src/kernel/gmxdump.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <stdio.h>
  40 #include <string.h>
  41 #include <math.h>
  42 #include "main.h"
  43 #include "macros.h"
  44 #include "futil.h"
  45 #include "statutil.h"
  46 #include "copyrite.h"
  47 #include "sysstuff.h"
  48 #include "txtdump.h"
  49 #include "gmx_fatal.h"
  50 #include "xtcio.h"
  51 #include "enxio.h"
  52 #include "smalloc.h"
  53 #include "names.h"
  54 #include "gmxfio.h"
  55 #include "tpxio.h"
  56 #include "trnio.h"
  57 #include "txtdump.h"
  58 #include "gmxcpp.h"
  59 #include "checkpoint.h"
  60 #include "mtop_util.h"
  61 #include "sparsematrix.h"
  62 #include "mtxio.h"
  63
  64 static void dump_top(FILE *fp,t_topology *top,char *tpr)
  65 {
  66   int i,j,k,*types;
  67
  68   fprintf(fp,"; Topology generated from %s by program %s\n",tpr,Program());
  69   fprintf(fp,"[ defaults ]\n 1 1 no 1.0 1.0\n\n");
  70   fprintf(fp,"[ atomtypes ]\n");
  71   fprintf(fp,";name  at.num    mass      charge ptype        c6        c12\n");
  72   snew(types,top->atomtypes.nr);
  73   for(i=0; (i<top->atomtypes.nr); i++) {
  74     for(j=0; (j<top->atoms.nr) && (top->atoms.atom[j].type != i); j++)
  75       ;
  76     if (j<top->atoms.nr) {
  77       types[i] = j;
  78       fprintf(fp,"%5s  %4d   %8.4f   %8.4f  %2s  %8.3f  %8.3f\n",
  79               *(top->atoms.atomtype[j]),top->atomtypes.atomnumber[i],
  80               0.0,0.0,"A",0.0,0.0);
  81     }
  82   }
  83   fprintf(fp,"[ nonbonded_params ]\n");
  84   for(i=k=0; (i<top->idef.ntypes); i++) {
  85     for(j=0; (j<top->idef.ntypes); j++,k++) {
  86       fprintf(fp,"%12s  %12s  1  %12.5e  %12.5e\n",
  87               *(top->atoms.atomtype[types[i]]),
  88               *(top->atoms.atomtype[types[j]]),
  89               top->idef.iparams[k].lj.c12,top->idef.iparams[k].lj.c6);
  90     }
  91   }
  92   sfree(types);
  93 }
  94
  95 static void list_tpx(const char *fn, bool bShowNumbers,const char *mdpfn,
  96                      bool bSysTop)
  97 {
  98   FILE *gp;
  99   int         fp,indent,i,j,**gcount,atot;
 100   t_state     state;
 101   rvec        *f=NULL;
 102   t_inputrec  ir;
 103   t_tpxheader tpx;
 104   gmx_mtop_t  mtop;
 105   gmx_groups_t *groups;
 106   t_topology  top;
 107
 108   read_tpxheader(fn,&tpx,TRUE,NULL,NULL);
 109
 110   read_tpx_state(fn,
 111                  tpx.bIr  ? &ir : NULL,
 112                  &state,tpx.bF ? f : NULL,
 113                  tpx.bTop ? &mtop: NULL);
 114
 115   if (mdpfn && tpx.bIr) {
 116     gp = gmx_fio_fopen(mdpfn,"w");
 117     pr_inputrec(gp,0,NULL,&(ir),TRUE);
 118     gmx_fio_fclose(gp);
 119   }
 120
 121   if (!mdpfn) {
 122     if (bSysTop)
 123       top = gmx_mtop_t_to_t_topology(&mtop);
 124
 125     if (available(stdout,&tpx,0,fn)) {
 126       indent=0;
 127       indent=pr_title(stdout,indent,fn);
 128       pr_inputrec(stdout,0,"inputrec",tpx.bIr ? &(ir) : NULL,FALSE);
 129
 130       indent = 0;
 131       pr_header(stdout,indent,"header",&(tpx));
 132
 133       if (!bSysTop)
 134         pr_mtop(stdout,indent,"topology",&(mtop),bShowNumbers);
 135       else
 136         pr_top(stdout,indent,"topology",&(top),bShowNumbers);
 137
 138       pr_rvecs(stdout,indent,"box",tpx.bBox ? state.box : NULL,DIM);
 139       pr_rvecs(stdout,indent,"box_rel",tpx.bBox ? state.box_rel : NULL,DIM);
 140       pr_rvecs(stdout,indent,"boxv",tpx.bBox ? state.boxv : NULL,DIM);
 141       pr_rvecs(stdout,indent,"pres_prev",tpx.bBox ? state.pres_prev : NULL,DIM);
 142       pr_rvecs(stdout,indent,"svir_prev",tpx.bBox ? state.svir_prev : NULL,DIM);
 143       pr_rvecs(stdout,indent,"fvir_prev",tpx.bBox ? state.fvir_prev : NULL,DIM);
 144       /* leave nosehoover_xi in for now to match the tpr version */
 145       pr_doubles(stdout,indent,"nosehoover_xi",state.nosehoover_xi,state.ngtc);
 146       /*pr_doubles(stdout,indent,"nosehoover_vxi",state.nosehoover_vxi,state.ngtc);*/
 147       /*pr_doubles(stdout,indent,"therm_integral",state.therm_integral,state.ngtc);*/
 148       pr_rvecs(stdout,indent,"x",tpx.bX ? state.x : NULL,state.natoms);
 149       pr_rvecs(stdout,indent,"v",tpx.bV ? state.v : NULL,state.natoms);
 150       if (state,tpx.bF) {
 151         pr_rvecs(stdout,indent,"f",f,state.natoms);
 152       }
 153     }
 154
 155     groups = &mtop.groups;
 156
 157     snew(gcount,egcNR);
 158     for(i=0; (i<egcNR); i++)
 159       snew(gcount[i],groups->grps[i].nr);
 160
 161     for(i=0; (i<mtop.natoms); i++) {
 162       for(j=0; (j<egcNR); j++)
 163         gcount[j][ggrpnr(groups,j,i)]++;
 164     }
 165     printf("Group statistics\n");
 166     for(i=0; (i<egcNR); i++) {
 167       atot=0;
 168       printf("%-12s: ",gtypes[i]);
 169       for(j=0; (j<groups->grps[i].nr); j++) {
 170         printf("  %5d",gcount[i][j]);
 171         atot+=gcount[i][j];
 172       }
 173       printf("  (total %d atoms)\n",atot);
 174       sfree(gcount[i]);
 175     }
 176     sfree(gcount);
 177   }
 178   done_state(&state);
 179   sfree(f);
 180 }
 181
 182 static void list_top(const char *fn)
 183 {
 184   int status,done;
 185 #define BUFLEN 256
 186   char buf[BUFLEN];
 187   gmx_cpp_t handle;
 188   char *cppopts[] = { NULL };
 189
 190   status = cpp_open_file(fn,&handle,cppopts);
 191   if (status != 0)
 192     gmx_fatal(FARGS,cpp_error(&handle,status));
 193   do {
 194     status = cpp_read_line(&handle,BUFLEN,buf);
 195     done = (status == eCPP_EOF);
 196     if (!done) {
 197       if (status != eCPP_OK)
 198         gmx_fatal(FARGS,cpp_error(&handle,status));
 199       else
 200         printf("%s\n",buf);
 201     }
 202   } while (!done);
 203   status = cpp_close_file(&handle);
 204   if (status != eCPP_OK)
 205     gmx_fatal(FARGS,cpp_error(&handle,status));
 206 }
 207
 208 static void list_trn(const char *fn)
 209 {
 210   int         fpread,fpwrite,nframe,indent;
 211   char        buf[256];
 212   rvec        *x,*v,*f;
 213   matrix      box;
 214   t_trnheader trn;
 215   bool        bOK;
 216
 217   fpread  = open_trn(fn,"r");
 218   fpwrite = open_tpx(NULL,"w");
 219   gmx_fio_setdebug(fpwrite,TRUE);
 220
 221   nframe = 0;
 222   while (fread_trnheader(fpread,&trn,&bOK)) {
 223     snew(x,trn.natoms);
 224     snew(v,trn.natoms);
 225     snew(f,trn.natoms);
 226     if (fread_htrn(fpread,&trn,
 227                    trn.box_size ? box : NULL,
 228                    trn.x_size   ? x : NULL,
 229                    trn.v_size   ? v : NULL,
 230                    trn.f_size   ? f : NULL)) {
 231       sprintf(buf,"%s frame %d",fn,nframe);
 232       indent=0;
 233       indent=pr_title(stdout,indent,buf);
 234       pr_indent(stdout,indent);
 235       fprintf(stdout,"natoms=%10d  step=%10d  time=%12.7e  lambda=%10g\n",
 236               trn.natoms,trn.step,trn.t,trn.lambda);
 237       if (trn.box_size)
 238         pr_rvecs(stdout,indent,"box",box,DIM);
 239       if (trn.x_size)
 240         pr_rvecs(stdout,indent,"x",x,trn.natoms);
 241       if (trn.v_size)
 242         pr_rvecs(stdout,indent,"v",v,trn.natoms);
 243       if (trn.f_size)
 244         pr_rvecs(stdout,indent,"f",f,trn.natoms);
 245     }
 246     else
 247       fprintf(stderr,"\nWARNING: Incomplete frame: nr %d, t=%g\n",
 248               nframe,trn.t);
 249
 250     sfree(x);
 251     sfree(v);
 252     sfree(f);
 253     nframe++;
 254   }
 255   if (!bOK)
 256     fprintf(stderr,"\nWARNING: Incomplete frame header: nr %d, t=%g\n",
 257             nframe,trn.t);
 258   close_tpx(fpwrite);
 259   close_trn(fpread);
 260 }
 261
 262 void list_xtc(const char *fn, bool bXVG)
 263 {
 264   int    xd,indent;
 265   char   buf[256];
 266   rvec   *x;
 267   matrix box;
 268   int    nframe,natoms,step;
 269   real   prec,time;
 270   bool   bOK;
 271
 272   xd = open_xtc(fn,"r");
 273   read_first_xtc(xd,&natoms,&step,&time,box,&x,&prec,&bOK);
 274
 275   nframe=0;
 276   do {
 277     if (bXVG) {
 278       int i,d;
 279
 280       fprintf(stdout,"%g",time);
 281       for(i=0; i<natoms; i++)
 282         for(d=0; d<DIM; d++)
 283           fprintf(stdout," %g",x[i][d]);
 284       fprintf(stdout,"\n");
 285     } else {
 286       sprintf(buf,"%s frame %d",fn,nframe);
 287       indent=0;
 288       indent=pr_title(stdout,indent,buf);
 289       pr_indent(stdout,indent);
 290       fprintf(stdout,"natoms=%10d  step=%10d  time=%12.7e  prec=%10g\n",
 291             natoms,step,time,prec);
 292       pr_rvecs(stdout,indent,"box",box,DIM);
 293       pr_rvecs(stdout,indent,"x",x,natoms);
 294     }
 295     nframe++;
 296   } while (read_next_xtc(xd,natoms,&step,&time,box,x,&prec,&bOK));
 297   if (!bOK)
 298     fprintf(stderr,"\nWARNING: Incomplete frame at time %g\n",time);
 299   close_xtc(xd);
 300 }
 301
 302 void list_trx(const char *fn,bool bXVG)
 303 {
 304   int ftp;
 305
 306   ftp = fn2ftp(fn);
 307   if (ftp == efXTC)
 308     list_xtc(fn,bXVG);
 309   else if ((ftp == efTRR) || (ftp == efTRJ))
 310     list_trn(fn);
 311   else
 312     fprintf(stderr,"File %s not supported. Try using more %s\n",
 313             fn,fn);
 314 }
 315
 316 void list_ene(const char *fn)
 317 {
 318   int        ndr;
 319   ener_file_t in;
 320   bool       bCont;
 321   gmx_enxnm_t *enm=NULL;
 322   t_enxframe *fr;
 323   int        i,nre,b;
 324   real       rav,minthird;
 325   char       buf[22];
 326
 327   printf("gmxdump: %s\n",fn);
 328   in = open_enx(fn,"r");
 329   do_enxnms(in,&nre,&enm);
 330
 331   printf("energy components:\n");
 332   for(i=0; (i<nre); i++)
 333     printf("%5d  %-24s (%s)\n",i,enm[i].name,enm[i].unit);
 334
 335   minthird=-1.0/3.0;
 336   snew(fr,1);
 337   do {
 338     bCont=do_enx(in,fr);
 339
 340     if (bCont) {
 341       printf("\n%24s  %12.5e  %12s  %12s\n","time:",
 342              fr->t,"step:",gmx_step_str(fr->step,buf));
 343       printf("%24s  %12s  %12s  %12s\n",
 344              "","","nsteps:",gmx_step_str(fr->nsteps,buf));
 345       printf("%24s  %12s  %12s  %12s\n",
 346              "","","sum steps:",gmx_step_str(fr->nsum,buf));
 347       if (fr->nre == nre) {
 348         printf("%24s  %12s  %12s  %12s\n",
 349                "Component","Energy","Av. Energy","Sum Energy");
 350         if (fr->nsum > 0) {
 351           for(i=0; (i<nre); i++)
 352             printf("%24s  %12.5e  %12.5e  %12.5e\n",
 353                    enm[i].name,fr->ener[i].e,fr->ener[i].eav,fr->ener[i].esum);
 354         } else {
 355           for(i=0; (i<nre); i++)
 356             printf("%24s  %12.5e\n",
 357                    enm[i].name,fr->ener[i].e);
 358         }
 359       }
 360       if (fr->ndisre > 0) {
 361         printf("Distance restraint %8s  %8s\n","r(t)","<r^-3>^-3");
 362         for(i=0; i<fr->ndisre; i++) {
 363           rav=pow(fr->disre_rm3tav[i],minthird);
 364           printf("%17d  %8.4f  %8.4f\n",i,fr->disre_rt[i],rav);
 365         }
 366       }
 367       for(b=0; b<fr->nblock; b++)
 368         if (fr->nr[b] > 0) {
 369           printf("Block data %2d (%4d elm.) %8s\n",b,fr->nr[b],"value");
 370           for(i=0; i<fr->nr[b]; i++)
 371             printf("%24d  %8.4f\n",i,fr->block[b][i]);
 372         }
 373     }
 374   } while (bCont);
 375
 376   close_enx(in);
 377
 378   free_enxframe(fr);
 379   sfree(fr);
 380   sfree(enm);
 381 }
 382
 383 static void list_mtx(const char *fn)
 384 {
 385   int  nrow,ncol,i,j,k;
 386   real *full=NULL,value;
 387   gmx_sparsematrix_t * sparse=NULL;
 388
 389   gmx_mtxio_read(fn,&nrow,&ncol,&full,&sparse);
 390
 391   if (full == NULL) {
 392     snew(full,nrow*ncol);
 393     for(i=0;i<nrow*ncol;i++) {
 394       full[i] = 0;
 395     }
 396
 397     for(i=0;i<sparse->nrow;i++) {
 398         for(j=0;j<sparse->ndata[i];j++) {
 399           k     = sparse->data[i][j].col;
 400           value = sparse->data[i][j].value;
 401           full[i*ncol+k] = value;
 402           full[k*ncol+i] = value;
 403         }
 404     }
 405     gmx_sparsematrix_destroy(sparse);
 406   }
 407
 408   printf("%d %d\n",nrow,ncol);
 409   for(i=0; i<nrow; i++) {
 410     for(j=0; j<ncol; j++) {
 411       printf(" %g",full[i*ncol+j]);
 412     }
 413     printf("\n");
 414   }
 415
 416   sfree(full);
 417 }
 418
 419 int main(int argc,char *argv[])
 420 {
 421   const char *desc[] = {
 422     "gmxdump reads a run input file ([TT].tpa[tt]/[TT].tpr[tt]/[TT].tpb[tt]),",
 423     "a trajectory ([TT].trj[tt]/[TT].trr[tt]/[TT].xtc[tt]), an energy",
 424     "file ([TT].ene[tt]/[TT].edr[tt]), or a checkpoint file ([TT].cpt[tt])",
 425     "and prints that to standard output in a readable format.",
 426     "This program is essential for checking your run input file in case of",
 427     "problems.[PAR]",
 428     "The program can also preprocess a topology to help finding problems.",
 429     "Note that currently setting GMXLIB is the only way to customize",
 430     "directories used for searching include files.",
 431   };
 432   t_filenm fnm[] = {
 433     { efTPX, "-s", NULL, ffOPTRD },
 434     { efTRX, "-f", NULL, ffOPTRD },
 435     { efEDR, "-e", NULL, ffOPTRD },
 436     { efCPT, NULL, NULL, ffOPTRD },
 437     { efTOP, "-p", NULL, ffOPTRD },
 438     { efMTX, "-mtx", "hessian", ffOPTRD },
 439     { efMDP, "-om", NULL, ffOPTWR }
 440   };
 441 #define NFILE asize(fnm)
 442
 443   output_env_t oenv;
 444   /* Command line options */
 445   static bool bXVG=FALSE;
 446   static bool bShowNumbers=TRUE;
 447   static bool bSysTop=FALSE;
 448   t_pargs pa[] = {
 449     { "-xvg", FALSE, etBOOL, {&bXVG}, "HIDDENXVG layout for xtc" },
 450     { "-nr",FALSE, etBOOL, {&bShowNumbers},"Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)" },
 451     { "-sys", FALSE, etBOOL, {&bSysTop}, "List the atoms and bonded interactions for the whole system instead of for each molecule type" }
 452   };
 453
 454   CopyRight(stderr,argv[0]);
 455   parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
 456                     asize(desc),desc,0,NULL,&oenv);
 457
 458
 459   if (ftp2bSet(efTPX,NFILE,fnm))
 460     list_tpx(ftp2fn(efTPX,NFILE,fnm),bShowNumbers,
 461              ftp2fn_null(efMDP,NFILE,fnm),bSysTop);
 462   else if (ftp2bSet(efTRX,NFILE,fnm))
 463     list_trx(ftp2fn(efTRX,NFILE,fnm),bXVG);
 464   else if (ftp2bSet(efEDR,NFILE,fnm))
 465     list_ene(ftp2fn(efEDR,NFILE,fnm));
 466   else if (ftp2bSet(efCPT,NFILE,fnm))
 467     list_checkpoint(ftp2fn(efCPT,NFILE,fnm),stdout);
 468   else if (ftp2bSet(efTOP,NFILE,fnm))
 469     list_top(ftp2fn(efTOP,NFILE,fnm));
 470   else if (ftp2bSet(efMTX,NFILE,fnm))
 471     list_mtx(ftp2fn(efMTX,NFILE,fnm));
 472
 473   thanx(stderr);
 474
 475   return 0;
 476 }