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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/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/vec.h"
77 #include "gromacs/math/vectypes.h"
78 #include "gromacs/mdlib/checkpointhandler.h"
79 #include "gromacs/mdlib/compute_io.h"
80 #include "gromacs/mdlib/constr.h"
81 #include "gromacs/mdlib/coupling.h"
82 #include "gromacs/mdlib/ebin.h"
83 #include "gromacs/mdlib/enerdata_utils.h"
84 #include "gromacs/mdlib/energyoutput.h"
85 #include "gromacs/mdlib/expanded.h"
86 #include "gromacs/mdlib/force.h"
87 #include "gromacs/mdlib/force_flags.h"
88 #include "gromacs/mdlib/forcerec.h"
89 #include "gromacs/mdlib/md_support.h"
90 #include "gromacs/mdlib/mdatoms.h"
91 #include "gromacs/mdlib/mdoutf.h"
92 #include "gromacs/mdlib/membed.h"
93 #include "gromacs/mdlib/resethandler.h"
94 #include "gromacs/mdlib/sighandler.h"
95 #include "gromacs/mdlib/simulationsignal.h"
96 #include "gromacs/mdlib/stat.h"
97 #include "gromacs/mdlib/stophandler.h"
98 #include "gromacs/mdlib/tgroup.h"
99 #include "gromacs/mdlib/trajectory_writing.h"
100 #include "gromacs/mdlib/update.h"
101 #include "gromacs/mdlib/update_constrain_gpu.h"
102 #include "gromacs/mdlib/vcm.h"
103 #include "gromacs/mdlib/vsite.h"
104 #include "gromacs/mdrunutility/handlerestart.h"
105 #include "gromacs/mdrunutility/multisim.h"
106 #include "gromacs/mdrunutility/printtime.h"
107 #include "gromacs/mdtypes/awh_history.h"
108 #include "gromacs/mdtypes/awh_params.h"
109 #include "gromacs/mdtypes/commrec.h"
110 #include "gromacs/mdtypes/df_history.h"
111 #include "gromacs/mdtypes/energyhistory.h"
112 #include "gromacs/mdtypes/fcdata.h"
113 #include "gromacs/mdtypes/forcerec.h"
114 #include "gromacs/mdtypes/group.h"
115 #include "gromacs/mdtypes/inputrec.h"
116 #include "gromacs/mdtypes/interaction_const.h"
117 #include "gromacs/mdtypes/md_enums.h"
118 #include "gromacs/mdtypes/mdatom.h"
119 #include "gromacs/mdtypes/mdrunoptions.h"
120 #include "gromacs/mdtypes/observableshistory.h"
121 #include "gromacs/mdtypes/pullhistory.h"
122 #include "gromacs/mdtypes/simulation_workload.h"
123 #include "gromacs/mdtypes/state.h"
124 #include "gromacs/mdtypes/state_propagator_data_gpu.h"
125 #include "gromacs/modularsimulator/energydata.h"
126 #include "gromacs/nbnxm/gpu_data_mgmt.h"
127 #include "gromacs/nbnxm/nbnxm.h"
128 #include "gromacs/pbcutil/pbc.h"
129 #include "gromacs/pulling/output.h"
130 #include "gromacs/pulling/pull.h"
131 #include "gromacs/swap/swapcoords.h"
132 #include "gromacs/timing/wallcycle.h"
133 #include "gromacs/timing/walltime_accounting.h"
134 #include "gromacs/topology/atoms.h"
135 #include "gromacs/topology/idef.h"
136 #include "gromacs/topology/mtop_util.h"
137 #include "gromacs/topology/topology.h"
138 #include "gromacs/trajectory/trajectoryframe.h"
139 #include "gromacs/utility/basedefinitions.h"
140 #include "gromacs/utility/cstringutil.h"
141 #include "gromacs/utility/fatalerror.h"
142 #include "gromacs/utility/logger.h"
143 #include "gromacs/utility/real.h"
144 #include "gromacs/utility/smalloc.h"
146 #include "legacysimulator.h"
147 #include "replicaexchange.h"
151 # include "corewrap.h"
154 using gmx::SimulationSignaller;
156 void gmx::LegacySimulator::do_md()
158 // TODO Historically, the EM and MD "integrators" used different
159 // names for the t_inputrec *parameter, but these must have the
160 // same name, now that it's a member of a struct. We use this ir
161 // alias to avoid a large ripple of nearly useless changes.
162 // t_inputrec is being replaced by IMdpOptionsProvider, so this
163 // will go away eventually.
164 t_inputrec* ir = inputrec;
165 int64_t step, step_rel;
166 double t, t0 = ir->init_t, lam0[efptNR];
167 gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, bCalcEner;
168 gmx_bool bNS = FALSE, bNStList, bStopCM, bFirstStep, bInitStep, bLastStep = FALSE;
169 gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
170 gmx_bool do_ene, do_log, do_verbose;
171 gmx_bool bMasterState;
172 unsigned int force_flags;
173 tensor force_vir = { { 0 } }, shake_vir = { { 0 } }, total_vir = { { 0 } }, pres = { { 0 } };
176 matrix pressureCouplingMu, M;
177 gmx_repl_ex_t repl_ex = nullptr;
178 PaddedHostVector<gmx::RVec> f{};
179 gmx_global_stat_t gstat;
180 gmx_shellfc_t* shellfc;
181 gmx_bool bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
182 gmx_bool bTemp, bPres, bTrotter;
184 std::vector<RVec> cbuf;
190 real saved_conserved_quantity = 0;
193 char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
195 /* PME load balancing data for GPU kernels */
196 gmx_bool bPMETune = FALSE;
197 gmx_bool bPMETunePrinting = FALSE;
199 bool bInteractiveMDstep = false;
201 /* Domain decomposition could incorrectly miss a bonded
202 interaction, but checking for that requires a global
203 communication stage, which does not otherwise happen in DD
204 code. So we do that alongside the first global energy reduction
205 after a new DD is made. These variables handle whether the
206 check happens, and the result it returns. */
207 bool shouldCheckNumberOfBondedInteractions = false;
208 int totalNumberOfBondedInteractions = -1;
210 SimulationSignals signals;
211 // Most global communnication stages don't propagate mdrun
212 // signals, and will use this object to achieve that.
213 SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
215 if (!mdrunOptions.writeConfout)
217 // This is on by default, and the main known use case for
218 // turning it off is for convenience in benchmarking, which is
219 // something that should not show up in the general user
224 "The -noconfout functionality is deprecated, and may be removed in a "
228 /* md-vv uses averaged full step velocities for T-control
229 md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
230 md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
231 bTrotter = (EI_VV(ir->eI)
232 && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir) || inputrecNvtTrotter(ir)));
234 const bool bRerunMD = false;
236 int nstglobalcomm = computeGlobalCommunicationPeriod(mdlog, ir, cr);
237 bGStatEveryStep = (nstglobalcomm == 1);
239 const SimulationGroups* groups = &top_global->groups;
241 std::unique_ptr<EssentialDynamics> ed = nullptr;
242 if (opt2bSet("-ei", nfile, fnm))
244 /* Initialize essential dynamics sampling */
245 ed = init_edsam(mdlog, opt2fn_null("-ei", nfile, fnm), opt2fn("-eo", nfile, fnm), top_global,
246 ir, cr, constr, state_global, observablesHistory, oenv, startingBehavior);
248 else if (observablesHistory->edsamHistory)
251 "The checkpoint is from a run with essential dynamics sampling, "
252 "but the current run did not specify the -ei option. "
253 "Either specify the -ei option to mdrun, or do not use this checkpoint file.");
256 int* fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
257 gmx::ArrayRef<real> lambda = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
258 initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda, lam0);
259 Update upd(*ir, deform);
260 const bool doSimulatedAnnealing = initSimulatedAnnealing(ir, &upd);
261 const bool useReplicaExchange = (replExParams.exchangeInterval > 0);
263 const t_fcdata& fcdata = fr->listedForces->fcdata();
265 bool simulationsShareState = false;
266 int nstSignalComm = nstglobalcomm;
268 // TODO This implementation of ensemble orientation restraints is nasty because
269 // a user can't just do multi-sim with single-sim orientation restraints.
270 bool usingEnsembleRestraints =
271 (fcdata.disres->nsystems > 1) || ((ms != nullptr) && (fcdata.orires->nr != 0));
272 bool awhUsesMultiSim = (ir->bDoAwh && ir->awhParams->shareBiasMultisim && (ms != nullptr));
274 // Replica exchange, ensemble restraints and AWH need all
275 // simulations to remain synchronized, so they need
276 // checkpoints and stop conditions to act on the same step, so
277 // the propagation of such signals must take place between
278 // simulations, not just within simulations.
279 // TODO: Make algorithm initializers set these flags.
280 simulationsShareState = useReplicaExchange || usingEnsembleRestraints || awhUsesMultiSim;
282 if (simulationsShareState)
284 // Inter-simulation signal communication does not need to happen
285 // often, so we use a minimum of 200 steps to reduce overhead.
286 const int c_minimumInterSimulationSignallingInterval = 200;
287 nstSignalComm = ((c_minimumInterSimulationSignallingInterval + nstglobalcomm - 1) / nstglobalcomm)
292 if (startingBehavior != StartingBehavior::RestartWithAppending)
294 pleaseCiteCouplingAlgorithms(fplog, *ir);
297 init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, mdModulesNotifier, ir,
298 top_global, oenv, wcycle, startingBehavior, simulationsShareState, ms);
299 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work,
300 mdoutf_get_fp_dhdl(outf), false, startingBehavior, mdModulesNotifier);
302 gstat = global_stat_init(ir);
304 /* Check for polarizable models and flexible constraints */
305 shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
306 ir->nstcalcenergy, DOMAINDECOMP(cr));
309 double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
310 if ((io > 2000) && MASTER(cr))
312 fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
316 // Local state only becomes valid now.
317 std::unique_ptr<t_state> stateInstance;
321 gmx_localtop_t top(top_global->ffparams);
323 auto mdatoms = mdAtoms->mdatoms();
325 std::unique_ptr<UpdateConstrainGpu> integrator;
327 if (DOMAINDECOMP(cr))
329 stateInstance = std::make_unique<t_state>();
330 state = stateInstance.get();
331 dd_init_local_state(cr->dd, state_global, state);
333 /* Distribute the charge groups over the nodes from the master node */
334 dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
335 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
336 nrnb, nullptr, FALSE);
337 shouldCheckNumberOfBondedInteractions = true;
338 upd.setNumAtoms(state->natoms);
342 state_change_natoms(state_global, state_global->natoms);
343 /* Copy the pointer to the global state */
344 state = state_global;
346 /* Generate and initialize new topology */
347 mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
349 upd.setNumAtoms(state->natoms);
352 const auto& simulationWork = runScheduleWork->simulationWork;
353 const bool useGpuForPme = simulationWork.useGpuPme;
354 const bool useGpuForNonbonded = simulationWork.useGpuNonbonded;
355 const bool useGpuForBufferOps = simulationWork.useGpuBufferOps;
356 const bool useGpuForUpdate = simulationWork.useGpuUpdate;
358 StatePropagatorDataGpu* stateGpu = fr->stateGpu;
360 // TODO: the assertions below should be handled by UpdateConstraintsBuilder.
363 GMX_RELEASE_ASSERT(!DOMAINDECOMP(cr) || ddUsesUpdateGroups(*cr->dd) || constr == nullptr
364 || constr->numConstraintsTotal() == 0,
365 "Constraints in domain decomposition are only supported with update "
366 "groups if using GPU update.\n");
367 GMX_RELEASE_ASSERT(ir->eConstrAlg != econtSHAKE || constr == nullptr
368 || constr->numConstraintsTotal() == 0,
369 "SHAKE is not supported with GPU update.");
370 GMX_RELEASE_ASSERT(useGpuForPme || (useGpuForNonbonded && simulationWork.useGpuBufferOps),
371 "Either PME or short-ranged non-bonded interaction tasks must run on "
372 "the GPU to use GPU update.\n");
373 GMX_RELEASE_ASSERT(ir->eI == eiMD,
374 "Only the md integrator is supported with the GPU update.\n");
376 ir->etc != etcNOSEHOOVER,
377 "Nose-Hoover temperature coupling is not supported with the GPU update.\n");
378 GMX_RELEASE_ASSERT(ir->epc == epcNO || ir->epc == epcPARRINELLORAHMAN || ir->epc == epcBERENDSEN,
379 "Only Parrinello-Rahman and Berendsen pressure coupling are supported "
380 "with the GPU update.\n");
381 GMX_RELEASE_ASSERT(!mdatoms->haveVsites,
382 "Virtual sites are not supported with the GPU update.\n");
383 GMX_RELEASE_ASSERT(ed == nullptr,
384 "Essential dynamics is not supported with the GPU update.\n");
385 GMX_RELEASE_ASSERT(!ir->bPull || !pull_have_constraint(ir->pull),
386 "Constraints pulling is not supported with the GPU update.\n");
387 GMX_RELEASE_ASSERT(fcdata.orires->nr == 0,
388 "Orientation restraints are not supported with the GPU update.\n");
391 || (!haveFreeEnergyType(*ir, efptBONDED) && !haveFreeEnergyType(*ir, efptMASS)),
392 "Free energy perturbation of masses and constraints are not supported with the GPU "
395 if (constr != nullptr && constr->numConstraintsTotal() > 0)
399 .appendText("Updating coordinates and applying constraints on the GPU.");
403 GMX_LOG(mdlog.info).asParagraph().appendText("Updating coordinates on the GPU.");
405 GMX_RELEASE_ASSERT(fr->deviceStreamManager != nullptr,
406 "Device stream manager should be initialized in order to use GPU "
407 "update-constraints.");
409 fr->deviceStreamManager->streamIsValid(gmx::DeviceStreamType::UpdateAndConstraints),
410 "Update stream should be initialized in order to use GPU "
411 "update-constraints.");
412 integrator = std::make_unique<UpdateConstrainGpu>(
413 *ir, *top_global, fr->deviceStreamManager->context(),
414 fr->deviceStreamManager->stream(gmx::DeviceStreamType::UpdateAndConstraints),
415 stateGpu->xUpdatedOnDevice());
417 integrator->setPbc(PbcType::Xyz, state->box);
420 if (useGpuForPme || (useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
422 changePinningPolicy(&state->x, PinningPolicy::PinnedIfSupported);
424 if ((useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
426 changePinningPolicy(&f, PinningPolicy::PinnedIfSupported);
430 changePinningPolicy(&state->v, PinningPolicy::PinnedIfSupported);
433 // NOTE: The global state is no longer used at this point.
434 // But state_global is still used as temporary storage space for writing
435 // the global state to file and potentially for replica exchange.
436 // (Global topology should persist.)
438 update_mdatoms(mdatoms, state->lambda[efptMASS]);
442 /* Check nstexpanded here, because the grompp check was broken */
443 if (ir->expandedvals->nstexpanded % ir->nstcalcenergy != 0)
446 "With expanded ensemble, nstexpanded should be a multiple of nstcalcenergy");
448 init_expanded_ensemble(startingBehavior != StartingBehavior::NewSimulation, ir, state->dfhist);
453 EnergyData::initializeEnergyHistory(startingBehavior, observablesHistory, &energyOutput);
456 preparePrevStepPullCom(ir, pull_work, mdatoms->massT, state, state_global, cr,
457 startingBehavior != StartingBehavior::NewSimulation);
459 // TODO: Remove this by converting AWH into a ForceProvider
460 auto awh = prepareAwhModule(fplog, *ir, state_global, cr, ms,
461 startingBehavior != StartingBehavior::NewSimulation,
462 shellfc != nullptr, opt2fn("-awh", nfile, fnm), pull_work);
464 if (useReplicaExchange && MASTER(cr))
466 repl_ex = init_replica_exchange(fplog, ms, top_global->natoms, ir, replExParams);
468 /* PME tuning is only supported in the Verlet scheme, with PME for
469 * Coulomb. It is not supported with only LJ PME. */
470 bPMETune = (mdrunOptions.tunePme && EEL_PME(fr->ic->eeltype) && !mdrunOptions.reproducible
471 && ir->cutoff_scheme != ecutsGROUP);
473 pme_load_balancing_t* pme_loadbal = nullptr;
476 pme_loadbal_init(&pme_loadbal, cr, mdlog, *ir, state->box, *fr->ic, *fr->nbv, fr->pmedata,
480 if (!ir->bContinuation)
482 if (state->flags & (1U << estV))
484 auto v = makeArrayRef(state->v);
485 /* Set the velocities of vsites, shells and frozen atoms to zero */
486 for (i = 0; i < mdatoms->homenr; i++)
488 if (mdatoms->ptype[i] == eptVSite || mdatoms->ptype[i] == eptShell)
492 else if (mdatoms->cFREEZE)
494 for (m = 0; m < DIM; m++)
496 if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
507 /* Constrain the initial coordinates and velocities */
508 do_constrain_first(fplog, constr, ir, mdatoms->nr, mdatoms->homenr,
509 state->x.arrayRefWithPadding(), state->v.arrayRefWithPadding(),
510 state->box, state->lambda[efptBONDED]);
514 /* Construct the virtual sites for the initial configuration */
515 vsite->construct(state->x, ir->delta_t, {}, state->box);
519 if (ir->efep != efepNO)
521 /* Set free energy calculation frequency as the greatest common
522 * denominator of nstdhdl and repl_ex_nst. */
523 nstfep = ir->fepvals->nstdhdl;
526 nstfep = std::gcd(ir->expandedvals->nstexpanded, nstfep);
528 if (useReplicaExchange)
530 nstfep = std::gcd(replExParams.exchangeInterval, nstfep);
534 /* Be REALLY careful about what flags you set here. You CANNOT assume
535 * this is the first step, since we might be restarting from a checkpoint,
536 * and in that case we should not do any modifications to the state.
538 bStopCM = (ir->comm_mode != ecmNO && !ir->bContinuation);
540 // When restarting from a checkpoint, it can be appropriate to
541 // initialize ekind from quantities in the checkpoint. Otherwise,
542 // compute_globals must initialize ekind before the simulation
543 // starts/restarts. However, only the master rank knows what was
544 // found in the checkpoint file, so we have to communicate in
545 // order to coordinate the restart.
547 // TODO Consider removing this communication if/when checkpoint
548 // reading directly follows .tpr reading, because all ranks can
549 // agree on hasReadEkinState at that time.
550 bool hasReadEkinState = MASTER(cr) ? state_global->ekinstate.hasReadEkinState : false;
553 gmx_bcast(sizeof(hasReadEkinState), &hasReadEkinState, cr->mpi_comm_mygroup);
555 if (hasReadEkinState)
557 restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
560 unsigned int cglo_flags =
561 (CGLO_TEMPERATURE | CGLO_GSTAT | (EI_VV(ir->eI) ? CGLO_PRESSURE : 0)
562 | (EI_VV(ir->eI) ? CGLO_CONSTRAINT : 0) | (hasReadEkinState ? CGLO_READEKIN : 0));
564 bSumEkinhOld = FALSE;
566 t_vcm vcm(top_global->groups, *ir);
567 reportComRemovalInfo(fplog, vcm);
569 /* To minimize communication, compute_globals computes the COM velocity
570 * and the kinetic energy for the velocities without COM motion removed.
571 * Thus to get the kinetic energy without the COM contribution, we need
572 * to call compute_globals twice.
574 for (int cgloIteration = 0; cgloIteration < (bStopCM ? 2 : 1); cgloIteration++)
576 unsigned int cglo_flags_iteration = cglo_flags;
577 if (bStopCM && cgloIteration == 0)
579 cglo_flags_iteration |= CGLO_STOPCM;
580 cglo_flags_iteration &= ~CGLO_TEMPERATURE;
582 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
583 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
584 enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
585 state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
587 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
589 if (cglo_flags_iteration & CGLO_STOPCM)
591 /* At initialization, do not pass x with acceleration-correction mode
592 * to avoid (incorrect) correction of the initial coordinates.
594 auto x = (vcm.mode == ecmLINEAR_ACCELERATION_CORRECTION) ? ArrayRef<RVec>()
595 : makeArrayRef(state->x);
596 process_and_stopcm_grp(fplog, &vcm, *mdatoms, x, makeArrayRef(state->v));
597 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
600 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
601 makeConstArrayRef(state->x), state->box,
602 &shouldCheckNumberOfBondedInteractions);
603 if (ir->eI == eiVVAK)
605 /* a second call to get the half step temperature initialized as well */
606 /* we do the same call as above, but turn the pressure off -- internally to
607 compute_globals, this is recognized as a velocity verlet half-step
608 kinetic energy calculation. This minimized excess variables, but
609 perhaps loses some logic?*/
611 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
612 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
613 enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
614 state->box, nullptr, &bSumEkinhOld, cglo_flags & ~CGLO_PRESSURE);
617 /* Calculate the initial half step temperature, and save the ekinh_old */
618 if (startingBehavior == StartingBehavior::NewSimulation)
620 for (i = 0; (i < ir->opts.ngtc); i++)
622 copy_mat(ekind->tcstat[i].ekinh, ekind->tcstat[i].ekinh_old);
626 /* need to make an initiation call to get the Trotter variables set, as well as other constants
627 for non-trotter temperature control */
628 auto trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
632 if (!ir->bContinuation)
634 if (constr && ir->eConstrAlg == econtLINCS)
636 fprintf(fplog, "RMS relative constraint deviation after constraining: %.2e\n",
639 if (EI_STATE_VELOCITY(ir->eI))
641 real temp = enerd->term[F_TEMP];
644 /* Result of Ekin averaged over velocities of -half
645 * and +half step, while we only have -half step here.
649 fprintf(fplog, "Initial temperature: %g K\n", temp);
654 fprintf(stderr, "starting mdrun '%s'\n", *(top_global->name));
657 sprintf(tbuf, "%8.1f", (ir->init_step + ir->nsteps) * ir->delta_t);
661 sprintf(tbuf, "%s", "infinite");
663 if (ir->init_step > 0)
665 fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
666 gmx_step_str(ir->init_step + ir->nsteps, sbuf), tbuf,
667 gmx_step_str(ir->init_step, sbuf2), ir->init_step * ir->delta_t);
671 fprintf(stderr, "%s steps, %s ps.\n", gmx_step_str(ir->nsteps, sbuf), tbuf);
673 fprintf(fplog, "\n");
676 walltime_accounting_start_time(walltime_accounting);
677 wallcycle_start(wcycle, ewcRUN);
678 print_start(fplog, cr, walltime_accounting, "mdrun");
681 /* safest point to do file checkpointing is here. More general point would be immediately before integrator call */
682 int chkpt_ret = fcCheckPointParallel(cr->nodeid, NULL, 0);
685 gmx_fatal(3, __FILE__, __LINE__, "Checkpoint error on step %d\n", 0);
689 /***********************************************************
693 ************************************************************/
696 /* Skip the first Nose-Hoover integration when we get the state from tpx */
697 bInitStep = startingBehavior == StartingBehavior::NewSimulation || EI_VV(ir->eI);
698 bSumEkinhOld = FALSE;
700 bNeedRepartition = FALSE;
702 step = ir->init_step;
705 auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
706 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), simulationsShareState,
707 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstSignalComm,
708 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
710 auto checkpointHandler = std::make_unique<CheckpointHandler>(
711 compat::make_not_null<SimulationSignal*>(&signals[eglsCHKPT]), simulationsShareState,
712 ir->nstlist == 0, MASTER(cr), mdrunOptions.writeConfout,
713 mdrunOptions.checkpointOptions.period);
715 const bool resetCountersIsLocal = true;
716 auto resetHandler = std::make_unique<ResetHandler>(
717 compat::make_not_null<SimulationSignal*>(&signals[eglsRESETCOUNTERS]),
718 !resetCountersIsLocal, ir->nsteps, MASTER(cr), mdrunOptions.timingOptions.resetHalfway,
719 mdrunOptions.maximumHoursToRun, mdlog, wcycle, walltime_accounting);
721 const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
723 if (MASTER(cr) && isMultiSim(ms) && !useReplicaExchange)
725 logInitialMultisimStatus(ms, cr, mdlog, simulationsShareState, ir->nsteps, ir->init_step);
728 /* and stop now if we should */
729 bLastStep = (bLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
733 /* Determine if this is a neighbor search step */
734 bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
736 if (bPMETune && bNStList)
738 // This has to be here because PME load balancing is called so early.
739 // TODO: Move to after all booleans are defined.
740 if (useGpuForUpdate && !bFirstStep)
742 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
743 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
745 /* PME grid + cut-off optimization with GPUs or PME nodes */
746 pme_loadbal_do(pme_loadbal, cr, (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
747 fplog, mdlog, *ir, fr, state->box, state->x, wcycle, step, step_rel,
748 &bPMETunePrinting, simulationWork.useGpuPmePpCommunication);
751 wallcycle_start(wcycle, ewcSTEP);
753 bLastStep = (step_rel == ir->nsteps);
754 t = t0 + step * ir->delta_t;
756 // TODO Refactor this, so that nstfep does not need a default value of zero
757 if (ir->efep != efepNO || ir->bSimTemp)
759 /* find and set the current lambdas */
760 setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
762 bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
763 bDoFEP = ((ir->efep != efepNO) && do_per_step(step, nstfep));
764 bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded) && (ir->bExpanded)
768 bDoReplEx = (useReplicaExchange && (step > 0) && !bLastStep
769 && do_per_step(step, replExParams.exchangeInterval));
771 if (doSimulatedAnnealing)
773 update_annealing_target_temp(ir, t, &upd);
776 /* Stop Center of Mass motion */
777 bStopCM = (ir->comm_mode != ecmNO && do_per_step(step, ir->nstcomm));
779 /* Determine whether or not to do Neighbour Searching */
780 bNS = (bFirstStep || bNStList || bExchanged || bNeedRepartition);
782 /* Note that the stopHandler will cause termination at nstglobalcomm
783 * steps. Since this concides with nstcalcenergy, nsttcouple and/or
784 * nstpcouple steps, we have computed the half-step kinetic energy
785 * of the previous step and can always output energies at the last step.
787 bLastStep = bLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
789 /* do_log triggers energy and virial calculation. Because this leads
790 * to different code paths, forces can be different. Thus for exact
791 * continuation we should avoid extra log output.
792 * Note that the || bLastStep can result in non-exact continuation
793 * beyond the last step. But we don't consider that to be an issue.
795 do_log = (do_per_step(step, ir->nstlog)
796 || (bFirstStep && startingBehavior == StartingBehavior::NewSimulation) || bLastStep);
797 do_verbose = mdrunOptions.verbose
798 && (step % mdrunOptions.verboseStepPrintInterval == 0 || bFirstStep || bLastStep);
800 if (useGpuForUpdate && !bFirstStep && bNS)
802 // Copy velocities from the GPU on search steps to keep a copy on host (device buffers are reinitialized).
803 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
804 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
805 // Copy coordinate from the GPU when needed at the search step.
806 // NOTE: The cases when coordinates needed on CPU for force evaluation are handled in sim_utils.
807 // NOTE: If the coordinates are to be written into output file they are also copied separately before the output.
808 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
809 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
812 if (bNS && !(bFirstStep && ir->bContinuation))
814 bMasterState = FALSE;
815 /* Correct the new box if it is too skewed */
816 if (inputrecDynamicBox(ir))
818 if (correct_box(fplog, step, state->box))
821 // If update is offloaded, it should be informed about the box size change
824 integrator->setPbc(PbcType::Xyz, state->box);
828 if (DOMAINDECOMP(cr) && bMasterState)
830 dd_collect_state(cr->dd, state, state_global);
833 if (DOMAINDECOMP(cr))
835 /* Repartition the domain decomposition */
836 dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
837 *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
838 fr, vsite, constr, nrnb, wcycle, do_verbose && !bPMETunePrinting);
839 shouldCheckNumberOfBondedInteractions = true;
840 upd.setNumAtoms(state->natoms);
842 // Allocate or re-size GPU halo exchange object, if necessary
843 if (havePPDomainDecomposition(cr) && simulationWork.useGpuHaloExchange
844 && useGpuForNonbonded && is1D(*cr->dd))
846 GMX_RELEASE_ASSERT(fr->deviceStreamManager != nullptr,
847 "GPU device manager has to be initialized to use GPU "
848 "version of halo exchange.");
849 // TODO remove need to pass local stream into GPU halo exchange - Issue #3093
850 constructGpuHaloExchange(mdlog, *cr, *fr->deviceStreamManager, wcycle);
855 if (MASTER(cr) && do_log)
857 gmx::EnergyOutput::printHeader(fplog, step,
858 t); /* can we improve the information printed here? */
861 if (ir->efep != efepNO)
863 update_mdatoms(mdatoms, state->lambda[efptMASS]);
869 /* We need the kinetic energy at minus the half step for determining
870 * the full step kinetic energy and possibly for T-coupling.*/
871 /* This may not be quite working correctly yet . . . . */
872 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
873 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
874 enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
875 state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
876 CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
877 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
878 &top, makeConstArrayRef(state->x), state->box,
879 &shouldCheckNumberOfBondedInteractions);
881 clear_mat(force_vir);
883 checkpointHandler->decideIfCheckpointingThisStep(bNS, bFirstStep, bLastStep);
885 /* Determine the energy and pressure:
886 * at nstcalcenergy steps and at energy output steps (set below).
888 if (EI_VV(ir->eI) && (!bInitStep))
890 bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
891 bCalcVir = bCalcEnerStep
893 && (do_per_step(step, ir->nstpcouple) || do_per_step(step - 1, ir->nstpcouple)));
897 bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
898 bCalcVir = bCalcEnerStep || (ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
900 bCalcEner = bCalcEnerStep;
902 do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
904 if (do_ene || do_log || bDoReplEx)
910 /* Do we need global communication ? */
911 bGStat = (bCalcVir || bCalcEner || bStopCM || do_per_step(step, nstglobalcomm)
912 || (EI_VV(ir->eI) && inputrecNvtTrotter(ir) && do_per_step(step - 1, nstglobalcomm)));
914 force_flags = (GMX_FORCE_STATECHANGED | ((inputrecDynamicBox(ir)) ? GMX_FORCE_DYNAMICBOX : 0)
915 | GMX_FORCE_ALLFORCES | (bCalcVir ? GMX_FORCE_VIRIAL : 0)
916 | (bCalcEner ? GMX_FORCE_ENERGY : 0) | (bDoFEP ? GMX_FORCE_DHDL : 0));
920 /* Now is the time to relax the shells */
921 relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
922 imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
923 state->natoms, state->x.arrayRefWithPadding(),
924 state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
925 f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, shellfc,
926 fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
930 /* The AWH history need to be saved _before_ doing force calculations where the AWH bias
931 is updated (or the AWH update will be performed twice for one step when continuing).
932 It would be best to call this update function from do_md_trajectory_writing but that
933 would occur after do_force. One would have to divide the update_awh function into one
934 function applying the AWH force and one doing the AWH bias update. The update AWH
935 bias function could then be called after do_md_trajectory_writing (then containing
936 update_awh_history). The checkpointing will in the future probably moved to the start
937 of the md loop which will rid of this issue. */
938 if (awh && checkpointHandler->isCheckpointingStep() && MASTER(cr))
940 awh->updateHistory(state_global->awhHistory.get());
943 /* The coordinates (x) are shifted (to get whole molecules)
945 * This is parallellized as well, and does communication too.
946 * Check comments in sim_util.c
948 do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step,
949 nrnb, wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
950 f.arrayRefWithPadding(), force_vir, mdatoms, enerd, state->lambda, fr,
951 runScheduleWork, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
952 (bNS ? GMX_FORCE_NS : 0) | force_flags, ddBalanceRegionHandler);
955 // VV integrators do not need the following velocity half step
956 // if it is the first step after starting from a checkpoint.
957 // That is, the half step is needed on all other steps, and
958 // also the first step when starting from a .tpr file.
959 if (EI_VV(ir->eI) && (!bFirstStep || startingBehavior == StartingBehavior::NewSimulation))
960 /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
962 rvec* vbuf = nullptr;
964 wallcycle_start(wcycle, ewcUPDATE);
965 if (ir->eI == eiVV && bInitStep)
967 /* if using velocity verlet with full time step Ekin,
968 * take the first half step only to compute the
969 * virial for the first step. From there,
970 * revert back to the initial coordinates
971 * so that the input is actually the initial step.
973 snew(vbuf, state->natoms);
974 copy_rvecn(state->v.rvec_array(), vbuf, 0,
975 state->natoms); /* should make this better for parallelizing? */
979 /* this is for NHC in the Ekin(t+dt/2) version of vv */
980 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ,
981 trotter_seq, ettTSEQ1);
984 upd.update_coords(*ir, step, mdatoms, state, f.arrayRefWithPadding(), fcdata, ekind, M,
985 etrtVELOCITY1, cr, constr != nullptr);
987 wallcycle_stop(wcycle, ewcUPDATE);
988 constrain_velocities(constr, do_log, do_ene, step, state, nullptr, bCalcVir, shake_vir);
989 wallcycle_start(wcycle, ewcUPDATE);
990 /* if VV, compute the pressure and constraints */
991 /* For VV2, we strictly only need this if using pressure
992 * control, but we really would like to have accurate pressures
994 * Think about ways around this in the future?
995 * For now, keep this choice in comments.
997 /*bPres = (ir->eI==eiVV || inputrecNptTrotter(ir)); */
998 /*bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK && inputrecNptTrotter(ir)));*/
1000 bTemp = ((ir->eI == eiVV && (!bInitStep)) || (ir->eI == eiVVAK));
1001 if (bCalcEner && ir->eI == eiVVAK)
1003 bSumEkinhOld = TRUE;
1005 /* for vv, the first half of the integration actually corresponds to the previous step.
1006 So we need information from the last step in the first half of the integration */
1007 if (bGStat || do_per_step(step - 1, nstglobalcomm))
1009 wallcycle_stop(wcycle, ewcUPDATE);
1010 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
1011 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
1012 enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
1013 state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
1014 (bGStat ? CGLO_GSTAT : 0) | (bCalcEner ? CGLO_ENERGY : 0)
1015 | (bTemp ? CGLO_TEMPERATURE : 0) | (bPres ? CGLO_PRESSURE : 0)
1016 | (bPres ? CGLO_CONSTRAINT : 0) | (bStopCM ? CGLO_STOPCM : 0)
1017 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
1020 /* explanation of above:
1021 a) We compute Ekin at the full time step
1022 if 1) we are using the AveVel Ekin, and it's not the
1023 initial step, or 2) if we are using AveEkin, but need the full
1024 time step kinetic energy for the pressure (always true now, since we want accurate statistics).
1025 b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
1026 EkinAveVel because it's needed for the pressure */
1027 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
1028 top_global, &top, makeConstArrayRef(state->x),
1029 state->box, &shouldCheckNumberOfBondedInteractions);
1032 process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
1033 makeArrayRef(state->v));
1034 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
1036 wallcycle_start(wcycle, ewcUPDATE);
1038 /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
1043 m_add(force_vir, shake_vir,
1044 total_vir); /* we need the un-dispersion corrected total vir here */
1045 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ,
1046 trotter_seq, ettTSEQ2);
1048 /* TODO This is only needed when we're about to write
1049 * a checkpoint, because we use it after the restart
1050 * (in a kludge?). But what should we be doing if
1051 * the startingBehavior is NewSimulation or bInitStep are true? */
1052 if (inputrecNptTrotter(ir) || inputrecNphTrotter(ir))
1054 copy_mat(shake_vir, state->svir_prev);
1055 copy_mat(force_vir, state->fvir_prev);
1057 if (inputrecNvtTrotter(ir) && ir->eI == eiVV)
1059 /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
1060 enerd->term[F_TEMP] =
1061 sum_ekin(&(ir->opts), ekind, nullptr, (ir->eI == eiVV), FALSE);
1062 enerd->term[F_EKIN] = trace(ekind->ekin);
1065 else if (bExchanged)
1067 wallcycle_stop(wcycle, ewcUPDATE);
1068 /* We need the kinetic energy at minus the half step for determining
1069 * the full step kinetic energy and possibly for T-coupling.*/
1070 /* This may not be quite working correctly yet . . . . */
1071 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
1072 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
1073 enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
1074 state->box, nullptr, &bSumEkinhOld, CGLO_GSTAT | CGLO_TEMPERATURE);
1075 wallcycle_start(wcycle, ewcUPDATE);
1078 /* if it's the initial step, we performed this first step just to get the constraint virial */
1079 if (ir->eI == eiVV && bInitStep)
1081 copy_rvecn(vbuf, state->v.rvec_array(), 0, state->natoms);
1084 wallcycle_stop(wcycle, ewcUPDATE);
1087 /* compute the conserved quantity */
1090 saved_conserved_quantity = NPT_energy(ir, state, &MassQ);
1093 last_ekin = enerd->term[F_EKIN];
1095 if ((ir->eDispCorr != edispcEnerPres) && (ir->eDispCorr != edispcAllEnerPres))
1097 saved_conserved_quantity -= enerd->term[F_DISPCORR];
1099 /* sum up the foreign kinetic energy and dK/dl terms for vv. currently done every step so that dhdl is correct in the .edr */
1100 if (ir->efep != efepNO)
1102 accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
1106 /* ######## END FIRST UPDATE STEP ############## */
1107 /* ######## If doing VV, we now have v(dt) ###### */
1110 /* perform extended ensemble sampling in lambda - we don't
1111 actually move to the new state before outputting
1112 statistics, but if performing simulated tempering, we
1113 do update the velocities and the tau_t. */
1115 lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, state->fep_state,
1116 state->dfhist, step, state->v.rvec_array(), mdatoms);
1117 /* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
1120 copy_df_history(state_global->dfhist, state->dfhist);
1124 // Copy coordinate from the GPU for the output/checkpointing if the update is offloaded and
1125 // coordinates have not already been copied for i) search or ii) CPU force tasks.
1126 if (useGpuForUpdate && !bNS && !runScheduleWork->domainWork.haveCpuLocalForceWork
1127 && (do_per_step(step, ir->nstxout) || do_per_step(step, ir->nstxout_compressed)
1128 || checkpointHandler->isCheckpointingStep()))
1130 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
1131 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
1133 // Copy velocities if needed for the output/checkpointing.
1134 // NOTE: Copy on the search steps is done at the beginning of the step.
1135 if (useGpuForUpdate && !bNS
1136 && (do_per_step(step, ir->nstvout) || checkpointHandler->isCheckpointingStep()))
1138 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
1139 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
1141 // Copy forces for the output if the forces were reduced on the GPU (not the case on virial steps)
1142 // and update is offloaded hence forces are kept on the GPU for update and have not been
1143 // already transferred in do_force().
1144 // TODO: There should be an improved, explicit mechanism that ensures this copy is only executed
1145 // when the forces are ready on the GPU -- the same synchronizer should be used as the one
1146 // prior to GPU update.
1147 // TODO: When the output flags will be included in step workload, this copy can be combined with the
1148 // copy call in do_force(...).
1149 // NOTE: The forces should not be copied here if the vsites are present, since they were modified
1150 // on host after the D2H copy in do_force(...).
1151 if (runScheduleWork->stepWork.useGpuFBufferOps && (simulationWork.useGpuUpdate && !vsite)
1152 && do_per_step(step, ir->nstfout))
1154 stateGpu->copyForcesFromGpu(ArrayRef<RVec>(f), AtomLocality::Local);
1155 stateGpu->waitForcesReadyOnHost(AtomLocality::Local);
1157 /* Now we have the energies and forces corresponding to the
1158 * coordinates at time t. We must output all of this before
1161 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state, state_global,
1162 observablesHistory, top_global, fr, outf, energyOutput, ekind, f,
1163 checkpointHandler->isCheckpointingStep(), bRerunMD, bLastStep,
1164 mdrunOptions.writeConfout, bSumEkinhOld);
1165 /* Check if IMD step and do IMD communication, if bIMD is TRUE. */
1166 bInteractiveMDstep = imdSession->run(step, bNS, state->box, state->x.rvec_array(), t);
1168 /* kludge -- virial is lost with restart for MTTK NPT control. Must reload (saved earlier). */
1169 if (startingBehavior != StartingBehavior::NewSimulation && bFirstStep
1170 && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir)))
1172 copy_mat(state->svir_prev, shake_vir);
1173 copy_mat(state->fvir_prev, force_vir);
1176 stopHandler->setSignal();
1177 resetHandler->setSignal(walltime_accounting);
1179 if (bGStat || !PAR(cr))
1181 /* In parallel we only have to check for checkpointing in steps
1182 * where we do global communication,
1183 * otherwise the other nodes don't know.
1185 checkpointHandler->setSignal(walltime_accounting);
1188 /* ######### START SECOND UPDATE STEP ################# */
1190 /* at the start of step, randomize or scale the velocities ((if vv. Restriction of Andersen
1191 controlled in preprocessing */
1193 if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
1195 gmx_bool bIfRandomize;
1196 bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
1197 /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
1198 if (constr && bIfRandomize)
1200 constrain_velocities(constr, do_log, do_ene, step, state, nullptr, false, nullptr);
1203 /* Box is changed in update() when we do pressure coupling,
1204 * but we should still use the old box for energy corrections and when
1205 * writing it to the energy file, so it matches the trajectory files for
1206 * the same timestep above. Make a copy in a separate array.
1208 copy_mat(state->box, lastbox);
1212 wallcycle_start(wcycle, ewcUPDATE);
1213 /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
1216 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
1217 /* We can only do Berendsen coupling after we have summed
1218 * the kinetic energy or virial. Since the happens
1219 * in global_state after update, we should only do it at
1220 * step % nstlist = 1 with bGStatEveryStep=FALSE.
1225 update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
1226 update_pcouple_before_coordinates(fplog, step, ir, state, pressureCouplingMu, M, bInitStep);
1231 /* velocity half-step update */
1232 upd.update_coords(*ir, step, mdatoms, state, f.arrayRefWithPadding(), fcdata, ekind, M,
1233 etrtVELOCITY2, cr, constr != nullptr);
1236 /* Above, initialize just copies ekinh into ekin,
1237 * it doesn't copy position (for VV),
1238 * and entire integrator for MD.
1241 if (ir->eI == eiVVAK)
1243 cbuf.resize(state->x.size());
1244 std::copy(state->x.begin(), state->x.end(), cbuf.begin());
1247 /* With leap-frog type integrators we compute the kinetic energy
1248 * at a whole time step as the average of the half-time step kinetic
1249 * energies of two subsequent steps. Therefore we need to compute the
1250 * half step kinetic energy also if we need energies at the next step.
1252 const bool needHalfStepKineticEnergy =
1253 (!EI_VV(ir->eI) && (do_per_step(step + 1, nstglobalcomm) || step_rel + 1 == ir->nsteps));
1255 // Parrinello-Rahman requires the pressure to be availible before the update to compute
1256 // the velocity scaling matrix. Hence, it runs one step after the nstpcouple step.
1257 const bool doParrinelloRahman = (ir->epc == epcPARRINELLORAHMAN
1258 && do_per_step(step + ir->nstpcouple - 1, ir->nstpcouple));
1260 if (useGpuForUpdate)
1262 if (bNS && (bFirstStep || DOMAINDECOMP(cr)))
1264 integrator->set(stateGpu->getCoordinates(), stateGpu->getVelocities(),
1265 stateGpu->getForces(), top.idef, *mdatoms, ekind->ngtc);
1267 // Copy data to the GPU after buffers might have being reinitialized
1268 stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
1269 stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
1272 // If the buffer ops were not offloaded this step, the forces are on the host and have to be copied
1273 if (!runScheduleWork->stepWork.useGpuFBufferOps)
1275 stateGpu->copyForcesToGpu(ArrayRef<RVec>(f), AtomLocality::Local);
1278 const bool doTemperatureScaling =
1279 (ir->etc != etcNO && do_per_step(step + ir->nsttcouple - 1, ir->nsttcouple));
1281 // This applies Leap-Frog, LINCS and SETTLE in succession
1282 integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
1283 AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
1284 ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
1285 ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
1287 // Copy velocities D2H after update if:
1288 // - Globals are computed this step (includes the energy output steps).
1289 // - Temperature is needed for the next step.
1290 if (bGStat || needHalfStepKineticEnergy)
1292 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
1293 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
1298 upd.update_coords(*ir, step, mdatoms, state, f.arrayRefWithPadding(), fcdata, ekind, M,
1299 etrtPOSITION, cr, constr != nullptr);
1301 wallcycle_stop(wcycle, ewcUPDATE);
1303 constrain_coordinates(constr, do_log, do_ene, step, state,
1304 upd.xp()->arrayRefWithPadding(), &dvdl_constr, bCalcVir, shake_vir);
1306 upd.update_sd_second_half(*ir, step, &dvdl_constr, mdatoms, state, cr, nrnb, wcycle,
1307 constr, do_log, do_ene);
1308 upd.finish_update(*ir, mdatoms, state, wcycle, constr != nullptr);
1311 if (ir->bPull && ir->pull->bSetPbcRefToPrevStepCOM)
1313 updatePrevStepPullCom(pull_work, state);
1316 if (ir->eI == eiVVAK)
1318 /* erase F_EKIN and F_TEMP here? */
1319 /* just compute the kinetic energy at the half step to perform a trotter step */
1320 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
1321 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle, enerd,
1322 force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, lastbox,
1323 nullptr, &bSumEkinhOld, (bGStat ? CGLO_GSTAT : 0) | CGLO_TEMPERATURE);
1324 wallcycle_start(wcycle, ewcUPDATE);
1325 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ4);
1326 /* now we know the scaling, we can compute the positions again */
1327 std::copy(cbuf.begin(), cbuf.end(), state->x.begin());
1329 upd.update_coords(*ir, step, mdatoms, state, f.arrayRefWithPadding(), fcdata, ekind, M,
1330 etrtPOSITION, cr, constr != nullptr);
1331 wallcycle_stop(wcycle, ewcUPDATE);
1333 /* do we need an extra constraint here? just need to copy out of as_rvec_array(state->v.data()) to upd->xp? */
1334 /* are the small terms in the shake_vir here due
1335 * to numerical errors, or are they important
1336 * physically? I'm thinking they are just errors, but not completely sure.
1337 * For now, will call without actually constraining, constr=NULL*/
1338 upd.finish_update(*ir, mdatoms, state, wcycle, false);
1342 /* this factor or 2 correction is necessary
1343 because half of the constraint force is removed
1344 in the vv step, so we have to double it. See
1345 the Issue #1255. It is not yet clear
1346 if the factor of 2 is exact, or just a very
1347 good approximation, and this will be
1348 investigated. The next step is to see if this
1349 can be done adding a dhdl contribution from the
1350 rattle step, but this is somewhat more
1351 complicated with the current code. Will be
1352 investigated, hopefully for 4.6.3. However,
1353 this current solution is much better than
1354 having it completely wrong.
1356 enerd->term[F_DVDL_CONSTR] += 2 * dvdl_constr;
1360 enerd->term[F_DVDL_CONSTR] += dvdl_constr;
1363 if (vsite != nullptr)
1365 wallcycle_start(wcycle, ewcVSITECONSTR);
1366 vsite->construct(state->x, ir->delta_t, state->v, state->box);
1367 wallcycle_stop(wcycle, ewcVSITECONSTR);
1370 /* ############## IF NOT VV, Calculate globals HERE ############ */
1371 /* With Leap-Frog we can skip compute_globals at
1372 * non-communication steps, but we need to calculate
1373 * the kinetic energy one step before communication.
1376 // Organize to do inter-simulation signalling on steps if
1377 // and when algorithms require it.
1378 const bool doInterSimSignal = (simulationsShareState && do_per_step(step, nstSignalComm));
1380 if (bGStat || needHalfStepKineticEnergy || doInterSimSignal)
1382 // Copy coordinates when needed to stop the CM motion.
1383 if (useGpuForUpdate && !EI_VV(ir->eI) && bStopCM)
1385 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
1386 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
1388 // Since we're already communicating at this step, we
1389 // can propagate intra-simulation signals. Note that
1390 // check_nstglobalcomm has the responsibility for
1391 // choosing the value of nstglobalcomm that is one way
1392 // bGStat becomes true, so we can't get into a
1393 // situation where e.g. checkpointing can't be
1395 bool doIntraSimSignal = true;
1396 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
1398 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
1399 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm,
1400 wcycle, enerd, force_vir, shake_vir, total_vir, pres, constr,
1401 &signaller, lastbox, &totalNumberOfBondedInteractions, &bSumEkinhOld,
1402 (bGStat ? CGLO_GSTAT : 0) | (!EI_VV(ir->eI) && bCalcEner ? CGLO_ENERGY : 0)
1403 | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
1404 | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
1405 | (!EI_VV(ir->eI) ? CGLO_PRESSURE : 0) | CGLO_CONSTRAINT
1406 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
1408 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
1409 top_global, &top, makeConstArrayRef(state->x),
1410 state->box, &shouldCheckNumberOfBondedInteractions);
1411 if (!EI_VV(ir->eI) && bStopCM)
1413 process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
1414 makeArrayRef(state->v));
1415 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
1417 // TODO: The special case of removing CM motion should be dealt more gracefully
1418 if (useGpuForUpdate)
1420 stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
1421 // Here we block until the H2D copy completes because event sync with the
1422 // force kernels that use the coordinates on the next steps is not implemented
1423 // (not because of a race on state->x being modified on the CPU while H2D is in progress).
1424 stateGpu->waitCoordinatesCopiedToDevice(AtomLocality::Local);
1425 // If the COM removal changed the velocities on the CPU, this has to be accounted for.
1426 if (vcm.mode != ecmNO)
1428 stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
1435 /* ############# END CALC EKIN AND PRESSURE ################# */
1437 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
1438 the virial that should probably be addressed eventually. state->veta has better properies,
1439 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
1440 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
1442 if (ir->efep != efepNO && !EI_VV(ir->eI))
1444 /* Sum up the foreign energy and dK/dl terms for md and sd.
1445 Currently done every step so that dH/dl is correct in the .edr */
1446 accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
1449 update_pcouple_after_coordinates(fplog, step, ir, mdatoms, pres, force_vir, shake_vir,
1450 pressureCouplingMu, state, nrnb, upd.deform(), !useGpuForUpdate);
1452 const bool doBerendsenPressureCoupling =
1453 (inputrec->epc == epcBERENDSEN && do_per_step(step, inputrec->nstpcouple));
1454 if (useGpuForUpdate && (doBerendsenPressureCoupling || doParrinelloRahman))
1456 integrator->scaleCoordinates(pressureCouplingMu);
1457 integrator->setPbc(PbcType::Xyz, state->box);
1460 /* ################# END UPDATE STEP 2 ################# */
1461 /* #### We now have r(t+dt) and v(t+dt/2) ############# */
1463 /* The coordinates (x) were unshifted in update */
1466 /* We will not sum ekinh_old,
1467 * so signal that we still have to do it.
1469 bSumEkinhOld = TRUE;
1474 /* ######### BEGIN PREPARING EDR OUTPUT ########### */
1476 /* use the directly determined last velocity, not actually the averaged half steps */
1477 if (bTrotter && ir->eI == eiVV)
1479 enerd->term[F_EKIN] = last_ekin;
1481 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
1483 if (integratorHasConservedEnergyQuantity(ir))
1487 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
1491 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + NPT_energy(ir, state, &MassQ);
1494 /* ######### END PREPARING EDR OUTPUT ########### */
1500 if (fplog && do_log && bDoExpanded)
1502 /* only needed if doing expanded ensemble */
1503 PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals,
1504 ir->bSimTemp ? ir->simtempvals : nullptr,
1505 state_global->dfhist, state->fep_state, ir->nstlog, step);
1509 energyOutput.addDataAtEnergyStep(bDoDHDL, bCalcEnerStep, t, mdatoms->tmass, enerd, state,
1510 ir->fepvals, ir->expandedvals, lastbox, shake_vir,
1511 force_vir, total_vir, pres, ekind, mu_tot, constr);
1515 energyOutput.recordNonEnergyStep();
1518 gmx_bool do_dr = do_per_step(step, ir->nstdisreout);
1519 gmx_bool do_or = do_per_step(step, ir->nstorireout);
1521 if (doSimulatedAnnealing)
1523 gmx::EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups,
1526 if (do_log || do_ene || do_dr || do_or)
1528 energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
1529 do_log ? fplog : nullptr, step, t,
1530 &fr->listedForces->fcdata(), awh.get());
1535 pull_print_output(pull_work, step, t);
1538 if (do_per_step(step, ir->nstlog))
1540 if (fflush(fplog) != 0)
1542 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
1548 /* Have to do this part _after_ outputting the logfile and the edr file */
1549 /* Gets written into the state at the beginning of next loop*/
1550 state->fep_state = lamnew;
1552 /* Print the remaining wall clock time for the run */
1553 if (isMasterSimMasterRank(ms, MASTER(cr)) && (do_verbose || gmx_got_usr_signal()) && !bPMETunePrinting)
1557 fprintf(stderr, "\n");
1559 print_time(stderr, walltime_accounting, step, ir, cr);
1562 /* Ion/water position swapping.
1563 * Not done in last step since trajectory writing happens before this call
1564 * in the MD loop and exchanges would be lost anyway. */
1565 bNeedRepartition = FALSE;
1566 if ((ir->eSwapCoords != eswapNO) && (step > 0) && !bLastStep && do_per_step(step, ir->swap->nstswap))
1569 do_swapcoords(cr, step, t, ir, swap, wcycle, as_rvec_array(state->x.data()),
1570 state->box, MASTER(cr) && mdrunOptions.verbose, bRerunMD);
1572 if (bNeedRepartition && DOMAINDECOMP(cr))
1574 dd_collect_state(cr->dd, state, state_global);
1578 /* Replica exchange */
1582 bExchanged = replica_exchange(fplog, cr, ms, repl_ex, state_global, enerd, state, step, t);
1585 if ((bExchanged || bNeedRepartition) && DOMAINDECOMP(cr))
1587 dd_partition_system(fplog, mdlog, step, cr, TRUE, 1, state_global, *top_global, ir,
1588 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
1589 nrnb, wcycle, FALSE);
1590 shouldCheckNumberOfBondedInteractions = true;
1591 upd.setNumAtoms(state->natoms);
1597 /* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
1598 /* With all integrators, except VV, we need to retain the pressure
1599 * at the current step for coupling at the next step.
1601 if ((state->flags & (1U << estPRES_PREV))
1602 && (bGStatEveryStep || (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
1604 /* Store the pressure in t_state for pressure coupling
1605 * at the next MD step.
1607 copy_mat(pres, state->pres_prev);
1610 /* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
1612 if ((membed != nullptr) && (!bLastStep))
1614 rescale_membed(step_rel, membed, as_rvec_array(state_global->x.data()));
1617 cycles = wallcycle_stop(wcycle, ewcSTEP);
1618 if (DOMAINDECOMP(cr) && wcycle)
1620 dd_cycles_add(cr->dd, cycles, ddCyclStep);
1623 /* increase the MD step number */
1627 resetHandler->resetCounters(step, step_rel, mdlog, fplog, cr, fr->nbv.get(), nrnb,
1628 fr->pmedata, pme_loadbal, wcycle, walltime_accounting);
1630 /* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
1631 imdSession->updateEnergyRecordAndSendPositionsAndEnergies(bInteractiveMDstep, step, bCalcEner);
1633 /* End of main MD loop */
1635 /* Closing TNG files can include compressing data. Therefore it is good to do that
1636 * before stopping the time measurements. */
1637 mdoutf_tng_close(outf);
1639 /* Stop measuring walltime */
1640 walltime_accounting_end_time(walltime_accounting);
1642 if (!thisRankHasDuty(cr, DUTY_PME))
1644 /* Tell the PME only node to finish */
1645 gmx_pme_send_finish(cr);
1650 if (ir->nstcalcenergy > 0)
1652 gmx::EnergyOutput::printAnnealingTemperatures(fplog, groups, &(ir->opts));
1653 energyOutput.printAverages(fplog, groups);
1660 pme_loadbal_done(pme_loadbal, fplog, mdlog, fr->nbv->useGpu());
1663 done_shellfc(fplog, shellfc, step_rel);
1665 if (useReplicaExchange && MASTER(cr))
1667 print_replica_exchange_statistics(fplog, repl_ex);
1670 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
1672 global_stat_destroy(gstat);