Date: Sun, 10 Feb 2013 07:56:49 +0000 (UTC) From: Martin Wilke <miwi@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r312002 - in head/science/gromacs: . files Message-ID: <201302100756.r1A7unIW073062@svn.freebsd.org>
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Author: miwi Date: Sun Feb 10 07:56:49 2013 New Revision: 312002 URL: http://svnweb.freebsd.org/changeset/ports/312002 Log: - Update to 4.6 PR: 175589 Submitted by: Ports Fury Deleted: head/science/gromacs/files/ Modified: head/science/gromacs/Makefile head/science/gromacs/distinfo (contents, props changed) head/science/gromacs/pkg-plist (contents, props changed) Modified: head/science/gromacs/Makefile ============================================================================== --- head/science/gromacs/Makefile Sun Feb 10 07:55:45 2013 (r312001) +++ head/science/gromacs/Makefile Sun Feb 10 07:56:49 2013 (r312002) @@ -2,198 +2,139 @@ # $FreeBSD$ PORTNAME= gromacs -PORTVERSION= 4.5.5 -PORTREVISION= 1 +PORTVERSION= 4.6 CATEGORIES= science MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/ MAINTAINER= ports@FreeBSD.org COMMENT= Compute molecular dynamics -USE_GNOME= libxml2 -USE_GMAKE= yes -USE_AUTOTOOLS= libtool -USE_LDCONFIG= yes -CPPFLAGS+= -I${LOCALBASE}/include -LDFLAGS+= -L${LOCALBASE}/lib -CONFIGURE_ARGS= --exec-prefix=${PREFIX} --program-suffix="" --enable-shared - -PLIST_SUB= BUILD=${MACHINE_ARCH}-portbld-freebsd${OSREL} - -OPTIONS_DEFINE= FFTW GSL FLOAT X11 MPI -OPTIONS_DEFAULT= FFTW FFTW3 GSL X11 -OPTIONS_SINGLE= FFTW MPI -OPTIONS_SINGLE_FFTW= FFTW2 FFTW3 -OPTIONS_SINGLE_MPI= MPICH OMPI - -FFTW_DESC= Use FFT routines -FFTW2_DESC= Use FFT routines from math/fftw -FFTW3_DESC= Use FFT routines from math/fftw3 -GSL_DESC= Enable extra analysis using math/gsl -FLOAT_DESC= Use single instead of double precision -MPI_DESC= Enable MPI support -MPICH_DESC= Enable MPI support using net/mpich2 -OMPI_DESC= Enable MPI support using net/openmpi +LICENSE= LGPL21 + +OPTIONS_DEFINE= ATLAS FLOAT GSL SIMD X11 +OPTIONS_DEFAULT= FLOAT GSL X11 +OPTIONS_RADIO= MPI +OPTIONS_RADIO_MPI= MPICH OMPI -.include <bsd.port.pre.mk> +ATLAS_DESC= Use ATLAS for BLAS and LAPACK +FLOAT_DESC= Use single instead of double precision +GSL_DESC= Extra analysis using math/gsl +MPICH_DESC= MPI support using net/mpich2 +OMPI_DESC= MPI support using net/openmpi + +USE_FORTRAN= yes +USE_PERL5= yes +USE_PKGCONFIG= build +USE_CMAKE= yes +CMAKE_ARGS= -DBLAS_LIBRARIES:FILEPATH="${BLAS_LIBS}" \ + -DLAPACK_LIBRARIES:FILEPATH="${LAPACK_LIBS}" +USE_LDCONFIG= yes +MAKE_JOBS_SAFE= yes -.if ${ARCH} == i386 -CONFIGURE_ARGS+= --disable-ia32-sse +MAN1= do_dssp.1 editconf.1 eneconv.1 g_anadock.1 \ + g_anaeig.1 g_analyze.1 g_angle.1 g_bar.1 \ + g_bond.1 g_bundle.1 g_chi.1 g_cluster.1 \ + g_clustsize.1 g_confrms.1 g_covar.1 g_current.1 \ + g_density.1 g_densmap.1 g_densorder.1 g_dielectric.1 \ + g_dipoles.1 g_disre.1 g_dist.1 g_dos.1 \ + g_dyecoupl.1 g_dyndom.1 g_enemat.1 g_energy.1 \ + g_filter.1 g_gyrate.1 g_h2order.1 g_hbond.1 \ + g_helix.1 g_helixorient.1 g_hydorder.1 g_kinetics.1 \ + g_lie.1 g_mdmat.1 g_membed.1 g_mindist.1 \ + g_morph.1 g_msd.1 g_nmeig.1 g_nmens.1 \ + g_nmtraj.1 g_order.1 g_pme_error.1 g_polystat.1 \ + g_potential.1 g_principal.1 g_protonate.1 g_rama.1 \ + g_rdf.1 g_rms.1 g_rmsdist.1 g_rmsf.1 \ + g_rotacf.1 g_rotmat.1 g_saltbr.1 g_sans.1 \ + g_sas.1 g_select.1 g_sgangle.1 g_sham.1 \ + g_sigeps.1 g_sorient.1 g_spatial.1 g_spol.1 \ + g_tcaf.1 g_traj.1 g_tune_pme.1 g_vanhove.1 \ + g_velacc.1 g_wham.1 g_wheel.1 g_x2top.1 \ + genbox.1 genconf.1 genion.1 genrestr.1 \ + gmxcheck.1 gmxdump.1 grompp.1 make_edi.1 \ + make_ndx.1 mdrun.1 mk_angndx.1 pdb2gmx.1 \ + tpbconv.1 trjcat.1 trjconv.1 trjorder.1 \ + xpm2ps.1 +MAN7= gromacs.7 + +.include <bsd.port.options.mk> + +.if ${PORT_OPTIONS:MATLAS} +LIB_DEPENDS+= alapack:${PORTSDIR}/math/atlas +BLAS_LIBS= ${LOCALBASE}/lib/libcblas.so;${LOCALBASE}/lib/libf77blas.so +LAPACK_LIBS= ${LOCALBASE}/lib/libalapack.so +.else +LIB_DEPENDS+= blas:${PORTSDIR}/math/blas \ + lapack:${PORTSDIR}/math/lapack +BLAS_LIBS= ${LOCALBASE}/lib/libblas.so +LAPACK_LIBS= ${LOCALBASE}/lib/liblapack.so .endif -.if ${PORT_OPTIONS:MFFTW3} -CONFIGURE_ARGS+= --with-fft=fftw3 -. if ${PORT_OPTIONS:MFLOAT} +.if ${PORT_OPTIONS:MFLOAT} +BUILD_DEPENDS+= fftw3>0:${PORTSDIR}/math/fftw3 LIB_DEPENDS+= fftw3f:${PORTSDIR}/math/fftw3-float -. else -LIB_DEPENDS+= fftw3:${PORTSDIR}/math/fftw3 -. endif +CMAKE_ARGS+= -DGMX_DOUBLE:BOOL=OFF +PLIST_SUB+= SUFFIX_D="" .else -. if ${PORT_OPTIONS:MFFTW2} -CONFIGURE_ARGS+= --with-fft=fftw2 -. if ${PORT_OPTIONS:MFLOAT} -LIB_DEPENDS+= sfftw.2:${PORTSDIR}/math/fftw-float -. else -LIB_DEPENDS+= fftw.2:${PORTSDIR}/math/fftw -. endif -. else -CONFIGURE_ARGS+= --with-fft=fftpack -. endif +LIB_DEPENDS+= fftw3:${PORTSDIR}/math/fftw3 +CMAKE_ARGS+= -DGMX_DOUBLE:BOOL=ON +PLIST_SUB+= SUFFIX_D="_d" .endif .if ${PORT_OPTIONS:MGSL} -CONFIGURE_ARGS+= --with-gsl -LIB_DEPENDS+= gsl.16:${PORTSDIR}/math/gsl +LIB_DEPENDS+= gsl:${PORTSDIR}/math/gsl +CMAKE_ARGS+= -DGMX_GSL:BOOL=ON .else -CONFIGURE_ARGS+= --without-gsl +CMAKE_ARGS+= -DGMX_GSL:BOOL=OFF +.endif + +.if empty(PORT_OPTIONS:MSIMD) +CMAKE_ARGS+= -DGMX_CPU_ACCELERATION:STRING="None" .endif .if ${PORT_OPTIONS:MX11} +USE_XORG= xext x11 +CMAKE_ARGS+= -DGMX_X11:BOOL=ON PLIST_SUB+= X11="" -CONFIGURE_ARGS+= --with-x -USE_XORG= x11 +MAN1+= g_xrama.1 ngmx.1 .else +CMAKE_ARGS+= -DGMX_X11:BOOL=OFF PLIST_SUB+= X11="@comment " -CONFIGURE_ARGS+= --without-x .endif -.if ${PORT_OPTIONS:MFLOAT} -PLIST_SUB+= SUFFIX_D="" SUFFIX_DOUBLE="" +.if ${PORT_OPTIONS:MMPICH} || ${PORT_OPTIONS:MOMPI} +CMAKE_ARGS+= -DGMX_MPI:BOOL=ON \ + -DMPI_C_COMPILER:FILEPATH="${MPICC}" +PLIST_SUB+= SUFFIX_MPI="_mpi" .else -CONFIGURE_ARGS+= --disable-float -PLIST_SUB+= SUFFIX_D=_d SUFFIX_DOUBLE=_double +CMAKE_ARGS+= -DGMX_MPI:BOOL=OFF +PLIST_SUB+= SUFFIX_MPI="" .endif -.if ${PORT_OPTIONS:MMPICH} || ${PORT_OPTIONS:MOMPI} -CONFIGURE_ARGS+= --enable-mpi .if ${PORT_OPTIONS:MMPICH} -CONFIGURE_ENV+= MPICC=${PREFIX}/bin/mpicc BUILD_DEPENDS+= ${LOCALBASE}/bin/mpicc:${PORTSDIR}/net/mpich2 RUN_DEPENDS+= ${LOCALBASE}/bin/mpicc:${PORTSDIR}/net/mpich2 -.elif ${PORT_OPTIONS:MOMPI} -CONFIGURE_ENV+= MPICC=${PREFIX}/mpi/openmpi/bin/mpicc +MPICC= ${LOCALBASE}/bin/mpicc +.endif + +.if ${PORT_OPTIONS:MOMPI} BUILD_DEPENDS+= ${LOCALBASE}/mpi/openmpi/bin/mpicc:${PORTSDIR}/net/openmpi RUN_DEPENDS+= ${LOCALBASE}/mpi/openmpi/bin/mpicc:${PORTSDIR}/net/openmpi +MPICC= ${LOCALBASE}/mpi/openmpi/bin/mpicc .endif -PLIST_SUB+= SUFFIX_MPI="_mpi" MPI="" -.else -PLIST_SUB+= SUFFIX_MPI="" MPI="@comment " -.endif - -MAN1= do_dssp.1 \ - editconf.1 \ - eneconv.1 \ - g_anadock.1 \ - g_anaeig.1 \ - g_analyze.1 \ - g_angle.1 \ - g_bar.1 \ - g_bond.1 \ - g_bundle.1 \ - g_chi.1 \ - g_cluster.1 \ - g_clustsize.1 \ - g_confrms.1 \ - g_covar.1 \ - g_current.1 \ - g_density.1 \ - g_densmap.1 \ - g_densorder.1 \ - g_dielectric.1 \ - g_dih.1 \ - g_dipoles.1 \ - g_disre.1 \ - g_dist.1 \ - g_dyndom.1 \ - g_enemat.1 \ - g_energy.1 \ - g_filter.1 \ - g_gyrate.1 \ - g_h2order.1 \ - g_hbond.1 \ - g_helix.1 \ - g_helixorient.1 \ - g_hydorder.1 \ - g_lie.1 \ - g_mdmat.1 \ - g_membed.1 \ - g_mindist.1 \ - g_morph.1 \ - g_msd.1 \ - g_nmeig.1 \ - g_nmens.1 \ - g_nmtraj.1 \ - g_options.1 \ - g_order.1 \ - g_pme_error.1 \ - g_polystat.1 \ - g_potential.1 \ - g_principal.1 \ - g_protonate.1 \ - g_rama.1 \ - g_rdf.1 \ - g_rms.1 \ - g_rmsdist.1 \ - g_rmsf.1 \ - g_rotacf.1 \ - g_rotmat.1 \ - g_saltbr.1 \ - g_sas.1 \ - g_select.1 \ - g_sgangle.1 \ - g_sham.1 \ - g_sigeps.1 \ - g_sorient.1 \ - g_spatial.1 \ - g_spol.1 \ - g_tcaf.1 \ - g_traj.1 \ - g_tune_pme.1 \ - g_vanhove.1 \ - g_velacc.1 \ - g_wham.1 \ - g_wheel.1 \ - g_x2top.1 \ - g_xrama.1 \ - genbox.1 \ - genconf.1 \ - genion.1 \ - genrestr.1 \ - gmxcheck.1 \ - gmxdump.1 \ - grompp.1 \ - make_edi.1 \ - make_ndx.1 \ - mdrun.1 \ - mk_angndx.1 \ - ngmx.1 \ - pdb2gmx.1 \ - tpbconv.1 \ - trjcat.1 \ - trjconv.1 \ - trjorder.1 \ - xpm2ps.1 -MAN7= gromacs.7 +post-patch: + @${FIND} ${WRKSRC} -name "CMakeLists.txt" | ${XARGS} \ + ${REINPLACE_CMD} -e \ + 's|share/man|man| ; \ + s|-lpthread|${PTHREAD_LIBS}| ; \ + /pkgconfig/s|LIB_INSTALL_DIR}|CMAKE_INSTALL_PREFIX}/libdata|' + @${FIND} ${WRKSRC} -name "GMXRC.*" | ${XARGS} ${REINPLACE_CMD} -e \ + 's|LDLIB/pkgconfig|LDLIB/../libdata/pkgconfig| ; \ + s|LDLIB}/pkgconfig|LDLIB}/../libdata/pkgconfig|' + @${FIND} ${WRKSRC} -name "*.pl" | ${XARGS} ${REINPLACE_CMD} -e \ + 's|/usr/bin/perl|${PERL}|' + @${FIND} ${WRKSRC} -name "*.sh" | ${XARGS} ${REINPLACE_CMD} -e \ + 's|/bin/bash|/bin/sh|' -.include <bsd.port.post.mk> +.include <bsd.port.mk> Modified: head/science/gromacs/distinfo ============================================================================== --- head/science/gromacs/distinfo Sun Feb 10 07:55:45 2013 (r312001) +++ head/science/gromacs/distinfo Sun Feb 10 07:56:49 2013 (r312002) @@ -1,2 +1,2 @@ -SHA256 (gromacs-4.5.5.tar.gz) = e0605e4810b0d552a8761fef5540c545beeaf85893f4a6e21df9905a33f871ba -SIZE (gromacs-4.5.5.tar.gz) = 10398178 +SHA256 (gromacs-4.6.tar.gz) = f695ea814b10cb9afa8d69241fed703c6e20156bab96ed4b25f817ad85a8dbde +SIZE (gromacs-4.6.tar.gz) = 10098687 Modified: head/science/gromacs/pkg-plist ============================================================================== --- head/science/gromacs/pkg-plist Sun Feb 10 07:55:45 2013 (r312001) +++ head/science/gromacs/pkg-plist Sun Feb 10 07:56:49 2013 (r312002) @@ -6,104 +6,106 @@ bin/completion.bash bin/completion.csh bin/completion.zsh bin/demux.pl -bin/do_dssp -bin/editconf -bin/eneconv -bin/g_anadock -bin/g_anaeig -bin/g_analyze -bin/g_angle -bin/g_bar -bin/g_bond -bin/g_bundle -bin/g_chi -bin/g_cluster -bin/g_clustsize -bin/g_confrms -bin/g_covar -bin/g_current -bin/g_density -bin/g_densmap -bin/g_densorder -bin/g_dielectric -bin/g_dih -bin/g_dipoles -bin/g_disre -bin/g_dist -bin/g_dos -bin/g_dyndom -bin/g_enemat -bin/g_energy -bin/g_filter -bin/g_gyrate -bin/g_h2order -bin/g_hbond -bin/g_helix -bin/g_helixorient -bin/g_hydorder -bin/g_kinetics -bin/g_lie -bin/g_luck -bin/g_mdmat -bin/g_membed -bin/g_mindist -bin/g_morph -bin/g_msd -bin/g_nmeig -bin/g_nmens -bin/g_nmtraj -bin/g_options -bin/g_order -bin/g_pme_error -bin/g_polystat -bin/g_potential -bin/g_principal -bin/g_protonate -bin/g_rama -bin/g_rdf -bin/g_rms -bin/g_rmsdist -bin/g_rmsf -bin/g_rotacf -bin/g_rotmat -bin/g_saltbr -bin/g_sas -bin/g_select -bin/g_sgangle -bin/g_sham -bin/g_sigeps -bin/g_sorient -bin/g_spatial -bin/g_spol -bin/g_tcaf -bin/g_traj -bin/g_tune_pme -bin/g_vanhove -bin/g_velacc -bin/g_wham -bin/g_wheel -bin/g_x2top -%%X11%%bin/g_xrama -bin/genbox -bin/genconf -bin/genion -bin/genrestr -bin/gmxcheck -bin/gmxdump -bin/grompp -bin/make_edi -bin/make_ndx -bin/mdrun -bin/mk_angndx -%%X11%%bin/ngmx -bin/pdb2gmx -bin/tpbconv -bin/trjcat -bin/trjconv -bin/trjorder +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_kinetics%%SUFFIX_MPI%%%%SUFFIX_D%% +bin/g_lie%%SUFFIX_MPI%%%%SUFFIX_D%% +bin/g_luck%%SUFFIX_MPI%%%%SUFFIX_D%% +bin/g_mdmat%%SUFFIX_MPI%%%%SUFFIX_D%% +bin/g_membed%%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_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%% +%%X11%%bin/g_xrama%%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/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%% +%%X11%%bin/ngmx%%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 +bin/xpm2ps%%SUFFIX_MPI%%%%SUFFIX_D%% include/gromacs/3dview.h +include/gromacs/CTestTestfile.cmake include/gromacs/assert.h include/gromacs/atomprop.h include/gromacs/bondf.h @@ -117,7 +119,6 @@ include/gromacs/confio.h include/gromacs/constr.h include/gromacs/copyrite.h include/gromacs/coulomb.h -include/gromacs/dihre.h include/gromacs/displacement.h include/gromacs/disre.h include/gromacs/do_fit.h @@ -134,27 +135,48 @@ include/gromacs/gbutil.h include/gromacs/gen_ad.h include/gromacs/genborn.h include/gromacs/gmx_ana.h -include/gromacs/gmx_arpack.h -include/gromacs/gmx_blas.h +include/gromacs/gmx_avx_double.h +include/gromacs/gmx_avx_single.h +include/gromacs/gmx_cpuid.h include/gromacs/gmx_cyclecounter.h +include/gromacs/gmx_detect_hardware.h include/gromacs/gmx_fatal.h +include/gromacs/gmx_fatal_collective.h include/gromacs/gmx_fft.h include/gromacs/gmx_ga2la.h -include/gromacs/gmx_lapack.h +include/gromacs/gmx_hash.h +include/gromacs/gmx_header_config.h +include/gromacs/gmx_math_x86_avx_128_fma_double.h +include/gromacs/gmx_math_x86_avx_128_fma_single.h +include/gromacs/gmx_math_x86_avx_256_double.h +include/gromacs/gmx_math_x86_avx_256_single.h +include/gromacs/gmx_math_x86_sse2_double.h +include/gromacs/gmx_math_x86_sse2_single.h +include/gromacs/gmx_math_x86_sse4_1_double.h +include/gromacs/gmx_math_x86_sse4_1_single.h include/gromacs/gmx_matrix.h +include/gromacs/gmx_omp.h +include/gromacs/gmx_omp_nthreads.h include/gromacs/gmx_parallel_3dfft.h include/gromacs/gmx_random.h +include/gromacs/gmx_simd_macros.h include/gromacs/gmx_sort.h -include/gromacs/gmx_sse2_double.h -include/gromacs/gmx_sse2_single.h include/gromacs/gmx_statistics.h include/gromacs/gmx_system_xdr.h +include/gromacs/gmx_thread_affinity.h include/gromacs/gmx_wallcycle.h +include/gromacs/gmx_x86_avx_128_fma.h +include/gromacs/gmx_x86_avx_256.h +include/gromacs/gmx_x86_simd_double.h +include/gromacs/gmx_x86_simd_single.h +include/gromacs/gmx_x86_sse2.h +include/gromacs/gmx_x86_sse4_1.h include/gromacs/gmxcomplex.h include/gromacs/gmxcpp.h include/gromacs/gmxfio.h include/gromacs/gpp_atomtype.h include/gromacs/gpp_nextnb.h +include/gromacs/gpu_utils.h include/gromacs/grompp.h include/gromacs/gstat.h include/gromacs/hackblock.h @@ -164,22 +186,23 @@ include/gromacs/indexutil.h include/gromacs/inputrec.h include/gromacs/invblock.h include/gromacs/macros.h -include/gromacs/magic.h include/gromacs/main.h include/gromacs/mainpage.h include/gromacs/maths.h include/gromacs/matio.h include/gromacs/md5.h +include/gromacs/md_logging.h +include/gromacs/md_support.h include/gromacs/mdatoms.h include/gromacs/mdebin.h include/gromacs/mdrun.h -include/gromacs/molfile_plugin.h include/gromacs/mpelogging.h include/gromacs/mshift.h include/gromacs/mtop_util.h include/gromacs/mtxio.h include/gromacs/mvdata.h include/gromacs/names.h +include/gromacs/nbnxn_cuda_data_mgmt.h include/gromacs/nbsearch.h include/gromacs/network.h include/gromacs/nonbonded.h @@ -196,16 +219,16 @@ include/gromacs/pdb2top.h include/gromacs/pdbio.h include/gromacs/perf_est.h include/gromacs/physics.h +include/gromacs/pmalloc_cuda.h include/gromacs/pme.h include/gromacs/poscalc.h include/gromacs/position.h -include/gromacs/pppm.h include/gromacs/princ.h include/gromacs/pull.h +include/gromacs/pull_rotation.h include/gromacs/qmmm.h include/gromacs/random.h include/gromacs/rbin.h -include/gromacs/rdgroup.h include/gromacs/readinp.h include/gromacs/resall.h include/gromacs/rmpbc.h @@ -217,6 +240,7 @@ include/gromacs/sfactor.h include/gromacs/shellfc.h include/gromacs/shift.h include/gromacs/sighandler.h +include/gromacs/sim_util.h include/gromacs/smalloc.h include/gromacs/sortwater.h include/gromacs/sparsematrix.h @@ -227,6 +251,7 @@ include/gromacs/strdb.h include/gromacs/string2.h include/gromacs/symtab.h include/gromacs/sysstuff.h +include/gromacs/tables.h include/gromacs/tgroup.h include/gromacs/thread_mpi.h include/gromacs/thread_mpi/atomic.h @@ -238,16 +263,21 @@ include/gromacs/thread_mpi/atomic/gcc_pp include/gromacs/thread_mpi/atomic/gcc_spinlock.h include/gromacs/thread_mpi/atomic/gcc_x86.h include/gromacs/thread_mpi/atomic/msvc.h +include/gromacs/thread_mpi/atomic/suncc-sparc.h include/gromacs/thread_mpi/atomic/xlc_ppc.h include/gromacs/thread_mpi/barrier.h include/gromacs/thread_mpi/collective.h include/gromacs/thread_mpi/event.h +include/gromacs/thread_mpi/hwinfo.h include/gromacs/thread_mpi/list.h include/gromacs/thread_mpi/lock.h include/gromacs/thread_mpi/mpi_bindings.h +include/gromacs/thread_mpi/mutex.h include/gromacs/thread_mpi/numa_malloc.h +include/gromacs/thread_mpi/system_error.h include/gromacs/thread_mpi/threads.h include/gromacs/thread_mpi/tmpi.h +include/gromacs/thread_mpi/visibility.h include/gromacs/thread_mpi/wait.h include/gromacs/tmpi.h include/gromacs/topsort.h @@ -265,19 +295,26 @@ include/gromacs/types/energy.h include/gromacs/types/enums.h include/gromacs/types/fcdata.h include/gromacs/types/filenm.h +include/gromacs/types/force_flags.h include/gromacs/types/forcerec.h include/gromacs/types/genborn.h include/gromacs/types/globsig.h include/gromacs/types/graph.h include/gromacs/types/group.h +include/gromacs/types/hw_info.h include/gromacs/types/idef.h include/gromacs/types/ifunc.h include/gromacs/types/inputrec.h +include/gromacs/types/interaction_const.h include/gromacs/types/ishift.h include/gromacs/types/iteratedconstraints.h include/gromacs/types/matrix.h include/gromacs/types/mdatom.h +include/gromacs/types/membedt.h +include/gromacs/types/nb_verlet.h include/gromacs/types/nblist.h +include/gromacs/types/nbnxn_cuda_types_ext.h +include/gromacs/types/nbnxn_pairlist.h include/gromacs/types/nlistheuristics.h include/gromacs/types/nrnb.h include/gromacs/types/ns.h @@ -294,10 +331,9 @@ include/gromacs/types/trx.h include/gromacs/update.h include/gromacs/vcm.h include/gromacs/vec.h +include/gromacs/version.h include/gromacs/viewit.h -include/gromacs/vmddlopen.h -include/gromacs/vmdio.h -include/gromacs/vmdplugin.h +include/gromacs/visibility.h include/gromacs/vsite.h include/gromacs/warninp.h include/gromacs/wgms.h @@ -306,26 +342,22 @@ include/gromacs/writeps.h include/gromacs/xdrf.h include/gromacs/xtcio.h include/gromacs/xvgr.h -lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.a -lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.la lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.so lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6 -lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.a -lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.la lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.so lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6 -lib/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.a -lib/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.la lib/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.so lib/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6 -lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.a -lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.la lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.so lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6 libdata/pkgconfig/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.pc libdata/pkgconfig/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.pc libdata/pkgconfig/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.pc libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.pc +%%DATADIR%%/COPYING +%%DATADIR%%/CTestTestfile.cmake +%%DATADIR%%/README.tutor +%%DATADIR%%/README_FreeEnergyModifications.txt %%DATADIR%%/html/gmxfaq.html %%DATADIR%%/html/images/1ctf-0.2.jpg %%DATADIR%%/html/images/1ctf-0.5.jpg @@ -354,14 +386,16 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%S %%DATADIR%%/html/images/flow_vline.gif %%DATADIR%%/html/images/flow_vrule.gif %%DATADIR%%/html/images/gmxlogo_small.jpg +%%DATADIR%%/html/images/gmxlogo_small.png %%DATADIR%%/html/images/links.gif %%DATADIR%%/html/images/mail.gif %%DATADIR%%/html/images/manual.gif %%DATADIR%%/html/images/plotje.gif +%%DATADIR%%/html/images/rainbow.gif %%DATADIR%%/html/images/software.gif %%DATADIR%%/html/images/topologies.gif %%DATADIR%%/html/images/xvgr.gif -%%DATADIR%%/html/online.html +%%DATADIR%%/html/online/ADD_INCLUDE %%DATADIR%%/html/online/cpt.html %%DATADIR%%/html/online/dat.html %%DATADIR%%/html/online/dlg.html @@ -377,57 +411,79 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%S %%DATADIR%%/html/online/flow.html %%DATADIR%%/html/online/g87.html %%DATADIR%%/html/online/g96.html +%%DATADIR%%/html/online/g_anadock.html %%DATADIR%%/html/online/g_anaeig.html %%DATADIR%%/html/online/g_analyze.html %%DATADIR%%/html/online/g_angle.html +%%DATADIR%%/html/online/g_bar.html %%DATADIR%%/html/online/g_bond.html %%DATADIR%%/html/online/g_bundle.html %%DATADIR%%/html/online/g_chi.html %%DATADIR%%/html/online/g_cluster.html +%%DATADIR%%/html/online/g_clustsize.html %%DATADIR%%/html/online/g_confrms.html %%DATADIR%%/html/online/g_covar.html +%%DATADIR%%/html/online/g_current.html %%DATADIR%%/html/online/g_density.html %%DATADIR%%/html/online/g_densmap.html %%DATADIR%%/html/online/g_densorder.html %%DATADIR%%/html/online/g_dielectric.html -%%DATADIR%%/html/online/g_dih.html %%DATADIR%%/html/online/g_dipoles.html %%DATADIR%%/html/online/g_disre.html %%DATADIR%%/html/online/g_dist.html %%DATADIR%%/html/online/g_dyndom.html %%DATADIR%%/html/online/g_enemat.html %%DATADIR%%/html/online/g_energy.html +%%DATADIR%%/html/online/g_filter.html %%DATADIR%%/html/online/g_gyrate.html %%DATADIR%%/html/online/g_h2order.html %%DATADIR%%/html/online/g_hbond.html %%DATADIR%%/html/online/g_helix.html +%%DATADIR%%/html/online/g_helixorient.html %%DATADIR%%/html/online/g_lie.html %%DATADIR%%/html/online/g_mdmat.html +%%DATADIR%%/html/online/g_membed.html %%DATADIR%%/html/online/g_mindist.html %%DATADIR%%/html/online/g_morph.html %%DATADIR%%/html/online/g_msd.html %%DATADIR%%/html/online/g_nmeig.html %%DATADIR%%/html/online/g_nmens.html +%%DATADIR%%/html/online/g_nmtraj.html %%DATADIR%%/html/online/g_order.html +%%DATADIR%%/html/online/g_polystat.html %%DATADIR%%/html/online/g_potential.html +%%DATADIR%%/html/online/g_principal.html +%%DATADIR%%/html/online/g_protonate.html %%DATADIR%%/html/online/g_rama.html %%DATADIR%%/html/online/g_rdf.html %%DATADIR%%/html/online/g_rms.html %%DATADIR%%/html/online/g_rmsdist.html %%DATADIR%%/html/online/g_rmsf.html %%DATADIR%%/html/online/g_rotacf.html +%%DATADIR%%/html/online/g_rotmat.html %%DATADIR%%/html/online/g_saltbr.html %%DATADIR%%/html/online/g_sas.html +%%DATADIR%%/html/online/g_select.html %%DATADIR%%/html/online/g_sgangle.html %%DATADIR%%/html/online/g_sham.html +%%DATADIR%%/html/online/g_sigeps.html %%DATADIR%%/html/online/g_sorient.html +%%DATADIR%%/html/online/g_spatial.html +%%DATADIR%%/html/online/g_spol.html %%DATADIR%%/html/online/g_tcaf.html %%DATADIR%%/html/online/g_traj.html +%%DATADIR%%/html/online/g_tune_pme.html +%%DATADIR%%/html/online/g_vanhove.html %%DATADIR%%/html/online/g_velacc.html +%%DATADIR%%/html/online/g_wham.html +%%DATADIR%%/html/online/g_wheel.html +%%DATADIR%%/html/online/g_x2top.html +%%DATADIR%%/html/online/g_xrama.html %%DATADIR%%/html/online/genbox.html %%DATADIR%%/html/online/genconf.html %%DATADIR%%/html/online/genion.html %%DATADIR%%/html/online/genpr.html +%%DATADIR%%/html/online/genrestr.html %%DATADIR%%/html/online/getting_started.html %%DATADIR%%/html/online/gmxcheck.html %%DATADIR%%/html/online/gmxdemo.html @@ -482,9 +538,11 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%S %%DATADIR%%/html/online/xtc.html %%DATADIR%%/html/online/xvg.html %%DATADIR%%/html/online/yourown.html -%%DATADIR%%/template/Makefile.%%BUILD%%%%SUFFIX_DOUBLE%% +%%DATADIR%%/html/online.html +%%DATADIR%%/template/CMakeLists.txt %%DATADIR%%/template/Makefile.pkg %%DATADIR%%/template/README +%%DATADIR%%/template/cmake/FindGROMACS.cmake %%DATADIR%%/template/template.c %%DATADIR%%/top/amber03.ff/aminoacids.arn %%DATADIR%%/top/amber03.ff/aminoacids.c.tdb @@ -711,10 +769,10 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%S %%DATADIR%%/top/charmm27.ff/aminoacids.vsd %%DATADIR%%/top/charmm27.ff/atomtypes.atp %%DATADIR%%/top/charmm27.ff/cmap.itp +%%DATADIR%%/top/charmm27.ff/dna.arn +%%DATADIR%%/top/charmm27.ff/dna.c.tdb %%DATADIR%%/top/charmm27.ff/dna.hdb %%DATADIR%%/top/charmm27.ff/dna.n.tdb -%%DATADIR%%/top/charmm27.ff/dna.c.tdb -%%DATADIR%%/top/charmm27.ff/dna.arn %%DATADIR%%/top/charmm27.ff/dna.rtp %%DATADIR%%/top/charmm27.ff/ffbonded.itp %%DATADIR%%/top/charmm27.ff/ffnabonded.itp @@ -726,10 +784,10 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%S %%DATADIR%%/top/charmm27.ff/ions.itp %%DATADIR%%/top/charmm27.ff/lipids.hdb %%DATADIR%%/top/charmm27.ff/lipids.rtp +%%DATADIR%%/top/charmm27.ff/rna.arn +%%DATADIR%%/top/charmm27.ff/rna.c.tdb %%DATADIR%%/top/charmm27.ff/rna.hdb %%DATADIR%%/top/charmm27.ff/rna.n.tdb -%%DATADIR%%/top/charmm27.ff/rna.c.tdb -%%DATADIR%%/top/charmm27.ff/rna.arn %%DATADIR%%/top/charmm27.ff/rna.r2b %%DATADIR%%/top/charmm27.ff/rna.rtp %%DATADIR%%/top/charmm27.ff/spc.itp @@ -925,6 +983,7 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%S %%DATADIR%%/top/highway.dat %%DATADIR%%/top/ions.itp %%DATADIR%%/top/links.dat +%%DATADIR%%/top/nsfactor.dat %%DATADIR%%/top/oplsaa.ff/1propanol.itp %%DATADIR%%/top/oplsaa.ff/aminoacids.c.tdb %%DATADIR%%/top/oplsaa.ff/aminoacids.hdb @@ -952,6 +1011,8 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%S %%DATADIR%%/top/ps.m2p %%DATADIR%%/top/random.dat %%DATADIR%%/top/refi_aa.dat +%%DATADIR%%/top/residues.dtd +%%DATADIR%%/top/residues.xml %%DATADIR%%/top/residuetypes.dat %%DATADIR%%/top/sfactor.dat %%DATADIR%%/top/spc.itp @@ -970,47 +1031,9 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%S %%DATADIR%%/top/tip4p.gro %%DATADIR%%/top/tip4p.itp %%DATADIR%%/top/tip5p.gro +%%DATADIR%%/top/vdw-msms.dat %%DATADIR%%/top/vdwradii.dat %%DATADIR%%/top/xlateat.dat -%%DATADIR%%/tutor/gmxdemo/cpeptide.pdb -%%DATADIR%%/tutor/gmxdemo/demo -%%DATADIR%%/tutor/methanol/conf.gro -%%DATADIR%%/tutor/methanol/grompp.mdp -%%DATADIR%%/tutor/methanol/index.ndx -%%DATADIR%%/tutor/methanol/methanol.itp -%%DATADIR%%/tutor/methanol/methanol.pdb -%%DATADIR%%/tutor/methanol/topol.top -%%DATADIR%%/tutor/mixed/conf.gro -%%DATADIR%%/tutor/mixed/grompp.mdp -%%DATADIR%%/tutor/mixed/index.ndx -%%DATADIR%%/tutor/mixed/mixed.pdb -%%DATADIR%%/tutor/mixed/topol.top -%%DATADIR%%/tutor/nmr1/conf.gro -%%DATADIR%%/tutor/nmr1/grompp.mdp -%%DATADIR%%/tutor/nmr1/pep.pdb -%%DATADIR%%/tutor/nmr1/topol.top -%%DATADIR%%/tutor/nmr2/conf.gro -%%DATADIR%%/tutor/nmr2/genconf.gcp -%%DATADIR%%/tutor/nmr2/grompp.mdp -%%DATADIR%%/tutor/nmr2/pep.pdb -%%DATADIR%%/tutor/nmr2/topol.top -%%DATADIR%%/tutor/speptide/em.mdp -%%DATADIR%%/tutor/speptide/full.mdp -%%DATADIR%%/tutor/speptide/pr.mdp -%%DATADIR%%/tutor/speptide/speptide.pdb -%%DATADIR%%/tutor/water/conf.gro -%%DATADIR%%/tutor/water/grompp.mdp -%%DATADIR%%/tutor/water/index.ndx -%%DATADIR%%/tutor/water/spc216.pdb -%%DATADIR%%/tutor/water/topol.top -@dirrm %%DATADIR%%/tutor/water -@dirrm %%DATADIR%%/tutor/speptide -@dirrm %%DATADIR%%/tutor/nmr2 -@dirrm %%DATADIR%%/tutor/nmr1 -@dirrm %%DATADIR%%/tutor/mixed -@dirrm %%DATADIR%%/tutor/methanol -@dirrm %%DATADIR%%/tutor/gmxdemo -@dirrm %%DATADIR%%/tutor @dirrm %%DATADIR%%/top/oplsaa.ff @dirrm %%DATADIR%%/top/gromos53a6.ff @dirrm %%DATADIR%%/top/gromos53a5.ff @@ -1030,6 +1053,7 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%S @dirrm %%DATADIR%%/top/amber94.ff @dirrm %%DATADIR%%/top/amber03.ff @dirrm %%DATADIR%%/top +@dirrm %%DATADIR%%/template/cmake @dirrm %%DATADIR%%/template @dirrm %%DATADIR%%/html/online @dirrm %%DATADIR%%/html/images
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