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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, mdModulesNotifier);
302 gstat = global_stat_init(ir);
304 const auto& simulationWork = runScheduleWork->simulationWork;
305 const bool useGpuForPme = simulationWork.useGpuPme;
306 const bool useGpuForNonbonded = simulationWork.useGpuNonbonded;
307 const bool useGpuForBufferOps = simulationWork.useGpuBufferOps;
308 const bool useGpuForUpdate = simulationWork.useGpuUpdate;
310 /* Check for polarizable models and flexible constraints */
311 shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
312 ir->nstcalcenergy, DOMAINDECOMP(cr), useGpuForPme);
315 double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
316 if ((io > 2000) && MASTER(cr))
318 fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
322 // Local state only becomes valid now.
323 std::unique_ptr<t_state> stateInstance;
326 gmx_localtop_t top(top_global->ffparams);
328 auto mdatoms = mdAtoms->mdatoms();
330 ForceBuffers f(fr->useMts, ((useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
331 ? PinningPolicy::PinnedIfSupported
332 : PinningPolicy::CannotBePinned);
333 if (DOMAINDECOMP(cr))
335 stateInstance = std::make_unique<t_state>();
336 state = stateInstance.get();
337 dd_init_local_state(cr->dd, state_global, state);
339 /* Distribute the charge groups over the nodes from the master node */
340 dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
341 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
342 nrnb, nullptr, FALSE);
343 shouldCheckNumberOfBondedInteractions = true;
344 upd.setNumAtoms(state->natoms);
348 state_change_natoms(state_global, state_global->natoms);
349 /* Copy the pointer to the global state */
350 state = state_global;
352 /* Generate and initialize new topology */
353 mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
355 upd.setNumAtoms(state->natoms);
358 std::unique_ptr<UpdateConstrainGpu> integrator;
360 StatePropagatorDataGpu* stateGpu = fr->stateGpu;
362 // TODO: the assertions below should be handled by UpdateConstraintsBuilder.
365 GMX_RELEASE_ASSERT(!DOMAINDECOMP(cr) || ddUsesUpdateGroups(*cr->dd) || constr == nullptr
366 || constr->numConstraintsTotal() == 0,
367 "Constraints in domain decomposition are only supported with update "
368 "groups if using GPU update.\n");
369 GMX_RELEASE_ASSERT(ir->eConstrAlg != econtSHAKE || constr == nullptr
370 || constr->numConstraintsTotal() == 0,
371 "SHAKE is not supported with GPU update.");
372 GMX_RELEASE_ASSERT(useGpuForPme || (useGpuForNonbonded && simulationWork.useGpuBufferOps),
373 "Either PME or short-ranged non-bonded interaction tasks must run on "
374 "the GPU to use GPU update.\n");
375 GMX_RELEASE_ASSERT(ir->eI == eiMD,
376 "Only the md integrator is supported with the GPU update.\n");
378 ir->etc != etcNOSEHOOVER,
379 "Nose-Hoover temperature coupling is not supported with the GPU update.\n");
381 ir->epc == epcNO || ir->epc == epcPARRINELLORAHMAN || ir->epc == epcBERENDSEN
382 || ir->epc == epcCRESCALE,
383 "Only Parrinello-Rahman, Berendsen, and C-rescale pressure coupling are supported "
384 "with the GPU update.\n");
385 GMX_RELEASE_ASSERT(!mdatoms->haveVsites,
386 "Virtual sites are not supported with the GPU update.\n");
387 GMX_RELEASE_ASSERT(ed == nullptr,
388 "Essential dynamics is not supported with the GPU update.\n");
389 GMX_RELEASE_ASSERT(!ir->bPull || !pull_have_constraint(*ir->pull),
390 "Constraints pulling is not supported with the GPU update.\n");
391 GMX_RELEASE_ASSERT(fcdata.orires->nr == 0,
392 "Orientation restraints are not supported with the GPU update.\n");
395 || (!haveFreeEnergyType(*ir, efptBONDED) && !haveFreeEnergyType(*ir, efptMASS)),
396 "Free energy perturbation of masses and constraints are not supported with the GPU "
399 if (constr != nullptr && constr->numConstraintsTotal() > 0)
403 .appendText("Updating coordinates and applying constraints on the GPU.");
407 GMX_LOG(mdlog.info).asParagraph().appendText("Updating coordinates on the GPU.");
409 GMX_RELEASE_ASSERT(fr->deviceStreamManager != nullptr,
410 "Device stream manager should be initialized in order to use GPU "
411 "update-constraints.");
413 fr->deviceStreamManager->streamIsValid(gmx::DeviceStreamType::UpdateAndConstraints),
414 "Update stream should be initialized in order to use GPU "
415 "update-constraints.");
416 integrator = std::make_unique<UpdateConstrainGpu>(
417 *ir, *top_global, fr->deviceStreamManager->context(),
418 fr->deviceStreamManager->stream(gmx::DeviceStreamType::UpdateAndConstraints),
419 stateGpu->xUpdatedOnDevice(), wcycle);
421 integrator->setPbc(PbcType::Xyz, state->box);
424 if (useGpuForPme || (useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
426 changePinningPolicy(&state->x, 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 nstfep = std::gcd(ir->awhParams->nstSampleCoord, nstfep);
538 /* Be REALLY careful about what flags you set here. You CANNOT assume
539 * this is the first step, since we might be restarting from a checkpoint,
540 * and in that case we should not do any modifications to the state.
542 bStopCM = (ir->comm_mode != ecmNO && !ir->bContinuation);
544 // When restarting from a checkpoint, it can be appropriate to
545 // initialize ekind from quantities in the checkpoint. Otherwise,
546 // compute_globals must initialize ekind before the simulation
547 // starts/restarts. However, only the master rank knows what was
548 // found in the checkpoint file, so we have to communicate in
549 // order to coordinate the restart.
551 // TODO Consider removing this communication if/when checkpoint
552 // reading directly follows .tpr reading, because all ranks can
553 // agree on hasReadEkinState at that time.
554 bool hasReadEkinState = MASTER(cr) ? state_global->ekinstate.hasReadEkinState : false;
557 gmx_bcast(sizeof(hasReadEkinState), &hasReadEkinState, cr->mpi_comm_mygroup);
559 if (hasReadEkinState)
561 restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
564 unsigned int cglo_flags =
565 (CGLO_TEMPERATURE | CGLO_GSTAT | (EI_VV(ir->eI) ? CGLO_PRESSURE : 0)
566 | (EI_VV(ir->eI) ? CGLO_CONSTRAINT : 0) | (hasReadEkinState ? CGLO_READEKIN : 0));
568 bSumEkinhOld = FALSE;
570 t_vcm vcm(top_global->groups, *ir);
571 reportComRemovalInfo(fplog, vcm);
573 /* To minimize communication, compute_globals computes the COM velocity
574 * and the kinetic energy for the velocities without COM motion removed.
575 * Thus to get the kinetic energy without the COM contribution, we need
576 * to call compute_globals twice.
578 for (int cgloIteration = 0; cgloIteration < (bStopCM ? 2 : 1); cgloIteration++)
580 unsigned int cglo_flags_iteration = cglo_flags;
581 if (bStopCM && cgloIteration == 0)
583 cglo_flags_iteration |= CGLO_STOPCM;
584 cglo_flags_iteration &= ~CGLO_TEMPERATURE;
586 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
587 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
588 enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
589 state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
591 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
593 if (cglo_flags_iteration & CGLO_STOPCM)
595 /* At initialization, do not pass x with acceleration-correction mode
596 * to avoid (incorrect) correction of the initial coordinates.
598 auto x = (vcm.mode == ecmLINEAR_ACCELERATION_CORRECTION) ? ArrayRef<RVec>()
599 : makeArrayRef(state->x);
600 process_and_stopcm_grp(fplog, &vcm, *mdatoms, x, makeArrayRef(state->v));
601 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
604 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
605 makeConstArrayRef(state->x), state->box,
606 &shouldCheckNumberOfBondedInteractions);
607 if (ir->eI == eiVVAK)
609 /* a second call to get the half step temperature initialized as well */
610 /* we do the same call as above, but turn the pressure off -- internally to
611 compute_globals, this is recognized as a velocity verlet half-step
612 kinetic energy calculation. This minimized excess variables, but
613 perhaps loses some logic?*/
615 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
616 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
617 enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
618 state->box, nullptr, &bSumEkinhOld, cglo_flags & ~CGLO_PRESSURE);
621 /* Calculate the initial half step temperature, and save the ekinh_old */
622 if (startingBehavior == StartingBehavior::NewSimulation)
624 for (i = 0; (i < ir->opts.ngtc); i++)
626 copy_mat(ekind->tcstat[i].ekinh, ekind->tcstat[i].ekinh_old);
630 /* need to make an initiation call to get the Trotter variables set, as well as other constants
631 for non-trotter temperature control */
632 auto trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
636 if (!ir->bContinuation)
638 if (constr && ir->eConstrAlg == econtLINCS)
640 fprintf(fplog, "RMS relative constraint deviation after constraining: %.2e\n",
643 if (EI_STATE_VELOCITY(ir->eI))
645 real temp = enerd->term[F_TEMP];
648 /* Result of Ekin averaged over velocities of -half
649 * and +half step, while we only have -half step here.
653 fprintf(fplog, "Initial temperature: %g K\n", temp);
658 fprintf(stderr, "starting mdrun '%s'\n", *(top_global->name));
661 sprintf(tbuf, "%8.1f", (ir->init_step + ir->nsteps) * ir->delta_t);
665 sprintf(tbuf, "%s", "infinite");
667 if (ir->init_step > 0)
669 fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
670 gmx_step_str(ir->init_step + ir->nsteps, sbuf), tbuf,
671 gmx_step_str(ir->init_step, sbuf2), ir->init_step * ir->delta_t);
675 fprintf(stderr, "%s steps, %s ps.\n", gmx_step_str(ir->nsteps, sbuf), tbuf);
677 fprintf(fplog, "\n");
680 walltime_accounting_start_time(walltime_accounting);
681 wallcycle_start(wcycle, ewcRUN);
682 print_start(fplog, cr, walltime_accounting, "mdrun");
684 /***********************************************************
688 ************************************************************/
691 /* Skip the first Nose-Hoover integration when we get the state from tpx */
692 bInitStep = startingBehavior == StartingBehavior::NewSimulation || EI_VV(ir->eI);
693 bSumEkinhOld = FALSE;
695 bNeedRepartition = FALSE;
697 step = ir->init_step;
700 auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
701 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), simulationsShareState,
702 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstSignalComm,
703 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
705 auto checkpointHandler = std::make_unique<CheckpointHandler>(
706 compat::make_not_null<SimulationSignal*>(&signals[eglsCHKPT]), simulationsShareState,
707 ir->nstlist == 0, MASTER(cr), mdrunOptions.writeConfout,
708 mdrunOptions.checkpointOptions.period);
710 const bool resetCountersIsLocal = true;
711 auto resetHandler = std::make_unique<ResetHandler>(
712 compat::make_not_null<SimulationSignal*>(&signals[eglsRESETCOUNTERS]),
713 !resetCountersIsLocal, ir->nsteps, MASTER(cr), mdrunOptions.timingOptions.resetHalfway,
714 mdrunOptions.maximumHoursToRun, mdlog, wcycle, walltime_accounting);
716 const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
718 if (MASTER(cr) && isMultiSim(ms) && !useReplicaExchange)
720 logInitialMultisimStatus(ms, cr, mdlog, simulationsShareState, ir->nsteps, ir->init_step);
723 /* and stop now if we should */
724 bLastStep = (bLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
728 /* Determine if this is a neighbor search step */
729 bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
731 if (bPMETune && bNStList)
733 // This has to be here because PME load balancing is called so early.
734 // TODO: Move to after all booleans are defined.
735 if (useGpuForUpdate && !bFirstStep)
737 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
738 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
740 /* PME grid + cut-off optimization with GPUs or PME nodes */
741 pme_loadbal_do(pme_loadbal, cr, (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
742 fplog, mdlog, *ir, fr, state->box, state->x, wcycle, step, step_rel,
743 &bPMETunePrinting, simulationWork.useGpuPmePpCommunication);
746 wallcycle_start(wcycle, ewcSTEP);
748 bLastStep = (step_rel == ir->nsteps);
749 t = t0 + step * ir->delta_t;
751 // TODO Refactor this, so that nstfep does not need a default value of zero
752 if (ir->efep != efepNO || ir->bSimTemp)
754 /* find and set the current lambdas */
755 state->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
757 bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
758 bDoFEP = ((ir->efep != efepNO) && do_per_step(step, nstfep));
759 bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded) && (ir->bExpanded)
763 bDoReplEx = (useReplicaExchange && (step > 0) && !bLastStep
764 && do_per_step(step, replExParams.exchangeInterval));
766 if (doSimulatedAnnealing)
768 update_annealing_target_temp(ir, t, &upd);
771 /* Stop Center of Mass motion */
772 bStopCM = (ir->comm_mode != ecmNO && do_per_step(step, ir->nstcomm));
774 /* Determine whether or not to do Neighbour Searching */
775 bNS = (bFirstStep || bNStList || bExchanged || bNeedRepartition);
777 /* Note that the stopHandler will cause termination at nstglobalcomm
778 * steps. Since this concides with nstcalcenergy, nsttcouple and/or
779 * nstpcouple steps, we have computed the half-step kinetic energy
780 * of the previous step and can always output energies at the last step.
782 bLastStep = bLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
784 /* do_log triggers energy and virial calculation. Because this leads
785 * to different code paths, forces can be different. Thus for exact
786 * continuation we should avoid extra log output.
787 * Note that the || bLastStep can result in non-exact continuation
788 * beyond the last step. But we don't consider that to be an issue.
790 do_log = (do_per_step(step, ir->nstlog)
791 || (bFirstStep && startingBehavior == StartingBehavior::NewSimulation) || bLastStep);
792 do_verbose = mdrunOptions.verbose
793 && (step % mdrunOptions.verboseStepPrintInterval == 0 || bFirstStep || bLastStep);
795 if (useGpuForUpdate && !bFirstStep && bNS)
797 // Copy velocities from the GPU on search steps to keep a copy on host (device buffers are reinitialized).
798 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
799 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
800 // Copy coordinate from the GPU when needed at the search step.
801 // NOTE: The cases when coordinates needed on CPU for force evaluation are handled in sim_utils.
802 // NOTE: If the coordinates are to be written into output file they are also copied separately before the output.
803 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
804 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
807 if (bNS && !(bFirstStep && ir->bContinuation))
809 bMasterState = FALSE;
810 /* Correct the new box if it is too skewed */
811 if (inputrecDynamicBox(ir))
813 if (correct_box(fplog, step, state->box))
816 // If update is offloaded, it should be informed about the box size change
819 integrator->setPbc(PbcType::Xyz, state->box);
823 if (DOMAINDECOMP(cr) && bMasterState)
825 dd_collect_state(cr->dd, state, state_global);
828 if (DOMAINDECOMP(cr))
830 /* Repartition the domain decomposition */
831 dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
832 *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
833 fr, vsite, constr, nrnb, wcycle, do_verbose && !bPMETunePrinting);
834 shouldCheckNumberOfBondedInteractions = true;
835 upd.setNumAtoms(state->natoms);
839 // Allocate or re-size GPU halo exchange object, if necessary
840 if (bNS && havePPDomainDecomposition(cr) && simulationWork.useGpuHaloExchange)
842 GMX_RELEASE_ASSERT(fr->deviceStreamManager != nullptr,
843 "GPU device manager has to be initialized to use GPU "
844 "version of halo exchange.");
845 constructGpuHaloExchange(mdlog, *cr, *fr->deviceStreamManager, wcycle);
848 if (MASTER(cr) && do_log)
850 gmx::EnergyOutput::printHeader(fplog, step,
851 t); /* can we improve the information printed here? */
854 if (ir->efep != efepNO)
856 update_mdatoms(mdatoms, state->lambda[efptMASS]);
861 /* We need the kinetic energy at minus the half step for determining
862 * the full step kinetic energy and possibly for T-coupling.*/
863 /* This may not be quite working correctly yet . . . . */
864 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
865 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
866 enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
867 state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
868 CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
869 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
870 &top, makeConstArrayRef(state->x), state->box,
871 &shouldCheckNumberOfBondedInteractions);
873 clear_mat(force_vir);
875 checkpointHandler->decideIfCheckpointingThisStep(bNS, bFirstStep, bLastStep);
877 /* Determine the energy and pressure:
878 * at nstcalcenergy steps and at energy output steps (set below).
880 if (EI_VV(ir->eI) && (!bInitStep))
882 bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
883 bCalcVir = bCalcEnerStep
885 && (do_per_step(step, ir->nstpcouple) || do_per_step(step - 1, ir->nstpcouple)));
889 bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
890 bCalcVir = bCalcEnerStep || (ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
892 bCalcEner = bCalcEnerStep;
894 do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
896 if (do_ene || do_log || bDoReplEx)
902 /* Do we need global communication ? */
903 bGStat = (bCalcVir || bCalcEner || bStopCM || do_per_step(step, nstglobalcomm)
904 || (EI_VV(ir->eI) && inputrecNvtTrotter(ir) && do_per_step(step - 1, nstglobalcomm)));
906 force_flags = (GMX_FORCE_STATECHANGED | ((inputrecDynamicBox(ir)) ? GMX_FORCE_DYNAMICBOX : 0)
907 | GMX_FORCE_ALLFORCES | (bCalcVir ? GMX_FORCE_VIRIAL : 0)
908 | (bCalcEner ? GMX_FORCE_ENERGY : 0) | (bDoFEP ? GMX_FORCE_DHDL : 0));
909 if (fr->useMts && !do_per_step(step, ir->nstfout))
911 force_flags |= GMX_FORCE_DO_NOT_NEED_NORMAL_FORCE;
916 /* Now is the time to relax the shells */
917 relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
918 imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
919 state->natoms, state->x.arrayRefWithPadding(),
920 state->v.arrayRefWithPadding(), state->box, state->lambda,
921 &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
922 fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
926 /* The AWH history need to be saved _before_ doing force calculations where the AWH bias
927 is updated (or the AWH update will be performed twice for one step when continuing).
928 It would be best to call this update function from do_md_trajectory_writing but that
929 would occur after do_force. One would have to divide the update_awh function into one
930 function applying the AWH force and one doing the AWH bias update. The update AWH
931 bias function could then be called after do_md_trajectory_writing (then containing
932 update_awh_history). The checkpointing will in the future probably moved to the start
933 of the md loop which will rid of this issue. */
934 if (awh && checkpointHandler->isCheckpointingStep() && MASTER(cr))
936 awh->updateHistory(state_global->awhHistory.get());
939 /* The coordinates (x) are shifted (to get whole molecules)
941 * This is parallellized as well, and does communication too.
942 * Check comments in sim_util.c
944 do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step,
945 nrnb, wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
946 &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
947 vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
948 (bNS ? GMX_FORCE_NS : 0) | force_flags, ddBalanceRegionHandler);
951 // VV integrators do not need the following velocity half step
952 // if it is the first step after starting from a checkpoint.
953 // That is, the half step is needed on all other steps, and
954 // also the first step when starting from a .tpr file.
957 integrateVVFirstStep(step, bFirstStep, bInitStep, startingBehavior, nstglobalcomm, ir,
958 fr, cr, state, mdatoms, fcdata, &MassQ, &vcm, top_global, top, enerd,
959 ekind, gstat, &last_ekin, bCalcVir, total_vir, shake_vir, force_vir,
960 pres, M, do_log, do_ene, bCalcEner, bGStat, bStopCM, bTrotter,
961 bExchanged, &bSumEkinhOld, &shouldCheckNumberOfBondedInteractions,
962 &saved_conserved_quantity, &f, &upd, constr, &nullSignaller,
963 trotter_seq, nrnb, mdlog, fplog, wcycle);
966 /* ######## END FIRST UPDATE STEP ############## */
967 /* ######## If doing VV, we now have v(dt) ###### */
970 /* perform extended ensemble sampling in lambda - we don't
971 actually move to the new state before outputting
972 statistics, but if performing simulated tempering, we
973 do update the velocities and the tau_t. */
975 lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, state->fep_state,
976 state->dfhist, step, state->v.rvec_array(), mdatoms);
977 /* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
980 copy_df_history(state_global->dfhist, state->dfhist);
984 // Copy coordinate from the GPU for the output/checkpointing if the update is offloaded and
985 // coordinates have not already been copied for i) search or ii) CPU force tasks.
986 if (useGpuForUpdate && !bNS && !runScheduleWork->domainWork.haveCpuLocalForceWork
987 && (do_per_step(step, ir->nstxout) || do_per_step(step, ir->nstxout_compressed)
988 || checkpointHandler->isCheckpointingStep()))
990 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
991 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
993 // Copy velocities if needed for the output/checkpointing.
994 // NOTE: Copy on the search steps is done at the beginning of the step.
995 if (useGpuForUpdate && !bNS
996 && (do_per_step(step, ir->nstvout) || checkpointHandler->isCheckpointingStep()))
998 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
999 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
1001 // Copy forces for the output if the forces were reduced on the GPU (not the case on virial steps)
1002 // and update is offloaded hence forces are kept on the GPU for update and have not been
1003 // already transferred in do_force().
1004 // TODO: There should be an improved, explicit mechanism that ensures this copy is only executed
1005 // when the forces are ready on the GPU -- the same synchronizer should be used as the one
1006 // prior to GPU update.
1007 // TODO: When the output flags will be included in step workload, this copy can be combined with the
1008 // copy call in do_force(...).
1009 // NOTE: The forces should not be copied here if the vsites are present, since they were modified
1010 // on host after the D2H copy in do_force(...).
1011 if (runScheduleWork->stepWork.useGpuFBufferOps && (simulationWork.useGpuUpdate && !vsite)
1012 && do_per_step(step, ir->nstfout))
1014 stateGpu->copyForcesFromGpu(f.view().force(), AtomLocality::Local);
1015 stateGpu->waitForcesReadyOnHost(AtomLocality::Local);
1017 /* Now we have the energies and forces corresponding to the
1018 * coordinates at time t. We must output all of this before
1021 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state, state_global,
1022 observablesHistory, top_global, fr, outf, energyOutput, ekind,
1023 f.view().force(), checkpointHandler->isCheckpointingStep(),
1024 bRerunMD, bLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
1025 /* Check if IMD step and do IMD communication, if bIMD is TRUE. */
1026 bInteractiveMDstep = imdSession->run(step, bNS, state->box, state->x.rvec_array(), t);
1028 /* kludge -- virial is lost with restart for MTTK NPT control. Must reload (saved earlier). */
1029 if (startingBehavior != StartingBehavior::NewSimulation && bFirstStep
1030 && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir)))
1032 copy_mat(state->svir_prev, shake_vir);
1033 copy_mat(state->fvir_prev, force_vir);
1036 stopHandler->setSignal();
1037 resetHandler->setSignal(walltime_accounting);
1039 if (bGStat || !PAR(cr))
1041 /* In parallel we only have to check for checkpointing in steps
1042 * where we do global communication,
1043 * otherwise the other nodes don't know.
1045 checkpointHandler->setSignal(walltime_accounting);
1048 /* ######### START SECOND UPDATE STEP ################# */
1050 /* at the start of step, randomize or scale the velocities ((if vv. Restriction of Andersen
1051 controlled in preprocessing */
1053 if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
1055 gmx_bool bIfRandomize;
1056 bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
1057 /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
1058 if (constr && bIfRandomize)
1060 constrain_velocities(constr, do_log, do_ene, step, state, nullptr, false, nullptr);
1063 /* Box is changed in update() when we do pressure coupling,
1064 * but we should still use the old box for energy corrections and when
1065 * writing it to the energy file, so it matches the trajectory files for
1066 * the same timestep above. Make a copy in a separate array.
1068 copy_mat(state->box, lastbox);
1072 wallcycle_start(wcycle, ewcUPDATE);
1073 /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
1076 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
1077 /* We can only do Berendsen coupling after we have summed
1078 * the kinetic energy or virial. Since the happens
1079 * in global_state after update, we should only do it at
1080 * step % nstlist = 1 with bGStatEveryStep=FALSE.
1085 update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
1086 update_pcouple_before_coordinates(fplog, step, ir, state, pressureCouplingMu, M, bInitStep);
1089 /* With leap-frog type integrators we compute the kinetic energy
1090 * at a whole time step as the average of the half-time step kinetic
1091 * energies of two subsequent steps. Therefore we need to compute the
1092 * half step kinetic energy also if we need energies at the next step.
1094 const bool needHalfStepKineticEnergy =
1095 (!EI_VV(ir->eI) && (do_per_step(step + 1, nstglobalcomm) || step_rel + 1 == ir->nsteps));
1097 // Parrinello-Rahman requires the pressure to be availible before the update to compute
1098 // the velocity scaling matrix. Hence, it runs one step after the nstpcouple step.
1099 const bool doParrinelloRahman = (ir->epc == epcPARRINELLORAHMAN
1100 && do_per_step(step + ir->nstpcouple - 1, ir->nstpcouple));
1104 GMX_ASSERT(!useGpuForUpdate, "GPU update is not supported with VVAK integrator.");
1106 integrateVVSecondStep(step, ir, fr, cr, state, mdatoms, fcdata, &MassQ, &vcm, pull_work,
1107 enerd, ekind, gstat, &dvdl_constr, bCalcVir, total_vir, shake_vir,
1108 force_vir, pres, M, lastbox, do_log, do_ene, bGStat, &bSumEkinhOld,
1109 &f, &cbuf, &upd, constr, &nullSignaller, trotter_seq, nrnb, wcycle);
1113 if (useGpuForUpdate)
1116 wallcycle_stop(wcycle, ewcUPDATE);
1118 if (bNS && (bFirstStep || DOMAINDECOMP(cr)))
1120 integrator->set(stateGpu->getCoordinates(), stateGpu->getVelocities(),
1121 stateGpu->getForces(), top.idef, *mdatoms, ekind->ngtc);
1123 // Copy data to the GPU after buffers might have being reinitialized
1124 stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
1125 stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
1128 if (simulationWork.useGpuPme && !runScheduleWork->simulationWork.useGpuPmePpCommunication
1129 && !thisRankHasDuty(cr, DUTY_PME))
1131 // The PME forces were recieved to the host, so have to be copied
1132 stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::All);
1134 else if (!runScheduleWork->stepWork.useGpuFBufferOps)
1136 // The buffer ops were not offloaded this step, so the forces are on the
1137 // host and have to be copied
1138 stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::Local);
1141 const bool doTemperatureScaling =
1142 (ir->etc != etcNO && do_per_step(step + ir->nsttcouple - 1, ir->nsttcouple));
1144 // This applies Leap-Frog, LINCS and SETTLE in succession
1145 integrator->integrate(
1146 stateGpu->getForcesReadyOnDeviceEvent(
1147 AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
1148 ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling, ekind->tcstat,
1149 doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
1151 // Copy velocities D2H after update if:
1152 // - Globals are computed this step (includes the energy output steps).
1153 // - Temperature is needed for the next step.
1154 if (bGStat || needHalfStepKineticEnergy)
1156 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
1157 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
1162 /* With multiple time stepping we need to do an additional normal
1163 * update step to obtain the virial, as the actual MTS integration
1164 * using an acceleration where the slow forces are multiplied by mtsFactor.
1165 * Using that acceleration would result in a virial with the slow
1166 * force contribution would be a factor mtsFactor too large.
1168 if (fr->useMts && bCalcVir && constr != nullptr)
1170 upd.update_for_constraint_virial(*ir, *mdatoms, *state,
1171 f.view().forceWithPadding(), *ekind);
1173 constrain_coordinates(constr, do_log, do_ene, step, state,
1174 upd.xp()->arrayRefWithPadding(), &dvdl_constr, bCalcVir,
1178 ArrayRefWithPadding<const RVec> forceCombined =
1179 (fr->useMts && step % ir->mtsLevels[1].stepFactor == 0)
1180 ? f.view().forceMtsCombinedWithPadding()
1181 : f.view().forceWithPadding();
1182 upd.update_coords(*ir, step, mdatoms, state, forceCombined, fcdata, ekind, M,
1183 etrtPOSITION, cr, constr != nullptr);
1185 wallcycle_stop(wcycle, ewcUPDATE);
1187 constrain_coordinates(constr, do_log, do_ene, step, state,
1188 upd.xp()->arrayRefWithPadding(), &dvdl_constr,
1189 bCalcVir && !fr->useMts, shake_vir);
1191 upd.update_sd_second_half(*ir, step, &dvdl_constr, mdatoms, state, cr, nrnb, wcycle,
1192 constr, do_log, do_ene);
1193 upd.finish_update(*ir, mdatoms, state, wcycle, constr != nullptr);
1196 if (ir->bPull && ir->pull->bSetPbcRefToPrevStepCOM)
1198 updatePrevStepPullCom(pull_work, state);
1201 enerd->term[F_DVDL_CONSTR] += dvdl_constr;
1204 if (vsite != nullptr)
1206 wallcycle_start(wcycle, ewcVSITECONSTR);
1207 vsite->construct(state->x, ir->delta_t, state->v, state->box);
1208 wallcycle_stop(wcycle, ewcVSITECONSTR);
1211 /* ############## IF NOT VV, Calculate globals HERE ############ */
1212 /* With Leap-Frog we can skip compute_globals at
1213 * non-communication steps, but we need to calculate
1214 * the kinetic energy one step before communication.
1217 // Organize to do inter-simulation signalling on steps if
1218 // and when algorithms require it.
1219 const bool doInterSimSignal = (simulationsShareState && do_per_step(step, nstSignalComm));
1221 if (bGStat || needHalfStepKineticEnergy || doInterSimSignal)
1223 // Copy coordinates when needed to stop the CM motion.
1224 if (useGpuForUpdate && !EI_VV(ir->eI) && bStopCM)
1226 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
1227 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
1229 // Since we're already communicating at this step, we
1230 // can propagate intra-simulation signals. Note that
1231 // check_nstglobalcomm has the responsibility for
1232 // choosing the value of nstglobalcomm that is one way
1233 // bGStat becomes true, so we can't get into a
1234 // situation where e.g. checkpointing can't be
1236 bool doIntraSimSignal = true;
1237 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
1239 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
1240 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm,
1241 wcycle, enerd, force_vir, shake_vir, total_vir, pres, constr,
1242 &signaller, lastbox, &totalNumberOfBondedInteractions, &bSumEkinhOld,
1243 (bGStat ? CGLO_GSTAT : 0) | (!EI_VV(ir->eI) && bCalcEner ? CGLO_ENERGY : 0)
1244 | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
1245 | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
1246 | (!EI_VV(ir->eI) ? CGLO_PRESSURE : 0) | CGLO_CONSTRAINT
1247 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
1249 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
1250 top_global, &top, makeConstArrayRef(state->x),
1251 state->box, &shouldCheckNumberOfBondedInteractions);
1252 if (!EI_VV(ir->eI) && bStopCM)
1254 process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
1255 makeArrayRef(state->v));
1256 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
1258 // TODO: The special case of removing CM motion should be dealt more gracefully
1259 if (useGpuForUpdate)
1261 stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
1262 // Here we block until the H2D copy completes because event sync with the
1263 // force kernels that use the coordinates on the next steps is not implemented
1264 // (not because of a race on state->x being modified on the CPU while H2D is in progress).
1265 stateGpu->waitCoordinatesCopiedToDevice(AtomLocality::Local);
1266 // If the COM removal changed the velocities on the CPU, this has to be accounted for.
1267 if (vcm.mode != ecmNO)
1269 stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
1276 /* ############# END CALC EKIN AND PRESSURE ################# */
1278 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
1279 the virial that should probably be addressed eventually. state->veta has better properies,
1280 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
1281 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
1283 if (ir->efep != efepNO && !EI_VV(ir->eI))
1285 /* Sum up the foreign energy and dK/dl terms for md and sd.
1286 Currently done every step so that dH/dl is correct in the .edr */
1287 accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
1290 update_pcouple_after_coordinates(fplog, step, ir, mdatoms, pres, force_vir, shake_vir,
1291 pressureCouplingMu, state, nrnb, upd.deform(), !useGpuForUpdate);
1293 const bool doBerendsenPressureCoupling =
1294 (inputrec->epc == epcBERENDSEN && do_per_step(step, inputrec->nstpcouple));
1295 const bool doCRescalePressureCoupling =
1296 (inputrec->epc == epcCRESCALE && do_per_step(step, inputrec->nstpcouple));
1298 && (doBerendsenPressureCoupling || doCRescalePressureCoupling || doParrinelloRahman))
1300 integrator->scaleCoordinates(pressureCouplingMu);
1301 if (doCRescalePressureCoupling)
1303 matrix pressureCouplingInvMu;
1304 gmx::invertBoxMatrix(pressureCouplingMu, pressureCouplingInvMu);
1305 integrator->scaleVelocities(pressureCouplingInvMu);
1307 integrator->setPbc(PbcType::Xyz, state->box);
1310 /* ################# END UPDATE STEP 2 ################# */
1311 /* #### We now have r(t+dt) and v(t+dt/2) ############# */
1313 /* The coordinates (x) were unshifted in update */
1316 /* We will not sum ekinh_old,
1317 * so signal that we still have to do it.
1319 bSumEkinhOld = TRUE;
1324 /* ######### BEGIN PREPARING EDR OUTPUT ########### */
1326 /* use the directly determined last velocity, not actually the averaged half steps */
1327 if (bTrotter && ir->eI == eiVV)
1329 enerd->term[F_EKIN] = last_ekin;
1331 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
1333 if (integratorHasConservedEnergyQuantity(ir))
1337 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
1341 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + NPT_energy(ir, state, &MassQ);
1344 /* ######### END PREPARING EDR OUTPUT ########### */
1350 if (fplog && do_log && bDoExpanded)
1352 /* only needed if doing expanded ensemble */
1353 PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals,
1354 ir->bSimTemp ? ir->simtempvals : nullptr,
1355 state_global->dfhist, state->fep_state, ir->nstlog, step);
1359 energyOutput.addDataAtEnergyStep(
1360 bDoDHDL, bCalcEnerStep, t, mdatoms->tmass, enerd, ir->fepvals,
1361 ir->expandedvals, lastbox,
1362 PTCouplingArrays{ state->boxv, state->nosehoover_xi, state->nosehoover_vxi,
1363 state->nhpres_xi, state->nhpres_vxi },
1364 state->fep_state, shake_vir, force_vir, total_vir, pres, ekind, mu_tot, constr);
1368 energyOutput.recordNonEnergyStep();
1371 gmx_bool do_dr = do_per_step(step, ir->nstdisreout);
1372 gmx_bool do_or = do_per_step(step, ir->nstorireout);
1374 if (doSimulatedAnnealing)
1376 gmx::EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups,
1379 if (do_log || do_ene || do_dr || do_or)
1381 energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
1382 do_log ? fplog : nullptr, step, t,
1383 fr->fcdata.get(), awh.get());
1385 if (do_log && ir->bDoAwh && awh->hasFepLambdaDimension())
1387 const bool isInitialOutput = false;
1388 printLambdaStateToLog(fplog, state->lambda, isInitialOutput);
1393 pull_print_output(pull_work, step, t);
1396 if (do_per_step(step, ir->nstlog))
1398 if (fflush(fplog) != 0)
1400 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
1406 /* Have to do this part _after_ outputting the logfile and the edr file */
1407 /* Gets written into the state at the beginning of next loop*/
1408 state->fep_state = lamnew;
1410 else if (ir->bDoAwh && awh->needForeignEnergyDifferences(step))
1412 state->fep_state = awh->fepLambdaState();
1414 /* Print the remaining wall clock time for the run */
1415 if (isMasterSimMasterRank(ms, MASTER(cr)) && (do_verbose || gmx_got_usr_signal()) && !bPMETunePrinting)
1419 fprintf(stderr, "\n");
1421 print_time(stderr, walltime_accounting, step, ir, cr);
1424 /* Ion/water position swapping.
1425 * Not done in last step since trajectory writing happens before this call
1426 * in the MD loop and exchanges would be lost anyway. */
1427 bNeedRepartition = FALSE;
1428 if ((ir->eSwapCoords != eswapNO) && (step > 0) && !bLastStep && do_per_step(step, ir->swap->nstswap))
1431 do_swapcoords(cr, step, t, ir, swap, wcycle, as_rvec_array(state->x.data()),
1432 state->box, MASTER(cr) && mdrunOptions.verbose, bRerunMD);
1434 if (bNeedRepartition && DOMAINDECOMP(cr))
1436 dd_collect_state(cr->dd, state, state_global);
1440 /* Replica exchange */
1444 bExchanged = replica_exchange(fplog, cr, ms, repl_ex, state_global, enerd, state, step, t);
1447 if ((bExchanged || bNeedRepartition) && DOMAINDECOMP(cr))
1449 dd_partition_system(fplog, mdlog, step, cr, TRUE, 1, state_global, *top_global, ir,
1450 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
1451 nrnb, wcycle, FALSE);
1452 shouldCheckNumberOfBondedInteractions = true;
1453 upd.setNumAtoms(state->natoms);
1459 /* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
1460 /* With all integrators, except VV, we need to retain the pressure
1461 * at the current step for coupling at the next step.
1463 if ((state->flags & (1U << estPRES_PREV))
1464 && (bGStatEveryStep || (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
1466 /* Store the pressure in t_state for pressure coupling
1467 * at the next MD step.
1469 copy_mat(pres, state->pres_prev);
1472 /* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
1474 if ((membed != nullptr) && (!bLastStep))
1476 rescale_membed(step_rel, membed, as_rvec_array(state_global->x.data()));
1479 cycles = wallcycle_stop(wcycle, ewcSTEP);
1480 if (DOMAINDECOMP(cr) && wcycle)
1482 dd_cycles_add(cr->dd, cycles, ddCyclStep);
1485 /* increase the MD step number */
1492 fcReportProgress(ir->nsteps + ir->init_step, step);
1496 resetHandler->resetCounters(step, step_rel, mdlog, fplog, cr, fr->nbv.get(), nrnb,
1497 fr->pmedata, pme_loadbal, wcycle, walltime_accounting);
1499 /* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
1500 imdSession->updateEnergyRecordAndSendPositionsAndEnergies(bInteractiveMDstep, step, bCalcEner);
1502 /* End of main MD loop */
1504 /* Closing TNG files can include compressing data. Therefore it is good to do that
1505 * before stopping the time measurements. */
1506 mdoutf_tng_close(outf);
1508 /* Stop measuring walltime */
1509 walltime_accounting_end_time(walltime_accounting);
1511 if (!thisRankHasDuty(cr, DUTY_PME))
1513 /* Tell the PME only node to finish */
1514 gmx_pme_send_finish(cr);
1519 if (ir->nstcalcenergy > 0)
1521 gmx::EnergyOutput::printAnnealingTemperatures(fplog, groups, &(ir->opts));
1522 energyOutput.printAverages(fplog, groups);
1529 pme_loadbal_done(pme_loadbal, fplog, mdlog, fr->nbv->useGpu());
1532 done_shellfc(fplog, shellfc, step_rel);
1534 if (useReplicaExchange && MASTER(cr))
1536 print_replica_exchange_statistics(fplog, repl_ex);
1539 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
1541 global_stat_destroy(gstat);