src/gmxlib/txtdump.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
   2  *
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.2.0
  11  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  12  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  13  * Copyright (c) 2001-2004, The GROMACS development team,
  14  * check out http://www.gromacs.org for more information.
  15
  16  * This program is free software; you can redistribute it and/or
  17  * modify it under the terms of the GNU General Public License
  18  * as published by the Free Software Foundation; either version 2
  19  * of the License, or (at your option) any later version.
  20  *
  21  * If you want to redistribute modifications, please consider that
  22  * scientific software is very special. Version control is crucial -
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  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.
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  31  * For more info, check our website at http://www.gromacs.org
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  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
  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                          EBOOL(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_simtempvals(FILE *fp,int indent,t_simtemp *simtemp, int n_lambda, gmx_bool bMDPformat)
 496 {
 497     PR("simtemp_low",simtemp->simtemp_low);
 498     PR("simtemp_high",simtemp->simtemp_high);
 499     PS("simulated-tempering-scaling",ESIMTEMP(simtemp->eSimTempScale));
 500     pr_rvec(fp,indent,"simulated tempering temperatures",simtemp->temperatures,n_lambda,TRUE);
 501 }
 502
 503 static void pr_expandedvals(FILE *fp,int indent,t_expanded *expand, int n_lambda, gmx_bool bMDPformat)
 504 {
 505
 506     PI("nstexpanded", expand->nstexpanded);
 507     PS("lambda-stats", elamstats_names[expand->elamstats]);
 508     PS("lambda-mc-move", elmcmove_names[expand->elmcmove]);
 509     PI("lmc-repeats",expand->lmc_repeats);
 510     PI("lmc-gibbsdelta",expand->gibbsdeltalam);
 511     PI("lmc-nstart",expand->lmc_forced_nstart);
 512     PS("symmetrized-transition-matrix", EBOOL(expand->bSymmetrizedTMatrix));
 513     PI("nst-transition-matrix",expand->nstTij);
 514     PI("mininum-var-min",expand->minvarmin); /*default is reasonable */
 515     PI("weight-c-range",expand->c_range); /* default is just C=0 */
 516     PR("wl-scale",expand->wl_scale);
 517     PR("init-wl-delta",expand->init_wl_delta);
 518     PR("wl-ratio",expand->wl_ratio);
 519     PS("bWLoneovert",EBOOL(expand->bWLoneovert));
 520     PI("lmc-seed",expand->lmc_seed);
 521     PR("mc-temperature",expand->mc_temp);
 522     PS("lmc-weights-equil",elmceq_names[expand->elmceq]);
 523     if (expand->elmceq == elmceqNUMATLAM)
 524     {
 525         PI("weight-equil-number-all-lambda",expand->equil_n_at_lam);
 526     }
 527     if (expand->elmceq == elmceqSAMPLES)
 528     {
 529         PI("weight-equil-number-samples",expand->equil_samples);
 530     }
 531     if (expand->elmceq == elmceqSTEPS)
 532     {
 533         PI("weight-equil-number-steps",expand->equil_steps);
 534     }
 535     if (expand->elmceq == elmceqWLDELTA)
 536     {
 537         PR("weight-equil-wl-delta",expand->equil_wl_delta);
 538     }
 539     if (expand->elmceq == elmceqRATIO)
 540     {
 541         PR("weight-equil-count-ratio",expand->equil_ratio);
 542     }
 543
 544     pr_indent(fp,indent);
 545     pr_rvec(fp,indent,"init-lambda-weights",expand->init_lambda_weights,n_lambda,TRUE);
 546     PS("init-weights",EBOOL(expand->bInit_weights));
 547 }
 548
 549 static void pr_fepvals(FILE *fp,int indent,t_lambda *fep, gmx_bool bMDPformat)
 550 {
 551     int i,j;
 552
 553     PI("nstdhdl",fep->nstdhdl);
 554     PI("init-lambda-state",fep->init_fep_state);
 555     PR("init-lambda",fep->init_lambda);
 556     PR("delta-lambda",fep->delta_lambda);
 557     if (!bMDPformat)
 558     {
 559         PI("n-lambdas",fep->n_lambda);
 560     }
 561     if (fep->n_lambda > 0)
 562     {
 563         pr_indent(fp,indent);
 564         fprintf(fp,"all-lambdas%s\n",bMDPformat ? " = " : ":");
 565         for(i=0; i<efptNR; i++) {
 566             fprintf(fp,"%18s = ",efpt_names[i]);
 567             for(j=0; j<fep->n_lambda; j++)
 568             {
 569                 fprintf(fp,"  %10g",fep->all_lambda[i][j]);
 570             }
 571             fprintf(fp,"\n");
 572         }
 573     }
 574
 575     PR("sc-alpha",fep->sc_alpha);
 576     PS("bScCoul",EBOOL(fep->bScCoul));
 577     PS("bScPrintEnergy",EBOOL(fep->bPrintEnergy));
 578     PI("sc-power",fep->sc_power);
 579     PR("sc-r-power",fep->sc_r_power);
 580     PR("sc-sigma",fep->sc_sigma);
 581     PR("sc-sigma-min",fep->sc_sigma_min);
 582     PS("separate-dhdl-file", SEPDHDLFILETYPE(fep->separate_dhdl_file));
 583     PS("dhdl-derivatives", DHDLDERIVATIVESTYPE(fep->dhdl_derivatives));
 584     PI("dh-hist-size", fep->dh_hist_size);
 585     PD("dh-hist-spacing", fep->dh_hist_spacing);
 586 };
 587
 588 static void pr_pull(FILE *fp,int indent,t_pull *pull)
 589 {
 590   int g;
 591
 592   PS("pull-geometry",EPULLGEOM(pull->eGeom));
 593   pr_ivec(fp,indent,"pull-dim",pull->dim,DIM,TRUE);
 594   PR("pull-r1",pull->cyl_r1);
 595   PR("pull-r0",pull->cyl_r0);
 596   PR("pull-constr-tol",pull->constr_tol);
 597   PI("pull-nstxout",pull->nstxout);
 598   PI("pull-nstfout",pull->nstfout);
 599   PI("pull-ngrp",pull->ngrp);
 600   for(g=0; g<pull->ngrp+1; g++)
 601     pr_pullgrp(fp,indent,g,&pull->grp[g]);
 602 }
 603
 604 static void pr_rotgrp(FILE *fp,int indent,int g,t_rotgrp *rotg)
 605 {
 606   pr_indent(fp,indent);
 607   fprintf(fp,"rotation_group %d:\n",g);
 608   indent += 2;
 609   PS("type",EROTGEOM(rotg->eType));
 610   PS("massw",EBOOL(rotg->bMassW));
 611   pr_ivec_block(fp,indent,"atom",rotg->ind,rotg->nat,TRUE);
 612   pr_rvecs(fp,indent,"x_ref",rotg->x_ref,rotg->nat);
 613   pr_rvec(fp,indent,"vec",rotg->vec,DIM,TRUE);
 614   pr_rvec(fp,indent,"pivot",rotg->pivot,DIM,TRUE);
 615   PR("rate",rotg->rate);
 616   PR("k",rotg->k);
 617   PR("slab_dist",rotg->slab_dist);
 618   PR("min_gaussian",rotg->min_gaussian);
 619   PR("epsilon",rotg->eps);
 620   PS("fit_method",EROTFIT(rotg->eFittype));
 621   PI("potfitangle_nstep",rotg->PotAngle_nstep);
 622   PR("potfitangle_step",rotg->PotAngle_step);
 623 }
 624
 625 static void pr_rot(FILE *fp,int indent,t_rot *rot)
 626 {
 627   int g;
 628
 629   PI("rot_nstrout",rot->nstrout);
 630   PI("rot_nstsout",rot->nstsout);
 631   PI("rot_ngrp",rot->ngrp);
 632   for(g=0; g<rot->ngrp; g++)
 633     pr_rotgrp(fp,indent,g,&rot->grp[g]);
 634 }
 635
 636 void pr_inputrec(FILE *fp,int indent,const char *title,t_inputrec *ir,
 637                  gmx_bool bMDPformat)
 638 {
 639   const char *infbuf="inf";
 640   int  i;
 641
 642   if (available(fp,ir,indent,title)) {
 643     if (!bMDPformat)
 644       indent=pr_title(fp,indent,title);
 645     PS("integrator",EI(ir->eI));
 646     PSTEP("nsteps",ir->nsteps);
 647     PSTEP("init-step",ir->init_step);
 648     PS("cutoff-scheme",ECUTSCHEME(ir->cutoff_scheme));
 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     PR("fourierspacing",ir->fourier_spacing);
 666     PI("nkx",ir->nkx);
 667     PI("nky",ir->nky);
 668     PI("nkz",ir->nkz);
 669     PI("pme-order",ir->pme_order);
 670     PR("ewald-rtol",ir->ewald_rtol);
 671     PR("ewald-geometry",ir->ewald_geometry);
 672     PR("epsilon-surface",ir->epsilon_surface);
 673     PS("optimize-fft",EBOOL(ir->bOptFFT));
 674     PS("ePBC",EPBC(ir->ePBC));
 675     PS("bPeriodicMols",EBOOL(ir->bPeriodicMols));
 676     PS("bContinuation",EBOOL(ir->bContinuation));
 677     PS("bShakeSOR",EBOOL(ir->bShakeSOR));
 678     PS("etc",ETCOUPLTYPE(ir->etc));
 679     PS("bPrintNHChains",EBOOL(ir->bPrintNHChains));
 680     PI("nsttcouple",ir->nsttcouple);
 681     PS("epc",EPCOUPLTYPE(ir->epc));
 682     PS("epctype",EPCOUPLTYPETYPE(ir->epct));
 683     PI("nstpcouple",ir->nstpcouple);
 684     PR("tau-p",ir->tau_p);
 685     pr_matrix(fp,indent,"ref-p",ir->ref_p,bMDPformat);
 686     pr_matrix(fp,indent,"compress",ir->compress,bMDPformat);
 687     PS("refcoord-scaling",EREFSCALINGTYPE(ir->refcoord_scaling));
 688     if (bMDPformat)
 689       fprintf(fp,"posres-com  = %g %g %g\n",ir->posres_com[XX],
 690               ir->posres_com[YY],ir->posres_com[ZZ]);
 691     else
 692       pr_rvec(fp,indent,"posres-com",ir->posres_com,DIM,TRUE);
 693     if (bMDPformat)
 694       fprintf(fp,"posres-comB = %g %g %g\n",ir->posres_comB[XX],
 695               ir->posres_comB[YY],ir->posres_comB[ZZ]);
 696     else
 697       pr_rvec(fp,indent,"posres-comB",ir->posres_comB,DIM,TRUE);
 698     PR("verlet-buffer-drift",ir->verletbuf_drift);
 699     PR("rlist",ir->rlist);
 700     PR("rlistlong",ir->rlistlong);
 701     PR("rtpi",ir->rtpi);
 702     PS("coulombtype",EELTYPE(ir->coulombtype));
 703     PR("rcoulomb-switch",ir->rcoulomb_switch);
 704     PR("rcoulomb",ir->rcoulomb);
 705     PS("vdwtype",EVDWTYPE(ir->vdwtype));
 706     PR("rvdw-switch",ir->rvdw_switch);
 707     PR("rvdw",ir->rvdw);
 708     if (ir->epsilon_r != 0)
 709       PR("epsilon-r",ir->epsilon_r);
 710     else
 711       PS("epsilon-r",infbuf);
 712     if (ir->epsilon_rf != 0)
 713       PR("epsilon-rf",ir->epsilon_rf);
 714     else
 715       PS("epsilon-rf",infbuf);
 716     PR("tabext",ir->tabext);
 717     PS("implicit-solvent",EIMPLICITSOL(ir->implicit_solvent));
 718     PS("gb-algorithm",EGBALGORITHM(ir->gb_algorithm));
 719     PR("gb-epsilon-solvent",ir->gb_epsilon_solvent);
 720     PI("nstgbradii",ir->nstgbradii);
 721     PR("rgbradii",ir->rgbradii);
 722     PR("gb-saltconc",ir->gb_saltconc);
 723     PR("gb-obc-alpha",ir->gb_obc_alpha);
 724     PR("gb-obc-beta",ir->gb_obc_beta);
 725     PR("gb-obc-gamma",ir->gb_obc_gamma);
 726     PR("gb-dielectric-offset",ir->gb_dielectric_offset);
 727     PS("sa-algorithm",ESAALGORITHM(ir->gb_algorithm));
 728     PR("sa-surface-tension",ir->sa_surface_tension);
 729     PS("DispCorr",EDISPCORR(ir->eDispCorr));
 730     PS("bSimTemp",EBOOL(ir->bSimTemp));
 731     if (ir->bSimTemp) {
 732         pr_simtempvals(fp,indent,ir->simtempvals,ir->fepvals->n_lambda,bMDPformat);
 733     }
 734     PS("free-energy",EFEPTYPE(ir->efep));
 735     if (ir->efep != efepNO || ir->bSimTemp) {
 736         pr_fepvals(fp,indent,ir->fepvals,bMDPformat);
 737     }
 738     if (ir->bExpanded) {
 739         pr_expandedvals(fp,indent,ir->expandedvals,ir->fepvals->n_lambda,bMDPformat);
 740     }
 741
 742     PI("nwall",ir->nwall);
 743     PS("wall-type",EWALLTYPE(ir->wall_type));
 744     PI("wall-atomtype[0]",ir->wall_atomtype[0]);
 745     PI("wall-atomtype[1]",ir->wall_atomtype[1]);
 746     PR("wall-density[0]",ir->wall_density[0]);
 747     PR("wall-density[1]",ir->wall_density[1]);
 748     PR("wall-ewald-zfac",ir->wall_ewald_zfac);
 749
 750     PS("pull",EPULLTYPE(ir->ePull));
 751     if (ir->ePull != epullNO)
 752       pr_pull(fp,indent,ir->pull);
 753
 754     PS("rotation",EBOOL(ir->bRot));
 755     if (ir->bRot)
 756       pr_rot(fp,indent,ir->rot);
 757
 758     PS("disre",EDISRETYPE(ir->eDisre));
 759     PS("disre-weighting",EDISREWEIGHTING(ir->eDisreWeighting));
 760     PS("disre-mixed",EBOOL(ir->bDisreMixed));
 761     PR("dr-fc",ir->dr_fc);
 762     PR("dr-tau",ir->dr_tau);
 763     PR("nstdisreout",ir->nstdisreout);
 764     PR("orires-fc",ir->orires_fc);
 765     PR("orires-tau",ir->orires_tau);
 766     PR("nstorireout",ir->nstorireout);
 767
 768     PR("dihre-fc",ir->dihre_fc);
 769
 770     PR("em-stepsize",ir->em_stepsize);
 771     PR("em-tol",ir->em_tol);
 772     PI("niter",ir->niter);
 773     PR("fc-stepsize",ir->fc_stepsize);
 774     PI("nstcgsteep",ir->nstcgsteep);
 775     PI("nbfgscorr",ir->nbfgscorr);
 776
 777     PS("ConstAlg",ECONSTRTYPE(ir->eConstrAlg));
 778     PR("shake-tol",ir->shake_tol);
 779     PI("lincs-order",ir->nProjOrder);
 780     PR("lincs-warnangle",ir->LincsWarnAngle);
 781     PI("lincs-iter",ir->nLincsIter);
 782     PR("bd-fric",ir->bd_fric);
 783     PI("ld-seed",ir->ld_seed);
 784     PR("cos-accel",ir->cos_accel);
 785     pr_matrix(fp,indent,"deform",ir->deform,bMDPformat);
 786
 787     PS("adress",EBOOL(ir->bAdress));
 788     if (ir->bAdress){
 789         PS("adress_type",EADRESSTYPE(ir->adress->type));
 790         PR("adress_const_wf",ir->adress->const_wf);
 791         PR("adress_ex_width",ir->adress->ex_width);
 792         PR("adress_hy_width",ir->adress->hy_width);
 793         PS("adress_interface_correction",EADRESSICTYPE(ir->adress->icor));
 794         PS("adress_site",EADRESSSITETYPE(ir->adress->site));
 795         PR("adress_ex_force_cap",ir->adress->ex_forcecap);
 796         PS("adress_do_hybridpairs", EBOOL(ir->adress->do_hybridpairs));
 797
 798         pr_rvec(fp,indent,"adress_reference_coords",ir->adress->refs,DIM,TRUE);
 799     }
 800     PI("userint1",ir->userint1);
 801     PI("userint2",ir->userint2);
 802     PI("userint3",ir->userint3);
 803     PI("userint4",ir->userint4);
 804     PR("userreal1",ir->userreal1);
 805     PR("userreal2",ir->userreal2);
 806     PR("userreal3",ir->userreal3);
 807     PR("userreal4",ir->userreal4);
 808     pr_grp_opts(fp,indent,"grpopts",&(ir->opts),bMDPformat);
 809     pr_cosine(fp,indent,"efield-x",&(ir->ex[XX]),bMDPformat);
 810     pr_cosine(fp,indent,"efield-xt",&(ir->et[XX]),bMDPformat);
 811     pr_cosine(fp,indent,"efield-y",&(ir->ex[YY]),bMDPformat);
 812     pr_cosine(fp,indent,"efield-yt",&(ir->et[YY]),bMDPformat);
 813     pr_cosine(fp,indent,"efield-z",&(ir->ex[ZZ]),bMDPformat);
 814     pr_cosine(fp,indent,"efield-zt",&(ir->et[ZZ]),bMDPformat);
 815     PS("bQMMM",EBOOL(ir->bQMMM));
 816     PI("QMconstraints",ir->QMconstraints);
 817     PI("QMMMscheme",ir->QMMMscheme);
 818     PR("scalefactor",ir->scalefactor);
 819     pr_qm_opts(fp,indent,"qm-opts",&(ir->opts));
 820   }
 821 }
 822 #undef PS
 823 #undef PR
 824 #undef PI
 825
 826 static void pr_harm(FILE *fp,t_iparams *iparams,const char *r,const char *kr)
 827 {
 828   fprintf(fp,"%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e\n",
 829           r,iparams->harmonic.rA,kr,iparams->harmonic.krA,
 830           r,iparams->harmonic.rB,kr,iparams->harmonic.krB);
 831 }
 832
 833 void pr_iparams(FILE *fp,t_functype ftype,t_iparams *iparams)
 834 {
 835   int i;
 836   real VA[4],VB[4],*rbcA,*rbcB;
 837
 838   switch (ftype) {
 839   case F_ANGLES:
 840   case F_G96ANGLES:
 841     pr_harm(fp,iparams,"th","ct");
 842     break;
 843   case F_CROSS_BOND_BONDS:
 844     fprintf(fp,"r1e=%15.8e, r2e=%15.8e, krr=%15.8e\n",
 845             iparams->cross_bb.r1e,iparams->cross_bb.r2e,
 846             iparams->cross_bb.krr);
 847     break;
 848   case F_CROSS_BOND_ANGLES:
 849     fprintf(fp,"r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e\n",
 850             iparams->cross_ba.r1e,iparams->cross_ba.r2e,
 851             iparams->cross_ba.r3e,iparams->cross_ba.krt);
 852     break;
 853   case F_LINEAR_ANGLES:
 854     fprintf(fp,"klinA=%15.8e, aA=%15.8e, klinB=%15.8e, aB=%15.8e\n",
 855             iparams->linangle.klinA,iparams->linangle.aA,
 856             iparams->linangle.klinB,iparams->linangle.aB);
 857     break;
 858   case F_UREY_BRADLEY:
 859       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);
 860     break;
 861   case F_QUARTIC_ANGLES:
 862     fprintf(fp,"theta=%15.8e",iparams->qangle.theta);
 863     for(i=0; i<5; i++)
 864       fprintf(fp,", c%c=%15.8e",'0'+i,iparams->qangle.c[i]);
 865     fprintf(fp,"\n");
 866     break;
 867   case F_BHAM:
 868     fprintf(fp,"a=%15.8e, b=%15.8e, c=%15.8e\n",
 869             iparams->bham.a,iparams->bham.b,iparams->bham.c);
 870     break;
 871   case F_BONDS:
 872   case F_G96BONDS:
 873   case F_HARMONIC:
 874     pr_harm(fp,iparams,"b0","cb");
 875     break;
 876   case F_IDIHS:
 877     pr_harm(fp,iparams,"xi","cx");
 878     break;
 879   case F_MORSE:
 880     fprintf(fp,"b0A=%15.8e, cbA=%15.8e, betaA=%15.8e, b0B=%15.8e, cbB=%15.8e, betaB=%15.8e\n",
 881             iparams->morse.b0A,iparams->morse.cbA,iparams->morse.betaA,
 882             iparams->morse.b0B,iparams->morse.cbB,iparams->morse.betaB);
 883     break;
 884   case F_CUBICBONDS:
 885     fprintf(fp,"b0=%15.8e, kb=%15.8e, kcub=%15.8e\n",
 886             iparams->cubic.b0,iparams->cubic.kb,iparams->cubic.kcub);
 887     break;
 888   case F_CONNBONDS:
 889     fprintf(fp,"\n");
 890     break;
 891   case F_FENEBONDS:
 892     fprintf(fp,"bm=%15.8e, kb=%15.8e\n",iparams->fene.bm,iparams->fene.kb);
 893     break;
 894   case F_RESTRBONDS:
 895       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",
 896               iparams->restraint.lowA,iparams->restraint.up1A,
 897               iparams->restraint.up2A,iparams->restraint.kA,
 898               iparams->restraint.lowB,iparams->restraint.up1B,
 899               iparams->restraint.up2B,iparams->restraint.kB);
 900       break;
 901   case F_TABBONDS:
 902   case F_TABBONDSNC:
 903   case F_TABANGLES:
 904   case F_TABDIHS:
 905     fprintf(fp,"tab=%d, kA=%15.8e, kB=%15.8e\n",
 906             iparams->tab.table,iparams->tab.kA,iparams->tab.kB);
 907     break;
 908   case F_POLARIZATION:
 909     fprintf(fp,"alpha=%15.8e\n",iparams->polarize.alpha);
 910     break;
 911   case F_ANHARM_POL:
 912     fprintf(fp,"alpha=%15.8e drcut=%15.8e khyp=%15.8e\n",
 913             iparams->anharm_polarize.alpha,
 914             iparams->anharm_polarize.drcut,
 915             iparams->anharm_polarize.khyp);
 916     break;
 917   case F_THOLE_POL:
 918     fprintf(fp,"a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e\n",
 919             iparams->thole.a,iparams->thole.alpha1,iparams->thole.alpha2,
 920             iparams->thole.rfac);
 921     break;
 922   case F_WATER_POL:
 923     fprintf(fp,"al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f\n",
 924             iparams->wpol.al_x,iparams->wpol.al_y,iparams->wpol.al_z,
 925             iparams->wpol.rOH,iparams->wpol.rHH,iparams->wpol.rOD);
 926     break;
 927   case F_LJ:
 928     fprintf(fp,"c6=%15.8e, c12=%15.8e\n",iparams->lj.c6,iparams->lj.c12);
 929     break;
 930   case F_LJ14:
 931     fprintf(fp,"c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e\n",
 932             iparams->lj14.c6A,iparams->lj14.c12A,
 933             iparams->lj14.c6B,iparams->lj14.c12B);
 934     break;
 935   case F_LJC14_Q:
 936     fprintf(fp,"fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
 937             iparams->ljc14.fqq,
 938             iparams->ljc14.qi,iparams->ljc14.qj,
 939             iparams->ljc14.c6,iparams->ljc14.c12);
 940     break;
 941   case F_LJC_PAIRS_NB:
 942     fprintf(fp,"qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
 943             iparams->ljcnb.qi,iparams->ljcnb.qj,
 944             iparams->ljcnb.c6,iparams->ljcnb.c12);
 945     break;
 946   case F_PDIHS:
 947   case F_PIDIHS:
 948   case F_ANGRES:
 949   case F_ANGRESZ:
 950     fprintf(fp,"phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d\n",
 951             iparams->pdihs.phiA,iparams->pdihs.cpA,
 952             iparams->pdihs.phiB,iparams->pdihs.cpB,
 953             iparams->pdihs.mult);
 954     break;
 955   case F_DISRES:
 956     fprintf(fp,"label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)\n",
 957             iparams->disres.label,iparams->disres.type,
 958             iparams->disres.low,iparams->disres.up1,
 959             iparams->disres.up2,iparams->disres.kfac);
 960     break;
 961   case F_ORIRES:
 962     fprintf(fp,"ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)\n",
 963             iparams->orires.ex,iparams->orires.label,iparams->orires.power,
 964             iparams->orires.c,iparams->orires.obs,iparams->orires.kfac);
 965     break;
 966   case F_DIHRES:
 967       fprintf(fp,"phiA=%15.8e, dphiA=%15.8e, kfacA=%15.8e, phiB=%15.8e, dphiB=%15.8e, kfacB=%15.8e\n",
 968               iparams->dihres.phiA,iparams->dihres.dphiA,iparams->dihres.kfacA,
 969               iparams->dihres.phiB,iparams->dihres.dphiB,iparams->dihres.kfacB);
 970     break;
 971   case F_POSRES:
 972     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",
 973             iparams->posres.pos0A[XX],iparams->posres.pos0A[YY],
 974             iparams->posres.pos0A[ZZ],iparams->posres.fcA[XX],
 975             iparams->posres.fcA[YY],iparams->posres.fcA[ZZ],
 976             iparams->posres.pos0B[XX],iparams->posres.pos0B[YY],
 977             iparams->posres.pos0B[ZZ],iparams->posres.fcB[XX],
 978             iparams->posres.fcB[YY],iparams->posres.fcB[ZZ]);
 979     break;
 980   case F_RBDIHS:
 981     for (i=0; i<NR_RBDIHS; i++)
 982       fprintf(fp,"%srbcA[%d]=%15.8e",i==0?"":", ",i,iparams->rbdihs.rbcA[i]);
 983     fprintf(fp,"\n");
 984     for (i=0; i<NR_RBDIHS; i++)
 985       fprintf(fp,"%srbcB[%d]=%15.8e",i==0?"":", ",i,iparams->rbdihs.rbcB[i]);
 986     fprintf(fp,"\n");
 987     break;
 988   case F_FOURDIHS:
 989     /* Use the OPLS -> Ryckaert-Bellemans formula backwards to get the
 990      * OPLS potential constants back.
 991      */
 992     rbcA = iparams->rbdihs.rbcA;
 993     rbcB = iparams->rbdihs.rbcB;
 994
 995     VA[3] = -0.25*rbcA[4];
 996     VA[2] = -0.5*rbcA[3];
 997     VA[1] = 4.0*VA[3]-rbcA[2];
 998     VA[0] = 3.0*VA[2]-2.0*rbcA[1];
 999
1000     VB[3] = -0.25*rbcB[4];
1001     VB[2] = -0.5*rbcB[3];
1002     VB[1] = 4.0*VB[3]-rbcB[2];
1003     VB[0] = 3.0*VB[2]-2.0*rbcB[1];
1004
1005     for (i=0; i<NR_FOURDIHS; i++)
1006       fprintf(fp,"%sFourA[%d]=%15.8e",i==0?"":", ",i,VA[i]);
1007     fprintf(fp,"\n");
1008     for (i=0; i<NR_FOURDIHS; i++)
1009       fprintf(fp,"%sFourB[%d]=%15.8e",i==0?"":", ",i,VB[i]);
1010     fprintf(fp,"\n");
1011     break;
1012
1013   case F_CONSTR:
1014   case F_CONSTRNC:
1015     fprintf(fp,"dA=%15.8e, dB=%15.8e\n",iparams->constr.dA,iparams->constr.dB);
1016     break;
1017   case F_SETTLE:
1018     fprintf(fp,"doh=%15.8e, dhh=%15.8e\n",iparams->settle.doh,
1019             iparams->settle.dhh);
1020     break;
1021   case F_VSITE2:
1022     fprintf(fp,"a=%15.8e\n",iparams->vsite.a);
1023     break;
1024   case F_VSITE3:
1025   case F_VSITE3FD:
1026   case F_VSITE3FAD:
1027     fprintf(fp,"a=%15.8e, b=%15.8e\n",iparams->vsite.a,iparams->vsite.b);
1028     break;
1029   case F_VSITE3OUT:
1030   case F_VSITE4FD:
1031   case F_VSITE4FDN:
1032     fprintf(fp,"a=%15.8e, b=%15.8e, c=%15.8e\n",
1033             iparams->vsite.a,iparams->vsite.b,iparams->vsite.c);
1034     break;
1035   case F_VSITEN:
1036     fprintf(fp,"n=%2d, a=%15.8e\n",iparams->vsiten.n,iparams->vsiten.a);
1037     break;
1038   case F_GB12:
1039   case F_GB13:
1040   case F_GB14:
1041     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);
1042     break;
1043   case F_CMAP:
1044     fprintf(fp, "cmapA=%1d, cmapB=%1d\n",iparams->cmap.cmapA, iparams->cmap.cmapB);
1045     break;
1046   default:
1047     gmx_fatal(FARGS,"unknown function type %d (%s) in %s line %d",
1048               ftype,interaction_function[ftype].name,__FILE__,__LINE__);
1049   }
1050 }
1051
1052 void pr_ilist(FILE *fp,int indent,const char *title,
1053               t_functype *functype,t_ilist *ilist, gmx_bool bShowNumbers)
1054 {
1055     int i,j,k,type,ftype;
1056     t_iatom *iatoms;
1057
1058     if (available(fp,ilist,indent,title) && ilist->nr > 0)
1059     {
1060         indent=pr_title(fp,indent,title);
1061         (void) pr_indent(fp,indent);
1062         fprintf(fp,"nr: %d\n",ilist->nr);
1063         if (ilist->nr > 0) {
1064             (void) pr_indent(fp,indent);
1065             fprintf(fp,"iatoms:\n");
1066             iatoms=ilist->iatoms;
1067             for (i=j=0; i<ilist->nr;) {
1068 #ifndef DEBUG
1069                 (void) pr_indent(fp,indent+INDENT);
1070                 type=*(iatoms++);
1071                 ftype=functype[type];
1072                 (void) fprintf(fp,"%d type=%d (%s)",
1073                                bShowNumbers?j:-1,bShowNumbers?type:-1,
1074                                interaction_function[ftype].name);
1075                 j++;
1076                 for (k=0; k<interaction_function[ftype].nratoms; k++)
1077                     (void) fprintf(fp," %u",*(iatoms++));
1078                 (void) fprintf(fp,"\n");
1079                 i+=1+interaction_function[ftype].nratoms;
1080 #else
1081                 fprintf(fp,"%5d%5d\n",i,iatoms[i]);
1082                 i++;
1083 #endif
1084             }
1085         }
1086     }
1087 }
1088
1089 static void pr_cmap(FILE *fp, int indent, const char *title,
1090                     gmx_cmap_t *cmap_grid, gmx_bool bShowNumbers)
1091 {
1092     int i,j,nelem;
1093     real dx,idx;
1094
1095     dx    = 360.0 / cmap_grid->grid_spacing;
1096     nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
1097
1098     if(available(fp,cmap_grid,indent,title))
1099     {
1100         fprintf(fp,"%s\n",title);
1101
1102         for(i=0;i<cmap_grid->ngrid;i++)
1103         {
1104             idx = -180.0;
1105             fprintf(fp,"%8s %8s %8s %8s\n","V","dVdx","dVdy","d2dV");
1106
1107             fprintf(fp,"grid[%3d]={\n",bShowNumbers?i:-1);
1108
1109             for(j=0;j<nelem;j++)
1110             {
1111                 if( (j%cmap_grid->grid_spacing)==0)
1112                 {
1113                     fprintf(fp,"%8.1f\n",idx);
1114                     idx+=dx;
1115                 }
1116
1117                 fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4]);
1118                 fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4+1]);
1119                 fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4+2]);
1120                 fprintf(fp,"%8.3f\n",cmap_grid->cmapdata[i].cmap[j*4+3]);
1121             }
1122             fprintf(fp,"\n");
1123         }
1124     }
1125
1126 }
1127
1128 void pr_ffparams(FILE *fp,int indent,const char *title,
1129                  gmx_ffparams_t *ffparams,
1130                  gmx_bool bShowNumbers)
1131 {
1132   int i,j;
1133
1134   indent=pr_title(fp,indent,title);
1135   (void) pr_indent(fp,indent);
1136   (void) fprintf(fp,"atnr=%d\n",ffparams->atnr);
1137   (void) pr_indent(fp,indent);
1138   (void) fprintf(fp,"ntypes=%d\n",ffparams->ntypes);
1139   for (i=0; i<ffparams->ntypes; i++) {
1140       (void) pr_indent(fp,indent+INDENT);
1141       (void) fprintf(fp,"functype[%d]=%s, ",
1142                      bShowNumbers?i:-1,
1143                      interaction_function[ffparams->functype[i]].name);
1144       pr_iparams(fp,ffparams->functype[i],&ffparams->iparams[i]);
1145   }
1146   (void) pr_double(fp,indent,"reppow",ffparams->reppow);
1147   (void) pr_real(fp,indent,"fudgeQQ",ffparams->fudgeQQ);
1148   pr_cmap(fp,indent,"cmap",&ffparams->cmap_grid,bShowNumbers);
1149 }
1150
1151 void pr_idef(FILE *fp,int indent,const char *title,t_idef *idef, gmx_bool bShowNumbers)
1152 {
1153   int i,j;
1154
1155   if (available(fp,idef,indent,title)) {
1156     indent=pr_title(fp,indent,title);
1157     (void) pr_indent(fp,indent);
1158     (void) fprintf(fp,"atnr=%d\n",idef->atnr);
1159     (void) pr_indent(fp,indent);
1160     (void) fprintf(fp,"ntypes=%d\n",idef->ntypes);
1161     for (i=0; i<idef->ntypes; i++) {
1162       (void) pr_indent(fp,indent+INDENT);
1163       (void) fprintf(fp,"functype[%d]=%s, ",
1164                      bShowNumbers?i:-1,
1165                      interaction_function[idef->functype[i]].name);
1166       pr_iparams(fp,idef->functype[i],&idef->iparams[i]);
1167     }
1168     (void) pr_real(fp,indent,"fudgeQQ",idef->fudgeQQ);
1169
1170     for(j=0; (j<F_NRE); j++)
1171       pr_ilist(fp,indent,interaction_function[j].longname,
1172                idef->functype,&idef->il[j],bShowNumbers);
1173   }
1174 }
1175
1176 static int pr_block_title(FILE *fp,int indent,const char *title,t_block *block)
1177 {
1178   int i;
1179
1180   if (available(fp,block,indent,title))
1181     {
1182       indent=pr_title(fp,indent,title);
1183       (void) pr_indent(fp,indent);
1184       (void) fprintf(fp,"nr=%d\n",block->nr);
1185     }
1186   return indent;
1187 }
1188
1189 static int pr_blocka_title(FILE *fp,int indent,const char *title,t_blocka *block)
1190 {
1191   int i;
1192
1193   if (available(fp,block,indent,title))
1194     {
1195       indent=pr_title(fp,indent,title);
1196       (void) pr_indent(fp,indent);
1197       (void) fprintf(fp,"nr=%d\n",block->nr);
1198       (void) pr_indent(fp,indent);
1199       (void) fprintf(fp,"nra=%d\n",block->nra);
1200     }
1201   return indent;
1202 }
1203
1204 static void low_pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block, gmx_bool bShowNumbers)
1205 {
1206   int i;
1207
1208   if (available(fp,block,indent,title))
1209     {
1210       indent=pr_blocka_title(fp,indent,title,block);
1211       for (i=0; i<=block->nr; i++)
1212         {
1213           (void) pr_indent(fp,indent+INDENT);
1214           (void) fprintf(fp,"%s->index[%d]=%u\n",
1215                          title,bShowNumbers?i:-1,block->index[i]);
1216         }
1217       for (i=0; i<block->nra; i++)
1218         {
1219           (void) pr_indent(fp,indent+INDENT);
1220           (void) fprintf(fp,"%s->a[%d]=%u\n",
1221                          title,bShowNumbers?i:-1,block->a[i]);
1222         }
1223     }
1224 }
1225
1226 void pr_block(FILE *fp,int indent,const char *title,t_block *block,gmx_bool bShowNumbers)
1227 {
1228   int i,j,ok,size,start,end;
1229
1230   if (available(fp,block,indent,title))
1231     {
1232       indent=pr_block_title(fp,indent,title,block);
1233       start=0;
1234       end=start;
1235       if ((ok=(block->index[start]==0))==0)
1236         (void) fprintf(fp,"block->index[%d] should be 0\n",start);
1237       else
1238         for (i=0; i<block->nr; i++)
1239           {
1240             end=block->index[i+1];
1241             size=pr_indent(fp,indent);
1242             if (end<=start)
1243               size+=fprintf(fp,"%s[%d]={}\n",title,i);
1244             else
1245               size+=fprintf(fp,"%s[%d]={%d..%d}\n",
1246                             title,bShowNumbers?i:-1,
1247                             bShowNumbers?start:-1,bShowNumbers?end-1:-1);
1248             start=end;
1249           }
1250     }
1251 }
1252
1253 void pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block,gmx_bool bShowNumbers)
1254 {
1255   int i,j,ok,size,start,end;
1256
1257   if (available(fp,block,indent,title))
1258     {
1259       indent=pr_blocka_title(fp,indent,title,block);
1260       start=0;
1261       end=start;
1262       if ((ok=(block->index[start]==0))==0)
1263         (void) fprintf(fp,"block->index[%d] should be 0\n",start);
1264       else
1265         for (i=0; i<block->nr; i++)
1266           {
1267             end=block->index[i+1];
1268             size=pr_indent(fp,indent);
1269             if (end<=start)
1270               size+=fprintf(fp,"%s[%d]={",title,i);
1271             else
1272               size+=fprintf(fp,"%s[%d][%d..%d]={",
1273                             title,bShowNumbers?i:-1,
1274                             bShowNumbers?start:-1,bShowNumbers?end-1:-1);
1275             for (j=start; j<end; j++)
1276               {
1277                 if (j>start) size+=fprintf(fp,", ");
1278                 if ((size)>(USE_WIDTH))
1279                   {
1280                     (void) fprintf(fp,"\n");
1281                     size=pr_indent(fp,indent+INDENT);
1282                   }
1283                 size+=fprintf(fp,"%u",block->a[j]);
1284               }
1285             (void) fprintf(fp,"}\n");
1286             start=end;
1287           }
1288       if ((end!=block->nra)||(!ok))
1289         {
1290           (void) pr_indent(fp,indent);
1291           (void) fprintf(fp,"tables inconsistent, dumping complete tables:\n");
1292           low_pr_blocka(fp,indent,title,block,bShowNumbers);
1293         }
1294     }
1295 }
1296
1297 static void pr_strings(FILE *fp,int indent,const char *title,char ***nm,int n, gmx_bool bShowNumbers)
1298 {
1299   int i;
1300
1301   if (available(fp,nm,indent,title))
1302     {
1303       indent=pr_title_n(fp,indent,title,n);
1304       for (i=0; i<n; i++)
1305         {
1306           (void) pr_indent(fp,indent);
1307           (void) fprintf(fp,"%s[%d]={name=\"%s\"}\n",
1308                          title,bShowNumbers?i:-1,*(nm[i]));
1309         }
1310     }
1311 }
1312
1313 static void pr_strings2(FILE *fp,int indent,const char *title,
1314                         char ***nm,char ***nmB,int n, gmx_bool bShowNumbers)
1315 {
1316   int i;
1317
1318   if (available(fp,nm,indent,title))
1319     {
1320       indent=pr_title_n(fp,indent,title,n);
1321       for (i=0; i<n; i++)
1322         {
1323           (void) pr_indent(fp,indent);
1324           (void) fprintf(fp,"%s[%d]={name=\"%s\",nameB=\"%s\"}\n",
1325                          title,bShowNumbers?i:-1,*(nm[i]),*(nmB[i]));
1326         }
1327     }
1328 }
1329
1330 static void pr_resinfo(FILE *fp,int indent,const char *title,t_resinfo *resinfo,int n, gmx_bool bShowNumbers)
1331 {
1332     int i;
1333
1334     if (available(fp,resinfo,indent,title))
1335     {
1336         indent=pr_title_n(fp,indent,title,n);
1337         for (i=0; i<n; i++)
1338         {
1339             (void) pr_indent(fp,indent);
1340             (void) fprintf(fp,"%s[%d]={name=\"%s\", nr=%d, ic='%c'}\n",
1341                            title,bShowNumbers?i:-1,
1342                            *(resinfo[i].name),resinfo[i].nr,
1343                            (resinfo[i].ic == '\0') ? ' ' : resinfo[i].ic);
1344         }
1345     }
1346 }
1347
1348 static void pr_atom(FILE *fp,int indent,const char *title,t_atom *atom,int n)
1349 {
1350   int i,j;
1351
1352   if (available(fp,atom,indent,title)) {
1353     indent=pr_title_n(fp,indent,title,n);
1354     for (i=0; i<n; i++) {
1355       (void) pr_indent(fp,indent);
1356       fprintf(fp,"%s[%6d]={type=%3d, typeB=%3d, ptype=%8s, m=%12.5e, "
1357               "q=%12.5e, mB=%12.5e, qB=%12.5e, resind=%5d, atomnumber=%3d}\n",
1358               title,i,atom[i].type,atom[i].typeB,ptype_str[atom[i].ptype],
1359               atom[i].m,atom[i].q,atom[i].mB,atom[i].qB,
1360               atom[i].resind,atom[i].atomnumber);
1361     }
1362   }
1363 }
1364
1365 static void pr_grps(FILE *fp,int indent,const char *title,t_grps grps[],
1366                     char **grpname[], gmx_bool bShowNumbers)
1367 {
1368     int i,j;
1369
1370     for(i=0; (i<egcNR); i++)
1371     {
1372         fprintf(fp,"%s[%-12s] nr=%d, name=[",title,gtypes[i],grps[i].nr);
1373         for(j=0; (j<grps[i].nr); j++)
1374         {
1375             fprintf(fp," %s",*(grpname[grps[i].nm_ind[j]]));
1376         }
1377         fprintf(fp,"]\n");
1378     }
1379 }
1380
1381 static void pr_groups(FILE *fp,int indent,const char *title,
1382                       gmx_groups_t *groups,
1383                       gmx_bool bShowNumbers)
1384 {
1385     int grpnr[egcNR];
1386     int nat_max,i,g;
1387
1388     pr_grps(fp,indent,"grp",groups->grps,groups->grpname,bShowNumbers);
1389     pr_strings(fp,indent,"grpname",groups->grpname,groups->ngrpname,bShowNumbers);
1390
1391     (void) pr_indent(fp,indent);
1392     fprintf(fp,"groups          ");
1393     for(g=0; g<egcNR; g++)
1394     {
1395        printf(" %5.5s",gtypes[g]);
1396     }
1397     printf("\n");
1398
1399     (void) pr_indent(fp,indent);
1400     fprintf(fp,"allocated       ");
1401     nat_max = 0;
1402     for(g=0; g<egcNR; g++)
1403     {
1404         printf(" %5d",groups->ngrpnr[g]);
1405         nat_max = max(nat_max,groups->ngrpnr[g]);
1406     }
1407     printf("\n");
1408
1409     if (nat_max == 0)
1410     {
1411         (void) pr_indent(fp,indent);
1412         fprintf(fp,"groupnr[%5s] =","*");
1413         for(g=0; g<egcNR; g++)
1414         {
1415             fprintf(fp,"  %3d ",0);
1416         }
1417         fprintf(fp,"\n");
1418     }
1419     else
1420     {
1421         for(i=0; i<nat_max; i++)
1422         {
1423             (void) pr_indent(fp,indent);
1424             fprintf(fp,"groupnr[%5d] =",i);
1425             for(g=0; g<egcNR; g++)
1426             {
1427                 fprintf(fp,"  %3d ",
1428                         groups->grpnr[g] ? groups->grpnr[g][i] : 0);
1429             }
1430             fprintf(fp,"\n");
1431         }
1432     }
1433 }
1434
1435 void pr_atoms(FILE *fp,int indent,const char *title,t_atoms *atoms,
1436               gmx_bool bShownumbers)
1437 {
1438   if (available(fp,atoms,indent,title))
1439     {
1440       indent=pr_title(fp,indent,title);
1441       pr_atom(fp,indent,"atom",atoms->atom,atoms->nr);
1442       pr_strings(fp,indent,"atom",atoms->atomname,atoms->nr,bShownumbers);
1443       pr_strings2(fp,indent,"type",atoms->atomtype,atoms->atomtypeB,atoms->nr,bShownumbers);
1444       pr_resinfo(fp,indent,"residue",atoms->resinfo,atoms->nres,bShownumbers);
1445     }
1446 }
1447
1448
1449 void pr_atomtypes(FILE *fp,int indent,const char *title,t_atomtypes *atomtypes,
1450                   gmx_bool bShowNumbers)
1451 {
1452   int i;
1453   if (available(fp,atomtypes,indent,title))
1454   {
1455     indent=pr_title(fp,indent,title);
1456     for(i=0;i<atomtypes->nr;i++) {
1457       pr_indent(fp,indent);
1458                 fprintf(fp,
1459                                 "atomtype[%3d]={radius=%12.5e, volume=%12.5e, gb_radius=%12.5e, surftens=%12.5e, atomnumber=%4d, S_hct=%12.5e)}\n",
1460                                 bShowNumbers?i:-1,atomtypes->radius[i],atomtypes->vol[i],
1461                                 atomtypes->gb_radius[i],
1462                                 atomtypes->surftens[i],atomtypes->atomnumber[i],atomtypes->S_hct[i]);
1463     }
1464   }
1465 }
1466
1467 static void pr_moltype(FILE *fp,int indent,const char *title,
1468                        gmx_moltype_t *molt,int n,
1469                        gmx_ffparams_t *ffparams,
1470                        gmx_bool bShowNumbers)
1471 {
1472     int j;
1473
1474     indent = pr_title_n(fp,indent,title,n);
1475     (void) pr_indent(fp,indent);
1476     (void) fprintf(fp,"name=\"%s\"\n",*(molt->name));
1477     pr_atoms(fp,indent,"atoms",&(molt->atoms),bShowNumbers);
1478     pr_block(fp,indent,"cgs",&molt->cgs, bShowNumbers);
1479     pr_blocka(fp,indent,"excls",&molt->excls, bShowNumbers);
1480     for(j=0; (j<F_NRE); j++) {
1481         pr_ilist(fp,indent,interaction_function[j].longname,
1482                  ffparams->functype,&molt->ilist[j],bShowNumbers);
1483     }
1484 }
1485
1486 static void pr_molblock(FILE *fp,int indent,const char *title,
1487                         gmx_molblock_t *molb,int n,
1488                         gmx_moltype_t *molt,
1489                         gmx_bool bShowNumbers)
1490 {
1491     indent = pr_title_n(fp,indent,title,n);
1492     (void) pr_indent(fp,indent);
1493     (void) fprintf(fp,"%-20s = %d \"%s\"\n",
1494                    "moltype",molb->type,*(molt[molb->type].name));
1495     pr_int(fp,indent,"#molecules",molb->nmol);
1496     pr_int(fp,indent,"#atoms_mol",molb->natoms_mol);
1497     pr_int(fp,indent,"#posres_xA",molb->nposres_xA);
1498     if (molb->nposres_xA > 0) {
1499         pr_rvecs(fp,indent,"posres_xA",molb->posres_xA,molb->nposres_xA);
1500     }
1501     pr_int(fp,indent,"#posres_xB",molb->nposres_xB);
1502     if (molb->nposres_xB > 0) {
1503         pr_rvecs(fp,indent,"posres_xB",molb->posres_xB,molb->nposres_xB);
1504     }
1505 }
1506
1507 void pr_mtop(FILE *fp,int indent,const char *title,gmx_mtop_t *mtop,
1508              gmx_bool bShowNumbers)
1509 {
1510     int mt,mb;
1511
1512     if (available(fp,mtop,indent,title)) {
1513         indent=pr_title(fp,indent,title);
1514         (void) pr_indent(fp,indent);
1515         (void) fprintf(fp,"name=\"%s\"\n",*(mtop->name));
1516         pr_int(fp,indent,"#atoms",mtop->natoms);
1517         pr_int(fp,indent,"#molblock",mtop->nmolblock);
1518         for(mb=0; mb<mtop->nmolblock; mb++) {
1519             pr_molblock(fp,indent,"molblock",&mtop->molblock[mb],mb,
1520                         mtop->moltype,bShowNumbers);
1521         }
1522         pr_ffparams(fp,indent,"ffparams",&(mtop->ffparams),bShowNumbers);
1523         pr_atomtypes(fp,indent,"atomtypes",&(mtop->atomtypes),bShowNumbers);
1524         for(mt=0; mt<mtop->nmoltype; mt++) {
1525             pr_moltype(fp,indent,"moltype",&mtop->moltype[mt],mt,
1526                        &mtop->ffparams,bShowNumbers);
1527         }
1528         pr_groups(fp,indent,"groups",&mtop->groups,bShowNumbers);
1529     }
1530 }
1531
1532 void pr_top(FILE *fp,int indent,const char *title,t_topology *top, gmx_bool bShowNumbers)
1533 {
1534   if (available(fp,top,indent,title)) {
1535     indent=pr_title(fp,indent,title);
1536     (void) pr_indent(fp,indent);
1537     (void) fprintf(fp,"name=\"%s\"\n",*(top->name));
1538     pr_atoms(fp,indent,"atoms",&(top->atoms),bShowNumbers);
1539     pr_atomtypes(fp,indent,"atomtypes",&(top->atomtypes),bShowNumbers);
1540     pr_block(fp,indent,"cgs",&top->cgs, bShowNumbers);
1541     pr_block(fp,indent,"mols",&top->mols, bShowNumbers);
1542     pr_blocka(fp,indent,"excls",&top->excls, bShowNumbers);
1543     pr_idef(fp,indent,"idef",&top->idef,bShowNumbers);
1544   }
1545 }
1546
1547 void pr_header(FILE *fp,int indent,const char *title,t_tpxheader *sh)
1548 {
1549   char buf[22];
1550
1551   if (available(fp,sh,indent,title))
1552     {
1553       indent=pr_title(fp,indent,title);
1554       pr_indent(fp,indent);
1555       fprintf(fp,"bIr    = %spresent\n",sh->bIr?"":"not ");
1556       pr_indent(fp,indent);
1557       fprintf(fp,"bBox   = %spresent\n",sh->bBox?"":"not ");
1558       pr_indent(fp,indent);
1559       fprintf(fp,"bTop   = %spresent\n",sh->bTop?"":"not ");
1560       pr_indent(fp,indent);
1561       fprintf(fp,"bX     = %spresent\n",sh->bX?"":"not ");
1562       pr_indent(fp,indent);
1563       fprintf(fp,"bV     = %spresent\n",sh->bV?"":"not ");
1564       pr_indent(fp,indent);
1565       fprintf(fp,"bF     = %spresent\n",sh->bF?"":"not ");
1566
1567       pr_indent(fp,indent);
1568       fprintf(fp,"natoms = %d\n",sh->natoms);
1569       pr_indent(fp,indent);
1570       fprintf(fp,"lambda = %e\n",sh->lambda);
1571     }
1572 }
1573
1574 void pr_commrec(FILE *fp,int indent,t_commrec *cr)
1575 {
1576   pr_indent(fp,indent);
1577   fprintf(fp,"commrec:\n");
1578   indent+=2;
1579   pr_indent(fp,indent);
1580   fprintf(fp,"nodeid    = %d\n",cr->nodeid);
1581   pr_indent(fp,indent);
1582   fprintf(fp,"nnodes    = %d\n",cr->nnodes);
1583   pr_indent(fp,indent);
1584   fprintf(fp,"npmenodes = %d\n",cr->npmenodes);
1585   /*
1586   pr_indent(fp,indent);
1587   fprintf(fp,"threadid  = %d\n",cr->threadid);
1588   pr_indent(fp,indent);
1589   fprintf(fp,"nthreads  = %d\n",cr->nthreads);
1590   */
1591 }