diff --git a/science/abinit/Makefile b/science/abinit/Makefile index 099a63b63abf..f0fed6fadc27 100644 --- a/science/abinit/Makefile +++ b/science/abinit/Makefile @@ -1,137 +1,137 @@ PORTNAME= abinit DISTVERSION= 10.6.5 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Full-featured atomic-scale first-principles simulation software WWW= https://www.abinit.org \ https://github.com/abinit/abinit LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING ONLY_FOR_ARCHS= amd64 powerpc64 powerpc64le BUILD_DEPENDS= gm4:devel/m4 \ ${PYTHON_PKGNAMEPREFIX}numpy1>=1.16:math/py-numpy1@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pygments>=0:textproc/py-pygments@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}graphviz>0:graphics/py-graphviz@${PY_FLAVOR} LIB_DEPENDS= libelpa.so:math/elpa \ libsz.so:science/libaec \ libxc.so:science/libxc \ libfftw3.so:math/fftw3 \ libfftw3f.so:math/fftw3-float \ libhdf5.so:science/hdf5 \ libnetcdf.so:science/netcdf \ libxmlf90.so:textproc/xmlf90 \ libwannier.so:science/wannier90 \ libnetcdff.so:science/netcdf-fortran RUN_DEPENDS= atompaw:science/atompaw TEST_DEPENDS= bash:shells/bash \ ${PYTHON_PKGNAMEPREFIX}numpy1>=1.16:math/py-numpy1@${PY_FLAVOR} \ libyaml>0:textproc/libyaml USES= autoreconf:build blaslapack:netlib fortran gmake gnome localbase:ldflags \ python shebangfix USE_GITHUB= yes USE_GNOME= libxml2 SHEBANG_FILES= config/scripts/* doc/tutorial/paral_bandpw_assets/abinit.sub.* SHEBANG_GLOB= *.py *.sh GNU_CONFIGURE= yes CONFIGURE_ENV= H5CC="${LOCALBASE}/bin/h5cc" \ HDF5_CFLAGS="-I${LOCALBASE}/include" \ HDF5_LDFLAGS="-L${LOCALBASE}/lib -lhdf5" \ LINALG_FCFLAGS="-I${LOCALBASE}/include/elpa-2019.05.002/modules" \ LINALG_LIBS="${BLASLIB} ${LAPACKLIB} -lelpa" \ NETCDF_FORTRAN_FCFLAGS=-I${LOCALBASE}/include \ XMLF90_FCFLAGS=-I${LOCALBASE}/include/xmlf90 \ WANNIER90_LIBS="${BLASLIB} ${LAPACKLIB} -lwannier" CONFIGURE_ARGS= --with-fft --with-libxc --with-libxml2 --with-netcdf \ --with-netcdf-fortran --with-wannier90 --with-xmlf90 FCFLAGS+= -ffree-line-length-none TEST_TARGET= tests_abirules tests_buildsys # Many tests print RuntimeError, https://github.com/abinit/abinit/issues/64 TEST_WRKSRC= ${WRKSRC}/abichecks PORTDOCS= * BINARY_ALIAS= git=false \ gfortran=gfortran${GCC_DEFAULT} # for tests OPTIONS_DEFINE= DOCS OPENMP OPTIONS_DEFAULT= MPICH OPTIONS_RADIO= MPIX OPTIONS_RADIO_MPIX= NOMPI MPICH OPENMPI OPENMP_CONFIGURE_ENABLE= openmp OPENMP_LDFLAGS= -lomp MIX_DESC= MPI options NOMPI_DESC= Do not use MPI NOMPI_CONFIGURE_ON= CC_LDFLAGS="${LDFLAGS}" CXX_LDFLAGS="${LDFLAGS}" \ FC_LDFLAGS="${LDFLAGS}" CFLAGS="${CFLAGS}" OPENMPI_USES= mpi:openmpi OPENMPI_CONFIGURE_ON= mpi=yes OPENMPI_VARS= FCFLAGS+="`pkg-config --cflags ompi-fort`" \ CFLAGS+="${MPI_CFLAGS}" \ LDFLAGS+="${MPI_LDFLAGS}" OPENMPI_CONFIGURE_ENV= ${MPIX_CONFIGURE_ENV} \ MPI_FCFLAGS="`pkg-config --cflags ompi-fort`" MPICH_USES= mpi:mpich MPICH_CONFIGURE_ON= mpi=yes MPICH_VARS= FFLAGS+=-I${LOCALBASE}/include FCFLAGS+=-I${LOCALBASE}/include \ CONFIGURE_ENV+=MPI_LIBS="`pkg-config --libs mpich` -lmpifort" \ CONFIGURE_ENV+MPI_LDFLAGS="`pkg-config --libs mpich` -lmpifort" MPICH_CONFIGURE_ENV= ${MPIX_CONFIGURE_ENV} MPIX_CONFIGURE_ENV= CC_LDFLAGS="${MPI_LIBS} ${LDFLAGS}" \ CXX_LDFLAGS="${MPI_LIBS} ${LDFLAGS}" \ FC_LDFLAGS="${MPI_LIBS} ${LDFLAGS}" \ CFLAGS="${MPI_CFLAGS} ${CFLAGS} ${CFLAGS_F2018}" \ MPI_CPPFLAGS="${MPI_CFLAGS}" \ MPI_LIBS="${MPI_LIBS}" \ MPI_LDFLAGS="${MPI_LIBS}" # When OpenMPI is enabled, put its related variables 1st to avoid conflicts with MPICH .if defined(WITH_LEVMAR) # --with-levmar seems deprecated LIB_DEPENDS+= liblevmar.so:math/levmar CONFIGURE_ENV+= LEVMAR_LIBS="-llevmar ${BLASLIB} ${LAPACKLIB}" CONFIGURE_ARGS+= --with-levmar .endif .include .if ${GCC_DEFAULT} >= 10 FCFLAGS+= -fallow-argument-mismatch # see https://github.com/abinit/abinit/issues/41 .endif pre-configure: # version lines below are workaround for https://github.com/abinit/abinit/issues/75 @cd ${WRKSRC} && \ ${ECHO} ${PORTVERSION} > .version && \ ${ECHO} ${PORTVERSION} > .tarball-version && \ ./autogen.sh post-install-DOCS-on: ${REINPLACE_CMD} -e 's|/usr/bin/env python|${PYTHON_CMD}|' \ ${WRKSRC}/doc/tutorial/paral_moldyn_assets/diag_moldyn.py ${RM} ${WRKSRC}/doc/tutorial/paral_moldyn_assets/diag_moldyn.py.bak @${MKDIR} ${STAGEDIR}${DOCSDIR} ${CP} -R ${WRKSRC}/doc/tutorial ${STAGEDIR}${DOCSDIR} pre-test: ${TOUCH} ${TEST_WRKSRC}/make.log test-long: # run all examples from tutorial/Input @cd ${WRKSRC}/tests/tutorial/Input && \ for abi in `${LS} *.abi`; do \ ${ECHO} "===> Running example $$abi" && \ ${SETENV} PATH=${STAGEDIR}${PREFIX}/bin:${PATH} ABI_PSPDIR=${WRKSRC}/tests/Psps_for_tests abinit $$abi; \ done # fftw3 not enabled because libfftw3_mpi is required but not packaged .include diff --git a/science/atompaw/Makefile b/science/atompaw/Makefile index 0178900bea72..081e7e39ec7d 100644 --- a/science/atompaw/Makefile +++ b/science/atompaw/Makefile @@ -1,31 +1,32 @@ PORTNAME= atompaw DISTVERSION= 4.2.0.5 +PORTREVISION= 1 CATEGORIES= science MASTER_SITES= http://users.wfu.edu/natalie/papers/pwpaw/ MAINTAINER= yuri@FreeBSD.org COMMENT= Tool for projector augmented wave functions for molecular simulations WWW= https://users.wfu.edu/natalie/papers/pwpaw/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING USES= blaslapack:openblas fortran gmake libtool MAKE_JOBS_UNSAFE=yes GNU_CONFIGURE= yes CONFIGURE_ARGS= --with-linalg-prefix=${LOCALBASE} \ --with-linalg-libs=${BLASLIB} OPTIONS_DEFINE= DOCS LIBXC OPTIONS_DEFAULT= LIBXC LIBXC_DESC= Build with libxc LIBXC_CONFIGURE_ENABLE= libxc LIBXC_LIB_DEPENDS= libxc.so:science/libxc PORTDOCS= * PLIST_FILES= bin/atompaw \ bin/atompaw_aeonly .include diff --git a/science/bagel/Makefile b/science/bagel/Makefile index cdc1992d6691..dbb2db20d02d 100644 --- a/science/bagel/Makefile +++ b/science/bagel/Makefile @@ -1,62 +1,62 @@ PORTNAME= bagel DISTVERSIONPREFIX= v DISTVERSION= 1.2.2-132 -PORTREVISION= 18 DISTVERSIONSUFFIX= -g2955e4d1a +PORTREVISION= 19 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Brilliantly Advanced General Electronic-structure Library WWW= https://nubakery.org/ \ https://github.com/qsimulate-open/bagel LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING BROKEN_armv7= error: static_assert failed "size_t is assumed to be the same size as unsigned long long" BROKEN_i386= error: static_assert failed "size_t is assumed to be the same size as unsigned long long" LIB_DEPENDS= libboost_serialization.so:devel/boost-libs TEST_DEPENDS= cblas>0:math/cblas USES= autoreconf blaslapack:openblas compiler:c++11-lang fortran gmake libtool localbase python:build USE_CXXSTD= c++11 USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= qsimulate-open GNU_CONFIGURE= yes CONFIGURE_ARGS= --datarootdir=${DATADIR} INSTALL_TARGET= install-strip 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= scalapack SCALAPACK_VARS= LDFLAGS+="-lscalapack" SCALAPACK_VARS_OFF= LDFLAGS+="${BLASLIB} ${LAPACKLIB}" # -llapack -lblas are a replacement of libscalapack SCALAPACK_LIB_DEPENDS= libscalapack.so:math/scalapack SCALAPACK_IMPLIES= MPI SMITH_DESC= Compile SMITH generated code SMITH_CONFIGURE_ENABLE= smith SMITH_IMPLIES= MPI TEST_TARGET= check TEST_ARGS= LDFLAGS+="-lcblas -lblas" ${TEST_TARGET} post-test: # tests fail, see https://github.com/qsimulate-open/bagel/issues/248 @cd ${WRKSRC}/src && ./TestSuite --log_level=all .include diff --git a/science/bagel/files/patch-src_scf_ks_xcfunc.h b/science/bagel/files/patch-src_scf_ks_xcfunc.h new file mode 100644 index 000000000000..0004f3c0ac0d --- /dev/null +++ b/science/bagel/files/patch-src_scf_ks_xcfunc.h @@ -0,0 +1,10 @@ +--- src/scf/ks/xcfunc.h.orig 2026-04-20 18:27:14 UTC ++++ src/scf/ks/xcfunc.h +@@ -33,6 +33,7 @@ + #include + #ifdef HAVE_XC_H + #include // header provided by libxc ++#include + #endif + + namespace bagel { diff --git a/science/helfem/Makefile b/science/helfem/Makefile index 8b9147f44dd0..314a717586c7 100644 --- a/science/helfem/Makefile +++ b/science/helfem/Makefile @@ -1,29 +1,29 @@ PORTNAME= helfem DISTVERSION= g20251026 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= Finite element methods for electronic structure calculations WWW= https://github.com/susilehtola/HelFEM LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libarmadillo.so:math/armadillo \ libgsl.so:math/gsl \ libhdf5_cpp.so:science/hdf5 \ libsz.so:science/libaec \ libxc.so:science/libxc USES= cmake fortran USE_CXXSTD= c++14 USE_GITHUB= yes GH_ACCOUNT= susilehtola GH_PROJECT= HelFEM GH_TAGNAME= ca3fa54 CMAKE_ON= HELFEM_FIND_DEPS BUILD_SHARED_LIBS .include diff --git a/science/jdftx/Makefile b/science/jdftx/Makefile index 96c88a2564c6..0091a26e0b0c 100644 --- a/science/jdftx/Makefile +++ b/science/jdftx/Makefile @@ -1,58 +1,58 @@ PORTNAME= jdftx DISTVERSIONPREFIX= v DISTVERSION= 1.7.0 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Software for joint density functional theory in chemistry WWW= https://jdftx.org/ 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= compiler:c++11-lang cmake 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= ${PORTNAME} CMAKE_ARGS= -DLAPACK_LIBRARIES:STRING="-llapack -lblas" OPTIONS_DEFINE= MPI LIBXC HDF5 SCALAPACK OCTAVE OPTIONS_DEFAULT= MPI LIBXC MPI_CMAKE_BOOL= EnableMPI MPI_LIB_DEPENDS= libmpich.so:net/mpich LIBXC_DESC= Use LibXC for additional exchange-correlation functionals LIBXC_CMAKE_BOOL= EnableLibXC LIBXC_LIB_DEPENDS= libxc.so:science/libxc HDF5_CMAKE_BOOL= EnableHDF5 HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 HDF5_BROKEN= use of undeclared identifier 'H5Pset_dxpl_mpio' # https://github.com/shankar1729/jdftx/issues/37 SCALAPACK_DESC= Enable ScaLAPACK support SCALAPACK_CMAKE_BOOL= EnableScaLAPACK SCALAPACK_LIB_DEPENDS= libscalapack.so:math/scalapack OCTAVE_DESC= With Octave support (only for one script: dryRunToPDB) OCTAVE_RUN_DEPENDS= octave:math/octave .include diff --git a/science/jdftx/files/patch-CMakeLists.txt b/science/jdftx/files/patch-CMakeLists.txt index 3c9bf7e13e53..65a3be9891ab 100644 --- a/science/jdftx/files/patch-CMakeLists.txt +++ b/science/jdftx/files/patch-CMakeLists.txt @@ -1,37 +1,37 @@ ---- CMakeLists.txt.orig 2018-08-24 15:03:02 UTC +--- CMakeLists.txt.orig 2022-01-04 20:31:13 UTC +++ CMakeLists.txt -@@ -97,7 +97,7 @@ if(EnableMPI) +@@ -104,7 +104,7 @@ endif() add_definitions("-DMPI_ENABLED") endif() -option(EnableLibXC "Use LibXC to provide additional exchange-correlation functionals") +option(EnableLibXC "Use LibXC to provide additional exchange-correlation functionals" OFF) if(EnableLibXC) find_package(LIBXC REQUIRED) include_directories(${LIBXC_INCLUDE_DIR}) -@@ -223,7 +223,7 @@ endif() +@@ -232,7 +232,7 @@ add_library(jdftxlib ${LINK_TYPE} ${jdftxlibSources}) #Library with all the functionality: FILE(GLOB jdftxlibSources core/*.cpp fluid/*.cpp electronic/*.cpp commands/*.cpp) add_library(jdftxlib ${LINK_TYPE} ${jdftxlibSources}) -target_link_libraries(jdftxlib ${EXTERNAL_LIBS}) +target_link_libraries(jdftxlib ${EXTERNAL_LIBS} -lexecinfo) # execinfo only for libxc? set_target_properties(jdftxlib PROPERTIES OUTPUT_NAME "jdftx") + install(TARGETS jdftxlib LIBRARY DESTINATION lib ARCHIVE DESTINATION lib) set_JDFTx_flags(jdftxlib OFF) - -@@ -232,6 +232,16 @@ set_JDFTx_flags(jdftxlib OFF) +@@ -241,6 +241,16 @@ option(EnableCuSolver "Whether to use cuSolver GPU LAP + #----- Add another set of libraries and executables with a _gpu suffix option(EnableCUDA "Enable NVIDIA GPU support using CUDA" OFF) option(EnableCuSolver "Whether to use cuSolver GPU LAPACK (Requires CUDA >= 9)" OFF) - ++ +include(CheckFunctionExists) +CHECK_FUNCTION_EXISTS(sincos HAVE_SINCOS_FUNCTION) + +if(NOT HAVE_SINCOS_FUNCTION) + MESSAGE("Do not have function sincos") + add_definitions("-DMISSING_SINCOS_FUNCTION") +else() + MESSAGE("Found function sincos") +endif() -+ + if(EnableCUDA) find_package(CUDA REQUIRED) - set(CUDA_ARCH "compute_35" CACHE STRING "CUDA virtual architecture to compile for") diff --git a/science/jdftx/files/patch-commands_elec__ex__corr.cpp b/science/jdftx/files/patch-commands_elec__ex__corr.cpp new file mode 100644 index 000000000000..b8a37ceff13b --- /dev/null +++ b/science/jdftx/files/patch-commands_elec__ex__corr.cpp @@ -0,0 +1,10 @@ +--- commands/elec_ex_corr.cpp.orig 2026-04-20 16:31:08 UTC ++++ commands/elec_ex_corr.cpp +@@ -76,6 +76,7 @@ EnumStringMap kineticDescriptionMap( + + #ifdef LIBXC_ENABLED + #include ++#include + #include //autogenerated during cmake + + //Get description by temporarily initializing functional: diff --git a/science/libxc/Makefile b/science/libxc/Makefile index 38fa9487e013..3e9696cd14f9 100644 --- a/science/libxc/Makefile +++ b/science/libxc/Makefile @@ -1,28 +1,29 @@ PORTNAME= libxc -DISTVERSION= 6.2.2 +DISTVERSION= 7.0.0 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Library of exchange-correlation functionals for DFT WWW= https://gitlab.com/libxc/libxc LICENSE= MPL20 LICENSE_FILE= ${WRKSRC}/COPYING TEST_DEPENDS= bash:shells/bash USES= cmake:testing fortran python USE_LDCONFIG= yes USE_GITLAB= yes -GL_TAGNAME= 0a19bedb24d258b2019eb2d027c1b1039d3e6503 CMAKE_ON= BUILD_SHARED_LIBS ENABLE_FORTRAN ENABLE_PYTHON CMAKE_OFF= BUILD_TESTING DISABLE_KXC ENABLE_XHOST pre-configure: ${REINPLACE_CMD} -e 's|$${CMAKE_INSTALL_LIBDIR}/pylibxc$$|${PYTHONPREFIX_SITELIBDIR}/pylibxc|' \ -e 's|$${CMAKE_INSTALL_PREFIX}/$${CMAKE_INSTALL_LIBDIR}/pylibxc/|${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pylibxc/|'\ ${WRKSRC}/CMakeLists.txt +# tests as of 7.0.0: 100% tests passed, 0 tests failed out of 20556 + .include diff --git a/science/libxc/distinfo b/science/libxc/distinfo index ddd838272150..f884d610dac1 100644 --- a/science/libxc/distinfo +++ b/science/libxc/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1712202616 -SHA256 (libxc-libxc-0a19bedb24d258b2019eb2d027c1b1039d3e6503_GL0.tar.gz) = a32d358c7e83715333cd351b8fbd4ad890b81dd53a9e54a5c9ba5e9341210e9a -SIZE (libxc-libxc-0a19bedb24d258b2019eb2d027c1b1039d3e6503_GL0.tar.gz) = 65298815 +TIMESTAMP = 1776702032 +SHA256 (libxc-7.0.0.tar.bz2) = e9ae69f8966d8de6b7585abd9fab588794ada1fab8f689337959a35abbf9527d +SIZE (libxc-7.0.0.tar.bz2) = 52408700 diff --git a/science/libxc/pkg-plist b/science/libxc/pkg-plist index 45cc2260d2a1..61ad4a33522e 100644 --- a/science/libxc/pkg-plist +++ b/science/libxc/pkg-plist @@ -1,31 +1,28 @@ bin/xc-info include/xc.h +include/xc_f03_funcs_m.mod include/xc_f03_lib_m.mod -include/xc_f90_lib_m.mod include/xc_funcs.h include/xc_funcs_removed.h include/xc_funcs_worker.h include/xc_version.h lib/cmake/Libxc/LibxcConfig.cmake lib/cmake/Libxc/LibxcConfigVersion.cmake lib/cmake/Libxc/LibxcTargets-C-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/Libxc/LibxcTargets-C.cmake lib/cmake/Libxc/LibxcTargets-Fortran-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/Libxc/LibxcTargets-Fortran.cmake lib/libxc.so -lib/libxc.so.12 +lib/libxc.so.15 lib/libxcf03.so -lib/libxcf03.so.12 -lib/libxcf90.so -lib/libxcf90.so.12 +lib/libxcf03.so.15 %%PYTHON_SITELIBDIR%%/pylibxc/__init__.py %%PYTHON_SITELIBDIR%%/pylibxc/core.py %%PYTHON_SITELIBDIR%%/pylibxc/flags.py %%PYTHON_SITELIBDIR%%/pylibxc/functional.py %%PYTHON_SITELIBDIR%%/pylibxc/libxc.so %%PYTHON_SITELIBDIR%%/pylibxc/structs.py %%PYTHON_SITELIBDIR%%/pylibxc/util.py %%PYTHON_SITELIBDIR%%/pylibxc/version.py libdata/pkgconfig/libxc.pc libdata/pkgconfig/libxcf03.pc -libdata/pkgconfig/libxcf90.pc diff --git a/science/madness/Makefile b/science/madness/Makefile index 16b551ac2834..cf7c2571253e 100644 --- a/science/madness/Makefile +++ b/science/madness/Makefile @@ -1,35 +1,35 @@ PORTNAME= madness DISTVERSION= 0.10.1.20180823 -PORTREVISION= 18 +PORTREVISION= 19 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Multiresolution adaptive numeric environment for scientific simulation WWW= https://github.com/m-a-d-n-e-s-s/madness LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= libsysinfo>0:devel/libsysinfo LIB_DEPENDS= libblas.so:math/blas \ liblapack.so:math/lapack \ libmpich.so:net/mpich \ libtcmalloc.so:devel/google-perftools \ libxc.so:science/libxc USES= cmake compiler:c++14-lang fortran localbase:ldflags python:build USE_GITHUB= yes GH_ACCOUNT= m-a-d-n-e-s-s GH_TAGNAME= ebb3fd7 USE_LDCONFIG= yes CMAKE_ARGS= -DLAPACK_LIBRARIES:STRING="-L${LOCALBASE}/lib -llapack -lblas -L${LOCALBASE}/lib/gcc${GCC_DEFAULT} -lgcc_s" -DPYTHON_EXECUTABLE=${PYTHON_CMD} OPTIONS_DEFINE= TBB #OPTIONS_DEFAULT= TBB # oneTBB support needs to be fixed: https://github.com/m-a-d-n-e-s-s/madness/issues/366 TBB_DESC= Enables use of Intel Thread Building Blocks TBB_CMAKE_BOOL= ENABLE_TBB TBB_LIB_DEPENDS= libtbb.so:devel/tbb .include diff --git a/science/openmolcas/Makefile b/science/openmolcas/Makefile index 0485a6c8d024..0a9357a84d81 100644 --- a/science/openmolcas/Makefile +++ b/science/openmolcas/Makefile @@ -1,66 +1,67 @@ PORTNAME= openmolcas DISTVERSION= 26.02 +PORTREVISION= 1 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= Quantum chemistry software package WWW= https://gitlab.com/Molcas/OpenMolcas LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_armv7= build breaks: Symbol 'maxfilesize' at (1) has no IMPLICIT type; did you mean 'mxfile'? - see https://gitlab.com/Molcas/OpenMolcas/-/issues/375 BROKEN_i386= build breaks: Symbol 'maxfilesize' at (1) has no IMPLICIT type; did you mean 'mxfile'? - see https://gitlab.com/Molcas/OpenMolcas/-/issues/375 BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pyparsing>0:devel/py-pyparsing@${PY_FLAVOR} \ chemps2:science/chemps2 LIB_DEPENDS= libhdf5.so:science/hdf5 \ libsz.so:science/libaec \ libxc.so:science/libxc USES= cmake:testing fortran python shebangfix USE_GCC= yes # see https://gitlab.com/Molcas/OpenMolcas/-/issues/351 USE_GITLAB= yes GL_ACCOUNT= Molcas GL_PROJECT= OpenMolcas GL_TAGNAME= 3cb6f2cd61a5d482611d85c47dcb61f8d51d50ba USE_GITHUB= nodefault GH_TUPLE= Reference-LAPACK:lapack:04b044e0:lapack/External/lapack \ ilyak:libefp:7d1ff5fd:libefp/External/efp \ mcodev31:libmsym:0e0b831c:libmsym/External/libmsym \ libwfa:libwfa:a44aca25:libwfa/External/libwfa SHEBANG_FILES= sbin/help_doc sbin/help_func sbin/help_basis sbin/setup sbin/verify sbin/version SHEBANG_GLOB= *.py CMAKE_ON= CHEMPS2 EFPLIB MSYM # TODO GEN1INT - package doesn't install itself, WFA - breaks due to https://gitlab.com/conradsnicta/armadillo-code/-/issues/216 CMAKE_ARGS= -DEXTERNAL_LIBXC:STRING=${LOCALBASE} \ -DFREEBSD_PYTHON_VER:STRING=${PYTHON_VER} CMAKE_OFF= BUILD_TESTING CMAKE_INSTALL_PREFIX= ${DATADIR} # installed into DATADIR because it doesn't respect UNIX file path conventions, see https://gitlab.com/Molcas/OpenMolcas/-/issues/352 BINARY_ALIAS= cpp=${CPP} # cpp is called from cmake scripts BINARY_ALIAS+= python3=${PYTHON_CMD} # cpp is called from cmake scripts post-patch: # fix python path @${REINPLACE_CMD} -e "s|'/usr/bin/env python3'|'${PYTHON_CMD}'|" ${WRKSRC}/Tools/pymolcas/export.py post-install: # remove unused static libraries, see https://gitlab.com/Molcas/OpenMolcas/-/issues/354 @${RM} -r ${STAGEDIR}${CMAKE_INSTALL_PREFIX}/lib # remove unnecessary fines @${RM} ${STAGEDIR}${CMAKE_INSTALL_PREFIX}/CONTRIBUTORS.md @${RM} ${STAGEDIR}${CMAKE_INSTALL_PREFIX}/LICENSE # remove empty include directory @${RMDIR} ${STAGEDIR}${DATADIR}/include # remove empty doc directory @${RMDIR} ${STAGEDIR}${DATADIR}/doc post-test: # A total of 5 test(s) failed, with 3 critical failure(s), see https://gitlab.com/Molcas/OpenMolcas/-/issues/369 @cd ${BUILD_WRKSRC} && ${STAGEDIR}${DATADIR}/pymolcas verify .include diff --git a/science/sirius/Makefile b/science/sirius/Makefile index b3c68c5de6f3..820d98aa8df4 100644 --- a/science/sirius/Makefile +++ b/science/sirius/Makefile @@ -1,51 +1,52 @@ PORTNAME= sirius DISTVERSIONPREFIX= v DISTVERSION= 7.10.0 +PORTREVISION= 1 CATEGORIES= science PKGNAMESUFFIX= -quantum-chemistry # other software also has the name "sirius" MAINTAINER= yuri@FreeBSD.org COMMENT= Domain specific library for electronic structure calculations WWW= https://github.com/electronic-structure/SIRIUS/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libcosta.so:math/costa \ libfmt.so:devel/libfmt \ libgsl.so:math/gsl \ libhdf5.so:science/hdf5 \ libopenblas.so:math/openblas \ libscalapack.so:math/scalapack \ libspfft.so:math/spfft \ libspla.so:math/spla \ libsymspg.so:science/spglib \ libxc.so:science/libxc USES= cmake:testing compiler:c++14-lang eigen:3,test fortran pkgconfig USE_GITHUB= yes GH_ACCOUNT= electronic-structure GH_PROJECT= SIRIUS USE_LDCONFIG= yes CMAKE_OFF= SIRIUS_USE_MEMORY_POOL # depends on umpire - not yet ported OPTIONS_DEFAULT= MPICH # NLCGLIB OPTIONS_DEFINE= NLCGLIB OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI NLCGLIB_DESC= Enable nlcglib MPICH_USES= mpi:mpich NLCGLIB_LIB_DEPENDS= libnlcglib.so:science/nlcglib \ libkokkoscore.so:devel/kokkos NLCGLIB_CMAKE_BOOL= USE_NLCGLIB OPENMPI_USES= mpi:openmpi # pre-7.4.0: many tests fail, see https://github.com/electronic-structure/SIRIUS/issues/760 # 7.6.0: several tests fail: Can't divide 1 ranks into groups of size 4 # 7.7.0: tests fail to compile, see https://github.com/electronic-structure/SIRIUS/issues/1070 .include diff --git a/science/votca/Makefile b/science/votca/Makefile index 34386f43f3c4..f5b20734bd72 100644 --- a/science/votca/Makefile +++ b/science/votca/Makefile @@ -1,77 +1,79 @@ PORTNAME= votca DISTVERSIONPREFIX= v DISTVERSION= 2026 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= CSG and XTP: libraries for atomistic simulations WWW= https://www.votca.org/ \ https://github.com/votca/votca LICENSE= APACHE20 BROKEN_i386= undefined reference to `__atomic_load' # ' PY_DEPENDS= \ ${PYTHON_PKGNAMEPREFIX}ase>0:science/py-ase@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}xmltodict>0:devel/py-xmltodict@${PY_FLAVOR} \ rdkit>0:science/rdkit BUILD_DEPENDS= bash:shells/bash \ lmp:science/lammps \ ${PY_DEPENDS} LIB_DEPENDS= libboost_program_options.so:devel/boost-libs \ libecpint.so:science/libecpint \ libexpat.so:textproc/expat2 \ libfftw3.so:math/fftw3 \ libgromacs_d.so:science/gromacs \ libhdf5.so:science/hdf5 \ libint2.so:science/libint2 \ libsz.so:science/libaec \ libxc.so:science/libxc RUN_DEPENDS= bash:shells/bash \ ${PYTHON_PKGNAMEPREFIX}numpy1>=1.16:math/py-numpy1@${PY_FLAVOR} \ ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} USES= cmake compiler:c++14-lang eigen:3 perl5 pkgconfig python:run \ shebangfix USE_GITHUB= yes USE_LDCONFIG= yes SHEBANG_GLOB= *.sh *.pl *.py SHEBANG_FILES= tools/scripts/votca_compare tools/scripts/votca_help2doc \ xtp/scripts/xtp_update_mapfile xtp/scripts/xtp_basisset xtp/share/benchmark/xtp_benchmark xtp/scripts/xtp_autogen_mapping \ xtp/scripts/xtp_modify_jobfile \ xtp/scripts/xtp_qmmm2qm CXXFLAGS+= -DBOOST_TIMER_ENABLE_DEPRECATED CMAKE_ON= BUILD_XTP \ CMAKE_DISABLE_FIND_PACKAGE_SPHINX CMAKE_OFF= INJECT_MARCH_NATIVE CMAKE_ARGS= -DLOCALBASE=${LOCALBASE} -DPython_EXECUTABLE=${PYTHON_CMD} +CONFIGURE_ENV+= PYTHONDONTWRITEBYTECODE=1 +MAKE_ENV+= PYTHONDONTWRITEBYTECODE=1 -BINARY_ALIAS= python3=${PYTHON_CMD} +BINARY_ALIAS= python3=${PYTHON_CMD} gfortran=gfortran14 OPTIONS_DEFINE= APPS OPTIONS_DEFAULT= APPS OPTIONS_SUB= yes APPS_DESC= Build applications APPS_CMAKE_BOOL= INSTALL_CSGAPPS post-install: # workaround for https://github.com/votca/votca/issues/1173 @${RM} -r ${STAGEDIR}${PREFIX}/lib/python. do-test: # several tests fail, see https://github.com/votca/votca/issues/1098 @cd ${BUILD_WRKSRC} && \ ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DENABLE_TESTING:BOOL=ON ${CMAKE_SOURCE_PATH} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test # tests as of 2026: 100% tests passed, 0 tests failed out of 248 .include diff --git a/science/votca/files/patch-xtp_include_votca_xtp_qmstate.h b/science/votca/files/patch-xtp_include_votca_xtp_qmstate.h index 9c37972ef3f9..904c7baec5f8 100644 --- a/science/votca/files/patch-xtp_include_votca_xtp_qmstate.h +++ b/science/votca/files/patch-xtp_include_votca_xtp_qmstate.h @@ -1,10 +1,10 @@ ---- xtp/include/votca/xtp/qmstate.h.orig 2025-10-03 18:44:55 UTC +--- xtp/include/votca/xtp/qmstate.h.orig 2026-03-09 18:52:35 UTC +++ xtp/include/votca/xtp/qmstate.h -@@ -23,6 +23,7 @@ - +@@ -24,6 +24,7 @@ // Standard includes + #include #include +#include // VOTCA includes #include diff --git a/science/votca/files/patch-xtp_src_pyxtp_pyproject.toml b/science/votca/files/patch-xtp_src_pyxtp_pyproject.toml new file mode 100644 index 000000000000..30702c515856 --- /dev/null +++ b/science/votca/files/patch-xtp_src_pyxtp_pyproject.toml @@ -0,0 +1,11 @@ +--- xtp/src/pyxtp/pyproject.toml.orig 2026-04-20 19:20:56 UTC ++++ xtp/src/pyxtp/pyproject.toml +@@ -9,7 +9,7 @@ authors = [ + { name="Bjoern Baumeier", email="bjoernbaumeier@gmail.com" }, + ] + +-dependencies = ["ase", "xmltodict", "h5py", "lxml", "rdkit"] ++dependencies = ["ase", "xmltodict", "h5py", "lxml"] + + [tool.pytest.ini_options] + addopts = [