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39 * \brief Implements the integrator for normal molecular dynamics simulations
41 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
42 * \ingroup module_mdrun
55 #include "gromacs/applied_forces/awh/awh.h"
56 #include "gromacs/commandline/filenm.h"
57 #include "gromacs/domdec/collect.h"
58 #include "gromacs/domdec/dlbtiming.h"
59 #include "gromacs/domdec/domdec.h"
60 #include "gromacs/domdec/domdec_network.h"
61 #include "gromacs/domdec/domdec_struct.h"
62 #include "gromacs/domdec/gpuhaloexchange.h"
63 #include "gromacs/domdec/mdsetup.h"
64 #include "gromacs/domdec/partition.h"
65 #include "gromacs/essentialdynamics/edsam.h"
66 #include "gromacs/ewald/pme_load_balancing.h"
67 #include "gromacs/ewald/pme_pp.h"
68 #include "gromacs/fileio/trxio.h"
69 #include "gromacs/gmxlib/network.h"
70 #include "gromacs/gmxlib/nrnb.h"
71 #include "gromacs/gpu_utils/device_stream_manager.h"
72 #include "gromacs/gpu_utils/gpu_utils.h"
73 #include "gromacs/imd/imd.h"
74 #include "gromacs/listed_forces/listed_forces.h"
75 #include "gromacs/math/functions.h"
76 #include "gromacs/math/invertmatrix.h"
77 #include "gromacs/math/vec.h"
78 #include "gromacs/math/vectypes.h"
79 #include "gromacs/mdlib/checkpointhandler.h"
80 #include "gromacs/mdlib/compute_io.h"
81 #include "gromacs/mdlib/constr.h"
82 #include "gromacs/mdlib/coupling.h"
83 #include "gromacs/mdlib/ebin.h"
84 #include "gromacs/mdlib/enerdata_utils.h"
85 #include "gromacs/mdlib/energyoutput.h"
86 #include "gromacs/mdlib/expanded.h"
87 #include "gromacs/mdlib/force.h"
88 #include "gromacs/mdlib/force_flags.h"
89 #include "gromacs/mdlib/forcerec.h"
90 #include "gromacs/mdlib/freeenergyparameters.h"
91 #include "gromacs/mdlib/md_support.h"
92 #include "gromacs/mdlib/mdatoms.h"
93 #include "gromacs/mdlib/mdoutf.h"
94 #include "gromacs/mdlib/membed.h"
95 #include "gromacs/mdlib/resethandler.h"
96 #include "gromacs/mdlib/sighandler.h"
97 #include "gromacs/mdlib/simulationsignal.h"
98 #include "gromacs/mdlib/stat.h"
99 #include "gromacs/mdlib/stophandler.h"
100 #include "gromacs/mdlib/tgroup.h"
101 #include "gromacs/mdlib/trajectory_writing.h"
102 #include "gromacs/mdlib/update.h"
103 #include "gromacs/mdlib/update_constrain_gpu.h"
104 #include "gromacs/mdlib/update_vv.h"
105 #include "gromacs/mdlib/vcm.h"
106 #include "gromacs/mdlib/vsite.h"
107 #include "gromacs/mdrunutility/handlerestart.h"
108 #include "gromacs/mdrunutility/multisim.h"
109 #include "gromacs/mdrunutility/printtime.h"
110 #include "gromacs/mdtypes/awh_history.h"
111 #include "gromacs/mdtypes/awh_params.h"
112 #include "gromacs/mdtypes/commrec.h"
113 #include "gromacs/mdtypes/df_history.h"
114 #include "gromacs/mdtypes/energyhistory.h"
115 #include "gromacs/mdtypes/fcdata.h"
116 #include "gromacs/mdtypes/forcebuffers.h"
117 #include "gromacs/mdtypes/forcerec.h"
118 #include "gromacs/mdtypes/group.h"
119 #include "gromacs/mdtypes/inputrec.h"
120 #include "gromacs/mdtypes/interaction_const.h"
121 #include "gromacs/mdtypes/md_enums.h"
122 #include "gromacs/mdtypes/mdatom.h"
123 #include "gromacs/mdtypes/mdrunoptions.h"
124 #include "gromacs/mdtypes/multipletimestepping.h"
125 #include "gromacs/mdtypes/observableshistory.h"
126 #include "gromacs/mdtypes/pullhistory.h"
127 #include "gromacs/mdtypes/simulation_workload.h"
128 #include "gromacs/mdtypes/state.h"
129 #include "gromacs/mdtypes/state_propagator_data_gpu.h"
130 #include "gromacs/modularsimulator/energydata.h"
131 #include "gromacs/nbnxm/gpu_data_mgmt.h"
132 #include "gromacs/nbnxm/nbnxm.h"
133 #include "gromacs/pbcutil/pbc.h"
134 #include "gromacs/pulling/output.h"
135 #include "gromacs/pulling/pull.h"
136 #include "gromacs/swap/swapcoords.h"
137 #include "gromacs/timing/wallcycle.h"
138 #include "gromacs/timing/walltime_accounting.h"
139 #include "gromacs/topology/atoms.h"
140 #include "gromacs/topology/idef.h"
141 #include "gromacs/topology/mtop_util.h"
142 #include "gromacs/topology/topology.h"
143 #include "gromacs/trajectory/trajectoryframe.h"
144 #include "gromacs/utility/basedefinitions.h"
145 #include "gromacs/utility/cstringutil.h"
146 #include "gromacs/utility/fatalerror.h"
147 #include "gromacs/utility/logger.h"
148 #include "gromacs/utility/real.h"
149 #include "gromacs/utility/smalloc.h"
151 #include "legacysimulator.h"
152 #include "replicaexchange.h"
155 using gmx::SimulationSignaller;
157 void gmx::LegacySimulator::do_md()
159 // TODO Historically, the EM and MD "integrators" used different
160 // names for the t_inputrec *parameter, but these must have the
161 // same name, now that it's a member of a struct. We use this ir
162 // alias to avoid a large ripple of nearly useless changes.
163 // t_inputrec is being replaced by IMdpOptionsProvider, so this
164 // will go away eventually.
165 const t_inputrec* ir = inputrec;
167 int64_t step, step_rel;
168 double t, t0 = ir->init_t;
169 gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, bCalcEner;
170 gmx_bool bNS = FALSE, bNStList, bStopCM, bFirstStep, bInitStep, bLastStep = FALSE;
171 gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
172 gmx_bool do_ene, do_log, do_verbose;
173 gmx_bool bMasterState;
174 unsigned int force_flags;
175 tensor force_vir = { { 0 } }, shake_vir = { { 0 } }, total_vir = { { 0 } }, pres = { { 0 } };
178 matrix pressureCouplingMu, M;
179 gmx_repl_ex_t repl_ex = nullptr;
180 gmx_global_stat_t gstat;
181 gmx_shellfc_t* shellfc;
182 gmx_bool bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
185 std::vector<RVec> cbuf;
191 real saved_conserved_quantity = 0;
194 char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
196 /* PME load balancing data for GPU kernels */
197 gmx_bool bPMETune = FALSE;
198 gmx_bool bPMETunePrinting = FALSE;
200 bool bInteractiveMDstep = false;
202 /* Domain decomposition could incorrectly miss a bonded
203 interaction, but checking for that requires a global
204 communication stage, which does not otherwise happen in DD
205 code. So we do that alongside the first global energy reduction
206 after a new DD is made. These variables handle whether the
207 check happens, and the result it returns. */
208 bool shouldCheckNumberOfBondedInteractions = false;
209 int totalNumberOfBondedInteractions = -1;
211 SimulationSignals signals;
212 // Most global communnication stages don't propagate mdrun
213 // signals, and will use this object to achieve that.
214 SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
216 if (!mdrunOptions.writeConfout)
218 // This is on by default, and the main known use case for
219 // turning it off is for convenience in benchmarking, which is
220 // something that should not show up in the general user
225 "The -noconfout functionality is deprecated, and may be removed in a "
229 /* md-vv uses averaged full step velocities for T-control
230 md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
231 md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
232 bTrotter = (EI_VV(ir->eI)
233 && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir) || inputrecNvtTrotter(ir)));
235 const bool bRerunMD = false;
237 int nstglobalcomm = computeGlobalCommunicationPeriod(mdlog, ir, cr);
238 bGStatEveryStep = (nstglobalcomm == 1);
240 const SimulationGroups* groups = &top_global->groups;
242 std::unique_ptr<EssentialDynamics> ed = nullptr;
243 if (opt2bSet("-ei", nfile, fnm))
245 /* Initialize essential dynamics sampling */
246 ed = init_edsam(mdlog,
247 opt2fn_null("-ei", nfile, fnm),
248 opt2fn("-eo", nfile, fnm),
258 else if (observablesHistory->edsamHistory)
261 "The checkpoint is from a run with essential dynamics sampling, "
262 "but the current run did not specify the -ei option. "
263 "Either specify the -ei option to mdrun, or do not use this checkpoint file.");
266 int* fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
267 gmx::ArrayRef<real> lambda = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
268 initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
269 Update upd(*ir, deform);
270 bool doSimulatedAnnealing = false;
272 // TODO: Avoid changing inputrec (#3854)
273 // Simulated annealing updates the reference temperature.
274 auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
275 doSimulatedAnnealing = initSimulatedAnnealing(nonConstInputrec, &upd);
277 const bool useReplicaExchange = (replExParams.exchangeInterval > 0);
279 const t_fcdata& fcdata = *fr->fcdata;
281 bool simulationsShareState = false;
282 int nstSignalComm = nstglobalcomm;
284 // TODO This implementation of ensemble orientation restraints is nasty because
285 // a user can't just do multi-sim with single-sim orientation restraints.
286 bool usingEnsembleRestraints =
287 (fcdata.disres->nsystems > 1) || ((ms != nullptr) && (fcdata.orires->nr != 0));
288 bool awhUsesMultiSim = (ir->bDoAwh && ir->awhParams->shareBiasMultisim && (ms != nullptr));
290 // Replica exchange, ensemble restraints and AWH need all
291 // simulations to remain synchronized, so they need
292 // checkpoints and stop conditions to act on the same step, so
293 // the propagation of such signals must take place between
294 // simulations, not just within simulations.
295 // TODO: Make algorithm initializers set these flags.
296 simulationsShareState = useReplicaExchange || usingEnsembleRestraints || awhUsesMultiSim;
298 if (simulationsShareState)
300 // Inter-simulation signal communication does not need to happen
301 // often, so we use a minimum of 200 steps to reduce overhead.
302 const int c_minimumInterSimulationSignallingInterval = 200;
303 nstSignalComm = ((c_minimumInterSimulationSignallingInterval + nstglobalcomm - 1) / nstglobalcomm)
308 if (startingBehavior != StartingBehavior::RestartWithAppending)
310 pleaseCiteCouplingAlgorithms(fplog, *ir);
312 gmx_mdoutf* outf = init_mdoutf(fplog,
324 simulationsShareState,
326 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
330 mdoutf_get_fp_dhdl(outf),
333 simulationsShareState,
336 gstat = global_stat_init(ir);
338 const auto& simulationWork = runScheduleWork->simulationWork;
339 const bool useGpuForPme = simulationWork.useGpuPme;
340 const bool useGpuForNonbonded = simulationWork.useGpuNonbonded;
341 const bool useGpuForBufferOps = simulationWork.useGpuBufferOps;
342 const bool useGpuForUpdate = simulationWork.useGpuUpdate;
344 /* Check for polarizable models and flexible constraints */
345 shellfc = init_shell_flexcon(fplog,
347 constr ? constr->numFlexibleConstraints() : 0,
353 double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
354 if ((io > 2000) && MASTER(cr))
356 fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
360 // Local state only becomes valid now.
361 std::unique_ptr<t_state> stateInstance;
364 gmx_localtop_t top(top_global->ffparams);
366 auto mdatoms = mdAtoms->mdatoms();
368 ForceBuffers f(fr->useMts,
369 ((useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
370 ? PinningPolicy::PinnedIfSupported
371 : PinningPolicy::CannotBePinned);
372 if (DOMAINDECOMP(cr))
374 stateInstance = std::make_unique<t_state>();
375 state = stateInstance.get();
376 dd_init_local_state(cr->dd, state_global, state);
378 /* Distribute the charge groups over the nodes from the master node */
379 dd_partition_system(fplog,
400 shouldCheckNumberOfBondedInteractions = true;
401 upd.setNumAtoms(state->natoms);
405 state_change_natoms(state_global, state_global->natoms);
406 /* Copy the pointer to the global state */
407 state = state_global;
409 /* Generate and initialize new topology */
410 mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
412 upd.setNumAtoms(state->natoms);
415 std::unique_ptr<UpdateConstrainGpu> integrator;
417 StatePropagatorDataGpu* stateGpu = fr->stateGpu;
419 // TODO: the assertions below should be handled by UpdateConstraintsBuilder.
422 GMX_RELEASE_ASSERT(!DOMAINDECOMP(cr) || ddUsesUpdateGroups(*cr->dd) || constr == nullptr
423 || constr->numConstraintsTotal() == 0,
424 "Constraints in domain decomposition are only supported with update "
425 "groups if using GPU update.\n");
426 GMX_RELEASE_ASSERT(ir->eConstrAlg != econtSHAKE || constr == nullptr
427 || constr->numConstraintsTotal() == 0,
428 "SHAKE is not supported with GPU update.");
429 GMX_RELEASE_ASSERT(useGpuForPme || (useGpuForNonbonded && simulationWork.useGpuBufferOps),
430 "Either PME or short-ranged non-bonded interaction tasks must run on "
431 "the GPU to use GPU update.\n");
432 GMX_RELEASE_ASSERT(ir->eI == eiMD,
433 "Only the md integrator is supported with the GPU update.\n");
435 ir->etc != TemperatureCoupling::NoseHoover,
436 "Nose-Hoover temperature coupling is not supported with the GPU update.\n");
438 ir->epc == PressureCoupling::No || ir->epc == PressureCoupling::ParrinelloRahman
439 || ir->epc == PressureCoupling::Berendsen || ir->epc == PressureCoupling::CRescale,
440 "Only Parrinello-Rahman, Berendsen, and C-rescale pressure coupling are supported "
441 "with the GPU update.\n");
442 GMX_RELEASE_ASSERT(!mdatoms->haveVsites,
443 "Virtual sites are not supported with the GPU update.\n");
444 GMX_RELEASE_ASSERT(ed == nullptr,
445 "Essential dynamics is not supported with the GPU update.\n");
446 GMX_RELEASE_ASSERT(!ir->bPull || !pull_have_constraint(*ir->pull),
447 "Constraints pulling is not supported with the GPU update.\n");
448 GMX_RELEASE_ASSERT(fcdata.orires->nr == 0,
449 "Orientation restraints are not supported with the GPU update.\n");
452 || (!haveFepPerturbedMasses(*top_global) && !havePerturbedConstraints(*top_global)),
453 "Free energy perturbation of masses and constraints are not supported with the GPU "
456 if (constr != nullptr && constr->numConstraintsTotal() > 0)
460 .appendText("Updating coordinates and applying constraints on the GPU.");
464 GMX_LOG(mdlog.info).asParagraph().appendText("Updating coordinates on the GPU.");
466 GMX_RELEASE_ASSERT(fr->deviceStreamManager != nullptr,
467 "Device stream manager should be initialized in order to use GPU "
468 "update-constraints.");
470 fr->deviceStreamManager->streamIsValid(gmx::DeviceStreamType::UpdateAndConstraints),
471 "Update stream should be initialized in order to use GPU "
472 "update-constraints.");
473 integrator = std::make_unique<UpdateConstrainGpu>(
476 fr->deviceStreamManager->context(),
477 fr->deviceStreamManager->stream(gmx::DeviceStreamType::UpdateAndConstraints),
478 stateGpu->xUpdatedOnDevice(),
481 integrator->setPbc(PbcType::Xyz, state->box);
484 if (useGpuForPme || (useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
486 changePinningPolicy(&state->x, PinningPolicy::PinnedIfSupported);
490 changePinningPolicy(&state->v, PinningPolicy::PinnedIfSupported);
493 // NOTE: The global state is no longer used at this point.
494 // But state_global is still used as temporary storage space for writing
495 // the global state to file and potentially for replica exchange.
496 // (Global topology should persist.)
498 update_mdatoms(mdatoms, state->lambda[efptMASS]);
502 /* Check nstexpanded here, because the grompp check was broken */
503 if (ir->expandedvals->nstexpanded % ir->nstcalcenergy != 0)
506 "With expanded ensemble, nstexpanded should be a multiple of nstcalcenergy");
508 init_expanded_ensemble(startingBehavior != StartingBehavior::NewSimulation, ir, state->dfhist);
513 EnergyData::initializeEnergyHistory(startingBehavior, observablesHistory, &energyOutput);
516 preparePrevStepPullCom(
517 ir, pull_work, mdatoms->massT, state, state_global, cr, startingBehavior != StartingBehavior::NewSimulation);
519 // TODO: Remove this by converting AWH into a ForceProvider
520 auto awh = prepareAwhModule(fplog,
525 startingBehavior != StartingBehavior::NewSimulation,
527 opt2fn("-awh", nfile, fnm),
530 if (useReplicaExchange && MASTER(cr))
532 repl_ex = init_replica_exchange(fplog, ms, top_global->natoms, ir, replExParams);
534 /* PME tuning is only supported in the Verlet scheme, with PME for
535 * Coulomb. It is not supported with only LJ PME. */
536 bPMETune = (mdrunOptions.tunePme && EEL_PME(fr->ic->eeltype) && !mdrunOptions.reproducible
537 && ir->cutoff_scheme != ecutsGROUP);
539 pme_load_balancing_t* pme_loadbal = nullptr;
543 &pme_loadbal, cr, mdlog, *ir, state->box, *fr->ic, *fr->nbv, fr->pmedata, fr->nbv->useGpu());
546 if (!ir->bContinuation)
548 if (state->flags & (1U << estV))
550 auto v = makeArrayRef(state->v);
551 /* Set the velocities of vsites, shells and frozen atoms to zero */
552 for (i = 0; i < mdatoms->homenr; i++)
554 if (mdatoms->ptype[i] == eptVSite || mdatoms->ptype[i] == eptShell)
558 else if (mdatoms->cFREEZE)
560 for (m = 0; m < DIM; m++)
562 if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
573 /* Constrain the initial coordinates and velocities */
574 do_constrain_first(fplog,
579 state->x.arrayRefWithPadding(),
580 state->v.arrayRefWithPadding(),
582 state->lambda[efptBONDED]);
586 /* Construct the virtual sites for the initial configuration */
587 vsite->construct(state->x, ir->delta_t, {}, state->box);
591 if (ir->efep != efepNO)
593 /* Set free energy calculation frequency as the greatest common
594 * denominator of nstdhdl and repl_ex_nst. */
595 nstfep = ir->fepvals->nstdhdl;
598 nstfep = std::gcd(ir->expandedvals->nstexpanded, nstfep);
600 if (useReplicaExchange)
602 nstfep = std::gcd(replExParams.exchangeInterval, nstfep);
606 nstfep = std::gcd(ir->awhParams->nstSampleCoord, nstfep);
610 /* Be REALLY careful about what flags you set here. You CANNOT assume
611 * this is the first step, since we might be restarting from a checkpoint,
612 * and in that case we should not do any modifications to the state.
614 bStopCM = (ir->comm_mode != ecmNO && !ir->bContinuation);
616 // When restarting from a checkpoint, it can be appropriate to
617 // initialize ekind from quantities in the checkpoint. Otherwise,
618 // compute_globals must initialize ekind before the simulation
619 // starts/restarts. However, only the master rank knows what was
620 // found in the checkpoint file, so we have to communicate in
621 // order to coordinate the restart.
623 // TODO Consider removing this communication if/when checkpoint
624 // reading directly follows .tpr reading, because all ranks can
625 // agree on hasReadEkinState at that time.
626 bool hasReadEkinState = MASTER(cr) ? state_global->ekinstate.hasReadEkinState : false;
629 gmx_bcast(sizeof(hasReadEkinState), &hasReadEkinState, cr->mpi_comm_mygroup);
631 if (hasReadEkinState)
633 restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
636 unsigned int cglo_flags =
637 (CGLO_TEMPERATURE | CGLO_GSTAT | (EI_VV(ir->eI) ? CGLO_PRESSURE : 0)
638 | (EI_VV(ir->eI) ? CGLO_CONSTRAINT : 0) | (hasReadEkinState ? CGLO_READEKIN : 0));
640 bSumEkinhOld = FALSE;
642 t_vcm vcm(top_global->groups, *ir);
643 reportComRemovalInfo(fplog, vcm);
645 /* To minimize communication, compute_globals computes the COM velocity
646 * and the kinetic energy for the velocities without COM motion removed.
647 * Thus to get the kinetic energy without the COM contribution, we need
648 * to call compute_globals twice.
650 for (int cgloIteration = 0; cgloIteration < (bStopCM ? 2 : 1); cgloIteration++)
652 unsigned int cglo_flags_iteration = cglo_flags;
653 if (bStopCM && cgloIteration == 0)
655 cglo_flags_iteration |= CGLO_STOPCM;
656 cglo_flags_iteration &= ~CGLO_TEMPERATURE;
658 compute_globals(gstat,
663 makeConstArrayRef(state->x),
664 makeConstArrayRef(state->v),
675 gmx::ArrayRef<real>{},
678 &totalNumberOfBondedInteractions,
681 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
683 if (cglo_flags_iteration & CGLO_STOPCM)
685 /* At initialization, do not pass x with acceleration-correction mode
686 * to avoid (incorrect) correction of the initial coordinates.
688 auto x = (vcm.mode == ecmLINEAR_ACCELERATION_CORRECTION) ? ArrayRef<RVec>()
689 : makeArrayRef(state->x);
690 process_and_stopcm_grp(fplog, &vcm, *mdatoms, x, makeArrayRef(state->v));
691 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
694 checkNumberOfBondedInteractions(mdlog,
696 totalNumberOfBondedInteractions,
699 makeConstArrayRef(state->x),
701 &shouldCheckNumberOfBondedInteractions);
702 if (ir->eI == eiVVAK)
704 /* a second call to get the half step temperature initialized as well */
705 /* we do the same call as above, but turn the pressure off -- internally to
706 compute_globals, this is recognized as a velocity verlet half-step
707 kinetic energy calculation. This minimized excess variables, but
708 perhaps loses some logic?*/
710 compute_globals(gstat,
715 makeConstArrayRef(state->x),
716 makeConstArrayRef(state->v),
727 gmx::ArrayRef<real>{},
732 cglo_flags & ~CGLO_PRESSURE);
735 /* Calculate the initial half step temperature, and save the ekinh_old */
736 if (startingBehavior == StartingBehavior::NewSimulation)
738 for (i = 0; (i < ir->opts.ngtc); i++)
740 copy_mat(ekind->tcstat[i].ekinh, ekind->tcstat[i].ekinh_old);
744 /* need to make an initiation call to get the Trotter variables set, as well as other constants
745 for non-trotter temperature control */
746 auto trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
750 if (!ir->bContinuation)
752 if (constr && ir->eConstrAlg == econtLINCS)
755 "RMS relative constraint deviation after constraining: %.2e\n",
758 if (EI_STATE_VELOCITY(ir->eI))
760 real temp = enerd->term[F_TEMP];
763 /* Result of Ekin averaged over velocities of -half
764 * and +half step, while we only have -half step here.
768 fprintf(fplog, "Initial temperature: %g K\n", temp);
773 fprintf(stderr, "starting mdrun '%s'\n", *(top_global->name));
776 sprintf(tbuf, "%8.1f", (ir->init_step + ir->nsteps) * ir->delta_t);
780 sprintf(tbuf, "%s", "infinite");
782 if (ir->init_step > 0)
785 "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
786 gmx_step_str(ir->init_step + ir->nsteps, sbuf),
788 gmx_step_str(ir->init_step, sbuf2),
789 ir->init_step * ir->delta_t);
793 fprintf(stderr, "%s steps, %s ps.\n", gmx_step_str(ir->nsteps, sbuf), tbuf);
795 fprintf(fplog, "\n");
798 walltime_accounting_start_time(walltime_accounting);
799 wallcycle_start(wcycle, ewcRUN);
800 print_start(fplog, cr, walltime_accounting, "mdrun");
802 /***********************************************************
806 ************************************************************/
809 /* Skip the first Nose-Hoover integration when we get the state from tpx */
810 bInitStep = startingBehavior == StartingBehavior::NewSimulation || EI_VV(ir->eI);
811 bSumEkinhOld = FALSE;
813 bNeedRepartition = FALSE;
815 step = ir->init_step;
818 auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
819 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
820 simulationsShareState,
823 mdrunOptions.reproducible,
825 mdrunOptions.maximumHoursToRun,
830 walltime_accounting);
832 auto checkpointHandler = std::make_unique<CheckpointHandler>(
833 compat::make_not_null<SimulationSignal*>(&signals[eglsCHKPT]),
834 simulationsShareState,
837 mdrunOptions.writeConfout,
838 mdrunOptions.checkpointOptions.period);
840 const bool resetCountersIsLocal = true;
841 auto resetHandler = std::make_unique<ResetHandler>(
842 compat::make_not_null<SimulationSignal*>(&signals[eglsRESETCOUNTERS]),
843 !resetCountersIsLocal,
846 mdrunOptions.timingOptions.resetHalfway,
847 mdrunOptions.maximumHoursToRun,
850 walltime_accounting);
852 const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
854 if (MASTER(cr) && isMultiSim(ms) && !useReplicaExchange)
856 logInitialMultisimStatus(ms, cr, mdlog, simulationsShareState, ir->nsteps, ir->init_step);
859 /* and stop now if we should */
860 bLastStep = (bLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
864 /* Determine if this is a neighbor search step */
865 bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
867 if (bPMETune && bNStList)
869 // This has to be here because PME load balancing is called so early.
870 // TODO: Move to after all booleans are defined.
871 if (useGpuForUpdate && !bFirstStep)
873 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
874 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
876 /* PME grid + cut-off optimization with GPUs or PME nodes */
877 pme_loadbal_do(pme_loadbal,
879 (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
890 simulationWork.useGpuPmePpCommunication);
893 wallcycle_start(wcycle, ewcSTEP);
895 bLastStep = (step_rel == ir->nsteps);
896 t = t0 + step * ir->delta_t;
898 // TODO Refactor this, so that nstfep does not need a default value of zero
899 if (ir->efep != efepNO || ir->bSimTemp)
901 /* find and set the current lambdas */
902 state->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
904 bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
905 bDoFEP = ((ir->efep != efepNO) && do_per_step(step, nstfep));
906 bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded) && (ir->bExpanded)
910 bDoReplEx = (useReplicaExchange && (step > 0) && !bLastStep
911 && do_per_step(step, replExParams.exchangeInterval));
913 if (doSimulatedAnnealing)
915 // TODO: Avoid changing inputrec (#3854)
916 // Simulated annealing updates the reference temperature.
917 auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
918 update_annealing_target_temp(nonConstInputrec, t, &upd);
921 /* Stop Center of Mass motion */
922 bStopCM = (ir->comm_mode != ecmNO && do_per_step(step, ir->nstcomm));
924 /* Determine whether or not to do Neighbour Searching */
925 bNS = (bFirstStep || bNStList || bExchanged || bNeedRepartition);
927 /* Note that the stopHandler will cause termination at nstglobalcomm
928 * steps. Since this concides with nstcalcenergy, nsttcouple and/or
929 * nstpcouple steps, we have computed the half-step kinetic energy
930 * of the previous step and can always output energies at the last step.
932 bLastStep = bLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
934 /* do_log triggers energy and virial calculation. Because this leads
935 * to different code paths, forces can be different. Thus for exact
936 * continuation we should avoid extra log output.
937 * Note that the || bLastStep can result in non-exact continuation
938 * beyond the last step. But we don't consider that to be an issue.
940 do_log = (do_per_step(step, ir->nstlog)
941 || (bFirstStep && startingBehavior == StartingBehavior::NewSimulation) || bLastStep);
942 do_verbose = mdrunOptions.verbose
943 && (step % mdrunOptions.verboseStepPrintInterval == 0 || bFirstStep || bLastStep);
945 if (useGpuForUpdate && !bFirstStep && bNS)
947 // Copy velocities from the GPU on search steps to keep a copy on host (device buffers are reinitialized).
948 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
949 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
950 // Copy coordinate from the GPU when needed at the search step.
951 // NOTE: The cases when coordinates needed on CPU for force evaluation are handled in sim_utils.
952 // NOTE: If the coordinates are to be written into output file they are also copied separately before the output.
953 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
954 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
957 if (bNS && !(bFirstStep && ir->bContinuation))
959 bMasterState = FALSE;
960 /* Correct the new box if it is too skewed */
961 if (inputrecDynamicBox(ir))
963 if (correct_box(fplog, step, state->box))
966 // If update is offloaded, it should be informed about the box size change
969 integrator->setPbc(PbcType::Xyz, state->box);
973 if (DOMAINDECOMP(cr) && bMasterState)
975 dd_collect_state(cr->dd, state, state_global);
978 if (DOMAINDECOMP(cr))
980 /* Repartition the domain decomposition */
981 dd_partition_system(fplog,
1001 do_verbose && !bPMETunePrinting);
1002 shouldCheckNumberOfBondedInteractions = true;
1003 upd.setNumAtoms(state->natoms);
1007 // Allocate or re-size GPU halo exchange object, if necessary
1008 if (bNS && havePPDomainDecomposition(cr) && simulationWork.useGpuHaloExchange)
1010 GMX_RELEASE_ASSERT(fr->deviceStreamManager != nullptr,
1011 "GPU device manager has to be initialized to use GPU "
1012 "version of halo exchange.");
1013 constructGpuHaloExchange(mdlog, *cr, *fr->deviceStreamManager, wcycle);
1016 if (MASTER(cr) && do_log)
1018 gmx::EnergyOutput::printHeader(
1019 fplog, step, t); /* can we improve the information printed here? */
1022 if (ir->efep != efepNO)
1024 update_mdatoms(mdatoms, state->lambda[efptMASS]);
1029 /* We need the kinetic energy at minus the half step for determining
1030 * the full step kinetic energy and possibly for T-coupling.*/
1031 /* This may not be quite working correctly yet . . . . */
1032 compute_globals(gstat,
1037 makeConstArrayRef(state->x),
1038 makeConstArrayRef(state->v),
1049 gmx::ArrayRef<real>{},
1052 &totalNumberOfBondedInteractions,
1054 CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
1055 checkNumberOfBondedInteractions(mdlog,
1057 totalNumberOfBondedInteractions,
1060 makeConstArrayRef(state->x),
1062 &shouldCheckNumberOfBondedInteractions);
1064 clear_mat(force_vir);
1066 checkpointHandler->decideIfCheckpointingThisStep(bNS, bFirstStep, bLastStep);
1068 /* Determine the energy and pressure:
1069 * at nstcalcenergy steps and at energy output steps (set below).
1071 if (EI_VV(ir->eI) && (!bInitStep))
1073 bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
1074 bCalcVir = bCalcEnerStep
1075 || (ir->epc != PressureCoupling::No
1076 && (do_per_step(step, ir->nstpcouple) || do_per_step(step - 1, ir->nstpcouple)));
1080 bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
1081 bCalcVir = bCalcEnerStep
1082 || (ir->epc != PressureCoupling::No && do_per_step(step, ir->nstpcouple));
1084 bCalcEner = bCalcEnerStep;
1086 do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
1088 if (do_ene || do_log || bDoReplEx)
1094 /* Do we need global communication ? */
1095 bGStat = (bCalcVir || bCalcEner || bStopCM || do_per_step(step, nstglobalcomm)
1096 || (EI_VV(ir->eI) && inputrecNvtTrotter(ir) && do_per_step(step - 1, nstglobalcomm)));
1098 force_flags = (GMX_FORCE_STATECHANGED | ((inputrecDynamicBox(ir)) ? GMX_FORCE_DYNAMICBOX : 0)
1099 | GMX_FORCE_ALLFORCES | (bCalcVir ? GMX_FORCE_VIRIAL : 0)
1100 | (bCalcEner ? GMX_FORCE_ENERGY : 0) | (bDoFEP ? GMX_FORCE_DHDL : 0));
1101 if (fr->useMts && !do_per_step(step, ir->nstfout))
1103 force_flags |= GMX_FORCE_DO_NOT_NEED_NORMAL_FORCE;
1108 /* Now is the time to relax the shells */
1109 relax_shell_flexcon(fplog,
1112 mdrunOptions.verbose,
1124 state->x.arrayRefWithPadding(),
1125 state->v.arrayRefWithPadding(),
1140 ddBalanceRegionHandler);
1144 /* The AWH history need to be saved _before_ doing force calculations where the AWH bias
1145 is updated (or the AWH update will be performed twice for one step when continuing).
1146 It would be best to call this update function from do_md_trajectory_writing but that
1147 would occur after do_force. One would have to divide the update_awh function into one
1148 function applying the AWH force and one doing the AWH bias update. The update AWH
1149 bias function could then be called after do_md_trajectory_writing (then containing
1150 update_awh_history). The checkpointing will in the future probably moved to the start
1151 of the md loop which will rid of this issue. */
1152 if (awh && checkpointHandler->isCheckpointingStep() && MASTER(cr))
1154 awh->updateHistory(state_global->awhHistory.get());
1157 /* The coordinates (x) are shifted (to get whole molecules)
1159 * This is parallellized as well, and does communication too.
1160 * Check comments in sim_util.c
1175 state->x.arrayRefWithPadding(),
1187 ed ? ed->getLegacyED() : nullptr,
1188 (bNS ? GMX_FORCE_NS : 0) | force_flags,
1189 ddBalanceRegionHandler);
1192 // VV integrators do not need the following velocity half step
1193 // if it is the first step after starting from a checkpoint.
1194 // That is, the half step is needed on all other steps, and
1195 // also the first step when starting from a .tpr file.
1198 integrateVVFirstStep(step,
1231 &shouldCheckNumberOfBondedInteractions,
1232 &saved_conserved_quantity,
1244 /* ######## END FIRST UPDATE STEP ############## */
1245 /* ######## If doing VV, we now have v(dt) ###### */
1248 /* perform extended ensemble sampling in lambda - we don't
1249 actually move to the new state before outputting
1250 statistics, but if performing simulated tempering, we
1251 do update the velocities and the tau_t. */
1252 // TODO: Avoid changing inputrec (#3854)
1253 // Simulated tempering updates the reference temperature.
1254 // Expanded ensemble without simulated tempering does not change the inputrec.
1255 auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
1256 lamnew = ExpandedEnsembleDynamics(fplog,
1264 state->v.rvec_array(),
1266 /* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
1269 copy_df_history(state_global->dfhist, state->dfhist);
1273 // Copy coordinate from the GPU for the output/checkpointing if the update is offloaded and
1274 // coordinates have not already been copied for i) search or ii) CPU force tasks.
1275 if (useGpuForUpdate && !bNS && !runScheduleWork->domainWork.haveCpuLocalForceWork
1276 && (do_per_step(step, ir->nstxout) || do_per_step(step, ir->nstxout_compressed)
1277 || checkpointHandler->isCheckpointingStep()))
1279 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
1280 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
1282 // Copy velocities if needed for the output/checkpointing.
1283 // NOTE: Copy on the search steps is done at the beginning of the step.
1284 if (useGpuForUpdate && !bNS
1285 && (do_per_step(step, ir->nstvout) || checkpointHandler->isCheckpointingStep()))
1287 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
1288 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
1290 // Copy forces for the output if the forces were reduced on the GPU (not the case on virial steps)
1291 // and update is offloaded hence forces are kept on the GPU for update and have not been
1292 // already transferred in do_force().
1293 // TODO: There should be an improved, explicit mechanism that ensures this copy is only executed
1294 // when the forces are ready on the GPU -- the same synchronizer should be used as the one
1295 // prior to GPU update.
1296 // TODO: When the output flags will be included in step workload, this copy can be combined with the
1297 // copy call in do_force(...).
1298 // NOTE: The forces should not be copied here if the vsites are present, since they were modified
1299 // on host after the D2H copy in do_force(...).
1300 if (runScheduleWork->stepWork.useGpuFBufferOps && (simulationWork.useGpuUpdate && !vsite)
1301 && do_per_step(step, ir->nstfout))
1303 stateGpu->copyForcesFromGpu(f.view().force(), AtomLocality::Local);
1304 stateGpu->waitForcesReadyOnHost(AtomLocality::Local);
1306 /* Now we have the energies and forces corresponding to the
1307 * coordinates at time t. We must output all of this before
1310 do_md_trajectory_writing(fplog,
1327 checkpointHandler->isCheckpointingStep(),
1330 mdrunOptions.writeConfout,
1332 /* Check if IMD step and do IMD communication, if bIMD is TRUE. */
1333 bInteractiveMDstep = imdSession->run(step, bNS, state->box, state->x.rvec_array(), t);
1335 /* kludge -- virial is lost with restart for MTTK NPT control. Must reload (saved earlier). */
1336 if (startingBehavior != StartingBehavior::NewSimulation && bFirstStep
1337 && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir)))
1339 copy_mat(state->svir_prev, shake_vir);
1340 copy_mat(state->fvir_prev, force_vir);
1343 stopHandler->setSignal();
1344 resetHandler->setSignal(walltime_accounting);
1346 if (bGStat || !PAR(cr))
1348 /* In parallel we only have to check for checkpointing in steps
1349 * where we do global communication,
1350 * otherwise the other nodes don't know.
1352 checkpointHandler->setSignal(walltime_accounting);
1355 /* ######### START SECOND UPDATE STEP ################# */
1357 /* at the start of step, randomize or scale the velocities ((if vv. Restriction of Andersen
1358 controlled in preprocessing */
1360 if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
1362 gmx_bool bIfRandomize;
1363 bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
1364 /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
1365 if (constr && bIfRandomize)
1367 constrain_velocities(constr, do_log, do_ene, step, state, nullptr, false, nullptr);
1370 /* Box is changed in update() when we do pressure coupling,
1371 * but we should still use the old box for energy corrections and when
1372 * writing it to the energy file, so it matches the trajectory files for
1373 * the same timestep above. Make a copy in a separate array.
1375 copy_mat(state->box, lastbox);
1379 if (!useGpuForUpdate)
1381 wallcycle_start(wcycle, ewcUPDATE);
1383 /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
1386 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
1387 /* We can only do Berendsen coupling after we have summed
1388 * the kinetic energy or virial. Since the happens
1389 * in global_state after update, we should only do it at
1390 * step % nstlist = 1 with bGStatEveryStep=FALSE.
1395 update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
1396 update_pcouple_before_coordinates(fplog, step, ir, state, pressureCouplingMu, M, bInitStep);
1399 /* With leap-frog type integrators we compute the kinetic energy
1400 * at a whole time step as the average of the half-time step kinetic
1401 * energies of two subsequent steps. Therefore we need to compute the
1402 * half step kinetic energy also if we need energies at the next step.
1404 const bool needHalfStepKineticEnergy =
1405 (!EI_VV(ir->eI) && (do_per_step(step + 1, nstglobalcomm) || step_rel + 1 == ir->nsteps));
1407 // Parrinello-Rahman requires the pressure to be availible before the update to compute
1408 // the velocity scaling matrix. Hence, it runs one step after the nstpcouple step.
1409 const bool doParrinelloRahman = (ir->epc == PressureCoupling::ParrinelloRahman
1410 && do_per_step(step + ir->nstpcouple - 1, ir->nstpcouple));
1414 GMX_ASSERT(!useGpuForUpdate, "GPU update is not supported with VVAK integrator.");
1416 integrateVVSecondStep(step,
1452 if (useGpuForUpdate)
1455 wallcycle_stop(wcycle, ewcUPDATE);
1457 if (bNS && (bFirstStep || DOMAINDECOMP(cr)))
1459 integrator->set(stateGpu->getCoordinates(),
1460 stateGpu->getVelocities(),
1461 stateGpu->getForces(),
1466 // Copy data to the GPU after buffers might have being reinitialized
1467 stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
1468 stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
1471 if (simulationWork.useGpuPme && !runScheduleWork->simulationWork.useGpuPmePpCommunication
1472 && !thisRankHasDuty(cr, DUTY_PME))
1474 // The PME forces were recieved to the host, so have to be copied
1475 stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::All);
1477 else if (!runScheduleWork->stepWork.useGpuFBufferOps)
1479 // The buffer ops were not offloaded this step, so the forces are on the
1480 // host and have to be copied
1481 stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::Local);
1484 const bool doTemperatureScaling =
1485 (ir->etc != TemperatureCoupling::No
1486 && do_per_step(step + ir->nsttcouple - 1, ir->nsttcouple));
1488 // This applies Leap-Frog, LINCS and SETTLE in succession
1489 integrator->integrate(
1490 stateGpu->getForcesReadyOnDeviceEvent(
1491 AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
1496 doTemperatureScaling,
1499 ir->nstpcouple * ir->delta_t,
1502 // Copy velocities D2H after update if:
1503 // - Globals are computed this step (includes the energy output steps).
1504 // - Temperature is needed for the next step.
1505 if (bGStat || needHalfStepKineticEnergy)
1507 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
1508 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
1513 /* With multiple time stepping we need to do an additional normal
1514 * update step to obtain the virial, as the actual MTS integration
1515 * using an acceleration where the slow forces are multiplied by mtsFactor.
1516 * Using that acceleration would result in a virial with the slow
1517 * force contribution would be a factor mtsFactor too large.
1519 if (fr->useMts && bCalcVir && constr != nullptr)
1521 upd.update_for_constraint_virial(
1522 *ir, *mdatoms, *state, f.view().forceWithPadding(), *ekind);
1524 constrain_coordinates(constr,
1529 upd.xp()->arrayRefWithPadding(),
1535 ArrayRefWithPadding<const RVec> forceCombined =
1536 (fr->useMts && step % ir->mtsLevels[1].stepFactor == 0)
1537 ? f.view().forceMtsCombinedWithPadding()
1538 : f.view().forceWithPadding();
1540 *ir, step, mdatoms, state, forceCombined, fcdata, ekind, M, etrtPOSITION, cr, constr != nullptr);
1542 wallcycle_stop(wcycle, ewcUPDATE);
1544 constrain_coordinates(constr,
1549 upd.xp()->arrayRefWithPadding(),
1551 bCalcVir && !fr->useMts,
1554 upd.update_sd_second_half(
1555 *ir, step, &dvdl_constr, mdatoms, state, cr, nrnb, wcycle, constr, do_log, do_ene);
1556 upd.finish_update(*ir, mdatoms, state, wcycle, constr != nullptr);
1559 if (ir->bPull && ir->pull->bSetPbcRefToPrevStepCOM)
1561 updatePrevStepPullCom(pull_work, state);
1564 enerd->term[F_DVDL_CONSTR] += dvdl_constr;
1567 if (vsite != nullptr)
1569 wallcycle_start(wcycle, ewcVSITECONSTR);
1570 vsite->construct(state->x, ir->delta_t, state->v, state->box);
1571 wallcycle_stop(wcycle, ewcVSITECONSTR);
1574 /* ############## IF NOT VV, Calculate globals HERE ############ */
1575 /* With Leap-Frog we can skip compute_globals at
1576 * non-communication steps, but we need to calculate
1577 * the kinetic energy one step before communication.
1580 // Organize to do inter-simulation signalling on steps if
1581 // and when algorithms require it.
1582 const bool doInterSimSignal = (simulationsShareState && do_per_step(step, nstSignalComm));
1584 if (bGStat || needHalfStepKineticEnergy || doInterSimSignal)
1586 // Copy coordinates when needed to stop the CM motion.
1587 if (useGpuForUpdate && !EI_VV(ir->eI) && bStopCM)
1589 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
1590 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
1592 // Since we're already communicating at this step, we
1593 // can propagate intra-simulation signals. Note that
1594 // check_nstglobalcomm has the responsibility for
1595 // choosing the value of nstglobalcomm that is one way
1596 // bGStat becomes true, so we can't get into a
1597 // situation where e.g. checkpointing can't be
1599 bool doIntraSimSignal = true;
1600 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
1608 makeConstArrayRef(state->x),
1609 makeConstArrayRef(state->v),
1620 (!EI_VV(ir->eI) && bCalcEner && constr != nullptr) ? constr->rmsdData()
1621 : gmx::ArrayRef<real>{},
1624 &totalNumberOfBondedInteractions,
1626 (bGStat ? CGLO_GSTAT : 0) | (!EI_VV(ir->eI) && bCalcEner ? CGLO_ENERGY : 0)
1627 | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
1628 | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
1629 | (!EI_VV(ir->eI) ? CGLO_PRESSURE : 0) | CGLO_CONSTRAINT
1630 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
1632 checkNumberOfBondedInteractions(mdlog,
1634 totalNumberOfBondedInteractions,
1637 makeConstArrayRef(state->x),
1639 &shouldCheckNumberOfBondedInteractions);
1640 if (!EI_VV(ir->eI) && bStopCM)
1642 process_and_stopcm_grp(
1643 fplog, &vcm, *mdatoms, makeArrayRef(state->x), makeArrayRef(state->v));
1644 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
1646 // TODO: The special case of removing CM motion should be dealt more gracefully
1647 if (useGpuForUpdate)
1649 stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
1650 // Here we block until the H2D copy completes because event sync with the
1651 // force kernels that use the coordinates on the next steps is not implemented
1652 // (not because of a race on state->x being modified on the CPU while H2D is in progress).
1653 stateGpu->waitCoordinatesCopiedToDevice(AtomLocality::Local);
1654 // If the COM removal changed the velocities on the CPU, this has to be accounted for.
1655 if (vcm.mode != ecmNO)
1657 stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
1664 /* ############# END CALC EKIN AND PRESSURE ################# */
1666 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
1667 the virial that should probably be addressed eventually. state->veta has better properies,
1668 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
1669 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
1671 if (ir->efep != efepNO && !EI_VV(ir->eI))
1673 /* Sum up the foreign energy and dK/dl terms for md and sd.
1674 Currently done every step so that dH/dl is correct in the .edr */
1675 accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
1678 update_pcouple_after_coordinates(
1679 fplog, step, ir, mdatoms, pres, force_vir, shake_vir, pressureCouplingMu, state, nrnb, upd.deform(), !useGpuForUpdate);
1681 const bool doBerendsenPressureCoupling = (inputrec->epc == PressureCoupling::Berendsen
1682 && do_per_step(step, inputrec->nstpcouple));
1683 const bool doCRescalePressureCoupling = (inputrec->epc == PressureCoupling::CRescale
1684 && do_per_step(step, inputrec->nstpcouple));
1686 && (doBerendsenPressureCoupling || doCRescalePressureCoupling || doParrinelloRahman))
1688 integrator->scaleCoordinates(pressureCouplingMu);
1689 if (doCRescalePressureCoupling)
1691 matrix pressureCouplingInvMu;
1692 gmx::invertBoxMatrix(pressureCouplingMu, pressureCouplingInvMu);
1693 integrator->scaleVelocities(pressureCouplingInvMu);
1695 integrator->setPbc(PbcType::Xyz, state->box);
1698 /* ################# END UPDATE STEP 2 ################# */
1699 /* #### We now have r(t+dt) and v(t+dt/2) ############# */
1701 /* The coordinates (x) were unshifted in update */
1704 /* We will not sum ekinh_old,
1705 * so signal that we still have to do it.
1707 bSumEkinhOld = TRUE;
1712 /* ######### BEGIN PREPARING EDR OUTPUT ########### */
1714 /* use the directly determined last velocity, not actually the averaged half steps */
1715 if (bTrotter && ir->eI == eiVV)
1717 enerd->term[F_EKIN] = last_ekin;
1719 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
1721 if (integratorHasConservedEnergyQuantity(ir))
1725 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
1729 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + NPT_energy(ir, state, &MassQ);
1732 /* ######### END PREPARING EDR OUTPUT ########### */
1738 if (fplog && do_log && bDoExpanded)
1740 /* only needed if doing expanded ensemble */
1741 PrintFreeEnergyInfoToFile(fplog,
1744 ir->bSimTemp ? ir->simtempvals : nullptr,
1745 state_global->dfhist,
1752 energyOutput.addDataAtEnergyStep(bDoDHDL,
1760 PTCouplingArrays{ state->boxv,
1761 state->nosehoover_xi,
1762 state->nosehoover_vxi,
1764 state->nhpres_vxi },
1776 energyOutput.recordNonEnergyStep();
1779 gmx_bool do_dr = do_per_step(step, ir->nstdisreout);
1780 gmx_bool do_or = do_per_step(step, ir->nstorireout);
1782 if (doSimulatedAnnealing)
1784 gmx::EnergyOutput::printAnnealingTemperatures(
1785 do_log ? fplog : nullptr, groups, &(ir->opts));
1787 if (do_log || do_ene || do_dr || do_or)
1789 energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
1793 do_log ? fplog : nullptr,
1799 if (do_log && ir->bDoAwh && awh->hasFepLambdaDimension())
1801 const bool isInitialOutput = false;
1802 printLambdaStateToLog(fplog, state->lambda, isInitialOutput);
1807 pull_print_output(pull_work, step, t);
1810 if (do_per_step(step, ir->nstlog))
1812 if (fflush(fplog) != 0)
1814 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
1820 /* Have to do this part _after_ outputting the logfile and the edr file */
1821 /* Gets written into the state at the beginning of next loop*/
1822 state->fep_state = lamnew;
1824 else if (ir->bDoAwh && awh->needForeignEnergyDifferences(step))
1826 state->fep_state = awh->fepLambdaState();
1828 /* Print the remaining wall clock time for the run */
1829 if (isMasterSimMasterRank(ms, MASTER(cr)) && (do_verbose || gmx_got_usr_signal()) && !bPMETunePrinting)
1833 fprintf(stderr, "\n");
1835 print_time(stderr, walltime_accounting, step, ir, cr);
1838 /* Ion/water position swapping.
1839 * Not done in last step since trajectory writing happens before this call
1840 * in the MD loop and exchanges would be lost anyway. */
1841 bNeedRepartition = FALSE;
1842 if ((ir->eSwapCoords != eswapNO) && (step > 0) && !bLastStep && do_per_step(step, ir->swap->nstswap))
1844 bNeedRepartition = do_swapcoords(cr,
1850 as_rvec_array(state->x.data()),
1852 MASTER(cr) && mdrunOptions.verbose,
1855 if (bNeedRepartition && DOMAINDECOMP(cr))
1857 dd_collect_state(cr->dd, state, state_global);
1861 /* Replica exchange */
1865 bExchanged = replica_exchange(fplog, cr, ms, repl_ex, state_global, enerd, state, step, t);
1868 if ((bExchanged || bNeedRepartition) && DOMAINDECOMP(cr))
1870 dd_partition_system(fplog,
1891 shouldCheckNumberOfBondedInteractions = true;
1892 upd.setNumAtoms(state->natoms);
1898 /* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
1899 /* With all integrators, except VV, we need to retain the pressure
1900 * at the current step for coupling at the next step.
1902 if ((state->flags & (1U << estPRES_PREV))
1903 && (bGStatEveryStep || (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
1905 /* Store the pressure in t_state for pressure coupling
1906 * at the next MD step.
1908 copy_mat(pres, state->pres_prev);
1911 /* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
1913 if ((membed != nullptr) && (!bLastStep))
1915 rescale_membed(step_rel, membed, as_rvec_array(state_global->x.data()));
1918 cycles = wallcycle_stop(wcycle, ewcSTEP);
1919 if (DOMAINDECOMP(cr) && wcycle)
1921 dd_cycles_add(cr->dd, cycles, ddCyclStep);
1924 /* increase the MD step number */
1931 fcReportProgress(ir->nsteps + ir->init_step, step);
1935 resetHandler->resetCounters(
1936 step, step_rel, mdlog, fplog, cr, fr->nbv.get(), nrnb, fr->pmedata, pme_loadbal, wcycle, walltime_accounting);
1938 /* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
1939 imdSession->updateEnergyRecordAndSendPositionsAndEnergies(bInteractiveMDstep, step, bCalcEner);
1941 /* End of main MD loop */
1943 /* Closing TNG files can include compressing data. Therefore it is good to do that
1944 * before stopping the time measurements. */
1945 mdoutf_tng_close(outf);
1947 /* Stop measuring walltime */
1948 walltime_accounting_end_time(walltime_accounting);
1950 if (!thisRankHasDuty(cr, DUTY_PME))
1952 /* Tell the PME only node to finish */
1953 gmx_pme_send_finish(cr);
1958 if (ir->nstcalcenergy > 0)
1960 energyOutput.printEnergyConservation(fplog, ir->simulation_part, EI_MD(ir->eI));
1962 gmx::EnergyOutput::printAnnealingTemperatures(fplog, groups, &(ir->opts));
1963 energyOutput.printAverages(fplog, groups);
1970 pme_loadbal_done(pme_loadbal, fplog, mdlog, fr->nbv->useGpu());
1973 done_shellfc(fplog, shellfc, step_rel);
1975 if (useReplicaExchange && MASTER(cr))
1977 print_replica_exchange_statistics(fplog, repl_ex);
1980 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
1982 global_stat_destroy(gstat);