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56 #include "md_support.h"
57 #include "md_logging.h"
73 #include "domdec_network.h"
79 #include "compute_io.h"
81 #include "checkpoint.h"
82 #include "mtop_util.h"
83 #include "sighandler.h"
86 #include "pme_loadbal.h"
89 #include "types/nlistheuristics.h"
90 #include "types/iteratedconstraints.h"
91 #include "nbnxn_cuda_data_mgmt.h"
101 #include "corewrap.h"
104 static void reset_all_counters(FILE *fplog,t_commrec *cr,
105 gmx_large_int_t step,
106 gmx_large_int_t *step_rel,t_inputrec *ir,
107 gmx_wallcycle_t wcycle,t_nrnb *nrnb,
108 gmx_runtime_t *runtime,
109 nbnxn_cuda_ptr_t cu_nbv)
111 char sbuf[STEPSTRSIZE];
113 /* Reset all the counters related to performance over the run */
114 md_print_warn(cr,fplog,"step %s: resetting all time and cycle counters\n",
115 gmx_step_str(step,sbuf));
119 nbnxn_cuda_reset_timings(cu_nbv);
122 wallcycle_stop(wcycle,ewcRUN);
123 wallcycle_reset_all(wcycle);
124 if (DOMAINDECOMP(cr))
126 reset_dd_statistics_counters(cr->dd);
129 ir->init_step += *step_rel;
130 ir->nsteps -= *step_rel;
132 wallcycle_start(wcycle,ewcRUN);
133 runtime_start(runtime);
134 print_date_and_time(fplog,cr->nodeid,"Restarted time",runtime);
137 double do_md(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
138 const output_env_t oenv, gmx_bool bVerbose,gmx_bool bCompact,
140 gmx_vsite_t *vsite,gmx_constr_t constr,
141 int stepout,t_inputrec *ir,
142 gmx_mtop_t *top_global,
144 t_state *state_global,
146 t_nrnb *nrnb,gmx_wallcycle_t wcycle,
147 gmx_edsam_t ed,t_forcerec *fr,
148 int repl_ex_nst,int repl_ex_nex,int repl_ex_seed,gmx_membed_t membed,
149 real cpt_period,real max_hours,
150 const char *deviceOptions,
152 gmx_runtime_t *runtime)
155 gmx_large_int_t step,step_rel;
157 double t,t0,lam0[efptNR];
158 gmx_bool bGStatEveryStep,bGStat,bCalcVir,bCalcEner;
159 gmx_bool bNS,bNStList,bSimAnn,bStopCM,bRerunMD,bNotLastFrame=FALSE,
160 bFirstStep,bStateFromCP,bStateFromTPX,bInitStep,bLastStep,
161 bBornRadii,bStartingFromCpt;
162 gmx_bool bDoDHDL=FALSE,bDoFEP=FALSE,bDoExpanded=FALSE;
163 gmx_bool do_ene,do_log,do_verbose,bRerunWarnNoV=TRUE,
164 bForceUpdate=FALSE,bCPT;
166 gmx_bool bMasterState;
167 int force_flags,cglo_flags;
168 tensor force_vir,shake_vir,total_vir,tmp_vir,pres;
173 t_state *bufstate=NULL;
174 matrix *scale_tot,pcoupl_mu,M,ebox;
177 gmx_repl_ex_t repl_ex=NULL;
180 t_mdebin *mdebin=NULL;
181 df_history_t df_history;
186 gmx_enerdata_t *enerd;
188 gmx_global_stat_t gstat;
189 gmx_update_t upd=NULL;
192 gmx_rng_t mcrng=NULL;
194 gmx_groups_t *groups;
195 gmx_ekindata_t *ekind, *ekind_save;
196 gmx_shellfc_t shellfc;
197 int count,nconverged=0;
200 gmx_bool bIonize=FALSE;
201 gmx_bool bTCR=FALSE,bConverged=TRUE,bOK,bSumEkinhOld,bExchanged;
203 gmx_bool bResetCountersHalfMaxH=FALSE;
204 gmx_bool bVV,bIterations,bFirstIterate,bTemp,bPres,bTrotter;
205 gmx_bool bUpdateDoLR;
208 atom_id *grpindex=NULL;
210 t_coupl_rec *tcr=NULL;
211 rvec *xcopy=NULL,*vcopy=NULL,*cbuf=NULL;
212 matrix boxcopy={{0}},lastbox;
214 real fom,oldfom,veta_save,pcurr,scalevir,tracevir;
222 real saved_conserved_quantity = 0;
227 char sbuf[STEPSTRSIZE],sbuf2[STEPSTRSIZE];
228 int handled_stop_condition=gmx_stop_cond_none; /* compare to get_stop_condition*/
229 gmx_iterate_t iterate;
230 gmx_large_int_t multisim_nsteps=-1; /* number of steps to do before first multisim
231 simulation stops. If equal to zero, don't
232 communicate any more between multisims.*/
233 /* PME load balancing data for GPU kernels */
234 pme_load_balancing_t pme_loadbal=NULL;
236 gmx_bool bPMETuneTry=FALSE,bPMETuneRunning=FALSE;
239 /* Temporary addition for FAHCORE checkpointing */
243 /* Check for special mdrun options */
244 bRerunMD = (Flags & MD_RERUN);
245 bIonize = (Flags & MD_IONIZE);
246 bFFscan = (Flags & MD_FFSCAN);
247 bAppend = (Flags & MD_APPENDFILES);
248 if (Flags & MD_RESETCOUNTERSHALFWAY)
252 /* Signal to reset the counters half the simulation steps. */
253 wcycle_set_reset_counters(wcycle,ir->nsteps/2);
255 /* Signal to reset the counters halfway the simulation time. */
256 bResetCountersHalfMaxH = (max_hours > 0);
259 /* md-vv uses averaged full step velocities for T-control
260 md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
261 md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
263 if (bVV) /* to store the initial velocities while computing virial */
265 snew(cbuf,top_global->natoms);
267 /* all the iteratative cases - only if there are constraints */
268 bIterations = ((IR_NPH_TROTTER(ir) || IR_NPT_TROTTER(ir)) && (constr) && (!bRerunMD));
269 bTrotter = (bVV && (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir) || IR_NVT_TROTTER(ir)));
273 /* Since we don't know if the frames read are related in any way,
274 * rebuild the neighborlist at every step.
277 ir->nstcalcenergy = 1;
281 check_ir_old_tpx_versions(cr,fplog,ir,top_global);
283 nstglobalcomm = check_nstglobalcomm(fplog,cr,nstglobalcomm,ir);
284 bGStatEveryStep = (nstglobalcomm == 1);
286 if (!bGStatEveryStep && ir->nstlist == -1 && fplog != NULL)
289 "To reduce the energy communication with nstlist = -1\n"
290 "the neighbor list validity should not be checked at every step,\n"
291 "this means that exact integration is not guaranteed.\n"
292 "The neighbor list validity is checked after:\n"
293 " <n.list life time> - 2*std.dev.(n.list life time) steps.\n"
294 "In most cases this will result in exact integration.\n"
295 "This reduces the energy communication by a factor of 2 to 3.\n"
296 "If you want less energy communication, set nstlist > 3.\n\n");
299 if (bRerunMD || bFFscan)
303 groups = &top_global->groups;
306 init_md(fplog,cr,ir,oenv,&t,&t0,state_global->lambda,
307 &(state_global->fep_state),lam0,
308 nrnb,top_global,&upd,
309 nfile,fnm,&outf,&mdebin,
310 force_vir,shake_vir,mu_tot,&bSimAnn,&vcm,state_global,Flags);
312 clear_mat(total_vir);
314 /* Energy terms and groups */
316 init_enerdata(top_global->groups.grps[egcENER].nr,ir->fepvals->n_lambda,
318 if (DOMAINDECOMP(cr))
324 snew(f,top_global->natoms);
327 /* lambda Monte carlo random number generator */
330 mcrng = gmx_rng_init(ir->expandedvals->lmc_seed);
332 /* copy the state into df_history */
333 copy_df_history(&df_history,&state_global->dfhist);
335 /* Kinetic energy data */
337 init_ekindata(fplog,top_global,&(ir->opts),ekind);
338 /* needed for iteration of constraints */
340 init_ekindata(fplog,top_global,&(ir->opts),ekind_save);
341 /* Copy the cos acceleration to the groups struct */
342 ekind->cosacc.cos_accel = ir->cos_accel;
344 gstat = global_stat_init(ir);
347 /* Check for polarizable models and flexible constraints */
348 shellfc = init_shell_flexcon(fplog,
349 top_global,n_flexible_constraints(constr),
350 (ir->bContinuation ||
351 (DOMAINDECOMP(cr) && !MASTER(cr))) ?
352 NULL : state_global->x);
356 #ifdef GMX_THREAD_MPI
357 tMPI_Thread_mutex_lock(&deform_init_box_mutex);
359 set_deform_reference_box(upd,
360 deform_init_init_step_tpx,
361 deform_init_box_tpx);
362 #ifdef GMX_THREAD_MPI
363 tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
368 double io = compute_io(ir,top_global->natoms,groups,mdebin->ebin->nener,1);
369 if ((io > 2000) && MASTER(cr))
371 "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
375 if (DOMAINDECOMP(cr)) {
376 top = dd_init_local_top(top_global);
379 dd_init_local_state(cr->dd,state_global,state);
381 if (DDMASTER(cr->dd) && ir->nstfout) {
382 snew(f_global,state_global->natoms);
386 /* Initialize the particle decomposition and split the topology */
387 top = split_system(fplog,top_global,ir,cr);
389 pd_cg_range(cr,&fr->cg0,&fr->hcg);
390 pd_at_range(cr,&a0,&a1);
392 top = gmx_mtop_generate_local_top(top_global,ir);
395 a1 = top_global->natoms;
398 forcerec_set_excl_load(fr,top,cr);
400 state = partdec_init_local_state(cr,state_global);
403 atoms2md(top_global,ir,0,NULL,a0,a1-a0,mdatoms);
406 set_vsite_top(vsite,top,mdatoms,cr);
409 if (ir->ePBC != epbcNONE && !fr->bMolPBC) {
410 graph = mk_graph(fplog,&(top->idef),0,top_global->natoms,FALSE,FALSE);
414 make_local_shells(cr,mdatoms,shellfc);
417 init_bonded_thread_force_reduction(fr,&top->idef);
419 if (ir->pull && PAR(cr)) {
420 dd_make_local_pull_groups(NULL,ir->pull,mdatoms);
424 if (DOMAINDECOMP(cr))
426 /* Distribute the charge groups over the nodes from the master node */
427 dd_partition_system(fplog,ir->init_step,cr,TRUE,1,
428 state_global,top_global,ir,
429 state,&f,mdatoms,top,fr,
430 vsite,shellfc,constr,
435 update_mdatoms(mdatoms,state->lambda[efptMASS]);
437 if (opt2bSet("-cpi",nfile,fnm))
439 bStateFromCP = gmx_fexist_master(opt2fn_master("-cpi",nfile,fnm,cr),cr);
443 bStateFromCP = FALSE;
450 /* Update mdebin with energy history if appending to output files */
451 if ( Flags & MD_APPENDFILES )
453 restore_energyhistory_from_state(mdebin,&state_global->enerhist);
457 /* We might have read an energy history from checkpoint,
458 * free the allocated memory and reset the counts.
460 done_energyhistory(&state_global->enerhist);
461 init_energyhistory(&state_global->enerhist);
464 /* Set the initial energy history in state by updating once */
465 update_energyhistory(&state_global->enerhist,mdebin);
468 if ((state->flags & (1<<estLD_RNG)) && (Flags & MD_READ_RNG))
470 /* Set the random state if we read a checkpoint file */
471 set_stochd_state(upd,state);
474 if (state->flags & (1<<estMC_RNG))
476 set_mc_state(mcrng,state);
479 /* Initialize constraints */
481 if (!DOMAINDECOMP(cr))
482 set_constraints(constr,top,ir,mdatoms,cr);
485 /* Check whether we have to GCT stuff */
486 bTCR = ftp2bSet(efGCT,nfile,fnm);
489 fprintf(stderr,"Will do General Coupling Theory!\n");
491 gnx = top_global->mols.nr;
493 for(i=0; (i<gnx); i++) {
500 /* We need to be sure replica exchange can only occur
501 * when the energies are current */
502 check_nst_param(fplog,cr,"nstcalcenergy",ir->nstcalcenergy,
503 "repl_ex_nst",&repl_ex_nst);
504 /* This check needs to happen before inter-simulation
505 * signals are initialized, too */
507 if (repl_ex_nst > 0 && MASTER(cr))
509 repl_ex = init_replica_exchange(fplog,cr->ms,state_global,ir,
510 repl_ex_nst,repl_ex_nex,repl_ex_seed);
513 /* PME tuning is only supported with GPUs or PME nodes and not with rerun */
514 if ((Flags & MD_TUNEPME) &&
515 EEL_PME(fr->eeltype) &&
516 ( (fr->cutoff_scheme == ecutsVERLET && fr->nbv->bUseGPU) || !(cr->duty & DUTY_PME)) &&
519 pme_loadbal_init(&pme_loadbal,ir,state->box,fr->ic,fr->pmedata);
521 if (cr->duty & DUTY_PME)
523 /* Start tuning right away, as we can't measure the load */
524 bPMETuneRunning = TRUE;
528 /* Separate PME nodes, we can measure the PP/PME load balance */
533 if (!ir->bContinuation && !bRerunMD)
535 if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
537 /* Set the velocities of frozen particles to zero */
538 for(i=mdatoms->start; i<mdatoms->start+mdatoms->homenr; i++)
542 if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
552 /* Constrain the initial coordinates and velocities */
553 do_constrain_first(fplog,constr,ir,mdatoms,state,f,
554 graph,cr,nrnb,fr,top,shake_vir);
558 /* Construct the virtual sites for the initial configuration */
559 construct_vsites(fplog,vsite,state->x,nrnb,ir->delta_t,NULL,
560 top->idef.iparams,top->idef.il,
561 fr->ePBC,fr->bMolPBC,graph,cr,state->box);
567 /* set free energy calculation frequency as the minimum of nstdhdl, nstexpanded, and nstrepl_ex_nst*/
568 nstfep = ir->fepvals->nstdhdl;
569 if (ir->bExpanded && (nstfep > ir->expandedvals->nstexpanded))
571 nstfep = ir->expandedvals->nstexpanded;
573 if (repl_ex_nst > 0 && repl_ex_nst > nstfep)
575 nstfep = repl_ex_nst;
578 /* I'm assuming we need global communication the first time! MRS */
579 cglo_flags = (CGLO_TEMPERATURE | CGLO_GSTAT
580 | ((ir->comm_mode != ecmNO) ? CGLO_STOPCM:0)
581 | (bVV ? CGLO_PRESSURE:0)
582 | (bVV ? CGLO_CONSTRAINT:0)
583 | (bRerunMD ? CGLO_RERUNMD:0)
584 | ((Flags & MD_READ_EKIN) ? CGLO_READEKIN:0));
586 bSumEkinhOld = FALSE;
587 compute_globals(fplog,gstat,cr,ir,fr,ekind,state,state_global,mdatoms,nrnb,vcm,
588 NULL,enerd,force_vir,shake_vir,total_vir,pres,mu_tot,
589 constr,NULL,FALSE,state->box,
590 top_global,&pcurr,top_global->natoms,&bSumEkinhOld,cglo_flags);
591 if (ir->eI == eiVVAK) {
592 /* a second call to get the half step temperature initialized as well */
593 /* we do the same call as above, but turn the pressure off -- internally to
594 compute_globals, this is recognized as a velocity verlet half-step
595 kinetic energy calculation. This minimized excess variables, but
596 perhaps loses some logic?*/
598 compute_globals(fplog,gstat,cr,ir,fr,ekind,state,state_global,mdatoms,nrnb,vcm,
599 NULL,enerd,force_vir,shake_vir,total_vir,pres,mu_tot,
600 constr,NULL,FALSE,state->box,
601 top_global,&pcurr,top_global->natoms,&bSumEkinhOld,
602 cglo_flags &~ (CGLO_STOPCM | CGLO_PRESSURE));
605 /* Calculate the initial half step temperature, and save the ekinh_old */
606 if (!(Flags & MD_STARTFROMCPT))
608 for(i=0; (i<ir->opts.ngtc); i++)
610 copy_mat(ekind->tcstat[i].ekinh,ekind->tcstat[i].ekinh_old);
615 enerd->term[F_TEMP] *= 2; /* result of averages being done over previous and current step,
616 and there is no previous step */
619 /* if using an iterative algorithm, we need to create a working directory for the state. */
622 bufstate = init_bufstate(state);
626 snew(xcopy,state->natoms);
627 snew(vcopy,state->natoms);
628 copy_rvecn(state->x,xcopy,0,state->natoms);
629 copy_rvecn(state->v,vcopy,0,state->natoms);
630 copy_mat(state->box,boxcopy);
633 /* need to make an initiation call to get the Trotter variables set, as well as other constants for non-trotter
634 temperature control */
635 trotter_seq = init_npt_vars(ir,state,&MassQ,bTrotter);
639 if (constr && !ir->bContinuation && ir->eConstrAlg == econtLINCS)
642 "RMS relative constraint deviation after constraining: %.2e\n",
643 constr_rmsd(constr,FALSE));
645 if (EI_STATE_VELOCITY(ir->eI))
647 fprintf(fplog,"Initial temperature: %g K\n",enerd->term[F_TEMP]);
651 fprintf(stderr,"starting md rerun '%s', reading coordinates from"
652 " input trajectory '%s'\n\n",
653 *(top_global->name),opt2fn("-rerun",nfile,fnm));
656 fprintf(stderr,"Calculated time to finish depends on nsteps from "
657 "run input file,\nwhich may not correspond to the time "
658 "needed to process input trajectory.\n\n");
664 fprintf(stderr,"starting mdrun '%s'\n",
665 *(top_global->name));
668 sprintf(tbuf,"%8.1f",(ir->init_step+ir->nsteps)*ir->delta_t);
672 sprintf(tbuf,"%s","infinite");
674 if (ir->init_step > 0)
676 fprintf(stderr,"%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
677 gmx_step_str(ir->init_step+ir->nsteps,sbuf),tbuf,
678 gmx_step_str(ir->init_step,sbuf2),
679 ir->init_step*ir->delta_t);
683 fprintf(stderr,"%s steps, %s ps.\n",
684 gmx_step_str(ir->nsteps,sbuf),tbuf);
690 /* Set and write start time */
691 runtime_start(runtime);
692 print_date_and_time(fplog,cr->nodeid,"Started mdrun",runtime);
693 wallcycle_start(wcycle,ewcRUN);
699 /* safest point to do file checkpointing is here. More general point would be immediately before integrator call */
701 chkpt_ret=fcCheckPointParallel( cr->nodeid,
703 if ( chkpt_ret == 0 )
704 gmx_fatal( 3,__FILE__,__LINE__, "Checkpoint error on step %d\n", 0 );
708 /***********************************************************
712 ************************************************************/
714 /* if rerunMD then read coordinates and velocities from input trajectory */
717 if (getenv("GMX_FORCE_UPDATE"))
725 bNotLastFrame = read_first_frame(oenv,&status,
726 opt2fn("-rerun",nfile,fnm),
727 &rerun_fr,TRX_NEED_X | TRX_READ_V);
728 if (rerun_fr.natoms != top_global->natoms)
731 "Number of atoms in trajectory (%d) does not match the "
732 "run input file (%d)\n",
733 rerun_fr.natoms,top_global->natoms);
735 if (ir->ePBC != epbcNONE)
739 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);
741 if (max_cutoff2(ir->ePBC,rerun_fr.box) < sqr(fr->rlistlong))
743 gmx_fatal(FARGS,"Rerun trajectory frame step %d time %f has too small box dimensions",rerun_fr.step,rerun_fr.time);
750 rerun_parallel_comm(cr,&rerun_fr,&bNotLastFrame);
753 if (ir->ePBC != epbcNONE)
755 /* Set the shift vectors.
756 * Necessary here when have a static box different from the tpr box.
758 calc_shifts(rerun_fr.box,fr->shift_vec);
762 /* loop over MD steps or if rerunMD to end of input trajectory */
764 /* Skip the first Nose-Hoover integration when we get the state from tpx */
765 bStateFromTPX = !bStateFromCP;
766 bInitStep = bFirstStep && (bStateFromTPX || bVV);
767 bStartingFromCpt = (Flags & MD_STARTFROMCPT) && bInitStep;
769 bSumEkinhOld = FALSE;
772 init_global_signals(&gs,cr,ir,repl_ex_nst);
774 step = ir->init_step;
777 if (ir->nstlist == -1)
779 init_nlistheuristics(&nlh,bGStatEveryStep,step);
782 if (MULTISIM(cr) && (repl_ex_nst <=0 ))
784 /* check how many steps are left in other sims */
785 multisim_nsteps=get_multisim_nsteps(cr, ir->nsteps);
789 /* and stop now if we should */
790 bLastStep = (bRerunMD || (ir->nsteps >= 0 && step_rel > ir->nsteps) ||
791 ((multisim_nsteps >= 0) && (step_rel >= multisim_nsteps )));
792 while (!bLastStep || (bRerunMD && bNotLastFrame)) {
794 wallcycle_start(wcycle,ewcSTEP);
797 if (rerun_fr.bStep) {
798 step = rerun_fr.step;
799 step_rel = step - ir->init_step;
801 if (rerun_fr.bTime) {
811 bLastStep = (step_rel == ir->nsteps);
812 t = t0 + step*ir->delta_t;
815 if (ir->efep != efepNO || ir->bSimTemp)
817 /* find and set the current lambdas. If rerunning, we either read in a state, or a lambda value,
818 requiring different logic. */
820 set_current_lambdas(step,ir->fepvals,bRerunMD,&rerun_fr,state_global,state,lam0);
821 bDoDHDL = do_per_step(step,ir->fepvals->nstdhdl);
822 bDoFEP = (do_per_step(step,nstfep) && (ir->efep != efepNO));
823 bDoExpanded = (do_per_step(step,ir->expandedvals->nstexpanded) && (ir->bExpanded) && (step > 0));
828 update_annealing_target_temp(&(ir->opts),t);
833 if (!(DOMAINDECOMP(cr) && !MASTER(cr)))
835 for(i=0; i<state_global->natoms; i++)
837 copy_rvec(rerun_fr.x[i],state_global->x[i]);
841 for(i=0; i<state_global->natoms; i++)
843 copy_rvec(rerun_fr.v[i],state_global->v[i]);
848 for(i=0; i<state_global->natoms; i++)
850 clear_rvec(state_global->v[i]);
854 fprintf(stderr,"\nWARNING: Some frames do not contain velocities.\n"
855 " Ekin, temperature and pressure are incorrect,\n"
856 " the virial will be incorrect when constraints are present.\n"
858 bRerunWarnNoV = FALSE;
862 copy_mat(rerun_fr.box,state_global->box);
863 copy_mat(state_global->box,state->box);
865 if (vsite && (Flags & MD_RERUN_VSITE))
867 if (DOMAINDECOMP(cr))
869 gmx_fatal(FARGS,"Vsite recalculation with -rerun is not implemented for domain decomposition, use particle decomposition");
873 /* Following is necessary because the graph may get out of sync
874 * with the coordinates if we only have every N'th coordinate set
876 mk_mshift(fplog,graph,fr->ePBC,state->box,state->x);
877 shift_self(graph,state->box,state->x);
879 construct_vsites(fplog,vsite,state->x,nrnb,ir->delta_t,state->v,
880 top->idef.iparams,top->idef.il,
881 fr->ePBC,fr->bMolPBC,graph,cr,state->box);
884 unshift_self(graph,state->box,state->x);
889 /* Stop Center of Mass motion */
890 bStopCM = (ir->comm_mode != ecmNO && do_per_step(step,ir->nstcomm));
892 /* Copy back starting coordinates in case we're doing a forcefield scan */
895 for(ii=0; (ii<state->natoms); ii++)
897 copy_rvec(xcopy[ii],state->x[ii]);
898 copy_rvec(vcopy[ii],state->v[ii]);
900 copy_mat(boxcopy,state->box);
905 /* for rerun MD always do Neighbour Searching */
906 bNS = (bFirstStep || ir->nstlist != 0);
911 /* Determine whether or not to do Neighbour Searching and LR */
912 bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
914 bNS = (bFirstStep || bExchanged || bNStList || bDoFEP ||
915 (ir->nstlist == -1 && nlh.nabnsb > 0));
917 if (bNS && ir->nstlist == -1)
919 set_nlistheuristics(&nlh,bFirstStep || bExchanged || bDoFEP, step);
923 /* check whether we should stop because another simulation has
927 if ( (multisim_nsteps >= 0) && (step_rel >= multisim_nsteps) &&
928 (multisim_nsteps != ir->nsteps) )
935 "Stopping simulation %d because another one has finished\n",
939 gs.sig[eglsCHKPT] = 1;
944 /* < 0 means stop at next step, > 0 means stop at next NS step */
945 if ( (gs.set[eglsSTOPCOND] < 0 ) ||
946 ( (gs.set[eglsSTOPCOND] > 0 ) && ( bNS || ir->nstlist==0)) )
951 /* Determine whether or not to update the Born radii if doing GB */
952 bBornRadii=bFirstStep;
953 if (ir->implicit_solvent && (step % ir->nstgbradii==0))
958 do_log = do_per_step(step,ir->nstlog) || bFirstStep || bLastStep;
959 do_verbose = bVerbose &&
960 (step % stepout == 0 || bFirstStep || bLastStep);
962 if (bNS && !(bFirstStep && ir->bContinuation && !bRerunMD))
970 bMasterState = FALSE;
971 /* Correct the new box if it is too skewed */
972 if (DYNAMIC_BOX(*ir))
974 if (correct_box(fplog,step,state->box,graph))
979 if (DOMAINDECOMP(cr) && bMasterState)
981 dd_collect_state(cr->dd,state,state_global);
985 if (DOMAINDECOMP(cr))
987 /* Repartition the domain decomposition */
988 wallcycle_start(wcycle,ewcDOMDEC);
989 dd_partition_system(fplog,step,cr,
990 bMasterState,nstglobalcomm,
991 state_global,top_global,ir,
992 state,&f,mdatoms,top,fr,
993 vsite,shellfc,constr,
995 do_verbose && !bPMETuneRunning);
996 wallcycle_stop(wcycle,ewcDOMDEC);
997 /* If using an iterative integrator, reallocate space to match the decomposition */
1001 if (MASTER(cr) && do_log && !bFFscan)
1003 print_ebin_header(fplog,step,t,state->lambda[efptFEP]); /* can we improve the information printed here? */
1006 if (ir->efep != efepNO)
1008 update_mdatoms(mdatoms,state->lambda[efptMASS]);
1011 if ((bRerunMD && rerun_fr.bV) || bExchanged)
1014 /* We need the kinetic energy at minus the half step for determining
1015 * the full step kinetic energy and possibly for T-coupling.*/
1016 /* This may not be quite working correctly yet . . . . */
1017 compute_globals(fplog,gstat,cr,ir,fr,ekind,state,state_global,mdatoms,nrnb,vcm,
1018 wcycle,enerd,NULL,NULL,NULL,NULL,mu_tot,
1019 constr,NULL,FALSE,state->box,
1020 top_global,&pcurr,top_global->natoms,&bSumEkinhOld,
1021 CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
1023 clear_mat(force_vir);
1025 /* Ionize the atoms if necessary */
1028 ionize(fplog,oenv,mdatoms,top_global,t,ir,state->x,state->v,
1029 mdatoms->start,mdatoms->start+mdatoms->homenr,state->box,cr);
1032 /* Update force field in ffscan program */
1035 if (update_forcefield(fplog,
1037 mdatoms->nr,state->x,state->box))
1045 /* We write a checkpoint at this MD step when:
1046 * either at an NS step when we signalled through gs,
1047 * or at the last step (but not when we do not want confout),
1048 * but never at the first step or with rerun.
1050 bCPT = (((gs.set[eglsCHKPT] && (bNS || ir->nstlist == 0)) ||
1051 (bLastStep && (Flags & MD_CONFOUT))) &&
1052 step > ir->init_step && !bRerunMD);
1055 gs.set[eglsCHKPT] = 0;
1058 /* Determine the energy and pressure:
1059 * at nstcalcenergy steps and at energy output steps (set below).
1061 if (EI_VV(ir->eI) && (!bInitStep))
1063 /* for vv, the first half actually corresponds to the last step */
1064 bCalcEner = do_per_step(step-1,ir->nstcalcenergy);
1068 bCalcEner = do_per_step(step,ir->nstcalcenergy);
1070 bCalcVir = bCalcEner ||
1071 (ir->epc != epcNO && do_per_step(step,ir->nstpcouple));
1073 /* Do we need global communication ? */
1074 bGStat = (bCalcVir || bCalcEner || bStopCM ||
1075 do_per_step(step,nstglobalcomm) ||
1076 (ir->nstlist == -1 && !bRerunMD && step >= nlh.step_nscheck));
1078 do_ene = (do_per_step(step,ir->nstenergy) || bLastStep);
1080 if (do_ene || do_log)
1087 /* these CGLO_ options remain the same throughout the iteration */
1088 cglo_flags = ((bRerunMD ? CGLO_RERUNMD : 0) |
1089 (bGStat ? CGLO_GSTAT : 0)
1092 force_flags = (GMX_FORCE_STATECHANGED |
1093 ((DYNAMIC_BOX(*ir) || bRerunMD) ? GMX_FORCE_DYNAMICBOX : 0) |
1094 GMX_FORCE_ALLFORCES |
1096 (bCalcVir ? GMX_FORCE_VIRIAL : 0) |
1097 (bCalcEner ? GMX_FORCE_ENERGY : 0) |
1098 (bDoFEP ? GMX_FORCE_DHDL : 0)
1103 if(do_per_step(step,ir->nstcalclr))
1105 force_flags |= GMX_FORCE_DO_LR;
1111 /* Now is the time to relax the shells */
1112 count=relax_shell_flexcon(fplog,cr,bVerbose,bFFscan ? step+1 : step,
1114 bStopCM,top,top_global,
1116 state,f,force_vir,mdatoms,
1117 nrnb,wcycle,graph,groups,
1118 shellfc,fr,bBornRadii,t,mu_tot,
1119 state->natoms,&bConverged,vsite,
1130 /* The coordinates (x) are shifted (to get whole molecules)
1132 * This is parallellized as well, and does communication too.
1133 * Check comments in sim_util.c
1135 do_force(fplog,cr,ir,step,nrnb,wcycle,top,top_global,groups,
1136 state->box,state->x,&state->hist,
1137 f,force_vir,mdatoms,enerd,fcd,
1138 state->lambda,graph,
1139 fr,vsite,mu_tot,t,outf->fp_field,ed,bBornRadii,
1140 (bNS ? GMX_FORCE_NS : 0) | force_flags);
1145 mu_aver = calc_mu_aver(cr,state->x,mdatoms->chargeA,
1146 mu_tot,&top_global->mols,mdatoms,gnx,grpindex);
1149 if (bTCR && bFirstStep)
1151 tcr=init_coupling(fplog,nfile,fnm,cr,fr,mdatoms,&(top->idef));
1152 fprintf(fplog,"Done init_coupling\n");
1156 if (bVV && !bStartingFromCpt && !bRerunMD)
1157 /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
1159 if (ir->eI==eiVV && bInitStep)
1161 /* if using velocity verlet with full time step Ekin,
1162 * take the first half step only to compute the
1163 * virial for the first step. From there,
1164 * revert back to the initial coordinates
1165 * so that the input is actually the initial step.
1167 copy_rvecn(state->v,cbuf,0,state->natoms); /* should make this better for parallelizing? */
1169 /* this is for NHC in the Ekin(t+dt/2) version of vv */
1170 trotter_update(ir,step,ekind,enerd,state,total_vir,mdatoms,&MassQ,trotter_seq,ettTSEQ1);
1173 /* If we are using twin-range interactions where the long-range component
1174 * is only evaluated every nstcalclr>1 steps, we should do a special update
1175 * step to combine the long-range forces on these steps.
1176 * For nstcalclr=1 this is not done, since the forces would have been added
1177 * directly to the short-range forces already.
1179 bUpdateDoLR = (fr->bTwinRange && do_per_step(step,ir->nstcalclr));
1181 update_coords(fplog,step,ir,mdatoms,state,fr->bMolPBC,
1182 f,bUpdateDoLR,fr->f_twin,fcd,
1183 ekind,M,wcycle,upd,bInitStep,etrtVELOCITY1,
1184 cr,nrnb,constr,&top->idef);
1188 gmx_iterate_init(&iterate,bIterations && !bInitStep);
1190 /* for iterations, we save these vectors, as we will be self-consistently iterating
1193 /*#### UPDATE EXTENDED VARIABLES IN TROTTER FORMULATION */
1195 /* save the state */
1196 if (bIterations && iterate.bIterate) {
1197 copy_coupling_state(state,bufstate,ekind,ekind_save,&(ir->opts));
1200 bFirstIterate = TRUE;
1201 while (bFirstIterate || (bIterations && iterate.bIterate))
1203 if (bIterations && iterate.bIterate)
1205 copy_coupling_state(bufstate,state,ekind_save,ekind,&(ir->opts));
1206 if (bFirstIterate && bTrotter)
1208 /* The first time through, we need a decent first estimate
1209 of veta(t+dt) to compute the constraints. Do
1210 this by computing the box volume part of the
1211 trotter integration at this time. Nothing else
1212 should be changed by this routine here. If
1213 !(first time), we start with the previous value
1216 veta_save = state->veta;
1217 trotter_update(ir,step,ekind,enerd,state,total_vir,mdatoms,&MassQ,trotter_seq,ettTSEQ0);
1218 vetanew = state->veta;
1219 state->veta = veta_save;
1224 if ( !bRerunMD || rerun_fr.bV || bForceUpdate) { /* Why is rerun_fr.bV here? Unclear. */
1227 update_constraints(fplog,step,&dvdl,ir,ekind,mdatoms,
1228 state,fr->bMolPBC,graph,f,
1229 &top->idef,shake_vir,NULL,
1230 cr,nrnb,wcycle,upd,constr,
1231 bInitStep,TRUE,bCalcVir,vetanew);
1233 if (!bOK && !bFFscan)
1235 gmx_fatal(FARGS,"Constraint error: Shake, Lincs or Settle could not solve the constrains");
1240 { /* Need to unshift here if a do_force has been
1241 called in the previous step */
1242 unshift_self(graph,state->box,state->x);
1246 /* if VV, compute the pressure and constraints */
1247 /* For VV2, we strictly only need this if using pressure
1248 * control, but we really would like to have accurate pressures
1250 * Think about ways around this in the future?
1251 * For now, keep this choice in comments.
1253 /*bPres = (ir->eI==eiVV || IR_NPT_TROTTER(ir)); */
1254 /*bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK && IR_NPT_TROTTER(ir)));*/
1256 bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK));
1257 if (bCalcEner && ir->eI==eiVVAK) /*MRS: 7/9/2010 -- this still doesn't fix it?*/
1259 bSumEkinhOld = TRUE;
1261 compute_globals(fplog,gstat,cr,ir,fr,ekind,state,state_global,mdatoms,nrnb,vcm,
1262 wcycle,enerd,force_vir,shake_vir,total_vir,pres,mu_tot,
1263 constr,NULL,FALSE,state->box,
1264 top_global,&pcurr,top_global->natoms,&bSumEkinhOld,
1267 | (bStopCM ? CGLO_STOPCM : 0)
1268 | (bTemp ? CGLO_TEMPERATURE:0)
1269 | (bPres ? CGLO_PRESSURE : 0)
1270 | (bPres ? CGLO_CONSTRAINT : 0)
1271 | ((bIterations && iterate.bIterate) ? CGLO_ITERATE : 0)
1272 | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
1275 /* explanation of above:
1276 a) We compute Ekin at the full time step
1277 if 1) we are using the AveVel Ekin, and it's not the
1278 initial step, or 2) if we are using AveEkin, but need the full
1279 time step kinetic energy for the pressure (always true now, since we want accurate statistics).
1280 b) If we are using EkinAveEkin for the kinetic energy for the temperture control, we still feed in
1281 EkinAveVel because it's needed for the pressure */
1283 /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
1288 trotter_update(ir,step,ekind,enerd,state,total_vir,mdatoms,&MassQ,trotter_seq,ettTSEQ2);
1295 /* We need the kinetic energy at minus the half step for determining
1296 * the full step kinetic energy and possibly for T-coupling.*/
1297 /* This may not be quite working correctly yet . . . . */
1298 compute_globals(fplog,gstat,cr,ir,fr,ekind,state,state_global,mdatoms,nrnb,vcm,
1299 wcycle,enerd,NULL,NULL,NULL,NULL,mu_tot,
1300 constr,NULL,FALSE,state->box,
1301 top_global,&pcurr,top_global->natoms,&bSumEkinhOld,
1302 CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
1306 update_tcouple(fplog,step,ir,state,ekind,wcycle,upd,&MassQ,mdatoms);
1311 done_iterating(cr,fplog,step,&iterate,bFirstIterate,
1312 state->veta,&vetanew))
1316 bFirstIterate = FALSE;
1319 if (bTrotter && !bInitStep) {
1320 enerd->term[F_DVDL_BONDED] += dvdl; /* only add after iterations */
1321 copy_mat(shake_vir,state->svir_prev);
1322 copy_mat(force_vir,state->fvir_prev);
1323 if (IR_NVT_TROTTER(ir) && ir->eI==eiVV) {
1324 /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
1325 enerd->term[F_TEMP] = sum_ekin(&(ir->opts),ekind,NULL,(ir->eI==eiVV),FALSE,FALSE);
1326 enerd->term[F_EKIN] = trace(ekind->ekin);
1329 /* if it's the initial step, we performed this first step just to get the constraint virial */
1330 if (bInitStep && ir->eI==eiVV) {
1331 copy_rvecn(cbuf,state->v,0,state->natoms);
1334 if (fr->bSepDVDL && fplog && do_log)
1336 fprintf(fplog,sepdvdlformat,"Constraint",0.0,dvdl);
1338 enerd->term[F_DVDL_BONDED] += dvdl;
1341 /* MRS -- now done iterating -- compute the conserved quantity */
1343 saved_conserved_quantity = compute_conserved_from_auxiliary(ir,state,&MassQ);
1346 last_ekin = enerd->term[F_EKIN];
1348 if ((ir->eDispCorr != edispcEnerPres) && (ir->eDispCorr != edispcAllEnerPres))
1350 saved_conserved_quantity -= enerd->term[F_DISPCORR];
1352 /* sum up the foreign energy and dhdl terms for vv. currently done every step so that dhdl is correct in the .edr */
1353 sum_dhdl(enerd,state->lambda,ir->fepvals);
1356 /* ######## END FIRST UPDATE STEP ############## */
1357 /* ######## If doing VV, we now have v(dt) ###### */
1359 /* perform extended ensemble sampling in lambda - we don't
1360 actually move to the new state before outputting
1361 statistics, but if performing simulated tempering, we
1362 do update the velocities and the tau_t. */
1364 lamnew = ExpandedEnsembleDynamics(fplog,ir,enerd,state,&MassQ,&df_history,step,mcrng,state->v,mdatoms);
1366 /* ################## START TRAJECTORY OUTPUT ################# */
1368 /* Now we have the energies and forces corresponding to the
1369 * coordinates at time t. We must output all of this before
1371 * for RerunMD t is read from input trajectory
1374 if (do_per_step(step,ir->nstxout)) { mdof_flags |= MDOF_X; }
1375 if (do_per_step(step,ir->nstvout)) { mdof_flags |= MDOF_V; }
1376 if (do_per_step(step,ir->nstfout)) { mdof_flags |= MDOF_F; }
1377 if (do_per_step(step,ir->nstxtcout)) { mdof_flags |= MDOF_XTC; }
1378 if (bCPT) { mdof_flags |= MDOF_CPT; };
1380 #if defined(GMX_FAHCORE) || defined(GMX_WRITELASTSTEP)
1383 /* Enforce writing positions and velocities at end of run */
1384 mdof_flags |= (MDOF_X | MDOF_V);
1389 fcReportProgress( ir->nsteps, step );
1391 /* sync bCPT and fc record-keeping */
1392 if (bCPT && MASTER(cr))
1393 fcRequestCheckPoint();
1396 if (mdof_flags != 0)
1398 wallcycle_start(wcycle,ewcTRAJ);
1401 if (state->flags & (1<<estLD_RNG))
1403 get_stochd_state(upd,state);
1405 if (state->flags & (1<<estMC_RNG))
1407 get_mc_state(mcrng,state);
1413 state_global->ekinstate.bUpToDate = FALSE;
1417 update_ekinstate(&state_global->ekinstate,ekind);
1418 state_global->ekinstate.bUpToDate = TRUE;
1420 update_energyhistory(&state_global->enerhist,mdebin);
1421 if (ir->efep!=efepNO || ir->bSimTemp)
1423 state_global->fep_state = state->fep_state; /* MRS: seems kludgy. The code should be
1424 structured so this isn't necessary.
1425 Note this reassignment is only necessary
1426 for single threads.*/
1427 copy_df_history(&state_global->dfhist,&df_history);
1431 write_traj(fplog,cr,outf,mdof_flags,top_global,
1432 step,t,state,state_global,f,f_global,&n_xtc,&x_xtc);
1439 if (bLastStep && step_rel == ir->nsteps &&
1440 (Flags & MD_CONFOUT) && MASTER(cr) &&
1441 !bRerunMD && !bFFscan)
1443 /* x and v have been collected in write_traj,
1444 * because a checkpoint file will always be written
1447 fprintf(stderr,"\nWriting final coordinates.\n");
1450 /* Make molecules whole only for confout writing */
1451 do_pbc_mtop(fplog,ir->ePBC,state->box,top_global,state_global->x);
1453 write_sto_conf_mtop(ftp2fn(efSTO,nfile,fnm),
1454 *top_global->name,top_global,
1455 state_global->x,state_global->v,
1456 ir->ePBC,state->box);
1459 wallcycle_stop(wcycle,ewcTRAJ);
1462 /* kludge -- virial is lost with restart for NPT control. Must restart */
1463 if (bStartingFromCpt && bVV)
1465 copy_mat(state->svir_prev,shake_vir);
1466 copy_mat(state->fvir_prev,force_vir);
1468 /* ################## END TRAJECTORY OUTPUT ################ */
1470 /* Determine the wallclock run time up till now */
1471 run_time = gmx_gettime() - (double)runtime->real;
1473 /* Check whether everything is still allright */
1474 if (((int)gmx_get_stop_condition() > handled_stop_condition)
1475 #ifdef GMX_THREAD_MPI
1480 /* this is just make gs.sig compatible with the hack
1481 of sending signals around by MPI_Reduce with together with
1483 if ( gmx_get_stop_condition() == gmx_stop_cond_next_ns )
1484 gs.sig[eglsSTOPCOND]=1;
1485 if ( gmx_get_stop_condition() == gmx_stop_cond_next )
1486 gs.sig[eglsSTOPCOND]=-1;
1487 /* < 0 means stop at next step, > 0 means stop at next NS step */
1491 "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
1492 gmx_get_signal_name(),
1493 gs.sig[eglsSTOPCOND]==1 ? "NS " : "");
1497 "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
1498 gmx_get_signal_name(),
1499 gs.sig[eglsSTOPCOND]==1 ? "NS " : "");
1501 handled_stop_condition=(int)gmx_get_stop_condition();
1503 else if (MASTER(cr) && (bNS || ir->nstlist <= 0) &&
1504 (max_hours > 0 && run_time > max_hours*60.0*60.0*0.99) &&
1505 gs.sig[eglsSTOPCOND] == 0 && gs.set[eglsSTOPCOND] == 0)
1507 /* Signal to terminate the run */
1508 gs.sig[eglsSTOPCOND] = 1;
1511 fprintf(fplog,"\nStep %s: Run time exceeded %.3f hours, will terminate the run\n",gmx_step_str(step,sbuf),max_hours*0.99);
1513 fprintf(stderr, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n",gmx_step_str(step,sbuf),max_hours*0.99);
1516 if (bResetCountersHalfMaxH && MASTER(cr) &&
1517 run_time > max_hours*60.0*60.0*0.495)
1519 gs.sig[eglsRESETCOUNTERS] = 1;
1522 if (ir->nstlist == -1 && !bRerunMD)
1524 /* When bGStatEveryStep=FALSE, global_stat is only called
1525 * when we check the atom displacements, not at NS steps.
1526 * This means that also the bonded interaction count check is not
1527 * performed immediately after NS. Therefore a few MD steps could
1528 * be performed with missing interactions.
1529 * But wrong energies are never written to file,
1530 * since energies are only written after global_stat
1533 if (step >= nlh.step_nscheck)
1535 nlh.nabnsb = natoms_beyond_ns_buffer(ir,fr,&top->cgs,
1536 nlh.scale_tot,state->x);
1540 /* This is not necessarily true,
1541 * but step_nscheck is determined quite conservatively.
1547 /* In parallel we only have to check for checkpointing in steps
1548 * where we do global communication,
1549 * otherwise the other nodes don't know.
1551 if (MASTER(cr) && ((bGStat || !PAR(cr)) &&
1554 run_time >= nchkpt*cpt_period*60.0)) &&
1555 gs.set[eglsCHKPT] == 0)
1557 gs.sig[eglsCHKPT] = 1;
1561 /* at the start of step, randomize the velocities */
1562 if (ETC_ANDERSEN(ir->etc) && EI_VV(ir->eI))
1564 gmx_bool bDoAndersenConstr;
1565 bDoAndersenConstr = (constr && update_randomize_velocities(ir,step,mdatoms,state,upd,&top->idef,constr));
1566 /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
1567 if (bDoAndersenConstr)
1569 update_constraints(fplog,step,&dvdl,ir,ekind,mdatoms,
1570 state,fr->bMolPBC,graph,f,
1571 &top->idef,tmp_vir,NULL,
1572 cr,nrnb,wcycle,upd,constr,
1573 bInitStep,TRUE,bCalcVir,vetanew);
1579 gmx_iterate_init(&iterate,bIterations);
1582 /* for iterations, we save these vectors, as we will be redoing the calculations */
1583 if (bIterations && iterate.bIterate)
1585 copy_coupling_state(state,bufstate,ekind,ekind_save,&(ir->opts));
1587 bFirstIterate = TRUE;
1588 while (bFirstIterate || (bIterations && iterate.bIterate))
1590 /* We now restore these vectors to redo the calculation with improved extended variables */
1593 copy_coupling_state(bufstate,state,ekind_save,ekind,&(ir->opts));
1596 /* We make the decision to break or not -after- the calculation of Ekin and Pressure,
1597 so scroll down for that logic */
1599 /* ######### START SECOND UPDATE STEP ################# */
1600 /* Box is changed in update() when we do pressure coupling,
1601 * but we should still use the old box for energy corrections and when
1602 * writing it to the energy file, so it matches the trajectory files for
1603 * the same timestep above. Make a copy in a separate array.
1605 copy_mat(state->box,lastbox);
1608 if (!(bRerunMD && !rerun_fr.bV && !bForceUpdate))
1610 wallcycle_start(wcycle,ewcUPDATE);
1612 /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
1615 if (bIterations && iterate.bIterate)
1623 /* we use a new value of scalevir to converge the iterations faster */
1624 scalevir = tracevir/trace(shake_vir);
1626 msmul(shake_vir,scalevir,shake_vir);
1627 m_add(force_vir,shake_vir,total_vir);
1628 clear_mat(shake_vir);
1630 trotter_update(ir,step,ekind,enerd,state,total_vir,mdatoms,&MassQ,trotter_seq,ettTSEQ3);
1631 /* We can only do Berendsen coupling after we have summed
1632 * the kinetic energy or virial. Since the happens
1633 * in global_state after update, we should only do it at
1634 * step % nstlist = 1 with bGStatEveryStep=FALSE.
1639 update_tcouple(fplog,step,ir,state,ekind,wcycle,upd,&MassQ,mdatoms);
1640 update_pcouple(fplog,step,ir,state,pcoupl_mu,M,wcycle,
1646 bUpdateDoLR = (fr->bTwinRange && do_per_step(step,ir->nstcalclr));
1648 /* velocity half-step update */
1649 update_coords(fplog,step,ir,mdatoms,state,fr->bMolPBC,f,
1650 bUpdateDoLR,fr->f_twin,fcd,
1651 ekind,M,wcycle,upd,FALSE,etrtVELOCITY2,
1652 cr,nrnb,constr,&top->idef);
1655 /* Above, initialize just copies ekinh into ekin,
1656 * it doesn't copy position (for VV),
1657 * and entire integrator for MD.
1662 copy_rvecn(state->x,cbuf,0,state->natoms);
1664 bUpdateDoLR = (fr->bTwinRange && do_per_step(step,ir->nstcalclr));
1666 update_coords(fplog,step,ir,mdatoms,state,fr->bMolPBC,f,
1667 bUpdateDoLR,fr->f_twin,fcd,
1668 ekind,M,wcycle,upd,bInitStep,etrtPOSITION,cr,nrnb,constr,&top->idef);
1669 wallcycle_stop(wcycle,ewcUPDATE);
1671 update_constraints(fplog,step,&dvdl,ir,ekind,mdatoms,state,
1672 fr->bMolPBC,graph,f,
1673 &top->idef,shake_vir,force_vir,
1674 cr,nrnb,wcycle,upd,constr,
1675 bInitStep,FALSE,bCalcVir,state->veta);
1679 /* erase F_EKIN and F_TEMP here? */
1680 /* just compute the kinetic energy at the half step to perform a trotter step */
1681 compute_globals(fplog,gstat,cr,ir,fr,ekind,state,state_global,mdatoms,nrnb,vcm,
1682 wcycle,enerd,force_vir,shake_vir,total_vir,pres,mu_tot,
1683 constr,NULL,FALSE,lastbox,
1684 top_global,&pcurr,top_global->natoms,&bSumEkinhOld,
1685 cglo_flags | CGLO_TEMPERATURE
1687 wallcycle_start(wcycle,ewcUPDATE);
1688 trotter_update(ir,step,ekind,enerd,state,total_vir,mdatoms,&MassQ,trotter_seq,ettTSEQ4);
1689 /* now we know the scaling, we can compute the positions again again */
1690 copy_rvecn(cbuf,state->x,0,state->natoms);
1692 bUpdateDoLR = (fr->bTwinRange && do_per_step(step,ir->nstcalclr));
1694 update_coords(fplog,step,ir,mdatoms,state,fr->bMolPBC,f,
1695 bUpdateDoLR,fr->f_twin,fcd,
1696 ekind,M,wcycle,upd,bInitStep,etrtPOSITION,cr,nrnb,constr,&top->idef);
1697 wallcycle_stop(wcycle,ewcUPDATE);
1699 /* do we need an extra constraint here? just need to copy out of state->v to upd->xp? */
1700 /* are the small terms in the shake_vir here due
1701 * to numerical errors, or are they important
1702 * physically? I'm thinking they are just errors, but not completely sure.
1703 * For now, will call without actually constraining, constr=NULL*/
1704 update_constraints(fplog,step,&dvdl,ir,ekind,mdatoms,
1705 state,fr->bMolPBC,graph,f,
1706 &top->idef,tmp_vir,force_vir,
1707 cr,nrnb,wcycle,upd,NULL,
1708 bInitStep,FALSE,bCalcVir,
1711 if (!bOK && !bFFscan)
1713 gmx_fatal(FARGS,"Constraint error: Shake, Lincs or Settle could not solve the constrains");
1716 if (fr->bSepDVDL && fplog && do_log)
1718 fprintf(fplog,sepdvdlformat,"Constraint dV/dl",0.0,dvdl);
1720 enerd->term[F_DVDL_BONDED] += dvdl;
1724 /* Need to unshift here */
1725 unshift_self(graph,state->box,state->x);
1730 wallcycle_start(wcycle,ewcVSITECONSTR);
1733 shift_self(graph,state->box,state->x);
1735 construct_vsites(fplog,vsite,state->x,nrnb,ir->delta_t,state->v,
1736 top->idef.iparams,top->idef.il,
1737 fr->ePBC,fr->bMolPBC,graph,cr,state->box);
1741 unshift_self(graph,state->box,state->x);
1743 wallcycle_stop(wcycle,ewcVSITECONSTR);
1746 /* ############## IF NOT VV, Calculate globals HERE, also iterate constraints ############ */
1747 /* With Leap-Frog we can skip compute_globals at
1748 * non-communication steps, but we need to calculate
1749 * the kinetic energy one step before communication.
1751 if (bGStat || do_per_step(step+1,nstglobalcomm) ||
1754 if (ir->nstlist == -1 && bFirstIterate)
1756 gs.sig[eglsNABNSB] = nlh.nabnsb;
1758 compute_globals(fplog,gstat,cr,ir,fr,ekind,state,state_global,mdatoms,nrnb,vcm,
1759 wcycle,enerd,force_vir,shake_vir,total_vir,pres,mu_tot,
1761 bFirstIterate ? &gs : NULL,
1762 (step_rel % gs.nstms == 0) &&
1763 (multisim_nsteps<0 || (step_rel<multisim_nsteps)),
1765 top_global,&pcurr,top_global->natoms,&bSumEkinhOld,
1767 | (!EI_VV(ir->eI) ? CGLO_ENERGY : 0)
1768 | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
1769 | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
1770 | (!EI_VV(ir->eI) || bRerunMD ? CGLO_PRESSURE : 0)
1771 | (bIterations && iterate.bIterate ? CGLO_ITERATE : 0)
1772 | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
1775 if (ir->nstlist == -1 && bFirstIterate)
1777 nlh.nabnsb = gs.set[eglsNABNSB];
1778 gs.set[eglsNABNSB] = 0;
1781 /* bIterate is set to keep it from eliminating the old ekin kinetic energy terms */
1782 /* ############# END CALC EKIN AND PRESSURE ################# */
1784 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
1785 the virial that should probably be addressed eventually. state->veta has better properies,
1786 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
1787 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
1790 done_iterating(cr,fplog,step,&iterate,bFirstIterate,
1791 trace(shake_vir),&tracevir))
1795 bFirstIterate = FALSE;
1798 /* only add constraint dvdl after constraints */
1799 enerd->term[F_DVDL_BONDED] += dvdl;
1802 /* sum up the foreign energy and dhdl terms for md and sd. currently done every step so that dhdl is correct in the .edr */
1803 sum_dhdl(enerd,state->lambda,ir->fepvals);
1805 update_box(fplog,step,ir,mdatoms,state,graph,f,
1806 ir->nstlist==-1 ? &nlh.scale_tot : NULL,pcoupl_mu,nrnb,wcycle,upd,bInitStep,FALSE);
1808 /* ################# END UPDATE STEP 2 ################# */
1809 /* #### We now have r(t+dt) and v(t+dt/2) ############# */
1811 /* The coordinates (x) were unshifted in update */
1812 if (bFFscan && (shellfc==NULL || bConverged))
1814 if (print_forcefield(fplog,enerd->term,mdatoms->homenr,
1816 &(top_global->mols),mdatoms->massT,pres))
1820 fprintf(stderr,"\n");
1826 /* We will not sum ekinh_old,
1827 * so signal that we still have to do it.
1829 bSumEkinhOld = TRUE;
1834 /* Only do GCT when the relaxation of shells (minimization) has converged,
1835 * otherwise we might be coupling to bogus energies.
1836 * In parallel we must always do this, because the other sims might
1840 /* Since this is called with the new coordinates state->x, I assume
1841 * we want the new box state->box too. / EL 20040121
1843 do_coupling(fplog,oenv,nfile,fnm,tcr,t,step,enerd->term,fr,
1845 mdatoms,&(top->idef),mu_aver,
1846 top_global->mols.nr,cr,
1847 state->box,total_vir,pres,
1848 mu_tot,state->x,f,bConverged);
1852 /* ######### BEGIN PREPARING EDR OUTPUT ########### */
1854 /* use the directly determined last velocity, not actually the averaged half steps */
1855 if (bTrotter && ir->eI==eiVV)
1857 enerd->term[F_EKIN] = last_ekin;
1859 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
1863 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
1867 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + compute_conserved_from_auxiliary(ir,state,&MassQ);
1869 /* Check for excessively large energies */
1873 real etot_max = 1e200;
1875 real etot_max = 1e30;
1877 if (fabs(enerd->term[F_ETOT]) > etot_max)
1879 fprintf(stderr,"Energy too large (%g), giving up\n",
1880 enerd->term[F_ETOT]);
1883 /* ######### END PREPARING EDR OUTPUT ########### */
1885 /* Time for performance */
1886 if (((step % stepout) == 0) || bLastStep)
1888 runtime_upd_proc(runtime);
1894 gmx_bool do_dr,do_or;
1896 if (fplog && do_log && bDoExpanded)
1898 /* only needed if doing expanded ensemble */
1899 PrintFreeEnergyInfoToFile(fplog,ir->fepvals,ir->expandedvals,ir->bSimTemp?ir->simtempvals:NULL,
1900 &df_history,state->fep_state,ir->nstlog,step);
1902 if (!(bStartingFromCpt && (EI_VV(ir->eI))))
1906 upd_mdebin(mdebin,bDoDHDL, TRUE,
1907 t,mdatoms->tmass,enerd,state,
1908 ir->fepvals,ir->expandedvals,lastbox,
1909 shake_vir,force_vir,total_vir,pres,
1910 ekind,mu_tot,constr);
1914 upd_mdebin_step(mdebin);
1917 do_dr = do_per_step(step,ir->nstdisreout);
1918 do_or = do_per_step(step,ir->nstorireout);
1920 print_ebin(outf->fp_ene,do_ene,do_dr,do_or,do_log?fplog:NULL,
1922 eprNORMAL,bCompact,mdebin,fcd,groups,&(ir->opts));
1924 if (ir->ePull != epullNO)
1926 pull_print_output(ir->pull,step,t);
1929 if (do_per_step(step,ir->nstlog))
1931 if(fflush(fplog) != 0)
1933 gmx_fatal(FARGS,"Cannot flush logfile - maybe you are out of disk space?");
1939 /* Have to do this part after outputting the logfile and the edr file */
1940 state->fep_state = lamnew;
1941 for (i=0;i<efptNR;i++)
1943 state->lambda[i] = ir->fepvals->all_lambda[i][lamnew];
1946 /* Remaining runtime */
1947 if (MULTIMASTER(cr) && (do_verbose || gmx_got_usr_signal()) && !bPMETuneRunning)
1951 fprintf(stderr,"\n");
1953 print_time(stderr,runtime,step,ir,cr);
1956 /* Replica exchange */
1958 if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
1959 do_per_step(step,repl_ex_nst))
1961 bExchanged = replica_exchange(fplog,cr,repl_ex,
1965 if (bExchanged && DOMAINDECOMP(cr))
1967 dd_partition_system(fplog,step,cr,TRUE,1,
1968 state_global,top_global,ir,
1969 state,&f,mdatoms,top,fr,
1970 vsite,shellfc,constr,
1977 bStartingFromCpt = FALSE;
1979 /* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
1980 /* With all integrators, except VV, we need to retain the pressure
1981 * at the current step for coupling at the next step.
1983 if ((state->flags & (1<<estPRES_PREV)) &&
1985 (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
1987 /* Store the pressure in t_state for pressure coupling
1988 * at the next MD step.
1990 copy_mat(pres,state->pres_prev);
1993 /* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
1995 if ( (membed!=NULL) && (!bLastStep) )
1997 rescale_membed(step_rel,membed,state_global->x);
2004 /* read next frame from input trajectory */
2005 bNotLastFrame = read_next_frame(oenv,status,&rerun_fr);
2010 rerun_parallel_comm(cr,&rerun_fr,&bNotLastFrame);
2014 if (!bRerunMD || !rerun_fr.bStep)
2016 /* increase the MD step number */
2021 cycles = wallcycle_stop(wcycle,ewcSTEP);
2022 if (DOMAINDECOMP(cr) && wcycle)
2024 dd_cycles_add(cr->dd,cycles,ddCyclStep);
2027 if (bPMETuneRunning || bPMETuneTry)
2029 /* PME grid + cut-off optimization with GPUs or PME nodes */
2031 /* Count the total cycles over the last steps */
2032 cycles_pmes += cycles;
2034 /* We can only switch cut-off at NS steps */
2035 if (step % ir->nstlist == 0)
2037 /* PME grid + cut-off optimization with GPUs or PME nodes */
2040 if (DDMASTER(cr->dd))
2042 /* PME node load is too high, start tuning */
2043 bPMETuneRunning = (dd_pme_f_ratio(cr->dd) >= 1.05);
2045 dd_bcast(cr->dd,sizeof(gmx_bool),&bPMETuneRunning);
2047 if (bPMETuneRunning || step_rel > ir->nstlist*50)
2049 bPMETuneTry = FALSE;
2052 if (bPMETuneRunning)
2054 /* init_step might not be a multiple of nstlist,
2055 * but the first cycle is always skipped anyhow.
2058 pme_load_balance(pme_loadbal,cr,
2059 (bVerbose && MASTER(cr)) ? stderr : NULL,
2061 ir,state,cycles_pmes,
2062 fr->ic,fr->nbv,&fr->pmedata,
2065 /* Update constants in forcerec/inputrec to keep them in sync with fr->ic */
2066 fr->ewaldcoeff = fr->ic->ewaldcoeff;
2067 fr->rlist = fr->ic->rlist;
2068 fr->rlistlong = fr->ic->rlistlong;
2069 fr->rcoulomb = fr->ic->rcoulomb;
2070 fr->rvdw = fr->ic->rvdw;
2076 if (step_rel == wcycle_get_reset_counters(wcycle) ||
2077 gs.set[eglsRESETCOUNTERS] != 0)
2079 /* Reset all the counters related to performance over the run */
2080 reset_all_counters(fplog,cr,step,&step_rel,ir,wcycle,nrnb,runtime,
2081 fr->nbv != NULL && fr->nbv->bUseGPU ? fr->nbv->cu_nbv : NULL);
2082 wcycle_set_reset_counters(wcycle,-1);
2083 /* Correct max_hours for the elapsed time */
2084 max_hours -= run_time/(60.0*60.0);
2085 bResetCountersHalfMaxH = FALSE;
2086 gs.set[eglsRESETCOUNTERS] = 0;
2090 /* End of main MD loop */
2094 runtime_end(runtime);
2096 if (bRerunMD && MASTER(cr))
2101 if (!(cr->duty & DUTY_PME))
2103 /* Tell the PME only node to finish */
2104 gmx_pme_send_finish(cr);
2109 if (ir->nstcalcenergy > 0 && !bRerunMD)
2111 print_ebin(outf->fp_ene,FALSE,FALSE,FALSE,fplog,step,t,
2112 eprAVER,FALSE,mdebin,fcd,groups,&(ir->opts));
2120 if (ir->nstlist == -1 && nlh.nns > 0 && fplog)
2122 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)));
2123 fprintf(fplog,"Average number of atoms that crossed the half buffer length: %.1f\n\n",nlh.ab/nlh.nns);
2126 if (pme_loadbal != NULL)
2128 pme_loadbal_done(pme_loadbal,fplog);
2131 if (shellfc && fplog)
2133 fprintf(fplog,"Fraction of iterations that converged: %.2f %%\n",
2134 (nconverged*100.0)/step_rel);
2135 fprintf(fplog,"Average number of force evaluations per MD step: %.2f\n\n",
2139 if (repl_ex_nst > 0 && MASTER(cr))
2141 print_replica_exchange_statistics(fplog,repl_ex);
2144 runtime->nsteps_done = step_rel;