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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/domdec/collect.h"
57 #include "gromacs/domdec/dlbtiming.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/mdsetup.h"
62 #include "gromacs/domdec/partition.h"
63 #include "gromacs/essentialdynamics/edsam.h"
64 #include "gromacs/ewald/pme.h"
65 #include "gromacs/ewald/pme_load_balancing.h"
66 #include "gromacs/fileio/trxio.h"
67 #include "gromacs/gmxlib/network.h"
68 #include "gromacs/gmxlib/nrnb.h"
69 #include "gromacs/gpu_utils/gpu_utils.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/enerdata_utils.h"
80 #include "gromacs/mdlib/energyoutput.h"
81 #include "gromacs/mdlib/expanded.h"
82 #include "gromacs/mdlib/force.h"
83 #include "gromacs/mdlib/force_flags.h"
84 #include "gromacs/mdlib/forcerec.h"
85 #include "gromacs/mdlib/md_support.h"
86 #include "gromacs/mdlib/mdatoms.h"
87 #include "gromacs/mdlib/mdoutf.h"
88 #include "gromacs/mdlib/membed.h"
89 #include "gromacs/mdlib/resethandler.h"
90 #include "gromacs/mdlib/sighandler.h"
91 #include "gromacs/mdlib/simulationsignal.h"
92 #include "gromacs/mdlib/stat.h"
93 #include "gromacs/mdlib/stophandler.h"
94 #include "gromacs/mdlib/tgroup.h"
95 #include "gromacs/mdlib/trajectory_writing.h"
96 #include "gromacs/mdlib/update.h"
97 #include "gromacs/mdlib/vcm.h"
98 #include "gromacs/mdlib/vsite.h"
99 #include "gromacs/mdrunutility/handlerestart.h"
100 #include "gromacs/mdrunutility/multisim.h"
101 #include "gromacs/mdrunutility/printtime.h"
102 #include "gromacs/mdtypes/awh_history.h"
103 #include "gromacs/mdtypes/awh_params.h"
104 #include "gromacs/mdtypes/commrec.h"
105 #include "gromacs/mdtypes/df_history.h"
106 #include "gromacs/mdtypes/energyhistory.h"
107 #include "gromacs/mdtypes/fcdata.h"
108 #include "gromacs/mdtypes/forcerec.h"
109 #include "gromacs/mdtypes/group.h"
110 #include "gromacs/mdtypes/inputrec.h"
111 #include "gromacs/mdtypes/interaction_const.h"
112 #include "gromacs/mdtypes/md_enums.h"
113 #include "gromacs/mdtypes/mdatom.h"
114 #include "gromacs/mdtypes/mdrunoptions.h"
115 #include "gromacs/mdtypes/observableshistory.h"
116 #include "gromacs/mdtypes/state.h"
117 #include "gromacs/mimic/utilities.h"
118 #include "gromacs/pbcutil/mshift.h"
119 #include "gromacs/pbcutil/pbc.h"
120 #include "gromacs/pulling/pull.h"
121 #include "gromacs/swap/swapcoords.h"
122 #include "gromacs/timing/wallcycle.h"
123 #include "gromacs/timing/walltime_accounting.h"
124 #include "gromacs/topology/atoms.h"
125 #include "gromacs/topology/idef.h"
126 #include "gromacs/topology/mtop_util.h"
127 #include "gromacs/topology/topology.h"
128 #include "gromacs/trajectory/trajectoryframe.h"
129 #include "gromacs/utility/basedefinitions.h"
130 #include "gromacs/utility/cstringutil.h"
131 #include "gromacs/utility/fatalerror.h"
132 #include "gromacs/utility/logger.h"
133 #include "gromacs/utility/real.h"
134 #include "gromacs/utility/smalloc.h"
136 #include "legacysimulator.h"
137 #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::LegacySimulator::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;
202 unsigned int force_flags;
203 tensor force_vir, shake_vir, total_vir, pres;
204 t_trxstatus *status = nullptr;
208 PaddedVector<gmx::RVec> f {};
209 gmx_global_stat_t gstat;
210 t_graph *graph = nullptr;
211 gmx_shellfc_t *shellfc;
215 /* Domain decomposition could incorrectly miss a bonded
216 interaction, but checking for that requires a global
217 communication stage, which does not otherwise happen in DD
218 code. So we do that alongside the first global energy reduction
219 after a new DD is made. These variables handle whether the
220 check happens, and the result it returns. */
221 bool shouldCheckNumberOfBondedInteractions = false;
222 int totalNumberOfBondedInteractions = -1;
224 SimulationSignals signals;
225 // Most global communnication stages don't propagate mdrun
226 // signals, and will use this object to achieve that.
227 SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
229 GMX_LOG(mdlog.info).asParagraph().
230 appendText("Note that it is planned that the command gmx mdrun -rerun will "
231 "be available in a different form in a future version of GROMACS, "
232 "e.g. gmx rerun -f.");
234 if (ir->efep != efepNO && (mdAtoms->mdatoms()->nMassPerturbed > 0 ||
235 (constr && constr->havePerturbedConstraints())))
237 gmx_fatal(FARGS, "Perturbed masses or constraints are not supported by rerun. "
238 "Either make a .tpr without mass and constraint perturbation, "
239 "or use GROMACS 2018.4, 2018.5 or later 2018 version.");
243 gmx_fatal(FARGS, "Expanded ensemble not supported by rerun.");
247 gmx_fatal(FARGS, "Simulated tempering not supported by rerun.");
251 gmx_fatal(FARGS, "AWH not supported by rerun.");
253 if (replExParams.exchangeInterval > 0)
255 gmx_fatal(FARGS, "Replica exchange not supported by rerun.");
257 if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
259 gmx_fatal(FARGS, "Essential dynamics not supported by rerun.");
263 gmx_fatal(FARGS, "Interactive MD not supported by rerun.");
267 gmx_fatal(FARGS, "Multiple simulations not supported by rerun.");
269 if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
270 [](int i){return i != eannNO; }))
272 gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
275 /* Rerun can't work if an output file name is the same as the input file name.
276 * If this is the case, the user will get an error telling them what the issue is.
278 if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0 ||
279 strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
281 gmx_fatal(FARGS, "When using mdrun -rerun, the name of the input trajectory file "
282 "%s cannot be identical to the name of an output file (whether "
283 "given explicitly with -o or -x, or by default)",
284 opt2fn("-rerun", nfile, fnm));
287 /* Settings for rerun */
289 ir->nstcalcenergy = 1;
290 int nstglobalcomm = 1;
291 const bool bNS = true;
293 ir->nstxout_compressed = 0;
294 SimulationGroups *groups = &top_global->groups;
295 if (ir->eI == eiMimic)
297 top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
300 initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
301 gmx_mdoutf *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, mdModulesNotifier, ir, top_global, oenv, wcycle,
302 StartingBehavior::NewSimulation);
303 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work, mdoutf_get_fp_dhdl(outf), true, mdModulesNotifier);
305 gstat = global_stat_init(ir);
307 /* Check for polarizable models and flexible constraints */
308 shellfc = init_shell_flexcon(fplog,
309 top_global, constr ? constr->numFlexibleConstraints() : 0,
310 ir->nstcalcenergy, DOMAINDECOMP(cr));
313 double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
314 if ((io > 2000) && MASTER(cr))
317 "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
322 // Local state only becomes valid now.
323 std::unique_ptr<t_state> stateInstance;
326 if (DOMAINDECOMP(cr))
328 dd_init_local_top(*top_global, &top);
330 stateInstance = std::make_unique<t_state>();
331 state = stateInstance.get();
332 dd_init_local_state(cr->dd, state_global, state);
334 /* Distribute the charge groups over the nodes from the master node */
335 dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1,
336 state_global, *top_global, ir, imdSession,
338 state, &f, mdAtoms, &top, fr,
340 nrnb, nullptr, FALSE);
341 shouldCheckNumberOfBondedInteractions = true;
345 state_change_natoms(state_global, state_global->natoms);
346 /* We need to allocate one element extra, since we might use
347 * (unaligned) 4-wide SIMD loads to access rvec entries.
349 f.resizeWithPadding(state_global->natoms);
350 /* Copy the pointer to the global state */
351 state = state_global;
353 mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr,
354 &graph, mdAtoms, constr, vsite, shellfc);
357 auto mdatoms = mdAtoms->mdatoms();
359 // NOTE: The global state is no longer used at this point.
360 // But state_global is still used as temporary storage space for writing
361 // the global state to file and potentially for replica exchange.
362 // (Global topology should persist.)
364 update_mdatoms(mdatoms, state->lambda[efptMASS]);
366 if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
368 doFreeEnergyPerturbation = true;
372 int cglo_flags = (CGLO_GSTAT |
373 (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
374 bool bSumEkinhOld = false;
375 t_vcm *vcm = nullptr;
376 compute_globals(gstat, cr, ir, fr, ekind,
377 state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
379 nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
380 constr, &nullSignaller, state->box,
381 &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
383 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
384 top_global, &top, state->x.rvec_array(), state->box,
385 &shouldCheckNumberOfBondedInteractions);
389 fprintf(stderr, "starting md rerun '%s', reading coordinates from"
390 " input trajectory '%s'\n\n",
391 *(top_global->name), opt2fn("-rerun", nfile, fnm));
392 if (mdrunOptions.verbose)
394 fprintf(stderr, "Calculated time to finish depends on nsteps from "
395 "run input file,\nwhich may not correspond to the time "
396 "needed to process input trajectory.\n\n");
398 fprintf(fplog, "\n");
401 walltime_accounting_start_time(walltime_accounting);
402 wallcycle_start(wcycle, ewcRUN);
403 print_start(fplog, cr, walltime_accounting, "mdrun");
405 /***********************************************************
409 ************************************************************/
413 GMX_LOG(mdlog.info).asParagraph().
414 appendText("Simulations has constraints. Rerun does not recalculate constraints.");
420 isLastStep = !read_first_frame(oenv, &status,
421 opt2fn("-rerun", nfile, fnm),
422 &rerun_fr, TRX_NEED_X);
423 if (rerun_fr.natoms != top_global->natoms)
426 "Number of atoms in trajectory (%d) does not match the "
427 "run input file (%d)\n",
428 rerun_fr.natoms, top_global->natoms);
431 if (ir->ePBC != epbcNONE)
435 gmx_fatal(FARGS, "Rerun trajectory frame step %" PRId64 " time %f "
436 "does not contain a box, while pbc is used",
437 rerun_fr.step, rerun_fr.time);
439 if (max_cutoff2(ir->ePBC, rerun_fr.box) < gmx::square(fr->rlist))
441 gmx_fatal(FARGS, "Rerun trajectory frame step %" PRId64 " time %f "
442 "has too small box dimensions", rerun_fr.step, rerun_fr.time);
447 GMX_LOG(mdlog.info).asParagraph().
448 appendText("Rerun does not report kinetic energy, total energy, temperature, virial and pressure.");
452 rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
455 if (ir->ePBC != epbcNONE)
457 /* Set the shift vectors.
458 * Necessary here when have a static box different from the tpr box.
460 calc_shifts(rerun_fr.box, fr->shift_vec);
463 auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
464 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false,
465 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstglobalcomm,
466 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
468 // we don't do counter resetting in rerun - finish will always be valid
469 walltime_accounting_set_valid_finish(walltime_accounting);
471 const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
473 step = ir->init_step;
476 /* and stop now if we should */
477 isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
480 wallcycle_start(wcycle, ewcSTEP);
484 step = rerun_fr.step;
485 step_rel = step - ir->init_step;
496 if (ir->efep != efepNO && MASTER(cr))
498 setCurrentLambdasRerun(step, ir->fepvals, &rerun_fr, lam0, state_global);
503 const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
504 if (constructVsites && DOMAINDECOMP(cr))
506 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
507 "use a single rank");
509 prepareRerunState(rerun_fr, state_global, constructVsites, vsite, top.idef, ir->delta_t, *fr, graph);
512 isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
514 if (DOMAINDECOMP(cr))
516 /* Repartition the domain decomposition */
517 const bool bMasterState = true;
518 dd_partition_system(fplog, mdlog, step, cr,
519 bMasterState, nstglobalcomm,
520 state_global, *top_global, ir, imdSession,
522 state, &f, mdAtoms, &top, fr,
525 mdrunOptions.verbose);
526 shouldCheckNumberOfBondedInteractions = true;
531 energyOutput.printHeader(fplog, step, t); /* can we improve the information printed here? */
534 if (ir->efep != efepNO)
536 update_mdatoms(mdatoms, state->lambda[efptMASS]);
539 force_flags = (GMX_FORCE_STATECHANGED |
540 GMX_FORCE_DYNAMICBOX |
541 GMX_FORCE_ALLFORCES |
542 (GMX_GPU ? GMX_FORCE_VIRIAL : 0) | // TODO: Get rid of this once #2649 is solved
544 (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
548 /* Now is the time to relax the shells */
549 relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
550 enforcedRotation, step,
551 ir, imdSession, pull_work, bNS, force_flags, &top,
554 state->x.arrayRefWithPadding(),
555 state->v.arrayRefWithPadding(),
559 f.arrayRefWithPadding(), force_vir, mdatoms,
561 shellfc, fr, mdScheduleWork, t, mu_tot,
563 ddBalanceRegionHandler);
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, imdSession,
576 step, nrnb, wcycle, &top,
577 state->box, state->x.arrayRefWithPadding(), &state->hist,
578 f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
579 state->lambda, graph,
580 fr, mdScheduleWork, vsite, mu_tot, t, ed,
581 GMX_FORCE_NS | force_flags,
582 ddBalanceRegionHandler);
585 /* Now we have the energies and forces corresponding to the
586 * coordinates at time t.
589 const bool isCheckpointingStep = false;
590 const bool doRerun = true;
591 const bool bSumEkinhOld = false;
592 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
593 ir, state, state_global, observablesHistory,
595 outf, energyOutput, ekind, f,
596 isCheckpointingStep, doRerun, isLastStep,
597 mdrunOptions.writeConfout,
601 stopHandler->setSignal();
605 /* Need to unshift here */
606 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
609 if (vsite != nullptr)
611 wallcycle_start(wcycle, ewcVSITECONSTR);
612 if (graph != nullptr)
614 shift_self(graph, state->box, as_rvec_array(state->x.data()));
616 construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
617 top.idef.iparams, top.idef.il,
618 fr->ePBC, fr->bMolPBC, cr, state->box);
620 if (graph != nullptr)
622 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
624 wallcycle_stop(wcycle, ewcVSITECONSTR);
628 const bool doInterSimSignal = false;
629 const bool doIntraSimSignal = true;
630 bool bSumEkinhOld = false;
631 t_vcm *vcm = nullptr;
632 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
634 compute_globals(gstat, cr, ir, fr, ekind,
635 state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
637 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
640 &totalNumberOfBondedInteractions, &bSumEkinhOld,
641 CGLO_GSTAT | CGLO_ENERGY
642 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
644 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
645 top_global, &top, state->x.rvec_array(), state->box,
646 &shouldCheckNumberOfBondedInteractions);
649 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
650 the virial that should probably be addressed eventually. state->veta has better properies,
651 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
652 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
654 if (ir->efep != efepNO)
656 /* Sum up the foreign energy and dhdl terms for md and sd.
657 Currently done every step so that dhdl is correct in the .edr */
658 sum_dhdl(enerd, state->lambda, ir->fepvals);
664 const bool bCalcEnerStep = true;
665 energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep,
666 t, mdatoms->tmass, enerd, state,
667 ir->fepvals, ir->expandedvals, state->box,
668 shake_vir, force_vir, total_vir, pres,
672 const bool do_ene = true;
673 const bool do_log = true;
675 const bool do_dr = ir->nstdisreout != 0;
676 const bool do_or = ir->nstorireout != 0;
678 energyOutput.printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
679 energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
680 do_log ? fplog : nullptr,
684 if (do_per_step(step, ir->nstlog))
686 if (fflush(fplog) != 0)
688 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
693 /* Print the remaining wall clock time for the run */
694 if (isMasterSimMasterRank(ms, MASTER(cr)) &&
695 (mdrunOptions.verbose || gmx_got_usr_signal()))
699 fprintf(stderr, "\n");
701 print_time(stderr, walltime_accounting, step, ir, cr);
704 /* Ion/water position swapping.
705 * Not done in last step since trajectory writing happens before this call
706 * in the MD loop and exchanges would be lost anyway. */
707 if ((ir->eSwapCoords != eswapNO) && (step > 0) && !isLastStep &&
708 do_per_step(step, ir->swap->nstswap))
710 const bool doRerun = true;
711 do_swapcoords(cr, step, t, ir, swap, wcycle,
714 MASTER(cr) && mdrunOptions.verbose,
720 /* read next frame from input trajectory */
721 isLastStep = !read_next_frame(oenv, status, &rerun_fr);
726 rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
729 cycles = wallcycle_stop(wcycle, ewcSTEP);
730 if (DOMAINDECOMP(cr) && wcycle)
732 dd_cycles_add(cr->dd, cycles, ddCyclStep);
737 /* increase the MD step number */
742 /* End of main MD loop */
744 /* Closing TNG files can include compressing data. Therefore it is good to do that
745 * before stopping the time measurements. */
746 mdoutf_tng_close(outf);
748 /* Stop measuring walltime */
749 walltime_accounting_end_time(walltime_accounting);
756 if (!thisRankHasDuty(cr, DUTY_PME))
758 /* Tell the PME only node to finish */
759 gmx_pme_send_finish(cr);
764 done_shellfc(fplog, shellfc, step_rel);
766 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);