src/gromacs/modularsimulator/simulatoralgorithm.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2020,2021, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
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   8  *
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  11  * as published by the Free Software Foundation; either version 2.1
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  35 /*! \internal \file
  36  * \brief Defines the modular simulator algorithm
  37  *
  38  * \author Pascal Merz <pascal.merz@me.com>
  39  * \ingroup module_modularsimulator
  40  */
  41
  42 #include "gmxpre.h"
  43
  44 #include "simulatoralgorithm.h"
  45
  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/nrnb.h"
  52 #include "gromacs/listed_forces/listed_forces.h"
  53 #include "gromacs/mdlib/checkpointhandler.h"
  54 #include "gromacs/mdlib/constr.h"
  55 #include "gromacs/mdlib/energyoutput.h"
  56 #include "gromacs/mdlib/md_support.h"
  57 #include "gromacs/mdlib/mdatoms.h"
  58 #include "gromacs/mdlib/resethandler.h"
  59 #include "gromacs/mdlib/stat.h"
  60 #include "gromacs/mdrun/replicaexchange.h"
  61 #include "gromacs/mdrun/shellfc.h"
  62 #include "gromacs/mdrunutility/freeenergy.h"
  63 #include "gromacs/mdrunutility/handlerestart.h"
  64 #include "gromacs/mdrunutility/printtime.h"
  65 #include "gromacs/mdtypes/commrec.h"
  66 #include "gromacs/mdtypes/fcdata.h"
  67 #include "gromacs/mdtypes/forcerec.h"
  68 #include "gromacs/mdtypes/inputrec.h"
  69 #include "gromacs/mdtypes/mdatom.h"
  70 #include "gromacs/mdtypes/mdrunoptions.h"
  71 #include "gromacs/mdtypes/observableshistory.h"
  72 #include "gromacs/nbnxm/nbnxm.h"
  73 #include "gromacs/timing/walltime_accounting.h"
  74 #include "gromacs/topology/topology.h"
  75 #include "gromacs/utility/cstringutil.h"
  76 #include "gromacs/utility/fatalerror.h"
  77
  78 #include "checkpointhelper.h"
  79 #include "domdechelper.h"
  80 #include "energydata.h"
  81 #include "firstorderpressurecoupling.h"
  82 #include "freeenergyperturbationdata.h"
  83 #include "modularsimulator.h"
  84 #include "pmeloadbalancehelper.h"
  85 #include "propagator.h"
  86 #include "referencetemperaturemanager.h"
  87 #include "statepropagatordata.h"
  88
  89 namespace gmx
  90 {
  91 ModularSimulatorAlgorithm::ModularSimulatorAlgorithm(std::string              topologyName,
  92                                                      FILE*                    fplog,
  93                                                      t_commrec*               cr,
  94                                                      const MDLogger&          mdlog,
  95                                                      const MdrunOptions&      mdrunOptions,
  96                                                      const t_inputrec*        inputrec,
  97                                                      t_nrnb*                  nrnb,
  98                                                      gmx_wallcycle*           wcycle,
  99                                                      t_forcerec*              fr,
 100                                                      gmx_walltime_accounting* walltime_accounting) :
 101     taskIterator_(taskQueue_.end()),
 102     statePropagatorData_(nullptr),
 103     energyData_(nullptr),
 104     freeEnergyPerturbationData_(nullptr),
 105     step_(-1),
 106     runFinished_(false),
 107     topologyName_(std::move(topologyName)),
 108     fplog(fplog),
 109     cr(cr),
 110     mdlog(mdlog),
 111     mdrunOptions(mdrunOptions),
 112     inputrec(inputrec),
 113     nrnb(nrnb),
 114     wcycle(wcycle),
 115     fr(fr),
 116     walltime_accounting(walltime_accounting)
 117 {
 118     signalHelper_ = std::make_unique<SignalHelper>();
 119 }
 120
 121 void ModularSimulatorAlgorithm::setup()
 122 {
 123     simulatorSetup();
 124     for (auto& signaller : signallerList_)
 125     {
 126         signaller->setup();
 127     }
 128     if (domDecHelper_)
 129     {
 130         domDecHelper_->setup();
 131     }
 132
 133     for (auto& element : elementSetupTeardownList_)
 134     {
 135         element->elementSetup();
 136     }
 137     statePropagatorData_->setup();
 138     if (pmeLoadBalanceHelper_)
 139     {
 140         // State must have been initialized so pmeLoadBalanceHelper_ gets a valid box
 141         pmeLoadBalanceHelper_->setup();
 142     }
 143 }
 144
 145 const SimulatorRunFunction* ModularSimulatorAlgorithm::getNextTask()
 146 {
 147     if (!taskQueue_.empty())
 148     {
 149         taskIterator_++;
 150     }
 151     if (taskIterator_ == taskQueue_.end())
 152     {
 153         if (runFinished_)
 154         {
 155             return nullptr;
 156         }
 157         updateTaskQueue();
 158         taskIterator_ = taskQueue_.begin();
 159     }
 160     return &*taskIterator_;
 161 }
 162
 163 void ModularSimulatorAlgorithm::updateTaskQueue()
 164 {
 165     // For now, we'll just clean the task queue and then re-populate
 166     // TODO: If tasks are periodic around updates of the task queue,
 167     //       we should reuse it instead
 168     taskQueue_.clear();
 169     populateTaskQueue();
 170 }
 171
 172 void ModularSimulatorAlgorithm::teardown()
 173 {
 174     for (auto& element : elementSetupTeardownList_)
 175     {
 176         element->elementTeardown();
 177     }
 178     energyData_->teardown();
 179     if (pmeLoadBalanceHelper_)
 180     {
 181         pmeLoadBalanceHelper_->teardown();
 182     }
 183     simulatorTeardown();
 184 }
 185
 186 void ModularSimulatorAlgorithm::simulatorSetup()
 187 {
 188     if (!mdrunOptions.writeConfout)
 189     {
 190         // This is on by default, and the main known use case for
 191         // turning it off is for convenience in benchmarking, which is
 192         // something that should not show up in the general user
 193         // interface.
 194         GMX_LOG(mdlog.info)
 195                 .asParagraph()
 196                 .appendText(
 197                         "The -noconfout functionality is deprecated, and "
 198                         "may be removed in a future version.");
 199     }
 200
 201     if (MASTER(cr))
 202     {
 203         char        sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
 204         std::string timeString;
 205         fprintf(stderr, "starting mdrun '%s'\n", topologyName_.c_str());
 206         if (inputrec->nsteps >= 0)
 207         {
 208             timeString = formatString(
 209                     "%8.1f", static_cast<double>(inputrec->init_step + inputrec->nsteps) * inputrec->delta_t);
 210         }
 211         else
 212         {
 213             timeString = "infinite";
 214         }
 215         if (inputrec->init_step > 0)
 216         {
 217             fprintf(stderr,
 218                     "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
 219                     gmx_step_str(inputrec->init_step + inputrec->nsteps, sbuf),
 220                     timeString.c_str(),
 221                     gmx_step_str(inputrec->init_step, sbuf2),
 222                     inputrec->init_step * inputrec->delta_t);
 223         }
 224         else
 225         {
 226             fprintf(stderr, "%s steps, %s ps.\n", gmx_step_str(inputrec->nsteps, sbuf), timeString.c_str());
 227         }
 228         fprintf(fplog, "\n");
 229     }
 230
 231     walltime_accounting_start_time(walltime_accounting);
 232     wallcycle_start(wcycle, WallCycleCounter::Run);
 233     print_start(fplog, cr, walltime_accounting, "mdrun");
 234
 235     step_ = inputrec->init_step;
 236 }
 237
 238 void ModularSimulatorAlgorithm::simulatorTeardown()
 239 {
 240
 241     // Stop measuring walltime
 242     walltime_accounting_end_time(walltime_accounting);
 243
 244     if (!thisRankHasDuty(cr, DUTY_PME))
 245     {
 246         /* Tell the PME only node to finish */
 247         gmx_pme_send_finish(cr);
 248     }
 249
 250     walltime_accounting_set_nsteps_done(walltime_accounting, step_ - inputrec->init_step);
 251 }
 252
 253 void ModularSimulatorAlgorithm::preStep(Step step, Time gmx_unused time, bool isNeighborSearchingStep)
 254 {
 255     if (stopHandler_->stoppingAfterCurrentStep(isNeighborSearchingStep) && step != signalHelper_->lastStep_)
 256     {
 257         /*
 258          * Stop handler wants to stop after the current step, which was
 259          * not known when building the current task queue. This happens
 260          * e.g. when a stop is signalled by OS. We therefore want to purge
 261          * the task queue now, and re-schedule this step as last step.
 262          */
 263         // clear task queue
 264         taskQueue_.clear();
 265         // rewind step
 266         step_ = step;
 267         return;
 268     }
 269
 270     resetHandler_->setSignal(walltime_accounting);
 271     // This is a hack to avoid having to rewrite StopHandler to be a NeighborSearchSignaller
 272     // and accept the step as input. Eventually, we want to do that, but currently this would
 273     // require introducing NeighborSearchSignaller in the legacy do_md or a lot of code
 274     // duplication.
 275     stophandlerIsNSStep_    = isNeighborSearchingStep;
 276     stophandlerCurrentStep_ = step;
 277     stopHandler_->setSignal();
 278
 279     wallcycle_start(wcycle, WallCycleCounter::Step);
 280 }
 281
 282 void ModularSimulatorAlgorithm::postStep(Step step, Time gmx_unused time)
 283 {
 284     // Output stuff
 285     if (MASTER(cr))
 286     {
 287         if (do_per_step(step, inputrec->nstlog))
 288         {
 289             if (fflush(fplog) != 0)
 290             {
 291                 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 292             }
 293         }
 294     }
 295     const bool do_verbose = mdrunOptions.verbose
 296                             && (step % mdrunOptions.verboseStepPrintInterval == 0
 297                                 || step == inputrec->init_step || step == signalHelper_->lastStep_);
 298     // Print the remaining wall clock time for the run
 299     if (MASTER(cr) && (do_verbose || gmx_got_usr_signal())
 300         && !(pmeLoadBalanceHelper_ && pmeLoadBalanceHelper_->pmePrinting()))
 301     {
 302         print_time(stderr, walltime_accounting, step, inputrec, cr);
 303     }
 304
 305     double cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
 306     if (DOMAINDECOMP(cr) && wcycle)
 307     {
 308         dd_cycles_add(cr->dd, static_cast<float>(cycles), ddCyclStep);
 309     }
 310
 311     resetHandler_->resetCounters(step,
 312                                  step - inputrec->init_step,
 313                                  mdlog,
 314                                  fplog,
 315                                  cr,
 316                                  fr->nbv.get(),
 317                                  nrnb,
 318                                  fr->pmedata,
 319                                  pmeLoadBalanceHelper_ ? pmeLoadBalanceHelper_->loadBalancingObject() : nullptr,
 320                                  wcycle,
 321                                  walltime_accounting);
 322 }
 323
 324 void ModularSimulatorAlgorithm::populateTaskQueue()
 325 {
 326     /*
 327      * The registerRunFunction emplaces functions to the task queue.
 328      * All elements are owned by the ModularSimulatorAlgorithm, as is the task queue.
 329      * Elements can hence register lambdas capturing their `this` pointers without expecting
 330      * life time issues, as the task queue and the elements are in the same scope.
 331      */
 332     auto registerRunFunction = [this](SimulatorRunFunction function) {
 333         taskQueue_.emplace_back(std::move(function));
 334     };
 335
 336     Time startTime = inputrec->init_t;
 337     Time timeStep  = inputrec->delta_t;
 338     Time time      = startTime + step_ * timeStep;
 339
 340     // Run an initial call to the signallers
 341     for (auto& signaller : signallerList_)
 342     {
 343         signaller->signal(step_, time);
 344     }
 345
 346     if (checkpointHelper_)
 347     {
 348         checkpointHelper_->run(step_, time);
 349     }
 350
 351     if (pmeLoadBalanceHelper_)
 352     {
 353         pmeLoadBalanceHelper_->run(step_, time);
 354     }
 355     if (domDecHelper_)
 356     {
 357         domDecHelper_->run(step_, time);
 358     }
 359
 360     do
 361     {
 362         // local variables for lambda capturing
 363         const int  step     = step_;
 364         const bool isNSStep = step == signalHelper_->nextNSStep_;
 365
 366         // register pre-step (task queue is local, so no problem with `this`)
 367         registerRunFunction([this, step, time, isNSStep]() { preStep(step, time, isNSStep); });
 368         // register pre step functions
 369         for (const auto& schedulingFunction : preStepScheduling_)
 370         {
 371             schedulingFunction(step_, time, registerRunFunction);
 372         }
 373         // register elements for step
 374         for (auto& element : elementCallList_)
 375         {
 376             element->scheduleTask(step_, time, registerRunFunction);
 377         }
 378         // register post step functions
 379         for (const auto& schedulingFunction : postStepScheduling_)
 380         {
 381             schedulingFunction(step_, time, registerRunFunction);
 382         }
 383         // register post-step (task queue is local, so no problem with `this`)
 384         registerRunFunction([this, step, time]() { postStep(step, time); });
 385
 386         // prepare next step
 387         step_++;
 388         time = startTime + step_ * timeStep;
 389         for (auto& signaller : signallerList_)
 390         {
 391             signaller->signal(step_, time);
 392         }
 393     } while (step_ != signalHelper_->nextNSStep_ && step_ <= signalHelper_->lastStep_);
 394
 395     runFinished_ = (step_ > signalHelper_->lastStep_);
 396
 397     if (runFinished_)
 398     {
 399         // task queue is local, so no problem with `this`
 400         registerRunFunction([this]() { teardown(); });
 401     }
 402 }
 403
 404 ModularSimulatorAlgorithmBuilder::ModularSimulatorAlgorithmBuilder(
 405         compat::not_null<LegacySimulatorData*>    legacySimulatorData,
 406         std::unique_ptr<ReadCheckpointDataHolder> checkpointDataHolder) :
 407     legacySimulatorData_(legacySimulatorData),
 408     signals_(std::make_unique<SimulationSignals>()),
 409     elementAdditionHelper_(this),
 410     globalCommunicationHelper_(computeGlobalCommunicationPeriod(legacySimulatorData->mdlog,
 411                                                                 legacySimulatorData->inputrec,
 412                                                                 legacySimulatorData->cr),
 413                                signals_.get()),
 414     observablesReducer_(legacySimulatorData->observablesReducerBuilder->build()),
 415     checkpointHelperBuilder_(std::move(checkpointDataHolder),
 416                              legacySimulatorData->startingBehavior,
 417                              legacySimulatorData->cr)
 418 {
 419     if (legacySimulatorData->inputrec->efep != FreeEnergyPerturbationType::No)
 420     {
 421         freeEnergyPerturbationData_ = std::make_unique<FreeEnergyPerturbationData>(
 422                 legacySimulatorData->fplog, *legacySimulatorData->inputrec, legacySimulatorData->mdAtoms);
 423         registerExistingElement(freeEnergyPerturbationData_->element());
 424     }
 425
 426     statePropagatorData_ = std::make_unique<StatePropagatorData>(
 427             legacySimulatorData->top_global.natoms,
 428             legacySimulatorData->fplog,
 429             legacySimulatorData->cr,
 430             legacySimulatorData->state_global,
 431             legacySimulatorData->fr->nbv->useGpu(),
 432             legacySimulatorData->fr->bMolPBC,
 433             legacySimulatorData->mdrunOptions.writeConfout,
 434             opt2fn("-c", legacySimulatorData->nfile, legacySimulatorData->fnm),
 435             legacySimulatorData->inputrec,
 436             legacySimulatorData->mdAtoms->mdatoms(),
 437             legacySimulatorData->top_global);
 438     registerExistingElement(statePropagatorData_->element());
 439
 440     // Multi sim is turned off
 441     const bool simulationsShareState = false;
 442
 443     energyData_ = std::make_unique<EnergyData>(statePropagatorData_.get(),
 444                                                freeEnergyPerturbationData_.get(),
 445                                                legacySimulatorData->top_global,
 446                                                legacySimulatorData->inputrec,
 447                                                legacySimulatorData->mdAtoms,
 448                                                legacySimulatorData->enerd,
 449                                                legacySimulatorData->ekind,
 450                                                legacySimulatorData->constr,
 451                                                legacySimulatorData->fplog,
 452                                                legacySimulatorData->fr->fcdata.get(),
 453                                                legacySimulatorData->mdModulesNotifiers,
 454                                                MASTER(legacySimulatorData->cr),
 455                                                legacySimulatorData->observablesHistory,
 456                                                legacySimulatorData->startingBehavior,
 457                                                simulationsShareState);
 458     registerExistingElement(energyData_->element());
 459
 460     // This is the only modular simulator object which changes the inputrec
 461     // TODO: Avoid changing inputrec (#3854)
 462     storeSimulationData(
 463             "ReferenceTemperatureManager",
 464             ReferenceTemperatureManager(const_cast<t_inputrec*>(legacySimulatorData->inputrec)));
 465     auto* referenceTemperatureManager =
 466             simulationData<ReferenceTemperatureManager>("ReferenceTemperatureManager").value();
 467
 468     // State propagator data is scaling velocities if reference temperature is updated
 469     auto* statePropagatorDataPtr = statePropagatorData_.get();
 470     referenceTemperatureManager->registerUpdateCallback(
 471             [statePropagatorDataPtr](ArrayRef<const real>                temperatures,
 472                                      ReferenceTemperatureChangeAlgorithm algorithm) {
 473                 statePropagatorDataPtr->updateReferenceTemperature(temperatures, algorithm);
 474             });
 475 }
 476
 477 ModularSimulatorAlgorithm ModularSimulatorAlgorithmBuilder::build()
 478 {
 479     if (algorithmHasBeenBuilt_)
 480     {
 481         GMX_THROW(SimulationAlgorithmSetupError(
 482                 "Tried to build ModularSimulationAlgorithm more than once."));
 483     }
 484     algorithmHasBeenBuilt_ = true;
 485
 486     // Connect propagators with thermostat / barostat
 487     for (const auto& registrationFunction : pressureTemperatureControlRegistrationFunctions_)
 488     {
 489         for (const auto& connection : propagatorConnections_)
 490         {
 491             registrationFunction(connection);
 492         }
 493     }
 494
 495     ModularSimulatorAlgorithm algorithm(*(legacySimulatorData_->top_global.name),
 496                                         legacySimulatorData_->fplog,
 497                                         legacySimulatorData_->cr,
 498                                         legacySimulatorData_->mdlog,
 499                                         legacySimulatorData_->mdrunOptions,
 500                                         legacySimulatorData_->inputrec,
 501                                         legacySimulatorData_->nrnb,
 502                                         legacySimulatorData_->wcycle,
 503                                         legacySimulatorData_->fr,
 504                                         legacySimulatorData_->walltime_accounting);
 505     registerWithInfrastructureAndSignallers(algorithm.signalHelper_.get());
 506     algorithm.statePropagatorData_        = std::move(statePropagatorData_);
 507     algorithm.energyData_                 = std::move(energyData_);
 508     algorithm.freeEnergyPerturbationData_ = std::move(freeEnergyPerturbationData_);
 509     algorithm.signals_                    = std::move(signals_);
 510     algorithm.simulationData_             = std::move(simulationData_);
 511
 512     // Multi sim is turned off
 513     const bool simulationsShareState = false;
 514
 515     // Build stop handler
 516     algorithm.stopHandler_ = legacySimulatorData_->stopHandlerBuilder->getStopHandlerMD(
 517             compat::not_null<SimulationSignal*>(
 518                     &(*globalCommunicationHelper_.simulationSignals())[eglsSTOPCOND]),
 519             simulationsShareState,
 520             MASTER(legacySimulatorData_->cr),
 521             legacySimulatorData_->inputrec->nstlist,
 522             legacySimulatorData_->mdrunOptions.reproducible,
 523             globalCommunicationHelper_.nstglobalcomm(),
 524             legacySimulatorData_->mdrunOptions.maximumHoursToRun,
 525             legacySimulatorData_->inputrec->nstlist == 0,
 526             legacySimulatorData_->fplog,
 527             algorithm.stophandlerCurrentStep_,
 528             algorithm.stophandlerIsNSStep_,
 529             legacySimulatorData_->walltime_accounting);
 530
 531     // Build reset handler
 532     const bool simulationsShareResetCounters = false;
 533     algorithm.resetHandler_                  = std::make_unique<ResetHandler>(
 534             compat::make_not_null<SimulationSignal*>(
 535                     &(*globalCommunicationHelper_.simulationSignals())[eglsRESETCOUNTERS]),
 536             simulationsShareResetCounters,
 537             legacySimulatorData_->inputrec->nsteps,
 538             MASTER(legacySimulatorData_->cr),
 539             legacySimulatorData_->mdrunOptions.timingOptions.resetHalfway,
 540             legacySimulatorData_->mdrunOptions.maximumHoursToRun,
 541             legacySimulatorData_->mdlog,
 542             legacySimulatorData_->wcycle,
 543             legacySimulatorData_->walltime_accounting);
 544
 545     // Build topology holder
 546     algorithm.topologyHolder_ = topologyHolderBuilder_.build(legacySimulatorData_->top_global,
 547                                                              legacySimulatorData_->cr,
 548                                                              legacySimulatorData_->inputrec,
 549                                                              legacySimulatorData_->fr,
 550                                                              legacySimulatorData_->mdAtoms,
 551                                                              legacySimulatorData_->constr,
 552                                                              legacySimulatorData_->vsite);
 553     registerWithInfrastructureAndSignallers(algorithm.topologyHolder_.get());
 554
 555     // Build PME load balance helper
 556     if (PmeLoadBalanceHelper::doPmeLoadBalancing(legacySimulatorData_->mdrunOptions,
 557                                                  legacySimulatorData_->inputrec,
 558                                                  legacySimulatorData_->fr))
 559     {
 560         algorithm.pmeLoadBalanceHelper_ =
 561                 std::make_unique<PmeLoadBalanceHelper>(legacySimulatorData_->mdrunOptions.verbose,
 562                                                        algorithm.statePropagatorData_.get(),
 563                                                        legacySimulatorData_->fplog,
 564                                                        legacySimulatorData_->cr,
 565                                                        legacySimulatorData_->mdlog,
 566                                                        legacySimulatorData_->inputrec,
 567                                                        legacySimulatorData_->wcycle,
 568                                                        legacySimulatorData_->fr);
 569         registerWithInfrastructureAndSignallers(algorithm.pmeLoadBalanceHelper_.get());
 570     }
 571
 572     // Build trajectory element
 573     auto trajectoryElement = trajectoryElementBuilder_.build(legacySimulatorData_->fplog,
 574                                                              legacySimulatorData_->nfile,
 575                                                              legacySimulatorData_->fnm,
 576                                                              legacySimulatorData_->mdrunOptions,
 577                                                              legacySimulatorData_->cr,
 578                                                              legacySimulatorData_->outputProvider,
 579                                                              legacySimulatorData_->mdModulesNotifiers,
 580                                                              legacySimulatorData_->inputrec,
 581                                                              legacySimulatorData_->top_global,
 582                                                              legacySimulatorData_->oenv,
 583                                                              legacySimulatorData_->wcycle,
 584                                                              legacySimulatorData_->startingBehavior,
 585                                                              simulationsShareState);
 586     registerWithInfrastructureAndSignallers(trajectoryElement.get());
 587
 588     // Build domdec helper
 589     if (DOMAINDECOMP(legacySimulatorData_->cr))
 590     {
 591         algorithm.domDecHelper_ =
 592                 domDecHelperBuilder_.build(legacySimulatorData_->mdrunOptions.verbose,
 593                                            legacySimulatorData_->mdrunOptions.verboseStepPrintInterval,
 594                                            algorithm.statePropagatorData_.get(),
 595                                            algorithm.topologyHolder_.get(),
 596                                            globalCommunicationHelper_.nstglobalcomm(),
 597                                            legacySimulatorData_->fplog,
 598                                            legacySimulatorData_->cr,
 599                                            legacySimulatorData_->mdlog,
 600                                            legacySimulatorData_->constr,
 601                                            legacySimulatorData_->inputrec,
 602                                            legacySimulatorData_->mdAtoms,
 603                                            legacySimulatorData_->nrnb,
 604                                            legacySimulatorData_->wcycle,
 605                                            legacySimulatorData_->fr,
 606                                            legacySimulatorData_->vsite,
 607                                            legacySimulatorData_->imdSession,
 608                                            legacySimulatorData_->pull_work);
 609         registerWithInfrastructureAndSignallers(algorithm.domDecHelper_.get());
 610     }
 611     // Build checkpoint helper (do this last so everyone else can be a checkpoint client!)
 612     {
 613         checkpointHelperBuilder_.setCheckpointHandler(std::make_unique<CheckpointHandler>(
 614                 compat::make_not_null<SimulationSignal*>(&(*algorithm.signals_)[eglsCHKPT]),
 615                 simulationsShareState,
 616                 legacySimulatorData_->inputrec->nstlist == 0,
 617                 MASTER(legacySimulatorData_->cr),
 618                 legacySimulatorData_->mdrunOptions.writeConfout,
 619                 legacySimulatorData_->mdrunOptions.checkpointOptions.period));
 620         algorithm.checkpointHelper_ =
 621                 checkpointHelperBuilder_.build(legacySimulatorData_->inputrec->init_step,
 622                                                trajectoryElement.get(),
 623                                                legacySimulatorData_->fplog,
 624                                                legacySimulatorData_->cr,
 625                                                legacySimulatorData_->observablesHistory,
 626                                                legacySimulatorData_->walltime_accounting,
 627                                                legacySimulatorData_->state_global,
 628                                                legacySimulatorData_->mdrunOptions.writeConfout);
 629         registerWithInfrastructureAndSignallers(algorithm.checkpointHelper_.get());
 630     }
 631
 632     // Build signallers
 633     {
 634         /* Signallers need to be called in an exact order. Some signallers are clients
 635          * of other signallers, which requires the clients signallers to be called
 636          * _after_ any signaller they are registered to - otherwise, they couldn't
 637          * adapt their behavior to the information they got signalled.
 638          *
 639          * Signallers being clients of other signallers require registration.
 640          * That registration happens during construction, which in turn means that
 641          * we want to construct the signallers in the reverse order of their later
 642          * call order.
 643          *
 644          * For the above reasons, the `addSignaller` lambda defined below emplaces
 645          * added signallers at the beginning of the signaller list, which will yield
 646          * a signaller list which is inverse to the build order (and hence equal to
 647          * the intended call order).
 648          */
 649         auto addSignaller = [this, &algorithm](auto signaller) {
 650             registerWithInfrastructureAndSignallers(signaller.get());
 651             algorithm.signallerList_.emplace(algorithm.signallerList_.begin(), std::move(signaller));
 652         };
 653         const auto* inputrec   = legacySimulatorData_->inputrec;
 654         auto        virialMode = EnergySignallerVirialMode::Off;
 655         if (inputrec->epc != PressureCoupling::No)
 656         {
 657             if (EI_VV(inputrec->eI))
 658             {
 659                 virialMode = EnergySignallerVirialMode::OnStepAndNext;
 660             }
 661             else
 662             {
 663                 virialMode = EnergySignallerVirialMode::OnStep;
 664             }
 665         }
 666         addSignaller(energySignallerBuilder_.build(
 667                 inputrec->nstcalcenergy,
 668                 computeFepPeriod(*inputrec, legacySimulatorData_->replExParams),
 669                 inputrec->nstpcouple,
 670                 virialMode));
 671         addSignaller(trajectorySignallerBuilder_.build(inputrec->nstxout,
 672                                                        inputrec->nstvout,
 673                                                        inputrec->nstfout,
 674                                                        inputrec->nstxout_compressed,
 675                                                        trajectoryElement->tngBoxOut(),
 676                                                        trajectoryElement->tngLambdaOut(),
 677                                                        trajectoryElement->tngBoxOutCompressed(),
 678                                                        trajectoryElement->tngLambdaOutCompressed(),
 679                                                        inputrec->nstenergy));
 680         addSignaller(loggingSignallerBuilder_.build(
 681                 inputrec->nstlog, inputrec->init_step, legacySimulatorData_->startingBehavior));
 682         addSignaller(lastStepSignallerBuilder_.build(
 683                 inputrec->nsteps, inputrec->init_step, algorithm.stopHandler_.get()));
 684         addSignaller(neighborSearchSignallerBuilder_.build(
 685                 inputrec->nstlist, inputrec->init_step, inputrec->init_t));
 686     }
 687
 688     // Move setup / teardown list
 689     algorithm.elementSetupTeardownList_ = std::move(setupAndTeardownList_);
 690     // Move pre- / post-step scheduling lists
 691     algorithm.preStepScheduling_  = std::move(preStepScheduling_);
 692     algorithm.postStepScheduling_ = std::move(postStepScheduling_);
 693
 694     // Create element list
 695     // Checkpoint helper needs to be in the call list (as first element!) to react to last step
 696     algorithm.elementCallList_.emplace_back(algorithm.checkpointHelper_.get());
 697     // Next, update the free energy lambda vector if needed
 698     if (algorithm.freeEnergyPerturbationData_)
 699     {
 700         algorithm.elementCallList_.emplace_back(algorithm.freeEnergyPerturbationData_->element());
 701     }
 702     // Then, move the built algorithm
 703     algorithm.elementsOwnershipList_.insert(algorithm.elementsOwnershipList_.end(),
 704                                             std::make_move_iterator(elements_.begin()),
 705                                             std::make_move_iterator(elements_.end()));
 706     algorithm.elementCallList_.insert(algorithm.elementCallList_.end(),
 707                                       std::make_move_iterator(callList_.begin()),
 708                                       std::make_move_iterator(callList_.end()));
 709     // Finally, all trajectory writing is happening after the step
 710     // (relevant data was stored by elements through energy signaller)
 711     algorithm.elementsOwnershipList_.emplace_back(std::move(trajectoryElement));
 712     algorithm.elementCallList_.emplace_back(algorithm.elementsOwnershipList_.back().get());
 713     algorithm.elementSetupTeardownList_.emplace_back(algorithm.elementsOwnershipList_.back().get());
 714
 715     algorithm.setup();
 716     return algorithm;
 717 }
 718
 719 bool ModularSimulatorAlgorithmBuilder::elementExists(const ISimulatorElement* element) const
 720 {
 721     // Check whether element exists in element list
 722     if (std::any_of(elements_.begin(), elements_.end(), [element](auto& existingElement) {
 723             return element == existingElement.get();
 724         }))
 725     {
 726         return true;
 727     }
 728     // Check whether element exists in other places controlled by *this
 729     return ((statePropagatorData_ && statePropagatorData_->element() == element)
 730             || (energyData_ && energyData_->element() == element)
 731             || (freeEnergyPerturbationData_ && freeEnergyPerturbationData_->element() == element));
 732 }
 733
 734 std::optional<SignallerCallback> ModularSimulatorAlgorithm::SignalHelper::registerLastStepCallback()
 735 {
 736     return [this](Step step, Time gmx_unused time) { this->lastStep_ = step; };
 737 }
 738
 739 std::optional<SignallerCallback> ModularSimulatorAlgorithm::SignalHelper::registerNSCallback()
 740 {
 741     return [this](Step step, Time gmx_unused time) { this->nextNSStep_ = step; };
 742 }
 743
 744 GlobalCommunicationHelper::GlobalCommunicationHelper(int nstglobalcomm, SimulationSignals* simulationSignals) :
 745     nstglobalcomm_(nstglobalcomm), simulationSignals_(simulationSignals)
 746 {
 747 }
 748
 749 int GlobalCommunicationHelper::nstglobalcomm() const
 750 {
 751     return nstglobalcomm_;
 752 }
 753
 754 SimulationSignals* GlobalCommunicationHelper::simulationSignals()
 755 {
 756     return simulationSignals_;
 757 }
 758
 759 ModularSimulatorAlgorithmBuilderHelper::ModularSimulatorAlgorithmBuilderHelper(
 760         ModularSimulatorAlgorithmBuilder* builder) :
 761     builder_(builder)
 762 {
 763 }
 764
 765 bool ModularSimulatorAlgorithmBuilderHelper::elementIsStored(const ISimulatorElement* element) const
 766 {
 767     return builder_->elementExists(element);
 768 }
 769
 770 [[maybe_unused]] void ModularSimulatorAlgorithmBuilderHelper::registerPreStepScheduling(SchedulingFunction schedulingFunction)
 771 {
 772     builder_->preStepScheduling_.emplace_back(std::move(schedulingFunction));
 773 }
 774
 775 [[maybe_unused]] void ModularSimulatorAlgorithmBuilderHelper::registerPostStepScheduling(SchedulingFunction schedulingFunction)
 776 {
 777     builder_->postStepScheduling_.emplace_back(std::move(schedulingFunction));
 778 }
 779
 780 std::optional<std::any> ModularSimulatorAlgorithmBuilderHelper::builderData(const std::string& key) const
 781 {
 782     const auto iter = builder_->builderData_.find(key);
 783     if (iter == builder_->builderData_.end())
 784     {
 785         return std::nullopt;
 786     }
 787     else
 788     {
 789         return iter->second;
 790     }
 791 }
 792
 793 void ModularSimulatorAlgorithmBuilderHelper::registerTemperaturePressureControl(
 794         std::function<void(const PropagatorConnection&)> registrationFunction)
 795 {
 796     builder_->pressureTemperatureControlRegistrationFunctions_.emplace_back(std::move(registrationFunction));
 797 }
 798
 799 void ModularSimulatorAlgorithmBuilderHelper::registerPropagator(PropagatorConnection connectionData)
 800 {
 801     builder_->propagatorConnections_.emplace_back(std::move(connectionData));
 802 }
 803
 804 void ModularSimulatorAlgorithmBuilderHelper::registerReferenceTemperatureUpdate(
 805         ReferenceTemperatureCallback referenceTemperatureCallback)
 806 {
 807     auto* referenceTemperatureManager =
 808             simulationData<ReferenceTemperatureManager>("ReferenceTemperatureManager").value();
 809     referenceTemperatureManager->registerUpdateCallback(std::move(referenceTemperatureCallback));
 810 }
 811
 812 ReferenceTemperatureCallback ModularSimulatorAlgorithmBuilderHelper::changeReferenceTemperatureCallback()
 813 {
 814     // Capture is safe because SimulatorAlgorithm will manage life time of both the
 815     // recipient of the callback and the reference temperature manager
 816     auto* referenceTemperatureManager =
 817             simulationData<ReferenceTemperatureManager>("ReferenceTemperatureManager").value();
 818     return [referenceTemperatureManager](ArrayRef<const real>                temperatures,
 819                                          ReferenceTemperatureChangeAlgorithm algorithm) {
 820         referenceTemperatureManager->setReferenceTemperature(temperatures, algorithm);
 821     };
 822 }
 823
 824 } // namespace gmx