+++ /dev/null
-double do_md_openmm(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)
-{
- int fp_trn=0,fp_xtc=0;
- ener_file_t fp_ene=NULL;
- gmx_large_int_t step,step_rel;
- const char *fn_cpt;
- FILE *fp_dhdl=NULL,*fp_field=NULL;
- double run_time;
- double t,t0,lam0;
- bool bGStatEveryStep,bGStat,bNstEner,bCalcPres,bCalcEner;
- 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,bX,bV,bF,bXTC,bCPT=FALSE;
- 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;
- /* Booleans (disguised as a reals) to checkpoint and terminate mdrun */
- real chkpt=0,terminate=0,terminate_now=0;
-
- 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;
-
- 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 reset_counters=0,reset_counters_now=0;
- real last_conserved = 0;
- real last_ekin = 0;
- int iter_i;
- t_extmass MassQ;
- int **trotter_seq;
- char sbuf[22],sbuf2[22];
- bool bHandledSignal=FALSE;
- gmx_iterate_t iterate;
-
-//#ifdef GMX_OPENMM
- const char *ommOptions = NULL;
-//#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-vv2 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,&fp_trn,&fp_xtc,&fp_ene,&fn_cpt,
- &fp_dhdl,&fp_field,&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);
- }
-
- /* If not DD, copy gb data */
- if(ir->implicit_solvent && !DOMAINDECOMP(cr))
- {
- make_local_gb(cr,fr->born,ir->gb_algorithm);
- }
-
- update_mdatoms(mdatoms,state->lambda);
-//#ifdef GMX_OPENMM
-
- if(deviceOptions[0]=='\0')
- {
- /* empty options, which should default to OpenMM in this build */
- ommOptions=deviceOptions;
- }
- else
- {
- if(gmx_strncasecmp(deviceOptions,"OpenMM",6)!=0)
- {
- gmx_fatal(FARGS, "This Gromacs version currently only works with OpenMM. Use -device \"OpenMM:<options>\"");
- }
- else
- {
- ommOptions=strchr(deviceOptions,':');
- if(NULL!=ommOptions)
- {
- /* Increase the pointer to skip the colon */
- ommOptions++;
- }
- }
- }
- void* openmmData = openmm_init(fplog, ommOptions, cr, ir, top_global, top, mdatoms, fr, state);
-//#endif
-
- 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,NULL,NULL,NULL,NULL,
- NULL,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,NULL,NULL,NULL,NULL,NULL,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 (!EI_VV(ir->eI))
- {
- 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 */
-
- 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;
-
- 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);
-
-//#ifdef GMX_OPENMM
- openmm_take_one_step(openmmData);
- step_rel++;
- step++;
- bLastStep = (step_rel == ir->nsteps);
- do_log = do_per_step(step,ir->nstlog) || bFirstStep || bLastStep;
- do_verbose = bVerbose &&
- (step % stepout == 0 || bFirstStep || bLastStep);
-//#else
- /* 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);
-
- bX = do_per_step(step,ir->nstxout);
- bV = do_per_step(step,ir->nstvout);
- bF = do_per_step(step,ir->nstfout);
- bXTC = do_per_step(step,ir->nstxtcout);
-
-//#ifdef GMX_OPENMM
- do_ene = do_per_step(step,ir->nstenergy);
- if (bX || bV || bF || bXTC || do_ene) {
- wallcycle_start(wcycle,ewcTRAJ);
- openmm_copy_state(openmmData, state, &t, f, enerd, bX||bXTC, bV||bXTC, bF||bXTC, do_ene);
- upd_mdebin(mdebin,fp_dhdl,bGStatEveryStep && !bRerunMD,
- t,mdatoms->tmass,enerd,state,lastbox,
- shake_vir,force_vir,total_vir,pres,
- ekind,mu_tot,constr);
- print_ebin(fp_ene,do_ene,FALSE,FALSE,do_log?fplog:NULL,step,t,
- eprNORMAL,bCompact,mdebin,fcd,groups,&(ir->opts)); // XXX check this do_log stuff!
-//#else
-
- write_traj(fplog,cr,fp_trn,bX,bV,bF,fp_xtc,bXTC,ir->xtcprec,
- fn_cpt,bCPT,top_global,ir->eI,ir->simulation_part,
- step,t,state,state_global,f,f_global,&n_xtc,&x_xtc);
- debug_gmx();
- if (bLastStep && step_rel == ir->nsteps &&
- (Flags & MD_CONFOUT) && MASTER(cr) &&
- !bRerunMD && !bFFscan)
- {
- /* x and v have been collected in write_traj */
- 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);
-
- }
- /* End of main MD loop */
- debug_gmx();
-
-//#ifdef GMX_OPENMM
- openmm_cleanup(fplog, openmmData);
-//#endif
-
- /* 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 (bGStatEveryStep && !bRerunMD)
- {
- print_ebin(fp_ene,FALSE,FALSE,FALSE,fplog,step,t,
- eprAVER,FALSE,mdebin,fcd,groups,&(ir->opts));
- }
- close_enx(fp_ene);
- if (ir->nstxtcout)
- {
- close_xtc(fp_xtc);
- }
- close_trn(fp_trn);
- if (fp_dhdl)
- {
- gmx_fio_fclose(fp_dhdl);
- }
- if (fp_field)
- {
- gmx_fio_fclose(fp_field);
- }
- }
- 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;
-}
-
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff