src/gromacs/modularsimulator/modularsimulator.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2019,2020, 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
  37  *
  38  * \author Pascal Merz <pascal.merz@me.com>
  39  * \ingroup module_modularsimulator
  40  */
  41
  42 #include "gmxpre.h"
  43
  44 #include "modularsimulator.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/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/mdatoms.h"
  58 #include "gromacs/mdlib/resethandler.h"
  59 #include "gromacs/mdlib/stat.h"
  60 #include "gromacs/mdlib/update.h"
  61 #include "gromacs/mdrun/replicaexchange.h"
  62 #include "gromacs/mdrun/shellfc.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/mdtypes/state.h"
  73 #include "gromacs/nbnxm/nbnxm.h"
  74 #include "gromacs/timing/walltime_accounting.h"
  75 #include "gromacs/topology/topology.h"
  76 #include "gromacs/utility/cstringutil.h"
  77 #include "gromacs/utility/fatalerror.h"
  78
  79 #include "compositesimulatorelement.h"
  80 #include "computeglobalselement.h"
  81 #include "constraintelement.h"
  82 #include "energyelement.h"
  83 #include "forceelement.h"
  84 #include "freeenergyperturbationelement.h"
  85 #include "parrinellorahmanbarostat.h"
  86 #include "propagator.h"
  87 #include "shellfcelement.h"
  88 #include "signallers.h"
  89 #include "statepropagatordata.h"
  90 #include "trajectoryelement.h"
  91 #include "vrescalethermostat.h"
  92
  93 namespace gmx
  94 {
  95 void ModularSimulator::run()
  96 {
  97     GMX_LOG(mdlog.info).asParagraph().appendText("Using the modular simulator.");
  98     constructElementsAndSignallers();
  99     simulatorSetup();
 100     for (auto& signaller : signallerCallList_)
 101     {
 102         signaller->signallerSetup();
 103     }
 104     if (domDecHelper_)
 105     {
 106         domDecHelper_->setup();
 107     }
 108
 109     for (auto& element : elementsOwnershipList_)
 110     {
 111         element->elementSetup();
 112     }
 113     if (pmeLoadBalanceHelper_)
 114     {
 115         // State must have been initialized so pmeLoadBalanceHelper_ gets a valid box
 116         pmeLoadBalanceHelper_->setup();
 117     }
 118
 119     while (step_ <= signalHelper_->lastStep_)
 120     {
 121         populateTaskQueue();
 122
 123         while (!taskQueue_.empty())
 124         {
 125             auto task = std::move(taskQueue_.front());
 126             taskQueue_.pop();
 127             // run function
 128             (*task)();
 129         }
 130     }
 131
 132     for (auto& element : elementsOwnershipList_)
 133     {
 134         element->elementTeardown();
 135     }
 136     if (pmeLoadBalanceHelper_)
 137     {
 138         pmeLoadBalanceHelper_->teardown();
 139     }
 140     simulatorTeardown();
 141 }
 142
 143 void ModularSimulator::simulatorSetup()
 144 {
 145     if (!mdrunOptions.writeConfout)
 146     {
 147         // This is on by default, and the main known use case for
 148         // turning it off is for convenience in benchmarking, which is
 149         // something that should not show up in the general user
 150         // interface.
 151         GMX_LOG(mdlog.info)
 152                 .asParagraph()
 153                 .appendText(
 154                         "The -noconfout functionality is deprecated, and "
 155                         "may be removed in a future version.");
 156     }
 157
 158     if (MASTER(cr))
 159     {
 160         char        sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
 161         std::string timeString;
 162         fprintf(stderr, "starting mdrun '%s'\n", *(top_global->name));
 163         if (inputrec->nsteps >= 0)
 164         {
 165             timeString = formatString("%8.1f", static_cast<double>(inputrec->init_step + inputrec->nsteps)
 166                                                        * inputrec->delta_t);
 167         }
 168         else
 169         {
 170             timeString = "infinite";
 171         }
 172         if (inputrec->init_step > 0)
 173         {
 174             fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
 175                     gmx_step_str(inputrec->init_step + inputrec->nsteps, sbuf), timeString.c_str(),
 176                     gmx_step_str(inputrec->init_step, sbuf2), inputrec->init_step * inputrec->delta_t);
 177         }
 178         else
 179         {
 180             fprintf(stderr, "%s steps, %s ps.\n", gmx_step_str(inputrec->nsteps, sbuf),
 181                     timeString.c_str());
 182         }
 183         fprintf(fplog, "\n");
 184     }
 185
 186     walltime_accounting_start_time(walltime_accounting);
 187     wallcycle_start(wcycle, ewcRUN);
 188     print_start(fplog, cr, walltime_accounting, "mdrun");
 189
 190     step_ = inputrec->init_step;
 191 }
 192
 193 void ModularSimulator::preStep(Step step, Time gmx_unused time, bool isNeighborSearchingStep)
 194 {
 195     if (stopHandler_->stoppingAfterCurrentStep(isNeighborSearchingStep) && step != signalHelper_->lastStep_)
 196     {
 197         /*
 198          * Stop handler wants to stop after the current step, which was
 199          * not known when building the current task queue. This happens
 200          * e.g. when a stop is signalled by OS. We therefore want to purge
 201          * the task queue now, and re-schedule this step as last step.
 202          */
 203         // clear task queue
 204         std::queue<SimulatorRunFunctionPtr>().swap(taskQueue_);
 205         // rewind step
 206         step_ = step;
 207         return;
 208     }
 209
 210     resetHandler_->setSignal(walltime_accounting);
 211     // This is a hack to avoid having to rewrite StopHandler to be a NeighborSearchSignaller
 212     // and accept the step as input. Eventually, we want to do that, but currently this would
 213     // require introducing NeighborSearchSignaller in the legacy do_md or a lot of code
 214     // duplication.
 215     stophandlerIsNSStep_    = isNeighborSearchingStep;
 216     stophandlerCurrentStep_ = step;
 217     stopHandler_->setSignal();
 218
 219     wallcycle_start(wcycle, ewcSTEP);
 220 }
 221
 222 void ModularSimulator::postStep(Step step, Time gmx_unused time)
 223 {
 224     // Output stuff
 225     if (MASTER(cr))
 226     {
 227         if (do_per_step(step, inputrec->nstlog))
 228         {
 229             if (fflush(fplog) != 0)
 230             {
 231                 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 232             }
 233         }
 234     }
 235     const bool do_verbose = mdrunOptions.verbose
 236                             && (step % mdrunOptions.verboseStepPrintInterval == 0
 237                                 || step == inputrec->init_step || step == signalHelper_->lastStep_);
 238     // Print the remaining wall clock time for the run
 239     if (MASTER(cr) && (do_verbose || gmx_got_usr_signal())
 240         && !(pmeLoadBalanceHelper_ && pmeLoadBalanceHelper_->pmePrinting()))
 241     {
 242         print_time(stderr, walltime_accounting, step, inputrec, cr);
 243     }
 244
 245     double cycles = wallcycle_stop(wcycle, ewcSTEP);
 246     if (DOMAINDECOMP(cr) && wcycle)
 247     {
 248         dd_cycles_add(cr->dd, static_cast<float>(cycles), ddCyclStep);
 249     }
 250
 251     resetHandler_->resetCounters(
 252             step, step - inputrec->init_step, mdlog, fplog, cr, fr->nbv.get(), nrnb, fr->pmedata,
 253             pmeLoadBalanceHelper_ ? pmeLoadBalanceHelper_->loadBalancingObject() : nullptr, wcycle,
 254             walltime_accounting);
 255 }
 256
 257 void ModularSimulator::simulatorTeardown()
 258 {
 259
 260     // Stop measuring walltime
 261     walltime_accounting_end_time(walltime_accounting);
 262
 263     if (!thisRankHasDuty(cr, DUTY_PME))
 264     {
 265         /* Tell the PME only node to finish */
 266         gmx_pme_send_finish(cr);
 267     }
 268
 269     walltime_accounting_set_nsteps_done(walltime_accounting, step_ - inputrec->init_step);
 270 }
 271
 272 void ModularSimulator::populateTaskQueue()
 273 {
 274     auto registerRunFunction = std::make_unique<RegisterRunFunction>(
 275             [this](SimulatorRunFunctionPtr ptr) { taskQueue_.push(std::move(ptr)); });
 276
 277     Time startTime = inputrec->init_t;
 278     Time timeStep  = inputrec->delta_t;
 279     Time time      = startTime + step_ * timeStep;
 280
 281     // Run an initial call to the signallers
 282     for (auto& signaller : signallerCallList_)
 283     {
 284         signaller->signal(step_, time);
 285     }
 286
 287     if (checkpointHelper_)
 288     {
 289         checkpointHelper_->run(step_, time);
 290     }
 291
 292     if (pmeLoadBalanceHelper_)
 293     {
 294         pmeLoadBalanceHelper_->run(step_, time);
 295     }
 296     if (domDecHelper_)
 297     {
 298         domDecHelper_->run(step_, time);
 299     }
 300
 301     do
 302     {
 303         // local variables for lambda capturing
 304         const int  step     = step_;
 305         const bool isNSStep = step == signalHelper_->nextNSStep_;
 306
 307         // register pre-step
 308         (*registerRunFunction)(std::make_unique<SimulatorRunFunction>(
 309                 [this, step, time, isNSStep]() { preStep(step, time, isNSStep); }));
 310         // register elements for step
 311         for (auto& element : elementCallList_)
 312         {
 313             element->scheduleTask(step_, time, registerRunFunction);
 314         }
 315         // register post-step
 316         (*registerRunFunction)(
 317                 std::make_unique<SimulatorRunFunction>([this, step, time]() { postStep(step, time); }));
 318
 319         // prepare next step
 320         step_++;
 321         time = startTime + step_ * timeStep;
 322         for (auto& signaller : signallerCallList_)
 323         {
 324             signaller->signal(step_, time);
 325         }
 326     } while (step_ != signalHelper_->nextNSStep_ && step_ <= signalHelper_->lastStep_);
 327 }
 328
 329 void ModularSimulator::constructElementsAndSignallers()
 330 {
 331     /* When restarting from a checkpoint, it can be appropriate to
 332      * initialize ekind from quantities in the checkpoint. Otherwise,
 333      * compute_globals must initialize ekind before the simulation
 334      * starts/restarts. However, only the master rank knows what was
 335      * found in the checkpoint file, so we have to communicate in
 336      * order to coordinate the restart.
 337      *
 338      * TODO (modular) This should become obsolete when checkpoint reading
 339      *      happens within the modular simulator framework: The energy
 340      *      element should read its data from the checkpoint file pointer,
 341      *      and signal to the compute globals element if it needs anything
 342      *      reduced.
 343      *
 344      * TODO (legacy) Consider removing this communication if/when checkpoint
 345      *      reading directly follows .tpr reading, because all ranks can
 346      *      agree on hasReadEkinState at that time.
 347      */
 348     bool hasReadEkinState = MASTER(cr) ? state_global->ekinstate.hasReadEkinState : false;
 349     if (PAR(cr))
 350     {
 351         gmx_bcast(sizeof(hasReadEkinState), &hasReadEkinState, cr);
 352     }
 353     if (hasReadEkinState)
 354     {
 355         restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
 356     }
 357
 358     /*
 359      * Build data structures
 360      */
 361     topologyHolder_ =
 362             std::make_unique<TopologyHolder>(*top_global, cr, inputrec, fr, mdAtoms, constr, vsite);
 363
 364     std::unique_ptr<FreeEnergyPerturbationElement> freeEnergyPerturbationElement    = nullptr;
 365     FreeEnergyPerturbationElement*                 freeEnergyPerturbationElementPtr = nullptr;
 366     if (inputrec->efep != efepNO)
 367     {
 368         freeEnergyPerturbationElement =
 369                 std::make_unique<FreeEnergyPerturbationElement>(fplog, inputrec, mdAtoms);
 370         freeEnergyPerturbationElementPtr = freeEnergyPerturbationElement.get();
 371     }
 372
 373     auto statePropagatorData = std::make_unique<StatePropagatorData>(
 374             top_global->natoms, fplog, cr, state_global, inputrec->nstxout, inputrec->nstvout,
 375             inputrec->nstfout, inputrec->nstxout_compressed, fr->nbv->useGpu(),
 376             freeEnergyPerturbationElementPtr, topologyHolder_.get(), fr->bMolPBC,
 377             mdrunOptions.writeConfout, opt2fn("-c", nfile, fnm), inputrec, mdAtoms->mdatoms());
 378     auto statePropagatorDataPtr = compat::make_not_null(statePropagatorData.get());
 379
 380     auto energyElement = std::make_unique<EnergyElement>(
 381             statePropagatorDataPtr, freeEnergyPerturbationElementPtr, top_global, inputrec, mdAtoms,
 382             enerd, ekind, constr, fplog, fcd, mdModulesNotifier, MASTER(cr), observablesHistory,
 383             startingBehavior);
 384     auto energyElementPtr = compat::make_not_null(energyElement.get());
 385
 386     /*
 387      * Build stop handler
 388      */
 389     const bool simulationsShareState = false;
 390     stopHandler_                     = stopHandlerBuilder->getStopHandlerMD(
 391             compat::not_null<SimulationSignal*>(&signals_[eglsSTOPCOND]), simulationsShareState,
 392             MASTER(cr), inputrec->nstlist, mdrunOptions.reproducible, nstglobalcomm_,
 393             mdrunOptions.maximumHoursToRun, inputrec->nstlist == 0, fplog, stophandlerCurrentStep_,
 394             stophandlerIsNSStep_, walltime_accounting);
 395
 396     /*
 397      * Create simulator builders
 398      */
 399     SignallerBuilder<NeighborSearchSignaller> neighborSearchSignallerBuilder;
 400     SignallerBuilder<LastStepSignaller>       lastStepSignallerBuilder;
 401     SignallerBuilder<LoggingSignaller>        loggingSignallerBuilder;
 402     SignallerBuilder<EnergySignaller>         energySignallerBuilder;
 403     TrajectoryElementBuilder                  trajectoryElementBuilder;
 404
 405     /*
 406      * Register data structures to signallers
 407      */
 408     trajectoryElementBuilder.registerWriterClient(statePropagatorDataPtr);
 409     trajectoryElementBuilder.registerSignallerClient(statePropagatorDataPtr);
 410     lastStepSignallerBuilder.registerSignallerClient(statePropagatorDataPtr);
 411
 412     trajectoryElementBuilder.registerWriterClient(energyElementPtr);
 413     trajectoryElementBuilder.registerSignallerClient(energyElementPtr);
 414     energySignallerBuilder.registerSignallerClient(energyElementPtr);
 415
 416     // Register the simulator itself to the neighbor search / last step signaller
 417     neighborSearchSignallerBuilder.registerSignallerClient(compat::make_not_null(signalHelper_.get()));
 418     lastStepSignallerBuilder.registerSignallerClient(compat::make_not_null(signalHelper_.get()));
 419
 420     /*
 421      * Build integrator - this takes care of force calculation, propagation,
 422      * constraining, and of the place the statePropagatorData and the energy element
 423      * have a full timestep state.
 424      */
 425     // TODO: Make a CheckpointHelperBuilder
 426     std::vector<ICheckpointHelperClient*> checkpointClients = { statePropagatorDataPtr, energyElementPtr,
 427                                                                 freeEnergyPerturbationElementPtr };
 428     CheckBondedInteractionsCallbackPtr checkBondedInteractionsCallback = nullptr;
 429     auto                               integrator =
 430             buildIntegrator(&neighborSearchSignallerBuilder, &energySignallerBuilder,
 431                             &loggingSignallerBuilder, &trajectoryElementBuilder, &checkpointClients,
 432                             &checkBondedInteractionsCallback, statePropagatorDataPtr,
 433                             energyElementPtr, freeEnergyPerturbationElementPtr, hasReadEkinState);
 434
 435     /*
 436      * Build infrastructure elements
 437      */
 438
 439     if (PmeLoadBalanceHelper::doPmeLoadBalancing(mdrunOptions, inputrec, fr))
 440     {
 441         pmeLoadBalanceHelper_ = std::make_unique<PmeLoadBalanceHelper>(
 442                 mdrunOptions.verbose, statePropagatorDataPtr, fplog, cr, mdlog, inputrec, wcycle, fr);
 443         neighborSearchSignallerBuilder.registerSignallerClient(
 444                 compat::make_not_null(pmeLoadBalanceHelper_.get()));
 445     }
 446
 447     if (DOMAINDECOMP(cr))
 448     {
 449         GMX_ASSERT(checkBondedInteractionsCallback,
 450                    "Domain decomposition needs a callback for check the number of bonded "
 451                    "interactions.");
 452         domDecHelper_ = std::make_unique<DomDecHelper>(
 453                 mdrunOptions.verbose, mdrunOptions.verboseStepPrintInterval, statePropagatorDataPtr,
 454                 topologyHolder_.get(), std::move(checkBondedInteractionsCallback), nstglobalcomm_, fplog,
 455                 cr, mdlog, constr, inputrec, mdAtoms, nrnb, wcycle, fr, vsite, imdSession, pull_work);
 456         neighborSearchSignallerBuilder.registerSignallerClient(compat::make_not_null(domDecHelper_.get()));
 457     }
 458
 459     const bool simulationsShareResetCounters = false;
 460     resetHandler_                            = std::make_unique<ResetHandler>(
 461             compat::make_not_null<SimulationSignal*>(&signals_[eglsRESETCOUNTERS]),
 462             simulationsShareResetCounters, inputrec->nsteps, MASTER(cr),
 463             mdrunOptions.timingOptions.resetHalfway, mdrunOptions.maximumHoursToRun, mdlog, wcycle,
 464             walltime_accounting);
 465
 466     /*
 467      * Build signaller list
 468      *
 469      * Note that as signallers depend on each others, the order of calling the signallers
 470      * matters. It is the responsibility of this builder to ensure that the order is
 471      * maintained.
 472      */
 473     auto energySignaller = energySignallerBuilder.build(
 474             inputrec->nstcalcenergy, inputrec->fepvals->nstdhdl, inputrec->nstpcouple);
 475     trajectoryElementBuilder.registerSignallerClient(compat::make_not_null(energySignaller.get()));
 476     loggingSignallerBuilder.registerSignallerClient(compat::make_not_null(energySignaller.get()));
 477     auto trajectoryElement = trajectoryElementBuilder.build(
 478             fplog, nfile, fnm, mdrunOptions, cr, outputProvider, mdModulesNotifier, inputrec,
 479             top_global, oenv, wcycle, startingBehavior);
 480     loggingSignallerBuilder.registerSignallerClient(compat::make_not_null(trajectoryElement.get()));
 481
 482     // Add checkpoint helper here since we need a pointer to the trajectory element and
 483     // need to register it with the lastStepSignallerBuilder
 484     auto checkpointHandler = std::make_unique<CheckpointHandler>(
 485             compat::make_not_null<SimulationSignal*>(&signals_[eglsCHKPT]), simulationsShareState,
 486             inputrec->nstlist == 0, MASTER(cr), mdrunOptions.writeConfout,
 487             mdrunOptions.checkpointOptions.period);
 488     checkpointHelper_ = std::make_unique<CheckpointHelper>(
 489             std::move(checkpointClients), std::move(checkpointHandler), inputrec->init_step,
 490             trajectoryElement.get(), top_global->natoms, fplog, cr, observablesHistory,
 491             walltime_accounting, state_global, mdrunOptions.writeConfout);
 492     lastStepSignallerBuilder.registerSignallerClient(compat::make_not_null(checkpointHelper_.get()));
 493
 494     lastStepSignallerBuilder.registerSignallerClient(compat::make_not_null(trajectoryElement.get()));
 495     auto loggingSignaller =
 496             loggingSignallerBuilder.build(inputrec->nstlog, inputrec->init_step, inputrec->init_t);
 497     lastStepSignallerBuilder.registerSignallerClient(compat::make_not_null(loggingSignaller.get()));
 498     auto lastStepSignaller =
 499             lastStepSignallerBuilder.build(inputrec->nsteps, inputrec->init_step, stopHandler_.get());
 500     neighborSearchSignallerBuilder.registerSignallerClient(compat::make_not_null(lastStepSignaller.get()));
 501     auto neighborSearchSignaller = neighborSearchSignallerBuilder.build(
 502             inputrec->nstlist, inputrec->init_step, inputrec->init_t);
 503
 504     addToCallListAndMove(std::move(neighborSearchSignaller), signallerCallList_, signallersOwnershipList_);
 505     addToCallListAndMove(std::move(lastStepSignaller), signallerCallList_, signallersOwnershipList_);
 506     addToCallListAndMove(std::move(loggingSignaller), signallerCallList_, signallersOwnershipList_);
 507     addToCallList(trajectoryElement, signallerCallList_);
 508     addToCallListAndMove(std::move(energySignaller), signallerCallList_, signallersOwnershipList_);
 509
 510     /*
 511      * Build the element list
 512      *
 513      * This is the actual sequence of (non-infrastructure) elements to be run.
 514      * For NVE, the trajectory element is used outside of the integrator
 515      * (composite) element, as well as the checkpoint helper. The checkpoint
 516      * helper should be on top of the loop, and is only part of the simulator
 517      * call list to be able to react to the last step being signalled.
 518      */
 519     addToCallList(checkpointHelper_, elementCallList_);
 520     if (freeEnergyPerturbationElement)
 521     {
 522         addToCallListAndMove(std::move(freeEnergyPerturbationElement), elementCallList_,
 523                              elementsOwnershipList_);
 524     }
 525     addToCallListAndMove(std::move(integrator), elementCallList_, elementsOwnershipList_);
 526     addToCallListAndMove(std::move(trajectoryElement), elementCallList_, elementsOwnershipList_);
 527     // for vv, we need to setup statePropagatorData after the compute
 528     // globals so that we reset the right velocities
 529     // TODO: Avoid this by getting rid of the need of resetting velocities in vv
 530     elementsOwnershipList_.emplace_back(std::move(statePropagatorData));
 531     elementsOwnershipList_.emplace_back(std::move(energyElement));
 532 }
 533
 534 std::unique_ptr<ISimulatorElement>
 535 ModularSimulator::buildForces(SignallerBuilder<NeighborSearchSignaller>* neighborSearchSignallerBuilder,
 536                               SignallerBuilder<EnergySignaller>*         energySignallerBuilder,
 537                               StatePropagatorData*                       statePropagatorDataPtr,
 538                               EnergyElement*                             energyElementPtr,
 539                               FreeEnergyPerturbationElement* freeEnergyPerturbationElement)
 540 {
 541     const bool isVerbose    = mdrunOptions.verbose;
 542     const bool isDynamicBox = inputrecDynamicBox(inputrec);
 543     // Check for polarizable models and flexible constraints
 544     if (ShellFCElement::doShellsOrFlexConstraints(topologyHolder_->globalTopology(),
 545                                                   constr ? constr->numFlexibleConstraints() : 0))
 546     {
 547         auto shellFCElement = std::make_unique<ShellFCElement>(
 548                 statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElement, isVerbose,
 549                 isDynamicBox, fplog, cr, inputrec, mdAtoms, nrnb, fr, fcd, wcycle, runScheduleWork, vsite,
 550                 imdSession, pull_work, constr, &topologyHolder_->globalTopology(), enforcedRotation);
 551         topologyHolder_->registerClient(shellFCElement.get());
 552         neighborSearchSignallerBuilder->registerSignallerClient(
 553                 compat::make_not_null(shellFCElement.get()));
 554         energySignallerBuilder->registerSignallerClient(compat::make_not_null(shellFCElement.get()));
 555
 556         // std::move *should* not be needed with c++-14, but clang-3.6 still requires it
 557         return std::move(shellFCElement);
 558     }
 559     else
 560     {
 561         auto forceElement = std::make_unique<ForceElement>(
 562                 statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElement,
 563                 isDynamicBox, fplog, cr, inputrec, mdAtoms, nrnb, fr, fcd, wcycle, runScheduleWork,
 564                 vsite, imdSession, pull_work, enforcedRotation);
 565         topologyHolder_->registerClient(forceElement.get());
 566         neighborSearchSignallerBuilder->registerSignallerClient(compat::make_not_null(forceElement.get()));
 567         energySignallerBuilder->registerSignallerClient(compat::make_not_null(forceElement.get()));
 568
 569         // std::move *should* not be needed with c++-14, but clang-3.6 still requires it
 570         return std::move(forceElement);
 571     }
 572 }
 573
 574 std::unique_ptr<ISimulatorElement> ModularSimulator::buildIntegrator(
 575         SignallerBuilder<NeighborSearchSignaller>* neighborSearchSignallerBuilder,
 576         SignallerBuilder<EnergySignaller>*         energySignallerBuilder,
 577         SignallerBuilder<LoggingSignaller>*        loggingSignallerBuilder,
 578         TrajectoryElementBuilder*                  trajectoryElementBuilder,
 579         std::vector<ICheckpointHelperClient*>*     checkpointClients,
 580         CheckBondedInteractionsCallbackPtr*        checkBondedInteractionsCallback,
 581         compat::not_null<StatePropagatorData*>     statePropagatorDataPtr,
 582         compat::not_null<EnergyElement*>           energyElementPtr,
 583         FreeEnergyPerturbationElement*             freeEnergyPerturbationElementPtr,
 584         bool                                       hasReadEkinState)
 585 {
 586     auto forceElement =
 587             buildForces(neighborSearchSignallerBuilder, energySignallerBuilder,
 588                         statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr);
 589
 590     // list of elements owned by the simulator composite object
 591     std::vector<std::unique_ptr<ISimulatorElement>> elementsOwnershipList;
 592     // call list of the simulator composite object
 593     std::vector<compat::not_null<ISimulatorElement*>> elementCallList;
 594
 595     std::function<void()> needToCheckNumberOfBondedInteractions;
 596     if (inputrec->eI == eiMD)
 597     {
 598         auto computeGlobalsElement =
 599                 std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>>(
 600                         statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
 601                         &signals_, nstglobalcomm_, fplog, mdlog, cr, inputrec, mdAtoms, nrnb,
 602                         wcycle, fr, &topologyHolder_->globalTopology(), constr, hasReadEkinState);
 603         topologyHolder_->registerClient(computeGlobalsElement.get());
 604         energySignallerBuilder->registerSignallerClient(compat::make_not_null(computeGlobalsElement.get()));
 605         trajectoryElementBuilder->registerSignallerClient(
 606                 compat::make_not_null(computeGlobalsElement.get()));
 607
 608         *checkBondedInteractionsCallback =
 609                 computeGlobalsElement->getCheckNumberOfBondedInteractionsCallback();
 610
 611         auto propagator = std::make_unique<Propagator<IntegrationStep::LeapFrog>>(
 612                 inputrec->delta_t, statePropagatorDataPtr, mdAtoms, wcycle);
 613
 614         addToCallListAndMove(std::move(forceElement), elementCallList, elementsOwnershipList);
 615         addToCallList(statePropagatorDataPtr, elementCallList); // we have a full microstate at time t here!
 616         if (inputrec->etc == etcVRESCALE)
 617         {
 618             // TODO: With increased complexity of the propagator, this will need further development,
 619             //       e.g. using propagators templated for velocity propagation policies and a builder
 620             propagator->setNumVelocityScalingVariables(inputrec->opts.ngtc);
 621             auto thermostat = std::make_unique<VRescaleThermostat>(
 622                     inputrec->nsttcouple, -1, false, inputrec->ld_seed, inputrec->opts.ngtc,
 623                     inputrec->delta_t * inputrec->nsttcouple, inputrec->opts.ref_t, inputrec->opts.tau_t,
 624                     inputrec->opts.nrdf, energyElementPtr, propagator->viewOnVelocityScaling(),
 625                     propagator->velocityScalingCallback(), state_global, cr, inputrec->bContinuation);
 626             checkpointClients->emplace_back(thermostat.get());
 627             energyElementPtr->setVRescaleThermostat(thermostat.get());
 628             addToCallListAndMove(std::move(thermostat), elementCallList, elementsOwnershipList);
 629         }
 630
 631         std::unique_ptr<ParrinelloRahmanBarostat> prBarostat = nullptr;
 632         if (inputrec->epc == epcPARRINELLORAHMAN)
 633         {
 634             // Building the PR barostat here since it needs access to the propagator
 635             // and we want to be able to move the propagator object
 636             prBarostat = std::make_unique<ParrinelloRahmanBarostat>(
 637                     inputrec->nstpcouple, -1, inputrec->delta_t * inputrec->nstpcouple,
 638                     inputrec->init_step, propagator->viewOnPRScalingMatrix(),
 639                     propagator->prScalingCallback(), statePropagatorDataPtr, energyElementPtr,
 640                     fplog, inputrec, mdAtoms, state_global, cr, inputrec->bContinuation);
 641             energyElementPtr->setParrinelloRahamnBarostat(prBarostat.get());
 642             checkpointClients->emplace_back(prBarostat.get());
 643         }
 644         addToCallListAndMove(std::move(propagator), elementCallList, elementsOwnershipList);
 645         if (constr)
 646         {
 647             auto constraintElement = std::make_unique<ConstraintsElement<ConstraintVariable::Positions>>(
 648                     constr, statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
 649                     MASTER(cr), fplog, inputrec, mdAtoms->mdatoms());
 650             auto constraintElementPtr = compat::make_not_null(constraintElement.get());
 651             energySignallerBuilder->registerSignallerClient(constraintElementPtr);
 652             trajectoryElementBuilder->registerSignallerClient(constraintElementPtr);
 653             loggingSignallerBuilder->registerSignallerClient(constraintElementPtr);
 654
 655             addToCallListAndMove(std::move(constraintElement), elementCallList, elementsOwnershipList);
 656         }
 657
 658         addToCallListAndMove(std::move(computeGlobalsElement), elementCallList, elementsOwnershipList);
 659         addToCallList(energyElementPtr, elementCallList); // we have the energies at time t here!
 660         if (prBarostat)
 661         {
 662             addToCallListAndMove(std::move(prBarostat), elementCallList, elementsOwnershipList);
 663         }
 664     }
 665     else if (inputrec->eI == eiVV)
 666     {
 667         auto computeGlobalsElement =
 668                 std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>(
 669                         statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
 670                         &signals_, nstglobalcomm_, fplog, mdlog, cr, inputrec, mdAtoms, nrnb,
 671                         wcycle, fr, &topologyHolder_->globalTopology(), constr, hasReadEkinState);
 672         topologyHolder_->registerClient(computeGlobalsElement.get());
 673         energySignallerBuilder->registerSignallerClient(compat::make_not_null(computeGlobalsElement.get()));
 674         trajectoryElementBuilder->registerSignallerClient(
 675                 compat::make_not_null(computeGlobalsElement.get()));
 676
 677         *checkBondedInteractionsCallback =
 678                 computeGlobalsElement->getCheckNumberOfBondedInteractionsCallback();
 679
 680         auto propagatorVelocities = std::make_unique<Propagator<IntegrationStep::VelocitiesOnly>>(
 681                 inputrec->delta_t * 0.5, statePropagatorDataPtr, mdAtoms, wcycle);
 682         auto propagatorVelocitiesAndPositions =
 683                 std::make_unique<Propagator<IntegrationStep::VelocityVerletPositionsAndVelocities>>(
 684                         inputrec->delta_t, statePropagatorDataPtr, mdAtoms, wcycle);
 685
 686         addToCallListAndMove(std::move(forceElement), elementCallList, elementsOwnershipList);
 687
 688         std::unique_ptr<ParrinelloRahmanBarostat> prBarostat = nullptr;
 689         if (inputrec->epc == epcPARRINELLORAHMAN)
 690         {
 691             // Building the PR barostat here since it needs access to the propagator
 692             // and we want to be able to move the propagator object
 693             prBarostat = std::make_unique<ParrinelloRahmanBarostat>(
 694                     inputrec->nstpcouple, -1, inputrec->delta_t * inputrec->nstpcouple,
 695                     inputrec->init_step, propagatorVelocities->viewOnPRScalingMatrix(),
 696                     propagatorVelocities->prScalingCallback(), statePropagatorDataPtr, energyElementPtr,
 697                     fplog, inputrec, mdAtoms, state_global, cr, inputrec->bContinuation);
 698             energyElementPtr->setParrinelloRahamnBarostat(prBarostat.get());
 699             checkpointClients->emplace_back(prBarostat.get());
 700         }
 701         addToCallListAndMove(std::move(propagatorVelocities), elementCallList, elementsOwnershipList);
 702         if (constr)
 703         {
 704             auto constraintElement = std::make_unique<ConstraintsElement<ConstraintVariable::Velocities>>(
 705                     constr, statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
 706                     MASTER(cr), fplog, inputrec, mdAtoms->mdatoms());
 707             energySignallerBuilder->registerSignallerClient(compat::make_not_null(constraintElement.get()));
 708             trajectoryElementBuilder->registerSignallerClient(
 709                     compat::make_not_null(constraintElement.get()));
 710             loggingSignallerBuilder->registerSignallerClient(
 711                     compat::make_not_null(constraintElement.get()));
 712
 713             addToCallListAndMove(std::move(constraintElement), elementCallList, elementsOwnershipList);
 714         }
 715         addToCallList(compat::make_not_null(computeGlobalsElement.get()), elementCallList);
 716         addToCallList(statePropagatorDataPtr, elementCallList); // we have a full microstate at time t here!
 717         if (inputrec->etc == etcVRESCALE)
 718         {
 719             // TODO: With increased complexity of the propagator, this will need further development,
 720             //       e.g. using propagators templated for velocity propagation policies and a builder
 721             propagatorVelocitiesAndPositions->setNumVelocityScalingVariables(inputrec->opts.ngtc);
 722             auto thermostat = std::make_unique<VRescaleThermostat>(
 723                     inputrec->nsttcouple, 0, true, inputrec->ld_seed, inputrec->opts.ngtc,
 724                     inputrec->delta_t * inputrec->nsttcouple, inputrec->opts.ref_t,
 725                     inputrec->opts.tau_t, inputrec->opts.nrdf, energyElementPtr,
 726                     propagatorVelocitiesAndPositions->viewOnVelocityScaling(),
 727                     propagatorVelocitiesAndPositions->velocityScalingCallback(), state_global, cr,
 728                     inputrec->bContinuation);
 729             checkpointClients->emplace_back(thermostat.get());
 730             energyElementPtr->setVRescaleThermostat(thermostat.get());
 731             addToCallListAndMove(std::move(thermostat), elementCallList, elementsOwnershipList);
 732         }
 733         addToCallListAndMove(std::move(propagatorVelocitiesAndPositions), elementCallList,
 734                              elementsOwnershipList);
 735         if (constr)
 736         {
 737             auto constraintElement = std::make_unique<ConstraintsElement<ConstraintVariable::Positions>>(
 738                     constr, statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
 739                     MASTER(cr), fplog, inputrec, mdAtoms->mdatoms());
 740             energySignallerBuilder->registerSignallerClient(compat::make_not_null(constraintElement.get()));
 741             trajectoryElementBuilder->registerSignallerClient(
 742                     compat::make_not_null(constraintElement.get()));
 743             loggingSignallerBuilder->registerSignallerClient(
 744                     compat::make_not_null(constraintElement.get()));
 745
 746             addToCallListAndMove(std::move(constraintElement), elementCallList, elementsOwnershipList);
 747         }
 748         addToCallListAndMove(std::move(computeGlobalsElement), elementCallList, elementsOwnershipList);
 749         addToCallList(energyElementPtr, elementCallList); // we have the energies at time t here!
 750         if (prBarostat)
 751         {
 752             addToCallListAndMove(std::move(prBarostat), elementCallList, elementsOwnershipList);
 753         }
 754     }
 755     else
 756     {
 757         gmx_fatal(FARGS, "Integrator not implemented for the modular simulator.");
 758     }
 759
 760     auto integrator = std::make_unique<CompositeSimulatorElement>(std::move(elementCallList),
 761                                                                   std::move(elementsOwnershipList));
 762     // std::move *should* not be needed with c++-14, but clang-3.6 still requires it
 763     return std::move(integrator);
 764 }
 765
 766 bool ModularSimulator::isInputCompatible(bool                             exitOnFailure,
 767                                          const t_inputrec*                inputrec,
 768                                          bool                             doRerun,
 769                                          const gmx_vsite_t*               vsite,
 770                                          const gmx_multisim_t*            ms,
 771                                          const ReplicaExchangeParameters& replExParams,
 772                                          const t_fcdata*                  fcd,
 773                                          int                              nfile,
 774                                          const t_filenm*                  fnm,
 775                                          ObservablesHistory*              observablesHistory,
 776                                          const gmx_membed_t*              membed)
 777 {
 778     auto conditionalAssert = [exitOnFailure](bool condition, const char* message) {
 779         if (exitOnFailure)
 780         {
 781             GMX_RELEASE_ASSERT(condition, message);
 782         }
 783         return condition;
 784     };
 785
 786     bool isInputCompatible = true;
 787
 788     // GMX_USE_MODULAR_SIMULATOR allows to use modular simulator also for non-standard uses,
 789     // such as the leap-frog integrator
 790     const auto modularSimulatorExplicitlyTurnedOn = (getenv("GMX_USE_MODULAR_SIMULATOR") != nullptr);
 791     // GMX_USE_MODULAR_SIMULATOR allows to use disable modular simulator for all uses,
 792     // including the velocity-verlet integrator used by default
 793     const auto modularSimulatorExplicitlyTurnedOff = (getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
 794
 795     GMX_RELEASE_ASSERT(
 796             !(modularSimulatorExplicitlyTurnedOn && modularSimulatorExplicitlyTurnedOff),
 797             "Cannot have both GMX_USE_MODULAR_SIMULATOR=ON and GMX_DISABLE_MODULAR_SIMULATOR=ON. "
 798             "Unset one of the two environment variables to explicitly chose which simulator to "
 799             "use, "
 800             "or unset both to recover default behavior.");
 801
 802     GMX_RELEASE_ASSERT(
 803             !(modularSimulatorExplicitlyTurnedOff && inputrec->eI == eiVV
 804               && inputrec->epc == epcPARRINELLORAHMAN),
 805             "Cannot use a Parrinello-Rahman barostat with md-vv and "
 806             "GMX_DISABLE_MODULAR_SIMULATOR=ON, "
 807             "as the Parrinello-Rahman barostat is not implemented in the legacy simulator. Unset "
 808             "GMX_DISABLE_MODULAR_SIMULATOR or use a different pressure control algorithm.");
 809
 810     isInputCompatible =
 811             isInputCompatible
 812             && conditionalAssert(
 813                        inputrec->eI == eiMD || inputrec->eI == eiVV,
 814                        "Only integrators md and md-vv are supported by the modular simulator.");
 815     isInputCompatible = isInputCompatible
 816                         && conditionalAssert(inputrec->eI != eiMD || modularSimulatorExplicitlyTurnedOn,
 817                                              "Set GMX_USE_MODULAR_SIMULATOR=ON to use the modular "
 818                                              "simulator with integrator md.");
 819     isInputCompatible =
 820             isInputCompatible
 821             && conditionalAssert(!doRerun, "Rerun is not supported by the modular simulator.");
 822     isInputCompatible =
 823             isInputCompatible
 824             && conditionalAssert(
 825                        inputrec->etc == etcNO || inputrec->etc == etcVRESCALE,
 826                        "Only v-rescale thermostat is supported by the modular simulator.");
 827     isInputCompatible =
 828             isInputCompatible
 829             && conditionalAssert(
 830                        inputrec->epc == epcNO || inputrec->epc == epcPARRINELLORAHMAN,
 831                        "Only Parrinello-Rahman barostat is supported by the modular simulator.");
 832     isInputCompatible =
 833             isInputCompatible
 834             && conditionalAssert(
 835                        !(inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec)
 836                          || inputrecNvtTrotter(inputrec)),
 837                        "Legacy Trotter decomposition is not supported by the modular simulator.");
 838     isInputCompatible = isInputCompatible
 839                         && conditionalAssert(inputrec->efep == efepNO || inputrec->efep == efepYES
 840                                                      || inputrec->efep == efepSLOWGROWTH,
 841                                              "Expanded ensemble free energy calculation is not "
 842                                              "supported by the modular simulator.");
 843     isInputCompatible = isInputCompatible
 844                         && conditionalAssert(!inputrec->bPull,
 845                                              "Pulling is not supported by the modular simulator.");
 846     isInputCompatible =
 847             isInputCompatible
 848             && conditionalAssert(inputrec->opts.ngacc == 1 && inputrec->opts.acc[0][XX] == 0.0
 849                                          && inputrec->opts.acc[0][YY] == 0.0
 850                                          && inputrec->opts.acc[0][ZZ] == 0.0 && inputrec->cos_accel == 0.0,
 851                                  "Acceleration is not supported by the modular simulator.");
 852     isInputCompatible =
 853             isInputCompatible
 854             && conditionalAssert(inputrec->opts.ngfrz == 1 && inputrec->opts.nFreeze[0][XX] == 0
 855                                          && inputrec->opts.nFreeze[0][YY] == 0
 856                                          && inputrec->opts.nFreeze[0][ZZ] == 0,
 857                                  "Freeze groups are not supported by the modular simulator.");
 858     isInputCompatible =
 859             isInputCompatible
 860             && conditionalAssert(
 861                        inputrec->deform[XX][XX] == 0.0 && inputrec->deform[XX][YY] == 0.0
 862                                && inputrec->deform[XX][ZZ] == 0.0 && inputrec->deform[YY][XX] == 0.0
 863                                && inputrec->deform[YY][YY] == 0.0 && inputrec->deform[YY][ZZ] == 0.0
 864                                && inputrec->deform[ZZ][XX] == 0.0 && inputrec->deform[ZZ][YY] == 0.0
 865                                && inputrec->deform[ZZ][ZZ] == 0.0,
 866                        "Deformation is not supported by the modular simulator.");
 867     isInputCompatible =
 868             isInputCompatible
 869             && conditionalAssert(vsite == nullptr,
 870                                  "Virtual sites are not supported by the modular simulator.");
 871     isInputCompatible = isInputCompatible
 872                         && conditionalAssert(!inputrec->bDoAwh,
 873                                              "AWH is not supported by the modular simulator.");
 874     isInputCompatible =
 875             isInputCompatible
 876             && conditionalAssert(ms == nullptr,
 877                                  "Multi-sim are not supported by the modular simulator.");
 878     isInputCompatible =
 879             isInputCompatible
 880             && conditionalAssert(replExParams.exchangeInterval == 0,
 881                                  "Replica exchange is not supported by the modular simulator.");
 882     isInputCompatible =
 883             isInputCompatible
 884             && conditionalAssert(fcd->disres.nsystems <= 1,
 885                                  "Ensemble restraints are not supported by the modular simulator.");
 886     isInputCompatible =
 887             isInputCompatible
 888             && conditionalAssert(!doSimulatedAnnealing(inputrec),
 889                                  "Simulated annealing is not supported by the modular simulator.");
 890     isInputCompatible =
 891             isInputCompatible
 892             && conditionalAssert(!inputrec->bSimTemp,
 893                                  "Simulated tempering is not supported by the modular simulator.");
 894     isInputCompatible = isInputCompatible
 895                         && conditionalAssert(!inputrec->bExpanded,
 896                                              "Expanded ensemble simulations are not supported by "
 897                                              "the modular simulator.");
 898     isInputCompatible =
 899             isInputCompatible
 900             && conditionalAssert(
 901                        !(opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr),
 902                        "Essential dynamics is not supported by the modular simulator.");
 903     isInputCompatible = isInputCompatible
 904                         && conditionalAssert(inputrec->eSwapCoords == eswapNO,
 905                                              "Ion / water position swapping is not supported by "
 906                                              "the modular simulator.");
 907     isInputCompatible =
 908             isInputCompatible
 909             && conditionalAssert(!inputrec->bIMD,
 910                                  "Interactive MD is not supported by the modular simulator.");
 911     isInputCompatible =
 912             isInputCompatible
 913             && conditionalAssert(membed == nullptr,
 914                                  "Membrane embedding is not supported by the modular simulator.");
 915     // TODO: Change this to the boolean passed when we merge the user interface change for the GPU update.
 916     isInputCompatible =
 917             isInputCompatible
 918             && conditionalAssert(
 919                        getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") == nullptr,
 920                        "Integration on the GPU is not supported by the modular simulator.");
 921     // Modular simulator is centered around NS updates
 922     // TODO: think how to handle nstlist == 0
 923     isInputCompatible = isInputCompatible
 924                         && conditionalAssert(inputrec->nstlist != 0,
 925                                              "Simulations without neighbor list update are not "
 926                                              "supported by the modular simulator.");
 927     isInputCompatible = isInputCompatible
 928                         && conditionalAssert(!GMX_FAHCORE,
 929                                              "GMX_FAHCORE not supported by the modular simulator.");
 930
 931     return isInputCompatible;
 932 }
 933
 934 void ModularSimulator::checkInputForDisabledFunctionality()
 935 {
 936     isInputCompatible(true, inputrec, doRerun, vsite, ms, replExParams, fcd, nfile, fnm,
 937                       observablesHistory, membed);
 938 }
 939
 940 SignallerCallbackPtr ModularSimulator::SignalHelper::registerLastStepCallback()
 941 {
 942     return std::make_unique<SignallerCallback>(
 943             [this](Step step, Time gmx_unused time) { this->lastStep_ = step; });
 944 }
 945
 946 SignallerCallbackPtr ModularSimulator::SignalHelper::registerNSCallback()
 947 {
 948     return std::make_unique<SignallerCallback>(
 949             [this](Step step, Time gmx_unused time) { this->nextNSStep_ = step; });
 950 }
 951 } // namespace gmx