src/gmxlib/txtdump.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
   2  *
   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 3.2.0
  11  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  12  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  13  * Copyright (c) 2001-2004, The GROMACS development team,
  14  * check out http://www.gromacs.org for more information.
  15
  16  * This program is free software; you can redistribute it and/or
  17  * modify it under the terms of the GNU General Public License
  18  * as published by the Free Software Foundation; either version 2
  19  * of the License, or (at your option) any later version.
  20  *
  21  * If you want to redistribute modifications, please consider that
  22  * scientific software is very special. Version control is crucial -
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  26  * files - if they are missing, get the official version at www.gromacs.org.
  27  *
  28  * To help us fund GROMACS development, we humbly ask that you cite
  29  * the papers on the package - you can find them in the top README file.
  30  *
  31  * For more info, check our website at http://www.gromacs.org
  32  *
  33  * And Hey:
  34  * GROningen Mixture of Alchemy and Childrens' Stories
  35  */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 /* This file is completely threadsafe - please keep it that way! */
  41 #ifdef GMX_THREADS
  42 #include <thread_mpi.h>
  43 #endif
  44
  45
  46 #include <stdio.h>
  47 #include "smalloc.h"
  48 #include "typedefs.h"
  49 #include "names.h"
  50 #include "txtdump.h"
  51 #include "string2.h"
  52 #include "vec.h"
  53
  54
  55 int pr_indent(FILE *fp,int n)
  56 {
  57   int i;
  58
  59   for (i=0; i<n; i++) (void) fprintf(fp," ");
  60   return n;
  61 }
  62
  63 int available(FILE *fp,void *p,int indent,const char *title)
  64 {
  65   if (!p) {
  66     if (indent > 0)
  67       pr_indent(fp,indent);
  68     (void) fprintf(fp,"%s: not available\n",title);
  69   }
  70   return (p!=NULL);
  71 }
  72
  73 int pr_title(FILE *fp,int indent,const char *title)
  74 {
  75   (void) pr_indent(fp,indent);
  76   (void) fprintf(fp,"%s:\n",title);
  77   return (indent+INDENT);
  78 }
  79
  80 int pr_title_n(FILE *fp,int indent,const char *title,int n)
  81 {
  82   (void) pr_indent(fp,indent);
  83   (void) fprintf(fp,"%s (%d):\n",title,n);
  84   return (indent+INDENT);
  85 }
  86
  87 int pr_title_nxn(FILE *fp,int indent,const char *title,int n1,int n2)
  88 {
  89   (void) pr_indent(fp,indent);
  90   (void) fprintf(fp,"%s (%dx%d):\n",title,n1,n2);
  91   return (indent+INDENT);
  92 }
  93
  94 void pr_ivec(FILE *fp,int indent,const char *title,int vec[],int n, bool bShowNumbers)
  95 {
  96   int i;
  97
  98   if (available(fp,vec,indent,title))
  99     {
 100       indent=pr_title_n(fp,indent,title,n);
 101       for (i=0; i<n; i++)
 102         {
 103           (void) pr_indent(fp,indent);
 104           (void) fprintf(fp,"%s[%d]=%d\n",title,bShowNumbers?i:-1,vec[i]);
 105         }
 106     }
 107 }
 108
 109 void pr_ivec_block(FILE *fp,int indent,const char *title,int vec[],int n, bool bShowNumbers)
 110 {
 111     int i,j;
 112
 113     if (available(fp,vec,indent,title))
 114     {
 115         indent=pr_title_n(fp,indent,title,n);
 116         i = 0;
 117         while (i < n)
 118         {
 119             j = i+1;
 120             while (j < n && vec[j] == vec[j-1]+1)
 121             {
 122                 j++;
 123             }
 124             /* Print consecutive groups of 3 or more as blocks */
 125             if (j - i < 3)
 126             {
 127                 while(i < j)
 128                 {
 129                     (void) pr_indent(fp,indent);
 130                     (void) fprintf(fp,"%s[%d]=%d\n",
 131                                    title,bShowNumbers?i:-1,vec[i]);
 132                     i++;
 133                 }
 134             }
 135             else
 136             {
 137                 (void) pr_indent(fp,indent);
 138                 (void) fprintf(fp,"%s[%d,...,%d] = {%d,...,%d}\n",
 139                                title,
 140                                bShowNumbers?i:-1,
 141                                bShowNumbers?j-1:-1,
 142                                vec[i],vec[j-1]);
 143                 i = j;
 144             }
 145         }
 146     }
 147 }
 148
 149 void pr_bvec(FILE *fp,int indent,const char *title,bool vec[],int n, bool bShowNumbers)
 150 {
 151   int i;
 152
 153   if (available(fp,vec,indent,title))
 154     {
 155       indent=pr_title_n(fp,indent,title,n);
 156       for (i=0; i<n; i++)
 157         {
 158           (void) pr_indent(fp,indent);
 159           (void) fprintf(fp,"%s[%d]=%s\n",title,bShowNumbers?i:-1,
 160                          BOOL(vec[i]));
 161         }
 162     }
 163 }
 164
 165 void pr_ivecs(FILE *fp,int indent,const char *title,ivec vec[],int n, bool bShowNumbers)
 166 {
 167   int i,j;
 168
 169   if (available(fp,vec,indent,title))
 170     {
 171       indent=pr_title_nxn(fp,indent,title,n,DIM);
 172       for (i=0; i<n; i++)
 173         {
 174           (void) pr_indent(fp,indent);
 175           (void) fprintf(fp,"%s[%d]={",title,bShowNumbers?i:-1);
 176           for (j=0; j<DIM; j++)
 177             {
 178               if (j!=0) (void) fprintf(fp,", ");
 179               fprintf(fp,"%d",vec[i][j]);
 180             }
 181           (void) fprintf(fp,"}\n");
 182         }
 183     }
 184 }
 185
 186 void pr_rvec(FILE *fp,int indent,const char *title,real vec[],int n, bool bShowNumbers)
 187 {
 188   int i;
 189
 190   if (available(fp,vec,indent,title))
 191     {
 192       indent=pr_title_n(fp,indent,title,n);
 193       for (i=0; i<n; i++)
 194         {
 195           pr_indent(fp,indent);
 196           fprintf(fp,"%s[%d]=%12.5e\n",title,bShowNumbers?i:-1,vec[i]);
 197         }
 198     }
 199 }
 200
 201 void pr_dvec(FILE *fp,int indent,const char *title,double vec[],int n, bool bShowNumbers)
 202 {
 203         int i;
 204
 205         if (available(fp,vec,indent,title))
 206     {
 207                 indent=pr_title_n(fp,indent,title,n);
 208                 for (i=0; i<n; i++)
 209         {
 210                         pr_indent(fp,indent);
 211                         fprintf(fp,"%s[%d]=%12.5e\n",title,bShowNumbers?i:-1,vec[i]);
 212         }
 213     }
 214 }
 215
 216
 217 /*
 218 void pr_mat(FILE *fp,int indent,char *title,matrix m)
 219 {
 220   int i,j;
 221
 222   if (available(fp,m,indent,title)) {
 223     indent=pr_title_n(fp,indent,title,n);
 224     for(i=0; i<n; i++) {
 225       pr_indent(fp,indent);
 226       fprintf(fp,"%s[%d]=%12.5e %12.5e %12.5e\n",
 227               title,bShowNumbers?i:-1,m[i][XX],m[i][YY],m[i][ZZ]);
 228     }
 229   }
 230 }
 231 */
 232
 233 void pr_rvecs_len(FILE *fp,int indent,const char *title,rvec vec[],int n)
 234 {
 235   int i,j;
 236
 237   if (available(fp,vec,indent,title)) {
 238     indent=pr_title_nxn(fp,indent,title,n,DIM);
 239     for (i=0; i<n; i++) {
 240       (void) pr_indent(fp,indent);
 241       (void) fprintf(fp,"%s[%5d]={",title,i);
 242       for (j=0; j<DIM; j++) {
 243         if (j != 0)
 244           (void) fprintf(fp,", ");
 245         (void) fprintf(fp,"%12.5e",vec[i][j]);
 246       }
 247       (void) fprintf(fp,"} len=%12.5e\n",norm(vec[i]));
 248     }
 249   }
 250 }
 251
 252 void pr_rvecs(FILE *fp,int indent,const char *title,rvec vec[],int n)
 253 {
 254   const char *fshort = "%12.5e";
 255   const char *flong  = "%15.8e";
 256   const char *format;
 257   int i,j;
 258
 259   if (getenv("LONGFORMAT") != NULL)
 260     format = flong;
 261   else
 262     format = fshort;
 263
 264   if (available(fp,vec,indent,title)) {
 265     indent=pr_title_nxn(fp,indent,title,n,DIM);
 266     for (i=0; i<n; i++) {
 267       (void) pr_indent(fp,indent);
 268       (void) fprintf(fp,"%s[%5d]={",title,i);
 269       for (j=0; j<DIM; j++) {
 270         if (j != 0)
 271           (void) fprintf(fp,", ");
 272         (void) fprintf(fp,format,vec[i][j]);
 273       }
 274       (void) fprintf(fp,"}\n");
 275     }
 276   }
 277 }
 278
 279
 280 void pr_reals(FILE *fp,int indent,const char *title,real *vec,int n)
 281 {
 282   int i;
 283
 284   if (available(fp,vec,indent,title)) {
 285     (void) pr_indent(fp,indent);
 286     (void) fprintf(fp,"%s:\t",title);
 287     for(i=0; i<n; i++)
 288       fprintf(fp,"  %10g",vec[i]);
 289     (void) fprintf(fp,"\n");
 290   }
 291 }
 292
 293 void pr_doubles(FILE *fp,int indent,const char *title,double *vec,int n)
 294 {
 295   int i;
 296
 297   if (available(fp,vec,indent,title)) {
 298     (void) pr_indent(fp,indent);
 299     (void) fprintf(fp,"%s:\t",title);
 300     for(i=0; i<n; i++)
 301       fprintf(fp,"  %10g",vec[i]);
 302     (void) fprintf(fp,"\n");
 303   }
 304 }
 305
 306 static void pr_int(FILE *fp,int indent,const char *title,int i)
 307 {
 308   pr_indent(fp,indent);
 309   fprintf(fp,"%-20s = %d\n",title,i);
 310 }
 311
 312 static void pr_gmx_large_int(FILE *fp,int indent,const char *title,gmx_large_int_t i)
 313 {
 314   char buf[STEPSTRSIZE];
 315
 316   pr_indent(fp,indent);
 317   fprintf(fp,"%-20s = %s\n",title,gmx_step_str(i,buf));
 318 }
 319
 320 static void pr_real(FILE *fp,int indent,const char *title,real r)
 321 {
 322   pr_indent(fp,indent);
 323   fprintf(fp,"%-20s = %g\n",title,r);
 324 }
 325
 326 static void pr_double(FILE *fp,int indent,const char *title,double d)
 327 {
 328   pr_indent(fp,indent);
 329   fprintf(fp,"%-20s = %g\n",title,d);
 330 }
 331
 332 static void pr_str(FILE *fp,int indent,const char *title,const char *s)
 333 {
 334   pr_indent(fp,indent);
 335   fprintf(fp,"%-20s = %s\n",title,s);
 336 }
 337
 338 void pr_qm_opts(FILE *fp,int indent,const char *title,t_grpopts *opts)
 339 {
 340   int i,m,j;
 341
 342   fprintf(fp,"%s:\n",title);
 343
 344   pr_int(fp,indent,"ngQM",opts->ngQM);
 345   if (opts->ngQM > 0) {
 346     pr_ivec(fp,indent,"QMmethod",opts->QMmethod,opts->ngQM,FALSE);
 347     pr_ivec(fp,indent,"QMbasis",opts->QMbasis,opts->ngQM,FALSE);
 348     pr_ivec(fp,indent,"QMcharge",opts->QMcharge,opts->ngQM,FALSE);
 349     pr_ivec(fp,indent,"QMmult",opts->QMmult,opts->ngQM,FALSE);
 350     pr_bvec(fp,indent,"bSH",opts->bSH,opts->ngQM,FALSE);
 351     pr_ivec(fp,indent,"CASorbitals",opts->CASorbitals,opts->ngQM,FALSE);
 352     pr_ivec(fp,indent,"CASelectrons",opts->CASelectrons,opts->ngQM,FALSE);
 353     pr_rvec(fp,indent,"SAon",opts->SAon,opts->ngQM,FALSE);
 354     pr_rvec(fp,indent,"SAon",opts->SAon,opts->ngQM,FALSE);
 355     pr_ivec(fp,indent,"SAsteps",opts->SAsteps,opts->ngQM,FALSE);
 356     pr_bvec(fp,indent,"bOPT",opts->bOPT,opts->ngQM,FALSE);
 357     pr_bvec(fp,indent,"bTS",opts->bTS,opts->ngQM,FALSE);
 358   }
 359 }
 360
 361 static void pr_grp_opts(FILE *out,int indent,const char *title,t_grpopts *opts,
 362                         bool bMDPformat)
 363 {
 364   int i,m,j;
 365
 366   if (!bMDPformat)
 367     fprintf(out,"%s:\n",title);
 368
 369   pr_indent(out,indent);
 370   fprintf(out,"nrdf%s",bMDPformat ? " = " : ":");
 371   for(i=0; (i<opts->ngtc); i++)
 372     fprintf(out,"  %10g",opts->nrdf[i]);
 373   fprintf(out,"\n");
 374
 375   pr_indent(out,indent);
 376   fprintf(out,"ref_t%s",bMDPformat ? " = " : ":");
 377   for(i=0; (i<opts->ngtc); i++)
 378     fprintf(out,"  %10g",opts->ref_t[i]);
 379   fprintf(out,"\n");
 380
 381   pr_indent(out,indent);
 382   fprintf(out,"tau_t%s",bMDPformat ? " = " : ":");
 383   for(i=0; (i<opts->ngtc); i++)
 384     fprintf(out,"  %10g",opts->tau_t[i]);
 385   fprintf(out,"\n");
 386
 387   /* Pretty-print the simulated annealing info */
 388   fprintf(out,"anneal%s",bMDPformat ? " = " : ":");
 389   for(i=0; (i<opts->ngtc); i++)
 390     fprintf(out,"  %10s",EANNEAL(opts->annealing[i]));
 391   fprintf(out,"\n");
 392
 393   fprintf(out,"ann_npoints%s",bMDPformat ? " = " : ":");
 394   for(i=0; (i<opts->ngtc); i++)
 395     fprintf(out,"  %10d",opts->anneal_npoints[i]);
 396   fprintf(out,"\n");
 397
 398   for(i=0; (i<opts->ngtc); i++) {
 399     if(opts->anneal_npoints[i]>0) {
 400       fprintf(out,"ann. times [%d]:\t",i);
 401       for(j=0; (j<opts->anneal_npoints[i]); j++)
 402         fprintf(out,"  %10.1f",opts->anneal_time[i][j]);
 403       fprintf(out,"\n");
 404       fprintf(out,"ann. temps [%d]:\t",i);
 405       for(j=0; (j<opts->anneal_npoints[i]); j++)
 406         fprintf(out,"  %10.1f",opts->anneal_temp[i][j]);
 407       fprintf(out,"\n");
 408     }
 409   }
 410
 411   pr_indent(out,indent);
 412   fprintf(out,"acc:\t");
 413   for(i=0; (i<opts->ngacc); i++)
 414     for(m=0; (m<DIM); m++)
 415       fprintf(out,"  %10g",opts->acc[i][m]);
 416   fprintf(out,"\n");
 417
 418   pr_indent(out,indent);
 419   fprintf(out,"nfreeze:");
 420   for(i=0; (i<opts->ngfrz); i++)
 421     for(m=0; (m<DIM); m++)
 422       fprintf(out,"  %10s",opts->nFreeze[i][m] ? "Y" : "N");
 423   fprintf(out,"\n");
 424
 425
 426   for(i=0; (i<opts->ngener); i++) {
 427     pr_indent(out,indent);
 428     fprintf(out,"energygrp_flags[%3d]:",i);
 429     for(m=0; (m<opts->ngener); m++)
 430       fprintf(out," %d",opts->egp_flags[opts->ngener*i+m]);
 431     fprintf(out,"\n");
 432   }
 433
 434   fflush(out);
 435 }
 436
 437 static void pr_matrix(FILE *fp,int indent,const char *title,rvec *m,
 438                       bool bMDPformat)
 439 {
 440   if (bMDPformat)
 441     fprintf(fp,"%-10s    = %g %g %g %g %g %g\n",title,
 442             m[XX][XX],m[YY][YY],m[ZZ][ZZ],m[XX][YY],m[XX][ZZ],m[YY][ZZ]);
 443   else
 444     pr_rvecs(fp,indent,title,m,DIM);
 445 }
 446
 447 static void pr_cosine(FILE *fp,int indent,const char *title,t_cosines *cos,
 448                       bool bMDPformat)
 449 {
 450   int j;
 451
 452   if (bMDPformat) {
 453     fprintf(fp,"%s = %d\n",title,cos->n);
 454   }
 455   else {
 456     indent=pr_title(fp,indent,title);
 457     (void) pr_indent(fp,indent);
 458     fprintf(fp,"n = %d\n",cos->n);
 459     if (cos->n > 0) {
 460       (void) pr_indent(fp,indent+2);
 461       fprintf(fp,"a =");
 462       for(j=0; (j<cos->n); j++)
 463         fprintf(fp," %e",cos->a[j]);
 464       fprintf(fp,"\n");
 465       (void) pr_indent(fp,indent+2);
 466       fprintf(fp,"phi =");
 467       for(j=0; (j<cos->n); j++)
 468         fprintf(fp," %e",cos->phi[j]);
 469       fprintf(fp,"\n");
 470     }
 471   }
 472 }
 473
 474 #define PS(t,s) pr_str(fp,indent,t,s)
 475 #define PI(t,s) pr_int(fp,indent,t,s)
 476 #define PSTEP(t,s) pr_gmx_large_int(fp,indent,t,s)
 477 #define PR(t,s) pr_real(fp,indent,t,s)
 478 #define PD(t,s) pr_double(fp,indent,t,s)
 479
 480 static void pr_pullgrp(FILE *fp,int indent,int g,t_pullgrp *pg)
 481 {
 482   pr_indent(fp,indent);
 483   fprintf(fp,"pull_group %d:\n",g);
 484   indent += 2;
 485   pr_ivec_block(fp,indent,"atom",pg->ind,pg->nat,TRUE);
 486   pr_rvec(fp,indent,"weight",pg->weight,pg->nweight,TRUE);
 487   PI("pbcatom",pg->pbcatom);
 488   pr_rvec(fp,indent,"vec",pg->vec,DIM,TRUE);
 489   pr_rvec(fp,indent,"init",pg->init,DIM,TRUE);
 490   PR("rate",pg->rate);
 491   PR("k",pg->k);
 492   PR("kB",pg->kB);
 493 }
 494
 495 static void pr_pull(FILE *fp,int indent,t_pull *pull)
 496 {
 497   int g;
 498
 499   PS("pull_geometry",EPULLGEOM(pull->eGeom));
 500   pr_ivec(fp,indent,"pull_dim",pull->dim,DIM,TRUE);
 501   PR("pull_r1",pull->cyl_r1);
 502   PR("pull_r0",pull->cyl_r0);
 503   PR("pull_constr_tol",pull->constr_tol);
 504   PI("pull_nstxout",pull->nstxout);
 505   PI("pull_nstfout",pull->nstfout);
 506   PI("pull_ngrp",pull->ngrp);
 507   for(g=0; g<pull->ngrp+1; g++)
 508     pr_pullgrp(fp,indent,g,&pull->grp[g]);
 509 }
 510
 511 void pr_inputrec(FILE *fp,int indent,const char *title,t_inputrec *ir,
 512                  bool bMDPformat)
 513 {
 514   const char *infbuf="inf";
 515   int  i;
 516
 517   if (available(fp,ir,indent,title)) {
 518     if (!bMDPformat)
 519       indent=pr_title(fp,indent,title);
 520     PS("integrator",EI(ir->eI));
 521     PSTEP("nsteps",ir->nsteps);
 522     PSTEP("init_step",ir->init_step);
 523     PI("nstcalcenergy",ir->nstcalcenergy);
 524     PS("ns_type",ENS(ir->ns_type));
 525     PI("nstlist",ir->nstlist);
 526     PI("ndelta",ir->ndelta);
 527     PI("nstcomm",ir->nstcomm);
 528     PS("comm_mode",ECOM(ir->comm_mode));
 529     PI("nstlog",ir->nstlog);
 530     PI("nstxout",ir->nstxout);
 531     PI("nstvout",ir->nstvout);
 532     PI("nstfout",ir->nstfout);
 533     PI("nstenergy",ir->nstenergy);
 534     PI("nstxtcout",ir->nstxtcout);
 535     PR("init_t",ir->init_t);
 536     PR("delta_t",ir->delta_t);
 537
 538     PR("xtcprec",ir->xtcprec);
 539     PI("nkx",ir->nkx);
 540     PI("nky",ir->nky);
 541     PI("nkz",ir->nkz);
 542     PI("pme_order",ir->pme_order);
 543     PR("ewald_rtol",ir->ewald_rtol);
 544     PR("ewald_geometry",ir->ewald_geometry);
 545     PR("epsilon_surface",ir->epsilon_surface);
 546     PS("optimize_fft",BOOL(ir->bOptFFT));
 547     PS("ePBC",EPBC(ir->ePBC));
 548     PS("bPeriodicMols",BOOL(ir->bPeriodicMols));
 549     PS("bContinuation",BOOL(ir->bContinuation));
 550     PS("bShakeSOR",BOOL(ir->bShakeSOR));
 551     PS("etc",ETCOUPLTYPE(ir->etc));
 552     PI("nsttcouple",ir->nsttcouple);
 553     PS("epc",EPCOUPLTYPE(ir->epc));
 554     PS("epctype",EPCOUPLTYPETYPE(ir->epct));
 555     PI("nstpcouple",ir->nstpcouple);
 556     PR("tau_p",ir->tau_p);
 557     pr_matrix(fp,indent,"ref_p",ir->ref_p,bMDPformat);
 558     pr_matrix(fp,indent,"compress",ir->compress,bMDPformat);
 559     PS("refcoord_scaling",EREFSCALINGTYPE(ir->refcoord_scaling));
 560     if (bMDPformat)
 561       fprintf(fp,"posres_com  = %g %g %g\n",ir->posres_com[XX],
 562               ir->posres_com[YY],ir->posres_com[ZZ]);
 563     else
 564       pr_rvec(fp,indent,"posres_com",ir->posres_com,DIM,TRUE);
 565     if (bMDPformat)
 566       fprintf(fp,"posres_comB = %g %g %g\n",ir->posres_comB[XX],
 567               ir->posres_comB[YY],ir->posres_comB[ZZ]);
 568     else
 569       pr_rvec(fp,indent,"posres_comB",ir->posres_comB,DIM,TRUE);
 570     PI("andersen_seed",ir->andersen_seed);
 571     PR("rlist",ir->rlist);
 572     PR("rlistlong",ir->rlistlong);
 573     PR("rtpi",ir->rtpi);
 574     PS("coulombtype",EELTYPE(ir->coulombtype));
 575     PR("rcoulomb_switch",ir->rcoulomb_switch);
 576     PR("rcoulomb",ir->rcoulomb);
 577     PS("vdwtype",EVDWTYPE(ir->vdwtype));
 578     PR("rvdw_switch",ir->rvdw_switch);
 579     PR("rvdw",ir->rvdw);
 580     if (ir->epsilon_r != 0)
 581       PR("epsilon_r",ir->epsilon_r);
 582     else
 583       PS("epsilon_r",infbuf);
 584     if (ir->epsilon_rf != 0)
 585       PR("epsilon_rf",ir->epsilon_rf);
 586     else
 587       PS("epsilon_rf",infbuf);
 588     PR("tabext",ir->tabext);
 589     PS("implicit_solvent",EIMPLICITSOL(ir->implicit_solvent));
 590     PS("gb_algorithm",EGBALGORITHM(ir->gb_algorithm));
 591     PR("gb_epsilon_solvent",ir->gb_epsilon_solvent);
 592     PI("nstgbradii",ir->nstgbradii);
 593     PR("rgbradii",ir->rgbradii);
 594     PR("gb_saltconc",ir->gb_saltconc);
 595     PR("gb_obc_alpha",ir->gb_obc_alpha);
 596     PR("gb_obc_beta",ir->gb_obc_beta);
 597     PR("gb_obc_gamma",ir->gb_obc_gamma);
 598     PR("gb_dielectric_offset",ir->gb_dielectric_offset);
 599     PS("sa_algorithm",ESAALGORITHM(ir->gb_algorithm));
 600     PR("sa_surface_tension",ir->sa_surface_tension);
 601
 602     PS("DispCorr",EDISPCORR(ir->eDispCorr));
 603     PS("free_energy",EFEPTYPE(ir->efep));
 604     PR("init_lambda",ir->init_lambda);
 605     PR("delta_lambda",ir->delta_lambda);
 606     if (!bMDPformat)
 607     {
 608         PI("n_foreign_lambda",ir->n_flambda);
 609     }
 610     if (ir->n_flambda > 0)
 611     {
 612         pr_indent(fp,indent);
 613         fprintf(fp,"foreign_lambda%s",bMDPformat ? " = " : ":");
 614         for(i=0; i<ir->n_flambda; i++)
 615         {
 616             fprintf(fp,"  %10g",ir->flambda[i]);
 617         }
 618         fprintf(fp,"\n");
 619     }
 620     PR("sc_alpha",ir->sc_alpha);
 621     PI("sc_power",ir->sc_power);
 622     PR("sc_sigma",ir->sc_sigma);
 623     PI("nstdhdl", ir->nstdhdl);
 624     PI("dh_table_size", ir->dh_table_size);
 625     PD("dh_table_spacing", ir->dh_table_spacing);
 626
 627     PI("nwall",ir->nwall);
 628     PS("wall_type",EWALLTYPE(ir->wall_type));
 629     PI("wall_atomtype[0]",ir->wall_atomtype[0]);
 630     PI("wall_atomtype[1]",ir->wall_atomtype[1]);
 631     PR("wall_density[0]",ir->wall_density[0]);
 632     PR("wall_density[1]",ir->wall_density[1]);
 633     PR("wall_ewald_zfac",ir->wall_ewald_zfac);
 634
 635     PS("pull",EPULLTYPE(ir->ePull));
 636     if (ir->ePull != epullNO)
 637       pr_pull(fp,indent,ir->pull);
 638
 639     PS("disre",EDISRETYPE(ir->eDisre));
 640     PS("disre_weighting",EDISREWEIGHTING(ir->eDisreWeighting));
 641     PS("disre_mixed",BOOL(ir->bDisreMixed));
 642     PR("dr_fc",ir->dr_fc);
 643     PR("dr_tau",ir->dr_tau);
 644     PR("nstdisreout",ir->nstdisreout);
 645     PR("orires_fc",ir->orires_fc);
 646     PR("orires_tau",ir->orires_tau);
 647     PR("nstorireout",ir->nstorireout);
 648
 649     PR("dihre-fc",ir->dihre_fc);
 650
 651     PR("em_stepsize",ir->em_stepsize);
 652     PR("em_tol",ir->em_tol);
 653     PI("niter",ir->niter);
 654     PR("fc_stepsize",ir->fc_stepsize);
 655     PI("nstcgsteep",ir->nstcgsteep);
 656     PI("nbfgscorr",ir->nbfgscorr);
 657
 658     PS("ConstAlg",ECONSTRTYPE(ir->eConstrAlg));
 659     PR("shake_tol",ir->shake_tol);
 660     PI("lincs_order",ir->nProjOrder);
 661     PR("lincs_warnangle",ir->LincsWarnAngle);
 662     PI("lincs_iter",ir->nLincsIter);
 663     PR("bd_fric",ir->bd_fric);
 664     PI("ld_seed",ir->ld_seed);
 665     PR("cos_accel",ir->cos_accel);
 666     pr_matrix(fp,indent,"deform",ir->deform,bMDPformat);
 667     PI("userint1",ir->userint1);
 668     PI("userint2",ir->userint2);
 669     PI("userint3",ir->userint3);
 670     PI("userint4",ir->userint4);
 671     PR("userreal1",ir->userreal1);
 672     PR("userreal2",ir->userreal2);
 673     PR("userreal3",ir->userreal3);
 674     PR("userreal4",ir->userreal4);
 675     pr_grp_opts(fp,indent,"grpopts",&(ir->opts),bMDPformat);
 676     pr_cosine(fp,indent,"efield-x",&(ir->ex[XX]),bMDPformat);
 677     pr_cosine(fp,indent,"efield-xt",&(ir->et[XX]),bMDPformat);
 678     pr_cosine(fp,indent,"efield-y",&(ir->ex[YY]),bMDPformat);
 679     pr_cosine(fp,indent,"efield-yt",&(ir->et[YY]),bMDPformat);
 680     pr_cosine(fp,indent,"efield-z",&(ir->ex[ZZ]),bMDPformat);
 681     pr_cosine(fp,indent,"efield-zt",&(ir->et[ZZ]),bMDPformat);
 682     PS("bQMMM",BOOL(ir->bQMMM));
 683     PI("QMconstraints",ir->QMconstraints);
 684     PI("QMMMscheme",ir->QMMMscheme);
 685     PR("scalefactor",ir->scalefactor);
 686     pr_qm_opts(fp,indent,"qm_opts",&(ir->opts));
 687   }
 688 }
 689 #undef PS
 690 #undef PR
 691 #undef PI
 692
 693 static void pr_harm(FILE *fp,t_iparams *iparams,const char *r,const char *kr)
 694 {
 695   fprintf(fp,"%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e\n",
 696           r,iparams->harmonic.rA,kr,iparams->harmonic.krA,
 697           r,iparams->harmonic.rB,kr,iparams->harmonic.krB);
 698 }
 699
 700 void pr_iparams(FILE *fp,t_functype ftype,t_iparams *iparams)
 701 {
 702   int i;
 703   real VA[4],VB[4],*rbcA,*rbcB;
 704
 705   switch (ftype) {
 706   case F_ANGLES:
 707   case F_G96ANGLES:
 708     pr_harm(fp,iparams,"th","ct");
 709     break;
 710   case F_CROSS_BOND_BONDS:
 711     fprintf(fp,"r1e=%15.8e, r2e=%15.8e, krr=%15.8e\n",
 712             iparams->cross_bb.r1e,iparams->cross_bb.r2e,
 713             iparams->cross_bb.krr);
 714     break;
 715   case F_CROSS_BOND_ANGLES:
 716     fprintf(fp,"r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e\n",
 717             iparams->cross_ba.r1e,iparams->cross_ba.r2e,
 718             iparams->cross_ba.r3e,iparams->cross_ba.krt);
 719     break;
 720   case F_UREY_BRADLEY:
 721     fprintf(fp,"theta=%15.8e, ktheta=%15.8e, r13=%15.8e, kUB=%15.8e\n",
 722             iparams->u_b.theta,iparams->u_b.ktheta,iparams->u_b.r13,iparams->u_b.kUB);
 723     break;
 724   case F_QUARTIC_ANGLES:
 725     fprintf(fp,"theta=%15.8e",iparams->qangle.theta);
 726     for(i=0; i<5; i++)
 727       fprintf(fp,", c%c=%15.8e",'0'+i,iparams->qangle.c[i]);
 728     fprintf(fp,"\n");
 729     break;
 730   case F_BHAM:
 731     fprintf(fp,"a=%15.8e, b=%15.8e, c=%15.8e\n",
 732             iparams->bham.a,iparams->bham.b,iparams->bham.c);
 733     break;
 734   case F_BONDS:
 735   case F_G96BONDS:
 736   case F_HARMONIC:
 737     pr_harm(fp,iparams,"b0","cb");
 738     break;
 739   case F_IDIHS:
 740     pr_harm(fp,iparams,"xi","cx");
 741     break;
 742   case F_MORSE:
 743     fprintf(fp,"b0=%15.8e, cb=%15.8e, beta=%15.8e\n",
 744             iparams->morse.b0,iparams->morse.cb,iparams->morse.beta);
 745     break;
 746   case F_CUBICBONDS:
 747     fprintf(fp,"b0=%15.8e, kb=%15.8e, kcub=%15.8e\n",
 748             iparams->cubic.b0,iparams->cubic.kb,iparams->cubic.kcub);
 749     break;
 750   case F_CONNBONDS:
 751     fprintf(fp,"\n");
 752     break;
 753   case F_FENEBONDS:
 754     fprintf(fp,"bm=%15.8e, kb=%15.8e\n",iparams->fene.bm,iparams->fene.kb);
 755     break;
 756   case F_RESTRBONDS:
 757       fprintf(fp,"lowA=%15.8e, up1A=%15.8e, up2A=%15.8e, kA=%15.8e, lowB=%15.8e, up1B=%15.8e, up2B=%15.8e, kB=%15.8e,\n",
 758               iparams->restraint.lowA,iparams->restraint.up1A,
 759               iparams->restraint.up2A,iparams->restraint.kA,
 760               iparams->restraint.lowB,iparams->restraint.up1B,
 761               iparams->restraint.up2B,iparams->restraint.kB);
 762       break;
 763   case F_TABBONDS:
 764   case F_TABBONDSNC:
 765   case F_TABANGLES:
 766   case F_TABDIHS:
 767     fprintf(fp,"tab=%d, kA=%15.8e, kB=%15.8e\n",
 768             iparams->tab.table,iparams->tab.kA,iparams->tab.kB);
 769     break;
 770   case F_POLARIZATION:
 771     fprintf(fp,"alpha=%15.8e\n",iparams->polarize.alpha);
 772     break;
 773   case F_THOLE_POL:
 774     fprintf(fp,"a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e\n",
 775             iparams->thole.a,iparams->thole.alpha1,iparams->thole.alpha2,
 776             iparams->thole.rfac);
 777     break;
 778   case F_WATER_POL:
 779     fprintf(fp,"al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f\n",
 780             iparams->wpol.al_x,iparams->wpol.al_y,iparams->wpol.al_z,
 781             iparams->wpol.rOH,iparams->wpol.rHH,iparams->wpol.rOD);
 782     break;
 783   case F_LJ:
 784     fprintf(fp,"c6=%15.8e, c12=%15.8e\n",iparams->lj.c6,iparams->lj.c12);
 785     break;
 786   case F_LJ14:
 787     fprintf(fp,"c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e\n",
 788             iparams->lj14.c6A,iparams->lj14.c12A,
 789             iparams->lj14.c6B,iparams->lj14.c12B);
 790     break;
 791   case F_LJC14_Q:
 792     fprintf(fp,"fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
 793             iparams->ljc14.fqq,
 794             iparams->ljc14.qi,iparams->ljc14.qj,
 795             iparams->ljc14.c6,iparams->ljc14.c12);
 796     break;
 797   case F_LJC_PAIRS_NB:
 798     fprintf(fp,"qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
 799             iparams->ljcnb.qi,iparams->ljcnb.qj,
 800             iparams->ljcnb.c6,iparams->ljcnb.c12);
 801     break;
 802   case F_PDIHS:
 803   case F_ANGRES:
 804   case F_ANGRESZ:
 805     fprintf(fp,"phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d\n",
 806             iparams->pdihs.phiA,iparams->pdihs.cpA,
 807             iparams->pdihs.phiB,iparams->pdihs.cpB,
 808             iparams->pdihs.mult);
 809     break;
 810   case F_DISRES:
 811     fprintf(fp,"label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)\n",
 812             iparams->disres.label,iparams->disres.type,
 813             iparams->disres.low,iparams->disres.up1,
 814             iparams->disres.up2,iparams->disres.kfac);
 815     break;
 816   case F_ORIRES:
 817     fprintf(fp,"ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)\n",
 818             iparams->orires.ex,iparams->orires.label,iparams->orires.power,
 819             iparams->orires.c,iparams->orires.obs,iparams->orires.kfac);
 820     break;
 821   case F_DIHRES:
 822     fprintf(fp,"label=%d, power=%4d phi=%15.8e, dphi=%15.8e, kfac=%15.8e)\n",
 823             iparams->dihres.label,iparams->dihres.power,
 824             iparams->dihres.phi,iparams->dihres.dphi,iparams->dihres.kfac);
 825     break;
 826   case F_POSRES:
 827     fprintf(fp,"pos0A=(%15.8e,%15.8e,%15.8e), fcA=(%15.8e,%15.8e,%15.8e), pos0B=(%15.8e,%15.8e,%15.8e), fcB=(%15.8e,%15.8e,%15.8e)\n",
 828             iparams->posres.pos0A[XX],iparams->posres.pos0A[YY],
 829             iparams->posres.pos0A[ZZ],iparams->posres.fcA[XX],
 830             iparams->posres.fcA[YY],iparams->posres.fcA[ZZ],
 831             iparams->posres.pos0B[XX],iparams->posres.pos0B[YY],
 832             iparams->posres.pos0B[ZZ],iparams->posres.fcB[XX],
 833             iparams->posres.fcB[YY],iparams->posres.fcB[ZZ]);
 834     break;
 835   case F_RBDIHS:
 836     for (i=0; i<NR_RBDIHS; i++)
 837       fprintf(fp,"%srbcA[%d]=%15.8e",i==0?"":", ",i,iparams->rbdihs.rbcA[i]);
 838     fprintf(fp,"\n");
 839     for (i=0; i<NR_RBDIHS; i++)
 840       fprintf(fp,"%srbcB[%d]=%15.8e",i==0?"":", ",i,iparams->rbdihs.rbcB[i]);
 841     fprintf(fp,"\n");
 842     break;
 843   case F_FOURDIHS:
 844     /* Use the OPLS -> Ryckaert-Bellemans formula backwards to get the
 845      * OPLS potential constants back.
 846      */
 847     rbcA = iparams->rbdihs.rbcA;
 848     rbcB = iparams->rbdihs.rbcB;
 849
 850     VA[3] = -0.25*rbcA[4];
 851     VA[2] = -0.5*rbcA[3];
 852     VA[1] = 4.0*VA[3]-rbcA[2];
 853     VA[0] = 3.0*VA[2]-2.0*rbcA[1];
 854
 855     VB[3] = -0.25*rbcB[4];
 856     VB[2] = -0.5*rbcB[3];
 857     VB[1] = 4.0*VB[3]-rbcB[2];
 858     VB[0] = 3.0*VB[2]-2.0*rbcB[1];
 859
 860     for (i=0; i<NR_FOURDIHS; i++)
 861       fprintf(fp,"%sFourA[%d]=%15.8e",i==0?"":", ",i,VA[i]);
 862     fprintf(fp,"\n");
 863     for (i=0; i<NR_FOURDIHS; i++)
 864       fprintf(fp,"%sFourB[%d]=%15.8e",i==0?"":", ",i,VB[i]);
 865     fprintf(fp,"\n");
 866     break;
 867
 868   case F_CONSTR:
 869   case F_CONSTRNC:
 870     fprintf(fp,"dA=%15.8e, dB=%15.8e\n",iparams->constr.dA,iparams->constr.dB);
 871     break;
 872   case F_SETTLE:
 873     fprintf(fp,"doh=%15.8e, dhh=%15.8e\n",iparams->settle.doh,
 874             iparams->settle.dhh);
 875     break;
 876   case F_VSITE2:
 877     fprintf(fp,"a=%15.8e\n",iparams->vsite.a);
 878     break;
 879   case F_VSITE3:
 880   case F_VSITE3FD:
 881   case F_VSITE3FAD:
 882     fprintf(fp,"a=%15.8e, b=%15.8e\n",iparams->vsite.a,iparams->vsite.b);
 883     break;
 884   case F_VSITE3OUT:
 885   case F_VSITE4FD:
 886   case F_VSITE4FDN:
 887     fprintf(fp,"a=%15.8e, b=%15.8e, c=%15.8e\n",
 888             iparams->vsite.a,iparams->vsite.b,iparams->vsite.c);
 889     break;
 890   case F_VSITEN:
 891     fprintf(fp,"n=%2d, a=%15.8e\n",iparams->vsiten.n,iparams->vsiten.a);
 892     break;
 893   case F_GB12:
 894   case F_GB13:
 895   case F_GB14:
 896     fprintf(fp, "sar=%15.8e, st=%15.8e, pi=%15.8e, gbr=%15.8e, bmlt=%15.8e\n",iparams->gb.sar,iparams->gb.st,iparams->gb.pi,iparams->gb.gbr,iparams->gb.bmlt);
 897     break;
 898   case F_CMAP:
 899     fprintf(fp, "cmapA=%1d, cmapB=%1d\n",iparams->cmap.cmapA, iparams->cmap.cmapB);
 900     break;
 901   default:
 902     gmx_fatal(FARGS,"unknown function type %d (%s) in %s line %d",
 903               ftype,interaction_function[ftype].name,__FILE__,__LINE__);
 904   }
 905 }
 906
 907 void pr_ilist(FILE *fp,int indent,const char *title,
 908               t_functype *functype,t_ilist *ilist, bool bShowNumbers)
 909 {
 910     int i,j,k,type,ftype;
 911     t_iatom *iatoms;
 912
 913     if (available(fp,ilist,indent,title) && ilist->nr > 0)
 914     {
 915         indent=pr_title(fp,indent,title);
 916         (void) pr_indent(fp,indent);
 917         fprintf(fp,"nr: %d\n",ilist->nr);
 918         if (ilist->nr > 0) {
 919             (void) pr_indent(fp,indent);
 920             fprintf(fp,"iatoms:\n");
 921             iatoms=ilist->iatoms;
 922             for (i=j=0; i<ilist->nr;) {
 923 #ifndef DEBUG
 924                 (void) pr_indent(fp,indent+INDENT);
 925                 type=*(iatoms++);
 926                 ftype=functype[type];
 927                 (void) fprintf(fp,"%d type=%d (%s)",
 928                                bShowNumbers?j:-1,bShowNumbers?type:-1,
 929                                interaction_function[ftype].name);
 930                 j++;
 931                 for (k=0; k<interaction_function[ftype].nratoms; k++)
 932                     (void) fprintf(fp," %u",*(iatoms++));
 933                 (void) fprintf(fp,"\n");
 934                 i+=1+interaction_function[ftype].nratoms;
 935 #else
 936                 fprintf(fp,"%5d%5d\n",i,iatoms[i]);
 937                 i++;
 938 #endif
 939             }
 940         }
 941     }
 942 }
 943
 944 static void pr_cmap(FILE *fp, int indent, const char *title,
 945                     gmx_cmap_t *cmap_grid, bool bShowNumbers)
 946 {
 947     int i,j,nelem;
 948     real dx,idx;
 949
 950     dx    = 360.0 / cmap_grid->grid_spacing;
 951     nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
 952
 953     if(available(fp,cmap_grid,indent,title))
 954     {
 955         fprintf(fp,"%s\n",title);
 956
 957         for(i=0;i<cmap_grid->ngrid;i++)
 958         {
 959             idx = -180.0;
 960             fprintf(fp,"%8s %8s %8s %8s\n","V","dVdx","dVdy","d2dV");
 961
 962             fprintf(fp,"grid[%3d]={\n",bShowNumbers?i:-1);
 963
 964             for(j=0;j<nelem;j++)
 965             {
 966                 if( (j%cmap_grid->grid_spacing)==0)
 967                 {
 968                     fprintf(fp,"%8.1f\n",idx);
 969                     idx+=dx;
 970                 }
 971
 972                 fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4]);
 973                 fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4+1]);
 974                 fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4+2]);
 975                 fprintf(fp,"%8.3f\n",cmap_grid->cmapdata[i].cmap[j*4+3]);
 976             }
 977             fprintf(fp,"\n");
 978         }
 979     }
 980
 981 }
 982
 983 void pr_ffparams(FILE *fp,int indent,const char *title,
 984                  gmx_ffparams_t *ffparams,
 985                  bool bShowNumbers)
 986 {
 987   int i,j;
 988
 989   indent=pr_title(fp,indent,title);
 990   (void) pr_indent(fp,indent);
 991   (void) fprintf(fp,"atnr=%d\n",ffparams->atnr);
 992   (void) pr_indent(fp,indent);
 993   (void) fprintf(fp,"ntypes=%d\n",ffparams->ntypes);
 994   for (i=0; i<ffparams->ntypes; i++) {
 995       (void) pr_indent(fp,indent+INDENT);
 996       (void) fprintf(fp,"functype[%d]=%s, ",
 997                      bShowNumbers?i:-1,
 998                      interaction_function[ffparams->functype[i]].name);
 999       pr_iparams(fp,ffparams->functype[i],&ffparams->iparams[i]);
1000   }
1001   (void) pr_double(fp,indent,"reppow",ffparams->reppow);
1002   (void) pr_real(fp,indent,"fudgeQQ",ffparams->fudgeQQ);
1003   pr_cmap(fp,indent,"cmap",&ffparams->cmap_grid,bShowNumbers);
1004 }
1005
1006 void pr_idef(FILE *fp,int indent,const char *title,t_idef *idef, bool bShowNumbers)
1007 {
1008   int i,j;
1009
1010   if (available(fp,idef,indent,title)) {
1011     indent=pr_title(fp,indent,title);
1012     (void) pr_indent(fp,indent);
1013     (void) fprintf(fp,"atnr=%d\n",idef->atnr);
1014     (void) pr_indent(fp,indent);
1015     (void) fprintf(fp,"ntypes=%d\n",idef->ntypes);
1016     for (i=0; i<idef->ntypes; i++) {
1017       (void) pr_indent(fp,indent+INDENT);
1018       (void) fprintf(fp,"functype[%d]=%s, ",
1019                      bShowNumbers?i:-1,
1020                      interaction_function[idef->functype[i]].name);
1021       pr_iparams(fp,idef->functype[i],&idef->iparams[i]);
1022     }
1023     (void) pr_real(fp,indent,"fudgeQQ",idef->fudgeQQ);
1024
1025     for(j=0; (j<F_NRE); j++)
1026       pr_ilist(fp,indent,interaction_function[j].longname,
1027                idef->functype,&idef->il[j],bShowNumbers);
1028   }
1029 }
1030
1031 static int pr_block_title(FILE *fp,int indent,const char *title,t_block *block)
1032 {
1033   int i;
1034
1035   if (available(fp,block,indent,title))
1036     {
1037       indent=pr_title(fp,indent,title);
1038       (void) pr_indent(fp,indent);
1039       (void) fprintf(fp,"nr=%d\n",block->nr);
1040     }
1041   return indent;
1042 }
1043
1044 static int pr_blocka_title(FILE *fp,int indent,const char *title,t_blocka *block)
1045 {
1046   int i;
1047
1048   if (available(fp,block,indent,title))
1049     {
1050       indent=pr_title(fp,indent,title);
1051       (void) pr_indent(fp,indent);
1052       (void) fprintf(fp,"nr=%d\n",block->nr);
1053       (void) pr_indent(fp,indent);
1054       (void) fprintf(fp,"nra=%d\n",block->nra);
1055     }
1056   return indent;
1057 }
1058
1059 static void low_pr_block(FILE *fp,int indent,const char *title,t_block *block, bool bShowNumbers)
1060 {
1061   int i;
1062
1063   if (available(fp,block,indent,title))
1064     {
1065       indent=pr_block_title(fp,indent,title,block);
1066       for (i=0; i<=block->nr; i++)
1067         {
1068           (void) pr_indent(fp,indent+INDENT);
1069           (void) fprintf(fp,"%s->index[%d]=%u\n",
1070                          title,bShowNumbers?i:-1,block->index[i]);
1071         }
1072     }
1073 }
1074
1075 static void low_pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block, bool bShowNumbers)
1076 {
1077   int i;
1078
1079   if (available(fp,block,indent,title))
1080     {
1081       indent=pr_blocka_title(fp,indent,title,block);
1082       for (i=0; i<=block->nr; i++)
1083         {
1084           (void) pr_indent(fp,indent+INDENT);
1085           (void) fprintf(fp,"%s->index[%d]=%u\n",
1086                          title,bShowNumbers?i:-1,block->index[i]);
1087         }
1088       for (i=0; i<block->nra; i++)
1089         {
1090           (void) pr_indent(fp,indent+INDENT);
1091           (void) fprintf(fp,"%s->a[%d]=%u\n",
1092                          title,bShowNumbers?i:-1,block->a[i]);
1093         }
1094     }
1095 }
1096
1097 void pr_block(FILE *fp,int indent,const char *title,t_block *block,bool bShowNumbers)
1098 {
1099   int i,j,ok,size,start,end;
1100
1101   if (available(fp,block,indent,title))
1102     {
1103       indent=pr_block_title(fp,indent,title,block);
1104       start=0;
1105       end=start;
1106       if ((ok=(block->index[start]==0))==0)
1107         (void) fprintf(fp,"block->index[%d] should be 0\n",start);
1108       else
1109         for (i=0; i<block->nr; i++)
1110           {
1111             end=block->index[i+1];
1112             size=pr_indent(fp,indent);
1113             if (end<=start)
1114               size+=fprintf(fp,"%s[%d]={}\n",title,i);
1115             else
1116               size+=fprintf(fp,"%s[%d]={%d..%d}\n",
1117                             title,bShowNumbers?i:-1,
1118                             bShowNumbers?start:-1,bShowNumbers?end-1:-1);
1119             start=end;
1120           }
1121     }
1122 }
1123
1124 void pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block,bool bShowNumbers)
1125 {
1126   int i,j,ok,size,start,end;
1127
1128   if (available(fp,block,indent,title))
1129     {
1130       indent=pr_blocka_title(fp,indent,title,block);
1131       start=0;
1132       end=start;
1133       if ((ok=(block->index[start]==0))==0)
1134         (void) fprintf(fp,"block->index[%d] should be 0\n",start);
1135       else
1136         for (i=0; i<block->nr; i++)
1137           {
1138             end=block->index[i+1];
1139             size=pr_indent(fp,indent);
1140             if (end<=start)
1141               size+=fprintf(fp,"%s[%d]={",title,i);
1142             else
1143               size+=fprintf(fp,"%s[%d][%d..%d]={",
1144                             title,bShowNumbers?i:-1,
1145                             bShowNumbers?start:-1,bShowNumbers?end-1:-1);
1146             for (j=start; j<end; j++)
1147               {
1148                 if (j>start) size+=fprintf(fp,", ");
1149                 if ((size)>(USE_WIDTH))
1150                   {
1151                     (void) fprintf(fp,"\n");
1152                     size=pr_indent(fp,indent+INDENT);
1153                   }
1154                 size+=fprintf(fp,"%u",block->a[j]);
1155               }
1156             (void) fprintf(fp,"}\n");
1157             start=end;
1158           }
1159       if ((end!=block->nra)||(!ok))
1160         {
1161           (void) pr_indent(fp,indent);
1162           (void) fprintf(fp,"tables inconsistent, dumping complete tables:\n");
1163           low_pr_blocka(fp,indent,title,block,bShowNumbers);
1164         }
1165     }
1166 }
1167
1168 static void pr_strings(FILE *fp,int indent,const char *title,char ***nm,int n, bool bShowNumbers)
1169 {
1170   int i;
1171
1172   if (available(fp,nm,indent,title))
1173     {
1174       indent=pr_title_n(fp,indent,title,n);
1175       for (i=0; i<n; i++)
1176         {
1177           (void) pr_indent(fp,indent);
1178           (void) fprintf(fp,"%s[%d]={name=\"%s\"}\n",
1179                          title,bShowNumbers?i:-1,*(nm[i]));
1180         }
1181     }
1182 }
1183
1184 static void pr_strings2(FILE *fp,int indent,const char *title,
1185                         char ***nm,char ***nmB,int n, bool bShowNumbers)
1186 {
1187   int i;
1188
1189   if (available(fp,nm,indent,title))
1190     {
1191       indent=pr_title_n(fp,indent,title,n);
1192       for (i=0; i<n; i++)
1193         {
1194           (void) pr_indent(fp,indent);
1195           (void) fprintf(fp,"%s[%d]={name=\"%s\",nameB=\"%s\"}\n",
1196                          title,bShowNumbers?i:-1,*(nm[i]),*(nmB[i]));
1197         }
1198     }
1199 }
1200
1201 static void pr_resinfo(FILE *fp,int indent,const char *title,t_resinfo *resinfo,int n, bool bShowNumbers)
1202 {
1203     int i;
1204
1205     if (available(fp,resinfo,indent,title))
1206     {
1207         indent=pr_title_n(fp,indent,title,n);
1208         for (i=0; i<n; i++)
1209         {
1210             (void) pr_indent(fp,indent);
1211             (void) fprintf(fp,"%s[%d]={name=\"%s\", nr=%d, ic='%c'}\n",
1212                            title,bShowNumbers?i:-1,
1213                            *(resinfo[i].name),resinfo[i].nr,
1214                            (resinfo[i].ic == '\0') ? ' ' : resinfo[i].ic);
1215         }
1216     }
1217 }
1218
1219 static void pr_atom(FILE *fp,int indent,const char *title,t_atom *atom,int n)
1220 {
1221   int i,j;
1222
1223   if (available(fp,atom,indent,title)) {
1224     indent=pr_title_n(fp,indent,title,n);
1225     for (i=0; i<n; i++) {
1226       (void) pr_indent(fp,indent);
1227       fprintf(fp,"%s[%6d]={type=%3d, typeB=%3d, ptype=%8s, m=%12.5e, "
1228               "q=%12.5e, mB=%12.5e, qB=%12.5e, resind=%5d, atomnumber=%3d}\n",
1229               title,i,atom[i].type,atom[i].typeB,ptype_str[atom[i].ptype],
1230               atom[i].m,atom[i].q,atom[i].mB,atom[i].qB,
1231               atom[i].resind,atom[i].atomnumber);
1232     }
1233   }
1234 }
1235
1236 static void pr_grps(FILE *fp,int indent,const char *title,t_grps grps[],int ngrp,
1237                     char **grpname[], bool bShowNumbers)
1238 {
1239     int i,j;
1240
1241   for(i=0; (i<ngrp); i++) {
1242     fprintf(fp,"%s[%d] nr=%d, name=[",title,bShowNumbers?i:-1,grps[i].nr);
1243     for(j=0; (j<grps[i].nr); j++)
1244       fprintf(fp," %s",*(grpname[grps[i].nm_ind[j]]));
1245     fprintf(fp,"]\n");
1246   }
1247 }
1248
1249 static void pr_groups(FILE *fp,int indent,const char *title,
1250                       gmx_groups_t *groups,
1251                       bool bShowNumbers)
1252 {
1253     int grpnr[egcNR];
1254     int nat_max,i,g;
1255
1256     pr_grps(fp,indent,"grp",groups->grps,egcNR,groups->grpname,bShowNumbers);
1257     pr_strings(fp,indent,"grpname",groups->grpname,groups->ngrpname,bShowNumbers);
1258
1259     (void) pr_indent(fp,indent);
1260     fprintf(fp,"groups          ");
1261     for(g=0; g<egcNR; g++)
1262     {
1263        printf(" %5.5s",gtypes[g]);
1264     }
1265     printf("\n");
1266
1267     (void) pr_indent(fp,indent);
1268     fprintf(fp,"allocated       ");
1269     nat_max = 0;
1270     for(g=0; g<egcNR; g++)
1271     {
1272         printf(" %5d",groups->ngrpnr[g]);
1273         nat_max = max(nat_max,groups->ngrpnr[g]);
1274     }
1275     printf("\n");
1276
1277     if (nat_max == 0)
1278     {
1279         (void) pr_indent(fp,indent);
1280         fprintf(fp,"groupnr[%5s] =","*");
1281         for(g=0; g<egcNR; g++)
1282         {
1283             fprintf(fp,"  %3d ",0);
1284         }
1285         fprintf(fp,"\n");
1286     }
1287     else
1288     {
1289         for(i=0; i<nat_max; i++)
1290         {
1291             (void) pr_indent(fp,indent);
1292             fprintf(fp,"groupnr[%5d] =",i);
1293             for(g=0; g<egcNR; g++)
1294             {
1295                 fprintf(fp,"  %3d ",
1296                         groups->grpnr[g] ? groups->grpnr[g][i] : 0);
1297             }
1298             fprintf(fp,"\n");
1299         }
1300     }
1301 }
1302
1303 void pr_atoms(FILE *fp,int indent,const char *title,t_atoms *atoms,
1304               bool bShownumbers)
1305 {
1306   if (available(fp,atoms,indent,title))
1307     {
1308       indent=pr_title(fp,indent,title);
1309       pr_atom(fp,indent,"atom",atoms->atom,atoms->nr);
1310       pr_strings(fp,indent,"atom",atoms->atomname,atoms->nr,bShownumbers);
1311       pr_strings2(fp,indent,"type",atoms->atomtype,atoms->atomtypeB,atoms->nr,bShownumbers);
1312       pr_resinfo(fp,indent,"residue",atoms->resinfo,atoms->nres,bShownumbers);
1313     }
1314 }
1315
1316
1317 void pr_atomtypes(FILE *fp,int indent,const char *title,t_atomtypes *atomtypes,
1318                   bool bShowNumbers)
1319 {
1320   int i;
1321   if (available(fp,atomtypes,indent,title))
1322   {
1323     indent=pr_title(fp,indent,title);
1324     for(i=0;i<atomtypes->nr;i++) {
1325       pr_indent(fp,indent);
1326                 fprintf(fp,
1327                                 "atomtype[%3d]={radius=%12.5e, volume=%12.5e, gb_radius=%12.5e, surftens=%12.5e, atomnumber=%4d, S_hct=%12.5e)}\n",
1328                                 bShowNumbers?i:-1,atomtypes->radius[i],atomtypes->vol[i],
1329                                 atomtypes->gb_radius[i],
1330                                 atomtypes->surftens[i],atomtypes->atomnumber[i],atomtypes->S_hct[i]);
1331     }
1332   }
1333 }
1334
1335 static void pr_moltype(FILE *fp,int indent,const char *title,
1336                        gmx_moltype_t *molt,int n,
1337                        gmx_ffparams_t *ffparams,
1338                        bool bShowNumbers)
1339 {
1340     int j;
1341
1342     indent = pr_title_n(fp,indent,title,n);
1343     (void) pr_indent(fp,indent);
1344     (void) fprintf(fp,"name=\"%s\"\n",*(molt->name));
1345     pr_atoms(fp,indent,"atoms",&(molt->atoms),bShowNumbers);
1346     pr_block(fp,indent,"cgs",&molt->cgs, bShowNumbers);
1347     pr_blocka(fp,indent,"excls",&molt->excls, bShowNumbers);
1348     for(j=0; (j<F_NRE); j++) {
1349         pr_ilist(fp,indent,interaction_function[j].longname,
1350                  ffparams->functype,&molt->ilist[j],bShowNumbers);
1351     }
1352 }
1353
1354 static void pr_molblock(FILE *fp,int indent,const char *title,
1355                         gmx_molblock_t *molb,int n,
1356                         gmx_moltype_t *molt,
1357                         bool bShowNumbers)
1358 {
1359     indent = pr_title_n(fp,indent,title,n);
1360     (void) pr_indent(fp,indent);
1361     (void) fprintf(fp,"%-20s = %d \"%s\"\n",
1362                    "moltype",molb->type,*(molt[molb->type].name));
1363     pr_int(fp,indent,"#molecules",molb->nmol);
1364     pr_int(fp,indent,"#atoms_mol",molb->natoms_mol);
1365     pr_int(fp,indent,"#posres_xA",molb->nposres_xA);
1366     if (molb->nposres_xA > 0) {
1367         pr_rvecs(fp,indent,"posres_xA",molb->posres_xA,molb->nposres_xA);
1368     }
1369     pr_int(fp,indent,"#posres_xB",molb->nposres_xB);
1370     if (molb->nposres_xB > 0) {
1371         pr_rvecs(fp,indent,"posres_xB",molb->posres_xB,molb->nposres_xB);
1372     }
1373 }
1374
1375 void pr_mtop(FILE *fp,int indent,const char *title,gmx_mtop_t *mtop,
1376              bool bShowNumbers)
1377 {
1378     int mt,mb;
1379
1380     if (available(fp,mtop,indent,title)) {
1381         indent=pr_title(fp,indent,title);
1382         (void) pr_indent(fp,indent);
1383         (void) fprintf(fp,"name=\"%s\"\n",*(mtop->name));
1384         pr_int(fp,indent,"#atoms",mtop->natoms);
1385         for(mb=0; mb<mtop->nmolblock; mb++) {
1386             pr_molblock(fp,indent,"molblock",&mtop->molblock[mb],mb,
1387                         mtop->moltype,bShowNumbers);
1388         }
1389         pr_ffparams(fp,indent,"ffparams",&(mtop->ffparams),bShowNumbers);
1390         pr_atomtypes(fp,indent,"atomtypes",&(mtop->atomtypes),bShowNumbers);
1391         for(mt=0; mt<mtop->nmoltype; mt++) {
1392             pr_moltype(fp,indent,"moltype",&mtop->moltype[mt],mt,
1393                        &mtop->ffparams,bShowNumbers);
1394         }
1395         pr_groups(fp,indent,"groups",&mtop->groups,bShowNumbers);
1396     }
1397 }
1398
1399 void pr_top(FILE *fp,int indent,const char *title,t_topology *top, bool bShowNumbers)
1400 {
1401   if (available(fp,top,indent,title)) {
1402     indent=pr_title(fp,indent,title);
1403     (void) pr_indent(fp,indent);
1404     (void) fprintf(fp,"name=\"%s\"\n",*(top->name));
1405     pr_atoms(fp,indent,"atoms",&(top->atoms),bShowNumbers);
1406     pr_atomtypes(fp,indent,"atomtypes",&(top->atomtypes),bShowNumbers);
1407     pr_block(fp,indent,"cgs",&top->cgs, bShowNumbers);
1408     pr_block(fp,indent,"mols",&top->mols, bShowNumbers);
1409     pr_blocka(fp,indent,"excls",&top->excls, bShowNumbers);
1410     pr_idef(fp,indent,"idef",&top->idef,bShowNumbers);
1411   }
1412 }
1413
1414 void pr_header(FILE *fp,int indent,const char *title,t_tpxheader *sh)
1415 {
1416   char buf[22];
1417
1418   if (available(fp,sh,indent,title))
1419     {
1420       indent=pr_title(fp,indent,title);
1421       pr_indent(fp,indent);
1422       fprintf(fp,"bIr    = %spresent\n",sh->bIr?"":"not ");
1423       pr_indent(fp,indent);
1424       fprintf(fp,"bBox   = %spresent\n",sh->bBox?"":"not ");
1425       pr_indent(fp,indent);
1426       fprintf(fp,"bTop   = %spresent\n",sh->bTop?"":"not ");
1427       pr_indent(fp,indent);
1428       fprintf(fp,"bX     = %spresent\n",sh->bX?"":"not ");
1429       pr_indent(fp,indent);
1430       fprintf(fp,"bV     = %spresent\n",sh->bV?"":"not ");
1431       pr_indent(fp,indent);
1432       fprintf(fp,"bF     = %spresent\n",sh->bF?"":"not ");
1433
1434       pr_indent(fp,indent);
1435       fprintf(fp,"natoms = %d\n",sh->natoms);
1436       pr_indent(fp,indent);
1437       fprintf(fp,"lambda = %e\n",sh->lambda);
1438     }
1439 }
1440
1441 void pr_commrec(FILE *fp,int indent,t_commrec *cr)
1442 {
1443   pr_indent(fp,indent);
1444   fprintf(fp,"commrec:\n");
1445   indent+=2;
1446   pr_indent(fp,indent);
1447   fprintf(fp,"nodeid    = %d\n",cr->nodeid);
1448   pr_indent(fp,indent);
1449   fprintf(fp,"nnodes    = %d\n",cr->nnodes);
1450   pr_indent(fp,indent);
1451   fprintf(fp,"npmenodes = %d\n",cr->npmenodes);
1452   pr_indent(fp,indent);
1453   fprintf(fp,"threadid  = %d\n",cr->threadid);
1454   pr_indent(fp,indent);
1455   fprintf(fp,"nthreads  = %d\n",cr->nthreads);
1456 }