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51 #include "thread_mpi/threads.h"
53 #include "gromacs/awh/awh.h"
54 #include "gromacs/commandline/filenm.h"
55 #include "gromacs/compat/make_unique.h"
56 #include "gromacs/domdec/domdec.h"
57 #include "gromacs/domdec/domdec_network.h"
58 #include "gromacs/domdec/domdec_struct.h"
59 #include "gromacs/essentialdynamics/edsam.h"
60 #include "gromacs/ewald/pme.h"
61 #include "gromacs/ewald/pme-load-balancing.h"
62 #include "gromacs/fileio/trxio.h"
63 #include "gromacs/gmxlib/network.h"
64 #include "gromacs/gmxlib/nrnb.h"
65 #include "gromacs/gpu_utils/gpu_utils.h"
66 #include "gromacs/imd/imd.h"
67 #include "gromacs/listed-forces/manage-threading.h"
68 #include "gromacs/math/functions.h"
69 #include "gromacs/math/utilities.h"
70 #include "gromacs/math/vec.h"
71 #include "gromacs/math/vectypes.h"
72 #include "gromacs/mdlib/compute_io.h"
73 #include "gromacs/mdlib/constr.h"
74 #include "gromacs/mdlib/ebin.h"
75 #include "gromacs/mdlib/expanded.h"
76 #include "gromacs/mdlib/force.h"
77 #include "gromacs/mdlib/force_flags.h"
78 #include "gromacs/mdlib/forcerec.h"
79 #include "gromacs/mdlib/md_support.h"
80 #include "gromacs/mdlib/mdatoms.h"
81 #include "gromacs/mdlib/mdebin.h"
82 #include "gromacs/mdlib/mdoutf.h"
83 #include "gromacs/mdlib/mdrun.h"
84 #include "gromacs/mdlib/mdsetup.h"
85 #include "gromacs/mdlib/nb_verlet.h"
86 #include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
87 #include "gromacs/mdlib/ns.h"
88 #include "gromacs/mdlib/shellfc.h"
89 #include "gromacs/mdlib/sighandler.h"
90 #include "gromacs/mdlib/sim_util.h"
91 #include "gromacs/mdlib/simulationsignal.h"
92 #include "gromacs/mdlib/tgroup.h"
93 #include "gromacs/mdlib/trajectory_writing.h"
94 #include "gromacs/mdlib/update.h"
95 #include "gromacs/mdlib/vcm.h"
96 #include "gromacs/mdlib/vsite.h"
97 #include "gromacs/mdtypes/awh-history.h"
98 #include "gromacs/mdtypes/commrec.h"
99 #include "gromacs/mdtypes/df_history.h"
100 #include "gromacs/mdtypes/energyhistory.h"
101 #include "gromacs/mdtypes/fcdata.h"
102 #include "gromacs/mdtypes/forcerec.h"
103 #include "gromacs/mdtypes/group.h"
104 #include "gromacs/mdtypes/inputrec.h"
105 #include "gromacs/mdtypes/interaction_const.h"
106 #include "gromacs/mdtypes/md_enums.h"
107 #include "gromacs/mdtypes/mdatom.h"
108 #include "gromacs/mdtypes/observableshistory.h"
109 #include "gromacs/mdtypes/state.h"
110 #include "gromacs/pbcutil/mshift.h"
111 #include "gromacs/pbcutil/pbc.h"
112 #include "gromacs/pulling/pull.h"
113 #include "gromacs/swap/swapcoords.h"
114 #include "gromacs/timing/wallcycle.h"
115 #include "gromacs/timing/walltime_accounting.h"
116 #include "gromacs/topology/atoms.h"
117 #include "gromacs/topology/idef.h"
118 #include "gromacs/topology/mtop_util.h"
119 #include "gromacs/topology/topology.h"
120 #include "gromacs/trajectory/trajectoryframe.h"
121 #include "gromacs/utility/basedefinitions.h"
122 #include "gromacs/utility/cstringutil.h"
123 #include "gromacs/utility/fatalerror.h"
124 #include "gromacs/utility/logger.h"
125 #include "gromacs/utility/real.h"
126 #include "gromacs/utility/smalloc.h"
133 #include "corewrap.h"
136 using gmx::SimulationSignaller;
138 /*! \brief Check whether bonded interactions are missing, if appropriate
140 * \param[in] fplog Log file pointer
141 * \param[in] cr Communication object
142 * \param[in] totalNumberOfBondedInteractions Result of the global reduction over the number of bonds treated in each domain
143 * \param[in] top_global Global topology for the error message
144 * \param[in] top_local Local topology for the error message
145 * \param[in] state Global state for the error message
146 * \param[inout] shouldCheckNumberOfBondedInteractions Whether we should do the check.
148 * \return Nothing, except that shouldCheckNumberOfBondedInteractions
149 * is always set to false after exit.
151 static void checkNumberOfBondedInteractions(FILE *fplog, t_commrec *cr, int totalNumberOfBondedInteractions,
152 gmx_mtop_t *top_global, gmx_localtop_t *top_local, t_state *state,
153 bool *shouldCheckNumberOfBondedInteractions)
155 if (*shouldCheckNumberOfBondedInteractions)
157 if (totalNumberOfBondedInteractions != cr->dd->nbonded_global)
159 dd_print_missing_interactions(fplog, cr, totalNumberOfBondedInteractions, top_global, top_local, state); // Does not return
161 *shouldCheckNumberOfBondedInteractions = false;
165 static void reset_all_counters(FILE *fplog, const gmx::MDLogger &mdlog, t_commrec *cr,
167 gmx_int64_t *step_rel, t_inputrec *ir,
168 gmx_wallcycle_t wcycle, t_nrnb *nrnb,
169 gmx_walltime_accounting_t walltime_accounting,
170 struct nonbonded_verlet_t *nbv,
171 struct gmx_pme_t *pme)
173 char sbuf[STEPSTRSIZE];
175 /* Reset all the counters related to performance over the run */
176 GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
177 "step %s: resetting all time and cycle counters",
178 gmx_step_str(step, sbuf));
182 nbnxn_gpu_reset_timings(nbv);
185 if (pme_gpu_task_enabled(pme))
187 pme_gpu_reset_timings(pme);
190 if (use_GPU(nbv) || pme_gpu_task_enabled(pme))
195 wallcycle_stop(wcycle, ewcRUN);
196 wallcycle_reset_all(wcycle);
197 if (DOMAINDECOMP(cr))
199 reset_dd_statistics_counters(cr->dd);
202 ir->init_step += *step_rel;
203 ir->nsteps -= *step_rel;
205 wallcycle_start(wcycle, ewcRUN);
206 walltime_accounting_start(walltime_accounting);
207 print_date_and_time(fplog, cr->nodeid, "Restarted time", gmx_gettime());
210 /*! \brief Copy the state from \p rerunFrame to \p globalState and, if requested, construct vsites
212 * \param[in] rerunFrame The trajectory frame to compute energy/forces for
213 * \param[in,out] globalState The global state container
214 * \param[in] constructVsites When true, vsite coordinates are constructed
215 * \param[in] vsite Vsite setup, can be nullptr when \p constructVsites = false
216 * \param[in] idef Topology parameters, used for constructing vsites
217 * \param[in] timeStep Time step, used for constructing vsites
218 * \param[in] forceRec Force record, used for constructing vsites
219 * \param[in,out] graph The molecular graph, used for constructing vsites when != nullptr
220 * \param[in,out] warnWhenNoV When true, issue a warning when no velocities are present in \p rerunFrame; is set to false when a warning was issued
222 static void prepareRerunState(const t_trxframe &rerunFrame,
223 t_state *globalState,
224 bool constructVsites,
225 const gmx_vsite_t *vsite,
228 const t_forcerec &forceRec,
230 gmx_bool *warnWhenNoV)
232 for (int i = 0; i < globalState->natoms; i++)
234 copy_rvec(rerunFrame.x[i], globalState->x[i]);
238 for (int i = 0; i < globalState->natoms; i++)
240 copy_rvec(rerunFrame.v[i], globalState->v[i]);
245 for (int i = 0; i < globalState->natoms; i++)
247 clear_rvec(globalState->v[i]);
251 fprintf(stderr, "\nWARNING: Some frames do not contain velocities.\n"
252 " Ekin, temperature and pressure are incorrect,\n"
253 " the virial will be incorrect when constraints are present.\n"
255 *warnWhenNoV = FALSE;
258 copy_mat(rerunFrame.box, globalState->box);
262 GMX_ASSERT(vsite, "Need valid vsite for constructing vsites");
266 /* Following is necessary because the graph may get out of sync
267 * with the coordinates if we only have every N'th coordinate set
269 mk_mshift(nullptr, graph, forceRec.ePBC, globalState->box, as_rvec_array(globalState->x.data()));
270 shift_self(graph, globalState->box, as_rvec_array(globalState->x.data()));
272 construct_vsites(vsite, as_rvec_array(globalState->x.data()), timeStep, as_rvec_array(globalState->v.data()),
273 idef.iparams, idef.il,
274 forceRec.ePBC, forceRec.bMolPBC, nullptr, globalState->box);
277 unshift_self(graph, globalState->box, as_rvec_array(globalState->x.data()));
283 \copydoc integrator_t (FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
284 int nfile, const t_filenm fnm[],
285 const gmx_output_env_t *oenv,
286 const MdrunOptions &mdrunOptions,
287 gmx_vsite_t *vsite, gmx_constr_t constr,
288 gmx::IMDOutputProvider *outputProvider,
289 t_inputrec *inputrec,
290 gmx_mtop_t *top_global, t_fcdata *fcd,
291 t_state *state_global,
293 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
295 const ReplicaExchangeParameters &replExParams,
296 gmx_membed_t *membed,
297 gmx_walltime_accounting_t walltime_accounting)
299 double gmx::do_md(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
300 int nfile, const t_filenm fnm[],
301 const gmx_output_env_t *oenv,
302 const MdrunOptions &mdrunOptions,
303 gmx_vsite_t *vsite, gmx_constr_t constr,
304 gmx::IMDOutputProvider *outputProvider,
306 gmx_mtop_t *top_global,
308 t_state *state_global,
309 ObservablesHistory *observablesHistory,
310 gmx::MDAtoms *mdAtoms,
311 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
313 const ReplicaExchangeParameters &replExParams,
314 gmx_membed_t *membed,
315 gmx_walltime_accounting_t walltime_accounting)
317 gmx_mdoutf_t outf = nullptr;
318 gmx_int64_t step, step_rel;
320 double t, t0, lam0[efptNR];
321 gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, bCalcEner;
322 gmx_bool bNS, bNStList, bSimAnn, bStopCM,
323 bFirstStep, bInitStep, bLastStep = FALSE,
324 bUsingEnsembleRestraints;
325 gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
326 gmx_bool do_ene, do_log, do_verbose, bRerunWarnNoV = TRUE,
327 bForceUpdate = FALSE, bCPT;
328 gmx_bool bMasterState;
329 int force_flags, cglo_flags;
330 tensor force_vir, shake_vir, total_vir, tmp_vir, pres;
335 matrix parrinellorahmanMu, M;
337 gmx_repl_ex_t repl_ex = nullptr;
340 t_mdebin *mdebin = nullptr;
341 gmx_enerdata_t *enerd;
342 PaddedRVecVector f {};
343 gmx_global_stat_t gstat;
344 gmx_update_t *upd = nullptr;
345 t_graph *graph = nullptr;
346 gmx_groups_t *groups;
347 gmx_ekindata_t *ekind;
348 gmx_shellfc_t *shellfc;
349 gmx_bool bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
350 gmx_bool bResetCountersHalfMaxH = FALSE;
351 gmx_bool bTemp, bPres, bTrotter;
353 rvec *cbuf = nullptr;
360 real saved_conserved_quantity = 0;
364 char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
365 int handled_stop_condition = gmx_stop_cond_none; /* compare to get_stop_condition*/
368 /* PME load balancing data for GPU kernels */
369 pme_load_balancing_t *pme_loadbal = nullptr;
370 gmx_bool bPMETune = FALSE;
371 gmx_bool bPMETunePrinting = FALSE;
374 gmx_bool bIMDstep = FALSE;
377 /* Temporary addition for FAHCORE checkpointing */
380 /* Domain decomposition could incorrectly miss a bonded
381 interaction, but checking for that requires a global
382 communication stage, which does not otherwise happen in DD
383 code. So we do that alongside the first global energy reduction
384 after a new DD is made. These variables handle whether the
385 check happens, and the result it returns. */
386 bool shouldCheckNumberOfBondedInteractions = false;
387 int totalNumberOfBondedInteractions = -1;
389 SimulationSignals signals;
390 // Most global communnication stages don't propagate mdrun
391 // signals, and will use this object to achieve that.
392 SimulationSignaller nullSignaller(nullptr, nullptr, false, false);
394 if (!mdrunOptions.writeConfout)
396 // This is on by default, and the main known use case for
397 // turning it off is for convenience in benchmarking, which is
398 // something that should not show up in the general user
400 GMX_LOG(mdlog.info).asParagraph().
401 appendText("The -noconfout functionality is deprecated, and may be removed in a future version.");
403 if (mdrunOptions.timingOptions.resetHalfway)
405 GMX_LOG(mdlog.info).asParagraph().
406 appendText("The -resethway functionality is deprecated, and may be removed in a future version.");
409 /* Signal to reset the counters half the simulation steps. */
410 wcycle_set_reset_counters(wcycle, ir->nsteps/2);
412 /* Signal to reset the counters halfway the simulation time. */
413 bResetCountersHalfMaxH = (mdrunOptions.maximumHoursToRun > 0);
416 /* md-vv uses averaged full step velocities for T-control
417 md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
418 md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
419 bTrotter = (EI_VV(ir->eI) && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir) || inputrecNvtTrotter(ir)));
421 const gmx_bool bRerunMD = mdrunOptions.rerun;
422 int nstglobalcomm = mdrunOptions.globalCommunicationInterval;
426 /* Since we don't know if the frames read are related in any way,
427 * rebuild the neighborlist at every step.
430 ir->nstcalcenergy = 1;
434 nstglobalcomm = check_nstglobalcomm(mdlog, nstglobalcomm, ir);
435 bGStatEveryStep = (nstglobalcomm == 1);
439 ir->nstxout_compressed = 0;
441 groups = &top_global->groups;
443 gmx_edsam *ed = nullptr;
444 if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
446 /* Initialize essential dynamics sampling */
447 ed = init_edsam(opt2fn_null("-ei", nfile, fnm), opt2fn("-eo", nfile, fnm),
450 state_global, observablesHistory,
451 oenv, mdrunOptions.continuationOptions.appendFiles);
454 if (ir->eSwapCoords != eswapNO)
456 /* Initialize ion swapping code */
457 init_swapcoords(fplog, ir, opt2fn_master("-swap", nfile, fnm, cr),
459 state_global, observablesHistory,
460 cr, oenv, mdrunOptions);
464 init_md(fplog, cr, outputProvider, ir, oenv, mdrunOptions,
465 &t, &t0, state_global, lam0,
466 nrnb, top_global, &upd,
467 nfile, fnm, &outf, &mdebin,
468 force_vir, shake_vir, mu_tot, &bSimAnn, &vcm, wcycle);
470 clear_mat(total_vir);
472 /* Energy terms and groups */
474 init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
477 /* Kinetic energy data */
479 init_ekindata(fplog, top_global, &(ir->opts), ekind);
480 /* Copy the cos acceleration to the groups struct */
481 ekind->cosacc.cos_accel = ir->cos_accel;
483 gstat = global_stat_init(ir);
485 /* Check for polarizable models and flexible constraints */
486 shellfc = init_shell_flexcon(fplog,
487 top_global, n_flexible_constraints(constr),
488 ir->nstcalcenergy, DOMAINDECOMP(cr));
490 if (shellfc && ir->nstcalcenergy != 1)
492 gmx_fatal(FARGS, "You have nstcalcenergy set to a value (%d) that is different from 1.\nThis is not supported in combinations with shell particles.\nPlease make a new tpr file.", ir->nstcalcenergy);
494 if (shellfc && DOMAINDECOMP(cr))
496 gmx_fatal(FARGS, "Shell particles are not implemented with domain decomposition, use a single rank");
498 if (shellfc && ir->bDoAwh)
500 gmx_fatal(FARGS, "AWH biasing does not support shell particles.");
503 if (inputrecDeform(ir))
505 tMPI_Thread_mutex_lock(&deform_init_box_mutex);
506 set_deform_reference_box(upd,
507 deform_init_init_step_tpx,
508 deform_init_box_tpx);
509 tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
513 double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
514 if ((io > 2000) && MASTER(cr))
517 "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
522 // Local state only becomes valid now.
523 std::unique_ptr<t_state> stateInstance;
526 if (DOMAINDECOMP(cr))
528 top = dd_init_local_top(top_global);
530 stateInstance = gmx::compat::make_unique<t_state>();
531 state = stateInstance.get();
532 dd_init_local_state(cr->dd, state_global, state);
536 state_change_natoms(state_global, state_global->natoms);
537 /* We need to allocate one element extra, since we might use
538 * (unaligned) 4-wide SIMD loads to access rvec entries.
540 f.resize(gmx::paddedRVecVectorSize(state_global->natoms));
541 /* Copy the pointer to the global state */
542 state = state_global;
545 mdAlgorithmsSetupAtomData(cr, ir, top_global, top, fr,
546 &graph, mdAtoms, vsite, shellfc);
548 update_realloc(upd, state->natoms);
551 /* Set up interactive MD (IMD) */
552 init_IMD(ir, cr, top_global, fplog, ir->nstcalcenergy, MASTER(cr) ? as_rvec_array(state_global->x.data()) : nullptr,
553 nfile, fnm, oenv, mdrunOptions);
555 if (DOMAINDECOMP(cr))
557 /* Distribute the charge groups over the nodes from the master node */
558 dd_partition_system(fplog, ir->init_step, cr, TRUE, 1,
559 state_global, top_global, ir,
560 state, &f, mdAtoms, top, fr,
562 nrnb, nullptr, FALSE);
563 shouldCheckNumberOfBondedInteractions = true;
564 update_realloc(upd, state->natoms);
567 auto mdatoms = mdAtoms->mdatoms();
569 // NOTE: The global state is no longer used at this point.
570 // But state_global is still used as temporary storage space for writing
571 // the global state to file and potentially for replica exchange.
572 // (Global topology should persist.)
574 update_mdatoms(mdatoms, state->lambda[efptMASS]);
576 const ContinuationOptions &continuationOptions = mdrunOptions.continuationOptions;
577 bool startingFromCheckpoint = continuationOptions.startedFromCheckpoint;
581 init_expanded_ensemble(startingFromCheckpoint, ir, state->dfhist);
586 if (startingFromCheckpoint)
588 /* Update mdebin with energy history if appending to output files */
589 if (continuationOptions.appendFiles)
591 restore_energyhistory_from_state(mdebin, observablesHistory->energyHistory.get());
593 else if (observablesHistory->energyHistory.get() != nullptr)
595 /* We might have read an energy history from checkpoint.
596 * As we are not appending, we want to restart the statistics.
597 * Free the allocated memory and reset the counts.
599 observablesHistory->energyHistory = {};
602 if (observablesHistory->energyHistory.get() == nullptr)
604 observablesHistory->energyHistory = std::unique_ptr<energyhistory_t>(new energyhistory_t {});
606 /* Set the initial energy history in state by updating once */
607 update_energyhistory(observablesHistory->energyHistory.get(), mdebin);
610 /* Initialize constraints */
611 if (constr && !DOMAINDECOMP(cr))
613 set_constraints(constr, top, ir, mdatoms, cr);
616 /* Initialize AWH and restore state from history in checkpoint if needed. */
619 ir->awh = new gmx::Awh(fplog, *ir, cr, *ir->awhParams, opt2fn("-awh", nfile, fnm), ir->pull_work);
621 if (startingFromCheckpoint)
623 /* Restore the AWH history read from checkpoint */
624 ir->awh->restoreStateFromHistory(MASTER(cr) ? state_global->awhHistory.get() : nullptr);
628 /* Initialize the AWH history here */
629 state_global->awhHistory = ir->awh->initHistoryFromState();
633 const bool useReplicaExchange = (replExParams.exchangeInterval > 0);
634 if (useReplicaExchange && MASTER(cr))
636 repl_ex = init_replica_exchange(fplog, cr->ms, top_global->natoms, ir,
640 /* PME tuning is only supported in the Verlet scheme, with PME for
641 * Coulomb. It is not supported with only LJ PME, or for
643 bPMETune = (mdrunOptions.tunePme && EEL_PME(fr->ic->eeltype) && !bRerunMD &&
644 !mdrunOptions.reproducible && ir->cutoff_scheme != ecutsGROUP);
647 pme_loadbal_init(&pme_loadbal, cr, mdlog, ir, state->box,
648 fr->ic, fr->nbv->listParams.get(), fr->pmedata, use_GPU(fr->nbv),
652 if (!ir->bContinuation && !bRerunMD)
654 if (state->flags & (1 << estV))
656 /* Set the velocities of vsites, shells and frozen atoms to zero */
657 for (i = 0; i < mdatoms->homenr; i++)
659 if (mdatoms->ptype[i] == eptVSite ||
660 mdatoms->ptype[i] == eptShell)
662 clear_rvec(state->v[i]);
664 else if (mdatoms->cFREEZE)
666 for (m = 0; m < DIM; m++)
668 if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
679 /* Constrain the initial coordinates and velocities */
680 do_constrain_first(fplog, constr, ir, mdatoms, state,
685 /* Construct the virtual sites for the initial configuration */
686 construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, nullptr,
687 top->idef.iparams, top->idef.il,
688 fr->ePBC, fr->bMolPBC, cr, state->box);
692 if (ir->efep != efepNO)
694 /* Set free energy calculation frequency as the greatest common
695 * denominator of nstdhdl and repl_ex_nst. */
696 nstfep = ir->fepvals->nstdhdl;
699 nstfep = gmx_greatest_common_divisor(ir->expandedvals->nstexpanded, nstfep);
701 if (useReplicaExchange)
703 nstfep = gmx_greatest_common_divisor(replExParams.exchangeInterval, nstfep);
707 /* Be REALLY careful about what flags you set here. You CANNOT assume
708 * this is the first step, since we might be restarting from a checkpoint,
709 * and in that case we should not do any modifications to the state.
711 bStopCM = (ir->comm_mode != ecmNO && !ir->bContinuation);
713 if (continuationOptions.haveReadEkin)
715 restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
718 cglo_flags = (CGLO_INITIALIZATION | CGLO_TEMPERATURE | CGLO_GSTAT
719 | (EI_VV(ir->eI) ? CGLO_PRESSURE : 0)
720 | (EI_VV(ir->eI) ? CGLO_CONSTRAINT : 0)
721 | (continuationOptions.haveReadEkin ? CGLO_READEKIN : 0));
723 bSumEkinhOld = FALSE;
724 /* To minimize communication, compute_globals computes the COM velocity
725 * and the kinetic energy for the velocities without COM motion removed.
726 * Thus to get the kinetic energy without the COM contribution, we need
727 * to call compute_globals twice.
729 for (int cgloIteration = 0; cgloIteration < (bStopCM ? 2 : 1); cgloIteration++)
731 int cglo_flags_iteration = cglo_flags;
732 if (bStopCM && cgloIteration == 0)
734 cglo_flags_iteration |= CGLO_STOPCM;
735 cglo_flags_iteration &= ~CGLO_TEMPERATURE;
737 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
738 nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
739 constr, &nullSignaller, state->box,
740 &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags_iteration
741 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
743 checkNumberOfBondedInteractions(fplog, cr, totalNumberOfBondedInteractions,
744 top_global, top, state,
745 &shouldCheckNumberOfBondedInteractions);
746 if (ir->eI == eiVVAK)
748 /* a second call to get the half step temperature initialized as well */
749 /* we do the same call as above, but turn the pressure off -- internally to
750 compute_globals, this is recognized as a velocity verlet half-step
751 kinetic energy calculation. This minimized excess variables, but
752 perhaps loses some logic?*/
754 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
755 nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
756 constr, &nullSignaller, state->box,
757 nullptr, &bSumEkinhOld,
758 cglo_flags & ~CGLO_PRESSURE);
761 /* Calculate the initial half step temperature, and save the ekinh_old */
762 if (!continuationOptions.startedFromCheckpoint)
764 for (i = 0; (i < ir->opts.ngtc); i++)
766 copy_mat(ekind->tcstat[i].ekinh, ekind->tcstat[i].ekinh_old);
770 /* need to make an initiation call to get the Trotter variables set, as well as other constants for non-trotter
771 temperature control */
772 trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
776 if (!ir->bContinuation)
778 if (constr && ir->eConstrAlg == econtLINCS)
781 "RMS relative constraint deviation after constraining: %.2e\n",
782 constr_rmsd(constr));
784 if (EI_STATE_VELOCITY(ir->eI))
786 real temp = enerd->term[F_TEMP];
789 /* Result of Ekin averaged over velocities of -half
790 * and +half step, while we only have -half step here.
794 fprintf(fplog, "Initial temperature: %g K\n", temp);
800 fprintf(stderr, "starting md rerun '%s', reading coordinates from"
801 " input trajectory '%s'\n\n",
802 *(top_global->name), opt2fn("-rerun", nfile, fnm));
803 if (mdrunOptions.verbose)
805 fprintf(stderr, "Calculated time to finish depends on nsteps from "
806 "run input file,\nwhich may not correspond to the time "
807 "needed to process input trajectory.\n\n");
813 fprintf(stderr, "starting mdrun '%s'\n",
814 *(top_global->name));
817 sprintf(tbuf, "%8.1f", (ir->init_step+ir->nsteps)*ir->delta_t);
821 sprintf(tbuf, "%s", "infinite");
823 if (ir->init_step > 0)
825 fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
826 gmx_step_str(ir->init_step+ir->nsteps, sbuf), tbuf,
827 gmx_step_str(ir->init_step, sbuf2),
828 ir->init_step*ir->delta_t);
832 fprintf(stderr, "%s steps, %s ps.\n",
833 gmx_step_str(ir->nsteps, sbuf), tbuf);
836 fprintf(fplog, "\n");
839 walltime_accounting_start(walltime_accounting);
840 wallcycle_start(wcycle, ewcRUN);
841 print_start(fplog, cr, walltime_accounting, "mdrun");
843 /* safest point to do file checkpointing is here. More general point would be immediately before integrator call */
845 chkpt_ret = fcCheckPointParallel( cr->nodeid,
849 gmx_fatal( 3, __FILE__, __LINE__, "Checkpoint error on step %d\n", 0 );
853 /***********************************************************
857 ************************************************************/
859 /* if rerunMD then read coordinates and velocities from input trajectory */
862 if (getenv("GMX_FORCE_UPDATE"))
870 bLastStep = !read_first_frame(oenv, &status,
871 opt2fn("-rerun", nfile, fnm),
872 &rerun_fr, TRX_NEED_X | TRX_READ_V);
873 if (rerun_fr.natoms != top_global->natoms)
876 "Number of atoms in trajectory (%d) does not match the "
877 "run input file (%d)\n",
878 rerun_fr.natoms, top_global->natoms);
880 if (ir->ePBC != epbcNONE)
884 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);
886 if (max_cutoff2(ir->ePBC, rerun_fr.box) < gmx::square(fr->rlist))
888 gmx_fatal(FARGS, "Rerun trajectory frame step %d time %f has too small box dimensions", rerun_fr.step, rerun_fr.time);
895 rerun_parallel_comm(cr, &rerun_fr, &bLastStep);
898 if (ir->ePBC != epbcNONE)
900 /* Set the shift vectors.
901 * Necessary here when have a static box different from the tpr box.
903 calc_shifts(rerun_fr.box, fr->shift_vec);
907 /* Loop over MD steps or if rerunMD to end of input trajectory,
908 * or, if max_hours>0, until max_hours is reached.
910 real max_hours = mdrunOptions.maximumHoursToRun;
912 /* Skip the first Nose-Hoover integration when we get the state from tpx */
913 bInitStep = !startingFromCheckpoint || EI_VV(ir->eI);
914 bSumEkinhOld = FALSE;
916 bNeedRepartition = FALSE;
917 // TODO This implementation of ensemble orientation restraints is nasty because
918 // a user can't just do multi-sim with single-sim orientation restraints.
919 bUsingEnsembleRestraints = (fcd->disres.nsystems > 1) || (cr->ms && fcd->orires.nr);
922 // Replica exchange and ensemble restraints need all
923 // simulations to remain synchronized, so they need
924 // checkpoints and stop conditions to act on the same step, so
925 // the propagation of such signals must take place between
926 // simulations, not just within simulations.
927 bool checkpointIsLocal = !useReplicaExchange && !bUsingEnsembleRestraints;
928 bool stopConditionIsLocal = !useReplicaExchange && !bUsingEnsembleRestraints;
929 bool resetCountersIsLocal = true;
930 signals[eglsCHKPT] = SimulationSignal(checkpointIsLocal);
931 signals[eglsSTOPCOND] = SimulationSignal(stopConditionIsLocal);
932 signals[eglsRESETCOUNTERS] = SimulationSignal(resetCountersIsLocal);
935 DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion = (DOMAINDECOMP(cr) ? DdOpenBalanceRegionBeforeForceComputation::yes : DdOpenBalanceRegionBeforeForceComputation::no);
936 DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion = (DOMAINDECOMP(cr) ? DdCloseBalanceRegionAfterForceComputation::yes : DdCloseBalanceRegionAfterForceComputation::no);
938 step = ir->init_step;
941 // TODO extract this to new multi-simulation module
942 if (MASTER(cr) && isMultiSim(cr->ms) && !useReplicaExchange)
944 if (!multisim_int_all_are_equal(cr->ms, ir->nsteps))
946 GMX_LOG(mdlog.warning).appendText(
947 "Note: The number of steps is not consistent across multi simulations,\n"
948 "but we are proceeding anyway!");
950 if (!multisim_int_all_are_equal(cr->ms, ir->init_step))
952 GMX_LOG(mdlog.warning).appendText(
953 "Note: The initial step is not consistent across multi simulations,\n"
954 "but we are proceeding anyway!");
958 /* and stop now if we should */
959 bLastStep = (bLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
963 /* Determine if this is a neighbor search step */
964 bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
966 if (bPMETune && bNStList)
968 /* PME grid + cut-off optimization with GPUs or PME nodes */
969 pme_loadbal_do(pme_loadbal, cr,
970 (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
978 wallcycle_start(wcycle, ewcSTEP);
984 step = rerun_fr.step;
985 step_rel = step - ir->init_step;
998 bLastStep = (step_rel == ir->nsteps);
999 t = t0 + step*ir->delta_t;
1002 // TODO Refactor this, so that nstfep does not need a default value of zero
1003 if (ir->efep != efepNO || ir->bSimTemp)
1005 /* find and set the current lambdas. If rerunning, we either read in a state, or a lambda value,
1006 requiring different logic. */
1011 setCurrentLambdasRerun(step, ir->fepvals, &rerun_fr, lam0, state_global);
1016 setCurrentLambdasLocal(step, ir->fepvals, lam0, state);
1018 bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
1019 bDoFEP = ((ir->efep != efepNO) && do_per_step(step, nstfep));
1020 bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded)
1021 && (ir->bExpanded) && (step > 0) && (!startingFromCheckpoint));
1024 bDoReplEx = (useReplicaExchange && (step > 0) && !bLastStep &&
1025 do_per_step(step, replExParams.exchangeInterval));
1029 update_annealing_target_temp(ir, t, upd);
1032 if (bRerunMD && MASTER(cr))
1034 const bool constructVsites = (vsite && mdrunOptions.rerunConstructVsites);
1035 if (constructVsites && DOMAINDECOMP(cr))
1037 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, use a single rank");
1039 prepareRerunState(rerun_fr, state_global, constructVsites, vsite, top->idef, ir->delta_t, *fr, graph, &bRerunWarnNoV);
1042 /* Stop Center of Mass motion */
1043 bStopCM = (ir->comm_mode != ecmNO && do_per_step(step, ir->nstcomm));
1047 /* for rerun MD always do Neighbour Searching */
1048 bNS = (bFirstStep || ir->nstlist != 0);
1052 /* Determine whether or not to do Neighbour Searching */
1053 bNS = (bFirstStep || bNStList || bExchanged || bNeedRepartition);
1056 /* < 0 means stop at next step, > 0 means stop at next NS step */
1057 if ( (signals[eglsSTOPCOND].set < 0) ||
1058 ( (signals[eglsSTOPCOND].set > 0 ) && ( bNS || ir->nstlist == 0)))
1063 /* do_log triggers energy and virial calculation. Because this leads
1064 * to different code paths, forces can be different. Thus for exact
1065 * continuation we should avoid extra log output.
1066 * Note that the || bLastStep can result in non-exact continuation
1067 * beyond the last step. But we don't consider that to be an issue.
1069 do_log = do_per_step(step, ir->nstlog) || (bFirstStep && !startingFromCheckpoint) || bLastStep || bRerunMD;
1070 do_verbose = mdrunOptions.verbose &&
1071 (step % mdrunOptions.verboseStepPrintInterval == 0 || bFirstStep || bLastStep || bRerunMD);
1073 if (bNS && !(bFirstStep && ir->bContinuation && !bRerunMD))
1077 bMasterState = TRUE;
1081 bMasterState = FALSE;
1082 /* Correct the new box if it is too skewed */
1083 if (inputrecDynamicBox(ir))
1085 if (correct_box(fplog, step, state->box, graph))
1087 bMasterState = TRUE;
1090 if (DOMAINDECOMP(cr) && bMasterState)
1092 dd_collect_state(cr->dd, state, state_global);
1096 if (DOMAINDECOMP(cr))
1098 /* Repartition the domain decomposition */
1099 dd_partition_system(fplog, step, cr,
1100 bMasterState, nstglobalcomm,
1101 state_global, top_global, ir,
1102 state, &f, mdAtoms, top, fr,
1105 do_verbose && !bPMETunePrinting);
1106 shouldCheckNumberOfBondedInteractions = true;
1107 update_realloc(upd, state->natoms);
1111 if (MASTER(cr) && do_log)
1113 print_ebin_header(fplog, step, t); /* can we improve the information printed here? */
1116 if (ir->efep != efepNO)
1118 update_mdatoms(mdatoms, state->lambda[efptMASS]);
1121 if ((bRerunMD && rerun_fr.bV) || bExchanged)
1124 /* We need the kinetic energy at minus the half step for determining
1125 * the full step kinetic energy and possibly for T-coupling.*/
1126 /* This may not be quite working correctly yet . . . . */
1127 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
1128 wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
1129 constr, &nullSignaller, state->box,
1130 &totalNumberOfBondedInteractions, &bSumEkinhOld,
1131 CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
1132 checkNumberOfBondedInteractions(fplog, cr, totalNumberOfBondedInteractions,
1133 top_global, top, state,
1134 &shouldCheckNumberOfBondedInteractions);
1136 clear_mat(force_vir);
1138 /* We write a checkpoint at this MD step when:
1139 * either at an NS step when we signalled through gs,
1140 * or at the last step (but not when we do not want confout),
1141 * but never at the first step or with rerun.
1143 bCPT = (((signals[eglsCHKPT].set && (bNS || ir->nstlist == 0)) ||
1144 (bLastStep && mdrunOptions.writeConfout)) &&
1145 step > ir->init_step && !bRerunMD);
1148 signals[eglsCHKPT].set = 0;
1151 /* Determine the energy and pressure:
1152 * at nstcalcenergy steps and at energy output steps (set below).
1154 if (EI_VV(ir->eI) && (!bInitStep))
1156 /* for vv, the first half of the integration actually corresponds
1157 to the previous step. bCalcEner is only required to be evaluated on the 'next' step,
1158 but the virial needs to be calculated on both the current step and the 'next' step. Future
1159 reorganization may be able to get rid of one of the bCalcVir=TRUE steps. */
1161 /* TODO: This is probably not what we want, we will write to energy file one step after nstcalcenergy steps. */
1162 bCalcEnerStep = do_per_step(step - 1, ir->nstcalcenergy);
1163 bCalcVir = bCalcEnerStep ||
1164 (ir->epc != epcNO && (do_per_step(step, ir->nstpcouple) || do_per_step(step-1, ir->nstpcouple)));
1168 bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
1169 bCalcVir = bCalcEnerStep ||
1170 (ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
1172 bCalcEner = bCalcEnerStep;
1174 do_ene = (do_per_step(step, ir->nstenergy) || bLastStep || bRerunMD);
1176 if (do_ene || do_log || bDoReplEx)
1182 /* Do we need global communication ? */
1183 bGStat = (bCalcVir || bCalcEner || bStopCM ||
1184 do_per_step(step, nstglobalcomm) ||
1185 (EI_VV(ir->eI) && inputrecNvtTrotter(ir) && do_per_step(step-1, nstglobalcomm)));
1187 force_flags = (GMX_FORCE_STATECHANGED |
1188 ((inputrecDynamicBox(ir) || bRerunMD) ? GMX_FORCE_DYNAMICBOX : 0) |
1189 GMX_FORCE_ALLFORCES |
1190 (bCalcVir ? GMX_FORCE_VIRIAL : 0) |
1191 (bCalcEner ? GMX_FORCE_ENERGY : 0) |
1192 (bDoFEP ? GMX_FORCE_DHDL : 0)
1197 /* Now is the time to relax the shells */
1198 relax_shell_flexcon(fplog, cr, mdrunOptions.verbose, step,
1199 ir, bNS, force_flags, top,
1201 state, &f, force_vir, mdatoms,
1202 nrnb, wcycle, graph, groups,
1203 shellfc, fr, t, mu_tot,
1205 ddOpenBalanceRegion, ddCloseBalanceRegion);
1209 /* The AWH history need to be saved _before_ doing force calculations where the AWH bias is updated
1210 (or the AWH update will be performed twice for one step when continuing). It would be best to
1211 call this update function from do_md_trajectory_writing but that would occur after do_force.
1212 One would have to divide the update_awh function into one function applying the AWH force
1213 and one doing the AWH bias update. The update AWH bias function could then be called after
1214 do_md_trajectory_writing (then containing update_awh_history).
1215 The checkpointing will in the future probably moved to the start of the md loop which will
1216 rid of this issue. */
1217 if (ir->bDoAwh && bCPT && MASTER(cr))
1219 ir->awh->updateHistory(state_global->awhHistory.get());
1222 /* The coordinates (x) are shifted (to get whole molecules)
1224 * This is parallellized as well, and does communication too.
1225 * Check comments in sim_util.c
1227 do_force(fplog, cr, ir, step, nrnb, wcycle, top, groups,
1228 state->box, state->x, &state->hist,
1229 f, force_vir, mdatoms, enerd, fcd,
1230 state->lambda, graph,
1231 fr, vsite, mu_tot, t, ed,
1232 (bNS ? GMX_FORCE_NS : 0) | force_flags,
1233 ddOpenBalanceRegion, ddCloseBalanceRegion);
1236 if (EI_VV(ir->eI) && !startingFromCheckpoint && !bRerunMD)
1237 /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
1239 rvec *vbuf = nullptr;
1241 wallcycle_start(wcycle, ewcUPDATE);
1242 if (ir->eI == eiVV && bInitStep)
1244 /* if using velocity verlet with full time step Ekin,
1245 * take the first half step only to compute the
1246 * virial for the first step. From there,
1247 * revert back to the initial coordinates
1248 * so that the input is actually the initial step.
1250 snew(vbuf, state->natoms);
1251 copy_rvecn(as_rvec_array(state->v.data()), vbuf, 0, state->natoms); /* should make this better for parallelizing? */
1255 /* this is for NHC in the Ekin(t+dt/2) version of vv */
1256 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ1);
1259 update_coords(fplog, step, ir, mdatoms, state, f, fcd,
1260 ekind, M, upd, etrtVELOCITY1,
1263 if (!bRerunMD || rerun_fr.bV || bForceUpdate) /* Why is rerun_fr.bV here? Unclear. */
1265 wallcycle_stop(wcycle, ewcUPDATE);
1266 update_constraints(fplog, step, nullptr, ir, mdatoms,
1267 state, fr->bMolPBC, graph, f,
1268 &top->idef, shake_vir,
1269 cr, nrnb, wcycle, upd, constr,
1271 wallcycle_start(wcycle, ewcUPDATE);
1275 /* Need to unshift here if a do_force has been
1276 called in the previous step */
1277 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
1279 /* if VV, compute the pressure and constraints */
1280 /* For VV2, we strictly only need this if using pressure
1281 * control, but we really would like to have accurate pressures
1283 * Think about ways around this in the future?
1284 * For now, keep this choice in comments.
1286 /*bPres = (ir->eI==eiVV || inputrecNptTrotter(ir)); */
1287 /*bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK && inputrecNptTrotter(ir)));*/
1289 bTemp = ((ir->eI == eiVV && (!bInitStep)) || (ir->eI == eiVVAK));
1290 if (bCalcEner && ir->eI == eiVVAK)
1292 bSumEkinhOld = TRUE;
1294 /* for vv, the first half of the integration actually corresponds to the previous step.
1295 So we need information from the last step in the first half of the integration */
1296 if (bGStat || do_per_step(step-1, nstglobalcomm))
1298 wallcycle_stop(wcycle, ewcUPDATE);
1299 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
1300 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
1301 constr, &nullSignaller, state->box,
1302 &totalNumberOfBondedInteractions, &bSumEkinhOld,
1303 (bGStat ? CGLO_GSTAT : 0)
1305 | (bTemp ? CGLO_TEMPERATURE : 0)
1306 | (bPres ? CGLO_PRESSURE : 0)
1307 | (bPres ? CGLO_CONSTRAINT : 0)
1308 | (bStopCM ? CGLO_STOPCM : 0)
1309 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
1312 /* explanation of above:
1313 a) We compute Ekin at the full time step
1314 if 1) we are using the AveVel Ekin, and it's not the
1315 initial step, or 2) if we are using AveEkin, but need the full
1316 time step kinetic energy for the pressure (always true now, since we want accurate statistics).
1317 b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
1318 EkinAveVel because it's needed for the pressure */
1319 checkNumberOfBondedInteractions(fplog, cr, totalNumberOfBondedInteractions,
1320 top_global, top, state,
1321 &shouldCheckNumberOfBondedInteractions);
1322 wallcycle_start(wcycle, ewcUPDATE);
1324 /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
1329 m_add(force_vir, shake_vir, total_vir); /* we need the un-dispersion corrected total vir here */
1330 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ2);
1332 /* TODO This is only needed when we're about to write
1333 * a checkpoint, because we use it after the restart
1334 * (in a kludge?). But what should we be doing if
1335 * startingFromCheckpoint or bInitStep are true? */
1336 if (inputrecNptTrotter(ir) || inputrecNphTrotter(ir))
1338 copy_mat(shake_vir, state->svir_prev);
1339 copy_mat(force_vir, state->fvir_prev);
1341 if (inputrecNvtTrotter(ir) && ir->eI == eiVV)
1343 /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
1344 enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, nullptr, (ir->eI == eiVV), FALSE);
1345 enerd->term[F_EKIN] = trace(ekind->ekin);
1348 else if (bExchanged)
1350 wallcycle_stop(wcycle, ewcUPDATE);
1351 /* We need the kinetic energy at minus the half step for determining
1352 * the full step kinetic energy and possibly for T-coupling.*/
1353 /* This may not be quite working correctly yet . . . . */
1354 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
1355 wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
1356 constr, &nullSignaller, state->box,
1357 nullptr, &bSumEkinhOld,
1358 CGLO_GSTAT | CGLO_TEMPERATURE);
1359 wallcycle_start(wcycle, ewcUPDATE);
1362 /* if it's the initial step, we performed this first step just to get the constraint virial */
1363 if (ir->eI == eiVV && bInitStep)
1365 copy_rvecn(vbuf, as_rvec_array(state->v.data()), 0, state->natoms);
1368 wallcycle_stop(wcycle, ewcUPDATE);
1371 /* compute the conserved quantity */
1374 saved_conserved_quantity = NPT_energy(ir, state, &MassQ);
1377 last_ekin = enerd->term[F_EKIN];
1379 if ((ir->eDispCorr != edispcEnerPres) && (ir->eDispCorr != edispcAllEnerPres))
1381 saved_conserved_quantity -= enerd->term[F_DISPCORR];
1383 /* sum up the foreign energy and dhdl terms for vv. currently done every step so that dhdl is correct in the .edr */
1384 if (ir->efep != efepNO && !bRerunMD)
1386 sum_dhdl(enerd, state->lambda, ir->fepvals);
1390 /* ######## END FIRST UPDATE STEP ############## */
1391 /* ######## If doing VV, we now have v(dt) ###### */
1394 /* perform extended ensemble sampling in lambda - we don't
1395 actually move to the new state before outputting
1396 statistics, but if performing simulated tempering, we
1397 do update the velocities and the tau_t. */
1399 lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, state->fep_state, state->dfhist, step, as_rvec_array(state->v.data()), mdatoms);
1400 /* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
1403 copy_df_history(state_global->dfhist, state->dfhist);
1407 /* Now we have the energies and forces corresponding to the
1408 * coordinates at time t. We must output all of this before
1411 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
1412 ir, state, state_global, observablesHistory,
1414 outf, mdebin, ekind, f,
1416 bCPT, bRerunMD, bLastStep,
1417 mdrunOptions.writeConfout,
1419 /* Check if IMD step and do IMD communication, if bIMD is TRUE. */
1420 bIMDstep = do_IMD(ir->bIMD, step, cr, bNS, state->box, as_rvec_array(state->x.data()), ir, t, wcycle);
1422 /* kludge -- virial is lost with restart for MTTK NPT control. Must reload (saved earlier). */
1423 if (startingFromCheckpoint && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir)))
1425 copy_mat(state->svir_prev, shake_vir);
1426 copy_mat(state->fvir_prev, force_vir);
1429 elapsed_time = walltime_accounting_get_current_elapsed_time(walltime_accounting);
1431 /* Check whether everything is still allright */
1432 if (((int)gmx_get_stop_condition() > handled_stop_condition)
1438 int nsteps_stop = -1;
1440 /* this just makes signals[].sig compatible with the hack
1441 of sending signals around by MPI_Reduce together with
1443 if ((gmx_get_stop_condition() == gmx_stop_cond_next_ns) ||
1444 (mdrunOptions.reproducible &&
1445 gmx_get_stop_condition() == gmx_stop_cond_next))
1447 /* We need at least two global communication steps to pass
1448 * around the signal. We stop at a pair-list creation step
1449 * to allow for exact continuation, when possible.
1451 signals[eglsSTOPCOND].sig = 1;
1452 nsteps_stop = std::max(ir->nstlist, 2*nstglobalcomm);
1454 else if (gmx_get_stop_condition() == gmx_stop_cond_next)
1456 /* Stop directly after the next global communication step.
1457 * This breaks exact continuation.
1459 signals[eglsSTOPCOND].sig = -1;
1460 nsteps_stop = nstglobalcomm + 1;
1465 "\n\nReceived the %s signal, stopping within %d steps\n\n",
1466 gmx_get_signal_name(), nsteps_stop);
1470 "\n\nReceived the %s signal, stopping within %d steps\n\n",
1471 gmx_get_signal_name(), nsteps_stop);
1473 handled_stop_condition = (int)gmx_get_stop_condition();
1475 else if (MASTER(cr) && (bNS || ir->nstlist <= 0) &&
1476 (max_hours > 0 && elapsed_time > max_hours*60.0*60.0*0.99) &&
1477 signals[eglsSTOPCOND].sig == 0 && signals[eglsSTOPCOND].set == 0)
1479 /* Signal to terminate the run */
1480 signals[eglsSTOPCOND].sig = 1;
1483 fprintf(fplog, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
1485 fprintf(stderr, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
1488 if (bResetCountersHalfMaxH && MASTER(cr) &&
1489 elapsed_time > max_hours*60.0*60.0*0.495)
1491 /* Set flag that will communicate the signal to all ranks in the simulation */
1492 signals[eglsRESETCOUNTERS].sig = 1;
1495 /* In parallel we only have to check for checkpointing in steps
1496 * where we do global communication,
1497 * otherwise the other nodes don't know.
1499 const real cpt_period = mdrunOptions.checkpointOptions.period;
1500 if (MASTER(cr) && ((bGStat || !PAR(cr)) &&
1503 elapsed_time >= nchkpt*cpt_period*60.0)) &&
1504 signals[eglsCHKPT].set == 0)
1506 signals[eglsCHKPT].sig = 1;
1509 /* ######### START SECOND UPDATE STEP ################# */
1511 /* at the start of step, randomize or scale the velocities ((if vv. Restriction of Andersen controlled
1514 if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
1516 gmx_bool bIfRandomize;
1517 bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state, upd, constr);
1518 /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
1519 if (constr && bIfRandomize)
1521 update_constraints(fplog, step, nullptr, ir, mdatoms,
1522 state, fr->bMolPBC, graph, f,
1523 &top->idef, tmp_vir,
1524 cr, nrnb, wcycle, upd, constr,
1528 /* Box is changed in update() when we do pressure coupling,
1529 * but we should still use the old box for energy corrections and when
1530 * writing it to the energy file, so it matches the trajectory files for
1531 * the same timestep above. Make a copy in a separate array.
1533 copy_mat(state->box, lastbox);
1537 if (!bRerunMD || rerun_fr.bV || bForceUpdate)
1539 wallcycle_start(wcycle, ewcUPDATE);
1540 /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
1543 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
1544 /* We can only do Berendsen coupling after we have summed
1545 * the kinetic energy or virial. Since the happens
1546 * in global_state after update, we should only do it at
1547 * step % nstlist = 1 with bGStatEveryStep=FALSE.
1552 update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
1553 update_pcouple_before_coordinates(fplog, step, ir, state,
1554 parrinellorahmanMu, M,
1560 /* velocity half-step update */
1561 update_coords(fplog, step, ir, mdatoms, state, f, fcd,
1562 ekind, M, upd, etrtVELOCITY2,
1566 /* Above, initialize just copies ekinh into ekin,
1567 * it doesn't copy position (for VV),
1568 * and entire integrator for MD.
1571 if (ir->eI == eiVVAK)
1573 /* We probably only need md->homenr, not state->natoms */
1574 if (state->natoms > cbuf_nalloc)
1576 cbuf_nalloc = state->natoms;
1577 srenew(cbuf, cbuf_nalloc);
1579 copy_rvecn(as_rvec_array(state->x.data()), cbuf, 0, state->natoms);
1582 update_coords(fplog, step, ir, mdatoms, state, f, fcd,
1583 ekind, M, upd, etrtPOSITION, cr, constr);
1584 wallcycle_stop(wcycle, ewcUPDATE);
1586 update_constraints(fplog, step, &dvdl_constr, ir, mdatoms, state,
1587 fr->bMolPBC, graph, f,
1588 &top->idef, shake_vir,
1589 cr, nrnb, wcycle, upd, constr,
1592 if (ir->eI == eiVVAK)
1594 /* erase F_EKIN and F_TEMP here? */
1595 /* just compute the kinetic energy at the half step to perform a trotter step */
1596 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
1597 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
1598 constr, &nullSignaller, lastbox,
1599 nullptr, &bSumEkinhOld,
1600 (bGStat ? CGLO_GSTAT : 0) | CGLO_TEMPERATURE
1602 wallcycle_start(wcycle, ewcUPDATE);
1603 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ4);
1604 /* now we know the scaling, we can compute the positions again again */
1605 copy_rvecn(cbuf, as_rvec_array(state->x.data()), 0, state->natoms);
1607 update_coords(fplog, step, ir, mdatoms, state, f, fcd,
1608 ekind, M, upd, etrtPOSITION, cr, constr);
1609 wallcycle_stop(wcycle, ewcUPDATE);
1611 /* do we need an extra constraint here? just need to copy out of as_rvec_array(state->v.data()) to upd->xp? */
1612 /* are the small terms in the shake_vir here due
1613 * to numerical errors, or are they important
1614 * physically? I'm thinking they are just errors, but not completely sure.
1615 * For now, will call without actually constraining, constr=NULL*/
1616 update_constraints(fplog, step, nullptr, ir, mdatoms,
1617 state, fr->bMolPBC, graph, f,
1618 &top->idef, tmp_vir,
1619 cr, nrnb, wcycle, upd, nullptr,
1624 /* this factor or 2 correction is necessary
1625 because half of the constraint force is removed
1626 in the vv step, so we have to double it. See
1627 the Redmine issue #1255. It is not yet clear
1628 if the factor of 2 is exact, or just a very
1629 good approximation, and this will be
1630 investigated. The next step is to see if this
1631 can be done adding a dhdl contribution from the
1632 rattle step, but this is somewhat more
1633 complicated with the current code. Will be
1634 investigated, hopefully for 4.6.3. However,
1635 this current solution is much better than
1636 having it completely wrong.
1638 enerd->term[F_DVDL_CONSTR] += 2*dvdl_constr;
1642 enerd->term[F_DVDL_CONSTR] += dvdl_constr;
1647 /* Need to unshift here */
1648 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
1651 if (vsite != nullptr)
1653 wallcycle_start(wcycle, ewcVSITECONSTR);
1654 if (graph != nullptr)
1656 shift_self(graph, state->box, as_rvec_array(state->x.data()));
1658 construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
1659 top->idef.iparams, top->idef.il,
1660 fr->ePBC, fr->bMolPBC, cr, state->box);
1662 if (graph != nullptr)
1664 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
1666 wallcycle_stop(wcycle, ewcVSITECONSTR);
1669 /* ############## IF NOT VV, Calculate globals HERE ############ */
1670 /* With Leap-Frog we can skip compute_globals at
1671 * non-communication steps, but we need to calculate
1672 * the kinetic energy one step before communication.
1675 // Organize to do inter-simulation signalling on steps if
1676 // and when algorithms require it.
1677 bool doInterSimSignal = (!bFirstStep && bDoReplEx) || bUsingEnsembleRestraints;
1679 if (bGStat || (!EI_VV(ir->eI) && do_per_step(step+1, nstglobalcomm)) || doInterSimSignal)
1681 // Since we're already communicating at this step, we
1682 // can propagate intra-simulation signals. Note that
1683 // check_nstglobalcomm has the responsibility for
1684 // choosing the value of nstglobalcomm that is one way
1685 // bGStat becomes true, so we can't get into a
1686 // situation where e.g. checkpointing can't be
1688 bool doIntraSimSignal = true;
1689 SimulationSignaller signaller(&signals, cr, doInterSimSignal, doIntraSimSignal);
1691 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
1692 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
1695 &totalNumberOfBondedInteractions, &bSumEkinhOld,
1696 (bGStat ? CGLO_GSTAT : 0)
1697 | (!EI_VV(ir->eI) || bRerunMD ? CGLO_ENERGY : 0)
1698 | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
1699 | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
1700 | (!EI_VV(ir->eI) || bRerunMD ? CGLO_PRESSURE : 0)
1702 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
1704 checkNumberOfBondedInteractions(fplog, cr, totalNumberOfBondedInteractions,
1705 top_global, top, state,
1706 &shouldCheckNumberOfBondedInteractions);
1710 /* ############# END CALC EKIN AND PRESSURE ################# */
1712 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
1713 the virial that should probably be addressed eventually. state->veta has better properies,
1714 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
1715 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
1717 if (ir->efep != efepNO && (!EI_VV(ir->eI) || bRerunMD))
1719 /* Sum up the foreign energy and dhdl terms for md and sd.
1720 Currently done every step so that dhdl is correct in the .edr */
1721 sum_dhdl(enerd, state->lambda, ir->fepvals);
1724 update_pcouple_after_coordinates(fplog, step, ir, mdatoms,
1725 pres, force_vir, shake_vir,
1729 /* ################# END UPDATE STEP 2 ################# */
1730 /* #### We now have r(t+dt) and v(t+dt/2) ############# */
1732 /* The coordinates (x) were unshifted in update */
1735 /* We will not sum ekinh_old,
1736 * so signal that we still have to do it.
1738 bSumEkinhOld = TRUE;
1743 /* ######### BEGIN PREPARING EDR OUTPUT ########### */
1745 /* use the directly determined last velocity, not actually the averaged half steps */
1746 if (bTrotter && ir->eI == eiVV)
1748 enerd->term[F_EKIN] = last_ekin;
1750 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
1752 if (integratorHasConservedEnergyQuantity(ir))
1756 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
1760 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + NPT_energy(ir, state, &MassQ);
1763 /* ######### END PREPARING EDR OUTPUT ########### */
1769 if (fplog && do_log && bDoExpanded)
1771 /* only needed if doing expanded ensemble */
1772 PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : nullptr,
1773 state_global->dfhist, state->fep_state, ir->nstlog, step);
1777 upd_mdebin(mdebin, bDoDHDL, bCalcEnerStep,
1778 t, mdatoms->tmass, enerd, state,
1779 ir->fepvals, ir->expandedvals, lastbox,
1780 shake_vir, force_vir, total_vir, pres,
1781 ekind, mu_tot, constr);
1785 upd_mdebin_step(mdebin);
1788 gmx_bool do_dr = do_per_step(step, ir->nstdisreout);
1789 gmx_bool do_or = do_per_step(step, ir->nstorireout);
1791 print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : nullptr,
1793 eprNORMAL, mdebin, fcd, groups, &(ir->opts), ir->awh);
1797 pull_print_output(ir->pull_work, step, t);
1800 if (do_per_step(step, ir->nstlog))
1802 if (fflush(fplog) != 0)
1804 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
1810 /* Have to do this part _after_ outputting the logfile and the edr file */
1811 /* Gets written into the state at the beginning of next loop*/
1812 state->fep_state = lamnew;
1814 /* Print the remaining wall clock time for the run */
1815 if (isMasterSimMasterRank(cr->ms, cr) &&
1816 (do_verbose || gmx_got_usr_signal()) &&
1821 fprintf(stderr, "\n");
1823 print_time(stderr, walltime_accounting, step, ir, cr);
1826 /* Ion/water position swapping.
1827 * Not done in last step since trajectory writing happens before this call
1828 * in the MD loop and exchanges would be lost anyway. */
1829 bNeedRepartition = FALSE;
1830 if ((ir->eSwapCoords != eswapNO) && (step > 0) && !bLastStep &&
1831 do_per_step(step, ir->swap->nstswap))
1833 bNeedRepartition = do_swapcoords(cr, step, t, ir, wcycle,
1834 bRerunMD ? rerun_fr.x : as_rvec_array(state->x.data()),
1835 bRerunMD ? rerun_fr.box : state->box,
1836 MASTER(cr) && mdrunOptions.verbose,
1839 if (bNeedRepartition && DOMAINDECOMP(cr))
1841 dd_collect_state(cr->dd, state, state_global);
1845 /* Replica exchange */
1849 bExchanged = replica_exchange(fplog, cr, repl_ex,
1850 state_global, enerd,
1854 if ( (bExchanged || bNeedRepartition) && DOMAINDECOMP(cr) )
1856 dd_partition_system(fplog, step, cr, TRUE, 1,
1857 state_global, top_global, ir,
1858 state, &f, mdAtoms, top, fr,
1860 nrnb, wcycle, FALSE);
1861 shouldCheckNumberOfBondedInteractions = true;
1862 update_realloc(upd, state->natoms);
1867 startingFromCheckpoint = false;
1869 /* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
1870 /* With all integrators, except VV, we need to retain the pressure
1871 * at the current step for coupling at the next step.
1873 if ((state->flags & (1<<estPRES_PREV)) &&
1875 (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
1877 /* Store the pressure in t_state for pressure coupling
1878 * at the next MD step.
1880 copy_mat(pres, state->pres_prev);
1883 /* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
1885 if ( (membed != nullptr) && (!bLastStep) )
1887 rescale_membed(step_rel, membed, as_rvec_array(state_global->x.data()));
1894 /* read next frame from input trajectory */
1895 bLastStep = !read_next_frame(oenv, status, &rerun_fr);
1900 rerun_parallel_comm(cr, &rerun_fr, &bLastStep);
1904 cycles = wallcycle_stop(wcycle, ewcSTEP);
1905 if (DOMAINDECOMP(cr) && wcycle)
1907 dd_cycles_add(cr->dd, cycles, ddCyclStep);
1910 if (!bRerunMD || !rerun_fr.bStep)
1912 /* increase the MD step number */
1917 /* TODO make a counter-reset module */
1918 /* If it is time to reset counters, set a flag that remains
1919 true until counters actually get reset */
1920 if (step_rel == wcycle_get_reset_counters(wcycle) ||
1921 signals[eglsRESETCOUNTERS].set != 0)
1923 if (pme_loadbal_is_active(pme_loadbal))
1925 /* Do not permit counter reset while PME load
1926 * balancing is active. The only purpose for resetting
1927 * counters is to measure reliable performance data,
1928 * and that can't be done before balancing
1931 * TODO consider fixing this by delaying the reset
1932 * until after load balancing completes,
1933 * e.g. https://gerrit.gromacs.org/#/c/4964/2 */
1934 gmx_fatal(FARGS, "PME tuning was still active when attempting to "
1935 "reset mdrun counters at step %" GMX_PRId64 ". Try "
1936 "resetting counters later in the run, e.g. with gmx "
1937 "mdrun -resetstep.", step);
1939 reset_all_counters(fplog, mdlog, cr, step, &step_rel, ir, wcycle, nrnb, walltime_accounting,
1940 use_GPU(fr->nbv) ? fr->nbv : nullptr, fr->pmedata);
1941 wcycle_set_reset_counters(wcycle, -1);
1942 if (!thisRankHasDuty(cr, DUTY_PME))
1944 /* Tell our PME node to reset its counters */
1945 gmx_pme_send_resetcounters(cr, step);
1947 /* Correct max_hours for the elapsed time */
1948 max_hours -= elapsed_time/(60.0*60.0);
1949 /* If mdrun -maxh -resethway was active, it can only trigger once */
1950 bResetCountersHalfMaxH = FALSE; /* TODO move this to where signals[eglsRESETCOUNTERS].sig is set */
1951 /* Reset can only happen once, so clear the triggering flag. */
1952 signals[eglsRESETCOUNTERS].set = 0;
1955 /* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
1956 IMD_prep_energies_send_positions(ir->bIMD && MASTER(cr), bIMDstep, ir->imd, enerd, step, bCalcEner, wcycle);
1959 /* End of main MD loop */
1961 /* Closing TNG files can include compressing data. Therefore it is good to do that
1962 * before stopping the time measurements. */
1963 mdoutf_tng_close(outf);
1965 /* Stop measuring walltime */
1966 walltime_accounting_end(walltime_accounting);
1968 if (bRerunMD && MASTER(cr))
1973 if (!thisRankHasDuty(cr, DUTY_PME))
1975 /* Tell the PME only node to finish */
1976 gmx_pme_send_finish(cr);
1981 if (ir->nstcalcenergy > 0 && !bRerunMD)
1983 print_ebin(mdoutf_get_fp_ene(outf), FALSE, FALSE, FALSE, fplog, step, t,
1984 eprAVER, mdebin, fcd, groups, &(ir->opts), ir->awh);
1992 pme_loadbal_done(pme_loadbal, fplog, mdlog, use_GPU(fr->nbv));
1995 done_shellfc(fplog, shellfc, step_rel);
1997 if (useReplicaExchange && MASTER(cr))
1999 print_replica_exchange_statistics(fplog, repl_ex);
2007 // Clean up swapcoords
2008 if (ir->eSwapCoords != eswapNO)
2010 finish_swapcoords(ir->swap);
2013 /* Do essential dynamics cleanup if needed. Close .edo file */
2016 /* IMD cleanup, if bIMD is TRUE. */
2017 IMD_finalize(ir->bIMD, ir->imd);
2019 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
2020 if (step_rel >= wcycle_get_reset_counters(wcycle) &&
2021 signals[eglsRESETCOUNTERS].set == 0 &&
2022 !bResetCountersHalfMaxH)
2024 walltime_accounting_set_valid_finish(walltime_accounting);