src/gromacs/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 -
  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
  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_THREAD_MPI
  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 #include "macros.h"
  54
  55
  56 int pr_indent(FILE *fp,int n)
  57 {
  58   int i;
  59
  60   for (i=0; i<n; i++) (void) fprintf(fp," ");
  61   return n;
  62 }
  63
  64 int available(FILE *fp,void *p,int indent,const char *title)
  65 {
  66   if (!p) {
  67     if (indent > 0)
  68       pr_indent(fp,indent);
  69     (void) fprintf(fp,"%s: not available\n",title);
  70   }
  71   return (p!=NULL);
  72 }
  73
  74 int pr_title(FILE *fp,int indent,const char *title)
  75 {
  76   (void) pr_indent(fp,indent);
  77   (void) fprintf(fp,"%s:\n",title);
  78   return (indent+INDENT);
  79 }
  80
  81 int pr_title_n(FILE *fp,int indent,const char *title,int n)
  82 {
  83   (void) pr_indent(fp,indent);
  84   (void) fprintf(fp,"%s (%d):\n",title,n);
  85   return (indent+INDENT);
  86 }
  87
  88 int pr_title_nxn(FILE *fp,int indent,const char *title,int n1,int n2)
  89 {
  90   (void) pr_indent(fp,indent);
  91   (void) fprintf(fp,"%s (%dx%d):\n",title,n1,n2);
  92   return (indent+INDENT);
  93 }
  94
  95 void pr_ivec(FILE *fp,int indent,const char *title,int vec[],int n, gmx_bool bShowNumbers)
  96 {
  97   int i;
  98
  99   if (available(fp,vec,indent,title))
 100     {
 101       indent=pr_title_n(fp,indent,title,n);
 102       for (i=0; i<n; i++)
 103         {
 104           (void) pr_indent(fp,indent);
 105           (void) fprintf(fp,"%s[%d]=%d\n",title,bShowNumbers?i:-1,vec[i]);
 106         }
 107     }
 108 }
 109
 110 void pr_ivec_block(FILE *fp,int indent,const char *title,int vec[],int n, gmx_bool bShowNumbers)
 111 {
 112     int i,j;
 113
 114     if (available(fp,vec,indent,title))
 115     {
 116         indent=pr_title_n(fp,indent,title,n);
 117         i = 0;
 118         while (i < n)
 119         {
 120             j = i+1;
 121             while (j < n && vec[j] == vec[j-1]+1)
 122             {
 123                 j++;
 124             }
 125             /* Print consecutive groups of 3 or more as blocks */
 126             if (j - i < 3)
 127             {
 128                 while(i < j)
 129                 {
 130                     (void) pr_indent(fp,indent);
 131                     (void) fprintf(fp,"%s[%d]=%d\n",
 132                                    title,bShowNumbers?i:-1,vec[i]);
 133                     i++;
 134                 }
 135             }
 136             else
 137             {
 138                 (void) pr_indent(fp,indent);
 139                 (void) fprintf(fp,"%s[%d,...,%d] = {%d,...,%d}\n",
 140                                title,
 141                                bShowNumbers?i:-1,
 142                                bShowNumbers?j-1:-1,
 143                                vec[i],vec[j-1]);
 144                 i = j;
 145             }
 146         }
 147     }
 148 }
 149
 150 void pr_bvec(FILE *fp,int indent,const char *title,gmx_bool vec[],int n, gmx_bool bShowNumbers)
 151 {
 152   int i;
 153
 154   if (available(fp,vec,indent,title))
 155     {
 156       indent=pr_title_n(fp,indent,title,n);
 157       for (i=0; i<n; i++)
 158         {
 159           (void) pr_indent(fp,indent);
 160           (void) fprintf(fp,"%s[%d]=%s\n",title,bShowNumbers?i:-1,
 161                          EBOOL(vec[i]));
 162         }
 163     }
 164 }
 165
 166 void pr_ivecs(FILE *fp,int indent,const char *title,ivec vec[],int n, gmx_bool bShowNumbers)
 167 {
 168   int i,j;
 169
 170   if (available(fp,vec,indent,title))
 171     {
 172       indent=pr_title_nxn(fp,indent,title,n,DIM);
 173       for (i=0; i<n; i++)
 174         {
 175           (void) pr_indent(fp,indent);
 176           (void) fprintf(fp,"%s[%d]={",title,bShowNumbers?i:-1);
 177           for (j=0; j<DIM; j++)
 178             {
 179               if (j!=0) (void) fprintf(fp,", ");
 180               fprintf(fp,"%d",vec[i][j]);
 181             }
 182           (void) fprintf(fp,"}\n");
 183         }
 184     }
 185 }
 186
 187 void pr_rvec(FILE *fp,int indent,const char *title,real vec[],int n, gmx_bool bShowNumbers)
 188 {
 189   int i;
 190
 191   if (available(fp,vec,indent,title))
 192     {
 193       indent=pr_title_n(fp,indent,title,n);
 194       for (i=0; i<n; i++)
 195         {
 196           pr_indent(fp,indent);
 197           fprintf(fp,"%s[%d]=%12.5e\n",title,bShowNumbers?i:-1,vec[i]);
 198         }
 199     }
 200 }
 201
 202 void pr_dvec(FILE *fp,int indent,const char *title,double vec[],int n, gmx_bool bShowNumbers)
 203 {
 204         int i;
 205
 206         if (available(fp,vec,indent,title))
 207     {
 208                 indent=pr_title_n(fp,indent,title,n);
 209                 for (i=0; i<n; i++)
 210         {
 211                         pr_indent(fp,indent);
 212                         fprintf(fp,"%s[%d]=%12.5e\n",title,bShowNumbers?i:-1,vec[i]);
 213         }
 214     }
 215 }
 216
 217
 218 /*
 219 void pr_mat(FILE *fp,int indent,char *title,matrix m)
 220 {
 221   int i,j;
 222
 223   if (available(fp,m,indent,title)) {
 224     indent=pr_title_n(fp,indent,title,n);
 225     for(i=0; i<n; i++) {
 226       pr_indent(fp,indent);
 227       fprintf(fp,"%s[%d]=%12.5e %12.5e %12.5e\n",
 228               title,bShowNumbers?i:-1,m[i][XX],m[i][YY],m[i][ZZ]);
 229     }
 230   }
 231 }
 232 */
 233
 234 void pr_rvecs_len(FILE *fp,int indent,const char *title,rvec vec[],int n)
 235 {
 236   int i,j;
 237
 238   if (available(fp,vec,indent,title)) {
 239     indent=pr_title_nxn(fp,indent,title,n,DIM);
 240     for (i=0; i<n; i++) {
 241       (void) pr_indent(fp,indent);
 242       (void) fprintf(fp,"%s[%5d]={",title,i);
 243       for (j=0; j<DIM; j++) {
 244         if (j != 0)
 245           (void) fprintf(fp,", ");
 246         (void) fprintf(fp,"%12.5e",vec[i][j]);
 247       }
 248       (void) fprintf(fp,"} len=%12.5e\n",norm(vec[i]));
 249     }
 250   }
 251 }
 252
 253 void pr_rvecs(FILE *fp,int indent,const char *title,rvec vec[],int n)
 254 {
 255   const char *fshort = "%12.5e";
 256   const char *flong  = "%15.8e";
 257   const char *format;
 258   int i,j;
 259
 260   if (getenv("LONGFORMAT") != NULL)
 261     format = flong;
 262   else
 263     format = fshort;
 264
 265   if (available(fp,vec,indent,title)) {
 266     indent=pr_title_nxn(fp,indent,title,n,DIM);
 267     for (i=0; i<n; i++) {
 268       (void) pr_indent(fp,indent);
 269       (void) fprintf(fp,"%s[%5d]={",title,i);
 270       for (j=0; j<DIM; j++) {
 271         if (j != 0)
 272           (void) fprintf(fp,", ");
 273         (void) fprintf(fp,format,vec[i][j]);
 274       }
 275       (void) fprintf(fp,"}\n");
 276     }
 277   }
 278 }
 279
 280
 281 void pr_reals(FILE *fp,int indent,const char *title,real *vec,int n)
 282 {
 283   int i;
 284
 285   if (available(fp,vec,indent,title)) {
 286     (void) pr_indent(fp,indent);
 287     (void) fprintf(fp,"%s:\t",title);
 288     for(i=0; i<n; i++)
 289       fprintf(fp,"  %10g",vec[i]);
 290     (void) fprintf(fp,"\n");
 291   }
 292 }
 293
 294 void pr_doubles(FILE *fp,int indent,const char *title,double *vec,int n)
 295 {
 296   int i;
 297
 298   if (available(fp,vec,indent,title)) {
 299     (void) pr_indent(fp,indent);
 300     (void) fprintf(fp,"%s:\t",title);
 301     for(i=0; i<n; i++)
 302       fprintf(fp,"  %10g",vec[i]);
 303     (void) fprintf(fp,"\n");
 304   }
 305 }
 306
 307 static void pr_int(FILE *fp,int indent,const char *title,int i)
 308 {
 309   pr_indent(fp,indent);
 310   fprintf(fp,"%-20s = %d\n",title,i);
 311 }
 312
 313 static void pr_gmx_large_int(FILE *fp,int indent,const char *title,gmx_large_int_t i)
 314 {
 315   char buf[STEPSTRSIZE];
 316
 317   pr_indent(fp,indent);
 318   fprintf(fp,"%-20s = %s\n",title,gmx_step_str(i,buf));
 319 }
 320
 321 static void pr_real(FILE *fp,int indent,const char *title,real r)
 322 {
 323   pr_indent(fp,indent);
 324   fprintf(fp,"%-20s = %g\n",title,r);
 325 }
 326
 327 static void pr_double(FILE *fp,int indent,const char *title,double d)
 328 {
 329   pr_indent(fp,indent);
 330   fprintf(fp,"%-20s = %g\n",title,d);
 331 }
 332
 333 static void pr_str(FILE *fp,int indent,const char *title,const char *s)
 334 {
 335   pr_indent(fp,indent);
 336   fprintf(fp,"%-20s = %s\n",title,s);
 337 }
 338
 339 void pr_qm_opts(FILE *fp,int indent,const char *title,t_grpopts *opts)
 340 {
 341   int i,m,j;
 342
 343   fprintf(fp,"%s:\n",title);
 344
 345   pr_int(fp,indent,"ngQM",opts->ngQM);
 346   if (opts->ngQM > 0) {
 347     pr_ivec(fp,indent,"QMmethod",opts->QMmethod,opts->ngQM,FALSE);
 348     pr_ivec(fp,indent,"QMbasis",opts->QMbasis,opts->ngQM,FALSE);
 349     pr_ivec(fp,indent,"QMcharge",opts->QMcharge,opts->ngQM,FALSE);
 350     pr_ivec(fp,indent,"QMmult",opts->QMmult,opts->ngQM,FALSE);
 351     pr_bvec(fp,indent,"bSH",opts->bSH,opts->ngQM,FALSE);
 352     pr_ivec(fp,indent,"CASorbitals",opts->CASorbitals,opts->ngQM,FALSE);
 353     pr_ivec(fp,indent,"CASelectrons",opts->CASelectrons,opts->ngQM,FALSE);
 354     pr_rvec(fp,indent,"SAon",opts->SAon,opts->ngQM,FALSE);
 355     pr_rvec(fp,indent,"SAon",opts->SAon,opts->ngQM,FALSE);
 356     pr_ivec(fp,indent,"SAsteps",opts->SAsteps,opts->ngQM,FALSE);
 357     pr_bvec(fp,indent,"bOPT",opts->bOPT,opts->ngQM,FALSE);
 358     pr_bvec(fp,indent,"bTS",opts->bTS,opts->ngQM,FALSE);
 359   }
 360 }
 361
 362 static void pr_grp_opts(FILE *out,int indent,const char *title,t_grpopts *opts,
 363                         gmx_bool bMDPformat)
 364 {
 365   int i,m,j;
 366
 367   if (!bMDPformat)
 368     fprintf(out,"%s:\n",title);
 369
 370   pr_indent(out,indent);
 371   fprintf(out,"nrdf%s",bMDPformat ? " = " : ":");
 372   for(i=0; (i<opts->ngtc); i++)
 373     fprintf(out,"  %10g",opts->nrdf[i]);
 374   fprintf(out,"\n");
 375
 376   pr_indent(out,indent);
 377   fprintf(out,"ref-t%s",bMDPformat ? " = " : ":");
 378   for(i=0; (i<opts->ngtc); i++)
 379     fprintf(out,"  %10g",opts->ref_t[i]);
 380   fprintf(out,"\n");
 381
 382   pr_indent(out,indent);
 383   fprintf(out,"tau-t%s",bMDPformat ? " = " : ":");
 384   for(i=0; (i<opts->ngtc); i++)
 385     fprintf(out,"  %10g",opts->tau_t[i]);
 386   fprintf(out,"\n");
 387
 388   /* Pretty-print the simulated annealing info */
 389   fprintf(out,"anneal%s",bMDPformat ? " = " : ":");
 390   for(i=0; (i<opts->ngtc); i++)
 391     fprintf(out,"  %10s",EANNEAL(opts->annealing[i]));
 392   fprintf(out,"\n");
 393
 394   fprintf(out,"ann-npoints%s",bMDPformat ? " = " : ":");
 395   for(i=0; (i<opts->ngtc); i++)
 396     fprintf(out,"  %10d",opts->anneal_npoints[i]);
 397   fprintf(out,"\n");
 398
 399   for(i=0; (i<opts->ngtc); i++) {
 400     if(opts->anneal_npoints[i]>0) {
 401       fprintf(out,"ann. times [%d]:\t",i);
 402       for(j=0; (j<opts->anneal_npoints[i]); j++)
 403         fprintf(out,"  %10.1f",opts->anneal_time[i][j]);
 404       fprintf(out,"\n");
 405       fprintf(out,"ann. temps [%d]:\t",i);
 406       for(j=0; (j<opts->anneal_npoints[i]); j++)
 407         fprintf(out,"  %10.1f",opts->anneal_temp[i][j]);
 408       fprintf(out,"\n");
 409     }
 410   }
 411
 412   pr_indent(out,indent);
 413   fprintf(out,"acc:\t");
 414   for(i=0; (i<opts->ngacc); i++)
 415     for(m=0; (m<DIM); m++)
 416       fprintf(out,"  %10g",opts->acc[i][m]);
 417   fprintf(out,"\n");
 418
 419   pr_indent(out,indent);
 420   fprintf(out,"nfreeze:");
 421   for(i=0; (i<opts->ngfrz); i++)
 422     for(m=0; (m<DIM); m++)
 423       fprintf(out,"  %10s",opts->nFreeze[i][m] ? "Y" : "N");
 424   fprintf(out,"\n");
 425
 426
 427   for(i=0; (i<opts->ngener); i++) {
 428     pr_indent(out,indent);
 429     fprintf(out,"energygrp-flags[%3d]:",i);
 430     for(m=0; (m<opts->ngener); m++)
 431       fprintf(out," %d",opts->egp_flags[opts->ngener*i+m]);
 432     fprintf(out,"\n");
 433   }
 434
 435   fflush(out);
 436 }
 437
 438 static void pr_matrix(FILE *fp,int indent,const char *title,rvec *m,
 439                       gmx_bool bMDPformat)
 440 {
 441   if (bMDPformat)
 442     fprintf(fp,"%-10s    = %g %g %g %g %g %g\n",title,
 443             m[XX][XX],m[YY][YY],m[ZZ][ZZ],m[XX][YY],m[XX][ZZ],m[YY][ZZ]);
 444   else
 445     pr_rvecs(fp,indent,title,m,DIM);
 446 }
 447
 448 static void pr_cosine(FILE *fp,int indent,const char *title,t_cosines *cos,
 449                       gmx_bool bMDPformat)
 450 {
 451   int j;
 452
 453   if (bMDPformat) {
 454     fprintf(fp,"%s = %d\n",title,cos->n);
 455   }
 456   else {
 457     indent=pr_title(fp,indent,title);
 458     (void) pr_indent(fp,indent);
 459     fprintf(fp,"n = %d\n",cos->n);
 460     if (cos->n > 0) {
 461       (void) pr_indent(fp,indent+2);
 462       fprintf(fp,"a =");
 463       for(j=0; (j<cos->n); j++)
 464         fprintf(fp," %e",cos->a[j]);
 465       fprintf(fp,"\n");
 466       (void) pr_indent(fp,indent+2);
 467       fprintf(fp,"phi =");
 468       for(j=0; (j<cos->n); j++)
 469         fprintf(fp," %e",cos->phi[j]);
 470       fprintf(fp,"\n");
 471     }
 472   }
 473 }
 474
 475 #define PS(t,s) pr_str(fp,indent,t,s)
 476 #define PI(t,s) pr_int(fp,indent,t,s)
 477 #define PSTEP(t,s) pr_gmx_large_int(fp,indent,t,s)
 478 #define PR(t,s) pr_real(fp,indent,t,s)
 479 #define PD(t,s) pr_double(fp,indent,t,s)
 480
 481 static void pr_pullgrp(FILE *fp,int indent,int g,t_pullgrp *pg)
 482 {
 483   pr_indent(fp,indent);
 484   fprintf(fp,"pull-group %d:\n",g);
 485   indent += 2;
 486   pr_ivec_block(fp,indent,"atom",pg->ind,pg->nat,TRUE);
 487   pr_rvec(fp,indent,"weight",pg->weight,pg->nweight,TRUE);
 488   PI("pbcatom",pg->pbcatom);
 489   pr_rvec(fp,indent,"vec",pg->vec,DIM,TRUE);
 490   pr_rvec(fp,indent,"init",pg->init,DIM,TRUE);
 491   PR("rate",pg->rate);
 492   PR("k",pg->k);
 493   PR("kB",pg->kB);
 494 }
 495
 496 static void pr_simtempvals(FILE *fp,int indent,t_simtemp *simtemp, int n_lambda, gmx_bool bMDPformat)
 497 {
 498     PR("simtemp_low",simtemp->simtemp_low);
 499     PR("simtemp_high",simtemp->simtemp_high);
 500     PS("simulated-tempering-scaling",ESIMTEMP(simtemp->eSimTempScale));
 501     pr_rvec(fp,indent,"simulated tempering temperatures",simtemp->temperatures,n_lambda,TRUE);
 502 }
 503
 504 static void pr_expandedvals(FILE *fp,int indent,t_expanded *expand, int n_lambda, gmx_bool bMDPformat)
 505 {
 506
 507     PI("nstexpanded", expand->nstexpanded);
 508     PS("lambda-stats", elamstats_names[expand->elamstats]);
 509     PS("lambda-mc-move", elmcmove_names[expand->elmcmove]);
 510     PI("lmc-repeats",expand->lmc_repeats);
 511     PI("lmc-gibbsdelta",expand->gibbsdeltalam);
 512     PI("lmc-nstart",expand->lmc_forced_nstart);
 513     PS("symmetrized-transition-matrix", EBOOL(expand->bSymmetrizedTMatrix));
 514     PI("nst-transition-matrix",expand->nstTij);
 515     PI("mininum-var-min",expand->minvarmin); /*default is reasonable */
 516     PI("weight-c-range",expand->c_range); /* default is just C=0 */
 517     PR("wl-scale",expand->wl_scale);
 518     PR("init-wl-delta",expand->init_wl_delta);
 519     PR("wl-ratio",expand->wl_ratio);
 520     PS("bWLoneovert",EBOOL(expand->bWLoneovert));
 521     PI("lmc-seed",expand->lmc_seed);
 522     PR("mc-temperature",expand->mc_temp);
 523     PS("lmc-weights-equil",elmceq_names[expand->elmceq]);
 524     if (expand->elmceq == elmceqNUMATLAM)
 525     {
 526         PI("weight-equil-number-all-lambda",expand->equil_n_at_lam);
 527     }
 528     if (expand->elmceq == elmceqSAMPLES)
 529     {
 530         PI("weight-equil-number-samples",expand->equil_samples);
 531     }
 532     if (expand->elmceq == elmceqSTEPS)
 533     {
 534         PI("weight-equil-number-steps",expand->equil_steps);
 535     }
 536     if (expand->elmceq == elmceqWLDELTA)
 537     {
 538         PR("weight-equil-wl-delta",expand->equil_wl_delta);
 539     }
 540     if (expand->elmceq == elmceqRATIO)
 541     {
 542         PR("weight-equil-count-ratio",expand->equil_ratio);
 543     }
 544
 545     pr_indent(fp,indent);
 546     pr_rvec(fp,indent,"init-lambda-weights",expand->init_lambda_weights,n_lambda,TRUE);
 547     PS("init-weights",EBOOL(expand->bInit_weights));
 548 }
 549
 550 static void pr_fepvals(FILE *fp,int indent,t_lambda *fep, gmx_bool bMDPformat)
 551 {
 552     int i,j;
 553
 554     PI("nstdhdl",fep->nstdhdl);
 555     PI("init-lambda-state",fep->init_fep_state);
 556     PR("init-lambda",fep->init_lambda);
 557     PR("delta-lambda",fep->delta_lambda);
 558     if (!bMDPformat)
 559     {
 560         PI("n-lambdas",fep->n_lambda);
 561     }
 562     if (fep->n_lambda > 0)
 563     {
 564         pr_indent(fp,indent);
 565         fprintf(fp,"all-lambdas%s\n",bMDPformat ? " = " : ":");
 566         for(i=0; i<efptNR; i++) {
 567             fprintf(fp,"%18s = ",efpt_names[i]);
 568             for(j=0; j<fep->n_lambda; j++)
 569             {
 570                 fprintf(fp,"  %10g",fep->all_lambda[i][j]);
 571             }
 572             fprintf(fp,"\n");
 573         }
 574     }
 575
 576     PR("sc-alpha",fep->sc_alpha);
 577     PS("bScCoul",EBOOL(fep->bScCoul));
 578     PS("bScPrintEnergy",EBOOL(fep->bPrintEnergy));
 579     PI("sc-power",fep->sc_power);
 580     PR("sc-r-power",fep->sc_r_power);
 581     PR("sc-sigma",fep->sc_sigma);
 582     PR("sc-sigma-min",fep->sc_sigma_min);
 583     PS("separate-dhdl-file", SEPDHDLFILETYPE(fep->separate_dhdl_file));
 584     PS("dhdl-derivatives", DHDLDERIVATIVESTYPE(fep->dhdl_derivatives));
 585     PI("dh-hist-size", fep->dh_hist_size);
 586     PD("dh-hist-spacing", fep->dh_hist_spacing);
 587 };
 588
 589 static void pr_pull(FILE *fp,int indent,t_pull *pull)
 590 {
 591   int g;
 592
 593   PS("pull-geometry",EPULLGEOM(pull->eGeom));
 594   pr_ivec(fp,indent,"pull-dim",pull->dim,DIM,TRUE);
 595   PR("pull-r1",pull->cyl_r1);
 596   PR("pull-r0",pull->cyl_r0);
 597   PR("pull-constr-tol",pull->constr_tol);
 598   PI("pull-nstxout",pull->nstxout);
 599   PI("pull-nstfout",pull->nstfout);
 600   PI("pull-ngrp",pull->ngrp);
 601   for(g=0; g<pull->ngrp+1; g++)
 602     pr_pullgrp(fp,indent,g,&pull->grp[g]);
 603 }
 604
 605 static void pr_rotgrp(FILE *fp,int indent,int g,t_rotgrp *rotg)
 606 {
 607   pr_indent(fp,indent);
 608   fprintf(fp,"rotation_group %d:\n",g);
 609   indent += 2;
 610   PS("type",EROTGEOM(rotg->eType));
 611   PS("massw",EBOOL(rotg->bMassW));
 612   pr_ivec_block(fp,indent,"atom",rotg->ind,rotg->nat,TRUE);
 613   pr_rvecs(fp,indent,"x_ref",rotg->x_ref,rotg->nat);
 614   pr_rvec(fp,indent,"vec",rotg->vec,DIM,TRUE);
 615   pr_rvec(fp,indent,"pivot",rotg->pivot,DIM,TRUE);
 616   PR("rate",rotg->rate);
 617   PR("k",rotg->k);
 618   PR("slab_dist",rotg->slab_dist);
 619   PR("min_gaussian",rotg->min_gaussian);
 620   PR("epsilon",rotg->eps);
 621   PS("fit_method",EROTFIT(rotg->eFittype));
 622   PI("potfitangle_nstep",rotg->PotAngle_nstep);
 623   PR("potfitangle_step",rotg->PotAngle_step);
 624 }
 625
 626 static void pr_rot(FILE *fp,int indent,t_rot *rot)
 627 {
 628   int g;
 629
 630   PI("rot_nstrout",rot->nstrout);
 631   PI("rot_nstsout",rot->nstsout);
 632   PI("rot_ngrp",rot->ngrp);
 633   for(g=0; g<rot->ngrp; g++)
 634     pr_rotgrp(fp,indent,g,&rot->grp[g]);
 635 }
 636
 637 void pr_inputrec(FILE *fp,int indent,const char *title,t_inputrec *ir,
 638                  gmx_bool bMDPformat)
 639 {
 640   const char *infbuf="inf";
 641   int  i;
 642
 643   if (available(fp,ir,indent,title)) {
 644     if (!bMDPformat)
 645       indent=pr_title(fp,indent,title);
 646     PS("integrator",EI(ir->eI));
 647     PSTEP("nsteps",ir->nsteps);
 648     PSTEP("init-step",ir->init_step);
 649     PS("ns-type",ENS(ir->ns_type));
 650     PI("nstlist",ir->nstlist);
 651     PI("ndelta",ir->ndelta);
 652     PI("nstcomm",ir->nstcomm);
 653     PS("comm-mode",ECOM(ir->comm_mode));
 654     PI("nstlog",ir->nstlog);
 655     PI("nstxout",ir->nstxout);
 656     PI("nstvout",ir->nstvout);
 657     PI("nstfout",ir->nstfout);
 658     PI("nstcalcenergy",ir->nstcalcenergy);
 659     PI("nstenergy",ir->nstenergy);
 660     PI("nstxtcout",ir->nstxtcout);
 661     PR("init-t",ir->init_t);
 662     PR("delta-t",ir->delta_t);
 663
 664     PR("xtcprec",ir->xtcprec);
 665     PI("nkx",ir->nkx);
 666     PI("nky",ir->nky);
 667     PI("nkz",ir->nkz);
 668     PI("pme-order",ir->pme_order);
 669     PR("ewald-rtol",ir->ewald_rtol);
 670     PR("ewald-geometry",ir->ewald_geometry);
 671     PR("epsilon-surface",ir->epsilon_surface);
 672     PS("optimize-fft",EBOOL(ir->bOptFFT));
 673     PS("ePBC",EPBC(ir->ePBC));
 674     PS("bPeriodicMols",EBOOL(ir->bPeriodicMols));
 675     PS("bContinuation",EBOOL(ir->bContinuation));
 676     PS("bShakeSOR",EBOOL(ir->bShakeSOR));
 677     PS("etc",ETCOUPLTYPE(ir->etc));
 678     PS("bPrintNHChains",EBOOL(ir->bPrintNHChains));
 679     PI("nsttcouple",ir->nsttcouple);
 680     PS("epc",EPCOUPLTYPE(ir->epc));
 681     PS("epctype",EPCOUPLTYPETYPE(ir->epct));
 682     PI("nstpcouple",ir->nstpcouple);
 683     PR("tau-p",ir->tau_p);
 684     pr_matrix(fp,indent,"ref-p",ir->ref_p,bMDPformat);
 685     pr_matrix(fp,indent,"compress",ir->compress,bMDPformat);
 686     PS("refcoord-scaling",EREFSCALINGTYPE(ir->refcoord_scaling));
 687     if (bMDPformat)
 688       fprintf(fp,"posres-com  = %g %g %g\n",ir->posres_com[XX],
 689               ir->posres_com[YY],ir->posres_com[ZZ]);
 690     else
 691       pr_rvec(fp,indent,"posres-com",ir->posres_com,DIM,TRUE);
 692     if (bMDPformat)
 693       fprintf(fp,"posres-comB = %g %g %g\n",ir->posres_comB[XX],
 694               ir->posres_comB[YY],ir->posres_comB[ZZ]);
 695     else
 696       pr_rvec(fp,indent,"posres-comB",ir->posres_comB,DIM,TRUE);
 697     PR("rlist",ir->rlist);
 698     PR("rlistlong",ir->rlistlong);
 699     PR("rtpi",ir->rtpi);
 700     PS("coulombtype",EELTYPE(ir->coulombtype));
 701     PR("rcoulomb-switch",ir->rcoulomb_switch);
 702     PR("rcoulomb",ir->rcoulomb);
 703     PS("vdwtype",EVDWTYPE(ir->vdwtype));
 704     PR("rvdw-switch",ir->rvdw_switch);
 705     PR("rvdw",ir->rvdw);
 706     if (ir->epsilon_r != 0)
 707       PR("epsilon-r",ir->epsilon_r);
 708     else
 709       PS("epsilon-r",infbuf);
 710     if (ir->epsilon_rf != 0)
 711       PR("epsilon-rf",ir->epsilon_rf);
 712     else
 713       PS("epsilon-rf",infbuf);
 714     PR("tabext",ir->tabext);
 715     PS("implicit-solvent",EIMPLICITSOL(ir->implicit_solvent));
 716     PS("gb-algorithm",EGBALGORITHM(ir->gb_algorithm));
 717     PR("gb-epsilon-solvent",ir->gb_epsilon_solvent);
 718     PI("nstgbradii",ir->nstgbradii);
 719     PR("rgbradii",ir->rgbradii);
 720     PR("gb-saltconc",ir->gb_saltconc);
 721     PR("gb-obc-alpha",ir->gb_obc_alpha);
 722     PR("gb-obc-beta",ir->gb_obc_beta);
 723     PR("gb-obc-gamma",ir->gb_obc_gamma);
 724     PR("gb-dielectric-offset",ir->gb_dielectric_offset);
 725     PS("sa-algorithm",ESAALGORITHM(ir->gb_algorithm));
 726     PR("sa-surface-tension",ir->sa_surface_tension);
 727     PS("DispCorr",EDISPCORR(ir->eDispCorr));
 728     PS("bSimTemp",EBOOL(ir->bSimTemp));
 729     if (ir->bSimTemp) {
 730         pr_simtempvals(fp,indent,ir->simtempvals,ir->fepvals->n_lambda,bMDPformat);
 731     }
 732     PS("free-energy",EFEPTYPE(ir->efep));
 733     if (ir->efep != efepNO || ir->bSimTemp) {
 734         pr_fepvals(fp,indent,ir->fepvals,bMDPformat);
 735     }
 736     if (ir->bExpanded) {
 737         pr_expandedvals(fp,indent,ir->expandedvals,ir->fepvals->n_lambda,bMDPformat);
 738     }
 739
 740     PI("nwall",ir->nwall);
 741     PS("wall-type",EWALLTYPE(ir->wall_type));
 742     PI("wall-atomtype[0]",ir->wall_atomtype[0]);
 743     PI("wall-atomtype[1]",ir->wall_atomtype[1]);
 744     PR("wall-density[0]",ir->wall_density[0]);
 745     PR("wall-density[1]",ir->wall_density[1]);
 746     PR("wall-ewald-zfac",ir->wall_ewald_zfac);
 747
 748     PS("pull",EPULLTYPE(ir->ePull));
 749     if (ir->ePull != epullNO)
 750       pr_pull(fp,indent,ir->pull);
 751
 752     PS("rotation",EBOOL(ir->bRot));
 753     if (ir->bRot)
 754       pr_rot(fp,indent,ir->rot);
 755
 756     PS("disre",EDISRETYPE(ir->eDisre));
 757     PS("disre-weighting",EDISREWEIGHTING(ir->eDisreWeighting));
 758     PS("disre-mixed",EBOOL(ir->bDisreMixed));
 759     PR("dr-fc",ir->dr_fc);
 760     PR("dr-tau",ir->dr_tau);
 761     PR("nstdisreout",ir->nstdisreout);
 762     PR("orires-fc",ir->orires_fc);
 763     PR("orires-tau",ir->orires_tau);
 764     PR("nstorireout",ir->nstorireout);
 765
 766     PR("dihre-fc",ir->dihre_fc);
 767
 768     PR("em-stepsize",ir->em_stepsize);
 769     PR("em-tol",ir->em_tol);
 770     PI("niter",ir->niter);
 771     PR("fc-stepsize",ir->fc_stepsize);
 772     PI("nstcgsteep",ir->nstcgsteep);
 773     PI("nbfgscorr",ir->nbfgscorr);
 774
 775     PS("ConstAlg",ECONSTRTYPE(ir->eConstrAlg));
 776     PR("shake-tol",ir->shake_tol);
 777     PI("lincs-order",ir->nProjOrder);
 778     PR("lincs-warnangle",ir->LincsWarnAngle);
 779     PI("lincs-iter",ir->nLincsIter);
 780     PR("bd-fric",ir->bd_fric);
 781     PI("ld-seed",ir->ld_seed);
 782     PR("cos-accel",ir->cos_accel);
 783     pr_matrix(fp,indent,"deform",ir->deform,bMDPformat);
 784
 785     PS("adress",EBOOL(ir->bAdress));
 786     if (ir->bAdress){
 787         PS("adress_type",EADRESSTYPE(ir->adress->type));
 788         PR("adress_const_wf",ir->adress->const_wf);
 789         PR("adress_ex_width",ir->adress->ex_width);
 790         PR("adress_hy_width",ir->adress->hy_width);
 791         PS("adress_interface_correction",EADRESSICTYPE(ir->adress->icor));
 792         PS("adress_site",EADRESSSITETYPE(ir->adress->site));
 793         PR("adress_ex_force_cap",ir->adress->ex_forcecap);
 794         PS("adress_do_hybridpairs", EBOOL(ir->adress->do_hybridpairs));
 795
 796         pr_rvec(fp,indent,"adress_reference_coords",ir->adress->refs,DIM,TRUE);
 797     }
 798     PI("userint1",ir->userint1);
 799     PI("userint2",ir->userint2);
 800     PI("userint3",ir->userint3);
 801     PI("userint4",ir->userint4);
 802     PR("userreal1",ir->userreal1);
 803     PR("userreal2",ir->userreal2);
 804     PR("userreal3",ir->userreal3);
 805     PR("userreal4",ir->userreal4);
 806     pr_grp_opts(fp,indent,"grpopts",&(ir->opts),bMDPformat);
 807     pr_cosine(fp,indent,"efield-x",&(ir->ex[XX]),bMDPformat);
 808     pr_cosine(fp,indent,"efield-xt",&(ir->et[XX]),bMDPformat);
 809     pr_cosine(fp,indent,"efield-y",&(ir->ex[YY]),bMDPformat);
 810     pr_cosine(fp,indent,"efield-yt",&(ir->et[YY]),bMDPformat);
 811     pr_cosine(fp,indent,"efield-z",&(ir->ex[ZZ]),bMDPformat);
 812     pr_cosine(fp,indent,"efield-zt",&(ir->et[ZZ]),bMDPformat);
 813     PS("bQMMM",EBOOL(ir->bQMMM));
 814     PI("QMconstraints",ir->QMconstraints);
 815     PI("QMMMscheme",ir->QMMMscheme);
 816     PR("scalefactor",ir->scalefactor);
 817     pr_qm_opts(fp,indent,"qm-opts",&(ir->opts));
 818   }
 819 }
 820 #undef PS
 821 #undef PR
 822 #undef PI
 823
 824 static void pr_harm(FILE *fp,t_iparams *iparams,const char *r,const char *kr)
 825 {
 826   fprintf(fp,"%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e\n",
 827           r,iparams->harmonic.rA,kr,iparams->harmonic.krA,
 828           r,iparams->harmonic.rB,kr,iparams->harmonic.krB);
 829 }
 830
 831 void pr_iparams(FILE *fp,t_functype ftype,t_iparams *iparams)
 832 {
 833   int i;
 834   real VA[4],VB[4],*rbcA,*rbcB;
 835
 836   switch (ftype) {
 837   case F_ANGLES:
 838   case F_G96ANGLES:
 839     pr_harm(fp,iparams,"th","ct");
 840     break;
 841   case F_CROSS_BOND_BONDS:
 842     fprintf(fp,"r1e=%15.8e, r2e=%15.8e, krr=%15.8e\n",
 843             iparams->cross_bb.r1e,iparams->cross_bb.r2e,
 844             iparams->cross_bb.krr);
 845     break;
 846   case F_CROSS_BOND_ANGLES:
 847     fprintf(fp,"r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e\n",
 848             iparams->cross_ba.r1e,iparams->cross_ba.r2e,
 849             iparams->cross_ba.r3e,iparams->cross_ba.krt);
 850     break;
 851   case F_LINEAR_ANGLES:
 852     fprintf(fp,"klinA=%15.8e, aA=%15.8e, klinB=%15.8e, aB=%15.8e\n",
 853             iparams->linangle.klinA,iparams->linangle.aA,
 854             iparams->linangle.klinB,iparams->linangle.aB);
 855     break;
 856   case F_UREY_BRADLEY:
 857       fprintf(fp,"thetaA=%15.8e, kthetaA=%15.8e, r13A=%15.8e, kUBA=%15.8e, thetaB=%15.8e, kthetaB=%15.8e, r13B=%15.8e, kUBB=%15.8e\n",iparams->u_b.thetaA,iparams->u_b.kthetaA,iparams->u_b.r13A,iparams->u_b.kUBA,iparams->u_b.thetaB,iparams->u_b.kthetaB,iparams->u_b.r13B,iparams->u_b.kUBB);
 858     break;
 859   case F_QUARTIC_ANGLES:
 860     fprintf(fp,"theta=%15.8e",iparams->qangle.theta);
 861     for(i=0; i<5; i++)
 862       fprintf(fp,", c%c=%15.8e",'0'+i,iparams->qangle.c[i]);
 863     fprintf(fp,"\n");
 864     break;
 865   case F_BHAM:
 866     fprintf(fp,"a=%15.8e, b=%15.8e, c=%15.8e\n",
 867             iparams->bham.a,iparams->bham.b,iparams->bham.c);
 868     break;
 869   case F_BONDS:
 870   case F_G96BONDS:
 871   case F_HARMONIC:
 872     pr_harm(fp,iparams,"b0","cb");
 873     break;
 874   case F_IDIHS:
 875     pr_harm(fp,iparams,"xi","cx");
 876     break;
 877   case F_MORSE:
 878     fprintf(fp,"b0A=%15.8e, cbA=%15.8e, betaA=%15.8e, b0B=%15.8e, cbB=%15.8e, betaB=%15.8e\n",
 879             iparams->morse.b0A,iparams->morse.cbA,iparams->morse.betaA,
 880             iparams->morse.b0B,iparams->morse.cbB,iparams->morse.betaB);
 881     break;
 882   case F_CUBICBONDS:
 883     fprintf(fp,"b0=%15.8e, kb=%15.8e, kcub=%15.8e\n",
 884             iparams->cubic.b0,iparams->cubic.kb,iparams->cubic.kcub);
 885     break;
 886   case F_CONNBONDS:
 887     fprintf(fp,"\n");
 888     break;
 889   case F_FENEBONDS:
 890     fprintf(fp,"bm=%15.8e, kb=%15.8e\n",iparams->fene.bm,iparams->fene.kb);
 891     break;
 892   case F_RESTRBONDS:
 893       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",
 894               iparams->restraint.lowA,iparams->restraint.up1A,
 895               iparams->restraint.up2A,iparams->restraint.kA,
 896               iparams->restraint.lowB,iparams->restraint.up1B,
 897               iparams->restraint.up2B,iparams->restraint.kB);
 898       break;
 899   case F_TABBONDS:
 900   case F_TABBONDSNC:
 901   case F_TABANGLES:
 902   case F_TABDIHS:
 903     fprintf(fp,"tab=%d, kA=%15.8e, kB=%15.8e\n",
 904             iparams->tab.table,iparams->tab.kA,iparams->tab.kB);
 905     break;
 906   case F_POLARIZATION:
 907     fprintf(fp,"alpha=%15.8e\n",iparams->polarize.alpha);
 908     break;
 909   case F_ANHARM_POL:
 910     fprintf(fp,"alpha=%15.8e drcut=%15.8e khyp=%15.8e\n",
 911             iparams->anharm_polarize.alpha,
 912             iparams->anharm_polarize.drcut,
 913             iparams->anharm_polarize.khyp);
 914     break;
 915   case F_THOLE_POL:
 916     fprintf(fp,"a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e\n",
 917             iparams->thole.a,iparams->thole.alpha1,iparams->thole.alpha2,
 918             iparams->thole.rfac);
 919     break;
 920   case F_WATER_POL:
 921     fprintf(fp,"al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f\n",
 922             iparams->wpol.al_x,iparams->wpol.al_y,iparams->wpol.al_z,
 923             iparams->wpol.rOH,iparams->wpol.rHH,iparams->wpol.rOD);
 924     break;
 925   case F_LJ:
 926     fprintf(fp,"c6=%15.8e, c12=%15.8e\n",iparams->lj.c6,iparams->lj.c12);
 927     break;
 928   case F_LJ14:
 929     fprintf(fp,"c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e\n",
 930             iparams->lj14.c6A,iparams->lj14.c12A,
 931             iparams->lj14.c6B,iparams->lj14.c12B);
 932     break;
 933   case F_LJC14_Q:
 934     fprintf(fp,"fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
 935             iparams->ljc14.fqq,
 936             iparams->ljc14.qi,iparams->ljc14.qj,
 937             iparams->ljc14.c6,iparams->ljc14.c12);
 938     break;
 939   case F_LJC_PAIRS_NB:
 940     fprintf(fp,"qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
 941             iparams->ljcnb.qi,iparams->ljcnb.qj,
 942             iparams->ljcnb.c6,iparams->ljcnb.c12);
 943     break;
 944   case F_PDIHS:
 945   case F_PIDIHS:
 946   case F_ANGRES:
 947   case F_ANGRESZ:
 948     fprintf(fp,"phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d\n",
 949             iparams->pdihs.phiA,iparams->pdihs.cpA,
 950             iparams->pdihs.phiB,iparams->pdihs.cpB,
 951             iparams->pdihs.mult);
 952     break;
 953   case F_DISRES:
 954     fprintf(fp,"label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)\n",
 955             iparams->disres.label,iparams->disres.type,
 956             iparams->disres.low,iparams->disres.up1,
 957             iparams->disres.up2,iparams->disres.kfac);
 958     break;
 959   case F_ORIRES:
 960     fprintf(fp,"ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)\n",
 961             iparams->orires.ex,iparams->orires.label,iparams->orires.power,
 962             iparams->orires.c,iparams->orires.obs,iparams->orires.kfac);
 963     break;
 964   case F_DIHRES:
 965       fprintf(fp,"phiA=%15.8e, dphiA=%15.8e, kfacA=%15.8e, phiB=%15.8e, dphiB=%15.8e, kfacB=%15.8e\n",
 966               iparams->dihres.phiA,iparams->dihres.dphiA,iparams->dihres.kfacA,
 967               iparams->dihres.phiB,iparams->dihres.dphiB,iparams->dihres.kfacB);
 968     break;
 969   case F_POSRES:
 970     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",
 971             iparams->posres.pos0A[XX],iparams->posres.pos0A[YY],
 972             iparams->posres.pos0A[ZZ],iparams->posres.fcA[XX],
 973             iparams->posres.fcA[YY],iparams->posres.fcA[ZZ],
 974             iparams->posres.pos0B[XX],iparams->posres.pos0B[YY],
 975             iparams->posres.pos0B[ZZ],iparams->posres.fcB[XX],
 976             iparams->posres.fcB[YY],iparams->posres.fcB[ZZ]);
 977     break;
 978   case F_RBDIHS:
 979     for (i=0; i<NR_RBDIHS; i++)
 980       fprintf(fp,"%srbcA[%d]=%15.8e",i==0?"":", ",i,iparams->rbdihs.rbcA[i]);
 981     fprintf(fp,"\n");
 982     for (i=0; i<NR_RBDIHS; i++)
 983       fprintf(fp,"%srbcB[%d]=%15.8e",i==0?"":", ",i,iparams->rbdihs.rbcB[i]);
 984     fprintf(fp,"\n");
 985     break;
 986   case F_FOURDIHS:
 987     /* Use the OPLS -> Ryckaert-Bellemans formula backwards to get the
 988      * OPLS potential constants back.
 989      */
 990     rbcA = iparams->rbdihs.rbcA;
 991     rbcB = iparams->rbdihs.rbcB;
 992
 993     VA[3] = -0.25*rbcA[4];
 994     VA[2] = -0.5*rbcA[3];
 995     VA[1] = 4.0*VA[3]-rbcA[2];
 996     VA[0] = 3.0*VA[2]-2.0*rbcA[1];
 997
 998     VB[3] = -0.25*rbcB[4];
 999     VB[2] = -0.5*rbcB[3];
1000     VB[1] = 4.0*VB[3]-rbcB[2];
1001     VB[0] = 3.0*VB[2]-2.0*rbcB[1];
1002
1003     for (i=0; i<NR_FOURDIHS; i++)
1004       fprintf(fp,"%sFourA[%d]=%15.8e",i==0?"":", ",i,VA[i]);
1005     fprintf(fp,"\n");
1006     for (i=0; i<NR_FOURDIHS; i++)
1007       fprintf(fp,"%sFourB[%d]=%15.8e",i==0?"":", ",i,VB[i]);
1008     fprintf(fp,"\n");
1009     break;
1010
1011   case F_CONSTR:
1012   case F_CONSTRNC:
1013     fprintf(fp,"dA=%15.8e, dB=%15.8e\n",iparams->constr.dA,iparams->constr.dB);
1014     break;
1015   case F_SETTLE:
1016     fprintf(fp,"doh=%15.8e, dhh=%15.8e\n",iparams->settle.doh,
1017             iparams->settle.dhh);
1018     break;
1019   case F_VSITE2:
1020     fprintf(fp,"a=%15.8e\n",iparams->vsite.a);
1021     break;
1022   case F_VSITE3:
1023   case F_VSITE3FD:
1024   case F_VSITE3FAD:
1025     fprintf(fp,"a=%15.8e, b=%15.8e\n",iparams->vsite.a,iparams->vsite.b);
1026     break;
1027   case F_VSITE3OUT:
1028   case F_VSITE4FD:
1029   case F_VSITE4FDN:
1030     fprintf(fp,"a=%15.8e, b=%15.8e, c=%15.8e\n",
1031             iparams->vsite.a,iparams->vsite.b,iparams->vsite.c);
1032     break;
1033   case F_VSITEN:
1034     fprintf(fp,"n=%2d, a=%15.8e\n",iparams->vsiten.n,iparams->vsiten.a);
1035     break;
1036   case F_GB12:
1037   case F_GB13:
1038   case F_GB14:
1039     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);
1040     break;
1041   case F_CMAP:
1042     fprintf(fp, "cmapA=%1d, cmapB=%1d\n",iparams->cmap.cmapA, iparams->cmap.cmapB);
1043     break;
1044   default:
1045     gmx_fatal(FARGS,"unknown function type %d (%s) in %s line %d",
1046               ftype,interaction_function[ftype].name,__FILE__,__LINE__);
1047   }
1048 }
1049
1050 void pr_ilist(FILE *fp,int indent,const char *title,
1051               t_functype *functype,t_ilist *ilist, gmx_bool bShowNumbers)
1052 {
1053     int i,j,k,type,ftype;
1054     t_iatom *iatoms;
1055
1056     if (available(fp,ilist,indent,title) && ilist->nr > 0)
1057     {
1058         indent=pr_title(fp,indent,title);
1059         (void) pr_indent(fp,indent);
1060         fprintf(fp,"nr: %d\n",ilist->nr);
1061         if (ilist->nr > 0) {
1062             (void) pr_indent(fp,indent);
1063             fprintf(fp,"iatoms:\n");
1064             iatoms=ilist->iatoms;
1065             for (i=j=0; i<ilist->nr;) {
1066 #ifndef DEBUG
1067                 (void) pr_indent(fp,indent+INDENT);
1068                 type=*(iatoms++);
1069                 ftype=functype[type];
1070                 (void) fprintf(fp,"%d type=%d (%s)",
1071                                bShowNumbers?j:-1,bShowNumbers?type:-1,
1072                                interaction_function[ftype].name);
1073                 j++;
1074                 for (k=0; k<interaction_function[ftype].nratoms; k++)
1075                     (void) fprintf(fp," %u",*(iatoms++));
1076                 (void) fprintf(fp,"\n");
1077                 i+=1+interaction_function[ftype].nratoms;
1078 #else
1079                 fprintf(fp,"%5d%5d\n",i,iatoms[i]);
1080                 i++;
1081 #endif
1082             }
1083         }
1084     }
1085 }
1086
1087 static void pr_cmap(FILE *fp, int indent, const char *title,
1088                     gmx_cmap_t *cmap_grid, gmx_bool bShowNumbers)
1089 {
1090     int i,j,nelem;
1091     real dx,idx;
1092
1093     dx    = 360.0 / cmap_grid->grid_spacing;
1094     nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
1095
1096     if(available(fp,cmap_grid,indent,title))
1097     {
1098         fprintf(fp,"%s\n",title);
1099
1100         for(i=0;i<cmap_grid->ngrid;i++)
1101         {
1102             idx = -180.0;
1103             fprintf(fp,"%8s %8s %8s %8s\n","V","dVdx","dVdy","d2dV");
1104
1105             fprintf(fp,"grid[%3d]={\n",bShowNumbers?i:-1);
1106
1107             for(j=0;j<nelem;j++)
1108             {
1109                 if( (j%cmap_grid->grid_spacing)==0)
1110                 {
1111                     fprintf(fp,"%8.1f\n",idx);
1112                     idx+=dx;
1113                 }
1114
1115                 fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4]);
1116                 fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4+1]);
1117                 fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4+2]);
1118                 fprintf(fp,"%8.3f\n",cmap_grid->cmapdata[i].cmap[j*4+3]);
1119             }
1120             fprintf(fp,"\n");
1121         }
1122     }
1123
1124 }
1125
1126 void pr_ffparams(FILE *fp,int indent,const char *title,
1127                  gmx_ffparams_t *ffparams,
1128                  gmx_bool bShowNumbers)
1129 {
1130   int i,j;
1131
1132   indent=pr_title(fp,indent,title);
1133   (void) pr_indent(fp,indent);
1134   (void) fprintf(fp,"atnr=%d\n",ffparams->atnr);
1135   (void) pr_indent(fp,indent);
1136   (void) fprintf(fp,"ntypes=%d\n",ffparams->ntypes);
1137   for (i=0; i<ffparams->ntypes; i++) {
1138       (void) pr_indent(fp,indent+INDENT);
1139       (void) fprintf(fp,"functype[%d]=%s, ",
1140                      bShowNumbers?i:-1,
1141                      interaction_function[ffparams->functype[i]].name);
1142       pr_iparams(fp,ffparams->functype[i],&ffparams->iparams[i]);
1143   }
1144   (void) pr_double(fp,indent,"reppow",ffparams->reppow);
1145   (void) pr_real(fp,indent,"fudgeQQ",ffparams->fudgeQQ);
1146   pr_cmap(fp,indent,"cmap",&ffparams->cmap_grid,bShowNumbers);
1147 }
1148
1149 void pr_idef(FILE *fp,int indent,const char *title,t_idef *idef, gmx_bool bShowNumbers)
1150 {
1151   int i,j;
1152
1153   if (available(fp,idef,indent,title)) {
1154     indent=pr_title(fp,indent,title);
1155     (void) pr_indent(fp,indent);
1156     (void) fprintf(fp,"atnr=%d\n",idef->atnr);
1157     (void) pr_indent(fp,indent);
1158     (void) fprintf(fp,"ntypes=%d\n",idef->ntypes);
1159     for (i=0; i<idef->ntypes; i++) {
1160       (void) pr_indent(fp,indent+INDENT);
1161       (void) fprintf(fp,"functype[%d]=%s, ",
1162                      bShowNumbers?i:-1,
1163                      interaction_function[idef->functype[i]].name);
1164       pr_iparams(fp,idef->functype[i],&idef->iparams[i]);
1165     }
1166     (void) pr_real(fp,indent,"fudgeQQ",idef->fudgeQQ);
1167
1168     for(j=0; (j<F_NRE); j++)
1169       pr_ilist(fp,indent,interaction_function[j].longname,
1170                idef->functype,&idef->il[j],bShowNumbers);
1171   }
1172 }
1173
1174 static int pr_block_title(FILE *fp,int indent,const char *title,t_block *block)
1175 {
1176   int i;
1177
1178   if (available(fp,block,indent,title))
1179     {
1180       indent=pr_title(fp,indent,title);
1181       (void) pr_indent(fp,indent);
1182       (void) fprintf(fp,"nr=%d\n",block->nr);
1183     }
1184   return indent;
1185 }
1186
1187 static int pr_blocka_title(FILE *fp,int indent,const char *title,t_blocka *block)
1188 {
1189   int i;
1190
1191   if (available(fp,block,indent,title))
1192     {
1193       indent=pr_title(fp,indent,title);
1194       (void) pr_indent(fp,indent);
1195       (void) fprintf(fp,"nr=%d\n",block->nr);
1196       (void) pr_indent(fp,indent);
1197       (void) fprintf(fp,"nra=%d\n",block->nra);
1198     }
1199   return indent;
1200 }
1201
1202 static void low_pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block, gmx_bool bShowNumbers)
1203 {
1204   int i;
1205
1206   if (available(fp,block,indent,title))
1207     {
1208       indent=pr_blocka_title(fp,indent,title,block);
1209       for (i=0; i<=block->nr; i++)
1210         {
1211           (void) pr_indent(fp,indent+INDENT);
1212           (void) fprintf(fp,"%s->index[%d]=%u\n",
1213                          title,bShowNumbers?i:-1,block->index[i]);
1214         }
1215       for (i=0; i<block->nra; i++)
1216         {
1217           (void) pr_indent(fp,indent+INDENT);
1218           (void) fprintf(fp,"%s->a[%d]=%u\n",
1219                          title,bShowNumbers?i:-1,block->a[i]);
1220         }
1221     }
1222 }
1223
1224 void pr_block(FILE *fp,int indent,const char *title,t_block *block,gmx_bool bShowNumbers)
1225 {
1226   int i,j,ok,size,start,end;
1227
1228   if (available(fp,block,indent,title))
1229     {
1230       indent=pr_block_title(fp,indent,title,block);
1231       start=0;
1232       end=start;
1233       if ((ok=(block->index[start]==0))==0)
1234         (void) fprintf(fp,"block->index[%d] should be 0\n",start);
1235       else
1236         for (i=0; i<block->nr; i++)
1237           {
1238             end=block->index[i+1];
1239             size=pr_indent(fp,indent);
1240             if (end<=start)
1241               size+=fprintf(fp,"%s[%d]={}\n",title,i);
1242             else
1243               size+=fprintf(fp,"%s[%d]={%d..%d}\n",
1244                             title,bShowNumbers?i:-1,
1245                             bShowNumbers?start:-1,bShowNumbers?end-1:-1);
1246             start=end;
1247           }
1248     }
1249 }
1250
1251 void pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block,gmx_bool bShowNumbers)
1252 {
1253   int i,j,ok,size,start,end;
1254
1255   if (available(fp,block,indent,title))
1256     {
1257       indent=pr_blocka_title(fp,indent,title,block);
1258       start=0;
1259       end=start;
1260       if ((ok=(block->index[start]==0))==0)
1261         (void) fprintf(fp,"block->index[%d] should be 0\n",start);
1262       else
1263         for (i=0; i<block->nr; i++)
1264           {
1265             end=block->index[i+1];
1266             size=pr_indent(fp,indent);
1267             if (end<=start)
1268               size+=fprintf(fp,"%s[%d]={",title,i);
1269             else
1270               size+=fprintf(fp,"%s[%d][%d..%d]={",
1271                             title,bShowNumbers?i:-1,
1272                             bShowNumbers?start:-1,bShowNumbers?end-1:-1);
1273             for (j=start; j<end; j++)
1274               {
1275                 if (j>start) size+=fprintf(fp,", ");
1276                 if ((size)>(USE_WIDTH))
1277                   {
1278                     (void) fprintf(fp,"\n");
1279                     size=pr_indent(fp,indent+INDENT);
1280                   }
1281                 size+=fprintf(fp,"%u",block->a[j]);
1282               }
1283             (void) fprintf(fp,"}\n");
1284             start=end;
1285           }
1286       if ((end!=block->nra)||(!ok))
1287         {
1288           (void) pr_indent(fp,indent);
1289           (void) fprintf(fp,"tables inconsistent, dumping complete tables:\n");
1290           low_pr_blocka(fp,indent,title,block,bShowNumbers);
1291         }
1292     }
1293 }
1294
1295 static void pr_strings(FILE *fp,int indent,const char *title,char ***nm,int n, gmx_bool bShowNumbers)
1296 {
1297   int i;
1298
1299   if (available(fp,nm,indent,title))
1300     {
1301       indent=pr_title_n(fp,indent,title,n);
1302       for (i=0; i<n; i++)
1303         {
1304           (void) pr_indent(fp,indent);
1305           (void) fprintf(fp,"%s[%d]={name=\"%s\"}\n",
1306                          title,bShowNumbers?i:-1,*(nm[i]));
1307         }
1308     }
1309 }
1310
1311 static void pr_strings2(FILE *fp,int indent,const char *title,
1312                         char ***nm,char ***nmB,int n, gmx_bool bShowNumbers)
1313 {
1314   int i;
1315
1316   if (available(fp,nm,indent,title))
1317     {
1318       indent=pr_title_n(fp,indent,title,n);
1319       for (i=0; i<n; i++)
1320         {
1321           (void) pr_indent(fp,indent);
1322           (void) fprintf(fp,"%s[%d]={name=\"%s\",nameB=\"%s\"}\n",
1323                          title,bShowNumbers?i:-1,*(nm[i]),*(nmB[i]));
1324         }
1325     }
1326 }
1327
1328 static void pr_resinfo(FILE *fp,int indent,const char *title,t_resinfo *resinfo,int n, gmx_bool bShowNumbers)
1329 {
1330     int i;
1331
1332     if (available(fp,resinfo,indent,title))
1333     {
1334         indent=pr_title_n(fp,indent,title,n);
1335         for (i=0; i<n; i++)
1336         {
1337             (void) pr_indent(fp,indent);
1338             (void) fprintf(fp,"%s[%d]={name=\"%s\", nr=%d, ic='%c'}\n",
1339                            title,bShowNumbers?i:-1,
1340                            *(resinfo[i].name),resinfo[i].nr,
1341                            (resinfo[i].ic == '\0') ? ' ' : resinfo[i].ic);
1342         }
1343     }
1344 }
1345
1346 static void pr_atom(FILE *fp,int indent,const char *title,t_atom *atom,int n)
1347 {
1348   int i,j;
1349
1350   if (available(fp,atom,indent,title)) {
1351     indent=pr_title_n(fp,indent,title,n);
1352     for (i=0; i<n; i++) {
1353       (void) pr_indent(fp,indent);
1354       fprintf(fp,"%s[%6d]={type=%3d, typeB=%3d, ptype=%8s, m=%12.5e, "
1355               "q=%12.5e, mB=%12.5e, qB=%12.5e, resind=%5d, atomnumber=%3d}\n",
1356               title,i,atom[i].type,atom[i].typeB,ptype_str[atom[i].ptype],
1357               atom[i].m,atom[i].q,atom[i].mB,atom[i].qB,
1358               atom[i].resind,atom[i].atomnumber);
1359     }
1360   }
1361 }
1362
1363 static void pr_grps(FILE *fp,int indent,const char *title,t_grps grps[],
1364                     char **grpname[], gmx_bool bShowNumbers)
1365 {
1366     int i,j;
1367
1368     for(i=0; (i<egcNR); i++)
1369     {
1370         fprintf(fp,"%s[%-12s] nr=%d, name=[",title,gtypes[i],grps[i].nr);
1371         for(j=0; (j<grps[i].nr); j++)
1372         {
1373             fprintf(fp," %s",*(grpname[grps[i].nm_ind[j]]));
1374         }
1375         fprintf(fp,"]\n");
1376     }
1377 }
1378
1379 static void pr_groups(FILE *fp,int indent,const char *title,
1380                       gmx_groups_t *groups,
1381                       gmx_bool bShowNumbers)
1382 {
1383     int grpnr[egcNR];
1384     int nat_max,i,g;
1385
1386     pr_grps(fp,indent,"grp",groups->grps,groups->grpname,bShowNumbers);
1387     pr_strings(fp,indent,"grpname",groups->grpname,groups->ngrpname,bShowNumbers);
1388
1389     (void) pr_indent(fp,indent);
1390     fprintf(fp,"groups          ");
1391     for(g=0; g<egcNR; g++)
1392     {
1393        printf(" %5.5s",gtypes[g]);
1394     }
1395     printf("\n");
1396
1397     (void) pr_indent(fp,indent);
1398     fprintf(fp,"allocated       ");
1399     nat_max = 0;
1400     for(g=0; g<egcNR; g++)
1401     {
1402         printf(" %5d",groups->ngrpnr[g]);
1403         nat_max = max(nat_max,groups->ngrpnr[g]);
1404     }
1405     printf("\n");
1406
1407     if (nat_max == 0)
1408     {
1409         (void) pr_indent(fp,indent);
1410         fprintf(fp,"groupnr[%5s] =","*");
1411         for(g=0; g<egcNR; g++)
1412         {
1413             fprintf(fp,"  %3d ",0);
1414         }
1415         fprintf(fp,"\n");
1416     }
1417     else
1418     {
1419         for(i=0; i<nat_max; i++)
1420         {
1421             (void) pr_indent(fp,indent);
1422             fprintf(fp,"groupnr[%5d] =",i);
1423             for(g=0; g<egcNR; g++)
1424             {
1425                 fprintf(fp,"  %3d ",
1426                         groups->grpnr[g] ? groups->grpnr[g][i] : 0);
1427             }
1428             fprintf(fp,"\n");
1429         }
1430     }
1431 }
1432
1433 void pr_atoms(FILE *fp,int indent,const char *title,t_atoms *atoms,
1434               gmx_bool bShownumbers)
1435 {
1436   if (available(fp,atoms,indent,title))
1437     {
1438       indent=pr_title(fp,indent,title);
1439       pr_atom(fp,indent,"atom",atoms->atom,atoms->nr);
1440       pr_strings(fp,indent,"atom",atoms->atomname,atoms->nr,bShownumbers);
1441       pr_strings2(fp,indent,"type",atoms->atomtype,atoms->atomtypeB,atoms->nr,bShownumbers);
1442       pr_resinfo(fp,indent,"residue",atoms->resinfo,atoms->nres,bShownumbers);
1443     }
1444 }
1445
1446
1447 void pr_atomtypes(FILE *fp,int indent,const char *title,t_atomtypes *atomtypes,
1448                   gmx_bool bShowNumbers)
1449 {
1450   int i;
1451   if (available(fp,atomtypes,indent,title))
1452   {
1453     indent=pr_title(fp,indent,title);
1454     for(i=0;i<atomtypes->nr;i++) {
1455       pr_indent(fp,indent);
1456                 fprintf(fp,
1457                                 "atomtype[%3d]={radius=%12.5e, volume=%12.5e, gb_radius=%12.5e, surftens=%12.5e, atomnumber=%4d, S_hct=%12.5e)}\n",
1458                                 bShowNumbers?i:-1,atomtypes->radius[i],atomtypes->vol[i],
1459                                 atomtypes->gb_radius[i],
1460                                 atomtypes->surftens[i],atomtypes->atomnumber[i],atomtypes->S_hct[i]);
1461     }
1462   }
1463 }
1464
1465 static void pr_moltype(FILE *fp,int indent,const char *title,
1466                        gmx_moltype_t *molt,int n,
1467                        gmx_ffparams_t *ffparams,
1468                        gmx_bool bShowNumbers)
1469 {
1470     int j;
1471
1472     indent = pr_title_n(fp,indent,title,n);
1473     (void) pr_indent(fp,indent);
1474     (void) fprintf(fp,"name=\"%s\"\n",*(molt->name));
1475     pr_atoms(fp,indent,"atoms",&(molt->atoms),bShowNumbers);
1476     pr_block(fp,indent,"cgs",&molt->cgs, bShowNumbers);
1477     pr_blocka(fp,indent,"excls",&molt->excls, bShowNumbers);
1478     for(j=0; (j<F_NRE); j++) {
1479         pr_ilist(fp,indent,interaction_function[j].longname,
1480                  ffparams->functype,&molt->ilist[j],bShowNumbers);
1481     }
1482 }
1483
1484 static void pr_molblock(FILE *fp,int indent,const char *title,
1485                         gmx_molblock_t *molb,int n,
1486                         gmx_moltype_t *molt,
1487                         gmx_bool bShowNumbers)
1488 {
1489     indent = pr_title_n(fp,indent,title,n);
1490     (void) pr_indent(fp,indent);
1491     (void) fprintf(fp,"%-20s = %d \"%s\"\n",
1492                    "moltype",molb->type,*(molt[molb->type].name));
1493     pr_int(fp,indent,"#molecules",molb->nmol);
1494     pr_int(fp,indent,"#atoms_mol",molb->natoms_mol);
1495     pr_int(fp,indent,"#posres_xA",molb->nposres_xA);
1496     if (molb->nposres_xA > 0) {
1497         pr_rvecs(fp,indent,"posres_xA",molb->posres_xA,molb->nposres_xA);
1498     }
1499     pr_int(fp,indent,"#posres_xB",molb->nposres_xB);
1500     if (molb->nposres_xB > 0) {
1501         pr_rvecs(fp,indent,"posres_xB",molb->posres_xB,molb->nposres_xB);
1502     }
1503 }
1504
1505 void pr_mtop(FILE *fp,int indent,const char *title,gmx_mtop_t *mtop,
1506              gmx_bool bShowNumbers)
1507 {
1508     int mt,mb;
1509
1510     if (available(fp,mtop,indent,title)) {
1511         indent=pr_title(fp,indent,title);
1512         (void) pr_indent(fp,indent);
1513         (void) fprintf(fp,"name=\"%s\"\n",*(mtop->name));
1514         pr_int(fp,indent,"#atoms",mtop->natoms);
1515         for(mb=0; mb<mtop->nmolblock; mb++) {
1516             pr_molblock(fp,indent,"molblock",&mtop->molblock[mb],mb,
1517                         mtop->moltype,bShowNumbers);
1518         }
1519         pr_ffparams(fp,indent,"ffparams",&(mtop->ffparams),bShowNumbers);
1520         pr_atomtypes(fp,indent,"atomtypes",&(mtop->atomtypes),bShowNumbers);
1521         for(mt=0; mt<mtop->nmoltype; mt++) {
1522             pr_moltype(fp,indent,"moltype",&mtop->moltype[mt],mt,
1523                        &mtop->ffparams,bShowNumbers);
1524         }
1525         pr_groups(fp,indent,"groups",&mtop->groups,bShowNumbers);
1526     }
1527 }
1528
1529 void pr_top(FILE *fp,int indent,const char *title,t_topology *top, gmx_bool bShowNumbers)
1530 {
1531   if (available(fp,top,indent,title)) {
1532     indent=pr_title(fp,indent,title);
1533     (void) pr_indent(fp,indent);
1534     (void) fprintf(fp,"name=\"%s\"\n",*(top->name));
1535     pr_atoms(fp,indent,"atoms",&(top->atoms),bShowNumbers);
1536     pr_atomtypes(fp,indent,"atomtypes",&(top->atomtypes),bShowNumbers);
1537     pr_block(fp,indent,"cgs",&top->cgs, bShowNumbers);
1538     pr_block(fp,indent,"mols",&top->mols, bShowNumbers);
1539     pr_blocka(fp,indent,"excls",&top->excls, bShowNumbers);
1540     pr_idef(fp,indent,"idef",&top->idef,bShowNumbers);
1541   }
1542 }
1543
1544 void pr_header(FILE *fp,int indent,const char *title,t_tpxheader *sh)
1545 {
1546   char buf[22];
1547
1548   if (available(fp,sh,indent,title))
1549     {
1550       indent=pr_title(fp,indent,title);
1551       pr_indent(fp,indent);
1552       fprintf(fp,"bIr    = %spresent\n",sh->bIr?"":"not ");
1553       pr_indent(fp,indent);
1554       fprintf(fp,"bBox   = %spresent\n",sh->bBox?"":"not ");
1555       pr_indent(fp,indent);
1556       fprintf(fp,"bTop   = %spresent\n",sh->bTop?"":"not ");
1557       pr_indent(fp,indent);
1558       fprintf(fp,"bX     = %spresent\n",sh->bX?"":"not ");
1559       pr_indent(fp,indent);
1560       fprintf(fp,"bV     = %spresent\n",sh->bV?"":"not ");
1561       pr_indent(fp,indent);
1562       fprintf(fp,"bF     = %spresent\n",sh->bF?"":"not ");
1563
1564       pr_indent(fp,indent);
1565       fprintf(fp,"natoms = %d\n",sh->natoms);
1566       pr_indent(fp,indent);
1567       fprintf(fp,"lambda = %e\n",sh->lambda);
1568     }
1569 }
1570
1571 void pr_commrec(FILE *fp,int indent,t_commrec *cr)
1572 {
1573   pr_indent(fp,indent);
1574   fprintf(fp,"commrec:\n");
1575   indent+=2;
1576   pr_indent(fp,indent);
1577   fprintf(fp,"nodeid    = %d\n",cr->nodeid);
1578   pr_indent(fp,indent);
1579   fprintf(fp,"nnodes    = %d\n",cr->nnodes);
1580   pr_indent(fp,indent);
1581   fprintf(fp,"npmenodes = %d\n",cr->npmenodes);
1582   /*
1583   pr_indent(fp,indent);
1584   fprintf(fp,"threadid  = %d\n",cr->threadid);
1585   pr_indent(fp,indent);
1586   fprintf(fp,"nthreads  = %d\n",cr->nthreads);
1587   */
1588 }