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37 * \brief Implements the loop for simulation reruns
39 * \author Pascal Merz <pascal.merz@colorado.edu>
40 * \ingroup module_mdrun
54 #include "gromacs/awh/awh.h"
55 #include "gromacs/commandline/filenm.h"
56 #include "gromacs/compat/make_unique.h"
57 #include "gromacs/domdec/collect.h"
58 #include "gromacs/domdec/domdec.h"
59 #include "gromacs/domdec/domdec_network.h"
60 #include "gromacs/domdec/domdec_struct.h"
61 #include "gromacs/domdec/partition.h"
62 #include "gromacs/essentialdynamics/edsam.h"
63 #include "gromacs/ewald/pme.h"
64 #include "gromacs/ewald/pme-load-balancing.h"
65 #include "gromacs/fileio/trxio.h"
66 #include "gromacs/gmxlib/network.h"
67 #include "gromacs/gmxlib/nrnb.h"
68 #include "gromacs/gpu_utils/gpu_utils.h"
69 #include "gromacs/imd/imd.h"
70 #include "gromacs/listed_forces/manage-threading.h"
71 #include "gromacs/math/functions.h"
72 #include "gromacs/math/utilities.h"
73 #include "gromacs/math/vec.h"
74 #include "gromacs/math/vectypes.h"
75 #include "gromacs/mdlib/checkpointhandler.h"
76 #include "gromacs/mdlib/compute_io.h"
77 #include "gromacs/mdlib/constr.h"
78 #include "gromacs/mdlib/ebin.h"
79 #include "gromacs/mdlib/expanded.h"
80 #include "gromacs/mdlib/force.h"
81 #include "gromacs/mdlib/force_flags.h"
82 #include "gromacs/mdlib/forcerec.h"
83 #include "gromacs/mdlib/md_support.h"
84 #include "gromacs/mdlib/mdatoms.h"
85 #include "gromacs/mdlib/mdebin.h"
86 #include "gromacs/mdlib/mdoutf.h"
87 #include "gromacs/mdlib/mdrun.h"
88 #include "gromacs/mdlib/mdsetup.h"
89 #include "gromacs/mdlib/membed.h"
90 #include "gromacs/mdlib/nb_verlet.h"
91 #include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
92 #include "gromacs/mdlib/ns.h"
93 #include "gromacs/mdlib/resethandler.h"
94 #include "gromacs/mdlib/shellfc.h"
95 #include "gromacs/mdlib/sighandler.h"
96 #include "gromacs/mdlib/sim_util.h"
97 #include "gromacs/mdlib/simulationsignal.h"
98 #include "gromacs/mdlib/stophandler.h"
99 #include "gromacs/mdlib/tgroup.h"
100 #include "gromacs/mdlib/trajectory_writing.h"
101 #include "gromacs/mdlib/update.h"
102 #include "gromacs/mdlib/vcm.h"
103 #include "gromacs/mdlib/vsite.h"
104 #include "gromacs/mdtypes/awh-history.h"
105 #include "gromacs/mdtypes/awh-params.h"
106 #include "gromacs/mdtypes/commrec.h"
107 #include "gromacs/mdtypes/df_history.h"
108 #include "gromacs/mdtypes/energyhistory.h"
109 #include "gromacs/mdtypes/fcdata.h"
110 #include "gromacs/mdtypes/forcerec.h"
111 #include "gromacs/mdtypes/group.h"
112 #include "gromacs/mdtypes/inputrec.h"
113 #include "gromacs/mdtypes/interaction_const.h"
114 #include "gromacs/mdtypes/md_enums.h"
115 #include "gromacs/mdtypes/mdatom.h"
116 #include "gromacs/mdtypes/observableshistory.h"
117 #include "gromacs/mdtypes/state.h"
118 #include "gromacs/mimic/MimicUtils.h"
119 #include "gromacs/pbcutil/mshift.h"
120 #include "gromacs/pbcutil/pbc.h"
121 #include "gromacs/pulling/pull.h"
122 #include "gromacs/swap/swapcoords.h"
123 #include "gromacs/timing/wallcycle.h"
124 #include "gromacs/timing/walltime_accounting.h"
125 #include "gromacs/topology/atoms.h"
126 #include "gromacs/topology/idef.h"
127 #include "gromacs/topology/mtop_util.h"
128 #include "gromacs/topology/topology.h"
129 #include "gromacs/trajectory/trajectoryframe.h"
130 #include "gromacs/utility/basedefinitions.h"
131 #include "gromacs/utility/cstringutil.h"
132 #include "gromacs/utility/fatalerror.h"
133 #include "gromacs/utility/logger.h"
134 #include "gromacs/utility/real.h"
135 #include "gromacs/utility/smalloc.h"
137 #include "integrator.h"
138 #include "replicaexchange.h"
140 using gmx::SimulationSignaller;
142 /*! \brief Copy the state from \p rerunFrame to \p globalState and, if requested, construct vsites
144 * \param[in] rerunFrame The trajectory frame to compute energy/forces for
145 * \param[in,out] globalState The global state container
146 * \param[in] constructVsites When true, vsite coordinates are constructed
147 * \param[in] vsite Vsite setup, can be nullptr when \p constructVsites = false
148 * \param[in] idef Topology parameters, used for constructing vsites
149 * \param[in] timeStep Time step, used for constructing vsites
150 * \param[in] forceRec Force record, used for constructing vsites
151 * \param[in,out] graph The molecular graph, used for constructing vsites when != nullptr
153 static void prepareRerunState(const t_trxframe &rerunFrame,
154 t_state *globalState,
155 bool constructVsites,
156 const gmx_vsite_t *vsite,
159 const t_forcerec &forceRec,
162 auto x = makeArrayRef(globalState->x);
163 auto rerunX = arrayRefFromArray(reinterpret_cast<gmx::RVec *>(rerunFrame.x), globalState->natoms);
164 std::copy(rerunX.begin(), rerunX.end(), x.begin());
165 copy_mat(rerunFrame.box, globalState->box);
169 GMX_ASSERT(vsite, "Need valid vsite for constructing vsites");
173 /* Following is necessary because the graph may get out of sync
174 * with the coordinates if we only have every N'th coordinate set
176 mk_mshift(nullptr, graph, forceRec.ePBC, globalState->box, globalState->x.rvec_array());
177 shift_self(graph, globalState->box, as_rvec_array(globalState->x.data()));
179 construct_vsites(vsite, globalState->x.rvec_array(), timeStep, globalState->v.rvec_array(),
180 idef.iparams, idef.il,
181 forceRec.ePBC, forceRec.bMolPBC, nullptr, globalState->box);
184 unshift_self(graph, globalState->box, globalState->x.rvec_array());
189 void gmx::Integrator::do_rerun()
191 // TODO Historically, the EM and MD "integrators" used different
192 // names for the t_inputrec *parameter, but these must have the
193 // same name, now that it's a member of a struct. We use this ir
194 // alias to avoid a large ripple of nearly useless changes.
195 // t_inputrec is being replaced by IMdpOptionsProvider, so this
196 // will go away eventually.
197 t_inputrec *ir = inputrec;
198 int64_t step, step_rel;
199 double t, lam0[efptNR];
200 bool isLastStep = false;
201 bool doFreeEnergyPerturbation = false;
203 tensor force_vir, shake_vir, total_vir, pres;
208 gmx_enerdata_t *enerd;
209 PaddedVector<gmx::RVec> f {};
210 gmx_global_stat_t gstat;
211 t_graph *graph = nullptr;
212 gmx_groups_t *groups;
213 gmx_shellfc_t *shellfc;
217 /* Domain decomposition could incorrectly miss a bonded
218 interaction, but checking for that requires a global
219 communication stage, which does not otherwise happen in DD
220 code. So we do that alongside the first global energy reduction
221 after a new DD is made. These variables handle whether the
222 check happens, and the result it returns. */
223 bool shouldCheckNumberOfBondedInteractions = false;
224 int totalNumberOfBondedInteractions = -1;
226 SimulationSignals signals;
227 // Most global communnication stages don't propagate mdrun
228 // signals, and will use this object to achieve that.
229 SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
231 GMX_LOG(mdlog.info).asParagraph().
232 appendText("Note that it is planned that the command gmx mdrun -rerun will "
233 "be available in a different form in a future version of GROMACS, "
234 "e.g. gmx rerun -f.");
238 gmx_fatal(FARGS, "Expanded ensemble not supported by rerun.");
242 gmx_fatal(FARGS, "Simulated tempering not supported by rerun.");
246 gmx_fatal(FARGS, "AWH not supported by rerun.");
248 if (replExParams.exchangeInterval > 0)
250 gmx_fatal(FARGS, "Replica exchange not supported by rerun.");
252 if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
254 gmx_fatal(FARGS, "Essential dynamics not supported by rerun.");
258 gmx_fatal(FARGS, "Interactive MD not supported by rerun.");
262 gmx_fatal(FARGS, "Multiple simulations not supported by rerun.");
264 if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
265 [](int i){return i != eannNO; }))
267 gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
270 /* Rerun can't work if an output file name is the same as the input file name.
271 * If this is the case, the user will get an error telling them what the issue is.
273 if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0 ||
274 strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
276 gmx_fatal(FARGS, "When using mdrun -rerun, the name of the input trajectory file "
277 "%s cannot be identical to the name of an output file (whether "
278 "given explicitly with -o or -x, or by default)",
279 opt2fn("-rerun", nfile, fnm));
282 /* Settings for rerun */
284 ir->nstcalcenergy = 1;
285 int nstglobalcomm = 1;
286 const bool bNS = true;
288 ir->nstxout_compressed = 0;
289 groups = &top_global->groups;
290 if (ir->eI == eiMimic)
292 top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
295 initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
298 gmx_mdoutf *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, oenv, wcycle);
299 t_mdebin *mdebin = init_mdebin(mdrunOptions.continuationOptions.appendFiles ? nullptr : mdoutf_get_fp_ene(outf),
300 top_global, ir, mdoutf_get_fp_dhdl(outf), true);
302 /* Energy terms and groups */
304 init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
307 /* Kinetic energy data */
308 std::unique_ptr<gmx_ekindata_t> eKinData = compat::make_unique<gmx_ekindata_t>();
309 gmx_ekindata_t *ekind = eKinData.get();
310 init_ekindata(fplog, top_global, &(ir->opts), ekind);
311 /* Copy the cos acceleration to the groups struct */
312 ekind->cosacc.cos_accel = ir->cos_accel;
314 gstat = global_stat_init(ir);
316 /* Check for polarizable models and flexible constraints */
317 shellfc = init_shell_flexcon(fplog,
318 top_global, constr ? constr->numFlexibleConstraints() : 0,
319 ir->nstcalcenergy, DOMAINDECOMP(cr));
322 double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
323 if ((io > 2000) && MASTER(cr))
326 "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
331 // Local state only becomes valid now.
332 std::unique_ptr<t_state> stateInstance;
335 if (DOMAINDECOMP(cr))
337 dd_init_local_top(*top_global, &top);
339 stateInstance = compat::make_unique<t_state>();
340 state = stateInstance.get();
341 dd_init_local_state(cr->dd, state_global, state);
343 /* Distribute the charge groups over the nodes from the master node */
344 dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1,
345 state_global, *top_global, ir,
346 state, &f, mdAtoms, &top, fr,
348 nrnb, nullptr, FALSE);
349 shouldCheckNumberOfBondedInteractions = true;
353 state_change_natoms(state_global, state_global->natoms);
354 /* We need to allocate one element extra, since we might use
355 * (unaligned) 4-wide SIMD loads to access rvec entries.
357 f.resizeWithPadding(state_global->natoms);
358 /* Copy the pointer to the global state */
359 state = state_global;
361 mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr,
362 &graph, mdAtoms, constr, vsite, shellfc);
365 auto mdatoms = mdAtoms->mdatoms();
367 // NOTE: The global state is no longer used at this point.
368 // But state_global is still used as temporary storage space for writing
369 // the global state to file and potentially for replica exchange.
370 // (Global topology should persist.)
372 update_mdatoms(mdatoms, state->lambda[efptMASS]);
374 if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
376 doFreeEnergyPerturbation = true;
380 int cglo_flags = (CGLO_INITIALIZATION | CGLO_GSTAT |
381 (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
382 bool bSumEkinhOld = false;
383 t_vcm *vcm = nullptr;
384 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
385 nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
386 constr, &nullSignaller, state->box,
387 &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
389 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
390 top_global, &top, state,
391 &shouldCheckNumberOfBondedInteractions);
395 fprintf(stderr, "starting md rerun '%s', reading coordinates from"
396 " input trajectory '%s'\n\n",
397 *(top_global->name), opt2fn("-rerun", nfile, fnm));
398 if (mdrunOptions.verbose)
400 fprintf(stderr, "Calculated time to finish depends on nsteps from "
401 "run input file,\nwhich may not correspond to the time "
402 "needed to process input trajectory.\n\n");
404 fprintf(fplog, "\n");
407 walltime_accounting_start_time(walltime_accounting);
408 wallcycle_start(wcycle, ewcRUN);
409 print_start(fplog, cr, walltime_accounting, "mdrun");
411 /***********************************************************
415 ************************************************************/
419 GMX_LOG(mdlog.info).asParagraph().
420 appendText("Simulations has constraints. Rerun does not recalculate constraints.");
426 isLastStep = !read_first_frame(oenv, &status,
427 opt2fn("-rerun", nfile, fnm),
428 &rerun_fr, TRX_NEED_X);
429 if (rerun_fr.natoms != top_global->natoms)
432 "Number of atoms in trajectory (%d) does not match the "
433 "run input file (%d)\n",
434 rerun_fr.natoms, top_global->natoms);
437 if (ir->ePBC != epbcNONE)
441 gmx_fatal(FARGS, "Rerun trajectory frame step %" PRId64 " time %f "
442 "does not contain a box, while pbc is used",
443 rerun_fr.step, rerun_fr.time);
445 if (max_cutoff2(ir->ePBC, rerun_fr.box) < gmx::square(fr->rlist))
447 gmx_fatal(FARGS, "Rerun trajectory frame step %" PRId64 " time %f "
448 "has too small box dimensions", rerun_fr.step, rerun_fr.time);
453 GMX_LOG(mdlog.info).asParagraph().
454 appendText("Rerun does not report kinetic energy, total energy, temperature, virial and pressure.");
458 rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
461 if (ir->ePBC != epbcNONE)
463 /* Set the shift vectors.
464 * Necessary here when have a static box different from the tpr box.
466 calc_shifts(rerun_fr.box, fr->shift_vec);
469 auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
470 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false,
471 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstglobalcomm,
472 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
474 // we don't do counter resetting in rerun - finish will always be valid
475 walltime_accounting_set_valid_finish(walltime_accounting);
477 DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion = (DOMAINDECOMP(cr) ? DdOpenBalanceRegionBeforeForceComputation::yes : DdOpenBalanceRegionBeforeForceComputation::no);
478 DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion = (DOMAINDECOMP(cr) ? DdCloseBalanceRegionAfterForceComputation::yes : DdCloseBalanceRegionAfterForceComputation::no);
480 step = ir->init_step;
483 /* and stop now if we should */
484 isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
487 wallcycle_start(wcycle, ewcSTEP);
491 step = rerun_fr.step;
492 step_rel = step - ir->init_step;
503 if (ir->efep != efepNO && MASTER(cr))
505 setCurrentLambdasRerun(step, ir->fepvals, &rerun_fr, lam0, state_global);
510 const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
511 if (constructVsites && DOMAINDECOMP(cr))
513 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
514 "use a single rank");
516 prepareRerunState(rerun_fr, state_global, constructVsites, vsite, top.idef, ir->delta_t, *fr, graph);
519 isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
521 if (DOMAINDECOMP(cr))
523 /* Repartition the domain decomposition */
524 const bool bMasterState = true;
525 dd_partition_system(fplog, mdlog, step, cr,
526 bMasterState, nstglobalcomm,
527 state_global, *top_global, ir,
528 state, &f, mdAtoms, &top, fr,
531 mdrunOptions.verbose);
532 shouldCheckNumberOfBondedInteractions = true;
537 print_ebin_header(fplog, step, t); /* can we improve the information printed here? */
540 if (ir->efep != efepNO)
542 update_mdatoms(mdatoms, state->lambda[efptMASS]);
545 force_flags = (GMX_FORCE_STATECHANGED |
546 GMX_FORCE_DYNAMICBOX |
547 GMX_FORCE_ALLFORCES |
548 (GMX_GPU ? GMX_FORCE_VIRIAL : 0) | // TODO: Get rid of this once #2649 is solved
550 (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
554 /* Now is the time to relax the shells */
555 relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
556 enforcedRotation, step,
557 ir, bNS, force_flags, &top,
559 state, f.arrayRefWithPadding(), force_vir, mdatoms,
560 nrnb, wcycle, graph, groups,
561 shellfc, fr, ppForceWorkload, t, mu_tot,
563 ddOpenBalanceRegion, ddCloseBalanceRegion);
567 /* The coordinates (x) are shifted (to get whole molecules)
569 * This is parallellized as well, and does communication too.
570 * Check comments in sim_util.c
573 gmx_edsam *ed = nullptr;
574 do_force(fplog, cr, ms, ir, awh, enforcedRotation,
575 step, nrnb, wcycle, &top, groups,
576 state->box, state->x.arrayRefWithPadding(), &state->hist,
577 f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
578 state->lambda, graph,
579 fr, ppForceWorkload, vsite, mu_tot, t, ed,
580 GMX_FORCE_NS | force_flags,
581 ddOpenBalanceRegion, ddCloseBalanceRegion);
584 /* Now we have the energies and forces corresponding to the
585 * coordinates at time t.
588 const bool isCheckpointingStep = false;
589 const bool doRerun = true;
590 const bool bSumEkinhOld = false;
591 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
592 ir, state, state_global, observablesHistory,
594 outf, mdebin, ekind, f,
595 isCheckpointingStep, doRerun, isLastStep,
596 mdrunOptions.writeConfout,
600 stopHandler->setSignal();
604 /* Need to unshift here */
605 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
608 if (vsite != nullptr)
610 wallcycle_start(wcycle, ewcVSITECONSTR);
611 if (graph != nullptr)
613 shift_self(graph, state->box, as_rvec_array(state->x.data()));
615 construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
616 top.idef.iparams, top.idef.il,
617 fr->ePBC, fr->bMolPBC, cr, state->box);
619 if (graph != nullptr)
621 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
623 wallcycle_stop(wcycle, ewcVSITECONSTR);
627 const bool doInterSimSignal = false;
628 const bool doIntraSimSignal = true;
629 bool bSumEkinhOld = false;
630 t_vcm *vcm = nullptr;
631 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
633 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
634 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
637 &totalNumberOfBondedInteractions, &bSumEkinhOld,
638 CGLO_GSTAT | CGLO_ENERGY
639 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
641 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
642 top_global, &top, state,
643 &shouldCheckNumberOfBondedInteractions);
646 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
647 the virial that should probably be addressed eventually. state->veta has better properies,
648 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
649 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
651 if (ir->efep != efepNO)
653 /* Sum up the foreign energy and dhdl terms for md and sd.
654 Currently done every step so that dhdl is correct in the .edr */
655 sum_dhdl(enerd, state->lambda, ir->fepvals);
661 const bool bCalcEnerStep = true;
662 upd_mdebin(mdebin, doFreeEnergyPerturbation, bCalcEnerStep,
663 t, mdatoms->tmass, enerd, state,
664 ir->fepvals, ir->expandedvals, rerun_fr.box,
665 shake_vir, force_vir, total_vir, pres,
666 ekind, mu_tot, constr);
668 const bool do_ene = true;
669 const bool do_log = true;
671 const bool do_dr = ir->nstdisreout != 0;
672 const bool do_or = ir->nstorireout != 0;
674 print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : nullptr,
676 eprNORMAL, mdebin, fcd, groups, &(ir->opts), awh);
678 if (do_per_step(step, ir->nstlog))
680 if (fflush(fplog) != 0)
682 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
687 /* Print the remaining wall clock time for the run */
688 if (isMasterSimMasterRank(ms, cr) &&
689 (mdrunOptions.verbose || gmx_got_usr_signal()))
693 fprintf(stderr, "\n");
695 print_time(stderr, walltime_accounting, step, ir, cr);
698 /* Ion/water position swapping.
699 * Not done in last step since trajectory writing happens before this call
700 * in the MD loop and exchanges would be lost anyway. */
701 if ((ir->eSwapCoords != eswapNO) && (step > 0) && !isLastStep &&
702 do_per_step(step, ir->swap->nstswap))
704 const bool doRerun = true;
705 do_swapcoords(cr, step, t, ir, wcycle,
708 MASTER(cr) && mdrunOptions.verbose,
714 /* read next frame from input trajectory */
715 isLastStep = !read_next_frame(oenv, status, &rerun_fr);
720 rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
723 cycles = wallcycle_stop(wcycle, ewcSTEP);
724 if (DOMAINDECOMP(cr) && wcycle)
726 dd_cycles_add(cr->dd, cycles, ddCyclStep);
731 /* increase the MD step number */
736 /* End of main MD loop */
738 /* Closing TNG files can include compressing data. Therefore it is good to do that
739 * before stopping the time measurements. */
740 mdoutf_tng_close(outf);
742 /* Stop measuring walltime */
743 walltime_accounting_end_time(walltime_accounting);
750 if (!thisRankHasDuty(cr, DUTY_PME))
752 /* Tell the PME only node to finish */
753 gmx_pme_send_finish(cr);
759 done_shellfc(fplog, shellfc, step_rel);
761 // Clean up swapcoords
762 if (ir->eSwapCoords != eswapNO)
764 finish_swapcoords(ir->swap);
767 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
769 destroy_enerdata(enerd);