/*
 * 
 *                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:
 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
 */
/* This file is completely threadsafe - keep it that way! */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <math.h>
#include <stdio.h>
#include <string.h>
#include "main.h"
#include "macros.h"
#include "smalloc.h"
#include "futil.h"
#include "statutil.h"
#include "sysstuff.h"
#include "txtdump.h"
#include "gmx_fatal.h"
#include "names.h"
#include "tpxio.h"
#include "enxio.h"
#include "mtop_util.h"
#include "string2.h"

static void cmp_int(FILE *fp,const char *s,int index,int i1,int i2)
{
  if (i1 != i2) {
    if (index != -1)
      fprintf(fp,"%s[%d] (%d - %d)\n",s,index,i1,i2);
    else
      fprintf(fp,"%s (%d - %d)\n",s,i1,i2);
  }
}

static void cmp_gmx_large_int(FILE *fp,const char *s,gmx_large_int_t i1,gmx_large_int_t i2)
{
  if (i1 != i2) {
    fprintf(fp,"%s (",s);
    fprintf(fp,gmx_large_int_pfmt,i1);
    fprintf(fp," - ");
    fprintf(fp,gmx_large_int_pfmt,i2);
    fprintf(fp,")\n");
  }
}

static void cmp_us(FILE *fp,const char *s,int index,unsigned short i1,unsigned short i2)
{
  if (i1 != i2) {
    if (index != -1)
      fprintf(fp,"%s[%d] (%d - %d)\n",s,index,i1,i2);
    else
      fprintf(fp,"%s (%d - %d)\n",s,i1,i2);
  }
}

static void cmp_uc(FILE *fp,const char *s,int index,unsigned char i1,unsigned char i2)
{
  if (i1 != i2) {
    if (index != -1)
      fprintf(fp,"%s[%d] (%d - %d)\n",s,index,i1,i2);
    else
      fprintf(fp,"%s (%d - %d)\n",s,i1,i2);
  }
}

static gmx_bool cmp_bool(FILE *fp, const char *s, int index, gmx_bool b1, gmx_bool b2)
{
  if (b1) {
    b1 = 1;
  } else {
    b1 = 0;
  }
  if (b2) {
    b2 = 1;
  } else {
    b2 = 0;
  }
  if (b1 != b2) {
    if (index != -1)
      fprintf(fp,"%s[%d] (%s - %s)\n",s,index,
	      bool_names[b1],bool_names[b2]);
    else
      fprintf(fp,"%s (%s - %s)\n",s,
	      bool_names[b1],bool_names[b2]);
  }
  return b1 && b2;
}

static void cmp_str(FILE *fp, const char *s, int index,
		    const char *s1, const char *s2)
{
  if (strcmp(s1,s2) != 0) {
    if (index != -1)
      fprintf(fp,"%s[%d] (%s - %s)\n",s,index,s1,s2);
    else
      fprintf(fp,"%s (%s - %s)\n",s,s1,s2);
  }
}

static gmx_bool equal_real(real i1,real i2,real ftol,real abstol)
{
    return ( ( 2*fabs(i1 - i2) <= (fabs(i1) + fabs(i2))*ftol ) || fabs(i1-i2)<=abstol );
}

static gmx_bool equal_float(float i1,float i2,float ftol,float abstol)
{
    return ( ( 2*fabs(i1 - i2) <= (fabs(i1) + fabs(i2))*ftol ) || fabs(i1-i2)<=abstol );
}

static gmx_bool equal_double(double i1,double i2,real ftol,real abstol)
{
    return ( ( 2*fabs(i1 - i2) <= (fabs(i1) + fabs(i2))*ftol ) || fabs(i1-i2)<=abstol );
}

static void 
cmp_real(FILE *fp,const char *s,int index,real i1,real i2,real ftol,real abstol)
{
  if (!equal_real(i1,i2,ftol,abstol)) {
    if (index != -1)
      fprintf(fp,"%s[%2d] (%e - %e)\n",s,index,i1,i2);
    else
      fprintf(fp,"%s (%e - %e)\n",s,i1,i2);
  }
}

static void 
cmp_float(FILE *fp,const char *s,int index,float i1,float i2,float ftol,float abstol)
{
  if (!equal_float(i1,i2,ftol,abstol)) {
    if (index != -1)
      fprintf(fp,"%s[%2d] (%e - %e)\n",s,index,i1,i2);
    else
      fprintf(fp,"%s (%e - %e)\n",s,i1,i2);
  }
}



static void 
cmp_double(FILE *fp,const char *s,int index,double i1,double i2,double ftol,double abstol)
{
  if (!equal_double(i1,i2,ftol,abstol)) {
    if (index != -1)
      fprintf(fp,"%s[%2d] (%16.9e - %16.9e)\n",s,index,i1,i2);
    else
      fprintf(fp,"%s (%16.9e - %16.9e)\n",s,i1,i2);
  }
}

static void cmp_rvec(FILE *fp,const char *s,int index,rvec i1,rvec i2,real ftol,real abstol)
{
    if(!equal_real(i1[XX],i2[XX],ftol,abstol) ||
       !equal_real(i1[YY],i2[YY],ftol,abstol) ||
       !equal_real(i1[ZZ],i2[ZZ],ftol,abstol))
    {
        if (index != -1)
            fprintf(fp,"%s[%5d] (%12.5e %12.5e %12.5e) - (%12.5e %12.5e %12.5e)\n",
                    s,index,i1[XX],i1[YY],i1[ZZ],i2[XX],i2[YY],i2[ZZ]);
        else
            fprintf(fp,"%s (%12.5e %12.5e %12.5e) - (%12.5e %12.5e %12.5e)\n",
                    s,i1[XX],i1[YY],i1[ZZ],i2[XX],i2[YY],i2[ZZ]);
    }
}

static void cmp_ivec(FILE *fp,const char *s,int index,ivec i1,ivec i2)
{
  if ((i1[XX] != i2[XX]) || (i1[YY] != i2[YY]) || (i1[ZZ] != i2[ZZ])) {
    if (index != -1)
      fprintf(fp,"%s[%5d] (%8d,%8d,%8d - %8d,%8d,%8d)\n",s,index,
	      i1[XX],i1[YY],i1[ZZ],i2[XX],i2[YY],i2[ZZ]);
    else
      fprintf(fp,"%s (%8d,%8d,%8d - %8d,%8d,%8d)\n",s,
	      i1[XX],i1[YY],i1[ZZ],i2[XX],i2[YY],i2[ZZ]);
  }
}

static void cmp_ilist(FILE *fp,int ftype,t_ilist *il1,t_ilist *il2)
{
  int i;
  char buf[256];
 
  fprintf(fp,"comparing ilist %s\n",interaction_function[ftype].name);
  sprintf(buf,"%s->nr",interaction_function[ftype].name);
  cmp_int(fp,buf,-1,il1->nr,il2->nr);
  sprintf(buf,"%s->iatoms",interaction_function[ftype].name);
  if (((il1->nr > 0) && (!il1->iatoms)) || 
      ((il2->nr > 0) && (!il2->iatoms)) ||
      ((il1->nr != il2->nr)))
    fprintf(fp,"Comparing radically different topologies - %s is different\n",
	    buf);
  else
    for(i=0; (i<il1->nr); i++) 
      cmp_int(fp,buf,i,il1->iatoms[i],il2->iatoms[i]);
}

void cmp_iparm(FILE *fp,const char *s,t_functype ft,
	       t_iparams ip1,t_iparams ip2,real ftol,real abstol) 
{
  int i;
  gmx_bool bDiff;
  
  bDiff=FALSE;
  for(i=0; i<MAXFORCEPARAM && !bDiff; i++)
    bDiff = !equal_real(ip1.generic.buf[i],ip2.generic.buf[i],ftol,abstol);
  if (bDiff) {
    fprintf(fp,"%s1: ",s);
    pr_iparams(fp,ft,&ip1);
    fprintf(fp,"%s2: ",s);
    pr_iparams(fp,ft,&ip2);
  }
}

void cmp_iparm_AB(FILE *fp,const char *s,t_functype ft,t_iparams ip1,real ftol,real abstol) 
{
  int nrfpA,nrfpB,p0,i;
  gmx_bool bDiff;
  
  /* Normally the first parameter is perturbable */
  p0 = 0;
  nrfpA = interaction_function[ft].nrfpA;
  nrfpB = interaction_function[ft].nrfpB;
  if (ft == F_PDIHS) {
    nrfpB = 2;
  } else if (interaction_function[ft].flags & IF_TABULATED) {
    /* For tabulated interactions only the second parameter is perturbable */
    p0 = 1;
    nrfpB = 1;
  }
  bDiff=FALSE;
  for(i=0; i<nrfpB && !bDiff; i++) {
    bDiff = !equal_real(ip1.generic.buf[p0+i],ip1.generic.buf[nrfpA+i],ftol,abstol);
  }
  if (bDiff) {
    fprintf(fp,"%s: ",s);
    pr_iparams(fp,ft,&ip1);
  }
}

static void cmp_idef(FILE *fp,t_idef *id1,t_idef *id2,real ftol,real abstol)
{
  int i;
  char buf1[64],buf2[64];
  
  fprintf(fp,"comparing idef\n");
  if (id2) {
    cmp_int(fp,"idef->ntypes",-1,id1->ntypes,id2->ntypes);
    cmp_int(fp,"idef->atnr",  -1,id1->atnr,id2->atnr);
    for(i=0; (i<id1->ntypes); i++) {
      sprintf(buf1,"idef->functype[%d]",i);
      sprintf(buf2,"idef->iparam[%d]",i);
      cmp_int(fp,buf1,i,(int)id1->functype[i],(int)id2->functype[i]);
      cmp_iparm(fp,buf2,id1->functype[i],
		id1->iparams[i],id2->iparams[i],ftol,abstol);
    }
    cmp_real(fp,"fudgeQQ",-1,id1->fudgeQQ,id2->fudgeQQ,ftol,abstol);
    for(i=0; (i<F_NRE); i++)
      cmp_ilist(fp,i,&(id1->il[i]),&(id2->il[i]));
  } else {
    for(i=0; (i<id1->ntypes); i++)
      cmp_iparm_AB(fp,"idef->iparam",id1->functype[i],id1->iparams[i],ftol,abstol);
  }
}

static void cmp_block(FILE *fp,t_block *b1,t_block *b2,const char *s)
{
  int i,j,k;
  char buf[32];
  
  fprintf(fp,"comparing block %s\n",s);
  sprintf(buf,"%s.nr",s);
  cmp_int(fp,buf,-1,b1->nr,b2->nr);
} 

static void cmp_blocka(FILE *fp,t_blocka *b1,t_blocka *b2,const char *s)
{
  int i,j,k;
  char buf[32];
  
  fprintf(fp,"comparing blocka %s\n",s);
  sprintf(buf,"%s.nr",s);
  cmp_int(fp,buf,-1,b1->nr,b2->nr);
  sprintf(buf,"%s.nra",s);
  cmp_int(fp,buf,-1,b1->nra,b2->nra);
} 

static void cmp_atom(FILE *fp,int index,t_atom *a1,t_atom *a2,real ftol,real abstol)
{
  int  i;
  char buf[256];

  if (a2) {
    cmp_us(fp,"atom.type",index,a1->type,a2->type);
    cmp_us(fp,"atom.ptype",index,a1->ptype,a2->ptype);
    cmp_int(fp,"atom.resind",index,a1->resind,a2->resind);
    cmp_int(fp,"atom.atomnumber",index,a1->atomnumber,a2->atomnumber);
    cmp_real(fp,"atom.m",index,a1->m,a2->m,ftol,abstol);
    cmp_real(fp,"atom.q",index,a1->q,a2->q,ftol,abstol);
    cmp_us(fp,"atom.typeB",index,a1->typeB,a2->typeB);
    cmp_real(fp,"atom.mB",index,a1->mB,a2->mB,ftol,abstol);
    cmp_real(fp,"atom.qB",index,a1->qB,a2->qB,ftol,abstol);
  } else {
    cmp_us(fp,"atom.type",index,a1->type,a1->typeB);
    cmp_real(fp,"atom.m",index,a1->m,a1->mB,ftol,abstol);
    cmp_real(fp,"atom.q",index,a1->q,a1->qB,ftol,abstol);
  }
}

static void cmp_atoms(FILE *fp,t_atoms *a1,t_atoms *a2,real ftol, real abstol)
{
  int i;
  
  fprintf(fp,"comparing atoms\n");

  if (a2) {
    cmp_int(fp,"atoms->nr",-1,a1->nr,a2->nr);
    for(i=0; (i<a1->nr); i++)
      cmp_atom(fp,i,&(a1->atom[i]),&(a2->atom[i]),ftol,abstol);
  } else {
    for(i=0; (i<a1->nr); i++)
      cmp_atom(fp,i,&(a1->atom[i]),NULL,ftol,abstol);
  }
}

static void cmp_top(FILE *fp,t_topology *t1,t_topology *t2,real ftol, real abstol)
{
  int i;
  
  fprintf(fp,"comparing top\n");
  if (t2) {
    cmp_idef(fp,&(t1->idef),&(t2->idef),ftol,abstol);
    cmp_atoms(fp,&(t1->atoms),&(t2->atoms),ftol,abstol);
    cmp_block(fp,&t1->cgs,&t2->cgs,"cgs");
    cmp_block(fp,&t1->mols,&t2->mols,"mols");
    cmp_blocka(fp,&t1->excls,&t2->excls,"excls");
  } else {
    cmp_idef(fp,&(t1->idef),NULL,ftol,abstol);
    cmp_atoms(fp,&(t1->atoms),NULL,ftol,abstol);
  }
}

static void cmp_groups(FILE *fp,gmx_groups_t *g0,gmx_groups_t *g1,
		       int natoms0,int natoms1)
{
  int  i,j,ndiff;
  char buf[32];

  fprintf(fp,"comparing groups\n");

  for(i=0; i<egcNR; i++) {
    sprintf(buf,"grps[%d].nr",i);
    cmp_int(fp,buf,-1,g0->grps[i].nr,g1->grps[i].nr);
    if (g0->grps[i].nr == g1->grps[i].nr) {
      for(j=0; j<g0->grps[i].nr; j++) {
          sprintf(buf,"grps[%d].name[%d]",i,j);
          cmp_str(fp,buf,-1,
                  *g0->grpname[g0->grps[i].nm_ind[j]],
                  *g1->grpname[g1->grps[i].nm_ind[j]]);
      }
    }
    cmp_int(fp,"ngrpnr",i,g0->ngrpnr[i],g1->ngrpnr[i]);
    if (g0->ngrpnr[i] == g1->ngrpnr[i] && natoms0 == natoms1 && 
	(g0->grpnr[i] != NULL || g1->grpnr[i] != NULL)) {
      for(j=0; j<natoms0; j++) {
	cmp_int(fp,gtypes[i],j,ggrpnr(g0,i,j),ggrpnr(g1,i,j));
      }
    }
  }
  /* We have compared the names in the groups lists,
   * so we can skip the grpname list comparison.
   */
}

static void cmp_rvecs(FILE *fp,const char *title,int n,rvec x1[],rvec x2[],
		      gmx_bool bRMSD,real ftol,real abstol)
{
  int i,m;
  double d,ssd;

  if (bRMSD) {
    ssd = 0;
    for(i=0; (i<n); i++) {
      for(m=0; m<DIM; m++) {
	d = x1[i][m] - x2[i][m];
	ssd += d*d;
      }
    }
    fprintf(fp,"%s RMSD %g\n",title,sqrt(ssd/n));
  } else {
    for(i=0; (i<n); i++) {
      cmp_rvec(fp,title,i,x1[i],x2[i],ftol,abstol);
    }
  }
}

static void cmp_grpopts(FILE *fp,t_grpopts *opt1,t_grpopts *opt2,real ftol, real abstol)
{
  int i,j;
  char buf1[256],buf2[256];
  
  cmp_int(fp,"inputrec->grpopts.ngtc",-1,  opt1->ngtc,opt2->ngtc);
  cmp_int(fp,"inputrec->grpopts.ngacc",-1, opt1->ngacc,opt2->ngacc);
  cmp_int(fp,"inputrec->grpopts.ngfrz",-1, opt1->ngfrz,opt2->ngfrz);
  cmp_int(fp,"inputrec->grpopts.ngener",-1,opt1->ngener,opt2->ngener);
  for(i=0; (i<min(opt1->ngtc,opt2->ngtc)); i++) {
    cmp_real(fp,"inputrec->grpopts.nrdf",i,opt1->nrdf[i],opt2->nrdf[i],ftol,abstol);
    cmp_real(fp,"inputrec->grpopts.ref_t",i,opt1->ref_t[i],opt2->ref_t[i],ftol,abstol);
    cmp_real(fp,"inputrec->grpopts.tau_t",i,opt1->tau_t[i],opt2->tau_t[i],ftol,abstol);
    cmp_int(fp,"inputrec->grpopts.annealing",i,opt1->annealing[i],opt2->annealing[i]);
    cmp_int(fp,"inputrec->grpopts.anneal_npoints",i,
	    opt1->anneal_npoints[i],opt2->anneal_npoints[i]);
    if(opt1->anneal_npoints[i]==opt2->anneal_npoints[i]) {
      sprintf(buf1,"inputrec->grpopts.anneal_time[%d]",i);
      sprintf(buf2,"inputrec->grpopts.anneal_temp[%d]",i);
      for(j=0;j<opt1->anneal_npoints[i];j++) {
	cmp_real(fp,buf1,j,opt1->anneal_time[i][j],opt2->anneal_time[i][j],ftol,abstol);
	cmp_real(fp,buf2,j,opt1->anneal_temp[i][j],opt2->anneal_temp[i][j],ftol,abstol);
      }
    }
  }
  if (opt1->ngener == opt2->ngener) {
    for(i=0; i<opt1->ngener; i++)
      for(j=i; j<opt1->ngener; j++) {
	sprintf(buf1,"inputrec->grpopts.egp_flags[%d]",i);
	cmp_int(fp,buf1,j,
		opt1->egp_flags[opt1->ngener*i+j],
		opt2->egp_flags[opt1->ngener*i+j]);
      }
  }
  for(i=0; (i<min(opt1->ngacc,opt2->ngacc)); i++)
    cmp_rvec(fp,"inputrec->grpopts.acc",i,opt1->acc[i],opt2->acc[i],ftol,abstol);
  for(i=0; (i<min(opt1->ngfrz,opt2->ngfrz)); i++)
    cmp_ivec(fp,"inputrec->grpopts.nFreeze",i,opt1->nFreeze[i],opt2->nFreeze[i]);
}

static void cmp_cosines(FILE *fp,const char *s,t_cosines c1[DIM],t_cosines c2[DIM],real ftol, real abstol)
{
  int i,m;
  char buf[256];
  
  for(m=0; (m<DIM); m++) {
    sprintf(buf,"inputrec->%s[%d]",s,m);
    cmp_int(fp,buf,0,c1->n,c2->n);
    for(i=0; (i<min(c1->n,c2->n)); i++) {
      cmp_real(fp,buf,i,c1->a[i],c2->a[i],ftol,abstol);
      cmp_real(fp,buf,i,c1->phi[i],c2->phi[i],ftol,abstol);
    }
  }
}

static void cmp_pull(FILE *fp,t_pull *pull1,t_pull *pull2,real ftol, real abstol)
{
  fprintf(fp,"WARNING: Both files use COM pulling, but comparing of the pull struct is not implemented (yet). The pull parameters could be the same or different.\n");
}

static void cmp_inputrec(FILE *fp,t_inputrec *ir1,t_inputrec *ir2,real ftol, real abstol)
{
  int i;

  fprintf(fp,"comparing inputrec\n");

  /* gcc 2.96 doesnt like these defines at all, but issues a huge list
   * of warnings. Maybe it will change in future versions, but for the
   * moment I've spelled them out instead. /EL 000820 
   * #define CIB(s) cmp_int(fp,"inputrec->"#s,0,ir1->##s,ir2->##s)
   * #define CII(s) cmp_int(fp,"inputrec->"#s,0,ir1->##s,ir2->##s)
   * #define CIR(s) cmp_real(fp,"inputrec->"#s,0,ir1->##s,ir2->##s,ftol)
   */
  cmp_int(fp,"inputrec->eI",-1,ir1->eI,ir2->eI);
  cmp_gmx_large_int(fp,"inputrec->nsteps",ir1->nsteps,ir2->nsteps);
  cmp_gmx_large_int(fp,"inputrec->init_step",ir1->init_step,ir2->init_step);
  cmp_int(fp,"inputrec->simulation_part",-1,ir1->simulation_part,ir2->simulation_part);
  cmp_int(fp,"inputrec->ePBC",-1,ir1->ePBC,ir2->ePBC);
  cmp_int(fp,"inputrec->bPeriodicMols",-1,ir1->bPeriodicMols,ir2->bPeriodicMols);
  cmp_int(fp,"inputrec->ns_type",-1,ir1->ns_type,ir2->ns_type);
  cmp_int(fp,"inputrec->nstlist",-1,ir1->nstlist,ir2->nstlist);
  cmp_int(fp,"inputrec->ndelta",-1,ir1->ndelta,ir2->ndelta);
  cmp_int(fp,"inputrec->nstcomm",-1,ir1->nstcomm,ir2->nstcomm);
  cmp_int(fp,"inputrec->comm_mode",-1,ir1->comm_mode,ir2->comm_mode);
  cmp_int(fp,"inputrec->nstcheckpoint",-1,ir1->nstcheckpoint,ir2->nstcheckpoint);
  cmp_int(fp,"inputrec->nstlog",-1,ir1->nstlog,ir2->nstlog);
  cmp_int(fp,"inputrec->nstxout",-1,ir1->nstxout,ir2->nstxout);
  cmp_int(fp,"inputrec->nstvout",-1,ir1->nstvout,ir2->nstvout);
  cmp_int(fp,"inputrec->nstfout",-1,ir1->nstfout,ir2->nstfout);
  cmp_int(fp,"inputrec->nstcalcenergy",-1,ir1->nstcalcenergy,ir2->nstcalcenergy);
  cmp_int(fp,"inputrec->nstenergy",-1,ir1->nstenergy,ir2->nstenergy);
  cmp_int(fp,"inputrec->nstxtcout",-1,ir1->nstxtcout,ir2->nstxtcout);
  cmp_double(fp,"inputrec->init_t",-1,ir1->init_t,ir2->init_t,ftol,abstol);
  cmp_double(fp,"inputrec->delta_t",-1,ir1->delta_t,ir2->delta_t,ftol,abstol);
  cmp_real(fp,"inputrec->xtcprec",-1,ir1->xtcprec,ir2->xtcprec,ftol,abstol);
  cmp_int(fp,"inputrec->nkx",-1,ir1->nkx,ir2->nkx);
  cmp_int(fp,"inputrec->nky",-1,ir1->nky,ir2->nky);
  cmp_int(fp,"inputrec->nkz",-1,ir1->nkz,ir2->nkz);
  cmp_int(fp,"inputrec->pme_order",-1,ir1->pme_order,ir2->pme_order);
  cmp_real(fp,"inputrec->ewald_rtol",-1,ir1->ewald_rtol,ir2->ewald_rtol,ftol,abstol);
  cmp_int(fp,"inputrec->ewald_geometry",-1,ir1->ewald_geometry,ir2->ewald_geometry);
  cmp_real(fp,"inputrec->epsilon_surface",-1,ir1->epsilon_surface,ir2->epsilon_surface,ftol,abstol);
  cmp_int(fp,"inputrec->bOptFFT",-1,ir1->bOptFFT,ir2->bOptFFT);
  cmp_int(fp,"inputrec->bContinuation",-1,ir1->bContinuation,ir2->bContinuation);
  cmp_int(fp,"inputrec->bShakeSOR",-1,ir1->bShakeSOR,ir2->bShakeSOR);
  cmp_int(fp,"inputrec->etc",-1,ir1->etc,ir2->etc);
  cmp_int(fp,"inputrec->epc",-1,ir1->epc,ir2->epc);
  cmp_int(fp,"inputrec->epct",-1,ir1->epct,ir2->epct);
  cmp_real(fp,"inputrec->tau_p",-1,ir1->tau_p,ir2->tau_p,ftol,abstol);
  cmp_rvec(fp,"inputrec->ref_p(x)",-1,ir1->ref_p[XX],ir2->ref_p[XX],ftol,abstol);
  cmp_rvec(fp,"inputrec->ref_p(y)",-1,ir1->ref_p[YY],ir2->ref_p[YY],ftol,abstol);
  cmp_rvec(fp,"inputrec->ref_p(z)",-1,ir1->ref_p[ZZ],ir2->ref_p[ZZ],ftol,abstol);
  cmp_rvec(fp,"inputrec->compress(x)",-1,ir1->compress[XX],ir2->compress[XX],ftol,abstol);
  cmp_rvec(fp,"inputrec->compress(y)",-1,ir1->compress[YY],ir2->compress[YY],ftol,abstol);
  cmp_rvec(fp,"inputrec->compress(z)",-1,ir1->compress[ZZ],ir2->compress[ZZ],ftol,abstol);
  cmp_int(fp,"refcoord_scaling",-1,ir1->refcoord_scaling,ir2->refcoord_scaling);
   cmp_rvec(fp,"inputrec->posres_com",-1,ir1->posres_com,ir2->posres_com,ftol,abstol);
   cmp_rvec(fp,"inputrec->posres_comB",-1,ir1->posres_comB,ir2->posres_comB,ftol,abstol);
   cmp_int(fp,"inputrec->andersen_seed",-1,ir1->andersen_seed,ir2->andersen_seed);
  cmp_real(fp,"inputrec->rlist",-1,ir1->rlist,ir2->rlist,ftol,abstol);
  cmp_real(fp,"inputrec->rlistlong",-1,ir1->rlistlong,ir2->rlistlong,ftol,abstol);
  cmp_real(fp,"inputrec->rtpi",-1,ir1->rtpi,ir2->rtpi,ftol,abstol);
  cmp_int(fp,"inputrec->coulombtype",-1,ir1->coulombtype,ir2->coulombtype);
  cmp_real(fp,"inputrec->rcoulomb_switch",-1,ir1->rcoulomb_switch,ir2->rcoulomb_switch,ftol,abstol);
  cmp_real(fp,"inputrec->rcoulomb",-1,ir1->rcoulomb,ir2->rcoulomb,ftol,abstol);
  cmp_int(fp,"inputrec->vdwtype",-1,ir1->vdwtype,ir2->vdwtype);
  cmp_real(fp,"inputrec->rvdw_switch",-1,ir1->rvdw_switch,ir2->rvdw_switch,ftol,abstol);
  cmp_real(fp,"inputrec->rvdw",-1,ir1->rvdw,ir2->rvdw,ftol,abstol);
  cmp_real(fp,"inputrec->epsilon_r",-1,ir1->epsilon_r,ir2->epsilon_r,ftol,abstol);
  cmp_real(fp,"inputrec->epsilon_rf",-1,ir1->epsilon_rf,ir2->epsilon_rf,ftol,abstol);
  cmp_real(fp,"inputrec->tabext",-1,ir1->tabext,ir2->tabext,ftol,abstol);
  cmp_int(fp,"inputrec->implicit_solvent",-1,ir1->implicit_solvent,ir2->implicit_solvent);
  cmp_int(fp,"inputrec->gb_algorithm",-1,ir1->gb_algorithm,ir2->gb_algorithm);
  cmp_int(fp,"inputrec->nstgbradii",-1,ir1->nstgbradii,ir2->nstgbradii);
  cmp_real(fp,"inputrec->rgbradii",-1,ir1->rgbradii,ir2->rgbradii,ftol,abstol);
  cmp_real(fp,"inputrec->gb_saltconc",-1,ir1->gb_saltconc,ir2->gb_saltconc,ftol,abstol);
  cmp_real(fp,"inputrec->gb_epsilon_solvent",-1,ir1->gb_epsilon_solvent,ir2->gb_epsilon_solvent,ftol,abstol);
  cmp_real(fp,"inputrec->gb_obc_alpha",-1,ir1->gb_obc_alpha,ir2->gb_obc_alpha,ftol,abstol);
  cmp_real(fp,"inputrec->gb_obc_beta",-1,ir1->gb_obc_beta,ir2->gb_obc_beta,ftol,abstol);
  cmp_real(fp,"inputrec->gb_obc_gamma",-1,ir1->gb_obc_gamma,ir2->gb_obc_gamma,ftol,abstol);
  cmp_real(fp,"inputrec->gb_dielectric_offset",-1,ir1->gb_dielectric_offset,ir2->gb_dielectric_offset,ftol,abstol);
  cmp_int(fp,"inputrec->sa_algorithm",-1,ir1->sa_algorithm,ir2->sa_algorithm);
  cmp_real(fp,"inputrec->sa_surface_tension",-1,ir1->sa_surface_tension,ir2->sa_surface_tension,ftol,abstol);	

  cmp_int(fp,"inputrec->eDispCorr",-1,ir1->eDispCorr,ir2->eDispCorr);
  cmp_real(fp,"inputrec->shake_tol",-1,ir1->shake_tol,ir2->shake_tol,ftol,abstol);
  cmp_int(fp,"inputrec->efep",-1,ir1->efep,ir2->efep);
  cmp_double(fp,"inputrec->init_lambda",-1,ir1->init_lambda,ir2->init_lambda,ftol,abstol);
  cmp_double(fp,"inputrec->delta_lambda",-1,ir1->delta_lambda,ir2->delta_lambda,ftol,abstol);
  cmp_int(fp,"inputrec->n_foreign_lambda",-1,ir1->n_flambda,ir2->n_flambda);
  for(i=0; i<min(ir1->n_flambda,ir2->n_flambda); i++) {
    cmp_double(fp,"inputrec->foreign_lambda",-1,ir1->flambda[i],ir2->flambda[i],ftol,abstol);
  }
  cmp_real(fp,"inputrec->sc_alpha",-1,ir1->sc_alpha,ir2->sc_alpha,ftol,abstol);
  cmp_int(fp,"inputrec->sc_power",-1,ir1->sc_power,ir2->sc_power);
  cmp_real(fp,"inputrec->sc_sigma",-1,ir1->sc_sigma,ir2->sc_sigma,ftol,abstol);
  cmp_real(fp,"inputrec->sc_sigma_min",-1,ir1->sc_sigma_min,ir2->sc_sigma_min,ftol,abstol);
  cmp_int(fp,"inputrec->nstdhdl",-1,ir1->nstdhdl,ir2->nstdhdl);
  cmp_int(fp,"inputrec->separate_dhdl_file",-1,ir1->separate_dhdl_file,ir2->separate_dhdl_file);
  cmp_int(fp,"inputrec->dhdl_derivatives",-1,ir1->dhdl_derivatives,ir2->dhdl_derivatives);
  cmp_int(fp,"inputrec->dh_hist_size",-1,ir1->dh_hist_size,ir2->dh_hist_size);
  cmp_double(fp,"inputrec->dh_hist_spacing",-1,ir1->dh_hist_spacing,ir2->dh_hist_spacing,ftol,abstol);

  cmp_int(fp,"inputrec->nwall",-1,ir1->nwall,ir2->nwall);
  cmp_int(fp,"inputrec->wall_type",-1,ir1->wall_type,ir2->wall_type);
  cmp_int(fp,"inputrec->wall_atomtype[0]",-1,ir1->wall_atomtype[0],ir2->wall_atomtype[0]);
  cmp_int(fp,"inputrec->wall_atomtype[1]",-1,ir1->wall_atomtype[1],ir2->wall_atomtype[1]);
  cmp_real(fp,"inputrec->wall_density[0]",-1,ir1->wall_density[0],ir2->wall_density[0],ftol,abstol);
  cmp_real(fp,"inputrec->wall_density[1]",-1,ir1->wall_density[1],ir2->wall_density[1],ftol,abstol);
  cmp_real(fp,"inputrec->wall_ewald_zfac",-1,ir1->wall_ewald_zfac,ir2->wall_ewald_zfac,ftol,abstol);

  cmp_int(fp,"inputrec->ePull",-1,ir1->ePull,ir2->ePull);
  if (ir1->ePull == ir2->ePull && ir1->ePull != epullNO)
    cmp_pull(fp,ir1->pull,ir2->pull,ftol,abstol);
  
  cmp_int(fp,"inputrec->eDisre",-1,ir1->eDisre,ir2->eDisre);
  cmp_real(fp,"inputrec->dr_fc",-1,ir1->dr_fc,ir2->dr_fc,ftol,abstol);
  cmp_int(fp,"inputrec->eDisreWeighting",-1,ir1->eDisreWeighting,ir2->eDisreWeighting);
  cmp_int(fp,"inputrec->bDisreMixed",-1,ir1->bDisreMixed,ir2->bDisreMixed);
  cmp_int(fp,"inputrec->nstdisreout",-1,ir1->nstdisreout,ir2->nstdisreout);
  cmp_real(fp,"inputrec->dr_tau",-1,ir1->dr_tau,ir2->dr_tau,ftol,abstol);
  cmp_real(fp,"inputrec->orires_fc",-1,ir1->orires_fc,ir2->orires_fc,ftol,abstol);
  cmp_real(fp,"inputrec->orires_tau",-1,ir1->orires_tau,ir2->orires_tau,ftol,abstol);
  cmp_int(fp,"inputrec->nstorireout",-1,ir1->nstorireout,ir2->nstorireout);
  cmp_real(fp,"inputrec->dihre_fc",-1,ir1->dihre_fc,ir2->dihre_fc,ftol,abstol);
  cmp_real(fp,"inputrec->em_stepsize",-1,ir1->em_stepsize,ir2->em_stepsize,ftol,abstol);
  cmp_real(fp,"inputrec->em_tol",-1,ir1->em_tol,ir2->em_tol,ftol,abstol);
  cmp_int(fp,"inputrec->niter",-1,ir1->niter,ir2->niter);
  cmp_real(fp,"inputrec->fc_stepsize",-1,ir1->fc_stepsize,ir2->fc_stepsize,ftol,abstol);
  cmp_int(fp,"inputrec->nstcgsteep",-1,ir1->nstcgsteep,ir2->nstcgsteep);
  cmp_int(fp,"inputrec->nbfgscorr",0,ir1->nbfgscorr,ir2->nbfgscorr);
  cmp_int(fp,"inputrec->eConstrAlg",-1,ir1->eConstrAlg,ir2->eConstrAlg);
  cmp_int(fp,"inputrec->nProjOrder",-1,ir1->nProjOrder,ir2->nProjOrder);
  cmp_real(fp,"inputrec->LincsWarnAngle",-1,ir1->LincsWarnAngle,ir2->LincsWarnAngle,ftol,abstol);
  cmp_int(fp,"inputrec->nLincsIter",-1,ir1->nLincsIter,ir2->nLincsIter);
  cmp_real(fp,"inputrec->bd_fric",-1,ir1->bd_fric,ir2->bd_fric,ftol,abstol);
  cmp_int(fp,"inputrec->ld_seed",-1,ir1->ld_seed,ir2->ld_seed);
  cmp_real(fp,"inputrec->cos_accel",-1,ir1->cos_accel,ir2->cos_accel,ftol,abstol);
  cmp_rvec(fp,"inputrec->deform(a)",-1,ir1->deform[XX],ir2->deform[XX],ftol,abstol);
  cmp_rvec(fp,"inputrec->deform(b)",-1,ir1->deform[YY],ir2->deform[YY],ftol,abstol);
  cmp_rvec(fp,"inputrec->deform(c)",-1,ir1->deform[ZZ],ir2->deform[ZZ],ftol,abstol);
  cmp_int(fp,"inputrec->userint1",-1,ir1->userint1,ir2->userint1);
  cmp_int(fp,"inputrec->userint2",-1,ir1->userint2,ir2->userint2);
  cmp_int(fp,"inputrec->userint3",-1,ir1->userint3,ir2->userint3);
  cmp_int(fp,"inputrec->userint4",-1,ir1->userint4,ir2->userint4);
  cmp_real(fp,"inputrec->userreal1",-1,ir1->userreal1,ir2->userreal1,ftol,abstol);
  cmp_real(fp,"inputrec->userreal2",-1,ir1->userreal2,ir2->userreal2,ftol,abstol);
  cmp_real(fp,"inputrec->userreal3",-1,ir1->userreal3,ir2->userreal3,ftol,abstol);
  cmp_real(fp,"inputrec->userreal4",-1,ir1->userreal4,ir2->userreal4,ftol,abstol);
  cmp_grpopts(fp,&(ir1->opts),&(ir2->opts),ftol,abstol);
  cmp_cosines(fp,"ex",ir1->ex,ir2->ex,ftol,abstol);
  cmp_cosines(fp,"et",ir1->et,ir2->et,ftol,abstol);
}

static void comp_pull_AB(FILE *fp,t_pull *pull,real ftol,real abstol)
{
  int i;

  for(i=0; i<pull->ngrp+1; i++) {
    fprintf(fp,"comparing pull group %d\n",i);
    cmp_real(fp,"pullgrp->k",-1,pull->grp[i].k,pull->grp[i].kB,ftol,abstol);
  }
}

static void comp_state(t_state *st1, t_state *st2,
		       gmx_bool bRMSD,real ftol,real abstol)
{
  int i,j,nc;

  fprintf(stdout,"comparing flags\n");
  cmp_int(stdout,"flags",-1,st1->flags,st2->flags);
  fprintf(stdout,"comparing box\n");
  cmp_rvecs(stdout,"box",DIM,st1->box,st2->box,FALSE,ftol,abstol);
  fprintf(stdout,"comparing box_rel\n");
  cmp_rvecs(stdout,"box_rel",DIM,st1->box_rel,st2->box_rel,FALSE,ftol,abstol);
  fprintf(stdout,"comparing boxv\n");
  cmp_rvecs(stdout,"boxv",DIM,st1->boxv,st2->boxv,FALSE,ftol,abstol);
  if (st1->flags & (1<<estSVIR_PREV)) {
    fprintf(stdout,"comparing shake vir_prev\n");
    cmp_rvecs(stdout,"svir_prev",DIM,st1->svir_prev,st2->svir_prev,FALSE,ftol,abstol);
  }
  if (st1->flags & (1<<estFVIR_PREV)) {
    fprintf(stdout,"comparing force vir_prev\n");
    cmp_rvecs(stdout,"fvir_prev",DIM,st1->fvir_prev,st2->fvir_prev,FALSE,ftol,abstol);
  }
  if (st1->flags & (1<<estPRES_PREV)) {
    fprintf(stdout,"comparing prev_pres\n");
    cmp_rvecs(stdout,"pres_prev",DIM,st1->pres_prev,st2->pres_prev,FALSE,ftol,abstol);
  }
  cmp_int(stdout,"ngtc",-1,st1->ngtc,st2->ngtc);
  cmp_int(stdout,"nhchainlength",-1,st1->nhchainlength,st2->nhchainlength);
  if (st1->ngtc == st2->ngtc && st1->nhchainlength == st2->nhchainlength){
    for(i=0; i<st1->ngtc; i++) {
      nc = i*st1->nhchainlength;
      for(j=0; j<nc; j++) {
	cmp_real(stdout,"nosehoover_xi",
		 i,st1->nosehoover_xi[nc+j],st2->nosehoover_xi[nc+j],ftol,abstol);
      }
    }
  }
  cmp_int(stdout,"nnhpres",-1,st1->nnhpres,st2->nnhpres);
  if (st1->nnhpres == st2->nnhpres && st1->nhchainlength == st2->nhchainlength) {
    for(i=0; i<st1->nnhpres; i++) {
      nc = i*st1->nhchainlength;
      for(j=0; j<nc; j++) {
	cmp_real(stdout,"nosehoover_xi",
		 i,st1->nhpres_xi[nc+j],st2->nhpres_xi[nc+j],ftol,abstol);
      }
    }
  }

  cmp_int(stdout,"natoms",-1,st1->natoms,st2->natoms);
  if (st1->natoms == st2->natoms) {
    if ((st1->flags & (1<<estX)) && (st2->flags & (1<<estX))) {
      fprintf(stdout,"comparing x\n");
      cmp_rvecs(stdout,"x",st1->natoms,st1->x,st2->x,bRMSD,ftol,abstol);
    }
    if ((st1->flags & (1<<estV)) && (st2->flags & (1<<estV))) {
      fprintf(stdout,"comparing v\n");
      cmp_rvecs(stdout,"v",st1->natoms,st1->v,st2->v,bRMSD,ftol,abstol);
    }
  }
}

void comp_tpx(const char *fn1,const char *fn2,
	      gmx_bool bRMSD,real ftol,real abstol)
{
  const char  *ff[2];
  t_tpxheader sh[2];
  t_inputrec  ir[2];
  t_state     state[2];
  gmx_mtop_t  mtop[2];
  t_topology  top[2];
  int         i;

  ff[0]=fn1;
  ff[1]=fn2;
  for(i=0; i<(fn2 ? 2 : 1); i++) {
    read_tpx_state(ff[i],&(ir[i]),&state[i],NULL,&(mtop[i]));
  }
  if (fn2) {
    cmp_inputrec(stdout,&ir[0],&ir[1],ftol,abstol);
    /* Convert gmx_mtop_t to t_topology.
     * We should implement direct mtop comparison,
     * but it might be useful to keep t_topology comparison as an option.
     */
    top[0] = gmx_mtop_t_to_t_topology(&mtop[0]);
    top[1] = gmx_mtop_t_to_t_topology(&mtop[1]);
    cmp_top(stdout,&top[0],&top[1],ftol,abstol);
    cmp_groups(stdout,&mtop[0].groups,&mtop[1].groups,
	       mtop[0].natoms,mtop[1].natoms);
    comp_state(&state[0],&state[1],bRMSD,ftol,abstol);
  } else {
    if (ir[0].efep == efepNO) {
      fprintf(stdout,"inputrec->efep = %s\n",efep_names[ir[0].efep]);
    } else {
      if (ir[0].ePull != epullNO) {
	comp_pull_AB(stdout,ir->pull,ftol,abstol);
      }
      /* Convert gmx_mtop_t to t_topology.
       * We should implement direct mtop comparison,
       * but it might be useful to keep t_topology comparison as an option.
       */
      top[0] = gmx_mtop_t_to_t_topology(&mtop[0]);
      cmp_top(stdout,&top[0],NULL,ftol,abstol);
    }
  }
}

void comp_frame(FILE *fp, t_trxframe *fr1, t_trxframe *fr2,
		gmx_bool bRMSD, real ftol,real abstol)
{
  fprintf(fp,"\n");
  cmp_int(fp,"flags",-1,fr1->flags,fr2->flags);
  cmp_int(fp,"not_ok",-1,fr1->not_ok,fr2->not_ok);
  cmp_int(fp,"natoms",-1,fr1->natoms,fr2->natoms);
  cmp_real(fp,"t0",-1,fr1->t0,fr2->t0,ftol,abstol);
  if (cmp_bool(fp,"bTitle",-1,fr1->bTitle,fr2->bTitle))
    cmp_str(fp,"title", -1, fr1->title, fr2->title);
  if (cmp_bool(fp,"bStep",-1,fr1->bStep,fr2->bStep))
    cmp_int(fp,"step",-1,fr1->step,fr2->step);
  cmp_int(fp,"step",-1,fr1->step,fr2->step);
  if (cmp_bool(fp,"bTime",-1,fr1->bTime,fr2->bTime))   
    cmp_real(fp,"time",-1,fr1->time,fr2->time,ftol,abstol);
  if (cmp_bool(fp,"bLambda",-1,fr1->bLambda,fr2->bLambda)) 
    cmp_real(fp,"lambda",-1,fr1->lambda,fr2->lambda,ftol,abstol);
  if (cmp_bool(fp,"bAtoms",-1,fr1->bAtoms,fr2->bAtoms))
    cmp_atoms(fp,fr1->atoms,fr2->atoms,ftol,abstol);
  if (cmp_bool(fp,"bPrec",-1,fr1->bPrec,fr2->bPrec))
    cmp_real(fp,"prec",-1,fr1->prec,fr2->prec,ftol,abstol);
  if (cmp_bool(fp,"bX",-1,fr1->bX,fr2->bX))
    cmp_rvecs(fp,"x",min(fr1->natoms,fr2->natoms),fr1->x,fr2->x,bRMSD,ftol,abstol);
  if (cmp_bool(fp,"bV",-1,fr1->bV,fr2->bV))
    cmp_rvecs(fp,"v",min(fr1->natoms,fr2->natoms),fr1->v,fr2->v,bRMSD,ftol,abstol);
  if (cmp_bool(fp,"bF",-1,fr1->bF,fr2->bF))
    cmp_rvecs(fp,"f",min(fr1->natoms,fr2->natoms),fr1->f,fr2->f,bRMSD,ftol,abstol);
  if (cmp_bool(fp,"bBox",-1,fr1->bBox,fr2->bBox))
    cmp_rvecs(fp,"box",3,fr1->box,fr2->box,FALSE,ftol,abstol);
}

void comp_trx(const output_env_t oenv,const char *fn1, const char *fn2, 
              gmx_bool bRMSD,real ftol,real abstol)
{
  int i;
  const char *fn[2];
  t_trxframe fr[2];
  t_trxstatus *status[2];
  gmx_bool b[2];
  
  fn[0]=fn1;
  fn[1]=fn2;
  fprintf(stderr,"Comparing trajectory files %s and %s\n",fn1,fn2);
  for (i=0; i<2; i++)
    b[i] = read_first_frame(oenv,&status[i],fn[i],&fr[i],TRX_READ_X|TRX_READ_V|TRX_READ_F);
  
  if (b[0] && b[1]) { 
    do {
      comp_frame(stdout, &(fr[0]), &(fr[1]), bRMSD, ftol, abstol);
      
      for (i=0; i<2; i++)
	b[i] = read_next_frame(oenv,status[i],&fr[i]);
    } while (b[0] && b[1]);
    
    for (i=0; i<2; i++) {
      if (b[i] && !b[1-i])
	fprintf(stdout,"\nEnd of file on %s but not on %s\n",fn[i],fn[1-i]);
      close_trj(status[i]);
    }
  }
  if (!b[0] && !b[1])
    fprintf(stdout,"\nBoth files read correctly\n");
}

static real ener_tensor_diag(int n,int *ind1,int *ind2,
			     gmx_enxnm_t *enm1,
			     int *tensi,int i,
			     t_energy e1[],t_energy e2[])
{
  int  d1,d2;
  int  len;
  int  j;
  real prod1,prod2;
  int  nfound;

  d1 = tensi[i]/DIM;
  d2 = tensi[i] - d1*DIM;
  
  /* Find the diagonal elements d1 and d2 */
  len = strlen(enm1[ind1[i]].name);
  prod1 = 1;
  prod2 = 1;
  nfound = 0;
  for(j=0; j<n; j++) {
    if (tensi[j] >= 0 &&
	strlen(enm1[ind1[j]].name) == len &&
	strncmp(enm1[ind1[i]].name,enm1[ind1[j]].name,len-2) == 0 &&
	(tensi[j] == d1*DIM+d1 || tensi[j] == d2*DIM+d2)) {
      prod1 *= fabs(e1[ind1[j]].e);
      prod2 *= fabs(e2[ind2[j]].e);
      nfound++;
    }
  }

  if (nfound == 2) {
    return 0.5*(sqrt(prod1) + sqrt(prod2));
  } else {
    return 0;
  }
}

static gmx_bool enernm_equal(const char *nm1,const char *nm2)
{
  int len1,len2;

  len1 = strlen(nm1);
  len2 = strlen(nm2);

  /* Remove " (bar)" at the end of a name */
  if (len1 > 6 && strcmp(nm1+len1-6," (bar)") == 0) {
    len1 -= 6;
  }
  if (len2 > 6 && strcmp(nm2+len2-6," (bar)") == 0) {
    len2 -= 6;
  }

  return (len1 == len2 && gmx_strncasecmp(nm1,nm2,len1) == 0);
}

static void cmp_energies(FILE *fp,int step1,int step2,
			 t_energy e1[],t_energy e2[],
			 gmx_enxnm_t *enm1,gmx_enxnm_t *enm2,
			 real ftol,real abstol,
			 int nre,int *ind1,int *ind2,int maxener)
{
  int  i,ii;
  int  *tensi,len,d1,d2;
  real ftol_i,abstol_i;

  snew(tensi,maxener);
  /* Check for tensor elements ending on "-XX", "-XY", ... , "-ZZ" */
  for(i=0; (i<maxener); i++) {
    ii = ind1[i];
    tensi[i] = -1;
    len = strlen(enm1[ii].name);
    if (len > 3 && enm1[ii].name[len-3] == '-') {
      d1 = enm1[ii].name[len-2] - 'X';
      d2 = enm1[ii].name[len-1] - 'X';
      if (d1 >= 0 && d1 < DIM &&
	  d2 >= 0 && d2 < DIM) {
	tensi[i] = d1*DIM + d2;
      }
    }
  }
  
  for(i=0; (i<maxener); i++) {
    /* Check if this is an off-diagonal tensor element */
    if (tensi[i] >= 0 && tensi[i] != 0 && tensi[i] != 4 && tensi[i] != 8) {
      /* Turn on the relative tolerance check (4 is maximum relative diff.) */
      ftol_i = 5;
      /* Do the relative tolerance through an absolute tolerance times
       * the size of diagonal components of the tensor.
       */
      abstol_i = ftol*ener_tensor_diag(nre,ind1,ind2,enm1,tensi,i,e1,e2);
      if (debug) {
	fprintf(debug,"tensor '%s' val %f diag %f\n",
		enm1[i].name,e1[i].e,abstol_i/ftol);
      }
      if (abstol_i > 0) {
	/* We found a diagonal, we need to check with the minimum tolerance */
	abstol_i = min(abstol_i,abstol);
      } else {
	/* We did not find a diagonal, ignore the relative tolerance check */
	abstol_i = abstol;
      }
    } else {
      ftol_i   = ftol;
      abstol_i = abstol;
    }
    if (!equal_real(e1[ind1[i]].e,e2[ind2[i]].e,ftol_i,abstol_i)) {
      fprintf(fp,"%-15s  step %3d:  %12g,  step %3d: %12g\n",
	      enm1[ind1[i]].name,
	      step1,e1[ind1[i]].e,
	      step2,e2[ind2[i]].e);
    }
  }

  sfree(tensi);
}

#if 0
static void cmp_disres(t_enxframe *fr1,t_enxframe *fr2,real ftol, real abstol)
{
  int i;
  char bav[64],bt[64],bs[22];
    
  cmp_int(stdout,"ndisre",-1,fr1->ndisre,fr2->ndisre);
  if ((fr1->ndisre == fr2->ndisre) && (fr1->ndisre > 0)) {
    sprintf(bav,"step %s: disre rav",gmx_step_str(fr1->step,bs));
    sprintf(bt, "step %s: disre  rt",gmx_step_str(fr1->step,bs));
    for(i=0; (i<fr1->ndisre); i++) {
      cmp_real(stdout,bav,i,fr1->disre_rm3tav[i],fr2->disre_rm3tav[i],ftol,abstol);
      cmp_real(stdout,bt ,i,fr1->disre_rt[i]    ,fr2->disre_rt[i]    ,ftol,abstol);
    }
  }
}
#endif

static void cmp_eblocks(t_enxframe *fr1,t_enxframe *fr2,real ftol, real abstol)
{
    int i,j,k;
    char buf[64],bs[22];

    cmp_int(stdout,"nblock",-1,fr1->nblock,fr2->nblock);  
    if ((fr1->nblock == fr2->nblock) && (fr1->nblock > 0)) 
    {
        for(j=0; (j<fr1->nblock); j++) 
        {
            t_enxblock *b1, *b2; /* convenience vars */

            b1=&(fr1->block[j]);
            b2=&(fr2->block[j]);

            sprintf(buf,"step %s: block[%d]",gmx_step_str(fr1->step,bs),j);
            cmp_int(stdout,buf,-1,b1->nsub,b2->nsub);
            cmp_int(stdout,buf,-1,b1->id,b2->id);

            if ( (b1->nsub==b2->nsub) && (b1->id==b2->id) )
            {
                for(i=0;i<b1->nsub;i++)
                {
                    t_enxsubblock *s1, *s2;

                    s1=&(b1->sub[i]);
                    s2=&(b2->sub[i]);

                    cmp_int(stdout, buf, -1, (int)s1->type, (int)s2->type);
                    cmp_gmx_large_int(stdout, buf, s1->nr, s2->nr);

                    if ((s1->type == s2->type) && (s1->nr == s2->nr))
                    {
                        switch(s1->type)
                        {
                            case xdr_datatype_float:
                                for(k=0;k<s1->nr;k++)
                                {
                                    cmp_float(stdout, buf, i,
                                             s1->fval[k], s2->fval[k], 
                                             ftol, abstol);
                                }
                                break;
                            case xdr_datatype_double:
                                for(k=0;k<s1->nr;k++)
                                {
                                    cmp_double(stdout, buf, i,
                                             s1->dval[k], s2->dval[k], 
                                             ftol, abstol);
                                }
                                break;
                            case xdr_datatype_int:
                                for(k=0;k<s1->nr;k++)
                                {
                                    cmp_int(stdout, buf, i,
                                            s1->ival[k], s2->ival[k]);
                                }
                                break;
                            case xdr_datatype_large_int:
                                for(k=0;k<s1->nr;k++)
                                {
                                    cmp_gmx_large_int(stdout, buf, 
                                                      s1->lval[k], s2->lval[k]);
                                }
                                break;
                            case xdr_datatype_char:
                                for(k=0;k<s1->nr;k++)
                                {
                                    cmp_uc(stdout, buf, i,
                                           s1->cval[k], s2->cval[k]);
                                }
                                break;
                            case xdr_datatype_string:
                                for(k=0;k<s1->nr;k++)
                                {
                                    cmp_str(stdout, buf, i,
                                            s1->sval[k], s2->sval[k]);
                                }
                                break;
                            default:
                                gmx_incons("Unknown data type!!");
                        }
                    }
                }
            }
        }
    }
}

void comp_enx(const char *fn1,const char *fn2,real ftol,real abstol,const char *lastener)
{
  int        nre,nre1,nre2,block;
  ener_file_t in1, in2;
  int        i,j,maxener,*ind1,*ind2,*have;
  char       buf[256];
  gmx_enxnm_t *enm1=NULL,*enm2=NULL;
  t_enxframe *fr1,*fr2;
  gmx_bool       b1,b2;
  
  fprintf(stdout,"comparing energy file %s and %s\n\n",fn1,fn2);

  in1 = open_enx(fn1,"r");
  in2 = open_enx(fn2,"r");
  do_enxnms(in1,&nre1,&enm1);
  do_enxnms(in2,&nre2,&enm2);
  if (nre1 != nre2) {
    fprintf(stdout,"There are %d and %d terms in the energy files\n\n",
	    nre1,nre2);
  } else {
    fprintf(stdout,"There are %d terms in the energy files\n\n",nre1);
  }

  snew(ind1,nre1);
  snew(ind2,nre2);
  snew(have,nre2);
  nre = 0;
  for(i=0; i<nre1; i++) {
    for(j=0; j<nre2; j++) {
      if (enernm_equal(enm1[i].name,enm2[j].name)) {
	ind1[nre] = i;
	ind2[nre] = j;
	have[j] = 1;
	nre++;
	break;
      }
    }
    if (nre == 0 || ind1[nre-1] != i) {
      cmp_str(stdout,"enm",i,enm1[i].name,"-");
    }
  }
  for(i=0; i<nre2; i++) {
    if (have[i] == 0) {
      cmp_str(stdout,"enm",i,"-",enm2[i].name);
    }
  }

  maxener = nre;
  for(i=0; i<nre; i++) {
    if ((lastener != NULL) && (strstr(enm1[i].name,lastener) != NULL)) {
      maxener=i+1;
      break;
    }
  }

  fprintf(stdout,"There are %d terms to compare in the energy files\n\n",
	  maxener);

  for(i=0; i<maxener; i++) {
    cmp_str(stdout,"unit",i,enm1[ind1[i]].unit,enm2[ind2[i]].unit);
  }
  
  snew(fr1,1);
  snew(fr2,1);
  do { 
    b1 = do_enx(in1,fr1);
    b2 = do_enx(in2,fr2);
    if (b1 && !b2)
      fprintf(stdout,"\nEnd of file on %s but not on %s\n",fn2,fn1);
    else if (!b1 && b2) 
      fprintf(stdout,"\nEnd of file on %s but not on %s\n",fn1,fn2);
    else if (!b1 && !b2)
      fprintf(stdout,"\nFiles read successfully\n");
    else {
      cmp_real(stdout,"t",-1,fr1->t,fr2->t,ftol,abstol);
      cmp_int(stdout,"step",-1,fr1->step,fr2->step);
      /* We don't want to print the nre mismatch for every frame */
      /* cmp_int(stdout,"nre",-1,fr1->nre,fr2->nre); */
      if ((fr1->nre >= nre) && (fr2->nre >= nre))
	cmp_energies(stdout,fr1->step,fr1->step,fr1->ener,fr2->ener,
		     enm1,enm2,ftol,abstol,nre,ind1,ind2,maxener);
      /*cmp_disres(fr1,fr2,ftol,abstol);*/
      cmp_eblocks(fr1,fr2,ftol,abstol);
    }
  } while (b1 && b2);
    
  close_enx(in1);
  close_enx(in2);
  
  free_enxframe(fr2);
  sfree(fr2);
  free_enxframe(fr1);
  sfree(fr1);
}
