From b61ce1e54f90e571b34b0fc3b0effacd3cb0ff1c Mon Sep 17 00:00:00 2001 From: Jason Bacon Date: Tue, 5 Feb 2019 08:35:15 -0600 Subject: [PATCH] gromac2018: Contains features not available in 2019 --- Makefile | 1 + gromacs2018/DESCR | 10 + gromacs2018/Makefile | 35 +++ gromacs2018/PLIST | 699 +++++++++++++++++++++++++++++++++++++++++ gromacs2018/distinfo | 6 + gromacs2018/options.mk | 28 ++ 6 files changed, 779 insertions(+) create mode 100644 gromacs2018/DESCR create mode 100644 gromacs2018/Makefile create mode 100644 gromacs2018/PLIST create mode 100644 gromacs2018/distinfo create mode 100644 gromacs2018/options.mk diff --git a/Makefile b/Makefile index 9262df82f9..16c6ffa976 100644 --- a/Makefile +++ b/Makefile @@ -1195,6 +1195,7 @@ SUBDIR+= greybird-theme SUBDIR+= grilo-plugins SUBDIR+= grisbi SUBDIR+= gromacs +SUBDIR+= gromacs2018 SUBDIR+= groovy SUBDIR+= grpc-java SUBDIR+= grsync diff --git a/gromacs2018/DESCR b/gromacs2018/DESCR new file mode 100644 index 0000000000..17d86649e9 --- /dev/null +++ b/gromacs2018/DESCR @@ -0,0 +1,10 @@ +GROMACS is a versatile package to perform molecular dynamics, +i.e. simulate the Newtonian equations of motion for systems with +hundreds to millions of particles. + +It is primarily designed for biochemical molecules like proteins, +lipids and nucleic acids that have a lot of complicated bonded +interactions, but since GROMACS is extremely fast at calculating +the nonbonded interactions (that usually dominate simulations) +many groups are also using it for research on non-biological +systems, e.g. polymers. diff --git a/gromacs2018/Makefile b/gromacs2018/Makefile new file mode 100644 index 0000000000..4c91529d8e --- /dev/null +++ b/gromacs2018/Makefile @@ -0,0 +1,35 @@ +# $NetBSD: Makefile,v 1.17 2018/08/22 09:42:59 wiz Exp $ +# + +DISTNAME= gromacs-2018.4 +CATEGORIES= science +MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/ + +MAINTAINER= bacon@NetBSD.org +HOMEPAGE= http://www.gromacs.org/ +COMMENT= Molecular dynamics package +LICENSE= gnu-gpl-v2 + +USE_LANGUAGES= c c++ +USE_TOOLS+= cmake pkg-config +USE_CMAKE= yes + +.include "options.mk" + +USE_TOOLS+= perl:run +REPLACE_PERL= scripts/demux.pl scripts/xplor2gmx.pl + +CHECK_INTERPRETER_SKIP+= share/gromacs/tutor/gmxdemo/demo + +.include "../../mk/bsd.prefs.mk" + +.if $(MACHINE_ARCH) == "i386" +CFLAGS+= -msse -msse2 +.endif + +.include "../../math/fftw/buildlink3.mk" +.include "../../math/fftwf/buildlink3.mk" +.include "../../math/gsl/buildlink3.mk" # optional +.include "../../parallel/hwloc/buildlink3.mk" +.include "../../textproc/libxml2/buildlink3.mk" # optional +.include "../../mk/bsd.pkg.mk" diff --git a/gromacs2018/PLIST b/gromacs2018/PLIST new file mode 100644 index 0000000000..72c5ee7d82 --- /dev/null +++ b/gromacs2018/PLIST @@ -0,0 +1,699 @@ +@comment $NetBSD$ +bin/GMXRC +bin/GMXRC.bash +bin/GMXRC.csh +bin/GMXRC.zsh +bin/demux.pl +bin/gmx +bin/gmx-completion-gmx.bash +bin/gmx-completion.bash +bin/xplor2gmx.pl +include/gromacs/analysisdata.h +include/gromacs/analysisdata/abstractdata.h +include/gromacs/analysisdata/analysisdata.h +include/gromacs/analysisdata/arraydata.h +include/gromacs/analysisdata/dataframe.h +include/gromacs/analysisdata/datamodule.h +include/gromacs/analysisdata/modules/average.h +include/gromacs/analysisdata/modules/displacement.h +include/gromacs/analysisdata/modules/histogram.h +include/gromacs/analysisdata/modules/lifetime.h +include/gromacs/analysisdata/modules/plot.h +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/filetypes.h +include/gromacs/fileio/gmxfio.h +include/gromacs/fileio/matio.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/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/gpu_utils/hostallocator.h +include/gromacs/linearalgebra/eigensolver.h +include/gromacs/linearalgebra/matrix.h +include/gromacs/linearalgebra/sparsematrix.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/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 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+PKG_SUPPORTED_OPTIONS+= mpich x11 +PKG_SUGGESTED_OPTIONS+= x11 + +.include "../../mk/bsd.options.mk" + +PLIST_VARS= x11 + +# MPI support: +.if !empty(PKG_OPTIONS:Mmpich) +CONFIGURE_ARGS+= --enable-mpi +PLIST_SUBST+= MPI=_mpi +.include "../../mk/mpi.buildlink3.mk" +.else +PLIST_SUBST+= MPI= +.endif + +# X support: +.if !empty(PKG_OPTIONS:Mx11) +CONFIGURE_ARGS+= --with-x +PLIST.x11= yes + +.include "../../x11/libX11/buildlink3.mk" +.include "../../x11/libICE/buildlink3.mk" +.include "../../x11/libSM/buildlink3.mk" +.endif