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File gromacs-3.3.1.dif of Package gromacs
Index: acinclude.m4 =================================================================== --- acinclude.m4.orig +++ acinclude.m4 @@ -1268,6423 +1268,3 @@ else fi AC_LANG_RESTORE ])dnl ACX_PTHREAD - - - - -# Libtool file included from libtool.m4 - -# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, -# 2005 Free Software Foundation, Inc. -# This file is free software; the Free Software Foundation -# gives unlimited permission to copy and/or distribute it, -# with or without modifications, as long as this notice is preserved. - -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY, to the extent permitted by law; without -# even the implied warranty of MERCHANTABILITY or FITNESS FOR A -# PARTICULAR PURPOSE. - -# libtool.m4 - Configure libtool for the host system. -*-Autoconf-*- - - -# AC_PROVIDE_IFELSE(MACRO-NAME, IF-PROVIDED, IF-NOT-PROVIDED) -# ----------------------------------------------------------- -# If this macro is not defined by Autoconf, define it here. -m4_ifdef([AC_PROVIDE_IFELSE], - [], - [m4_define([AC_PROVIDE_IFELSE], - [m4_ifdef([AC_PROVIDE_$1], - [$2], [$3])])]) - - -# AC_PROG_LIBTOOL -# --------------- -AC_DEFUN([AC_PROG_LIBTOOL], -[AC_REQUIRE([_AC_PROG_LIBTOOL])dnl -dnl If AC_PROG_CXX has already been expanded, run AC_LIBTOOL_CXX -dnl immediately, otherwise, hook it in at the end of AC_PROG_CXX. - AC_PROVIDE_IFELSE([AC_PROG_CXX], - [AC_LIBTOOL_CXX], - [define([AC_PROG_CXX], defn([AC_PROG_CXX])[AC_LIBTOOL_CXX - ])]) -dnl And a similar setup for Fortran 77 support - AC_PROVIDE_IFELSE([AC_PROG_F77], - [AC_LIBTOOL_F77], - [define([AC_PROG_F77], defn([AC_PROG_F77])[AC_LIBTOOL_F77 -])]) - -dnl Quote A][M_PROG_GCJ so that aclocal doesn't bring it in needlessly. -dnl If either AC_PROG_GCJ or A][M_PROG_GCJ have already been expanded, run -dnl AC_LIBTOOL_GCJ immediately, otherwise, hook it in at the end of both. - AC_PROVIDE_IFELSE([AC_PROG_GCJ], - [AC_LIBTOOL_GCJ], - [AC_PROVIDE_IFELSE([A][M_PROG_GCJ], - [AC_LIBTOOL_GCJ], - [AC_PROVIDE_IFELSE([LT_AC_PROG_GCJ], - [AC_LIBTOOL_GCJ], - [ifdef([AC_PROG_GCJ], - [define([AC_PROG_GCJ], defn([AC_PROG_GCJ])[AC_LIBTOOL_GCJ])]) - ifdef([A][M_PROG_GCJ], - [define([A][M_PROG_GCJ], defn([A][M_PROG_GCJ])[AC_LIBTOOL_GCJ])]) - ifdef([LT_AC_PROG_GCJ], - [define([LT_AC_PROG_GCJ], - defn([LT_AC_PROG_GCJ])[AC_LIBTOOL_GCJ])])])]) -])])# AC_PROG_LIBTOOL - - -# _AC_PROG_LIBTOOL -# ---------------- -AC_DEFUN([_AC_PROG_LIBTOOL], -[AC_REQUIRE([AC_LIBTOOL_SETUP])dnl -AC_BEFORE([$0],[AC_LIBTOOL_CXX])dnl -AC_BEFORE([$0],[AC_LIBTOOL_F77])dnl -AC_BEFORE([$0],[AC_LIBTOOL_GCJ])dnl - -# This can be used to rebuild libtool when needed -LIBTOOL_DEPS="$ac_aux_dir/ltmain.sh" - -# Always use our own libtool. -LIBTOOL='$(SHELL) $(top_builddir)/libtool' -AC_SUBST(LIBTOOL)dnl - -# Prevent multiple expansion -define([AC_PROG_LIBTOOL], []) -])# _AC_PROG_LIBTOOL - - -# AC_LIBTOOL_SETUP -# ---------------- -AC_DEFUN([AC_LIBTOOL_SETUP], -[AC_PREREQ(2.50)dnl -AC_REQUIRE([AC_ENABLE_SHARED])dnl -AC_REQUIRE([AC_ENABLE_STATIC])dnl -AC_REQUIRE([AC_ENABLE_FAST_INSTALL])dnl -AC_REQUIRE([AC_CANONICAL_HOST])dnl -AC_REQUIRE([AC_CANONICAL_BUILD])dnl -AC_REQUIRE([AC_PROG_CC])dnl -AC_REQUIRE([AC_PROG_LD])dnl -AC_REQUIRE([AC_PROG_LD_RELOAD_FLAG])dnl -AC_REQUIRE([AC_PROG_NM])dnl - -AC_REQUIRE([AC_PROG_LN_S])dnl -AC_REQUIRE([AC_DEPLIBS_CHECK_METHOD])dnl -# Autoconf 2.13's AC_OBJEXT and AC_EXEEXT macros only works for C compilers! -AC_REQUIRE([AC_OBJEXT])dnl -AC_REQUIRE([AC_EXEEXT])dnl -dnl - -AC_LIBTOOL_SYS_MAX_CMD_LEN -AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE -AC_LIBTOOL_OBJDIR - -AC_REQUIRE([_LT_AC_SYS_COMPILER])dnl -_LT_AC_PROG_ECHO_BACKSLASH - -case $host_os in -aix3*) - # AIX sometimes has problems with the GCC collect2 program. 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Bond lengths etc. are read from the topology. Pairs of atoms that can form hydrogen bonds are given a lowest possible distance of @@ -62,7 +62,7 @@ of to generate a topology with all dihedrals in there. If the optional pdb file is given, weights are read from the occupancy field, so that -not all atoms are part of the disco run, only those of which one of the +not all atoms are part of the g_disco run, only those of which one of the weights is non-zero. @@ -75,7 +75,7 @@ directory. The program can read a file with distances from NMR distance restraints (-d option). Note that these distance are treated slightly different -in the disco program, and therefore these distance should be NMR +in the g_disco program, and therefore these distance should be NMR derived distance restraints only. @@ -192,7 +192,7 @@ with each other. Maximum distance between any pair of atoms .BI "-[no]add" " no" - Write restraints in format of additional restraints for disco + Write restraints in format of additional restraints for g_disco .BI "-[no]vir" " no" Use virtual particles Index: man/man1/disco.1 =================================================================== --- man/man1/disco.1.orig +++ man/man1/disco.1 @@ -1,9 +1,9 @@ -.TH disco 1 "Mon 29 Aug 2005" +.TH g_disco 1 "Mon 29 Aug 2005" .SH NAME -disco +g_disco .B VERSION 3.3_beta_20050823 .SH SYNOPSIS -\f3disco\fP +\f3g_disco\fP .BI "-g" " disco.log " .BI "-f" " conf.gro " .BI "-d" " cdist.dat " @@ -36,17 +36,19 @@ disco .BI "-box" " vector " .BI "-grow" " int " .SH DESCRIPTION -disco reads a topology (tpr) file and runs distance geometry +g_disco reads a topology (tpr) file and runs distance geometry calculations based on the distances defined in the distance-restraints section of the topology. An appropriate tpr file may be generated by the cdist program. +In the original gromacs distribution, this file was named disco +but it conflicts with a file from the mono package. The algorithm is the CONCOORD algorithm of De Groot et al., which in turn is derived from the SHAKE alogrithm. -A parallel version of disco is under development whihc uses a +A parallel version of g_disco is under development which uses a master-slave approach. Slaves work asynchronously, and it is no problem when nodes are not equally fast, or when a node dies, unless it is the master node. Index: scripts/completion.bash =================================================================== --- scripts/completion.bash.orig +++ scripts/completion.bash @@ -44,7 +44,7 @@ case "$p" in -keep) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));; -viol) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));; esac } -complete -F _disco_compl disco +complete -F _disco_compl g_disco shopt -s extglob _do_dssp_compl() { local p c Index: scripts/completion.csh =================================================================== --- scripts/completion.csh.orig +++ scripts/completion.csh @@ -1,6 +1,6 @@ complete anadock "n/-f/f:*.pdb{,.gz,.Z}/" "n/-ox/f:*.pdb{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "c/-/( f ox od of g h nice noxvgr free norms cutoff)/" complete cdist "n/-sm/( none tri tetra)/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-q/f:*.pdb{,.gz,.Z}/" "n/-d/f:*.dat{,.gz,.Z}/" "n/-o/f:*.dat{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-dom/f:*.ndx{,.gz,.Z}/" "c/-/( s g q d o n dom h nice noengh bm am pm rr ar er vm lm il dm im nm hm hb nobon nonb measure maxdist add vir sm)/" -complete disco "n/-g/f:*.log{,.gz,.Z}/" "n/-f/f:*.{gro,g96,pdb,brk,ent,esp,tpr,tpb,tpa}{,.gz,.Z}/" "n/-d/f:*.dat{,.gz,.Z}/" "n/-do/f:*.dat{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent,esp}{,.gz,.Z}/" "n/-center/f:*.{gro,g96,pdb,brk,ent,esp}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-keep/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-viol/f:*.pdb{,.gz,.Z}/" "c/-/( g f d do c center n o keep viol h nice nf nit nov nochiral nopep lower weighted dump cubic explicit fit nbcheck nstprint ranlist noranlistfirst lowdev seed box grow)/" +complete g_disco "n/-g/f:*.log{,.gz,.Z}/" "n/-f/f:*.{gro,g96,pdb,brk,ent,esp,tpr,tpb,tpa}{,.gz,.Z}/" "n/-d/f:*.dat{,.gz,.Z}/" "n/-do/f:*.dat{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent,esp}{,.gz,.Z}/" "n/-center/f:*.{gro,g96,pdb,brk,ent,esp}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-keep/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-viol/f:*.pdb{,.gz,.Z}/" "c/-/( g f d do c center n o keep viol h nice nf nit nov nochiral nopep lower weighted dump cubic explicit fit nbcheck nstprint ranlist noranlistfirst lowdev seed box grow)/" complete do_dssp "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-ssdump/f:*.dat{,.gz,.Z}/" "n/-map/f:*.map{,.gz,.Z}/" "n/-o/f:*.xpm{,.gz,.Z}/" "n/-sc/f:*.xvg{,.gz,.Z}/" "n/-a/f:*.xpm{,.gz,.Z}/" "n/-ta/f:*.xvg{,.gz,.Z}/" "n/-aa/f:*.xvg{,.gz,.Z}/" "c/-/( f s n ssdump map o sc a ta aa h nice b e dt tu w noxvgr sss)/" complete editconf "n/-bt/( tric cubic dodecahedron octahedron)/" "n/-f/f:*.{gro,g96,pdb,brk,ent,esp,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent,esp}{,.gz,.Z}/" "n/-mead/f:*.pqr{,.gz,.Z}/" "n/-bf/f:*.dat{,.gz,.Z}/" "c/-/( f n o mead bf h nice w ndef bt box angles d c center translate rotate princ scale density novol pbc grasp rvdw sig56 vdwread atom legend label)/" complete eneconv "n/-f/f:*.{edr,ene}{,.gz,.Z}/" "n/-o/f:*.{edr,ene}{,.gz,.Z}/" "c/-/( f o h nice b e dt offset settime nosort scalefac noerror)/" Index: scripts/completion.zsh =================================================================== --- scripts/completion.zsh.orig +++ scripts/completion.zsh @@ -1,6 +1,6 @@ compctl -x 's[-]' -s " f ox od of g h nice noxvgr free norms cutoff" - 'c[-1,-f]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-ox]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' -- anadock compctl -x 's[-]' -s " s g q d o n dom h nice noengh bm am pm rr ar er vm lm il dm im nm hm hb nobon nonb measure maxdist add vir sm" - 'c[-1,-sm]' -s " none tri tetra" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-dom]' -g '*.ndx(|.gz|.Z) *(/)' -- cdist -compctl -x 's[-]' -s " g f d do c center n o keep viol h nice nf nit nov nochiral nopep lower weighted dump cubic explicit fit nbcheck nstprint ranlist noranlistfirst lowdev seed box grow" - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|esp|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-do]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|esp)(|.gz|.Z) *(/)' - 'c[-1,-center]' -g '*.(gro|g96|pdb|brk|ent|esp)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-keep]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-viol]' -g '*.pdb(|.gz|.Z) *(/)' -- disco +compctl -x 's[-]' -s " g f d do c center n o keep viol h nice nf nit nov nochiral nopep lower weighted dump cubic explicit fit nbcheck nstprint ranlist noranlistfirst lowdev seed box grow" - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|esp|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-do]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|esp)(|.gz|.Z) *(/)' - 'c[-1,-center]' -g '*.(gro|g96|pdb|brk|ent|esp)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-keep]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-viol]' -g '*.pdb(|.gz|.Z) *(/)' -- g_disco compctl -x 's[-]' -s " f s n ssdump map o sc a ta aa h nice b e dt tu w noxvgr sss" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-ssdump]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-map]' -g '*.map(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-sc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-a]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-ta]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-aa]' -g '*.xvg(|.gz|.Z) *(/)' -- do_dssp compctl -x 's[-]' -s " f n o mead bf h nice w ndef bt box angles d c center translate rotate princ scale density novol pbc grasp rvdw sig56 vdwread atom legend label" - 'c[-1,-bt]' -s " tric cubic dodecahedron octahedron" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|esp|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent|esp)(|.gz|.Z) *(/)' - 'c[-1,-mead]' -g '*.pqr(|.gz|.Z) *(/)' - 'c[-1,-bf]' -g '*.dat(|.gz|.Z) *(/)' -- editconf compctl -x 's[-]' -s " f o h nice b e dt offset settime nosort scalefac noerror" - 'c[-1,-f]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(edr|ene)(|.gz|.Z) *(/)' -- eneconv Index: share/html/online.html =================================================================== --- share/html/online.html.orig +++ share/html/online.html @@ -48,7 +48,7 @@ Sun 28 Aug 2005</B></td> <br> <br><a href=online/anadock.html>anadock</a> <br><a href=online/cdist.html>cdist</a> -<br><a href=online/disco.html>disco</a> +<br><a href=online/disco.html>g_disco</a> <br><a href=online/do_dssp.html>do_dssp</a> <br><a href=online/editconf.html>editconf</a> <br><a href=online/eneconv.html>eneconv</a> @@ -231,8 +231,8 @@ Sun 28 Aug 2005</B></td> <TR><TD><A HREF="online/g_confrms.html">g_confrms</A></TD><TD>fits two structures and calculates the rmsd </TD> <TR><TD><A HREF="online/g_cluster.html">g_cluster</A></TD><TD>clusters structures</TD> <TR><TD><A HREF="online/g_rmsf.html">g_rmsf</A></TD><TD>calculates atomic fluctuations</TD> -<TR><TD><A HREF="online/disco.html">disco</A></TD><TD>distance geometry calculation with the CONCOORD algorithm</TD> -<TR><TD><A HREF="online/cdist.html">cdist</A></TD><TD>create input for disco</TD> +<TR><TD><A HREF="online/disco.html">g_disco</A></TD><TD>distance geometry calculation with the CONCOORD algorithm</TD> +<TR><TD><A HREF="online/cdist.html">cdist</A></TD><TD>create input for g_disco</TD> </TABLE> <A NAME="HNR8"> @@ -280,8 +280,8 @@ Sun 28 Aug 2005</B></td> <TR><TD><A HREF="online/g_bundle.html">g_bundle</A></TD><TD>analyzes bundles of axes, e.g. helices</TD> <TR><TD><A HREF="online/g_disre.html">g_disre</A></TD><TD>analyzes distance restraints</TD> <TR><TD><A HREF="online/g_clustsize.html">g_clustsize</A></TD><TD>calculate size distributions of atomic clusters</TD> -<TR><TD><A HREF="online/disco.html">disco</A></TD><TD>distance geometry calculation with the CONCOORD algorithm</TD> -<TR><TD><A HREF="online/cdist.html">cdist</A></TD><TD>create input for disco</TD> +<TR><TD><A HREF="online/disco.html">g_disco</A></TD><TD>distance geometry calculation with the CONCOORD algorithm</TD> +<TR><TD><A HREF="online/cdist.html">cdist</A></TD><TD>create input for g_disco</TD> <TR><TD><A HREF="online/anadock.html">anadock</A></TD><TD>cluster structures from Autodock runs</TD> </TABLE> Index: share/top/Makefile.am =================================================================== --- share/top/Makefile.am.orig +++ share/top/Makefile.am @@ -50,7 +50,7 @@ topol_DATA = \ export.dlg bonds.dlg ss.map ps.m2p \ table6-10.xvg table6-11.xvg table6-12.xvg table6-8.xvg \ table6-9.xvg atom_nom.tbl gromacs.dtd tip5p.gro \ - tip5p.itp sw.itp + tip5p.itp sw.itp FF.dat EXTRA_DIST = ${topol_DATA} Index: src/gmxlib/nonbonded/nb_kernel/Makefile.am =================================================================== --- src/gmxlib/nonbonded/nb_kernel/Makefile.am.orig +++ src/gmxlib/nonbonded/nb_kernel/Makefile.am @@ -148,7 +148,7 @@ EXTRA_DIST = \ -BUILD_COMPILE = $(CC_FOR_BUILD) $(DEFS) $(DEFAULT_INCLUDES) +BUILD_COMPILE = $(CC_FOR_BUILD) $(DEFS) $(DEFAULT_INCLUDES) $(CCFLAGS) Index: src/gmxlib/nonbonded/nb_kernel/Makefile.am~ =================================================================== --- /dev/null +++ src/gmxlib/nonbonded/nb_kernel/Makefile.am~ @@ -0,0 +1,214 @@ + +AM_CPPFLAGS= -I$(top_srcdir)/include -DGMXLIBDIR=\"$(datadir)/top\" + +noinst_LTLIBRARIES = libnb_kernel.la + + +FORTRAN_KERNEL_OBJS = \ + nb_kernel010_f.lo nb_kernel020_f.lo nb_kernel030_f.lo nb_kernel100_f.lo \ + nb_kernel101_f.lo nb_kernel102_f.lo nb_kernel103_f.lo nb_kernel104_f.lo \ + nb_kernel110_f.lo nb_kernel111_f.lo nb_kernel112_f.lo nb_kernel113_f.lo \ + nb_kernel114_f.lo nb_kernel120_f.lo nb_kernel121_f.lo nb_kernel122_f.lo \ + nb_kernel123_f.lo nb_kernel124_f.lo nb_kernel130_f.lo nb_kernel131_f.lo \ + nb_kernel132_f.lo nb_kernel133_f.lo nb_kernel134_f.lo nb_kernel200_f.lo \ + nb_kernel201_f.lo nb_kernel202_f.lo nb_kernel203_f.lo nb_kernel204_f.lo \ + nb_kernel210_f.lo nb_kernel211_f.lo nb_kernel212_f.lo nb_kernel213_f.lo \ + nb_kernel214_f.lo nb_kernel220_f.lo nb_kernel221_f.lo nb_kernel222_f.lo \ + nb_kernel223_f.lo nb_kernel224_f.lo nb_kernel230_f.lo nb_kernel231_f.lo \ + nb_kernel232_f.lo nb_kernel233_f.lo nb_kernel234_f.lo nb_kernel300_f.lo \ + nb_kernel301_f.lo nb_kernel302_f.lo nb_kernel303_f.lo nb_kernel304_f.lo \ + nb_kernel310_f.lo nb_kernel311_f.lo nb_kernel312_f.lo nb_kernel313_f.lo \ + nb_kernel314_f.lo nb_kernel320_f.lo nb_kernel321_f.lo nb_kernel322_f.lo \ + nb_kernel323_f.lo nb_kernel324_f.lo nb_kernel330_f.lo nb_kernel331_f.lo \ + nb_kernel332_f.lo nb_kernel333_f.lo nb_kernel334_f.lo nb_kernel400_f.lo \ + nb_kernel410_f.lo nb_kernel420_f.lo nb_kernel430_f.lo + +FORTRAN_KERNEL_SOURCES = \ + nb_kernel010_f.f nb_kernel020_f.f nb_kernel030_f.f nb_kernel100_f.f \ + nb_kernel101_f.f nb_kernel102_f.f nb_kernel103_f.f nb_kernel104_f.f \ + nb_kernel110_f.f nb_kernel111_f.f nb_kernel112_f.f nb_kernel113_f.f \ + nb_kernel114_f.f nb_kernel120_f.f nb_kernel121_f.f nb_kernel122_f.f \ + nb_kernel123_f.f nb_kernel124_f.f nb_kernel130_f.f nb_kernel131_f.f \ + nb_kernel132_f.f nb_kernel133_f.f nb_kernel134_f.f nb_kernel200_f.f \ + nb_kernel201_f.f nb_kernel202_f.f nb_kernel203_f.f nb_kernel204_f.f \ + nb_kernel210_f.f nb_kernel211_f.f nb_kernel212_f.f nb_kernel213_f.f \ + nb_kernel214_f.f nb_kernel220_f.f nb_kernel221_f.f nb_kernel222_f.f \ + nb_kernel223_f.f nb_kernel224_f.f nb_kernel230_f.f nb_kernel231_f.f \ + nb_kernel232_f.f nb_kernel233_f.f nb_kernel234_f.f nb_kernel300_f.f \ + nb_kernel301_f.f nb_kernel302_f.f nb_kernel303_f.f nb_kernel304_f.f \ + nb_kernel310_f.f nb_kernel311_f.f nb_kernel312_f.f nb_kernel313_f.f \ + nb_kernel314_f.f nb_kernel320_f.f nb_kernel321_f.f nb_kernel322_f.f \ + nb_kernel323_f.f nb_kernel324_f.f nb_kernel330_f.f nb_kernel331_f.f \ + nb_kernel332_f.f nb_kernel333_f.f nb_kernel334_f.f nb_kernel400_f.f \ + nb_kernel410_f.f nb_kernel420_f.f nb_kernel430_f.f + + +# + +C_KERNEL_OBJS = \ + nb_kernel010_c.lo nb_kernel020_c.lo nb_kernel030_c.lo nb_kernel100_c.lo \ + nb_kernel101_c.lo nb_kernel102_c.lo nb_kernel103_c.lo nb_kernel104_c.lo \ + nb_kernel110_c.lo nb_kernel111_c.lo nb_kernel112_c.lo nb_kernel113_c.lo \ + nb_kernel114_c.lo nb_kernel120_c.lo nb_kernel121_c.lo nb_kernel122_c.lo \ + nb_kernel123_c.lo nb_kernel124_c.lo nb_kernel130_c.lo nb_kernel131_c.lo \ + nb_kernel132_c.lo nb_kernel133_c.lo nb_kernel134_c.lo nb_kernel200_c.lo \ + nb_kernel201_c.lo nb_kernel202_c.lo nb_kernel203_c.lo nb_kernel204_c.lo \ + nb_kernel210_c.lo nb_kernel211_c.lo nb_kernel212_c.lo nb_kernel213_c.lo \ + nb_kernel214_c.lo nb_kernel220_c.lo nb_kernel221_c.lo nb_kernel222_c.lo \ + nb_kernel223_c.lo nb_kernel224_c.lo nb_kernel230_c.lo nb_kernel231_c.lo \ + nb_kernel232_c.lo nb_kernel233_c.lo nb_kernel234_c.lo nb_kernel300_c.lo \ + nb_kernel301_c.lo nb_kernel302_c.lo nb_kernel303_c.lo nb_kernel304_c.lo \ + nb_kernel310_c.lo nb_kernel311_c.lo nb_kernel312_c.lo nb_kernel313_c.lo \ + nb_kernel314_c.lo nb_kernel320_c.lo nb_kernel321_c.lo nb_kernel322_c.lo \ + nb_kernel323_c.lo nb_kernel324_c.lo nb_kernel330_c.lo nb_kernel331_c.lo \ + nb_kernel332_c.lo nb_kernel333_c.lo nb_kernel334_c.lo nb_kernel400_c.lo \ + nb_kernel410_c.lo nb_kernel420_c.lo nb_kernel430_c.lo + + +C_KERNEL_SOURCES = \ + nb_kernel010_c.c nb_kernel020_c.c nb_kernel030_c.c nb_kernel100_c.c \ + nb_kernel101_c.c nb_kernel102_c.c nb_kernel103_c.c nb_kernel104_c.c \ + nb_kernel110_c.c nb_kernel111_c.c nb_kernel112_c.c nb_kernel113_c.c \ + nb_kernel114_c.c nb_kernel120_c.c nb_kernel121_c.c nb_kernel122_c.c \ + nb_kernel123_c.c nb_kernel124_c.c nb_kernel130_c.c nb_kernel131_c.c \ + nb_kernel132_c.c nb_kernel133_c.c nb_kernel134_c.c nb_kernel200_c.c \ + nb_kernel201_c.c nb_kernel202_c.c nb_kernel203_c.c nb_kernel204_c.c \ + nb_kernel210_c.c nb_kernel211_c.c nb_kernel212_c.c nb_kernel213_c.c \ + nb_kernel214_c.c nb_kernel220_c.c nb_kernel221_c.c nb_kernel222_c.c \ + nb_kernel223_c.c nb_kernel224_c.c nb_kernel230_c.c nb_kernel231_c.c \ + nb_kernel232_c.c nb_kernel233_c.c nb_kernel234_c.c nb_kernel300_c.c \ + nb_kernel301_c.c nb_kernel302_c.c nb_kernel303_c.c nb_kernel304_c.c \ + nb_kernel310_c.c nb_kernel311_c.c nb_kernel312_c.c nb_kernel313_c.c \ + nb_kernel314_c.c nb_kernel320_c.c nb_kernel321_c.c nb_kernel322_c.c \ + nb_kernel323_c.c nb_kernel324_c.c nb_kernel330_c.c nb_kernel331_c.c \ + nb_kernel332_c.c nb_kernel333_c.c nb_kernel334_c.c nb_kernel400_c.c \ + nb_kernel410_c.c nb_kernel420_c.c nb_kernel430_c.c + + + +if GMX_FORTRAN + KERNEL_OBJS = $(FORTRAN_KERNEL_OBJS) nb_kernel_f77sync.lo +else + KERNEL_OBJS = $(C_KERNEL_OBJS) +endif + +# +# This is a virtual target for all the kernels, to ensure it is only run +# by one CPU even if you run make in parallel. +# The mknb program will generate the kernel-stamp file when done. +# +BUILT_SOURCES = kernel-stamp + +libnb_kernel_la_LIBADD = $(KERNEL_OBJS) +libnb_kernel_la_DEPENDENCIES = $(KERNEL_OBJS) + + +libnb_kernel_la_SOURCES = \ + nb_kernel010.h nb_kernel020.h nb_kernel030.h nb_kernel100.h \ + nb_kernel101.h nb_kernel102.h nb_kernel103.h nb_kernel104.h \ + nb_kernel110.h nb_kernel111.h nb_kernel112.h nb_kernel113.h \ + nb_kernel114.h nb_kernel120.h nb_kernel121.h nb_kernel122.h \ + nb_kernel123.h nb_kernel124.h nb_kernel130.h nb_kernel131.h \ + nb_kernel132.h nb_kernel133.h nb_kernel134.h nb_kernel200.h \ + nb_kernel201.h nb_kernel202.h nb_kernel203.h nb_kernel204.h \ + nb_kernel210.h nb_kernel211.h nb_kernel212.h nb_kernel213.h \ + nb_kernel214.h nb_kernel220.h nb_kernel221.h nb_kernel222.h \ + nb_kernel223.h nb_kernel224.h nb_kernel230.h nb_kernel231.h \ + nb_kernel232.h nb_kernel233.h nb_kernel234.h nb_kernel300.h \ + nb_kernel301.h nb_kernel302.h nb_kernel303.h nb_kernel304.h \ + nb_kernel310.h nb_kernel311.h nb_kernel312.h nb_kernel313.h \ + nb_kernel314.h nb_kernel320.h nb_kernel321.h nb_kernel322.h \ + nb_kernel323.h nb_kernel324.h nb_kernel330.h nb_kernel331.h \ + nb_kernel332.h nb_kernel333.h nb_kernel334.h nb_kernel400.h \ + nb_kernel410.h nb_kernel420.h nb_kernel430.h \ + nb_kernel.c nb_kernel.h + + + +EXTRA_libnb_kernel_la_SOURCES = nb_kernel_f77sync.c + + +# sources built at compile time +nodist_EXTRA_libnb_kernel_la_SOURCES = $(FORTRAN_KERNEL_SOURCES) $(C_KERNEL_SOURCES) + + + +# mknb is special - we cant use a noinst_PROGRAMS target, since it might have +# to be compiled with a non-MPI compiler whose files can be executed by make: + +EXTRA_DIST = \ + mknb.c \ + mknb_metacode.c mknb_metacode.h \ + mknb_common.c mknb_common.h \ + mknb_declarations.c mknb_declarations.h \ + mknb_outerloop.c mknb_outerloop.h \ + mknb_innerloop.c mknb_innerloop.h \ + mknb_interactions.c mknb_interactions.h + + + + +BUILD_COMPILE = $(CC_FOR_BUILD) $(DEFS) $(DEFAULT_INCLUDES) + + + +mknb.o: mknb.c + $(BUILD_COMPILE) -c -o $@ $< +mknb_common.o: mknb_common.c + $(BUILD_COMPILE) -c -o $@ $< +mknb_metacode.o: mknb_metacode.c + $(BUILD_COMPILE) -c -o $@ $< +mknb_declarations.o: mknb_declarations.c + $(BUILD_COMPILE) -c -o $@ $< +mknb_outerloop.o: mknb_outerloop.c + $(BUILD_COMPILE) -c -o $@ $< +mknb_innerloop.o: mknb_innerloop.c + $(BUILD_COMPILE) -c -o $@ $< +mknb_interactions.o: mknb_interactions.c + $(BUILD_COMPILE) -c -o $@ $< + +MKNB_OBJ = \ + mknb.o mknb_metacode.o mknb_common.o mknb_declarations.o \ + mknb_outerloop.o mknb_innerloop.o mknb_interactions.o + +mknb: $(MKNB_OBJ) + $(BUILD_COMPILE) -o $@ $(MKNB_OBJ) + + +if GMX_DOUBLE + DOUBLEFLAG = -double +endif + +if GMX_THREAD + THREADFLAG = -threads +endif + +if GMX_SOFTWARE_SQRT + SQRTFLAG = -software_invsqrt +endif + +if GMX_PREFETCH_FORCES + PREFETCHFLAG = -prefetch_forces +endif + +if GMX_FORTRAN + FORTRANFLAG = -fortran +endif + +MKNB_FLAGS = $(DOUBLEFLAG) $(THREADFLAG) $(SQRTFLAG) \ + $(PREFETCHFLAG) $(FORTRANFLAG) + +# +# The kernels should only be built once, instead of once per +# source file when using parallel builds (make -j N). To solve this +# the mknb program writes out a stamp file after the kernels, which +# we use as a dummy/virtual target. +# +kernel-stamp: mknb + rm -f kernel-stamp + ./mknb $(MKNB_FLAGS) + + + +CLEANFILES = *.la *~ \\\#* mknb nb_kernel*_f.f nb_kernel*_c.c cg kernel-stamp + Index: src/mdlib/calcmu.c =================================================================== --- src/mdlib/calcmu.c.orig +++ src/mdlib/calcmu.c @@ -82,7 +82,7 @@ bool read_mu(FILE *fp,rvec mu,real *vol) /* For backward compatibility */ real mmm[4]; - if (fread(mmm,(size_t)(4*sizeof(mmm)),1,fp) != 1) + if (fread(mmm,(size_t)(4*sizeof(real)),1,fp) != 1) return FALSE; copy_rvec(mmm,mu); Index: src/mdlib/calcmu.c~ =================================================================== --- /dev/null +++ src/mdlib/calcmu.c~ @@ -0,0 +1,93 @@ +/* + * $Id: calcmu.c,v 1.11 2005/03/01 09:00:38 hess Exp $ + * + * This source code is part of + * + * G R O M A C S + * + * GROningen MAchine for Chemical Simulations + * + * VERSION 3.2.0 + * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. + * Copyright (c) 1991-2000, University of Groningen, The Netherlands. + * Copyright (c) 2001-2004, The GROMACS development team, + * check out http://www.gromacs.org for more information. + + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * If you want to redistribute modifications, please consider that + * scientific software is very special. Version control is crucial - + * bugs must be traceable. We will be happy to consider code for + * inclusion in the official distribution, but derived work must not + * be called official GROMACS. Details are found in the README & COPYING + * files - if they are missing, get the official version at www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the papers on the package - you can find them in the top README file. + * + * For more info, check our website at http://www.gromacs.org + * + * And Hey: + * GROwing Monsters And Cloning Shrimps + */ +/* This file is completely threadsafe - keep it that way! */ +#ifdef HAVE_CONFIG_H +#include <config.h> +#endif + +#include <stdio.h> +#include <stdlib.h> +#include "typedefs.h" +#include "network.h" +#include "vec.h" +#include "fatal.h" +#include "physics.h" +#include "nsb.h" +#include "main.h" + +void calc_mu(t_nsborder *nsb,rvec x[],real q[],real qB[], + bool bFreeEnergy, + rvec mu,rvec mu_B) +{ + int i,start,end,m; + /* temporary double prec. to maintain precision */ + dvec tmpmu; + + start = START(nsb); + end = start + HOMENR(nsb); + + clear_dvec(tmpmu); + for(i=start; (i<end); i++) + for(m=0; (m<DIM); m++) + tmpmu[m] += q[i]*x[i][m]; + + for(m=0; (m<DIM); m++) + mu[m] = tmpmu[m] * ENM2DEBYE; + + if (bFreeEnergy) { + clear_dvec(tmpmu); + for(i=start; (i<end); i++) + for(m=0; (m<DIM); m++) + tmpmu[m] += qB[i]*x[i][m]; + } + for(m=0; (m<DIM); m++) + mu_B[m] = tmpmu[m] * ENM2DEBYE; +} + +bool read_mu(FILE *fp,rvec mu,real *vol) +{ + /* For backward compatibility */ + real mmm[4]; + + if (fread(mmm,(size_t)(4*sizeof(mmm)),1,fp) != 1) + return FALSE; + + copy_rvec(mmm,mu); + *vol = mmm[3]; + + return TRUE; +} +
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