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36 * \brief Defines the modular simulator
38 * \author Pascal Merz <pascal.merz@me.com>
39 * \ingroup module_modularsimulator
44 #include "modularsimulator.h"
46 #include "gromacs/commandline/filenm.h"
47 #include "gromacs/domdec/domdec.h"
48 #include "gromacs/ewald/pme.h"
49 #include "gromacs/ewald/pme_load_balancing.h"
50 #include "gromacs/ewald/pme_pp.h"
51 #include "gromacs/gmxlib/network.h"
52 #include "gromacs/gmxlib/nrnb.h"
53 #include "gromacs/math/vec.h"
54 #include "gromacs/mdlib/checkpointhandler.h"
55 #include "gromacs/mdlib/constr.h"
56 #include "gromacs/mdlib/energyoutput.h"
57 #include "gromacs/mdlib/forcerec.h"
58 #include "gromacs/mdlib/mdatoms.h"
59 #include "gromacs/mdlib/resethandler.h"
60 #include "gromacs/mdlib/stat.h"
61 #include "gromacs/mdlib/update.h"
62 #include "gromacs/mdrun/replicaexchange.h"
63 #include "gromacs/mdrun/shellfc.h"
64 #include "gromacs/mdrunutility/handlerestart.h"
65 #include "gromacs/mdrunutility/printtime.h"
66 #include "gromacs/mdtypes/commrec.h"
67 #include "gromacs/mdtypes/fcdata.h"
68 #include "gromacs/mdtypes/forcerec.h"
69 #include "gromacs/mdtypes/inputrec.h"
70 #include "gromacs/mdtypes/mdatom.h"
71 #include "gromacs/mdtypes/mdrunoptions.h"
72 #include "gromacs/mdtypes/observableshistory.h"
73 #include "gromacs/mdtypes/state.h"
74 #include "gromacs/nbnxm/nbnxm.h"
75 #include "gromacs/timing/walltime_accounting.h"
76 #include "gromacs/topology/mtop_util.h"
77 #include "gromacs/topology/topology.h"
78 #include "gromacs/utility/cstringutil.h"
79 #include "gromacs/utility/fatalerror.h"
81 #include "compositesimulatorelement.h"
82 #include "computeglobalselement.h"
83 #include "constraintelement.h"
84 #include "energyelement.h"
85 #include "forceelement.h"
86 #include "freeenergyperturbationelement.h"
87 #include "parrinellorahmanbarostat.h"
88 #include "propagator.h"
89 #include "signallers.h"
90 #include "statepropagatordata.h"
91 #include "trajectoryelement.h"
92 #include "vrescalethermostat.h"
96 void ModularSimulator::run()
98 GMX_LOG(mdlog.info).asParagraph().appendText("Using the modular simulator.");
99 constructElementsAndSignallers();
101 for (auto& signaller : signallerCallList_)
103 signaller->signallerSetup();
107 domDecHelper_->setup();
110 for (auto& element : elementsOwnershipList_)
112 element->elementSetup();
114 if (pmeLoadBalanceHelper_)
116 // State must have been initialized so pmeLoadBalanceHelper_ gets a valid box
117 pmeLoadBalanceHelper_->setup();
120 while (step_ <= signalHelper_->lastStep_)
124 while (!taskQueue_.empty())
126 auto task = std::move(taskQueue_.front());
133 for (auto& element : elementsOwnershipList_)
135 element->elementTeardown();
137 if (pmeLoadBalanceHelper_)
139 pmeLoadBalanceHelper_->teardown();
144 void ModularSimulator::simulatorSetup()
146 if (!mdrunOptions.writeConfout)
148 // This is on by default, and the main known use case for
149 // turning it off is for convenience in benchmarking, which is
150 // something that should not show up in the general user
155 "The -noconfout functionality is deprecated, and "
156 "may be removed in a future version.");
161 char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
162 std::string timeString;
163 fprintf(stderr, "starting mdrun '%s'\n", *(top_global->name));
164 if (inputrec->nsteps >= 0)
166 timeString = formatString("%8.1f", static_cast<double>(inputrec->init_step + inputrec->nsteps)
167 * inputrec->delta_t);
171 timeString = "infinite";
173 if (inputrec->init_step > 0)
175 fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
176 gmx_step_str(inputrec->init_step + inputrec->nsteps, sbuf), timeString.c_str(),
177 gmx_step_str(inputrec->init_step, sbuf2), inputrec->init_step * inputrec->delta_t);
181 fprintf(stderr, "%s steps, %s ps.\n", gmx_step_str(inputrec->nsteps, sbuf),
184 fprintf(fplog, "\n");
187 walltime_accounting_start_time(walltime_accounting);
188 wallcycle_start(wcycle, ewcRUN);
189 print_start(fplog, cr, walltime_accounting, "mdrun");
191 step_ = inputrec->init_step;
194 void ModularSimulator::preStep(Step step, Time gmx_unused time, bool isNeighborSearchingStep)
196 if (stopHandler_->stoppingAfterCurrentStep(isNeighborSearchingStep) && step != signalHelper_->lastStep_)
199 * Stop handler wants to stop after the current step, which was
200 * not known when building the current task queue. This happens
201 * e.g. when a stop is signalled by OS. We therefore want to purge
202 * the task queue now, and re-schedule this step as last step.
205 std::queue<SimulatorRunFunctionPtr>().swap(taskQueue_);
211 resetHandler_->setSignal(walltime_accounting);
212 // This is a hack to avoid having to rewrite StopHandler to be a NeighborSearchSignaller
213 // and accept the step as input. Eventually, we want to do that, but currently this would
214 // require introducing NeighborSearchSignaller in the legacy do_md or a lot of code
216 stophandlerIsNSStep_ = isNeighborSearchingStep;
217 stophandlerCurrentStep_ = step;
218 stopHandler_->setSignal();
220 wallcycle_start(wcycle, ewcSTEP);
223 void ModularSimulator::postStep(Step step, Time gmx_unused time)
228 if (do_per_step(step, inputrec->nstlog))
230 if (fflush(fplog) != 0)
232 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
236 const bool do_verbose = mdrunOptions.verbose
237 && (step % mdrunOptions.verboseStepPrintInterval == 0
238 || step == inputrec->init_step || step == signalHelper_->lastStep_);
239 // Print the remaining wall clock time for the run
240 if (MASTER(cr) && (do_verbose || gmx_got_usr_signal())
241 && !(pmeLoadBalanceHelper_ && pmeLoadBalanceHelper_->pmePrinting()))
243 print_time(stderr, walltime_accounting, step, inputrec, cr);
246 double cycles = wallcycle_stop(wcycle, ewcSTEP);
247 if (DOMAINDECOMP(cr) && wcycle)
249 dd_cycles_add(cr->dd, static_cast<float>(cycles), ddCyclStep);
252 resetHandler_->resetCounters(
253 step, step - inputrec->init_step, mdlog, fplog, cr, fr->nbv.get(), nrnb, fr->pmedata,
254 pmeLoadBalanceHelper_ ? pmeLoadBalanceHelper_->loadBalancingObject() : nullptr, wcycle,
255 walltime_accounting);
258 void ModularSimulator::simulatorTeardown()
261 // Stop measuring walltime
262 walltime_accounting_end_time(walltime_accounting);
264 if (!thisRankHasDuty(cr, DUTY_PME))
266 /* Tell the PME only node to finish */
267 gmx_pme_send_finish(cr);
270 walltime_accounting_set_nsteps_done(walltime_accounting, step_ - inputrec->init_step);
273 void ModularSimulator::populateTaskQueue()
275 auto registerRunFunction = std::make_unique<RegisterRunFunction>(
276 [this](SimulatorRunFunctionPtr ptr) { taskQueue_.push(std::move(ptr)); });
278 Time startTime = inputrec->init_t;
279 Time timeStep = inputrec->delta_t;
280 Time time = startTime + step_ * timeStep;
282 // Run an initial call to the signallers
283 for (auto& signaller : signallerCallList_)
285 signaller->signal(step_, time);
288 if (checkpointHelper_)
290 checkpointHelper_->run(step_, time);
293 if (pmeLoadBalanceHelper_)
295 pmeLoadBalanceHelper_->run(step_, time);
299 domDecHelper_->run(step_, time);
304 // local variables for lambda capturing
305 const int step = step_;
306 const bool isNSStep = step == signalHelper_->nextNSStep_;
309 (*registerRunFunction)(std::make_unique<SimulatorRunFunction>(
310 [this, step, time, isNSStep]() { preStep(step, time, isNSStep); }));
311 // register elements for step
312 for (auto& element : elementCallList_)
314 element->scheduleTask(step_, time, registerRunFunction);
316 // register post-step
317 (*registerRunFunction)(
318 std::make_unique<SimulatorRunFunction>([this, step, time]() { postStep(step, time); }));
322 time = startTime + step_ * timeStep;
323 for (auto& signaller : signallerCallList_)
325 signaller->signal(step_, time);
327 } while (step_ != signalHelper_->nextNSStep_ && step_ <= signalHelper_->lastStep_);
330 void ModularSimulator::constructElementsAndSignallers()
332 /* When restarting from a checkpoint, it can be appropriate to
333 * initialize ekind from quantities in the checkpoint. Otherwise,
334 * compute_globals must initialize ekind before the simulation
335 * starts/restarts. However, only the master rank knows what was
336 * found in the checkpoint file, so we have to communicate in
337 * order to coordinate the restart.
339 * TODO (modular) This should become obsolete when checkpoint reading
340 * happens within the modular simulator framework: The energy
341 * element should read its data from the checkpoint file pointer,
342 * and signal to the compute globals element if it needs anything
345 * TODO (legacy) Consider removing this communication if/when checkpoint
346 * reading directly follows .tpr reading, because all ranks can
347 * agree on hasReadEkinState at that time.
349 bool hasReadEkinState = MASTER(cr) ? state_global->ekinstate.hasReadEkinState : false;
352 gmx_bcast(sizeof(hasReadEkinState), &hasReadEkinState, cr->mpi_comm_mygroup);
354 if (hasReadEkinState)
356 restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
360 * Build data structures
363 std::make_unique<TopologyHolder>(*top_global, cr, inputrec, fr, mdAtoms, constr, vsite);
365 std::unique_ptr<FreeEnergyPerturbationElement> freeEnergyPerturbationElement = nullptr;
366 FreeEnergyPerturbationElement* freeEnergyPerturbationElementPtr = nullptr;
367 if (inputrec->efep != efepNO)
369 freeEnergyPerturbationElement =
370 std::make_unique<FreeEnergyPerturbationElement>(fplog, inputrec, mdAtoms);
371 freeEnergyPerturbationElementPtr = freeEnergyPerturbationElement.get();
374 auto statePropagatorData = std::make_unique<StatePropagatorData>(
375 top_global->natoms, fplog, cr, state_global, inputrec->nstxout, inputrec->nstvout,
376 inputrec->nstfout, inputrec->nstxout_compressed, fr->nbv->useGpu(),
377 freeEnergyPerturbationElementPtr, topologyHolder_.get(), fr->bMolPBC,
378 mdrunOptions.writeConfout, opt2fn("-c", nfile, fnm), inputrec, mdAtoms->mdatoms());
379 auto statePropagatorDataPtr = compat::make_not_null(statePropagatorData.get());
381 auto energyElement = std::make_unique<EnergyElement>(
382 statePropagatorDataPtr, freeEnergyPerturbationElementPtr, top_global, inputrec, mdAtoms,
383 enerd, ekind, constr, fplog, fcd, mdModulesNotifier, MASTER(cr), observablesHistory,
385 auto energyElementPtr = compat::make_not_null(energyElement.get());
390 const bool simulationsShareState = false;
391 stopHandler_ = stopHandlerBuilder->getStopHandlerMD(
392 compat::not_null<SimulationSignal*>(&signals_[eglsSTOPCOND]), simulationsShareState,
393 MASTER(cr), inputrec->nstlist, mdrunOptions.reproducible, nstglobalcomm_,
394 mdrunOptions.maximumHoursToRun, inputrec->nstlist == 0, fplog, stophandlerCurrentStep_,
395 stophandlerIsNSStep_, walltime_accounting);
398 * Create simulator builders
400 SignallerBuilder<NeighborSearchSignaller> neighborSearchSignallerBuilder;
401 SignallerBuilder<LastStepSignaller> lastStepSignallerBuilder;
402 SignallerBuilder<LoggingSignaller> loggingSignallerBuilder;
403 SignallerBuilder<EnergySignaller> energySignallerBuilder;
404 TrajectoryElementBuilder trajectoryElementBuilder;
407 * Register data structures to signallers
409 trajectoryElementBuilder.registerWriterClient(statePropagatorDataPtr);
410 trajectoryElementBuilder.registerSignallerClient(statePropagatorDataPtr);
411 lastStepSignallerBuilder.registerSignallerClient(statePropagatorDataPtr);
413 trajectoryElementBuilder.registerWriterClient(energyElementPtr);
414 trajectoryElementBuilder.registerSignallerClient(energyElementPtr);
415 energySignallerBuilder.registerSignallerClient(energyElementPtr);
417 // Register the simulator itself to the neighbor search / last step signaller
418 neighborSearchSignallerBuilder.registerSignallerClient(compat::make_not_null(signalHelper_.get()));
419 lastStepSignallerBuilder.registerSignallerClient(compat::make_not_null(signalHelper_.get()));
422 * Build integrator - this takes care of force calculation, propagation,
423 * constraining, and of the place the statePropagatorData and the energy element
424 * have a full timestep state.
426 // TODO: Make a CheckpointHelperBuilder
427 std::vector<ICheckpointHelperClient*> checkpointClients = { statePropagatorDataPtr, energyElementPtr,
428 freeEnergyPerturbationElementPtr };
429 CheckBondedInteractionsCallbackPtr checkBondedInteractionsCallback = nullptr;
431 buildIntegrator(&neighborSearchSignallerBuilder, &energySignallerBuilder,
432 &loggingSignallerBuilder, &trajectoryElementBuilder, &checkpointClients,
433 &checkBondedInteractionsCallback, statePropagatorDataPtr,
434 energyElementPtr, freeEnergyPerturbationElementPtr, hasReadEkinState);
437 * Build infrastructure elements
440 if (PmeLoadBalanceHelper::doPmeLoadBalancing(mdrunOptions, inputrec, fr))
442 pmeLoadBalanceHelper_ = std::make_unique<PmeLoadBalanceHelper>(
443 mdrunOptions.verbose, statePropagatorDataPtr, fplog, cr, mdlog, inputrec, wcycle, fr);
444 neighborSearchSignallerBuilder.registerSignallerClient(
445 compat::make_not_null(pmeLoadBalanceHelper_.get()));
448 if (DOMAINDECOMP(cr))
450 GMX_ASSERT(checkBondedInteractionsCallback,
451 "Domain decomposition needs a callback for check the number of bonded "
453 domDecHelper_ = std::make_unique<DomDecHelper>(
454 mdrunOptions.verbose, mdrunOptions.verboseStepPrintInterval, statePropagatorDataPtr,
455 topologyHolder_.get(), std::move(checkBondedInteractionsCallback), nstglobalcomm_, fplog,
456 cr, mdlog, constr, inputrec, mdAtoms, nrnb, wcycle, fr, vsite, imdSession, pull_work);
457 neighborSearchSignallerBuilder.registerSignallerClient(compat::make_not_null(domDecHelper_.get()));
460 const bool simulationsShareResetCounters = false;
461 resetHandler_ = std::make_unique<ResetHandler>(
462 compat::make_not_null<SimulationSignal*>(&signals_[eglsRESETCOUNTERS]),
463 simulationsShareResetCounters, inputrec->nsteps, MASTER(cr),
464 mdrunOptions.timingOptions.resetHalfway, mdrunOptions.maximumHoursToRun, mdlog, wcycle,
465 walltime_accounting);
468 * Build signaller list
470 * Note that as signallers depend on each others, the order of calling the signallers
471 * matters. It is the responsibility of this builder to ensure that the order is
474 auto energySignaller = energySignallerBuilder.build(
475 inputrec->nstcalcenergy, inputrec->fepvals->nstdhdl, inputrec->nstpcouple);
476 trajectoryElementBuilder.registerSignallerClient(compat::make_not_null(energySignaller.get()));
477 loggingSignallerBuilder.registerSignallerClient(compat::make_not_null(energySignaller.get()));
478 auto trajectoryElement = trajectoryElementBuilder.build(
479 fplog, nfile, fnm, mdrunOptions, cr, outputProvider, mdModulesNotifier, inputrec,
480 top_global, oenv, wcycle, startingBehavior, simulationsShareState);
481 loggingSignallerBuilder.registerSignallerClient(compat::make_not_null(trajectoryElement.get()));
483 // Add checkpoint helper here since we need a pointer to the trajectory element and
484 // need to register it with the lastStepSignallerBuilder
485 auto checkpointHandler = std::make_unique<CheckpointHandler>(
486 compat::make_not_null<SimulationSignal*>(&signals_[eglsCHKPT]), simulationsShareState,
487 inputrec->nstlist == 0, MASTER(cr), mdrunOptions.writeConfout,
488 mdrunOptions.checkpointOptions.period);
489 checkpointHelper_ = std::make_unique<CheckpointHelper>(
490 std::move(checkpointClients), std::move(checkpointHandler), inputrec->init_step,
491 trajectoryElement.get(), top_global->natoms, fplog, cr, observablesHistory,
492 walltime_accounting, state_global, mdrunOptions.writeConfout);
493 lastStepSignallerBuilder.registerSignallerClient(compat::make_not_null(checkpointHelper_.get()));
495 lastStepSignallerBuilder.registerSignallerClient(compat::make_not_null(trajectoryElement.get()));
496 auto loggingSignaller =
497 loggingSignallerBuilder.build(inputrec->nstlog, inputrec->init_step, inputrec->init_t);
498 lastStepSignallerBuilder.registerSignallerClient(compat::make_not_null(loggingSignaller.get()));
499 auto lastStepSignaller =
500 lastStepSignallerBuilder.build(inputrec->nsteps, inputrec->init_step, stopHandler_.get());
501 neighborSearchSignallerBuilder.registerSignallerClient(compat::make_not_null(lastStepSignaller.get()));
502 auto neighborSearchSignaller = neighborSearchSignallerBuilder.build(
503 inputrec->nstlist, inputrec->init_step, inputrec->init_t);
505 addToCallListAndMove(std::move(neighborSearchSignaller), signallerCallList_, signallersOwnershipList_);
506 addToCallListAndMove(std::move(lastStepSignaller), signallerCallList_, signallersOwnershipList_);
507 addToCallListAndMove(std::move(loggingSignaller), signallerCallList_, signallersOwnershipList_);
508 addToCallList(trajectoryElement, signallerCallList_);
509 addToCallListAndMove(std::move(energySignaller), signallerCallList_, signallersOwnershipList_);
512 * Build the element list
514 * This is the actual sequence of (non-infrastructure) elements to be run.
515 * For NVE, the trajectory element is used outside of the integrator
516 * (composite) element, as well as the checkpoint helper. The checkpoint
517 * helper should be on top of the loop, and is only part of the simulator
518 * call list to be able to react to the last step being signalled.
520 addToCallList(checkpointHelper_, elementCallList_);
521 if (freeEnergyPerturbationElement)
523 addToCallListAndMove(std::move(freeEnergyPerturbationElement), elementCallList_,
524 elementsOwnershipList_);
526 addToCallListAndMove(std::move(integrator), elementCallList_, elementsOwnershipList_);
527 addToCallListAndMove(std::move(trajectoryElement), elementCallList_, elementsOwnershipList_);
528 // for vv, we need to setup statePropagatorData after the compute
529 // globals so that we reset the right velocities
530 // TODO: Avoid this by getting rid of the need of resetting velocities in vv
531 elementsOwnershipList_.emplace_back(std::move(statePropagatorData));
532 elementsOwnershipList_.emplace_back(std::move(energyElement));
535 std::unique_ptr<ISimulatorElement>
536 ModularSimulator::buildForces(SignallerBuilder<NeighborSearchSignaller>* neighborSearchSignallerBuilder,
537 SignallerBuilder<EnergySignaller>* energySignallerBuilder,
538 StatePropagatorData* statePropagatorDataPtr,
539 EnergyElement* energyElementPtr,
540 FreeEnergyPerturbationElement* freeEnergyPerturbationElement)
542 const bool isVerbose = mdrunOptions.verbose;
543 const bool isDynamicBox = inputrecDynamicBox(inputrec);
545 auto forceElement = std::make_unique<ForceElement>(
546 statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElement, isVerbose,
547 isDynamicBox, fplog, cr, inputrec, mdAtoms, nrnb, fr, fcd, wcycle, runScheduleWork, vsite,
548 imdSession, pull_work, constr, &topologyHolder_->globalTopology(), enforcedRotation);
549 topologyHolder_->registerClient(forceElement.get());
550 neighborSearchSignallerBuilder->registerSignallerClient(compat::make_not_null(forceElement.get()));
551 energySignallerBuilder->registerSignallerClient(compat::make_not_null(forceElement.get()));
553 // std::move *should* not be needed with c++-14, but clang-3.6 still requires it
554 return std::move(forceElement);
557 std::unique_ptr<ISimulatorElement> ModularSimulator::buildIntegrator(
558 SignallerBuilder<NeighborSearchSignaller>* neighborSearchSignallerBuilder,
559 SignallerBuilder<EnergySignaller>* energySignallerBuilder,
560 SignallerBuilder<LoggingSignaller>* loggingSignallerBuilder,
561 TrajectoryElementBuilder* trajectoryElementBuilder,
562 std::vector<ICheckpointHelperClient*>* checkpointClients,
563 CheckBondedInteractionsCallbackPtr* checkBondedInteractionsCallback,
564 compat::not_null<StatePropagatorData*> statePropagatorDataPtr,
565 compat::not_null<EnergyElement*> energyElementPtr,
566 FreeEnergyPerturbationElement* freeEnergyPerturbationElementPtr,
567 bool hasReadEkinState)
570 buildForces(neighborSearchSignallerBuilder, energySignallerBuilder,
571 statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr);
573 // list of elements owned by the simulator composite object
574 std::vector<std::unique_ptr<ISimulatorElement>> elementsOwnershipList;
575 // call list of the simulator composite object
576 std::vector<compat::not_null<ISimulatorElement*>> elementCallList;
578 std::function<void()> needToCheckNumberOfBondedInteractions;
579 if (inputrec->eI == eiMD)
581 auto computeGlobalsElement =
582 std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>>(
583 statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
584 &signals_, nstglobalcomm_, fplog, mdlog, cr, inputrec, mdAtoms, nrnb,
585 wcycle, fr, &topologyHolder_->globalTopology(), constr, hasReadEkinState);
586 topologyHolder_->registerClient(computeGlobalsElement.get());
587 energySignallerBuilder->registerSignallerClient(compat::make_not_null(computeGlobalsElement.get()));
588 trajectoryElementBuilder->registerSignallerClient(
589 compat::make_not_null(computeGlobalsElement.get()));
591 *checkBondedInteractionsCallback =
592 computeGlobalsElement->getCheckNumberOfBondedInteractionsCallback();
594 auto propagator = std::make_unique<Propagator<IntegrationStep::LeapFrog>>(
595 inputrec->delta_t, statePropagatorDataPtr, mdAtoms, wcycle);
597 addToCallListAndMove(std::move(forceElement), elementCallList, elementsOwnershipList);
598 addToCallList(statePropagatorDataPtr, elementCallList); // we have a full microstate at time t here!
599 if (inputrec->etc == etcVRESCALE)
601 // TODO: With increased complexity of the propagator, this will need further development,
602 // e.g. using propagators templated for velocity propagation policies and a builder
603 propagator->setNumVelocityScalingVariables(inputrec->opts.ngtc);
604 auto thermostat = std::make_unique<VRescaleThermostat>(
605 inputrec->nsttcouple, -1, false, inputrec->ld_seed, inputrec->opts.ngtc,
606 inputrec->delta_t * inputrec->nsttcouple, inputrec->opts.ref_t, inputrec->opts.tau_t,
607 inputrec->opts.nrdf, energyElementPtr, propagator->viewOnVelocityScaling(),
608 propagator->velocityScalingCallback(), state_global, cr, inputrec->bContinuation);
609 checkpointClients->emplace_back(thermostat.get());
610 energyElementPtr->setVRescaleThermostat(thermostat.get());
611 addToCallListAndMove(std::move(thermostat), elementCallList, elementsOwnershipList);
614 std::unique_ptr<ParrinelloRahmanBarostat> prBarostat = nullptr;
615 if (inputrec->epc == epcPARRINELLORAHMAN)
617 // Building the PR barostat here since it needs access to the propagator
618 // and we want to be able to move the propagator object
619 prBarostat = std::make_unique<ParrinelloRahmanBarostat>(
620 inputrec->nstpcouple, -1, inputrec->delta_t * inputrec->nstpcouple,
621 inputrec->init_step, propagator->viewOnPRScalingMatrix(),
622 propagator->prScalingCallback(), statePropagatorDataPtr, energyElementPtr,
623 fplog, inputrec, mdAtoms, state_global, cr, inputrec->bContinuation);
624 energyElementPtr->setParrinelloRahamnBarostat(prBarostat.get());
625 checkpointClients->emplace_back(prBarostat.get());
627 addToCallListAndMove(std::move(propagator), elementCallList, elementsOwnershipList);
630 auto constraintElement = std::make_unique<ConstraintsElement<ConstraintVariable::Positions>>(
631 constr, statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
632 MASTER(cr), fplog, inputrec, mdAtoms->mdatoms());
633 auto constraintElementPtr = compat::make_not_null(constraintElement.get());
634 energySignallerBuilder->registerSignallerClient(constraintElementPtr);
635 trajectoryElementBuilder->registerSignallerClient(constraintElementPtr);
636 loggingSignallerBuilder->registerSignallerClient(constraintElementPtr);
638 addToCallListAndMove(std::move(constraintElement), elementCallList, elementsOwnershipList);
641 addToCallListAndMove(std::move(computeGlobalsElement), elementCallList, elementsOwnershipList);
642 addToCallList(energyElementPtr, elementCallList); // we have the energies at time t here!
645 addToCallListAndMove(std::move(prBarostat), elementCallList, elementsOwnershipList);
648 else if (inputrec->eI == eiVV)
650 auto computeGlobalsElement =
651 std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>(
652 statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
653 &signals_, nstglobalcomm_, fplog, mdlog, cr, inputrec, mdAtoms, nrnb,
654 wcycle, fr, &topologyHolder_->globalTopology(), constr, hasReadEkinState);
655 topologyHolder_->registerClient(computeGlobalsElement.get());
656 energySignallerBuilder->registerSignallerClient(compat::make_not_null(computeGlobalsElement.get()));
657 trajectoryElementBuilder->registerSignallerClient(
658 compat::make_not_null(computeGlobalsElement.get()));
660 *checkBondedInteractionsCallback =
661 computeGlobalsElement->getCheckNumberOfBondedInteractionsCallback();
663 auto propagatorVelocities = std::make_unique<Propagator<IntegrationStep::VelocitiesOnly>>(
664 inputrec->delta_t * 0.5, statePropagatorDataPtr, mdAtoms, wcycle);
665 auto propagatorVelocitiesAndPositions =
666 std::make_unique<Propagator<IntegrationStep::VelocityVerletPositionsAndVelocities>>(
667 inputrec->delta_t, statePropagatorDataPtr, mdAtoms, wcycle);
669 addToCallListAndMove(std::move(forceElement), elementCallList, elementsOwnershipList);
671 std::unique_ptr<ParrinelloRahmanBarostat> prBarostat = nullptr;
672 if (inputrec->epc == epcPARRINELLORAHMAN)
674 // Building the PR barostat here since it needs access to the propagator
675 // and we want to be able to move the propagator object
676 prBarostat = std::make_unique<ParrinelloRahmanBarostat>(
677 inputrec->nstpcouple, -1, inputrec->delta_t * inputrec->nstpcouple,
678 inputrec->init_step, propagatorVelocities->viewOnPRScalingMatrix(),
679 propagatorVelocities->prScalingCallback(), statePropagatorDataPtr, energyElementPtr,
680 fplog, inputrec, mdAtoms, state_global, cr, inputrec->bContinuation);
681 energyElementPtr->setParrinelloRahamnBarostat(prBarostat.get());
682 checkpointClients->emplace_back(prBarostat.get());
684 addToCallListAndMove(std::move(propagatorVelocities), elementCallList, elementsOwnershipList);
687 auto constraintElement = std::make_unique<ConstraintsElement<ConstraintVariable::Velocities>>(
688 constr, statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
689 MASTER(cr), fplog, inputrec, mdAtoms->mdatoms());
690 energySignallerBuilder->registerSignallerClient(compat::make_not_null(constraintElement.get()));
691 trajectoryElementBuilder->registerSignallerClient(
692 compat::make_not_null(constraintElement.get()));
693 loggingSignallerBuilder->registerSignallerClient(
694 compat::make_not_null(constraintElement.get()));
696 addToCallListAndMove(std::move(constraintElement), elementCallList, elementsOwnershipList);
698 addToCallList(compat::make_not_null(computeGlobalsElement.get()), elementCallList);
699 addToCallList(statePropagatorDataPtr, elementCallList); // we have a full microstate at time t here!
700 if (inputrec->etc == etcVRESCALE)
702 // TODO: With increased complexity of the propagator, this will need further development,
703 // e.g. using propagators templated for velocity propagation policies and a builder
704 propagatorVelocitiesAndPositions->setNumVelocityScalingVariables(inputrec->opts.ngtc);
705 auto thermostat = std::make_unique<VRescaleThermostat>(
706 inputrec->nsttcouple, 0, true, inputrec->ld_seed, inputrec->opts.ngtc,
707 inputrec->delta_t * inputrec->nsttcouple, inputrec->opts.ref_t,
708 inputrec->opts.tau_t, inputrec->opts.nrdf, energyElementPtr,
709 propagatorVelocitiesAndPositions->viewOnVelocityScaling(),
710 propagatorVelocitiesAndPositions->velocityScalingCallback(), state_global, cr,
711 inputrec->bContinuation);
712 checkpointClients->emplace_back(thermostat.get());
713 energyElementPtr->setVRescaleThermostat(thermostat.get());
714 addToCallListAndMove(std::move(thermostat), elementCallList, elementsOwnershipList);
716 addToCallListAndMove(std::move(propagatorVelocitiesAndPositions), elementCallList,
717 elementsOwnershipList);
720 auto constraintElement = std::make_unique<ConstraintsElement<ConstraintVariable::Positions>>(
721 constr, statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
722 MASTER(cr), fplog, inputrec, mdAtoms->mdatoms());
723 energySignallerBuilder->registerSignallerClient(compat::make_not_null(constraintElement.get()));
724 trajectoryElementBuilder->registerSignallerClient(
725 compat::make_not_null(constraintElement.get()));
726 loggingSignallerBuilder->registerSignallerClient(
727 compat::make_not_null(constraintElement.get()));
729 addToCallListAndMove(std::move(constraintElement), elementCallList, elementsOwnershipList);
731 addToCallListAndMove(std::move(computeGlobalsElement), elementCallList, elementsOwnershipList);
732 addToCallList(energyElementPtr, elementCallList); // we have the energies at time t here!
735 addToCallListAndMove(std::move(prBarostat), elementCallList, elementsOwnershipList);
740 gmx_fatal(FARGS, "Integrator not implemented for the modular simulator.");
743 auto integrator = std::make_unique<CompositeSimulatorElement>(std::move(elementCallList),
744 std::move(elementsOwnershipList));
745 // std::move *should* not be needed with c++-14, but clang-3.6 still requires it
746 return std::move(integrator);
749 bool ModularSimulator::isInputCompatible(bool exitOnFailure,
750 const t_inputrec* inputrec,
752 const gmx_mtop_t& globalTopology,
753 const gmx_multisim_t* ms,
754 const ReplicaExchangeParameters& replExParams,
756 bool doEssentialDynamics,
759 auto conditionalAssert = [exitOnFailure](bool condition, const char* message) {
762 GMX_RELEASE_ASSERT(condition, message);
767 bool isInputCompatible = true;
769 // GMX_USE_MODULAR_SIMULATOR allows to use modular simulator also for non-standard uses,
770 // such as the leap-frog integrator
771 const auto modularSimulatorExplicitlyTurnedOn = (getenv("GMX_USE_MODULAR_SIMULATOR") != nullptr);
772 // GMX_USE_MODULAR_SIMULATOR allows to use disable modular simulator for all uses,
773 // including the velocity-verlet integrator used by default
774 const auto modularSimulatorExplicitlyTurnedOff = (getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
777 !(modularSimulatorExplicitlyTurnedOn && modularSimulatorExplicitlyTurnedOff),
778 "Cannot have both GMX_USE_MODULAR_SIMULATOR=ON and GMX_DISABLE_MODULAR_SIMULATOR=ON. "
779 "Unset one of the two environment variables to explicitly chose which simulator to "
781 "or unset both to recover default behavior.");
784 !(modularSimulatorExplicitlyTurnedOff && inputrec->eI == eiVV
785 && inputrec->epc == epcPARRINELLORAHMAN),
786 "Cannot use a Parrinello-Rahman barostat with md-vv and "
787 "GMX_DISABLE_MODULAR_SIMULATOR=ON, "
788 "as the Parrinello-Rahman barostat is not implemented in the legacy simulator. Unset "
789 "GMX_DISABLE_MODULAR_SIMULATOR or use a different pressure control algorithm.");
793 && conditionalAssert(
794 inputrec->eI == eiMD || inputrec->eI == eiVV,
795 "Only integrators md and md-vv are supported by the modular simulator.");
796 isInputCompatible = isInputCompatible
797 && conditionalAssert(inputrec->eI != eiMD || modularSimulatorExplicitlyTurnedOn,
798 "Set GMX_USE_MODULAR_SIMULATOR=ON to use the modular "
799 "simulator with integrator md.");
802 && conditionalAssert(!doRerun, "Rerun is not supported by the modular simulator.");
805 && conditionalAssert(
806 inputrec->etc == etcNO || inputrec->etc == etcVRESCALE,
807 "Only v-rescale thermostat is supported by the modular simulator.");
810 && conditionalAssert(
811 inputrec->epc == epcNO || inputrec->epc == epcPARRINELLORAHMAN,
812 "Only Parrinello-Rahman barostat is supported by the modular simulator.");
815 && conditionalAssert(
816 !(inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec)
817 || inputrecNvtTrotter(inputrec)),
818 "Legacy Trotter decomposition is not supported by the modular simulator.");
819 isInputCompatible = isInputCompatible
820 && conditionalAssert(inputrec->efep == efepNO || inputrec->efep == efepYES
821 || inputrec->efep == efepSLOWGROWTH,
822 "Expanded ensemble free energy calculation is not "
823 "supported by the modular simulator.");
824 isInputCompatible = isInputCompatible
825 && conditionalAssert(!inputrec->bPull,
826 "Pulling is not supported by the modular simulator.");
829 && conditionalAssert(inputrec->opts.ngacc == 1 && inputrec->opts.acc[0][XX] == 0.0
830 && inputrec->opts.acc[0][YY] == 0.0
831 && inputrec->opts.acc[0][ZZ] == 0.0 && inputrec->cos_accel == 0.0,
832 "Acceleration is not supported by the modular simulator.");
835 && conditionalAssert(inputrec->opts.ngfrz == 1 && inputrec->opts.nFreeze[0][XX] == 0
836 && inputrec->opts.nFreeze[0][YY] == 0
837 && inputrec->opts.nFreeze[0][ZZ] == 0,
838 "Freeze groups are not supported by the modular simulator.");
841 && conditionalAssert(
842 inputrec->deform[XX][XX] == 0.0 && inputrec->deform[XX][YY] == 0.0
843 && inputrec->deform[XX][ZZ] == 0.0 && inputrec->deform[YY][XX] == 0.0
844 && inputrec->deform[YY][YY] == 0.0 && inputrec->deform[YY][ZZ] == 0.0
845 && inputrec->deform[ZZ][XX] == 0.0 && inputrec->deform[ZZ][YY] == 0.0
846 && inputrec->deform[ZZ][ZZ] == 0.0,
847 "Deformation is not supported by the modular simulator.");
850 && conditionalAssert(gmx_mtop_interaction_count(globalTopology, IF_VSITE) == 0,
851 "Virtual sites are not supported by the modular simulator.");
852 isInputCompatible = isInputCompatible
853 && conditionalAssert(!inputrec->bDoAwh,
854 "AWH is not supported by the modular simulator.");
857 && conditionalAssert(gmx_mtop_ftype_count(globalTopology, F_DISRES) == 0,
858 "Distance restraints are not supported by the modular simulator.");
861 && conditionalAssert(
862 gmx_mtop_ftype_count(globalTopology, F_ORIRES) == 0,
863 "Orientation restraints are not supported by the modular simulator.");
866 && conditionalAssert(ms == nullptr,
867 "Multi-sim are not supported by the modular simulator.");
870 && conditionalAssert(replExParams.exchangeInterval == 0,
871 "Replica exchange is not supported by the modular simulator.");
873 int numEnsembleRestraintSystems;
876 numEnsembleRestraintSystems = fcd->disres.nsystems;
880 auto distantRestraintEnsembleEnvVar = getenv("GMX_DISRE_ENSEMBLE_SIZE");
881 numEnsembleRestraintSystems =
882 (ms != nullptr && distantRestraintEnsembleEnvVar != nullptr)
883 ? static_cast<int>(strtol(distantRestraintEnsembleEnvVar, nullptr, 10))
888 && conditionalAssert(numEnsembleRestraintSystems <= 1,
889 "Ensemble restraints are not supported by the modular simulator.");
892 && conditionalAssert(!doSimulatedAnnealing(inputrec),
893 "Simulated annealing is not supported by the modular simulator.");
896 && conditionalAssert(!inputrec->bSimTemp,
897 "Simulated tempering is not supported by the modular simulator.");
898 isInputCompatible = isInputCompatible
899 && conditionalAssert(!inputrec->bExpanded,
900 "Expanded ensemble simulations are not supported by "
901 "the modular simulator.");
904 && conditionalAssert(!doEssentialDynamics,
905 "Essential dynamics is not supported by the modular simulator.");
906 isInputCompatible = isInputCompatible
907 && conditionalAssert(inputrec->eSwapCoords == eswapNO,
908 "Ion / water position swapping is not supported by "
909 "the modular simulator.");
912 && conditionalAssert(!inputrec->bIMD,
913 "Interactive MD is not supported by the modular simulator.");
916 && conditionalAssert(!doMembed,
917 "Membrane embedding is not supported by the modular simulator.");
918 // TODO: Change this to the boolean passed when we merge the user interface change for the GPU update.
921 && conditionalAssert(
922 getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") == nullptr,
923 "Integration on the GPU is not supported by the modular simulator.");
924 // Modular simulator is centered around NS updates
925 // TODO: think how to handle nstlist == 0
926 isInputCompatible = isInputCompatible
927 && conditionalAssert(inputrec->nstlist != 0,
928 "Simulations without neighbor list update are not "
929 "supported by the modular simulator.");
930 isInputCompatible = isInputCompatible
931 && conditionalAssert(!GMX_FAHCORE,
932 "GMX_FAHCORE not supported by the modular simulator.");
934 return isInputCompatible;
937 void ModularSimulator::checkInputForDisabledFunctionality()
939 isInputCompatible(true, inputrec, doRerun, *top_global, ms, replExParams, fcd,
940 opt2bSet("-ei", nfile, fnm), membed != nullptr);
941 if (observablesHistory->edsamHistory)
944 "The checkpoint is from a run with essential dynamics sampling, "
945 "but the current run did not specify the -ei option. "
946 "Either specify the -ei option to mdrun, or do not use this checkpoint file.");
950 SignallerCallbackPtr ModularSimulator::SignalHelper::registerLastStepCallback()
952 return std::make_unique<SignallerCallback>(
953 [this](Step step, Time gmx_unused time) { this->lastStep_ = step; });
956 SignallerCallbackPtr ModularSimulator::SignalHelper::registerNSCallback()
958 return std::make_unique<SignallerCallback>(
959 [this](Step step, Time gmx_unused time) { this->nextNSStep_ = step; });