/* -*- 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
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 * GROwing Monsters And Cloning Shrimps
 */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <string.h>
#include <time.h>
#include <math.h>
#include "sysstuff.h"
#include "string2.h"
#include "network.h"
#include "confio.h"
#include "copyrite.h"
#include "smalloc.h"
#include "nrnb.h"
#include "main.h"
#include "chargegroup.h"
#include "force.h"
#include "macros.h"
#include "random.h"
#include "names.h"
#include "gmx_fatal.h"
#include "txtdump.h"
#include "typedefs.h"
#include "update.h"
#include "random.h"
#include "constr.h"
#include "vec.h"
#include "statutil.h"
#include "tgroup.h"
#include "mdebin.h"
#include "vsite.h"
#include "force.h"
#include "mdrun.h"
#include "domdec.h"
#include "partdec.h"
#include "gmx_random.h"
#include "physics.h"
#include "xvgr.h"
#include "mdatoms.h"
#include "ns.h"
#include "gmx_wallcycle.h"
#include "mtop_util.h"
#include "gmxfio.h"
#include "pme.h"
#include "gbutil.h"

#if ( defined(GMX_IA32_SSE) || defined(GMX_X86_64_SSE) || defined(GMX_X86_64_SSE2) )
#if defined(GMX_DOUBLE)
#include "gmx_sse2_double.h"
#else
#include "gmx_sse2_single.h"
#endif
#endif


static void global_max(t_commrec *cr,int *n)
{
  int *sum,i;

  snew(sum,cr->nnodes);
  sum[cr->nodeid] = *n;
  gmx_sumi(cr->nnodes,sum,cr);
  for(i=0; i<cr->nnodes; i++)
    *n = max(*n,sum[i]);
  
  sfree(sum);
}

static void realloc_bins(double **bin,int *nbin,int nbin_new)
{
  int i;

  if (nbin_new != *nbin) {
    srenew(*bin,nbin_new);
    for(i=*nbin; i<nbin_new; i++)
      (*bin)[i] = 0;
    *nbin = nbin_new;
  }
}

double do_tpi(FILE *fplog,t_commrec *cr,
              int nfile, const t_filenm fnm[],
              const output_env_t oenv, gmx_bool bVerbose,gmx_bool bCompact,
              int nstglobalcomm,
              gmx_vsite_t *vsite,gmx_constr_t constr,
              int stepout,
              t_inputrec *inputrec,
              gmx_mtop_t *top_global,t_fcdata *fcd,
              t_state *state,
              t_mdatoms *mdatoms,
              t_nrnb *nrnb,gmx_wallcycle_t wcycle,
              gmx_edsam_t ed,
              t_forcerec *fr,
              int repl_ex_nst,int repl_ex_seed,
              real cpt_period,real max_hours,
              const char *deviceOptions,
              unsigned long Flags,
              gmx_runtime_t *runtime)
{
  const char *TPI="Test Particle Insertion"; 
  gmx_localtop_t *top;
  gmx_groups_t *groups;
  gmx_enerdata_t *enerd;
  rvec   *f;
  real   lambda,t,temp,beta,drmax,epot;
  double embU,sum_embU,*sum_UgembU,V,V_all,VembU_all;
  t_trxstatus   *status;
  t_trxframe rerun_fr;
  gmx_bool   bDispCorr,bCharge,bRFExcl,bNotLastFrame,bStateChanged,bNS,bOurStep;
  tensor force_vir,shake_vir,vir,pres;
  int    cg_tp,a_tp0,a_tp1,ngid,gid_tp,nener,e;
  rvec   *x_mol;
  rvec   mu_tot,x_init,dx,x_tp;
  int    nnodes,frame,nsteps,step;
  int    i,start,end;
  gmx_rng_t tpi_rand;
  FILE   *fp_tpi=NULL;
  char   *ptr,*dump_pdb,**leg,str[STRLEN],str2[STRLEN];
  double dbl,dump_ener;
  gmx_bool   bCavity;
  int    nat_cavity=0,d;
  real   *mass_cavity=NULL,mass_tot;
  int    nbin;
  double invbinw,*bin,refvolshift,logV,bUlogV;
  real dvdl,prescorr,enercorr,dvdlcorr;
  gmx_bool bEnergyOutOfBounds;
  const char *tpid_leg[2]={"direct","reweighted"};

  /* Since there is no upper limit to the insertion energies,
   * we need to set an upper limit for the distribution output.
   */
  real bU_bin_limit      = 50;
  real bU_logV_bin_limit = bU_bin_limit + 10;

  nnodes = cr->nnodes;

  top = gmx_mtop_generate_local_top(top_global,inputrec);

  groups = &top_global->groups;

  bCavity = (inputrec->eI == eiTPIC);
  if (bCavity) {
    ptr = getenv("GMX_TPIC_MASSES");
    if (ptr == NULL) {
      nat_cavity = 1;
    } else {
      /* Read (multiple) masses from env var GMX_TPIC_MASSES,
       * The center of mass of the last atoms is then used for TPIC.
       */
      nat_cavity = 0;
      while (sscanf(ptr,"%lf%n",&dbl,&i) > 0) {
	srenew(mass_cavity,nat_cavity+1);
	mass_cavity[nat_cavity] = dbl;
	fprintf(fplog,"mass[%d] = %f\n",
		nat_cavity+1,mass_cavity[nat_cavity]);
	nat_cavity++;
	ptr += i;
      }
      if (nat_cavity == 0)
	gmx_fatal(FARGS,"Found %d masses in GMX_TPIC_MASSES",nat_cavity);
    }
  }

  /*
  init_em(fplog,TPI,inputrec,&lambda,nrnb,mu_tot,
  state->box,fr,mdatoms,top,cr,nfile,fnm,NULL,NULL);*/
  /* We never need full pbc for TPI */
  fr->ePBC = epbcXYZ;
  /* Determine the temperature for the Boltzmann weighting */
  temp = inputrec->opts.ref_t[0];
  if (fplog) {
    for(i=1; (i<inputrec->opts.ngtc); i++) {
      if (inputrec->opts.ref_t[i] != temp) {
	fprintf(fplog,"\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
	fprintf(stderr,"\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
      }
    }
    fprintf(fplog,
	    "\n  The temperature for test particle insertion is %.3f K\n\n",
	    temp);
  }
  beta = 1.0/(BOLTZ*temp);

  /* Number of insertions per frame */
  nsteps = inputrec->nsteps; 

  /* Use the same neighborlist with more insertions points
   * in a sphere of radius drmax around the initial point
   */
  /* This should be a proper mdp parameter */
  drmax = inputrec->rtpi;

  /* An environment variable can be set to dump all configurations
   * to pdb with an insertion energy <= this value.
   */
  dump_pdb = getenv("GMX_TPI_DUMP");
  dump_ener = 0;
  if (dump_pdb)
    sscanf(dump_pdb,"%lf",&dump_ener);

  atoms2md(top_global,inputrec,0,NULL,0,top_global->natoms,mdatoms);
  update_mdatoms(mdatoms,inputrec->init_lambda);

  snew(enerd,1);
  init_enerdata(groups->grps[egcENER].nr,inputrec->n_flambda,enerd);
  snew(f,top_global->natoms);

  /* Print to log file  */
  runtime_start(runtime);
  print_date_and_time(fplog,cr->nodeid,
                      "Started Test Particle Insertion",runtime); 
  wallcycle_start(wcycle,ewcRUN);

  /* The last charge group is the group to be inserted */
  cg_tp = top->cgs.nr - 1;
  a_tp0 = top->cgs.index[cg_tp];
  a_tp1 = top->cgs.index[cg_tp+1];
  if (debug)
    fprintf(debug,"TPI cg %d, atoms %d-%d\n",cg_tp,a_tp0,a_tp1);
  if (a_tp1 - a_tp0 > 1 &&
      (inputrec->rlist < inputrec->rcoulomb ||
       inputrec->rlist < inputrec->rvdw))
    gmx_fatal(FARGS,"Can not do TPI for multi-atom molecule with a twin-range cut-off");
  snew(x_mol,a_tp1-a_tp0);

  bDispCorr = (inputrec->eDispCorr != edispcNO);
  bCharge = FALSE;
  for(i=a_tp0; i<a_tp1; i++) {
    /* Copy the coordinates of the molecule to be insterted */
    copy_rvec(state->x[i],x_mol[i-a_tp0]);
    /* Check if we need to print electrostatic energies */
    bCharge |= (mdatoms->chargeA[i] != 0 ||
		(mdatoms->chargeB && mdatoms->chargeB[i] != 0));
  }
  bRFExcl = (bCharge && EEL_RF(fr->eeltype) && fr->eeltype!=eelRF_NEC);

  calc_cgcm(fplog,cg_tp,cg_tp+1,&(top->cgs),state->x,fr->cg_cm);
  if (bCavity) {
    if (norm(fr->cg_cm[cg_tp]) > 0.5*inputrec->rlist && fplog) {
      fprintf(fplog, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
      fprintf(stderr,"WARNING: Your TPI molecule is not centered at 0,0,0\n");
    }
  } else {
    /* Center the molecule to be inserted at zero */
     for(i=0; i<a_tp1-a_tp0; i++)
      rvec_dec(x_mol[i],fr->cg_cm[cg_tp]);
  }

  if (fplog) {
    fprintf(fplog,"\nWill insert %d atoms %s partial charges\n",
	    a_tp1-a_tp0,bCharge ? "with" : "without");
    
    fprintf(fplog,"\nWill insert %d times in each frame of %s\n",
	    nsteps,opt2fn("-rerun",nfile,fnm));
  }
  
    if (!bCavity)
    {
        if (inputrec->nstlist > 1)
        {
            if (drmax==0 && a_tp1-a_tp0==1)
            {
                gmx_fatal(FARGS,"Re-using the neighborlist %d times for insertions of a single atom in a sphere of radius %f does not make sense",inputrec->nstlist,drmax);
            }
            if (fplog)
            {
                fprintf(fplog,"Will use the same neighborlist for %d insertions in a sphere of radius %f\n",inputrec->nstlist,drmax);
            }
        }
    }
    else
    {
        if (fplog)
        {
            fprintf(fplog,"Will insert randomly in a sphere of radius %f around the center of the cavity\n",drmax);
        }
    }

  ngid = groups->grps[egcENER].nr;
  gid_tp = GET_CGINFO_GID(fr->cginfo[cg_tp]);
  nener = 1 + ngid;
  if (bDispCorr)
    nener += 1;
  if (bCharge) {
    nener += ngid;
    if (bRFExcl)
      nener += 1;
    if (EEL_FULL(fr->eeltype))
      nener += 1;
  }
  snew(sum_UgembU,nener);

  /* Initialize random generator */
  tpi_rand = gmx_rng_init(inputrec->ld_seed);

  if (MASTER(cr)) {
    fp_tpi = xvgropen(opt2fn("-tpi",nfile,fnm),
		      "TPI energies","Time (ps)",
		      "(kJ mol\\S-1\\N) / (nm\\S3\\N)",oenv);
    xvgr_subtitle(fp_tpi,"f. are averages over one frame",oenv);
    snew(leg,4+nener);
    e = 0;
    sprintf(str,"-kT log(<Ve\\S-\\betaU\\N>/<V>)");
    leg[e++] = strdup(str);
    sprintf(str,"f. -kT log<e\\S-\\betaU\\N>");
    leg[e++] = strdup(str);
    sprintf(str,"f. <e\\S-\\betaU\\N>");
    leg[e++] = strdup(str);
    sprintf(str,"f. V");
    leg[e++] = strdup(str);
    sprintf(str,"f. <Ue\\S-\\betaU\\N>");
    leg[e++] = strdup(str);
    for(i=0; i<ngid; i++) {
      sprintf(str,"f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>",
	      *(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
      leg[e++] = strdup(str);
    }
    if (bDispCorr) {
      sprintf(str,"f. <U\\sdisp c\\Ne\\S-\\betaU\\N>");
      leg[e++] = strdup(str);
    }
    if (bCharge) {
      for(i=0; i<ngid; i++) {
	sprintf(str,"f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>",
		*(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
	leg[e++] = strdup(str);
      }
      if (bRFExcl) {
	sprintf(str,"f. <U\\sRF excl\\Ne\\S-\\betaU\\N>");
	leg[e++] = strdup(str);
      }
      if (EEL_FULL(fr->eeltype)) {
	sprintf(str,"f. <U\\sCoul recip\\Ne\\S-\\betaU\\N>");
	leg[e++] = strdup(str);
      }
    }
    xvgr_legend(fp_tpi,4+nener,(const char**)leg,oenv);
    for(i=0; i<4+nener; i++)
      sfree(leg[i]);
    sfree(leg);
  }
  clear_rvec(x_init);
  V_all = 0;
  VembU_all = 0;

  invbinw = 10;
  nbin = 10;
  snew(bin,nbin);

  bNotLastFrame = read_first_frame(oenv,&status,opt2fn("-rerun",nfile,fnm),
				   &rerun_fr,TRX_NEED_X);
  frame = 0;

  if (rerun_fr.natoms - (bCavity ? nat_cavity : 0) !=
      mdatoms->nr - (a_tp1 - a_tp0))
    gmx_fatal(FARGS,"Number of atoms in trajectory (%d)%s "
	      "is not equal the number in the run input file (%d) "
	      "minus the number of atoms to insert (%d)\n",
	      rerun_fr.natoms,bCavity ? " minus one" : "",
	      mdatoms->nr,a_tp1-a_tp0);

  refvolshift = log(det(rerun_fr.box));

#if ( defined(GMX_IA32_SSE) || defined(GMX_X86_64_SSE) || defined(GMX_X86_64_SSE2) )
    /* Make sure we don't detect SSE overflow generated before this point */
    gmx_mm_check_and_reset_overflow();
#endif

    while (bNotLastFrame)
    {
        lambda = rerun_fr.lambda;
        t = rerun_fr.time;
        
        sum_embU = 0;
        for(e=0; e<nener; e++)
        {
            sum_UgembU[e] = 0;
        }
        
        /* Copy the coordinates from the input trajectory */
        for(i=0; i<rerun_fr.natoms; i++)
        {
            copy_rvec(rerun_fr.x[i],state->x[i]);
        }
        
        V = det(rerun_fr.box);
        logV = log(V);
        
        bStateChanged = TRUE;
        bNS = TRUE;
        for(step=0; step<nsteps; step++)
        {
            /* In parallel all nodes generate all random configurations.
             * In that way the result is identical to a single cpu tpi run.
             */
            if (!bCavity)
            {
                /* Random insertion in the whole volume */
                bNS = (step % inputrec->nstlist == 0);
                if (bNS)
                {
                    /* Generate a random position in the box */
                    x_init[XX] = gmx_rng_uniform_real(tpi_rand)*state->box[XX][XX];
                    x_init[YY] = gmx_rng_uniform_real(tpi_rand)*state->box[YY][YY];
                    x_init[ZZ] = gmx_rng_uniform_real(tpi_rand)*state->box[ZZ][ZZ];
                }
                if (inputrec->nstlist == 1)
                {
                    copy_rvec(x_init,x_tp);
                }
                else
                {
                    /* Generate coordinates within |dx|=drmax of x_init */
                    do
                    {
                        dx[XX] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
                        dx[YY] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
                        dx[ZZ] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
                    }
                    while (norm2(dx) > drmax*drmax);
                    rvec_add(x_init,dx,x_tp);
                }
            }
            else
            {
                /* Random insertion around a cavity location
                 * given by the last coordinate of the trajectory.
                 */
                if (step == 0)
                {
                    if (nat_cavity == 1)
                    {
                        /* Copy the location of the cavity */
                        copy_rvec(rerun_fr.x[rerun_fr.natoms-1],x_init);
                    }
                    else
                    {
                        /* Determine the center of mass of the last molecule */
                        clear_rvec(x_init);
                        mass_tot = 0;
                        for(i=0; i<nat_cavity; i++)
                        {
                            for(d=0; d<DIM; d++)
                            {
                                x_init[d] +=
                                    mass_cavity[i]*rerun_fr.x[rerun_fr.natoms-nat_cavity+i][d];
                            }
                            mass_tot += mass_cavity[i];
                        }
                        for(d=0; d<DIM; d++)
                        {
                            x_init[d] /= mass_tot;
                        }
                    }
                }
                /* Generate coordinates within |dx|=drmax of x_init */
                do
                {
                    dx[XX] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
                    dx[YY] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
                    dx[ZZ] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
                }
                while (norm2(dx) > drmax*drmax);
                rvec_add(x_init,dx,x_tp);
            }
            
            if (a_tp1 - a_tp0 == 1)
            {
                /* Insert a single atom, just copy the insertion location */
	copy_rvec(x_tp,state->x[a_tp0]);
            }
            else
            {
                /* Copy the coordinates from the top file */
                for(i=a_tp0; i<a_tp1; i++)
                {
                    copy_rvec(x_mol[i-a_tp0],state->x[i]);
                }
                /* Rotate the molecule randomly */
                rotate_conf(a_tp1-a_tp0,state->x+a_tp0,NULL,
                            2*M_PI*gmx_rng_uniform_real(tpi_rand),
                            2*M_PI*gmx_rng_uniform_real(tpi_rand),
                            2*M_PI*gmx_rng_uniform_real(tpi_rand));
                /* Shift to the insertion location */
                for(i=a_tp0; i<a_tp1; i++)
                {
                    rvec_inc(state->x[i],x_tp);
                }
            }
            
            /* Check if this insertion belongs to this node */
            bOurStep = TRUE;
            if (PAR(cr))
            {
                switch (inputrec->eI)
                {
                case eiTPI:
                    bOurStep = ((step / inputrec->nstlist) % nnodes == cr->nodeid);
                    break;
                case eiTPIC:
                    bOurStep = (step % nnodes == cr->nodeid);
                    break;
                default:
                    gmx_fatal(FARGS,"Unknown integrator %s",ei_names[inputrec->eI]);
                }
            }
            if (bOurStep)
            {
                /* Clear some matrix variables  */
                clear_mat(force_vir); 
                clear_mat(shake_vir);
                clear_mat(vir);
                clear_mat(pres);
                
                /* Set the charge group center of mass of the test particle */
                copy_rvec(x_init,fr->cg_cm[top->cgs.nr-1]);
                
                /* Calc energy (no forces) on new positions.
                 * Since we only need the intermolecular energy
                 * and the RF exclusion terms of the inserted molecule occur
                 * within a single charge group we can pass NULL for the graph.
                 * This also avoids shifts that would move charge groups
                 * out of the box.
                 *
                 * Some checks above ensure than we can not have
                 * twin-range interactions together with nstlist > 1,
                 * therefore we do not need to remember the LR energies.
                 */
                /* Make do_force do a single node force calculation */
                cr->nnodes = 1;
                do_force(fplog,cr,inputrec,
                         step,nrnb,wcycle,top,top_global,&top_global->groups,
                         rerun_fr.box,state->x,&state->hist,
                         f,force_vir,mdatoms,enerd,fcd,
                         lambda,NULL,fr,NULL,mu_tot,t,NULL,NULL,FALSE,
                         GMX_FORCE_NONBONDED |
                         (bNS ? GMX_FORCE_NS | GMX_FORCE_DOLR : 0) |
                         (bStateChanged ? GMX_FORCE_STATECHANGED : 0)); 
                cr->nnodes = nnodes;
                bStateChanged = FALSE;
                bNS = FALSE;
                
                /* Calculate long range corrections to pressure and energy */
                calc_dispcorr(fplog,inputrec,fr,step,top_global->natoms,rerun_fr.box,
                              lambda,pres,vir,&prescorr,&enercorr,&dvdlcorr);
                /* figure out how to rearrange the next 4 lines MRS 8/4/2009 */
                enerd->term[F_DISPCORR] = enercorr;
                enerd->term[F_EPOT] += enercorr;
                enerd->term[F_PRES] += prescorr;
                enerd->term[F_DVDL] += dvdlcorr;

                epot = enerd->term[F_EPOT];
                bEnergyOutOfBounds = FALSE;
#if ( defined(GMX_IA32_SSE) || defined(GMX_X86_64_SSE) || defined(GMX_X86_64_SSE2) )
                /* With SSE the energy can overflow, check for this */
                if (gmx_mm_check_and_reset_overflow())
                {
                    if (debug)
                    {
                        fprintf(debug,"Found an SSE overflow, assuming the energy is out of bounds\n");
                    }
                    bEnergyOutOfBounds = TRUE;
                }
#endif
                /* If the compiler doesn't optimize this check away
                 * we catch the NAN energies.
                 * The epot>GMX_REAL_MAX check catches inf values,
                 * which should nicely result in embU=0 through the exp below,
                 * but it does not hurt to check anyhow.
                 */
                /* Non-bonded Interaction usually diverge at r=0.
                 * With tabulated interaction functions the first few entries
                 * should be capped in a consistent fashion between
                 * repulsion, dispersion and Coulomb to avoid accidental
                 * negative values in the total energy.
                 * The table generation code in tables.c does this.
                 * With user tbales the user should take care of this.
                 */
                if (epot != epot || epot > GMX_REAL_MAX)
                {
                    bEnergyOutOfBounds = TRUE;
                }
                if (bEnergyOutOfBounds)
                {
                    if (debug)
                    {
                        fprintf(debug,"\n  time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n",t,step,epot);
                    }
                    embU = 0;
                }
                else
                {
                    embU = exp(-beta*epot);
                    sum_embU += embU;
                    /* Determine the weighted energy contributions of each energy group */
                    e = 0;
                    sum_UgembU[e++] += epot*embU;
                    if (fr->bBHAM)
                    {
                        for(i=0; i<ngid; i++)
                        {
                            sum_UgembU[e++] +=
                                (enerd->grpp.ener[egBHAMSR][GID(i,gid_tp,ngid)] +
                                 enerd->grpp.ener[egBHAMLR][GID(i,gid_tp,ngid)])*embU;
                        }
                    }
                    else
                    {
                        for(i=0; i<ngid; i++)
                        {
                            sum_UgembU[e++] +=
                                (enerd->grpp.ener[egLJSR][GID(i,gid_tp,ngid)] +
                                 enerd->grpp.ener[egLJLR][GID(i,gid_tp,ngid)])*embU;
                        }
                    }
                    if (bDispCorr)
                    {
                        sum_UgembU[e++] += enerd->term[F_DISPCORR]*embU;
                    }
                    if (bCharge)
                    {
                        for(i=0; i<ngid; i++)
                        {
                            sum_UgembU[e++] +=
                                (enerd->grpp.ener[egCOULSR][GID(i,gid_tp,ngid)] +
                                 enerd->grpp.ener[egCOULLR][GID(i,gid_tp,ngid)])*embU;
                        }
                        if (bRFExcl)
                        {
                            sum_UgembU[e++] += enerd->term[F_RF_EXCL]*embU;
                        }
                        if (EEL_FULL(fr->eeltype))
                        {
                            sum_UgembU[e++] += enerd->term[F_COUL_RECIP]*embU;
                        }
                    }
                }
                
                if (embU == 0 || beta*epot > bU_bin_limit)
                {
                    bin[0]++;
                }
                else
                {
                    i = (int)((bU_logV_bin_limit
                               - (beta*epot - logV + refvolshift))*invbinw
                              + 0.5);
                    if (i < 0)
                    {
                        i = 0;
                    }
                    if (i >= nbin)
                    {
                        realloc_bins(&bin,&nbin,i+10);
                    }
                    bin[i]++;
                }
                
                if (debug)
                {
                    fprintf(debug,"TPI %7d %12.5e %12.5f %12.5f %12.5f\n",
                            step,epot,x_tp[XX],x_tp[YY],x_tp[ZZ]);
                }

                if (dump_pdb && epot <= dump_ener)
                {
                    sprintf(str,"t%g_step%d.pdb",t,step);
                    sprintf(str2,"t: %f step %d ener: %f",t,step,epot);
                    write_sto_conf_mtop(str,str2,top_global,state->x,state->v,
                                        inputrec->ePBC,state->box);
                }
            }
        }
        
        if (PAR(cr))
        {
            /* When running in parallel sum the energies over the processes */
            gmx_sumd(1,    &sum_embU, cr);
            gmx_sumd(nener,sum_UgembU,cr);
        }

        frame++;
        V_all += V;
        VembU_all += V*sum_embU/nsteps;
        
        if (fp_tpi)
        {
            if (bVerbose || frame%10==0 || frame<10)
            {
                fprintf(stderr,"mu %10.3e <mu> %10.3e\n",
                        -log(sum_embU/nsteps)/beta,-log(VembU_all/V_all)/beta);
            }
            
            fprintf(fp_tpi,"%10.3f %12.5e %12.5e %12.5e %12.5e",
                    t,
                    VembU_all==0 ? 20/beta : -log(VembU_all/V_all)/beta,
                    sum_embU==0  ? 20/beta : -log(sum_embU/nsteps)/beta,
                    sum_embU/nsteps,V);
            for(e=0; e<nener; e++)
            {
                fprintf(fp_tpi," %12.5e",sum_UgembU[e]/nsteps);
            }
            fprintf(fp_tpi,"\n");
            fflush(fp_tpi);
        }
        
        bNotLastFrame = read_next_frame(oenv, status,&rerun_fr);
    } /* End of the loop  */
    runtime_end(runtime);

    close_trj(status);

    if (fp_tpi != NULL)
    {
        gmx_fio_fclose(fp_tpi);
    }

    if (fplog != NULL)
    {
        fprintf(fplog,"\n");
        fprintf(fplog,"  <V>  = %12.5e nm^3\n",V_all/frame);
        fprintf(fplog,"  <mu> = %12.5e kJ/mol\n",-log(VembU_all/V_all)/beta);
    }
  
    /* Write the Boltzmann factor histogram */
    if (PAR(cr))
    {
        /* When running in parallel sum the bins over the processes */
        i = nbin;
        global_max(cr,&i);
        realloc_bins(&bin,&nbin,i);
        gmx_sumd(nbin,bin,cr);
    }
    if (MASTER(cr))
    {
        fp_tpi = xvgropen(opt2fn("-tpid",nfile,fnm),
                          "TPI energy distribution",
                          "\\betaU - log(V/<V>)","count",oenv);
        sprintf(str,"number \\betaU > %g: %9.3e",bU_bin_limit,bin[0]);
        xvgr_subtitle(fp_tpi,str,oenv);
        xvgr_legend(fp_tpi,2,(const char **)tpid_leg,oenv);
        for(i=nbin-1; i>0; i--)
        {
            bUlogV = -i/invbinw + bU_logV_bin_limit - refvolshift + log(V_all/frame);
            fprintf(fp_tpi,"%6.2f %10d %12.5e\n",
                    bUlogV,
                    (int)(bin[i]+0.5),
                    bin[i]*exp(-bUlogV)*V_all/VembU_all);
        }
        gmx_fio_fclose(fp_tpi);
    }
    sfree(bin);

    sfree(sum_UgembU);

    runtime->nsteps_done = frame*inputrec->nsteps;

    return 0;
}
