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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/applied_forces/awh/read_params.h"
57 #include "gromacs/commandline/filenm.h"
58 #include "gromacs/domdec/collect.h"
59 #include "gromacs/domdec/dlbtiming.h"
60 #include "gromacs/domdec/domdec.h"
61 #include "gromacs/domdec/domdec_network.h"
62 #include "gromacs/domdec/domdec_struct.h"
63 #include "gromacs/domdec/gpuhaloexchange.h"
64 #include "gromacs/domdec/mdsetup.h"
65 #include "gromacs/domdec/partition.h"
66 #include "gromacs/essentialdynamics/edsam.h"
67 #include "gromacs/ewald/pme_load_balancing.h"
68 #include "gromacs/ewald/pme_pp.h"
69 #include "gromacs/fileio/trxio.h"
70 #include "gromacs/gmxlib/network.h"
71 #include "gromacs/gmxlib/nrnb.h"
72 #include "gromacs/gpu_utils/device_stream_manager.h"
73 #include "gromacs/gpu_utils/gpu_utils.h"
74 #include "gromacs/imd/imd.h"
75 #include "gromacs/listed_forces/listed_forces.h"
76 #include "gromacs/math/functions.h"
77 #include "gromacs/math/invertmatrix.h"
78 #include "gromacs/math/vec.h"
79 #include "gromacs/math/vectypes.h"
80 #include "gromacs/mdlib/checkpointhandler.h"
81 #include "gromacs/mdlib/compute_io.h"
82 #include "gromacs/mdlib/constr.h"
83 #include "gromacs/mdlib/coupling.h"
84 #include "gromacs/mdlib/ebin.h"
85 #include "gromacs/mdlib/enerdata_utils.h"
86 #include "gromacs/mdlib/energyoutput.h"
87 #include "gromacs/mdlib/expanded.h"
88 #include "gromacs/mdlib/force.h"
89 #include "gromacs/mdlib/force_flags.h"
90 #include "gromacs/mdlib/forcerec.h"
91 #include "gromacs/mdlib/freeenergyparameters.h"
92 #include "gromacs/mdlib/md_support.h"
93 #include "gromacs/mdlib/mdatoms.h"
94 #include "gromacs/mdlib/mdoutf.h"
95 #include "gromacs/mdlib/membed.h"
96 #include "gromacs/mdlib/resethandler.h"
97 #include "gromacs/mdlib/sighandler.h"
98 #include "gromacs/mdlib/simulationsignal.h"
99 #include "gromacs/mdlib/stat.h"
100 #include "gromacs/mdlib/stophandler.h"
101 #include "gromacs/mdlib/tgroup.h"
102 #include "gromacs/mdlib/trajectory_writing.h"
103 #include "gromacs/mdlib/update.h"
104 #include "gromacs/mdlib/update_constrain_gpu.h"
105 #include "gromacs/mdlib/update_vv.h"
106 #include "gromacs/mdlib/vcm.h"
107 #include "gromacs/mdlib/vsite.h"
108 #include "gromacs/mdrunutility/handlerestart.h"
109 #include "gromacs/mdrunutility/multisim.h"
110 #include "gromacs/mdrunutility/printtime.h"
111 #include "gromacs/mdtypes/awh_history.h"
112 #include "gromacs/mdtypes/awh_params.h"
113 #include "gromacs/mdtypes/commrec.h"
114 #include "gromacs/mdtypes/df_history.h"
115 #include "gromacs/mdtypes/energyhistory.h"
116 #include "gromacs/mdtypes/fcdata.h"
117 #include "gromacs/mdtypes/forcebuffers.h"
118 #include "gromacs/mdtypes/forcerec.h"
119 #include "gromacs/mdtypes/group.h"
120 #include "gromacs/mdtypes/inputrec.h"
121 #include "gromacs/mdtypes/interaction_const.h"
122 #include "gromacs/mdtypes/md_enums.h"
123 #include "gromacs/mdtypes/mdatom.h"
124 #include "gromacs/mdtypes/mdrunoptions.h"
125 #include "gromacs/mdtypes/multipletimestepping.h"
126 #include "gromacs/mdtypes/observableshistory.h"
127 #include "gromacs/mdtypes/pullhistory.h"
128 #include "gromacs/mdtypes/simulation_workload.h"
129 #include "gromacs/mdtypes/state.h"
130 #include "gromacs/mdtypes/state_propagator_data_gpu.h"
131 #include "gromacs/modularsimulator/energydata.h"
132 #include "gromacs/nbnxm/gpu_data_mgmt.h"
133 #include "gromacs/nbnxm/nbnxm.h"
134 #include "gromacs/pbcutil/pbc.h"
135 #include "gromacs/pulling/output.h"
136 #include "gromacs/pulling/pull.h"
137 #include "gromacs/swap/swapcoords.h"
138 #include "gromacs/timing/wallcycle.h"
139 #include "gromacs/timing/walltime_accounting.h"
140 #include "gromacs/topology/atoms.h"
141 #include "gromacs/topology/idef.h"
142 #include "gromacs/topology/mtop_util.h"
143 #include "gromacs/topology/topology.h"
144 #include "gromacs/trajectory/trajectoryframe.h"
145 #include "gromacs/utility/basedefinitions.h"
146 #include "gromacs/utility/cstringutil.h"
147 #include "gromacs/utility/fatalerror.h"
148 #include "gromacs/utility/logger.h"
149 #include "gromacs/utility/real.h"
150 #include "gromacs/utility/smalloc.h"
152 #include "legacysimulator.h"
153 #include "replicaexchange.h"
156 using gmx::SimulationSignaller;
158 void gmx::LegacySimulator::do_md()
160 // TODO Historically, the EM and MD "integrators" used different
161 // names for the t_inputrec *parameter, but these must have the
162 // same name, now that it's a member of a struct. We use this ir
163 // alias to avoid a large ripple of nearly useless changes.
164 // t_inputrec is being replaced by IMdpOptionsProvider, so this
165 // will go away eventually.
166 const t_inputrec* ir = inputrec;
168 int64_t step, step_rel;
169 double t, t0 = ir->init_t;
170 gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, bCalcEner;
171 gmx_bool bNS = FALSE, bNStList, bStopCM, bFirstStep, bInitStep, bLastStep = FALSE;
172 gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
173 gmx_bool do_ene, do_log, do_verbose;
174 gmx_bool bMasterState;
175 unsigned int force_flags;
176 tensor force_vir = { { 0 } }, shake_vir = { { 0 } }, total_vir = { { 0 } }, pres = { { 0 } };
179 matrix pressureCouplingMu, M;
180 gmx_repl_ex_t repl_ex = nullptr;
181 gmx_global_stat_t gstat;
182 gmx_shellfc_t* shellfc;
183 gmx_bool bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
186 std::vector<RVec> cbuf;
192 real saved_conserved_quantity = 0;
195 char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
197 /* PME load balancing data for GPU kernels */
198 gmx_bool bPMETune = FALSE;
199 gmx_bool bPMETunePrinting = FALSE;
201 bool bInteractiveMDstep = false;
203 SimulationSignals signals;
204 // Most global communnication stages don't propagate mdrun
205 // signals, and will use this object to achieve that.
206 SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
208 if (!mdrunOptions.writeConfout)
210 // This is on by default, and the main known use case for
211 // turning it off is for convenience in benchmarking, which is
212 // something that should not show up in the general user
217 "The -noconfout functionality is deprecated, and may be removed in a "
221 /* md-vv uses averaged full step velocities for T-control
222 md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
223 md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
224 bTrotter = (EI_VV(ir->eI)
225 && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir) || inputrecNvtTrotter(ir)));
227 const bool bRerunMD = false;
229 int nstglobalcomm = computeGlobalCommunicationPeriod(mdlog, ir, cr);
230 bGStatEveryStep = (nstglobalcomm == 1);
232 const SimulationGroups* groups = &top_global.groups;
234 std::unique_ptr<EssentialDynamics> ed = nullptr;
235 if (opt2bSet("-ei", nfile, fnm))
237 /* Initialize essential dynamics sampling */
238 ed = init_edsam(mdlog,
239 opt2fn_null("-ei", nfile, fnm),
240 opt2fn("-eo", nfile, fnm),
250 else if (observablesHistory->edsamHistory)
253 "The checkpoint is from a run with essential dynamics sampling, "
254 "but the current run did not specify the -ei option. "
255 "Either specify the -ei option to mdrun, or do not use this checkpoint file.");
258 int* fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
259 gmx::ArrayRef<real> lambda = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
261 fplog, *ir, gmx::arrayRefFromArray(ir->opts.ref_t, ir->opts.ngtc), MASTER(cr), fep_state, lambda);
262 Update upd(*ir, deform);
263 bool doSimulatedAnnealing = false;
265 // TODO: Avoid changing inputrec (#3854)
266 // Simulated annealing updates the reference temperature.
267 auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
268 doSimulatedAnnealing = initSimulatedAnnealing(nonConstInputrec, &upd);
270 const bool useReplicaExchange = (replExParams.exchangeInterval > 0);
272 const t_fcdata& fcdata = *fr->fcdata;
274 bool simulationsShareState = false;
275 int nstSignalComm = nstglobalcomm;
277 // TODO This implementation of ensemble orientation restraints is nasty because
278 // a user can't just do multi-sim with single-sim orientation restraints.
279 bool usingEnsembleRestraints =
280 (fcdata.disres->nsystems > 1) || ((ms != nullptr) && (fcdata.orires->nr != 0));
281 bool awhUsesMultiSim = (ir->bDoAwh && ir->awhParams->shareBiasMultisim() && (ms != nullptr));
283 // Replica exchange, ensemble restraints and AWH need all
284 // simulations to remain synchronized, so they need
285 // checkpoints and stop conditions to act on the same step, so
286 // the propagation of such signals must take place between
287 // simulations, not just within simulations.
288 // TODO: Make algorithm initializers set these flags.
289 simulationsShareState = useReplicaExchange || usingEnsembleRestraints || awhUsesMultiSim;
291 if (simulationsShareState)
293 // Inter-simulation signal communication does not need to happen
294 // often, so we use a minimum of 200 steps to reduce overhead.
295 const int c_minimumInterSimulationSignallingInterval = 200;
296 nstSignalComm = ((c_minimumInterSimulationSignallingInterval + nstglobalcomm - 1) / nstglobalcomm)
301 if (startingBehavior != StartingBehavior::RestartWithAppending)
303 pleaseCiteCouplingAlgorithms(fplog, *ir);
305 gmx_mdoutf* outf = init_mdoutf(fplog,
317 simulationsShareState,
319 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
323 mdoutf_get_fp_dhdl(outf),
326 simulationsShareState,
329 gstat = global_stat_init(ir);
331 const auto& simulationWork = runScheduleWork->simulationWork;
332 const bool useGpuForPme = simulationWork.useGpuPme;
333 const bool useGpuForNonbonded = simulationWork.useGpuNonbonded;
334 const bool useGpuForBufferOps = simulationWork.useGpuBufferOps;
335 const bool useGpuForUpdate = simulationWork.useGpuUpdate;
337 /* Check for polarizable models and flexible constraints */
338 shellfc = init_shell_flexcon(fplog,
340 constr ? constr->numFlexibleConstraints() : 0,
346 double io = compute_io(ir, top_global.natoms, *groups, energyOutput.numEnergyTerms(), 1);
347 if ((io > 2000) && MASTER(cr))
349 fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
353 // Local state only becomes valid now.
354 std::unique_ptr<t_state> stateInstance;
357 gmx_localtop_t top(top_global.ffparams);
359 auto mdatoms = mdAtoms->mdatoms();
361 ForceBuffers f(fr->useMts,
362 ((useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
363 ? PinningPolicy::PinnedIfSupported
364 : PinningPolicy::CannotBePinned);
365 const t_mdatoms* md = mdAtoms->mdatoms();
366 if (DOMAINDECOMP(cr))
368 stateInstance = std::make_unique<t_state>();
369 state = stateInstance.get();
370 dd_init_local_state(*cr->dd, state_global, state);
372 /* Distribute the charge groups over the nodes from the master node */
373 dd_partition_system(fplog,
394 upd.updateAfterPartition(state->natoms,
395 md->cFREEZE ? gmx::arrayRefFromArray(md->cFREEZE, md->nr)
396 : gmx::ArrayRef<const unsigned short>(),
397 md->cTC ? gmx::arrayRefFromArray(md->cTC, md->nr)
398 : gmx::ArrayRef<const unsigned short>());
402 state_change_natoms(state_global, state_global->natoms);
403 /* Copy the pointer to the global state */
404 state = state_global;
406 /* Generate and initialize new topology */
407 mdAlgorithmsSetupAtomData(cr, *ir, top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
409 upd.updateAfterPartition(state->natoms,
410 md->cFREEZE ? gmx::arrayRefFromArray(md->cFREEZE, md->nr)
411 : gmx::ArrayRef<const unsigned short>(),
412 md->cTC ? gmx::arrayRefFromArray(md->cTC, md->nr)
413 : gmx::ArrayRef<const unsigned short>());
416 std::unique_ptr<UpdateConstrainGpu> integrator;
418 StatePropagatorDataGpu* stateGpu = fr->stateGpu;
420 // TODO: the assertions below should be handled by UpdateConstraintsBuilder.
423 GMX_RELEASE_ASSERT(!DOMAINDECOMP(cr) || ddUsesUpdateGroups(*cr->dd) || constr == nullptr
424 || constr->numConstraintsTotal() == 0,
425 "Constraints in domain decomposition are only supported with update "
426 "groups if using GPU update.\n");
427 GMX_RELEASE_ASSERT(ir->eConstrAlg != ConstraintAlgorithm::Shake || constr == nullptr
428 || constr->numConstraintsTotal() == 0,
429 "SHAKE is not supported with GPU update.");
430 GMX_RELEASE_ASSERT(useGpuForPme || (useGpuForNonbonded && simulationWork.useGpuBufferOps),
431 "Either PME or short-ranged non-bonded interaction tasks must run on "
432 "the GPU to use GPU update.\n");
433 GMX_RELEASE_ASSERT(ir->eI == IntegrationAlgorithm::MD,
434 "Only the md integrator is supported with the GPU update.\n");
436 ir->etc != TemperatureCoupling::NoseHoover,
437 "Nose-Hoover temperature coupling is not supported with the GPU update.\n");
439 ir->epc == PressureCoupling::No || ir->epc == PressureCoupling::ParrinelloRahman
440 || ir->epc == PressureCoupling::Berendsen || ir->epc == PressureCoupling::CRescale,
441 "Only Parrinello-Rahman, Berendsen, and C-rescale pressure coupling are supported "
442 "with the GPU update.\n");
443 GMX_RELEASE_ASSERT(!mdatoms->haveVsites,
444 "Virtual sites are not supported with the GPU update.\n");
445 GMX_RELEASE_ASSERT(ed == nullptr,
446 "Essential dynamics is not supported with the GPU update.\n");
447 GMX_RELEASE_ASSERT(!ir->bPull || !pull_have_constraint(*ir->pull),
448 "Constraints pulling is not supported with the GPU update.\n");
449 GMX_RELEASE_ASSERT(fcdata.orires->nr == 0,
450 "Orientation restraints are not supported with the GPU update.\n");
452 ir->efep == FreeEnergyPerturbationType::No
453 || (!haveFepPerturbedMasses(top_global) && !havePerturbedConstraints(top_global)),
454 "Free energy perturbation of masses and constraints are not supported with the GPU "
457 if (constr != nullptr && constr->numConstraintsTotal() > 0)
461 .appendText("Updating coordinates and applying constraints on the GPU.");
465 GMX_LOG(mdlog.info).asParagraph().appendText("Updating coordinates on the GPU.");
467 GMX_RELEASE_ASSERT(fr->deviceStreamManager != nullptr,
468 "Device stream manager should be initialized in order to use GPU "
469 "update-constraints.");
471 fr->deviceStreamManager->streamIsValid(gmx::DeviceStreamType::UpdateAndConstraints),
472 "Update stream should be initialized in order to use GPU "
473 "update-constraints.");
474 integrator = std::make_unique<UpdateConstrainGpu>(
478 fr->deviceStreamManager->context(),
479 fr->deviceStreamManager->stream(gmx::DeviceStreamType::UpdateAndConstraints),
480 stateGpu->xUpdatedOnDevice(),
483 integrator->setPbc(PbcType::Xyz, state->box);
486 if (useGpuForPme || (useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
488 changePinningPolicy(&state->x, PinningPolicy::PinnedIfSupported);
492 changePinningPolicy(&state->v, PinningPolicy::PinnedIfSupported);
495 // NOTE: The global state is no longer used at this point.
496 // But state_global is still used as temporary storage space for writing
497 // the global state to file and potentially for replica exchange.
498 // (Global topology should persist.)
500 update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
504 /* Check nstexpanded here, because the grompp check was broken */
505 if (ir->expandedvals->nstexpanded % ir->nstcalcenergy != 0)
508 "With expanded ensemble, nstexpanded should be a multiple of nstcalcenergy");
510 init_expanded_ensemble(startingBehavior != StartingBehavior::NewSimulation, ir, state->dfhist);
515 EnergyData::initializeEnergyHistory(startingBehavior, observablesHistory, &energyOutput);
518 preparePrevStepPullCom(ir,
520 gmx::arrayRefFromArray(mdatoms->massT, mdatoms->nr),
524 startingBehavior != StartingBehavior::NewSimulation);
526 // TODO: Remove this by converting AWH into a ForceProvider
527 auto awh = prepareAwhModule(fplog,
532 startingBehavior != StartingBehavior::NewSimulation,
534 opt2fn("-awh", nfile, fnm),
537 if (useReplicaExchange && MASTER(cr))
539 repl_ex = init_replica_exchange(fplog, ms, top_global.natoms, ir, replExParams);
541 /* PME tuning is only supported in the Verlet scheme, with PME for
542 * Coulomb. It is not supported with only LJ PME. */
543 bPMETune = (mdrunOptions.tunePme && EEL_PME(fr->ic->eeltype) && !mdrunOptions.reproducible
544 && ir->cutoff_scheme != CutoffScheme::Group);
546 pme_load_balancing_t* pme_loadbal = nullptr;
550 &pme_loadbal, cr, mdlog, *ir, state->box, *fr->ic, *fr->nbv, fr->pmedata, fr->nbv->useGpu());
553 if (!ir->bContinuation)
555 if (state->flags & enumValueToBitMask(StateEntry::V))
557 auto v = makeArrayRef(state->v);
558 /* Set the velocities of vsites, shells and frozen atoms to zero */
559 for (i = 0; i < mdatoms->homenr; i++)
561 if (mdatoms->ptype[i] == ParticleType::Shell)
565 else if (mdatoms->cFREEZE)
567 for (m = 0; m < DIM; m++)
569 if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
580 /* Constrain the initial coordinates and velocities */
581 do_constrain_first(fplog,
586 state->x.arrayRefWithPadding(),
587 state->v.arrayRefWithPadding(),
589 state->lambda[FreeEnergyPerturbationCouplingType::Bonded]);
593 if (ir->efep != FreeEnergyPerturbationType::No)
595 /* Set free energy calculation frequency as the greatest common
596 * denominator of nstdhdl and repl_ex_nst. */
597 nstfep = ir->fepvals->nstdhdl;
600 nstfep = std::gcd(ir->expandedvals->nstexpanded, nstfep);
602 if (useReplicaExchange)
604 nstfep = std::gcd(replExParams.exchangeInterval, nstfep);
608 nstfep = std::gcd(ir->awhParams->nstSampleCoord(), nstfep);
612 /* Be REALLY careful about what flags you set here. You CANNOT assume
613 * this is the first step, since we might be restarting from a checkpoint,
614 * and in that case we should not do any modifications to the state.
616 bStopCM = (ir->comm_mode != ComRemovalAlgorithm::No && !ir->bContinuation);
618 // When restarting from a checkpoint, it can be appropriate to
619 // initialize ekind from quantities in the checkpoint. Otherwise,
620 // compute_globals must initialize ekind before the simulation
621 // starts/restarts. However, only the master rank knows what was
622 // found in the checkpoint file, so we have to communicate in
623 // order to coordinate the restart.
625 // TODO Consider removing this communication if/when checkpoint
626 // reading directly follows .tpr reading, because all ranks can
627 // agree on hasReadEkinState at that time.
628 bool hasReadEkinState = MASTER(cr) ? state_global->ekinstate.hasReadEkinState : false;
631 gmx_bcast(sizeof(hasReadEkinState), &hasReadEkinState, cr->mpi_comm_mygroup);
633 if (hasReadEkinState)
635 restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
638 unsigned int cglo_flags =
639 (CGLO_TEMPERATURE | CGLO_GSTAT | (EI_VV(ir->eI) ? CGLO_PRESSURE : 0)
640 | (EI_VV(ir->eI) ? CGLO_CONSTRAINT : 0) | (hasReadEkinState ? CGLO_READEKIN : 0));
642 bSumEkinhOld = FALSE;
644 t_vcm vcm(top_global.groups, *ir);
645 reportComRemovalInfo(fplog, vcm);
647 /* To minimize communication, compute_globals computes the COM velocity
648 * and the kinetic energy for the velocities without COM motion removed.
649 * Thus to get the kinetic energy without the COM contribution, we need
650 * to call compute_globals twice.
652 for (int cgloIteration = 0; cgloIteration < (bStopCM ? 2 : 1); cgloIteration++)
654 unsigned int cglo_flags_iteration = cglo_flags;
655 if (bStopCM && cgloIteration == 0)
657 cglo_flags_iteration |= CGLO_STOPCM;
658 cglo_flags_iteration &= ~CGLO_TEMPERATURE;
660 if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd) && cgloIteration == 0)
662 cglo_flags_iteration |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
664 compute_globals(gstat,
669 makeConstArrayRef(state->x),
670 makeConstArrayRef(state->v),
681 gmx::ArrayRef<real>{},
685 cglo_flags_iteration);
686 if (cglo_flags_iteration & CGLO_STOPCM)
688 /* At initialization, do not pass x with acceleration-correction mode
689 * to avoid (incorrect) correction of the initial coordinates.
691 auto x = (vcm.mode == ComRemovalAlgorithm::LinearAccelerationCorrection)
693 : makeArrayRef(state->x);
694 process_and_stopcm_grp(fplog, &vcm, *mdatoms, x, makeArrayRef(state->v));
695 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
698 if (DOMAINDECOMP(cr))
700 checkNumberOfBondedInteractions(
701 mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
703 if (ir->eI == IntegrationAlgorithm::VVAK)
705 /* a second call to get the half step temperature initialized as well */
706 /* we do the same call as above, but turn the pressure off -- internally to
707 compute_globals, this is recognized as a velocity verlet half-step
708 kinetic energy calculation. This minimized excess variables, but
709 perhaps loses some logic?*/
711 compute_globals(gstat,
716 makeConstArrayRef(state->x),
717 makeConstArrayRef(state->v),
728 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 == ConstraintAlgorithm::Lincs)
755 "RMS relative constraint deviation after constraining: %.2e\n",
758 if (EI_STATE_VELOCITY(ir->eI))
760 real temp = enerd->term[F_TEMP];
761 if (ir->eI != IntegrationAlgorithm::VV)
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, WallCycleCounter::Run);
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, WallCycleCounter::Step);
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 != FreeEnergyPerturbationType::No || 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 != FreeEnergyPerturbationType::No) && 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 != ComRemovalAlgorithm::No && 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 // We only need to calculate virtual velocities if we are writing them in the current step
958 const bool needVirtualVelocitiesThisStep =
960 && (do_per_step(step, ir->nstvout) || checkpointHandler->isCheckpointingStep());
962 if (vsite != nullptr)
964 // Virtual sites need to be updated before domain decomposition and forces are calculated
965 wallcycle_start(wcycle, WallCycleCounter::VsiteConstr);
966 // md-vv calculates virtual velocities once it has full-step real velocities
967 vsite->construct(state->x,
970 (!EI_VV(inputrec->eI) && needVirtualVelocitiesThisStep)
971 ? VSiteOperation::PositionsAndVelocities
972 : VSiteOperation::Positions);
973 wallcycle_stop(wcycle, WallCycleCounter::VsiteConstr);
976 if (bNS && !(bFirstStep && ir->bContinuation))
978 bMasterState = FALSE;
979 /* Correct the new box if it is too skewed */
980 if (inputrecDynamicBox(ir))
982 if (correct_box(fplog, step, state->box))
985 // If update is offloaded, it should be informed about the box size change
988 integrator->setPbc(PbcType::Xyz, state->box);
992 if (DOMAINDECOMP(cr) && bMasterState)
994 dd_collect_state(cr->dd, state, state_global);
997 if (DOMAINDECOMP(cr))
999 /* Repartition the domain decomposition */
1000 dd_partition_system(fplog,
1020 do_verbose && !bPMETunePrinting);
1021 upd.updateAfterPartition(state->natoms,
1022 md->cFREEZE ? gmx::arrayRefFromArray(md->cFREEZE, md->nr)
1023 : gmx::ArrayRef<const unsigned short>(),
1024 md->cTC ? gmx::arrayRefFromArray(md->cTC, md->nr)
1025 : gmx::ArrayRef<const unsigned short>());
1029 // Allocate or re-size GPU halo exchange object, if necessary
1030 if (bNS && havePPDomainDecomposition(cr) && simulationWork.useGpuHaloExchange)
1032 GMX_RELEASE_ASSERT(fr->deviceStreamManager != nullptr,
1033 "GPU device manager has to be initialized to use GPU "
1034 "version of halo exchange.");
1035 constructGpuHaloExchange(mdlog, *cr, *fr->deviceStreamManager, wcycle);
1038 if (MASTER(cr) && do_log)
1040 gmx::EnergyOutput::printHeader(
1041 fplog, step, t); /* can we improve the information printed here? */
1044 if (ir->efep != FreeEnergyPerturbationType::No)
1046 update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
1051 /* We need the kinetic energy at minus the half step for determining
1052 * the full step kinetic energy and possibly for T-coupling.*/
1053 /* This may not be quite working correctly yet . . . . */
1054 int cglo_flags = CGLO_GSTAT | CGLO_TEMPERATURE;
1055 if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
1057 cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
1059 compute_globals(gstat,
1064 makeConstArrayRef(state->x),
1065 makeConstArrayRef(state->v),
1076 gmx::ArrayRef<real>{},
1081 if (DOMAINDECOMP(cr))
1083 checkNumberOfBondedInteractions(
1084 mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
1087 clear_mat(force_vir);
1089 checkpointHandler->decideIfCheckpointingThisStep(bNS, bFirstStep, bLastStep);
1091 /* Determine the energy and pressure:
1092 * at nstcalcenergy steps and at energy output steps (set below).
1094 if (EI_VV(ir->eI) && (!bInitStep))
1096 bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
1097 bCalcVir = bCalcEnerStep
1098 || (ir->epc != PressureCoupling::No
1099 && (do_per_step(step, ir->nstpcouple) || do_per_step(step - 1, ir->nstpcouple)));
1103 bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
1104 bCalcVir = bCalcEnerStep
1105 || (ir->epc != PressureCoupling::No && do_per_step(step, ir->nstpcouple));
1107 bCalcEner = bCalcEnerStep;
1109 do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
1111 if (do_ene || do_log || bDoReplEx)
1117 /* Do we need global communication ? */
1118 bGStat = (bCalcVir || bCalcEner || bStopCM || do_per_step(step, nstglobalcomm)
1119 || (EI_VV(ir->eI) && inputrecNvtTrotter(ir) && do_per_step(step - 1, nstglobalcomm)));
1121 force_flags = (GMX_FORCE_STATECHANGED | ((inputrecDynamicBox(ir)) ? GMX_FORCE_DYNAMICBOX : 0)
1122 | GMX_FORCE_ALLFORCES | (bCalcVir ? GMX_FORCE_VIRIAL : 0)
1123 | (bCalcEner ? GMX_FORCE_ENERGY : 0) | (bDoFEP ? GMX_FORCE_DHDL : 0));
1124 if (fr->useMts && !do_per_step(step, ir->nstfout))
1126 force_flags |= GMX_FORCE_DO_NOT_NEED_NORMAL_FORCE;
1131 /* Now is the time to relax the shells */
1132 relax_shell_flexcon(fplog,
1135 mdrunOptions.verbose,
1147 state->x.arrayRefWithPadding(),
1148 state->v.arrayRefWithPadding(),
1163 ddBalanceRegionHandler);
1167 /* The AWH history need to be saved _before_ doing force calculations where the AWH bias
1168 is updated (or the AWH update will be performed twice for one step when continuing).
1169 It would be best to call this update function from do_md_trajectory_writing but that
1170 would occur after do_force. One would have to divide the update_awh function into one
1171 function applying the AWH force and one doing the AWH bias update. The update AWH
1172 bias function could then be called after do_md_trajectory_writing (then containing
1173 update_awh_history). The checkpointing will in the future probably moved to the start
1174 of the md loop which will rid of this issue. */
1175 if (awh && checkpointHandler->isCheckpointingStep() && MASTER(cr))
1177 awh->updateHistory(state_global->awhHistory.get());
1180 /* The coordinates (x) are shifted (to get whole molecules)
1182 * This is parallellized as well, and does communication too.
1183 * Check comments in sim_util.c
1198 state->x.arrayRefWithPadding(),
1210 ed ? ed->getLegacyED() : nullptr,
1211 (bNS ? GMX_FORCE_NS : 0) | force_flags,
1212 ddBalanceRegionHandler);
1215 // VV integrators do not need the following velocity half step
1216 // if it is the first step after starting from a checkpoint.
1217 // That is, the half step is needed on all other steps, and
1218 // also the first step when starting from a .tpr file.
1221 integrateVVFirstStep(step,
1254 &saved_conserved_quantity,
1264 if (vsite != nullptr && needVirtualVelocitiesThisStep)
1266 // Positions were calculated earlier
1267 wallcycle_start(wcycle, WallCycleCounter::VsiteConstr);
1268 vsite->construct(state->x, state->v, state->box, VSiteOperation::Velocities);
1269 wallcycle_stop(wcycle, WallCycleCounter::VsiteConstr);
1273 /* ######## END FIRST UPDATE STEP ############## */
1274 /* ######## If doing VV, we now have v(dt) ###### */
1277 /* perform extended ensemble sampling in lambda - we don't
1278 actually move to the new state before outputting
1279 statistics, but if performing simulated tempering, we
1280 do update the velocities and the tau_t. */
1281 // TODO: Avoid changing inputrec (#3854)
1282 // Simulated tempering updates the reference temperature.
1283 // Expanded ensemble without simulated tempering does not change the inputrec.
1284 auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
1285 lamnew = ExpandedEnsembleDynamics(fplog,
1293 state->v.rvec_array(),
1295 /* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
1298 copy_df_history(state_global->dfhist, state->dfhist);
1302 // Copy coordinate from the GPU for the output/checkpointing if the update is offloaded and
1303 // coordinates have not already been copied for i) search or ii) CPU force tasks.
1304 if (useGpuForUpdate && !bNS && !runScheduleWork->domainWork.haveCpuLocalForceWork
1305 && (do_per_step(step, ir->nstxout) || do_per_step(step, ir->nstxout_compressed)
1306 || checkpointHandler->isCheckpointingStep()))
1308 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
1309 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
1311 // Copy velocities if needed for the output/checkpointing.
1312 // NOTE: Copy on the search steps is done at the beginning of the step.
1313 if (useGpuForUpdate && !bNS
1314 && (do_per_step(step, ir->nstvout) || checkpointHandler->isCheckpointingStep()))
1316 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
1317 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
1319 // Copy forces for the output if the forces were reduced on the GPU (not the case on virial steps)
1320 // and update is offloaded hence forces are kept on the GPU for update and have not been
1321 // already transferred in do_force().
1322 // TODO: There should be an improved, explicit mechanism that ensures this copy is only executed
1323 // when the forces are ready on the GPU -- the same synchronizer should be used as the one
1324 // prior to GPU update.
1325 // TODO: When the output flags will be included in step workload, this copy can be combined with the
1326 // copy call in do_force(...).
1327 // NOTE: The forces should not be copied here if the vsites are present, since they were modified
1328 // on host after the D2H copy in do_force(...).
1329 if (runScheduleWork->stepWork.useGpuFBufferOps && (simulationWork.useGpuUpdate && !vsite)
1330 && do_per_step(step, ir->nstfout))
1332 stateGpu->copyForcesFromGpu(f.view().force(), AtomLocality::Local);
1333 stateGpu->waitForcesReadyOnHost(AtomLocality::Local);
1335 /* Now we have the energies and forces corresponding to the
1336 * coordinates at time t. We must output all of this before
1339 do_md_trajectory_writing(fplog,
1356 checkpointHandler->isCheckpointingStep(),
1359 mdrunOptions.writeConfout,
1361 /* Check if IMD step and do IMD communication, if bIMD is TRUE. */
1362 bInteractiveMDstep = imdSession->run(step, bNS, state->box, state->x, t);
1364 /* kludge -- virial is lost with restart for MTTK NPT control. Must reload (saved earlier). */
1365 if (startingBehavior != StartingBehavior::NewSimulation && bFirstStep
1366 && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir)))
1368 copy_mat(state->svir_prev, shake_vir);
1369 copy_mat(state->fvir_prev, force_vir);
1372 stopHandler->setSignal();
1373 resetHandler->setSignal(walltime_accounting);
1375 if (bGStat || !PAR(cr))
1377 /* In parallel we only have to check for checkpointing in steps
1378 * where we do global communication,
1379 * otherwise the other nodes don't know.
1381 checkpointHandler->setSignal(walltime_accounting);
1384 /* ######### START SECOND UPDATE STEP ################# */
1386 /* at the start of step, randomize or scale the velocities ((if vv. Restriction of Andersen
1387 controlled in preprocessing */
1389 if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
1391 gmx_bool bIfRandomize;
1392 bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
1393 /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
1394 if (constr && bIfRandomize)
1396 constrain_velocities(constr, do_log, do_ene, step, state, nullptr, false, nullptr);
1399 /* Box is changed in update() when we do pressure coupling,
1400 * but we should still use the old box for energy corrections and when
1401 * writing it to the energy file, so it matches the trajectory files for
1402 * the same timestep above. Make a copy in a separate array.
1404 copy_mat(state->box, lastbox);
1408 if (!useGpuForUpdate)
1410 wallcycle_start(wcycle, WallCycleCounter::Update);
1412 /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
1415 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
1416 /* We can only do Berendsen coupling after we have summed
1417 * the kinetic energy or virial. Since the happens
1418 * in global_state after update, we should only do it at
1419 * step % nstlist = 1 with bGStatEveryStep=FALSE.
1424 update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
1425 update_pcouple_before_coordinates(fplog, step, ir, state, pressureCouplingMu, M, bInitStep);
1428 /* With leap-frog type integrators we compute the kinetic energy
1429 * at a whole time step as the average of the half-time step kinetic
1430 * energies of two subsequent steps. Therefore we need to compute the
1431 * half step kinetic energy also if we need energies at the next step.
1433 const bool needHalfStepKineticEnergy =
1434 (!EI_VV(ir->eI) && (do_per_step(step + 1, nstglobalcomm) || step_rel + 1 == ir->nsteps));
1436 // Parrinello-Rahman requires the pressure to be availible before the update to compute
1437 // the velocity scaling matrix. Hence, it runs one step after the nstpcouple step.
1438 const bool doParrinelloRahman = (ir->epc == PressureCoupling::ParrinelloRahman
1439 && do_per_step(step + ir->nstpcouple - 1, ir->nstpcouple));
1443 GMX_ASSERT(!useGpuForUpdate, "GPU update is not supported with VVAK integrator.");
1445 integrateVVSecondStep(step,
1481 if (useGpuForUpdate)
1483 if (bNS && (bFirstStep || DOMAINDECOMP(cr)))
1485 integrator->set(stateGpu->getCoordinates(),
1486 stateGpu->getVelocities(),
1487 stateGpu->getForces(),
1491 // Copy data to the GPU after buffers might have being reinitialized
1492 stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
1493 stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
1496 if (simulationWork.useGpuPme && !runScheduleWork->simulationWork.useGpuPmePpCommunication
1497 && !thisRankHasDuty(cr, DUTY_PME))
1499 // The PME forces were recieved to the host, so have to be copied
1500 stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::All);
1502 else if (!runScheduleWork->stepWork.useGpuFBufferOps)
1504 // The buffer ops were not offloaded this step, so the forces are on the
1505 // host and have to be copied
1506 stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::Local);
1509 const bool doTemperatureScaling =
1510 (ir->etc != TemperatureCoupling::No
1511 && do_per_step(step + ir->nsttcouple - 1, ir->nsttcouple));
1513 // This applies Leap-Frog, LINCS and SETTLE in succession
1514 integrator->integrate(
1515 stateGpu->getForcesReadyOnDeviceEvent(
1516 AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
1521 doTemperatureScaling,
1524 ir->nstpcouple * ir->delta_t,
1527 // Copy velocities D2H after update if:
1528 // - Globals are computed this step (includes the energy output steps).
1529 // - Temperature is needed for the next step.
1530 if (bGStat || needHalfStepKineticEnergy)
1532 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
1533 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
1538 /* With multiple time stepping we need to do an additional normal
1539 * update step to obtain the virial, as the actual MTS integration
1540 * using an acceleration where the slow forces are multiplied by mtsFactor.
1541 * Using that acceleration would result in a virial with the slow
1542 * force contribution would be a factor mtsFactor too large.
1544 if (fr->useMts && bCalcVir && constr != nullptr)
1546 upd.update_for_constraint_virial(
1549 mdatoms->havePartiallyFrozenAtoms,
1550 gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
1551 gmx::arrayRefFromArray(mdatoms->invMassPerDim, mdatoms->nr),
1553 f.view().forceWithPadding(),
1556 constrain_coordinates(constr,
1561 upd.xp()->arrayRefWithPadding(),
1567 ArrayRefWithPadding<const RVec> forceCombined =
1568 (fr->useMts && step % ir->mtsLevels[1].stepFactor == 0)
1569 ? f.view().forceMtsCombinedWithPadding()
1570 : f.view().forceWithPadding();
1571 upd.update_coords(*ir,
1574 mdatoms->havePartiallyFrozenAtoms,
1575 gmx::arrayRefFromArray(md->ptype, md->nr),
1576 gmx::arrayRefFromArray(md->invmass, md->nr),
1577 gmx::arrayRefFromArray(md->invMassPerDim, md->nr),
1587 wallcycle_stop(wcycle, WallCycleCounter::Update);
1589 constrain_coordinates(constr,
1594 upd.xp()->arrayRefWithPadding(),
1596 bCalcVir && !fr->useMts,
1599 upd.update_sd_second_half(*ir,
1603 gmx::arrayRefFromArray(md->ptype, md->nr),
1604 gmx::arrayRefFromArray(md->invmass, md->nr),
1612 upd.finish_update(*ir, mdatoms, state, wcycle, constr != nullptr);
1615 if (ir->bPull && ir->pull->bSetPbcRefToPrevStepCOM)
1617 updatePrevStepPullCom(pull_work, state);
1620 enerd->term[F_DVDL_CONSTR] += dvdl_constr;
1623 /* ############## IF NOT VV, Calculate globals HERE ############ */
1624 /* With Leap-Frog we can skip compute_globals at
1625 * non-communication steps, but we need to calculate
1626 * the kinetic energy one step before communication.
1629 // Organize to do inter-simulation signalling on steps if
1630 // and when algorithms require it.
1631 const bool doInterSimSignal = (simulationsShareState && do_per_step(step, nstSignalComm));
1633 if (bGStat || needHalfStepKineticEnergy || doInterSimSignal)
1635 // Copy coordinates when needed to stop the CM motion.
1636 if (useGpuForUpdate && !EI_VV(ir->eI) && bStopCM)
1638 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
1639 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
1641 // Since we're already communicating at this step, we
1642 // can propagate intra-simulation signals. Note that
1643 // check_nstglobalcomm has the responsibility for
1644 // choosing the value of nstglobalcomm that is one way
1645 // bGStat becomes true, so we can't get into a
1646 // situation where e.g. checkpointing can't be
1648 bool doIntraSimSignal = true;
1649 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
1657 makeConstArrayRef(state->x),
1658 makeConstArrayRef(state->v),
1669 (!EI_VV(ir->eI) && bCalcEner && constr != nullptr) ? constr->rmsdData()
1670 : gmx::ArrayRef<real>{},
1674 (bGStat ? CGLO_GSTAT : 0) | (!EI_VV(ir->eI) && bCalcEner ? CGLO_ENERGY : 0)
1675 | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
1676 | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
1677 | (!EI_VV(ir->eI) ? CGLO_PRESSURE : 0) | CGLO_CONSTRAINT
1678 | (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd)
1679 ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
1681 if (DOMAINDECOMP(cr))
1683 checkNumberOfBondedInteractions(
1684 mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
1686 if (!EI_VV(ir->eI) && bStopCM)
1688 process_and_stopcm_grp(
1689 fplog, &vcm, *mdatoms, makeArrayRef(state->x), makeArrayRef(state->v));
1690 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
1692 // TODO: The special case of removing CM motion should be dealt more gracefully
1693 if (useGpuForUpdate)
1695 stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
1696 // Here we block until the H2D copy completes because event sync with the
1697 // force kernels that use the coordinates on the next steps is not implemented
1698 // (not because of a race on state->x being modified on the CPU while H2D is in progress).
1699 stateGpu->waitCoordinatesCopiedToDevice(AtomLocality::Local);
1700 // If the COM removal changed the velocities on the CPU, this has to be accounted for.
1701 if (vcm.mode != ComRemovalAlgorithm::No)
1703 stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
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 != FreeEnergyPerturbationType::No && !EI_VV(ir->eI))
1719 /* Sum up the foreign energy and dK/dl terms for md and sd.
1720 Currently done every step so that dH/dl is correct in the .edr */
1721 accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
1724 update_pcouple_after_coordinates(
1725 fplog, step, ir, mdatoms, pres, force_vir, shake_vir, pressureCouplingMu, state, nrnb, upd.deform(), !useGpuForUpdate);
1727 const bool doBerendsenPressureCoupling = (inputrec->epc == PressureCoupling::Berendsen
1728 && do_per_step(step, inputrec->nstpcouple));
1729 const bool doCRescalePressureCoupling = (inputrec->epc == PressureCoupling::CRescale
1730 && do_per_step(step, inputrec->nstpcouple));
1732 && (doBerendsenPressureCoupling || doCRescalePressureCoupling || doParrinelloRahman))
1734 integrator->scaleCoordinates(pressureCouplingMu);
1735 if (doCRescalePressureCoupling)
1737 matrix pressureCouplingInvMu;
1738 gmx::invertBoxMatrix(pressureCouplingMu, pressureCouplingInvMu);
1739 integrator->scaleVelocities(pressureCouplingInvMu);
1741 integrator->setPbc(PbcType::Xyz, state->box);
1744 /* ################# END UPDATE STEP 2 ################# */
1745 /* #### We now have r(t+dt) and v(t+dt/2) ############# */
1747 /* The coordinates (x) were unshifted in update */
1750 /* We will not sum ekinh_old,
1751 * so signal that we still have to do it.
1753 bSumEkinhOld = TRUE;
1758 /* ######### BEGIN PREPARING EDR OUTPUT ########### */
1760 /* use the directly determined last velocity, not actually the averaged half steps */
1761 if (bTrotter && ir->eI == IntegrationAlgorithm::VV)
1763 enerd->term[F_EKIN] = last_ekin;
1765 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
1767 if (integratorHasConservedEnergyQuantity(ir))
1771 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
1775 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + NPT_energy(ir, state, &MassQ);
1778 /* ######### END PREPARING EDR OUTPUT ########### */
1784 if (fplog && do_log && bDoExpanded)
1786 /* only needed if doing expanded ensemble */
1787 PrintFreeEnergyInfoToFile(fplog,
1789 ir->expandedvals.get(),
1790 ir->bSimTemp ? ir->simtempvals.get() : nullptr,
1791 state_global->dfhist,
1798 energyOutput.addDataAtEnergyStep(bDoDHDL,
1804 ir->expandedvals.get(),
1806 PTCouplingArrays{ state->boxv,
1807 state->nosehoover_xi,
1808 state->nosehoover_vxi,
1810 state->nhpres_vxi },
1822 energyOutput.recordNonEnergyStep();
1825 gmx_bool do_dr = do_per_step(step, ir->nstdisreout);
1826 gmx_bool do_or = do_per_step(step, ir->nstorireout);
1828 if (doSimulatedAnnealing)
1830 gmx::EnergyOutput::printAnnealingTemperatures(
1831 do_log ? fplog : nullptr, groups, &(ir->opts));
1833 if (do_log || do_ene || do_dr || do_or)
1835 energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
1839 do_log ? fplog : nullptr,
1845 if (do_log && ir->bDoAwh && awh->hasFepLambdaDimension())
1847 const bool isInitialOutput = false;
1848 printLambdaStateToLog(fplog, state->lambda, isInitialOutput);
1853 pull_print_output(pull_work, step, t);
1856 if (do_per_step(step, ir->nstlog))
1858 if (fflush(fplog) != 0)
1860 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
1866 /* Have to do this part _after_ outputting the logfile and the edr file */
1867 /* Gets written into the state at the beginning of next loop*/
1868 state->fep_state = lamnew;
1870 else if (ir->bDoAwh && awh->needForeignEnergyDifferences(step))
1872 state->fep_state = awh->fepLambdaState();
1874 /* Print the remaining wall clock time for the run */
1875 if (isMasterSimMasterRank(ms, MASTER(cr)) && (do_verbose || gmx_got_usr_signal()) && !bPMETunePrinting)
1879 fprintf(stderr, "\n");
1881 print_time(stderr, walltime_accounting, step, ir, cr);
1884 /* Ion/water position swapping.
1885 * Not done in last step since trajectory writing happens before this call
1886 * in the MD loop and exchanges would be lost anyway. */
1887 bNeedRepartition = FALSE;
1888 if ((ir->eSwapCoords != SwapType::No) && (step > 0) && !bLastStep
1889 && do_per_step(step, ir->swap->nstswap))
1891 bNeedRepartition = do_swapcoords(cr,
1897 as_rvec_array(state->x.data()),
1899 MASTER(cr) && mdrunOptions.verbose,
1902 if (bNeedRepartition && DOMAINDECOMP(cr))
1904 dd_collect_state(cr->dd, state, state_global);
1908 /* Replica exchange */
1912 bExchanged = replica_exchange(fplog, cr, ms, repl_ex, state_global, enerd, state, step, t);
1915 if ((bExchanged || bNeedRepartition) && DOMAINDECOMP(cr))
1917 dd_partition_system(fplog,
1938 upd.updateAfterPartition(state->natoms,
1939 md->cFREEZE ? gmx::arrayRefFromArray(md->cFREEZE, md->nr)
1940 : gmx::ArrayRef<const unsigned short>(),
1941 md->cTC ? gmx::arrayRefFromArray(md->cTC, md->nr)
1942 : gmx::ArrayRef<const unsigned short>());
1948 /* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
1949 /* With all integrators, except VV, we need to retain the pressure
1950 * at the current step for coupling at the next step.
1952 if ((state->flags & enumValueToBitMask(StateEntry::PressurePrevious))
1953 && (bGStatEveryStep || (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
1955 /* Store the pressure in t_state for pressure coupling
1956 * at the next MD step.
1958 copy_mat(pres, state->pres_prev);
1961 /* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
1963 if ((membed != nullptr) && (!bLastStep))
1965 rescale_membed(step_rel, membed, as_rvec_array(state_global->x.data()));
1968 cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
1969 if (DOMAINDECOMP(cr) && wcycle)
1971 dd_cycles_add(cr->dd, cycles, ddCyclStep);
1974 /* increase the MD step number */
1981 fcReportProgress(ir->nsteps + ir->init_step, step);
1985 resetHandler->resetCounters(
1986 step, step_rel, mdlog, fplog, cr, fr->nbv.get(), nrnb, fr->pmedata, pme_loadbal, wcycle, walltime_accounting);
1988 /* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
1989 imdSession->updateEnergyRecordAndSendPositionsAndEnergies(bInteractiveMDstep, step, bCalcEner);
1991 /* End of main MD loop */
1993 /* Closing TNG files can include compressing data. Therefore it is good to do that
1994 * before stopping the time measurements. */
1995 mdoutf_tng_close(outf);
1997 /* Stop measuring walltime */
1998 walltime_accounting_end_time(walltime_accounting);
2000 if (!thisRankHasDuty(cr, DUTY_PME))
2002 /* Tell the PME only node to finish */
2003 gmx_pme_send_finish(cr);
2008 if (ir->nstcalcenergy > 0)
2010 energyOutput.printEnergyConservation(fplog, ir->simulation_part, EI_MD(ir->eI));
2012 gmx::EnergyOutput::printAnnealingTemperatures(fplog, groups, &(ir->opts));
2013 energyOutput.printAverages(fplog, groups);
2020 pme_loadbal_done(pme_loadbal, fplog, mdlog, fr->nbv->useGpu());
2023 done_shellfc(fplog, shellfc, step_rel);
2025 if (useReplicaExchange && MASTER(cr))
2027 print_replica_exchange_statistics(fplog, repl_ex);
2030 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
2032 global_stat_destroy(gstat);