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
  32  *
  33  * And Hey:
  34  * GROningen Mixture of Alchemy and Childrens' Stories
  35  */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 /* This file is completely threadsafe - please keep it that way! */
  41 #ifdef GMX_THREADS
  42 #include <thread_mpi.h>
  43 #endif
  44
  45
  46 #include <stdio.h>
  47 #include "smalloc.h"
  48 #include "typedefs.h"
  49 #include "names.h"
  50 #include "txtdump.h"
  51 #include "string2.h"
  52 #include "vec.h"
  53
  54
  55 int pr_indent(FILE *fp,int n)
  56 {
  57   int i;
  58
  59   for (i=0; i<n; i++) (void) fprintf(fp," ");
  60   return n;
  61 }
  62
  63 int available(FILE *fp,void *p,int indent,const char *title)
  64 {
  65   if (!p) {
  66     if (indent > 0)
  67       pr_indent(fp,indent);
  68     (void) fprintf(fp,"%s: not available\n",title);
  69   }
  70   return (p!=NULL);
  71 }
  72
  73 int pr_title(FILE *fp,int indent,const char *title)
  74 {
  75   (void) pr_indent(fp,indent);
  76   (void) fprintf(fp,"%s:\n",title);
  77   return (indent+INDENT);
  78 }
  79
  80 int pr_title_n(FILE *fp,int indent,const char *title,int n)
  81 {
  82   (void) pr_indent(fp,indent);
  83   (void) fprintf(fp,"%s (%d):\n",title,n);
  84   return (indent+INDENT);
  85 }
  86
  87 int pr_title_nxn(FILE *fp,int indent,const char *title,int n1,int n2)
  88 {
  89   (void) pr_indent(fp,indent);
  90   (void) fprintf(fp,"%s (%dx%d):\n",title,n1,n2);
  91   return (indent+INDENT);
  92 }
  93
  94 void pr_ivec(FILE *fp,int indent,const char *title,int vec[],int n, gmx_bool bShowNumbers)
  95 {
  96   int i;
  97
  98   if (available(fp,vec,indent,title))
  99     {
 100       indent=pr_title_n(fp,indent,title,n);
 101       for (i=0; i<n; i++)
 102         {
 103           (void) pr_indent(fp,indent);
 104           (void) fprintf(fp,"%s[%d]=%d\n",title,bShowNumbers?i:-1,vec[i]);
 105         }
 106     }
 107 }
 108
 109 void pr_ivec_block(FILE *fp,int indent,const char *title,int vec[],int n, gmx_bool bShowNumbers)
 110 {
 111     int i,j;
 112
 113     if (available(fp,vec,indent,title))
 114     {
 115         indent=pr_title_n(fp,indent,title,n);
 116         i = 0;
 117         while (i < n)
 118         {
 119             j = i+1;
 120             while (j < n && vec[j] == vec[j-1]+1)
 121             {
 122                 j++;
 123             }
 124             /* Print consecutive groups of 3 or more as blocks */
 125             if (j - i < 3)
 126             {
 127                 while(i < j)
 128                 {
 129                     (void) pr_indent(fp,indent);
 130                     (void) fprintf(fp,"%s[%d]=%d\n",
 131                                    title,bShowNumbers?i:-1,vec[i]);
 132                     i++;
 133                 }
 134             }
 135             else
 136             {
 137                 (void) pr_indent(fp,indent);
 138                 (void) fprintf(fp,"%s[%d,...,%d] = {%d,...,%d}\n",
 139                                title,
 140                                bShowNumbers?i:-1,
 141                                bShowNumbers?j-1:-1,
 142                                vec[i],vec[j-1]);
 143                 i = j;
 144             }
 145         }
 146     }
 147 }
 148
 149 void pr_bvec(FILE *fp,int indent,const char *title,gmx_bool vec[],int n, gmx_bool bShowNumbers)
 150 {
 151   int i;
 152
 153   if (available(fp,vec,indent,title))
 154     {
 155       indent=pr_title_n(fp,indent,title,n);
 156       for (i=0; i<n; i++)
 157         {
 158           (void) pr_indent(fp,indent);
 159           (void) fprintf(fp,"%s[%d]=%s\n",title,bShowNumbers?i:-1,
 160                          BOOL(vec[i]));
 161         }
 162     }
 163 }
 164
 165 void pr_ivecs(FILE *fp,int indent,const char *title,ivec vec[],int n, gmx_bool bShowNumbers)
 166 {
 167   int i,j;
 168
 169   if (available(fp,vec,indent,title))
 170     {
 171       indent=pr_title_nxn(fp,indent,title,n,DIM);
 172       for (i=0; i<n; i++)
 173         {
 174           (void) pr_indent(fp,indent);
 175           (void) fprintf(fp,"%s[%d]={",title,bShowNumbers?i:-1);
 176           for (j=0; j<DIM; j++)
 177             {
 178               if (j!=0) (void) fprintf(fp,", ");
 179               fprintf(fp,"%d",vec[i][j]);
 180             }
 181           (void) fprintf(fp,"}\n");
 182         }
 183     }
 184 }
 185
 186 void pr_rvec(FILE *fp,int indent,const char *title,real vec[],int n, gmx_bool bShowNumbers)
 187 {
 188   int i;
 189
 190   if (available(fp,vec,indent,title))
 191     {
 192       indent=pr_title_n(fp,indent,title,n);
 193       for (i=0; i<n; i++)
 194         {
 195           pr_indent(fp,indent);
 196           fprintf(fp,"%s[%d]=%12.5e\n",title,bShowNumbers?i:-1,vec[i]);
 197         }
 198     }
 199 }
 200
 201 void pr_dvec(FILE *fp,int indent,const char *title,double vec[],int n, gmx_bool bShowNumbers)
 202 {
 203         int i;
 204
 205         if (available(fp,vec,indent,title))
 206     {
 207                 indent=pr_title_n(fp,indent,title,n);
 208                 for (i=0; i<n; i++)
 209         {
 210                         pr_indent(fp,indent);
 211                         fprintf(fp,"%s[%d]=%12.5e\n",title,bShowNumbers?i:-1,vec[i]);
 212         }
 213     }
 214 }
 215
 216
 217 /*
 218 void pr_mat(FILE *fp,int indent,char *title,matrix m)
 219 {
 220   int i,j;
 221
 222   if (available(fp,m,indent,title)) {
 223     indent=pr_title_n(fp,indent,title,n);
 224     for(i=0; i<n; i++) {
 225       pr_indent(fp,indent);
 226       fprintf(fp,"%s[%d]=%12.5e %12.5e %12.5e\n",
 227               title,bShowNumbers?i:-1,m[i][XX],m[i][YY],m[i][ZZ]);
 228     }
 229   }
 230 }
 231 */
 232
 233 void pr_rvecs_len(FILE *fp,int indent,const char *title,rvec vec[],int n)
 234 {
 235   int i,j;
 236
 237   if (available(fp,vec,indent,title)) {
 238     indent=pr_title_nxn(fp,indent,title,n,DIM);
 239     for (i=0; i<n; i++) {
 240       (void) pr_indent(fp,indent);
 241       (void) fprintf(fp,"%s[%5d]={",title,i);
 242       for (j=0; j<DIM; j++) {
 243         if (j != 0)
 244           (void) fprintf(fp,", ");
 245         (void) fprintf(fp,"%12.5e",vec[i][j]);
 246       }
 247       (void) fprintf(fp,"} len=%12.5e\n",norm(vec[i]));
 248     }
 249   }
 250 }
 251
 252 void pr_rvecs(FILE *fp,int indent,const char *title,rvec vec[],int n)
 253 {
 254   const char *fshort = "%12.5e";
 255   const char *flong  = "%15.8e";
 256   const char *format;
 257   int i,j;
 258
 259   if (getenv("LONGFORMAT") != NULL)
 260     format = flong;
 261   else
 262     format = fshort;
 263
 264   if (available(fp,vec,indent,title)) {
 265     indent=pr_title_nxn(fp,indent,title,n,DIM);
 266     for (i=0; i<n; i++) {
 267       (void) pr_indent(fp,indent);
 268       (void) fprintf(fp,"%s[%5d]={",title,i);
 269       for (j=0; j<DIM; j++) {
 270         if (j != 0)
 271           (void) fprintf(fp,", ");
 272         (void) fprintf(fp,format,vec[i][j]);
 273       }
 274       (void) fprintf(fp,"}\n");
 275     }
 276   }
 277 }
 278
 279
 280 void pr_reals(FILE *fp,int indent,const char *title,real *vec,int n)
 281 {
 282   int i;
 283
 284   if (available(fp,vec,indent,title)) {
 285     (void) pr_indent(fp,indent);
 286     (void) fprintf(fp,"%s:\t",title);
 287     for(i=0; i<n; i++)
 288       fprintf(fp,"  %10g",vec[i]);
 289     (void) fprintf(fp,"\n");
 290   }
 291 }
 292
 293 void pr_doubles(FILE *fp,int indent,const char *title,double *vec,int n)
 294 {
 295   int i;
 296
 297   if (available(fp,vec,indent,title)) {
 298     (void) pr_indent(fp,indent);
 299     (void) fprintf(fp,"%s:\t",title);
 300     for(i=0; i<n; i++)
 301       fprintf(fp,"  %10g",vec[i]);
 302     (void) fprintf(fp,"\n");
 303   }
 304 }
 305
 306 static void pr_int(FILE *fp,int indent,const char *title,int i)
 307 {
 308   pr_indent(fp,indent);
 309   fprintf(fp,"%-20s = %d\n",title,i);
 310 }
 311
 312 static void pr_gmx_large_int(FILE *fp,int indent,const char *title,gmx_large_int_t i)
 313 {
 314   char buf[STEPSTRSIZE];
 315
 316   pr_indent(fp,indent);
 317   fprintf(fp,"%-20s = %s\n",title,gmx_step_str(i,buf));
 318 }
 319
 320 static void pr_real(FILE *fp,int indent,const char *title,real r)
 321 {
 322   pr_indent(fp,indent);
 323   fprintf(fp,"%-20s = %g\n",title,r);
 324 }
 325
 326 static void pr_double(FILE *fp,int indent,const char *title,double d)
 327 {
 328   pr_indent(fp,indent);
 329   fprintf(fp,"%-20s = %g\n",title,d);
 330 }
 331
 332 static void pr_str(FILE *fp,int indent,const char *title,const char *s)
 333 {
 334   pr_indent(fp,indent);
 335   fprintf(fp,"%-20s = %s\n",title,s);
 336 }
 337
 338 void pr_qm_opts(FILE *fp,int indent,const char *title,t_grpopts *opts)
 339 {
 340   int i,m,j;
 341
 342   fprintf(fp,"%s:\n",title);
 343
 344   pr_int(fp,indent,"ngQM",opts->ngQM);
 345   if (opts->ngQM > 0) {
 346     pr_ivec(fp,indent,"QMmethod",opts->QMmethod,opts->ngQM,FALSE);
 347     pr_ivec(fp,indent,"QMbasis",opts->QMbasis,opts->ngQM,FALSE);
 348     pr_ivec(fp,indent,"QMcharge",opts->QMcharge,opts->ngQM,FALSE);
 349     pr_ivec(fp,indent,"QMmult",opts->QMmult,opts->ngQM,FALSE);
 350     pr_bvec(fp,indent,"bSH",opts->bSH,opts->ngQM,FALSE);
 351     pr_ivec(fp,indent,"CASorbitals",opts->CASorbitals,opts->ngQM,FALSE);
 352     pr_ivec(fp,indent,"CASelectrons",opts->CASelectrons,opts->ngQM,FALSE);
 353     pr_rvec(fp,indent,"SAon",opts->SAon,opts->ngQM,FALSE);
 354     pr_rvec(fp,indent,"SAon",opts->SAon,opts->ngQM,FALSE);
 355     pr_ivec(fp,indent,"SAsteps",opts->SAsteps,opts->ngQM,FALSE);
 356     pr_bvec(fp,indent,"bOPT",opts->bOPT,opts->ngQM,FALSE);
 357     pr_bvec(fp,indent,"bTS",opts->bTS,opts->ngQM,FALSE);
 358   }
 359 }
 360
 361 static void pr_grp_opts(FILE *out,int indent,const char *title,t_grpopts *opts,
 362                         gmx_bool bMDPformat)
 363 {
 364   int i,m,j;
 365
 366   if (!bMDPformat)
 367     fprintf(out,"%s:\n",title);
 368
 369   pr_indent(out,indent);
 370   fprintf(out,"nrdf%s",bMDPformat ? " = " : ":");
 371   for(i=0; (i<opts->ngtc); i++)
 372     fprintf(out,"  %10g",opts->nrdf[i]);
 373   fprintf(out,"\n");
 374
 375   pr_indent(out,indent);
 376   fprintf(out,"ref_t%s",bMDPformat ? " = " : ":");
 377   for(i=0; (i<opts->ngtc); i++)
 378     fprintf(out,"  %10g",opts->ref_t[i]);
 379   fprintf(out,"\n");
 380
 381   pr_indent(out,indent);
 382   fprintf(out,"tau_t%s",bMDPformat ? " = " : ":");
 383   for(i=0; (i<opts->ngtc); i++)
 384     fprintf(out,"  %10g",opts->tau_t[i]);
 385   fprintf(out,"\n");
 386
 387   /* Pretty-print the simulated annealing info */
 388   fprintf(out,"anneal%s",bMDPformat ? " = " : ":");
 389   for(i=0; (i<opts->ngtc); i++)
 390     fprintf(out,"  %10s",EANNEAL(opts->annealing[i]));
 391   fprintf(out,"\n");
 392
 393   fprintf(out,"ann_npoints%s",bMDPformat ? " = " : ":");
 394   for(i=0; (i<opts->ngtc); i++)
 395     fprintf(out,"  %10d",opts->anneal_npoints[i]);
 396   fprintf(out,"\n");
 397
 398   for(i=0; (i<opts->ngtc); i++) {
 399     if(opts->anneal_npoints[i]>0) {
 400       fprintf(out,"ann. times [%d]:\t",i);
 401       for(j=0; (j<opts->anneal_npoints[i]); j++)
 402         fprintf(out,"  %10.1f",opts->anneal_time[i][j]);
 403       fprintf(out,"\n");
 404       fprintf(out,"ann. temps [%d]:\t",i);
 405       for(j=0; (j<opts->anneal_npoints[i]); j++)
 406         fprintf(out,"  %10.1f",opts->anneal_temp[i][j]);
 407       fprintf(out,"\n");
 408     }
 409   }
 410
 411   pr_indent(out,indent);
 412   fprintf(out,"acc:\t");
 413   for(i=0; (i<opts->ngacc); i++)
 414     for(m=0; (m<DIM); m++)
 415       fprintf(out,"  %10g",opts->acc[i][m]);
 416   fprintf(out,"\n");
 417
 418   pr_indent(out,indent);
 419   fprintf(out,"nfreeze:");
 420   for(i=0; (i<opts->ngfrz); i++)
 421     for(m=0; (m<DIM); m++)
 422       fprintf(out,"  %10s",opts->nFreeze[i][m] ? "Y" : "N");
 423   fprintf(out,"\n");
 424
 425
 426   for(i=0; (i<opts->ngener); i++) {
 427     pr_indent(out,indent);
 428     fprintf(out,"energygrp_flags[%3d]:",i);
 429     for(m=0; (m<opts->ngener); m++)
 430       fprintf(out," %d",opts->egp_flags[opts->ngener*i+m]);
 431     fprintf(out,"\n");
 432   }
 433
 434   fflush(out);
 435 }
 436
 437 static void pr_matrix(FILE *fp,int indent,const char *title,rvec *m,
 438                       gmx_bool bMDPformat)
 439 {
 440   if (bMDPformat)
 441     fprintf(fp,"%-10s    = %g %g %g %g %g %g\n",title,
 442             m[XX][XX],m[YY][YY],m[ZZ][ZZ],m[XX][YY],m[XX][ZZ],m[YY][ZZ]);
 443   else
 444     pr_rvecs(fp,indent,title,m,DIM);
 445 }
 446
 447 static void pr_cosine(FILE *fp,int indent,const char *title,t_cosines *cos,
 448                       gmx_bool bMDPformat)
 449 {
 450   int j;
 451
 452   if (bMDPformat) {
 453     fprintf(fp,"%s = %d\n",title,cos->n);
 454   }
 455   else {
 456     indent=pr_title(fp,indent,title);
 457     (void) pr_indent(fp,indent);
 458     fprintf(fp,"n = %d\n",cos->n);
 459     if (cos->n > 0) {
 460       (void) pr_indent(fp,indent+2);
 461       fprintf(fp,"a =");
 462       for(j=0; (j<cos->n); j++)
 463         fprintf(fp," %e",cos->a[j]);
 464       fprintf(fp,"\n");
 465       (void) pr_indent(fp,indent+2);
 466       fprintf(fp,"phi =");
 467       for(j=0; (j<cos->n); j++)
 468         fprintf(fp," %e",cos->phi[j]);
 469       fprintf(fp,"\n");
 470     }
 471   }
 472 }
 473
 474 #define PS(t,s) pr_str(fp,indent,t,s)
 475 #define PI(t,s) pr_int(fp,indent,t,s)
 476 #define PSTEP(t,s) pr_gmx_large_int(fp,indent,t,s)
 477 #define PR(t,s) pr_real(fp,indent,t,s)
 478 #define PD(t,s) pr_double(fp,indent,t,s)
 479
 480 static void pr_pullgrp(FILE *fp,int indent,int g,t_pullgrp *pg)
 481 {
 482   pr_indent(fp,indent);
 483   fprintf(fp,"pull_group %d:\n",g);
 484   indent += 2;
 485   pr_ivec_block(fp,indent,"atom",pg->ind,pg->nat,TRUE);
 486   pr_rvec(fp,indent,"weight",pg->weight,pg->nweight,TRUE);
 487   PI("pbcatom",pg->pbcatom);
 488   pr_rvec(fp,indent,"vec",pg->vec,DIM,TRUE);
 489   pr_rvec(fp,indent,"init",pg->init,DIM,TRUE);
 490   PR("rate",pg->rate);
 491   PR("k",pg->k);
 492   PR("kB",pg->kB);
 493 }
 494
 495 static void pr_pull(FILE *fp,int indent,t_pull *pull)
 496 {
 497   int g;
 498
 499   PS("pull_geometry",EPULLGEOM(pull->eGeom));
 500   pr_ivec(fp,indent,"pull_dim",pull->dim,DIM,TRUE);
 501   PR("pull_r1",pull->cyl_r1);
 502   PR("pull_r0",pull->cyl_r0);
 503   PR("pull_constr_tol",pull->constr_tol);
 504   PI("pull_nstxout",pull->nstxout);
 505   PI("pull_nstfout",pull->nstfout);
 506   PI("pull_ngrp",pull->ngrp);
 507   for(g=0; g<pull->ngrp+1; g++)
 508     pr_pullgrp(fp,indent,g,&pull->grp[g]);
 509 }
 510
 511 static void pr_rotgrp(FILE *fp,int indent,int g,t_rotgrp *rotg)
 512 {
 513   pr_indent(fp,indent);
 514   fprintf(fp,"rotation_group %d:\n",g);
 515   indent += 2;
 516   PS("type",EROTGEOM(rotg->eType));
 517   PS("massw",BOOL(rotg->bMassW));
 518   pr_ivec_block(fp,indent,"atom",rotg->ind,rotg->nat,TRUE);
 519   pr_rvecs(fp,indent,"x_ref",rotg->x_ref,rotg->nat);
 520   pr_rvec(fp,indent,"vec",rotg->vec,DIM,TRUE);
 521   pr_rvec(fp,indent,"pivot",rotg->pivot,DIM,TRUE);
 522   PR("rate",rotg->rate);
 523   PR("k",rotg->k);
 524   PR("slab_dist",rotg->slab_dist);
 525   PR("min_gaussian",rotg->min_gaussian);
 526   PR("epsilon",rotg->eps);
 527   PS("fit_method",EROTFIT(rotg->eFittype));
 528 }
 529
 530 static void pr_rot(FILE *fp,int indent,t_rot *rot)
 531 {
 532   int g;
 533
 534   PI("rot_nstrout",rot->nstrout);
 535   PI("rot_nstsout",rot->nstsout);
 536   PI("rot_ngrp",rot->ngrp);
 537   for(g=0; g<rot->ngrp; g++)
 538     pr_rotgrp(fp,indent,g,&rot->grp[g]);
 539 }
 540
 541 void pr_inputrec(FILE *fp,int indent,const char *title,t_inputrec *ir,
 542                  gmx_bool bMDPformat)
 543 {
 544   const char *infbuf="inf";
 545   int  i;
 546
 547   if (available(fp,ir,indent,title)) {
 548     if (!bMDPformat)
 549       indent=pr_title(fp,indent,title);
 550     PS("integrator",EI(ir->eI));
 551     PSTEP("nsteps",ir->nsteps);
 552     PSTEP("init_step",ir->init_step);
 553     PS("ns_type",ENS(ir->ns_type));
 554     PI("nstlist",ir->nstlist);
 555     PI("ndelta",ir->ndelta);
 556     PI("nstcomm",ir->nstcomm);
 557     PS("comm_mode",ECOM(ir->comm_mode));
 558     PI("nstlog",ir->nstlog);
 559     PI("nstxout",ir->nstxout);
 560     PI("nstvout",ir->nstvout);
 561     PI("nstfout",ir->nstfout);
 562     PI("nstcalcenergy",ir->nstcalcenergy);
 563     PI("nstenergy",ir->nstenergy);
 564     PI("nstxtcout",ir->nstxtcout);
 565     PR("init_t",ir->init_t);
 566     PR("delta_t",ir->delta_t);
 567
 568     PR("xtcprec",ir->xtcprec);
 569     PI("nkx",ir->nkx);
 570     PI("nky",ir->nky);
 571     PI("nkz",ir->nkz);
 572     PI("pme_order",ir->pme_order);
 573     PR("ewald_rtol",ir->ewald_rtol);
 574     PR("ewald_geometry",ir->ewald_geometry);
 575     PR("epsilon_surface",ir->epsilon_surface);
 576     PS("optimize_fft",BOOL(ir->bOptFFT));
 577     PS("ePBC",EPBC(ir->ePBC));
 578     PS("bPeriodicMols",BOOL(ir->bPeriodicMols));
 579     PS("bContinuation",BOOL(ir->bContinuation));
 580     PS("bShakeSOR",BOOL(ir->bShakeSOR));
 581     PS("etc",ETCOUPLTYPE(ir->etc));
 582     PI("nsttcouple",ir->nsttcouple);
 583     PS("epc",EPCOUPLTYPE(ir->epc));
 584     PS("epctype",EPCOUPLTYPETYPE(ir->epct));
 585     PI("nstpcouple",ir->nstpcouple);
 586     PR("tau_p",ir->tau_p);
 587     pr_matrix(fp,indent,"ref_p",ir->ref_p,bMDPformat);
 588     pr_matrix(fp,indent,"compress",ir->compress,bMDPformat);
 589     PS("refcoord_scaling",EREFSCALINGTYPE(ir->refcoord_scaling));
 590     if (bMDPformat)
 591       fprintf(fp,"posres_com  = %g %g %g\n",ir->posres_com[XX],
 592               ir->posres_com[YY],ir->posres_com[ZZ]);
 593     else
 594       pr_rvec(fp,indent,"posres_com",ir->posres_com,DIM,TRUE);
 595     if (bMDPformat)
 596       fprintf(fp,"posres_comB = %g %g %g\n",ir->posres_comB[XX],
 597               ir->posres_comB[YY],ir->posres_comB[ZZ]);
 598     else
 599       pr_rvec(fp,indent,"posres_comB",ir->posres_comB,DIM,TRUE);
 600     PI("andersen_seed",ir->andersen_seed);
 601     PR("rlist",ir->rlist);
 602     PR("rlistlong",ir->rlistlong);
 603     PR("rtpi",ir->rtpi);
 604     PS("coulombtype",EELTYPE(ir->coulombtype));
 605     PR("rcoulomb_switch",ir->rcoulomb_switch);
 606     PR("rcoulomb",ir->rcoulomb);
 607     PS("vdwtype",EVDWTYPE(ir->vdwtype));
 608     PR("rvdw_switch",ir->rvdw_switch);
 609     PR("rvdw",ir->rvdw);
 610     if (ir->epsilon_r != 0)
 611       PR("epsilon_r",ir->epsilon_r);
 612     else
 613       PS("epsilon_r",infbuf);
 614     if (ir->epsilon_rf != 0)
 615       PR("epsilon_rf",ir->epsilon_rf);
 616     else
 617       PS("epsilon_rf",infbuf);
 618     PR("tabext",ir->tabext);
 619     PS("implicit_solvent",EIMPLICITSOL(ir->implicit_solvent));
 620     PS("gb_algorithm",EGBALGORITHM(ir->gb_algorithm));
 621     PR("gb_epsilon_solvent",ir->gb_epsilon_solvent);
 622     PI("nstgbradii",ir->nstgbradii);
 623     PR("rgbradii",ir->rgbradii);
 624     PR("gb_saltconc",ir->gb_saltconc);
 625     PR("gb_obc_alpha",ir->gb_obc_alpha);
 626     PR("gb_obc_beta",ir->gb_obc_beta);
 627     PR("gb_obc_gamma",ir->gb_obc_gamma);
 628     PR("gb_dielectric_offset",ir->gb_dielectric_offset);
 629     PS("sa_algorithm",ESAALGORITHM(ir->gb_algorithm));
 630     PR("sa_surface_tension",ir->sa_surface_tension);
 631
 632     PS("DispCorr",EDISPCORR(ir->eDispCorr));
 633     PS("free_energy",EFEPTYPE(ir->efep));
 634     PR("init_lambda",ir->init_lambda);
 635     PR("delta_lambda",ir->delta_lambda);
 636     if (!bMDPformat)
 637     {
 638         PI("n_foreign_lambda",ir->n_flambda);
 639     }
 640     if (ir->n_flambda > 0)
 641     {
 642         pr_indent(fp,indent);
 643         fprintf(fp,"foreign_lambda%s",bMDPformat ? " = " : ":");
 644         for(i=0; i<ir->n_flambda; i++)
 645         {
 646             fprintf(fp,"  %10g",ir->flambda[i]);
 647         }
 648         fprintf(fp,"\n");
 649     }
 650     PR("sc_alpha",ir->sc_alpha);
 651     PI("sc_power",ir->sc_power);
 652     PR("sc_sigma",ir->sc_sigma);
 653     PR("sc_sigma_min",ir->sc_sigma_min);
 654     PI("nstdhdl", ir->nstdhdl);
 655     PS("separate_dhdl_file", SEPDHDLFILETYPE(ir->separate_dhdl_file));
 656     PS("dhdl_derivatives", DHDLDERIVATIVESTYPE(ir->dhdl_derivatives));
 657     PI("dh_hist_size", ir->dh_hist_size);
 658     PD("dh_hist_spacing", ir->dh_hist_spacing);
 659
 660     PI("nwall",ir->nwall);
 661     PS("wall_type",EWALLTYPE(ir->wall_type));
 662     PI("wall_atomtype[0]",ir->wall_atomtype[0]);
 663     PI("wall_atomtype[1]",ir->wall_atomtype[1]);
 664     PR("wall_density[0]",ir->wall_density[0]);
 665     PR("wall_density[1]",ir->wall_density[1]);
 666     PR("wall_ewald_zfac",ir->wall_ewald_zfac);
 667
 668     PS("pull",EPULLTYPE(ir->ePull));
 669     if (ir->ePull != epullNO)
 670       pr_pull(fp,indent,ir->pull);
 671
 672     PS("rotation",BOOL(ir->bRot));
 673     if (ir->bRot)
 674       pr_rot(fp,indent,ir->rot);
 675
 676     PS("disre",EDISRETYPE(ir->eDisre));
 677     PS("disre_weighting",EDISREWEIGHTING(ir->eDisreWeighting));
 678     PS("disre_mixed",BOOL(ir->bDisreMixed));
 679     PR("dr_fc",ir->dr_fc);
 680     PR("dr_tau",ir->dr_tau);
 681     PR("nstdisreout",ir->nstdisreout);
 682     PR("orires_fc",ir->orires_fc);
 683     PR("orires_tau",ir->orires_tau);
 684     PR("nstorireout",ir->nstorireout);
 685
 686     PR("dihre-fc",ir->dihre_fc);
 687
 688     PR("em_stepsize",ir->em_stepsize);
 689     PR("em_tol",ir->em_tol);
 690     PI("niter",ir->niter);
 691     PR("fc_stepsize",ir->fc_stepsize);
 692     PI("nstcgsteep",ir->nstcgsteep);
 693     PI("nbfgscorr",ir->nbfgscorr);
 694
 695     PS("ConstAlg",ECONSTRTYPE(ir->eConstrAlg));
 696     PR("shake_tol",ir->shake_tol);
 697     PI("lincs_order",ir->nProjOrder);
 698     PR("lincs_warnangle",ir->LincsWarnAngle);
 699     PI("lincs_iter",ir->nLincsIter);
 700     PR("bd_fric",ir->bd_fric);
 701     PI("ld_seed",ir->ld_seed);
 702     PR("cos_accel",ir->cos_accel);
 703     pr_matrix(fp,indent,"deform",ir->deform,bMDPformat);
 704
 705     PS("adress_type",EADRESSTYPE(ir->adress_type));
 706     PR("adress_const_wf",ir->adress_const_wf);
 707     PR("adress_ex_width",ir->adress_ex_width);
 708     PR("adress_hy_width",ir->adress_hy_width);
 709     PS("adress_interface_correction",EADRESSICTYPE(ir->adress_icor));
 710     PS("adress_tf_full_box",BOOL(ir->badress_tf_full_box));
 711     PS("adress_site",EADRESSSITETYPE(ir->adress_site));
 712     PR("adress_ex_force_cap",ir->adress_ex_forcecap);
 713     PS("adress_do_hybridpairs", BOOL(ir->adress_do_hybridpairs));
 714
 715     pr_rvecs(fp,indent,"adress_reference_coords",&(ir->adress_refs),bMDPformat);
 716
 717     PI("userint1",ir->userint1);
 718     PI("userint2",ir->userint2);
 719     PI("userint3",ir->userint3);
 720     PI("userint4",ir->userint4);
 721     PR("userreal1",ir->userreal1);
 722     PR("userreal2",ir->userreal2);
 723     PR("userreal3",ir->userreal3);
 724     PR("userreal4",ir->userreal4);
 725     pr_grp_opts(fp,indent,"grpopts",&(ir->opts),bMDPformat);
 726     pr_cosine(fp,indent,"efield-x",&(ir->ex[XX]),bMDPformat);
 727     pr_cosine(fp,indent,"efield-xt",&(ir->et[XX]),bMDPformat);
 728     pr_cosine(fp,indent,"efield-y",&(ir->ex[YY]),bMDPformat);
 729     pr_cosine(fp,indent,"efield-yt",&(ir->et[YY]),bMDPformat);
 730     pr_cosine(fp,indent,"efield-z",&(ir->ex[ZZ]),bMDPformat);
 731     pr_cosine(fp,indent,"efield-zt",&(ir->et[ZZ]),bMDPformat);
 732     PS("bQMMM",BOOL(ir->bQMMM));
 733     PI("QMconstraints",ir->QMconstraints);
 734     PI("QMMMscheme",ir->QMMMscheme);
 735     PR("scalefactor",ir->scalefactor);
 736     pr_qm_opts(fp,indent,"qm_opts",&(ir->opts));
 737   }
 738 }
 739 #undef PS
 740 #undef PR
 741 #undef PI
 742
 743 static void pr_harm(FILE *fp,t_iparams *iparams,const char *r,const char *kr)
 744 {
 745   fprintf(fp,"%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e\n",
 746           r,iparams->harmonic.rA,kr,iparams->harmonic.krA,
 747           r,iparams->harmonic.rB,kr,iparams->harmonic.krB);
 748 }
 749
 750 void pr_iparams(FILE *fp,t_functype ftype,t_iparams *iparams)
 751 {
 752   int i;
 753   real VA[4],VB[4],*rbcA,*rbcB;
 754
 755   switch (ftype) {
 756   case F_ANGLES:
 757   case F_G96ANGLES:
 758     pr_harm(fp,iparams,"th","ct");
 759     break;
 760   case F_CROSS_BOND_BONDS:
 761     fprintf(fp,"r1e=%15.8e, r2e=%15.8e, krr=%15.8e\n",
 762             iparams->cross_bb.r1e,iparams->cross_bb.r2e,
 763             iparams->cross_bb.krr);
 764     break;
 765   case F_CROSS_BOND_ANGLES:
 766     fprintf(fp,"r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e\n",
 767             iparams->cross_ba.r1e,iparams->cross_ba.r2e,
 768             iparams->cross_ba.r3e,iparams->cross_ba.krt);
 769     break;
 770   case F_UREY_BRADLEY:
 771     fprintf(fp,"theta=%15.8e, ktheta=%15.8e, r13=%15.8e, kUB=%15.8e\n",
 772             iparams->u_b.theta,iparams->u_b.ktheta,iparams->u_b.r13,iparams->u_b.kUB);
 773     break;
 774   case F_QUARTIC_ANGLES:
 775     fprintf(fp,"theta=%15.8e",iparams->qangle.theta);
 776     for(i=0; i<5; i++)
 777       fprintf(fp,", c%c=%15.8e",'0'+i,iparams->qangle.c[i]);
 778     fprintf(fp,"\n");
 779     break;
 780   case F_BHAM:
 781     fprintf(fp,"a=%15.8e, b=%15.8e, c=%15.8e\n",
 782             iparams->bham.a,iparams->bham.b,iparams->bham.c);
 783     break;
 784   case F_BONDS:
 785   case F_G96BONDS:
 786   case F_HARMONIC:
 787     pr_harm(fp,iparams,"b0","cb");
 788     break;
 789   case F_IDIHS:
 790     pr_harm(fp,iparams,"xi","cx");
 791     break;
 792   case F_MORSE:
 793     fprintf(fp,"b0=%15.8e, cb=%15.8e, beta=%15.8e\n",
 794             iparams->morse.b0,iparams->morse.cb,iparams->morse.beta);
 795     break;
 796   case F_CUBICBONDS:
 797     fprintf(fp,"b0=%15.8e, kb=%15.8e, kcub=%15.8e\n",
 798             iparams->cubic.b0,iparams->cubic.kb,iparams->cubic.kcub);
 799     break;
 800   case F_CONNBONDS:
 801     fprintf(fp,"\n");
 802     break;
 803   case F_FENEBONDS:
 804     fprintf(fp,"bm=%15.8e, kb=%15.8e\n",iparams->fene.bm,iparams->fene.kb);
 805     break;
 806   case F_RESTRBONDS:
 807       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",
 808               iparams->restraint.lowA,iparams->restraint.up1A,
 809               iparams->restraint.up2A,iparams->restraint.kA,
 810               iparams->restraint.lowB,iparams->restraint.up1B,
 811               iparams->restraint.up2B,iparams->restraint.kB);
 812       break;
 813   case F_TABBONDS:
 814   case F_TABBONDSNC:
 815   case F_TABANGLES:
 816   case F_TABDIHS:
 817     fprintf(fp,"tab=%d, kA=%15.8e, kB=%15.8e\n",
 818             iparams->tab.table,iparams->tab.kA,iparams->tab.kB);
 819     break;
 820   case F_POLARIZATION:
 821     fprintf(fp,"alpha=%15.8e\n",iparams->polarize.alpha);
 822     break;
 823   case F_THOLE_POL:
 824     fprintf(fp,"a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e\n",
 825             iparams->thole.a,iparams->thole.alpha1,iparams->thole.alpha2,
 826             iparams->thole.rfac);
 827     break;
 828   case F_WATER_POL:
 829     fprintf(fp,"al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f\n",
 830             iparams->wpol.al_x,iparams->wpol.al_y,iparams->wpol.al_z,
 831             iparams->wpol.rOH,iparams->wpol.rHH,iparams->wpol.rOD);
 832     break;
 833   case F_LJ:
 834     fprintf(fp,"c6=%15.8e, c12=%15.8e\n",iparams->lj.c6,iparams->lj.c12);
 835     break;
 836   case F_LJ14:
 837     fprintf(fp,"c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e\n",
 838             iparams->lj14.c6A,iparams->lj14.c12A,
 839             iparams->lj14.c6B,iparams->lj14.c12B);
 840     break;
 841   case F_LJC14_Q:
 842     fprintf(fp,"fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
 843             iparams->ljc14.fqq,
 844             iparams->ljc14.qi,iparams->ljc14.qj,
 845             iparams->ljc14.c6,iparams->ljc14.c12);
 846     break;
 847   case F_LJC_PAIRS_NB:
 848     fprintf(fp,"qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
 849             iparams->ljcnb.qi,iparams->ljcnb.qj,
 850             iparams->ljcnb.c6,iparams->ljcnb.c12);
 851     break;
 852   case F_PDIHS:
 853   case F_PIDIHS:
 854   case F_ANGRES:
 855   case F_ANGRESZ:
 856     fprintf(fp,"phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d\n",
 857             iparams->pdihs.phiA,iparams->pdihs.cpA,
 858             iparams->pdihs.phiB,iparams->pdihs.cpB,
 859             iparams->pdihs.mult);
 860     break;
 861   case F_DISRES:
 862     fprintf(fp,"label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)\n",
 863             iparams->disres.label,iparams->disres.type,
 864             iparams->disres.low,iparams->disres.up1,
 865             iparams->disres.up2,iparams->disres.kfac);
 866     break;
 867   case F_ORIRES:
 868     fprintf(fp,"ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)\n",
 869             iparams->orires.ex,iparams->orires.label,iparams->orires.power,
 870             iparams->orires.c,iparams->orires.obs,iparams->orires.kfac);
 871     break;
 872   case F_DIHRES:
 873     fprintf(fp,"label=%d, power=%4d phi=%15.8e, dphi=%15.8e, kfac=%15.8e)\n",
 874             iparams->dihres.label,iparams->dihres.power,
 875             iparams->dihres.phi,iparams->dihres.dphi,iparams->dihres.kfac);
 876     break;
 877   case F_POSRES:
 878     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",
 879             iparams->posres.pos0A[XX],iparams->posres.pos0A[YY],
 880             iparams->posres.pos0A[ZZ],iparams->posres.fcA[XX],
 881             iparams->posres.fcA[YY],iparams->posres.fcA[ZZ],
 882             iparams->posres.pos0B[XX],iparams->posres.pos0B[YY],
 883             iparams->posres.pos0B[ZZ],iparams->posres.fcB[XX],
 884             iparams->posres.fcB[YY],iparams->posres.fcB[ZZ]);
 885     break;
 886   case F_RBDIHS:
 887     for (i=0; i<NR_RBDIHS; i++)
 888       fprintf(fp,"%srbcA[%d]=%15.8e",i==0?"":", ",i,iparams->rbdihs.rbcA[i]);
 889     fprintf(fp,"\n");
 890     for (i=0; i<NR_RBDIHS; i++)
 891       fprintf(fp,"%srbcB[%d]=%15.8e",i==0?"":", ",i,iparams->rbdihs.rbcB[i]);
 892     fprintf(fp,"\n");
 893     break;
 894   case F_FOURDIHS:
 895     /* Use the OPLS -> Ryckaert-Bellemans formula backwards to get the
 896      * OPLS potential constants back.
 897      */
 898     rbcA = iparams->rbdihs.rbcA;
 899     rbcB = iparams->rbdihs.rbcB;
 900
 901     VA[3] = -0.25*rbcA[4];
 902     VA[2] = -0.5*rbcA[3];
 903     VA[1] = 4.0*VA[3]-rbcA[2];
 904     VA[0] = 3.0*VA[2]-2.0*rbcA[1];
 905
 906     VB[3] = -0.25*rbcB[4];
 907     VB[2] = -0.5*rbcB[3];
 908     VB[1] = 4.0*VB[3]-rbcB[2];
 909     VB[0] = 3.0*VB[2]-2.0*rbcB[1];
 910
 911     for (i=0; i<NR_FOURDIHS; i++)
 912       fprintf(fp,"%sFourA[%d]=%15.8e",i==0?"":", ",i,VA[i]);
 913     fprintf(fp,"\n");
 914     for (i=0; i<NR_FOURDIHS; i++)
 915       fprintf(fp,"%sFourB[%d]=%15.8e",i==0?"":", ",i,VB[i]);
 916     fprintf(fp,"\n");
 917     break;
 918
 919   case F_CONSTR:
 920   case F_CONSTRNC:
 921     fprintf(fp,"dA=%15.8e, dB=%15.8e\n",iparams->constr.dA,iparams->constr.dB);
 922     break;
 923   case F_SETTLE:
 924     fprintf(fp,"doh=%15.8e, dhh=%15.8e\n",iparams->settle.doh,
 925             iparams->settle.dhh);
 926     break;
 927   case F_VSITE2:
 928     fprintf(fp,"a=%15.8e\n",iparams->vsite.a);
 929     break;
 930   case F_VSITE3:
 931   case F_VSITE3FD:
 932   case F_VSITE3FAD:
 933     fprintf(fp,"a=%15.8e, b=%15.8e\n",iparams->vsite.a,iparams->vsite.b);
 934     break;
 935   case F_VSITE3OUT:
 936   case F_VSITE4FD:
 937   case F_VSITE4FDN:
 938     fprintf(fp,"a=%15.8e, b=%15.8e, c=%15.8e\n",
 939             iparams->vsite.a,iparams->vsite.b,iparams->vsite.c);
 940     break;
 941   case F_VSITEN:
 942     fprintf(fp,"n=%2d, a=%15.8e\n",iparams->vsiten.n,iparams->vsiten.a);
 943     break;
 944   case F_GB12:
 945   case F_GB13:
 946   case F_GB14:
 947     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);
 948     break;
 949   case F_CMAP:
 950     fprintf(fp, "cmapA=%1d, cmapB=%1d\n",iparams->cmap.cmapA, iparams->cmap.cmapB);
 951     break;
 952   default:
 953     gmx_fatal(FARGS,"unknown function type %d (%s) in %s line %d",
 954               ftype,interaction_function[ftype].name,__FILE__,__LINE__);
 955   }
 956 }
 957
 958 void pr_ilist(FILE *fp,int indent,const char *title,
 959               t_functype *functype,t_ilist *ilist, gmx_bool bShowNumbers)
 960 {
 961     int i,j,k,type,ftype;
 962     t_iatom *iatoms;
 963
 964     if (available(fp,ilist,indent,title) && ilist->nr > 0)
 965     {
 966         indent=pr_title(fp,indent,title);
 967         (void) pr_indent(fp,indent);
 968         fprintf(fp,"nr: %d\n",ilist->nr);
 969         if (ilist->nr > 0) {
 970             (void) pr_indent(fp,indent);
 971             fprintf(fp,"iatoms:\n");
 972             iatoms=ilist->iatoms;
 973             for (i=j=0; i<ilist->nr;) {
 974 #ifndef DEBUG
 975                 (void) pr_indent(fp,indent+INDENT);
 976                 type=*(iatoms++);
 977                 ftype=functype[type];
 978                 (void) fprintf(fp,"%d type=%d (%s)",
 979                                bShowNumbers?j:-1,bShowNumbers?type:-1,
 980                                interaction_function[ftype].name);
 981                 j++;
 982                 for (k=0; k<interaction_function[ftype].nratoms; k++)
 983                     (void) fprintf(fp," %u",*(iatoms++));
 984                 (void) fprintf(fp,"\n");
 985                 i+=1+interaction_function[ftype].nratoms;
 986 #else
 987                 fprintf(fp,"%5d%5d\n",i,iatoms[i]);
 988                 i++;
 989 #endif
 990             }
 991         }
 992     }
 993 }
 994
 995 static void pr_cmap(FILE *fp, int indent, const char *title,
 996                     gmx_cmap_t *cmap_grid, gmx_bool bShowNumbers)
 997 {
 998     int i,j,nelem;
 999     real dx,idx;
1000
1001     dx    = 360.0 / cmap_grid->grid_spacing;
1002     nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
1003
1004     if(available(fp,cmap_grid,indent,title))
1005     {
1006         fprintf(fp,"%s\n",title);
1007
1008         for(i=0;i<cmap_grid->ngrid;i++)
1009         {
1010             idx = -180.0;
1011             fprintf(fp,"%8s %8s %8s %8s\n","V","dVdx","dVdy","d2dV");
1012
1013             fprintf(fp,"grid[%3d]={\n",bShowNumbers?i:-1);
1014
1015             for(j=0;j<nelem;j++)
1016             {
1017                 if( (j%cmap_grid->grid_spacing)==0)
1018                 {
1019                     fprintf(fp,"%8.1f\n",idx);
1020                     idx+=dx;
1021                 }
1022
1023                 fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4]);
1024                 fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4+1]);
1025                 fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4+2]);
1026                 fprintf(fp,"%8.3f\n",cmap_grid->cmapdata[i].cmap[j*4+3]);
1027             }
1028             fprintf(fp,"\n");
1029         }
1030     }
1031
1032 }
1033
1034 void pr_ffparams(FILE *fp,int indent,const char *title,
1035                  gmx_ffparams_t *ffparams,
1036                  gmx_bool bShowNumbers)
1037 {
1038   int i,j;
1039
1040   indent=pr_title(fp,indent,title);
1041   (void) pr_indent(fp,indent);
1042   (void) fprintf(fp,"atnr=%d\n",ffparams->atnr);
1043   (void) pr_indent(fp,indent);
1044   (void) fprintf(fp,"ntypes=%d\n",ffparams->ntypes);
1045   for (i=0; i<ffparams->ntypes; i++) {
1046       (void) pr_indent(fp,indent+INDENT);
1047       (void) fprintf(fp,"functype[%d]=%s, ",
1048                      bShowNumbers?i:-1,
1049                      interaction_function[ffparams->functype[i]].name);
1050       pr_iparams(fp,ffparams->functype[i],&ffparams->iparams[i]);
1051   }
1052   (void) pr_double(fp,indent,"reppow",ffparams->reppow);
1053   (void) pr_real(fp,indent,"fudgeQQ",ffparams->fudgeQQ);
1054   pr_cmap(fp,indent,"cmap",&ffparams->cmap_grid,bShowNumbers);
1055 }
1056
1057 void pr_idef(FILE *fp,int indent,const char *title,t_idef *idef, gmx_bool bShowNumbers)
1058 {
1059   int i,j;
1060
1061   if (available(fp,idef,indent,title)) {
1062     indent=pr_title(fp,indent,title);
1063     (void) pr_indent(fp,indent);
1064     (void) fprintf(fp,"atnr=%d\n",idef->atnr);
1065     (void) pr_indent(fp,indent);
1066     (void) fprintf(fp,"ntypes=%d\n",idef->ntypes);
1067     for (i=0; i<idef->ntypes; i++) {
1068       (void) pr_indent(fp,indent+INDENT);
1069       (void) fprintf(fp,"functype[%d]=%s, ",
1070                      bShowNumbers?i:-1,
1071                      interaction_function[idef->functype[i]].name);
1072       pr_iparams(fp,idef->functype[i],&idef->iparams[i]);
1073     }
1074     (void) pr_real(fp,indent,"fudgeQQ",idef->fudgeQQ);
1075
1076     for(j=0; (j<F_NRE); j++)
1077       pr_ilist(fp,indent,interaction_function[j].longname,
1078                idef->functype,&idef->il[j],bShowNumbers);
1079   }
1080 }
1081
1082 static int pr_block_title(FILE *fp,int indent,const char *title,t_block *block)
1083 {
1084   int i;
1085
1086   if (available(fp,block,indent,title))
1087     {
1088       indent=pr_title(fp,indent,title);
1089       (void) pr_indent(fp,indent);
1090       (void) fprintf(fp,"nr=%d\n",block->nr);
1091     }
1092   return indent;
1093 }
1094
1095 static int pr_blocka_title(FILE *fp,int indent,const char *title,t_blocka *block)
1096 {
1097   int i;
1098
1099   if (available(fp,block,indent,title))
1100     {
1101       indent=pr_title(fp,indent,title);
1102       (void) pr_indent(fp,indent);
1103       (void) fprintf(fp,"nr=%d\n",block->nr);
1104       (void) pr_indent(fp,indent);
1105       (void) fprintf(fp,"nra=%d\n",block->nra);
1106     }
1107   return indent;
1108 }
1109
1110 static void low_pr_block(FILE *fp,int indent,const char *title,t_block *block, gmx_bool bShowNumbers)
1111 {
1112   int i;
1113
1114   if (available(fp,block,indent,title))
1115     {
1116       indent=pr_block_title(fp,indent,title,block);
1117       for (i=0; i<=block->nr; i++)
1118         {
1119           (void) pr_indent(fp,indent+INDENT);
1120           (void) fprintf(fp,"%s->index[%d]=%u\n",
1121                          title,bShowNumbers?i:-1,block->index[i]);
1122         }
1123     }
1124 }
1125
1126 static void low_pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block, gmx_bool bShowNumbers)
1127 {
1128   int i;
1129
1130   if (available(fp,block,indent,title))
1131     {
1132       indent=pr_blocka_title(fp,indent,title,block);
1133       for (i=0; i<=block->nr; i++)
1134         {
1135           (void) pr_indent(fp,indent+INDENT);
1136           (void) fprintf(fp,"%s->index[%d]=%u\n",
1137                          title,bShowNumbers?i:-1,block->index[i]);
1138         }
1139       for (i=0; i<block->nra; i++)
1140         {
1141           (void) pr_indent(fp,indent+INDENT);
1142           (void) fprintf(fp,"%s->a[%d]=%u\n",
1143                          title,bShowNumbers?i:-1,block->a[i]);
1144         }
1145     }
1146 }
1147
1148 void pr_block(FILE *fp,int indent,const char *title,t_block *block,gmx_bool bShowNumbers)
1149 {
1150   int i,j,ok,size,start,end;
1151
1152   if (available(fp,block,indent,title))
1153     {
1154       indent=pr_block_title(fp,indent,title,block);
1155       start=0;
1156       end=start;
1157       if ((ok=(block->index[start]==0))==0)
1158         (void) fprintf(fp,"block->index[%d] should be 0\n",start);
1159       else
1160         for (i=0; i<block->nr; i++)
1161           {
1162             end=block->index[i+1];
1163             size=pr_indent(fp,indent);
1164             if (end<=start)
1165               size+=fprintf(fp,"%s[%d]={}\n",title,i);
1166             else
1167               size+=fprintf(fp,"%s[%d]={%d..%d}\n",
1168                             title,bShowNumbers?i:-1,
1169                             bShowNumbers?start:-1,bShowNumbers?end-1:-1);
1170             start=end;
1171           }
1172     }
1173 }
1174
1175 void pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block,gmx_bool bShowNumbers)
1176 {
1177   int i,j,ok,size,start,end;
1178
1179   if (available(fp,block,indent,title))
1180     {
1181       indent=pr_blocka_title(fp,indent,title,block);
1182       start=0;
1183       end=start;
1184       if ((ok=(block->index[start]==0))==0)
1185         (void) fprintf(fp,"block->index[%d] should be 0\n",start);
1186       else
1187         for (i=0; i<block->nr; i++)
1188           {
1189             end=block->index[i+1];
1190             size=pr_indent(fp,indent);
1191             if (end<=start)
1192               size+=fprintf(fp,"%s[%d]={",title,i);
1193             else
1194               size+=fprintf(fp,"%s[%d][%d..%d]={",
1195                             title,bShowNumbers?i:-1,
1196                             bShowNumbers?start:-1,bShowNumbers?end-1:-1);
1197             for (j=start; j<end; j++)
1198               {
1199                 if (j>start) size+=fprintf(fp,", ");
1200                 if ((size)>(USE_WIDTH))
1201                   {
1202                     (void) fprintf(fp,"\n");
1203                     size=pr_indent(fp,indent+INDENT);
1204                   }
1205                 size+=fprintf(fp,"%u",block->a[j]);
1206               }
1207             (void) fprintf(fp,"}\n");
1208             start=end;
1209           }
1210       if ((end!=block->nra)||(!ok))
1211         {
1212           (void) pr_indent(fp,indent);
1213           (void) fprintf(fp,"tables inconsistent, dumping complete tables:\n");
1214           low_pr_blocka(fp,indent,title,block,bShowNumbers);
1215         }
1216     }
1217 }
1218
1219 static void pr_strings(FILE *fp,int indent,const char *title,char ***nm,int n, gmx_bool bShowNumbers)
1220 {
1221   int i;
1222
1223   if (available(fp,nm,indent,title))
1224     {
1225       indent=pr_title_n(fp,indent,title,n);
1226       for (i=0; i<n; i++)
1227         {
1228           (void) pr_indent(fp,indent);
1229           (void) fprintf(fp,"%s[%d]={name=\"%s\"}\n",
1230                          title,bShowNumbers?i:-1,*(nm[i]));
1231         }
1232     }
1233 }
1234
1235 static void pr_strings2(FILE *fp,int indent,const char *title,
1236                         char ***nm,char ***nmB,int n, gmx_bool bShowNumbers)
1237 {
1238   int i;
1239
1240   if (available(fp,nm,indent,title))
1241     {
1242       indent=pr_title_n(fp,indent,title,n);
1243       for (i=0; i<n; i++)
1244         {
1245           (void) pr_indent(fp,indent);
1246           (void) fprintf(fp,"%s[%d]={name=\"%s\",nameB=\"%s\"}\n",
1247                          title,bShowNumbers?i:-1,*(nm[i]),*(nmB[i]));
1248         }
1249     }
1250 }
1251
1252 static void pr_resinfo(FILE *fp,int indent,const char *title,t_resinfo *resinfo,int n, gmx_bool bShowNumbers)
1253 {
1254     int i;
1255
1256     if (available(fp,resinfo,indent,title))
1257     {
1258         indent=pr_title_n(fp,indent,title,n);
1259         for (i=0; i<n; i++)
1260         {
1261             (void) pr_indent(fp,indent);
1262             (void) fprintf(fp,"%s[%d]={name=\"%s\", nr=%d, ic='%c'}\n",
1263                            title,bShowNumbers?i:-1,
1264                            *(resinfo[i].name),resinfo[i].nr,
1265                            (resinfo[i].ic == '\0') ? ' ' : resinfo[i].ic);
1266         }
1267     }
1268 }
1269
1270 static void pr_atom(FILE *fp,int indent,const char *title,t_atom *atom,int n)
1271 {
1272   int i,j;
1273
1274   if (available(fp,atom,indent,title)) {
1275     indent=pr_title_n(fp,indent,title,n);
1276     for (i=0; i<n; i++) {
1277       (void) pr_indent(fp,indent);
1278       fprintf(fp,"%s[%6d]={type=%3d, typeB=%3d, ptype=%8s, m=%12.5e, "
1279               "q=%12.5e, mB=%12.5e, qB=%12.5e, resind=%5d, atomnumber=%3d}\n",
1280               title,i,atom[i].type,atom[i].typeB,ptype_str[atom[i].ptype],
1281               atom[i].m,atom[i].q,atom[i].mB,atom[i].qB,
1282               atom[i].resind,atom[i].atomnumber);
1283     }
1284   }
1285 }
1286
1287 static void pr_grps(FILE *fp,int indent,const char *title,t_grps grps[],
1288                     char **grpname[], gmx_bool bShowNumbers)
1289 {
1290     int i,j;
1291
1292     for(i=0; (i<egcNR); i++)
1293     {
1294         fprintf(fp,"%s[%-12s] nr=%d, name=[",title,gtypes[i],grps[i].nr);
1295         for(j=0; (j<grps[i].nr); j++)
1296         {
1297             fprintf(fp," %s",*(grpname[grps[i].nm_ind[j]]));
1298         }
1299         fprintf(fp,"]\n");
1300     }
1301 }
1302
1303 static void pr_groups(FILE *fp,int indent,const char *title,
1304                       gmx_groups_t *groups,
1305                       gmx_bool bShowNumbers)
1306 {
1307     int grpnr[egcNR];
1308     int nat_max,i,g;
1309
1310     pr_grps(fp,indent,"grp",groups->grps,groups->grpname,bShowNumbers);
1311     pr_strings(fp,indent,"grpname",groups->grpname,groups->ngrpname,bShowNumbers);
1312
1313     (void) pr_indent(fp,indent);
1314     fprintf(fp,"groups          ");
1315     for(g=0; g<egcNR; g++)
1316     {
1317        printf(" %5.5s",gtypes[g]);
1318     }
1319     printf("\n");
1320
1321     (void) pr_indent(fp,indent);
1322     fprintf(fp,"allocated       ");
1323     nat_max = 0;
1324     for(g=0; g<egcNR; g++)
1325     {
1326         printf(" %5d",groups->ngrpnr[g]);
1327         nat_max = max(nat_max,groups->ngrpnr[g]);
1328     }
1329     printf("\n");
1330
1331     if (nat_max == 0)
1332     {
1333         (void) pr_indent(fp,indent);
1334         fprintf(fp,"groupnr[%5s] =","*");
1335         for(g=0; g<egcNR; g++)
1336         {
1337             fprintf(fp,"  %3d ",0);
1338         }
1339         fprintf(fp,"\n");
1340     }
1341     else
1342     {
1343         for(i=0; i<nat_max; i++)
1344         {
1345             (void) pr_indent(fp,indent);
1346             fprintf(fp,"groupnr[%5d] =",i);
1347             for(g=0; g<egcNR; g++)
1348             {
1349                 fprintf(fp,"  %3d ",
1350                         groups->grpnr[g] ? groups->grpnr[g][i] : 0);
1351             }
1352             fprintf(fp,"\n");
1353         }
1354     }
1355 }
1356
1357 void pr_atoms(FILE *fp,int indent,const char *title,t_atoms *atoms,
1358               gmx_bool bShownumbers)
1359 {
1360   if (available(fp,atoms,indent,title))
1361     {
1362       indent=pr_title(fp,indent,title);
1363       pr_atom(fp,indent,"atom",atoms->atom,atoms->nr);
1364       pr_strings(fp,indent,"atom",atoms->atomname,atoms->nr,bShownumbers);
1365       pr_strings2(fp,indent,"type",atoms->atomtype,atoms->atomtypeB,atoms->nr,bShownumbers);
1366       pr_resinfo(fp,indent,"residue",atoms->resinfo,atoms->nres,bShownumbers);
1367     }
1368 }
1369
1370
1371 void pr_atomtypes(FILE *fp,int indent,const char *title,t_atomtypes *atomtypes,
1372                   gmx_bool bShowNumbers)
1373 {
1374   int i;
1375   if (available(fp,atomtypes,indent,title))
1376   {
1377     indent=pr_title(fp,indent,title);
1378     for(i=0;i<atomtypes->nr;i++) {
1379       pr_indent(fp,indent);
1380                 fprintf(fp,
1381                                 "atomtype[%3d]={radius=%12.5e, volume=%12.5e, gb_radius=%12.5e, surftens=%12.5e, atomnumber=%4d, S_hct=%12.5e)}\n",
1382                                 bShowNumbers?i:-1,atomtypes->radius[i],atomtypes->vol[i],
1383                                 atomtypes->gb_radius[i],
1384                                 atomtypes->surftens[i],atomtypes->atomnumber[i],atomtypes->S_hct[i]);
1385     }
1386   }
1387 }
1388
1389 static void pr_moltype(FILE *fp,int indent,const char *title,
1390                        gmx_moltype_t *molt,int n,
1391                        gmx_ffparams_t *ffparams,
1392                        gmx_bool bShowNumbers)
1393 {
1394     int j;
1395
1396     indent = pr_title_n(fp,indent,title,n);
1397     (void) pr_indent(fp,indent);
1398     (void) fprintf(fp,"name=\"%s\"\n",*(molt->name));
1399     pr_atoms(fp,indent,"atoms",&(molt->atoms),bShowNumbers);
1400     pr_block(fp,indent,"cgs",&molt->cgs, bShowNumbers);
1401     pr_blocka(fp,indent,"excls",&molt->excls, bShowNumbers);
1402     for(j=0; (j<F_NRE); j++) {
1403         pr_ilist(fp,indent,interaction_function[j].longname,
1404                  ffparams->functype,&molt->ilist[j],bShowNumbers);
1405     }
1406 }
1407
1408 static void pr_molblock(FILE *fp,int indent,const char *title,
1409                         gmx_molblock_t *molb,int n,
1410                         gmx_moltype_t *molt,
1411                         gmx_bool bShowNumbers)
1412 {
1413     indent = pr_title_n(fp,indent,title,n);
1414     (void) pr_indent(fp,indent);
1415     (void) fprintf(fp,"%-20s = %d \"%s\"\n",
1416                    "moltype",molb->type,*(molt[molb->type].name));
1417     pr_int(fp,indent,"#molecules",molb->nmol);
1418     pr_int(fp,indent,"#atoms_mol",molb->natoms_mol);
1419     pr_int(fp,indent,"#posres_xA",molb->nposres_xA);
1420     if (molb->nposres_xA > 0) {
1421         pr_rvecs(fp,indent,"posres_xA",molb->posres_xA,molb->nposres_xA);
1422     }
1423     pr_int(fp,indent,"#posres_xB",molb->nposres_xB);
1424     if (molb->nposres_xB > 0) {
1425         pr_rvecs(fp,indent,"posres_xB",molb->posres_xB,molb->nposres_xB);
1426     }
1427 }
1428
1429 void pr_mtop(FILE *fp,int indent,const char *title,gmx_mtop_t *mtop,
1430              gmx_bool bShowNumbers)
1431 {
1432     int mt,mb;
1433
1434     if (available(fp,mtop,indent,title)) {
1435         indent=pr_title(fp,indent,title);
1436         (void) pr_indent(fp,indent);
1437         (void) fprintf(fp,"name=\"%s\"\n",*(mtop->name));
1438         pr_int(fp,indent,"#atoms",mtop->natoms);
1439         for(mb=0; mb<mtop->nmolblock; mb++) {
1440             pr_molblock(fp,indent,"molblock",&mtop->molblock[mb],mb,
1441                         mtop->moltype,bShowNumbers);
1442         }
1443         pr_ffparams(fp,indent,"ffparams",&(mtop->ffparams),bShowNumbers);
1444         pr_atomtypes(fp,indent,"atomtypes",&(mtop->atomtypes),bShowNumbers);
1445         for(mt=0; mt<mtop->nmoltype; mt++) {
1446             pr_moltype(fp,indent,"moltype",&mtop->moltype[mt],mt,
1447                        &mtop->ffparams,bShowNumbers);
1448         }
1449         pr_groups(fp,indent,"groups",&mtop->groups,bShowNumbers);
1450     }
1451 }
1452
1453 void pr_top(FILE *fp,int indent,const char *title,t_topology *top, gmx_bool bShowNumbers)
1454 {
1455   if (available(fp,top,indent,title)) {
1456     indent=pr_title(fp,indent,title);
1457     (void) pr_indent(fp,indent);
1458     (void) fprintf(fp,"name=\"%s\"\n",*(top->name));
1459     pr_atoms(fp,indent,"atoms",&(top->atoms),bShowNumbers);
1460     pr_atomtypes(fp,indent,"atomtypes",&(top->atomtypes),bShowNumbers);
1461     pr_block(fp,indent,"cgs",&top->cgs, bShowNumbers);
1462     pr_block(fp,indent,"mols",&top->mols, bShowNumbers);
1463     pr_blocka(fp,indent,"excls",&top->excls, bShowNumbers);
1464     pr_idef(fp,indent,"idef",&top->idef,bShowNumbers);
1465   }
1466 }
1467
1468 void pr_header(FILE *fp,int indent,const char *title,t_tpxheader *sh)
1469 {
1470   char buf[22];
1471
1472   if (available(fp,sh,indent,title))
1473     {
1474       indent=pr_title(fp,indent,title);
1475       pr_indent(fp,indent);
1476       fprintf(fp,"bIr    = %spresent\n",sh->bIr?"":"not ");
1477       pr_indent(fp,indent);
1478       fprintf(fp,"bBox   = %spresent\n",sh->bBox?"":"not ");
1479       pr_indent(fp,indent);
1480       fprintf(fp,"bTop   = %spresent\n",sh->bTop?"":"not ");
1481       pr_indent(fp,indent);
1482       fprintf(fp,"bX     = %spresent\n",sh->bX?"":"not ");
1483       pr_indent(fp,indent);
1484       fprintf(fp,"bV     = %spresent\n",sh->bV?"":"not ");
1485       pr_indent(fp,indent);
1486       fprintf(fp,"bF     = %spresent\n",sh->bF?"":"not ");
1487
1488       pr_indent(fp,indent);
1489       fprintf(fp,"natoms = %d\n",sh->natoms);
1490       pr_indent(fp,indent);
1491       fprintf(fp,"lambda = %e\n",sh->lambda);
1492     }
1493 }
1494
1495 void pr_commrec(FILE *fp,int indent,t_commrec *cr)
1496 {
1497   pr_indent(fp,indent);
1498   fprintf(fp,"commrec:\n");
1499   indent+=2;
1500   pr_indent(fp,indent);
1501   fprintf(fp,"nodeid    = %d\n",cr->nodeid);
1502   pr_indent(fp,indent);
1503   fprintf(fp,"nnodes    = %d\n",cr->nnodes);
1504   pr_indent(fp,indent);
1505   fprintf(fp,"npmenodes = %d\n",cr->npmenodes);
1506   /*
1507   pr_indent(fp,indent);
1508   fprintf(fp,"threadid  = %d\n",cr->threadid);
1509   pr_indent(fp,indent);
1510   fprintf(fp,"nthreads  = %d\n",cr->nthreads);
1511   */
1512 }