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
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  23  * bugs must be traceable. We will be happy to consider code for
  24  * inclusion in the official distribution, but derived work must not
  25  * be called official GROMACS. Details are found in the README & COPYING
  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
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  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, gmx_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, gmx_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,gmx_bool vec[],int n, gmx_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, gmx_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, gmx_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, gmx_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                         gmx_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                       gmx_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                       gmx_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                  gmx_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     PS("ns-type",ENS(ir->ns_type));
 524     PI("nstlist",ir->nstlist);
 525     PI("ndelta",ir->ndelta);
 526     PI("nstcomm",ir->nstcomm);
 527     PS("comm-mode",ECOM(ir->comm_mode));
 528     PI("nstlog",ir->nstlog);
 529     PI("nstxout",ir->nstxout);
 530     PI("nstvout",ir->nstvout);
 531     PI("nstfout",ir->nstfout);
 532     PI("nstcalcenergy",ir->nstcalcenergy);
 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     PR("sc-sigma-min",ir->sc_sigma_min);
 624     PI("nstdhdl", ir->nstdhdl);
 625     PS("separate-dhdl-file", SEPDHDLFILETYPE(ir->separate_dhdl_file));
 626     PS("dhdl-derivatives", DHDLDERIVATIVESTYPE(ir->dhdl_derivatives));
 627     PI("dh-hist-size", ir->dh_hist_size);
 628     PD("dh-hist-spacing", ir->dh_hist_spacing);
 629
 630     PI("nwall",ir->nwall);
 631     PS("wall-type",EWALLTYPE(ir->wall_type));
 632     PI("wall-atomtype[0]",ir->wall_atomtype[0]);
 633     PI("wall-atomtype[1]",ir->wall_atomtype[1]);
 634     PR("wall-density[0]",ir->wall_density[0]);
 635     PR("wall-density[1]",ir->wall_density[1]);
 636     PR("wall-ewald-zfac",ir->wall_ewald_zfac);
 637
 638     PS("pull",EPULLTYPE(ir->ePull));
 639     if (ir->ePull != epullNO)
 640       pr_pull(fp,indent,ir->pull);
 641
 642     PS("disre",EDISRETYPE(ir->eDisre));
 643     PS("disre-weighting",EDISREWEIGHTING(ir->eDisreWeighting));
 644     PS("disre-mixed",BOOL(ir->bDisreMixed));
 645     PR("dr-fc",ir->dr_fc);
 646     PR("dr-tau",ir->dr_tau);
 647     PR("nstdisreout",ir->nstdisreout);
 648     PR("orires-fc",ir->orires_fc);
 649     PR("orires-tau",ir->orires_tau);
 650     PR("nstorireout",ir->nstorireout);
 651
 652     PR("dihre-fc",ir->dihre_fc);
 653
 654     PR("em-stepsize",ir->em_stepsize);
 655     PR("em-tol",ir->em_tol);
 656     PI("niter",ir->niter);
 657     PR("fc-stepsize",ir->fc_stepsize);
 658     PI("nstcgsteep",ir->nstcgsteep);
 659     PI("nbfgscorr",ir->nbfgscorr);
 660
 661     PS("ConstAlg",ECONSTRTYPE(ir->eConstrAlg));
 662     PR("shake-tol",ir->shake_tol);
 663     PI("lincs-order",ir->nProjOrder);
 664     PR("lincs-warnangle",ir->LincsWarnAngle);
 665     PI("lincs-iter",ir->nLincsIter);
 666     PR("bd-fric",ir->bd_fric);
 667     PI("ld-seed",ir->ld_seed);
 668     PR("cos-accel",ir->cos_accel);
 669     pr_matrix(fp,indent,"deform",ir->deform,bMDPformat);
 670     PI("userint1",ir->userint1);
 671     PI("userint2",ir->userint2);
 672     PI("userint3",ir->userint3);
 673     PI("userint4",ir->userint4);
 674     PR("userreal1",ir->userreal1);
 675     PR("userreal2",ir->userreal2);
 676     PR("userreal3",ir->userreal3);
 677     PR("userreal4",ir->userreal4);
 678     pr_grp_opts(fp,indent,"grpopts",&(ir->opts),bMDPformat);
 679     pr_cosine(fp,indent,"efield-x",&(ir->ex[XX]),bMDPformat);
 680     pr_cosine(fp,indent,"efield-xt",&(ir->et[XX]),bMDPformat);
 681     pr_cosine(fp,indent,"efield-y",&(ir->ex[YY]),bMDPformat);
 682     pr_cosine(fp,indent,"efield-yt",&(ir->et[YY]),bMDPformat);
 683     pr_cosine(fp,indent,"efield-z",&(ir->ex[ZZ]),bMDPformat);
 684     pr_cosine(fp,indent,"efield-zt",&(ir->et[ZZ]),bMDPformat);
 685     PS("bQMMM",BOOL(ir->bQMMM));
 686     PI("QMconstraints",ir->QMconstraints);
 687     PI("QMMMscheme",ir->QMMMscheme);
 688     PR("scalefactor",ir->scalefactor);
 689     pr_qm_opts(fp,indent,"qm-opts",&(ir->opts));
 690   }
 691 }
 692 #undef PS
 693 #undef PR
 694 #undef PI
 695
 696 static void pr_harm(FILE *fp,t_iparams *iparams,const char *r,const char *kr)
 697 {
 698   fprintf(fp,"%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e\n",
 699           r,iparams->harmonic.rA,kr,iparams->harmonic.krA,
 700           r,iparams->harmonic.rB,kr,iparams->harmonic.krB);
 701 }
 702
 703 void pr_iparams(FILE *fp,t_functype ftype,t_iparams *iparams)
 704 {
 705   int i;
 706   real VA[4],VB[4],*rbcA,*rbcB;
 707
 708   switch (ftype) {
 709   case F_ANGLES:
 710   case F_G96ANGLES:
 711     pr_harm(fp,iparams,"th","ct");
 712     break;
 713   case F_CROSS_BOND_BONDS:
 714     fprintf(fp,"r1e=%15.8e, r2e=%15.8e, krr=%15.8e\n",
 715             iparams->cross_bb.r1e,iparams->cross_bb.r2e,
 716             iparams->cross_bb.krr);
 717     break;
 718   case F_CROSS_BOND_ANGLES:
 719     fprintf(fp,"r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e\n",
 720             iparams->cross_ba.r1e,iparams->cross_ba.r2e,
 721             iparams->cross_ba.r3e,iparams->cross_ba.krt);
 722     break;
 723   case F_UREY_BRADLEY:
 724     fprintf(fp,"theta=%15.8e, ktheta=%15.8e, r13=%15.8e, kUB=%15.8e\n",
 725             iparams->u_b.theta,iparams->u_b.ktheta,iparams->u_b.r13,iparams->u_b.kUB);
 726     break;
 727   case F_QUARTIC_ANGLES:
 728     fprintf(fp,"theta=%15.8e",iparams->qangle.theta);
 729     for(i=0; i<5; i++)
 730       fprintf(fp,", c%c=%15.8e",'0'+i,iparams->qangle.c[i]);
 731     fprintf(fp,"\n");
 732     break;
 733   case F_BHAM:
 734     fprintf(fp,"a=%15.8e, b=%15.8e, c=%15.8e\n",
 735             iparams->bham.a,iparams->bham.b,iparams->bham.c);
 736     break;
 737   case F_BONDS:
 738   case F_G96BONDS:
 739   case F_HARMONIC:
 740     pr_harm(fp,iparams,"b0","cb");
 741     break;
 742   case F_IDIHS:
 743     pr_harm(fp,iparams,"xi","cx");
 744     break;
 745   case F_MORSE:
 746     fprintf(fp,"b0=%15.8e, cb=%15.8e, beta=%15.8e\n",
 747             iparams->morse.b0,iparams->morse.cb,iparams->morse.beta);
 748     break;
 749   case F_CUBICBONDS:
 750     fprintf(fp,"b0=%15.8e, kb=%15.8e, kcub=%15.8e\n",
 751             iparams->cubic.b0,iparams->cubic.kb,iparams->cubic.kcub);
 752     break;
 753   case F_CONNBONDS:
 754     fprintf(fp,"\n");
 755     break;
 756   case F_FENEBONDS:
 757     fprintf(fp,"bm=%15.8e, kb=%15.8e\n",iparams->fene.bm,iparams->fene.kb);
 758     break;
 759   case F_RESTRBONDS:
 760       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",
 761               iparams->restraint.lowA,iparams->restraint.up1A,
 762               iparams->restraint.up2A,iparams->restraint.kA,
 763               iparams->restraint.lowB,iparams->restraint.up1B,
 764               iparams->restraint.up2B,iparams->restraint.kB);
 765       break;
 766   case F_TABBONDS:
 767   case F_TABBONDSNC:
 768   case F_TABANGLES:
 769   case F_TABDIHS:
 770     fprintf(fp,"tab=%d, kA=%15.8e, kB=%15.8e\n",
 771             iparams->tab.table,iparams->tab.kA,iparams->tab.kB);
 772     break;
 773   case F_POLARIZATION:
 774     fprintf(fp,"alpha=%15.8e\n",iparams->polarize.alpha);
 775     break;
 776   case F_THOLE_POL:
 777     fprintf(fp,"a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e\n",
 778             iparams->thole.a,iparams->thole.alpha1,iparams->thole.alpha2,
 779             iparams->thole.rfac);
 780     break;
 781   case F_WATER_POL:
 782     fprintf(fp,"al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f\n",
 783             iparams->wpol.al_x,iparams->wpol.al_y,iparams->wpol.al_z,
 784             iparams->wpol.rOH,iparams->wpol.rHH,iparams->wpol.rOD);
 785     break;
 786   case F_LJ:
 787     fprintf(fp,"c6=%15.8e, c12=%15.8e\n",iparams->lj.c6,iparams->lj.c12);
 788     break;
 789   case F_LJ14:
 790     fprintf(fp,"c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e\n",
 791             iparams->lj14.c6A,iparams->lj14.c12A,
 792             iparams->lj14.c6B,iparams->lj14.c12B);
 793     break;
 794   case F_LJC14_Q:
 795     fprintf(fp,"fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
 796             iparams->ljc14.fqq,
 797             iparams->ljc14.qi,iparams->ljc14.qj,
 798             iparams->ljc14.c6,iparams->ljc14.c12);
 799     break;
 800   case F_LJC_PAIRS_NB:
 801     fprintf(fp,"qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
 802             iparams->ljcnb.qi,iparams->ljcnb.qj,
 803             iparams->ljcnb.c6,iparams->ljcnb.c12);
 804     break;
 805   case F_PDIHS:
 806   case F_PIDIHS:
 807   case F_ANGRES:
 808   case F_ANGRESZ:
 809     fprintf(fp,"phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d\n",
 810             iparams->pdihs.phiA,iparams->pdihs.cpA,
 811             iparams->pdihs.phiB,iparams->pdihs.cpB,
 812             iparams->pdihs.mult);
 813     break;
 814   case F_DISRES:
 815     fprintf(fp,"label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)\n",
 816             iparams->disres.label,iparams->disres.type,
 817             iparams->disres.low,iparams->disres.up1,
 818             iparams->disres.up2,iparams->disres.kfac);
 819     break;
 820   case F_ORIRES:
 821     fprintf(fp,"ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)\n",
 822             iparams->orires.ex,iparams->orires.label,iparams->orires.power,
 823             iparams->orires.c,iparams->orires.obs,iparams->orires.kfac);
 824     break;
 825   case F_DIHRES:
 826     fprintf(fp,"label=%d, power=%4d phi=%15.8e, dphi=%15.8e, kfac=%15.8e)\n",
 827             iparams->dihres.label,iparams->dihres.power,
 828             iparams->dihres.phi,iparams->dihres.dphi,iparams->dihres.kfac);
 829     break;
 830   case F_POSRES:
 831     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",
 832             iparams->posres.pos0A[XX],iparams->posres.pos0A[YY],
 833             iparams->posres.pos0A[ZZ],iparams->posres.fcA[XX],
 834             iparams->posres.fcA[YY],iparams->posres.fcA[ZZ],
 835             iparams->posres.pos0B[XX],iparams->posres.pos0B[YY],
 836             iparams->posres.pos0B[ZZ],iparams->posres.fcB[XX],
 837             iparams->posres.fcB[YY],iparams->posres.fcB[ZZ]);
 838     break;
 839   case F_RBDIHS:
 840     for (i=0; i<NR_RBDIHS; i++)
 841       fprintf(fp,"%srbcA[%d]=%15.8e",i==0?"":", ",i,iparams->rbdihs.rbcA[i]);
 842     fprintf(fp,"\n");
 843     for (i=0; i<NR_RBDIHS; i++)
 844       fprintf(fp,"%srbcB[%d]=%15.8e",i==0?"":", ",i,iparams->rbdihs.rbcB[i]);
 845     fprintf(fp,"\n");
 846     break;
 847   case F_FOURDIHS:
 848     /* Use the OPLS -> Ryckaert-Bellemans formula backwards to get the
 849      * OPLS potential constants back.
 850      */
 851     rbcA = iparams->rbdihs.rbcA;
 852     rbcB = iparams->rbdihs.rbcB;
 853
 854     VA[3] = -0.25*rbcA[4];
 855     VA[2] = -0.5*rbcA[3];
 856     VA[1] = 4.0*VA[3]-rbcA[2];
 857     VA[0] = 3.0*VA[2]-2.0*rbcA[1];
 858
 859     VB[3] = -0.25*rbcB[4];
 860     VB[2] = -0.5*rbcB[3];
 861     VB[1] = 4.0*VB[3]-rbcB[2];
 862     VB[0] = 3.0*VB[2]-2.0*rbcB[1];
 863
 864     for (i=0; i<NR_FOURDIHS; i++)
 865       fprintf(fp,"%sFourA[%d]=%15.8e",i==0?"":", ",i,VA[i]);
 866     fprintf(fp,"\n");
 867     for (i=0; i<NR_FOURDIHS; i++)
 868       fprintf(fp,"%sFourB[%d]=%15.8e",i==0?"":", ",i,VB[i]);
 869     fprintf(fp,"\n");
 870     break;
 871
 872   case F_CONSTR:
 873   case F_CONSTRNC:
 874     fprintf(fp,"dA=%15.8e, dB=%15.8e\n",iparams->constr.dA,iparams->constr.dB);
 875     break;
 876   case F_SETTLE:
 877     fprintf(fp,"doh=%15.8e, dhh=%15.8e\n",iparams->settle.doh,
 878             iparams->settle.dhh);
 879     break;
 880   case F_VSITE2:
 881     fprintf(fp,"a=%15.8e\n",iparams->vsite.a);
 882     break;
 883   case F_VSITE3:
 884   case F_VSITE3FD:
 885   case F_VSITE3FAD:
 886     fprintf(fp,"a=%15.8e, b=%15.8e\n",iparams->vsite.a,iparams->vsite.b);
 887     break;
 888   case F_VSITE3OUT:
 889   case F_VSITE4FD:
 890   case F_VSITE4FDN:
 891     fprintf(fp,"a=%15.8e, b=%15.8e, c=%15.8e\n",
 892             iparams->vsite.a,iparams->vsite.b,iparams->vsite.c);
 893     break;
 894   case F_VSITEN:
 895     fprintf(fp,"n=%2d, a=%15.8e\n",iparams->vsiten.n,iparams->vsiten.a);
 896     break;
 897   case F_GB12:
 898   case F_GB13:
 899   case F_GB14:
 900     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);
 901     break;
 902   case F_CMAP:
 903     fprintf(fp, "cmapA=%1d, cmapB=%1d\n",iparams->cmap.cmapA, iparams->cmap.cmapB);
 904     break;
 905   default:
 906     gmx_fatal(FARGS,"unknown function type %d (%s) in %s line %d",
 907               ftype,interaction_function[ftype].name,__FILE__,__LINE__);
 908   }
 909 }
 910
 911 void pr_ilist(FILE *fp,int indent,const char *title,
 912               t_functype *functype,t_ilist *ilist, gmx_bool bShowNumbers)
 913 {
 914     int i,j,k,type,ftype;
 915     t_iatom *iatoms;
 916
 917     if (available(fp,ilist,indent,title) && ilist->nr > 0)
 918     {
 919         indent=pr_title(fp,indent,title);
 920         (void) pr_indent(fp,indent);
 921         fprintf(fp,"nr: %d\n",ilist->nr);
 922         if (ilist->nr > 0) {
 923             (void) pr_indent(fp,indent);
 924             fprintf(fp,"iatoms:\n");
 925             iatoms=ilist->iatoms;
 926             for (i=j=0; i<ilist->nr;) {
 927 #ifndef DEBUG
 928                 (void) pr_indent(fp,indent+INDENT);
 929                 type=*(iatoms++);
 930                 ftype=functype[type];
 931                 (void) fprintf(fp,"%d type=%d (%s)",
 932                                bShowNumbers?j:-1,bShowNumbers?type:-1,
 933                                interaction_function[ftype].name);
 934                 j++;
 935                 for (k=0; k<interaction_function[ftype].nratoms; k++)
 936                     (void) fprintf(fp," %u",*(iatoms++));
 937                 (void) fprintf(fp,"\n");
 938                 i+=1+interaction_function[ftype].nratoms;
 939 #else
 940                 fprintf(fp,"%5d%5d\n",i,iatoms[i]);
 941                 i++;
 942 #endif
 943             }
 944         }
 945     }
 946 }
 947
 948 static void pr_cmap(FILE *fp, int indent, const char *title,
 949                     gmx_cmap_t *cmap_grid, gmx_bool bShowNumbers)
 950 {
 951     int i,j,nelem;
 952     real dx,idx;
 953
 954     dx    = 360.0 / cmap_grid->grid_spacing;
 955     nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
 956
 957     if(available(fp,cmap_grid,indent,title))
 958     {
 959         fprintf(fp,"%s\n",title);
 960
 961         for(i=0;i<cmap_grid->ngrid;i++)
 962         {
 963             idx = -180.0;
 964             fprintf(fp,"%8s %8s %8s %8s\n","V","dVdx","dVdy","d2dV");
 965
 966             fprintf(fp,"grid[%3d]={\n",bShowNumbers?i:-1);
 967
 968             for(j=0;j<nelem;j++)
 969             {
 970                 if( (j%cmap_grid->grid_spacing)==0)
 971                 {
 972                     fprintf(fp,"%8.1f\n",idx);
 973                     idx+=dx;
 974                 }
 975
 976                 fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4]);
 977                 fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4+1]);
 978                 fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4+2]);
 979                 fprintf(fp,"%8.3f\n",cmap_grid->cmapdata[i].cmap[j*4+3]);
 980             }
 981             fprintf(fp,"\n");
 982         }
 983     }
 984
 985 }
 986
 987 void pr_ffparams(FILE *fp,int indent,const char *title,
 988                  gmx_ffparams_t *ffparams,
 989                  gmx_bool bShowNumbers)
 990 {
 991   int i,j;
 992
 993   indent=pr_title(fp,indent,title);
 994   (void) pr_indent(fp,indent);
 995   (void) fprintf(fp,"atnr=%d\n",ffparams->atnr);
 996   (void) pr_indent(fp,indent);
 997   (void) fprintf(fp,"ntypes=%d\n",ffparams->ntypes);
 998   for (i=0; i<ffparams->ntypes; i++) {
 999       (void) pr_indent(fp,indent+INDENT);
1000       (void) fprintf(fp,"functype[%d]=%s, ",
1001                      bShowNumbers?i:-1,
1002                      interaction_function[ffparams->functype[i]].name);
1003       pr_iparams(fp,ffparams->functype[i],&ffparams->iparams[i]);
1004   }
1005   (void) pr_double(fp,indent,"reppow",ffparams->reppow);
1006   (void) pr_real(fp,indent,"fudgeQQ",ffparams->fudgeQQ);
1007   pr_cmap(fp,indent,"cmap",&ffparams->cmap_grid,bShowNumbers);
1008 }
1009
1010 void pr_idef(FILE *fp,int indent,const char *title,t_idef *idef, gmx_bool bShowNumbers)
1011 {
1012   int i,j;
1013
1014   if (available(fp,idef,indent,title)) {
1015     indent=pr_title(fp,indent,title);
1016     (void) pr_indent(fp,indent);
1017     (void) fprintf(fp,"atnr=%d\n",idef->atnr);
1018     (void) pr_indent(fp,indent);
1019     (void) fprintf(fp,"ntypes=%d\n",idef->ntypes);
1020     for (i=0; i<idef->ntypes; i++) {
1021       (void) pr_indent(fp,indent+INDENT);
1022       (void) fprintf(fp,"functype[%d]=%s, ",
1023                      bShowNumbers?i:-1,
1024                      interaction_function[idef->functype[i]].name);
1025       pr_iparams(fp,idef->functype[i],&idef->iparams[i]);
1026     }
1027     (void) pr_real(fp,indent,"fudgeQQ",idef->fudgeQQ);
1028
1029     for(j=0; (j<F_NRE); j++)
1030       pr_ilist(fp,indent,interaction_function[j].longname,
1031                idef->functype,&idef->il[j],bShowNumbers);
1032   }
1033 }
1034
1035 static int pr_block_title(FILE *fp,int indent,const char *title,t_block *block)
1036 {
1037   int i;
1038
1039   if (available(fp,block,indent,title))
1040     {
1041       indent=pr_title(fp,indent,title);
1042       (void) pr_indent(fp,indent);
1043       (void) fprintf(fp,"nr=%d\n",block->nr);
1044     }
1045   return indent;
1046 }
1047
1048 static int pr_blocka_title(FILE *fp,int indent,const char *title,t_blocka *block)
1049 {
1050   int i;
1051
1052   if (available(fp,block,indent,title))
1053     {
1054       indent=pr_title(fp,indent,title);
1055       (void) pr_indent(fp,indent);
1056       (void) fprintf(fp,"nr=%d\n",block->nr);
1057       (void) pr_indent(fp,indent);
1058       (void) fprintf(fp,"nra=%d\n",block->nra);
1059     }
1060   return indent;
1061 }
1062
1063 static void low_pr_block(FILE *fp,int indent,const char *title,t_block *block, gmx_bool bShowNumbers)
1064 {
1065   int i;
1066
1067   if (available(fp,block,indent,title))
1068     {
1069       indent=pr_block_title(fp,indent,title,block);
1070       for (i=0; i<=block->nr; i++)
1071         {
1072           (void) pr_indent(fp,indent+INDENT);
1073           (void) fprintf(fp,"%s->index[%d]=%u\n",
1074                          title,bShowNumbers?i:-1,block->index[i]);
1075         }
1076     }
1077 }
1078
1079 static void low_pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block, gmx_bool bShowNumbers)
1080 {
1081   int i;
1082
1083   if (available(fp,block,indent,title))
1084     {
1085       indent=pr_blocka_title(fp,indent,title,block);
1086       for (i=0; i<=block->nr; i++)
1087         {
1088           (void) pr_indent(fp,indent+INDENT);
1089           (void) fprintf(fp,"%s->index[%d]=%u\n",
1090                          title,bShowNumbers?i:-1,block->index[i]);
1091         }
1092       for (i=0; i<block->nra; i++)
1093         {
1094           (void) pr_indent(fp,indent+INDENT);
1095           (void) fprintf(fp,"%s->a[%d]=%u\n",
1096                          title,bShowNumbers?i:-1,block->a[i]);
1097         }
1098     }
1099 }
1100
1101 void pr_block(FILE *fp,int indent,const char *title,t_block *block,gmx_bool bShowNumbers)
1102 {
1103   int i,j,ok,size,start,end;
1104
1105   if (available(fp,block,indent,title))
1106     {
1107       indent=pr_block_title(fp,indent,title,block);
1108       start=0;
1109       end=start;
1110       if ((ok=(block->index[start]==0))==0)
1111         (void) fprintf(fp,"block->index[%d] should be 0\n",start);
1112       else
1113         for (i=0; i<block->nr; i++)
1114           {
1115             end=block->index[i+1];
1116             size=pr_indent(fp,indent);
1117             if (end<=start)
1118               size+=fprintf(fp,"%s[%d]={}\n",title,i);
1119             else
1120               size+=fprintf(fp,"%s[%d]={%d..%d}\n",
1121                             title,bShowNumbers?i:-1,
1122                             bShowNumbers?start:-1,bShowNumbers?end-1:-1);
1123             start=end;
1124           }
1125     }
1126 }
1127
1128 void pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block,gmx_bool bShowNumbers)
1129 {
1130   int i,j,ok,size,start,end;
1131
1132   if (available(fp,block,indent,title))
1133     {
1134       indent=pr_blocka_title(fp,indent,title,block);
1135       start=0;
1136       end=start;
1137       if ((ok=(block->index[start]==0))==0)
1138         (void) fprintf(fp,"block->index[%d] should be 0\n",start);
1139       else
1140         for (i=0; i<block->nr; i++)
1141           {
1142             end=block->index[i+1];
1143             size=pr_indent(fp,indent);
1144             if (end<=start)
1145               size+=fprintf(fp,"%s[%d]={",title,i);
1146             else
1147               size+=fprintf(fp,"%s[%d][%d..%d]={",
1148                             title,bShowNumbers?i:-1,
1149                             bShowNumbers?start:-1,bShowNumbers?end-1:-1);
1150             for (j=start; j<end; j++)
1151               {
1152                 if (j>start) size+=fprintf(fp,", ");
1153                 if ((size)>(USE_WIDTH))
1154                   {
1155                     (void) fprintf(fp,"\n");
1156                     size=pr_indent(fp,indent+INDENT);
1157                   }
1158                 size+=fprintf(fp,"%u",block->a[j]);
1159               }
1160             (void) fprintf(fp,"}\n");
1161             start=end;
1162           }
1163       if ((end!=block->nra)||(!ok))
1164         {
1165           (void) pr_indent(fp,indent);
1166           (void) fprintf(fp,"tables inconsistent, dumping complete tables:\n");
1167           low_pr_blocka(fp,indent,title,block,bShowNumbers);
1168         }
1169     }
1170 }
1171
1172 static void pr_strings(FILE *fp,int indent,const char *title,char ***nm,int n, gmx_bool bShowNumbers)
1173 {
1174   int i;
1175
1176   if (available(fp,nm,indent,title))
1177     {
1178       indent=pr_title_n(fp,indent,title,n);
1179       for (i=0; i<n; i++)
1180         {
1181           (void) pr_indent(fp,indent);
1182           (void) fprintf(fp,"%s[%d]={name=\"%s\"}\n",
1183                          title,bShowNumbers?i:-1,*(nm[i]));
1184         }
1185     }
1186 }
1187
1188 static void pr_strings2(FILE *fp,int indent,const char *title,
1189                         char ***nm,char ***nmB,int n, gmx_bool bShowNumbers)
1190 {
1191   int i;
1192
1193   if (available(fp,nm,indent,title))
1194     {
1195       indent=pr_title_n(fp,indent,title,n);
1196       for (i=0; i<n; i++)
1197         {
1198           (void) pr_indent(fp,indent);
1199           (void) fprintf(fp,"%s[%d]={name=\"%s\",nameB=\"%s\"}\n",
1200                          title,bShowNumbers?i:-1,*(nm[i]),*(nmB[i]));
1201         }
1202     }
1203 }
1204
1205 static void pr_resinfo(FILE *fp,int indent,const char *title,t_resinfo *resinfo,int n, gmx_bool bShowNumbers)
1206 {
1207     int i;
1208
1209     if (available(fp,resinfo,indent,title))
1210     {
1211         indent=pr_title_n(fp,indent,title,n);
1212         for (i=0; i<n; i++)
1213         {
1214             (void) pr_indent(fp,indent);
1215             (void) fprintf(fp,"%s[%d]={name=\"%s\", nr=%d, ic='%c'}\n",
1216                            title,bShowNumbers?i:-1,
1217                            *(resinfo[i].name),resinfo[i].nr,
1218                            (resinfo[i].ic == '\0') ? ' ' : resinfo[i].ic);
1219         }
1220     }
1221 }
1222
1223 static void pr_atom(FILE *fp,int indent,const char *title,t_atom *atom,int n)
1224 {
1225   int i,j;
1226
1227   if (available(fp,atom,indent,title)) {
1228     indent=pr_title_n(fp,indent,title,n);
1229     for (i=0; i<n; i++) {
1230       (void) pr_indent(fp,indent);
1231       fprintf(fp,"%s[%6d]={type=%3d, typeB=%3d, ptype=%8s, m=%12.5e, "
1232               "q=%12.5e, mB=%12.5e, qB=%12.5e, resind=%5d, atomnumber=%3d}\n",
1233               title,i,atom[i].type,atom[i].typeB,ptype_str[atom[i].ptype],
1234               atom[i].m,atom[i].q,atom[i].mB,atom[i].qB,
1235               atom[i].resind,atom[i].atomnumber);
1236     }
1237   }
1238 }
1239
1240 static void pr_grps(FILE *fp,int indent,const char *title,t_grps grps[],
1241                     char **grpname[], gmx_bool bShowNumbers)
1242 {
1243     int i,j;
1244
1245     for(i=0; (i<egcNR); i++)
1246     {
1247         fprintf(fp,"%s[%-12s] nr=%d, name=[",title,gtypes[i],grps[i].nr);
1248         for(j=0; (j<grps[i].nr); j++)
1249         {
1250             fprintf(fp," %s",*(grpname[grps[i].nm_ind[j]]));
1251         }
1252         fprintf(fp,"]\n");
1253     }
1254 }
1255
1256 static void pr_groups(FILE *fp,int indent,const char *title,
1257                       gmx_groups_t *groups,
1258                       gmx_bool bShowNumbers)
1259 {
1260     int grpnr[egcNR];
1261     int nat_max,i,g;
1262
1263     pr_grps(fp,indent,"grp",groups->grps,groups->grpname,bShowNumbers);
1264     pr_strings(fp,indent,"grpname",groups->grpname,groups->ngrpname,bShowNumbers);
1265
1266     (void) pr_indent(fp,indent);
1267     fprintf(fp,"groups          ");
1268     for(g=0; g<egcNR; g++)
1269     {
1270        printf(" %5.5s",gtypes[g]);
1271     }
1272     printf("\n");
1273
1274     (void) pr_indent(fp,indent);
1275     fprintf(fp,"allocated       ");
1276     nat_max = 0;
1277     for(g=0; g<egcNR; g++)
1278     {
1279         printf(" %5d",groups->ngrpnr[g]);
1280         nat_max = max(nat_max,groups->ngrpnr[g]);
1281     }
1282     printf("\n");
1283
1284     if (nat_max == 0)
1285     {
1286         (void) pr_indent(fp,indent);
1287         fprintf(fp,"groupnr[%5s] =","*");
1288         for(g=0; g<egcNR; g++)
1289         {
1290             fprintf(fp,"  %3d ",0);
1291         }
1292         fprintf(fp,"\n");
1293     }
1294     else
1295     {
1296         for(i=0; i<nat_max; i++)
1297         {
1298             (void) pr_indent(fp,indent);
1299             fprintf(fp,"groupnr[%5d] =",i);
1300             for(g=0; g<egcNR; g++)
1301             {
1302                 fprintf(fp,"  %3d ",
1303                         groups->grpnr[g] ? groups->grpnr[g][i] : 0);
1304             }
1305             fprintf(fp,"\n");
1306         }
1307     }
1308 }
1309
1310 void pr_atoms(FILE *fp,int indent,const char *title,t_atoms *atoms,
1311               gmx_bool bShownumbers)
1312 {
1313   if (available(fp,atoms,indent,title))
1314     {
1315       indent=pr_title(fp,indent,title);
1316       pr_atom(fp,indent,"atom",atoms->atom,atoms->nr);
1317       pr_strings(fp,indent,"atom",atoms->atomname,atoms->nr,bShownumbers);
1318       pr_strings2(fp,indent,"type",atoms->atomtype,atoms->atomtypeB,atoms->nr,bShownumbers);
1319       pr_resinfo(fp,indent,"residue",atoms->resinfo,atoms->nres,bShownumbers);
1320     }
1321 }
1322
1323
1324 void pr_atomtypes(FILE *fp,int indent,const char *title,t_atomtypes *atomtypes,
1325                   gmx_bool bShowNumbers)
1326 {
1327   int i;
1328   if (available(fp,atomtypes,indent,title))
1329   {
1330     indent=pr_title(fp,indent,title);
1331     for(i=0;i<atomtypes->nr;i++) {
1332       pr_indent(fp,indent);
1333                 fprintf(fp,
1334                                 "atomtype[%3d]={radius=%12.5e, volume=%12.5e, gb_radius=%12.5e, surftens=%12.5e, atomnumber=%4d, S_hct=%12.5e)}\n",
1335                                 bShowNumbers?i:-1,atomtypes->radius[i],atomtypes->vol[i],
1336                                 atomtypes->gb_radius[i],
1337                                 atomtypes->surftens[i],atomtypes->atomnumber[i],atomtypes->S_hct[i]);
1338     }
1339   }
1340 }
1341
1342 static void pr_moltype(FILE *fp,int indent,const char *title,
1343                        gmx_moltype_t *molt,int n,
1344                        gmx_ffparams_t *ffparams,
1345                        gmx_bool bShowNumbers)
1346 {
1347     int j;
1348
1349     indent = pr_title_n(fp,indent,title,n);
1350     (void) pr_indent(fp,indent);
1351     (void) fprintf(fp,"name=\"%s\"\n",*(molt->name));
1352     pr_atoms(fp,indent,"atoms",&(molt->atoms),bShowNumbers);
1353     pr_block(fp,indent,"cgs",&molt->cgs, bShowNumbers);
1354     pr_blocka(fp,indent,"excls",&molt->excls, bShowNumbers);
1355     for(j=0; (j<F_NRE); j++) {
1356         pr_ilist(fp,indent,interaction_function[j].longname,
1357                  ffparams->functype,&molt->ilist[j],bShowNumbers);
1358     }
1359 }
1360
1361 static void pr_molblock(FILE *fp,int indent,const char *title,
1362                         gmx_molblock_t *molb,int n,
1363                         gmx_moltype_t *molt,
1364                         gmx_bool bShowNumbers)
1365 {
1366     indent = pr_title_n(fp,indent,title,n);
1367     (void) pr_indent(fp,indent);
1368     (void) fprintf(fp,"%-20s = %d \"%s\"\n",
1369                    "moltype",molb->type,*(molt[molb->type].name));
1370     pr_int(fp,indent,"#molecules",molb->nmol);
1371     pr_int(fp,indent,"#atoms_mol",molb->natoms_mol);
1372     pr_int(fp,indent,"#posres_xA",molb->nposres_xA);
1373     if (molb->nposres_xA > 0) {
1374         pr_rvecs(fp,indent,"posres_xA",molb->posres_xA,molb->nposres_xA);
1375     }
1376     pr_int(fp,indent,"#posres_xB",molb->nposres_xB);
1377     if (molb->nposres_xB > 0) {
1378         pr_rvecs(fp,indent,"posres_xB",molb->posres_xB,molb->nposres_xB);
1379     }
1380 }
1381
1382 void pr_mtop(FILE *fp,int indent,const char *title,gmx_mtop_t *mtop,
1383              gmx_bool bShowNumbers)
1384 {
1385     int mt,mb;
1386
1387     if (available(fp,mtop,indent,title)) {
1388         indent=pr_title(fp,indent,title);
1389         (void) pr_indent(fp,indent);
1390         (void) fprintf(fp,"name=\"%s\"\n",*(mtop->name));
1391         pr_int(fp,indent,"#atoms",mtop->natoms);
1392         for(mb=0; mb<mtop->nmolblock; mb++) {
1393             pr_molblock(fp,indent,"molblock",&mtop->molblock[mb],mb,
1394                         mtop->moltype,bShowNumbers);
1395         }
1396         pr_ffparams(fp,indent,"ffparams",&(mtop->ffparams),bShowNumbers);
1397         pr_atomtypes(fp,indent,"atomtypes",&(mtop->atomtypes),bShowNumbers);
1398         for(mt=0; mt<mtop->nmoltype; mt++) {
1399             pr_moltype(fp,indent,"moltype",&mtop->moltype[mt],mt,
1400                        &mtop->ffparams,bShowNumbers);
1401         }
1402         pr_groups(fp,indent,"groups",&mtop->groups,bShowNumbers);
1403     }
1404 }
1405
1406 void pr_top(FILE *fp,int indent,const char *title,t_topology *top, gmx_bool bShowNumbers)
1407 {
1408   if (available(fp,top,indent,title)) {
1409     indent=pr_title(fp,indent,title);
1410     (void) pr_indent(fp,indent);
1411     (void) fprintf(fp,"name=\"%s\"\n",*(top->name));
1412     pr_atoms(fp,indent,"atoms",&(top->atoms),bShowNumbers);
1413     pr_atomtypes(fp,indent,"atomtypes",&(top->atomtypes),bShowNumbers);
1414     pr_block(fp,indent,"cgs",&top->cgs, bShowNumbers);
1415     pr_block(fp,indent,"mols",&top->mols, bShowNumbers);
1416     pr_blocka(fp,indent,"excls",&top->excls, bShowNumbers);
1417     pr_idef(fp,indent,"idef",&top->idef,bShowNumbers);
1418   }
1419 }
1420
1421 void pr_header(FILE *fp,int indent,const char *title,t_tpxheader *sh)
1422 {
1423   char buf[22];
1424
1425   if (available(fp,sh,indent,title))
1426     {
1427       indent=pr_title(fp,indent,title);
1428       pr_indent(fp,indent);
1429       fprintf(fp,"bIr    = %spresent\n",sh->bIr?"":"not ");
1430       pr_indent(fp,indent);
1431       fprintf(fp,"bBox   = %spresent\n",sh->bBox?"":"not ");
1432       pr_indent(fp,indent);
1433       fprintf(fp,"bTop   = %spresent\n",sh->bTop?"":"not ");
1434       pr_indent(fp,indent);
1435       fprintf(fp,"bX     = %spresent\n",sh->bX?"":"not ");
1436       pr_indent(fp,indent);
1437       fprintf(fp,"bV     = %spresent\n",sh->bV?"":"not ");
1438       pr_indent(fp,indent);
1439       fprintf(fp,"bF     = %spresent\n",sh->bF?"":"not ");
1440
1441       pr_indent(fp,indent);
1442       fprintf(fp,"natoms = %d\n",sh->natoms);
1443       pr_indent(fp,indent);
1444       fprintf(fp,"lambda = %e\n",sh->lambda);
1445     }
1446 }
1447
1448 void pr_commrec(FILE *fp,int indent,t_commrec *cr)
1449 {
1450   pr_indent(fp,indent);
1451   fprintf(fp,"commrec:\n");
1452   indent+=2;
1453   pr_indent(fp,indent);
1454   fprintf(fp,"nodeid    = %d\n",cr->nodeid);
1455   pr_indent(fp,indent);
1456   fprintf(fp,"nnodes    = %d\n",cr->nnodes);
1457   pr_indent(fp,indent);
1458   fprintf(fp,"npmenodes = %d\n",cr->npmenodes);
1459   /*
1460   pr_indent(fp,indent);
1461   fprintf(fp,"threadid  = %d\n",cr->threadid);
1462   pr_indent(fp,indent);
1463   fprintf(fp,"nthreads  = %d\n",cr->nthreads);
1464   */
1465 }