src/kernel/gmxdump.c

   1 /*
   2  * $Id$
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.1
  11  * Copyright (c) 1991-2001, University of Groningen, The Netherlands
  12  * This program is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU General Public License
  14  * as published by the Free Software Foundation; either version 2
  15  * of the License, or (at your option) any later version.
  16  *
  17  * If you want to redistribute modifications, please consider that
  18  * scientific software is very special. Version control is crucial -
  19  * bugs must be traceable. We will be happy to consider code for
  20  * inclusion in the official distribution, but derived work must not
  21  * be called official GROMACS. Details are found in the README & COPYING
  22  * files - if they are missing, get the official version at www.gromacs.org.
  23  *
  24  * To help us fund GROMACS development, we humbly ask that you cite
  25  * the papers on the package - you can find them in the top README file.
  26  *
  27  * For more info, check our website at http://www.gromacs.org
  28  *
  29  * And Hey:
  30  * GROningen Mixture of Alchemy and Childrens' Stories
  31  */
  32 static char *SRCID_gmxdump_c = "$Id$";
  33 #include <stdio.h>
  34 #include <string.h>
  35 #include <math.h>
  36 #include "main.h"
  37 #include "macros.h"
  38 #include "futil.h"
  39 #include "statutil.h"
  40 #include "copyrite.h"
  41 #include "sysstuff.h"
  42 #include "txtdump.h"
  43 #include "fatal.h"
  44 #include "xtcio.h"
  45 #include "enxio.h"
  46 #include "assert.h"
  47 #include "smalloc.h"
  48 #include "names.h"
  49 #include "gmxfio.h"
  50 #include "tpxio.h"
  51 #include "trnio.h"
  52 #include "txtdump.h"
  53
  54 static void list_tpx(char *fn)
  55 {
  56   int         step,natoms,fp,indent,i,j,**gcount,atot;
  57   real        t,lambda;
  58   rvec        *x,*v,*f;
  59   matrix      box;
  60   t_inputrec  ir;
  61   t_tpxheader tpx;
  62   t_topology  top;
  63
  64   read_tpxheader(fn,&tpx);
  65   snew(x,tpx.natoms);
  66   snew(v,tpx.natoms);
  67   snew(f,tpx.natoms);
  68   read_tpx(fn,&step,&t,&lambda,
  69            tpx.bIr  ? &ir : NULL,
  70            tpx.bBox ? box : NULL,
  71            &natoms,
  72            tpx.bX   ? x : NULL,
  73            tpx.bV   ? v : NULL,
  74            tpx.bF   ? f : NULL,
  75            tpx.bTop ? &top: NULL);
  76
  77   if (available(stdout,&tpx,fn)) {
  78     indent=0;
  79     indent=pr_title(stdout,indent,fn);
  80     pr_header(stdout,indent,"header",&(tpx));
  81     pr_inputrec(stdout,indent,"ir",&(ir));
  82     pr_rvecs(stdout,indent,"box",box,DIM);
  83     pr_rvecs(stdout,indent,"x",x,natoms);
  84     pr_rvecs(stdout,indent,"v",v,natoms);
  85     pr_rvecs(stdout,indent,"f",f,natoms);
  86     pr_top(stdout,indent,"topology",&(top));
  87   }
  88
  89   snew(gcount,egcNR);
  90   for(i=0; (i<egcNR); i++)
  91     snew(gcount[i],top.atoms.grps[i].nr);
  92
  93   for(i=0; (i<top.atoms.nr); i++) {
  94     for(j=0; (j<egcNR); j++)
  95       gcount[j][top.atoms.atom[i].grpnr[j]]++;
  96   }
  97   printf("Group statistics\n");
  98   for(i=0; (i<egcNR); i++) {
  99     atot=0;
 100     printf("%-12s: ",gtypes[i]);
 101     for(j=0; (j<top.atoms.grps[i].nr); j++) {
 102       printf("  %5d",gcount[i][j]);
 103       atot+=gcount[i][j];
 104     }
 105     printf("  (total %d atoms)\n",atot);
 106     sfree(gcount[i]);
 107   }
 108   sfree(gcount);
 109
 110   sfree(x);
 111   sfree(v);
 112   sfree(f);
 113 }
 114
 115 static void list_trn(char *fn)
 116 {
 117   int         fpread,fpwrite,nframe,indent;
 118   char        buf[256];
 119   rvec        *x,*v,*f;
 120   matrix      box;
 121   t_trnheader trn;
 122   bool        bOK;
 123
 124   fpread  = open_trn(fn,"r");
 125   fpwrite = open_tpx(NULL,"w");
 126   fio_setdebug(fpwrite,TRUE);
 127
 128   nframe = 0;
 129   while (fread_trnheader(fpread,&trn,&bOK)) {
 130     snew(x,trn.natoms);
 131     snew(v,trn.natoms);
 132     snew(f,trn.natoms);
 133     if (fread_htrn(fpread,&trn,
 134                    trn.box_size ? box : NULL,
 135                    trn.x_size   ? x : NULL,
 136                    trn.v_size   ? v : NULL,
 137                    trn.f_size   ? f : NULL)) {
 138       sprintf(buf,"%s frame %d",fn,nframe);
 139       indent=0;
 140       indent=pr_title(stdout,indent,buf);
 141       pr_indent(stdout,indent);
 142       fprintf(stdout,"natoms=%10d  step=%10d  time=%10g  lambda=%10g\n",
 143               trn.natoms,trn.step,trn.t,trn.lambda);
 144       if (trn.box_size)
 145         pr_rvecs(stdout,indent,"box",box,DIM);
 146       if (trn.x_size)
 147         pr_rvecs(stdout,indent,"x",x,trn.natoms);
 148       if (trn.v_size)
 149         pr_rvecs(stdout,indent,"v",v,trn.natoms);
 150       if (trn.f_size)
 151         pr_rvecs(stdout,indent,"f",f,trn.natoms);
 152     }
 153     else
 154       fprintf(stderr,"\nWARNING: Incomplete frame: nr %d, t=%g\n",
 155               nframe,trn.t);
 156
 157     sfree(x);
 158     sfree(v);
 159     sfree(f);
 160     nframe++;
 161   }
 162   if (!bOK)
 163     fprintf(stderr,"\nWARNING: Incomplete frame header: nr %d, t=%g\n",
 164             nframe,trn.t);
 165   close_tpx(fpwrite);
 166   close_trn(fpread);
 167 }
 168
 169 void list_xtc(char *fn, bool bXVG)
 170 {
 171   int    xd,indent;
 172   char   buf[256];
 173   rvec   *x;
 174   matrix box;
 175   int    nframe,natoms,step;
 176   real   prec,time;
 177   bool   bOK;
 178
 179   xd = open_xtc(fn,"r");
 180   read_first_xtc(xd,&natoms,&step,&time,box,&x,&prec,&bOK);
 181
 182   nframe=0;
 183   do {
 184     if (bXVG) {
 185       int i,d;
 186
 187       fprintf(stdout,"%g",time);
 188       for(i=0; i<natoms; i++)
 189         for(d=0; d<DIM; d++)
 190           fprintf(stdout," %g",x[i][d]);
 191       fprintf(stdout,"\n");
 192     } else {
 193       sprintf(buf,"%s frame %d",fn,nframe);
 194       indent=0;
 195       indent=pr_title(stdout,indent,buf);
 196       pr_indent(stdout,indent);
 197       fprintf(stdout,"natoms=%10d  step=%10d  time=%10g  prec=%10g\n",
 198             natoms,step,time,prec);
 199       pr_rvecs(stdout,indent,"box",box,DIM);
 200       pr_rvecs(stdout,indent,"x",x,natoms);
 201     }
 202     nframe++;
 203   } while (read_next_xtc(xd,natoms,&step,&time,box,x,&prec,&bOK));
 204   if (!bOK)
 205     fprintf(stderr,"\nWARNING: Incomplete frame at time %g\n",time);
 206   close_xtc(xd);
 207 }
 208
 209 void list_trx(char *fn,bool bXVG)
 210 {
 211   int ftp;
 212
 213   ftp = fn2ftp(fn);
 214   if (ftp == efXTC)
 215     list_xtc(fn,bXVG);
 216   else if ((ftp == efTRR) || (ftp == efTRJ))
 217     list_trn(fn);
 218   else
 219     fprintf(stderr,"File %s not supported. Try using more %s\n",
 220             fn,fn);
 221 }
 222
 223 void list_ene(char *fn)
 224 {
 225   int        in,ndr;
 226   bool       bCont;
 227   t_enxframe *fr;
 228   int        i,nre,b;
 229   real       rav,minthird;
 230   char       **enm=NULL;
 231
 232   printf("gmxdump: %s\n",fn);
 233   in = open_enx(fn,"r");
 234   do_enxnms(in,&nre,&enm);
 235
 236   printf("energy components:\n");
 237   for(i=0; (i<nre); i++)
 238     printf("%5d  %s\n",i,enm[i]);
 239
 240   minthird=-1.0/3.0;
 241   snew(fr,1);
 242   do {
 243     bCont=do_enx(in,fr);
 244     assert(fr->nre==nre);
 245
 246     if (bCont) {
 247       printf("\n%24s  %12.5e  %12s  %12d\n","time:",
 248              fr->t,"step:",fr->step);
 249       printf("%24s  %12s  %12s  %12s\n",
 250              "Component","Energy","Av. Energy","Sum Energy");
 251       for(i=0; (i<nre); i++)
 252         printf("%24s  %12.5e  %12.5e  %12.5e\n",
 253                enm[i],fr->ener[i].e,fr->ener[i].eav,fr->ener[i].esum);
 254       if (fr->ndisre > 0) {
 255         printf("Distance restraint %8s  %8s\n","r(t)","< r >");
 256         for(i=0; i<fr->ndisre; i++) {
 257           rav=pow(fr->rav[i],minthird);
 258           printf("%17d  %8.4f  %8.4f\n",i,fr->rt[i],rav);
 259         }
 260       }
 261       for(b=0; b<fr->nblock; b++)
 262         if (fr->nr[b] > 0) {
 263           printf("Block data %2d (%4d elm.) %8s\n",b,fr->nr[b],"value");
 264           for(i=0; i<fr->nr[b]; i++)
 265             printf("%24d  %8.4f\n",i,fr->block[b][i]);
 266         }
 267     }
 268   } while (bCont);
 269
 270   close_enx(in);
 271
 272   free_enxframe(fr);
 273   sfree(fr);
 274   sfree(enm);
 275 }
 276
 277 int main(int argc,char *argv[])
 278 {
 279   static char *desc[] = {
 280     "gmxdump reads a run input file ([TT].tpa[tt]/[TT].tpr[tt]/[TT].tpb[tt]),",
 281     "a trajectory ([TT].trj[tt]/[TT].trr[tt]/[TT].xtc[tt]) or an energy",
 282     "file ([TT].ene[tt]/[TT].edr[tt]) and prints that to standard",
 283     "output in a readable format. This program is essential for",
 284     "checking your run input file in case of problems.[PAR]"
 285   };
 286   t_filenm fnm[] = {
 287     { efTPX, "-s", NULL, ffOPTRD },
 288     { efTRX, "-f", NULL, ffOPTRD },
 289     { efENX, "-e", NULL, ffOPTRD },
 290   };
 291 #define NFILE asize(fnm)
 292
 293   /* Command line options */
 294   static bool bXVG=FALSE;
 295   static bool bShowNumbers=TRUE;
 296   t_pargs pa[] = {
 297     { "-xvg", FALSE, etBOOL, {&bXVG}, "HIDDENXVG layout for xtc" },
 298     { "-nr",FALSE, etBOOL, {&bShowNumbers},"Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)" }
 299   };
 300
 301   CopyRight(stderr,argv[0]);
 302   parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
 303                     asize(desc),desc,0,NULL);
 304
 305   pr_shownumbers(bShowNumbers);
 306   if (ftp2bSet(efTPX,NFILE,fnm))
 307     list_tpx(ftp2fn(efTPX,NFILE,fnm));
 308
 309   if (ftp2bSet(efTRX,NFILE,fnm))
 310     list_trx(ftp2fn(efTRX,NFILE,fnm),bXVG);
 311
 312   if (ftp2bSet(efENX,NFILE,fnm))
 313     list_ene(ftp2fn(efENX,NFILE,fnm));
 314
 315   thanx(stderr);
 316
 317   return 0;
 318 }