3 files changed, 127 insertions, 407 deletions

diff --git a/science/gromacs/Makefile b/science/gromacs/Makefile
index a67b8f171272..7bcf303f9020 100644
--- a/science/gromacs/Makefile
+++ b/science/gromacs/Makefile
@@ -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="${LOCALBASE}/lib/libcblas.so;${LOCAL
 			-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>
-
-.if ${PORT_OPTIONS:MFLOAT}
-PLIST_SUB+=	SUFFIX_D=""
-.else
-PLIST_SUB+=	SUFFIX_D="_d"
-.endif
-
-.if ${PORT_OPTIONS:MMPICH2} || ${PORT_OPTIONS:MOPENMPI}
-CMAKE_ARGS+=	-DGMX_MPI:BOOL=ON
-PLIST_SUB+=	SUFFIX_MPI="_mpi"
-.else
-CMAKE_ARGS+=	-DGMX_MPI:BOOL=OFF
-PLIST_SUB+=	SUFFIX_MPI=""
-.endif
+MP_DESC=		Multiprocessing
+
+NOMP_DESC=		No multiprocessing support
+NOMP_PLIST_SUB=	SUFFIX_MPI=""
+
+MPICH2_LIB_DEPENDS=	libmpich.so:net/mpich2
+MPICH2_CMAKE_ON=	-DGMX_MPI:BOOL=ON \
+			-DMPI_C_COMPILER:FILEPATH="${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} \
diff --git a/science/gromacs/distinfo b/science/gromacs/distinfo
index f0b9b672f6d7..05e294f7c60d 100644
--- a/science/gromacs/distinfo
+++ b/science/gromacs/distinfo
@@ -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
diff --git a/science/gromacs/pkg-plist b/science/gromacs/pkg-plist
index 344e179d48a4..ab31b392c0e9 100644
--- a/science/gromacs/pkg-plist
+++ b/science/gromacs/pkg-plist
@@ -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
-%%DATADIR%%/html/images/flow_right+left.gif
-%%DATADIR%%/html/images/flow_right.gif
-%%DATADIR%%/html/images/flow_rightleftdown.gif
-%%DATADIR%%/html/images/flow_uprightleft.gif
-%%DATADIR%%/html/images/flow_vline.gif
-%%DATADIR%%/html/images/flow_vrule.gif
-%%DATADIR%%/html/images/gmxlogo_small.jpg
-%%DATADIR%%/html/images/plotje.gif
-%%DATADIR%%/html/images/xvgr.gif
-%%DATADIR%%/html/online.html
-%%DATADIR%%/html/online/cpt.html
-%%DATADIR%%/html/online/dat.html
-%%DATADIR%%/html/online/dlg.html
-%%DATADIR%%/html/online/edi.html
-%%DATADIR%%/html/online/edo.html
-%%DATADIR%%/html/online/edr.html
-%%DATADIR%%/html/online/ene.html
-%%DATADIR%%/html/online/eps.html
-%%DATADIR%%/html/online/files.html
-%%DATADIR%%/html/online/flow.html
-%%DATADIR%%/html/online/g96.html
-%%DATADIR%%/html/online/getting_started.html
-%%DATADIR%%/html/online/gro.html
-%%DATADIR%%/html/online/hdb.html
-%%DATADIR%%/html/online/itp.html
-%%DATADIR%%/html/online/log.html
-%%DATADIR%%/html/online/m2p.html
-%%DATADIR%%/html/online/map.html
-%%DATADIR%%/html/online/mdp.html
-%%DATADIR%%/html/online/mdp_opt.html
-%%DATADIR%%/html/online/mtx.html
-%%DATADIR%%/html/online/ndx.html
-%%DATADIR%%/html/online/options.html
-%%DATADIR%%/html/online/out.html
-%%DATADIR%%/html/online/pdb.html
-%%DATADIR%%/html/online/rtp.html
-%%DATADIR%%/html/online/style.css
-%%DATADIR%%/html/online/tex.html
-%%DATADIR%%/html/online/tng.html
-%%DATADIR%%/html/online/top.html
-%%DATADIR%%/html/online/tpa.html
-%%DATADIR%%/html/online/tpb.html
-%%DATADIR%%/html/online/tpr.html
-%%DATADIR%%/html/online/trj.html
-%%DATADIR%%/html/online/trr.html
-%%DATADIR%%/html/online/xpm.html
-%%DATADIR%%/html/online/xtc.html
-%%DATADIR%%/html/online/xvg.html
-%%DATADIR%%/html/programs/byname.html
-%%DATADIR%%/html/programs/bytopic.html
-%%DATADIR%%/html/programs/gmx-anadock.html
-%%DATADIR%%/html/programs/gmx-anaeig.html
-%%DATADIR%%/html/programs/gmx-analyze.html
-%%DATADIR%%/html/programs/gmx-angle.html
-%%DATADIR%%/html/programs/gmx-bar.html
-%%DATADIR%%/html/programs/gmx-bundle.html
-%%DATADIR%%/html/programs/gmx-check.html
-%%DATADIR%%/html/programs/gmx-chi.html
-%%DATADIR%%/html/programs/gmx-cluster.html
-%%DATADIR%%/html/programs/gmx-clustsize.html
-%%DATADIR%%/html/programs/gmx-confrms.html
-%%DATADIR%%/html/programs/gmx-convert-tpr.html
-%%DATADIR%%/html/programs/gmx-covar.html
-%%DATADIR%%/html/programs/gmx-current.html
-%%DATADIR%%/html/programs/gmx-density.html
-%%DATADIR%%/html/programs/gmx-densmap.html
-%%DATADIR%%/html/programs/gmx-densorder.html
-%%DATADIR%%/html/programs/gmx-dielectric.html
-%%DATADIR%%/html/programs/gmx-dipoles.html
-%%DATADIR%%/html/programs/gmx-disre.html
-%%DATADIR%%/html/programs/gmx-distance.html
-%%DATADIR%%/html/programs/gmx-do_dssp.html
-%%DATADIR%%/html/programs/gmx-dos.html
-%%DATADIR%%/html/programs/gmx-dump.html
-%%DATADIR%%/html/programs/gmx-dyecoupl.html
-%%DATADIR%%/html/programs/gmx-dyndom.html
-%%DATADIR%%/html/programs/gmx-editconf.html
-%%DATADIR%%/html/programs/gmx-eneconv.html
-%%DATADIR%%/html/programs/gmx-enemat.html
-%%DATADIR%%/html/programs/gmx-energy.html
-%%DATADIR%%/html/programs/gmx-filter.html
-%%DATADIR%%/html/programs/gmx-freevolume.html
-%%DATADIR%%/html/programs/gmx-gangle.html
-%%DATADIR%%/html/programs/gmx-genconf.html
-%%DATADIR%%/html/programs/gmx-genion.html
-%%DATADIR%%/html/programs/gmx-genrestr.html
-%%DATADIR%%/html/programs/gmx-grompp.html
-%%DATADIR%%/html/programs/gmx-gyrate.html
-%%DATADIR%%/html/programs/gmx-h2order.html
-%%DATADIR%%/html/programs/gmx-hbond.html
-%%DATADIR%%/html/programs/gmx-helix.html
-%%DATADIR%%/html/programs/gmx-helixorient.html
-%%DATADIR%%/html/programs/gmx-help.html
-%%DATADIR%%/html/programs/gmx-hydorder.html
-%%DATADIR%%/html/programs/gmx-insert-molecules.html
-%%DATADIR%%/html/programs/gmx-lie.html
-%%DATADIR%%/html/programs/gmx-make_edi.html
-%%DATADIR%%/html/programs/gmx-make_ndx.html
-%%DATADIR%%/html/programs/gmx-mdmat.html
-%%DATADIR%%/html/programs/gmx-mdrun.html
-%%DATADIR%%/html/programs/gmx-mindist.html
-%%DATADIR%%/html/programs/gmx-mk_angndx.html
-%%DATADIR%%/html/programs/gmx-morph.html
-%%DATADIR%%/html/programs/gmx-msd.html
-%%DATADIR%%/html/programs/gmx-nmeig.html
-%%DATADIR%%/html/programs/gmx-nmens.html
-%%DATADIR%%/html/programs/gmx-nmtraj.html
-%%DATADIR%%/html/programs/gmx-order.html
-%%DATADIR%%/html/programs/gmx-pdb2gmx.html
-%%DATADIR%%/html/programs/gmx-pme_error.html
-%%DATADIR%%/html/programs/gmx-polystat.html
-%%DATADIR%%/html/programs/gmx-potential.html
-%%DATADIR%%/html/programs/gmx-principal.html
-%%DATADIR%%/html/programs/gmx-protonate.html
-%%DATADIR%%/html/programs/gmx-rama.html
-%%DATADIR%%/html/programs/gmx-rdf.html
-%%DATADIR%%/html/programs/gmx-rms.html
-%%DATADIR%%/html/programs/gmx-rmsdist.html
-%%DATADIR%%/html/programs/gmx-rmsf.html
-%%DATADIR%%/html/programs/gmx-rotacf.html
-%%DATADIR%%/html/programs/gmx-rotmat.html
-%%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