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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>(
477 fr->deviceStreamManager->context(),
478 fr->deviceStreamManager->stream(gmx::DeviceStreamType::UpdateAndConstraints),
479 stateGpu->xUpdatedOnDevice(),
482 integrator->setPbc(PbcType::Xyz, state->box);
485 if (useGpuForPme || (useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
487 changePinningPolicy(&state->x, PinningPolicy::PinnedIfSupported);
491 changePinningPolicy(&state->v, PinningPolicy::PinnedIfSupported);
494 // NOTE: The global state is no longer used at this point.
495 // But state_global is still used as temporary storage space for writing
496 // the global state to file and potentially for replica exchange.
497 // (Global topology should persist.)
499 update_mdatoms(mdatoms, state->lambda[efptMASS]);
503 /* Check nstexpanded here, because the grompp check was broken */
504 if (ir->expandedvals->nstexpanded % ir->nstcalcenergy != 0)
507 "With expanded ensemble, nstexpanded should be a multiple of nstcalcenergy");
509 init_expanded_ensemble(startingBehavior != StartingBehavior::NewSimulation, ir, state->dfhist);
514 EnergyData::initializeEnergyHistory(startingBehavior, observablesHistory, &energyOutput);
517 preparePrevStepPullCom(
518 ir, pull_work, mdatoms->massT, state, state_global, cr, startingBehavior != StartingBehavior::NewSimulation);
520 // TODO: Remove this by converting AWH into a ForceProvider
521 auto awh = prepareAwhModule(fplog,
526 startingBehavior != StartingBehavior::NewSimulation,
528 opt2fn("-awh", nfile, fnm),
531 if (useReplicaExchange && MASTER(cr))
533 repl_ex = init_replica_exchange(fplog, ms, top_global->natoms, ir, replExParams);
535 /* PME tuning is only supported in the Verlet scheme, with PME for
536 * Coulomb. It is not supported with only LJ PME. */
537 bPMETune = (mdrunOptions.tunePme && EEL_PME(fr->ic->eeltype) && !mdrunOptions.reproducible
538 && ir->cutoff_scheme != ecutsGROUP);
540 pme_load_balancing_t* pme_loadbal = nullptr;
544 &pme_loadbal, cr, mdlog, *ir, state->box, *fr->ic, *fr->nbv, fr->pmedata, fr->nbv->useGpu());
547 if (!ir->bContinuation)
549 if (state->flags & (1U << estV))
551 auto v = makeArrayRef(state->v);
552 /* Set the velocities of vsites, shells and frozen atoms to zero */
553 for (i = 0; i < mdatoms->homenr; i++)
555 if (mdatoms->ptype[i] == eptShell)
559 else if (mdatoms->cFREEZE)
561 for (m = 0; m < DIM; m++)
563 if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
574 /* Constrain the initial coordinates and velocities */
575 do_constrain_first(fplog,
580 state->x.arrayRefWithPadding(),
581 state->v.arrayRefWithPadding(),
583 state->lambda[efptBONDED]);
587 if (ir->efep != efepNO)
589 /* Set free energy calculation frequency as the greatest common
590 * denominator of nstdhdl and repl_ex_nst. */
591 nstfep = ir->fepvals->nstdhdl;
594 nstfep = std::gcd(ir->expandedvals->nstexpanded, nstfep);
596 if (useReplicaExchange)
598 nstfep = std::gcd(replExParams.exchangeInterval, nstfep);
602 nstfep = std::gcd(ir->awhParams->nstSampleCoord, nstfep);
606 /* Be REALLY careful about what flags you set here. You CANNOT assume
607 * this is the first step, since we might be restarting from a checkpoint,
608 * and in that case we should not do any modifications to the state.
610 bStopCM = (ir->comm_mode != ecmNO && !ir->bContinuation);
612 // When restarting from a checkpoint, it can be appropriate to
613 // initialize ekind from quantities in the checkpoint. Otherwise,
614 // compute_globals must initialize ekind before the simulation
615 // starts/restarts. However, only the master rank knows what was
616 // found in the checkpoint file, so we have to communicate in
617 // order to coordinate the restart.
619 // TODO Consider removing this communication if/when checkpoint
620 // reading directly follows .tpr reading, because all ranks can
621 // agree on hasReadEkinState at that time.
622 bool hasReadEkinState = MASTER(cr) ? state_global->ekinstate.hasReadEkinState : false;
625 gmx_bcast(sizeof(hasReadEkinState), &hasReadEkinState, cr->mpi_comm_mygroup);
627 if (hasReadEkinState)
629 restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
632 unsigned int cglo_flags =
633 (CGLO_TEMPERATURE | CGLO_GSTAT | (EI_VV(ir->eI) ? CGLO_PRESSURE : 0)
634 | (EI_VV(ir->eI) ? CGLO_CONSTRAINT : 0) | (hasReadEkinState ? CGLO_READEKIN : 0));
636 bSumEkinhOld = FALSE;
638 t_vcm vcm(top_global->groups, *ir);
639 reportComRemovalInfo(fplog, vcm);
641 /* To minimize communication, compute_globals computes the COM velocity
642 * and the kinetic energy for the velocities without COM motion removed.
643 * Thus to get the kinetic energy without the COM contribution, we need
644 * to call compute_globals twice.
646 for (int cgloIteration = 0; cgloIteration < (bStopCM ? 2 : 1); cgloIteration++)
648 unsigned int cglo_flags_iteration = cglo_flags;
649 if (bStopCM && cgloIteration == 0)
651 cglo_flags_iteration |= CGLO_STOPCM;
652 cglo_flags_iteration &= ~CGLO_TEMPERATURE;
654 compute_globals(gstat,
659 makeConstArrayRef(state->x),
660 makeConstArrayRef(state->v),
671 gmx::ArrayRef<real>{},
674 &totalNumberOfBondedInteractions,
677 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
679 if (cglo_flags_iteration & CGLO_STOPCM)
681 /* At initialization, do not pass x with acceleration-correction mode
682 * to avoid (incorrect) correction of the initial coordinates.
684 auto x = (vcm.mode == ecmLINEAR_ACCELERATION_CORRECTION) ? ArrayRef<RVec>()
685 : makeArrayRef(state->x);
686 process_and_stopcm_grp(fplog, &vcm, *mdatoms, x, makeArrayRef(state->v));
687 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
690 checkNumberOfBondedInteractions(mdlog,
692 totalNumberOfBondedInteractions,
695 makeConstArrayRef(state->x),
697 &shouldCheckNumberOfBondedInteractions);
698 if (ir->eI == eiVVAK)
700 /* a second call to get the half step temperature initialized as well */
701 /* we do the same call as above, but turn the pressure off -- internally to
702 compute_globals, this is recognized as a velocity verlet half-step
703 kinetic energy calculation. This minimized excess variables, but
704 perhaps loses some logic?*/
706 compute_globals(gstat,
711 makeConstArrayRef(state->x),
712 makeConstArrayRef(state->v),
723 gmx::ArrayRef<real>{},
728 cglo_flags & ~CGLO_PRESSURE);
731 /* Calculate the initial half step temperature, and save the ekinh_old */
732 if (startingBehavior == StartingBehavior::NewSimulation)
734 for (i = 0; (i < ir->opts.ngtc); i++)
736 copy_mat(ekind->tcstat[i].ekinh, ekind->tcstat[i].ekinh_old);
740 /* need to make an initiation call to get the Trotter variables set, as well as other constants
741 for non-trotter temperature control */
742 auto trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
746 if (!ir->bContinuation)
748 if (constr && ir->eConstrAlg == econtLINCS)
751 "RMS relative constraint deviation after constraining: %.2e\n",
754 if (EI_STATE_VELOCITY(ir->eI))
756 real temp = enerd->term[F_TEMP];
759 /* Result of Ekin averaged over velocities of -half
760 * and +half step, while we only have -half step here.
764 fprintf(fplog, "Initial temperature: %g K\n", temp);
769 fprintf(stderr, "starting mdrun '%s'\n", *(top_global->name));
772 sprintf(tbuf, "%8.1f", (ir->init_step + ir->nsteps) * ir->delta_t);
776 sprintf(tbuf, "%s", "infinite");
778 if (ir->init_step > 0)
781 "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
782 gmx_step_str(ir->init_step + ir->nsteps, sbuf),
784 gmx_step_str(ir->init_step, sbuf2),
785 ir->init_step * ir->delta_t);
789 fprintf(stderr, "%s steps, %s ps.\n", gmx_step_str(ir->nsteps, sbuf), tbuf);
791 fprintf(fplog, "\n");
794 walltime_accounting_start_time(walltime_accounting);
795 wallcycle_start(wcycle, ewcRUN);
796 print_start(fplog, cr, walltime_accounting, "mdrun");
798 /***********************************************************
802 ************************************************************/
805 /* Skip the first Nose-Hoover integration when we get the state from tpx */
806 bInitStep = startingBehavior == StartingBehavior::NewSimulation || EI_VV(ir->eI);
807 bSumEkinhOld = FALSE;
809 bNeedRepartition = FALSE;
811 step = ir->init_step;
814 auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
815 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
816 simulationsShareState,
819 mdrunOptions.reproducible,
821 mdrunOptions.maximumHoursToRun,
826 walltime_accounting);
828 auto checkpointHandler = std::make_unique<CheckpointHandler>(
829 compat::make_not_null<SimulationSignal*>(&signals[eglsCHKPT]),
830 simulationsShareState,
833 mdrunOptions.writeConfout,
834 mdrunOptions.checkpointOptions.period);
836 const bool resetCountersIsLocal = true;
837 auto resetHandler = std::make_unique<ResetHandler>(
838 compat::make_not_null<SimulationSignal*>(&signals[eglsRESETCOUNTERS]),
839 !resetCountersIsLocal,
842 mdrunOptions.timingOptions.resetHalfway,
843 mdrunOptions.maximumHoursToRun,
846 walltime_accounting);
848 const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
850 if (MASTER(cr) && isMultiSim(ms) && !useReplicaExchange)
852 logInitialMultisimStatus(ms, cr, mdlog, simulationsShareState, ir->nsteps, ir->init_step);
855 /* and stop now if we should */
856 bLastStep = (bLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
860 /* Determine if this is a neighbor search step */
861 bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
863 if (bPMETune && bNStList)
865 // This has to be here because PME load balancing is called so early.
866 // TODO: Move to after all booleans are defined.
867 if (useGpuForUpdate && !bFirstStep)
869 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
870 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
872 /* PME grid + cut-off optimization with GPUs or PME nodes */
873 pme_loadbal_do(pme_loadbal,
875 (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
886 simulationWork.useGpuPmePpCommunication);
889 wallcycle_start(wcycle, ewcSTEP);
891 bLastStep = (step_rel == ir->nsteps);
892 t = t0 + step * ir->delta_t;
894 // TODO Refactor this, so that nstfep does not need a default value of zero
895 if (ir->efep != efepNO || ir->bSimTemp)
897 /* find and set the current lambdas */
898 state->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
900 bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
901 bDoFEP = ((ir->efep != efepNO) && do_per_step(step, nstfep));
902 bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded) && (ir->bExpanded)
906 bDoReplEx = (useReplicaExchange && (step > 0) && !bLastStep
907 && do_per_step(step, replExParams.exchangeInterval));
909 if (doSimulatedAnnealing)
911 // TODO: Avoid changing inputrec (#3854)
912 // Simulated annealing updates the reference temperature.
913 auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
914 update_annealing_target_temp(nonConstInputrec, t, &upd);
917 /* Stop Center of Mass motion */
918 bStopCM = (ir->comm_mode != ecmNO && do_per_step(step, ir->nstcomm));
920 /* Determine whether or not to do Neighbour Searching */
921 bNS = (bFirstStep || bNStList || bExchanged || bNeedRepartition);
923 /* Note that the stopHandler will cause termination at nstglobalcomm
924 * steps. Since this concides with nstcalcenergy, nsttcouple and/or
925 * nstpcouple steps, we have computed the half-step kinetic energy
926 * of the previous step and can always output energies at the last step.
928 bLastStep = bLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
930 /* do_log triggers energy and virial calculation. Because this leads
931 * to different code paths, forces can be different. Thus for exact
932 * continuation we should avoid extra log output.
933 * Note that the || bLastStep can result in non-exact continuation
934 * beyond the last step. But we don't consider that to be an issue.
936 do_log = (do_per_step(step, ir->nstlog)
937 || (bFirstStep && startingBehavior == StartingBehavior::NewSimulation) || bLastStep);
938 do_verbose = mdrunOptions.verbose
939 && (step % mdrunOptions.verboseStepPrintInterval == 0 || bFirstStep || bLastStep);
941 if (useGpuForUpdate && !bFirstStep && bNS)
943 // Copy velocities from the GPU on search steps to keep a copy on host (device buffers are reinitialized).
944 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
945 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
946 // Copy coordinate from the GPU when needed at the search step.
947 // NOTE: The cases when coordinates needed on CPU for force evaluation are handled in sim_utils.
948 // NOTE: If the coordinates are to be written into output file they are also copied separately before the output.
949 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
950 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
953 // We only need to calculate virtual velocities if we are writing them in the current step
954 const bool needVirtualVelocitiesThisStep =
956 && (do_per_step(step, ir->nstvout) || checkpointHandler->isCheckpointingStep());
958 if (vsite != nullptr)
960 // Virtual sites need to be updated before domain decomposition and forces are calculated
961 wallcycle_start(wcycle, ewcVSITECONSTR);
962 // md-vv calculates virtual velocities once it has full-step real velocities
963 vsite->construct(state->x,
966 (!EI_VV(inputrec->eI) && needVirtualVelocitiesThisStep)
967 ? VSiteOperation::PositionsAndVelocities
968 : VSiteOperation::Positions);
969 wallcycle_stop(wcycle, ewcVSITECONSTR);
972 if (bNS && !(bFirstStep && ir->bContinuation))
974 bMasterState = FALSE;
975 /* Correct the new box if it is too skewed */
976 if (inputrecDynamicBox(ir))
978 if (correct_box(fplog, step, state->box))
981 // If update is offloaded, it should be informed about the box size change
984 integrator->setPbc(PbcType::Xyz, state->box);
988 if (DOMAINDECOMP(cr) && bMasterState)
990 dd_collect_state(cr->dd, state, state_global);
993 if (DOMAINDECOMP(cr))
995 /* Repartition the domain decomposition */
996 dd_partition_system(fplog,
1016 do_verbose && !bPMETunePrinting);
1017 shouldCheckNumberOfBondedInteractions = true;
1018 upd.setNumAtoms(state->natoms);
1022 // Allocate or re-size GPU halo exchange object, if necessary
1023 if (bNS && havePPDomainDecomposition(cr) && simulationWork.useGpuHaloExchange)
1025 GMX_RELEASE_ASSERT(fr->deviceStreamManager != nullptr,
1026 "GPU device manager has to be initialized to use GPU "
1027 "version of halo exchange.");
1028 constructGpuHaloExchange(mdlog, *cr, *fr->deviceStreamManager, wcycle);
1031 if (MASTER(cr) && do_log)
1033 gmx::EnergyOutput::printHeader(
1034 fplog, step, t); /* can we improve the information printed here? */
1037 if (ir->efep != efepNO)
1039 update_mdatoms(mdatoms, state->lambda[efptMASS]);
1044 /* We need the kinetic energy at minus the half step for determining
1045 * the full step kinetic energy and possibly for T-coupling.*/
1046 /* This may not be quite working correctly yet . . . . */
1047 compute_globals(gstat,
1052 makeConstArrayRef(state->x),
1053 makeConstArrayRef(state->v),
1064 gmx::ArrayRef<real>{},
1067 &totalNumberOfBondedInteractions,
1069 CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
1070 checkNumberOfBondedInteractions(mdlog,
1072 totalNumberOfBondedInteractions,
1075 makeConstArrayRef(state->x),
1077 &shouldCheckNumberOfBondedInteractions);
1079 clear_mat(force_vir);
1081 checkpointHandler->decideIfCheckpointingThisStep(bNS, bFirstStep, bLastStep);
1083 /* Determine the energy and pressure:
1084 * at nstcalcenergy steps and at energy output steps (set below).
1086 if (EI_VV(ir->eI) && (!bInitStep))
1088 bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
1089 bCalcVir = bCalcEnerStep
1090 || (ir->epc != PressureCoupling::No
1091 && (do_per_step(step, ir->nstpcouple) || do_per_step(step - 1, ir->nstpcouple)));
1095 bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
1096 bCalcVir = bCalcEnerStep
1097 || (ir->epc != PressureCoupling::No && do_per_step(step, ir->nstpcouple));
1099 bCalcEner = bCalcEnerStep;
1101 do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
1103 if (do_ene || do_log || bDoReplEx)
1109 /* Do we need global communication ? */
1110 bGStat = (bCalcVir || bCalcEner || bStopCM || do_per_step(step, nstglobalcomm)
1111 || (EI_VV(ir->eI) && inputrecNvtTrotter(ir) && do_per_step(step - 1, nstglobalcomm)));
1113 force_flags = (GMX_FORCE_STATECHANGED | ((inputrecDynamicBox(ir)) ? GMX_FORCE_DYNAMICBOX : 0)
1114 | GMX_FORCE_ALLFORCES | (bCalcVir ? GMX_FORCE_VIRIAL : 0)
1115 | (bCalcEner ? GMX_FORCE_ENERGY : 0) | (bDoFEP ? GMX_FORCE_DHDL : 0));
1116 if (fr->useMts && !do_per_step(step, ir->nstfout))
1118 force_flags |= GMX_FORCE_DO_NOT_NEED_NORMAL_FORCE;
1123 /* Now is the time to relax the shells */
1124 relax_shell_flexcon(fplog,
1127 mdrunOptions.verbose,
1139 state->x.arrayRefWithPadding(),
1140 state->v.arrayRefWithPadding(),
1155 ddBalanceRegionHandler);
1159 /* The AWH history need to be saved _before_ doing force calculations where the AWH bias
1160 is updated (or the AWH update will be performed twice for one step when continuing).
1161 It would be best to call this update function from do_md_trajectory_writing but that
1162 would occur after do_force. One would have to divide the update_awh function into one
1163 function applying the AWH force and one doing the AWH bias update. The update AWH
1164 bias function could then be called after do_md_trajectory_writing (then containing
1165 update_awh_history). The checkpointing will in the future probably moved to the start
1166 of the md loop which will rid of this issue. */
1167 if (awh && checkpointHandler->isCheckpointingStep() && MASTER(cr))
1169 awh->updateHistory(state_global->awhHistory.get());
1172 /* The coordinates (x) are shifted (to get whole molecules)
1174 * This is parallellized as well, and does communication too.
1175 * Check comments in sim_util.c
1190 state->x.arrayRefWithPadding(),
1202 ed ? ed->getLegacyED() : nullptr,
1203 (bNS ? GMX_FORCE_NS : 0) | force_flags,
1204 ddBalanceRegionHandler);
1207 // VV integrators do not need the following velocity half step
1208 // if it is the first step after starting from a checkpoint.
1209 // That is, the half step is needed on all other steps, and
1210 // also the first step when starting from a .tpr file.
1213 integrateVVFirstStep(step,
1246 &shouldCheckNumberOfBondedInteractions,
1247 &saved_conserved_quantity,
1257 if (vsite != nullptr && needVirtualVelocitiesThisStep)
1259 // Positions were calculated earlier
1260 wallcycle_start(wcycle, ewcVSITECONSTR);
1261 vsite->construct(state->x, state->v, state->box, VSiteOperation::Velocities);
1262 wallcycle_stop(wcycle, ewcVSITECONSTR);
1266 /* ######## END FIRST UPDATE STEP ############## */
1267 /* ######## If doing VV, we now have v(dt) ###### */
1270 /* perform extended ensemble sampling in lambda - we don't
1271 actually move to the new state before outputting
1272 statistics, but if performing simulated tempering, we
1273 do update the velocities and the tau_t. */
1274 // TODO: Avoid changing inputrec (#3854)
1275 // Simulated tempering updates the reference temperature.
1276 // Expanded ensemble without simulated tempering does not change the inputrec.
1277 auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
1278 lamnew = ExpandedEnsembleDynamics(fplog,
1286 state->v.rvec_array(),
1288 /* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
1291 copy_df_history(state_global->dfhist, state->dfhist);
1295 // Copy coordinate from the GPU for the output/checkpointing if the update is offloaded and
1296 // coordinates have not already been copied for i) search or ii) CPU force tasks.
1297 if (useGpuForUpdate && !bNS && !runScheduleWork->domainWork.haveCpuLocalForceWork
1298 && (do_per_step(step, ir->nstxout) || do_per_step(step, ir->nstxout_compressed)
1299 || checkpointHandler->isCheckpointingStep()))
1301 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
1302 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
1304 // Copy velocities if needed for the output/checkpointing.
1305 // NOTE: Copy on the search steps is done at the beginning of the step.
1306 if (useGpuForUpdate && !bNS
1307 && (do_per_step(step, ir->nstvout) || checkpointHandler->isCheckpointingStep()))
1309 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
1310 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
1312 // Copy forces for the output if the forces were reduced on the GPU (not the case on virial steps)
1313 // and update is offloaded hence forces are kept on the GPU for update and have not been
1314 // already transferred in do_force().
1315 // TODO: There should be an improved, explicit mechanism that ensures this copy is only executed
1316 // when the forces are ready on the GPU -- the same synchronizer should be used as the one
1317 // prior to GPU update.
1318 // TODO: When the output flags will be included in step workload, this copy can be combined with the
1319 // copy call in do_force(...).
1320 // NOTE: The forces should not be copied here if the vsites are present, since they were modified
1321 // on host after the D2H copy in do_force(...).
1322 if (runScheduleWork->stepWork.useGpuFBufferOps && (simulationWork.useGpuUpdate && !vsite)
1323 && do_per_step(step, ir->nstfout))
1325 stateGpu->copyForcesFromGpu(f.view().force(), AtomLocality::Local);
1326 stateGpu->waitForcesReadyOnHost(AtomLocality::Local);
1328 /* Now we have the energies and forces corresponding to the
1329 * coordinates at time t. We must output all of this before
1332 do_md_trajectory_writing(fplog,
1349 checkpointHandler->isCheckpointingStep(),
1352 mdrunOptions.writeConfout,
1354 /* Check if IMD step and do IMD communication, if bIMD is TRUE. */
1355 bInteractiveMDstep = imdSession->run(step, bNS, state->box, state->x.rvec_array(), t);
1357 /* kludge -- virial is lost with restart for MTTK NPT control. Must reload (saved earlier). */
1358 if (startingBehavior != StartingBehavior::NewSimulation && bFirstStep
1359 && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir)))
1361 copy_mat(state->svir_prev, shake_vir);
1362 copy_mat(state->fvir_prev, force_vir);
1365 stopHandler->setSignal();
1366 resetHandler->setSignal(walltime_accounting);
1368 if (bGStat || !PAR(cr))
1370 /* In parallel we only have to check for checkpointing in steps
1371 * where we do global communication,
1372 * otherwise the other nodes don't know.
1374 checkpointHandler->setSignal(walltime_accounting);
1377 /* ######### START SECOND UPDATE STEP ################# */
1379 /* at the start of step, randomize or scale the velocities ((if vv. Restriction of Andersen
1380 controlled in preprocessing */
1382 if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
1384 gmx_bool bIfRandomize;
1385 bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
1386 /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
1387 if (constr && bIfRandomize)
1389 constrain_velocities(constr, do_log, do_ene, step, state, nullptr, false, nullptr);
1392 /* Box is changed in update() when we do pressure coupling,
1393 * but we should still use the old box for energy corrections and when
1394 * writing it to the energy file, so it matches the trajectory files for
1395 * the same timestep above. Make a copy in a separate array.
1397 copy_mat(state->box, lastbox);
1401 if (!useGpuForUpdate)
1403 wallcycle_start(wcycle, ewcUPDATE);
1405 /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
1408 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
1409 /* We can only do Berendsen coupling after we have summed
1410 * the kinetic energy or virial. Since the happens
1411 * in global_state after update, we should only do it at
1412 * step % nstlist = 1 with bGStatEveryStep=FALSE.
1417 update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
1418 update_pcouple_before_coordinates(fplog, step, ir, state, pressureCouplingMu, M, bInitStep);
1421 /* With leap-frog type integrators we compute the kinetic energy
1422 * at a whole time step as the average of the half-time step kinetic
1423 * energies of two subsequent steps. Therefore we need to compute the
1424 * half step kinetic energy also if we need energies at the next step.
1426 const bool needHalfStepKineticEnergy =
1427 (!EI_VV(ir->eI) && (do_per_step(step + 1, nstglobalcomm) || step_rel + 1 == ir->nsteps));
1429 // Parrinello-Rahman requires the pressure to be availible before the update to compute
1430 // the velocity scaling matrix. Hence, it runs one step after the nstpcouple step.
1431 const bool doParrinelloRahman = (ir->epc == PressureCoupling::ParrinelloRahman
1432 && do_per_step(step + ir->nstpcouple - 1, ir->nstpcouple));
1436 GMX_ASSERT(!useGpuForUpdate, "GPU update is not supported with VVAK integrator.");
1438 integrateVVSecondStep(step,
1474 if (useGpuForUpdate)
1477 wallcycle_stop(wcycle, ewcUPDATE);
1479 if (bNS && (bFirstStep || DOMAINDECOMP(cr)))
1481 integrator->set(stateGpu->getCoordinates(),
1482 stateGpu->getVelocities(),
1483 stateGpu->getForces(),
1487 // Copy data to the GPU after buffers might have being reinitialized
1488 stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
1489 stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
1492 if (simulationWork.useGpuPme && !runScheduleWork->simulationWork.useGpuPmePpCommunication
1493 && !thisRankHasDuty(cr, DUTY_PME))
1495 // The PME forces were recieved to the host, so have to be copied
1496 stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::All);
1498 else if (!runScheduleWork->stepWork.useGpuFBufferOps)
1500 // The buffer ops were not offloaded this step, so the forces are on the
1501 // host and have to be copied
1502 stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::Local);
1505 const bool doTemperatureScaling =
1506 (ir->etc != TemperatureCoupling::No
1507 && do_per_step(step + ir->nsttcouple - 1, ir->nsttcouple));
1509 // This applies Leap-Frog, LINCS and SETTLE in succession
1510 integrator->integrate(
1511 stateGpu->getForcesReadyOnDeviceEvent(
1512 AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
1517 doTemperatureScaling,
1520 ir->nstpcouple * ir->delta_t,
1523 // Copy velocities D2H after update if:
1524 // - Globals are computed this step (includes the energy output steps).
1525 // - Temperature is needed for the next step.
1526 if (bGStat || needHalfStepKineticEnergy)
1528 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
1529 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
1534 /* With multiple time stepping we need to do an additional normal
1535 * update step to obtain the virial, as the actual MTS integration
1536 * using an acceleration where the slow forces are multiplied by mtsFactor.
1537 * Using that acceleration would result in a virial with the slow
1538 * force contribution would be a factor mtsFactor too large.
1540 if (fr->useMts && bCalcVir && constr != nullptr)
1542 upd.update_for_constraint_virial(
1543 *ir, *mdatoms, *state, f.view().forceWithPadding(), *ekind);
1545 constrain_coordinates(constr,
1550 upd.xp()->arrayRefWithPadding(),
1556 ArrayRefWithPadding<const RVec> forceCombined =
1557 (fr->useMts && step % ir->mtsLevels[1].stepFactor == 0)
1558 ? f.view().forceMtsCombinedWithPadding()
1559 : f.view().forceWithPadding();
1561 *ir, step, mdatoms, state, forceCombined, fcdata, ekind, M, etrtPOSITION, cr, constr != nullptr);
1563 wallcycle_stop(wcycle, ewcUPDATE);
1565 constrain_coordinates(constr,
1570 upd.xp()->arrayRefWithPadding(),
1572 bCalcVir && !fr->useMts,
1575 upd.update_sd_second_half(
1576 *ir, step, &dvdl_constr, mdatoms, state, cr, nrnb, wcycle, constr, do_log, do_ene);
1577 upd.finish_update(*ir, mdatoms, state, wcycle, constr != nullptr);
1580 if (ir->bPull && ir->pull->bSetPbcRefToPrevStepCOM)
1582 updatePrevStepPullCom(pull_work, state);
1585 enerd->term[F_DVDL_CONSTR] += dvdl_constr;
1588 /* ############## IF NOT VV, Calculate globals HERE ############ */
1589 /* With Leap-Frog we can skip compute_globals at
1590 * non-communication steps, but we need to calculate
1591 * the kinetic energy one step before communication.
1594 // Organize to do inter-simulation signalling on steps if
1595 // and when algorithms require it.
1596 const bool doInterSimSignal = (simulationsShareState && do_per_step(step, nstSignalComm));
1598 if (bGStat || needHalfStepKineticEnergy || doInterSimSignal)
1600 // Copy coordinates when needed to stop the CM motion.
1601 if (useGpuForUpdate && !EI_VV(ir->eI) && bStopCM)
1603 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
1604 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
1606 // Since we're already communicating at this step, we
1607 // can propagate intra-simulation signals. Note that
1608 // check_nstglobalcomm has the responsibility for
1609 // choosing the value of nstglobalcomm that is one way
1610 // bGStat becomes true, so we can't get into a
1611 // situation where e.g. checkpointing can't be
1613 bool doIntraSimSignal = true;
1614 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
1622 makeConstArrayRef(state->x),
1623 makeConstArrayRef(state->v),
1634 (!EI_VV(ir->eI) && bCalcEner && constr != nullptr) ? constr->rmsdData()
1635 : gmx::ArrayRef<real>{},
1638 &totalNumberOfBondedInteractions,
1640 (bGStat ? CGLO_GSTAT : 0) | (!EI_VV(ir->eI) && bCalcEner ? CGLO_ENERGY : 0)
1641 | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
1642 | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
1643 | (!EI_VV(ir->eI) ? CGLO_PRESSURE : 0) | CGLO_CONSTRAINT
1644 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
1646 checkNumberOfBondedInteractions(mdlog,
1648 totalNumberOfBondedInteractions,
1651 makeConstArrayRef(state->x),
1653 &shouldCheckNumberOfBondedInteractions);
1654 if (!EI_VV(ir->eI) && bStopCM)
1656 process_and_stopcm_grp(
1657 fplog, &vcm, *mdatoms, makeArrayRef(state->x), makeArrayRef(state->v));
1658 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
1660 // TODO: The special case of removing CM motion should be dealt more gracefully
1661 if (useGpuForUpdate)
1663 stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
1664 // Here we block until the H2D copy completes because event sync with the
1665 // force kernels that use the coordinates on the next steps is not implemented
1666 // (not because of a race on state->x being modified on the CPU while H2D is in progress).
1667 stateGpu->waitCoordinatesCopiedToDevice(AtomLocality::Local);
1668 // If the COM removal changed the velocities on the CPU, this has to be accounted for.
1669 if (vcm.mode != ecmNO)
1671 stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
1678 /* ############# END CALC EKIN AND PRESSURE ################# */
1680 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
1681 the virial that should probably be addressed eventually. state->veta has better properies,
1682 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
1683 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
1685 if (ir->efep != efepNO && !EI_VV(ir->eI))
1687 /* Sum up the foreign energy and dK/dl terms for md and sd.
1688 Currently done every step so that dH/dl is correct in the .edr */
1689 accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
1692 update_pcouple_after_coordinates(
1693 fplog, step, ir, mdatoms, pres, force_vir, shake_vir, pressureCouplingMu, state, nrnb, upd.deform(), !useGpuForUpdate);
1695 const bool doBerendsenPressureCoupling = (inputrec->epc == PressureCoupling::Berendsen
1696 && do_per_step(step, inputrec->nstpcouple));
1697 const bool doCRescalePressureCoupling = (inputrec->epc == PressureCoupling::CRescale
1698 && do_per_step(step, inputrec->nstpcouple));
1700 && (doBerendsenPressureCoupling || doCRescalePressureCoupling || doParrinelloRahman))
1702 integrator->scaleCoordinates(pressureCouplingMu);
1703 if (doCRescalePressureCoupling)
1705 matrix pressureCouplingInvMu;
1706 gmx::invertBoxMatrix(pressureCouplingMu, pressureCouplingInvMu);
1707 integrator->scaleVelocities(pressureCouplingInvMu);
1709 integrator->setPbc(PbcType::Xyz, state->box);
1712 /* ################# END UPDATE STEP 2 ################# */
1713 /* #### We now have r(t+dt) and v(t+dt/2) ############# */
1715 /* The coordinates (x) were unshifted in update */
1718 /* We will not sum ekinh_old,
1719 * so signal that we still have to do it.
1721 bSumEkinhOld = TRUE;
1726 /* ######### BEGIN PREPARING EDR OUTPUT ########### */
1728 /* use the directly determined last velocity, not actually the averaged half steps */
1729 if (bTrotter && ir->eI == eiVV)
1731 enerd->term[F_EKIN] = last_ekin;
1733 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
1735 if (integratorHasConservedEnergyQuantity(ir))
1739 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
1743 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + NPT_energy(ir, state, &MassQ);
1746 /* ######### END PREPARING EDR OUTPUT ########### */
1752 if (fplog && do_log && bDoExpanded)
1754 /* only needed if doing expanded ensemble */
1755 PrintFreeEnergyInfoToFile(fplog,
1758 ir->bSimTemp ? ir->simtempvals : nullptr,
1759 state_global->dfhist,
1766 energyOutput.addDataAtEnergyStep(bDoDHDL,
1774 PTCouplingArrays{ state->boxv,
1775 state->nosehoover_xi,
1776 state->nosehoover_vxi,
1778 state->nhpres_vxi },
1790 energyOutput.recordNonEnergyStep();
1793 gmx_bool do_dr = do_per_step(step, ir->nstdisreout);
1794 gmx_bool do_or = do_per_step(step, ir->nstorireout);
1796 if (doSimulatedAnnealing)
1798 gmx::EnergyOutput::printAnnealingTemperatures(
1799 do_log ? fplog : nullptr, groups, &(ir->opts));
1801 if (do_log || do_ene || do_dr || do_or)
1803 energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
1807 do_log ? fplog : nullptr,
1813 if (do_log && ir->bDoAwh && awh->hasFepLambdaDimension())
1815 const bool isInitialOutput = false;
1816 printLambdaStateToLog(fplog, state->lambda, isInitialOutput);
1821 pull_print_output(pull_work, step, t);
1824 if (do_per_step(step, ir->nstlog))
1826 if (fflush(fplog) != 0)
1828 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
1834 /* Have to do this part _after_ outputting the logfile and the edr file */
1835 /* Gets written into the state at the beginning of next loop*/
1836 state->fep_state = lamnew;
1838 else if (ir->bDoAwh && awh->needForeignEnergyDifferences(step))
1840 state->fep_state = awh->fepLambdaState();
1842 /* Print the remaining wall clock time for the run */
1843 if (isMasterSimMasterRank(ms, MASTER(cr)) && (do_verbose || gmx_got_usr_signal()) && !bPMETunePrinting)
1847 fprintf(stderr, "\n");
1849 print_time(stderr, walltime_accounting, step, ir, cr);
1852 /* Ion/water position swapping.
1853 * Not done in last step since trajectory writing happens before this call
1854 * in the MD loop and exchanges would be lost anyway. */
1855 bNeedRepartition = FALSE;
1856 if ((ir->eSwapCoords != eswapNO) && (step > 0) && !bLastStep && do_per_step(step, ir->swap->nstswap))
1858 bNeedRepartition = do_swapcoords(cr,
1864 as_rvec_array(state->x.data()),
1866 MASTER(cr) && mdrunOptions.verbose,
1869 if (bNeedRepartition && DOMAINDECOMP(cr))
1871 dd_collect_state(cr->dd, state, state_global);
1875 /* Replica exchange */
1879 bExchanged = replica_exchange(fplog, cr, ms, repl_ex, state_global, enerd, state, step, t);
1882 if ((bExchanged || bNeedRepartition) && DOMAINDECOMP(cr))
1884 dd_partition_system(fplog,
1905 shouldCheckNumberOfBondedInteractions = true;
1906 upd.setNumAtoms(state->natoms);
1912 /* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
1913 /* With all integrators, except VV, we need to retain the pressure
1914 * at the current step for coupling at the next step.
1916 if ((state->flags & (1U << estPRES_PREV))
1917 && (bGStatEveryStep || (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
1919 /* Store the pressure in t_state for pressure coupling
1920 * at the next MD step.
1922 copy_mat(pres, state->pres_prev);
1925 /* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
1927 if ((membed != nullptr) && (!bLastStep))
1929 rescale_membed(step_rel, membed, as_rvec_array(state_global->x.data()));
1932 cycles = wallcycle_stop(wcycle, ewcSTEP);
1933 if (DOMAINDECOMP(cr) && wcycle)
1935 dd_cycles_add(cr->dd, cycles, ddCyclStep);
1938 /* increase the MD step number */
1945 fcReportProgress(ir->nsteps + ir->init_step, step);
1949 resetHandler->resetCounters(
1950 step, step_rel, mdlog, fplog, cr, fr->nbv.get(), nrnb, fr->pmedata, pme_loadbal, wcycle, walltime_accounting);
1952 /* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
1953 imdSession->updateEnergyRecordAndSendPositionsAndEnergies(bInteractiveMDstep, step, bCalcEner);
1955 /* End of main MD loop */
1957 /* Closing TNG files can include compressing data. Therefore it is good to do that
1958 * before stopping the time measurements. */
1959 mdoutf_tng_close(outf);
1961 /* Stop measuring walltime */
1962 walltime_accounting_end_time(walltime_accounting);
1964 if (!thisRankHasDuty(cr, DUTY_PME))
1966 /* Tell the PME only node to finish */
1967 gmx_pme_send_finish(cr);
1972 if (ir->nstcalcenergy > 0)
1974 energyOutput.printEnergyConservation(fplog, ir->simulation_part, EI_MD(ir->eI));
1976 gmx::EnergyOutput::printAnnealingTemperatures(fplog, groups, &(ir->opts));
1977 energyOutput.printAverages(fplog, groups);
1984 pme_loadbal_done(pme_loadbal, fplog, mdlog, fr->nbv->useGpu());
1987 done_shellfc(fplog, shellfc, step_rel);
1989 if (useReplicaExchange && MASTER(cr))
1991 print_replica_exchange_statistics(fplog, repl_ex);
1994 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
1996 global_stat_destroy(gstat);