Hi,
The format that is dumped by gmxdump is now the processed topology.
The bonded interactions are now only stored per molecule type.
I have made a option -sys to gmxdump, the source code is attached.
Could you try if this does what you want and report back?
Berk
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/*
* $Id: gmxdump.c,v 1.51 2008/09/19 08:09:34 lindahl 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.
*
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* 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:
* Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdio.h>
#include <string.h>
#include <math.h>
#include "main.h"
#include "macros.h"
#include "futil.h"
#include "statutil.h"
#include "copyrite.h"
#include "sysstuff.h"
#include "txtdump.h"
#include "gmx_fatal.h"
#include "xtcio.h"
#include "enxio.h"
#include "smalloc.h"
#include "names.h"
#include "gmxfio.h"
#include "tpxio.h"
#include "trnio.h"
#include "txtdump.h"
#include "gmxcpp.h"
#include "checkpoint.h"
#include "mtop_util.h"
static void dump_top(FILE *fp,t_topology *top,char *tpr)
{
int i,j,k,*types;
fprintf(fp,"; Topology generated from %s by program %s\n",tpr,Program());
fprintf(fp,"[ defaults ]\n 1 1 no 1.0 1.0\n\n");
fprintf(fp,"[ atomtypes ]\n");
fprintf(fp,";name at.num mass charge ptype c6 c12\n");
snew(types,top->atomtypes.nr);
for(i=0; (i<top->atomtypes.nr); i++) {
for(j=0; (j<top->atoms.nr) && (top->atoms.atom[j].type != i); j++)
;
if (j<top->atoms.nr) {
types[i] = j;
fprintf(fp,"%5s %4d %8.4f %8.4f %2s %8.3f %8.3f\n",
*(top->atoms.atomtype[j]),top->atomtypes.atomnumber[i],
0.0,0.0,"A",0.0,0.0);
}
}
fprintf(fp,"[ nonbonded_params ]\n");
for(i=k=0; (i<top->idef.ntypes); i++) {
for(j=0; (j<top->idef.ntypes); j++,k++) {
fprintf(fp,"%12s %12s 1 %12.5e %12.5e\n",
*(top->atoms.atomtype[types[i]]),
*(top->atoms.atomtype[types[j]]),
top->idef.iparams[k].lj.c12,top->idef.iparams[k].lj.c6);
}
}
sfree(types);
}
static void list_tpx(char *fn, bool bShowNumbers,char *mdpfn,bool bSysTop)
{
FILE *gp;
int step,fp,indent,i,j,**gcount,atot;
real t;
t_state state;
rvec *f=NULL;
t_inputrec ir;
t_tpxheader tpx;
gmx_mtop_t mtop;
gmx_groups_t *groups;
t_topology top;
read_tpxheader(fn,&tpx,TRUE,NULL,NULL);
read_tpx_state(fn,&step,&t,
tpx.bIr ? &ir : NULL,
&state,tpx.bF ? f : NULL,
tpx.bTop ? &mtop: NULL);
if (mdpfn && tpx.bIr) {
gp = gmx_fio_fopen(mdpfn,"w");
pr_inputrec(gp,0,NULL,&(ir),TRUE);
gmx_fio_fclose(gp);
}
if (!mdpfn) {
if (bSysTop)
top = gmx_mtop_t_to_t_topology(&mtop);
if (available(stdout,&tpx,0,fn)) {
indent=0;
indent=pr_title(stdout,indent,fn);
pr_inputrec(stdout,0,"inputrec",tpx.bIr ? &(ir) : NULL,FALSE);
indent = 0;
pr_header(stdout,indent,"header",&(tpx));
if (!bSysTop)
pr_mtop(stdout,indent,"topology",&(mtop),bShowNumbers);
else
pr_top(stdout,indent,"topology",&(top),bShowNumbers);
pr_rvecs(stdout,indent,"box",tpx.bBox ? state.box : NULL,DIM);
pr_rvecs(stdout,indent,"box_rel",tpx.bBox ? state.box_rel : NULL,DIM);
pr_rvecs(stdout,indent,"boxv",tpx.bBox ? state.boxv : NULL,DIM);
pr_rvecs(stdout,indent,"pres_prev",tpx.bBox ? state.pres_prev : NULL,DIM);
pr_reals(stdout,indent,"nosehoover_xi",state.nosehoover_xi,state.ngtc);
pr_rvecs(stdout,indent,"x",tpx.bX ? state.x : NULL,state.natoms);
pr_rvecs(stdout,indent,"v",tpx.bV ? state.v : NULL,state.natoms);
if (state,tpx.bF) {
pr_rvecs(stdout,indent,"f",f,state.natoms);
}
}
groups = &mtop.groups;
snew(gcount,egcNR);
for(i=0; (i<egcNR); i++)
snew(gcount[i],groups->grps[i].nr);
for(i=0; (i<mtop.natoms); i++) {
for(j=0; (j<egcNR); j++)
gcount[j][ggrpnr(groups,j,i)]++;
}
printf("Group statistics\n");
for(i=0; (i<egcNR); i++) {
atot=0;
printf("%-12s: ",gtypes[i]);
for(j=0; (j<groups->grps[i].nr); j++) {
printf(" %5d",gcount[i][j]);
atot+=gcount[i][j];
}
printf(" (total %d atoms)\n",atot);
sfree(gcount[i]);
}
sfree(gcount);
}
done_state(&state);
sfree(f);
}
static void list_top(char *fn)
{
int status,done;
#define BUFLEN 256
char buf[BUFLEN];
gmx_cpp_t handle;
char *cppopts[] = { NULL };
status = cpp_open_file(fn,&handle,cppopts);
if (status != 0)
gmx_fatal(FARGS,cpp_error(&handle,status));
do {
status = cpp_read_line(&handle,BUFLEN,buf);
done = (status == eCPP_EOF);
if (!done) {
if (status != eCPP_OK)
gmx_fatal(FARGS,cpp_error(&handle,status));
else
printf("%s\n",buf);
}
} while (!done);
status = cpp_close_file(&handle);
if (status != eCPP_OK)
gmx_fatal(FARGS,cpp_error(&handle,status));
}
static void list_trn(char *fn)
{
int fpread,fpwrite,nframe,indent;
char buf[256];
rvec *x,*v,*f;
matrix box;
t_trnheader trn;
bool bOK;
fpread = open_trn(fn,"r");
fpwrite = open_tpx(NULL,"w");
gmx_fio_setdebug(fpwrite,TRUE);
nframe = 0;
while (fread_trnheader(fpread,&trn,&bOK)) {
snew(x,trn.natoms);
snew(v,trn.natoms);
snew(f,trn.natoms);
if (fread_htrn(fpread,&trn,
trn.box_size ? box : NULL,
trn.x_size ? x : NULL,
trn.v_size ? v : NULL,
trn.f_size ? f : NULL)) {
sprintf(buf,"%s frame %d",fn,nframe);
indent=0;
indent=pr_title(stdout,indent,buf);
pr_indent(stdout,indent);
fprintf(stdout,"natoms=%10d step=%10d time=%12.7e lambda=%10g\n",
trn.natoms,trn.step,trn.t,trn.lambda);
if (trn.box_size)
pr_rvecs(stdout,indent,"box",box,DIM);
if (trn.x_size)
pr_rvecs(stdout,indent,"x",x,trn.natoms);
if (trn.v_size)
pr_rvecs(stdout,indent,"v",v,trn.natoms);
if (trn.f_size)
pr_rvecs(stdout,indent,"f",f,trn.natoms);
}
else
fprintf(stderr,"\nWARNING: Incomplete frame: nr %d, t=%g\n",
nframe,trn.t);
sfree(x);
sfree(v);
sfree(f);
nframe++;
}
if (!bOK)
fprintf(stderr,"\nWARNING: Incomplete frame header: nr %d, t=%g\n",
nframe,trn.t);
close_tpx(fpwrite);
close_trn(fpread);
}
void list_xtc(char *fn, bool bXVG)
{
int xd,indent;
char buf[256];
rvec *x;
matrix box;
int nframe,natoms,step;
real prec,time;
bool bOK;
xd = open_xtc(fn,"r");
read_first_xtc(xd,&natoms,&step,&time,box,&x,&prec,&bOK);
nframe=0;
do {
if (bXVG) {
int i,d;
fprintf(stdout,"%g",time);
for(i=0; i<natoms; i++)
for(d=0; d<DIM; d++)
fprintf(stdout," %g",x[i][d]);
fprintf(stdout,"\n");
} else {
sprintf(buf,"%s frame %d",fn,nframe);
indent=0;
indent=pr_title(stdout,indent,buf);
pr_indent(stdout,indent);
fprintf(stdout,"natoms=%10d step=%10d time=%12.7e prec=%10g\n",
natoms,step,time,prec);
pr_rvecs(stdout,indent,"box",box,DIM);
pr_rvecs(stdout,indent,"x",x,natoms);
}
nframe++;
} while (read_next_xtc(xd,natoms,&step,&time,box,x,&prec,&bOK));
if (!bOK)
fprintf(stderr,"\nWARNING: Incomplete frame at time %g\n",time);
close_xtc(xd);
}
void list_trx(char *fn,bool bXVG)
{
int ftp;
ftp = fn2ftp(fn);
if (ftp == efXTC)
list_xtc(fn,bXVG);
else if ((ftp == efTRR) || (ftp == efTRJ))
list_trn(fn);
else
fprintf(stderr,"File %s not supported. Try using more %s\n",
fn,fn);
}
void list_ene(char *fn)
{
int in,ndr;
bool bCont;
t_enxframe *fr;
int i,nre,b;
real rav,minthird;
char **enm=NULL;
printf("gmxdump: %s\n",fn);
in = open_enx(fn,"r");
do_enxnms(in,&nre,&enm);
printf("energy components:\n");
for(i=0; (i<nre); i++)
printf("%5d %s\n",i,enm[i]);
minthird=-1.0/3.0;
snew(fr,1);
do {
bCont=do_enx(in,fr);
if (bCont) {
printf("\n%24s %12.5e %12s %12d\n","time:",
fr->t,"step:",fr->step);
if (fr->nre == nre) {
printf("%24s %12s %12s %12s\n",
"Component","Energy","Av. Energy","Sum Energy");
for(i=0; (i<nre); i++)
printf("%24s %12.5e %12.5e %12.5e\n",
enm[i],fr->ener[i].e,fr->ener[i].eav,fr->ener[i].esum);
}
if (fr->ndisre > 0) {
printf("Distance restraint %8s %8s\n","r(t)","<r^-3>^-3");
for(i=0; i<fr->ndisre; i++) {
rav=pow(fr->disre_rm3tav[i],minthird);
printf("%17d %8.4f %8.4f\n",i,fr->disre_rt[i],rav);
}
}
for(b=0; b<fr->nblock; b++)
if (fr->nr[b] > 0) {
printf("Block data %2d (%4d elm.) %8s\n",b,fr->nr[b],"value");
for(i=0; i<fr->nr[b]; i++)
printf("%24d %8.4f\n",i,fr->block[b][i]);
}
}
} while (bCont);
close_enx(in);
free_enxframe(fr);
sfree(fr);
sfree(enm);
}
int main(int argc,char *argv[])
{
static char *desc[] = {
"gmxdump reads a run input file ([TT].tpa[tt]/[TT].tpr[tt]/[TT].tpb[tt]),",
"a trajectory ([TT].trj[tt]/[TT].trr[tt]/[TT].xtc[tt]) or an energy",
"file ([TT].ene[tt]/[TT].edr[tt]) and prints that to standard",
"output in a readable format. This program is essential for",
"checking your run input file in case of problems.[PAR]",
"When requesting to dump a topology file the program will dump",
"the processed topology, since not all original information is maintained",
"in tpr files."
};
t_filenm fnm[] = {
{ efTPX, "-s", NULL, ffOPTRD },
{ efTRX, "-f", NULL, ffOPTRD },
{ efENX, "-e", NULL, ffOPTRD },
{ efCPT, NULL, NULL, ffOPTRD },
{ efMDP, "-om", NULL, ffOPTWR }
};
#define NFILE asize(fnm)
/* Command line options */
static bool bXVG=FALSE;
static bool bShowNumbers=TRUE;
static bool bSysTop=FALSE;
t_pargs pa[] = {
{ "-xvg", FALSE, etBOOL, {&bXVG}, "HIDDENXVG layout for xtc" },
{ "-nr",FALSE, etBOOL, {&bShowNumbers},"Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)" },
{ "-sys", FALSE, etBOOL, {&bSysTop}, "List the atoms and bonded interactions for the whole system instead of for each molecule type" }
};
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL);
if (ftp2bSet(efTPX,NFILE,fnm))
list_tpx(ftp2fn(efTPX,NFILE,fnm),bShowNumbers,
ftp2fn_null(efMDP,NFILE,fnm),bSysTop);
else if (ftp2bSet(efTRX,NFILE,fnm))
list_trx(ftp2fn(efTRX,NFILE,fnm),bXVG);
else if (ftp2bSet(efENX,NFILE,fnm))
list_ene(ftp2fn(efENX,NFILE,fnm));
else if (ftp2bSet(efCPT,NFILE,fnm))
list_checkpoint(ftp2fn(efCPT,NFILE,fnm),stdout);
thanx(stderr);
return 0;
}
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