diff options
author | asau <asau@pkgsrc.org> | 2010-03-15 14:08:49 +0000 |
---|---|---|
committer | asau <asau@pkgsrc.org> | 2010-03-15 14:08:49 +0000 |
commit | 29d1bdfacb547a15ec030ee9fb1c178cc09d7ff7 (patch) | |
tree | 91cfac1a1319742f4d3cee1344505397f59d7177 /biology | |
parent | ae213c3610fc3db7b848e5163e5b95ed3716b1b2 (diff) | |
download | pkgsrc-29d1bdfacb547a15ec030ee9fb1c178cc09d7ff7.tar.gz |
Import GROMACS 4.0.7 as biology/gromacs.
From pkgsrc-wip, packaged originally by Peter Ibsen Hansen.
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.
Diffstat (limited to 'biology')
-rw-r--r-- | biology/gromacs/DESCR | 10 | ||||
-rw-r--r-- | biology/gromacs/Makefile | 33 | ||||
-rw-r--r-- | biology/gromacs/PLIST | 684 | ||||
-rw-r--r-- | biology/gromacs/distinfo | 8 | ||||
-rw-r--r-- | biology/gromacs/options.mk | 19 | ||||
-rw-r--r-- | biology/gromacs/patches/patch-aa | 19 | ||||
-rw-r--r-- | biology/gromacs/patches/patch-ab | 24 | ||||
-rw-r--r-- | biology/gromacs/patches/patch-ac | 24 |
8 files changed, 821 insertions, 0 deletions
diff --git a/biology/gromacs/DESCR b/biology/gromacs/DESCR new file mode 100644 index 00000000000..17d86649e93 --- /dev/null +++ b/biology/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/biology/gromacs/Makefile b/biology/gromacs/Makefile new file mode 100644 index 00000000000..6a1c711d77e --- /dev/null +++ b/biology/gromacs/Makefile @@ -0,0 +1,33 @@ +# $NetBSD: Makefile,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $ +# + +DISTNAME= gromacs-4.0.7 +CATEGORIES= biology +MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/ + +MAINTAINER= pkgsrc-users@NetBSD.org +HOMEPAGE= http://www.gromacs.org/ +COMMENT= Molecular dynamics package +LICENSE= gnu-gpl-v2 + +PKG_DESTDIR_SUPPORT= user-destdir + +# Official recommendation is not to use the gcc 4.1.x set of compilers. + +GNU_CONFIGURE= yes +USE_LIBTOOL= yes +USE_PKGLOCALEDIR= yes + +CONFIGURE_ARGS+= --enable-shared +CONFIGURE_ARGS+= --enable-double --program-suffix= +CONFIGURE_ARGS+= --with-gsl + +.include "options.mk" + +USE_TOOLS+= perl:run +REPLACE_PERL= scripts/demux.pl scripts/xplor2gmx.pl + +.include "../../math/fftw/buildlink3.mk" +.include "../../math/gsl/buildlink3.mk" # optional +.include "../../textproc/libxml2/buildlink3.mk" # optional +.include "../../mk/bsd.pkg.mk" diff --git a/biology/gromacs/PLIST b/biology/gromacs/PLIST new file mode 100644 index 00000000000..1eefe4bba92 --- /dev/null +++ b/biology/gromacs/PLIST @@ -0,0 +1,684 @@ +@comment $NetBSD: PLIST,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $ +bin/GMXRC +bin/GMXRC.bash +bin/GMXRC.csh +bin/GMXRC.zsh +bin/anadock +bin/completion.bash +bin/completion.csh +bin/completion.zsh +bin/demux.pl +bin/do_dssp +bin/editconf +bin/eneconv +bin/g_anaeig +bin/g_analyze +bin/g_angle +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_dielectric +bin/g_dih +bin/g_dipoles +bin/g_disre +bin/g_dist +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_kinetics +bin/g_lie +bin/g_mdmat +bin/g_mindist +bin/g_morph +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 +bin/g_rmsdist +bin/g_rmsf +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/genrestr +bin/gmxcheck +bin/gmxdump +bin/grompp +${PLIST.x11}bin/highway +bin/luck +bin/make_edi +bin/make_ndx +bin/mdrun +bin/mk_angndx +${PLIST.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 +${PLIST.x11}bin/xrama +include/gromacs/3dview.h +include/gromacs/assert.h +include/gromacs/atomprop.h +include/gromacs/bondf.h +include/gromacs/calcgrid.h +include/gromacs/calch.h +include/gromacs/calcmu.h +include/gromacs/checkpoint.h +include/gromacs/confio.h +include/gromacs/constr.h +include/gromacs/copyrite.h +include/gromacs/coulomb.h +include/gromacs/dihre.h +include/gromacs/disre.h +include/gromacs/do_fit.h +include/gromacs/domdec.h +include/gromacs/domdec_network.h +include/gromacs/ebin.h +include/gromacs/edsam.h +include/gromacs/enxio.h +include/gromacs/ffscanf.h +include/gromacs/fftgrid.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/invblock.h +include/gromacs/macros.h +include/gromacs/magic.h +include/gromacs/main.h +include/gromacs/maths.h +include/gromacs/matio.h +include/gromacs/mdatoms.h +include/gromacs/mdebin.h +include/gromacs/mdrun.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/nonbonded.h +include/gromacs/nrama.h +include/gromacs/nrjac.h +include/gromacs/nrnb.h +include/gromacs/ns.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/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 +include/gromacs/readcomp.h +include/gromacs/readinp.h +include/gromacs/reorder.h +include/gromacs/rmpbc.h +include/gromacs/shellfc.h +include/gromacs/shift.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 +include/gromacs/string2.h +include/gromacs/struc2.h +include/gromacs/symtab.h +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 +include/gromacs/txtdump.h +include/gromacs/typedefs.h +include/gromacs/types/atoms.h +include/gromacs/types/block.h +include/gromacs/types/commrec.h +include/gromacs/types/constr.h +include/gromacs/types/energy.h +include/gromacs/types/enums.h +include/gromacs/types/fcdata.h +include/gromacs/types/filenm.h +include/gromacs/types/forcerec.h +include/gromacs/types/graph.h +include/gromacs/types/group.h +include/gromacs/types/idef.h +include/gromacs/types/ifunc.h +include/gromacs/types/inputrec.h +include/gromacs/types/ishift.h +include/gromacs/types/matrix.h +include/gromacs/types/mdatom.h +include/gromacs/types/nblist.h +include/gromacs/types/nbslist.h +include/gromacs/types/nrnb.h +include/gromacs/types/ns.h +include/gromacs/types/nsgrid.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 +include/gromacs/types/topology.h +include/gromacs/types/trx.h +include/gromacs/update.h +include/gromacs/utils.h +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/xdrf.h +include/gromacs/xtcio.h +include/gromacs/xvgr.h +lib/libgmx_d.la +lib/libgmxana_d.la +lib/libmd_d.la +man/man1/anadock.1 +man/man1/do_dssp.1 +man/man1/editconf.1 +man/man1/eneconv.1 +man/man1/g_anaeig.1 +man/man1/g_analyze.1 +man/man1/g_angle.1 +man/man1/g_bond.1 +man/man1/g_bundle.1 +man/man1/g_chi.1 +man/man1/g_cluster.1 +man/man1/g_clustsize.1 +man/man1/g_confrms.1 +man/man1/g_covar.1 +man/man1/g_current.1 +man/man1/g_density.1 +man/man1/g_densmap.1 +man/man1/g_dielectric.1 +man/man1/g_dih.1 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00000000000..39cee7939aa --- /dev/null +++ b/biology/gromacs/distinfo @@ -0,0 +1,8 @@ +$NetBSD: distinfo,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $ + +SHA1 (gromacs-4.0.7.tar.gz) = 8519bef2fa989fb487d54612b0a2d0228f228b30 +RMD160 (gromacs-4.0.7.tar.gz) = 4fa8e5c90f549ef627a98a907a166676692a4c4b +Size (gromacs-4.0.7.tar.gz) = 8404518 bytes +SHA1 (patch-aa) = dcf39e862c2087bca0cd4e577438633bf70fe57f +SHA1 (patch-ab) = 333fea1f0844f8628795f593de16c941744b11d2 +SHA1 (patch-ac) = 164a7b3e06ab4f4cc1142615c1281eec82adee9b diff --git a/biology/gromacs/options.mk b/biology/gromacs/options.mk new file mode 100644 index 00000000000..55502741ee5 --- /dev/null +++ b/biology/gromacs/options.mk @@ -0,0 +1,19 @@ +# $NetBSD: options.mk,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $ + +PKG_OPTIONS_VAR= PKG_OPTIONS.gromacs +PKG_SUPPORTED_OPTIONS+= x11 +PKG_SUGGESTED_OPTIONS+= x11 + +.include "../../mk/bsd.options.mk" + +PLIST_VARS= x11 + +# 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 diff --git a/biology/gromacs/patches/patch-aa b/biology/gromacs/patches/patch-aa new file mode 100644 index 00000000000..13d6487d231 --- /dev/null +++ b/biology/gromacs/patches/patch-aa @@ -0,0 +1,19 @@ +$NetBSD: patch-aa,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $ + +Allow flags to contain commas. + +--- share/template/Makefile.in.orig 2010-01-12 15:44:18.000000000 +0300 ++++ share/template/Makefile.in 2010-01-12 15:58:57.000000000 +0300 +@@ -389,9 +389,9 @@ + + Makefile.@host@ Makefile.@host@_double: Template.mak Makefile + cat $(srcdir)/Template.mak | \ +- sed 's,@LDFLAGS\@,$(LDFLAGS),' | \ +- sed 's,@LIBS\@,$(LIBS),' | \ +- sed 's,@CFLAGS\@,$(MYCFLAGS),' | \ ++ sed 's|@LDFLAGS\@|$(LDFLAGS)|' | \ ++ sed 's|@LIBS\@|$(LIBS)|' | \ ++ sed 's|@CFLAGS\@|$(MYCFLAGS)|' | \ + sed 's,@CC\@,$(CC),' | \ + sed 's,@host\@,@host@,' >$@ + # Tell versions [3.59,3.63) of GNU make to not export all variables. diff --git a/biology/gromacs/patches/patch-ab b/biology/gromacs/patches/patch-ab new file mode 100644 index 00000000000..a25ab310a3c --- /dev/null +++ b/biology/gromacs/patches/patch-ab @@ -0,0 +1,24 @@ +$NetBSD: patch-ab,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $ + +Avoid non-standard "==" in test. + +--- configure.ac.orig 2009-12-07 00:18:27.000000000 +0300 ++++ configure.ac 2010-03-15 16:02:27.000000000 +0300 +@@ -183,7 +183,7 @@ + [set --enable-ppc-sqrt=1 for better speed.])],, + enable_ppc_sqrt=no) + if test "$enable_ppc_sqrt" != "no"; then +- if test "$enable_ppc_sqrt" == "1"; then ++ if test "$enable_ppc_sqrt" = "1"; then + ppc_sqrt_niter=1; + else + ppc_sqrt_niter=2; +@@ -193,7 +193,7 @@ + enable_software_sqrt="no"; + fi + AM_CONDITIONAL([GMX_POWERPC_SQRT],[test "$enable_ppc_sqrt" != "no"]) +-AM_CONDITIONAL([GMX_POWERPC_SQRT_SINGLE_ITERATION],[test "$ppc_sqrt_niter" == "1"]) ++AM_CONDITIONAL([GMX_POWERPC_SQRT_SINGLE_ITERATION],[test "$ppc_sqrt_niter" = "1"]) + + + if test "$enable_software_sqrt" = "yes"; then diff --git a/biology/gromacs/patches/patch-ac b/biology/gromacs/patches/patch-ac new file mode 100644 index 00000000000..534f950d288 --- /dev/null +++ b/biology/gromacs/patches/patch-ac @@ -0,0 +1,24 @@ +$NetBSD: patch-ac,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $ + +Avoid non-standard "==" in test. + +--- configure.orig 2010-03-15 15:59:18.000000000 +0300 ++++ configure 2010-03-15 16:00:44.000000000 +0300 +@@ -2994,7 +2994,7 @@ + fi + + if test "$enable_ppc_sqrt" != "no"; then +- if test "$enable_ppc_sqrt" == "1"; then ++ if test "$enable_ppc_sqrt" = "1"; then + ppc_sqrt_niter=1; + else + ppc_sqrt_niter=2; +@@ -3015,7 +3015,7 @@ + GMX_POWERPC_SQRT_FALSE= + fi + +- if test "$ppc_sqrt_niter" == "1"; then ++ if test "$ppc_sqrt_niter" = "1"; then + GMX_POWERPC_SQRT_SINGLE_ITERATION_TRUE= + GMX_POWERPC_SQRT_SINGLE_ITERATION_FALSE='#' + else |