gromacs: Upgrade biology/gromacs to 2019 release

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: gromacs: Upgrade biology/gromacs to 2019 release
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Mon, 04 Feb 2019 19:14:39 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Mon Feb 4 13:14:39 2019 -0600
Changeset:	5f8897b8ab385e0da03acf4dc7fa6058485e07a5

Modified Files:
	Makefile
Added Files:
	gromacs/DESCR
	gromacs/Makefile
	gromacs/PLIST
	gromacs/distinfo
	gromacs/options.mk

Log Message:
gromacs: Upgrade biology/gromacs to 2019 release

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=5f8897b8ab385e0da03acf4dc7fa6058485e07a5

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile           |   1 +
 gromacs/DESCR      |  10 +
 gromacs/Makefile   |  35 +++
 gromacs/PLIST      | 699 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 gromacs/distinfo   |   6 +
 gromacs/options.mk |  28 +++
 6 files changed, 779 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index da02dc0ccd..2cf64f58f5 100644
--- a/Makefile
+++ b/Makefile
@@ -1193,6 +1193,7 @@ SUBDIR+=	gretl
 SUBDIR+=	greybird-theme
 SUBDIR+=	grilo-plugins
 SUBDIR+=	grisbi
+SUBDIR+=	gromacs
 SUBDIR+=	groovy
 SUBDIR+=	grpc-java
 SUBDIR+=	grsync
diff --git a/gromacs/DESCR b/gromacs/DESCR
new file mode 100644
index 0000000000..17d86649e9
--- /dev/null
+++ b/gromacs/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/gromacs/Makefile b/gromacs/Makefile
new file mode 100644
index 0000000000..0ff19eaec9
--- /dev/null
+++ b/gromacs/Makefile
@@ -0,0 +1,35 @@
+# $NetBSD: Makefile,v 1.17 2018/08/22 09:42:59 wiz Exp $
+#
+
+DISTNAME=		gromacs-2019
+CATEGORIES=		science
+MASTER_SITES=		ftp://ftp.gromacs.org/pub/gromacs/
+
+MAINTAINER=		bacon%NetBSD.org@localhost
+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/gromacs/PLIST b/gromacs/PLIST
new file mode 100644
index 0000000000..d59d493591
--- /dev/null
+++ b/gromacs/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/compat/make_unique.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/math/3dtransforms.h
+include/gromacs/math/arrayrefwithpadding.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/mdlib/simulationsignal.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/restraint/restraintpotential.h
+include/gromacs/selection.h
+include/gromacs/selection/indexutil.h
+include/gromacs/selection/nbsearch.h
+include/gromacs/selection/position.h
+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/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/forcefieldparameters.h
+include/gromacs/topology/idef.h
+include/gromacs/topology/ifunc.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/energyframe.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/trajectoryanalysis/topologyinformation.h
+include/gromacs/utility.h
+include/gromacs/utility/alignedallocator.h
+include/gromacs/utility/allocator.h
+include/gromacs/utility/arrayref.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/fatalerror.h
+include/gromacs/utility/fileptr.h
+include/gromacs/utility/flags.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/unique_cptr.h
+include/gromacs/version.h
+lib/libgromacs.so
+lib/libgromacs.so.4
+lib/libgromacs.so.4.0.0
+lib/pkgconfig/libgromacs.pc
+man/man1/gmx-anadock.1
+man/man1/gmx-anaeig.1
+man/man1/gmx-analyze.1
+man/man1/gmx-angle.1
+man/man1/gmx-awh.1
+man/man1/gmx-bar.1
+man/man1/gmx-bundle.1
+man/man1/gmx-check.1
+man/man1/gmx-chi.1
+man/man1/gmx-cluster.1
+man/man1/gmx-clustsize.1
+man/man1/gmx-confrms.1
+man/man1/gmx-convert-tpr.1
+man/man1/gmx-covar.1
+man/man1/gmx-current.1
+man/man1/gmx-density.1
+man/man1/gmx-densmap.1
+man/man1/gmx-densorder.1
+man/man1/gmx-dielectric.1
+man/man1/gmx-dipoles.1
+man/man1/gmx-disre.1
+man/man1/gmx-distance.1
+man/man1/gmx-do_dssp.1
+man/man1/gmx-dos.1
+man/man1/gmx-dump.1
+man/man1/gmx-dyecoupl.1
+man/man1/gmx-dyndom.1
+man/man1/gmx-editconf.1
+man/man1/gmx-eneconv.1
+man/man1/gmx-enemat.1
+man/man1/gmx-energy.1
+man/man1/gmx-filter.1
+man/man1/gmx-freevolume.1
+man/man1/gmx-gangle.1
+man/man1/gmx-genconf.1
+man/man1/gmx-genion.1
+man/man1/gmx-genrestr.1
+man/man1/gmx-grompp.1
+man/man1/gmx-gyrate.1
+man/man1/gmx-h2order.1
+man/man1/gmx-hbond.1
+man/man1/gmx-helix.1
+man/man1/gmx-helixorient.1
+man/man1/gmx-help.1
+man/man1/gmx-hydorder.1
+man/man1/gmx-insert-molecules.1
+man/man1/gmx-lie.1
+man/man1/gmx-make_edi.1
+man/man1/gmx-make_ndx.1
+man/man1/gmx-mdmat.1
+man/man1/gmx-mdrun.1
+man/man1/gmx-mindist.1
+man/man1/gmx-mk_angndx.1
+man/man1/gmx-morph.1
+man/man1/gmx-msd.1
+man/man1/gmx-nmeig.1
+man/man1/gmx-nmens.1
+man/man1/gmx-nmr.1
+man/man1/gmx-nmtraj.1
+man/man1/gmx-order.1
+man/man1/gmx-pairdist.1
+man/man1/gmx-pdb2gmx.1
+man/man1/gmx-pme_error.1
+man/man1/gmx-polystat.1
+man/man1/gmx-potential.1
+man/man1/gmx-principal.1
+man/man1/gmx-rama.1
+man/man1/gmx-rdf.1
+man/man1/gmx-report-methods.1
+man/man1/gmx-rms.1
+man/man1/gmx-rmsdist.1
+man/man1/gmx-rmsf.1
+man/man1/gmx-rotacf.1
+man/man1/gmx-rotmat.1
+man/man1/gmx-saltbr.1
+man/man1/gmx-sans.1
+man/man1/gmx-sasa.1
+man/man1/gmx-saxs.1
+man/man1/gmx-select.1
+man/man1/gmx-sham.1
+man/man1/gmx-sigeps.1
+man/man1/gmx-solvate.1
+man/man1/gmx-sorient.1
+man/man1/gmx-spatial.1
+man/man1/gmx-spol.1
+man/man1/gmx-tcaf.1
+man/man1/gmx-traj.1
+man/man1/gmx-trajectory.1
+man/man1/gmx-trjcat.1
+man/man1/gmx-trjconv.1
+man/man1/gmx-trjorder.1
+man/man1/gmx-tune_pme.1
+man/man1/gmx-vanhove.1
+man/man1/gmx-velacc.1
+man/man1/gmx-view.1
+man/man1/gmx-wham.1
+man/man1/gmx-wheel.1
+man/man1/gmx-x2top.1
+man/man1/gmx-xpm2ps.1
+man/man1/gmx.1
+share/cmake/gromacs/gromacs-config-version.cmake
+share/cmake/gromacs/gromacs-config.cmake
+share/cmake/gromacs/libgromacs-release.cmake
+share/cmake/gromacs/libgromacs.cmake
+share/gromacs/COPYING
+share/gromacs/README.tutor
+share/gromacs/README_FreeEnergyModifications.txt
+share/gromacs/template/CMakeLists.txt
+share/gromacs/template/Makefile.pkg
+share/gromacs/template/README
+share/gromacs/template/cmake/FindGROMACS.cmake
+share/gromacs/template/template.cpp
+share/gromacs/top/README
+share/gromacs/top/amber03.ff/aminoacids.arn
+share/gromacs/top/amber03.ff/aminoacids.c.tdb
+share/gromacs/top/amber03.ff/aminoacids.hdb
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+share/gromacs/top/amber94.ff/dna.rtp
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+share/gromacs/top/amber99.ff/aminoacids.arn
+share/gromacs/top/amber99.ff/aminoacids.c.tdb
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+share/gromacs/top/amber99.ff/aminoacids.rtp
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+share/gromacs/top/amber99.ff/atomtypes.atp
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+share/gromacs/top/amber99.ff/dna.hdb
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+share/gromacs/top/amber99.ff/forcefield.doc
+share/gromacs/top/amber99.ff/forcefield.itp
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+share/gromacs/top/amber99.ff/rna.arn
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+share/gromacs/top/amber99.ff/tip4p.itp
+share/gromacs/top/amber99.ff/tip4pew.itp
+share/gromacs/top/amber99.ff/tip5p.itp
+share/gromacs/top/amber99.ff/urea.itp
+share/gromacs/top/amber99.ff/watermodels.dat
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+share/gromacs/top/residues.xml
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diff --git a/gromacs/distinfo b/gromacs/distinfo
new file mode 100644
index 0000000000..2840dabe8f
--- /dev/null
+++ b/gromacs/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (gromacs-2019.tar.gz) = 89155f31489be22593b98d403113d5eb5881a792
+RMD160 (gromacs-2019.tar.gz) = 598f0b3b797a801ff5b4acef38cc248f69656fc2
+SHA512 (gromacs-2019.tar.gz) = 54b11530e8ff671461e3ae9418d991fe242957943c944798cddf6efe740eee670a562cd5201dbba68b045f4bafd3afa2dc8de27e0643c7def4e05eaf0ccb5769
+Size (gromacs-2019.tar.gz) = 33428725 bytes
diff --git a/gromacs/options.mk b/gromacs/options.mk
new file mode 100644
index 0000000000..c0e3f3653e
--- /dev/null
+++ b/gromacs/options.mk
@@ -0,0 +1,28 @@
+# $NetBSD: options.mk,v 1.2 2010/05/16 12:04:03 asau Exp $
+
+PKG_OPTIONS_VAR=		PKG_OPTIONS.gromacs
+PKG_SUPPORTED_OPTIONS+=		mpi x11
+PKG_SUGGESTED_OPTIONS+=		mpi x11
+
+.include "../../mk/bsd.options.mk"
+
+PLIST_VARS=	x11
+
+# MPI support:
+.if !empty(PKG_OPTIONS:Mmpi)
+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
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