Don't use POSIX fnmatch() for pattern matching.

[gromacs/qmmm-gamess-us.git] / src / gmxlib / txtdump.c

/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
 *
 * 
 *                This source code is part of
 * 
 *                 G   R   O   M   A   C   S
 * 
 *          GROningen MAchine for Chemical Simulations
 * 
 *                        VERSION 3.2.0
 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team,
 * check out http://www.gromacs.org for more information.

 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 * 
 * If you want to redistribute modifications, please consider that
 * scientific software is very special. Version control is crucial -
 * bugs must be traceable. We will be happy to consider code for
 * inclusion in the official distribution, but derived work must not
 * be called official GROMACS. Details are found in the README & COPYING
 * files - if they are missing, get the official version at www.gromacs.org.
 * 
 * To help us fund GROMACS development, we humbly ask that you cite
 * the papers on the package - you can find them in the top README file.
 * 
 * For more info, check our website at http://www.gromacs.org
 * 
 * And Hey:
 * GROningen Mixture of Alchemy and Childrens' Stories
 */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

/* This file is completely threadsafe - please keep it that way! */
#include <thread_mpi.h>


#include <stdio.h>
#include "smalloc.h"
#include "typedefs.h"
#include "names.h"
#include "txtdump.h"
#include "string2.h"
#include "vec.h"


int pr_indent(FILE *fp,int n)
{
  int i;

  for (i=0; i<n; i++) (void) fprintf(fp," ");
  return n;
}

int available(FILE *fp,void *p,int indent,const char *title)
{
  if (!p) {
    if (indent > 0)
      pr_indent(fp,indent);
    (void) fprintf(fp,"%s: not available\n",title);
  }
  return (p!=NULL);
}

int pr_title(FILE *fp,int indent,const char *title)
{
  (void) pr_indent(fp,indent);
  (void) fprintf(fp,"%s:\n",title);
  return (indent+INDENT);
}

int pr_title_n(FILE *fp,int indent,const char *title,int n)
{
  (void) pr_indent(fp,indent);
  (void) fprintf(fp,"%s (%d):\n",title,n);
  return (indent+INDENT);
}

int pr_title_nxn(FILE *fp,int indent,const char *title,int n1,int n2)
{
  (void) pr_indent(fp,indent);
  (void) fprintf(fp,"%s (%dx%d):\n",title,n1,n2);
  return (indent+INDENT);
}

void pr_ivec(FILE *fp,int indent,const char *title,int vec[],int n, bool bShowNumbers)
{
  int i;

  if (available(fp,vec,indent,title))
    {
      indent=pr_title_n(fp,indent,title,n);
      for (i=0; i<n; i++)
        {
          (void) pr_indent(fp,indent);
          (void) fprintf(fp,"%s[%d]=%d\n",title,bShowNumbers?i:-1,vec[i]);
        }
    }
}

void pr_ivec_block(FILE *fp,int indent,const char *title,int vec[],int n, bool bShowNumbers)
{
    int i,j;
    
    if (available(fp,vec,indent,title))
    {
        indent=pr_title_n(fp,indent,title,n);
        i = 0;
        while (i < n)
        {
            j = i+1;
            while (j < n && vec[j] == vec[j-1]+1)
            {
                j++;
            }
            /* Print consecutive groups of 3 or more as blocks */
            if (j - i < 3)
            {
                while(i < j)
                {
                    (void) pr_indent(fp,indent);
                    (void) fprintf(fp,"%s[%d]=%d\n",
                                   title,bShowNumbers?i:-1,vec[i]);
                    i++;
                }
            }
            else
            {
                (void) pr_indent(fp,indent);
                (void) fprintf(fp,"%s[%d,...,%d] = {%d,...,%d}\n",
                               title,
                               bShowNumbers?i:-1,
                               bShowNumbers?j-1:-1,
                               vec[i],vec[j-1]); 
                i = j;
            }
        }
    }
}

void pr_bvec(FILE *fp,int indent,const char *title,bool vec[],int n, bool bShowNumbers)
{
  int i;

  if (available(fp,vec,indent,title))
    {
      indent=pr_title_n(fp,indent,title,n);
      for (i=0; i<n; i++)
        {
          (void) pr_indent(fp,indent);
          (void) fprintf(fp,"%s[%d]=%s\n",title,bShowNumbers?i:-1,
                         BOOL(vec[i]));
        }
    }
}

void pr_ivecs(FILE *fp,int indent,const char *title,ivec vec[],int n, bool bShowNumbers)
{
  int i,j;

  if (available(fp,vec,indent,title))
    {  
      indent=pr_title_nxn(fp,indent,title,n,DIM);
      for (i=0; i<n; i++)
        {
          (void) pr_indent(fp,indent);
          (void) fprintf(fp,"%s[%d]={",title,bShowNumbers?i:-1);
          for (j=0; j<DIM; j++)
            {
              if (j!=0) (void) fprintf(fp,", ");
              fprintf(fp,"%d",vec[i][j]);
            }
          (void) fprintf(fp,"}\n");
        }
    }
}

void pr_rvec(FILE *fp,int indent,const char *title,real vec[],int n, bool bShowNumbers)
{
  int i;

  if (available(fp,vec,indent,title))
    {  
      indent=pr_title_n(fp,indent,title,n);
      for (i=0; i<n; i++)
        {
          pr_indent(fp,indent);
          fprintf(fp,"%s[%d]=%12.5e\n",title,bShowNumbers?i:-1,vec[i]);
        }
    }
}

void pr_dvec(FILE *fp,int indent,const char *title,double vec[],int n, bool bShowNumbers)
{
        int i;
        
        if (available(fp,vec,indent,title))
    {  
                indent=pr_title_n(fp,indent,title,n);
                for (i=0; i<n; i++)
        {
                        pr_indent(fp,indent);
                        fprintf(fp,"%s[%d]=%12.5e\n",title,bShowNumbers?i:-1,vec[i]);
        }
    }
}


/*
void pr_mat(FILE *fp,int indent,char *title,matrix m)
{
  int i,j;
  
  if (available(fp,m,indent,title)) {  
    indent=pr_title_n(fp,indent,title,n);
    for(i=0; i<n; i++) {
      pr_indent(fp,indent);
      fprintf(fp,"%s[%d]=%12.5e %12.5e %12.5e\n",
              title,bShowNumbers?i:-1,m[i][XX],m[i][YY],m[i][ZZ]);
    }
  }
}
*/

void pr_rvecs_len(FILE *fp,int indent,const char *title,rvec vec[],int n)
{
  int i,j;

  if (available(fp,vec,indent,title)) {  
    indent=pr_title_nxn(fp,indent,title,n,DIM);
    for (i=0; i<n; i++) {
      (void) pr_indent(fp,indent);
      (void) fprintf(fp,"%s[%5d]={",title,i);
      for (j=0; j<DIM; j++) {
        if (j != 0) 
          (void) fprintf(fp,", ");
        (void) fprintf(fp,"%12.5e",vec[i][j]);
      }
      (void) fprintf(fp,"} len=%12.5e\n",norm(vec[i]));
    }
  }
}

void pr_rvecs(FILE *fp,int indent,const char *title,rvec vec[],int n)
{
  const char *fshort = "%12.5e";
  const char *flong  = "%15.8e";
  const char *format;
  int i,j;

  if (getenv("LONGFORMAT") != NULL)
    format = flong;
  else
    format = fshort;
    
  if (available(fp,vec,indent,title)) {  
    indent=pr_title_nxn(fp,indent,title,n,DIM);
    for (i=0; i<n; i++) {
      (void) pr_indent(fp,indent);
      (void) fprintf(fp,"%s[%5d]={",title,i);
      for (j=0; j<DIM; j++) {
        if (j != 0) 
          (void) fprintf(fp,", ");
        (void) fprintf(fp,format,vec[i][j]);
      }
      (void) fprintf(fp,"}\n");
    }
  }
}


void pr_reals(FILE *fp,int indent,const char *title,real *vec,int n)
{
  int i;
    
  if (available(fp,vec,indent,title)) {  
    (void) pr_indent(fp,indent);
    (void) fprintf(fp,"%s:\t",title);
    for(i=0; i<n; i++)
      fprintf(fp,"  %10g",vec[i]);
    (void) fprintf(fp,"\n");
  }
}

void pr_doubles(FILE *fp,int indent,const char *title,double *vec,int n)
{
  int i;
    
  if (available(fp,vec,indent,title)) {  
    (void) pr_indent(fp,indent);
    (void) fprintf(fp,"%s:\t",title);
    for(i=0; i<n; i++)
      fprintf(fp,"  %10g",vec[i]);
    (void) fprintf(fp,"\n");
  }
}

static void pr_int(FILE *fp,int indent,const char *title,int i)
{
  pr_indent(fp,indent);
  fprintf(fp,"%-20s = %d\n",title,i);
}

static void pr_gmx_large_int(FILE *fp,int indent,const char *title,gmx_large_int_t i)
{
  char buf[22];

  pr_indent(fp,indent);
  fprintf(fp,"%-20s = %s\n",title,gmx_step_str(i,buf));
}

static void pr_real(FILE *fp,int indent,const char *title,real r)
{
  pr_indent(fp,indent);
  fprintf(fp,"%-20s = %g\n",title,r);
}

static void pr_double(FILE *fp,int indent,const char *title,double d)
{
  pr_indent(fp,indent);
  fprintf(fp,"%-20s = %g\n",title,d);
}

static void pr_str(FILE *fp,int indent,const char *title,const char *s)
{
  pr_indent(fp,indent);
  fprintf(fp,"%-20s = %s\n",title,s);
}

void pr_qm_opts(FILE *fp,int indent,const char *title,t_grpopts *opts)
{
  int i,m,j;

  fprintf(fp,"%s:\n",title);
  
  pr_int(fp,indent,"ngQM",opts->ngQM);
  if (opts->ngQM > 0) {
    pr_ivec(fp,indent,"QMmethod",opts->QMmethod,opts->ngQM,FALSE);
    pr_ivec(fp,indent,"QMbasis",opts->QMbasis,opts->ngQM,FALSE);
    pr_ivec(fp,indent,"QMcharge",opts->QMcharge,opts->ngQM,FALSE);
    pr_ivec(fp,indent,"QMmult",opts->QMmult,opts->ngQM,FALSE);
    pr_bvec(fp,indent,"bSH",opts->bSH,opts->ngQM,FALSE);
    pr_ivec(fp,indent,"CASorbitals",opts->CASorbitals,opts->ngQM,FALSE);
    pr_ivec(fp,indent,"CASelectrons",opts->CASelectrons,opts->ngQM,FALSE);
    pr_rvec(fp,indent,"SAon",opts->SAon,opts->ngQM,FALSE);
    pr_rvec(fp,indent,"SAon",opts->SAon,opts->ngQM,FALSE);
    pr_ivec(fp,indent,"SAsteps",opts->SAsteps,opts->ngQM,FALSE);
    pr_bvec(fp,indent,"bOPT",opts->bOPT,opts->ngQM,FALSE);
    pr_bvec(fp,indent,"bTS",opts->bTS,opts->ngQM,FALSE);
  }
}

static void pr_grp_opts(FILE *out,int indent,const char *title,t_grpopts *opts,
                        bool bMDPformat)
{
  int i,m,j;

  if (!bMDPformat)
    fprintf(out,"%s:\n",title);
  
  pr_indent(out,indent);
  fprintf(out,"nrdf%s",bMDPformat ? " = " : ":");
  for(i=0; (i<opts->ngtc); i++)
    fprintf(out,"  %10g",opts->nrdf[i]);
  fprintf(out,"\n");
  
  pr_indent(out,indent);
  fprintf(out,"ref_t%s",bMDPformat ? " = " : ":");
  for(i=0; (i<opts->ngtc); i++)
    fprintf(out,"  %10g",opts->ref_t[i]);
  fprintf(out,"\n");
  
  pr_indent(out,indent);
  fprintf(out,"tau_t%s",bMDPformat ? " = " : ":");
  for(i=0; (i<opts->ngtc); i++)
    fprintf(out,"  %10g",opts->tau_t[i]);
  fprintf(out,"\n");  
  
  /* Pretty-print the simulated annealing info */
  fprintf(out,"anneal%s",bMDPformat ? " = " : ":");
  for(i=0; (i<opts->ngtc); i++)
    fprintf(out,"  %10s",EANNEAL(opts->annealing[i]));
  fprintf(out,"\n");  
 
  fprintf(out,"ann_npoints%s",bMDPformat ? " = " : ":");
  for(i=0; (i<opts->ngtc); i++)
    fprintf(out,"  %10d",opts->anneal_npoints[i]);
  fprintf(out,"\n");  
 
  for(i=0; (i<opts->ngtc); i++) {
    if(opts->anneal_npoints[i]>0) {
      fprintf(out,"ann. times [%d]:\t",i);
      for(j=0; (j<opts->anneal_npoints[i]); j++)
        fprintf(out,"  %10.1f",opts->anneal_time[i][j]);
      fprintf(out,"\n");  
      fprintf(out,"ann. temps [%d]:\t",i);
      for(j=0; (j<opts->anneal_npoints[i]); j++)
        fprintf(out,"  %10.1f",opts->anneal_temp[i][j]);
      fprintf(out,"\n");  
    }
  }
  
  pr_indent(out,indent);
  fprintf(out,"acc:\t");
  for(i=0; (i<opts->ngacc); i++)
    for(m=0; (m<DIM); m++)
      fprintf(out,"  %10g",opts->acc[i][m]);
  fprintf(out,"\n");

  pr_indent(out,indent);
  fprintf(out,"nfreeze:");
  for(i=0; (i<opts->ngfrz); i++)
    for(m=0; (m<DIM); m++)
      fprintf(out,"  %10s",opts->nFreeze[i][m] ? "Y" : "N");
  fprintf(out,"\n");


  for(i=0; (i<opts->ngener); i++) {
    pr_indent(out,indent);
    fprintf(out,"energygrp_flags[%3d]:",i);
    for(m=0; (m<opts->ngener); m++)
      fprintf(out," %d",opts->egp_flags[opts->ngener*i+m]);
    fprintf(out,"\n");
  }

  fflush(out);
}

static void pr_matrix(FILE *fp,int indent,const char *title,rvec *m,
                      bool bMDPformat)
{
  if (bMDPformat)
    fprintf(fp,"%-10s    = %g %g %g %g %g %g\n",title,
            m[XX][XX],m[YY][YY],m[ZZ][ZZ],m[XX][YY],m[XX][ZZ],m[YY][ZZ]);
  else
    pr_rvecs(fp,indent,title,m,DIM);
}

static void pr_cosine(FILE *fp,int indent,const char *title,t_cosines *cos,
                      bool bMDPformat)
{
  int j;
  
  if (bMDPformat) {
    fprintf(fp,"%s = %d\n",title,cos->n);
  }
  else {
    indent=pr_title(fp,indent,title);
    (void) pr_indent(fp,indent);
    fprintf(fp,"n = %d\n",cos->n);
    if (cos->n > 0) {
      (void) pr_indent(fp,indent+2);
      fprintf(fp,"a =");
      for(j=0; (j<cos->n); j++)
        fprintf(fp," %e",cos->a[j]);
      fprintf(fp,"\n");
      (void) pr_indent(fp,indent+2);
      fprintf(fp,"phi =");
      for(j=0; (j<cos->n); j++)
        fprintf(fp," %e",cos->phi[j]);
      fprintf(fp,"\n");
    }
  }
}

#define PS(t,s) pr_str(fp,indent,t,s)
#define PI(t,s) pr_int(fp,indent,t,s)
#define PSTEP(t,s) pr_gmx_large_int(fp,indent,t,s)
#define PR(t,s) pr_real(fp,indent,t,s)

static void pr_pullgrp(FILE *fp,int indent,int g,t_pullgrp *pg)
{
  pr_indent(fp,indent);
  fprintf(fp,"pull_group %d:\n",g);
  indent += 2;
  pr_ivec_block(fp,indent,"atom",pg->ind,pg->nat,TRUE);
  pr_rvec(fp,indent,"weight",pg->weight,pg->nweight,TRUE);
  PI("pbcatom",pg->pbcatom);
  pr_rvec(fp,indent,"vec",pg->vec,DIM,TRUE);
  pr_rvec(fp,indent,"init",pg->init,DIM,TRUE);
  PR("rate",pg->rate);
  PR("k",pg->k);
  PR("kB",pg->kB);
}

static void pr_pull(FILE *fp,int indent,t_pull *pull)
{
  int g;

  PS("pull_geometry",EPULLGEOM(pull->eGeom));
  pr_ivec(fp,indent,"pull_dim",pull->dim,DIM,TRUE);
  PR("pull_r1",pull->cyl_r1);
  PR("pull_r0",pull->cyl_r0);
  PR("pull_constr_tol",pull->constr_tol);
  PI("pull_nstxout",pull->nstxout);
  PI("pull_nstfout",pull->nstfout);
  PI("pull_ngrp",pull->ngrp);
  for(g=0; g<pull->ngrp+1; g++)
    pr_pullgrp(fp,indent,g,&pull->grp[g]);
}

void pr_inputrec(FILE *fp,int indent,const char *title,t_inputrec *ir,
                 bool bMDPformat)
{
  const char *infbuf="inf";
  int  i;
  
  if (available(fp,ir,indent,title)) {
    if (!bMDPformat)
      indent=pr_title(fp,indent,title);
    PS("integrator",EI(ir->eI));
    PSTEP("nsteps",ir->nsteps);
    PSTEP("init_step",ir->init_step);
    PI("nstcalcenergy",ir->nstcalcenergy);
    PS("ns_type",ENS(ir->ns_type));
    PI("nstlist",ir->nstlist);
    PI("ndelta",ir->ndelta);
    PI("nstcomm",ir->nstcomm);
    PS("comm_mode",ECOM(ir->comm_mode));
    PI("nstlog",ir->nstlog);
    PI("nstxout",ir->nstxout);
    PI("nstvout",ir->nstvout);
    PI("nstfout",ir->nstfout);
    PI("nstenergy",ir->nstenergy);
    PI("nstxtcout",ir->nstxtcout);
    PR("init_t",ir->init_t);
    PR("delta_t",ir->delta_t);
    
    PR("xtcprec",ir->xtcprec);
    PI("nkx",ir->nkx);
    PI("nky",ir->nky);
    PI("nkz",ir->nkz);
    PI("pme_order",ir->pme_order);
    PR("ewald_rtol",ir->ewald_rtol);
    PR("ewald_geometry",ir->ewald_geometry);
    PR("epsilon_surface",ir->epsilon_surface);
    PS("optimize_fft",BOOL(ir->bOptFFT));
    PS("ePBC",EPBC(ir->ePBC));
    PS("bPeriodicMols",BOOL(ir->bPeriodicMols));
    PS("bContinuation",BOOL(ir->bContinuation));
    PS("bShakeSOR",BOOL(ir->bShakeSOR));
    PS("etc",ETCOUPLTYPE(ir->etc));
    PS("epc",EPCOUPLTYPE(ir->epc));
    PS("epctype",EPCOUPLTYPETYPE(ir->epct));
    PR("tau_p",ir->tau_p);
    pr_matrix(fp,indent,"ref_p",ir->ref_p,bMDPformat);
    pr_matrix(fp,indent,"compress",ir->compress,bMDPformat);
    PS("refcoord_scaling",EREFSCALINGTYPE(ir->refcoord_scaling));
    if (bMDPformat)
      fprintf(fp,"posres_com  = %g %g %g\n",ir->posres_com[XX],
              ir->posres_com[YY],ir->posres_com[ZZ]);
    else
      pr_rvec(fp,indent,"posres_com",ir->posres_com,DIM,TRUE);
    if (bMDPformat)
      fprintf(fp,"posres_comB = %g %g %g\n",ir->posres_comB[XX],
              ir->posres_comB[YY],ir->posres_comB[ZZ]);
    else
      pr_rvec(fp,indent,"posres_comB",ir->posres_comB,DIM,TRUE);
    PI("andersen_seed",ir->andersen_seed);
    PR("rlist",ir->rlist);
    PR("rlistlong",ir->rlistlong);
    PR("rtpi",ir->rtpi);
    PS("coulombtype",EELTYPE(ir->coulombtype));
    PR("rcoulomb_switch",ir->rcoulomb_switch);
    PR("rcoulomb",ir->rcoulomb);
    PS("vdwtype",EVDWTYPE(ir->vdwtype));
    PR("rvdw_switch",ir->rvdw_switch);
    PR("rvdw",ir->rvdw);
    if (ir->epsilon_r != 0)
      PR("epsilon_r",ir->epsilon_r);
    else
      PS("epsilon_r",infbuf);
    if (ir->epsilon_rf != 0)
      PR("epsilon_rf",ir->epsilon_rf);
    else
      PS("epsilon_rf",infbuf);
    PR("tabext",ir->tabext);
    PS("implicit_solvent",EIMPLICITSOL(ir->implicit_solvent));
    PS("gb_algorithm",EGBALGORITHM(ir->gb_algorithm));
    PR("gb_epsilon_solvent",ir->gb_epsilon_solvent);
    PI("nstgbradii",ir->nstgbradii);
    PR("rgbradii",ir->rgbradii);
    PR("gb_saltconc",ir->gb_saltconc);
    PR("gb_obc_alpha",ir->gb_obc_alpha);
    PR("gb_obc_beta",ir->gb_obc_beta);
    PR("gb_obc_gamma",ir->gb_obc_gamma);
    PR("gb_dielectric_offset",ir->gb_dielectric_offset);
    PS("sa_algorithm",ESAALGORITHM(ir->gb_algorithm));
    PR("sa_surface_tension",ir->sa_surface_tension);
          
    PS("DispCorr",EDISPCORR(ir->eDispCorr));
    PS("free_energy",EFEPTYPE(ir->efep));
    PR("init_lambda",ir->init_lambda);
    PR("delta_lambda",ir->delta_lambda);
    if (!bMDPformat)
    {
        PI("n_foreign_lambda",ir->n_flambda);
    }
    if (ir->n_flambda > 0)
    {
        pr_indent(fp,indent);
        fprintf(fp,"foreign_lambda%s",bMDPformat ? " = " : ":");
        for(i=0; i<ir->n_flambda; i++)
        {
            fprintf(fp,"  %10g",ir->flambda[i]);
        }
        fprintf(fp,"\n");
    }
    PR("sc_alpha",ir->sc_alpha);
    PI("sc_power",ir->sc_power);
    PR("sc_sigma",ir->sc_sigma);
    PI("nstdhdl", ir->nstdhdl);

    PI("nwall",ir->nwall);
    PS("wall_type",EWALLTYPE(ir->wall_type));
    PI("wall_atomtype[0]",ir->wall_atomtype[0]);
    PI("wall_atomtype[1]",ir->wall_atomtype[1]);
    PR("wall_density[0]",ir->wall_density[0]);
    PR("wall_density[1]",ir->wall_density[1]);
    PR("wall_ewald_zfac",ir->wall_ewald_zfac);

    PS("pull",EPULLTYPE(ir->ePull));
    if (ir->ePull != epullNO)
      pr_pull(fp,indent,ir->pull);

    PS("disre",EDISRETYPE(ir->eDisre));
    PS("disre_weighting",EDISREWEIGHTING(ir->eDisreWeighting));
    PS("disre_mixed",BOOL(ir->bDisreMixed));
    PR("dr_fc",ir->dr_fc);
    PR("dr_tau",ir->dr_tau);
    PR("nstdisreout",ir->nstdisreout);
    PR("orires_fc",ir->orires_fc);
    PR("orires_tau",ir->orires_tau);
    PR("nstorireout",ir->nstorireout);

    PR("dihre-fc",ir->dihre_fc);
    
    PR("em_stepsize",ir->em_stepsize);
    PR("em_tol",ir->em_tol);
    PI("niter",ir->niter);
    PR("fc_stepsize",ir->fc_stepsize);
    PI("nstcgsteep",ir->nstcgsteep);
    PI("nbfgscorr",ir->nbfgscorr);

    PS("ConstAlg",ECONSTRTYPE(ir->eConstrAlg));
    PR("shake_tol",ir->shake_tol);
    PI("lincs_order",ir->nProjOrder);
    PR("lincs_warnangle",ir->LincsWarnAngle);
    PI("lincs_iter",ir->nLincsIter);
    PR("bd_fric",ir->bd_fric);
    PI("ld_seed",ir->ld_seed);
    PR("cos_accel",ir->cos_accel);
    pr_matrix(fp,indent,"deform",ir->deform,bMDPformat);
    PI("userint1",ir->userint1);
    PI("userint2",ir->userint2);
    PI("userint3",ir->userint3);
    PI("userint4",ir->userint4);
    PR("userreal1",ir->userreal1);
    PR("userreal2",ir->userreal2);
    PR("userreal3",ir->userreal3);
    PR("userreal4",ir->userreal4);
    pr_grp_opts(fp,indent,"grpopts",&(ir->opts),bMDPformat);
    pr_cosine(fp,indent,"efield-x",&(ir->ex[XX]),bMDPformat);
    pr_cosine(fp,indent,"efield-xt",&(ir->et[XX]),bMDPformat);
    pr_cosine(fp,indent,"efield-y",&(ir->ex[YY]),bMDPformat);
    pr_cosine(fp,indent,"efield-yt",&(ir->et[YY]),bMDPformat);
    pr_cosine(fp,indent,"efield-z",&(ir->ex[ZZ]),bMDPformat);
    pr_cosine(fp,indent,"efield-zt",&(ir->et[ZZ]),bMDPformat);
    PS("bQMMM",BOOL(ir->bQMMM));
    PI("QMconstraints",ir->QMconstraints);
    PI("QMMMscheme",ir->QMMMscheme);
    PR("scalefactor",ir->scalefactor);
    pr_qm_opts(fp,indent,"qm_opts",&(ir->opts));
  }
}
#undef PS
#undef PR
#undef PI

static void pr_harm(FILE *fp,t_iparams *iparams,const char *r,const char *kr)
{
  fprintf(fp,"%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e\n",
          r,iparams->harmonic.rA,kr,iparams->harmonic.krA,
          r,iparams->harmonic.rB,kr,iparams->harmonic.krB);
}

void pr_iparams(FILE *fp,t_functype ftype,t_iparams *iparams)
{
  int i;
  real VA[4],VB[4],*rbcA,*rbcB;

  switch (ftype) {
  case F_ANGLES:
  case F_G96ANGLES:
    pr_harm(fp,iparams,"th","ct");
    break;
  case F_CROSS_BOND_BONDS:
    fprintf(fp,"r1e=%15.8e, r2e=%15.8e, krr=%15.8e\n",
            iparams->cross_bb.r1e,iparams->cross_bb.r2e,
            iparams->cross_bb.krr);
    break;
  case F_CROSS_BOND_ANGLES:
    fprintf(fp,"r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e\n",
            iparams->cross_ba.r1e,iparams->cross_ba.r2e,
            iparams->cross_ba.r3e,iparams->cross_ba.krt);
    break;
  case F_UREY_BRADLEY:
    fprintf(fp,"theta=%15.8e, ktheta=%15.8e, r13=%15.8e, kUB=%15.8e\n",
            iparams->u_b.theta,iparams->u_b.ktheta,iparams->u_b.r13,iparams->u_b.kUB);
    break;
  case F_QUARTIC_ANGLES:
    fprintf(fp,"theta=%15.8e",iparams->qangle.theta);
    for(i=0; i<5; i++)
      fprintf(fp,", c%c=%15.8e",'0'+i,iparams->qangle.c[i]);
    fprintf(fp,"\n");
    break;
  case F_BHAM:
    fprintf(fp,"a=%15.8e, b=%15.8e, c=%15.8e\n",
            iparams->bham.a,iparams->bham.b,iparams->bham.c);
    break;
  case F_BONDS:
  case F_G96BONDS:
  case F_HARMONIC:
    pr_harm(fp,iparams,"b0","cb");
    break;
  case F_IDIHS:
    pr_harm(fp,iparams,"xi","cx");
    break;
  case F_MORSE:
    fprintf(fp,"b0=%15.8e, cb=%15.8e, beta=%15.8e\n",
            iparams->morse.b0,iparams->morse.cb,iparams->morse.beta);
    break;
  case F_CUBICBONDS:
    fprintf(fp,"b0=%15.8e, kb=%15.8e, kcub=%15.8e\n",
            iparams->cubic.b0,iparams->cubic.kb,iparams->cubic.kcub);
    break;
  case F_CONNBONDS:
    fprintf(fp,"\n");
    break;
  case F_FENEBONDS:
    fprintf(fp,"bm=%15.8e, kb=%15.8e\n",iparams->fene.bm,iparams->fene.kb);
    break;
  case F_TABBONDS:
  case F_TABBONDSNC:
  case F_TABANGLES:
  case F_TABDIHS:
    fprintf(fp,"tab=%d, kA=%15.8e, kB=%15.8e\n",
            iparams->tab.table,iparams->tab.kA,iparams->tab.kB);
    break;
  case F_POLARIZATION:
    fprintf(fp,"alpha=%15.8e\n",iparams->polarize.alpha);
    break;
  case F_THOLE_POL:
    fprintf(fp,"a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e\n",
            iparams->thole.a,iparams->thole.alpha1,iparams->thole.alpha2,
            iparams->thole.rfac);
    break;
  case F_WATER_POL:
    fprintf(fp,"al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f\n",
            iparams->wpol.al_x,iparams->wpol.al_y,iparams->wpol.al_z,
            iparams->wpol.rOH,iparams->wpol.rHH,iparams->wpol.rOD);
    break;
  case F_LJ:
    fprintf(fp,"c6=%15.8e, c12=%15.8e\n",iparams->lj.c6,iparams->lj.c12);
    break;
  case F_LJ14:
    fprintf(fp,"c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e\n",
            iparams->lj14.c6A,iparams->lj14.c12A,
            iparams->lj14.c6B,iparams->lj14.c12B);
    break;
  case F_LJC14_Q:
    fprintf(fp,"fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
            iparams->ljc14.fqq,
            iparams->ljc14.qi,iparams->ljc14.qj,
            iparams->ljc14.c6,iparams->ljc14.c12);
    break;
  case F_LJC_PAIRS_NB:
    fprintf(fp,"qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
            iparams->ljcnb.qi,iparams->ljcnb.qj,
            iparams->ljcnb.c6,iparams->ljcnb.c12);
    break;
  case F_PDIHS:
  case F_ANGRES:
  case F_ANGRESZ:
    fprintf(fp,"phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d\n",
            iparams->pdihs.phiA,iparams->pdihs.cpA,
            iparams->pdihs.phiB,iparams->pdihs.cpB,
            iparams->pdihs.mult);
    break;
  case F_DISRES:
    fprintf(fp,"label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)\n",
            iparams->disres.label,iparams->disres.type,
            iparams->disres.low,iparams->disres.up1,
            iparams->disres.up2,iparams->disres.kfac);
    break;
  case F_ORIRES:
    fprintf(fp,"ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)\n",
            iparams->orires.ex,iparams->orires.label,iparams->orires.power,
            iparams->orires.c,iparams->orires.obs,iparams->orires.kfac);
    break;
  case F_DIHRES:
    fprintf(fp,"label=%d, power=%4d phi=%15.8e, dphi=%15.8e, kfac=%15.8e)\n",
            iparams->dihres.label,iparams->dihres.power,
            iparams->dihres.phi,iparams->dihres.dphi,iparams->dihres.kfac);
    break;
  case F_POSRES:
    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",
            iparams->posres.pos0A[XX],iparams->posres.pos0A[YY],
            iparams->posres.pos0A[ZZ],iparams->posres.fcA[XX],
            iparams->posres.fcA[YY],iparams->posres.fcA[ZZ],
            iparams->posres.pos0B[XX],iparams->posres.pos0B[YY],
            iparams->posres.pos0B[ZZ],iparams->posres.fcB[XX],
            iparams->posres.fcB[YY],iparams->posres.fcB[ZZ]);
    break;
  case F_RBDIHS:
    for (i=0; i<NR_RBDIHS; i++) 
      fprintf(fp,"%srbcA[%d]=%15.8e",i==0?"":", ",i,iparams->rbdihs.rbcA[i]);
    fprintf(fp,"\n");
    for (i=0; i<NR_RBDIHS; i++) 
      fprintf(fp,"%srbcB[%d]=%15.8e",i==0?"":", ",i,iparams->rbdihs.rbcB[i]);
    fprintf(fp,"\n");
    break;
  case F_FOURDIHS:
    /* Use the OPLS -> Ryckaert-Bellemans formula backwards to get the
     * OPLS potential constants back.
     */
    rbcA = iparams->rbdihs.rbcA;
    rbcB = iparams->rbdihs.rbcB;

    VA[3] = -0.25*rbcA[4];
    VA[2] = -0.5*rbcA[3];
    VA[1] = 4.0*VA[3]-rbcA[2];
    VA[0] = 3.0*VA[2]-2.0*rbcA[1];

    VB[3] = -0.25*rbcB[4];
    VB[2] = -0.5*rbcB[3];
    VB[1] = 4.0*VB[3]-rbcB[2];
    VB[0] = 3.0*VB[2]-2.0*rbcB[1];

    for (i=0; i<NR_FOURDIHS; i++) 
      fprintf(fp,"%sFourA[%d]=%15.8e",i==0?"":", ",i,VA[i]);
    fprintf(fp,"\n");
    for (i=0; i<NR_FOURDIHS; i++) 
      fprintf(fp,"%sFourB[%d]=%15.8e",i==0?"":", ",i,VB[i]);
    fprintf(fp,"\n");
    break;
   
  case F_CONSTR:
  case F_CONSTRNC:
    fprintf(fp,"dA=%15.8e, dB=%15.8e\n",iparams->constr.dA,iparams->constr.dB);
    break;
  case F_SETTLE:
    fprintf(fp,"doh=%15.8e, dhh=%15.8e\n",iparams->settle.doh,
            iparams->settle.dhh);
    break;
  case F_VSITE2:
    fprintf(fp,"a=%15.8e\n",iparams->vsite.a);
    break;
  case F_VSITE3:
  case F_VSITE3FD:
  case F_VSITE3FAD:
    fprintf(fp,"a=%15.8e, b=%15.8e\n",iparams->vsite.a,iparams->vsite.b);
    break;
  case F_VSITE3OUT:
  case F_VSITE4FD:
  case F_VSITE4FDN:
    fprintf(fp,"a=%15.8e, b=%15.8e, c=%15.8e\n",
            iparams->vsite.a,iparams->vsite.b,iparams->vsite.c);
    break;
  case F_VSITEN:
    fprintf(fp,"n=%2d, a=%15.8e\n",iparams->vsiten.n,iparams->vsiten.a);
    break;
  case F_GB12:
  case F_GB13:
  case F_GB14:
    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);
    break;                
  case F_CMAP:
    fprintf(fp, "cmapA=%1d, cmapB=%1d\n",iparams->cmap.cmapA, iparams->cmap.cmapB);
    break;                
  default:
    gmx_fatal(FARGS,"unknown function type %d (%s) in %s line %d",
              ftype,interaction_function[ftype].name,__FILE__,__LINE__);
  }
}

void pr_ilist(FILE *fp,int indent,const char *title,
              t_functype *functype,t_ilist *ilist, bool bShowNumbers)
{
    int i,j,k,type,ftype;
    t_iatom *iatoms;
    
    if (available(fp,ilist,indent,title) && ilist->nr > 0)
    {  
        indent=pr_title(fp,indent,title);
        (void) pr_indent(fp,indent);
        fprintf(fp,"nr: %d\n",ilist->nr);
        if (ilist->nr > 0) {
            (void) pr_indent(fp,indent);
            fprintf(fp,"iatoms:\n");
            iatoms=ilist->iatoms;
            for (i=j=0; i<ilist->nr;) {
#ifndef DEBUG
                (void) pr_indent(fp,indent+INDENT);
                type=*(iatoms++);
                ftype=functype[type];
                (void) fprintf(fp,"%d type=%d (%s)",
                               bShowNumbers?j:-1,bShowNumbers?type:-1,
                               interaction_function[ftype].name);
                j++;
                for (k=0; k<interaction_function[ftype].nratoms; k++)
                    (void) fprintf(fp," %u",*(iatoms++));
                (void) fprintf(fp,"\n");
                i+=1+interaction_function[ftype].nratoms;
#else
                fprintf(fp,"%5d%5d\n",i,iatoms[i]);
                i++;
#endif
            }
        }
    }
}

void pr_ffparams(FILE *fp,int indent,const char *title,
                 gmx_ffparams_t *ffparams,
                 bool bShowNumbers)
{
  int i,j;
  
  indent=pr_title(fp,indent,title);
  (void) pr_indent(fp,indent);
  (void) fprintf(fp,"atnr=%d\n",ffparams->atnr);
  (void) pr_indent(fp,indent);
  (void) fprintf(fp,"ntypes=%d\n",ffparams->ntypes);
  for (i=0; i<ffparams->ntypes; i++) {
      (void) pr_indent(fp,indent+INDENT);
      (void) fprintf(fp,"functype[%d]=%s, ",
                     bShowNumbers?i:-1,
                     interaction_function[ffparams->functype[i]].name);
      pr_iparams(fp,ffparams->functype[i],&ffparams->iparams[i]);
  }
  (void) pr_double(fp,indent,"reppow",ffparams->reppow);
  (void) pr_real(fp,indent,"fudgeQQ",ffparams->fudgeQQ);
}

void pr_idef(FILE *fp,int indent,const char *title,t_idef *idef, bool bShowNumbers)
{
  int i,j;
  
  if (available(fp,idef,indent,title)) {  
    indent=pr_title(fp,indent,title);
    (void) pr_indent(fp,indent);
    (void) fprintf(fp,"atnr=%d\n",idef->atnr);
    (void) pr_indent(fp,indent);
    (void) fprintf(fp,"ntypes=%d\n",idef->ntypes);
    for (i=0; i<idef->ntypes; i++) {
      (void) pr_indent(fp,indent+INDENT);
      (void) fprintf(fp,"functype[%d]=%s, ",
                     bShowNumbers?i:-1,
                     interaction_function[idef->functype[i]].name);
      pr_iparams(fp,idef->functype[i],&idef->iparams[i]);
    }
    (void) pr_real(fp,indent,"fudgeQQ",idef->fudgeQQ);

    for(j=0; (j<F_NRE); j++)
      pr_ilist(fp,indent,interaction_function[j].longname,
               idef->functype,&idef->il[j],bShowNumbers);
  }
}

static int pr_block_title(FILE *fp,int indent,const char *title,t_block *block)
{
  int i;

  if (available(fp,block,indent,title))
    {
      indent=pr_title(fp,indent,title);
      (void) pr_indent(fp,indent);
      (void) fprintf(fp,"nr=%d\n",block->nr);
    }
  return indent;
}

static int pr_blocka_title(FILE *fp,int indent,const char *title,t_blocka *block)
{
  int i;

  if (available(fp,block,indent,title))
    {
      indent=pr_title(fp,indent,title);
      (void) pr_indent(fp,indent);
      (void) fprintf(fp,"nr=%d\n",block->nr);
      (void) pr_indent(fp,indent);
      (void) fprintf(fp,"nra=%d\n",block->nra);
    }
  return indent;
}

static void low_pr_block(FILE *fp,int indent,const char *title,t_block *block, bool bShowNumbers)
{
  int i;
  
  if (available(fp,block,indent,title))
    {
      indent=pr_block_title(fp,indent,title,block);
      for (i=0; i<=block->nr; i++)
        {
          (void) pr_indent(fp,indent+INDENT);
          (void) fprintf(fp,"%s->index[%d]=%u\n",
                         title,bShowNumbers?i:-1,block->index[i]);
        }
    }
}

static void low_pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block, bool bShowNumbers)
{
  int i;
  
  if (available(fp,block,indent,title))
    {
      indent=pr_blocka_title(fp,indent,title,block);
      for (i=0; i<=block->nr; i++)
        {
          (void) pr_indent(fp,indent+INDENT);
          (void) fprintf(fp,"%s->index[%d]=%u\n",
                         title,bShowNumbers?i:-1,block->index[i]);
        }
      for (i=0; i<block->nra; i++)
        {
          (void) pr_indent(fp,indent+INDENT);
          (void) fprintf(fp,"%s->a[%d]=%u\n",
                         title,bShowNumbers?i:-1,block->a[i]);
        }
    }
}

void pr_block(FILE *fp,int indent,const char *title,t_block *block,bool bShowNumbers)
{
  int i,j,ok,size,start,end;
  
  if (available(fp,block,indent,title))
    {
      indent=pr_block_title(fp,indent,title,block);
      start=0;
      end=start;
      if ((ok=(block->index[start]==0))==0)
        (void) fprintf(fp,"block->index[%d] should be 0\n",start);
      else
        for (i=0; i<block->nr; i++)
          {
            end=block->index[i+1];
            size=pr_indent(fp,indent);
            if (end<=start)
              size+=fprintf(fp,"%s[%d]={}\n",title,i);
            else
              size+=fprintf(fp,"%s[%d]={%d..%d}\n",
                            title,bShowNumbers?i:-1,
                            bShowNumbers?start:-1,bShowNumbers?end-1:-1);
            start=end;
          }
    }
}

void pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block,bool bShowNumbers)
{
  int i,j,ok,size,start,end;
  
  if (available(fp,block,indent,title))
    {
      indent=pr_blocka_title(fp,indent,title,block);
      start=0;
      end=start;
      if ((ok=(block->index[start]==0))==0)
        (void) fprintf(fp,"block->index[%d] should be 0\n",start);
      else
        for (i=0; i<block->nr; i++)
          {
            end=block->index[i+1];
            size=pr_indent(fp,indent);
            if (end<=start)
              size+=fprintf(fp,"%s[%d]={",title,i);
            else
              size+=fprintf(fp,"%s[%d][%d..%d]={",
                            title,bShowNumbers?i:-1,
                            bShowNumbers?start:-1,bShowNumbers?end-1:-1);
            for (j=start; j<end; j++)
              {
                if (j>start) size+=fprintf(fp,", ");
                if ((size)>(USE_WIDTH))
                  {
                    (void) fprintf(fp,"\n");
                    size=pr_indent(fp,indent+INDENT);
                  }
                size+=fprintf(fp,"%u",block->a[j]);
              }
            (void) fprintf(fp,"}\n");
            start=end;
          }
      if ((end!=block->nra)||(!ok)) 
        {
          (void) pr_indent(fp,indent);
          (void) fprintf(fp,"tables inconsistent, dumping complete tables:\n");
          low_pr_blocka(fp,indent,title,block,bShowNumbers);
        }
    }
}

static void pr_strings(FILE *fp,int indent,const char *title,char ***nm,int n, bool bShowNumbers)
{
  int i;

  if (available(fp,nm,indent,title))
    {  
      indent=pr_title_n(fp,indent,title,n);
      for (i=0; i<n; i++)
        {
          (void) pr_indent(fp,indent);
          (void) fprintf(fp,"%s[%d]={name=\"%s\"}\n",
                         title,bShowNumbers?i:-1,*(nm[i]));
        }
    }
}

static void pr_strings2(FILE *fp,int indent,const char *title,
                        char ***nm,char ***nmB,int n, bool bShowNumbers)
{
  int i;

  if (available(fp,nm,indent,title))
    {  
      indent=pr_title_n(fp,indent,title,n);
      for (i=0; i<n; i++)
        {
          (void) pr_indent(fp,indent);
          (void) fprintf(fp,"%s[%d]={name=\"%s\",nameB=\"%s\"}\n",
                         title,bShowNumbers?i:-1,*(nm[i]),*(nmB[i]));
        }
    }
}

static void pr_resinfo(FILE *fp,int indent,const char *title,t_resinfo *resinfo,int n, bool bShowNumbers)
{
    int i;
    
    if (available(fp,resinfo,indent,title))
    {  
        indent=pr_title_n(fp,indent,title,n);
        for (i=0; i<n; i++)
        {
            (void) pr_indent(fp,indent);
            (void) fprintf(fp,"%s[%d]={name=\"%s\", nr=%d, ic='%c'}\n",
                           title,bShowNumbers?i:-1,
                           *(resinfo[i].name),resinfo[i].nr,
                           (resinfo[i].ic == '\0') ? ' ' : resinfo[i].ic);
        }
    }
}

static void pr_atom(FILE *fp,int indent,const char *title,t_atom *atom,int n)
{
  int i,j;
  
  if (available(fp,atom,indent,title)) {  
    indent=pr_title_n(fp,indent,title,n);
    for (i=0; i<n; i++) {
      (void) pr_indent(fp,indent);
      fprintf(fp,"%s[%6d]={type=%3d, typeB=%3d, ptype=%8s, m=%12.5e, "
              "q=%12.5e, mB=%12.5e, qB=%12.5e, resind=%5d, atomnumber=%3d}\n",
              title,i,atom[i].type,atom[i].typeB,ptype_str[atom[i].ptype],
              atom[i].m,atom[i].q,atom[i].mB,atom[i].qB,
              atom[i].resind,atom[i].atomnumber);
    }
  }
}

static void pr_grps(FILE *fp,int indent,const char *title,t_grps grps[],int ngrp,
                    char **grpname[], bool bShowNumbers)
{
    int i,j;

  for(i=0; (i<ngrp); i++) {
    fprintf(fp,"%s[%d] nr=%d, name=[",title,bShowNumbers?i:-1,grps[i].nr);
    for(j=0; (j<grps[i].nr); j++)
      fprintf(fp," %s",*(grpname[grps[i].nm_ind[j]]));
    fprintf(fp,"]\n");
  }
}

static void pr_groups(FILE *fp,int indent,const char *title,
                      gmx_groups_t *groups,
                      bool bShowNumbers)
{
    int grpnr[egcNR];
    int nat_max,i,g;

    pr_grps(fp,indent,"grp",groups->grps,egcNR,groups->grpname,bShowNumbers);
    pr_strings(fp,indent,"grpname",groups->grpname,groups->ngrpname,bShowNumbers);

    (void) pr_indent(fp,indent);
    fprintf(fp,"groups          ");
    for(g=0; g<egcNR; g++)
    {
       printf(" %5.5s",gtypes[g]);
    }
    printf("\n");

    (void) pr_indent(fp,indent);
    fprintf(fp,"allocated       ");
    nat_max = 0;
    for(g=0; g<egcNR; g++)
    {
        printf(" %5d",groups->ngrpnr[g]);
        nat_max = max(nat_max,groups->ngrpnr[g]);
    }
    printf("\n");

    if (nat_max == 0)
    {
        (void) pr_indent(fp,indent);
        fprintf(fp,"groupnr[%5s] =","*");
        for(g=0; g<egcNR; g++)
        {
            fprintf(fp,"  %3d ",0);
        }
        fprintf(fp,"\n");
    }
    else
    {
        for(i=0; i<nat_max; i++)
        {
            (void) pr_indent(fp,indent);
            fprintf(fp,"groupnr[%5d] =",i);
            for(g=0; g<egcNR; g++)
            {
                fprintf(fp,"  %3d ",
                        groups->grpnr[g] ? groups->grpnr[g][i] : 0);
            }
            fprintf(fp,"\n");
        }
    }
}

void pr_atoms(FILE *fp,int indent,const char *title,t_atoms *atoms, 
              bool bShownumbers)
{
  if (available(fp,atoms,indent,title))
    {
      indent=pr_title(fp,indent,title);
      pr_atom(fp,indent,"atom",atoms->atom,atoms->nr);
      pr_strings(fp,indent,"atom",atoms->atomname,atoms->nr,bShownumbers);
      pr_strings2(fp,indent,"type",atoms->atomtype,atoms->atomtypeB,atoms->nr,bShownumbers);
      pr_resinfo(fp,indent,"residue",atoms->resinfo,atoms->nres,bShownumbers);
    }
}

void pr_cmap(FILE *fp, int indent, const char *title, gmx_cmap_t *cmap_grid,
             bool bShowNumbers)
{
    int i,j,nelem;
    real dx,idx;
        
    dx    = 360.0 / cmap_grid->grid_spacing;
    nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
        
    if(available(fp,cmap_grid,indent,title))
    {
        fprintf(fp,"%s\n",title);
                
        for(i=0;i<cmap_grid->ngrid;i++)
        {
            idx = -180.0;
            fprintf(fp,"%8s %8s %8s %8s\n","V","dVdx","dVdy","d2dV");
                        
            fprintf(fp,"grid[%3d]={\n",bShowNumbers?i:-1);
                        
            for(j=0;j<nelem;j++)
            {
                if( (j%cmap_grid->grid_spacing)==0)
                {
                    fprintf(fp,"%8.1f\n",idx);
                    idx+=dx;
                }
                                
                fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4]);
                fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4+1]);
                fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4+2]);
                fprintf(fp,"%8.3f\n",cmap_grid->cmapdata[i].cmap[j*4+3]);
            }
            fprintf(fp,"\n");
        }
    }
        
}


void pr_atomtypes(FILE *fp,int indent,const char *title,t_atomtypes *atomtypes, 
                  bool bShowNumbers)
{
  int i;
  if (available(fp,atomtypes,indent,title)) 
  {
    indent=pr_title(fp,indent,title);
    for(i=0;i<atomtypes->nr;i++) {
      pr_indent(fp,indent);
                fprintf(fp,
                                "atomtype[%3d]={radius=%12.5e, volume=%12.5e, gb_radius=%12.5e, surftens=%12.5e, atomnumber=%4d, S_hct=%12.5e)}\n",
                                bShowNumbers?i:-1,atomtypes->radius[i],atomtypes->vol[i],
                                atomtypes->gb_radius[i],
                                atomtypes->surftens[i],atomtypes->atomnumber[i],atomtypes->S_hct[i]);
    }
  }
}

static void pr_moltype(FILE *fp,int indent,const char *title,
                       gmx_moltype_t *molt,int n,
                       gmx_ffparams_t *ffparams,
                       bool bShowNumbers)
{
    int j;

    indent = pr_title_n(fp,indent,title,n);
    (void) pr_indent(fp,indent);
    (void) fprintf(fp,"name=\"%s\"\n",*(molt->name));
    pr_atoms(fp,indent,"atoms",&(molt->atoms),bShowNumbers);
    pr_block(fp,indent,"cgs",&molt->cgs, bShowNumbers);
    pr_blocka(fp,indent,"excls",&molt->excls, bShowNumbers);
    for(j=0; (j<F_NRE); j++) {
        pr_ilist(fp,indent,interaction_function[j].longname,
                 ffparams->functype,&molt->ilist[j],bShowNumbers);
    }
}

static void pr_molblock(FILE *fp,int indent,const char *title,
                        gmx_molblock_t *molb,int n,
                        gmx_moltype_t *molt,
                        bool bShowNumbers)
{
    indent = pr_title_n(fp,indent,title,n);
    (void) pr_indent(fp,indent);
    (void) fprintf(fp,"%-20s = %d \"%s\"\n",
                   "moltype",molb->type,*(molt[molb->type].name));
    pr_int(fp,indent,"#molecules",molb->nmol);
    pr_int(fp,indent,"#atoms_mol",molb->natoms_mol);
    pr_int(fp,indent,"#posres_xA",molb->nposres_xA);
    if (molb->nposres_xA > 0) {
        pr_rvecs(fp,indent,"posres_xA",molb->posres_xA,molb->nposres_xA);
    }
    pr_int(fp,indent,"#posres_xB",molb->nposres_xB);
    if (molb->nposres_xB > 0) {
        pr_rvecs(fp,indent,"posres_xB",molb->posres_xB,molb->nposres_xB);
    }
}

void pr_mtop(FILE *fp,int indent,const char *title,gmx_mtop_t *mtop,
             bool bShowNumbers)
{
    int mt,mb;

    if (available(fp,mtop,indent,title)) {
        indent=pr_title(fp,indent,title);
        (void) pr_indent(fp,indent);
        (void) fprintf(fp,"name=\"%s\"\n",*(mtop->name));
        pr_int(fp,indent,"#atoms",mtop->natoms);
        for(mb=0; mb<mtop->nmolblock; mb++) {
            pr_molblock(fp,indent,"molblock",&mtop->molblock[mb],mb,
                        mtop->moltype,bShowNumbers);
        }
        pr_ffparams(fp,indent,"ffparams",&(mtop->ffparams),bShowNumbers);
        pr_atomtypes(fp,indent,"atomtypes",&(mtop->atomtypes),bShowNumbers);
        for(mt=0; mt<mtop->nmoltype; mt++) {
            pr_moltype(fp,indent,"moltype",&mtop->moltype[mt],mt,
                       &mtop->ffparams,bShowNumbers);
        }
        pr_groups(fp,indent,"groups",&mtop->groups,bShowNumbers);
        pr_cmap(fp,indent,"cmap",&mtop->cmap_grid,bShowNumbers);
    }
}

void pr_top(FILE *fp,int indent,const char *title,t_topology *top, bool bShowNumbers)
{
  if (available(fp,top,indent,title)) {
    indent=pr_title(fp,indent,title);
    (void) pr_indent(fp,indent);
    (void) fprintf(fp,"name=\"%s\"\n",*(top->name));
    pr_atoms(fp,indent,"atoms",&(top->atoms),bShowNumbers);
    pr_atomtypes(fp,indent,"atomtypes",&(top->atomtypes),bShowNumbers);
    pr_block(fp,indent,"cgs",&top->cgs, bShowNumbers);
    pr_block(fp,indent,"mols",&top->mols, bShowNumbers);
    pr_blocka(fp,indent,"excls",&top->excls, bShowNumbers);
    pr_idef(fp,indent,"idef",&top->idef,bShowNumbers);
  }
}

void pr_header(FILE *fp,int indent,const char *title,t_tpxheader *sh)
{
  char buf[22];
    
  if (available(fp,sh,indent,title))
    {
      indent=pr_title(fp,indent,title);
      pr_indent(fp,indent);
      fprintf(fp,"bIr    = %spresent\n",sh->bIr?"":"not ");
      pr_indent(fp,indent);
      fprintf(fp,"bBox   = %spresent\n",sh->bBox?"":"not ");
      pr_indent(fp,indent);
      fprintf(fp,"bTop   = %spresent\n",sh->bTop?"":"not ");
      pr_indent(fp,indent);
      fprintf(fp,"bX     = %spresent\n",sh->bX?"":"not ");
      pr_indent(fp,indent);
      fprintf(fp,"bV     = %spresent\n",sh->bV?"":"not ");
      pr_indent(fp,indent);
      fprintf(fp,"bF     = %spresent\n",sh->bF?"":"not ");
      
      pr_indent(fp,indent);
      fprintf(fp,"natoms = %d\n",sh->natoms);
      pr_indent(fp,indent);
      fprintf(fp,"lambda = %e\n",sh->lambda);
    }
}

void pr_commrec(FILE *fp,int indent,t_commrec *cr)
{
  pr_indent(fp,indent);
  fprintf(fp,"commrec:\n");
  indent+=2;
  pr_indent(fp,indent);
  fprintf(fp,"nodeid    = %d\n",cr->nodeid);
  pr_indent(fp,indent);
  fprintf(fp,"nnodes    = %d\n",cr->nnodes);
  pr_indent(fp,indent);
  fprintf(fp,"npmenodes = %d\n",cr->npmenodes);
  pr_indent(fp,indent);
  fprintf(fp,"threadid  = %d\n",cr->threadid);
  pr_indent(fp,indent);
  fprintf(fp,"nthreads  = %d\n",cr->nthreads);
}