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 2.0
  11  *
  12  * Copyright (c) 1991-1999
  13  * BIOSON Research Institute, Dept. of Biophysical Chemistry
  14  * University of Groningen, The Netherlands
  15  *
  16  * Please refer to:
  17  * GROMACS: A message-passing parallel molecular dynamics implementation
  18  * H.J.C. Berendsen, D. van der Spoel and R. van Drunen
  19  * Comp. Phys. Comm. 91, 43-56 (1995)
  20  *
  21  * Also check out our WWW page:
  22  * http://md.chem.rug.nl/~gmx
  23  * or e-mail to:
  24  * gromacs@chem.rug.nl
  25  *
  26  * And Hey:
  27  * GRowing Old MAkes el Chrono Sweat
  28  */
  29 static char *SRCID_gmxdump_c = "$Id$";
  30
  31 #include <stdio.h>
  32 #include <string.h>
  33 #include <math.h>
  34 #include "main.h"
  35 #include "macros.h"
  36 #include "futil.h"
  37 #include "statutil.h"
  38 #include "copyrite.h"
  39 #include "sysstuff.h"
  40 #include "txtdump.h"
  41 #include "fatal.h"
  42 #include "xtcio.h"
  43 #include "enxio.h"
  44 #include "assert.h"
  45 #include "smalloc.h"
  46 #include "names.h"
  47 #include "gmxfio.h"
  48 #include "tpxio.h"
  49 #include "trnio.h"
  50 #include "txtdump.h"
  51
  52 static void list_tpx(char *fn, bool bAltLayout)
  53 {
  54   int         step,natoms,fp,indent,i,j,**gcount,atot;
  55   real        t,lambda;
  56   rvec        *x,*v,*f;
  57   matrix      box;
  58   t_inputrec  ir;
  59   t_tpxheader tpx;
  60   t_topology  top;
  61
  62   read_tpxheader(fn,&tpx);
  63   snew(x,tpx.natoms);
  64   snew(v,tpx.natoms);
  65   snew(f,tpx.natoms);
  66   read_tpx(fn,&step,&t,&lambda,
  67            tpx.bIr  ? &ir : NULL,
  68            tpx.bBox ? box : NULL,
  69            &natoms,
  70            tpx.bX   ? x : NULL,
  71            tpx.bV   ? v : NULL,
  72            tpx.bF   ? f : NULL,
  73            tpx.bTop ? &top: NULL);
  74
  75   if (bAltLayout) {
  76     printf("----------- begin of %s ------------\n",fn);
  77     fp = open_tpx(NULL,"w");
  78     fio_setdebug(fp,TRUE);
  79     fwrite_tpx(fp,step,t,lambda,
  80                tpx.bIr  ? &ir : NULL,
  81                tpx.bBox ? box : NULL,
  82                natoms,
  83                tpx.bX   ? x : NULL,
  84                tpx.bV   ? v : NULL,
  85                tpx.bF   ? f : NULL,
  86                tpx.bTop ? &top : NULL);
  87     close_tpx(fp);
  88     printf("----------- end of %s ------------\n",fn);
  89   } else {
  90     if (available(stdout,&tpx,fn))
  91       {
  92         indent=0;
  93         indent=pr_title(stdout,indent,fn);
  94         pr_header(stdout,indent,"header",&(tpx));
  95         pr_inputrec(stdout,indent,"ir",&(ir));
  96         pr_rvecs(stdout,indent,"box",box,DIM);
  97         pr_rvecs(stdout,indent,"x",x,natoms);
  98         pr_rvecs(stdout,indent,"v",v,natoms);
  99         pr_rvecs(stdout,indent,"f",f,natoms);
 100         pr_top(stdout,indent,"topology",&(top));
 101       }
 102   }
 103   snew(gcount,egcNR);
 104   for(i=0; (i<egcNR); i++)
 105     snew(gcount[i],top.atoms.grps[i].nr);
 106
 107   for(i=0; (i<top.atoms.nr); i++) {
 108     for(j=0; (j<egcNR); j++)
 109       gcount[j][top.atoms.atom[i].grpnr[j]]++;
 110   }
 111   printf("Group statistics\n");
 112   for(i=0; (i<egcNR); i++) {
 113     atot=0;
 114     printf("%-12s: ",gtypes[i]);
 115     for(j=0; (j<top.atoms.grps[i].nr); j++) {
 116       printf("  %5d",gcount[i][j]);
 117       atot+=gcount[i][j];
 118     }
 119     printf("  (total %d atoms)\n",atot);
 120     sfree(gcount[i]);
 121   }
 122   sfree(gcount);
 123
 124   sfree(x);
 125   sfree(v);
 126   sfree(f);
 127 }
 128
 129 static void list_trn(char *fn,bool bAltLayout)
 130 {
 131   int         fpread,fpwrite,nframe,indent;
 132   char        buf[256];
 133   rvec        *x,*v,*f;
 134   matrix      box;
 135   t_trnheader trn;
 136   bool        bOK;
 137
 138   fpread  = open_trn(fn,"r");
 139   fpwrite = open_tpx(NULL,"w");
 140   fio_setdebug(fpwrite,TRUE);
 141
 142   nframe = 0;
 143   while (fread_trnheader(fpread,&trn,&bOK)) {
 144     snew(x,trn.natoms);
 145     snew(v,trn.natoms);
 146     snew(f,trn.natoms);
 147     if (fread_htrn(fpread,&trn,
 148                    trn.box_size ? box : NULL,
 149                    trn.x_size   ? x : NULL,
 150                    trn.v_size   ? v : NULL,
 151                    trn.f_size   ? f : NULL)) {
 152       if (bAltLayout) {
 153         printf("----------- begin of %s frame %d ------------\n",fn,nframe);
 154         fwrite_tpx(fpwrite,trn.step,trn.t,trn.lambda,NULL,
 155                    trn.box_size ? box : NULL,
 156                    trn.natoms,
 157                    trn.x_size   ? x : NULL,
 158                    trn.v_size   ? v : NULL,
 159                    trn.f_size   ? f : NULL,
 160                    NULL);
 161         printf("----------- end of %s frame %d ------------\n",fn,nframe);
 162       } else {
 163         sprintf(buf,"%s frame %d",fn,nframe);
 164         indent=0;
 165         indent=pr_title(stdout,indent,buf);
 166         pr_indent(stdout,indent);
 167         fprintf(stdout,"natoms=%10d  step=%10d  time=%10g  lambda=%10g\n",
 168                 trn.natoms,trn.step,trn.t,trn.lambda);
 169         if (trn.box_size)
 170           pr_rvecs(stdout,indent,"box",box,DIM);
 171         if (trn.x_size)
 172           pr_rvecs(stdout,indent,"x",x,trn.natoms);
 173         if (trn.v_size)
 174           pr_rvecs(stdout,indent,"v",v,trn.natoms);
 175         if (trn.f_size)
 176           pr_rvecs(stdout,indent,"f",f,trn.natoms);
 177       }
 178     } else
 179       fprintf(stderr,"\nWARNING: Incomplete frame: nr %d, t=%g\n",
 180               nframe,trn.t);
 181
 182     sfree(x);
 183     sfree(v);
 184     sfree(f);
 185     nframe++;
 186   }
 187   if (!bOK)
 188     fprintf(stderr,"\nWARNING: Incomplete frame header: nr %d, t=%g\n",
 189             nframe,trn.t);
 190   close_tpx(fpwrite);
 191   close_trn(fpread);
 192 }
 193
 194 void list_xtc(char *fn, bool bXVG)
 195 {
 196   int    xd,indent;
 197   char   buf[256];
 198   rvec   *x;
 199   matrix box;
 200   int    nframe,natoms,step;
 201   real   prec,time;
 202   bool   bOK;
 203
 204   xd = open_xtc(fn,"r");
 205   read_first_xtc(xd,&natoms,&step,&time,box,&x,&prec,&bOK);
 206
 207   nframe=0;
 208   do {
 209     if (bXVG) {
 210       int i,d;
 211
 212       fprintf(stdout,"%g",time);
 213       for(i=0; i<natoms; i++)
 214         for(d=0; d<DIM; d++)
 215           fprintf(stdout," %g",x[i][d]);
 216       fprintf(stdout,"\n");
 217     } else {
 218       sprintf(buf,"%s frame %d",fn,nframe);
 219       indent=0;
 220       indent=pr_title(stdout,indent,buf);
 221       pr_indent(stdout,indent);
 222       fprintf(stdout,"natoms=%10d  step=%10d  time=%10g  prec=%10g\n",
 223             natoms,step,time,prec);
 224       pr_rvecs(stdout,indent,"box",box,DIM);
 225       pr_rvecs(stdout,indent,"x",x,natoms);
 226     }
 227     nframe++;
 228   } while (read_next_xtc(xd,&natoms,&step,&time,box,x,&prec,&bOK));
 229   if (!bOK)
 230     fprintf(stderr,"\nWARNING: Incomplete frame at time %g\n",time);
 231   close_xtc(xd);
 232 }
 233
 234 void list_trx(char *fn,bool bAltLayout,bool bXVG)
 235 {
 236   int ftp;
 237
 238   ftp = fn2ftp(fn);
 239   if (ftp == efXTC)
 240     list_xtc(fn,bXVG);
 241   else if ((ftp == efTRR) || (ftp == efTRJ))
 242     list_trn(fn,bAltLayout);
 243   else
 244     fprintf(stderr,"File %s not supported. Try using more %s\n",
 245             fn,fn);
 246 }
 247
 248 void list_ene(char *fn,bool bEDR)
 249 {
 250   int       in,ndr;
 251   bool      bCont;
 252   t_energy  *ener;
 253   t_drblock drblock;
 254   int       i,nre,nre2,step;
 255   real      t,rav,minthird;
 256   char      **enm=NULL;
 257
 258   printf("gmxdump: %s\n",fn);
 259   in = open_enx(fn,"r");
 260   do_enxnms(in,&nre,&enm);
 261
 262   printf("energy components:\n");
 263   for(i=0; (i<nre); i++)
 264     printf("%5d  %s\n",i,enm[i]);
 265
 266   drblock.ndr=0;
 267   minthird=-1.0/3.0;
 268   snew(ener,nre);
 269   do {
 270     bCont=do_enx(in,&t,&step,&nre2,ener,&ndr,&drblock);
 271     assert(nre2==nre);
 272
 273     if (bCont) {
 274       printf("\n%24s  %12.5e  %12s  %12d\n","time:",t,"step:",step);
 275       printf("%24s  %12s  %12s  %12s\n",
 276              "Component","Energy","Av. Energy","Sum Energy");
 277       for(i=0; (i<nre); i++)
 278         printf("%24s  %12.5e  %12.5e  %12.5e\n",
 279                enm[i],ener[i].e,ener[i].eav,ener[i].esum);
 280       if (ndr > 0) {
 281         printf("Restraint %8s  %8s\n","r(t)","< r >");
 282         for(i=0; (i<drblock.ndr); i++) {
 283           rav=pow(drblock.rav[i],minthird);
 284           printf("%8d  %8.4f  %8.4f\n",i,drblock.rt[i],rav);
 285         }
 286       }
 287     }
 288   } while (bCont);
 289
 290   close_enx(in);
 291
 292   sfree(ener);
 293   sfree(enm);
 294   if (drblock.ndr) {
 295     sfree(drblock.rav);
 296     sfree(drblock.rt);
 297   }
 298 }
 299
 300 int main(int argc,char *argv[])
 301 {
 302   static char *desc[] = {
 303     "gmxdump reads a run input file ([TT].tpa[tt]/[TT].tpr[tt]/[TT].tpb[tt]),",
 304     "a trajectory ([TT].trj[tt]/[TT].trr[tt]/[TT].xtc[tt]) or an energy",
 305     "file ([TT].ene[tt]/[TT].edr[tt]) and prints that to standard",
 306     "output in a readable format. This program is essential for",
 307     "checking your run input file in case of problems.[PAR]"
 308   };
 309   t_filenm fnm[] = {
 310     { efTPX, "-s", NULL, ffOPTRD },
 311     { efTRX, "-f", NULL, ffOPTRD },
 312     { efENX, "-e", NULL, ffOPTRD },
 313   };
 314 #define NFILE asize(fnm)
 315
 316   /* Command line options */
 317   static bool bAltLayout=FALSE,bXVG=FALSE;
 318   static bool bShowNumbers=TRUE;
 319   t_pargs pa[] = {
 320     { "-a", FALSE, etBOOL, {&bAltLayout}, "HIDDENAlternative layout for run startup files" },
 321     { "-xvg", FALSE, etBOOL, {&bXVG}, "HIDDENXVG layout for xtc" },
 322     { "-nr",FALSE, etBOOL, {&bShowNumbers},"Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)" }
 323   };
 324
 325   CopyRight(stderr,argv[0]);
 326   parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,asize(pa),pa,
 327                     asize(desc),desc,0,NULL);
 328
 329   pr_shownumbers(bShowNumbers);
 330   if (ftp2bSet(efTPX,NFILE,fnm))
 331     list_tpx(ftp2fn(efTPX,NFILE,fnm), bAltLayout);
 332
 333   if (ftp2bSet(efTRX,NFILE,fnm))
 334     list_trx(ftp2fn(efTRX,NFILE,fnm), bAltLayout, bXVG);
 335
 336   if (ftp2bSet(efENX,NFILE,fnm))
 337     list_ene(ftp2fn(efENX,NFILE,fnm), FALSE);
 338
 339   thanx(stderr);
 340
 341   return 0;
 342 }