "on an Intel Penryn (2.5 GHz)." + cd "${S}"/tests + emake tests_min || ewarn "Minimal tests failed" + emake tests_paw || ewarn "PAW tests failed" + emake tests_gw || ewarn "GW tests failed" + emake tests_gw_paw || ewarn "GW-PAW tests failed" + emake tests tdft || ewarn "TDFT tests failed" + emake tests_bench || ewarn "Benchmarks failed" + + local REPORT + for REPORT in $(find . -name report); do + REPORT=3D${REPORT#*/} + elog "Parameters and unusual results for ${REPORT%%/*} tests" + echo "Parameters and unusual results for ${REPORT%%/*} tests" >>tests_= summary.txt + while read line; do + elog "${line}" + echo "${line}" >>tests_summary.txt + done \ + < <(grep -v -e succeeded -e passed ${REPORT}) + done + + local testdir + find . -name "tmp-test*" -print | \ + while read testdir; do + if [ -e summary_of_tests.tar ]; then + tar rvf summary_of_tests.tar ${testdir} + else tar cvf summary_of_tests.tar ${testdir} + fi + done + + elog "The full test results will be installed as summary_of_tests.tar.b= z2." + elog "Also a concise report tests_summary.txt is installed." +} + +src_install() { + emake DESTDIR=3D"${D}" install || die "make install failed" + + if use test; then + dodoc tests/tests_summary.txt || ewarn "Copying tests summary failed" + dodoc tests/summary_tests.tar || ewarn "Copying tests results failed" + dodoc tests/summary_of_tests.tar || ewarn "Copying tests results faile= d" + fi + + dodoc KNOWN_PROBLEMS README || die "Copying doc files failed" +} + +pkg_postinst() { + if use test; then + elog "The full test results will be installed as summary_tests.tar.bz2= ." + elog "Also a concise report tests_summary.txt is installed." + fi +} diff --git a/sci-physics/atompaw/ChangeLog b/sci-physics/atompaw/ChangeLo= g 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: $ =20 +*atompaw-3.0.1.3 (09 Nov 2011) + + 09 Nov 2011; Honza Mach=C3=A1=C4=8Dek + +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 Mach=C3=A1=C4=8Dek + +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 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/at= ompaw/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=3D3 + +inherit eutils fortran-2 multilib toolchain-funcs + +DESCRIPTION=3D"PAW atomic data generator" +HOMEPAGE=3D"http://www.wfu.edu/~natalie/papers/pwpaw/man.html" +SRC_URI=3D"http://www.wfu.edu/~natalie/papers/pwpaw/${P}.tar.gz + doc? ( http://www.wfu.edu/~natalie/papers/pwpaw/atompaw.pdf + http://www.wfu.edu/~natalie/papers/pwpaw/atompaw-usersguide.pdf + http://www.wfu.edu/~natalie/papers/pwpaw/notes/atompaw/atompawEqns.pdf= )" + +LICENSE=3D"GPL-2" +SLOT=3D"0" +KEYWORDS=3D"~amd64 ~x86" +IUSE=3D"doc libxc" + +RDEPEND=3D"virtual/lapack + virtual/blas + libxc? ( sci-libs/libxc[fortran] )" +DEPEND=3D"${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 ${FILESDIR}/3.0.1-longplot.patch =20 +} + +src_configure() { + local modules=3D"-I/usr/$(get_libdir)/finclude" + econf $(use_enable libxc) \ + --with-linalg-flavor=3Datlas \ + --with-linalg-libs=3D"$(pkg-config --libs lapack)" \ + --with-libxc-incs=3D"${modules}" \ + --with-libxc-libs=3D"${libs} -lxc" \ + FC=3D"$(tc-getFC)" FCFLAGS=3D"${FCFLAGS:- ${FFLAGS:- -O2}}" \ + CC=3D"$(tc-getCC)" LDFLAGS=3D"${LDFLAGS:- ${CFLAGS:- -O2}}" +} + +src_compile() { + emake -j1 || die "Make failed" +} + +src_test() { + emake check || die "Test failed" +} + +src_install() { + emake DESTDIR=3D"${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 d= oc failed" + fi +} diff --git a/sci-physics/atompaw/atompaw-3.0.1.3.ebuild b/sci-physics/ato= mpaw/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=3D3 + +inherit eutils fortran-2 multilib toolchain-funcs + +DESCRIPTION=3D"PAW atomic data generator" +HOMEPAGE=3D"http://www.wfu.edu/~natalie/papers/pwpaw/man.html" +SRC_URI=3D"http://www.wfu.edu/~natalie/papers/pwpaw/${P}.tar.gz + doc? ( http://www.wfu.edu/~natalie/papers/pwpaw/atompaw.pdf + http://www.wfu.edu/~natalie/papers/pwpaw/atompaw-usersguide.pdf + http://www.wfu.edu/~natalie/papers/pwpaw/notes/atompaw/atompawEqns.pdf= )" + +LICENSE=3D"GPL-2" +SLOT=3D"0" +KEYWORDS=3D"~amd64 ~x86" +IUSE=3D"doc libxc" + +RDEPEND=3D"virtual/lapack + virtual/blas + libxc? ( sci-libs/libxc[fortran] )" +DEPEND=3D"${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 ${FILESDIR}/3.0.1-longplot.patch =20 +} + +src_configure() { + local modules=3D"-I/usr/$(get_libdir)/finclude" + econf $(use_enable libxc) \ + --with-linalg-flavor=3Datlas \ + --with-linalg-libs=3D"$(pkg-config --libs lapack)" \ + --with-libxc-incs=3D"${modules}" \ + --with-libxc-libs=3D"${libs} -lxc" \ + FC=3D"$(tc-getFC)" FCFLAGS=3D"${FCFLAGS:- ${FFLAGS:- -O2}}" \ + CC=3D"$(tc-getCC)" LDFLAGS=3D"${LDFLAGS:- ${CFLAGS:- -O2}}" +} + +src_compile() { + emake -j1 || die "Make failed" +} + +src_test() { + emake check || die "Test failed" +} + +src_install() { + emake DESTDIR=3D"${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 d= oc 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/ato= mpaw_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=3D'wfn'//TRIM(flnm),form=3D'formatted') + WRITE(ifout,*) '# l=3D',PAW%l(io),'basis function with energy ',P= AW%eig(io) +- DO i=3D1,irc+50 ++ DO i=3D1,n + WRITE(ifout,'(1p,5e12.4)') r(i),PAW%ophi(i,io),PAW%otphi(i,io= ),PAW%otp(i,io) + ENDDO + CLOSE(ifout)