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
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  13  *
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  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/ewald/pme_pp.h"
  51 #include "gromacs/gmxlib/network.h"
  52 #include "gromacs/gmxlib/nrnb.h"
  53 #include "gromacs/listed_forces/listed_forces.h"
  54 #include "gromacs/mdlib/checkpointhandler.h"
  55 #include "gromacs/mdlib/constr.h"
  56 #include "gromacs/mdlib/coupling.h"
  57 #include "gromacs/mdlib/energyoutput.h"
  58 #include "gromacs/mdlib/mdatoms.h"
  59 #include "gromacs/mdlib/resethandler.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/nbnxm/nbnxm.h"
  73 #include "gromacs/topology/mtop_util.h"
  74 #include "gromacs/topology/topology.h"
  75 #include "gromacs/utility/fatalerror.h"
  76
  77 #include "compositesimulatorelement.h"
  78 #include "computeglobalselement.h"
  79 #include "constraintelement.h"
  80 #include "energydata.h"
  81 #include "forceelement.h"
  82 #include "freeenergyperturbationdata.h"
  83 #include "parrinellorahmanbarostat.h"
  84 #include "propagator.h"
  85 #include "signallers.h"
  86 #include "simulatoralgorithm.h"
  87 #include "statepropagatordata.h"
  88 #include "trajectoryelement.h"
  89 #include "vrescalethermostat.h"
  90
  91 namespace gmx
  92 {
  93 void ModularSimulator::run()
  94 {
  95     GMX_LOG(legacySimulatorData_->mdlog.info)
  96             .asParagraph()
  97             .appendText("Using the modular simulator.");
  98
  99     ModularSimulatorAlgorithmBuilder algorithmBuilder(compat::make_not_null(legacySimulatorData_.get()));
 100     auto                             algorithm = algorithmBuilder.build();
 101
 102     while (const auto* task = algorithm.getNextTask())
 103     {
 104         // execute task
 105         (*task)();
 106     }
 107 }
 108
 109 std::unique_ptr<ISimulatorElement> ModularSimulatorAlgorithmBuilder::buildForces(
 110         SignallerBuilder<NeighborSearchSignaller>* neighborSearchSignallerBuilder,
 111         SignallerBuilder<EnergySignaller>*         energySignallerBuilder,
 112         StatePropagatorData*                       statePropagatorDataPtr,
 113         EnergyData*                                energyDataPtr,
 114         FreeEnergyPerturbationData*                freeEnergyPerturbationDataPtr,
 115         TopologyHolder::Builder*                   topologyHolderBuilder)
 116 {
 117     const bool isVerbose    = legacySimulatorData_->mdrunOptions.verbose;
 118     const bool isDynamicBox = inputrecDynamicBox(legacySimulatorData_->inputrec);
 119
 120     auto forceElement = std::make_unique<ForceElement>(
 121             statePropagatorDataPtr, energyDataPtr, freeEnergyPerturbationDataPtr, isVerbose, isDynamicBox,
 122             legacySimulatorData_->fplog, legacySimulatorData_->cr, legacySimulatorData_->inputrec,
 123             legacySimulatorData_->mdAtoms, legacySimulatorData_->nrnb, legacySimulatorData_->fr,
 124             legacySimulatorData_->wcycle, legacySimulatorData_->runScheduleWork,
 125             legacySimulatorData_->vsite, legacySimulatorData_->imdSession,
 126             legacySimulatorData_->pull_work, legacySimulatorData_->constr,
 127             legacySimulatorData_->top_global, legacySimulatorData_->enforcedRotation);
 128     topologyHolderBuilder->registerClient(forceElement.get());
 129     neighborSearchSignallerBuilder->registerSignallerClient(compat::make_not_null(forceElement.get()));
 130     energySignallerBuilder->registerSignallerClient(compat::make_not_null(forceElement.get()));
 131
 132     // std::move *should* not be needed with c++-14, but clang-3.6 still requires it
 133     return std::move(forceElement);
 134 }
 135
 136 std::unique_ptr<ISimulatorElement> ModularSimulatorAlgorithmBuilder::buildIntegrator(
 137         SignallerBuilder<NeighborSearchSignaller>* neighborSearchSignallerBuilder,
 138         SignallerBuilder<LastStepSignaller>*       lastStepSignallerBuilder,
 139         SignallerBuilder<EnergySignaller>*         energySignallerBuilder,
 140         SignallerBuilder<LoggingSignaller>*        loggingSignallerBuilder,
 141         SignallerBuilder<TrajectorySignaller>*     trajectorySignallerBuilder,
 142         TrajectoryElementBuilder*                  trajectoryElementBuilder,
 143         std::vector<ICheckpointHelperClient*>*     checkpointClients,
 144         CheckBondedInteractionsCallbackPtr*        checkBondedInteractionsCallback,
 145         compat::not_null<StatePropagatorData*>     statePropagatorDataPtr,
 146         compat::not_null<EnergyData*>              energyDataPtr,
 147         FreeEnergyPerturbationData*                freeEnergyPerturbationDataPtr,
 148         bool                                       hasReadEkinState,
 149         TopologyHolder::Builder*                   topologyHolderBuilder,
 150         SimulationSignals*                         signals)
 151 {
 152     auto forceElement = buildForces(neighborSearchSignallerBuilder, energySignallerBuilder,
 153                                     statePropagatorDataPtr, energyDataPtr,
 154                                     freeEnergyPerturbationDataPtr, topologyHolderBuilder);
 155
 156     // list of elements owned by the simulator composite object
 157     std::vector<std::unique_ptr<ISimulatorElement>> elementsOwnershipList;
 158     // call list of the simulator composite object
 159     std::vector<compat::not_null<ISimulatorElement*>> elementCallList;
 160
 161     std::function<void()> needToCheckNumberOfBondedInteractions;
 162     if (legacySimulatorData_->inputrec->eI == eiMD)
 163     {
 164         auto computeGlobalsElement = std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>>(
 165                 statePropagatorDataPtr, energyDataPtr, freeEnergyPerturbationDataPtr, signals,
 166                 nstglobalcomm_, legacySimulatorData_->fplog, legacySimulatorData_->mdlog,
 167                 legacySimulatorData_->cr, legacySimulatorData_->inputrec, legacySimulatorData_->mdAtoms,
 168                 legacySimulatorData_->nrnb, legacySimulatorData_->wcycle, legacySimulatorData_->fr,
 169                 legacySimulatorData_->top_global, legacySimulatorData_->constr, hasReadEkinState);
 170         topologyHolderBuilder->registerClient(computeGlobalsElement.get());
 171         energySignallerBuilder->registerSignallerClient(compat::make_not_null(computeGlobalsElement.get()));
 172         trajectorySignallerBuilder->registerSignallerClient(
 173                 compat::make_not_null(computeGlobalsElement.get()));
 174
 175         *checkBondedInteractionsCallback =
 176                 computeGlobalsElement->getCheckNumberOfBondedInteractionsCallback();
 177
 178         auto propagator = std::make_unique<Propagator<IntegrationStep::LeapFrog>>(
 179                 legacySimulatorData_->inputrec->delta_t, statePropagatorDataPtr,
 180                 legacySimulatorData_->mdAtoms, legacySimulatorData_->wcycle);
 181
 182         addToCallListAndMove(std::move(forceElement), elementCallList, elementsOwnershipList);
 183         auto stateElement = compat::make_not_null(statePropagatorDataPtr->element());
 184         trajectoryElementBuilder->registerWriterClient(stateElement);
 185         trajectorySignallerBuilder->registerSignallerClient(stateElement);
 186         lastStepSignallerBuilder->registerSignallerClient(stateElement);
 187         checkpointClients->emplace_back(stateElement);
 188         // we have a full microstate at time t here!
 189         addToCallList(stateElement, elementCallList);
 190         if (legacySimulatorData_->inputrec->etc == etcVRESCALE)
 191         {
 192             // TODO: With increased complexity of the propagator, this will need further development,
 193             //       e.g. using propagators templated for velocity propagation policies and a builder
 194             propagator->setNumVelocityScalingVariables(legacySimulatorData_->inputrec->opts.ngtc);
 195             auto thermostat = std::make_unique<VRescaleThermostat>(
 196                     legacySimulatorData_->inputrec->nsttcouple, -1, false,
 197                     legacySimulatorData_->inputrec->ld_seed, legacySimulatorData_->inputrec->opts.ngtc,
 198                     legacySimulatorData_->inputrec->delta_t * legacySimulatorData_->inputrec->nsttcouple,
 199                     legacySimulatorData_->inputrec->opts.ref_t,
 200                     legacySimulatorData_->inputrec->opts.tau_t, legacySimulatorData_->inputrec->opts.nrdf,
 201                     energyDataPtr, propagator->viewOnVelocityScaling(),
 202                     propagator->velocityScalingCallback(), legacySimulatorData_->state_global,
 203                     legacySimulatorData_->cr, legacySimulatorData_->inputrec->bContinuation);
 204             checkpointClients->emplace_back(thermostat.get());
 205             energyDataPtr->setVRescaleThermostat(thermostat.get());
 206             addToCallListAndMove(std::move(thermostat), elementCallList, elementsOwnershipList);
 207         }
 208
 209         std::unique_ptr<ParrinelloRahmanBarostat> prBarostat = nullptr;
 210         if (legacySimulatorData_->inputrec->epc == epcPARRINELLORAHMAN)
 211         {
 212             // Building the PR barostat here since it needs access to the propagator
 213             // and we want to be able to move the propagator object
 214             prBarostat = std::make_unique<ParrinelloRahmanBarostat>(
 215                     legacySimulatorData_->inputrec->nstpcouple, -1,
 216                     legacySimulatorData_->inputrec->delta_t * legacySimulatorData_->inputrec->nstpcouple,
 217                     legacySimulatorData_->inputrec->init_step, propagator->viewOnPRScalingMatrix(),
 218                     propagator->prScalingCallback(), statePropagatorDataPtr, energyDataPtr,
 219                     legacySimulatorData_->fplog, legacySimulatorData_->inputrec,
 220                     legacySimulatorData_->mdAtoms, legacySimulatorData_->state_global,
 221                     legacySimulatorData_->cr, legacySimulatorData_->inputrec->bContinuation);
 222             energyDataPtr->setParrinelloRahamnBarostat(prBarostat.get());
 223             checkpointClients->emplace_back(prBarostat.get());
 224         }
 225         addToCallListAndMove(std::move(propagator), elementCallList, elementsOwnershipList);
 226         if (legacySimulatorData_->constr)
 227         {
 228             auto constraintElement = std::make_unique<ConstraintsElement<ConstraintVariable::Positions>>(
 229                     legacySimulatorData_->constr, statePropagatorDataPtr, energyDataPtr,
 230                     freeEnergyPerturbationDataPtr, MASTER(legacySimulatorData_->cr),
 231                     legacySimulatorData_->fplog, legacySimulatorData_->inputrec,
 232                     legacySimulatorData_->mdAtoms->mdatoms());
 233             auto constraintElementPtr = compat::make_not_null(constraintElement.get());
 234             energySignallerBuilder->registerSignallerClient(constraintElementPtr);
 235             trajectorySignallerBuilder->registerSignallerClient(constraintElementPtr);
 236             loggingSignallerBuilder->registerSignallerClient(constraintElementPtr);
 237
 238             addToCallListAndMove(std::move(constraintElement), elementCallList, elementsOwnershipList);
 239         }
 240
 241         addToCallListAndMove(std::move(computeGlobalsElement), elementCallList, elementsOwnershipList);
 242         auto energyElement = compat::make_not_null(energyDataPtr->element());
 243         trajectoryElementBuilder->registerWriterClient(energyElement);
 244         trajectorySignallerBuilder->registerSignallerClient(energyElement);
 245         energySignallerBuilder->registerSignallerClient(energyElement);
 246         checkpointClients->emplace_back(energyElement);
 247         // we have the energies at time t here!
 248         addToCallList(energyElement, elementCallList);
 249         if (prBarostat)
 250         {
 251             addToCallListAndMove(std::move(prBarostat), elementCallList, elementsOwnershipList);
 252         }
 253     }
 254     else if (legacySimulatorData_->inputrec->eI == eiVV)
 255     {
 256         auto computeGlobalsElement =
 257                 std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>(
 258                         statePropagatorDataPtr, energyDataPtr, freeEnergyPerturbationDataPtr, signals,
 259                         nstglobalcomm_, legacySimulatorData_->fplog, legacySimulatorData_->mdlog,
 260                         legacySimulatorData_->cr, legacySimulatorData_->inputrec,
 261                         legacySimulatorData_->mdAtoms, legacySimulatorData_->nrnb,
 262                         legacySimulatorData_->wcycle, legacySimulatorData_->fr,
 263                         legacySimulatorData_->top_global, legacySimulatorData_->constr, hasReadEkinState);
 264         topologyHolderBuilder->registerClient(computeGlobalsElement.get());
 265         energySignallerBuilder->registerSignallerClient(compat::make_not_null(computeGlobalsElement.get()));
 266         trajectorySignallerBuilder->registerSignallerClient(
 267                 compat::make_not_null(computeGlobalsElement.get()));
 268
 269         *checkBondedInteractionsCallback =
 270                 computeGlobalsElement->getCheckNumberOfBondedInteractionsCallback();
 271
 272         auto propagatorVelocities = std::make_unique<Propagator<IntegrationStep::VelocitiesOnly>>(
 273                 legacySimulatorData_->inputrec->delta_t * 0.5, statePropagatorDataPtr,
 274                 legacySimulatorData_->mdAtoms, legacySimulatorData_->wcycle);
 275         auto propagatorVelocitiesAndPositions =
 276                 std::make_unique<Propagator<IntegrationStep::VelocityVerletPositionsAndVelocities>>(
 277                         legacySimulatorData_->inputrec->delta_t, statePropagatorDataPtr,
 278                         legacySimulatorData_->mdAtoms, legacySimulatorData_->wcycle);
 279
 280         addToCallListAndMove(std::move(forceElement), elementCallList, elementsOwnershipList);
 281
 282         std::unique_ptr<ParrinelloRahmanBarostat> prBarostat = nullptr;
 283         if (legacySimulatorData_->inputrec->epc == epcPARRINELLORAHMAN)
 284         {
 285             // Building the PR barostat here since it needs access to the propagator
 286             // and we want to be able to move the propagator object
 287             prBarostat = std::make_unique<ParrinelloRahmanBarostat>(
 288                     legacySimulatorData_->inputrec->nstpcouple, -1,
 289                     legacySimulatorData_->inputrec->delta_t * legacySimulatorData_->inputrec->nstpcouple,
 290                     legacySimulatorData_->inputrec->init_step,
 291                     propagatorVelocities->viewOnPRScalingMatrix(),
 292                     propagatorVelocities->prScalingCallback(), statePropagatorDataPtr,
 293                     energyDataPtr, legacySimulatorData_->fplog, legacySimulatorData_->inputrec,
 294                     legacySimulatorData_->mdAtoms, legacySimulatorData_->state_global,
 295                     legacySimulatorData_->cr, legacySimulatorData_->inputrec->bContinuation);
 296             energyDataPtr->setParrinelloRahamnBarostat(prBarostat.get());
 297             checkpointClients->emplace_back(prBarostat.get());
 298         }
 299         addToCallListAndMove(std::move(propagatorVelocities), elementCallList, elementsOwnershipList);
 300         if (legacySimulatorData_->constr)
 301         {
 302             auto constraintElement = std::make_unique<ConstraintsElement<ConstraintVariable::Velocities>>(
 303                     legacySimulatorData_->constr, statePropagatorDataPtr, energyDataPtr,
 304                     freeEnergyPerturbationDataPtr, MASTER(legacySimulatorData_->cr),
 305                     legacySimulatorData_->fplog, legacySimulatorData_->inputrec,
 306                     legacySimulatorData_->mdAtoms->mdatoms());
 307             energySignallerBuilder->registerSignallerClient(compat::make_not_null(constraintElement.get()));
 308             trajectorySignallerBuilder->registerSignallerClient(
 309                     compat::make_not_null(constraintElement.get()));
 310             loggingSignallerBuilder->registerSignallerClient(
 311                     compat::make_not_null(constraintElement.get()));
 312
 313             addToCallListAndMove(std::move(constraintElement), elementCallList, elementsOwnershipList);
 314         }
 315         addToCallList(compat::make_not_null(computeGlobalsElement.get()), elementCallList);
 316         auto stateElement = compat::make_not_null(statePropagatorDataPtr->element());
 317         trajectoryElementBuilder->registerWriterClient(stateElement);
 318         trajectorySignallerBuilder->registerSignallerClient(stateElement);
 319         lastStepSignallerBuilder->registerSignallerClient(stateElement);
 320         checkpointClients->emplace_back(stateElement);
 321         // we have a full microstate at time t here!
 322         addToCallList(stateElement, elementCallList);
 323         if (legacySimulatorData_->inputrec->etc == etcVRESCALE)
 324         {
 325             // TODO: With increased complexity of the propagator, this will need further development,
 326             //       e.g. using propagators templated for velocity propagation policies and a builder
 327             propagatorVelocitiesAndPositions->setNumVelocityScalingVariables(
 328                     legacySimulatorData_->inputrec->opts.ngtc);
 329             auto thermostat = std::make_unique<VRescaleThermostat>(
 330                     legacySimulatorData_->inputrec->nsttcouple, 0, true,
 331                     legacySimulatorData_->inputrec->ld_seed, legacySimulatorData_->inputrec->opts.ngtc,
 332                     legacySimulatorData_->inputrec->delta_t * legacySimulatorData_->inputrec->nsttcouple,
 333                     legacySimulatorData_->inputrec->opts.ref_t,
 334                     legacySimulatorData_->inputrec->opts.tau_t, legacySimulatorData_->inputrec->opts.nrdf,
 335                     energyDataPtr, propagatorVelocitiesAndPositions->viewOnVelocityScaling(),
 336                     propagatorVelocitiesAndPositions->velocityScalingCallback(),
 337                     legacySimulatorData_->state_global, legacySimulatorData_->cr,
 338                     legacySimulatorData_->inputrec->bContinuation);
 339             checkpointClients->emplace_back(thermostat.get());
 340             energyDataPtr->setVRescaleThermostat(thermostat.get());
 341             addToCallListAndMove(std::move(thermostat), elementCallList, elementsOwnershipList);
 342         }
 343         addToCallListAndMove(std::move(propagatorVelocitiesAndPositions), elementCallList,
 344                              elementsOwnershipList);
 345         if (legacySimulatorData_->constr)
 346         {
 347             auto constraintElement = std::make_unique<ConstraintsElement<ConstraintVariable::Positions>>(
 348                     legacySimulatorData_->constr, statePropagatorDataPtr, energyDataPtr,
 349                     freeEnergyPerturbationDataPtr, MASTER(legacySimulatorData_->cr),
 350                     legacySimulatorData_->fplog, legacySimulatorData_->inputrec,
 351                     legacySimulatorData_->mdAtoms->mdatoms());
 352             energySignallerBuilder->registerSignallerClient(compat::make_not_null(constraintElement.get()));
 353             trajectorySignallerBuilder->registerSignallerClient(
 354                     compat::make_not_null(constraintElement.get()));
 355             loggingSignallerBuilder->registerSignallerClient(
 356                     compat::make_not_null(constraintElement.get()));
 357
 358             addToCallListAndMove(std::move(constraintElement), elementCallList, elementsOwnershipList);
 359         }
 360         addToCallListAndMove(std::move(computeGlobalsElement), elementCallList, elementsOwnershipList);
 361         auto energyElement = compat::make_not_null(energyDataPtr->element());
 362         trajectoryElementBuilder->registerWriterClient(energyElement);
 363         trajectorySignallerBuilder->registerSignallerClient(energyElement);
 364         energySignallerBuilder->registerSignallerClient(energyElement);
 365         checkpointClients->emplace_back(energyElement);
 366         // we have the energies at time t here!
 367         addToCallList(energyElement, elementCallList);
 368         if (prBarostat)
 369         {
 370             addToCallListAndMove(std::move(prBarostat), elementCallList, elementsOwnershipList);
 371         }
 372     }
 373     else
 374     {
 375         gmx_fatal(FARGS, "Integrator not implemented for the modular simulator.");
 376     }
 377
 378     auto integrator = std::make_unique<CompositeSimulatorElement>(std::move(elementCallList),
 379                                                                   std::move(elementsOwnershipList));
 380     // std::move *should* not be needed with c++-14, but clang-3.6 still requires it
 381     return std::move(integrator);
 382 }
 383
 384 bool ModularSimulator::isInputCompatible(bool                             exitOnFailure,
 385                                          const t_inputrec*                inputrec,
 386                                          bool                             doRerun,
 387                                          const gmx_mtop_t&                globalTopology,
 388                                          const gmx_multisim_t*            ms,
 389                                          const ReplicaExchangeParameters& replExParams,
 390                                          const t_fcdata*                  fcd,
 391                                          bool                             doEssentialDynamics,
 392                                          bool                             doMembed)
 393 {
 394     auto conditionalAssert = [exitOnFailure](bool condition, const char* message) {
 395         if (exitOnFailure)
 396         {
 397             GMX_RELEASE_ASSERT(condition, message);
 398         }
 399         return condition;
 400     };
 401
 402     bool isInputCompatible = true;
 403
 404     // GMX_USE_MODULAR_SIMULATOR allows to use modular simulator also for non-standard uses,
 405     // such as the leap-frog integrator
 406     const auto modularSimulatorExplicitlyTurnedOn = (getenv("GMX_USE_MODULAR_SIMULATOR") != nullptr);
 407     // GMX_USE_MODULAR_SIMULATOR allows to use disable modular simulator for all uses,
 408     // including the velocity-verlet integrator used by default
 409     const auto modularSimulatorExplicitlyTurnedOff = (getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
 410
 411     GMX_RELEASE_ASSERT(
 412             !(modularSimulatorExplicitlyTurnedOn && modularSimulatorExplicitlyTurnedOff),
 413             "Cannot have both GMX_USE_MODULAR_SIMULATOR=ON and GMX_DISABLE_MODULAR_SIMULATOR=ON. "
 414             "Unset one of the two environment variables to explicitly chose which simulator to "
 415             "use, "
 416             "or unset both to recover default behavior.");
 417
 418     GMX_RELEASE_ASSERT(
 419             !(modularSimulatorExplicitlyTurnedOff && inputrec->eI == eiVV
 420               && inputrec->epc == epcPARRINELLORAHMAN),
 421             "Cannot use a Parrinello-Rahman barostat with md-vv and "
 422             "GMX_DISABLE_MODULAR_SIMULATOR=ON, "
 423             "as the Parrinello-Rahman barostat is not implemented in the legacy simulator. Unset "
 424             "GMX_DISABLE_MODULAR_SIMULATOR or use a different pressure control algorithm.");
 425
 426     isInputCompatible =
 427             isInputCompatible
 428             && conditionalAssert(
 429                        inputrec->eI == eiMD || inputrec->eI == eiVV,
 430                        "Only integrators md and md-vv are supported by the modular simulator.");
 431     isInputCompatible = isInputCompatible
 432                         && conditionalAssert(inputrec->eI != eiMD || modularSimulatorExplicitlyTurnedOn,
 433                                              "Set GMX_USE_MODULAR_SIMULATOR=ON to use the modular "
 434                                              "simulator with integrator md.");
 435     isInputCompatible =
 436             isInputCompatible
 437             && conditionalAssert(!doRerun, "Rerun is not supported by the modular simulator.");
 438     isInputCompatible =
 439             isInputCompatible
 440             && conditionalAssert(
 441                        inputrec->etc == etcNO || inputrec->etc == etcVRESCALE,
 442                        "Only v-rescale thermostat is supported by the modular simulator.");
 443     isInputCompatible =
 444             isInputCompatible
 445             && conditionalAssert(
 446                        inputrec->epc == epcNO || inputrec->epc == epcPARRINELLORAHMAN,
 447                        "Only Parrinello-Rahman barostat is supported by the modular simulator.");
 448     isInputCompatible =
 449             isInputCompatible
 450             && conditionalAssert(
 451                        !(inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec)
 452                          || inputrecNvtTrotter(inputrec)),
 453                        "Legacy Trotter decomposition is not supported by the modular simulator.");
 454     isInputCompatible = isInputCompatible
 455                         && conditionalAssert(inputrec->efep == efepNO || inputrec->efep == efepYES
 456                                                      || inputrec->efep == efepSLOWGROWTH,
 457                                              "Expanded ensemble free energy calculation is not "
 458                                              "supported by the modular simulator.");
 459     isInputCompatible = isInputCompatible
 460                         && conditionalAssert(!inputrec->bPull,
 461                                              "Pulling is not supported by the modular simulator.");
 462     isInputCompatible =
 463             isInputCompatible
 464             && conditionalAssert(inputrec->opts.ngacc == 1 && inputrec->opts.acc[0][XX] == 0.0
 465                                          && inputrec->opts.acc[0][YY] == 0.0
 466                                          && inputrec->opts.acc[0][ZZ] == 0.0 && inputrec->cos_accel == 0.0,
 467                                  "Acceleration is not supported by the modular simulator.");
 468     isInputCompatible =
 469             isInputCompatible
 470             && conditionalAssert(inputrec->opts.ngfrz == 1 && inputrec->opts.nFreeze[0][XX] == 0
 471                                          && inputrec->opts.nFreeze[0][YY] == 0
 472                                          && inputrec->opts.nFreeze[0][ZZ] == 0,
 473                                  "Freeze groups are not supported by the modular simulator.");
 474     isInputCompatible =
 475             isInputCompatible
 476             && conditionalAssert(
 477                        inputrec->deform[XX][XX] == 0.0 && inputrec->deform[XX][YY] == 0.0
 478                                && inputrec->deform[XX][ZZ] == 0.0 && inputrec->deform[YY][XX] == 0.0
 479                                && inputrec->deform[YY][YY] == 0.0 && inputrec->deform[YY][ZZ] == 0.0
 480                                && inputrec->deform[ZZ][XX] == 0.0 && inputrec->deform[ZZ][YY] == 0.0
 481                                && inputrec->deform[ZZ][ZZ] == 0.0,
 482                        "Deformation is not supported by the modular simulator.");
 483     isInputCompatible =
 484             isInputCompatible
 485             && conditionalAssert(gmx_mtop_interaction_count(globalTopology, IF_VSITE) == 0,
 486                                  "Virtual sites are not supported by the modular simulator.");
 487     isInputCompatible = isInputCompatible
 488                         && conditionalAssert(!inputrec->bDoAwh,
 489                                              "AWH is not supported by the modular simulator.");
 490     isInputCompatible =
 491             isInputCompatible
 492             && conditionalAssert(gmx_mtop_ftype_count(globalTopology, F_DISRES) == 0,
 493                                  "Distance restraints are not supported by the modular simulator.");
 494     isInputCompatible =
 495             isInputCompatible
 496             && conditionalAssert(
 497                        gmx_mtop_ftype_count(globalTopology, F_ORIRES) == 0,
 498                        "Orientation restraints are not supported by the modular simulator.");
 499     isInputCompatible =
 500             isInputCompatible
 501             && conditionalAssert(ms == nullptr,
 502                                  "Multi-sim are not supported by the modular simulator.");
 503     isInputCompatible =
 504             isInputCompatible
 505             && conditionalAssert(replExParams.exchangeInterval == 0,
 506                                  "Replica exchange is not supported by the modular simulator.");
 507
 508     int numEnsembleRestraintSystems;
 509     if (fcd)
 510     {
 511         numEnsembleRestraintSystems = fcd->disres->nsystems;
 512     }
 513     else
 514     {
 515         auto distantRestraintEnsembleEnvVar = getenv("GMX_DISRE_ENSEMBLE_SIZE");
 516         numEnsembleRestraintSystems =
 517                 (ms != nullptr && distantRestraintEnsembleEnvVar != nullptr)
 518                         ? static_cast<int>(strtol(distantRestraintEnsembleEnvVar, nullptr, 10))
 519                         : 0;
 520     }
 521     isInputCompatible =
 522             isInputCompatible
 523             && conditionalAssert(numEnsembleRestraintSystems <= 1,
 524                                  "Ensemble restraints are not supported by the modular simulator.");
 525     isInputCompatible =
 526             isInputCompatible
 527             && conditionalAssert(!doSimulatedAnnealing(inputrec),
 528                                  "Simulated annealing is not supported by the modular simulator.");
 529     isInputCompatible =
 530             isInputCompatible
 531             && conditionalAssert(!inputrec->bSimTemp,
 532                                  "Simulated tempering is not supported by the modular simulator.");
 533     isInputCompatible = isInputCompatible
 534                         && conditionalAssert(!inputrec->bExpanded,
 535                                              "Expanded ensemble simulations are not supported by "
 536                                              "the modular simulator.");
 537     isInputCompatible =
 538             isInputCompatible
 539             && conditionalAssert(!doEssentialDynamics,
 540                                  "Essential dynamics is not supported by the modular simulator.");
 541     isInputCompatible = isInputCompatible
 542                         && conditionalAssert(inputrec->eSwapCoords == eswapNO,
 543                                              "Ion / water position swapping is not supported by "
 544                                              "the modular simulator.");
 545     isInputCompatible =
 546             isInputCompatible
 547             && conditionalAssert(!inputrec->bIMD,
 548                                  "Interactive MD is not supported by the modular simulator.");
 549     isInputCompatible =
 550             isInputCompatible
 551             && conditionalAssert(!doMembed,
 552                                  "Membrane embedding is not supported by the modular simulator.");
 553     // TODO: Change this to the boolean passed when we merge the user interface change for the GPU update.
 554     isInputCompatible =
 555             isInputCompatible
 556             && conditionalAssert(
 557                        getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") == nullptr,
 558                        "Integration on the GPU is not supported by the modular simulator.");
 559     // Modular simulator is centered around NS updates
 560     // TODO: think how to handle nstlist == 0
 561     isInputCompatible = isInputCompatible
 562                         && conditionalAssert(inputrec->nstlist != 0,
 563                                              "Simulations without neighbor list update are not "
 564                                              "supported by the modular simulator.");
 565     isInputCompatible = isInputCompatible
 566                         && conditionalAssert(!GMX_FAHCORE,
 567                                              "GMX_FAHCORE not supported by the modular simulator.");
 568
 569     return isInputCompatible;
 570 }
 571
 572 ModularSimulator::ModularSimulator(std::unique_ptr<LegacySimulatorData> legacySimulatorData) :
 573     legacySimulatorData_(std::move(legacySimulatorData))
 574 {
 575     checkInputForDisabledFunctionality();
 576 }
 577
 578 void ModularSimulator::checkInputForDisabledFunctionality()
 579 {
 580     isInputCompatible(true, legacySimulatorData_->inputrec,
 581                       legacySimulatorData_->mdrunOptions.rerun, *legacySimulatorData_->top_global,
 582                       legacySimulatorData_->ms, legacySimulatorData_->replExParams,
 583                       &legacySimulatorData_->fr->listedForces->fcdata(),
 584                       opt2bSet("-ei", legacySimulatorData_->nfile, legacySimulatorData_->fnm),
 585                       legacySimulatorData_->membed != nullptr);
 586     if (legacySimulatorData_->observablesHistory->edsamHistory)
 587     {
 588         gmx_fatal(FARGS,
 589                   "The checkpoint is from a run with essential dynamics sampling, "
 590                   "but the current run did not specify the -ei option. "
 591                   "Either specify the -ei option to mdrun, or do not use this checkpoint file.");
 592     }
 593 }
 594
 595 } // namespace gmx