Index: head/science/atom/Makefile =================================================================== --- head/science/atom/Makefile (revision 482632) +++ head/science/atom/Makefile (revision 482633) @@ -1,40 +1,40 @@ # $FreeBSD$ PORTNAME= atom DISTVERSION= 4.2.7-100 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MASTER_SITES= https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/ \ https://departments.icmab.es/leem/siesta/Pseudopotentials/:lic PKGNAMESUFFIX= -chemistry DISTFILES= ${DISTNAME}${EXTRACT_SUFX} atom_licence.html:lic DIST_SUBDIR= ${PORTNAME}${PKGNAMESUFFIX} EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org COMMENT= Program for DFT calculations in atoms LICENSE= ATOM_LICENSE LICENSE_NAME= ATOM ACADEMIC LICENCE LICENSE_FILE= ${DISTDIR}/${DIST_SUBDIR}/atom_licence.html -LICENSE_PERMS= no-dist-mirror no-pkg-mirror no-pkg-sell no-auto-accept +LICENSE_PERMS= # none LIB_DEPENDS= libGridXC.so:science/libgridxc \ libxc.so:science/libxc \ libxmlf90.so:textproc/xmlf90 USES= fortran gmake tar:tgz MAKE_ENV= XMLF90_ROOT=${LOCALBASE} GRIDXC_ROOT=${LOCALBASE} LIBXC_ROOT=${LOCALBASE} MAKE_ARGS= FC=gfortran${GCC_DEFAULT} LDFLAGS="${LDFLAGS}" ALL_TARGET= default PLIST_FILES= bin/atm post-patch: @${CP} ${WRKSRC}/arch.make.sample ${WRKSRC}/arch.make do-install: ${INSTALL_PROGRAM} ${WRKSRC}/atm ${STAGEDIR}${PREFIX}/bin/ .include Index: head/science/bagel/Makefile =================================================================== --- head/science/bagel/Makefile (revision 482632) +++ head/science/bagel/Makefile (revision 482633) @@ -1,53 +1,54 @@ # $FreeBSD$ PORTNAME= bagel DISTVERSIONPREFIX= v DISTVERSION= 1.1.2-21 DISTVERSIONSUFFIX= -g2a9472a50 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Brilliantly Advanced General Electronic-structure Library LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING BROKEN_i386= error: static_assert failed "size_t is assumed to be the same size as unsigned long long" BROKEN_FreeBSD_10= /usr/include/c++/v1/memory:4004:35: error: no viable overloaded '='; __e->__weak_this_ = *this; LIB_DEPENDS= libboost_serialization.so:devel/boost-libs \ libcblas.so:math/cblas USES= autoreconf compiler:c++11-lang fortran gmake libtool localbase python:build GNU_CONFIGURE= yes CONFIGURE_ARGS= --datarootdir=${DATADIR} USE_GITHUB= yes GH_ACCOUNT= nubakery USE_CXXSTD= c++11 USE_LDCONFIG= yes OPTIONS_DEFINE= MPI LIBXC SCALAPACK SMITH # SLATER (needs a separate lib) OPTIONS_DEFAULT= MPI LIBXC SCALAPACK SMITH MPI_CONFIGURE_ON= --with-mpi=openmpi MPI_CONFIGURE_OFF= --with-mpi=no MPI_LIB_DEPENDS= libmpicxx.so:net/mpich # openmpi option erroneously links to mpich (due to a name clash) LIBXC_DESC= Build DFT with libxc LIBXC_CONFIGURE_WITH= libxc LIBXC_LIB_DEPENDS= libxc.so:science/libxc SCALAPACK_DESC= Use ScaLapack library for parallelized linear algebra SCALAPACK_CONFIGURE_ENABLE= libxc SCALAPACK_MAKE_ARGS= EXTRA_LIBS="-lcblas" SCALAPACK_MAKE_ARGS_OFF= EXTRA_LIBS="-lcblas -llapack -lblas" # -llapack -lblas are a replacement of libscalapack SCALAPACK_LIB_DEPENDS= libscalapack.so:math/scalapack SCALAPACK_LIB_DEPENDS_OFF= liblapack.so:math/lapack \ libblas.so:math/blas SCALAPACK_IMPLIES= MPI SMITH_DESC= Compile SMITH generated code SMITH_CONFIGURE_ENABLE= smith SMITH_IMPLIES= MPI .include Index: head/science/jdftx/Makefile =================================================================== --- head/science/jdftx/Makefile (revision 482632) +++ head/science/jdftx/Makefile (revision 482633) @@ -1,60 +1,60 @@ # $FreeBSD$ PORTNAME= jdftx DISTVERSIONPREFIX= v DISTVERSION= 1.4.2-74 -PORTREVISION= 1 +PORTREVISION= 2 DISTVERSIONSUFFIX= -gba743849 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Software for joint density functional theory in chemistry LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libblas.so:math/blas \ libcblas.so:math/cblas \ libfftw3.so:math/fftw3 \ libgsl.so:math/gsl \ liblapack.so:math/lapack RUN_DEPENDS= bash:shells/bash TEST_DEPENDS= bash:shells/bash USES= cmake:outsource fortran localbase:ldflags shebangfix SHEBANG_GLOB= *.sh SHEBANG_FILES= scripts/* SHEBANG_LANG= octave USE_GITHUB= yes GH_ACCOUNT= shankar1729 USE_LDCONFIG= yes TEST_TARGET= test WRKSRC_SUBDIR= ${PORTNAME} CMAKE_ARGS= -DLAPACK_LIBRARIES:STRING="-llapack -lblas" OPTIONS_DEFINE= MPI LIBXC HDF5 SCALAPACK OCTAVE OPTIONS_DEFAULT= MPI LIBXC MPI_CMAKE_BOOL= EnableMPI MPI_LIB_DEPENDS= libmpich.so:net/mpich LIBXC_DESC= Use LibXC for additional exchange-correlation functionals LIBXC_CMAKE_BOOL= EnableLibXC LIBXC_LIB_DEPENDS= libxc.so:science/libxc HDF5_CMAKE_BOOL= EnableHDF5 HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 HDF5_BROKEN= use of undeclared identifier 'H5Pset_dxpl_mpio' # https://github.com/shankar1729/jdftx/issues/37 SCALAPACK_DESC= Enable ScaLAPACK support SCALAPACK_CMAKE_BOOL= EnableScaLAPACK SCALAPACK_LIB_DEPENDS= libscalapack.so:math/scalapack OCTAVE_DESC= With Octave support (only for one script: dryRunToPDB) OCTAVE_USES= octave .include Index: head/science/libgridxc/Makefile =================================================================== --- head/science/libgridxc/Makefile (revision 482632) +++ head/science/libgridxc/Makefile (revision 482633) @@ -1,58 +1,58 @@ # $FreeBSD$ PORTNAME= libgridxc DISTVERSION= 0.8.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MASTER_SITES= https://launchpad.net/${PORTNAME}/trunk/${DISTVERSION:R}/+download/ MAINTAINER= yuri@FreeBSD.org COMMENT= Library to compute the exchange and correlation energy and potentials LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/../BSD_LICENSE USES= fortran gmake tar:tgz USE_LDCONFIG= yes MAKEFILE= makefile ALL_TARGET= default WRKSRC_SUBDIR= src BUILD_WRKSRC= ${WRKSRC}/../build TMP_STAGEDIR= ${WRKDIR}/tmp_stage MAKE_ENV= INSTALL_DIR=${TMP_STAGEDIR}${PREFIX} FREEBSD_LOCALBASE=${LOCALBASE} BINARY_ALIAS= make=${GMAKE} OPTIONS_DEFINE= MPI LIBXC OPTIONS_DEFAULT= MPI LIBXC MPI_MAKE_ENV= WITH_MPI=1 MPI_LIB_DEPENDS= libmpich.so:net/mpich LIBXC_DESC= Use libxc for exchange-correlation functionals for DFT LIBXC_MAKE_ENV= WITH_LIBXC=1 LIBXC_LIB_DEPENDS= libxc.so:science/libxc post-patch: @${MKDIR} ${BUILD_WRKSRC} @${CAT} ${WRKSRC}/../extra/fortran.mk \ | ${SED} '\ s|FC_SERIAL=gfortran|&${GCC_DEFAULT}|; \ s|LIBXC_ROOT=/usr/local|LIBXC_ROOT=${LOCALBASE}|; \ s|FFLAGS= -O2|& -fPIC|' \ > ${BUILD_WRKSRC}/fortran.mk do-configure: @cd ${BUILD_WRKSRC} && ${SETENV} ${CONFIGURE_ENV} ${SH} ../src/config.sh do-build: @cd ${BUILD_WRKSRC} && ${MKDIR} ${TMP_STAGEDIR} && ${SETENV} ${MAKE_ENV} ${SH} ../src/build.sh do-install: cd ${TMP_STAGEDIR} && ${COPYTREE_SHARE} . ${STAGEDIR} ${MKDIR} ${STAGEDIR}${PREFIX}/share/mk && ${MV} ${STAGEDIR}${PREFIX}/*.mk ${STAGEDIR}${PREFIX}/share/mk .include Index: head/science/libxc/Makefile =================================================================== --- head/science/libxc/Makefile (revision 482632) +++ head/science/libxc/Makefile (revision 482633) @@ -1,27 +1,22 @@ # Created by: Johannes Dieterich # $FreeBSD$ PORTNAME= libxc -PORTVERSION= 3.0.0 -PORTREVISION= 5 +DISTVERSION= 4.2.3 CATEGORIES= science -MASTER_SITES= http://www.tddft.org/programs/octopus/download/libxc/ +MASTER_SITES= http://www.tddft.org/programs/octopus/download/libxc/${DISTVERSION}/ MAINTAINER= dieterich@ogolem.org COMMENT= Library of exchange-correlation functionals for DFT LICENSE= LGPL3+ LICENSE_FILE= ${WRKSRC}/COPYING USES= fortran gmake libtool perl5 GNU_CONFIGURE= yes -CONFIGURE_ARGS= --enable-shared +CONFIGURE_ARGS= --enable-shared --disable-static USE_LDCONFIG= yes INSTALL_TARGET= install-strip - -post-patch: - @${REINPLACE_CMD} -e '/^pkgconfigdir =/s,libdir),prefix)/libdata,' \ - ${WRKSRC}/build/Makefile.in .include Index: head/science/libxc/distinfo =================================================================== --- head/science/libxc/distinfo (revision 482632) +++ head/science/libxc/distinfo (revision 482633) @@ -1,2 +1,3 @@ -SHA256 (libxc-3.0.0.tar.gz) = 5542b99042c09b2925f2e3700d769cda4fb411b476d446c833ea28c6bfa8792a -SIZE (libxc-3.0.0.tar.gz) = 8388775 +TIMESTAMP = 1540063598 +SHA256 (libxc-4.2.3.tar.gz) = 02e49e9ba7d21d18df17e9e57eae861e6ce05e65e966e1e832475aa09e344256 +SIZE (libxc-4.2.3.tar.gz) = 15601356 Index: head/science/libxc/files/patch-src_xc.h =================================================================== --- head/science/libxc/files/patch-src_xc.h (nonexistent) +++ head/science/libxc/files/patch-src_xc.h (revision 482633) @@ -0,0 +1,11 @@ +--- src/xc.h.orig 2018-10-20 19:30:09 UTC ++++ src/xc.h +@@ -14,7 +14,7 @@ extern "C" { + #endif + + #ifdef HAVE_CONFIG_H +-#include "config.h" ++//#include "config.h" // "config.h" should never be included by the installed package: https://gitlab.com/libxc/libxc/issues/66 + #endif + + #include Property changes on: head/science/libxc/files/patch-src_xc.h ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/libxc/pkg-descr =================================================================== --- head/science/libxc/pkg-descr (revision 482632) +++ head/science/libxc/pkg-descr (revision 482633) @@ -1,9 +1,9 @@ Libxc is library of exchange-correlation functionals for density-functional -theory. The aim is to provide a portable, well tested and reliable set of +theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals that can be used by all the ETSF codes and also other codes. In libxc you can find different types of functionals: LDA, GGA, hybrids, and mGGA (experimental). -WWW: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc +WWW: http://www.tddft.org/programs/libxc/ Index: head/science/libxc/pkg-plist =================================================================== --- head/science/libxc/pkg-plist (revision 482632) +++ head/science/libxc/pkg-plist (revision 482633) @@ -1,23 +1,22 @@ bin/xc-info +bin/xc-threshold include/libxc_funcs_m.mod include/xc.h -include/xc_config.h include/xc_f03_lib_m.mod include/xc_f90_lib_m.mod include/xc_f90_types_m.mod include/xc_funcs.h -include/xc_unconfig.h +include/xc_funcs_removed.h include/xc_version.h -lib/libxc.a lib/libxc.so -lib/libxc.so.4 -lib/libxc.so.4.0.0 -lib/libxcf03.a +lib/libxc.so.5 +lib/libxc.so.5.2.3 lib/libxcf03.so -lib/libxcf03.so.4 -lib/libxcf03.so.4.0.0 -lib/libxcf90.a +lib/libxcf03.so.5 +lib/libxcf03.so.5.2.3 lib/libxcf90.so -lib/libxcf90.so.4 -lib/libxcf90.so.4.0.0 +lib/libxcf90.so.5 +lib/libxcf90.so.5.2.3 libdata/pkgconfig/libxc.pc +libdata/pkgconfig/libxcf03.pc +libdata/pkgconfig/libxcf90.pc Index: head/science/madness/Makefile =================================================================== --- head/science/madness/Makefile (revision 482632) +++ head/science/madness/Makefile (revision 482633) @@ -1,30 +1,30 @@ # $FreeBSD$ PORTNAME= madness DISTVERSION= 0.10.1.20180823 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Multiresolution adaptive numeric environment for scientific simulation LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= libsysinfo>0:devel/libsysinfo LIB_DEPENDS= libblas.so:math/blas \ liblapack.so:math/lapack \ libmpich.so:net/mpich \ libtbb.so:devel/tbb \ libtcmalloc.so:devel/google-perftools \ libxc.so:science/libxc USES= cmake:outsource compiler:c++14-lang fortran localbase:ldflags python:build USE_GITHUB= yes GH_ACCOUNT= m-a-d-n-e-s-s GH_TAGNAME= ebb3fd7 USE_LDCONFIG= yes CMAKE_ARGS= -DLAPACK_LIBRARIES:STRING="-L${LOCALBASE}/lib -llapack -lblas -L${LOCALBASE}/lib/gcc${GCC_DEFAULT} -lgcc_s" -DPYTHON_EXECUTABLE=${PYTHON_CMD} .include Index: head/science/octopus/Makefile =================================================================== --- head/science/octopus/Makefile (revision 482632) +++ head/science/octopus/Makefile (revision 482633) @@ -1,38 +1,38 @@ # $FreeBSD$ PORTNAME= octopus DISTVERSION= 8.2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MASTER_SITES= http://www.tddft.org/programs/${PORTNAME}/download/${DISTVERSION}/ MAINTAINER= yuri@FreeBSD.org COMMENT= Scientific program aimed at the ab initio virtual experimentation LICENSE= GPLv2 BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libarpack.so:math/arpack-ng \ libblas.so:math/blas \ libfftw3.so:math/fftw3 \ libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 \ libgd.so:graphics/gd \ libgsl.so:math/gsl \ liblapack.so:math/lapack \ libpng16.so:graphics/png \ libtiff.so:graphics/tiff \ libwebp.so:graphics/webp \ libxc.so:science/libxc USES= compiler:c++11-lang fortran gmake jpeg localbase:ldflags GNU_CONFIGURE= yes CONFIGURE_SHELL= ${PREFIX}/bin/bash USE_CXXSTD= c++11 FCFLAGS+= -I${LOCALBASE}/include -ffree-line-length-none post-stage: # https://gitlab.com/octopus-code/octopus/issues/108 @${RM} ${STAGEDIR}${PREFIX}/include/yaml.h .include Index: head/science/py-gpaw/Makefile =================================================================== --- head/science/py-gpaw/Makefile (revision 482632) +++ head/science/py-gpaw/Makefile (revision 482633) @@ -1,31 +1,31 @@ # $FreeBSD$ PORTNAME= gpaw DISTVERSION= 1.4.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= DFT and beyond within the projector-augmented wave method in chemistry LICENSE= GPLv3+ BUILD_DEPENDS= ${PYNUMPY} LIB_DEPENDS= libmpich.so:net/mpich \ libopenblas.so:math/openblas \ libxc.so:science/libxc RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}ase>0:science/py-ase@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${PYNUMPY} USES= gettext-runtime localbase python shebangfix GH_ACCOUNT= psychopy USE_PYTHON= distutils concurrent autoplist SHEBANG_FILES= tools/* post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/gpaw-python ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/_gpaw.so .include