- Update to 4.0.3

PR:		131655
Submitted by:	Joerg Pulz <Joerg.Pulz@frm2.tum.de>
Approved by:	maintainer

1 files changed, 136 insertions, 103 deletions

diff --git a/science/gromacs/Makefile b/science/gromacs/Makefile
index 1d210075014f..3e1346b8c686 100644
--- a/science/gromacs/Makefile
+++ b/science/gromacs/Makefile
@@ -6,153 +6,186 @@
 #
 
 PORTNAME=	gromacs
-PORTVERSION=	3.2.1
-PORTREVISION=	4
+PORTVERSION=	4.0.3
 CATEGORIES=	science
 MASTER_SITES=	ftp://ftp.gromacs.org/pub/gromacs/
 
 MAINTAINER=	stephen@math.missouri.edu
 COMMENT=	Compute molecular dynamics
 
-.ifndef WITHOUT_FFTW
-LIB_DEPENDS=	fftw:${PORTSDIR}/math/fftw:install
-.endif
-.ifdef WITH_MPI
-BUILD_DEPENDS=	${LOCALBASE}/mpich/bin/mpicc:${PORTSDIR}/net/mpich
-RUN_DEPENDS=	${LOCALBASE}/mpich/bin/mpicc:${PORTSDIR}/net/mpich
-.endif
-
+USE_GNOME=	libxml2
 USE_GMAKE=	yes
 USE_AUTOTOOLS=	libtool:15
 USE_LDCONFIG=	yes
 CONFIGURE_ENV=	CPPFLAGS=-I${LOCALBASE}/include LDFLAGS=-L${LOCALBASE}/lib
-CONFIGURE_ARGS=	--exec-prefix=${PREFIX}
+CONFIGURE_ARGS=	--exec-prefix=${PREFIX} --program-suffix="" --enable-shared
 
 PLIST_SUB=	BUILD=${MACHINE_ARCH}-portbld-freebsd${OSREL}
 
-.ifndef WITHOUT_FFTW
-.ifdef WITH_FLOAT
-IGNORE=		Cannot currently build with fftw and single precision floating point
-.elifdef WITH_MPI
-IGNORE=		Cannot currently build with fftw and mpi support
+OPTIONS=	FFTW3	"Use FFT routines from math/fftw3"		on  \
+		FFTW2	"Use FFT routines from math/fftw"		off \
+		GSL	"Enable extra analysis using math/gsl"		on  \
+		FLOAT	"Use single instead of double precision"	off \
+		X11	"Build and install X11 programs"		on  \
+		MPICH	"Enable MPI support using net/mpich"		off \
+		OMPI	"Enable MPI support using net/openmpi"		off
+
+.include <bsd.port.pre.mk>
+
+.if !defined(WITHOUT_FFTW3) && defined(WITH_FFTW2)
+IGNORE=		Cannot build with FFTW3 and FFTW2. Run 'make config' again and choose only one of them.
 .endif
+
+.if defined(WITH_MPICH) && defined(WITH_OMPI)
+IGNORE=		Cannot build with MPICH and OpenMPI support. Run 'make config' again and choose only one of them.
 .endif
 
-.ifdef WITHOUT_X
-PLIST_SUB+=	WITHOUT_X="@comment "
-CONFIGURE_ARGS+=	--without-x
+.if !defined(WITHOUT_FFTW3)
+CONFIGURE_ARGS+=	--with-fft=fftw3
+. if defined(WITH_FLOAT)
+LIB_DEPENDS+=	fftw3f.4:${PORTSDIR}/math/fftw3-float
+. else
+LIB_DEPENDS+=	fftw3.4:${PORTSDIR}/math/fftw3
+. endif
 .else
-PLIST_SUB+=	WITHOUT_X=
-CONFIGURE_ARGS+=	--with-x
-USE_XORG=	x11
+. if defined(WITH_FFTW2)
+CONFIGURE_ARGS+=	--with-fft=fftw2
+.  if defined(WITH_FLOAT)
+LIB_DEPENDS+=	sfftw.2:${PORTSDIR}/math/fftw-float
+.  else
+LIB_DEPENDS+=	fftw.2:${PORTSDIR}/math/fftw
+.  endif
+. else
+CONFIGURE_ARGS+=	--with-fft=fftpack
+. endif
 .endif
 
-.ifndef WITH_FLOAT
-CONFIGURE_ARGS+=	--disable-float --program-suffix=
-PLIST_SUB+=	SUFFIX_D=_d SUFFIX_DOUBLE=_double
+.if !defined(WITHOUT_GSL)
+CONFIGURE_ARGS+=	--with-gsl
+LIB_DEPENDS+=	gsl.13:${PORTSDIR}/math/gsl
 .else
-PLIST_SUB+=	SUFFIX_D= SUFFIX_DOUBLE=
+CONFIGURE_ARGS+=	--without-gsl
 .endif
 
-.ifdef WITHOUT_FFTW
-CONFIGURE_ARGS+=	--without-fftw
+.if !defined(WITHOUT_X11)
+PLIST_SUB+=	X11=""
+CONFIGURE_ARGS+=	--with-x
+USE_XORG=	x11
+.else
+PLIST_SUB+=	X11="@comment "
+CONFIGURE_ARGS+=	--without-x
 .endif
 
-.ifdef WITH_MPI
+.if defined(WITH_FLOAT)
+PLIST_SUB+=	SUFFIX_D="" SUFFIX_DOUBLE=""
+.else
+CONFIGURE_ARGS+=	--disable-float
+PLIST_SUB+=	SUFFIX_D=_d SUFFIX_DOUBLE=_double
+.endif
+
+.if defined(WITH_MPICH) || defined(WITH_OMPI)
 CONFIGURE_ARGS+=	--enable-mpi
+. if defined(WITH_MPICH)
 CONFIGURE_ENV+=	MPICC=${PREFIX}/mpich/bin/mpicc
-PLIST_SUB+=	WITH_MPI= SUFFIX_MPI=_mpi WITHOUT_MPI="@comment "
+BUILD_DEPENDS+=	${PREFIX}/mpich/bin/mpicc:${PORTSDIR}/net/mpich
+RUN_DEPENDS+=	${PREFIX}/mpich/bin/mpicc:${PORTSDIR}/net/mpich
+. else
+CONFIGURE_ENV+=	MPICC=${PREFIX}/mpi/openmpi/bin/mpicc
+BUILD_DEPENDS+=	${PREFIX}/mpi/openmpi/bin/mpicc:${PORTSDIR}/net/openmpi
+RUN_DEPENDS+=	${PREFIX}/mpi/openmpi/bin/mpicc:${PORTSDIR}/net/openmpi
+. endif
+PLIST_SUB+=	SUFFIX_MPI="_mpi" MPI=""
 .else
-PLIST_SUB+=	WITH_MPI="@comment " SUFFIX_MPI= WITHOUT_MPI=
+PLIST_SUB+=	SUFFIX_MPI="" MPI="@comment "
 .endif
 
 MAN1=	anadock.1 \
+	do_dssp.1 \
+	editconf.1 \
+	eneconv.1 \
+	g_anaeig.1 \
+	g_analyze.1 \
+	g_angle.1 \
+	g_bond.1 \
+	g_bundle.1 \
+	g_chi.1 \
 	g_cluster.1 \
-	g_filter.1 \
-	g_potential.1 \
-	g_velacc.1 \
-	ngmx.1 \
-	cdist.1 \
 	g_clustsize.1 \
-	g_gyrate.1 \
-	g_rama.1 \
-	g_wham.1 \
-	pdb2gmx.1 \
-	disco.1 \
 	g_confrms.1 \
-	g_h2order.1 \
-	g_rdf.1 \
-	genbox.1 \
-	protonate.1 \
-	do_dssp.1 \
 	g_covar.1 \
-	g_hbond.1 \
-	g_rms.1 \
-	genconf.1 \
-	tpbconv.1 \
-	editconf.1 \
+	g_current.1 \
 	g_density.1 \
-	g_helix.1 \
-	g_rmsdist.1 \
-	genion.1 \
-	trjcat.1 \
-	eneconv.1 \
+	g_densmap.1 \
 	g_dielectric.1 \
-	g_lie.1 \
-	g_rmsf.1 \
-	genpr.1 \
-	trjconv.1 \
-	ffscan.1 \
 	g_dih.1 \
-	g_mdmat.1 \
-	g_rotacf.1 \
-	gmxcheck.1 \
-	trjorder.1 \
-	g_anaeig.1 \
 	g_dipoles.1 \
-	g_mindist.1 \
-	g_saltbr.1 \
-	gmxdump.1 \
-	wheel.1 \
-	g_analyze.1 \
 	g_disre.1 \
-	g_morph.1 \
-	g_sas.1 \
-	grompp.1 \
-	x2top.1 \
-	g_angle.1 \
 	g_dist.1 \
-	g_msd.1 \
-	g_sgangle.1 \
-	highway.1 \
-	xpm2ps.1 \
-	g_bond.1 \
 	g_dyndom.1 \
-	g_nmeig.1 \
-	g_sorient.1 \
-	make_ndx.1 \
-	xrama.1 \
-	g_bundle.1 \
 	g_enemat.1 \
-	g_nmens.1 \
-	g_tcaf.1 \
-	mdrun.1 \
-	g_chi.1 \
 	g_energy.1 \
+	g_filter.1 \
+	g_gyrate.1 \
+	g_h2order.1 \
+	g_hbond.1 \
+	g_helix.1 \
+	g_helixorient.1 \
+	g_kinetics.1 \
+	g_lie.1 \
+	g_mdmat.1 \
+	g_mindist.1 \
+	g_morph.1 \
+	g_msd.1 \
+	g_nmeig.1 \
+	g_nmens.1 \
+	g_nmtraj.1 \
 	g_order.1 \
+	g_polystat.1 \
+	g_potential.1 \
+	g_principal.1 \
+	g_rama.1 \
+	g_rdf.1 \
+	g_rms.1 \
+	g_rmsdist.1 \
+	g_rmsf.1 \
+	g_rotacf.1 \
+	g_saltbr.1 \
+	g_sas.1 \
+	g_sdf.1 \
+	g_sgangle.1 \
+	g_sham.1 \
+	g_sorient.1 \
+	g_spatial.1 \
+	g_spol.1 \
+	g_tcaf.1 \
 	g_traj.1 \
-	mk_angndx.1
-
-.include <bsd.port.pre.mk>
-
-pre-fetch:
-	@${ECHO}
-	@${ECHO} "OPTIONS:"
-	@${ECHO}
-	@${ECHO} "To compile without X11: define WITHOUT_X"
-	@${ECHO} "To compile using single precision floating point: define WITH_FLOAT"
-	@${ECHO} "To compile without fftw: define WITHOUT_FFTW"
-	@${ECHO} "To compile with mpi: define WITH_MPI"
-	@${ECHO}
+	g_vanhove.1 \
+	g_velacc.1 \
+	g_wham.1 \
+	gen_table.1 \
+	genbox.1 \
+	genconf.1 \
+	genion.1 \
+	genrestr.1 \
+	gmxcheck.1 \
+	gmxdump.1 \
+	grompp.1 \
+	highway.1 \
+	make_edi.1 \
+	make_ndx.1 \
+	mdrun.1 \
+	mk_angndx.1 \
+	ngmx.1 \
+	pdb2gmx.1 \
+	protonate.1 \
+	sigeps.1 \
+	tpbconv.1 \
+	trjcat.1 \
+	trjconv.1 \
+	trjorder.1 \
+	wheel.1 \
+	x2top.1 \
+	xpm2ps.1 \
+	xrama.1
 
 .include <bsd.port.post.mk>