added Verlet scheme and NxN non-bonded functionality

[gromacs.git] / src / mdlib / sim_util.c

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

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

#ifdef GMX_CRAY_XT3
#include<catamount/dclock.h>
#endif


#include <stdio.h>
#include <time.h>
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
#include <math.h>
#include "typedefs.h"
#include "string2.h"
#include "gmxfio.h"
#include "smalloc.h"
#include "names.h"
#include "confio.h"
#include "mvdata.h"
#include "txtdump.h"
#include "pbc.h"
#include "chargegroup.h"
#include "vec.h"
#include <time.h>
#include "nrnb.h"
#include "mshift.h"
#include "mdrun.h"
#include "sim_util.h"
#include "update.h"
#include "physics.h"
#include "main.h"
#include "mdatoms.h"
#include "force.h"
#include "bondf.h"
#include "pme.h"
#include "disre.h"
#include "orires.h"
#include "network.h"
#include "calcmu.h"
#include "constr.h"
#include "xvgr.h"
#include "trnio.h"
#include "xtcio.h"
#include "copyrite.h"
#include "pull_rotation.h"
#include "gmx_random.h"
#include "mpelogging.h"
#include "domdec.h"
#include "partdec.h"
#include "gmx_wallcycle.h"
#include "genborn.h"
#include "nbnxn_search.h"
#include "nbnxn_kernels/nbnxn_kernel_ref.h"
#include "nbnxn_kernels/nbnxn_kernel_x86_simd128.h"
#include "nbnxn_kernels/nbnxn_kernel_x86_simd256.h"
#include "nbnxn_kernels/nbnxn_kernel_gpu_ref.h"

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

#include "adress.h"
#include "qmmm.h"

#include "nbnxn_cuda_data_mgmt.h"
#include "nbnxn_cuda/nbnxn_cuda.h"

#if 0
typedef struct gmx_timeprint {

} t_gmx_timeprint;
#endif

/* Portable version of ctime_r implemented in src/gmxlib/string2.c, but we do not want it declared in public installed headers */
char *
gmx_ctime_r(const time_t *clock,char *buf, int n);


double
gmx_gettime()
{
#ifdef HAVE_GETTIMEOFDAY
        struct timeval t;
        double seconds;

        gettimeofday(&t,NULL);

        seconds = (double) t.tv_sec + 1e-6*(double)t.tv_usec;

        return seconds;
#else
        double  seconds;

        seconds = time(NULL);

        return seconds;
#endif
}


#define difftime(end,start) ((double)(end)-(double)(start))

void print_time(FILE *out,gmx_runtime_t *runtime,gmx_large_int_t step,
                t_inputrec *ir, t_commrec *cr)
{
    time_t finish;
    char   timebuf[STRLEN];
    double dt;
    char buf[48];

#ifndef GMX_THREAD_MPI
    if (!PAR(cr))
#endif
    {
        fprintf(out,"\r");
    }
    fprintf(out,"step %s",gmx_step_str(step,buf));
    if ((step >= ir->nstlist))
    {
        runtime->last = gmx_gettime();
        dt = difftime(runtime->last,runtime->real);
        runtime->time_per_step = dt/(step - ir->init_step + 1);

        dt = (ir->nsteps + ir->init_step - step)*runtime->time_per_step;

        if (ir->nsteps >= 0)
        {
            if (dt >= 300)
            {
                finish = (time_t) (runtime->last + dt);
                gmx_ctime_r(&finish,timebuf,STRLEN);
                sprintf(buf,"%s",timebuf);
                buf[strlen(buf)-1]='\0';
                fprintf(out,", will finish %s",buf);
            }
            else
                fprintf(out,", remaining runtime: %5d s          ",(int)dt);
        }
        else
        {
            fprintf(out," performance: %.1f ns/day    ",
                    ir->delta_t/1000*24*60*60/runtime->time_per_step);
        }
    }
#ifndef GMX_THREAD_MPI
    if (PAR(cr))
    {
        fprintf(out,"\n");
    }
#endif

    fflush(out);
}

#ifdef NO_CLOCK
#define clock() -1
#endif

static double set_proctime(gmx_runtime_t *runtime)
{
    double diff;
#ifdef GMX_CRAY_XT3
    double prev;

    prev = runtime->proc;
    runtime->proc = dclock();

    diff = runtime->proc - prev;
#else
    clock_t prev;

    prev = runtime->proc;
    runtime->proc = clock();

    diff = (double)(runtime->proc - prev)/(double)CLOCKS_PER_SEC;
#endif
    if (diff < 0)
    {
        /* The counter has probably looped, ignore this data */
        diff = 0;
    }

    return diff;
}

void runtime_start(gmx_runtime_t *runtime)
{
    runtime->real = gmx_gettime();
    runtime->proc          = 0;
    set_proctime(runtime);
    runtime->realtime      = 0;
    runtime->proctime      = 0;
    runtime->last          = 0;
    runtime->time_per_step = 0;
}

void runtime_end(gmx_runtime_t *runtime)
{
    double now;

    now = gmx_gettime();

    runtime->proctime += set_proctime(runtime);
    runtime->realtime  = now - runtime->real;
    runtime->real      = now;
}

void runtime_upd_proc(gmx_runtime_t *runtime)
{
    runtime->proctime += set_proctime(runtime);
}

void print_date_and_time(FILE *fplog,int nodeid,const char *title,
                         const gmx_runtime_t *runtime)
{
    int i;
    char timebuf[STRLEN];
    char time_string[STRLEN];
    time_t tmptime;

    if (fplog)
    {
        if (runtime != NULL)
        {
            tmptime = (time_t) runtime->real;
            gmx_ctime_r(&tmptime,timebuf,STRLEN);
        }
        else
        {
            tmptime = (time_t) gmx_gettime();
            gmx_ctime_r(&tmptime,timebuf,STRLEN);
        }
        for(i=0; timebuf[i]>=' '; i++)
        {
            time_string[i]=timebuf[i];
        }
        time_string[i]='\0';

        fprintf(fplog,"%s on node %d %s\n",title,nodeid,time_string);
    }
}

static void sum_forces(int start,int end,rvec f[],rvec flr[])
{
  int i;

  if (gmx_debug_at) {
    pr_rvecs(debug,0,"fsr",f+start,end-start);
    pr_rvecs(debug,0,"flr",flr+start,end-start);
  }
  for(i=start; (i<end); i++)
    rvec_inc(f[i],flr[i]);
}

/*
 * calc_f_el calculates forces due to an electric field.
 *
 * force is kJ mol^-1 nm^-1 = e * kJ mol^-1 nm^-1 / e
 *
 * Et[] contains the parameters for the time dependent
 * part of the field (not yet used).
 * Ex[] contains the parameters for
 * the spatial dependent part of the field. You can have cool periodic
 * fields in principle, but only a constant field is supported
 * now.
 * The function should return the energy due to the electric field
 * (if any) but for now returns 0.
 *
 * WARNING:
 * There can be problems with the virial.
 * Since the field is not self-consistent this is unavoidable.
 * For neutral molecules the virial is correct within this approximation.
 * For neutral systems with many charged molecules the error is small.
 * But for systems with a net charge or a few charged molecules
 * the error can be significant when the field is high.
 * Solution: implement a self-consitent electric field into PME.
 */
static void calc_f_el(FILE *fp,int  start,int homenr,
                      real charge[],rvec x[],rvec f[],
                      t_cosines Ex[],t_cosines Et[],double t)
{
    rvec Ext;
    real t0;
    int  i,m;

    for(m=0; (m<DIM); m++)
    {
        if (Et[m].n > 0)
        {
            if (Et[m].n == 3)
            {
                t0 = Et[m].a[1];
                Ext[m] = cos(Et[m].a[0]*(t-t0))*exp(-sqr(t-t0)/(2.0*sqr(Et[m].a[2])));
            }
            else
            {
                Ext[m] = cos(Et[m].a[0]*t);
            }
        }
        else
        {
            Ext[m] = 1.0;
        }
        if (Ex[m].n > 0)
        {
            /* Convert the field strength from V/nm to MD-units */
            Ext[m] *= Ex[m].a[0]*FIELDFAC;
            for(i=start; (i<start+homenr); i++)
                f[i][m] += charge[i]*Ext[m];
        }
        else
        {
            Ext[m] = 0;
        }
    }
    if (fp != NULL)
    {
        fprintf(fp,"%10g  %10g  %10g  %10g #FIELD\n",t,
                Ext[XX]/FIELDFAC,Ext[YY]/FIELDFAC,Ext[ZZ]/FIELDFAC);
    }
}

static void calc_virial(FILE *fplog,int start,int homenr,rvec x[],rvec f[],
                        tensor vir_part,t_graph *graph,matrix box,
                        t_nrnb *nrnb,const t_forcerec *fr,int ePBC)
{
  int i,j;
  tensor virtest;

  /* The short-range virial from surrounding boxes */
  clear_mat(vir_part);
  calc_vir(fplog,SHIFTS,fr->shift_vec,fr->fshift,vir_part,ePBC==epbcSCREW,box);
  inc_nrnb(nrnb,eNR_VIRIAL,SHIFTS);

  /* Calculate partial virial, for local atoms only, based on short range.
   * Total virial is computed in global_stat, called from do_md
   */
  f_calc_vir(fplog,start,start+homenr,x,f,vir_part,graph,box);
  inc_nrnb(nrnb,eNR_VIRIAL,homenr);

  /* Add position restraint contribution */
  for(i=0; i<DIM; i++) {
    vir_part[i][i] += fr->vir_diag_posres[i];
  }

  /* Add wall contribution */
  for(i=0; i<DIM; i++) {
    vir_part[i][ZZ] += fr->vir_wall_z[i];
  }

  if (debug)
    pr_rvecs(debug,0,"vir_part",vir_part,DIM);
}

static void posres_wrapper(FILE *fplog,
                           int flags,
                           gmx_bool bSepDVDL,
                           t_inputrec *ir,
                           t_nrnb *nrnb,
                           gmx_localtop_t *top,
                           matrix box,rvec x[],
                           rvec f[],
                           gmx_enerdata_t *enerd,
                           real *lambda,
                           t_forcerec *fr)
{
    t_pbc pbc;
    real  v,dvdl;
    int   i;

    /* Position restraints always require full pbc */
    set_pbc(&pbc,ir->ePBC,box);
    dvdl = 0;
    v = posres(top->idef.il[F_POSRES].nr,top->idef.il[F_POSRES].iatoms,
               top->idef.iparams_posres,
               (const rvec*)x,fr->f_novirsum,fr->vir_diag_posres,
               ir->ePBC==epbcNONE ? NULL : &pbc,
               lambda[efptRESTRAINT],&dvdl,
               fr->rc_scaling,fr->ePBC,fr->posres_com,fr->posres_comB);
    if (bSepDVDL)
    {
        fprintf(fplog,sepdvdlformat,
                interaction_function[F_POSRES].longname,v,dvdl);
    }
    enerd->term[F_POSRES] += v;
    /* If just the force constant changes, the FEP term is linear,
     * but if k changes, it is not.
     */
    enerd->dvdl_nonlin[efptRESTRAINT] += dvdl;
    inc_nrnb(nrnb,eNR_POSRES,top->idef.il[F_POSRES].nr/2);

    if ((ir->fepvals->n_lambda > 0) && (flags & GMX_FORCE_DHDL))
    {
        for(i=0; i<enerd->n_lambda; i++)
        {
            real dvdl_dum,lambda_dum;

            lambda_dum = (i==0 ? lambda[efptRESTRAINT] : ir->fepvals->all_lambda[efptRESTRAINT][i-1]);
            v = posres(top->idef.il[F_POSRES].nr,top->idef.il[F_POSRES].iatoms,
                       top->idef.iparams_posres,
                       (const rvec*)x,NULL,NULL,
                       ir->ePBC==epbcNONE ? NULL : &pbc,lambda_dum,&dvdl,
                       fr->rc_scaling,fr->ePBC,fr->posres_com,fr->posres_comB);
            enerd->enerpart_lambda[i] += v;
        }
    }
}

static void pull_potential_wrapper(FILE *fplog,
                                   gmx_bool bSepDVDL,
                                   t_commrec *cr,
                                   t_inputrec *ir,
                                   matrix box,rvec x[],
                                   rvec f[],
                                   tensor vir_force,
                                   t_mdatoms *mdatoms,
                                   gmx_enerdata_t *enerd,
                                   real *lambda,
                                   double t)
{
    t_pbc  pbc;
    real   dvdl;

    /* Calculate the center of mass forces, this requires communication,
     * which is why pull_potential is called close to other communication.
     * The virial contribution is calculated directly,
     * which is why we call pull_potential after calc_virial.
     */
    set_pbc(&pbc,ir->ePBC,box);
    dvdl = 0; 
    enerd->term[F_COM_PULL] +=
        pull_potential(ir->ePull,ir->pull,mdatoms,&pbc,
                       cr,t,lambda[efptRESTRAINT],x,f,vir_force,&dvdl);
    if (bSepDVDL)
    {
        fprintf(fplog,sepdvdlformat,"Com pull",enerd->term[F_COM_PULL],dvdl);
    }
    enerd->dvdl_lin[efptRESTRAINT] += dvdl;
}

static void pme_receive_force_ener(FILE *fplog,
                                   gmx_bool bSepDVDL,
                                   t_commrec *cr,
                                   gmx_wallcycle_t wcycle,
                                   gmx_enerdata_t *enerd,
                                   t_forcerec *fr)
{
    real   e,v,dvdl;    
    float  cycles_ppdpme,cycles_seppme;

    cycles_ppdpme = wallcycle_stop(wcycle,ewcPPDURINGPME);
    dd_cycles_add(cr->dd,cycles_ppdpme,ddCyclPPduringPME);

    /* In case of node-splitting, the PP nodes receive the long-range 
     * forces, virial and energy from the PME nodes here.
     */    
    wallcycle_start(wcycle,ewcPP_PMEWAITRECVF);
    dvdl = 0;
    gmx_pme_receive_f(cr,fr->f_novirsum,fr->vir_el_recip,&e,&dvdl,
                      &cycles_seppme);
    if (bSepDVDL)
    {
        fprintf(fplog,sepdvdlformat,"PME mesh",e,dvdl);
    }
    enerd->term[F_COUL_RECIP] += e;
    enerd->dvdl_lin[efptCOUL] += dvdl;
    if (wcycle)
    {
        dd_cycles_add(cr->dd,cycles_seppme,ddCyclPME);
    }
    wallcycle_stop(wcycle,ewcPP_PMEWAITRECVF);
}

static void print_large_forces(FILE *fp,t_mdatoms *md,t_commrec *cr,
                               gmx_large_int_t step,real pforce,rvec *x,rvec *f)
{
  int  i;
  real pf2,fn2;
  char buf[STEPSTRSIZE];

  pf2 = sqr(pforce);
  for(i=md->start; i<md->start+md->homenr; i++) {
    fn2 = norm2(f[i]);
    /* We also catch NAN, if the compiler does not optimize this away. */
    if (fn2 >= pf2 || fn2 != fn2) {
      fprintf(fp,"step %s  atom %6d  x %8.3f %8.3f %8.3f  force %12.5e\n",
              gmx_step_str(step,buf),
              ddglatnr(cr->dd,i),x[i][XX],x[i][YY],x[i][ZZ],sqrt(fn2));
    }
  }
}

static void post_process_forces(FILE *fplog,
                                t_commrec *cr,
                                gmx_large_int_t step,
                                t_nrnb *nrnb,gmx_wallcycle_t wcycle,
                                gmx_localtop_t *top,
                                matrix box,rvec x[],
                                rvec f[],
                                tensor vir_force,
                                t_mdatoms *mdatoms,
                                t_graph *graph,
                                t_forcerec *fr,gmx_vsite_t *vsite,
                                int flags)
{
    if (fr->bF_NoVirSum)
    {
        if (vsite)
        {
            /* Spread the mesh force on virtual sites to the other particles... 
             * This is parallellized. MPI communication is performed
             * if the constructing atoms aren't local.
             */
            wallcycle_start(wcycle,ewcVSITESPREAD);
            spread_vsite_f(fplog,vsite,x,fr->f_novirsum,NULL,
                           (flags & GMX_FORCE_VIRIAL),fr->vir_el_recip,
                           nrnb,
                           &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
            wallcycle_stop(wcycle,ewcVSITESPREAD);
        }
        if (flags & GMX_FORCE_VIRIAL)
        {
            /* Now add the forces, this is local */
            if (fr->bDomDec)
            {
                sum_forces(0,fr->f_novirsum_n,f,fr->f_novirsum);
            }
            else
            {
                sum_forces(mdatoms->start,mdatoms->start+mdatoms->homenr,
                           f,fr->f_novirsum);
            }
            if (EEL_FULL(fr->eeltype))
            {
                /* Add the mesh contribution to the virial */
                m_add(vir_force,fr->vir_el_recip,vir_force);
            }
            if (debug)
            {
                pr_rvecs(debug,0,"vir_force",vir_force,DIM);
            }
        }
    }
    
    if (fr->print_force >= 0)
    {
        print_large_forces(stderr,mdatoms,cr,step,fr->print_force,x,f);
    }
}

static void do_nb_verlet(t_forcerec *fr,
                         interaction_const_t *ic,
                         gmx_enerdata_t *enerd,
                         int flags, int ilocality,
                         int clearF,
                         t_nrnb *nrnb,
                         gmx_wallcycle_t wcycle)
{
    int     nnbl, kernel_type, sh_e;
    char    *env;
    nonbonded_verlet_group_t  *nbvg;

    if (!(flags & GMX_FORCE_NONBONDED))
    {
        /* skip non-bonded calculation */
        return;
    }

    nbvg = &fr->nbv->grp[ilocality];

    /* CUDA kernel launch overhead is already timed separately */
    if (fr->cutoff_scheme != ecutsVERLET)
    {
        gmx_incons("Invalid cut-off scheme passed!");
    }

    if (nbvg->kernel_type != nbk8x8x8_CUDA)
    {
        wallcycle_sub_start(wcycle, ewcsNONBONDED);
    }
    switch (nbvg->kernel_type)
    {
        case nbk4x4_PlainC:
            nbnxn_kernel_ref(&nbvg->nbl_lists,
                             nbvg->nbat, ic,
                             fr->shift_vec,
                             flags,
                             clearF,
                             fr->fshift[0],
                             enerd->grpp.ener[egCOULSR],
                             fr->bBHAM ?
                             enerd->grpp.ener[egBHAMSR] :
                             enerd->grpp.ener[egLJSR]);
            break;
        
        case nbk4xN_X86_SIMD128:
            nbnxn_kernel_x86_simd128(&nbvg->nbl_lists,
                                     nbvg->nbat, ic,
                                     fr->shift_vec,
                                     flags,
                                     clearF,
                                     fr->fshift[0],
                                     enerd->grpp.ener[egCOULSR],
                                     fr->bBHAM ?
                                     enerd->grpp.ener[egBHAMSR] :
                                     enerd->grpp.ener[egLJSR]);
            break;
        case nbk4xN_X86_SIMD256:
            nbnxn_kernel_x86_simd256(&nbvg->nbl_lists,
                                     nbvg->nbat, ic,
                                     fr->shift_vec,
                                     flags,
                                     clearF,
                                     fr->fshift[0],
                                     enerd->grpp.ener[egCOULSR],
                                     fr->bBHAM ?
                                     enerd->grpp.ener[egBHAMSR] :
                                     enerd->grpp.ener[egLJSR]);
            break;

        case nbk8x8x8_CUDA:
            nbnxn_cuda_launch_kernel(fr->nbv->cu_nbv, nbvg->nbat, flags, ilocality);
            break;

        case nbk8x8x8_PlainC:
            nbnxn_kernel_gpu_ref(nbvg->nbl_lists.nbl[0],
                                 nbvg->nbat, ic,
                                 fr->shift_vec,
                                 flags,
                                 clearF,
                                 nbvg->nbat->out[0].f,
                                 fr->fshift[0],
                                 enerd->grpp.ener[egCOULSR],
                                 fr->bBHAM ?
                                 enerd->grpp.ener[egBHAMSR] :
                                 enerd->grpp.ener[egLJSR]);
            break;

        default:
            gmx_incons("Invalid nonbonded kernel type passed!");

    }
    if (nbvg->kernel_type != nbk8x8x8_CUDA)
    {
        wallcycle_sub_stop(wcycle, ewcsNONBONDED);
    }

    /* In eNR_??? the nbnxn F+E kernels are always the F kernel + 1 */
    sh_e = ((flags & GMX_FORCE_ENERGY) ? 1 : 0);
    inc_nrnb(nrnb,
             ((EEL_RF(ic->eeltype) || ic->eeltype == eelCUT) ?
              eNR_NBNXN_LJ_RF : eNR_NBNXN_LJ_TAB) + sh_e,
             nbvg->nbl_lists.natpair_ljq);
    inc_nrnb(nrnb,eNR_NBNXN_LJ+sh_e,nbvg->nbl_lists.natpair_lj);
    inc_nrnb(nrnb,
             ((EEL_RF(ic->eeltype) || ic->eeltype == eelCUT) ?
              eNR_NBNXN_RF : eNR_NBNXN_TAB)+sh_e,
             nbvg->nbl_lists.natpair_q);
}

void do_force_cutsVERLET(FILE *fplog,t_commrec *cr,
              t_inputrec *inputrec,
              gmx_large_int_t step,t_nrnb *nrnb,gmx_wallcycle_t wcycle,
              gmx_localtop_t *top,
              gmx_mtop_t *mtop,
              gmx_groups_t *groups,
              matrix box,rvec x[],history_t *hist,
              rvec f[],
              tensor vir_force,
              t_mdatoms *mdatoms,
              gmx_enerdata_t *enerd,t_fcdata *fcd,
              real *lambda,t_graph *graph,
              t_forcerec *fr, interaction_const_t *ic,
              gmx_vsite_t *vsite,rvec mu_tot,
              double t,FILE *field,gmx_edsam_t ed,
              gmx_bool bBornRadii,
              int flags)
{
    int     cg0,cg1,i,j;
    int     start,homenr;
    int     nb_kernel_type;
    double  mu[2*DIM];
    gmx_bool   bSepDVDL,bStateChanged,bNS,bFillGrid,bCalcCGCM,bBS;
    gmx_bool   bDoLongRange,bDoForces,bSepLRF,bUseGPU,bUseOrEmulGPU;
    gmx_bool   bDiffKernels=FALSE;
    matrix  boxs;
    rvec    vzero,box_diag;
    real    e,v,dvdl;
    float  cycles_pme,cycles_force;
    nonbonded_verlet_t *nbv;

    cycles_force = 0;
    nbv = fr->nbv;
    nb_kernel_type = fr->nbv->grp[0].kernel_type;

    start  = mdatoms->start;
    homenr = mdatoms->homenr;

    bSepDVDL = (fr->bSepDVDL && do_per_step(step,inputrec->nstlog));

    clear_mat(vir_force);

    cg0 = 0;
    if (DOMAINDECOMP(cr))
    {
        cg1 = cr->dd->ncg_tot;
    }
    else
    {
        cg1 = top->cgs.nr;
    }
    if (fr->n_tpi > 0)
    {
        cg1--;
    }

    bStateChanged = (flags & GMX_FORCE_STATECHANGED);
    bNS           = (flags & GMX_FORCE_NS) && (fr->bAllvsAll==FALSE); 
    bFillGrid     = (bNS && bStateChanged);
    bCalcCGCM     = (bFillGrid && !DOMAINDECOMP(cr));
    bDoLongRange  = (fr->bTwinRange && bNS && (flags & GMX_FORCE_DOLR));
    bDoForces     = (flags & GMX_FORCE_FORCES);
    bSepLRF       = (bDoLongRange && bDoForces && (flags & GMX_FORCE_SEPLRF));
    bUseGPU       = fr->nbv->bUseGPU;
    bUseOrEmulGPU = bUseGPU || (nbv->grp[0].kernel_type == nbk8x8x8_PlainC);

    if (bStateChanged)
    {
        update_forcerec(fplog,fr,box);

        if (NEED_MUTOT(*inputrec))
        {
            /* Calculate total (local) dipole moment in a temporary common array.
             * This makes it possible to sum them over nodes faster.
             */
            calc_mu(start,homenr,
                    x,mdatoms->chargeA,mdatoms->chargeB,mdatoms->nChargePerturbed,
                    mu,mu+DIM);
        }
    }

    if (fr->ePBC != epbcNONE) { 
        /* Compute shift vectors every step,
         * because of pressure coupling or box deformation!
         */
        if ((flags & GMX_FORCE_DYNAMICBOX) && bStateChanged)
            calc_shifts(box,fr->shift_vec);

        if (bCalcCGCM) { 
            put_atoms_in_box_omp(fr->ePBC,box,homenr,x);
            inc_nrnb(nrnb,eNR_SHIFTX,homenr);
        } 
        else if (EI_ENERGY_MINIMIZATION(inputrec->eI) && graph) {
            unshift_self(graph,box,x);
        }
    } 

    nbnxn_atomdata_copy_shiftvec(flags & GMX_FORCE_DYNAMICBOX,
                                  fr->shift_vec,nbv->grp[0].nbat);

#ifdef GMX_MPI
    if (!(cr->duty & DUTY_PME)) {
        /* Send particle coordinates to the pme nodes.
         * Since this is only implemented for domain decomposition
         * and domain decomposition does not use the graph,
         * we do not need to worry about shifting.
         */    

        wallcycle_start(wcycle,ewcPP_PMESENDX);
        GMX_MPE_LOG(ev_send_coordinates_start);

        bBS = (inputrec->nwall == 2);
        if (bBS) {
            copy_mat(box,boxs);
            svmul(inputrec->wall_ewald_zfac,boxs[ZZ],boxs[ZZ]);
        }

        gmx_pme_send_x(cr,bBS ? boxs : box,x,
                       mdatoms->nChargePerturbed,lambda[efptCOUL],
                       (flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY)),step);

        GMX_MPE_LOG(ev_send_coordinates_finish);
        wallcycle_stop(wcycle,ewcPP_PMESENDX);
    }
#endif /* GMX_MPI */

    /* do gridding for pair search */
    if (bNS)
    {
        if (graph && bStateChanged)
        {
            /* Calculate intramolecular shift vectors to make molecules whole */
            mk_mshift(fplog,graph,fr->ePBC,box,x);
        }

        clear_rvec(vzero);
        box_diag[XX] = box[XX][XX];
        box_diag[YY] = box[YY][YY];
        box_diag[ZZ] = box[ZZ][ZZ];

        wallcycle_start(wcycle,ewcNS);
        if (!fr->bDomDec)
        {
            wallcycle_sub_start(wcycle,ewcsNBS_GRID_LOCAL);
            nbnxn_put_on_grid(nbv->nbs,fr->ePBC,box,
                              0,vzero,box_diag,
                              0,mdatoms->homenr,-1,fr->cginfo,x,
                              0,NULL,
                              nbv->grp[eintLocal].kernel_type,
                              nbv->grp[eintLocal].nbat);
            wallcycle_sub_stop(wcycle,ewcsNBS_GRID_LOCAL);
        }
        else
        {
            wallcycle_sub_start(wcycle,ewcsNBS_GRID_NONLOCAL);
            nbnxn_put_on_grid_nonlocal(nbv->nbs,domdec_zones(cr->dd),
                                       fr->cginfo,x,
                                       nbv->grp[eintNonlocal].kernel_type,
                                       nbv->grp[eintNonlocal].nbat);
            wallcycle_sub_stop(wcycle,ewcsNBS_GRID_NONLOCAL);
        }

        if (nbv->ngrp == 1 ||
            nbv->grp[eintNonlocal].nbat == nbv->grp[eintLocal].nbat)
        {
            nbnxn_atomdata_set(nbv->grp[eintLocal].nbat,eatAll,
                                nbv->nbs,mdatoms,fr->cginfo);
        }
        else
        {
            nbnxn_atomdata_set(nbv->grp[eintLocal].nbat,eatLocal,
                                nbv->nbs,mdatoms,fr->cginfo);
            nbnxn_atomdata_set(nbv->grp[eintNonlocal].nbat,eatAll,
                                nbv->nbs,mdatoms,fr->cginfo);
        }
        wallcycle_stop(wcycle, ewcNS);
    }

    /* initialize the GPU atom data and copy shift vector */
    if (bUseGPU)
    {
        if (bNS)
        {
            wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
            nbnxn_cuda_init_atomdata(nbv->cu_nbv, nbv->grp[eintLocal].nbat);
            wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
        }

        wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
        nbnxn_cuda_upload_shiftvec(nbv->cu_nbv, nbv->grp[eintLocal].nbat);
        wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
    }

    /* do local pair search */
    if (bNS)
    {
        wallcycle_start_nocount(wcycle,ewcNS);
        wallcycle_sub_start(wcycle,ewcsNBS_SEARCH_LOCAL);
        nbnxn_make_pairlist(nbv->nbs,nbv->grp[eintLocal].nbat,
                            &top->excls,
                            ic->rlist,
                            nbv->min_ci_balanced,
                            &nbv->grp[eintLocal].nbl_lists,
                            eintLocal,
                            nbv->grp[eintLocal].kernel_type,
                            nrnb);
        wallcycle_sub_stop(wcycle,ewcsNBS_SEARCH_LOCAL);

        if (bUseGPU)
        {
            /* initialize local pair-list on the GPU */
            nbnxn_cuda_init_pairlist(nbv->cu_nbv,
                                     nbv->grp[eintLocal].nbl_lists.nbl[0],
                                     eintLocal);
        }
        wallcycle_stop(wcycle, ewcNS);
    }
    else
    {
        wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
        wallcycle_sub_start(wcycle, ewcsNB_X_BUF_OPS);
        nbnxn_atomdata_copy_x_to_nbat_x(nbv->nbs,eatLocal,FALSE,x,
                                        nbv->grp[eintLocal].nbat);
        wallcycle_sub_stop(wcycle, ewcsNB_X_BUF_OPS);
        wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
    }

    if (bUseGPU)
    {
        wallcycle_start(wcycle,ewcLAUNCH_GPU_NB);
        /* launch local nonbonded F on GPU */
        do_nb_verlet(fr, ic, enerd, flags, eintLocal, enbvClearFNo,
                     nrnb, wcycle);
        wallcycle_stop(wcycle,ewcLAUNCH_GPU_NB);
    }

    /* Communicate coordinates and sum dipole if necessary + 
       do non-local pair search */
    if (DOMAINDECOMP(cr))
    {
        bDiffKernels = (nbv->grp[eintNonlocal].kernel_type !=
                        nbv->grp[eintLocal].kernel_type);

        if (bDiffKernels)
        {
            /* With GPU+CPU non-bonded calculations we need to copy
             * the local coordinates to the non-local nbat struct
             * (in CPU format) as the non-local kernel call also
             * calculates the local - non-local interactions.
             */
            wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
            wallcycle_sub_start(wcycle, ewcsNB_X_BUF_OPS);
            nbnxn_atomdata_copy_x_to_nbat_x(nbv->nbs,eatLocal,TRUE,x,
                                             nbv->grp[eintNonlocal].nbat);
            wallcycle_sub_stop(wcycle, ewcsNB_X_BUF_OPS);
            wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
        }

        if (bNS)
        {
            wallcycle_start_nocount(wcycle,ewcNS);
            wallcycle_sub_start(wcycle,ewcsNBS_SEARCH_NONLOCAL);

            if (bDiffKernels)
            {
                nbnxn_grid_add_simple(nbv->nbs,nbv->grp[eintNonlocal].nbat);
            }

            nbnxn_make_pairlist(nbv->nbs,nbv->grp[eintNonlocal].nbat,
                                &top->excls,
                                ic->rlist,
                                nbv->min_ci_balanced,
                                &nbv->grp[eintNonlocal].nbl_lists,
                                eintNonlocal,
                                nbv->grp[eintNonlocal].kernel_type,
                                nrnb);

            wallcycle_sub_stop(wcycle,ewcsNBS_SEARCH_NONLOCAL);

            if (nbv->grp[eintNonlocal].kernel_type == nbk8x8x8_CUDA)
            {
                /* initialize non-local pair-list on the GPU */
                nbnxn_cuda_init_pairlist(nbv->cu_nbv,
                                         nbv->grp[eintNonlocal].nbl_lists.nbl[0],
                                         eintNonlocal);
            }
            wallcycle_stop(wcycle,ewcNS);
        } 
        else
        {
            wallcycle_start(wcycle,ewcMOVEX);
            dd_move_x(cr->dd,box,x);

            /* When we don't need the total dipole we sum it in global_stat */
            if (bStateChanged && NEED_MUTOT(*inputrec))
            {
                gmx_sumd(2*DIM,mu,cr);
            }
            wallcycle_stop(wcycle,ewcMOVEX);

            wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
            wallcycle_sub_start(wcycle, ewcsNB_X_BUF_OPS);
            nbnxn_atomdata_copy_x_to_nbat_x(nbv->nbs,eatNonlocal,FALSE,x,
                                            nbv->grp[eintNonlocal].nbat);
            wallcycle_sub_stop(wcycle, ewcsNB_X_BUF_OPS);
            cycles_force += wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
        }

        if (bUseGPU && !bDiffKernels)
        { 
            wallcycle_start(wcycle,ewcLAUNCH_GPU_NB);
            /* launch non-local nonbonded F on GPU */
            do_nb_verlet(fr, ic, enerd, flags, eintNonlocal, enbvClearFNo,
                         nrnb, wcycle);
            cycles_force += wallcycle_stop(wcycle,ewcLAUNCH_GPU_NB);
        }
    }

    if (bUseGPU)
    {
        /* launch D2H copy-back F */
        wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
        if (DOMAINDECOMP(cr) && !bDiffKernels)
        {
            nbnxn_cuda_launch_cpyback(nbv->cu_nbv, nbv->grp[eintNonlocal].nbat,
                                      flags, eatNonlocal);
        }
        nbnxn_cuda_launch_cpyback(nbv->cu_nbv, nbv->grp[eintLocal].nbat,
                                  flags, eatLocal);
        cycles_force += wallcycle_stop(wcycle,ewcLAUNCH_GPU_NB);
    }

    if (bStateChanged && NEED_MUTOT(*inputrec))
    {
        if (PAR(cr))
        {
            gmx_sumd(2*DIM,mu,cr);
        } 

        for(i=0; i<2; i++)
        {
            for(j=0;j<DIM;j++)
            {
                fr->mu_tot[i][j] = mu[i*DIM + j];
            }
        }
    }
    if (fr->efep == efepNO)
    {
        copy_rvec(fr->mu_tot[0],mu_tot);
    }
    else
    {
        for(j=0; j<DIM; j++)
        {
            mu_tot[j] =
                (1.0 - lambda[efptCOUL])*fr->mu_tot[0][j] +
                lambda[efptCOUL]*fr->mu_tot[1][j];
        }
    }

    /* Reset energies */
    reset_enerdata(&(inputrec->opts),fr,bNS,enerd,MASTER(cr));
    clear_rvecs(SHIFTS,fr->fshift);

    if (DOMAINDECOMP(cr))
    {
        if (!(cr->duty & DUTY_PME))
        {
            wallcycle_start(wcycle,ewcPPDURINGPME);
            dd_force_flop_start(cr->dd,nrnb);
        }
    }
    
    /* Start the force cycle counter.
     * This counter is stopped in do_forcelow_level.
     * No parallel communication should occur while this counter is running,
     * since that will interfere with the dynamic load balancing.
     */
    wallcycle_start(wcycle,ewcFORCE);
    if (bDoForces)
    {
        /* Reset forces for which the virial is calculated separately:
         * PME/Ewald forces if necessary */
        if (fr->bF_NoVirSum) 
        {
            if (flags & GMX_FORCE_VIRIAL)
            {
                fr->f_novirsum = fr->f_novirsum_alloc;
                GMX_BARRIER(cr->mpi_comm_mygroup);
                if (fr->bDomDec)
                {
                    clear_rvecs(fr->f_novirsum_n,fr->f_novirsum);
                }
                else
                {
                    clear_rvecs(homenr,fr->f_novirsum+start);
                }
                GMX_BARRIER(cr->mpi_comm_mygroup);
            }
            else
            {
                /* We are not calculating the pressure so we do not need
                 * a separate array for forces that do not contribute
                 * to the pressure.
                 */
                fr->f_novirsum = f;
            }
        }

        if (bSepLRF)
        {
            /* Add the long range forces to the short range forces */
            for(i=0; i<fr->natoms_force_constr; i++)
            {
                copy_rvec(fr->f_twin[i],f[i]);
            }
        }
        else if (!(fr->bTwinRange && bNS))
        {
            /* Clear the short-range forces */
            clear_rvecs(fr->natoms_force_constr,f);
        }

        clear_rvec(fr->vir_diag_posres);

        GMX_BARRIER(cr->mpi_comm_mygroup);
    }
    if (inputrec->ePull == epullCONSTRAINT)
    {
        clear_pull_forces(inputrec->pull);
    }

    /* update QMMMrec, if necessary */
    if(fr->bQMMM)
    {
        update_QMMMrec(cr,fr,x,mdatoms,box,top);
    }

    if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0)
    {
        posres_wrapper(fplog,flags,bSepDVDL,inputrec,nrnb,top,box,x,
                       f,enerd,lambda,fr);
    }

    /* Compute the bonded and non-bonded energies and optionally forces */    
    /* if we use the GPU turn off the nonbonded */
    do_force_lowlevel(fplog,step,fr,inputrec,&(top->idef),
                      cr,nrnb,wcycle,mdatoms,&(inputrec->opts),
                      x,hist,f,enerd,fcd,mtop,top,fr->born,
                      &(top->atomtypes),bBornRadii,box,
                      inputrec->fepvals,lambda,graph,&(top->excls),fr->mu_tot,
                      ((nb_kernel_type == nbk8x8x8_CUDA || nb_kernel_type == nbk8x8x8_PlainC) 
                        ? flags&~GMX_FORCE_NONBONDED : flags),
                      &cycles_pme);

    if (!bUseOrEmulGPU)
    {
        /* Maybe we should move this into do_force_lowlevel */
        do_nb_verlet(fr, ic, enerd, flags, eintLocal, enbvClearFYes,
                     nrnb, wcycle);
    }
        

    if (!bUseOrEmulGPU || bDiffKernels)
    {
        int aloc;

        if (DOMAINDECOMP(cr))
        {
            do_nb_verlet(fr, ic, enerd, flags, eintNonlocal,
                         bDiffKernels ? enbvClearFYes : enbvClearFNo,
                         nrnb, wcycle);
        }

        if (!bUseOrEmulGPU)
        {
            aloc = eintLocal;
        }
        else
        {
            aloc = eintNonlocal;
        }

        /* Add all the non-bonded force to the normal force array.
         * This can be split into a local a non-local part when overlapping
         * communication with calculation with domain decomposition.
         */
        cycles_force += wallcycle_stop(wcycle,ewcFORCE);
        wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
        wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
        nbnxn_atomdata_add_nbat_f_to_f(nbv->nbs,eatAll,nbv->grp[aloc].nbat,f);
        wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
        cycles_force += wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
        wallcycle_start_nocount(wcycle,ewcFORCE);

        /* if there are multiple fshift output buffers reduce them */
        if ((flags & GMX_FORCE_VIRIAL) &&
            nbv->grp[aloc].nbl_lists.nnbl > 1)
        {
            nbnxn_atomdata_add_nbat_fshift_to_fshift(nbv->grp[aloc].nbat,
                                                      fr->fshift);
        }
    }
    
    cycles_force += wallcycle_stop(wcycle,ewcFORCE);
    GMX_BARRIER(cr->mpi_comm_mygroup);
    
    if (ed)
    {
        do_flood(fplog,cr,x,f,ed,box,step,bNS);
    }

    if (bUseOrEmulGPU && !bDiffKernels)
    {
        /* wait for non-local forces (or calculate in emulation mode) */
        if (DOMAINDECOMP(cr))
        {
            if (bUseGPU)
            {
                wallcycle_start(wcycle,ewcWAIT_GPU_NB_NL);
                nbnxn_cuda_wait_gpu(nbv->cu_nbv,
                                    nbv->grp[eintNonlocal].nbat,
                                    flags, eatNonlocal,
                                    enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
                                    fr->fshift);
                cycles_force += wallcycle_stop(wcycle,ewcWAIT_GPU_NB_NL);
            }
            else
            {
                wallcycle_start_nocount(wcycle,ewcFORCE);
                do_nb_verlet(fr, ic, enerd, flags, eintNonlocal, enbvClearFYes,
                             nrnb, wcycle);
                cycles_force += wallcycle_stop(wcycle,ewcFORCE);
            }            
            wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
            wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
            /* skip the reduction if there was no non-local work to do */
            if (nbv->grp[eintLocal].nbl_lists.nbl[0]->nsci > 0)
            {
                nbnxn_atomdata_add_nbat_f_to_f(nbv->nbs,eatNonlocal,
                                               nbv->grp[eintNonlocal].nbat,f);
            }
            wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
            cycles_force += wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
        }
    }

    if (bDoForces)
    {
        /* Communicate the forces */
        if (PAR(cr))
        {
            wallcycle_start(wcycle,ewcMOVEF);
            if (DOMAINDECOMP(cr))
            {
                dd_move_f(cr->dd,f,fr->fshift);
                /* Do we need to communicate the separate force array
                 * for terms that do not contribute to the single sum virial?
                 * Position restraints and electric fields do not introduce
                 * inter-cg forces, only full electrostatics methods do.
                 * When we do not calculate the virial, fr->f_novirsum = f,
                 * so we have already communicated these forces.
                 */
                if (EEL_FULL(fr->eeltype) && cr->dd->n_intercg_excl &&
                    (flags & GMX_FORCE_VIRIAL))
                {
                    dd_move_f(cr->dd,fr->f_novirsum,NULL);
                }
                if (bSepLRF)
                {
                    /* We should not update the shift forces here,
                     * since f_twin is already included in f.
                     */
                    dd_move_f(cr->dd,fr->f_twin,NULL);
                }
            }
            wallcycle_stop(wcycle,ewcMOVEF);
        }
    }
 
    if (bUseOrEmulGPU)
    {
        /* wait for local forces (or calculate in emulation mode) */
        if (bUseGPU)
        {
            wallcycle_start(wcycle,ewcWAIT_GPU_NB_L);
            nbnxn_cuda_wait_gpu(nbv->cu_nbv,
                                nbv->grp[eintLocal].nbat,
                                flags, eatLocal,
                                enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
                                fr->fshift);
            wallcycle_stop(wcycle,ewcWAIT_GPU_NB_L);

            /* now clear the GPU outputs while we finish the step on the CPU */
            nbnxn_cuda_clear_outputs(nbv->cu_nbv, flags);
        }
        else
        {            
            wallcycle_start_nocount(wcycle,ewcFORCE);
            do_nb_verlet(fr, ic, enerd, flags, eintLocal,
                         DOMAINDECOMP(cr) ? enbvClearFNo : enbvClearFYes,
                         nrnb, wcycle);
            wallcycle_stop(wcycle,ewcFORCE);
        }
        wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
        wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
        if (nbv->grp[eintLocal].nbl_lists.nbl[0]->nsci > 0)
        {
            /* skip the reduction if there was no non-local work to do */
            nbnxn_atomdata_add_nbat_f_to_f(nbv->nbs,eatLocal,
                                           nbv->grp[eintLocal].nbat,f);
        }
        wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
        wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
    }
    
    if (DOMAINDECOMP(cr))
    {
        dd_force_flop_stop(cr->dd,nrnb);
        if (wcycle)
        {
            dd_cycles_add(cr->dd,cycles_force-cycles_pme,ddCyclF);
        }
    }

    if (bDoForces)
    {
        if (IR_ELEC_FIELD(*inputrec))
        {
            /* Compute forces due to electric field */
            calc_f_el(MASTER(cr) ? field : NULL,
                      start,homenr,mdatoms->chargeA,x,fr->f_novirsum,
                      inputrec->ex,inputrec->et,t);
        }

        /* If we have NoVirSum forces, but we do not calculate the virial,
         * we sum fr->f_novirum=f later.
         */
        if (vsite && !(fr->bF_NoVirSum && !(flags & GMX_FORCE_VIRIAL)))
        {
            wallcycle_start(wcycle,ewcVSITESPREAD);
            spread_vsite_f(fplog,vsite,x,f,fr->fshift,FALSE,NULL,nrnb,
                           &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
            wallcycle_stop(wcycle,ewcVSITESPREAD);

            if (bSepLRF)
            {
                wallcycle_start(wcycle,ewcVSITESPREAD);
                spread_vsite_f(fplog,vsite,x,fr->f_twin,NULL,FALSE,NULL,
                               nrnb,
                               &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
                wallcycle_stop(wcycle,ewcVSITESPREAD);
            }
        }

        if (flags & GMX_FORCE_VIRIAL)
        {
            /* Calculation of the virial must be done after vsites! */
            calc_virial(fplog,mdatoms->start,mdatoms->homenr,x,f,
                        vir_force,graph,box,nrnb,fr,inputrec->ePBC);
        }
    }

    if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F)
    {
        pull_potential_wrapper(fplog,bSepDVDL,cr,inputrec,box,x,
                               f,vir_force,mdatoms,enerd,lambda,t);
    }

    if (PAR(cr) && !(cr->duty & DUTY_PME))
    {
        /* In case of node-splitting, the PP nodes receive the long-range 
         * forces, virial and energy from the PME nodes here.
         */    
        pme_receive_force_ener(fplog,bSepDVDL,cr,wcycle,enerd,fr);
    }

    if (bDoForces)
    {
        post_process_forces(fplog,cr,step,nrnb,wcycle,
                            top,box,x,f,vir_force,mdatoms,graph,fr,vsite,
                            flags);
    }
    
    /* Sum the potential energy terms from group contributions */
    sum_epot(&(inputrec->opts),enerd);
}

void do_force_cutsGROUP(FILE *fplog,t_commrec *cr,
              t_inputrec *inputrec,
              gmx_large_int_t step,t_nrnb *nrnb,gmx_wallcycle_t wcycle,
              gmx_localtop_t *top,
              gmx_mtop_t *mtop,
              gmx_groups_t *groups,
              matrix box,rvec x[],history_t *hist,
              rvec f[],
              tensor vir_force,
              t_mdatoms *mdatoms,
              gmx_enerdata_t *enerd,t_fcdata *fcd,
              real *lambda,t_graph *graph,
              t_forcerec *fr,gmx_vsite_t *vsite,rvec mu_tot,
              double t,FILE *field,gmx_edsam_t ed,
              gmx_bool bBornRadii,
              int flags)
{
    int    cg0,cg1,i,j;
    int    start,homenr;
    double mu[2*DIM];
    gmx_bool   bSepDVDL,bStateChanged,bNS,bFillGrid,bCalcCGCM,bBS;
    gmx_bool   bDoLongRange,bDoForces,bSepLRF;
    gmx_bool   bDoAdressWF;
    matrix boxs;
    rvec   vzero,box_diag;
    real   e,v,dvdlambda[efptNR];
    t_pbc  pbc;
    float  cycles_pme,cycles_force;

    start  = mdatoms->start;
    homenr = mdatoms->homenr;

    bSepDVDL = (fr->bSepDVDL && do_per_step(step,inputrec->nstlog));

    clear_mat(vir_force);

    if (PARTDECOMP(cr))
    {
        pd_cg_range(cr,&cg0,&cg1);
    }
    else
    {
        cg0 = 0;
        if (DOMAINDECOMP(cr))
        {
            cg1 = cr->dd->ncg_tot;
        }
        else
        {
            cg1 = top->cgs.nr;
        }
        if (fr->n_tpi > 0)
        {
            cg1--;
        }
    }

    bStateChanged = (flags & GMX_FORCE_STATECHANGED);
    bNS           = (flags & GMX_FORCE_NS) && (fr->bAllvsAll==FALSE);
    bFillGrid     = (bNS && bStateChanged);
    bCalcCGCM     = (bFillGrid && !DOMAINDECOMP(cr));
    bDoLongRange  = (fr->bTwinRange && bNS && (flags & GMX_FORCE_DOLR));
    bDoForces     = (flags & GMX_FORCE_FORCES);
    bSepLRF       = (bDoLongRange && bDoForces && (flags & GMX_FORCE_SEPLRF));
    /* should probably move this to the forcerec since it doesn't change */
    bDoAdressWF   = ((fr->adress_type!=eAdressOff));

    if (bStateChanged)
    {
        update_forcerec(fplog,fr,box);

        if (NEED_MUTOT(*inputrec))
        {
            /* Calculate total (local) dipole moment in a temporary common array.
             * This makes it possible to sum them over nodes faster.
             */
            calc_mu(start,homenr,
                    x,mdatoms->chargeA,mdatoms->chargeB,mdatoms->nChargePerturbed,
                    mu,mu+DIM);
        }
    }

    if (fr->ePBC != epbcNONE) { 
        /* Compute shift vectors every step,
         * because of pressure coupling or box deformation!
         */
        if ((flags & GMX_FORCE_DYNAMICBOX) && bStateChanged)
            calc_shifts(box,fr->shift_vec);

        if (bCalcCGCM) { 
            put_charge_groups_in_box(fplog,cg0,cg1,fr->ePBC,box,
                    &(top->cgs),x,fr->cg_cm);
            inc_nrnb(nrnb,eNR_CGCM,homenr);
            inc_nrnb(nrnb,eNR_RESETX,cg1-cg0);
        } 
        else if (EI_ENERGY_MINIMIZATION(inputrec->eI) && graph) {
            unshift_self(graph,box,x);
        }
    } 
    else if (bCalcCGCM) {
        calc_cgcm(fplog,cg0,cg1,&(top->cgs),x,fr->cg_cm);
        inc_nrnb(nrnb,eNR_CGCM,homenr);
    }

    if (bCalcCGCM) {
        if (PAR(cr)) {
            move_cgcm(fplog,cr,fr->cg_cm);
        }
        if (gmx_debug_at)
            pr_rvecs(debug,0,"cgcm",fr->cg_cm,top->cgs.nr);
    }

#ifdef GMX_MPI
    if (!(cr->duty & DUTY_PME)) {
        /* Send particle coordinates to the pme nodes.
         * Since this is only implemented for domain decomposition
         * and domain decomposition does not use the graph,
         * we do not need to worry about shifting.
         */    

        wallcycle_start(wcycle,ewcPP_PMESENDX);
        GMX_MPE_LOG(ev_send_coordinates_start);

        bBS = (inputrec->nwall == 2);
        if (bBS) {
            copy_mat(box,boxs);
            svmul(inputrec->wall_ewald_zfac,boxs[ZZ],boxs[ZZ]);
        }

        gmx_pme_send_x(cr,bBS ? boxs : box,x,
                       mdatoms->nChargePerturbed,lambda[efptCOUL],
                       (flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY)),step);

        GMX_MPE_LOG(ev_send_coordinates_finish);
        wallcycle_stop(wcycle,ewcPP_PMESENDX);
    }
#endif /* GMX_MPI */

    /* Communicate coordinates and sum dipole if necessary */
    if (PAR(cr))
    {
        wallcycle_start(wcycle,ewcMOVEX);
        if (DOMAINDECOMP(cr))
        {
            dd_move_x(cr->dd,box,x);
        }
        else
        {
            move_x(fplog,cr,GMX_LEFT,GMX_RIGHT,x,nrnb);
        }
        wallcycle_stop(wcycle,ewcMOVEX);
    }

    /* update adress weight beforehand */
    if(bStateChanged && bDoAdressWF)
    {
        /* need pbc for adress weight calculation with pbc_dx */
        set_pbc(&pbc,inputrec->ePBC,box);
        if(fr->adress_site == eAdressSITEcog)
        {
            update_adress_weights_cog(top->idef.iparams,top->idef.il,x,fr,mdatoms,
                                      inputrec->ePBC==epbcNONE ? NULL : &pbc);
        }
        else if (fr->adress_site == eAdressSITEcom)
        {
            update_adress_weights_com(fplog,cg0,cg1,&(top->cgs),x,fr,mdatoms,
                                      inputrec->ePBC==epbcNONE ? NULL : &pbc);
        }
        else if (fr->adress_site == eAdressSITEatomatom){
            update_adress_weights_atom_per_atom(cg0,cg1,&(top->cgs),x,fr,mdatoms,
                                                inputrec->ePBC==epbcNONE ? NULL : &pbc);
        }
        else
        {
            update_adress_weights_atom(cg0,cg1,&(top->cgs),x,fr,mdatoms,
                                       inputrec->ePBC==epbcNONE ? NULL : &pbc);
        }
    }

    if (NEED_MUTOT(*inputrec))
    {

        if (bStateChanged)
        {
            if (PAR(cr))
            {
                gmx_sumd(2*DIM,mu,cr);
            }
            for(i=0; i<2; i++)
            {
                for(j=0;j<DIM;j++)
                {
                    fr->mu_tot[i][j] = mu[i*DIM + j];
                }
            }
        }
        if (fr->efep == efepNO)
        {
            copy_rvec(fr->mu_tot[0],mu_tot);
        }
        else
        {
            for(j=0; j<DIM; j++)
            {
                mu_tot[j] =
                    (1.0 - lambda[efptCOUL])*fr->mu_tot[0][j] + lambda[efptCOUL]*fr->mu_tot[1][j];
            }
        }
    }

    /* Reset energies */
    reset_enerdata(&(inputrec->opts),fr,bNS,enerd,MASTER(cr));
    clear_rvecs(SHIFTS,fr->fshift);

    if (bNS)
    {
        wallcycle_start(wcycle,ewcNS);

        if (graph && bStateChanged)
        {
            /* Calculate intramolecular shift vectors to make molecules whole */
            mk_mshift(fplog,graph,fr->ePBC,box,x);
        }

        /* Reset long range forces if necessary */
        if (fr->bTwinRange)
        {
            /* Reset the (long-range) forces if necessary */
            clear_rvecs(fr->natoms_force_constr,bSepLRF ? fr->f_twin : f);
        }

        /* Do the actual neighbour searching and if twin range electrostatics
         * also do the calculation of long range forces and energies.
         */
        for (i=0;i<efptNR;i++) {dvdlambda[i] = 0;}
        ns(fplog,fr,x,box,
           groups,&(inputrec->opts),top,mdatoms,
           cr,nrnb,lambda,dvdlambda,&enerd->grpp,bFillGrid,
           bDoLongRange,bDoForces,bSepLRF ? fr->f_twin : f);
        if (bSepDVDL)
        {
            fprintf(fplog,sepdvdlformat,"LR non-bonded",0.0,dvdlambda);
        }
        enerd->dvdl_lin[efptVDW] += dvdlambda[efptVDW];
        enerd->dvdl_lin[efptCOUL] += dvdlambda[efptCOUL];

        wallcycle_stop(wcycle,ewcNS);
    }

    if (inputrec->implicit_solvent && bNS)
    {
        make_gb_nblist(cr,inputrec->gb_algorithm,inputrec->rlist,
                       x,box,fr,&top->idef,graph,fr->born);
    }

    if (DOMAINDECOMP(cr))
    {
        if (!(cr->duty & DUTY_PME))
        {
            wallcycle_start(wcycle,ewcPPDURINGPME);
            dd_force_flop_start(cr->dd,nrnb);
        }
    }

    if (inputrec->bRot)
    {
        /* Enforced rotation has its own cycle counter that starts after the collective
         * coordinates have been communicated. It is added to ddCyclF to allow
         * for proper load-balancing */
        wallcycle_start(wcycle,ewcROT);
        do_rotation(cr,inputrec,box,x,t,step,wcycle,bNS);
        wallcycle_stop(wcycle,ewcROT);
    }

    /* Start the force cycle counter.
     * This counter is stopped in do_forcelow_level.
     * No parallel communication should occur while this counter is running,
     * since that will interfere with the dynamic load balancing.
     */
    wallcycle_start(wcycle,ewcFORCE);
    
    if (bDoForces)
    {
        /* Reset forces for which the virial is calculated separately:
         * PME/Ewald forces if necessary */
        if (fr->bF_NoVirSum)
        {
            if (flags & GMX_FORCE_VIRIAL)
            {
                fr->f_novirsum = fr->f_novirsum_alloc;
                GMX_BARRIER(cr->mpi_comm_mygroup);
                if (fr->bDomDec)
                {
                    clear_rvecs(fr->f_novirsum_n,fr->f_novirsum);
                }
                else
                {
                    clear_rvecs(homenr,fr->f_novirsum+start);
                }
                GMX_BARRIER(cr->mpi_comm_mygroup);
            }
            else
            {
                /* We are not calculating the pressure so we do not need
                 * a separate array for forces that do not contribute
                 * to the pressure.
                 */
                fr->f_novirsum = f;
            }
        }

        if (bSepLRF)
        {
            /* Add the long range forces to the short range forces */
            for(i=0; i<fr->natoms_force_constr; i++)
            {
                copy_rvec(fr->f_twin[i],f[i]);
            }
        }
        else if (!(fr->bTwinRange && bNS))
        {
            /* Clear the short-range forces */
            clear_rvecs(fr->natoms_force_constr,f);
        }

        clear_rvec(fr->vir_diag_posres);

        GMX_BARRIER(cr->mpi_comm_mygroup);
    }
    if (inputrec->ePull == epullCONSTRAINT)
    {
        clear_pull_forces(inputrec->pull);
    }

    /* update QMMMrec, if necessary */
    if(fr->bQMMM)
    {
        update_QMMMrec(cr,fr,x,mdatoms,box,top);
    }

    if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0)
    {
        posres_wrapper(fplog,flags,bSepDVDL,inputrec,nrnb,top,box,x,
                       f,enerd,lambda,fr);
    }

    /* Compute the bonded and non-bonded energies and optionally forces */
    do_force_lowlevel(fplog,step,fr,inputrec,&(top->idef),
                      cr,nrnb,wcycle,mdatoms,&(inputrec->opts),
                      x,hist,f,enerd,fcd,mtop,top,fr->born,
                      &(top->atomtypes),bBornRadii,box,
                      inputrec->fepvals,lambda,
                      graph,&(top->excls),fr->mu_tot,
                      flags,
                      &cycles_pme);

    cycles_force = wallcycle_stop(wcycle,ewcFORCE);
    GMX_BARRIER(cr->mpi_comm_mygroup);

    if (ed)
    {
        do_flood(fplog,cr,x,f,ed,box,step,bNS);
    }

    if (DOMAINDECOMP(cr))
    {
        dd_force_flop_stop(cr->dd,nrnb);
        if (wcycle)
        {
            dd_cycles_add(cr->dd,cycles_force-cycles_pme,ddCyclF);
        }
    }

    if (bDoForces)
    {
        if (IR_ELEC_FIELD(*inputrec))
        {
            /* Compute forces due to electric field */
            calc_f_el(MASTER(cr) ? field : NULL,
                      start,homenr,mdatoms->chargeA,x,fr->f_novirsum,
                      inputrec->ex,inputrec->et,t);
        }

        if (bDoAdressWF && fr->adress_icor == eAdressICThermoForce)
        {
            /* Compute thermodynamic force in hybrid AdResS region */
            adress_thermo_force(start,homenr,&(top->cgs),x,fr->f_novirsum,fr,mdatoms,
                                inputrec->ePBC==epbcNONE ? NULL : &pbc);
        }

        /* Communicate the forces */
        if (PAR(cr))
        {
            wallcycle_start(wcycle,ewcMOVEF);
            if (DOMAINDECOMP(cr))
            {
                dd_move_f(cr->dd,f,fr->fshift);
                /* Do we need to communicate the separate force array
                 * for terms that do not contribute to the single sum virial?
                 * Position restraints and electric fields do not introduce
                 * inter-cg forces, only full electrostatics methods do.
                 * When we do not calculate the virial, fr->f_novirsum = f,
                 * so we have already communicated these forces.
                 */
                if (EEL_FULL(fr->eeltype) && cr->dd->n_intercg_excl &&
                    (flags & GMX_FORCE_VIRIAL))
                {
                    dd_move_f(cr->dd,fr->f_novirsum,NULL);
                }
                if (bSepLRF)
                {
                    /* We should not update the shift forces here,
                     * since f_twin is already included in f.
                     */
                    dd_move_f(cr->dd,fr->f_twin,NULL);
                }
            }
            else
            {
                pd_move_f(cr,f,nrnb);
                if (bSepLRF)
                {
                    pd_move_f(cr,fr->f_twin,nrnb);
                }
            }
            wallcycle_stop(wcycle,ewcMOVEF);
        }

        /* If we have NoVirSum forces, but we do not calculate the virial,
         * we sum fr->f_novirum=f later.
         */
        if (vsite && !(fr->bF_NoVirSum && !(flags & GMX_FORCE_VIRIAL)))
        {
            wallcycle_start(wcycle,ewcVSITESPREAD);
            spread_vsite_f(fplog,vsite,x,f,fr->fshift,FALSE,NULL,nrnb,
                           &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
            wallcycle_stop(wcycle,ewcVSITESPREAD);

            if (bSepLRF)
            {
                wallcycle_start(wcycle,ewcVSITESPREAD);
                spread_vsite_f(fplog,vsite,x,fr->f_twin,NULL,FALSE,NULL,
                               nrnb,
                               &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
                wallcycle_stop(wcycle,ewcVSITESPREAD);
            }
        }

        if (flags & GMX_FORCE_VIRIAL)
        {
            /* Calculation of the virial must be done after vsites! */
            calc_virial(fplog,mdatoms->start,mdatoms->homenr,x,f,
                        vir_force,graph,box,nrnb,fr,inputrec->ePBC);
        }
    }

    if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F)
    {
        pull_potential_wrapper(fplog,bSepDVDL,cr,inputrec,box,x,
                               f,vir_force,mdatoms,enerd,lambda,t);
    }

    /* Add the forces from enforced rotation potentials (if any) */
    if (inputrec->bRot)
    {
        wallcycle_start(wcycle,ewcROTadd);
        enerd->term[F_COM_PULL] += add_rot_forces(inputrec->rot, f, cr,step,t);
        wallcycle_stop(wcycle,ewcROTadd);
    }

    if (PAR(cr) && !(cr->duty & DUTY_PME))
    {
        /* In case of node-splitting, the PP nodes receive the long-range 
         * forces, virial and energy from the PME nodes here.
         */
        pme_receive_force_ener(fplog,bSepDVDL,cr,wcycle,enerd,fr);
    }

    if (bDoForces)
    {
        post_process_forces(fplog,cr,step,nrnb,wcycle,
                            top,box,x,f,vir_force,mdatoms,graph,fr,vsite,
                            flags);
    }

    /* Sum the potential energy terms from group contributions */
    sum_epot(&(inputrec->opts),enerd);
}

void do_force(FILE *fplog,t_commrec *cr,
              t_inputrec *inputrec,
              gmx_large_int_t step,t_nrnb *nrnb,gmx_wallcycle_t wcycle,
              gmx_localtop_t *top,
              gmx_mtop_t *mtop,
              gmx_groups_t *groups,
              matrix box,rvec x[],history_t *hist,
              rvec f[],
              tensor vir_force,
              t_mdatoms *mdatoms,
              gmx_enerdata_t *enerd,t_fcdata *fcd,
              real *lambda,t_graph *graph,
              t_forcerec *fr,
              gmx_vsite_t *vsite,rvec mu_tot,
              double t,FILE *field,gmx_edsam_t ed,
              gmx_bool bBornRadii,
              int flags)
{
    /* modify force flag if not doing nonbonded */
    if (!fr->bNonbonded)
    {
        flags &= ~GMX_FORCE_NONBONDED;
    }

    switch (inputrec->cutoff_scheme)
    {
        case ecutsVERLET:
            do_force_cutsVERLET(fplog, cr, inputrec,
                                step, nrnb, wcycle,
                                top, mtop,
                                groups,
                                box, x, hist,
                                f, vir_force,
                                mdatoms,
                                enerd, fcd,
                                lambda, graph,
                                fr, fr->ic, 
                                vsite, mu_tot,
                                t, field, ed,
                                bBornRadii,
                                flags);
            break;
        case ecutsGROUP:
             do_force_cutsGROUP(fplog, cr, inputrec,
                                step, nrnb, wcycle,
                                top, mtop,
                                groups,
                                box, x, hist,
                                f, vir_force,
                                mdatoms,
                                enerd, fcd,
                                lambda, graph,
                                fr, vsite, mu_tot,
                                t, field, ed,
                                bBornRadii,
                                flags);
            break;
        default:
            gmx_incons("Invalid cut-off scheme passed!");
    }
}


void do_constrain_first(FILE *fplog,gmx_constr_t constr,
                        t_inputrec *ir,t_mdatoms *md,
                        t_state *state,rvec *f,
                        t_graph *graph,t_commrec *cr,t_nrnb *nrnb,
                        t_forcerec *fr, gmx_localtop_t *top, tensor shake_vir)
{
    int    i,m,start,end;
    gmx_large_int_t step;
    real   dt=ir->delta_t;
    real   dvdl_dum;
    rvec   *savex;

    snew(savex,state->natoms);

    start = md->start;
    end   = md->homenr + start;

    if (debug)
        fprintf(debug,"vcm: start=%d, homenr=%d, end=%d\n",
                start,md->homenr,end);
    /* Do a first constrain to reset particles... */
    step = ir->init_step;
    if (fplog)
    {
        char buf[STEPSTRSIZE];
        fprintf(fplog,"\nConstraining the starting coordinates (step %s)\n",
                gmx_step_str(step,buf));
    }
    dvdl_dum = 0;

    /* constrain the current position */
    constrain(NULL,TRUE,FALSE,constr,&(top->idef),
              ir,NULL,cr,step,0,md,
              state->x,state->x,NULL,
              fr->bMolPBC,state->box,
              state->lambda[efptBONDED],&dvdl_dum,
              NULL,NULL,nrnb,econqCoord,
              ir->epc==epcMTTK,state->veta,state->veta);
    if (EI_VV(ir->eI))
    {
        /* constrain the inital velocity, and save it */
        /* also may be useful if we need the ekin from the halfstep for velocity verlet */
        /* might not yet treat veta correctly */
        constrain(NULL,TRUE,FALSE,constr,&(top->idef),
                  ir,NULL,cr,step,0,md,
                  state->x,state->v,state->v,
                  fr->bMolPBC,state->box,
                  state->lambda[efptBONDED],&dvdl_dum,
                  NULL,NULL,nrnb,econqVeloc,
                  ir->epc==epcMTTK,state->veta,state->veta);
    }
    /* constrain the inital velocities at t-dt/2 */
    if (EI_STATE_VELOCITY(ir->eI) && ir->eI!=eiVV)
    {
        for(i=start; (i<end); i++)
        {
            for(m=0; (m<DIM); m++)
            {
                /* Reverse the velocity */
                state->v[i][m] = -state->v[i][m];
                /* Store the position at t-dt in buf */
                savex[i][m] = state->x[i][m] + dt*state->v[i][m];
            }
        }
    /* Shake the positions at t=-dt with the positions at t=0
     * as reference coordinates.
         */
        if (fplog)
        {
            char buf[STEPSTRSIZE];
            fprintf(fplog,"\nConstraining the coordinates at t0-dt (step %s)\n",
                    gmx_step_str(step,buf));
        }
        dvdl_dum = 0;
        constrain(NULL,TRUE,FALSE,constr,&(top->idef),
                  ir,NULL,cr,step,-1,md,
                  state->x,savex,NULL,
                  fr->bMolPBC,state->box,
                  state->lambda[efptBONDED],&dvdl_dum,
                  state->v,NULL,nrnb,econqCoord,
                  ir->epc==epcMTTK,state->veta,state->veta);
        
        for(i=start; i<end; i++) {
            for(m=0; m<DIM; m++) {
                /* Re-reverse the velocities */
                state->v[i][m] = -state->v[i][m];
            }
        }
    }
    sfree(savex);
}

void calc_enervirdiff(FILE *fplog,int eDispCorr,t_forcerec *fr)
{
  double eners[2],virs[2],enersum,virsum,y0,f,g,h;
  double r0,r1,r,rc3,rc9,ea,eb,ec,pa,pb,pc,pd;
  double invscale,invscale2,invscale3;
  int    ri0,ri1,ri,i,offstart,offset;
  real   scale,*vdwtab;

  fr->enershiftsix = 0;
  fr->enershifttwelve = 0;
  fr->enerdiffsix = 0;
  fr->enerdifftwelve = 0;
  fr->virdiffsix = 0;
  fr->virdifftwelve = 0;

  if (eDispCorr != edispcNO) {
    for(i=0; i<2; i++) {
      eners[i] = 0;
      virs[i]  = 0;
    }
    if ((fr->vdwtype == evdwSWITCH) || (fr->vdwtype == evdwSHIFT)) {
      if (fr->rvdw_switch == 0)
        gmx_fatal(FARGS,
                  "With dispersion correction rvdw-switch can not be zero "
                  "for vdw-type = %s",evdw_names[fr->vdwtype]);

      scale  = fr->nblists[0].tab.scale;
      vdwtab = fr->nblists[0].vdwtab;

      /* Round the cut-offs to exact table values for precision */
      ri0 = floor(fr->rvdw_switch*scale);
      ri1 = ceil(fr->rvdw*scale);
      r0  = ri0/scale;
      r1  = ri1/scale;
      rc3 = r0*r0*r0;
      rc9  = rc3*rc3*rc3;

      if (fr->vdwtype == evdwSHIFT) {
        /* Determine the constant energy shift below rvdw_switch */
        fr->enershiftsix    = (real)(-1.0/(rc3*rc3)) - vdwtab[8*ri0];
        fr->enershifttwelve = (real)( 1.0/(rc9*rc3)) - vdwtab[8*ri0 + 4];
      }
      /* Add the constant part from 0 to rvdw_switch.
       * This integration from 0 to rvdw_switch overcounts the number
       * of interactions by 1, as it also counts the self interaction.
       * We will correct for this later.
       */
      eners[0] += 4.0*M_PI*fr->enershiftsix*rc3/3.0;
      eners[1] += 4.0*M_PI*fr->enershifttwelve*rc3/3.0;

      invscale = 1.0/(scale);
      invscale2 = invscale*invscale;
      invscale3 = invscale*invscale2;

      /* following summation derived from cubic spline definition,
        Numerical Recipies in C, second edition, p. 113-116.  Exact
        for the cubic spline.  We first calculate the negative of
        the energy from rvdw to rvdw_switch, assuming that g(r)=1,
        and then add the more standard, abrupt cutoff correction to
        that result, yielding the long-range correction for a
        switched function.  We perform both the pressure and energy
        loops at the same time for simplicity, as the computational
        cost is low. */

      for (i=0;i<2;i++) {
        enersum = 0.0; virsum = 0.0;
        if (i==0)
          offstart = 0;
        else
          offstart = 4;
        for (ri=ri0; ri<ri1; ri++) {
          r = ri*invscale;
          ea = invscale3;
          eb = 2.0*invscale2*r;
          ec = invscale*r*r;

          pa = invscale3;
          pb = 3.0*invscale2*r;
          pc = 3.0*invscale*r*r;
          pd = r*r*r;

          /* this "8" is from the packing in the vdwtab array - perhaps
            should be #define'ed? */
          offset = 8*ri + offstart;
          y0 = vdwtab[offset];
          f = vdwtab[offset+1];
          g = vdwtab[offset+2];
          h = vdwtab[offset+3];

          enersum += y0*(ea/3 + eb/2 + ec) + f*(ea/4 + eb/3 + ec/2)+
            g*(ea/5 + eb/4 + ec/3) + h*(ea/6 + eb/5 + ec/4);
          virsum  +=  f*(pa/4 + pb/3 + pc/2 + pd) +
            2*g*(pa/5 + pb/4 + pc/3 + pd/2) + 3*h*(pa/6 + pb/5 + pc/4 + pd/3);

        }
        enersum *= 4.0*M_PI;
        virsum  *= 4.0*M_PI;
        eners[i] -= enersum;
        virs[i]  -= virsum;
      }

      /* now add the correction for rvdw_switch to infinity */
      eners[0] += -4.0*M_PI/(3.0*rc3);
      eners[1] +=  4.0*M_PI/(9.0*rc9);
      virs[0]  +=  8.0*M_PI/rc3;
      virs[1]  += -16.0*M_PI/(3.0*rc9);
    }
    else if ((fr->vdwtype == evdwCUT) || (fr->vdwtype == evdwUSER)) {
      if (fr->vdwtype == evdwUSER && fplog)
        fprintf(fplog,
                "WARNING: using dispersion correction with user tables\n");
      rc3  = fr->rvdw*fr->rvdw*fr->rvdw;
      rc9  = rc3*rc3*rc3;
      /* Contribution beyond the cut-off */
      eners[0] += -4.0*M_PI/(3.0*rc3);
      eners[1] +=  4.0*M_PI/(9.0*rc9);
      if (fr->cutoff_scheme == ecutsVERLET && fr->ic->sh_invrc6 != 0) {
          /* Contribution within the cut-off */
          eners[0] += -4.0*M_PI/(3.0*rc3);
          eners[1] +=  4.0*M_PI/(3.0*rc9);
      }
      /* Contribution beyond the cut-off */
      virs[0]  +=  8.0*M_PI/rc3;
      virs[1]  += -16.0*M_PI/(3.0*rc9);
    } else {
      gmx_fatal(FARGS,
                "Dispersion correction is not implemented for vdw-type = %s",
                evdw_names[fr->vdwtype]);
    }
    fr->enerdiffsix    = eners[0];
    fr->enerdifftwelve = eners[1];
    /* The 0.5 is due to the Gromacs definition of the virial */
    fr->virdiffsix     = 0.5*virs[0];
    fr->virdifftwelve  = 0.5*virs[1];
  }
}

void calc_dispcorr(FILE *fplog,t_inputrec *ir,t_forcerec *fr,
                   gmx_large_int_t step,int natoms,
                   matrix box,real lambda,tensor pres,tensor virial,
                   real *prescorr, real *enercorr, real *dvdlcorr)
{
    gmx_bool bCorrAll,bCorrPres;
    real dvdlambda,invvol,dens,ninter,avcsix,avctwelve,enerdiff,svir=0,spres=0;
    int  m;

    *prescorr = 0;
    *enercorr = 0;
    *dvdlcorr = 0;

    clear_mat(virial);
    clear_mat(pres);

    if (ir->eDispCorr != edispcNO) {
        bCorrAll  = (ir->eDispCorr == edispcAllEner ||
                     ir->eDispCorr == edispcAllEnerPres);
        bCorrPres = (ir->eDispCorr == edispcEnerPres ||
                     ir->eDispCorr == edispcAllEnerPres);

        invvol = 1/det(box);
        if (fr->n_tpi)
        {
            /* Only correct for the interactions with the inserted molecule */
            dens = (natoms - fr->n_tpi)*invvol;
            ninter = fr->n_tpi;
        }
        else
        {
            dens = natoms*invvol;
            ninter = 0.5*natoms;
        }

        if (ir->efep == efepNO)
        {
            avcsix    = fr->avcsix[0];
            avctwelve = fr->avctwelve[0];
        }
        else
        {
            avcsix    = (1 - lambda)*fr->avcsix[0]    + lambda*fr->avcsix[1];
            avctwelve = (1 - lambda)*fr->avctwelve[0] + lambda*fr->avctwelve[1];
        }

        enerdiff = ninter*(dens*fr->enerdiffsix - fr->enershiftsix);
        *enercorr += avcsix*enerdiff;
        dvdlambda = 0.0;
        if (ir->efep != efepNO)
        {
            dvdlambda += (fr->avcsix[1] - fr->avcsix[0])*enerdiff;
        }
        if (bCorrAll)
        {
            enerdiff = ninter*(dens*fr->enerdifftwelve - fr->enershifttwelve);
            *enercorr += avctwelve*enerdiff;
            if (fr->efep != efepNO)
            {
                dvdlambda += (fr->avctwelve[1] - fr->avctwelve[0])*enerdiff;
            }
        }

        if (bCorrPres)
        {
            svir = ninter*dens*avcsix*fr->virdiffsix/3.0;
            if (ir->eDispCorr == edispcAllEnerPres)
            {
                svir += ninter*dens*avctwelve*fr->virdifftwelve/3.0;
            }
            /* The factor 2 is because of the Gromacs virial definition */
            spres = -2.0*invvol*svir*PRESFAC;

            for(m=0; m<DIM; m++) {
                virial[m][m] += svir;
                pres[m][m] += spres;
            }
            *prescorr += spres;
        }

        /* Can't currently control when it prints, for now, just print when degugging */
        if (debug)
        {
            if (bCorrAll) {
                fprintf(debug,"Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
                        avcsix,avctwelve);
            }
            if (bCorrPres)
            {
                fprintf(debug,
                        "Long Range LJ corr.: Epot %10g, Pres: %10g, Vir: %10g\n",
                        *enercorr,spres,svir);
            }
            else
            {
                fprintf(debug,"Long Range LJ corr.: Epot %10g\n",*enercorr);
            }
        }

        if (fr->bSepDVDL && do_per_step(step,ir->nstlog))
        {
            fprintf(fplog,sepdvdlformat,"Dispersion correction",
                    *enercorr,dvdlambda);
        }
        if (fr->efep != efepNO)
        {
            *dvdlcorr += dvdlambda;
        }
    }
}

void do_pbc_first(FILE *fplog,matrix box,t_forcerec *fr,
                  t_graph *graph,rvec x[])
{
  if (fplog)
    fprintf(fplog,"Removing pbc first time\n");
  calc_shifts(box,fr->shift_vec);
  if (graph) {
    mk_mshift(fplog,graph,fr->ePBC,box,x);
    if (gmx_debug_at)
      p_graph(debug,"do_pbc_first 1",graph);
    shift_self(graph,box,x);
    /* By doing an extra mk_mshift the molecules that are broken
     * because they were e.g. imported from another software
     * will be made whole again. Such are the healing powers
     * of GROMACS.
     */
    mk_mshift(fplog,graph,fr->ePBC,box,x);
    if (gmx_debug_at)
      p_graph(debug,"do_pbc_first 2",graph);
  }
  if (fplog)
    fprintf(fplog,"Done rmpbc\n");
}

static void low_do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
                            gmx_mtop_t *mtop,rvec x[],
                            gmx_bool bFirst)
{
  t_graph *graph;
  int mb,as,mol;
  gmx_molblock_t *molb;

  if (bFirst && fplog)
    fprintf(fplog,"Removing pbc first time\n");

  snew(graph,1);
  as = 0;
  for(mb=0; mb<mtop->nmolblock; mb++) {
    molb = &mtop->molblock[mb];
    if (molb->natoms_mol == 1 ||
        (!bFirst && mtop->moltype[molb->type].cgs.nr == 1)) {
      /* Just one atom or charge group in the molecule, no PBC required */
      as += molb->nmol*molb->natoms_mol;
    } else {
      /* Pass NULL iso fplog to avoid graph prints for each molecule type */
      mk_graph_ilist(NULL,mtop->moltype[molb->type].ilist,
                     0,molb->natoms_mol,FALSE,FALSE,graph);

      for(mol=0; mol<molb->nmol; mol++) {
        mk_mshift(fplog,graph,ePBC,box,x+as);

        shift_self(graph,box,x+as);
        /* The molecule is whole now.
         * We don't need the second mk_mshift call as in do_pbc_first,
         * since we no longer need this graph.
         */

        as += molb->natoms_mol;
      }
      done_graph(graph);
    }
  }
  sfree(graph);
}

void do_pbc_first_mtop(FILE *fplog,int ePBC,matrix box,
                       gmx_mtop_t *mtop,rvec x[])
{
  low_do_pbc_mtop(fplog,ePBC,box,mtop,x,TRUE);
}

void do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
                 gmx_mtop_t *mtop,rvec x[])
{
  low_do_pbc_mtop(fplog,ePBC,box,mtop,x,FALSE);
}

void finish_run(FILE *fplog,t_commrec *cr,const char *confout,
                t_inputrec *inputrec,
                t_nrnb nrnb[],gmx_wallcycle_t wcycle,
                gmx_runtime_t *runtime,
                wallclock_gpu_t *gputimes,
                int omp_nth_pp,
                gmx_bool bWriteStat)
{
    int    i,j;
    t_nrnb *nrnb_tot=NULL;
    real   delta_t;
    double nbfs,mflop;

    wallcycle_sum(cr,wcycle);

    if (cr->nnodes > 1)
    {
        snew(nrnb_tot,1);
#ifdef GMX_MPI
        MPI_Allreduce(nrnb->n,nrnb_tot->n,eNRNB,MPI_DOUBLE,MPI_SUM,
                      cr->mpi_comm_mysim);
#endif
    }
    else
    {
        nrnb_tot = nrnb;
    }

#if defined(GMX_MPI) && !defined(GMX_THREAD_MPI)
    if (cr->nnodes > 1)
    {
        /* reduce nodetime over all MPI processes in the current simulation */
        double sum;
        MPI_Allreduce(&runtime->proctime,&sum,1,MPI_DOUBLE,MPI_SUM,
                      cr->mpi_comm_mysim);
        runtime->proctime = sum;
    }
#endif

    if (SIMMASTER(cr))
    {
        print_flop(fplog,nrnb_tot,&nbfs,&mflop);
    }
    if (cr->nnodes > 1)
    {
        sfree(nrnb_tot);
    }

    if ((cr->duty & DUTY_PP) && DOMAINDECOMP(cr))
    {
        print_dd_statistics(cr,inputrec,fplog);
    }

#ifdef GMX_MPI
    if (PARTDECOMP(cr))
    {
        if (MASTER(cr))
        {
            t_nrnb     *nrnb_all;
            int        s;
            MPI_Status stat;

            snew(nrnb_all,cr->nnodes);
            nrnb_all[0] = *nrnb;
            for(s=1; s<cr->nnodes; s++)
            {
                MPI_Recv(nrnb_all[s].n,eNRNB,MPI_DOUBLE,s,0,
                         cr->mpi_comm_mysim,&stat);
            }
            pr_load(fplog,cr,nrnb_all);
            sfree(nrnb_all);
        }
        else
        {
            MPI_Send(nrnb->n,eNRNB,MPI_DOUBLE,MASTERRANK(cr),0,
                     cr->mpi_comm_mysim);
        }
    }
#endif

    if (SIMMASTER(cr))
    {
        wallcycle_print(fplog,cr->nnodes,cr->npmenodes,runtime->realtime,
                        wcycle,gputimes);

        if (EI_DYNAMICS(inputrec->eI))
        {
            delta_t = inputrec->delta_t;
        }
        else
        {
            delta_t = 0;
        }

        if (fplog)
        {
            print_perf(fplog,runtime->proctime,runtime->realtime,
                       cr->nnodes-cr->npmenodes,
                       runtime->nsteps_done,delta_t,nbfs,mflop,
                       omp_nth_pp);
        }
        if (bWriteStat)
        {
            print_perf(stderr,runtime->proctime,runtime->realtime,
                       cr->nnodes-cr->npmenodes,
                       runtime->nsteps_done,delta_t,nbfs,mflop,
                       omp_nth_pp);
        }
    }
}

extern void initialize_lambdas(FILE *fplog,t_inputrec *ir,int *fep_state,real *lambda,double *lam0)
{
    /* this function works, but could probably use a logic rewrite to keep all the different
       types of efep straight. */

    int i;
    t_lambda *fep = ir->fepvals;

    if ((ir->efep==efepNO) && (ir->bSimTemp == FALSE)) {
        for (i=0;i<efptNR;i++)  {
            lambda[i] = 0.0;
            if (lam0)
            {
                lam0[i] = 0.0;
            }
        }
        return;
    } else {
        *fep_state = fep->init_fep_state; /* this might overwrite the checkpoint
                                             if checkpoint is set -- a kludge is in for now
                                             to prevent this.*/
        for (i=0;i<efptNR;i++)
        {
            /* overwrite lambda state with init_lambda for now for backwards compatibility */
            if (fep->init_lambda>=0) /* if it's -1, it was never initializd */
            {
                lambda[i] = fep->init_lambda;
                if (lam0) {
                    lam0[i] = lambda[i];
                }
            }
            else
            {
                lambda[i] = fep->all_lambda[i][*fep_state];
                if (lam0) {
                    lam0[i] = lambda[i];
                }
            }
        }
        if (ir->bSimTemp) {
            /* need to rescale control temperatures to match current state */
            for (i=0;i<ir->opts.ngtc;i++) {
                if (ir->opts.ref_t[i] > 0) {
                    ir->opts.ref_t[i] = ir->simtempvals->temperatures[*fep_state];
                }
            }
        }
    }

    /* Send to the log the information on the current lambdas */
    if (fplog != NULL)
    {
        fprintf(fplog,"Initial vector of lambda components:[ ");
        for (i=0;i<efptNR;i++)
        {
            fprintf(fplog,"%10.4f ",lambda[i]);
        }
        fprintf(fplog,"]\n");
    }
    return;
}


void init_md(FILE *fplog,
             t_commrec *cr,t_inputrec *ir,const output_env_t oenv,
             double *t,double *t0,
             real *lambda, int *fep_state, double *lam0,
             t_nrnb *nrnb,gmx_mtop_t *mtop,
             gmx_update_t *upd,
             int nfile,const t_filenm fnm[],
             gmx_mdoutf_t **outf,t_mdebin **mdebin,
             tensor force_vir,tensor shake_vir,rvec mu_tot,
             gmx_bool *bSimAnn,t_vcm **vcm, t_state *state, unsigned long Flags)
{
    int  i,j,n;
    real tmpt,mod;

    /* Initial values */
    *t = *t0       = ir->init_t;

    *bSimAnn=FALSE;
    for(i=0;i<ir->opts.ngtc;i++)
    {
        /* set bSimAnn if any group is being annealed */
        if(ir->opts.annealing[i]!=eannNO)
        {
            *bSimAnn = TRUE;
        }
    }
    if (*bSimAnn)
    {
        update_annealing_target_temp(&(ir->opts),ir->init_t);
    }

    /* Initialize lambda variables */
    initialize_lambdas(fplog,ir,fep_state,lambda,lam0);

    if (upd)
    {
        *upd = init_update(fplog,ir);
    }


    if (vcm != NULL)
    {
        *vcm = init_vcm(fplog,&mtop->groups,ir);
    }

    if (EI_DYNAMICS(ir->eI) && !(Flags & MD_APPENDFILES))
    {
        if (ir->etc == etcBERENDSEN)
        {
            please_cite(fplog,"Berendsen84a");
        }
        if (ir->etc == etcVRESCALE)
        {
            please_cite(fplog,"Bussi2007a");
        }
    }

    init_nrnb(nrnb);

    if (nfile != -1)
    {
        *outf = init_mdoutf(nfile,fnm,Flags,cr,ir,oenv);

        *mdebin = init_mdebin((Flags & MD_APPENDFILES) ? NULL : (*outf)->fp_ene,
                              mtop,ir, (*outf)->fp_dhdl);
    }

    if (ir->bAdress)
    {
      please_cite(fplog,"Fritsch12");
      please_cite(fplog,"Junghans10");
    }
    /* Initiate variables */
    clear_mat(force_vir);
    clear_mat(shake_vir);
    clear_rvec(mu_tot);

    debug_gmx();
}