diff --git a/science/dftbplus/Makefile b/science/dftbplus/Makefile index 0654ff7eb91f..15937ffe934d 100644 --- a/science/dftbplus/Makefile +++ b/science/dftbplus/Makefile @@ -1,109 +1,110 @@ PORTNAME= dftbplus DISTVERSION= 23.1 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= DFTB+: Package for performing fast atomistic simulations WWW= https://dftbplus.org/ LICENSE= GPLv3 # main code is under LGPL3+, the bundled dftd3-lib is under GPLv1+, this makes the result GPLv3 (based on https://www.gnu.org/licenses/gpl-faq.html#AllCompatibility) BROKEN_aarch64= Lack of IEEE754 support in gcc causes "Cannot find an intrinsic module named 'ieee_arithmetic'", see bug\#255890 BROKEN_FreeBSD_12_powerpc= Lack of IEEE754 support in gcc causes "Cannot find an intrinsic module named 'ieee_arithmetic'", see bug\#255890 BROKEN_FreeBSD_12_powerpc64= Lack of IEEE754 support in gcc causes "Cannot find an intrinsic module named 'ieee_arithmetic'", see bug\#255890 LIB_DEPENDS= libblas.so:math/blas \ liblapack.so:math/lapack \ libopenblas.so:math/openblas RUN_DEPENDS= ${PYNUMPY} TEST_DEPENDS= bash:shells/bash USES= cmake compiler:gcc-c++11-lib fortran pkgconfig python:build shebangfix USE_LDCONFIG= yes SHEBANG_FILES= tools/dptools/bin/* tools/misc/* utils/srcmanip/* utils/build/* external/fypp/bin/* utils/get_opt_externals \ external/fypp/bin/fypp utils/test/testlist_to_fypp SHEBANG_GLOB= *.py *.sh USE_GITHUB= yes GH_TUPLE= \ aradi:fytest:94e05ac:aradi_fytest/external/fytest/origin \ dftbplus:testparams:cd7536f:testparams/external/slakos/origin \ dftd4:dftd4:056491b:dftd4_dftd4/external/dftd4/origin TEST_TARGET= test BINARY_ALIAS= git=false CMAKE_ON= BLAS_DETECTION BUILD_SHARED_LIBS WITH_API ENABLE_DYNAMIC_LOADING CMAKE_ARGS= -DLAPACK_LIBRARY=lapack -DSCALAPACK_LIBRARY=scalapack BINARY_ALIAS= git=false python=${PYTHON_CMD} python3=${PYTHON_CMD} OPTIONS_DEFINE= ARPACK CHIMES DFTD3 MBD MPIX PLUMED POISSON PYTHON SOCKETS TBLITE TRANSPORT # see config.cmake for a complete list OPTIONS_DEFAULT= CHIMES DFTD3 MBD MPIX PLUMED POISSON TRANSPORT SOCKETS # PYTHON TBLITE OPTIONS_SUB= yes ARPACK_DESC= Build with ARPACK for large eigenvalue problems ARPACK_CMAKE_BOOL= WITH_ARPACK ARPACK_LIB_DEPENDS= libarpack.so:math/arpack-ng ARPACK_PREVENTS= MPIX # ARPACK is only used in a single-core application CHIMES_DESC= Build with ChIMES CHIMES_CMAKE_BOOL= WITH_CHIMES CHIMES_LIB_DEPENDS= libchimescalc.so:science/chimes-calculator DFTD3_DESC= Build with s-dft3 DFTD3_CMAKE_BOOL= WITH_SDFTD3 DFTD3_LIB_DEPENDS= libs-dftd3.so:science/simple-dftd3 \ libmctc-lib.so:science/mctc-lib \ libmstore.so:science/mstore \ libtoml-f.so:textproc/toml-f # binaries not linked with libtoml-f.so, see https://github.com/dftbplus/dftbplus/issues/1040 MBD_DESC= Build with many-body-dispersion support MBD_CMAKE_BOOL= WITH_MBD MBD_LIB_DEPENDS= libmbd.so:science/libmbd MPIX_DESC= MPI (Message Passing Interface) support # the MPI option name causes failure in MPI_USES=mpi:openmpi MPIX_CMAKE_BOOL= WITH_MPI MPIX_USES= mpi:mpich MPIX_LIB_DEPENDS= libmpich.so:net/mpich \ libmpifx.so:net/mpifx \ libscalapack.so:math/scalapack \ libscalapackfx.so:math/scalapackfx MPIX_LDFLAGS= ${LOCALBASE}/lib/libmpich.so ${LOCALBASE}/lib/libmpifort.so ${LOCALBASE}/lib/libmpi.so PLUMED_DESC= Do metadynamics via the PLUMED2 library PLUMED_CMAKE_BOOL= WITH_PLUMED PLUMED_LIB_DEPENDS= libplumed.so:science/plumed POISSON_DESC= Include Poisson-solver POISSON_CMAKE_BOOL= WITH_POISSON PYTHON_USES= python PYTHON_CMAKE_BOOL= WITH_PYTHON PYTHON_BROKEN= fails to install into stage directory: https://github.com/dftbplus/dftbplus/issues/931 SOCKETS_DESC= Build with sockets library SOCKETS_CMAKE_BOOL= WITH_SOCKETS SOCKETS_BINARY_ALIAS= gcc=${CC} TBLITE_DESC= Include xTB support via tblite TBLITE_CMAKE_BOOL= WITH_TBLITE TBLITE_BROKEN= fails to build, see https://github.com/dftbplus/dftbplus/issues/1041 TRANSPORT_DESC= Transport via libNEGF TRANSPORT_CMAKE_BOOL= WITH_TRANSPORT TRANSPORT_LIB_DEPENDS= libnegf.so:science/libnegf \ libmpi.so:net/mpich \ libmpifx.so:net/mpifx .include .if ${GCC_DEFAULT} >= 10 # workaround for Type mismatch between actual argument at (1) and actual argument at (2) (COMPLEX(8)/CHARACTER(*)). # in theory, this should set FCFLAGS, but the port does not conform FFLAGS+= -fallow-argument-mismatch .endif .include diff --git a/science/py-qcengine/Makefile b/science/py-qcengine/Makefile index 8f0ad75f16d2..d043a9e4501d 100644 --- a/science/py-qcengine/Makefile +++ b/science/py-qcengine/Makefile @@ -1,39 +1,39 @@ PORTNAME= qcengine DISTVERSION= 0.26.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python # chemistry MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Quantum chemistry program executor and IO standardizer (QCSchema) WWW= https://github.com/MolSSI/QCEngine LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}py-cpuinfo>0:sysutils/py-py-cpuinfo@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}psutil>0:sysutils/py-psutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pydantic>=1.8.2:devel/py-pydantic@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}qcelemental>=0.24.0:science/py-qcelemental@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}yaml>0:devel/py-yaml@${PY_FLAVOR} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \ dftd4:science/dftd4 \ mopac:science/mopac \ mp2d:science/mp2d \ mrchem:science/py-mrchem@${PY_FLAVOR} \ nwchem:science/nwchem \ rdkit>0:science/rdkit \ s-dftd3:science/simple-dftd3 \ xtb:science/xtb \ ${PYTHON_PKGNAMEPREFIX}msgpack>0:devel/py-msgpack@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyberny>0:science/py-pyberny@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}geometric>0:science/py-geometric@${PY_FLAVOR} # last dependencies above are for specific quantum chemistry packages to test with TODO torchani,openmm,psi4,torsiondrive,mdi USES= python USE_PYTHON= distutils concurrent autoplist pytest # 1 test fails, see https://github.com/MolSSI/QCEngine/issues/377, psi4 test hangs, see https://github.com/MolSSI/QCEngine/issues/390 NO_ARCH= yes .include diff --git a/science/simple-dftd3/Makefile b/science/simple-dftd3/Makefile index 7c635e492662..45ea69f41c27 100644 --- a/science/simple-dftd3/Makefile +++ b/science/simple-dftd3/Makefile @@ -1,32 +1,31 @@ PORTNAME= simple-dftd3 DISTVERSIONPREFIX= v -DISTVERSION= 0.6.0 -PORTREVISION= 2 +DISTVERSION= 1.0.0 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= Reimplementation of the DFT-D3 program WWW= https://github.com/awvwgk/simple-dftd3 LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING BROKEN_aarch64= cannot open module file 'ieee_arithmetic.mod' for reading at (1): No such file or directory BUILD_DEPENDS= mstore>0:science/mstore LIB_DEPENDS= libmctc-lib.so:science/mctc-lib \ libopenblas.so:math/openblas \ libtoml-f.so:textproc/toml-f USES= cmake:testing fortran USE_LDCONFIG= yes USE_GITHUB= yes -GH_ACCOUNT= awvwgk +GH_ACCOUNT= dftd3 CMAKE_ON= BUILD_SHARED_LIBS post-patch: # see https://github.com/toml-f/toml-f/issues/51 @${REINPLACE_CMD} -e 's|$${CMAKE_Fortran_COMPILER_ID}-$${CMAKE_Fortran_COMPILER_VERSION}||' ${WRKSRC}/config/CMakeLists.txt .include diff --git a/science/simple-dftd3/distinfo b/science/simple-dftd3/distinfo index 555df3aa249d..6039ed2ccdf8 100644 --- a/science/simple-dftd3/distinfo +++ b/science/simple-dftd3/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1651347900 -SHA256 (awvwgk-simple-dftd3-v0.6.0_GH0.tar.gz) = 4bef311f8e5a2c32141eddeea65615c3c8480f917cd884488ede059fb0962a50 -SIZE (awvwgk-simple-dftd3-v0.6.0_GH0.tar.gz) = 439438 +TIMESTAMP = 1690349962 +SHA256 (dftd3-simple-dftd3-v1.0.0_GH0.tar.gz) = fac3d9f785562b178dcf8e89f8d27782b8bda45fcd9dbaccc359b5def4fb1cf6 +SIZE (dftd3-simple-dftd3-v1.0.0_GH0.tar.gz) = 449042 diff --git a/science/simple-dftd3/pkg-plist b/science/simple-dftd3/pkg-plist index f248d5d1313c..9b87962049a6 100644 --- a/science/simple-dftd3/pkg-plist +++ b/science/simple-dftd3/pkg-plist @@ -1,38 +1,38 @@ bin/s-dftd3 include/dftd3.h include/s-dftd3.h include/s-dftd3/dftd3.mod include/s-dftd3/dftd3_api.mod include/s-dftd3/dftd3_blas.mod include/s-dftd3/dftd3_cutoff.mod include/s-dftd3/dftd3_damping.mod include/s-dftd3/dftd3_damping_atm.mod include/s-dftd3/dftd3_damping_mzero.mod include/s-dftd3/dftd3_damping_optimizedpower.mod include/s-dftd3/dftd3_damping_rational.mod include/s-dftd3/dftd3_damping_zero.mod include/s-dftd3/dftd3_data.mod include/s-dftd3/dftd3_data_covrad.mod include/s-dftd3/dftd3_data_r4r2.mod include/s-dftd3/dftd3_data_vdwrad.mod include/s-dftd3/dftd3_disp.mod include/s-dftd3/dftd3_model.mod include/s-dftd3/dftd3_ncoord.mod include/s-dftd3/dftd3_output.mod include/s-dftd3/dftd3_param.mod include/s-dftd3/dftd3_reference.mod include/s-dftd3/dftd3_utils.mod include/s-dftd3/dftd3_version.mod lib/cmake/s-dftd3/Findcustom-blas.cmake lib/cmake/s-dftd3/Findmctc-lib.cmake lib/cmake/s-dftd3/Findmstore.cmake lib/cmake/s-dftd3/Findtoml-f.cmake lib/cmake/s-dftd3/s-dftd3-config-version.cmake lib/cmake/s-dftd3/s-dftd3-config.cmake lib/cmake/s-dftd3/s-dftd3-targets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/s-dftd3/s-dftd3-targets.cmake lib/cmake/s-dftd3/s-dftd3-utils.cmake lib/libs-dftd3.so -lib/libs-dftd3.so.0 -lib/libs-dftd3.so.0.6.0 +lib/libs-dftd3.so.1 +lib/libs-dftd3.so.1.0.0 libdata/pkgconfig/s-dftd3.pc diff --git a/science/tblite/Makefile b/science/tblite/Makefile index ab9ac090200a..0900490bdbc1 100644 --- a/science/tblite/Makefile +++ b/science/tblite/Makefile @@ -1,34 +1,35 @@ PORTNAME= tblite DISTVERSIONPREFIX= v DISTVERSION= 0.3.0 +PORTREVISION= 1 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= Light-weight tight-binding framework WWW= https://github.com/tblite/tblite LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING .if !exists(/usr/include/omp.h) BROKEN= requires OpenMP support that is missing on this architecture .endif BUILD_DEPENDS= mstore>0:science/mstore # unclear if this is really needed LIB_DEPENDS= libdftd4.so:science/dftd4 \ libmctc-lib.so:science/mctc-lib \ libmulticharge.so:science/multicharge \ libopenblas.so:math/openblas \ libs-dftd3.so:science/simple-dftd3 \ libtoml-f.so:textproc/toml-f USES= cmake:testing fortran USE_GITHUB= yes USE_LDCONFIG= yes CMAKE_ON= BUILD_SHARED_LIBS post-patch: # see https://github.com/toml-f/toml-f/issues/51 @${REINPLACE_CMD} -e 's|$${CMAKE_Fortran_COMPILER_ID}-$${CMAKE_Fortran_COMPILER_VERSION}||' ${WRKSRC}/config/CMakeLists.txt .include