fixed some details for nstcalcenergy>1

[gromacs.git] / src / kernel / md.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 -
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 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
 */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <signal.h>
#include <stdlib.h>

#if ((defined WIN32 || defined _WIN32 || defined WIN64 || defined _WIN64) && !defined __CYGWIN__ && !defined __CYGWIN32__)
/* _isnan() */
#include <float.h>
#endif

#include "typedefs.h"
#include "smalloc.h"
#include "sysstuff.h"
#include "vec.h"
#include "statutil.h"
#include "vcm.h"
#include "mdebin.h"
#include "nrnb.h"
#include "calcmu.h"
#include "index.h"
#include "vsite.h"
#include "update.h"
#include "ns.h"
#include "trnio.h"
#include "xtcio.h"
#include "mdrun.h"
#include "confio.h"
#include "network.h"
#include "pull.h"
#include "xvgr.h"
#include "physics.h"
#include "names.h"
#include "xmdrun.h"
#include "ionize.h"
#include "disre.h"
#include "orires.h"
#include "dihre.h"
#include "pppm.h"
#include "pme.h"
#include "mdatoms.h"
#include "repl_ex.h"
#include "qmmm.h"
#include "mpelogging.h"
#include "domdec.h"
#include "partdec.h"
#include "topsort.h"
#include "coulomb.h"
#include "constr.h"
#include "shellfc.h"
#include "compute_io.h"
#include "mvdata.h"
#include "checkpoint.h"
#include "mtop_util.h"
#include "sighandler.h"

#ifdef GMX_LIB_MPI
#include <mpi.h>
#endif
#ifdef GMX_THREADS
#include "tmpi.h"
#endif

#ifdef GMX_FAHCORE
#include "corewrap.h"
#endif



enum { eglsNABNSB, eglsCHKPT, eglsTERM, eglsRESETCOUNTERS, eglsNR };
/* Is the signal in one simulation independent of other simulations? */
bool gs_simlocal[eglsNR] = { TRUE, FALSE, FALSE, TRUE };

typedef struct {
    int nstms;       /* The frequency for intersimulation communication */
    int sig[eglsNR]; /* The signal set by one process in do_md */
    int set[eglsNR]; /* The communicated signal, equal for all processes */
} globsig_t;


static int multisim_min(const gmx_multisim_t *ms,int nmin,int n)
{
    int  *buf;
    bool bPos,bEqual;
    int  s,d;

    snew(buf,ms->nsim);
    buf[ms->sim] = n;
    gmx_sumi_sim(ms->nsim,buf,ms);
    bPos   = TRUE;
    bEqual = TRUE;
    for(s=0; s<ms->nsim; s++)
    {
        bPos   = bPos   && (buf[s] > 0);
        bEqual = bEqual && (buf[s] == buf[0]);
    }
    if (bPos)
    {
        if (bEqual)
        {
            nmin = min(nmin,buf[0]);
        }
        else
        {
            /* Find the least common multiple */
            for(d=2; d<nmin; d++)
            {
                s = 0;
                while (s < ms->nsim && d % buf[s] == 0)
                {
                    s++;
                }
                if (s == ms->nsim)
                {
                    /* We found the LCM and it is less than nmin */
                    nmin = d;
                    break;
                }
            }
        }
    }
    sfree(buf);

    return nmin;
}

static int multisim_nstsimsync(const t_commrec *cr,
                               const t_inputrec *ir,int repl_ex_nst)
{
    int nmin;

    if (MASTER(cr))
    {
        nmin = INT_MAX;
        nmin = multisim_min(cr->ms,nmin,ir->nstlist);
        nmin = multisim_min(cr->ms,nmin,ir->nstcalcenergy);
        nmin = multisim_min(cr->ms,nmin,repl_ex_nst);
        if (nmin == INT_MAX)
        {
            gmx_fatal(FARGS,"Can not find an appropriate interval for inter-simulation communication, since nstlist, nstcalcenergy and -replex are all <= 0");
        }
        /* Avoid inter-simulation communication at every (second) step */
        if (nmin <= 2)
        {
            nmin = 10;
        }
    }

    gmx_bcast(sizeof(int),&nmin,cr);

    return nmin;
}

static void init_global_signals(globsig_t *gs,const t_commrec *cr,
                                const t_inputrec *ir,int repl_ex_nst)
{
    int i;

    if (MULTISIM(cr))
    {
        gs->nstms = multisim_nstsimsync(cr,ir,repl_ex_nst);
        if (debug)
        {
            fprintf(debug,"Syncing simulations for checkpointing and termination every %d steps\n",gs->nstms);
        }
    }
    else
    {
        gs->nstms = 1;
    }

    for(i=0; i<eglsNR; i++)
    {
        gs->sig[i] = 0;
        gs->set[i] = 0;
    }
}

static void copy_coupling_state(t_state *statea,t_state *stateb, 
                                gmx_ekindata_t *ekinda,gmx_ekindata_t *ekindb, t_grpopts* opts) 
{
    
    /* MRS note -- might be able to get rid of some of the arguments.  Look over it when it's all debugged */
    
    int i,j,nc;

    /* Make sure we have enough space for x and v */
    if (statea->nalloc > stateb->nalloc)
    {
        stateb->nalloc = statea->nalloc;
        srenew(stateb->x,stateb->nalloc);
        srenew(stateb->v,stateb->nalloc);
    }

    stateb->natoms     = statea->natoms;
    stateb->ngtc       = statea->ngtc;
    stateb->nnhpres    = statea->nnhpres;
    stateb->veta       = statea->veta;
    if (ekinda) 
    {
        copy_mat(ekinda->ekin,ekindb->ekin);
        for (i=0; i<stateb->ngtc; i++) 
        {
            ekindb->tcstat[i].T = ekinda->tcstat[i].T;
            ekindb->tcstat[i].Th = ekinda->tcstat[i].Th;
            copy_mat(ekinda->tcstat[i].ekinh,ekindb->tcstat[i].ekinh);
            copy_mat(ekinda->tcstat[i].ekinf,ekindb->tcstat[i].ekinf);
            ekindb->tcstat[i].ekinscalef_nhc =  ekinda->tcstat[i].ekinscalef_nhc;
            ekindb->tcstat[i].ekinscaleh_nhc =  ekinda->tcstat[i].ekinscaleh_nhc;
            ekindb->tcstat[i].vscale_nhc =  ekinda->tcstat[i].vscale_nhc;
        }
    }
    copy_rvecn(statea->x,stateb->x,0,stateb->natoms);
    copy_rvecn(statea->v,stateb->v,0,stateb->natoms);
    copy_mat(statea->box,stateb->box);
    copy_mat(statea->box_rel,stateb->box_rel);
    copy_mat(statea->boxv,stateb->boxv);

    for (i = 0; i<stateb->ngtc; i++) 
    { 
        nc = i*opts->nhchainlength;
        for (j=0; j<opts->nhchainlength; j++) 
        {
            stateb->nosehoover_xi[nc+j]  = statea->nosehoover_xi[nc+j];
            stateb->nosehoover_vxi[nc+j] = statea->nosehoover_vxi[nc+j];
        }
    }
    if (stateb->nhpres_xi != NULL)
    {
        for (i = 0; i<stateb->nnhpres; i++) 
        {
            nc = i*opts->nhchainlength;
            for (j=0; j<opts->nhchainlength; j++) 
            {
                stateb->nhpres_xi[nc+j]  = statea->nhpres_xi[nc+j];
                stateb->nhpres_vxi[nc+j] = statea->nhpres_vxi[nc+j];
            }
        }
    }
}

static void compute_globals(FILE *fplog, gmx_global_stat_t gstat, t_commrec *cr, t_inputrec *ir, 
                            t_forcerec *fr, gmx_ekindata_t *ekind, 
                            t_state *state, t_state *state_global, t_mdatoms *mdatoms, 
                            t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
                            gmx_enerdata_t *enerd,tensor force_vir, tensor shake_vir, tensor total_vir, 
                            tensor pres, rvec mu_tot, gmx_constr_t constr, 
                            globsig_t *gs,bool bInterSimGS,
                            matrix box, gmx_mtop_t *top_global, real *pcurr, 
                            int natoms, bool *bSumEkinhOld, int flags)
{
    int  i,gsi;
    real gs_buf[eglsNR];
    tensor corr_vir,corr_pres,shakeall_vir;
    bool bEner,bPres,bTemp, bVV;
    bool bRerunMD, bStopCM, bGStat, bNEMD, bIterate, 
        bFirstIterate,bReadEkin,bEkinAveVel,bScaleEkin, bConstrain;
    real ekin,temp,prescorr,enercorr,dvdlcorr;
    
    /* translate CGLO flags to booleans */
    bRerunMD = flags & CGLO_RERUNMD;
    bStopCM = flags & CGLO_STOPCM;
    bGStat = flags & CGLO_GSTAT;
    bNEMD = flags & CGLO_NEMD;
    bReadEkin = flags & CGLO_READEKIN;
    bScaleEkin = flags & CGLO_SCALEEKIN;
    bEner = flags & CGLO_ENERGY;
    bTemp = flags & CGLO_TEMPERATURE;
    bPres  = flags & CGLO_PRESSURE;
    bConstrain = flags & CGLO_CONSTRAINT;
    bIterate = flags & CGLO_ITERATE;
    bFirstIterate = flags & CGLO_FIRSTITERATE;

    /* we calculate a full state kinetic energy either with full-step velocity verlet
       or half step where we need the pressure */
    bEkinAveVel = (ir->eI==eiVV || (ir->eI==eiVVAK && IR_NPT_TROTTER(ir) && bPres) || bReadEkin);

    /* in initalization, it sums the shake virial in vv, and to 
       sums ekinh_old in leapfrog (or if we are calculating ekinh_old for other reasons */

    /* ########## Kinetic energy  ############## */
    
    if (bTemp) 
    {
        /* Non-equilibrium MD: this is parallellized, but only does communication
         * when there really is NEMD.
         */
        
        if (PAR(cr) && (bNEMD)) 
        {
            accumulate_u(cr,&(ir->opts),ekind);
        }
        debug_gmx();
        if (bReadEkin)
        {
            restore_ekinstate_from_state(cr,ekind,&state_global->ekinstate);
        }
        else 
        {

            calc_ke_part(state,&(ir->opts),mdatoms,ekind,nrnb,bEkinAveVel,bIterate);
        }
        
        debug_gmx();
        
        /* Calculate center of mass velocity if necessary, also parallellized */
        if (bStopCM && !bRerunMD && bEner) 
        {
            calc_vcm_grp(fplog,mdatoms->start,mdatoms->homenr,mdatoms,
                         state->x,state->v,vcm);
        }
    }

    if (bTemp || bPres || bEner || bConstrain) 
    {
        if (!bGStat)
        {
            /* We will not sum ekinh_old,                                                            
             * so signal that we still have to do it.                                                
             */
            *bSumEkinhOld = TRUE;

        }
        else
        {
            if (gs != NULL)
            {
                for(i=0; i<eglsNR; i++)
                {
                    gs_buf[i] = gs->sig[i];
                }
            }
            if (PAR(cr)) 
            {
                wallcycle_start(wcycle,ewcMoveE);
                GMX_MPE_LOG(ev_global_stat_start);
                global_stat(fplog,gstat,cr,enerd,force_vir,shake_vir,mu_tot,
                            ir,ekind,constr,vcm,
                            gs != NULL ? eglsNR : 0,gs_buf,
                            top_global,state,
                            *bSumEkinhOld,flags);
                GMX_MPE_LOG(ev_global_stat_finish);
                wallcycle_stop(wcycle,ewcMoveE);
            }
            if (gs != NULL)
            {
                if (MULTISIM(cr) && bInterSimGS)
                {
                    if (MASTER(cr))
                    {
                        /* Communicate the signals between the simulations */
                        gmx_sum_sim(eglsNR,gs_buf,cr->ms);
                    }
                    /* Communicate the signals form the master to the others */
                    gmx_bcast(eglsNR*sizeof(gs_buf[0]),gs_buf,cr);
                }
                for(i=0; i<eglsNR; i++)
                {
                    if (bInterSimGS || gs_simlocal[i])
                    {
                        /* Set the communicated signal only when it is non-zero,
                         * since signals might not be processed at each MD step.
                         */
                        gsi = (gs_buf[i] >= 0 ?
                               (int)(gs_buf[i] + 0.5) :
                               (int)(gs_buf[i] - 0.5));
                        if (gsi != 0)
                        {
                            gs->set[i] = gsi;
                        }
                        /* Turn off the local signal */
                        gs->sig[i] = 0;
                    }
                }
            }
            *bSumEkinhOld = FALSE;
        }
    }
    
    if (!bNEMD && debug && bTemp && (vcm->nr > 0))
    {
        correct_ekin(debug,
                     mdatoms->start,mdatoms->start+mdatoms->homenr,
                     state->v,vcm->group_p[0],
                     mdatoms->massT,mdatoms->tmass,ekind->ekin);
    }
    
    if (bEner) {
        /* Do center of mass motion removal */
        if (bStopCM && !bRerunMD) /* is this correct?  Does it get called too often with this logic? */
        {
            check_cm_grp(fplog,vcm,ir,1);
            do_stopcm_grp(fplog,mdatoms->start,mdatoms->homenr,mdatoms->cVCM,
                          state->x,state->v,vcm);
            inc_nrnb(nrnb,eNR_STOPCM,mdatoms->homenr);
        }
    }

    if (bTemp) 
    {
        /* Sum the kinetic energies of the groups & calc temp */
        /* compute full step kinetic energies if vv, or if vv-avek and we are computing the pressure with IR_NPT_TROTTER */
        /* three maincase:  VV with AveVel (md-vv), vv with AveEkin (md-vv-avek), leap with AveEkin (md).  
           Leap with AveVel is also an option for the future but not supported now.  
           bEkinAveVel: If TRUE, we simply multiply ekin by ekinscale to get a full step kinetic energy. 
           If FALSE, we average ekinh_old and ekinh*ekinscale_nhc to get an averaged half step kinetic energy.
           bSaveEkinOld: If TRUE (in the case of iteration = bIterate is TRUE), we don't reset the ekinscale_nhc.  
           If FALSE, we go ahead and erase over it.
        */ 
        enerd->term[F_TEMP] = sum_ekin(&(ir->opts),ekind,&(enerd->term[F_DKDL]),
                                       bEkinAveVel,bIterate,bScaleEkin);
 
        enerd->term[F_EKIN] = trace(ekind->ekin);
    }
    
    /* ##########  Long range energy information ###### */
    
    if (bEner || bPres || bConstrain) 
    {
        calc_dispcorr(fplog,ir,fr,0,top_global->natoms,box,state->lambda,
                      corr_pres,corr_vir,&prescorr,&enercorr,&dvdlcorr);
    }
    
    if (bEner && bFirstIterate) 
    {
        enerd->term[F_DISPCORR] = enercorr;
        enerd->term[F_EPOT] += enercorr;
        enerd->term[F_DVDL] += dvdlcorr;
        if (fr->efep != efepNO) {
            enerd->dvdl_lin += dvdlcorr;
        }
    }
    
    /* ########## Now pressure ############## */
    if (bPres || bConstrain) 
    {
        
        m_add(force_vir,shake_vir,total_vir);
        
        /* Calculate pressure and apply LR correction if PPPM is used.
         * Use the box from last timestep since we already called update().
         */
        
        enerd->term[F_PRES] = calc_pres(fr->ePBC,ir->nwall,box,ekind->ekin,total_vir,pres,
                                        (fr->eeltype==eelPPPM)?enerd->term[F_COUL_RECIP]:0.0);
        
        /* Calculate long range corrections to pressure and energy */
        /* this adds to enerd->term[F_PRES] and enerd->term[F_ETOT], 
           and computes enerd->term[F_DISPCORR].  Also modifies the 
           total_vir and pres tesors */
        
        m_add(total_vir,corr_vir,total_vir);
        m_add(pres,corr_pres,pres);
        enerd->term[F_PDISPCORR] = prescorr;
        enerd->term[F_PRES] += prescorr;
        *pcurr = enerd->term[F_PRES];
        /* calculate temperature using virial */
        enerd->term[F_VTEMP] = calc_temp(trace(total_vir),ir->opts.nrdf[0]);
        
    }    
}


/* Definitions for convergence of iterated constraints */

/* iterate constraints up to 50 times  */
#define MAXITERCONST       50

/* data type */
typedef struct
{
    real f,fprev,x,xprev;  
    int iter_i;
    bool bIterate;
    real allrelerr[MAXITERCONST+2];
    int num_close; /* number of "close" violations, caused by limited precision. */
} gmx_iterate_t;
  
#ifdef GMX_DOUBLE
#define CONVERGEITER  0.000000001
#define CLOSE_ENOUGH  0.000001000
#else
#define CONVERGEITER  0.0001
#define CLOSE_ENOUGH  0.0050
#endif

/* we want to keep track of the close calls.  If there are too many, there might be some other issues.
   so we make sure that it's either less than some predetermined number, or if more than that number,
   only some small fraction of the total. */
#define MAX_NUMBER_CLOSE        50
#define FRACTION_CLOSE       0.001
  
/* maximum length of cyclic traps to check, emerging from limited numerical precision  */
#define CYCLEMAX            20

static void gmx_iterate_init(gmx_iterate_t *iterate,bool bIterate)
{
    int i;

    iterate->iter_i = 0;
    iterate->bIterate = bIterate;
    iterate->num_close = 0;
    for (i=0;i<MAXITERCONST+2;i++) 
    {
        iterate->allrelerr[i] = 0;
    }
}

static bool done_iterating(const t_commrec *cr,FILE *fplog, int nsteps, gmx_iterate_t *iterate, bool bFirstIterate, real fom, real *newf) 
{    
    /* monitor convergence, and use a secant search to propose new
       values.  
                                                                  x_{i} - x_{i-1}
       The secant method computes x_{i+1} = x_{i} - f(x_{i}) * ---------------------
                                                                f(x_{i}) - f(x_{i-1})
       
       The function we are trying to zero is fom-x, where fom is the
       "figure of merit" which is the pressure (or the veta value) we
       would get by putting in an old value of the pressure or veta into
       the incrementor function for the step or half step.  I have
       verified that this gives the same answer as self consistent
       iteration, usually in many fewer steps, especially for small tau_p.
       
       We could possibly eliminate an iteration with proper use
       of the value from the previous step, but that would take a bit
       more bookkeeping, especially for veta, since tests indicate the
       function of veta on the last step is not sufficiently close to
       guarantee convergence this step. This is
       good enough for now.  On my tests, I could use tau_p down to
       0.02, which is smaller that would ever be necessary in
       practice. Generally, 3-5 iterations will be sufficient */

    real relerr,err,xmin;
    char buf[256];
    int i;
    bool incycle;
    
    if (bFirstIterate) 
    {
        iterate->x = fom;
        iterate->f = fom-iterate->x;
        iterate->xprev = 0;
        iterate->fprev = 0;
        *newf = fom;
    } 
    else 
    {
        iterate->f = fom-iterate->x; /* we want to zero this difference */
        if ((iterate->iter_i > 1) && (iterate->iter_i < MAXITERCONST)) 
        {
            if (iterate->f==iterate->fprev) 
            {
                *newf = iterate->f;
            } 
            else 
            {
                *newf = iterate->x - (iterate->x-iterate->xprev)*(iterate->f)/(iterate->f-iterate->fprev); 
            }
        } 
        else 
        {
            /* just use self-consistent iteration the first step to initialize, or 
               if it's not converging (which happens occasionally -- need to investigate why) */
            *newf = fom; 
        }
    }
    /* Consider a slight shortcut allowing us to exit one sooner -- we check the
       difference between the closest of x and xprev to the new
       value. To be 100% certain, we should check the difference between
       the last result, and the previous result, or
       
       relerr = (fabs((x-xprev)/fom));
       
       but this is pretty much never necessary under typical conditions.
       Checking numerically, it seems to lead to almost exactly the same
       trajectories, but there are small differences out a few decimal
       places in the pressure, and eventually in the v_eta, but it could
       save an interation.
       
       if (fabs(*newf-x) < fabs(*newf - xprev)) { xmin = x;} else { xmin = xprev;}
       relerr = (fabs((*newf-xmin) / *newf));
    */
    
    err = fabs((iterate->f-iterate->fprev));
    relerr = fabs(err/fom);

    iterate->allrelerr[iterate->iter_i] = relerr;
    
    if (iterate->iter_i > 0) 
    {
        if (debug) 
        {
            fprintf(debug,"Iterating NPT constraints: %6i %20.12f%14.6g%20.12f\n",
                    iterate->iter_i,fom,relerr,*newf);
        }
        
        if ((relerr < CONVERGEITER) || (err < CONVERGEITER) || (fom==0) || ((iterate->x == iterate->xprev) && iterate->iter_i > 1))
        {
            iterate->bIterate = FALSE;
            if (debug) 
            {
                fprintf(debug,"Iterating NPT constraints: CONVERGED\n");
            }
            return TRUE;
        }
        if (iterate->iter_i > MAXITERCONST)
        {
            if (relerr < CLOSE_ENOUGH)
            {
                incycle = FALSE;
                for (i=1;i<CYCLEMAX;i++) {
                    if ((iterate->allrelerr[iterate->iter_i-(1+i)] == iterate->allrelerr[iterate->iter_i-1]) &&
                        (iterate->allrelerr[iterate->iter_i-(1+i)] == iterate->allrelerr[iterate->iter_i-(1+2*i)])) {
                        incycle = TRUE;
                        if (debug) 
                        {
                            fprintf(debug,"Exiting from an NPT iterating cycle of length %d\n",i);
                        }
                        break;
                    }
                }
                
                if (incycle) {
                    /* step 1: trapped in a numerical attractor */
                    /* we are trapped in a numerical attractor, and can't converge any more, and are close to the final result.
                       Better to give up convergence here than have the simulation die.
                    */
                    iterate->num_close++;
                    return TRUE;
                } 
                else 
                {
                    /* Step #2: test if we are reasonably close for other reasons, then monitor the number.  If not, die */
                    
                    /* how many close calls have we had?  If less than a few, we're OK */
                    if (iterate->num_close < MAX_NUMBER_CLOSE) 
                    {
                        sprintf(buf,"Slight numerical convergence deviation with NPT at step %d, relative error only %10.5g, likely not a problem, continuing\n",nsteps,relerr);
                        md_print_warning(cr,fplog,buf);
                        iterate->num_close++;
                        return TRUE;
                        /* if more than a few, check the total fraction.  If too high, die. */
                    } else if (iterate->num_close/(double)nsteps > FRACTION_CLOSE) {
                        gmx_fatal(FARGS,"Could not converge NPT constraints, too many exceptions (%d%%\n",iterate->num_close/(double)nsteps);
                    } 
                }
            }
            else 
            {
                gmx_fatal(FARGS,"Could not converge NPT constraints\n");
            }
        }
    }
    
    iterate->xprev = iterate->x;
    iterate->x = *newf;
    iterate->fprev = iterate->f;
    iterate->iter_i++;
    
    return FALSE;
}

static void check_nst_param(FILE *fplog,t_commrec *cr,
                            const char *desc_nst,int nst,
                            const char *desc_p,int *p)
{
    char buf[STRLEN];

    if (*p > 0 && *p % nst != 0)
    {
        /* Round up to the next multiple of nst */
        *p = ((*p)/nst + 1)*nst;
        sprintf(buf,"NOTE: %s changes %s to %d\n",desc_nst,desc_p,*p);
        md_print_warning(cr,fplog,buf);
    }
}

static void reset_all_counters(FILE *fplog,t_commrec *cr,
                               gmx_large_int_t step,
                               gmx_large_int_t *step_rel,t_inputrec *ir,
                               gmx_wallcycle_t wcycle,t_nrnb *nrnb,
                               gmx_runtime_t *runtime)
{
    char buf[STRLEN],sbuf[STEPSTRSIZE];

    /* Reset all the counters related to performance over the run */
    sprintf(buf,"Step %s: resetting all time and cycle counters\n",
            gmx_step_str(step,sbuf));
    md_print_warning(cr,fplog,buf);

    wallcycle_stop(wcycle,ewcRUN);
    wallcycle_reset_all(wcycle);
    if (DOMAINDECOMP(cr))
    {
        reset_dd_statistics_counters(cr->dd);
    }
    init_nrnb(nrnb);
    ir->init_step += *step_rel;
    ir->nsteps    -= *step_rel;
    *step_rel = 0;
    wallcycle_start(wcycle,ewcRUN);
    runtime_start(runtime);
    print_date_and_time(fplog,cr->nodeid,"Restarted time",runtime);
}

static int check_nstglobalcomm(FILE *fplog,t_commrec *cr,
                               int nstglobalcomm,t_inputrec *ir)
{
    char buf[STRLEN];

    if (!EI_DYNAMICS(ir->eI))
    {
        nstglobalcomm = 1;
    }

    if (nstglobalcomm == -1)
    {
        if (ir->nstcalcenergy == 0 && ir->nstlist == 0)
        {
            nstglobalcomm = 10;
            if (ir->nstenergy > 0 && ir->nstenergy < nstglobalcomm)
            {
                nstglobalcomm = ir->nstenergy;
            }
        }
        else
        {
            /* We assume that if nstcalcenergy > nstlist,
             * nstcalcenergy is a multiple of nstlist.
             */
            if (ir->nstcalcenergy == 0 ||
                (ir->nstlist > 0 && ir->nstlist < ir->nstcalcenergy))
            {
                nstglobalcomm = ir->nstlist;
            }
            else
            {
                nstglobalcomm = ir->nstcalcenergy;
            }
        }
    }
    else
    {
        if (ir->nstlist > 0 &&
            nstglobalcomm > ir->nstlist && nstglobalcomm % ir->nstlist != 0)
        {
            nstglobalcomm = (nstglobalcomm / ir->nstlist)*ir->nstlist;
            sprintf(buf,"WARNING: nstglobalcomm is larger than nstlist, but not a multiple, setting it to %d\n",nstglobalcomm);
            md_print_warning(cr,fplog,buf);
        }
        if (nstglobalcomm > ir->nstcalcenergy)
        {
            check_nst_param(fplog,cr,"-gcom",nstglobalcomm,
                            "nstcalcenergy",&ir->nstcalcenergy);
        }

        check_nst_param(fplog,cr,"-gcom",nstglobalcomm,
                        "nstenergy",&ir->nstenergy);

        check_nst_param(fplog,cr,"-gcom",nstglobalcomm,
                        "nstlog",&ir->nstlog);
    }

    if (ir->comm_mode != ecmNO && ir->nstcomm < nstglobalcomm)
    {
        sprintf(buf,"WARNING: Changing nstcomm from %d to %d\n",
                ir->nstcomm,nstglobalcomm);
        md_print_warning(cr,fplog,buf);
        ir->nstcomm = nstglobalcomm;
    }

    return nstglobalcomm;
}

void check_ir_old_tpx_versions(t_commrec *cr,FILE *fplog,
                               t_inputrec *ir,gmx_mtop_t *mtop)
{
    /* Check required for old tpx files */
    if (IR_TWINRANGE(*ir) && ir->nstlist > 1 &&
        ir->nstcalcenergy % ir->nstlist != 0)
    {
        md_print_warning(cr,fplog,"Old tpr file with twin-range settings: modifying energy calculation and/or T/P-coupling frequencies");

        if (gmx_mtop_ftype_count(mtop,F_CONSTR) +
            gmx_mtop_ftype_count(mtop,F_CONSTRNC) > 0 &&
            ir->eConstrAlg == econtSHAKE)
        {
            md_print_warning(cr,fplog,"With twin-range cut-off's and SHAKE the virial and pressure are incorrect");
            if (ir->epc != epcNO)
            {
                gmx_fatal(FARGS,"Can not do pressure coupling with twin-range cut-off's and SHAKE");
            }
        }
        check_nst_param(fplog,cr,"nstlist",ir->nstlist,
                        "nstcalcenergy",&ir->nstcalcenergy);
    }
    check_nst_param(fplog,cr,"nstcalcenergy",ir->nstcalcenergy,
                    "nstenergy",&ir->nstenergy);
    check_nst_param(fplog,cr,"nstcalcenergy",ir->nstcalcenergy,
                    "nstlog",&ir->nstlog);
    if (ir->efep != efepNO)
    {
        check_nst_param(fplog,cr,"nstdhdl",ir->nstdhdl,
                        "nstenergy",&ir->nstenergy);
    }
}

typedef struct {
    bool       bGStatEveryStep;
    gmx_large_int_t step_ns;
    gmx_large_int_t step_nscheck;
    gmx_large_int_t nns;
    matrix     scale_tot;
    int        nabnsb;
    double     s1;
    double     s2;
    double     ab;
    double     lt_runav;
    double     lt_runav2;
} gmx_nlheur_t;

static void reset_nlistheuristics(gmx_nlheur_t *nlh,gmx_large_int_t step)
{
    nlh->lt_runav  = 0;
    nlh->lt_runav2 = 0;
    nlh->step_nscheck = step;
}

static void init_nlistheuristics(gmx_nlheur_t *nlh,
                                 bool bGStatEveryStep,gmx_large_int_t step)
{
    nlh->bGStatEveryStep = bGStatEveryStep;
    nlh->nns       = 0;
    nlh->nabnsb    = 0;
    nlh->s1        = 0;
    nlh->s2        = 0;
    nlh->ab        = 0;

    reset_nlistheuristics(nlh,step);
}

static void update_nliststatistics(gmx_nlheur_t *nlh,gmx_large_int_t step)
{
    gmx_large_int_t nl_lt;
    char sbuf[STEPSTRSIZE],sbuf2[STEPSTRSIZE];

    /* Determine the neighbor list life time */
    nl_lt = step - nlh->step_ns;
    if (debug)
    {
        fprintf(debug,"%d atoms beyond ns buffer, updating neighbor list after %s steps\n",nlh->nabnsb,gmx_step_str(nl_lt,sbuf));
    }
    nlh->nns++;
    nlh->s1 += nl_lt;
    nlh->s2 += nl_lt*nl_lt;
    nlh->ab += nlh->nabnsb;
    if (nlh->lt_runav == 0)
    {
        nlh->lt_runav  = nl_lt;
        /* Initialize the fluctuation average
         * such that at startup we check after 0 steps.
         */
        nlh->lt_runav2 = sqr(nl_lt/2.0);
    }
    /* Running average with 0.9 gives an exp. history of 9.5 */
    nlh->lt_runav2 = 0.9*nlh->lt_runav2 + 0.1*sqr(nlh->lt_runav - nl_lt);
    nlh->lt_runav  = 0.9*nlh->lt_runav  + 0.1*nl_lt;
    if (nlh->bGStatEveryStep)
    {
        /* Always check the nlist validity */
        nlh->step_nscheck = step;
    }
    else
    {
        /* We check after:  <life time> - 2*sigma
         * The factor 2 is quite conservative,
         * but we assume that with nstlist=-1 the user
         * prefers exact integration over performance.
         */
        nlh->step_nscheck = step
                  + (int)(nlh->lt_runav - 2.0*sqrt(nlh->lt_runav2)) - 1;
    }
    if (debug)
    {
        fprintf(debug,"nlist life time %s run av. %4.1f sig %3.1f check %s check with -gcom %d\n",
                gmx_step_str(nl_lt,sbuf),nlh->lt_runav,sqrt(nlh->lt_runav2),
                gmx_step_str(nlh->step_nscheck-step+1,sbuf2),
                (int)(nlh->lt_runav - 2.0*sqrt(nlh->lt_runav2)));
    }
}

static void set_nlistheuristics(gmx_nlheur_t *nlh,bool bReset,gmx_large_int_t step)
{
    int d;

    if (bReset)
    {
        reset_nlistheuristics(nlh,step);
    }
    else
    {
        update_nliststatistics(nlh,step);
    }

    nlh->step_ns = step;
    /* Initialize the cumulative coordinate scaling matrix */
    clear_mat(nlh->scale_tot);
    for(d=0; d<DIM; d++)
    {
        nlh->scale_tot[d][d] = 1.0;
    }
}

double do_md(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
             const output_env_t oenv, bool bVerbose,bool bCompact,
             int nstglobalcomm,
             gmx_vsite_t *vsite,gmx_constr_t constr,
             int stepout,t_inputrec *ir,
             gmx_mtop_t *top_global,
             t_fcdata *fcd,
             t_state *state_global,
             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)
{
    gmx_mdoutf_t *outf;
    gmx_large_int_t step,step_rel;
    double     run_time;
    double     t,t0,lam0;
    bool       bGStatEveryStep,bGStat,bNstEner,bCalcEnerPres;
    bool       bNS,bNStList,bSimAnn,bStopCM,bRerunMD,bNotLastFrame=FALSE,
               bFirstStep,bStateFromTPX,bInitStep,bLastStep,
               bBornRadii,bStartingFromCpt;
    bool       bDoDHDL=FALSE;
    bool       bNEMD,do_ene,do_log,do_verbose,bRerunWarnNoV=TRUE,
               bForceUpdate=FALSE,bCPT;
    int        mdof_flags;
    bool       bMasterState;
    int        force_flags,cglo_flags;
    tensor     force_vir,shake_vir,total_vir,tmp_vir,pres;
    int        i,m,status;
    rvec       mu_tot;
    t_vcm      *vcm;
    t_state    *bufstate=NULL;   
    matrix     *scale_tot,pcoupl_mu,M,ebox;
    gmx_nlheur_t nlh;
    t_trxframe rerun_fr;
    gmx_repl_ex_t repl_ex=NULL;
    int        nchkpt=1;

    gmx_localtop_t *top;        
    t_mdebin *mdebin=NULL;
    t_state    *state=NULL;
    rvec       *f_global=NULL;
    int        n_xtc=-1;
    rvec       *x_xtc=NULL;
    gmx_enerdata_t *enerd;
    rvec       *f=NULL;
    gmx_global_stat_t gstat;
    gmx_update_t upd=NULL;
    t_graph    *graph=NULL;
    globsig_t   gs;

    bool        bFFscan;
    gmx_groups_t *groups;
    gmx_ekindata_t *ekind, *ekind_save;
    gmx_shellfc_t shellfc;
    int         count,nconverged=0;
    real        timestep=0;
    double      tcount=0;
    bool        bIonize=FALSE;
    bool        bTCR=FALSE,bConverged=TRUE,bOK,bSumEkinhOld,bExchanged;
    bool        bAppend;
    bool        bResetCountersHalfMaxH=FALSE;
    bool        bVV,bIterations,bIterate,bFirstIterate,bTemp,bPres,bTrotter;
    real        temp0,mu_aver=0,dvdl;
    int         a0,a1,gnx=0,ii;
    atom_id     *grpindex=NULL;
    char        *grpname;
    t_coupl_rec *tcr=NULL;
    rvec        *xcopy=NULL,*vcopy=NULL,*cbuf=NULL;
    matrix      boxcopy={{0}},lastbox;
        tensor      tmpvir;
        real        fom,oldfom,veta_save,pcurr,scalevir,tracevir;
        real        vetanew = 0;
    double      cycles;
        real        last_conserved = 0;
    real        last_ekin = 0;
        int         iter_i;
        t_extmass   MassQ;
    int         **trotter_seq; 
    char        sbuf[STEPSTRSIZE],sbuf2[STEPSTRSIZE];
    int         handledSignal=-1; /* compare to last_signal_recvd */
    gmx_iterate_t iterate;
#ifdef GMX_FAHCORE
    /* Temporary addition for FAHCORE checkpointing */
    int chkpt_ret;
#endif

    /* Check for special mdrun options */
    bRerunMD = (Flags & MD_RERUN);
    bIonize  = (Flags & MD_IONIZE);
    bFFscan  = (Flags & MD_FFSCAN);
    bAppend  = (Flags & MD_APPENDFILES);
    if (Flags & MD_RESETCOUNTERSHALFWAY)
    {
        if (ir->nsteps > 0)
        {
            /* Signal to reset the counters half the simulation steps. */
            wcycle_set_reset_counters(wcycle,ir->nsteps/2);
        }
        /* Signal to reset the counters halfway the simulation time. */
        bResetCountersHalfMaxH = (max_hours > 0);
    }

    /* md-vv uses averaged full step velocities for T-control 
       md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
       md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
    bVV = EI_VV(ir->eI);
    if (bVV) /* to store the initial velocities while computing virial */
    {
        snew(cbuf,top_global->natoms);
    }
    /* all the iteratative cases - only if there are constraints */ 
    bIterations = ((IR_NPT_TROTTER(ir)) && (constr) && (!bRerunMD));
    bTrotter = (bVV && (IR_NPT_TROTTER(ir) || (IR_NVT_TROTTER(ir))));        
    
    if (bRerunMD)
    {
        /* Since we don't know if the frames read are related in any way,
         * rebuild the neighborlist at every step.
         */
        ir->nstlist       = 1;
        ir->nstcalcenergy = 1;
        nstglobalcomm     = 1;
    }

    check_ir_old_tpx_versions(cr,fplog,ir,top_global);

    nstglobalcomm = check_nstglobalcomm(fplog,cr,nstglobalcomm,ir);
    bGStatEveryStep = (nstglobalcomm == 1);

    if (!bGStatEveryStep && ir->nstlist == -1 && fplog != NULL)
    {
        fprintf(fplog,
                "To reduce the energy communication with nstlist = -1\n"
                "the neighbor list validity should not be checked at every step,\n"
                "this means that exact integration is not guaranteed.\n"
                "The neighbor list validity is checked after:\n"
                "  <n.list life time> - 2*std.dev.(n.list life time)  steps.\n"
                "In most cases this will result in exact integration.\n"
                "This reduces the energy communication by a factor of 2 to 3.\n"
                "If you want less energy communication, set nstlist > 3.\n\n");
    }

    if (bRerunMD || bFFscan)
    {
        ir->nstxtcout = 0;
    }
    groups = &top_global->groups;

    /* Initial values */
    init_md(fplog,cr,ir,oenv,&t,&t0,&state_global->lambda,&lam0,
            nrnb,top_global,&upd,
            nfile,fnm,&outf,&mdebin,
            force_vir,shake_vir,mu_tot,&bNEMD,&bSimAnn,&vcm,state_global,Flags);

    clear_mat(total_vir);
    clear_mat(pres);
    /* Energy terms and groups */
    snew(enerd,1);
    init_enerdata(top_global->groups.grps[egcENER].nr,ir->n_flambda,enerd);
    if (DOMAINDECOMP(cr))
    {
        f = NULL;
    }
    else
    {
        snew(f,top_global->natoms);
    }

    /* Kinetic energy data */
    snew(ekind,1);
    init_ekindata(fplog,top_global,&(ir->opts),ekind);
    /* needed for iteration of constraints */
    snew(ekind_save,1);
    init_ekindata(fplog,top_global,&(ir->opts),ekind_save);
    /* Copy the cos acceleration to the groups struct */    
    ekind->cosacc.cos_accel = ir->cos_accel;

    gstat = global_stat_init(ir);
    debug_gmx();

    /* Check for polarizable models and flexible constraints */
    shellfc = init_shell_flexcon(fplog,
                                 top_global,n_flexible_constraints(constr),
                                 (ir->bContinuation || 
                                  (DOMAINDECOMP(cr) && !MASTER(cr))) ?
                                 NULL : state_global->x);

    if (DEFORM(*ir))
    {
#ifdef GMX_THREADS
        tMPI_Thread_mutex_lock(&deform_init_box_mutex);
#endif
        set_deform_reference_box(upd,
                                 deform_init_init_step_tpx,
                                 deform_init_box_tpx);
#ifdef GMX_THREADS
        tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
#endif
    }

    {
        double io = compute_io(ir,top_global->natoms,groups,mdebin->ebin->nener,1);
        if ((io > 2000) && MASTER(cr))
            fprintf(stderr,
                    "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
                    io);
    }

    if (DOMAINDECOMP(cr)) {
        top = dd_init_local_top(top_global);

        snew(state,1);
        dd_init_local_state(cr->dd,state_global,state);

        if (DDMASTER(cr->dd) && ir->nstfout) {
            snew(f_global,state_global->natoms);
        }
    } else {
        if (PAR(cr)) {
            /* Initialize the particle decomposition and split the topology */
            top = split_system(fplog,top_global,ir,cr);

            pd_cg_range(cr,&fr->cg0,&fr->hcg);
            pd_at_range(cr,&a0,&a1);
        } else {
            top = gmx_mtop_generate_local_top(top_global,ir);

            a0 = 0;
            a1 = top_global->natoms;
        }

        state = partdec_init_local_state(cr,state_global);
        f_global = f;

        atoms2md(top_global,ir,0,NULL,a0,a1-a0,mdatoms);

        if (vsite) {
            set_vsite_top(vsite,top,mdatoms,cr);
        }

        if (ir->ePBC != epbcNONE && !ir->bPeriodicMols) {
            graph = mk_graph(fplog,&(top->idef),0,top_global->natoms,FALSE,FALSE);
        }

        if (shellfc) {
            make_local_shells(cr,mdatoms,shellfc);
        }

        if (ir->pull && PAR(cr)) {
            dd_make_local_pull_groups(NULL,ir->pull,mdatoms);
        }
    }

    if (DOMAINDECOMP(cr))
    {
        /* Distribute the charge groups over the nodes from the master node */
        dd_partition_system(fplog,ir->init_step,cr,TRUE,1,
                            state_global,top_global,ir,
                            state,&f,mdatoms,top,fr,
                            vsite,shellfc,constr,
                            nrnb,wcycle,FALSE);
    }

    update_mdatoms(mdatoms,state->lambda);

    if (MASTER(cr))
    {
        /* Update mdebin with energy history if appending to output files */
        if ( Flags & MD_APPENDFILES )
        {
            restore_energyhistory_from_state(mdebin,&state_global->enerhist);
        }
        /* Set the initial energy history in state to zero by updating once */
        update_energyhistory(&state_global->enerhist,mdebin);
    }   

    if ((state->flags & (1<<estLD_RNG)) && (Flags & MD_READ_RNG)) {
        /* Set the random state if we read a checkpoint file */
        set_stochd_state(upd,state);
    }

    /* Initialize constraints */
    if (constr) {
        if (!DOMAINDECOMP(cr))
            set_constraints(constr,top,ir,mdatoms,cr);
    }

    /* Check whether we have to GCT stuff */
    bTCR = ftp2bSet(efGCT,nfile,fnm);
    if (bTCR) {
        if (MASTER(cr)) {
            fprintf(stderr,"Will do General Coupling Theory!\n");
        }
        gnx = top_global->mols.nr;
        snew(grpindex,gnx);
        for(i=0; (i<gnx); i++) {
            grpindex[i] = i;
        }
    }

    if (repl_ex_nst > 0 && MASTER(cr))
        repl_ex = init_replica_exchange(fplog,cr->ms,state_global,ir,
                                        repl_ex_nst,repl_ex_seed);

    if (!ir->bContinuation && !bRerunMD)
    {
        if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
        {
            /* Set the velocities of frozen particles to zero */
            for(i=mdatoms->start; i<mdatoms->start+mdatoms->homenr; i++)
            {
                for(m=0; m<DIM; m++)
                {
                    if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
                    {
                        state->v[i][m] = 0;
                    }
                }
            }
        }

        if (constr)
        {
            /* Constrain the initial coordinates and velocities */
            do_constrain_first(fplog,constr,ir,mdatoms,state,f,
                               graph,cr,nrnb,fr,top,shake_vir);
        }
        if (vsite)
        {
            /* Construct the virtual sites for the initial configuration */
            construct_vsites(fplog,vsite,state->x,nrnb,ir->delta_t,NULL,
                             top->idef.iparams,top->idef.il,
                             fr->ePBC,fr->bMolPBC,graph,cr,state->box);
        }
    }

    debug_gmx();
  
    /* I'm assuming we need global communication the first time! MRS */
    cglo_flags = (CGLO_TEMPERATURE | CGLO_GSTAT
                  | (bVV ? CGLO_PRESSURE:0)
                  | (bVV ? CGLO_CONSTRAINT:0)
                  | (bRerunMD ? CGLO_RERUNMD:0)
                  | ((Flags & MD_READ_EKIN) ? CGLO_READEKIN:0));
    
    bSumEkinhOld = FALSE;
    compute_globals(fplog,gstat,cr,ir,fr,ekind,state,state_global,mdatoms,nrnb,vcm,
                    wcycle,enerd,force_vir,shake_vir,total_vir,pres,mu_tot,
                    constr,NULL,FALSE,state->box,
                    top_global,&pcurr,top_global->natoms,&bSumEkinhOld,cglo_flags);
    if (ir->eI == eiVVAK) {
        /* a second call to get the half step temperature initialized as well */ 
        /* we do the same call as above, but turn the pressure off -- internally, this 
           is recognized as a velocity verlet half-step kinetic energy calculation.
           This minimized excess variables, but perhaps loses some logic?*/
        
        compute_globals(fplog,gstat,cr,ir,fr,ekind,state,state_global,mdatoms,nrnb,vcm,
                        wcycle,enerd,force_vir,shake_vir,total_vir,pres,mu_tot,
                        constr,NULL,FALSE,state->box,
                        top_global,&pcurr,top_global->natoms,&bSumEkinhOld,
                        cglo_flags &~ CGLO_PRESSURE);
    }
    
    /* Calculate the initial half step temperature, and save the ekinh_old */
    if (!(Flags & MD_STARTFROMCPT)) 
    {
        for(i=0; (i<ir->opts.ngtc); i++) 
        {
            copy_mat(ekind->tcstat[i].ekinh,ekind->tcstat[i].ekinh_old);
        } 
    }
    temp0 = enerd->term[F_TEMP];
    
    /* if using an iterative algorithm, we need to create a working directory for the state. */
    if (bIterations) 
    {
            bufstate = init_bufstate(state);
    }
    if (bFFscan) 
    {
        snew(xcopy,state->natoms);
        snew(vcopy,state->natoms);
        copy_rvecn(state->x,xcopy,0,state->natoms);
        copy_rvecn(state->v,vcopy,0,state->natoms);
        copy_mat(state->box,boxcopy);
    } 
    
    /* need to make an initiation call to get the Trotter variables set, as well as other constants for non-trotter
       temperature control */
    trotter_seq = init_npt_vars(ir,state,&MassQ,bTrotter);
    
    if (MASTER(cr))
    {
        if (constr && !ir->bContinuation && ir->eConstrAlg == econtLINCS)
        {
            fprintf(fplog,
                    "RMS relative constraint deviation after constraining: %.2e\n",
                    constr_rmsd(constr,FALSE));
        }
        if (bVV) 
        {
            enerd->term[F_TEMP] *= 2; /* result of averages being done over previous and current step,
                                         and there is no previous step */
        }
        fprintf(fplog,"Initial temperature: %g K\n",enerd->term[F_TEMP]);
        if (bRerunMD)
        {
            fprintf(stderr,"starting md rerun '%s', reading coordinates from"
                    " input trajectory '%s'\n\n",
                    *(top_global->name),opt2fn("-rerun",nfile,fnm));
            if (bVerbose)
            {
                fprintf(stderr,"Calculated time to finish depends on nsteps from "
                        "run input file,\nwhich may not correspond to the time "
                        "needed to process input trajectory.\n\n");
            }
        }
        else
        {
            char tbuf[20];
            fprintf(stderr,"starting mdrun '%s'\n",
                    *(top_global->name));
            if (ir->nsteps >= 0)
            {
                sprintf(tbuf,"%8.1f",(ir->init_step+ir->nsteps)*ir->delta_t);
            }
            else
            {
                sprintf(tbuf,"%s","infinite");
            }
            if (ir->init_step > 0)
            {
                fprintf(stderr,"%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
                        gmx_step_str(ir->init_step+ir->nsteps,sbuf),tbuf,
                        gmx_step_str(ir->init_step,sbuf2),
                        ir->init_step*ir->delta_t);
            }
            else
            {
                fprintf(stderr,"%s steps, %s ps.\n",
                        gmx_step_str(ir->nsteps,sbuf),tbuf);
            }
        }
        fprintf(fplog,"\n");
    }

    /* Set and write start time */
    runtime_start(runtime);
    print_date_and_time(fplog,cr->nodeid,"Started mdrun",runtime);
    wallcycle_start(wcycle,ewcRUN);
    if (fplog)
        fprintf(fplog,"\n");

    /* safest point to do file checkpointing is here.  More general point would be immediately before integrator call */
#ifdef GMX_FAHCORE
    chkpt_ret=fcCheckPointParallel( cr->nodeid,
                                    NULL,0);
    if ( chkpt_ret == 0 ) 
        gmx_fatal( 3,__FILE__,__LINE__, "Checkpoint error on step %d\n", 0 );
#endif

    debug_gmx();
    /***********************************************************
     *
     *             Loop over MD steps 
     *
     ************************************************************/

    /* if rerunMD then read coordinates and velocities from input trajectory */
    if (bRerunMD)
    {
        if (getenv("GMX_FORCE_UPDATE"))
        {
            bForceUpdate = TRUE;
        }

        bNotLastFrame = read_first_frame(oenv,&status,
                                         opt2fn("-rerun",nfile,fnm),
                                         &rerun_fr,TRX_NEED_X | TRX_READ_V);
        if (rerun_fr.natoms != top_global->natoms)
        {
            gmx_fatal(FARGS,
                      "Number of atoms in trajectory (%d) does not match the "
                      "run input file (%d)\n",
                      rerun_fr.natoms,top_global->natoms);
        }
        if (ir->ePBC != epbcNONE)
        {
            if (!rerun_fr.bBox)
            {
                gmx_fatal(FARGS,"Rerun trajectory frame step %d time %f does not contain a box, while pbc is used",rerun_fr.step,rerun_fr.time);
            }
            if (max_cutoff2(ir->ePBC,rerun_fr.box) < sqr(fr->rlistlong))
            {
                gmx_fatal(FARGS,"Rerun trajectory frame step %d time %f has too small box dimensions",rerun_fr.step,rerun_fr.time);
            }

            /* Set the shift vectors.
             * Necessary here when have a static box different from the tpr box.
             */
            calc_shifts(rerun_fr.box,fr->shift_vec);
        }
    }

    /* loop over MD steps or if rerunMD to end of input trajectory */
    bFirstStep = TRUE;
    /* Skip the first Nose-Hoover integration when we get the state from tpx */
    bStateFromTPX = !opt2bSet("-cpi",nfile,fnm);
    bInitStep = bFirstStep && (bStateFromTPX || bVV);
    bStartingFromCpt = (Flags & MD_STARTFROMCPT) && bInitStep;
    bLastStep    = FALSE;
    bSumEkinhOld = FALSE;
    bExchanged   = FALSE;

    init_global_signals(&gs,cr,ir,repl_ex_nst);

    step = ir->init_step;
    step_rel = 0;

    if (ir->nstlist == -1)
    {
        init_nlistheuristics(&nlh,bGStatEveryStep,step);
    }

    bLastStep = (bRerunMD || (ir->nsteps >= 0 && step_rel > ir->nsteps));
    while (!bLastStep || (bRerunMD && bNotLastFrame)) {

        wallcycle_start(wcycle,ewcSTEP);

        GMX_MPE_LOG(ev_timestep1);

        if (bRerunMD) {
            if (rerun_fr.bStep) {
                step = rerun_fr.step;
                step_rel = step - ir->init_step;
            }
            if (rerun_fr.bTime) {
                t = rerun_fr.time;
            }
            else
            {
                t = step;
            }
        } 
        else 
        {
            bLastStep = (step_rel == ir->nsteps);
            t = t0 + step*ir->delta_t;
        }

        if (ir->efep != efepNO)
        {
            if (bRerunMD && rerun_fr.bLambda && (ir->delta_lambda!=0))
            {
                state_global->lambda = rerun_fr.lambda;
            }
            else
            {
                state_global->lambda = lam0 + step*ir->delta_lambda;
            }
            state->lambda = state_global->lambda;
            bDoDHDL = do_per_step(step,ir->nstdhdl);
        }

        if (bSimAnn) 
        {
            update_annealing_target_temp(&(ir->opts),t);
        }

        if (bRerunMD)
        {
            if (!(DOMAINDECOMP(cr) && !MASTER(cr)))
            {
                for(i=0; i<state_global->natoms; i++)
                {
                    copy_rvec(rerun_fr.x[i],state_global->x[i]);
                }
                if (rerun_fr.bV)
                {
                    for(i=0; i<state_global->natoms; i++)
                    {
                        copy_rvec(rerun_fr.v[i],state_global->v[i]);
                    }
                }
                else
                {
                    for(i=0; i<state_global->natoms; i++)
                    {
                        clear_rvec(state_global->v[i]);
                    }
                    if (bRerunWarnNoV)
                    {
                        fprintf(stderr,"\nWARNING: Some frames do not contain velocities.\n"
                                "         Ekin, temperature and pressure are incorrect,\n"
                                "         the virial will be incorrect when constraints are present.\n"
                                "\n");
                        bRerunWarnNoV = FALSE;
                    }
                }
            }
            copy_mat(rerun_fr.box,state_global->box);
            copy_mat(state_global->box,state->box);

            if (vsite && (Flags & MD_RERUN_VSITE))
            {
                if (DOMAINDECOMP(cr))
                {
                    gmx_fatal(FARGS,"Vsite recalculation with -rerun is not implemented for domain decomposition, use particle decomposition");
                }
                if (graph)
                {
                    /* Following is necessary because the graph may get out of sync
                     * with the coordinates if we only have every N'th coordinate set
                     */
                    mk_mshift(fplog,graph,fr->ePBC,state->box,state->x);
                    shift_self(graph,state->box,state->x);
                }
                construct_vsites(fplog,vsite,state->x,nrnb,ir->delta_t,state->v,
                                 top->idef.iparams,top->idef.il,
                                 fr->ePBC,fr->bMolPBC,graph,cr,state->box);
                if (graph)
                {
                    unshift_self(graph,state->box,state->x);
                }
            }
        }

        /* Stop Center of Mass motion */
        bStopCM = (ir->comm_mode != ecmNO && do_per_step(step,ir->nstcomm));

        /* Copy back starting coordinates in case we're doing a forcefield scan */
        if (bFFscan)
        {
            for(ii=0; (ii<state->natoms); ii++)
            {
                copy_rvec(xcopy[ii],state->x[ii]);
                copy_rvec(vcopy[ii],state->v[ii]);
            }
            copy_mat(boxcopy,state->box);
        }

        if (bRerunMD)
        {
            /* for rerun MD always do Neighbour Searching */
            bNS = (bFirstStep || ir->nstlist != 0);
            bNStList = bNS;
        }
        else
        {
            /* Determine whether or not to do Neighbour Searching and LR */
            bNStList = (ir->nstlist > 0  && step % ir->nstlist == 0);
            
            bNS = (bFirstStep || bExchanged || bNStList ||
                   (ir->nstlist == -1 && nlh.nabnsb > 0));

            if (bNS && ir->nstlist == -1)
            {
                set_nlistheuristics(&nlh,bFirstStep || bExchanged,step);
            }
        } 

        if (gs.set[eglsTERM] > 0 || (gs.set[eglsTERM] < 0 && bNS))
        {
            bLastStep = TRUE;
        }

        /* Determine whether or not to update the Born radii if doing GB */
        bBornRadii=bFirstStep;
        if (ir->implicit_solvent && (step % ir->nstgbradii==0))
        {
            bBornRadii=TRUE;
        }
        
        do_log = do_per_step(step,ir->nstlog) || bFirstStep || bLastStep;
        do_verbose = bVerbose &&
                  (step % stepout == 0 || bFirstStep || bLastStep);

        if (bNS && !(bFirstStep && ir->bContinuation && !bRerunMD))
        {
            if (bRerunMD)
            {
                bMasterState = TRUE;
            }
            else
            {
                bMasterState = FALSE;
                /* Correct the new box if it is too skewed */
                if (DYNAMIC_BOX(*ir))
                {
                    if (correct_box(fplog,step,state->box,graph))
                    {
                        bMasterState = TRUE;
                    }
                }
                if (DOMAINDECOMP(cr) && bMasterState)
                {
                    dd_collect_state(cr->dd,state,state_global);
                }
            }

            if (DOMAINDECOMP(cr))
            {
                /* Repartition the domain decomposition */
                wallcycle_start(wcycle,ewcDOMDEC);
                dd_partition_system(fplog,step,cr,
                                    bMasterState,nstglobalcomm,
                                    state_global,top_global,ir,
                                    state,&f,mdatoms,top,fr,
                                    vsite,shellfc,constr,
                                    nrnb,wcycle,do_verbose);
                wallcycle_stop(wcycle,ewcDOMDEC);
                /* If using an iterative integrator, reallocate space to match the decomposition */
            }
        }

        if (MASTER(cr) && do_log && !bFFscan)
        {
            print_ebin_header(fplog,step,t,state->lambda);
        }

        if (ir->efep != efepNO)
        {
            update_mdatoms(mdatoms,state->lambda); 
        }

        if (bRerunMD && rerun_fr.bV)
        {
            
            /* We need the kinetic energy at minus the half step for determining
             * the full step kinetic energy and possibly for T-coupling.*/
            /* This may not be quite working correctly yet . . . . */
            compute_globals(fplog,gstat,cr,ir,fr,ekind,state,state_global,mdatoms,nrnb,vcm,
                            wcycle,enerd,NULL,NULL,NULL,NULL,mu_tot,
                            constr,NULL,FALSE,state->box,
                            top_global,&pcurr,top_global->natoms,&bSumEkinhOld,
                            CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
        }
        clear_mat(force_vir);
        
        /* Ionize the atoms if necessary */
        if (bIonize)
        {
            ionize(fplog,oenv,mdatoms,top_global,t,ir,state->x,state->v,
                   mdatoms->start,mdatoms->start+mdatoms->homenr,state->box,cr);
        }
        
        /* Update force field in ffscan program */
        if (bFFscan)
        {
            if (update_forcefield(fplog,
                                  nfile,fnm,fr,
                                  mdatoms->nr,state->x,state->box)) {
                if (gmx_parallel_env_initialized())
                {
                    gmx_finalize();
                }
                exit(0);
            }
        }

        GMX_MPE_LOG(ev_timestep2);

        /* We write a checkpoint at this MD step when:
         * either at an NS step when we signalled through gs,
         * or at the last step (but not when we do not want confout),
         * but never at the first step or with rerun.
         */
        bCPT = (((gs.set[eglsCHKPT] && bNS) ||
                 (bLastStep && (Flags & MD_CONFOUT))) &&
                step > ir->init_step && !bRerunMD);
        if (bCPT)
        {
            gs.set[eglsCHKPT] = 0;
        }

        /* Determine the energy and pressure:
         * at nstcalcenergy steps and at energy output steps (set below).
         */
        bNstEner = (bGStatEveryStep || do_per_step(step,ir->nstcalcenergy));
        bCalcEnerPres = bNstEner;

        /* Do we need global communication ? */
        bGStat = (bCalcEnerPres || bStopCM ||
                  (ir->nstlist == -1 && !bRerunMD && step >= nlh.step_nscheck));

        do_ene = (do_per_step(step,ir->nstenergy) || bLastStep);

        if (do_ene || do_log)
        {
            bCalcEnerPres = TRUE;
            bGStat        = TRUE;
        }
        
        /* these CGLO_ options remain the same throughout the iteration */
        cglo_flags = ((bRerunMD ? CGLO_RERUNMD : 0) |
                      (bStopCM ? CGLO_STOPCM : 0) |
                      (bGStat ? CGLO_GSTAT : 0) |
                      (bNEMD ? CGLO_NEMD : 0)
            );
        
        force_flags = (GMX_FORCE_STATECHANGED |
                       ((DYNAMIC_BOX(*ir) || bRerunMD) ? GMX_FORCE_DYNAMICBOX : 0) |
                       GMX_FORCE_ALLFORCES |
                       (bNStList ? GMX_FORCE_DOLR : 0) |
                       GMX_FORCE_SEPLRF |
                       (bCalcEnerPres ? GMX_FORCE_VIRIAL : 0) |
                       (bDoDHDL ? GMX_FORCE_DHDL : 0)
            );
        
        if (shellfc)
        {
            /* Now is the time to relax the shells */
            count=relax_shell_flexcon(fplog,cr,bVerbose,bFFscan ? step+1 : step,
                                      ir,bNS,force_flags,
                                      bStopCM,top,top_global,
                                      constr,enerd,fcd,
                                      state,f,force_vir,mdatoms,
                                      nrnb,wcycle,graph,groups,
                                      shellfc,fr,bBornRadii,t,mu_tot,
                                      state->natoms,&bConverged,vsite,
                                      outf->fp_field);
            tcount+=count;

            if (bConverged)
            {
                nconverged++;
            }
        }
        else
        {
            /* The coordinates (x) are shifted (to get whole molecules)
             * in do_force.
             * This is parallellized as well, and does communication too. 
             * Check comments in sim_util.c
             */
        
            do_force(fplog,cr,ir,step,nrnb,wcycle,top,top_global,groups,
                     state->box,state->x,&state->hist,
                     f,force_vir,mdatoms,enerd,fcd,
                     state->lambda,graph,
                     fr,vsite,mu_tot,t,outf->fp_field,ed,bBornRadii,
                     (bNS ? GMX_FORCE_NS : 0) | force_flags);
        }
    
        GMX_BARRIER(cr->mpi_comm_mygroup);
        
        if (bTCR)
        {
            mu_aver = calc_mu_aver(cr,state->x,mdatoms->chargeA,
                                   mu_tot,&top_global->mols,mdatoms,gnx,grpindex);
        }
        
        if (bTCR && bFirstStep)
        {
            tcr=init_coupling(fplog,nfile,fnm,cr,fr,mdatoms,&(top->idef));
            fprintf(fplog,"Done init_coupling\n"); 
            fflush(fplog);
        }
        
        /*  ############### START FIRST UPDATE HALF-STEP ############### */
        
        if (!bStartingFromCpt && !bRerunMD)
        {
            if (ir->eI == eiVV)
            {
                if (bInitStep)
                {
                    /* if using velocity verlet with full time step Ekin,
                     * take the first half step only to compute the 
                     * virial for the first step. From there,
                     * revert back to the initial coordinates
                     * so that the input is actually the initial step.
                     */
                    copy_rvecn(state->v,cbuf,0,state->natoms); /* should make this better for parallelizing? */
                }
                
                /* this is for NHC in the Ekin(t+dt/2) version of vv */
                if (!bInitStep)
                {
                    trotter_update(ir,ekind,enerd,state,total_vir,mdatoms,&MassQ,trotter_seq[1]);            
                }
                
                update_coords(fplog,step,ir,mdatoms,state,
                              f,fr->bTwinRange && bNStList,fr->f_twin,fcd,
                              ekind,M,wcycle,upd,bInitStep,etrtVELOCITY,
                              cr,nrnb,constr,&top->idef);
                
                if (bIterations)
                {
                    gmx_iterate_init(&iterate,bIterations && !bInitStep);
                }
                /* for iterations, we save these vectors, as we will be self-consistently iterating
                   the calculations */
                /*#### UPDATE EXTENDED VARIABLES IN TROTTER FORMULATION */
                
                /* save the state */
                if (bIterations && iterate.bIterate) { 
                    copy_coupling_state(state,bufstate,ekind,ekind_save,&(ir->opts));
                }
            }
            
            bFirstIterate = TRUE;
            while (bFirstIterate || (bIterations && iterate.bIterate))
            {
                if (bIterations && iterate.bIterate) 
                {
                    copy_coupling_state(bufstate,state,ekind_save,ekind,&(ir->opts));
                    if (bFirstIterate && bTrotter) 
                    {
                        /* The first time through, we need a decent first estimate
                           of veta(t+dt) to compute the constraints.  Do
                           this by computing the box volume part of the
                           trotter integration at this time. Nothing else
                           should be changed by this routine here.  If
                           !(first time), we start with the previous value
                           of veta.  */
                        
                        veta_save = state->veta;
                        trotter_update(ir,ekind,enerd,state,total_vir,mdatoms,&MassQ,trotter_seq[0]);
                        vetanew = state->veta;
                        state->veta = veta_save;
                    } 
                } 
                
                bOK = TRUE;
                if ( !bRerunMD || rerun_fr.bV || bForceUpdate) {  /* Why is rerun_fr.bV here?  Unclear. */
                    dvdl = 0;
                    
                    update_constraints(fplog,step,&dvdl,ir,ekind,mdatoms,state,graph,f,
                                       &top->idef,shake_vir,NULL,
                                       cr,nrnb,wcycle,upd,constr,
                                       bInitStep,TRUE,bCalcEnerPres,vetanew);
                    
                    if (!bOK && !bFFscan)
                    {
                        gmx_fatal(FARGS,"Constraint error: Shake, Lincs or Settle could not solve the constrains");
                    }
                    
                } 
                else if (graph)
                { /* Need to unshift here if a do_force has been
                     called in the previous step */
                    unshift_self(graph,state->box,state->x);
                }
                
                
                if (bVV) {
                    /* if VV, compute the pressure and constraints */
                    /* if VV2, the pressure and constraints only if using pressure control.*/
                    bPres = (ir->eI==eiVV || IR_NPT_TROTTER(ir)); 
                    bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK && IR_NPT_TROTTER(ir)));
                    compute_globals(fplog,gstat,cr,ir,fr,ekind,state,state_global,mdatoms,nrnb,vcm,
                                    wcycle,enerd,force_vir,shake_vir,total_vir,pres,mu_tot,
                                    constr,NULL,FALSE,state->box,
                                    top_global,&pcurr,top_global->natoms,&bSumEkinhOld,
                                    cglo_flags 
                                    | CGLO_ENERGY 
                                    | (bTemp ? CGLO_TEMPERATURE:0) 
                                    | (bPres ? CGLO_PRESSURE : 0) 
                                    | (bPres ? CGLO_CONSTRAINT : 0)
                                    | (iterate.bIterate ? CGLO_ITERATE : 0)  
                                    | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
                                    | CGLO_SCALEEKIN 
                        );
                }
                /* explanation of above: 
                   a) We compute Ekin at the full time step
                   if 1) we are using the AveVel Ekin, and it's not the
                   initial step, or 2) if we are using AveEkin, but need the full
                   time step kinetic energy for the pressure.
                   b) If we are using EkinAveEkin for the kinetic energy for the temperture control, we still feed in 
                   EkinAveVel because it's needed for the pressure */
                
                /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
                if (bVV && !bInitStep) 
                {
                    trotter_update(ir,ekind,enerd,state,total_vir,mdatoms,&MassQ,trotter_seq[2]);
                }
                
                if (bIterations &&
                    done_iterating(cr,fplog,step,&iterate,bFirstIterate,
                                   state->veta,&vetanew)) 
                {
                    break;
                }
                bFirstIterate = FALSE;
            }

            if (bTrotter && !bInitStep) {
                copy_mat(shake_vir,state->svir_prev);
                copy_mat(force_vir,state->fvir_prev);
                if (IR_NVT_TROTTER(ir) && ir->eI==eiVV) {
                    /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
                    enerd->term[F_TEMP] = sum_ekin(&(ir->opts),ekind,NULL,(ir->eI==eiVV),FALSE,FALSE);
                    enerd->term[F_EKIN] = trace(ekind->ekin);
                }
            }
            /* if it's the initial step, we performed this first step just to get the constraint virial */
            if (bInitStep && ir->eI==eiVV) {
                copy_rvecn(cbuf,state->v,0,state->natoms);
            }
            
            if (fr->bSepDVDL && fplog && do_log) 
            {
                fprintf(fplog,sepdvdlformat,"Constraint",0.0,dvdl);
            }
            enerd->term[F_DHDL_CON] += dvdl;
            
            GMX_MPE_LOG(ev_timestep1);
            
        }
    
        /* MRS -- now done iterating -- compute the conserved quantity */
        if (bVV) {
            last_conserved = 0;
            if (IR_NVT_TROTTER(ir) || IR_NPT_TROTTER(ir))
            {
                last_conserved = 
                    NPT_energy(ir,state,&MassQ); 
                if ((ir->eDispCorr != edispcEnerPres) && (ir->eDispCorr != edispcAllEnerPres)) 
                {
                    last_conserved -= enerd->term[F_DISPCORR];
                }
            }
            if (ir->eI==eiVV) {
                last_ekin = enerd->term[F_EKIN]; /* does this get preserved through checkpointing? */
            }
        }
        
        /* ########  END FIRST UPDATE STEP  ############## */
        /* ########  If doing VV, we now have v(dt) ###### */
        
        /* ################## START TRAJECTORY OUTPUT ################# */
        
        /* Now we have the energies and forces corresponding to the 
         * coordinates at time t. We must output all of this before
         * the update.
         * for RerunMD t is read from input trajectory
         */
        GMX_MPE_LOG(ev_output_start);

        mdof_flags = 0;
        if (do_per_step(step,ir->nstxout)) { mdof_flags |= MDOF_X; }
        if (do_per_step(step,ir->nstvout)) { mdof_flags |= MDOF_V; }
        if (do_per_step(step,ir->nstfout)) { mdof_flags |= MDOF_F; }
        if (do_per_step(step,ir->nstxtcout)) { mdof_flags |= MDOF_XTC; }
        if (bCPT) { mdof_flags |= MDOF_CPT; };

#ifdef GMX_FAHCORE
        if (MASTER(cr))
            fcReportProgress( ir->nsteps, step );

        if (bLastStep)
        {
            /* Enforce writing positions and velocities at end of run */
            mdof_flags |= (MDOF_X | MDOF_V);
        }
        {
            int nthreads=(cr->nthreads==0 ? 1 : cr->nthreads);
            int nnodes=(cr->nnodes==0 ? 1 : cr->nnodes);
            
            /*Gromacs drives checkpointing; no ||  
              fcCheckPointPendingThreads(cr->nodeid,
              nthreads*nnodes);*/
            /* sync bCPT and fc record-keeping */
            if (bCPT && MASTER(cr))
                fcRequestCheckPoint();
        }
#endif
        
        if (mdof_flags != 0)
        {
            wallcycle_start(wcycle,ewcTRAJ);
            if (bCPT)
            {
                if (state->flags & (1<<estLD_RNG))
                {
                    get_stochd_state(upd,state);
                }
                if (MASTER(cr))
                {
                    if (bSumEkinhOld)
                    {
                        state_global->ekinstate.bUpToDate = FALSE;
                    }
                    else
                    {
                        update_ekinstate(&state_global->ekinstate,ekind);
                        state_global->ekinstate.bUpToDate = TRUE;
                    }
                    update_energyhistory(&state_global->enerhist,mdebin);
                }
            }
            write_traj(fplog,cr,outf,mdof_flags,top_global,
                       step,t,state,state_global,f,f_global,&n_xtc,&x_xtc);
            if (bCPT)
            {
                nchkpt++;
                bCPT = FALSE;
            }
            debug_gmx();
            if (bLastStep && step_rel == ir->nsteps &&
                (Flags & MD_CONFOUT) && MASTER(cr) &&
                !bRerunMD && !bFFscan)
            {
                /* x and v have been collected in write_traj,
                 * because a checkpoint file will always be written
                 * at the last step.
                 */
                fprintf(stderr,"\nWriting final coordinates.\n");
                if (ir->ePBC != epbcNONE && !ir->bPeriodicMols &&
                    DOMAINDECOMP(cr))
                {
                    /* Make molecules whole only for confout writing */
                    do_pbc_mtop(fplog,ir->ePBC,state->box,top_global,state_global->x);
                }
                write_sto_conf_mtop(ftp2fn(efSTO,nfile,fnm),
                                    *top_global->name,top_global,
                                    state_global->x,state_global->v,
                                    ir->ePBC,state->box);
                debug_gmx();
            }
            wallcycle_stop(wcycle,ewcTRAJ);
        }
        GMX_MPE_LOG(ev_output_finish);
        
        /* kludge -- virial is lost with restart for NPT control. Must restart */
        if (bStartingFromCpt && bVV) 
        {
            copy_mat(state->svir_prev,shake_vir);
            copy_mat(state->fvir_prev,force_vir);
        }
        /*  ################## END TRAJECTORY OUTPUT ################ */
        
        /* Determine the pressure:
         * always when we want exact averages in the energy file,
         * at ns steps when we have pressure coupling,
         * otherwise only at energy output steps (set below).
         */
    
        bNstEner = (bGStatEveryStep || do_per_step(step,ir->nstcalcenergy));
        bCalcEnerPres = bNstEner;
        
        /* Do we need global communication ? */
        bGStat = (bGStatEveryStep || bStopCM || bNS ||
                  (ir->nstlist == -1 && !bRerunMD && step >= nlh.step_nscheck));
        
        do_ene = (do_per_step(step,ir->nstenergy) || bLastStep);
        
        if (do_ene || do_log)
        {
            bCalcEnerPres = TRUE;
            bGStat        = TRUE;
        }

        /* Determine the wallclock run time up till now */
        run_time = gmx_gettime() - (double)runtime->real;

        /* Check whether everything is still allright */    
        if ((bGotStopNextStepSignal || bGotStopNextNSStepSignal) && 
            (handledSignal!=last_signal_number_recvd) &&
            MASTERTHREAD(cr))
        {
            if (bGotStopNextStepSignal || ir->nstlist == 0)
            {
                gs.sig[eglsTERM] = 1;
            }
            else
            {
                gs.sig[eglsTERM] = -1;
            }
            if (fplog)
            {
                fprintf(fplog,
                        "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
                        signal_name[last_signal_number_recvd], 
                        gs.sig[eglsTERM]==-1 ? "NS " : "");
                fflush(fplog);
            }
            fprintf(stderr,
                    "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
                    signal_name[last_signal_number_recvd], 
                    gs.sig[eglsTERM]==-1 ? "NS " : "");
            fflush(stderr);
            handledSignal=last_signal_number_recvd;
        }
        else if (MASTER(cr) && (bNS || ir->nstlist <= 0) &&
                 (max_hours > 0 && run_time > max_hours*60.0*60.0*0.99) &&
                 gs.sig[eglsTERM] == 0 && gs.set[eglsTERM] == 0)
        {
            /* Signal to terminate the run */
            gs.sig[eglsTERM] = (ir->nstlist == 0 ? 1 : -1);
            if (fplog)
            {
                fprintf(fplog,"\nStep %s: Run time exceeded %.3f hours, will terminate the run\n",gmx_step_str(step,sbuf),max_hours*0.99);
            }
            fprintf(stderr, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n",gmx_step_str(step,sbuf),max_hours*0.99);
        }
        
        if (bResetCountersHalfMaxH && MASTER(cr) &&
            run_time > max_hours*60.0*60.0*0.495)
        {
            gs.sig[eglsRESETCOUNTERS] = 1;
        }

        if (ir->nstlist == -1 && !bRerunMD)
        {
            /* When bGStatEveryStep=FALSE, global_stat is only called
             * when we check the atom displacements, not at NS steps.
             * This means that also the bonded interaction count check is not
             * performed immediately after NS. Therefore a few MD steps could
             * be performed with missing interactions.
             * But wrong energies are never written to file,
             * since energies are only written after global_stat
             * has been called.
             */
            if (step >= nlh.step_nscheck)
            {
                nlh.nabnsb = natoms_beyond_ns_buffer(ir,fr,&top->cgs,
                                                     nlh.scale_tot,state->x);
            }
            else
            {
                /* This is not necessarily true,
                 * but step_nscheck is determined quite conservatively.
                 */
                nlh.nabnsb = 0;
            }
        }

        /* In parallel we only have to check for checkpointing in steps
         * where we do global communication,
         *  otherwise the other nodes don't know.
         */
        if (MASTER(cr) && ((bGStat || !PAR(cr)) &&
                           cpt_period >= 0 &&
                           (cpt_period == 0 || 
                            run_time >= nchkpt*cpt_period*60.0)) &&
            gs.set[eglsCHKPT] == 0)
        {
            gs.sig[eglsCHKPT] = 1;
        }
  
        if (bIterations)
        {
            gmx_iterate_init(&iterate,bIterations);
        }
    
        /* for iterations, we save these vectors, as we will be redoing the calculations */
        if (bIterations && iterate.bIterate) 
        {
            copy_coupling_state(state,bufstate,ekind,ekind_save,&(ir->opts));
        }
        bFirstIterate = TRUE;
        while (bFirstIterate || (bIterations && iterate.bIterate))
        {
            /* We now restore these vectors to redo the calculation with improved extended variables */    
            if (bIterations) 
            { 
                copy_coupling_state(bufstate,state,ekind_save,ekind,&(ir->opts));
            }

            /* We make the decision to break or not -after- the calculation of Ekin and Pressure,
               so scroll down for that logic */
            
            /* #########   START SECOND UPDATE STEP ################# */
            GMX_MPE_LOG(ev_update_start);
            bOK = TRUE;
            if (!bRerunMD || rerun_fr.bV || bForceUpdate) 
            {
                wallcycle_start(wcycle,ewcUPDATE);
                dvdl = 0;
                /* Box is changed in update() when we do pressure coupling,
                 * but we should still use the old box for energy corrections and when
                 * writing it to the energy file, so it matches the trajectory files for
                 * the same timestep above. Make a copy in a separate array.
                 */
                copy_mat(state->box,lastbox);
                /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
                if (bTrotter) 
                {
                    if (bIterations && iterate.bIterate) 
                    {
                        if (bFirstIterate) 
                        {
                            scalevir = 1;
                        }
                        else 
                        {
                            /* we use a new value of scalevir to converge the iterations faster */
                            scalevir = tracevir/trace(shake_vir);
                        }
                        msmul(shake_vir,scalevir,shake_vir); 
                        m_add(force_vir,shake_vir,total_vir);
                        clear_mat(shake_vir);
                    }
                    trotter_update(ir,ekind,enerd,state,total_vir,mdatoms,&MassQ,trotter_seq[3]);
                }
                /* We can only do Berendsen coupling after we have summed
                 * the kinetic energy or virial. Since the happens
                 * in global_state after update, we should only do it at
                 * step % nstlist = 1 with bGStatEveryStep=FALSE.
                 */
                
                update_extended(fplog,step,ir,mdatoms,state,ekind,pcoupl_mu,M,wcycle,
                                upd,bInitStep,FALSE,&MassQ);

                /* velocity (for VV) */
                update_coords(fplog,step,ir,mdatoms,state,f,fr->bTwinRange && bNStList,fr->f_twin,fcd,
                              ekind,M,wcycle,upd,FALSE,etrtVELOCITY,cr,nrnb,constr,&top->idef);

                /* Above, initialize just copies ekinh into ekin,
                 * it doesn't copy position (for VV),
                 * and entire integrator for MD.
                 */
                
                if (ir->eI==eiVVAK) 
                {
                    copy_rvecn(state->x,cbuf,0,state->natoms);
                }
                
                update_coords(fplog,step,ir,mdatoms,state,f,fr->bTwinRange && bNStList,fr->f_twin,fcd,
                              ekind,M,wcycle,upd,bInitStep,etrtPOSITION,cr,nrnb,constr,&top->idef);
                wallcycle_stop(wcycle,ewcUPDATE);

                update_constraints(fplog,step,&dvdl,ir,ekind,mdatoms,state,graph,f,
                                   &top->idef,shake_vir,force_vir,
                                   cr,nrnb,wcycle,upd,constr,
                                   bInitStep,FALSE,bCalcEnerPres,state->veta);  
                
                if (ir->eI==eiVVAK) 
                {
                    /* erase F_EKIN and F_TEMP here? */
                    /* just compute the kinetic energy at the half step to perform a trotter step */
                    compute_globals(fplog,gstat,cr,ir,fr,ekind,state,state_global,mdatoms,nrnb,vcm,
                                    wcycle,enerd,force_vir,shake_vir,total_vir,pres,mu_tot,
                                    constr,NULL,FALSE,lastbox,
                                    top_global,&pcurr,top_global->natoms,&bSumEkinhOld,
                                    cglo_flags | CGLO_TEMPERATURE | CGLO_CONSTRAINT    
                        );
                    wallcycle_start(wcycle,ewcUPDATE);
                    trotter_update(ir,ekind,enerd,state,total_vir,mdatoms,&MassQ,trotter_seq[4]);            
                    /* now we know the scaling, we can compute the positions again again */
                    copy_rvecn(cbuf,state->x,0,state->natoms);

                    update_coords(fplog,step,ir,mdatoms,state,f,fr->bTwinRange && bNStList,fr->f_twin,fcd,
                                  ekind,M,wcycle,upd,bInitStep,etrtPOSITION,cr,nrnb,constr,&top->idef);
                    wallcycle_stop(wcycle,ewcUPDATE);

                    /* do we need an extra constraint here? just need to copy out of state->v to upd->xp? */
                    /* are the small terms in the shake_vir here due
                     * to numerical errors, or are they important
                     * physically? I'm thinking they are just errors, but not completely sure. 
                     * For now, will call without actually constraining, constr=NULL*/
                    update_constraints(fplog,step,&dvdl,ir,ekind,mdatoms,state,graph,f,
                                       &top->idef,tmp_vir,force_vir,
                                       cr,nrnb,wcycle,upd,NULL,
                                       bInitStep,FALSE,bCalcEnerPres,
                                       state->veta);  
                }
                if (!bOK && !bFFscan) 
                {
                    gmx_fatal(FARGS,"Constraint error: Shake, Lincs or Settle could not solve the constrains");
                }
                
                if (fr->bSepDVDL && fplog && do_log) 
                {
                    fprintf(fplog,sepdvdlformat,"Constraint",0.0,dvdl);
                }
                enerd->term[F_DHDL_CON] += dvdl;
            } 
            else if (graph) 
            {
                /* Need to unshift here */
                unshift_self(graph,state->box,state->x);
            }
            
            GMX_BARRIER(cr->mpi_comm_mygroup);
            GMX_MPE_LOG(ev_update_finish);

            if (vsite != NULL) 
            {
                wallcycle_start(wcycle,ewcVSITECONSTR);
                if (graph != NULL) 
                {
                    shift_self(graph,state->box,state->x);
                }
                construct_vsites(fplog,vsite,state->x,nrnb,ir->delta_t,state->v,
                                 top->idef.iparams,top->idef.il,
                                 fr->ePBC,fr->bMolPBC,graph,cr,state->box);
                
                if (graph != NULL) 
                {
                    unshift_self(graph,state->box,state->x);
                }
                wallcycle_stop(wcycle,ewcVSITECONSTR);
            }
            
            /* ############## IF NOT VV, Calculate globals HERE, also iterate constraints ############ */
            if (ir->nstlist == -1 && bFirstIterate)
            {
                gs.sig[eglsNABNSB] = nlh.nabnsb;
            }
            compute_globals(fplog,gstat,cr,ir,fr,ekind,state,state_global,mdatoms,nrnb,vcm,
                            wcycle,enerd,force_vir,shake_vir,total_vir,pres,mu_tot,
                            constr,
                            bFirstIterate ? &gs : NULL,(step % gs.nstms == 0),
                            lastbox,
                            top_global,&pcurr,top_global->natoms,&bSumEkinhOld,
                            cglo_flags 
                            | (!EI_VV(ir->eI) ? CGLO_ENERGY : 0) 
                            | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0) 
                            | (!EI_VV(ir->eI) || bRerunMD ? CGLO_PRESSURE : 0) 
                            | (bIterations && iterate.bIterate ? CGLO_ITERATE : 0) 
                            | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
                            | CGLO_CONSTRAINT 
                );
            if (ir->nstlist == -1 && bFirstIterate)
            {
                nlh.nabnsb = gs.set[eglsNABNSB];
                gs.set[eglsNABNSB] = 0;
            }
            /* bIterate is set to keep it from eliminating the old ekin kinetic energy terms */
            /* #############  END CALC EKIN AND PRESSURE ################# */
        
            /* Note: this is OK, but there are some numerical precision issues with using the convergence of
               the virial that should probably be addressed eventually. state->veta has better properies,
               but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
               generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */

            if (bIterations && 
                done_iterating(cr,fplog,step,&iterate,bFirstIterate,
                               trace(shake_vir),&tracevir)) 
            {
                break;
            }
            bFirstIterate = FALSE;
        }

        update_box(fplog,step,ir,mdatoms,state,graph,f,
                   ir->nstlist==-1 ? &nlh.scale_tot : NULL,pcoupl_mu,nrnb,wcycle,upd,bInitStep,FALSE);
        
        /* ################# END UPDATE STEP 2 ################# */
        /* #### We now have r(t+dt) and v(t+dt/2)  ############# */
    
        /* The coordinates (x) were unshifted in update */
        if (bFFscan && (shellfc==NULL || bConverged))
        {
            if (print_forcefield(fplog,enerd->term,mdatoms->homenr,
                                 f,NULL,xcopy,
                                 &(top_global->mols),mdatoms->massT,pres))
            {
                if (gmx_parallel_env_initialized())
                {
                    gmx_finalize();
                }
                fprintf(stderr,"\n");
                exit(0);
            }
        }
        if (!bGStat)
        {
            /* We will not sum ekinh_old,                                                            
             * so signal that we still have to do it.                                                
             */
            bSumEkinhOld = TRUE;
        }
        
        if (bTCR)
        {
            /* Only do GCT when the relaxation of shells (minimization) has converged,
             * otherwise we might be coupling to bogus energies. 
             * In parallel we must always do this, because the other sims might
             * update the FF.
             */

            /* Since this is called with the new coordinates state->x, I assume
             * we want the new box state->box too. / EL 20040121
             */
            do_coupling(fplog,oenv,nfile,fnm,tcr,t,step,enerd->term,fr,
                        ir,MASTER(cr),
                        mdatoms,&(top->idef),mu_aver,
                        top_global->mols.nr,cr,
                        state->box,total_vir,pres,
                        mu_tot,state->x,f,bConverged);
            debug_gmx();
        }

        /* #########  BEGIN PREPARING EDR OUTPUT  ###########  */
        
        sum_dhdl(enerd,state->lambda,ir);
        /* use the directly determined last velocity, not actually the averaged half steps */
        if (bTrotter && ir->eI==eiVV) 
        {
            enerd->term[F_EKIN] = last_ekin;
        }
        enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
        
        switch (ir->etc) 
        {
        case etcNO:
            break;
        case etcBERENDSEN:
            break;
        case etcNOSEHOOVER:
            if (IR_NVT_TROTTER(ir)) {
                enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + last_conserved;
            } else {
                enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + 
                    NPT_energy(ir,state,&MassQ);        
            }
            break;
        case etcVRESCALE:
            enerd->term[F_ECONSERVED] =
                enerd->term[F_ETOT] + vrescale_energy(&(ir->opts),
                                                      state->therm_integral);
            break;
        default:
            break;
        }
        
        /* Check for excessively large energies */
        if (bIonize) 
        {
#ifdef GMX_DOUBLE
            real etot_max = 1e200;
#else
            real etot_max = 1e30;
#endif
            if (fabs(enerd->term[F_ETOT]) > etot_max) 
            {
                fprintf(stderr,"Energy too large (%g), giving up\n",
                        enerd->term[F_ETOT]);
            }
        }
        /* #########  END PREPARING EDR OUTPUT  ###########  */
        
        /* Time for performance */
        if (((step % stepout) == 0) || bLastStep) 
        {
            runtime_upd_proc(runtime);
        }
        
        /* Output stuff */
        if (MASTER(cr))
        {
            bool do_dr,do_or;
            
            if (!(bStartingFromCpt && (EI_VV(ir->eI)))) 
            {
                if (bNstEner)
                {
                    upd_mdebin(mdebin,bDoDHDL ? outf->fp_dhdl : NULL,TRUE,
                               t,mdatoms->tmass,enerd,state,lastbox,
                               shake_vir,force_vir,total_vir,pres,
                               ekind,mu_tot,constr);
                }
                else
                {
                    upd_mdebin_step(mdebin);
                }
                
                do_dr  = do_per_step(step,ir->nstdisreout);
                do_or  = do_per_step(step,ir->nstorireout);
                
                print_ebin(outf->fp_ene,do_ene,do_dr,do_or,do_log?fplog:NULL,
                           step,t,
                           eprNORMAL,bCompact,mdebin,fcd,groups,&(ir->opts));
            }
            if (ir->ePull != epullNO)
            {
                pull_print_output(ir->pull,step,t);
            }
            
            if (do_per_step(step,ir->nstlog))
            {
                if(fflush(fplog) != 0)
                {
                    gmx_fatal(FARGS,"Cannot flush logfile - maybe you are out of quota?");
                }
            }
        }


        /* Remaining runtime */
        if (MULTIMASTER(cr) && do_verbose) 
        {
            if (shellfc) 
            {
                fprintf(stderr,"\n");
            }
            print_time(stderr,runtime,step,ir,cr);
        }

        /* Replica exchange */
        bExchanged = FALSE;
        if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
            do_per_step(step,repl_ex_nst)) 
        {
            bExchanged = replica_exchange(fplog,cr,repl_ex,
                                          state_global,enerd->term,
                                          state,step,t);
        }
        if (bExchanged && PAR(cr)) 
        {
            if (DOMAINDECOMP(cr)) 
            {
                dd_partition_system(fplog,step,cr,TRUE,1,
                                    state_global,top_global,ir,
                                    state,&f,mdatoms,top,fr,
                                    vsite,shellfc,constr,
                                    nrnb,wcycle,FALSE);
            } 
            else 
            {
                bcast_state(cr,state,FALSE);
            }
        }
        
        bFirstStep = FALSE;
        bInitStep = FALSE;
        bStartingFromCpt = FALSE;

        /* #######  SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
        /* Complicated conditional when bGStatEveryStep=FALSE.
         * We can not just use bGStat, since then the simulation results
         * would depend on nstenergy and nstlog or step_nscheck.
         */
        if (((state->flags & (1<<estPRES_PREV)) || 
             (state->flags & (1<<estSVIR_PREV)) ||
             (state->flags & (1<<estFVIR_PREV))) &&
            (bGStatEveryStep ||
             (ir->nstlist > 0 && step % ir->nstlist == 0) ||
             (ir->nstlist < 0 && nlh.nabnsb > 0) ||
             (ir->nstlist == 0 && bGStat))) 
        {
            /* Store the pressure in t_state for pressure coupling
             * at the next MD step.
             */
            if (state->flags & (1<<estPRES_PREV))
            {
                copy_mat(pres,state->pres_prev);
            }
        }
        
        /* #######  END SET VARIABLES FOR NEXT ITERATION ###### */
        
        if (bRerunMD) 
        {
            /* read next frame from input trajectory */
            bNotLastFrame = read_next_frame(oenv,status,&rerun_fr);
        }
        
        if (!bRerunMD || !rerun_fr.bStep)
        {
            /* increase the MD step number */
            step++;
            step_rel++;
        }
        
        cycles = wallcycle_stop(wcycle,ewcSTEP);
        if (DOMAINDECOMP(cr) && wcycle)
        {
            dd_cycles_add(cr->dd,cycles,ddCyclStep);
        }
        
        if (step_rel == wcycle_get_reset_counters(wcycle) ||
            gs.set[eglsRESETCOUNTERS] != 0)
        {
            /* Reset all the counters related to performance over the run */
            reset_all_counters(fplog,cr,step,&step_rel,ir,wcycle,nrnb,runtime);
            wcycle_set_reset_counters(wcycle,-1);
            bResetCountersHalfMaxH = FALSE;
            gs.set[eglsRESETCOUNTERS] = 0;
        }
    }
    /* End of main MD loop */
    debug_gmx();
    
    /* Stop the time */
    runtime_end(runtime);
    
    if (bRerunMD)
    {
        close_trj(status);
    }
    
    if (!(cr->duty & DUTY_PME))
    {
        /* Tell the PME only node to finish */
        gmx_pme_finish(cr);
    }
    
    if (MASTER(cr))
    {
        if (ir->nstcalcenergy > 0 && !bRerunMD) 
        {
            print_ebin(outf->fp_ene,FALSE,FALSE,FALSE,fplog,step,t,
                       eprAVER,FALSE,mdebin,fcd,groups,&(ir->opts));
        }
    }

    done_mdoutf(outf);

    debug_gmx();

    if (ir->nstlist == -1 && nlh.nns > 0 && fplog)
    {
        fprintf(fplog,"Average neighborlist lifetime: %.1f steps, std.dev.: %.1f steps\n",nlh.s1/nlh.nns,sqrt(nlh.s2/nlh.nns - sqr(nlh.s1/nlh.nns)));
        fprintf(fplog,"Average number of atoms that crossed the half buffer length: %.1f\n\n",nlh.ab/nlh.nns);
    }
    
    if (shellfc && fplog)
    {
        fprintf(fplog,"Fraction of iterations that converged:           %.2f %%\n",
                (nconverged*100.0)/step_rel);
        fprintf(fplog,"Average number of force evaluations per MD step: %.2f\n\n",
                tcount/step_rel);
    }
    
    if (repl_ex_nst > 0 && MASTER(cr))
    {
        print_replica_exchange_statistics(fplog,repl_ex);
    }
    
    runtime->nsteps_done = step_rel;
    
    return 0;
}