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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 t_inputrec* ir = inputrec;
166 int64_t step, step_rel;
167 double t, t0 = ir->init_t;
168 gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, bCalcEner;
169 gmx_bool bNS = FALSE, bNStList, bStopCM, bFirstStep, bInitStep, bLastStep = FALSE;
170 gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
171 gmx_bool do_ene, do_log, do_verbose;
172 gmx_bool bMasterState;
173 unsigned int force_flags;
174 tensor force_vir = { { 0 } }, shake_vir = { { 0 } }, total_vir = { { 0 } }, pres = { { 0 } };
177 matrix pressureCouplingMu, M;
178 gmx_repl_ex_t repl_ex = nullptr;
179 gmx_global_stat_t gstat;
180 gmx_shellfc_t* shellfc;
181 gmx_bool bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
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);
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->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,
301 simulationsShareState, mdModulesNotifier);
303 gstat = global_stat_init(ir);
305 const auto& simulationWork = runScheduleWork->simulationWork;
306 const bool useGpuForPme = simulationWork.useGpuPme;
307 const bool useGpuForNonbonded = simulationWork.useGpuNonbonded;
308 const bool useGpuForBufferOps = simulationWork.useGpuBufferOps;
309 const bool useGpuForUpdate = simulationWork.useGpuUpdate;
311 /* Check for polarizable models and flexible constraints */
312 shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
313 ir->nstcalcenergy, DOMAINDECOMP(cr), useGpuForPme);
316 double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
317 if ((io > 2000) && MASTER(cr))
319 fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
323 // Local state only becomes valid now.
324 std::unique_ptr<t_state> stateInstance;
327 gmx_localtop_t top(top_global->ffparams);
329 auto mdatoms = mdAtoms->mdatoms();
331 ForceBuffers f(fr->useMts, ((useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
332 ? PinningPolicy::PinnedIfSupported
333 : PinningPolicy::CannotBePinned);
334 if (DOMAINDECOMP(cr))
336 stateInstance = std::make_unique<t_state>();
337 state = stateInstance.get();
338 dd_init_local_state(cr->dd, state_global, state);
340 /* Distribute the charge groups over the nodes from the master node */
341 dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
342 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
343 nrnb, nullptr, FALSE);
344 shouldCheckNumberOfBondedInteractions = true;
345 upd.setNumAtoms(state->natoms);
349 state_change_natoms(state_global, state_global->natoms);
350 /* Copy the pointer to the global state */
351 state = state_global;
353 /* Generate and initialize new topology */
354 mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
356 upd.setNumAtoms(state->natoms);
359 std::unique_ptr<UpdateConstrainGpu> integrator;
361 StatePropagatorDataGpu* stateGpu = fr->stateGpu;
363 // TODO: the assertions below should be handled by UpdateConstraintsBuilder.
366 GMX_RELEASE_ASSERT(!DOMAINDECOMP(cr) || ddUsesUpdateGroups(*cr->dd) || constr == nullptr
367 || constr->numConstraintsTotal() == 0,
368 "Constraints in domain decomposition are only supported with update "
369 "groups if using GPU update.\n");
370 GMX_RELEASE_ASSERT(ir->eConstrAlg != econtSHAKE || constr == nullptr
371 || constr->numConstraintsTotal() == 0,
372 "SHAKE is not supported with GPU update.");
373 GMX_RELEASE_ASSERT(useGpuForPme || (useGpuForNonbonded && simulationWork.useGpuBufferOps),
374 "Either PME or short-ranged non-bonded interaction tasks must run on "
375 "the GPU to use GPU update.\n");
376 GMX_RELEASE_ASSERT(ir->eI == eiMD,
377 "Only the md integrator is supported with the GPU update.\n");
379 ir->etc != etcNOSEHOOVER,
380 "Nose-Hoover temperature coupling is not supported with the GPU update.\n");
382 ir->epc == epcNO || ir->epc == epcPARRINELLORAHMAN || ir->epc == epcBERENDSEN
383 || ir->epc == epcCRESCALE,
384 "Only Parrinello-Rahman, Berendsen, and C-rescale pressure coupling are supported "
385 "with the GPU update.\n");
386 GMX_RELEASE_ASSERT(!mdatoms->haveVsites,
387 "Virtual sites are not supported with the GPU update.\n");
388 GMX_RELEASE_ASSERT(ed == nullptr,
389 "Essential dynamics is not supported with the GPU update.\n");
390 GMX_RELEASE_ASSERT(!ir->bPull || !pull_have_constraint(*ir->pull),
391 "Constraints pulling is not supported with the GPU update.\n");
392 GMX_RELEASE_ASSERT(fcdata.orires->nr == 0,
393 "Orientation restraints are not supported with the GPU update.\n");
396 || (!haveFepPerturbedMasses(*top_global) && !havePerturbedConstraints(*top_global)),
397 "Free energy perturbation of masses and constraints are not supported with the GPU "
400 if (constr != nullptr && constr->numConstraintsTotal() > 0)
404 .appendText("Updating coordinates and applying constraints on the GPU.");
408 GMX_LOG(mdlog.info).asParagraph().appendText("Updating coordinates on the GPU.");
410 GMX_RELEASE_ASSERT(fr->deviceStreamManager != nullptr,
411 "Device stream manager should be initialized in order to use GPU "
412 "update-constraints.");
414 fr->deviceStreamManager->streamIsValid(gmx::DeviceStreamType::UpdateAndConstraints),
415 "Update stream should be initialized in order to use GPU "
416 "update-constraints.");
417 integrator = std::make_unique<UpdateConstrainGpu>(
418 *ir, *top_global, fr->deviceStreamManager->context(),
419 fr->deviceStreamManager->stream(gmx::DeviceStreamType::UpdateAndConstraints),
420 stateGpu->xUpdatedOnDevice(), wcycle);
422 integrator->setPbc(PbcType::Xyz, state->box);
425 if (useGpuForPme || (useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
427 changePinningPolicy(&state->x, PinningPolicy::PinnedIfSupported);
431 changePinningPolicy(&state->v, PinningPolicy::PinnedIfSupported);
434 // NOTE: The global state is no longer used at this point.
435 // But state_global is still used as temporary storage space for writing
436 // the global state to file and potentially for replica exchange.
437 // (Global topology should persist.)
439 update_mdatoms(mdatoms, state->lambda[efptMASS]);
443 /* Check nstexpanded here, because the grompp check was broken */
444 if (ir->expandedvals->nstexpanded % ir->nstcalcenergy != 0)
447 "With expanded ensemble, nstexpanded should be a multiple of nstcalcenergy");
449 init_expanded_ensemble(startingBehavior != StartingBehavior::NewSimulation, ir, state->dfhist);
454 EnergyData::initializeEnergyHistory(startingBehavior, observablesHistory, &energyOutput);
457 preparePrevStepPullCom(ir, pull_work, mdatoms->massT, state, state_global, cr,
458 startingBehavior != StartingBehavior::NewSimulation);
460 // TODO: Remove this by converting AWH into a ForceProvider
461 auto awh = prepareAwhModule(fplog, *ir, state_global, cr, ms,
462 startingBehavior != StartingBehavior::NewSimulation,
463 shellfc != nullptr, opt2fn("-awh", nfile, fnm), pull_work);
465 if (useReplicaExchange && MASTER(cr))
467 repl_ex = init_replica_exchange(fplog, ms, top_global->natoms, ir, replExParams);
469 /* PME tuning is only supported in the Verlet scheme, with PME for
470 * Coulomb. It is not supported with only LJ PME. */
471 bPMETune = (mdrunOptions.tunePme && EEL_PME(fr->ic->eeltype) && !mdrunOptions.reproducible
472 && ir->cutoff_scheme != ecutsGROUP);
474 pme_load_balancing_t* pme_loadbal = nullptr;
477 pme_loadbal_init(&pme_loadbal, cr, mdlog, *ir, state->box, *fr->ic, *fr->nbv, fr->pmedata,
481 if (!ir->bContinuation)
483 if (state->flags & (1U << estV))
485 auto v = makeArrayRef(state->v);
486 /* Set the velocities of vsites, shells and frozen atoms to zero */
487 for (i = 0; i < mdatoms->homenr; i++)
489 if (mdatoms->ptype[i] == eptVSite || mdatoms->ptype[i] == eptShell)
493 else if (mdatoms->cFREEZE)
495 for (m = 0; m < DIM; m++)
497 if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
508 /* Constrain the initial coordinates and velocities */
509 do_constrain_first(fplog, constr, ir, mdatoms->nr, mdatoms->homenr,
510 state->x.arrayRefWithPadding(), state->v.arrayRefWithPadding(),
511 state->box, state->lambda[efptBONDED]);
515 /* Construct the virtual sites for the initial configuration */
516 vsite->construct(state->x, ir->delta_t, {}, state->box);
520 if (ir->efep != efepNO)
522 /* Set free energy calculation frequency as the greatest common
523 * denominator of nstdhdl and repl_ex_nst. */
524 nstfep = ir->fepvals->nstdhdl;
527 nstfep = std::gcd(ir->expandedvals->nstexpanded, nstfep);
529 if (useReplicaExchange)
531 nstfep = std::gcd(replExParams.exchangeInterval, nstfep);
535 nstfep = std::gcd(ir->awhParams->nstSampleCoord, nstfep);
539 /* Be REALLY careful about what flags you set here. You CANNOT assume
540 * this is the first step, since we might be restarting from a checkpoint,
541 * and in that case we should not do any modifications to the state.
543 bStopCM = (ir->comm_mode != ecmNO && !ir->bContinuation);
545 // When restarting from a checkpoint, it can be appropriate to
546 // initialize ekind from quantities in the checkpoint. Otherwise,
547 // compute_globals must initialize ekind before the simulation
548 // starts/restarts. However, only the master rank knows what was
549 // found in the checkpoint file, so we have to communicate in
550 // order to coordinate the restart.
552 // TODO Consider removing this communication if/when checkpoint
553 // reading directly follows .tpr reading, because all ranks can
554 // agree on hasReadEkinState at that time.
555 bool hasReadEkinState = MASTER(cr) ? state_global->ekinstate.hasReadEkinState : false;
558 gmx_bcast(sizeof(hasReadEkinState), &hasReadEkinState, cr->mpi_comm_mygroup);
560 if (hasReadEkinState)
562 restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
565 unsigned int cglo_flags =
566 (CGLO_TEMPERATURE | CGLO_GSTAT | (EI_VV(ir->eI) ? CGLO_PRESSURE : 0)
567 | (EI_VV(ir->eI) ? CGLO_CONSTRAINT : 0) | (hasReadEkinState ? CGLO_READEKIN : 0));
569 bSumEkinhOld = FALSE;
571 t_vcm vcm(top_global->groups, *ir);
572 reportComRemovalInfo(fplog, vcm);
574 /* To minimize communication, compute_globals computes the COM velocity
575 * and the kinetic energy for the velocities without COM motion removed.
576 * Thus to get the kinetic energy without the COM contribution, we need
577 * to call compute_globals twice.
579 for (int cgloIteration = 0; cgloIteration < (bStopCM ? 2 : 1); cgloIteration++)
581 unsigned int cglo_flags_iteration = cglo_flags;
582 if (bStopCM && cgloIteration == 0)
584 cglo_flags_iteration |= CGLO_STOPCM;
585 cglo_flags_iteration &= ~CGLO_TEMPERATURE;
587 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
588 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
589 enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
590 state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
592 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
594 if (cglo_flags_iteration & CGLO_STOPCM)
596 /* At initialization, do not pass x with acceleration-correction mode
597 * to avoid (incorrect) correction of the initial coordinates.
599 auto x = (vcm.mode == ecmLINEAR_ACCELERATION_CORRECTION) ? ArrayRef<RVec>()
600 : makeArrayRef(state->x);
601 process_and_stopcm_grp(fplog, &vcm, *mdatoms, x, makeArrayRef(state->v));
602 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
605 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
606 makeConstArrayRef(state->x), state->box,
607 &shouldCheckNumberOfBondedInteractions);
608 if (ir->eI == eiVVAK)
610 /* a second call to get the half step temperature initialized as well */
611 /* we do the same call as above, but turn the pressure off -- internally to
612 compute_globals, this is recognized as a velocity verlet half-step
613 kinetic energy calculation. This minimized excess variables, but
614 perhaps loses some logic?*/
616 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
617 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
618 enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
619 state->box, nullptr, &bSumEkinhOld, cglo_flags & ~CGLO_PRESSURE);
622 /* Calculate the initial half step temperature, and save the ekinh_old */
623 if (startingBehavior == StartingBehavior::NewSimulation)
625 for (i = 0; (i < ir->opts.ngtc); i++)
627 copy_mat(ekind->tcstat[i].ekinh, ekind->tcstat[i].ekinh_old);
631 /* need to make an initiation call to get the Trotter variables set, as well as other constants
632 for non-trotter temperature control */
633 auto trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
637 if (!ir->bContinuation)
639 if (constr && ir->eConstrAlg == econtLINCS)
641 fprintf(fplog, "RMS relative constraint deviation after constraining: %.2e\n",
644 if (EI_STATE_VELOCITY(ir->eI))
646 real temp = enerd->term[F_TEMP];
649 /* Result of Ekin averaged over velocities of -half
650 * and +half step, while we only have -half step here.
654 fprintf(fplog, "Initial temperature: %g K\n", temp);
659 fprintf(stderr, "starting mdrun '%s'\n", *(top_global->name));
662 sprintf(tbuf, "%8.1f", (ir->init_step + ir->nsteps) * ir->delta_t);
666 sprintf(tbuf, "%s", "infinite");
668 if (ir->init_step > 0)
670 fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
671 gmx_step_str(ir->init_step + ir->nsteps, sbuf), tbuf,
672 gmx_step_str(ir->init_step, sbuf2), ir->init_step * ir->delta_t);
676 fprintf(stderr, "%s steps, %s ps.\n", gmx_step_str(ir->nsteps, sbuf), tbuf);
678 fprintf(fplog, "\n");
681 walltime_accounting_start_time(walltime_accounting);
682 wallcycle_start(wcycle, ewcRUN);
683 print_start(fplog, cr, walltime_accounting, "mdrun");
685 /***********************************************************
689 ************************************************************/
692 /* Skip the first Nose-Hoover integration when we get the state from tpx */
693 bInitStep = startingBehavior == StartingBehavior::NewSimulation || EI_VV(ir->eI);
694 bSumEkinhOld = FALSE;
696 bNeedRepartition = FALSE;
698 step = ir->init_step;
701 auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
702 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), simulationsShareState,
703 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstSignalComm,
704 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
706 auto checkpointHandler = std::make_unique<CheckpointHandler>(
707 compat::make_not_null<SimulationSignal*>(&signals[eglsCHKPT]), simulationsShareState,
708 ir->nstlist == 0, MASTER(cr), mdrunOptions.writeConfout,
709 mdrunOptions.checkpointOptions.period);
711 const bool resetCountersIsLocal = true;
712 auto resetHandler = std::make_unique<ResetHandler>(
713 compat::make_not_null<SimulationSignal*>(&signals[eglsRESETCOUNTERS]),
714 !resetCountersIsLocal, ir->nsteps, MASTER(cr), mdrunOptions.timingOptions.resetHalfway,
715 mdrunOptions.maximumHoursToRun, mdlog, wcycle, walltime_accounting);
717 const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
719 if (MASTER(cr) && isMultiSim(ms) && !useReplicaExchange)
721 logInitialMultisimStatus(ms, cr, mdlog, simulationsShareState, ir->nsteps, ir->init_step);
724 /* and stop now if we should */
725 bLastStep = (bLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
729 /* Determine if this is a neighbor search step */
730 bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
732 if (bPMETune && bNStList)
734 // This has to be here because PME load balancing is called so early.
735 // TODO: Move to after all booleans are defined.
736 if (useGpuForUpdate && !bFirstStep)
738 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
739 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
741 /* PME grid + cut-off optimization with GPUs or PME nodes */
742 pme_loadbal_do(pme_loadbal, cr, (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
743 fplog, mdlog, *ir, fr, state->box, state->x, wcycle, step, step_rel,
744 &bPMETunePrinting, simulationWork.useGpuPmePpCommunication);
747 wallcycle_start(wcycle, ewcSTEP);
749 bLastStep = (step_rel == ir->nsteps);
750 t = t0 + step * ir->delta_t;
752 // TODO Refactor this, so that nstfep does not need a default value of zero
753 if (ir->efep != efepNO || ir->bSimTemp)
755 /* find and set the current lambdas */
756 state->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
758 bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
759 bDoFEP = ((ir->efep != efepNO) && do_per_step(step, nstfep));
760 bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded) && (ir->bExpanded)
764 bDoReplEx = (useReplicaExchange && (step > 0) && !bLastStep
765 && do_per_step(step, replExParams.exchangeInterval));
767 if (doSimulatedAnnealing)
769 update_annealing_target_temp(ir, t, &upd);
772 /* Stop Center of Mass motion */
773 bStopCM = (ir->comm_mode != ecmNO && do_per_step(step, ir->nstcomm));
775 /* Determine whether or not to do Neighbour Searching */
776 bNS = (bFirstStep || bNStList || bExchanged || bNeedRepartition);
778 /* Note that the stopHandler will cause termination at nstglobalcomm
779 * steps. Since this concides with nstcalcenergy, nsttcouple and/or
780 * nstpcouple steps, we have computed the half-step kinetic energy
781 * of the previous step and can always output energies at the last step.
783 bLastStep = bLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
785 /* do_log triggers energy and virial calculation. Because this leads
786 * to different code paths, forces can be different. Thus for exact
787 * continuation we should avoid extra log output.
788 * Note that the || bLastStep can result in non-exact continuation
789 * beyond the last step. But we don't consider that to be an issue.
791 do_log = (do_per_step(step, ir->nstlog)
792 || (bFirstStep && startingBehavior == StartingBehavior::NewSimulation) || bLastStep);
793 do_verbose = mdrunOptions.verbose
794 && (step % mdrunOptions.verboseStepPrintInterval == 0 || bFirstStep || bLastStep);
796 if (useGpuForUpdate && !bFirstStep && bNS)
798 // Copy velocities from the GPU on search steps to keep a copy on host (device buffers are reinitialized).
799 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
800 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
801 // Copy coordinate from the GPU when needed at the search step.
802 // NOTE: The cases when coordinates needed on CPU for force evaluation are handled in sim_utils.
803 // NOTE: If the coordinates are to be written into output file they are also copied separately before the output.
804 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
805 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
808 if (bNS && !(bFirstStep && ir->bContinuation))
810 bMasterState = FALSE;
811 /* Correct the new box if it is too skewed */
812 if (inputrecDynamicBox(ir))
814 if (correct_box(fplog, step, state->box))
817 // If update is offloaded, it should be informed about the box size change
820 integrator->setPbc(PbcType::Xyz, state->box);
824 if (DOMAINDECOMP(cr) && bMasterState)
826 dd_collect_state(cr->dd, state, state_global);
829 if (DOMAINDECOMP(cr))
831 /* Repartition the domain decomposition */
832 dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
833 *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
834 fr, vsite, constr, nrnb, wcycle, do_verbose && !bPMETunePrinting);
835 shouldCheckNumberOfBondedInteractions = true;
836 upd.setNumAtoms(state->natoms);
840 // Allocate or re-size GPU halo exchange object, if necessary
841 if (bNS && havePPDomainDecomposition(cr) && simulationWork.useGpuHaloExchange)
843 GMX_RELEASE_ASSERT(fr->deviceStreamManager != nullptr,
844 "GPU device manager has to be initialized to use GPU "
845 "version of halo exchange.");
846 constructGpuHaloExchange(mdlog, *cr, *fr->deviceStreamManager, wcycle);
849 if (MASTER(cr) && do_log)
851 gmx::EnergyOutput::printHeader(fplog, step,
852 t); /* can we improve the information printed here? */
855 if (ir->efep != efepNO)
857 update_mdatoms(mdatoms, state->lambda[efptMASS]);
862 /* We need the kinetic energy at minus the half step for determining
863 * the full step kinetic energy and possibly for T-coupling.*/
864 /* This may not be quite working correctly yet . . . . */
865 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
866 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
867 enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
868 state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
869 CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
870 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
871 &top, makeConstArrayRef(state->x), state->box,
872 &shouldCheckNumberOfBondedInteractions);
874 clear_mat(force_vir);
876 checkpointHandler->decideIfCheckpointingThisStep(bNS, bFirstStep, bLastStep);
878 /* Determine the energy and pressure:
879 * at nstcalcenergy steps and at energy output steps (set below).
881 if (EI_VV(ir->eI) && (!bInitStep))
883 bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
884 bCalcVir = bCalcEnerStep
886 && (do_per_step(step, ir->nstpcouple) || do_per_step(step - 1, ir->nstpcouple)));
890 bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
891 bCalcVir = bCalcEnerStep || (ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
893 bCalcEner = bCalcEnerStep;
895 do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
897 if (do_ene || do_log || bDoReplEx)
903 /* Do we need global communication ? */
904 bGStat = (bCalcVir || bCalcEner || bStopCM || do_per_step(step, nstglobalcomm)
905 || (EI_VV(ir->eI) && inputrecNvtTrotter(ir) && do_per_step(step - 1, nstglobalcomm)));
907 force_flags = (GMX_FORCE_STATECHANGED | ((inputrecDynamicBox(ir)) ? GMX_FORCE_DYNAMICBOX : 0)
908 | GMX_FORCE_ALLFORCES | (bCalcVir ? GMX_FORCE_VIRIAL : 0)
909 | (bCalcEner ? GMX_FORCE_ENERGY : 0) | (bDoFEP ? GMX_FORCE_DHDL : 0));
910 if (fr->useMts && !do_per_step(step, ir->nstfout))
912 force_flags |= GMX_FORCE_DO_NOT_NEED_NORMAL_FORCE;
917 /* Now is the time to relax the shells */
918 relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
919 imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
920 state->natoms, state->x.arrayRefWithPadding(),
921 state->v.arrayRefWithPadding(), state->box, state->lambda,
922 &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
923 fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
927 /* The AWH history need to be saved _before_ doing force calculations where the AWH bias
928 is updated (or the AWH update will be performed twice for one step when continuing).
929 It would be best to call this update function from do_md_trajectory_writing but that
930 would occur after do_force. One would have to divide the update_awh function into one
931 function applying the AWH force and one doing the AWH bias update. The update AWH
932 bias function could then be called after do_md_trajectory_writing (then containing
933 update_awh_history). The checkpointing will in the future probably moved to the start
934 of the md loop which will rid of this issue. */
935 if (awh && checkpointHandler->isCheckpointingStep() && MASTER(cr))
937 awh->updateHistory(state_global->awhHistory.get());
940 /* The coordinates (x) are shifted (to get whole molecules)
942 * This is parallellized as well, and does communication too.
943 * Check comments in sim_util.c
945 do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step,
946 nrnb, wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
947 &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
948 vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
949 (bNS ? GMX_FORCE_NS : 0) | force_flags, ddBalanceRegionHandler);
952 // VV integrators do not need the following velocity half step
953 // if it is the first step after starting from a checkpoint.
954 // That is, the half step is needed on all other steps, and
955 // also the first step when starting from a .tpr file.
958 integrateVVFirstStep(step, bFirstStep, bInitStep, startingBehavior, nstglobalcomm, ir,
959 fr, cr, state, mdatoms, fcdata, &MassQ, &vcm, top_global, top, enerd,
960 ekind, gstat, &last_ekin, bCalcVir, total_vir, shake_vir, force_vir,
961 pres, M, do_log, do_ene, bCalcEner, bGStat, bStopCM, bTrotter,
962 bExchanged, &bSumEkinhOld, &shouldCheckNumberOfBondedInteractions,
963 &saved_conserved_quantity, &f, &upd, constr, &nullSignaller,
964 trotter_seq, nrnb, mdlog, fplog, wcycle);
967 /* ######## END FIRST UPDATE STEP ############## */
968 /* ######## If doing VV, we now have v(dt) ###### */
971 /* perform extended ensemble sampling in lambda - we don't
972 actually move to the new state before outputting
973 statistics, but if performing simulated tempering, we
974 do update the velocities and the tau_t. */
976 lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, state->fep_state,
977 state->dfhist, step, state->v.rvec_array(), mdatoms);
978 /* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
981 copy_df_history(state_global->dfhist, state->dfhist);
985 // Copy coordinate from the GPU for the output/checkpointing if the update is offloaded and
986 // coordinates have not already been copied for i) search or ii) CPU force tasks.
987 if (useGpuForUpdate && !bNS && !runScheduleWork->domainWork.haveCpuLocalForceWork
988 && (do_per_step(step, ir->nstxout) || do_per_step(step, ir->nstxout_compressed)
989 || checkpointHandler->isCheckpointingStep()))
991 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
992 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
994 // Copy velocities if needed for the output/checkpointing.
995 // NOTE: Copy on the search steps is done at the beginning of the step.
996 if (useGpuForUpdate && !bNS
997 && (do_per_step(step, ir->nstvout) || checkpointHandler->isCheckpointingStep()))
999 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
1000 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
1002 // Copy forces for the output if the forces were reduced on the GPU (not the case on virial steps)
1003 // and update is offloaded hence forces are kept on the GPU for update and have not been
1004 // already transferred in do_force().
1005 // TODO: There should be an improved, explicit mechanism that ensures this copy is only executed
1006 // when the forces are ready on the GPU -- the same synchronizer should be used as the one
1007 // prior to GPU update.
1008 // TODO: When the output flags will be included in step workload, this copy can be combined with the
1009 // copy call in do_force(...).
1010 // NOTE: The forces should not be copied here if the vsites are present, since they were modified
1011 // on host after the D2H copy in do_force(...).
1012 if (runScheduleWork->stepWork.useGpuFBufferOps && (simulationWork.useGpuUpdate && !vsite)
1013 && do_per_step(step, ir->nstfout))
1015 stateGpu->copyForcesFromGpu(f.view().force(), AtomLocality::Local);
1016 stateGpu->waitForcesReadyOnHost(AtomLocality::Local);
1018 /* Now we have the energies and forces corresponding to the
1019 * coordinates at time t. We must output all of this before
1022 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state, state_global,
1023 observablesHistory, top_global, fr, outf, energyOutput, ekind,
1024 f.view().force(), checkpointHandler->isCheckpointingStep(),
1025 bRerunMD, bLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
1026 /* Check if IMD step and do IMD communication, if bIMD is TRUE. */
1027 bInteractiveMDstep = imdSession->run(step, bNS, state->box, state->x.rvec_array(), t);
1029 /* kludge -- virial is lost with restart for MTTK NPT control. Must reload (saved earlier). */
1030 if (startingBehavior != StartingBehavior::NewSimulation && bFirstStep
1031 && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir)))
1033 copy_mat(state->svir_prev, shake_vir);
1034 copy_mat(state->fvir_prev, force_vir);
1037 stopHandler->setSignal();
1038 resetHandler->setSignal(walltime_accounting);
1040 if (bGStat || !PAR(cr))
1042 /* In parallel we only have to check for checkpointing in steps
1043 * where we do global communication,
1044 * otherwise the other nodes don't know.
1046 checkpointHandler->setSignal(walltime_accounting);
1049 /* ######### START SECOND UPDATE STEP ################# */
1051 /* at the start of step, randomize or scale the velocities ((if vv. Restriction of Andersen
1052 controlled in preprocessing */
1054 if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
1056 gmx_bool bIfRandomize;
1057 bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
1058 /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
1059 if (constr && bIfRandomize)
1061 constrain_velocities(constr, do_log, do_ene, step, state, nullptr, false, nullptr);
1064 /* Box is changed in update() when we do pressure coupling,
1065 * but we should still use the old box for energy corrections and when
1066 * writing it to the energy file, so it matches the trajectory files for
1067 * the same timestep above. Make a copy in a separate array.
1069 copy_mat(state->box, lastbox);
1073 if (!useGpuForUpdate)
1075 wallcycle_start(wcycle, ewcUPDATE);
1077 /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
1080 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
1081 /* We can only do Berendsen coupling after we have summed
1082 * the kinetic energy or virial. Since the happens
1083 * in global_state after update, we should only do it at
1084 * step % nstlist = 1 with bGStatEveryStep=FALSE.
1089 update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
1090 update_pcouple_before_coordinates(fplog, step, ir, state, pressureCouplingMu, M, bInitStep);
1093 /* With leap-frog type integrators we compute the kinetic energy
1094 * at a whole time step as the average of the half-time step kinetic
1095 * energies of two subsequent steps. Therefore we need to compute the
1096 * half step kinetic energy also if we need energies at the next step.
1098 const bool needHalfStepKineticEnergy =
1099 (!EI_VV(ir->eI) && (do_per_step(step + 1, nstglobalcomm) || step_rel + 1 == ir->nsteps));
1101 // Parrinello-Rahman requires the pressure to be availible before the update to compute
1102 // the velocity scaling matrix. Hence, it runs one step after the nstpcouple step.
1103 const bool doParrinelloRahman = (ir->epc == epcPARRINELLORAHMAN
1104 && do_per_step(step + ir->nstpcouple - 1, ir->nstpcouple));
1108 GMX_ASSERT(!useGpuForUpdate, "GPU update is not supported with VVAK integrator.");
1110 integrateVVSecondStep(step, ir, fr, cr, state, mdatoms, fcdata, &MassQ, &vcm, pull_work,
1111 enerd, ekind, gstat, &dvdl_constr, bCalcVir, total_vir, shake_vir,
1112 force_vir, pres, M, lastbox, do_log, do_ene, bGStat, &bSumEkinhOld,
1113 &f, &cbuf, &upd, constr, &nullSignaller, trotter_seq, nrnb, wcycle);
1117 if (useGpuForUpdate)
1120 wallcycle_stop(wcycle, ewcUPDATE);
1122 if (bNS && (bFirstStep || DOMAINDECOMP(cr)))
1124 integrator->set(stateGpu->getCoordinates(), stateGpu->getVelocities(),
1125 stateGpu->getForces(), top.idef, *mdatoms, ekind->ngtc);
1127 // Copy data to the GPU after buffers might have being reinitialized
1128 stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
1129 stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
1132 if (simulationWork.useGpuPme && !runScheduleWork->simulationWork.useGpuPmePpCommunication
1133 && !thisRankHasDuty(cr, DUTY_PME))
1135 // The PME forces were recieved to the host, so have to be copied
1136 stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::All);
1138 else if (!runScheduleWork->stepWork.useGpuFBufferOps)
1140 // The buffer ops were not offloaded this step, so the forces are on the
1141 // host and have to be copied
1142 stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::Local);
1145 const bool doTemperatureScaling =
1146 (ir->etc != etcNO && do_per_step(step + ir->nsttcouple - 1, ir->nsttcouple));
1148 // This applies Leap-Frog, LINCS and SETTLE in succession
1149 integrator->integrate(
1150 stateGpu->getForcesReadyOnDeviceEvent(
1151 AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
1152 ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling, ekind->tcstat,
1153 doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
1155 // Copy velocities D2H after update if:
1156 // - Globals are computed this step (includes the energy output steps).
1157 // - Temperature is needed for the next step.
1158 if (bGStat || needHalfStepKineticEnergy)
1160 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
1161 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
1166 /* With multiple time stepping we need to do an additional normal
1167 * update step to obtain the virial, as the actual MTS integration
1168 * using an acceleration where the slow forces are multiplied by mtsFactor.
1169 * Using that acceleration would result in a virial with the slow
1170 * force contribution would be a factor mtsFactor too large.
1172 if (fr->useMts && bCalcVir && constr != nullptr)
1174 upd.update_for_constraint_virial(*ir, *mdatoms, *state,
1175 f.view().forceWithPadding(), *ekind);
1177 constrain_coordinates(constr, do_log, do_ene, step, state,
1178 upd.xp()->arrayRefWithPadding(), &dvdl_constr, bCalcVir,
1182 ArrayRefWithPadding<const RVec> forceCombined =
1183 (fr->useMts && step % ir->mtsLevels[1].stepFactor == 0)
1184 ? f.view().forceMtsCombinedWithPadding()
1185 : f.view().forceWithPadding();
1186 upd.update_coords(*ir, step, mdatoms, state, forceCombined, fcdata, ekind, M,
1187 etrtPOSITION, cr, constr != nullptr);
1189 wallcycle_stop(wcycle, ewcUPDATE);
1191 constrain_coordinates(constr, do_log, do_ene, step, state,
1192 upd.xp()->arrayRefWithPadding(), &dvdl_constr,
1193 bCalcVir && !fr->useMts, shake_vir);
1195 upd.update_sd_second_half(*ir, step, &dvdl_constr, mdatoms, state, cr, nrnb, wcycle,
1196 constr, do_log, do_ene);
1197 upd.finish_update(*ir, mdatoms, state, wcycle, constr != nullptr);
1200 if (ir->bPull && ir->pull->bSetPbcRefToPrevStepCOM)
1202 updatePrevStepPullCom(pull_work, state);
1205 enerd->term[F_DVDL_CONSTR] += dvdl_constr;
1208 if (vsite != nullptr)
1210 wallcycle_start(wcycle, ewcVSITECONSTR);
1211 vsite->construct(state->x, ir->delta_t, state->v, state->box);
1212 wallcycle_stop(wcycle, ewcVSITECONSTR);
1215 /* ############## IF NOT VV, Calculate globals HERE ############ */
1216 /* With Leap-Frog we can skip compute_globals at
1217 * non-communication steps, but we need to calculate
1218 * the kinetic energy one step before communication.
1221 // Organize to do inter-simulation signalling on steps if
1222 // and when algorithms require it.
1223 const bool doInterSimSignal = (simulationsShareState && do_per_step(step, nstSignalComm));
1225 if (bGStat || needHalfStepKineticEnergy || doInterSimSignal)
1227 // Copy coordinates when needed to stop the CM motion.
1228 if (useGpuForUpdate && !EI_VV(ir->eI) && bStopCM)
1230 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
1231 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
1233 // Since we're already communicating at this step, we
1234 // can propagate intra-simulation signals. Note that
1235 // check_nstglobalcomm has the responsibility for
1236 // choosing the value of nstglobalcomm that is one way
1237 // bGStat becomes true, so we can't get into a
1238 // situation where e.g. checkpointing can't be
1240 bool doIntraSimSignal = true;
1241 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
1243 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
1244 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm,
1245 wcycle, enerd, force_vir, shake_vir, total_vir, pres, constr,
1246 &signaller, lastbox, &totalNumberOfBondedInteractions, &bSumEkinhOld,
1247 (bGStat ? CGLO_GSTAT : 0) | (!EI_VV(ir->eI) && bCalcEner ? CGLO_ENERGY : 0)
1248 | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
1249 | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
1250 | (!EI_VV(ir->eI) ? CGLO_PRESSURE : 0) | CGLO_CONSTRAINT
1251 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
1253 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
1254 top_global, &top, makeConstArrayRef(state->x),
1255 state->box, &shouldCheckNumberOfBondedInteractions);
1256 if (!EI_VV(ir->eI) && bStopCM)
1258 process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
1259 makeArrayRef(state->v));
1260 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
1262 // TODO: The special case of removing CM motion should be dealt more gracefully
1263 if (useGpuForUpdate)
1265 stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
1266 // Here we block until the H2D copy completes because event sync with the
1267 // force kernels that use the coordinates on the next steps is not implemented
1268 // (not because of a race on state->x being modified on the CPU while H2D is in progress).
1269 stateGpu->waitCoordinatesCopiedToDevice(AtomLocality::Local);
1270 // If the COM removal changed the velocities on the CPU, this has to be accounted for.
1271 if (vcm.mode != ecmNO)
1273 stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
1280 /* ############# END CALC EKIN AND PRESSURE ################# */
1282 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
1283 the virial that should probably be addressed eventually. state->veta has better properies,
1284 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
1285 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
1287 if (ir->efep != efepNO && !EI_VV(ir->eI))
1289 /* Sum up the foreign energy and dK/dl terms for md and sd.
1290 Currently done every step so that dH/dl is correct in the .edr */
1291 accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
1294 update_pcouple_after_coordinates(fplog, step, ir, mdatoms, pres, force_vir, shake_vir,
1295 pressureCouplingMu, state, nrnb, upd.deform(), !useGpuForUpdate);
1297 const bool doBerendsenPressureCoupling =
1298 (inputrec->epc == epcBERENDSEN && do_per_step(step, inputrec->nstpcouple));
1299 const bool doCRescalePressureCoupling =
1300 (inputrec->epc == epcCRESCALE && do_per_step(step, inputrec->nstpcouple));
1302 && (doBerendsenPressureCoupling || doCRescalePressureCoupling || doParrinelloRahman))
1304 integrator->scaleCoordinates(pressureCouplingMu);
1305 if (doCRescalePressureCoupling)
1307 matrix pressureCouplingInvMu;
1308 gmx::invertBoxMatrix(pressureCouplingMu, pressureCouplingInvMu);
1309 integrator->scaleVelocities(pressureCouplingInvMu);
1311 integrator->setPbc(PbcType::Xyz, state->box);
1314 /* ################# END UPDATE STEP 2 ################# */
1315 /* #### We now have r(t+dt) and v(t+dt/2) ############# */
1317 /* The coordinates (x) were unshifted in update */
1320 /* We will not sum ekinh_old,
1321 * so signal that we still have to do it.
1323 bSumEkinhOld = TRUE;
1328 /* ######### BEGIN PREPARING EDR OUTPUT ########### */
1330 /* use the directly determined last velocity, not actually the averaged half steps */
1331 if (bTrotter && ir->eI == eiVV)
1333 enerd->term[F_EKIN] = last_ekin;
1335 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
1337 if (integratorHasConservedEnergyQuantity(ir))
1341 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
1345 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + NPT_energy(ir, state, &MassQ);
1348 /* ######### END PREPARING EDR OUTPUT ########### */
1354 if (fplog && do_log && bDoExpanded)
1356 /* only needed if doing expanded ensemble */
1357 PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals,
1358 ir->bSimTemp ? ir->simtempvals : nullptr,
1359 state_global->dfhist, state->fep_state, ir->nstlog, step);
1363 energyOutput.addDataAtEnergyStep(
1364 bDoDHDL, bCalcEnerStep, t, mdatoms->tmass, enerd, ir->fepvals,
1365 ir->expandedvals, lastbox,
1366 PTCouplingArrays{ state->boxv, state->nosehoover_xi, state->nosehoover_vxi,
1367 state->nhpres_xi, state->nhpres_vxi },
1368 state->fep_state, shake_vir, force_vir, total_vir, pres, ekind, mu_tot, constr);
1372 energyOutput.recordNonEnergyStep();
1375 gmx_bool do_dr = do_per_step(step, ir->nstdisreout);
1376 gmx_bool do_or = do_per_step(step, ir->nstorireout);
1378 if (doSimulatedAnnealing)
1380 gmx::EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups,
1383 if (do_log || do_ene || do_dr || do_or)
1385 energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
1386 do_log ? fplog : nullptr, step, t,
1387 fr->fcdata.get(), awh.get());
1389 if (do_log && ir->bDoAwh && awh->hasFepLambdaDimension())
1391 const bool isInitialOutput = false;
1392 printLambdaStateToLog(fplog, state->lambda, isInitialOutput);
1397 pull_print_output(pull_work, step, t);
1400 if (do_per_step(step, ir->nstlog))
1402 if (fflush(fplog) != 0)
1404 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
1410 /* Have to do this part _after_ outputting the logfile and the edr file */
1411 /* Gets written into the state at the beginning of next loop*/
1412 state->fep_state = lamnew;
1414 else if (ir->bDoAwh && awh->needForeignEnergyDifferences(step))
1416 state->fep_state = awh->fepLambdaState();
1418 /* Print the remaining wall clock time for the run */
1419 if (isMasterSimMasterRank(ms, MASTER(cr)) && (do_verbose || gmx_got_usr_signal()) && !bPMETunePrinting)
1423 fprintf(stderr, "\n");
1425 print_time(stderr, walltime_accounting, step, ir, cr);
1428 /* Ion/water position swapping.
1429 * Not done in last step since trajectory writing happens before this call
1430 * in the MD loop and exchanges would be lost anyway. */
1431 bNeedRepartition = FALSE;
1432 if ((ir->eSwapCoords != eswapNO) && (step > 0) && !bLastStep && do_per_step(step, ir->swap->nstswap))
1435 do_swapcoords(cr, step, t, ir, swap, wcycle, as_rvec_array(state->x.data()),
1436 state->box, MASTER(cr) && mdrunOptions.verbose, bRerunMD);
1438 if (bNeedRepartition && DOMAINDECOMP(cr))
1440 dd_collect_state(cr->dd, state, state_global);
1444 /* Replica exchange */
1448 bExchanged = replica_exchange(fplog, cr, ms, repl_ex, state_global, enerd, state, step, t);
1451 if ((bExchanged || bNeedRepartition) && DOMAINDECOMP(cr))
1453 dd_partition_system(fplog, mdlog, step, cr, TRUE, 1, state_global, *top_global, ir,
1454 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
1455 nrnb, wcycle, FALSE);
1456 shouldCheckNumberOfBondedInteractions = true;
1457 upd.setNumAtoms(state->natoms);
1463 /* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
1464 /* With all integrators, except VV, we need to retain the pressure
1465 * at the current step for coupling at the next step.
1467 if ((state->flags & (1U << estPRES_PREV))
1468 && (bGStatEveryStep || (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
1470 /* Store the pressure in t_state for pressure coupling
1471 * at the next MD step.
1473 copy_mat(pres, state->pres_prev);
1476 /* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
1478 if ((membed != nullptr) && (!bLastStep))
1480 rescale_membed(step_rel, membed, as_rvec_array(state_global->x.data()));
1483 cycles = wallcycle_stop(wcycle, ewcSTEP);
1484 if (DOMAINDECOMP(cr) && wcycle)
1486 dd_cycles_add(cr->dd, cycles, ddCyclStep);
1489 /* increase the MD step number */
1496 fcReportProgress(ir->nsteps + ir->init_step, step);
1500 resetHandler->resetCounters(step, step_rel, mdlog, fplog, cr, fr->nbv.get(), nrnb,
1501 fr->pmedata, pme_loadbal, wcycle, walltime_accounting);
1503 /* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
1504 imdSession->updateEnergyRecordAndSendPositionsAndEnergies(bInteractiveMDstep, step, bCalcEner);
1506 /* End of main MD loop */
1508 /* Closing TNG files can include compressing data. Therefore it is good to do that
1509 * before stopping the time measurements. */
1510 mdoutf_tng_close(outf);
1512 /* Stop measuring walltime */
1513 walltime_accounting_end_time(walltime_accounting);
1515 if (!thisRankHasDuty(cr, DUTY_PME))
1517 /* Tell the PME only node to finish */
1518 gmx_pme_send_finish(cr);
1523 if (ir->nstcalcenergy > 0)
1525 energyOutput.printEnergyConservation(fplog, ir->simulation_part, EI_MD(ir->eI));
1527 gmx::EnergyOutput::printAnnealingTemperatures(fplog, groups, &(ir->opts));
1528 energyOutput.printAverages(fplog, groups);
1535 pme_loadbal_done(pme_loadbal, fplog, mdlog, fr->nbv->useGpu());
1538 done_shellfc(fplog, shellfc, step_rel);
1540 if (useReplicaExchange && MASTER(cr))
1542 print_replica_exchange_statistics(fplog, repl_ex);
1545 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
1547 global_stat_destroy(gstat);