Date: Thu, 19 Apr 2018 08:04:10 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r467753 - head/science/gromacs Message-ID: <201804190804.w3J84AGl038097@repo.freebsd.org>
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Author: yuri Date: Thu Apr 19 08:04:10 2018 New Revision: 467753 URL: https://svnweb.freebsd.org/changeset/ports/467753 Log: science/gromacs: Update 5.0.6 -> 2018.1 Port changes: * Take maintainership. * Modernize the port, now using option helpers. * Add the OPENCL option. * Add the THREAD_MPI option that is now the default multiprocessing option. * Add missing dependencies. Modified: head/science/gromacs/Makefile head/science/gromacs/distinfo head/science/gromacs/pkg-plist Modified: head/science/gromacs/Makefile ============================================================================== --- head/science/gromacs/Makefile Thu Apr 19 07:28:27 2018 (r467752) +++ head/science/gromacs/Makefile Thu Apr 19 08:04:10 2018 (r467753) @@ -2,17 +2,17 @@ # $FreeBSD$ PORTNAME= gromacs -PORTVERSION= 5.0.6 -PORTREVISION= 12 +DISTVERSION= 2018.1 CATEGORIES= science MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/ -MAINTAINER= ports@FreeBSD.org +MAINTAINER= yuri@FreeBSD.org COMMENT= Compute molecular dynamics LICENSE= LGPL21 BUILD_DEPENDS= boost-libs>=1.44:devel/boost-libs +LIB_DEPENDS= libhwloc.so:devel/hwloc USES= cmake fortran perl5 pkgconfig shebangfix SHEBANG_FILES= admin/*.sh scripts/*.pl scripts/*.sh src/gromacs/selection/*.sh @@ -22,10 +22,10 @@ CMAKE_ARGS= -DGMX_USE_RDTSCP:BOOL=OFF \ -DUSE_PYTHON_SCRIPTS:BOOL=OFF USE_LDCONFIG= yes -OPTIONS_DEFINE= ATLAS FLOAT OPENMP SIMD X11 -OPTIONS_RADIO= MPI -OPTIONS_RADIO_MPI= MPICH2 OPENMPI -OPTIONS_DEFAULT= FLOAT OPENMP X11 +OPTIONS_DEFINE= ATLAS FLOAT OPENCL OPENMP SIMD X11 +OPTIONS_SINGLE= MP +OPTIONS_SINGLE_MP= NOMP MPICH2 OPENMPI THREAD_MPI +OPTIONS_DEFAULT= FLOAT OPENMP THREAD_MPI X11 OPTIONS_SUB= yes ATLAS_DESC= Use ATLAS for BLAS and LAPACK @@ -35,40 +35,48 @@ ATLAS_CMAKE_ON= -DBLAS_LIBRARIES:FILEPATH="${LOCALBAS -DLAPACK_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libalapack.so" ATLAS_CMAKE_OFF= -DBLAS_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libblas.so" \ -DLAPACK_LIBRARIES:FILEPATH="${LOCALBASE}/lib/liblapack.so" + FLOAT_DESC= Use single instead of double precision FLOAT_BUILD_DEPENDS= fftw3>0:math/fftw3 FLOAT_LIB_DEPENDS= libfftw3f.so:math/fftw3-float FLOAT_LIB_DEPENDS_OFF= libfftw3.so:math/fftw3 FLOAT_CMAKE_ON= -DGMX_DOUBLE:BOOL=OFF FLOAT_CMAKE_OFF= -DGMX_DOUBLE:BOOL=ON -MPICH2_LIB_DEPENDS= libmpich.so:net/mpich2 -MPICH2_CMAKE_ON= -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/bin/mpicc" +FLOAT_PLIST_SUB= SUFFIX_D="" +FLOAT_PLIST_SUB_OFF= SUFFIX_D="_d" + +OPENCL_CMAKE_BOOL= GMX_USE_OPENCL GMX_GPU +OPENCL_LIB_DEPENDS= libOpenCL.so:devel/ocl-icd + OPENMP_USES= compiler:openmp OPENMP_CMAKE_ON= -DGMX_CXX11:BOOL=OFF OPENMP_CMAKE_OFF= -DGMX_OPENMP:BOOL=OFF -OPENMPI_BUILD_DEPENDS= openmpi>0:net/openmpi -OPENMPI_RUN_DEPENDS= openmpi>0:net/openmpi -OPENMPI_CMAKE_ON= -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/mpi/openmpi/bin/mpicc" + SIMD_CMAKE_OFF= -DGMX_SIMD:STRING="None" -X11_USE= XORG=xext,x11 + +X11_USE= XORG=ice,sm,xext,x11 X11_CMAKE_ON= -DGMX_X11:BOOL=ON X11_CMAKE_OFF= -DGMX_X11:BOOL=OFF -.include <bsd.port.options.mk> +MP_DESC= Multiprocessing -.if ${PORT_OPTIONS:MFLOAT} -PLIST_SUB+= SUFFIX_D="" -.else -PLIST_SUB+= SUFFIX_D="_d" -.endif +NOMP_DESC= No multiprocessing support +NOMP_PLIST_SUB= SUFFIX_MPI="" -.if ${PORT_OPTIONS:MMPICH2} || ${PORT_OPTIONS:MOPENMPI} -CMAKE_ARGS+= -DGMX_MPI:BOOL=ON -PLIST_SUB+= SUFFIX_MPI="_mpi" -.else -CMAKE_ARGS+= -DGMX_MPI:BOOL=OFF -PLIST_SUB+= SUFFIX_MPI="" -.endif +MPICH2_LIB_DEPENDS= libmpich.so:net/mpich2 +MPICH2_CMAKE_ON= -DGMX_MPI:BOOL=ON \ + -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/bin/mpicc" +MPICH2_PLIST_SUB= SUFFIX_MPI="_mpi" + +OPENMPI_BUILD_DEPENDS= openmpi>0:net/openmpi +OPENMPI_RUN_DEPENDS= openmpi>0:net/openmpi +OPENMPI_CMAKE_ON= -DGMX_MPI:BOOL=ON \ + -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/mpi/openmpi/bin/mpicc" +OPENMPI_PLIST_SUB= SUFFIX_MPI="_mpi" + +THREAD_MPI_DESC= Build a thread-MPI-based multithreaded version of GROMACS +THREAD_MPI_CMAKE_BOOL= GMX_THREAD_MPI +THREAD_MPI_PLIST_SUB= SUFFIX_MPI="" post-patch: @${FIND} ${WRKSRC} -name "CMakeLists.txt" | ${XARGS} \ Modified: head/science/gromacs/distinfo ============================================================================== --- head/science/gromacs/distinfo Thu Apr 19 07:28:27 2018 (r467752) +++ head/science/gromacs/distinfo Thu Apr 19 08:04:10 2018 (r467753) @@ -1,2 +1,3 @@ -SHA256 (gromacs-5.0.6.tar.gz) = e07e950c4cd6cb84b83b145b70a15c25338ad6a7d7d1a0a83cdbd51cad954952 -SIZE (gromacs-5.0.6.tar.gz) = 26351063 +TIMESTAMP = 1524116817 +SHA256 (gromacs-2018.1.tar.gz) = 4d3533340499323fece83b4a2d4251fa856376f2426c541e00b8e6b4c0d705cd +SIZE (gromacs-2018.1.tar.gz) = 29895119 Modified: head/science/gromacs/pkg-plist ============================================================================== --- head/science/gromacs/pkg-plist Thu Apr 19 07:28:27 2018 (r467752) +++ head/science/gromacs/pkg-plist Thu Apr 19 08:04:10 2018 (r467753) @@ -3,103 +3,10 @@ bin/GMXRC.bash bin/GMXRC.csh bin/GMXRC.zsh bin/demux.pl -bin/do_dssp%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/editconf%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/eneconv%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_anadock%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_anaeig%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_analyze%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_angle%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_bar%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_bond%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_bundle%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_chi%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_cluster%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_clustsize%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_confrms%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_covar%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_current%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_density%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_densmap%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_densorder%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_dielectric%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_dipoles%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_disre%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_dist%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_dos%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_dyecoupl%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_dyndom%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_enemat%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_energy%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_filter%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_gyrate%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_h2order%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_hbond%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_helix%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_helixorient%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_hydorder%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_lie%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_mdmat%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_mindist%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_morph%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_msd%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_nmeig%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_nmens%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_nmtraj%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_options%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_order%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_pme_error%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_polystat%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_potential%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_principal%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_protonate%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_rama%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_rdf%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_rms%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_rmsdist%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_rmsf%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_rotacf%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_rotmat%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_saltbr%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_sans%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_sas%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_saxs%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_select%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_sgangle%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_sham%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_sigeps%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_sorient%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_spatial%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_spol%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_tcaf%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_traj%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_tune_pme%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_vanhove%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_velacc%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_wham%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_wheel%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_x2top%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/genbox%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/genconf%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/genion%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/genrestr%%SUFFIX_MPI%%%%SUFFIX_D%% bin/gmx%%SUFFIX_MPI%%%%SUFFIX_D%% bin/gmx-completion-gmx%%SUFFIX_MPI%%%%SUFFIX_D%%.bash bin/gmx-completion.bash -bin/gmxcheck%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/gmxdump%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/grompp%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/make_edi%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/make_ndx%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/mdrun%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/mk_angndx%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/pdb2gmx%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/tpbconv%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/trjcat%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/trjconv%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/trjorder%%SUFFIX_MPI%%%%SUFFIX_D%% bin/xplor2gmx.pl -bin/xpm2ps%%SUFFIX_MPI%%%%SUFFIX_D%% include/gromacs/analysisdata.h include/gromacs/analysisdata/abstractdata.h include/gromacs/analysisdata/analysisdata.h @@ -115,153 +22,77 @@ include/gromacs/commandline.h include/gromacs/commandline/cmdlinehelpwriter.h include/gromacs/commandline/cmdlineinit.h include/gromacs/commandline/cmdlinemodule.h +include/gromacs/commandline/cmdlineoptionsmodule.h include/gromacs/commandline/cmdlineparser.h include/gromacs/commandline/cmdlineprogramcontext.h +include/gromacs/commandline/filenm.h include/gromacs/commandline/pargs.h +include/gromacs/commandline/viewit.h include/gromacs/fft/fft.h include/gromacs/fileio/confio.h include/gromacs/fileio/enxio.h -include/gromacs/fileio/filenm.h -include/gromacs/fileio/futil.h +include/gromacs/fileio/filetypes.h include/gromacs/fileio/gmxfio.h include/gromacs/fileio/matio.h -include/gromacs/fileio/mdoutf.h +include/gromacs/fileio/mtxio.h +include/gromacs/fileio/oenv.h include/gromacs/fileio/pdbio.h +include/gromacs/fileio/rgb.h include/gromacs/fileio/tpxio.h -include/gromacs/fileio/trajectory_writing.h -include/gromacs/fileio/trnio.h -include/gromacs/fileio/trx.h +include/gromacs/fileio/trrio.h include/gromacs/fileio/trxio.h include/gromacs/fileio/xdr_datatype.h include/gromacs/fileio/xtcio.h +include/gromacs/fileio/xvgr.h include/gromacs/gmxana/gstat.h -include/gromacs/legacyheaders/atomprop.h -include/gromacs/legacyheaders/bondf.h -include/gromacs/legacyheaders/calcgrid.h -include/gromacs/legacyheaders/calch.h -include/gromacs/legacyheaders/calcmu.h -include/gromacs/legacyheaders/chargegroup.h -include/gromacs/legacyheaders/checkpoint.h -include/gromacs/legacyheaders/constr.h -include/gromacs/legacyheaders/copyrite.h -include/gromacs/legacyheaders/coulomb.h -include/gromacs/legacyheaders/disre.h -include/gromacs/legacyheaders/domdec.h -include/gromacs/legacyheaders/domdec_network.h -include/gromacs/legacyheaders/ebin.h -include/gromacs/legacyheaders/force.h -include/gromacs/legacyheaders/genborn.h -include/gromacs/legacyheaders/gmx_cpuid.h -include/gromacs/legacyheaders/gmx_detect_hardware.h -include/gromacs/legacyheaders/gmx_fatal.h -include/gromacs/legacyheaders/gmx_fatal_collective.h -include/gromacs/legacyheaders/gmx_omp_nthreads.h -include/gromacs/legacyheaders/gmx_thread_affinity.h -include/gromacs/legacyheaders/index.h -include/gromacs/legacyheaders/inputrec.h -include/gromacs/legacyheaders/invblock.h -include/gromacs/legacyheaders/macros.h -include/gromacs/legacyheaders/main.h -include/gromacs/legacyheaders/md_logging.h -include/gromacs/legacyheaders/md_support.h -include/gromacs/legacyheaders/mdatoms.h -include/gromacs/legacyheaders/mdebin.h -include/gromacs/legacyheaders/mdrun.h -include/gromacs/legacyheaders/mshift.h -include/gromacs/legacyheaders/mtop_util.h -include/gromacs/legacyheaders/mvdata.h -include/gromacs/legacyheaders/names.h -include/gromacs/legacyheaders/network.h -include/gromacs/legacyheaders/nonbonded.h -include/gromacs/legacyheaders/nrnb.h -include/gromacs/legacyheaders/ns.h -include/gromacs/legacyheaders/nsgrid.h -include/gromacs/legacyheaders/oenv.h -include/gromacs/legacyheaders/orires.h -include/gromacs/legacyheaders/pbc.h -include/gromacs/legacyheaders/perf_est.h -include/gromacs/legacyheaders/physics.h -include/gromacs/legacyheaders/pme.h -include/gromacs/legacyheaders/princ.h -include/gromacs/legacyheaders/qmmm.h -include/gromacs/legacyheaders/rbin.h -include/gromacs/legacyheaders/readinp.h -include/gromacs/legacyheaders/rmpbc.h -include/gromacs/legacyheaders/sfactor.h -include/gromacs/legacyheaders/shellfc.h -include/gromacs/legacyheaders/shift.h -include/gromacs/legacyheaders/sighandler.h -include/gromacs/legacyheaders/sim_util.h -include/gromacs/legacyheaders/splitter.h -include/gromacs/legacyheaders/symtab.h -include/gromacs/legacyheaders/sysstuff.h -include/gromacs/legacyheaders/tables.h -include/gromacs/legacyheaders/tgroup.h -include/gromacs/legacyheaders/txtdump.h -include/gromacs/legacyheaders/typedefs.h -include/gromacs/legacyheaders/types/atoms.h -include/gromacs/legacyheaders/types/block.h -include/gromacs/legacyheaders/types/constr.h -include/gromacs/legacyheaders/types/energy.h -include/gromacs/legacyheaders/types/enums.h -include/gromacs/legacyheaders/types/fcdata.h -include/gromacs/legacyheaders/types/force_flags.h -include/gromacs/legacyheaders/types/forcerec.h -include/gromacs/legacyheaders/types/genborn.h -include/gromacs/legacyheaders/types/globsig.h -include/gromacs/legacyheaders/types/graph.h -include/gromacs/legacyheaders/types/group.h -include/gromacs/legacyheaders/types/hw_info.h -include/gromacs/legacyheaders/types/idef.h -include/gromacs/legacyheaders/types/ifunc.h -include/gromacs/legacyheaders/types/inputrec.h -include/gromacs/legacyheaders/types/interaction_const.h -include/gromacs/legacyheaders/types/ishift.h -include/gromacs/legacyheaders/types/iteratedconstraints.h -include/gromacs/legacyheaders/types/matrix.h -include/gromacs/legacyheaders/types/mdatom.h -include/gromacs/legacyheaders/types/membedt.h -include/gromacs/legacyheaders/types/nb_verlet.h -include/gromacs/legacyheaders/types/nblist.h -include/gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h -include/gromacs/legacyheaders/types/nbnxn_pairlist.h -include/gromacs/legacyheaders/types/nlistheuristics.h -include/gromacs/legacyheaders/types/nrnb.h -include/gromacs/legacyheaders/types/ns.h -include/gromacs/legacyheaders/types/nsgrid.h -include/gromacs/legacyheaders/types/oenv.h -include/gromacs/legacyheaders/types/pbc.h -include/gromacs/legacyheaders/types/qmmmrec.h -include/gromacs/legacyheaders/types/shellfc.h -include/gromacs/legacyheaders/types/simple.h -include/gromacs/legacyheaders/types/state.h -include/gromacs/legacyheaders/types/symtab.h -include/gromacs/legacyheaders/types/topology.h -include/gromacs/legacyheaders/update.h -include/gromacs/legacyheaders/vcm.h -include/gromacs/legacyheaders/vec.h -include/gromacs/legacyheaders/viewit.h -include/gromacs/legacyheaders/vsite.h -include/gromacs/legacyheaders/warninp.h -include/gromacs/legacyheaders/xvgr.h +include/gromacs/gpu_utils/hostallocator.h include/gromacs/linearalgebra/eigensolver.h include/gromacs/linearalgebra/matrix.h -include/gromacs/linearalgebra/mtxio.h include/gromacs/linearalgebra/sparsematrix.h -include/gromacs/math/3dview.h +include/gromacs/listed-forces/listed-forces.h +include/gromacs/math/3dtransforms.h include/gromacs/math/do_fit.h +include/gromacs/math/functions.h include/gromacs/math/gmxcomplex.h +include/gromacs/math/paddedvector.h +include/gromacs/math/units.h include/gromacs/math/utilities.h -include/gromacs/onlinehelp.h -include/gromacs/onlinehelp/helptopicinterface.h +include/gromacs/math/vec.h +include/gromacs/math/vectypes.h +include/gromacs/mdtypes/inputrec.h +include/gromacs/mdtypes/md_enums.h +include/gromacs/mdtypes/mdatom.h +include/gromacs/mdtypes/state.h include/gromacs/options.h include/gromacs/options/abstractoption.h +include/gromacs/options/abstractsection.h include/gromacs/options/basicoptions.h include/gromacs/options/filenameoption.h +include/gromacs/options/filenameoptionmanager.h +include/gromacs/options/ioptionsbehavior.h +include/gromacs/options/ioptionscontainer.h +include/gromacs/options/ioptionscontainerwithsections.h +include/gromacs/options/isectionstorage.h +include/gromacs/options/ivaluestore.h include/gromacs/options/optionfiletype.h include/gromacs/options/optionflags.h include/gromacs/options/options.h +include/gromacs/options/optionsection.h +include/gromacs/options/repeatingsection.h include/gromacs/options/timeunitmanager.h +include/gromacs/options/valuestore.h +include/gromacs/pbcutil/ishift.h +include/gromacs/pbcutil/pbc.h +include/gromacs/pbcutil/rmpbc.h +include/gromacs/random.h +include/gromacs/random/exponentialdistribution.h +include/gromacs/random/gammadistribution.h +include/gromacs/random/normaldistribution.h +include/gromacs/random/seed.h +include/gromacs/random/tabulatednormaldistribution.h +include/gromacs/random/threefry.h +include/gromacs/random/uniformintdistribution.h +include/gromacs/random/uniformrealdistribution.h include/gromacs/selection.h include/gromacs/selection/indexutil.h include/gromacs/selection/nbsearch.h @@ -270,38 +101,56 @@ include/gromacs/selection/selection.h include/gromacs/selection/selectioncollection.h include/gromacs/selection/selectionenums.h include/gromacs/selection/selectionoption.h +include/gromacs/selection/selectionoptionbehavior.h include/gromacs/selection/selectionoptionmanager.h -include/gromacs/swap/enums.h +include/gromacs/timing/wallcycle.h include/gromacs/timing/walltime_accounting.h +include/gromacs/topology/atomprop.h +include/gromacs/topology/atoms.h +include/gromacs/topology/block.h +include/gromacs/topology/idef.h +include/gromacs/topology/index.h +include/gromacs/topology/mtop_util.h +include/gromacs/topology/symtab.h +include/gromacs/topology/topology.h +include/gromacs/trajectory/energy.h +include/gromacs/trajectory/trajectoryframe.h include/gromacs/trajectoryanalysis.h include/gromacs/trajectoryanalysis/analysismodule.h include/gromacs/trajectoryanalysis/analysissettings.h include/gromacs/trajectoryanalysis/cmdlinerunner.h include/gromacs/utility.h +include/gromacs/utility/alignedallocator.h +include/gromacs/utility/allocator.h include/gromacs/utility/arrayref.h -include/gromacs/utility/common.h +include/gromacs/utility/arraysize.h +include/gromacs/utility/basedefinitions.h +include/gromacs/utility/baseversion.h +include/gromacs/utility/classhelpers.h include/gromacs/utility/cstringutil.h +include/gromacs/utility/current_function.h +include/gromacs/utility/datafilefinder.h include/gromacs/utility/errorcodes.h include/gromacs/utility/exceptions.h -include/gromacs/utility/file.h +include/gromacs/utility/fatalerror.h include/gromacs/utility/flags.h -include/gromacs/utility/gmx_header_config.h -include/gromacs/utility/gmx_header_config_gen.h +include/gromacs/utility/futil.h include/gromacs/utility/gmxassert.h include/gromacs/utility/init.h include/gromacs/utility/programcontext.h +include/gromacs/utility/real.h include/gromacs/utility/smalloc.h include/gromacs/utility/stringutil.h -include/gromacs/utility/uniqueptr.h include/gromacs/version.h lib/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.so -lib/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.so.0 -lib/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.so.0.0.0 +lib/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.so.3 +lib/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.so.3.1.0 libdata/pkgconfig/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.pc man/man1/gmx-anadock.1.gz man/man1/gmx-anaeig.1.gz man/man1/gmx-analyze.1.gz man/man1/gmx-angle.1.gz +man/man1/gmx-awh.1.gz man/man1/gmx-bar.1.gz man/man1/gmx-bundle.1.gz man/man1/gmx-check.1.gz @@ -354,14 +203,15 @@ man/man1/gmx-morph.1.gz man/man1/gmx-msd.1.gz man/man1/gmx-nmeig.1.gz man/man1/gmx-nmens.1.gz +man/man1/gmx-nmr.1.gz man/man1/gmx-nmtraj.1.gz man/man1/gmx-order.1.gz +man/man1/gmx-pairdist.1.gz man/man1/gmx-pdb2gmx.1.gz man/man1/gmx-pme_error.1.gz man/man1/gmx-polystat.1.gz man/man1/gmx-potential.1.gz man/man1/gmx-principal.1.gz -man/man1/gmx-protonate.1.gz man/man1/gmx-rama.1.gz man/man1/gmx-rdf.1.gz man/man1/gmx-rms.1.gz @@ -382,6 +232,7 @@ man/man1/gmx-spatial.1.gz man/man1/gmx-spol.1.gz man/man1/gmx-tcaf.1.gz man/man1/gmx-traj.1.gz +man/man1/gmx-trajectory.1.gz man/man1/gmx-trjcat.1.gz man/man1/gmx-trjconv.1.gz man/man1/gmx-trjorder.1.gz @@ -393,163 +244,24 @@ man/man1/gmx-wham.1.gz man/man1/gmx-wheel.1.gz man/man1/gmx-x2top.1.gz man/man1/gmx-xpm2ps.1.gz -man/man7/gromacs.7.gz +man/man1/gmx.1.gz +share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%-config-version.cmake +share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%-config.cmake +share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/libgromacs-%%CMAKE_BUILD_TYPE%%.cmake +share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/libgromacs.cmake %%DATADIR%%/COPYING %%DATADIR%%/README.tutor %%DATADIR%%/README_FreeEnergyModifications.txt -%%DATADIR%%/html/images/flow_down.gif -%%DATADIR%%/html/images/flow_downleft.gif -%%DATADIR%%/html/images/flow_hline.gif -%%DATADIR%%/html/images/flow_left.gif -%%DATADIR%%/html/images/flow_leftright.gif -%%DATADIR%%/html/images/flow_leftrightdown.gif -%%DATADIR%%/html/images/flow_leftrightup.gif -%%DATADIR%%/html/images/flow_leftup.gif 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-%%DATADIR%%/html/programs/gmx-saltbr.html -%%DATADIR%%/html/programs/gmx-sans.html -%%DATADIR%%/html/programs/gmx-sasa.html -%%DATADIR%%/html/programs/gmx-saxs.html -%%DATADIR%%/html/programs/gmx-select.html -%%DATADIR%%/html/programs/gmx-sham.html -%%DATADIR%%/html/programs/gmx-sigeps.html -%%DATADIR%%/html/programs/gmx-solvate.html -%%DATADIR%%/html/programs/gmx-sorient.html -%%DATADIR%%/html/programs/gmx-spatial.html -%%DATADIR%%/html/programs/gmx-spol.html -%%DATADIR%%/html/programs/gmx-tcaf.html -%%DATADIR%%/html/programs/gmx-traj.html -%%DATADIR%%/html/programs/gmx-trjcat.html -%%DATADIR%%/html/programs/gmx-trjconv.html -%%DATADIR%%/html/programs/gmx-trjorder.html -%%DATADIR%%/html/programs/gmx-tune_pme.html -%%DATADIR%%/html/programs/gmx-vanhove.html -%%DATADIR%%/html/programs/gmx-velacc.html -%%DATADIR%%/html/programs/gmx-view.html -%%DATADIR%%/html/programs/gmx-wham.html -%%DATADIR%%/html/programs/gmx-wheel.html -%%DATADIR%%/html/programs/gmx-x2top.html -%%DATADIR%%/html/programs/gmx-xpm2ps.html +%%OPENCL%%%%DATADIR%%/opencl/nbnxn_ocl_kernel_amd.clh +%%OPENCL%%%%DATADIR%%/opencl/nbnxn_ocl_kernel_nowarp.clh +%%OPENCL%%%%DATADIR%%/opencl/nbnxn_ocl_kernel_nvidia.clh +%%OPENCL%%%%DATADIR%%/opencl/nbnxn_ocl_kernel_pruneonly.clh +%%OPENCL%%%%DATADIR%%/opencl/nbnxn_ocl_kernel_utils.clh +%%OPENCL%%%%DATADIR%%/opencl/nbnxn_ocl_kernels.cl +%%OPENCL%%%%DATADIR%%/opencl/nbnxn_ocl_kernels.clh +%%OPENCL%%%%DATADIR%%/opencl/nbnxn_ocl_kernels_fastgen.clh +%%OPENCL%%%%DATADIR%%/opencl/nbnxn_ocl_kernels_fastgen_add_twincut.clh +%%OPENCL%%%%DATADIR%%/opencl/vectype_ops.clh %%DATADIR%%/template/CMakeLists.txt %%DATADIR%%/template/Makefile.pkg %%DATADIR%%/template/README @@ -769,7 +481,6 @@ man/man7/gromacs.7.gz %%DATADIR%%/top/atom_nom.tbl %%DATADIR%%/top/atommass.dat %%DATADIR%%/top/bonds.dlg -%%DATADIR%%/top/bromacs.dat %%DATADIR%%/top/ca-shift.dat %%DATADIR%%/top/cb-shift.dat %%DATADIR%%/top/charmm27.ff/aminoacids.arn @@ -940,7 +651,6 @@ man/man7/gromacs.7.gz %%DATADIR%%/top/gromos54a7.ff/tip4p.itp %%DATADIR%%/top/gromos54a7.ff/tmcl.itp %%DATADIR%%/top/gromos54a7.ff/watermodels.dat -%%DATADIR%%/top/gurgle.dat %%DATADIR%%/top/ha-shift.dat %%DATADIR%%/top/ions.itp %%DATADIR%%/top/nsfactor.dat @@ -965,6 +675,7 @@ man/man7/gromacs.7.gz %%DATADIR%%/top/oplsaa.ff/spce.itp %%DATADIR%%/top/oplsaa.ff/tip3p.itp %%DATADIR%%/top/oplsaa.ff/tip4p.itp +%%DATADIR%%/top/oplsaa.ff/tip4pew.itp %%DATADIR%%/top/oplsaa.ff/tip5p.itp %%DATADIR%%/top/oplsaa.ff/tip5pe.itp %%DATADIR%%/top/oplsaa.ff/watermodels.dat
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