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
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  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/gmxlib/network.h"
  51 #include "gromacs/gmxlib/nrnb.h"
  52 #include "gromacs/math/vec.h"
  53 #include "gromacs/mdlib/checkpointhandler.h"
  54 #include "gromacs/mdlib/constr.h"
  55 #include "gromacs/mdlib/energyoutput.h"
  56 #include "gromacs/mdlib/forcerec.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/inputrec.h"
  68 #include "gromacs/mdtypes/mdrunoptions.h"
  69 #include "gromacs/mdtypes/observableshistory.h"
  70 #include "gromacs/mdtypes/state.h"
  71 #include "gromacs/nbnxm/nbnxm.h"
  72 #include "gromacs/timing/walltime_accounting.h"
  73 #include "gromacs/topology/mtop_util.h"
  74 #include "gromacs/topology/topology.h"
  75 #include "gromacs/utility/cstringutil.h"
  76 #include "gromacs/utility/fatalerror.h"
  77
  78 #include "compositesimulatorelement.h"
  79 #include "computeglobalselement.h"
  80 #include "constraintelement.h"
  81 #include "energyelement.h"
  82 #include "forceelement.h"
  83 #include "freeenergyperturbationelement.h"
  84 #include "parrinellorahmanbarostat.h"
  85 #include "propagator.h"
  86 #include "shellfcelement.h"
  87 #include "signallers.h"
  88 #include "statepropagatordata.h"
  89 #include "trajectoryelement.h"
  90 #include "vrescalethermostat.h"
  91
  92 namespace gmx
  93 {
  94 void ModularSimulator::run()
  95 {
  96     GMX_LOG(mdlog.info).asParagraph().appendText("Using the modular simulator.");
  97     constructElementsAndSignallers();
  98     simulatorSetup();
  99     for (auto& signaller : signallerCallList_)
 100     {
 101         signaller->signallerSetup();
 102     }
 103     if (domDecHelper_)
 104     {
 105         domDecHelper_->setup();
 106     }
 107
 108     for (auto& element : elementsOwnershipList_)
 109     {
 110         element->elementSetup();
 111     }
 112     if (pmeLoadBalanceHelper_)
 113     {
 114         // State must have been initialized so pmeLoadBalanceHelper_ gets a valid box
 115         pmeLoadBalanceHelper_->setup();
 116     }
 117
 118     while (step_ <= signalHelper_->lastStep_)
 119     {
 120         populateTaskQueue();
 121
 122         while (!taskQueue_.empty())
 123         {
 124             auto task = std::move(taskQueue_.front());
 125             taskQueue_.pop();
 126             // run function
 127             (*task)();
 128         }
 129     }
 130
 131     for (auto& element : elementsOwnershipList_)
 132     {
 133         element->elementTeardown();
 134     }
 135     if (pmeLoadBalanceHelper_)
 136     {
 137         pmeLoadBalanceHelper_->teardown();
 138     }
 139     simulatorTeardown();
 140 }
 141
 142 void ModularSimulator::simulatorSetup()
 143 {
 144     if (!mdrunOptions.writeConfout)
 145     {
 146         // This is on by default, and the main known use case for
 147         // turning it off is for convenience in benchmarking, which is
 148         // something that should not show up in the general user
 149         // interface.
 150         GMX_LOG(mdlog.info)
 151                 .asParagraph()
 152                 .appendText(
 153                         "The -noconfout functionality is deprecated, and "
 154                         "may be removed in a future version.");
 155     }
 156
 157     if (MASTER(cr))
 158     {
 159         char        sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
 160         std::string timeString;
 161         fprintf(stderr, "starting mdrun '%s'\n", *(top_global->name));
 162         if (inputrec->nsteps >= 0)
 163         {
 164             timeString = formatString("%8.1f", static_cast<double>(inputrec->init_step + inputrec->nsteps)
 165                                                        * inputrec->delta_t);
 166         }
 167         else
 168         {
 169             timeString = "infinite";
 170         }
 171         if (inputrec->init_step > 0)
 172         {
 173             fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
 174                     gmx_step_str(inputrec->init_step + inputrec->nsteps, sbuf), timeString.c_str(),
 175                     gmx_step_str(inputrec->init_step, sbuf2), inputrec->init_step * inputrec->delta_t);
 176         }
 177         else
 178         {
 179             fprintf(stderr, "%s steps, %s ps.\n", gmx_step_str(inputrec->nsteps, sbuf),
 180                     timeString.c_str());
 181         }
 182         fprintf(fplog, "\n");
 183     }
 184
 185     walltime_accounting_start_time(walltime_accounting);
 186     wallcycle_start(wcycle, ewcRUN);
 187     print_start(fplog, cr, walltime_accounting, "mdrun");
 188
 189     step_ = inputrec->init_step;
 190 }
 191
 192 void ModularSimulator::preStep(Step step, Time gmx_unused time, bool isNeighborSearchingStep)
 193 {
 194     if (stopHandler_->stoppingAfterCurrentStep(isNeighborSearchingStep) && step != signalHelper_->lastStep_)
 195     {
 196         /*
 197          * Stop handler wants to stop after the current step, which was
 198          * not known when building the current task queue. This happens
 199          * e.g. when a stop is signalled by OS. We therefore want to purge
 200          * the task queue now, and re-schedule this step as last step.
 201          */
 202         // clear task queue
 203         std::queue<SimulatorRunFunctionPtr>().swap(taskQueue_);
 204         // rewind step
 205         step_ = step;
 206         return;
 207     }
 208
 209     resetHandler_->setSignal(walltime_accounting);
 210     // This is a hack to avoid having to rewrite StopHandler to be a NeighborSearchSignaller
 211     // and accept the step as input. Eventually, we want to do that, but currently this would
 212     // require introducing NeighborSearchSignaller in the legacy do_md or a lot of code
 213     // duplication.
 214     stophandlerIsNSStep_    = isNeighborSearchingStep;
 215     stophandlerCurrentStep_ = step;
 216     stopHandler_->setSignal();
 217
 218     wallcycle_start(wcycle, ewcSTEP);
 219 }
 220
 221 void ModularSimulator::postStep(Step step, Time gmx_unused time)
 222 {
 223     // Output stuff
 224     if (MASTER(cr))
 225     {
 226         if (do_per_step(step, inputrec->nstlog))
 227         {
 228             if (fflush(fplog) != 0)
 229             {
 230                 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 231             }
 232         }
 233     }
 234     const bool do_verbose = mdrunOptions.verbose
 235                             && (step % mdrunOptions.verboseStepPrintInterval == 0
 236                                 || step == inputrec->init_step || step == signalHelper_->lastStep_);
 237     // Print the remaining wall clock time for the run
 238     if (MASTER(cr) && (do_verbose || gmx_got_usr_signal())
 239         && !(pmeLoadBalanceHelper_ && pmeLoadBalanceHelper_->pmePrinting()))
 240     {
 241         print_time(stderr, walltime_accounting, step, inputrec, cr);
 242     }
 243
 244     double cycles = wallcycle_stop(wcycle, ewcSTEP);
 245     if (DOMAINDECOMP(cr) && wcycle)
 246     {
 247         dd_cycles_add(cr->dd, static_cast<float>(cycles), ddCyclStep);
 248     }
 249
 250     resetHandler_->resetCounters(
 251             step, step - inputrec->init_step, mdlog, fplog, cr, fr->nbv.get(), nrnb, fr->pmedata,
 252             pmeLoadBalanceHelper_ ? pmeLoadBalanceHelper_->loadBalancingObject() : nullptr, wcycle,
 253             walltime_accounting);
 254 }
 255
 256 void ModularSimulator::simulatorTeardown()
 257 {
 258
 259     // Stop measuring walltime
 260     walltime_accounting_end_time(walltime_accounting);
 261
 262     if (!thisRankHasDuty(cr, DUTY_PME))
 263     {
 264         /* Tell the PME only node to finish */
 265         gmx_pme_send_finish(cr);
 266     }
 267
 268     walltime_accounting_set_nsteps_done(walltime_accounting, step_ - inputrec->init_step);
 269 }
 270
 271 void ModularSimulator::populateTaskQueue()
 272 {
 273     auto registerRunFunction = std::make_unique<RegisterRunFunction>(
 274             [this](SimulatorRunFunctionPtr ptr) { taskQueue_.push(std::move(ptr)); });
 275
 276     Time startTime = inputrec->init_t;
 277     Time timeStep  = inputrec->delta_t;
 278     Time time      = startTime + step_ * timeStep;
 279
 280     // Run an initial call to the signallers
 281     for (auto& signaller : signallerCallList_)
 282     {
 283         signaller->signal(step_, time);
 284     }
 285
 286     if (checkpointHelper_)
 287     {
 288         checkpointHelper_->run(step_, time);
 289     }
 290
 291     if (pmeLoadBalanceHelper_)
 292     {
 293         pmeLoadBalanceHelper_->run(step_, time);
 294     }
 295     if (domDecHelper_)
 296     {
 297         domDecHelper_->run(step_, time);
 298     }
 299
 300     do
 301     {
 302         // local variables for lambda capturing
 303         const int  step     = step_;
 304         const bool isNSStep = step == signalHelper_->nextNSStep_;
 305
 306         // register pre-step
 307         (*registerRunFunction)(std::make_unique<SimulatorRunFunction>(
 308                 [this, step, time, isNSStep]() { preStep(step, time, isNSStep); }));
 309         // register elements for step
 310         for (auto& element : elementCallList_)
 311         {
 312             element->scheduleTask(step_, time, registerRunFunction);
 313         }
 314         // register post-step
 315         (*registerRunFunction)(
 316                 std::make_unique<SimulatorRunFunction>([this, step, time]() { postStep(step, time); }));
 317
 318         // prepare next step
 319         step_++;
 320         time = startTime + step_ * timeStep;
 321         for (auto& signaller : signallerCallList_)
 322         {
 323             signaller->signal(step_, time);
 324         }
 325     } while (step_ != signalHelper_->nextNSStep_ && step_ <= signalHelper_->lastStep_);
 326 }
 327
 328 void ModularSimulator::constructElementsAndSignallers()
 329 {
 330     /* When restarting from a checkpoint, it can be appropriate to
 331      * initialize ekind from quantities in the checkpoint. Otherwise,
 332      * compute_globals must initialize ekind before the simulation
 333      * starts/restarts. However, only the master rank knows what was
 334      * found in the checkpoint file, so we have to communicate in
 335      * order to coordinate the restart.
 336      *
 337      * TODO (modular) This should become obsolete when checkpoint reading
 338      *      happens within the modular simulator framework: The energy
 339      *      element should read its data from the checkpoint file pointer,
 340      *      and signal to the compute globals element if it needs anything
 341      *      reduced.
 342      *
 343      * TODO (legacy) Consider removing this communication if/when checkpoint
 344      *      reading directly follows .tpr reading, because all ranks can
 345      *      agree on hasReadEkinState at that time.
 346      */
 347     bool hasReadEkinState = MASTER(cr) ? state_global->ekinstate.hasReadEkinState : false;
 348     if (PAR(cr))
 349     {
 350         gmx_bcast(sizeof(hasReadEkinState), &hasReadEkinState, cr);
 351     }
 352     if (hasReadEkinState)
 353     {
 354         restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
 355     }
 356
 357     /*
 358      * Build data structures
 359      */
 360     topologyHolder_ =
 361             std::make_unique<TopologyHolder>(*top_global, cr, inputrec, fr, mdAtoms, constr, vsite);
 362
 363     std::unique_ptr<FreeEnergyPerturbationElement> freeEnergyPerturbationElement    = nullptr;
 364     FreeEnergyPerturbationElement*                 freeEnergyPerturbationElementPtr = nullptr;
 365     if (inputrec->efep != efepNO)
 366     {
 367         freeEnergyPerturbationElement =
 368                 std::make_unique<FreeEnergyPerturbationElement>(fplog, inputrec, mdAtoms);
 369         freeEnergyPerturbationElementPtr = freeEnergyPerturbationElement.get();
 370     }
 371
 372     auto statePropagatorData = std::make_unique<StatePropagatorData>(
 373             top_global->natoms, fplog, cr, state_global, inputrec->nstxout, inputrec->nstvout,
 374             inputrec->nstfout, inputrec->nstxout_compressed, fr->nbv->useGpu(),
 375             freeEnergyPerturbationElementPtr, topologyHolder_.get(), fr->bMolPBC,
 376             mdrunOptions.writeConfout, opt2fn("-c", nfile, fnm), inputrec, mdAtoms->mdatoms());
 377     auto statePropagatorDataPtr = compat::make_not_null(statePropagatorData.get());
 378
 379     auto energyElement = std::make_unique<EnergyElement>(
 380             statePropagatorDataPtr, freeEnergyPerturbationElementPtr, top_global, inputrec, mdAtoms,
 381             enerd, ekind, constr, fplog, fcd, mdModulesNotifier, MASTER(cr), observablesHistory,
 382             startingBehavior);
 383     auto energyElementPtr = compat::make_not_null(energyElement.get());
 384
 385     /*
 386      * Build stop handler
 387      */
 388     const bool simulationsShareState = false;
 389     stopHandler_                     = stopHandlerBuilder->getStopHandlerMD(
 390             compat::not_null<SimulationSignal*>(&signals_[eglsSTOPCOND]), simulationsShareState,
 391             MASTER(cr), inputrec->nstlist, mdrunOptions.reproducible, nstglobalcomm_,
 392             mdrunOptions.maximumHoursToRun, inputrec->nstlist == 0, fplog, stophandlerCurrentStep_,
 393             stophandlerIsNSStep_, walltime_accounting);
 394
 395     /*
 396      * Create simulator builders
 397      */
 398     SignallerBuilder<NeighborSearchSignaller> neighborSearchSignallerBuilder;
 399     SignallerBuilder<LastStepSignaller>       lastStepSignallerBuilder;
 400     SignallerBuilder<LoggingSignaller>        loggingSignallerBuilder;
 401     SignallerBuilder<EnergySignaller>         energySignallerBuilder;
 402     TrajectoryElementBuilder                  trajectoryElementBuilder;
 403
 404     /*
 405      * Register data structures to signallers
 406      */
 407     trajectoryElementBuilder.registerWriterClient(statePropagatorDataPtr);
 408     trajectoryElementBuilder.registerSignallerClient(statePropagatorDataPtr);
 409     lastStepSignallerBuilder.registerSignallerClient(statePropagatorDataPtr);
 410
 411     trajectoryElementBuilder.registerWriterClient(energyElementPtr);
 412     trajectoryElementBuilder.registerSignallerClient(energyElementPtr);
 413     energySignallerBuilder.registerSignallerClient(energyElementPtr);
 414
 415     // Register the simulator itself to the neighbor search / last step signaller
 416     neighborSearchSignallerBuilder.registerSignallerClient(compat::make_not_null(signalHelper_.get()));
 417     lastStepSignallerBuilder.registerSignallerClient(compat::make_not_null(signalHelper_.get()));
 418
 419     /*
 420      * Build integrator - this takes care of force calculation, propagation,
 421      * constraining, and of the place the statePropagatorData and the energy element
 422      * have a full timestep state.
 423      */
 424     // TODO: Make a CheckpointHelperBuilder
 425     std::vector<ICheckpointHelperClient*> checkpointClients = { statePropagatorDataPtr, energyElementPtr,
 426                                                                 freeEnergyPerturbationElementPtr };
 427     CheckBondedInteractionsCallbackPtr checkBondedInteractionsCallback = nullptr;
 428     auto                               integrator =
 429             buildIntegrator(&neighborSearchSignallerBuilder, &energySignallerBuilder,
 430                             &loggingSignallerBuilder, &trajectoryElementBuilder, &checkpointClients,
 431                             &checkBondedInteractionsCallback, statePropagatorDataPtr,
 432                             energyElementPtr, freeEnergyPerturbationElementPtr, hasReadEkinState);
 433
 434     /*
 435      * Build infrastructure elements
 436      */
 437
 438     if (PmeLoadBalanceHelper::doPmeLoadBalancing(mdrunOptions, inputrec, fr))
 439     {
 440         pmeLoadBalanceHelper_ = std::make_unique<PmeLoadBalanceHelper>(
 441                 mdrunOptions.verbose, statePropagatorDataPtr, fplog, cr, mdlog, inputrec, wcycle, fr);
 442         neighborSearchSignallerBuilder.registerSignallerClient(
 443                 compat::make_not_null(pmeLoadBalanceHelper_.get()));
 444     }
 445
 446     if (DOMAINDECOMP(cr))
 447     {
 448         GMX_ASSERT(checkBondedInteractionsCallback,
 449                    "Domain decomposition needs a callback for check the number of bonded "
 450                    "interactions.");
 451         domDecHelper_ = std::make_unique<DomDecHelper>(
 452                 mdrunOptions.verbose, mdrunOptions.verboseStepPrintInterval, statePropagatorDataPtr,
 453                 freeEnergyPerturbationElementPtr, topologyHolder_.get(),
 454                 std::move(checkBondedInteractionsCallback), nstglobalcomm_, fplog, cr, mdlog,
 455                 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, simulationsShareState);
 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 computeGlobalsElementAtFullTimeStep =
 668                 std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerletAtFullTimeStep>>(
 669                         statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
 670                         &signals_, nstglobalcomm_, fplog, mdlog, cr, inputrec, mdAtoms, nrnb,
 671                         wcycle, fr, &topologyHolder_->globalTopology(), constr, hasReadEkinState);
 672         topologyHolder_->registerClient(computeGlobalsElementAtFullTimeStep.get());
 673         energySignallerBuilder->registerSignallerClient(
 674                 compat::make_not_null(computeGlobalsElementAtFullTimeStep.get()));
 675         trajectoryElementBuilder->registerSignallerClient(
 676                 compat::make_not_null(computeGlobalsElementAtFullTimeStep.get()));
 677
 678         auto computeGlobalsElementAfterCoordinateUpdate =
 679                 std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerletAfterCoordinateUpdate>>(
 680                         statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
 681                         &signals_, nstglobalcomm_, fplog, mdlog, cr, inputrec, mdAtoms, nrnb,
 682                         wcycle, fr, &topologyHolder_->globalTopology(), constr, hasReadEkinState);
 683         topologyHolder_->registerClient(computeGlobalsElementAfterCoordinateUpdate.get());
 684         energySignallerBuilder->registerSignallerClient(
 685                 compat::make_not_null(computeGlobalsElementAfterCoordinateUpdate.get()));
 686         trajectoryElementBuilder->registerSignallerClient(
 687                 compat::make_not_null(computeGlobalsElementAfterCoordinateUpdate.get()));
 688
 689         *checkBondedInteractionsCallback =
 690                 computeGlobalsElementAfterCoordinateUpdate->getCheckNumberOfBondedInteractionsCallback();
 691
 692         auto propagatorVelocities = std::make_unique<Propagator<IntegrationStep::VelocitiesOnly>>(
 693                 inputrec->delta_t * 0.5, statePropagatorDataPtr, mdAtoms, wcycle);
 694         auto propagatorVelocitiesAndPositions =
 695                 std::make_unique<Propagator<IntegrationStep::VelocityVerletPositionsAndVelocities>>(
 696                         inputrec->delta_t, statePropagatorDataPtr, mdAtoms, wcycle);
 697
 698         addToCallListAndMove(std::move(forceElement), elementCallList, elementsOwnershipList);
 699
 700         std::unique_ptr<ParrinelloRahmanBarostat> prBarostat = nullptr;
 701         if (inputrec->epc == epcPARRINELLORAHMAN)
 702         {
 703             // Building the PR barostat here since it needs access to the propagator
 704             // and we want to be able to move the propagator object
 705             prBarostat = std::make_unique<ParrinelloRahmanBarostat>(
 706                     inputrec->nstpcouple, -1, inputrec->delta_t * inputrec->nstpcouple,
 707                     inputrec->init_step, propagatorVelocities->viewOnPRScalingMatrix(),
 708                     propagatorVelocities->prScalingCallback(), statePropagatorDataPtr, energyElementPtr,
 709                     fplog, inputrec, mdAtoms, state_global, cr, inputrec->bContinuation);
 710             energyElementPtr->setParrinelloRahamnBarostat(prBarostat.get());
 711             checkpointClients->emplace_back(prBarostat.get());
 712         }
 713         addToCallListAndMove(std::move(propagatorVelocities), elementCallList, elementsOwnershipList);
 714         if (constr)
 715         {
 716             auto constraintElement = std::make_unique<ConstraintsElement<ConstraintVariable::Velocities>>(
 717                     constr, statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
 718                     MASTER(cr), fplog, inputrec, mdAtoms->mdatoms());
 719             energySignallerBuilder->registerSignallerClient(compat::make_not_null(constraintElement.get()));
 720             trajectoryElementBuilder->registerSignallerClient(
 721                     compat::make_not_null(constraintElement.get()));
 722             loggingSignallerBuilder->registerSignallerClient(
 723                     compat::make_not_null(constraintElement.get()));
 724
 725             addToCallListAndMove(std::move(constraintElement), elementCallList, elementsOwnershipList);
 726         }
 727         addToCallListAndMove(std::move(computeGlobalsElementAtFullTimeStep), elementCallList,
 728                              elementsOwnershipList);
 729         addToCallList(statePropagatorDataPtr, elementCallList); // we have a full microstate at time t here!
 730         if (inputrec->etc == etcVRESCALE)
 731         {
 732             // TODO: With increased complexity of the propagator, this will need further development,
 733             //       e.g. using propagators templated for velocity propagation policies and a builder
 734             propagatorVelocitiesAndPositions->setNumVelocityScalingVariables(inputrec->opts.ngtc);
 735             auto thermostat = std::make_unique<VRescaleThermostat>(
 736                     inputrec->nsttcouple, 0, true, inputrec->ld_seed, inputrec->opts.ngtc,
 737                     inputrec->delta_t * inputrec->nsttcouple, inputrec->opts.ref_t,
 738                     inputrec->opts.tau_t, inputrec->opts.nrdf, energyElementPtr,
 739                     propagatorVelocitiesAndPositions->viewOnVelocityScaling(),
 740                     propagatorVelocitiesAndPositions->velocityScalingCallback(), state_global, cr,
 741                     inputrec->bContinuation);
 742             checkpointClients->emplace_back(thermostat.get());
 743             energyElementPtr->setVRescaleThermostat(thermostat.get());
 744             addToCallListAndMove(std::move(thermostat), elementCallList, elementsOwnershipList);
 745         }
 746         addToCallListAndMove(std::move(propagatorVelocitiesAndPositions), elementCallList,
 747                              elementsOwnershipList);
 748         if (constr)
 749         {
 750             auto constraintElement = std::make_unique<ConstraintsElement<ConstraintVariable::Positions>>(
 751                     constr, statePropagatorDataPtr, energyElementPtr, freeEnergyPerturbationElementPtr,
 752                     MASTER(cr), fplog, inputrec, mdAtoms->mdatoms());
 753             energySignallerBuilder->registerSignallerClient(compat::make_not_null(constraintElement.get()));
 754             trajectoryElementBuilder->registerSignallerClient(
 755                     compat::make_not_null(constraintElement.get()));
 756             loggingSignallerBuilder->registerSignallerClient(
 757                     compat::make_not_null(constraintElement.get()));
 758
 759             addToCallListAndMove(std::move(constraintElement), elementCallList, elementsOwnershipList);
 760         }
 761         addToCallListAndMove(std::move(computeGlobalsElementAfterCoordinateUpdate), elementCallList,
 762                              elementsOwnershipList);
 763         addToCallList(energyElementPtr, elementCallList); // we have the energies at time t here!
 764         if (prBarostat)
 765         {
 766             addToCallListAndMove(std::move(prBarostat), elementCallList, elementsOwnershipList);
 767         }
 768     }
 769     else
 770     {
 771         gmx_fatal(FARGS, "Integrator not implemented for the modular simulator.");
 772     }
 773
 774     auto integrator = std::make_unique<CompositeSimulatorElement>(std::move(elementCallList),
 775                                                                   std::move(elementsOwnershipList));
 776     // std::move *should* not be needed with c++-14, but clang-3.6 still requires it
 777     return std::move(integrator);
 778 }
 779
 780 bool ModularSimulator::isInputCompatible(bool                             exitOnFailure,
 781                                          const t_inputrec*                inputrec,
 782                                          bool                             doRerun,
 783                                          const gmx_mtop_t&                globalTopology,
 784                                          const gmx_multisim_t*            ms,
 785                                          const ReplicaExchangeParameters& replExParams,
 786                                          const t_fcdata*                  fcd,
 787                                          bool                             doEssentialDynamics,
 788                                          bool                             doMembed)
 789 {
 790     auto conditionalAssert = [exitOnFailure](bool condition, const char* message) {
 791         if (exitOnFailure)
 792         {
 793             GMX_RELEASE_ASSERT(condition, message);
 794         }
 795         return condition;
 796     };
 797
 798     bool isInputCompatible = true;
 799
 800     // GMX_USE_MODULAR_SIMULATOR allows to use modular simulator also for non-standard uses,
 801     // such as the leap-frog integrator
 802     const auto modularSimulatorExplicitlyTurnedOn = (getenv("GMX_USE_MODULAR_SIMULATOR") != nullptr);
 803     // GMX_USE_MODULAR_SIMULATOR allows to use disable modular simulator for all uses,
 804     // including the velocity-verlet integrator used by default
 805     const auto modularSimulatorExplicitlyTurnedOff = (getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
 806
 807     GMX_RELEASE_ASSERT(
 808             !(modularSimulatorExplicitlyTurnedOn && modularSimulatorExplicitlyTurnedOff),
 809             "Cannot have both GMX_USE_MODULAR_SIMULATOR=ON and GMX_DISABLE_MODULAR_SIMULATOR=ON. "
 810             "Unset one of the two environment variables to explicitly chose which simulator to "
 811             "use, "
 812             "or unset both to recover default behavior.");
 813
 814     GMX_RELEASE_ASSERT(
 815             !(modularSimulatorExplicitlyTurnedOff && inputrec->eI == eiVV
 816               && inputrec->epc == epcPARRINELLORAHMAN),
 817             "Cannot use a Parrinello-Rahman barostat with md-vv and "
 818             "GMX_DISABLE_MODULAR_SIMULATOR=ON, "
 819             "as the Parrinello-Rahman barostat is not implemented in the legacy simulator. Unset "
 820             "GMX_DISABLE_MODULAR_SIMULATOR or use a different pressure control algorithm.");
 821
 822     isInputCompatible =
 823             isInputCompatible
 824             && conditionalAssert(
 825                        inputrec->eI == eiMD || inputrec->eI == eiVV,
 826                        "Only integrators md and md-vv are supported by the modular simulator.");
 827     isInputCompatible = isInputCompatible
 828                         && conditionalAssert(inputrec->eI != eiMD || modularSimulatorExplicitlyTurnedOn,
 829                                              "Set GMX_USE_MODULAR_SIMULATOR=ON to use the modular "
 830                                              "simulator with integrator md.");
 831     isInputCompatible =
 832             isInputCompatible
 833             && conditionalAssert(!doRerun, "Rerun is not supported by the modular simulator.");
 834     isInputCompatible =
 835             isInputCompatible
 836             && conditionalAssert(
 837                        inputrec->etc == etcNO || inputrec->etc == etcVRESCALE,
 838                        "Only v-rescale thermostat is supported by the modular simulator.");
 839     isInputCompatible =
 840             isInputCompatible
 841             && conditionalAssert(
 842                        inputrec->epc == epcNO || inputrec->epc == epcPARRINELLORAHMAN,
 843                        "Only Parrinello-Rahman barostat is supported by the modular simulator.");
 844     isInputCompatible =
 845             isInputCompatible
 846             && conditionalAssert(
 847                        !(inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec)
 848                          || inputrecNvtTrotter(inputrec)),
 849                        "Legacy Trotter decomposition is not supported by the modular simulator.");
 850     isInputCompatible = isInputCompatible
 851                         && conditionalAssert(inputrec->efep == efepNO || inputrec->efep == efepYES
 852                                                      || inputrec->efep == efepSLOWGROWTH,
 853                                              "Expanded ensemble free energy calculation is not "
 854                                              "supported by the modular simulator.");
 855     isInputCompatible = isInputCompatible
 856                         && conditionalAssert(!inputrec->bPull,
 857                                              "Pulling is not supported by the modular simulator.");
 858     isInputCompatible =
 859             isInputCompatible
 860             && conditionalAssert(inputrec->opts.ngacc == 1 && inputrec->opts.acc[0][XX] == 0.0
 861                                          && inputrec->opts.acc[0][YY] == 0.0
 862                                          && inputrec->opts.acc[0][ZZ] == 0.0 && inputrec->cos_accel == 0.0,
 863                                  "Acceleration is not supported by the modular simulator.");
 864     isInputCompatible =
 865             isInputCompatible
 866             && conditionalAssert(inputrec->opts.ngfrz == 1 && inputrec->opts.nFreeze[0][XX] == 0
 867                                          && inputrec->opts.nFreeze[0][YY] == 0
 868                                          && inputrec->opts.nFreeze[0][ZZ] == 0,
 869                                  "Freeze groups are not supported by the modular simulator.");
 870     isInputCompatible =
 871             isInputCompatible
 872             && conditionalAssert(
 873                        inputrec->deform[XX][XX] == 0.0 && inputrec->deform[XX][YY] == 0.0
 874                                && inputrec->deform[XX][ZZ] == 0.0 && inputrec->deform[YY][XX] == 0.0
 875                                && inputrec->deform[YY][YY] == 0.0 && inputrec->deform[YY][ZZ] == 0.0
 876                                && inputrec->deform[ZZ][XX] == 0.0 && inputrec->deform[ZZ][YY] == 0.0
 877                                && inputrec->deform[ZZ][ZZ] == 0.0,
 878                        "Deformation is not supported by the modular simulator.");
 879     isInputCompatible =
 880             isInputCompatible
 881             && conditionalAssert(gmx_mtop_interaction_count(globalTopology, IF_VSITE) == 0,
 882                                  "Virtual sites are not supported by the modular simulator.");
 883     isInputCompatible = isInputCompatible
 884                         && conditionalAssert(!inputrec->bDoAwh,
 885                                              "AWH is not supported by the modular simulator.");
 886     isInputCompatible =
 887             isInputCompatible
 888             && conditionalAssert(gmx_mtop_ftype_count(globalTopology, F_DISRES) == 0,
 889                                  "Distance restraints are not supported by the modular simulator.");
 890     isInputCompatible =
 891             isInputCompatible
 892             && conditionalAssert(
 893                        gmx_mtop_ftype_count(globalTopology, F_ORIRES) == 0,
 894                        "Orientation restraints are not supported by the modular simulator.");
 895     isInputCompatible =
 896             isInputCompatible
 897             && conditionalAssert(ms == nullptr,
 898                                  "Multi-sim are not supported by the modular simulator.");
 899     isInputCompatible =
 900             isInputCompatible
 901             && conditionalAssert(replExParams.exchangeInterval == 0,
 902                                  "Replica exchange is not supported by the modular simulator.");
 903
 904     int numEnsembleRestraintSystems;
 905     if (fcd)
 906     {
 907         numEnsembleRestraintSystems = fcd->disres.nsystems;
 908     }
 909     else
 910     {
 911         auto distantRestraintEnsembleEnvVar = getenv("GMX_DISRE_ENSEMBLE_SIZE");
 912         numEnsembleRestraintSystems =
 913                 (ms != nullptr && distantRestraintEnsembleEnvVar != nullptr)
 914                         ? static_cast<int>(strtol(distantRestraintEnsembleEnvVar, nullptr, 10))
 915                         : 0;
 916     }
 917     isInputCompatible =
 918             isInputCompatible
 919             && conditionalAssert(numEnsembleRestraintSystems <= 1,
 920                                  "Ensemble restraints are not supported by the modular simulator.");
 921     isInputCompatible =
 922             isInputCompatible
 923             && conditionalAssert(!doSimulatedAnnealing(inputrec),
 924                                  "Simulated annealing is not supported by the modular simulator.");
 925     isInputCompatible =
 926             isInputCompatible
 927             && conditionalAssert(!inputrec->bSimTemp,
 928                                  "Simulated tempering is not supported by the modular simulator.");
 929     isInputCompatible = isInputCompatible
 930                         && conditionalAssert(!inputrec->bExpanded,
 931                                              "Expanded ensemble simulations are not supported by "
 932                                              "the modular simulator.");
 933     isInputCompatible =
 934             isInputCompatible
 935             && conditionalAssert(!doEssentialDynamics,
 936                                  "Essential dynamics is not supported by the modular simulator.");
 937     isInputCompatible = isInputCompatible
 938                         && conditionalAssert(inputrec->eSwapCoords == eswapNO,
 939                                              "Ion / water position swapping is not supported by "
 940                                              "the modular simulator.");
 941     isInputCompatible =
 942             isInputCompatible
 943             && conditionalAssert(!inputrec->bIMD,
 944                                  "Interactive MD is not supported by the modular simulator.");
 945     isInputCompatible =
 946             isInputCompatible
 947             && conditionalAssert(!doMembed,
 948                                  "Membrane embedding is not supported by the modular simulator.");
 949     const bool useGraph = !areMoleculesDistributedOverPbc(*inputrec, globalTopology, MDLogger());
 950     isInputCompatible =
 951             isInputCompatible
 952             && conditionalAssert(!useGraph, "Graph is not supported by the modular simulator.");
 953     // TODO: Change this to the boolean passed when we merge the user interface change for the GPU update.
 954     isInputCompatible =
 955             isInputCompatible
 956             && conditionalAssert(
 957                        getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") == nullptr,
 958                        "Integration on the GPU is not supported by the modular simulator.");
 959     // Modular simulator is centered around NS updates
 960     // TODO: think how to handle nstlist == 0
 961     isInputCompatible = isInputCompatible
 962                         && conditionalAssert(inputrec->nstlist != 0,
 963                                              "Simulations without neighbor list update are not "
 964                                              "supported by the modular simulator.");
 965     isInputCompatible = isInputCompatible
 966                         && conditionalAssert(!GMX_FAHCORE,
 967                                              "GMX_FAHCORE not supported by the modular simulator.");
 968
 969     return isInputCompatible;
 970 }
 971
 972 void ModularSimulator::checkInputForDisabledFunctionality()
 973 {
 974     isInputCompatible(true, inputrec, doRerun, *top_global, ms, replExParams, fcd,
 975                       opt2bSet("-ei", nfile, fnm), membed != nullptr);
 976     if (observablesHistory->edsamHistory)
 977     {
 978         gmx_fatal(FARGS,
 979                   "The checkpoint is from a run with essential dynamics sampling, "
 980                   "but the current run did not specify the -ei option. "
 981                   "Either specify the -ei option to mdrun, or do not use this checkpoint file.");
 982     }
 983 }
 984
 985 SignallerCallbackPtr ModularSimulator::SignalHelper::registerLastStepCallback()
 986 {
 987     return std::make_unique<SignallerCallback>(
 988             [this](Step step, Time gmx_unused time) { this->lastStep_ = step; });
 989 }
 990
 991 SignallerCallbackPtr ModularSimulator::SignalHelper::registerNSCallback()
 992 {
 993     return std::make_unique<SignallerCallback>(
 994             [this](Step step, Time gmx_unused time) { this->nextNSStep_ = step; });
 995 }
 996 } // namespace gmx