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44 #include "gromacs/math/vec.h"
54 #include "md_support.h"
55 #include "md_logging.h"
67 #include "domdec_network.h"
71 #include "gromacs/gmxpreprocess/compute_io.h"
72 #include "checkpoint.h"
73 #include "gromacs/topology/mtop_util.h"
74 #include "sighandler.h"
76 #include "gromacs/utility/cstringutil.h"
77 #include "pme_loadbal.h"
80 #include "types/nlistheuristics.h"
81 #include "types/iteratedconstraints.h"
82 #include "nbnxn_cuda_data_mgmt.h"
84 #include "gromacs/fileio/confio.h"
85 #include "gromacs/fileio/mdoutf.h"
86 #include "gromacs/fileio/trajectory_writing.h"
87 #include "gromacs/fileio/trnio.h"
88 #include "gromacs/fileio/trxio.h"
89 #include "gromacs/fileio/xtcio.h"
90 #include "gromacs/imd/imd.h"
91 #include "gromacs/pbcutil/mshift.h"
92 #include "gromacs/pbcutil/pbc.h"
93 #include "gromacs/pulling/pull.h"
94 #include "gromacs/swap/swapcoords.h"
95 #include "gromacs/timing/wallcycle.h"
96 #include "gromacs/timing/walltime_accounting.h"
97 #include "gromacs/utility/gmxmpi.h"
98 #include "gromacs/utility/smalloc.h"
101 #include "corewrap.h"
104 static void reset_all_counters(FILE *fplog, t_commrec *cr,
106 gmx_int64_t *step_rel, t_inputrec *ir,
107 gmx_wallcycle_t wcycle, t_nrnb *nrnb,
108 gmx_walltime_accounting_t walltime_accounting,
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 walltime_accounting_start(walltime_accounting);
134 print_date_and_time(fplog, cr->nodeid, "Restarted time", gmx_gettime());
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 gmx_unused *deviceOptions,
153 gmx_walltime_accounting_t walltime_accounting)
155 gmx_mdoutf_t outf = NULL;
156 gmx_int64_t step, step_rel;
158 double t, t0, lam0[efptNR];
159 gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEner;
160 gmx_bool bNS, bNStList, bSimAnn, bStopCM, bRerunMD, bNotLastFrame = FALSE,
161 bFirstStep, bStateFromCP, bStateFromTPX, bInitStep, bLastStep,
162 bBornRadii, bStartingFromCpt;
163 gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
164 gmx_bool do_ene, do_log, do_verbose, bRerunWarnNoV = TRUE,
165 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;
177 gmx_repl_ex_t repl_ex = NULL;
180 t_mdebin *mdebin = NULL;
181 t_state *state = NULL;
182 rvec *f_global = NULL;
183 gmx_enerdata_t *enerd;
185 gmx_global_stat_t gstat;
186 gmx_update_t upd = NULL;
187 t_graph *graph = NULL;
189 gmx_groups_t *groups;
190 gmx_ekindata_t *ekind, *ekind_save;
191 gmx_shellfc_t shellfc;
192 int count, nconverged = 0;
194 gmx_bool bConverged = TRUE, bOK, bSumEkinhOld, bExchanged, bNeedRepartition;
195 gmx_bool bResetCountersHalfMaxH = FALSE;
196 gmx_bool bVV, bIterativeCase, bFirstIterate, bTemp, bPres, bTrotter;
197 gmx_bool bUpdateDoLR;
201 real veta_save, scalevir, tracevir;
207 real saved_conserved_quantity = 0;
211 char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
212 int handled_stop_condition = gmx_stop_cond_none; /* compare to get_stop_condition*/
213 gmx_iterate_t iterate;
214 gmx_int64_t multisim_nsteps = -1; /* number of steps to do before first multisim
215 simulation stops. If equal to zero, don't
216 communicate any more between multisims.*/
217 /* PME load balancing data for GPU kernels */
218 pme_load_balancing_t pme_loadbal = NULL;
220 gmx_bool bPMETuneTry = FALSE, bPMETuneRunning = FALSE;
223 gmx_bool bIMDstep = FALSE;
226 /* Temporary addition for FAHCORE checkpointing */
230 /* Check for special mdrun options */
231 bRerunMD = (Flags & MD_RERUN);
232 if (Flags & MD_RESETCOUNTERSHALFWAY)
236 /* Signal to reset the counters half the simulation steps. */
237 wcycle_set_reset_counters(wcycle, ir->nsteps/2);
239 /* Signal to reset the counters halfway the simulation time. */
240 bResetCountersHalfMaxH = (max_hours > 0);
243 /* md-vv uses averaged full step velocities for T-control
244 md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
245 md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
247 if (bVV) /* to store the initial velocities while computing virial */
249 snew(cbuf, top_global->natoms);
251 /* all the iteratative cases - only if there are constraints */
252 bIterativeCase = ((IR_NPH_TROTTER(ir) || IR_NPT_TROTTER(ir)) && (constr) && (!bRerunMD));
253 gmx_iterate_init(&iterate, FALSE); /* The default value of iterate->bIterationActive is set to
254 false in this step. The correct value, true or false,
255 is set at each step, as it depends on the frequency of temperature
256 and pressure control.*/
257 bTrotter = (bVV && (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir) || IR_NVT_TROTTER(ir)));
261 /* Since we don't know if the frames read are related in any way,
262 * rebuild the neighborlist at every step.
265 ir->nstcalcenergy = 1;
269 check_ir_old_tpx_versions(cr, fplog, ir, top_global);
271 nstglobalcomm = check_nstglobalcomm(fplog, cr, nstglobalcomm, ir);
272 bGStatEveryStep = (nstglobalcomm == 1);
274 if (!bGStatEveryStep && ir->nstlist == -1 && fplog != NULL)
277 "To reduce the energy communication with nstlist = -1\n"
278 "the neighbor list validity should not be checked at every step,\n"
279 "this means that exact integration is not guaranteed.\n"
280 "The neighbor list validity is checked after:\n"
281 " <n.list life time> - 2*std.dev.(n.list life time) steps.\n"
282 "In most cases this will result in exact integration.\n"
283 "This reduces the energy communication by a factor of 2 to 3.\n"
284 "If you want less energy communication, set nstlist > 3.\n\n");
289 ir->nstxout_compressed = 0;
291 groups = &top_global->groups;
294 init_md(fplog, cr, ir, oenv, &t, &t0, state_global->lambda,
295 &(state_global->fep_state), lam0,
296 nrnb, top_global, &upd,
297 nfile, fnm, &outf, &mdebin,
298 force_vir, shake_vir, mu_tot, &bSimAnn, &vcm, Flags);
300 clear_mat(total_vir);
302 /* Energy terms and groups */
304 init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
306 if (DOMAINDECOMP(cr))
312 snew(f, top_global->natoms);
315 /* Kinetic energy data */
317 init_ekindata(fplog, top_global, &(ir->opts), ekind);
318 /* needed for iteration of constraints */
320 init_ekindata(fplog, top_global, &(ir->opts), ekind_save);
321 /* Copy the cos acceleration to the groups struct */
322 ekind->cosacc.cos_accel = ir->cos_accel;
324 gstat = global_stat_init(ir);
327 /* Check for polarizable models and flexible constraints */
328 shellfc = init_shell_flexcon(fplog, fr->cutoff_scheme == ecutsVERLET,
329 top_global, n_flexible_constraints(constr),
330 (ir->bContinuation ||
331 (DOMAINDECOMP(cr) && !MASTER(cr))) ?
332 NULL : state_global->x);
334 if (shellfc && ir->eI == eiNM)
336 /* Currently shells don't work with Normal Modes */
337 gmx_fatal(FARGS, "Normal Mode analysis is not supported with shells.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
340 if (vsite && ir->eI == eiNM)
342 /* Currently virtual sites don't work with Normal Modes */
343 gmx_fatal(FARGS, "Normal Mode analysis is not supported with virtual sites.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
348 tMPI_Thread_mutex_lock(&deform_init_box_mutex);
349 set_deform_reference_box(upd,
350 deform_init_init_step_tpx,
351 deform_init_box_tpx);
352 tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
356 double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
357 if ((io > 2000) && MASTER(cr))
360 "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
365 if (DOMAINDECOMP(cr))
367 top = dd_init_local_top(top_global);
370 dd_init_local_state(cr->dd, state_global, state);
372 if (DDMASTER(cr->dd) && ir->nstfout)
374 snew(f_global, state_global->natoms);
379 top = gmx_mtop_generate_local_top(top_global, ir);
381 forcerec_set_excl_load(fr, top);
383 state = serial_init_local_state(state_global);
386 atoms2md(top_global, ir, 0, NULL, top_global->natoms, mdatoms);
390 set_vsite_top(vsite, top, mdatoms, cr);
393 if (ir->ePBC != epbcNONE && !fr->bMolPBC)
395 graph = mk_graph(fplog, &(top->idef), 0, top_global->natoms, FALSE, FALSE);
400 make_local_shells(cr, mdatoms, shellfc);
403 setup_bonded_threading(fr, &top->idef);
406 /* Set up interactive MD (IMD) */
407 init_IMD(ir, cr, top_global, fplog, ir->nstcalcenergy, state_global->x,
408 nfile, fnm, oenv, imdport, Flags);
410 if (DOMAINDECOMP(cr))
412 /* Distribute the charge groups over the nodes from the master node */
413 dd_partition_system(fplog, ir->init_step, cr, TRUE, 1,
414 state_global, top_global, ir,
415 state, &f, mdatoms, top, fr,
416 vsite, shellfc, constr,
417 nrnb, wcycle, FALSE);
421 update_mdatoms(mdatoms, state->lambda[efptMASS]);
423 if (opt2bSet("-cpi", nfile, fnm))
425 bStateFromCP = gmx_fexist_master(opt2fn_master("-cpi", nfile, fnm, cr), cr);
429 bStateFromCP = FALSE;
434 init_expanded_ensemble(bStateFromCP, ir, &state->dfhist);
441 /* Update mdebin with energy history if appending to output files */
442 if (Flags & MD_APPENDFILES)
444 restore_energyhistory_from_state(mdebin, &state_global->enerhist);
448 /* We might have read an energy history from checkpoint,
449 * free the allocated memory and reset the counts.
451 done_energyhistory(&state_global->enerhist);
452 init_energyhistory(&state_global->enerhist);
455 /* Set the initial energy history in state by updating once */
456 update_energyhistory(&state_global->enerhist, mdebin);
459 /* Initialize constraints */
460 if (constr && !DOMAINDECOMP(cr))
462 set_constraints(constr, top, ir, mdatoms, cr);
467 /* We need to be sure replica exchange can only occur
468 * when the energies are current */
469 check_nst_param(fplog, cr, "nstcalcenergy", ir->nstcalcenergy,
470 "repl_ex_nst", &repl_ex_nst);
471 /* This check needs to happen before inter-simulation
472 * signals are initialized, too */
474 if (repl_ex_nst > 0 && MASTER(cr))
476 repl_ex = init_replica_exchange(fplog, cr->ms, state_global, ir,
477 repl_ex_nst, repl_ex_nex, repl_ex_seed);
480 /* PME tuning is only supported with GPUs or PME nodes and not with rerun.
481 * PME tuning is not supported with PME only for LJ and not for Coulomb.
483 if ((Flags & MD_TUNEPME) &&
484 EEL_PME(fr->eeltype) &&
485 ( (fr->cutoff_scheme == ecutsVERLET && fr->nbv->bUseGPU) || !(cr->duty & DUTY_PME)) &&
488 pme_loadbal_init(&pme_loadbal, ir, state->box, fr->ic, fr->pmedata);
490 if (cr->duty & DUTY_PME)
492 /* Start tuning right away, as we can't measure the load */
493 bPMETuneRunning = TRUE;
497 /* Separate PME nodes, we can measure the PP/PME load balance */
502 if (!ir->bContinuation && !bRerunMD)
504 if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
506 /* Set the velocities of frozen particles to zero */
507 for (i = 0; i < mdatoms->homenr; i++)
509 for (m = 0; m < DIM; m++)
511 if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
521 /* Constrain the initial coordinates and velocities */
522 do_constrain_first(fplog, constr, ir, mdatoms, state,
527 /* Construct the virtual sites for the initial configuration */
528 construct_vsites(vsite, state->x, ir->delta_t, NULL,
529 top->idef.iparams, top->idef.il,
530 fr->ePBC, fr->bMolPBC, cr, state->box);
536 /* set free energy calculation frequency as the minimum
537 greatest common denominator of nstdhdl, nstexpanded, and repl_ex_nst*/
538 nstfep = ir->fepvals->nstdhdl;
541 nstfep = gmx_greatest_common_divisor(ir->fepvals->nstdhdl, nstfep);
545 nstfep = gmx_greatest_common_divisor(repl_ex_nst, nstfep);
548 /* I'm assuming we need global communication the first time! MRS */
549 cglo_flags = (CGLO_TEMPERATURE | CGLO_GSTAT
550 | ((ir->comm_mode != ecmNO) ? CGLO_STOPCM : 0)
551 | (bVV ? CGLO_PRESSURE : 0)
552 | (bVV ? CGLO_CONSTRAINT : 0)
553 | (bRerunMD ? CGLO_RERUNMD : 0)
554 | ((Flags & MD_READ_EKIN) ? CGLO_READEKIN : 0));
556 bSumEkinhOld = FALSE;
557 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
558 NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
559 constr, NULL, FALSE, state->box,
560 top_global, &bSumEkinhOld, cglo_flags);
561 if (ir->eI == eiVVAK)
563 /* a second call to get the half step temperature initialized as well */
564 /* we do the same call as above, but turn the pressure off -- internally to
565 compute_globals, this is recognized as a velocity verlet half-step
566 kinetic energy calculation. This minimized excess variables, but
567 perhaps loses some logic?*/
569 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
570 NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
571 constr, NULL, FALSE, state->box,
572 top_global, &bSumEkinhOld,
573 cglo_flags &~(CGLO_STOPCM | CGLO_PRESSURE));
576 /* Calculate the initial half step temperature, and save the ekinh_old */
577 if (!(Flags & MD_STARTFROMCPT))
579 for (i = 0; (i < ir->opts.ngtc); i++)
581 copy_mat(ekind->tcstat[i].ekinh, ekind->tcstat[i].ekinh_old);
586 enerd->term[F_TEMP] *= 2; /* result of averages being done over previous and current step,
587 and there is no previous step */
590 /* if using an iterative algorithm, we need to create a working directory for the state. */
593 bufstate = init_bufstate(state);
596 /* need to make an initiation call to get the Trotter variables set, as well as other constants for non-trotter
597 temperature control */
598 trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
602 if (constr && !ir->bContinuation && ir->eConstrAlg == econtLINCS)
605 "RMS relative constraint deviation after constraining: %.2e\n",
606 constr_rmsd(constr, FALSE));
608 if (EI_STATE_VELOCITY(ir->eI))
610 fprintf(fplog, "Initial temperature: %g K\n", enerd->term[F_TEMP]);
614 fprintf(stderr, "starting md rerun '%s', reading coordinates from"
615 " input trajectory '%s'\n\n",
616 *(top_global->name), opt2fn("-rerun", nfile, fnm));
619 fprintf(stderr, "Calculated time to finish depends on nsteps from "
620 "run input file,\nwhich may not correspond to the time "
621 "needed to process input trajectory.\n\n");
627 fprintf(stderr, "starting mdrun '%s'\n",
628 *(top_global->name));
631 sprintf(tbuf, "%8.1f", (ir->init_step+ir->nsteps)*ir->delta_t);
635 sprintf(tbuf, "%s", "infinite");
637 if (ir->init_step > 0)
639 fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
640 gmx_step_str(ir->init_step+ir->nsteps, sbuf), tbuf,
641 gmx_step_str(ir->init_step, sbuf2),
642 ir->init_step*ir->delta_t);
646 fprintf(stderr, "%s steps, %s ps.\n",
647 gmx_step_str(ir->nsteps, sbuf), tbuf);
650 fprintf(fplog, "\n");
653 walltime_accounting_start(walltime_accounting);
654 wallcycle_start(wcycle, ewcRUN);
655 print_start(fplog, cr, walltime_accounting, "mdrun");
657 /* safest point to do file checkpointing is here. More general point would be immediately before integrator call */
659 chkpt_ret = fcCheckPointParallel( cr->nodeid,
663 gmx_fatal( 3, __FILE__, __LINE__, "Checkpoint error on step %d\n", 0 );
668 /***********************************************************
672 ************************************************************/
674 /* if rerunMD then read coordinates and velocities from input trajectory */
677 if (getenv("GMX_FORCE_UPDATE"))
685 bNotLastFrame = read_first_frame(oenv, &status,
686 opt2fn("-rerun", nfile, fnm),
687 &rerun_fr, TRX_NEED_X | TRX_READ_V);
688 if (rerun_fr.natoms != top_global->natoms)
691 "Number of atoms in trajectory (%d) does not match the "
692 "run input file (%d)\n",
693 rerun_fr.natoms, top_global->natoms);
695 if (ir->ePBC != epbcNONE)
699 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);
701 if (max_cutoff2(ir->ePBC, rerun_fr.box) < sqr(fr->rlistlong))
703 gmx_fatal(FARGS, "Rerun trajectory frame step %d time %f has too small box dimensions", rerun_fr.step, rerun_fr.time);
710 rerun_parallel_comm(cr, &rerun_fr, &bNotLastFrame);
713 if (ir->ePBC != epbcNONE)
715 /* Set the shift vectors.
716 * Necessary here when have a static box different from the tpr box.
718 calc_shifts(rerun_fr.box, fr->shift_vec);
722 /* loop over MD steps or if rerunMD to end of input trajectory */
724 /* Skip the first Nose-Hoover integration when we get the state from tpx */
725 bStateFromTPX = !bStateFromCP;
726 bInitStep = bFirstStep && (bStateFromTPX || bVV);
727 bStartingFromCpt = (Flags & MD_STARTFROMCPT) && bInitStep;
728 bSumEkinhOld = FALSE;
730 bNeedRepartition = FALSE;
732 init_global_signals(&gs, cr, ir, repl_ex_nst);
734 step = ir->init_step;
737 init_nlistheuristics(&nlh, bGStatEveryStep, step);
739 if (MULTISIM(cr) && (repl_ex_nst <= 0 ))
741 /* check how many steps are left in other sims */
742 multisim_nsteps = get_multisim_nsteps(cr, ir->nsteps);
746 /* and stop now if we should */
747 bLastStep = (bRerunMD || (ir->nsteps >= 0 && step_rel > ir->nsteps) ||
748 ((multisim_nsteps >= 0) && (step_rel >= multisim_nsteps )));
749 while (!bLastStep || (bRerunMD && bNotLastFrame))
752 wallcycle_start(wcycle, ewcSTEP);
758 step = rerun_fr.step;
759 step_rel = step - ir->init_step;
772 bLastStep = (step_rel == ir->nsteps);
773 t = t0 + step*ir->delta_t;
776 if (ir->efep != efepNO || ir->bSimTemp)
778 /* find and set the current lambdas. If rerunning, we either read in a state, or a lambda value,
779 requiring different logic. */
781 set_current_lambdas(step, ir->fepvals, bRerunMD, &rerun_fr, state_global, state, lam0);
782 bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
783 bDoFEP = (do_per_step(step, nstfep) && (ir->efep != efepNO));
784 bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded)
785 && (ir->bExpanded) && (step > 0) && (!bStartingFromCpt));
790 update_annealing_target_temp(&(ir->opts), t);
795 if (!DOMAINDECOMP(cr) || MASTER(cr))
797 for (i = 0; i < state_global->natoms; i++)
799 copy_rvec(rerun_fr.x[i], state_global->x[i]);
803 for (i = 0; i < state_global->natoms; i++)
805 copy_rvec(rerun_fr.v[i], state_global->v[i]);
810 for (i = 0; i < state_global->natoms; i++)
812 clear_rvec(state_global->v[i]);
816 fprintf(stderr, "\nWARNING: Some frames do not contain velocities.\n"
817 " Ekin, temperature and pressure are incorrect,\n"
818 " the virial will be incorrect when constraints are present.\n"
820 bRerunWarnNoV = FALSE;
824 copy_mat(rerun_fr.box, state_global->box);
825 copy_mat(state_global->box, state->box);
827 if (vsite && (Flags & MD_RERUN_VSITE))
829 if (DOMAINDECOMP(cr))
831 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, use a single rank");
835 /* Following is necessary because the graph may get out of sync
836 * with the coordinates if we only have every N'th coordinate set
838 mk_mshift(fplog, graph, fr->ePBC, state->box, state->x);
839 shift_self(graph, state->box, state->x);
841 construct_vsites(vsite, state->x, ir->delta_t, state->v,
842 top->idef.iparams, top->idef.il,
843 fr->ePBC, fr->bMolPBC, cr, state->box);
846 unshift_self(graph, state->box, state->x);
851 /* Stop Center of Mass motion */
852 bStopCM = (ir->comm_mode != ecmNO && do_per_step(step, ir->nstcomm));
856 /* for rerun MD always do Neighbour Searching */
857 bNS = (bFirstStep || ir->nstlist != 0);
862 /* Determine whether or not to do Neighbour Searching and LR */
863 bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
865 bNS = (bFirstStep || bExchanged || bNeedRepartition || bNStList || bDoFEP ||
866 (ir->nstlist == -1 && nlh.nabnsb > 0));
868 if (bNS && ir->nstlist == -1)
870 set_nlistheuristics(&nlh, bFirstStep || bExchanged || bNeedRepartition || bDoFEP, step);
874 /* check whether we should stop because another simulation has
878 if ( (multisim_nsteps >= 0) && (step_rel >= multisim_nsteps) &&
879 (multisim_nsteps != ir->nsteps) )
886 "Stopping simulation %d because another one has finished\n",
890 gs.sig[eglsCHKPT] = 1;
895 /* < 0 means stop at next step, > 0 means stop at next NS step */
896 if ( (gs.set[eglsSTOPCOND] < 0) ||
897 ( (gs.set[eglsSTOPCOND] > 0) && (bNStList || ir->nstlist == 0) ) )
902 /* Determine whether or not to update the Born radii if doing GB */
903 bBornRadii = bFirstStep;
904 if (ir->implicit_solvent && (step % ir->nstgbradii == 0))
909 do_log = do_per_step(step, ir->nstlog) || bFirstStep || bLastStep;
910 do_verbose = bVerbose &&
911 (step % stepout == 0 || bFirstStep || bLastStep);
913 if (bNS && !(bFirstStep && ir->bContinuation && !bRerunMD))
921 bMasterState = FALSE;
922 /* Correct the new box if it is too skewed */
923 if (DYNAMIC_BOX(*ir))
925 if (correct_box(fplog, step, state->box, graph))
930 if (DOMAINDECOMP(cr) && bMasterState)
932 dd_collect_state(cr->dd, state, state_global);
936 if (DOMAINDECOMP(cr))
938 /* Repartition the domain decomposition */
939 wallcycle_start(wcycle, ewcDOMDEC);
940 dd_partition_system(fplog, step, cr,
941 bMasterState, nstglobalcomm,
942 state_global, top_global, ir,
943 state, &f, mdatoms, top, fr,
944 vsite, shellfc, constr,
946 do_verbose && !bPMETuneRunning);
947 wallcycle_stop(wcycle, ewcDOMDEC);
948 /* If using an iterative integrator, reallocate space to match the decomposition */
952 if (MASTER(cr) && do_log)
954 print_ebin_header(fplog, step, t, state->lambda[efptFEP]); /* can we improve the information printed here? */
957 if (ir->efep != efepNO)
959 update_mdatoms(mdatoms, state->lambda[efptMASS]);
962 if ((bRerunMD && rerun_fr.bV) || bExchanged)
965 /* We need the kinetic energy at minus the half step for determining
966 * the full step kinetic energy and possibly for T-coupling.*/
967 /* This may not be quite working correctly yet . . . . */
968 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
969 wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
970 constr, NULL, FALSE, state->box,
971 top_global, &bSumEkinhOld,
972 CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
974 clear_mat(force_vir);
976 /* We write a checkpoint at this MD step when:
977 * either at an NS step when we signalled through gs,
978 * or at the last step (but not when we do not want confout),
979 * but never at the first step or with rerun.
981 bCPT = (((gs.set[eglsCHKPT] && (bNS || ir->nstlist == 0)) ||
982 (bLastStep && (Flags & MD_CONFOUT))) &&
983 step > ir->init_step && !bRerunMD);
986 gs.set[eglsCHKPT] = 0;
989 /* Determine the energy and pressure:
990 * at nstcalcenergy steps and at energy output steps (set below).
992 if (EI_VV(ir->eI) && (!bInitStep))
994 /* for vv, the first half of the integration actually corresponds
995 to the previous step. bCalcEner is only required to be evaluated on the 'next' step,
996 but the virial needs to be calculated on both the current step and the 'next' step. Future
997 reorganization may be able to get rid of one of the bCalcVir=TRUE steps. */
999 bCalcEner = do_per_step(step-1, ir->nstcalcenergy);
1000 bCalcVir = bCalcEner ||
1001 (ir->epc != epcNO && (do_per_step(step, ir->nstpcouple) || do_per_step(step-1, ir->nstpcouple)));
1005 bCalcEner = do_per_step(step, ir->nstcalcenergy);
1006 bCalcVir = bCalcEner ||
1007 (ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
1010 /* Do we need global communication ? */
1011 bGStat = (bCalcVir || bCalcEner || bStopCM ||
1012 do_per_step(step, nstglobalcomm) || (bVV && IR_NVT_TROTTER(ir) && do_per_step(step-1, nstglobalcomm)) ||
1013 (ir->nstlist == -1 && !bRerunMD && step >= nlh.step_nscheck));
1015 do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
1017 if (do_ene || do_log)
1024 /* these CGLO_ options remain the same throughout the iteration */
1025 cglo_flags = ((bRerunMD ? CGLO_RERUNMD : 0) |
1026 (bGStat ? CGLO_GSTAT : 0)
1029 force_flags = (GMX_FORCE_STATECHANGED |
1030 ((DYNAMIC_BOX(*ir) || bRerunMD) ? GMX_FORCE_DYNAMICBOX : 0) |
1031 GMX_FORCE_ALLFORCES |
1033 (bCalcVir ? GMX_FORCE_VIRIAL : 0) |
1034 (bCalcEner ? GMX_FORCE_ENERGY : 0) |
1035 (bDoFEP ? GMX_FORCE_DHDL : 0)
1040 if (do_per_step(step, ir->nstcalclr))
1042 force_flags |= GMX_FORCE_DO_LR;
1048 /* Now is the time to relax the shells */
1049 count = relax_shell_flexcon(fplog, cr, bVerbose, step,
1050 ir, bNS, force_flags,
1053 state, f, force_vir, mdatoms,
1054 nrnb, wcycle, graph, groups,
1055 shellfc, fr, bBornRadii, t, mu_tot,
1057 mdoutf_get_fp_field(outf));
1067 /* The coordinates (x) are shifted (to get whole molecules)
1069 * This is parallellized as well, and does communication too.
1070 * Check comments in sim_util.c
1072 do_force(fplog, cr, ir, step, nrnb, wcycle, top, groups,
1073 state->box, state->x, &state->hist,
1074 f, force_vir, mdatoms, enerd, fcd,
1075 state->lambda, graph,
1076 fr, vsite, mu_tot, t, mdoutf_get_fp_field(outf), ed, bBornRadii,
1077 (bNS ? GMX_FORCE_NS : 0) | force_flags);
1080 if (bVV && !bStartingFromCpt && !bRerunMD)
1081 /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
1083 if (ir->eI == eiVV && bInitStep)
1085 /* if using velocity verlet with full time step Ekin,
1086 * take the first half step only to compute the
1087 * virial for the first step. From there,
1088 * revert back to the initial coordinates
1089 * so that the input is actually the initial step.
1091 copy_rvecn(state->v, cbuf, 0, state->natoms); /* should make this better for parallelizing? */
1095 /* this is for NHC in the Ekin(t+dt/2) version of vv */
1096 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ1);
1099 /* If we are using twin-range interactions where the long-range component
1100 * is only evaluated every nstcalclr>1 steps, we should do a special update
1101 * step to combine the long-range forces on these steps.
1102 * For nstcalclr=1 this is not done, since the forces would have been added
1103 * directly to the short-range forces already.
1105 * TODO Remove various aspects of VV+twin-range in master
1106 * branch, because VV integrators did not ever support
1107 * twin-range multiple time stepping with constraints.
1109 bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
1111 update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC,
1112 f, bUpdateDoLR, fr->f_twin, fcd,
1113 ekind, M, upd, bInitStep, etrtVELOCITY1,
1114 cr, nrnb, constr, &top->idef);
1116 if (bIterativeCase && do_per_step(step-1, ir->nstpcouple) && !bInitStep)
1118 gmx_iterate_init(&iterate, TRUE);
1120 /* for iterations, we save these vectors, as we will be self-consistently iterating
1123 /*#### UPDATE EXTENDED VARIABLES IN TROTTER FORMULATION */
1125 /* save the state */
1126 if (iterate.bIterationActive)
1128 copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
1131 bFirstIterate = TRUE;
1132 while (bFirstIterate || iterate.bIterationActive)
1134 if (iterate.bIterationActive)
1136 copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
1137 if (bFirstIterate && bTrotter)
1139 /* The first time through, we need a decent first estimate
1140 of veta(t+dt) to compute the constraints. Do
1141 this by computing the box volume part of the
1142 trotter integration at this time. Nothing else
1143 should be changed by this routine here. If
1144 !(first time), we start with the previous value
1147 veta_save = state->veta;
1148 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ0);
1149 vetanew = state->veta;
1150 state->veta = veta_save;
1155 if (!bRerunMD || rerun_fr.bV || bForceUpdate) /* Why is rerun_fr.bV here? Unclear. */
1157 update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
1158 state, fr->bMolPBC, graph, f,
1159 &top->idef, shake_vir,
1160 cr, nrnb, wcycle, upd, constr,
1161 TRUE, bCalcVir, vetanew);
1165 gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
1171 /* Need to unshift here if a do_force has been
1172 called in the previous step */
1173 unshift_self(graph, state->box, state->x);
1176 /* if VV, compute the pressure and constraints */
1177 /* For VV2, we strictly only need this if using pressure
1178 * control, but we really would like to have accurate pressures
1180 * Think about ways around this in the future?
1181 * For now, keep this choice in comments.
1183 /*bPres = (ir->eI==eiVV || IR_NPT_TROTTER(ir)); */
1184 /*bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK && IR_NPT_TROTTER(ir)));*/
1186 bTemp = ((ir->eI == eiVV && (!bInitStep)) || (ir->eI == eiVVAK));
1187 if (bCalcEner && ir->eI == eiVVAK) /*MRS: 7/9/2010 -- this still doesn't fix it?*/
1189 bSumEkinhOld = TRUE;
1191 /* for vv, the first half of the integration actually corresponds to the previous step.
1192 So we need information from the last step in the first half of the integration */
1193 if (bGStat || do_per_step(step-1, nstglobalcomm))
1195 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
1196 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
1197 constr, NULL, FALSE, state->box,
1198 top_global, &bSumEkinhOld,
1201 | (bTemp ? CGLO_TEMPERATURE : 0)
1202 | (bPres ? CGLO_PRESSURE : 0)
1203 | (bPres ? CGLO_CONSTRAINT : 0)
1204 | ((iterate.bIterationActive) ? CGLO_ITERATE : 0)
1205 | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
1208 /* explanation of above:
1209 a) We compute Ekin at the full time step
1210 if 1) we are using the AveVel Ekin, and it's not the
1211 initial step, or 2) if we are using AveEkin, but need the full
1212 time step kinetic energy for the pressure (always true now, since we want accurate statistics).
1213 b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
1214 EkinAveVel because it's needed for the pressure */
1216 /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
1221 m_add(force_vir, shake_vir, total_vir); /* we need the un-dispersion corrected total vir here */
1222 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ2);
1229 /* We need the kinetic energy at minus the half step for determining
1230 * the full step kinetic energy and possibly for T-coupling.*/
1231 /* This may not be quite working correctly yet . . . . */
1232 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
1233 wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
1234 constr, NULL, FALSE, state->box,
1235 top_global, &bSumEkinhOld,
1236 CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
1241 if (iterate.bIterationActive &&
1242 done_iterating(cr, fplog, step, &iterate, bFirstIterate,
1243 state->veta, &vetanew))
1247 bFirstIterate = FALSE;
1250 if (bTrotter && !bInitStep)
1252 copy_mat(shake_vir, state->svir_prev);
1253 copy_mat(force_vir, state->fvir_prev);
1254 if (IR_NVT_TROTTER(ir) && ir->eI == eiVV)
1256 /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
1257 enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, NULL, (ir->eI == eiVV), FALSE);
1258 enerd->term[F_EKIN] = trace(ekind->ekin);
1261 /* if it's the initial step, we performed this first step just to get the constraint virial */
1262 if (bInitStep && ir->eI == eiVV)
1264 copy_rvecn(cbuf, state->v, 0, state->natoms);
1268 /* MRS -- now done iterating -- compute the conserved quantity */
1271 saved_conserved_quantity = compute_conserved_from_auxiliary(ir, state, &MassQ);
1274 last_ekin = enerd->term[F_EKIN];
1276 if ((ir->eDispCorr != edispcEnerPres) && (ir->eDispCorr != edispcAllEnerPres))
1278 saved_conserved_quantity -= enerd->term[F_DISPCORR];
1280 /* sum up the foreign energy and dhdl terms for vv. currently done every step so that dhdl is correct in the .edr */
1283 sum_dhdl(enerd, state->lambda, ir->fepvals);
1287 /* ######## END FIRST UPDATE STEP ############## */
1288 /* ######## If doing VV, we now have v(dt) ###### */
1291 /* perform extended ensemble sampling in lambda - we don't
1292 actually move to the new state before outputting
1293 statistics, but if performing simulated tempering, we
1294 do update the velocities and the tau_t. */
1296 lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, state->fep_state, &state->dfhist, step, state->v, mdatoms);
1297 /* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
1298 copy_df_history(&state_global->dfhist, &state->dfhist);
1301 /* Now we have the energies and forces corresponding to the
1302 * coordinates at time t. We must output all of this before
1305 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
1306 ir, state, state_global, top_global, fr,
1307 outf, mdebin, ekind, f, f_global,
1309 bCPT, bRerunMD, bLastStep, (Flags & MD_CONFOUT),
1311 /* Check if IMD step and do IMD communication, if bIMD is TRUE. */
1312 bIMDstep = do_IMD(ir->bIMD, step, cr, bNS, state->box, state->x, ir, t, wcycle);
1314 /* kludge -- virial is lost with restart for NPT control. Must restart */
1315 if (bStartingFromCpt && bVV)
1317 copy_mat(state->svir_prev, shake_vir);
1318 copy_mat(state->fvir_prev, force_vir);
1321 elapsed_time = walltime_accounting_get_current_elapsed_time(walltime_accounting);
1323 /* Check whether everything is still allright */
1324 if (((int)gmx_get_stop_condition() > handled_stop_condition)
1325 #ifdef GMX_THREAD_MPI
1330 /* this is just make gs.sig compatible with the hack
1331 of sending signals around by MPI_Reduce with together with
1333 if (gmx_get_stop_condition() == gmx_stop_cond_next_ns)
1335 gs.sig[eglsSTOPCOND] = 1;
1337 if (gmx_get_stop_condition() == gmx_stop_cond_next)
1339 gs.sig[eglsSTOPCOND] = -1;
1341 /* < 0 means stop at next step, > 0 means stop at next NS step */
1345 "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
1346 gmx_get_signal_name(),
1347 gs.sig[eglsSTOPCOND] == 1 ? "NS " : "");
1351 "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
1352 gmx_get_signal_name(),
1353 gs.sig[eglsSTOPCOND] == 1 ? "NS " : "");
1355 handled_stop_condition = (int)gmx_get_stop_condition();
1357 else if (MASTER(cr) && (bNS || ir->nstlist <= 0) &&
1358 (max_hours > 0 && elapsed_time > max_hours*60.0*60.0*0.99) &&
1359 gs.sig[eglsSTOPCOND] == 0 && gs.set[eglsSTOPCOND] == 0)
1361 /* Signal to terminate the run */
1362 gs.sig[eglsSTOPCOND] = 1;
1365 fprintf(fplog, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
1367 fprintf(stderr, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
1370 if (bResetCountersHalfMaxH && MASTER(cr) &&
1371 elapsed_time > max_hours*60.0*60.0*0.495)
1373 gs.sig[eglsRESETCOUNTERS] = 1;
1376 if (ir->nstlist == -1 && !bRerunMD)
1378 /* When bGStatEveryStep=FALSE, global_stat is only called
1379 * when we check the atom displacements, not at NS steps.
1380 * This means that also the bonded interaction count check is not
1381 * performed immediately after NS. Therefore a few MD steps could
1382 * be performed with missing interactions.
1383 * But wrong energies are never written to file,
1384 * since energies are only written after global_stat
1387 if (step >= nlh.step_nscheck)
1389 nlh.nabnsb = natoms_beyond_ns_buffer(ir, fr, &top->cgs,
1390 nlh.scale_tot, state->x);
1394 /* This is not necessarily true,
1395 * but step_nscheck is determined quite conservatively.
1401 /* In parallel we only have to check for checkpointing in steps
1402 * where we do global communication,
1403 * otherwise the other nodes don't know.
1405 if (MASTER(cr) && ((bGStat || !PAR(cr)) &&
1408 elapsed_time >= nchkpt*cpt_period*60.0)) &&
1409 gs.set[eglsCHKPT] == 0)
1411 gs.sig[eglsCHKPT] = 1;
1414 /* at the start of step, randomize or scale the velocities (trotter done elsewhere) */
1419 update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
1421 if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
1423 gmx_bool bIfRandomize;
1424 bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state, upd, constr);
1425 /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
1426 if (constr && bIfRandomize)
1428 update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
1429 state, fr->bMolPBC, graph, f,
1430 &top->idef, tmp_vir,
1431 cr, nrnb, wcycle, upd, constr,
1432 TRUE, bCalcVir, vetanew);
1437 if (bIterativeCase && do_per_step(step, ir->nstpcouple))
1439 gmx_iterate_init(&iterate, TRUE);
1440 /* for iterations, we save these vectors, as we will be redoing the calculations */
1441 copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
1444 bFirstIterate = TRUE;
1445 while (bFirstIterate || iterate.bIterationActive)
1447 /* We now restore these vectors to redo the calculation with improved extended variables */
1448 if (iterate.bIterationActive)
1450 copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
1453 /* We make the decision to break or not -after- the calculation of Ekin and Pressure,
1454 so scroll down for that logic */
1456 /* ######### START SECOND UPDATE STEP ################# */
1457 /* Box is changed in update() when we do pressure coupling,
1458 * but we should still use the old box for energy corrections and when
1459 * writing it to the energy file, so it matches the trajectory files for
1460 * the same timestep above. Make a copy in a separate array.
1462 copy_mat(state->box, lastbox);
1467 if (!(bRerunMD && !rerun_fr.bV && !bForceUpdate))
1469 wallcycle_start(wcycle, ewcUPDATE);
1470 /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
1473 if (iterate.bIterationActive)
1481 /* we use a new value of scalevir to converge the iterations faster */
1482 scalevir = tracevir/trace(shake_vir);
1484 msmul(shake_vir, scalevir, shake_vir);
1485 m_add(force_vir, shake_vir, total_vir);
1486 clear_mat(shake_vir);
1488 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
1489 /* We can only do Berendsen coupling after we have summed
1490 * the kinetic energy or virial. Since the happens
1491 * in global_state after update, we should only do it at
1492 * step % nstlist = 1 with bGStatEveryStep=FALSE.
1497 update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
1498 update_pcouple(fplog, step, ir, state, pcoupl_mu, M, bInitStep);
1503 bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
1505 /* velocity half-step update */
1506 update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
1507 bUpdateDoLR, fr->f_twin, fcd,
1508 ekind, M, upd, FALSE, etrtVELOCITY2,
1509 cr, nrnb, constr, &top->idef);
1512 /* Above, initialize just copies ekinh into ekin,
1513 * it doesn't copy position (for VV),
1514 * and entire integrator for MD.
1517 if (ir->eI == eiVVAK)
1519 copy_rvecn(state->x, cbuf, 0, state->natoms);
1521 bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
1523 update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
1524 bUpdateDoLR, fr->f_twin, fcd,
1525 ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
1526 wallcycle_stop(wcycle, ewcUPDATE);
1528 update_constraints(fplog, step, &dvdl_constr, ir, ekind, mdatoms, state,
1529 fr->bMolPBC, graph, f,
1530 &top->idef, shake_vir,
1531 cr, nrnb, wcycle, upd, constr,
1532 FALSE, bCalcVir, state->veta);
1534 if (ir->eI == eiVVAK)
1536 /* erase F_EKIN and F_TEMP here? */
1537 /* just compute the kinetic energy at the half step to perform a trotter step */
1538 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
1539 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
1540 constr, NULL, FALSE, lastbox,
1541 top_global, &bSumEkinhOld,
1542 cglo_flags | CGLO_TEMPERATURE
1544 wallcycle_start(wcycle, ewcUPDATE);
1545 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ4);
1546 /* now we know the scaling, we can compute the positions again again */
1547 copy_rvecn(cbuf, state->x, 0, state->natoms);
1549 bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
1551 update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
1552 bUpdateDoLR, fr->f_twin, fcd,
1553 ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
1554 wallcycle_stop(wcycle, ewcUPDATE);
1556 /* do we need an extra constraint here? just need to copy out of state->v to upd->xp? */
1557 /* are the small terms in the shake_vir here due
1558 * to numerical errors, or are they important
1559 * physically? I'm thinking they are just errors, but not completely sure.
1560 * For now, will call without actually constraining, constr=NULL*/
1561 update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
1562 state, fr->bMolPBC, graph, f,
1563 &top->idef, tmp_vir,
1564 cr, nrnb, wcycle, upd, NULL,
1570 gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
1573 if (fr->bSepDVDL && fplog && do_log)
1575 gmx_print_sepdvdl(fplog, "Constraint dV/dl", 0.0, dvdl_constr);
1579 /* this factor or 2 correction is necessary
1580 because half of the constraint force is removed
1581 in the vv step, so we have to double it. See
1582 the Redmine issue #1255. It is not yet clear
1583 if the factor of 2 is exact, or just a very
1584 good approximation, and this will be
1585 investigated. The next step is to see if this
1586 can be done adding a dhdl contribution from the
1587 rattle step, but this is somewhat more
1588 complicated with the current code. Will be
1589 investigated, hopefully for 4.6.3. However,
1590 this current solution is much better than
1591 having it completely wrong.
1593 enerd->term[F_DVDL_CONSTR] += 2*dvdl_constr;
1597 enerd->term[F_DVDL_CONSTR] += dvdl_constr;
1602 /* Need to unshift here */
1603 unshift_self(graph, state->box, state->x);
1608 wallcycle_start(wcycle, ewcVSITECONSTR);
1611 shift_self(graph, state->box, state->x);
1613 construct_vsites(vsite, state->x, ir->delta_t, state->v,
1614 top->idef.iparams, top->idef.il,
1615 fr->ePBC, fr->bMolPBC, cr, state->box);
1619 unshift_self(graph, state->box, state->x);
1621 wallcycle_stop(wcycle, ewcVSITECONSTR);
1624 /* ############## IF NOT VV, Calculate globals HERE, also iterate constraints ############ */
1625 /* With Leap-Frog we can skip compute_globals at
1626 * non-communication steps, but we need to calculate
1627 * the kinetic energy one step before communication.
1629 if (bGStat || (!EI_VV(ir->eI) && do_per_step(step+1, nstglobalcomm)))
1631 if (ir->nstlist == -1 && bFirstIterate)
1633 gs.sig[eglsNABNSB] = nlh.nabnsb;
1635 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
1636 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
1638 bFirstIterate ? &gs : NULL,
1639 (step_rel % gs.nstms == 0) &&
1640 (multisim_nsteps < 0 || (step_rel < multisim_nsteps)),
1642 top_global, &bSumEkinhOld,
1644 | (!EI_VV(ir->eI) || bRerunMD ? CGLO_ENERGY : 0)
1645 | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
1646 | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
1647 | (!EI_VV(ir->eI) || bRerunMD ? CGLO_PRESSURE : 0)
1648 | (iterate.bIterationActive ? CGLO_ITERATE : 0)
1649 | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
1652 if (ir->nstlist == -1 && bFirstIterate)
1654 nlh.nabnsb = gs.set[eglsNABNSB];
1655 gs.set[eglsNABNSB] = 0;
1658 /* bIterate is set to keep it from eliminating the old ekin kinetic energy terms */
1659 /* ############# END CALC EKIN AND PRESSURE ################# */
1661 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
1662 the virial that should probably be addressed eventually. state->veta has better properies,
1663 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
1664 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
1666 if (iterate.bIterationActive &&
1667 done_iterating(cr, fplog, step, &iterate, bFirstIterate,
1668 trace(shake_vir), &tracevir))
1672 bFirstIterate = FALSE;
1675 if (!bVV || bRerunMD)
1677 /* sum up the foreign energy and dhdl terms for md and sd. currently done every step so that dhdl is correct in the .edr */
1678 sum_dhdl(enerd, state->lambda, ir->fepvals);
1680 update_box(fplog, step, ir, mdatoms, state, f,
1681 ir->nstlist == -1 ? &nlh.scale_tot : NULL, pcoupl_mu, nrnb, upd);
1683 /* ################# END UPDATE STEP 2 ################# */
1684 /* #### We now have r(t+dt) and v(t+dt/2) ############# */
1686 /* The coordinates (x) were unshifted in update */
1689 /* We will not sum ekinh_old,
1690 * so signal that we still have to do it.
1692 bSumEkinhOld = TRUE;
1695 /* ######### BEGIN PREPARING EDR OUTPUT ########### */
1697 /* use the directly determined last velocity, not actually the averaged half steps */
1698 if (bTrotter && ir->eI == eiVV)
1700 enerd->term[F_EKIN] = last_ekin;
1702 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
1706 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
1710 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + compute_conserved_from_auxiliary(ir, state, &MassQ);
1712 /* ######### END PREPARING EDR OUTPUT ########### */
1717 gmx_bool do_dr, do_or;
1719 if (fplog && do_log && bDoExpanded)
1721 /* only needed if doing expanded ensemble */
1722 PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : NULL,
1723 &state_global->dfhist, state->fep_state, ir->nstlog, step);
1725 if (!(bStartingFromCpt && (EI_VV(ir->eI))))
1729 upd_mdebin(mdebin, bDoDHDL, TRUE,
1730 t, mdatoms->tmass, enerd, state,
1731 ir->fepvals, ir->expandedvals, lastbox,
1732 shake_vir, force_vir, total_vir, pres,
1733 ekind, mu_tot, constr);
1737 upd_mdebin_step(mdebin);
1740 do_dr = do_per_step(step, ir->nstdisreout);
1741 do_or = do_per_step(step, ir->nstorireout);
1743 print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : NULL,
1745 eprNORMAL, bCompact, mdebin, fcd, groups, &(ir->opts));
1747 if (ir->ePull != epullNO)
1749 pull_print_output(ir->pull, step, t);
1752 if (do_per_step(step, ir->nstlog))
1754 if (fflush(fplog) != 0)
1756 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
1762 /* Have to do this part _after_ outputting the logfile and the edr file */
1763 /* Gets written into the state at the beginning of next loop*/
1764 state->fep_state = lamnew;
1766 /* Print the remaining wall clock time for the run */
1767 if (MULTIMASTER(cr) && (do_verbose || gmx_got_usr_signal()) && !bPMETuneRunning)
1771 fprintf(stderr, "\n");
1773 print_time(stderr, walltime_accounting, step, ir, cr);
1776 /* Ion/water position swapping.
1777 * Not done in last step since trajectory writing happens before this call
1778 * in the MD loop and exchanges would be lost anyway. */
1779 bNeedRepartition = FALSE;
1780 if ((ir->eSwapCoords != eswapNO) && (step > 0) && !bLastStep &&
1781 do_per_step(step, ir->swap->nstswap))
1783 bNeedRepartition = do_swapcoords(cr, step, t, ir, wcycle,
1784 bRerunMD ? rerun_fr.x : state->x,
1785 bRerunMD ? rerun_fr.box : state->box,
1786 top_global, MASTER(cr) && bVerbose, bRerunMD);
1788 if (bNeedRepartition && DOMAINDECOMP(cr))
1790 dd_collect_state(cr->dd, state, state_global);
1794 /* Replica exchange */
1796 if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
1797 do_per_step(step, repl_ex_nst))
1799 bExchanged = replica_exchange(fplog, cr, repl_ex,
1800 state_global, enerd,
1804 if ( (bExchanged || bNeedRepartition) && DOMAINDECOMP(cr) )
1806 dd_partition_system(fplog, step, cr, TRUE, 1,
1807 state_global, top_global, ir,
1808 state, &f, mdatoms, top, fr,
1809 vsite, shellfc, constr,
1810 nrnb, wcycle, FALSE);
1815 bStartingFromCpt = FALSE;
1817 /* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
1818 /* With all integrators, except VV, we need to retain the pressure
1819 * at the current step for coupling at the next step.
1821 if ((state->flags & (1<<estPRES_PREV)) &&
1823 (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
1825 /* Store the pressure in t_state for pressure coupling
1826 * at the next MD step.
1828 copy_mat(pres, state->pres_prev);
1831 /* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
1833 if ( (membed != NULL) && (!bLastStep) )
1835 rescale_membed(step_rel, membed, state_global->x);
1842 /* read next frame from input trajectory */
1843 bNotLastFrame = read_next_frame(oenv, status, &rerun_fr);
1848 rerun_parallel_comm(cr, &rerun_fr, &bNotLastFrame);
1852 if (!bRerunMD || !rerun_fr.bStep)
1854 /* increase the MD step number */
1859 cycles = wallcycle_stop(wcycle, ewcSTEP);
1860 if (DOMAINDECOMP(cr) && wcycle)
1862 dd_cycles_add(cr->dd, cycles, ddCyclStep);
1865 if (bPMETuneRunning || bPMETuneTry)
1867 /* PME grid + cut-off optimization with GPUs or PME nodes */
1869 /* Count the total cycles over the last steps */
1870 cycles_pmes += cycles;
1872 /* We can only switch cut-off at NS steps */
1873 if (step % ir->nstlist == 0)
1875 /* PME grid + cut-off optimization with GPUs or PME nodes */
1878 if (DDMASTER(cr->dd))
1880 /* PME node load is too high, start tuning */
1881 bPMETuneRunning = (dd_pme_f_ratio(cr->dd) >= 1.05);
1883 dd_bcast(cr->dd, sizeof(gmx_bool), &bPMETuneRunning);
1885 if (bPMETuneRunning || step_rel > ir->nstlist*50)
1887 bPMETuneTry = FALSE;
1890 if (bPMETuneRunning)
1892 /* init_step might not be a multiple of nstlist,
1893 * but the first cycle is always skipped anyhow.
1896 pme_load_balance(pme_loadbal, cr,
1897 (bVerbose && MASTER(cr)) ? stderr : NULL,
1899 ir, state, cycles_pmes,
1900 fr->ic, fr->nbv, &fr->pmedata,
1903 /* Update constants in forcerec/inputrec to keep them in sync with fr->ic */
1904 fr->ewaldcoeff_q = fr->ic->ewaldcoeff_q;
1905 fr->ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
1906 fr->rlist = fr->ic->rlist;
1907 fr->rlistlong = fr->ic->rlistlong;
1908 fr->rcoulomb = fr->ic->rcoulomb;
1909 fr->rvdw = fr->ic->rvdw;
1911 if (ir->eDispCorr != edispcNO)
1913 calc_enervirdiff(NULL, ir->eDispCorr, fr);
1920 if (step_rel == wcycle_get_reset_counters(wcycle) ||
1921 gs.set[eglsRESETCOUNTERS] != 0)
1923 /* Reset all the counters related to performance over the run */
1924 reset_all_counters(fplog, cr, step, &step_rel, ir, wcycle, nrnb, walltime_accounting,
1925 fr->nbv != NULL && fr->nbv->bUseGPU ? fr->nbv->cu_nbv : NULL);
1926 wcycle_set_reset_counters(wcycle, -1);
1927 if (!(cr->duty & DUTY_PME))
1929 /* Tell our PME node to reset its counters */
1930 gmx_pme_send_resetcounters(cr, step);
1932 /* Correct max_hours for the elapsed time */
1933 max_hours -= elapsed_time/(60.0*60.0);
1934 bResetCountersHalfMaxH = FALSE;
1935 gs.set[eglsRESETCOUNTERS] = 0;
1938 /* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
1939 IMD_prep_energies_send_positions(ir->bIMD && MASTER(cr), bIMDstep, ir->imd, enerd, step, bCalcEner, wcycle);
1942 /* End of main MD loop */
1945 /* Stop measuring walltime */
1946 walltime_accounting_end(walltime_accounting);
1948 if (bRerunMD && MASTER(cr))
1953 if (!(cr->duty & DUTY_PME))
1955 /* Tell the PME only node to finish */
1956 gmx_pme_send_finish(cr);
1961 if (ir->nstcalcenergy > 0 && !bRerunMD)
1963 print_ebin(mdoutf_get_fp_ene(outf), FALSE, FALSE, FALSE, fplog, step, t,
1964 eprAVER, FALSE, mdebin, fcd, groups, &(ir->opts));
1971 if (ir->nstlist == -1 && nlh.nns > 0 && fplog)
1973 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)));
1974 fprintf(fplog, "Average number of atoms that crossed the half buffer length: %.1f\n\n", nlh.ab/nlh.nns);
1977 if (pme_loadbal != NULL)
1979 pme_loadbal_done(pme_loadbal, cr, fplog,
1980 fr->nbv != NULL && fr->nbv->bUseGPU);
1983 if (shellfc && fplog)
1985 fprintf(fplog, "Fraction of iterations that converged: %.2f %%\n",
1986 (nconverged*100.0)/step_rel);
1987 fprintf(fplog, "Average number of force evaluations per MD step: %.2f\n\n",
1991 if (repl_ex_nst > 0 && MASTER(cr))
1993 print_replica_exchange_statistics(fplog, repl_ex);
1996 /* IMD cleanup, if bIMD is TRUE. */
1997 IMD_finalize(ir->bIMD, ir->imd);
1999 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);