diff --git a/science/lammps/Makefile b/science/lammps/Makefile index 3d6da54b6a25..c9e658c6b332 100644 --- a/science/lammps/Makefile +++ b/science/lammps/Makefile @@ -1,128 +1,129 @@ PORTNAME= lammps PORTVERSION= ${GH_TAGNAME:C/(stable|patch)_([0-9]{1,2})([A-Z][a-z][a-z])([0-9]{4})/\4.\3.\2/S/Jan/01/S/Feb/02/S/Mar/03/S/Apr/04/S/May/05/S/Jun/06/S/Jul/07/S/Aug/08/S/Sep/09/S/Oct/10/S/Nov/11/S/Dec/12/} +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Classical molecular dynamics code with a focus on materials modeling LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_i386= undefined reference to `__atomic_load' CONFLICTS_BUILD= ga mpich mpich2 # conflicts with include/error.h from ga, already fixed in the head LIB_DEPENDS= libfftw3.so:math/fftw3 USES= blaslapack:openblas cmake:noninja compiler:c++11-lang eigen:3 fortran localbase:ldflags shebangfix USE_GITHUB= yes GH_TAGNAME= patch_8Apr2021 USE_LDCONFIG= yes SHEBANG_GLOB= *.sh *.bash SHEBANG_FILES= lib/kokkos/bin/nvcc_wrapper CMAKE_ON= BUILD_SHARED_LIBS CMAKE_SOURCE_PATH= ${WRKSRC}/cmake CMAKE_ARGS= -DBLA_VENDOR:STRING="OpenBLAS" ${CMAKE_ARGS_${CHOSEN_COMPILER_TYPE}} CMAKE_ARGS_gcc= -DBUILD_OMP:BOOL=false # enable packages (for a complete list see STANDARD_PACKAGES in cmake/CMakeLists.txt) CMAKE_ON+= PKG_ASPHERE PKG_BODY PKG_CLASS2 PKG_COLLOID PKG_COMPRESS PKG_DIPOLE CMAKE_ON+= PKG_GRANULAR PKG_KSPACE PKG_MANYBODY PKG_MC PKG_MESSAGE PKG_MISC PKG_MOLECULE PKG_PERI PKG_POEMS PKG_QEQ CMAKE_ON+= PKG_REPLICA PKG_RIGID PKG_SHOCK PKG_SPIN PKG_SNAP PKG_SRD CMAKE_ON+= PKG_USER-ATC PKG_USER-AWPMD PKG_USER-BOCS PKG_USER-CGDNA PKG_USER-MESODPD PKG_USER-CGSDK PKG_USER-COLVARS CMAKE_ON+= PKG_USER-DIFFRACTION PKG_USER-DPD PKG_USER-DRUDE PKG_USER-EFF PKG_USER-FEP CMAKE_ON+= PKG_USER-MANIFOLD PKG_USER-MEAMC PKG_USER-MGPT PKG_USER-MISC PKG_USER-MOFFF PKG_USER-MOLFILE CMAKE_ON+= PKG_USER-PHONON PKG_USER-PTM PKG_USER-QTB PKG_USER-REACTION CMAKE_ON+= PKG_USER-REAXC PKG_USER-SDPD PKG_USER-SMD PKG_USER-SMTBQ PKG_USER-SPH PKG_USER-TALLY CMAKE_ON+= PKG_USER-UEF PKG_USER-QMMM PKG_USER-YAFF # Packages requiring extra downloades or dependencies: PKG_MSCG PKG_USER-ADIOS2 PKG_USER-NETCDF PKG_USER-QUIP PKG_USER-SCAFACOS OPTIONS_DEFINE= EXCEPTIONS JPEG PNG GZIP FFMPEG OPTIONS_GROUP= PARALLEL PACKAGES OPTIONS_DEFAULT= EXCEPTIONS MPI OPENMP JPEG PNG GZIP FFMPEG H5MD KIM KOKKOS LATTE PLUMED VORONOI ${OPTIONS_DEFAULT_${CHOSEN_COMPILER_TYPE}} OPTIONS_SUB= yes PARALLEL_DESC= Enable parallelizations: PACKAGES_DESC= Enable packages: OPTIONS_GROUP_PARALLEL= MPI OPENMP ${OPTIONS_DEFINE_${CHOSEN_COMPILER_TYPE}} OPTIONS_GROUP_PACKAGES= H5MD KIM KOKKOS LATTE PLUMED VORONOI VTK EXCEPTIONS_DESC= Enable the use of C++ exceptions EXCEPTIONS_CMAKE_BOOL= LAMMPS_EXCEPTIONS MPI_CMAKE_BOOL= BUILD_MPI PKG_MPIIO PKG_USER-LB MPI_LIB_DEPENDS= libmpi.so:net/openmpi MPI_USES= compiler:c11 FFMPEG_CMAKE_BOOL= WITH_FFMPEG FFMPEG_BUILD_DEPENDS= ffmpeg:multimedia/ffmpeg FFMPEG_RUN_DEPENDS= ffmpeg:multimedia/ffmpeg JPEG_CMAKE_BOOL= WITH_JPEG JPEG_USES= jpeg PNG_CMAKE_BOOL= WITH_PNG PNG_LIB_DEPENDS= libpng.so:graphics/png GZIP_DESC= Enable GZIP support GZIP_CMAKE_BOOL= WITH_GZIP H5MD_DESC= USER-H5MD package based on libhdf5 H5MD_CMAKE_BOOL= PKG_USER-H5MD H5MD_LIB_DEPENDS= libhdf5.so:science/hdf5 \ libsz.so:science/szip KIM_DESC= KIM package based on the OpenKim library/repository KIM_USES= pkgconfig KIM_CMAKE_BOOL= PKG_KIM KIM_CMAKE_ON= -DDOWNLOAD_KIM:BOOL=OFF KIM_LIB_DEPENDS= libkim-api.so:science/kim-api \ libcurl.so:ftp/curl KIM_RUN_DEPENDS= openkim-models>0:science/openkim-models KOKKOS_DESC= kokkos package based on the libkokkos library KOKKOS_CMAKE_BOOL= PKG_KOKKOS EXTERNAL_KOKKOS KOKKOS_LIB_DEPENDS= libkokkoscore.so:devel/kokkos LATTE_DESC= latte package based on the liblatte library LATTE_CMAKE_BOOL= PKG_LATTE LATTE_LIB_DEPENDS= liblatte.so:science/latte PLUMED_DESC= plumed package based on the plumed library PLUMED_USES= pkgconfig PLUMED_CMAKE_BOOL= PKG_USER-PLUMED PLUMED_CMAKE_ON= -DPLUMED_MODE=shared PLUMED_LIB_DEPENDS= libplumed.so:science/plumed VORONOI_DESC= voro++, Voronoi tessellation package VORONOI_CMAKE_BOOL= PKG_VORONOI VORONOI_LIB_DEPENDS= libvoro++.so:science/voro++ VTK_DESC= USER-VTK package based on the external vtk package VTK_CMAKE_BOOL= PKG_USER-VTK VTK_CMAKE_ON= -DVTK_DIR:PATH=${LOCALBASE}/lib/vtk-8.2/cmake/vtk-8.2 VTK_USES= qt:5 xorg VTK_USE= qt=core,gui,sql,widgets xorg=ice,sm,x11,xext,xt VTK_LIB_DEPENDS= libvtkImagingMath-8.2.so:math/vtk8 \ libexpat.so:textproc/expat2 \ libfreetype.so:print/freetype2 \ libtiff.so:graphics/tiff PORTSCOUT= ignore:1 # due to a special version tagging scheme that this project uses portscout fails to find new versions, watching their GitHub release page instead .include .if ${PORT_OPTIONS:MOPENMP} CMAKE_ARGS+= -DBUILD_OMP:BOOL=true .endif post-patch: @${REINPLACE_CMD} 's|SHELL = /bin/bash|SHELL = ${LOCALBASE}/bin/bash|' ${WRKSRC}/src/Makefile post-patch-FFMPEG-off: @${REINPLACE_CMD} 's|find_program(FFMPEG_EXECUTABLE|#&|' ${WRKSRC}/cmake/CMakeLists.txt post-install: @${RM} -r ${STAGEDIR}${PREFIX}/lib/python* .include diff --git a/science/plumed/Makefile b/science/plumed/Makefile index 6ba187472002..baddc1a49f07 100644 --- a/science/plumed/Makefile +++ b/science/plumed/Makefile @@ -1,35 +1,35 @@ PORTNAME= plumed DISTVERSIONPREFIX= v -DISTVERSION= 2.7.0 +DISTVERSION= 2.7.1 CATEGORIES= science graphics MAINTAINER= yuri@FreeBSD.org COMMENT= PLUgin for MolEcular Dynamics LICENSE= LGPL3 LICENSE_FILE= ${WRKSRC}/COPYING.LESSER BROKEN_i386= undefined reference to `__atomic_load' BUILD_DEPENDS= bash:shells/bash \ xxd:editors/vim-console RUN_DEPENDS= bash:shells/bash USES= autoreconf compiler:c++11-lang gmake pkgconfig shebangfix SHEBANG_GLOB= *.sh SHEBANG_FILES= src/maketools/makecmd GNU_CONFIGURE= yes USE_GITHUB= yes GH_PROJECT= plumed2 USE_LDCONFIG= yes CONFIGURE_ARGS= --enable-shared --disable-python post-patch: @${REINPLACE_CMD} -e 's|#! /bin/bash|#! ${LOCALBASE}/bin/bash|' ${WRKSRC}/src/lib/Makefile post-install: @${RMDIR} ${STAGEDIR}${PREFIX}/lib/plumed/obj @cd ${STAGEDIR}${PREFIX} && ${STRIP_CMD} bin/plumed lib/plumed/plumed-runtime lib/libplumed.so lib/libplumedKernel.so .include diff --git a/science/plumed/distinfo b/science/plumed/distinfo index 917abafe0773..ac52ae498ac4 100644 --- a/science/plumed/distinfo +++ b/science/plumed/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1609653184 -SHA256 (plumed-plumed2-v2.7.0_GH0.tar.gz) = 14450ea566c25ac9bf71fd77bb9c0c95e9038462b5739c73a515be82e2011cd6 -SIZE (plumed-plumed2-v2.7.0_GH0.tar.gz) = 98823600 +TIMESTAMP = 1618623190 +SHA256 (plumed-plumed2-v2.7.1_GH0.tar.gz) = cb8b5735d8dd61980fa6441f3dde3f33544240ae4177da0f529fb5abb355cd4a +SIZE (plumed-plumed2-v2.7.1_GH0.tar.gz) = 106402167 diff --git a/science/plumed/pkg-plist b/science/plumed/pkg-plist index 83c2a1f4107f..46f81da872af 100644 --- a/science/plumed/pkg-plist +++ b/science/plumed/pkg-plist @@ -1,497 +1,520 @@ bin/plumed bin/plumed-config bin/plumed-patch include/plumed/analysis/AnalysisBase.h include/plumed/analysis/AverageVessel.h include/plumed/analysis/DataCollectionObject.h include/plumed/analysis/LandmarkSelectionBase.h include/plumed/analysis/ReadAnalysisFrames.h include/plumed/asmjit/arch.h include/plumed/asmjit/arm.h include/plumed/asmjit/asmjit.h include/plumed/asmjit/asmjit_apibegin.h include/plumed/asmjit/asmjit_apiend.h include/plumed/asmjit/asmjit_build.h include/plumed/asmjit/assembler.h include/plumed/asmjit/base.h include/plumed/asmjit/codebuilder.h include/plumed/asmjit/codecompiler.h include/plumed/asmjit/codeemitter.h include/plumed/asmjit/codeholder.h include/plumed/asmjit/constpool.h include/plumed/asmjit/cpuinfo.h include/plumed/asmjit/func.h include/plumed/asmjit/globals.h include/plumed/asmjit/inst.h include/plumed/asmjit/logging.h include/plumed/asmjit/misc_p.h include/plumed/asmjit/moved_string.h include/plumed/asmjit/operand.h include/plumed/asmjit/osutils.h include/plumed/asmjit/regalloc_p.h include/plumed/asmjit/runtime.h include/plumed/asmjit/simdtypes.h include/plumed/asmjit/utils.h include/plumed/asmjit/vmem.h include/plumed/asmjit/x86.h include/plumed/asmjit/x86assembler.h include/plumed/asmjit/x86builder.h include/plumed/asmjit/x86compiler.h include/plumed/asmjit/x86emitter.h include/plumed/asmjit/x86globals.h include/plumed/asmjit/x86inst.h include/plumed/asmjit/x86instimpl_p.h include/plumed/asmjit/x86internal_p.h include/plumed/asmjit/x86logging_p.h include/plumed/asmjit/x86misc.h include/plumed/asmjit/x86operand.h include/plumed/asmjit/x86regalloc_p.h include/plumed/asmjit/zone.h include/plumed/bias/ActionRegister.h include/plumed/bias/Bias.h include/plumed/bias/ReweightBase.h include/plumed/blas/blas.h include/plumed/blas/def_external.h include/plumed/blas/def_internal.h include/plumed/blas/real.h include/plumed/cltools/CLTool.h include/plumed/cltools/CLToolRegister.h include/plumed/colvar/ActionRegister.h include/plumed/colvar/Colvar.h include/plumed/colvar/CoordinationBase.h include/plumed/colvar/PathMSDBase.h include/plumed/config/Config.h include/plumed/config/version.h include/plumed/core/Action.h include/plumed/core/ActionAnyorder.h include/plumed/core/ActionAtomistic.h include/plumed/core/ActionPilot.h include/plumed/core/ActionRegister.h include/plumed/core/ActionSet.h include/plumed/core/ActionSetup.h include/plumed/core/ActionShortcut.h include/plumed/core/ActionWithArguments.h include/plumed/core/ActionWithValue.h include/plumed/core/ActionWithVirtualAtom.h include/plumed/core/Atoms.h include/plumed/core/CLTool.h include/plumed/core/CLToolMain.h include/plumed/core/CLToolRegister.h include/plumed/core/Colvar.h include/plumed/core/DataFetchingObject.h include/plumed/core/ExchangePatterns.h include/plumed/core/FlexibleBin.h include/plumed/core/GREX.h include/plumed/core/GenericMolInfo.h include/plumed/core/MDAtoms.h include/plumed/core/PlumedMain.h include/plumed/core/PlumedMainInitializer.h include/plumed/core/TargetDist.h include/plumed/core/Value.h include/plumed/core/WithCmd.h include/plumed/function/ActionRegister.h include/plumed/function/Function.h include/plumed/gridtools/ActionWithGrid.h include/plumed/gridtools/ActionWithInputGrid.h include/plumed/gridtools/ActionWithIntegral.h include/plumed/gridtools/AverageOnGrid.h include/plumed/gridtools/ContourFindingBase.h include/plumed/gridtools/GridPrintingBase.h include/plumed/gridtools/GridSearch.h include/plumed/gridtools/GridVessel.h include/plumed/gridtools/HistogramOnGrid.h include/plumed/isdb/MetainferenceBase.h include/plumed/lapack/def_external.h include/plumed/lapack/def_internal.h include/plumed/lapack/lapack.h include/plumed/lapack/lapack_limits.h include/plumed/lapack/real.h include/plumed/lepton/CompiledExpression.h include/plumed/lepton/CustomFunction.h include/plumed/lepton/Exception.h include/plumed/lepton/ExpressionProgram.h 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