ports/131655: science/gromacs: update to v4.0.3

Joerg Pulz Joerg.Pulz at frm2.tum.de
Fri Feb 13 18:50:04 UTC 2009 

>Number:         131655
>Category:       ports
>Synopsis:       science/gromacs: update to v4.0.3
>Confidential:   no
>Severity:       non-critical
>Priority:       medium
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          update
>Submitter-Id:   current-users
>Arrival-Date:   Fri Feb 13 18:50:03 UTC 2009
>Closed-Date:
>Last-Modified:
>Originator:     Joerg Pulz
>Release:        FreeBSD 7.1-RELEASE-p2 i386
>Organization:
Technische Universitaet Muenchen / ZWE FRM-II
>Environment:
System: FreeBSD hades.admin.frm2 7.1-RELEASE-p2 FreeBSD 7.1-RELEASE-p2 #0: Mon Jan 19 12:01:54 CET 2009 root at hades.admin.frm2:/usr/obj/usr/src/sys/HADES i386


	
>Description:
	Update the science/gromacs port to version 4.0.3.
	Changes:
	 Makefile
		- introduce OPTIONS and set reasonable defaults
		- update *_DEPENDS and CONFIGURE_ARGS
		- add manpages and sort alphabetically
		- allow to choose between different FFT libraries
		- allow to choose between MPI implementations
		  (very useful if you want to more then one core or coputers)
	 distinfo
		- regen for the new version
	 pkg-plist
		- update for the new version
		- sort alphabetically

>How-To-Repeat:
	
>Fix:

	- apply the patch
	- remove all zero-sized patches from ${FILESDIR}
	- add ${FILESDIR}/patch-configure

--- science_gromacs.diff begins here ---
Index: Makefile
===================================================================
RCS file: /home/ncvs/ports/science/gromacs/Makefile,v
retrieving revision 1.12
diff -u -r1.12 Makefile
--- Makefile	21 Aug 2008 06:18:12 -0000	1.12
+++ Makefile	10 Feb 2009 19:53:51 -0000
@@ -6,153 +6,187 @@
 #
 
 PORTNAME=	gromacs
-PORTVERSION=	3.2.1
-PORTREVISION=	4
+PORTVERSION=	4.0.3
+#PORTREVISION=	4
 CATEGORIES=	science
 MASTER_SITES=	ftp://ftp.gromacs.org/pub/gromacs/
 
 MAINTAINER=	stephen at 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>
Index: distinfo
===================================================================
RCS file: /home/ncvs/ports/science/gromacs/distinfo,v
retrieving revision 1.2
diff -u -r1.2 distinfo
--- distinfo	24 Jan 2006 01:01:33 -0000	1.2
+++ distinfo	10 Feb 2009 19:53:51 -0000
@@ -1,3 +1,3 @@
-MD5 (gromacs-3.2.1.tar.gz) = d298386495f6ee39b3155ce951984485
-SHA256 (gromacs-3.2.1.tar.gz) = de85710553202e17a3ac67049d2cf51117939d3d8944a34aa0909aa3771bef53
-SIZE (gromacs-3.2.1.tar.gz) = 3302723
+MD5 (gromacs-4.0.3.tar.gz) = 2902403671a0f9b0934ddf3ca586b7ec
+SHA256 (gromacs-4.0.3.tar.gz) = 6fc33ac9e1e9b208e2e8c73cb9e95940ed86969207fedc02bf30119f2ed58572
+SIZE (gromacs-4.0.3.tar.gz) = 8420556
Index: pkg-plist
===================================================================
RCS file: /home/ncvs/ports/science/gromacs/pkg-plist,v
retrieving revision 1.3
diff -u -r1.3 pkg-plist
--- pkg-plist	23 Feb 2006 10:38:50 -0000	1.3
+++ pkg-plist	10 Feb 2009 19:53:51 -0000
@@ -3,16 +3,13 @@
 bin/GMXRC.csh
 bin/GMXRC.zsh
 bin/anadock
-bin/average
-bin/cdist
 bin/completion.bash
 bin/completion.csh
 bin/completion.zsh
-bin/disco
+bin/demux.pl
 bin/do_dssp
 bin/editconf
 bin/eneconv
-bin/ffscan
 bin/g_anaeig
 bin/g_analyze
 bin/g_angle
@@ -23,7 +20,9 @@
 bin/g_clustsize
 bin/g_confrms
 bin/g_covar
+bin/g_current
 bin/g_density
+bin/g_densmap
 bin/g_dielectric
 bin/g_dih
 bin/g_dipoles
@@ -37,6 +36,8 @@
 bin/g_h2order
 bin/g_hbond
 bin/g_helix
+bin/g_helixorient
+bin/g_kinetics
 bin/g_lie
 bin/g_mdmat
 bin/g_mindist
@@ -44,8 +45,11 @@
 bin/g_msd
 bin/g_nmeig
 bin/g_nmens
+bin/g_nmtraj
 bin/g_order
+bin/g_polystat
 bin/g_potential
+bin/g_principal
 bin/g_rama
 bin/g_rdf
 bin/g_rms
@@ -54,77 +58,88 @@
 bin/g_rotacf
 bin/g_saltbr
 bin/g_sas
+bin/g_sdf
 bin/g_sgangle
+bin/g_sham
 bin/g_sorient
+bin/g_spatial
+bin/g_spol
 bin/g_tcaf
 bin/g_traj
+bin/g_vanhove
 bin/g_velacc
 bin/g_wham
 bin/genbox
 bin/genconf
 bin/genion
-bin/genpr
+bin/genrestr
 bin/gmxcheck
 bin/gmxdump
 bin/grompp
-%%WITHOUT_X%%bin/highway
+%%X11%%bin/highway
 bin/luck
 bin/make_edi
 bin/make_ndx
 bin/mdrun
 bin/mk_angndx
-%%WITHOUT_X%%bin/ngmx
+%%X11%%bin/ngmx
 bin/pdb2gmx
 bin/protonate
+bin/sigeps
 bin/tpbconv
 bin/trjcat
 bin/trjconv
 bin/trjorder
 bin/wheel
 bin/x2top
+bin/xplor2gmx.pl
 bin/xpm2ps
-%%WITHOUT_X%%bin/xrama
+%%X11%%bin/xrama
 include/gromacs/3dview.h
 include/gromacs/assert.h
 include/gromacs/atomprop.h
-include/gromacs/axp_asm.h
-include/gromacs/block_tx.h
 include/gromacs/bondf.h
 include/gromacs/calcgrid.h
 include/gromacs/calch.h
 include/gromacs/calcmu.h
-include/gromacs/callf77.h
+include/gromacs/checkpoint.h
 include/gromacs/confio.h
 include/gromacs/constr.h
 include/gromacs/copyrite.h
-include/gromacs/detectcpu.h
+include/gromacs/coulomb.h
 include/gromacs/dihre.h
 include/gromacs/disre.h
 include/gromacs/do_fit.h
-include/gromacs/do_md.h
-include/gromacs/dummies.h
+include/gromacs/domdec.h
+include/gromacs/domdec_network.h
 include/gromacs/ebin.h
 include/gromacs/edsam.h
 include/gromacs/enxio.h
-include/gromacs/ewald.h
-include/gromacs/ewald_util.h
-include/gromacs/fatal.h
 include/gromacs/ffscanf.h
 include/gromacs/fftgrid.h
-include/gromacs/fftw_wrapper.h
 include/gromacs/filenm.h
 include/gromacs/force.h
 include/gromacs/futil.h
 include/gromacs/gbutil.h
 include/gromacs/gmx_ana.h
+include/gromacs/gmx_arpack.h
+include/gromacs/gmx_blas.h
+include/gromacs/gmx_cyclecounter.h
+include/gromacs/gmx_fatal.h
+include/gromacs/gmx_fft.h
+include/gromacs/gmx_lapack.h
+include/gromacs/gmx_parallel_3dfft.h
 include/gromacs/gmx_random.h
 include/gromacs/gmx_system_xdr.h
+include/gromacs/gmx_thread.h
+include/gromacs/gmx_wallcycle.h
 include/gromacs/gmxcomplex.h
 include/gromacs/gmxfio.h
+include/gromacs/gpp_atomtype.h
+include/gromacs/gpp_nextnb.h
 include/gromacs/grompp.h
 include/gromacs/gstat.h
 include/gromacs/index.h
-include/gromacs/init.h
 include/gromacs/invblock.h
 include/gromacs/macros.h
 include/gromacs/magic.h
@@ -134,28 +149,31 @@
 include/gromacs/mdatoms.h
 include/gromacs/mdebin.h
 include/gromacs/mdrun.h
-include/gromacs/metacode.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/network.h
-include/gromacs/nr.h
+include/gromacs/nonbonded.h
 include/gromacs/nrama.h
 include/gromacs/nrjac.h
 include/gromacs/nrnb.h
 include/gromacs/ns.h
-include/gromacs/nsb.h
 include/gromacs/nsgrid.h
 include/gromacs/orires.h
+include/gromacs/partdec.h
 include/gromacs/pbc.h
 include/gromacs/pdbio.h
 include/gromacs/pdebug.h
+include/gromacs/perf_est.h
 include/gromacs/physics.h
 include/gromacs/pme.h
-include/gromacs/ppc_altivec.h
 include/gromacs/pppm.h
 include/gromacs/princ.h
 include/gromacs/pull.h
+include/gromacs/qmmm.h
 include/gromacs/random.h
 include/gromacs/rbin.h
 include/gromacs/rdgroup.h
@@ -163,12 +181,13 @@
 include/gromacs/readinp.h
 include/gromacs/reorder.h
 include/gromacs/rmpbc.h
-include/gromacs/sheader.h
+include/gromacs/shellfc.h
 include/gromacs/shift.h
-include/gromacs/shift_util.h
 include/gromacs/smalloc.h
 include/gromacs/sortwater.h
+include/gromacs/sparsematrix.h
 include/gromacs/split.h
+include/gromacs/splitter.h
 include/gromacs/statusio.h
 include/gromacs/statutil.h
 include/gromacs/strdb.h
@@ -178,6 +197,7 @@
 include/gromacs/sysstuff.h
 include/gromacs/tags.h
 include/gromacs/tgroup.h
+include/gromacs/topsort.h
 include/gromacs/tpxio.h
 include/gromacs/transfer.h
 include/gromacs/trnio.h
@@ -186,7 +206,7 @@
 include/gromacs/types/atoms.h
 include/gromacs/types/block.h
 include/gromacs/types/commrec.h
-include/gromacs/types/edsams.h
+include/gromacs/types/constr.h
 include/gromacs/types/energy.h
 include/gromacs/types/enums.h
 include/gromacs/types/fcdata.h
@@ -203,9 +223,11 @@
 include/gromacs/types/nblist.h
 include/gromacs/types/nbslist.h
 include/gromacs/types/nrnb.h
-include/gromacs/types/nsborder.h
+include/gromacs/types/ns.h
 include/gromacs/types/nsgrid.h
-include/gromacs/types/parm.h
+include/gromacs/types/pbc.h
+include/gromacs/types/qmmmrec.h
+include/gromacs/types/shellfc.h
 include/gromacs/types/simple.h
 include/gromacs/types/state.h
 include/gromacs/types/symtab.h
@@ -216,34 +238,27 @@
 include/gromacs/vcm.h
 include/gromacs/vec.h
 include/gromacs/viewit.h
+include/gromacs/vsite.h
 include/gromacs/wgms.h
 include/gromacs/wman.h
 include/gromacs/writeps.h
-include/gromacs/x86_3dnow.h
-include/gromacs/x86_sse.h
-include/gromacs/x86_sse2.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.3
-lib/libgmxana%%SUFFIX_D%%.a
-lib/libgmxana%%SUFFIX_D%%.la
-lib/libgmxana%%SUFFIX_D%%.so
-%%WITHOUT_MPI%%lib/libgmxana%%SUFFIX_D%%.a
-%%WITHOUT_MPI%%lib/libgmxana%%SUFFIX_D%%.la
-%%WITHOUT_MPI%%lib/libgmxana%%SUFFIX_D%%.so
-%%WITHOUT_MPI%%lib/libgmxana%%SUFFIX_D%%.so.3
-%%WITH_MPI%%lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.a
-%%WITH_MPI%%lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.la
-%%WITH_MPI%%lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.so
-%%WITH_MPI%%lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.so.3
+lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.so.5
+%%MPI%%lib/libgmxana%%SUFFIX_D%%.a
+%%MPI%%lib/libgmxana%%SUFFIX_D%%.so
+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.5
 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.3
+lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.so.5
 %%DATADIR%%/html/gmxfaq.html
 %%DATADIR%%/html/images/1ctf-0.2.jpg
 %%DATADIR%%/html/images/1ctf-0.5.jpg
@@ -280,6 +295,7 @@
 %%DATADIR%%/html/images/topologies.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/do_dssp.html
@@ -304,6 +320,7 @@
 %%DATADIR%%/html/online/g_confrms.html
 %%DATADIR%%/html/online/g_covar.html
 %%DATADIR%%/html/online/g_density.html
+%%DATADIR%%/html/online/g_densmap.html
 %%DATADIR%%/html/online/g_dielectric.html
 %%DATADIR%%/html/online/g_dih.html
 %%DATADIR%%/html/online/g_dipoles.html
@@ -334,6 +351,7 @@
 %%DATADIR%%/html/online/g_saltbr.html
 %%DATADIR%%/html/online/g_sas.html
 %%DATADIR%%/html/online/g_sgangle.html
+%%DATADIR%%/html/online/g_sham.html
 %%DATADIR%%/html/online/g_sorient.html
 %%DATADIR%%/html/online/g_tcaf.html
 %%DATADIR%%/html/online/g_traj.html
@@ -355,6 +373,7 @@
 %%DATADIR%%/html/online/itp.html
 %%DATADIR%%/html/online/log.html
 %%DATADIR%%/html/online/m2p.html
+%%DATADIR%%/html/online/make_edi.html
 %%DATADIR%%/html/online/make_ndx.html
 %%DATADIR%%/html/online/map.html
 %%DATADIR%%/html/online/mdp.html
@@ -419,7 +438,10 @@
 %%DATADIR%%/top/dmso.gro
 %%DATADIR%%/top/dmso.itp
 %%DATADIR%%/top/edissoc.dat
+%%DATADIR%%/top/electroneg.dat
+%%DATADIR%%/top/elements.dat
 %%DATADIR%%/top/export.dlg
+%%DATADIR%%/top/f3c.itp
 %%DATADIR%%/top/fa.itp
 %%DATADIR%%/top/ffG43a1-c.tdb
 %%DATADIR%%/top/ffG43a1-n.tdb
@@ -439,23 +461,57 @@
 %%DATADIR%%/top/ffG43a2.rtp
 %%DATADIR%%/top/ffG43a2bon.itp
 %%DATADIR%%/top/ffG43a2nb.itp
-%%DATADIR%%/top/ffG43b1-c.tdb
-%%DATADIR%%/top/ffG43b1-n.tdb
-%%DATADIR%%/top/ffG43b1.atp
-%%DATADIR%%/top/ffG43b1.ddb
-%%DATADIR%%/top/ffG43b1.hdb
-%%DATADIR%%/top/ffG43b1.itp
-%%DATADIR%%/top/ffG43b1.rtp
-%%DATADIR%%/top/ffG43b1bon.itp
-%%DATADIR%%/top/ffG43b1nb.itp
+%%DATADIR%%/top/ffG45a3-c.tdb
+%%DATADIR%%/top/ffG45a3-n.tdb
+%%DATADIR%%/top/ffG45a3.atp
+%%DATADIR%%/top/ffG45a3.ddb
+%%DATADIR%%/top/ffG45a3.hdb
+%%DATADIR%%/top/ffG45a3.itp
+%%DATADIR%%/top/ffG45a3.rtp
+%%DATADIR%%/top/ffG45a3bon.itp
+%%DATADIR%%/top/ffG45a3nb.itp
+%%DATADIR%%/top/ffG53a5-c.tdb
+%%DATADIR%%/top/ffG53a5-n.tdb
+%%DATADIR%%/top/ffG53a5.atp
+%%DATADIR%%/top/ffG53a5.ddb
+%%DATADIR%%/top/ffG53a5.hdb
+%%DATADIR%%/top/ffG53a5.itp
+%%DATADIR%%/top/ffG53a5.n2t
+%%DATADIR%%/top/ffG53a5.rtp
+%%DATADIR%%/top/ffG53a5bon.itp
+%%DATADIR%%/top/ffG53a5nb.itp
+%%DATADIR%%/top/ffG53a6-c.tdb
+%%DATADIR%%/top/ffG53a6-n.tdb
+%%DATADIR%%/top/ffG53a6.atp
+%%DATADIR%%/top/ffG53a6.ddb
+%%DATADIR%%/top/ffG53a6.hdb
+%%DATADIR%%/top/ffG53a6.itp
+%%DATADIR%%/top/ffG53a6.rtp
+%%DATADIR%%/top/ffG53a6bon.itp
+%%DATADIR%%/top/ffG53a6nb.itp
 %%DATADIR%%/top/ff_dum.itp
+%%DATADIR%%/top/ffencads-c.tdb
+%%DATADIR%%/top/ffencads-n.tdb
+%%DATADIR%%/top/ffencads.atp
+%%DATADIR%%/top/ffencads.hdb
+%%DATADIR%%/top/ffencads.itp
+%%DATADIR%%/top/ffencads.rtp
+%%DATADIR%%/top/ffencadsbon.itp
+%%DATADIR%%/top/ffencadsnb.itp
+%%DATADIR%%/top/ffencadv-c.tdb
+%%DATADIR%%/top/ffencadv-n.tdb
+%%DATADIR%%/top/ffencadv.atp
+%%DATADIR%%/top/ffencadv.hdb
+%%DATADIR%%/top/ffencadv.itp
+%%DATADIR%%/top/ffencadv.rtp
+%%DATADIR%%/top/ffencadvbon.itp
+%%DATADIR%%/top/ffencadvnb.itp
 %%DATADIR%%/top/ffgmx-c.tdb
 %%DATADIR%%/top/ffgmx-n.tdb
 %%DATADIR%%/top/ffgmx.atp
 %%DATADIR%%/top/ffgmx.ddb
 %%DATADIR%%/top/ffgmx.hdb
 %%DATADIR%%/top/ffgmx.itp
-%%DATADIR%%/top/ffgmx.n2t
 %%DATADIR%%/top/ffgmx.rtp
 %%DATADIR%%/top/ffgmx2-c.tdb
 %%DATADIR%%/top/ffgmx2-n.tdb
@@ -474,6 +530,7 @@
 %%DATADIR%%/top/ffoplsaa.ddb
 %%DATADIR%%/top/ffoplsaa.hdb
 %%DATADIR%%/top/ffoplsaa.itp
+%%DATADIR%%/top/ffoplsaa.n2t
 %%DATADIR%%/top/ffoplsaa.rtp
 %%DATADIR%%/top/ffoplsaabon.itp
 %%DATADIR%%/top/ffoplsaanb.itp
@@ -486,6 +543,7 @@
 %%DATADIR%%/top/h2p8o25.itp
 %%DATADIR%%/top/h2po4.itp
 %%DATADIR%%/top/ha-shift.dat
+%%DATADIR%%/top/highway.dat
 %%DATADIR%%/top/ions.itp
 %%DATADIR%%/top/links.dat
 %%DATADIR%%/top/methanol.itp
@@ -515,7 +573,6 @@
 %%DATADIR%%/top/urea.itp
 %%DATADIR%%/top/vdwradii.dat
 %%DATADIR%%/top/xlateat.dat
-%%DATADIR%%/tutor/cleanit
 %%DATADIR%%/tutor/gmxdemo/cpeptide.pdb
 %%DATADIR%%/tutor/gmxdemo/demo
 %%DATADIR%%/tutor/methanol/conf.gro
Index: files/patch-configure
===================================================================
RCS file: files/patch-configure
diff -N files/patch-configure
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ files/patch-configure	10 Feb 2009 19:53:51 -0000
@@ -0,0 +1,11 @@
+--- configure.orig	2009-02-10 17:49:39.000000000 +0100
++++ configure	2009-02-10 17:50:54.000000000 +0100
+@@ -29600,7 +29600,7 @@
+ # if it isnt there.
+ if test "$with_xml" = "yes"; then
+    ac_save_CPPFLAGS="$CPPFLAGS"
+-   CPPFLAGS="$ac_save_CPPFLAGS -I/usr/include/libxml2"
++   CPPFLAGS="$ac_save_CPPFLAGS -I/usr/local/include/libxml2"
+ 
+ for ac_header in libxml/parser.h
+ do
Index: files/patch-src::contrib::Makefile.in
===================================================================
RCS file: files/patch-src::contrib::Makefile.in
diff -N files/patch-src::contrib::Makefile.in
--- files/patch-src::contrib::Makefile.in	9 Dec 2004 22:45:33 -0000	1.1
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,15 +0,0 @@
---- src/contrib/Makefile.in.orig	Mon Mar  1 20:49:01 2004
-+++ src/contrib/Makefile.in	Thu Dec  9 19:54:56 2004
-@@ -307,10 +307,10 @@
- @AMDEP_TRUE@	./$(DEPDIR)/sigeps.Po
- COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
- 	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--LTCOMPILE = $(LIBTOOL) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) \
-+LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(DEFS) $(DEFAULT_INCLUDES) \
- 	$(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
- CCLD = $(CC)
--LINK = $(LIBTOOL) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
-+LINK = $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
- 	$(AM_LDFLAGS) $(LDFLAGS) -o $@
- F77COMPILE = $(F77) $(AM_FFLAGS) $(FFLAGS)
- LTF77COMPILE = $(LIBTOOL) --mode=compile $(F77) $(AM_FFLAGS) $(FFLAGS)
Index: files/patch-src::gmxlib::Makefile.in
===================================================================
RCS file: files/patch-src::gmxlib::Makefile.in
diff -N files/patch-src::gmxlib::Makefile.in
--- files/patch-src::gmxlib::Makefile.in	9 Dec 2004 22:45:33 -0000	1.1
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,22 +0,0 @@
---- src/gmxlib/Makefile.in.orig	Mon Mar  1 20:49:02 2004
-+++ src/gmxlib/Makefile.in	Thu Dec  9 00:11:00 2004
-@@ -292,16 +292,16 @@
- @AMDEP_TRUE@	./$(DEPDIR)/xtcio.Plo ./$(DEPDIR)/xvgr.Plo
- COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
- 	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--LTCOMPILE = $(LIBTOOL) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) \
-+LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(DEFS) $(DEFAULT_INCLUDES) \
- 	$(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
- CCLD = $(CC)
--LINK = $(LIBTOOL) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
-+LINK = $(LIBTOOL) --mode=link  --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
- 	$(AM_LDFLAGS) $(LDFLAGS) -o $@
- F77COMPILE = $(F77) $(AM_FFLAGS) $(FFLAGS)
- LTF77COMPILE = $(LIBTOOL) --mode=compile $(F77) $(AM_FFLAGS) $(FFLAGS)
- F77LD = $(F77)
- CCASCOMPILE = $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS)
--LTCCASCOMPILE = $(LIBTOOL) --mode=compile $(CCAS) $(AM_CCASFLAGS) \
-+LTCCASCOMPILE = $(LIBTOOL) --mode=compile  --tag=CC $(CCAS) $(AM_CCASFLAGS) \
- 	$(CCASFLAGS)
- DIST_SOURCES = $(libgmx at LIBSUFFIX@_la_SOURCES) \
- 	$(EXTRA_libgmx at LIBSUFFIX@_la_SOURCES)
Index: files/patch-src::kernel::Makefile.in
===================================================================
RCS file: files/patch-src::kernel::Makefile.in
diff -N files/patch-src::kernel::Makefile.in
--- files/patch-src::kernel::Makefile.in	9 Dec 2004 22:45:33 -0000	1.1
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,15 +0,0 @@
---- src/kernel/Makefile.in.orig	Mon Mar  1 20:49:03 2004
-+++ src/kernel/Makefile.in	Thu Dec  9 00:33:06 2004
-@@ -367,10 +367,10 @@
- @AMDEP_TRUE@	./$(DEPDIR)/xutils.Po
- COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
- 	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--LTCOMPILE = $(LIBTOOL) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) \
-+LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(DEFS) $(DEFAULT_INCLUDES) \
- 	$(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
- CCLD = $(CC)
--LINK = $(LIBTOOL) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
-+LINK = $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
- 	$(AM_LDFLAGS) $(LDFLAGS) -o $@
- DIST_SOURCES = $(ffscan_SOURCES) $(gmxcheck_SOURCES) gmxdump.c \
- 	$(grompp_SOURCES) luck.c $(mdrun_SOURCES) $(pdb2gmx_SOURCES) \
Index: files/patch-src::mdlib::Makefile.in
===================================================================
RCS file: files/patch-src::mdlib::Makefile.in
diff -N files/patch-src::mdlib::Makefile.in
--- files/patch-src::mdlib::Makefile.in	9 Dec 2004 22:45:33 -0000	1.1
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,15 +0,0 @@
---- src/mdlib/Makefile.in.orig	Mon Mar  1 20:49:03 2004
-+++ src/mdlib/Makefile.in	Thu Dec  9 00:22:03 2004
-@@ -233,10 +233,10 @@
- @AMDEP_TRUE@	./$(DEPDIR)/vcm.Plo ./$(DEPDIR)/wnblist.Plo
- COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
- 	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--LTCOMPILE = $(LIBTOOL) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) \
-+LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(DEFS) $(DEFAULT_INCLUDES) \
- 	$(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
- CCLD = $(CC)
--LINK = $(LIBTOOL) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
-+LINK = $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
- 	$(AM_LDFLAGS) $(LDFLAGS) -o $@
- F77COMPILE = $(F77) $(AM_FFLAGS) $(FFLAGS)
- LTF77COMPILE = $(LIBTOOL) --mode=compile $(F77) $(AM_FFLAGS) $(FFLAGS)
Index: files/patch-src::ngmx::Makefile.in
===================================================================
RCS file: files/patch-src::ngmx::Makefile.in
diff -N files/patch-src::ngmx::Makefile.in
--- files/patch-src::ngmx::Makefile.in	9 Dec 2004 22:45:33 -0000	1.1
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,15 +0,0 @@
---- src/ngmx/Makefile.in.orig	Mon Mar  1 20:49:04 2004
-+++ src/ngmx/Makefile.in	Thu Dec  9 19:53:57 2004
-@@ -272,10 +272,10 @@
- @AMDEP_TRUE@	./$(DEPDIR)/xrama.Po ./$(DEPDIR)/xutil.Po
- COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
- 	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--LTCOMPILE = $(LIBTOOL) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) \
-+LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(DEFS) $(DEFAULT_INCLUDES) \
- 	$(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
- CCLD = $(CC)
--LINK = $(LIBTOOL) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
-+LINK = $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
- 	$(AM_LDFLAGS) $(LDFLAGS) -o $@
- DIST_SOURCES = $(dlg_SOURCES) $(gmxlogo_SOURCES) $(highway_SOURCES) \
- 	$(ngmx_SOURCES) $(scrollw_SOURCES) $(showcol_SOURCES) \
Index: files/patch-src::tools::Makefile.in
===================================================================
RCS file: files/patch-src::tools::Makefile.in
diff -N files/patch-src::tools::Makefile.in
--- files/patch-src::tools::Makefile.in	9 Dec 2004 22:45:33 -0000	1.1
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,15 +0,0 @@
---- src/tools/Makefile.in.orig	Mon Mar  1 20:49:06 2004
-+++ src/tools/Makefile.in	Thu Dec  9 19:35:43 2004
-@@ -744,10 +744,10 @@
- @AMDEP_TRUE@	./$(DEPDIR)/xpm2ps.Po
- COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
- 	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
--LTCOMPILE = $(LIBTOOL) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) \
-+LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(DEFS) $(DEFAULT_INCLUDES) \
- 	$(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
- CCLD = $(CC)
--LINK = $(LIBTOOL) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
-+LINK = $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
- 	$(AM_LDFLAGS) $(LDFLAGS) -o $@
- DIST_SOURCES = $(libgmxana at LIBSUFFIX@_la_SOURCES) $(anadock_SOURCES) \
- 	average.c $(cdist_SOURCES) $(disco_SOURCES) do_dssp.c \
--- science_gromacs.diff ends here ---


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