src/gromacs/modularsimulator/modularsimulator.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   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.
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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/fileio/checkpoint.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/mdrun/replicaexchange.h"
  61 #include "gromacs/mdrun/shellfc.h"
  62 #include "gromacs/mdrunutility/handlerestart.h"
  63 #include "gromacs/mdrunutility/printtime.h"
  64 #include "gromacs/mdtypes/commrec.h"
  65 #include "gromacs/mdtypes/fcdata.h"
  66 #include "gromacs/mdtypes/forcerec.h"
  67 #include "gromacs/mdtypes/inputrec.h"
  68 #include "gromacs/mdtypes/mdatom.h"
  69 #include "gromacs/mdtypes/mdrunoptions.h"
  70 #include "gromacs/mdtypes/observableshistory.h"
  71 #include "gromacs/nbnxm/nbnxm.h"
  72 #include "gromacs/topology/mtop_util.h"
  73 #include "gromacs/topology/topology.h"
  74 #include "gromacs/trajectory/trajectoryframe.h"
  75 #include "gromacs/utility/fatalerror.h"
  76 #include "gromacs/utility/int64_to_int.h"
  77
  78 #include "andersentemperaturecoupling.h"
  79 #include "computeglobalselement.h"
  80 #include "constraintelement.h"
  81 #include "firstorderpressurecoupling.h"
  82 #include "forceelement.h"
  83 #include "mttk.h"
  84 #include "nosehooverchains.h"
  85 #include "parrinellorahmanbarostat.h"
  86 #include "simulatoralgorithm.h"
  87 #include "statepropagatordata.h"
  88 #include "velocityscalingtemperaturecoupling.h"
  89
  90 namespace gmx
  91 {
  92 void ModularSimulator::run()
  93 {
  94     GMX_LOG(legacySimulatorData_->mdlog.info)
  95             .asParagraph()
  96             .appendText("Using the modular simulator.");
  97
  98     ModularSimulatorAlgorithmBuilder algorithmBuilder(compat::make_not_null(legacySimulatorData_),
  99                                                       std::move(checkpointDataHolder_));
 100     addIntegrationElements(&algorithmBuilder);
 101     auto algorithm = algorithmBuilder.build();
 102
 103     while (const auto* task = algorithm.getNextTask())
 104     {
 105         // execute task
 106         (*task)();
 107     }
 108 }
 109
 110 void ModularSimulator::addIntegrationElements(ModularSimulatorAlgorithmBuilder* builder)
 111 {
 112     const bool isTrotter = inputrecNvtTrotter(legacySimulatorData_->inputrec)
 113                            || inputrecNptTrotter(legacySimulatorData_->inputrec)
 114                            || inputrecNphTrotter(legacySimulatorData_->inputrec);
 115     if (legacySimulatorData_->inputrec->eI == IntegrationAlgorithm::MD)
 116     {
 117         // The leap frog integration algorithm
 118         builder->add<ForceElement>();
 119         builder->add<StatePropagatorData::Element>();
 120         if (legacySimulatorData_->inputrec->etc == TemperatureCoupling::VRescale
 121             || legacySimulatorData_->inputrec->etc == TemperatureCoupling::Berendsen
 122             || legacySimulatorData_->inputrec->etc == TemperatureCoupling::NoseHoover)
 123         {
 124             builder->add<VelocityScalingTemperatureCoupling>(Offset(-1),
 125                                                              UseFullStepKE::No,
 126                                                              ReportPreviousStepConservedEnergy::No,
 127                                                              PropagatorTag("LeapFrogPropagator"));
 128         }
 129         builder->add<Propagator<IntegrationStage::LeapFrog>>(
 130                 PropagatorTag("LeapFrogPropagator"), TimeStep(legacySimulatorData_->inputrec->delta_t));
 131         if (legacySimulatorData_->constr)
 132         {
 133             builder->add<ConstraintsElement<ConstraintVariable::Positions>>();
 134         }
 135         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>>();
 136         if (legacySimulatorData_->inputrec->epc == PressureCoupling::ParrinelloRahman)
 137         {
 138             builder->add<ParrinelloRahmanBarostat>(Offset(-1), PropagatorTag("LeapFrogPropagator"));
 139         }
 140         else if (legacySimulatorData_->inputrec->epc == PressureCoupling::Berendsen
 141                  || legacySimulatorData_->inputrec->epc == PressureCoupling::CRescale)
 142         {
 143             builder->add<FirstOrderPressureCoupling>(0, ReportPreviousStepConservedEnergy::No);
 144         }
 145     }
 146     else if (legacySimulatorData_->inputrec->eI == IntegrationAlgorithm::VV && !isTrotter)
 147     {
 148         // The velocity verlet integration algorithm
 149         builder->add<ForceElement>();
 150         builder->add<Propagator<IntegrationStage::VelocitiesOnly>>(
 151                 PropagatorTag("VelocityHalfStep"), TimeStep(0.5 * legacySimulatorData_->inputrec->delta_t));
 152         if (legacySimulatorData_->constr)
 153         {
 154             builder->add<ConstraintsElement<ConstraintVariable::Velocities>>();
 155         }
 156         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
 157         builder->add<StatePropagatorData::Element>();
 158         if (legacySimulatorData_->inputrec->etc == TemperatureCoupling::VRescale
 159             || legacySimulatorData_->inputrec->etc == TemperatureCoupling::Berendsen)
 160         {
 161             builder->add<VelocityScalingTemperatureCoupling>(
 162                     Offset(0),
 163                     UseFullStepKE::Yes,
 164                     ReportPreviousStepConservedEnergy::Yes,
 165                     PropagatorTag("VelocityHalfAndPositionFullStep"));
 166         }
 167         else if (ETC_ANDERSEN(legacySimulatorData_->inputrec->etc))
 168         {
 169             builder->add<AndersenTemperatureCoupling>();
 170         }
 171         builder->add<Propagator<IntegrationStage::VelocityVerletPositionsAndVelocities>>(
 172                 PropagatorTag("VelocityHalfAndPositionFullStep"),
 173                 TimeStep(legacySimulatorData_->inputrec->delta_t));
 174         if (legacySimulatorData_->constr)
 175         {
 176             builder->add<ConstraintsElement<ConstraintVariable::Positions>>();
 177         }
 178         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
 179         if (legacySimulatorData_->inputrec->epc == PressureCoupling::ParrinelloRahman)
 180         {
 181             builder->add<ParrinelloRahmanBarostat>(Offset(-1), PropagatorTag("VelocityHalfStep"));
 182         }
 183         else if (legacySimulatorData_->inputrec->epc == PressureCoupling::Berendsen
 184                  || legacySimulatorData_->inputrec->epc == PressureCoupling::CRescale)
 185         {
 186             builder->add<FirstOrderPressureCoupling>(0, ReportPreviousStepConservedEnergy::Yes);
 187         }
 188     }
 189     else if (legacySimulatorData_->inputrec->eI == IntegrationAlgorithm::VV && isTrotter)
 190     {
 191         // For a new simulation, avoid the first Trotter half step
 192         const auto scheduleTrotterFirstHalfOnInitStep =
 193                 ((legacySimulatorData_->startingBehavior == StartingBehavior::NewSimulation)
 194                          ? ScheduleOnInitStep::No
 195                          : ScheduleOnInitStep::Yes);
 196
 197         builder->add<ForceElement>();
 198         // Propagate velocities from t-dt/2 to t
 199         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 200         {
 201             builder->add<Propagator<IntegrationStage::ScaleVelocities>>(
 202                     PropagatorTag("ScaleMTTKVPre1"));
 203         }
 204         builder->add<Propagator<IntegrationStage::VelocitiesOnly>>(
 205                 PropagatorTag("VelocityHalfStep1"),
 206                 TimeStep(0.5 * legacySimulatorData_->inputrec->delta_t));
 207         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 208         {
 209             builder->add<Propagator<IntegrationStage::ScaleVelocities>>(
 210                     PropagatorTag("ScaleMTTKVPost1"));
 211         }
 212         if (legacySimulatorData_->constr)
 213         {
 214             builder->add<ConstraintsElement<ConstraintVariable::Velocities>>();
 215         }
 216         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
 217
 218         // Propagate extended system variables from t-dt/2 to t
 219         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 220         {
 221             builder->add<MttkElement>(Offset(-1),
 222                                       scheduleTrotterFirstHalfOnInitStep,
 223                                       PropagatorTag("ScaleMTTKXPre"),
 224                                       PropagatorTag("ScaleMTTKXPost"),
 225                                       Offset(0),
 226                                       PropagatorTag("ScaleMTTKVPre1"),
 227                                       PropagatorTag("ScaleMTTKVPost1"),
 228                                       Offset(1),
 229                                       PropagatorTag("ScaleMTTKVPre2"),
 230                                       PropagatorTag("ScaleMTTKVPost2"),
 231                                       Offset(0));
 232         }
 233         if (legacySimulatorData_->inputrec->etc == TemperatureCoupling::NoseHoover)
 234         {
 235             builder->add<NoseHooverChainsElement>(NhcUsage::System,
 236                                                   Offset(-1),
 237                                                   UseFullStepKE::Yes,
 238                                                   scheduleTrotterFirstHalfOnInitStep,
 239                                                   PropagatorTag("ScaleNHC"));
 240             builder->add<Propagator<IntegrationStage::ScaleVelocities>>(PropagatorTag("ScaleNHC"));
 241         }
 242         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 243         {
 244             builder->add<NoseHooverChainsElement>(
 245                     NhcUsage::Barostat, Offset(-1), UseFullStepKE::Yes, scheduleTrotterFirstHalfOnInitStep);
 246         }
 247         // We have a full state at time t here
 248         builder->add<StatePropagatorData::Element>();
 249
 250         // Propagate extended system variables from t to t+dt/2
 251         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 252         {
 253             builder->add<NoseHooverChainsElement>(
 254                     NhcUsage::Barostat, Offset(0), UseFullStepKE::Yes, ScheduleOnInitStep::Yes);
 255         }
 256         if (legacySimulatorData_->inputrec->etc == TemperatureCoupling::NoseHoover)
 257         {
 258             builder->add<NoseHooverChainsElement>(NhcUsage::System,
 259                                                   Offset(0),
 260                                                   UseFullStepKE::Yes,
 261                                                   ScheduleOnInitStep::Yes,
 262                                                   PropagatorTag("VelocityHalfStep2"));
 263         }
 264         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 265         {
 266             builder->add<MttkElement>(Offset(0),
 267                                       ScheduleOnInitStep::Yes,
 268                                       PropagatorTag("ScaleMTTKXPre"),
 269                                       PropagatorTag("ScaleMTTKXPost"),
 270                                       Offset(0),
 271                                       PropagatorTag("ScaleMTTKVPre1"),
 272                                       PropagatorTag("ScaleMTTKVPost1"),
 273                                       Offset(1),
 274                                       PropagatorTag("ScaleMTTKVPre2"),
 275                                       PropagatorTag("ScaleMTTKVPost2"),
 276                                       Offset(0));
 277             builder->add<Propagator<IntegrationStage::ScaleVelocities>>(
 278                     PropagatorTag("ScaleMTTKVPre2"));
 279         }
 280
 281         // Propagate velocities from t to t+dt/2
 282         builder->add<Propagator<IntegrationStage::VelocitiesOnly>>(
 283                 PropagatorTag("VelocityHalfStep2"),
 284                 TimeStep(0.5 * legacySimulatorData_->inputrec->delta_t));
 285         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 286         {
 287             builder->add<Propagator<IntegrationStage::ScaleVelocities>>(
 288                     PropagatorTag("ScaleMTTKVPost2"));
 289             builder->add<Propagator<IntegrationStage::ScalePositions>>(
 290                     PropagatorTag("ScaleMTTKXPre"));
 291         }
 292         // Propagate positions from t to t+dt
 293         builder->add<Propagator<IntegrationStage::PositionsOnly>>(
 294                 PropagatorTag("PositionFullStep"), TimeStep(legacySimulatorData_->inputrec->delta_t));
 295         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 296         {
 297             builder->add<Propagator<IntegrationStage::ScalePositions>>(
 298                     PropagatorTag("ScaleMTTKXPost"));
 299         }
 300         if (legacySimulatorData_->constr)
 301         {
 302             builder->add<ConstraintsElement<ConstraintVariable::Positions>>();
 303         }
 304         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
 305
 306         // Propagate box from t to t+dt
 307         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 308         {
 309             builder->add<MttkBoxScaling>();
 310         }
 311         else if (legacySimulatorData_->inputrec->epc == PressureCoupling::CRescale)
 312         {
 313             // Legacy implementation allows combination of C-Rescale with Trotter Nose-Hoover
 314             builder->add<FirstOrderPressureCoupling>(0, ReportPreviousStepConservedEnergy::Yes);
 315         }
 316     }
 317     else
 318     {
 319         gmx_fatal(FARGS, "Integrator not implemented for the modular simulator.");
 320     }
 321     builder->add<EnergyData::Element>();
 322 }
 323
 324 bool ModularSimulator::isInputCompatible(bool                             exitOnFailure,
 325                                          const t_inputrec*                inputrec,
 326                                          bool                             doRerun,
 327                                          const gmx_mtop_t&                globalTopology,
 328                                          const gmx_multisim_t*            ms,
 329                                          const ReplicaExchangeParameters& replExParams,
 330                                          const t_fcdata*                  fcd,
 331                                          bool                             doEssentialDynamics,
 332                                          bool                             doMembed)
 333 {
 334     auto conditionalAssert = [exitOnFailure](bool condition, const char* message) {
 335         if (exitOnFailure)
 336         {
 337             GMX_RELEASE_ASSERT(condition, message);
 338         }
 339         return condition;
 340     };
 341
 342     // GMX_USE_MODULAR_SIMULATOR allows to use modular simulator also for non-standard uses,
 343     // such as the leap-frog integrator
 344     const auto modularSimulatorExplicitlyTurnedOn = (getenv("GMX_USE_MODULAR_SIMULATOR") != nullptr);
 345     // GMX_USE_MODULAR_SIMULATOR allows to use disable modular simulator for all uses,
 346     // including the velocity-verlet integrator used by default
 347     const auto modularSimulatorExplicitlyTurnedOff = (getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
 348
 349     GMX_RELEASE_ASSERT(
 350             !(modularSimulatorExplicitlyTurnedOn && modularSimulatorExplicitlyTurnedOff),
 351             "Cannot have both GMX_USE_MODULAR_SIMULATOR=ON and GMX_DISABLE_MODULAR_SIMULATOR=ON. "
 352             "Unset one of the two environment variables to explicitly chose which simulator to "
 353             "use, "
 354             "or unset both to recover default behavior.");
 355
 356     GMX_RELEASE_ASSERT(
 357             !(modularSimulatorExplicitlyTurnedOff && inputrec->eI == IntegrationAlgorithm::VV
 358               && inputrec->epc == PressureCoupling::ParrinelloRahman),
 359             "Cannot use a Parrinello-Rahman barostat with md-vv and "
 360             "GMX_DISABLE_MODULAR_SIMULATOR=ON, "
 361             "as the Parrinello-Rahman barostat is not implemented in the legacy simulator. Unset "
 362             "GMX_DISABLE_MODULAR_SIMULATOR or use a different pressure control algorithm.");
 363
 364     bool isInputCompatible = conditionalAssert(
 365             inputrec->eI == IntegrationAlgorithm::MD || inputrec->eI == IntegrationAlgorithm::VV,
 366             "Only integrators md and md-vv are supported by the modular simulator.");
 367     isInputCompatible = isInputCompatible
 368                         && conditionalAssert(inputrec->eI != IntegrationAlgorithm::MD
 369                                                      || modularSimulatorExplicitlyTurnedOn,
 370                                              "Set GMX_USE_MODULAR_SIMULATOR=ON to use the modular "
 371                                              "simulator with integrator md.");
 372     isInputCompatible =
 373             isInputCompatible
 374             && conditionalAssert(
 375                     !inputrec->useMts,
 376                     "Multiple time stepping is not supported by the modular simulator.");
 377     isInputCompatible =
 378             isInputCompatible
 379             && conditionalAssert(!doRerun, "Rerun is not supported by the modular simulator.");
 380     isInputCompatible =
 381             isInputCompatible
 382             && conditionalAssert(inputrec->efep == FreeEnergyPerturbationType::No
 383                                          || inputrec->efep == FreeEnergyPerturbationType::Yes
 384                                          || inputrec->efep == FreeEnergyPerturbationType::SlowGrowth,
 385                                  "Expanded ensemble free energy calculation is not "
 386                                  "supported by the modular simulator.");
 387     isInputCompatible = isInputCompatible
 388                         && conditionalAssert(!inputrec->bPull,
 389                                              "Pulling is not supported by the modular simulator.");
 390     isInputCompatible =
 391             isInputCompatible
 392             && conditionalAssert(inputrec->cos_accel == 0.0,
 393                                  "Acceleration is not supported by the modular simulator.");
 394     isInputCompatible =
 395             isInputCompatible
 396             && conditionalAssert(!inputrecFrozenAtoms(inputrec),
 397                                  "Freeze groups are not supported by the modular simulator.");
 398     isInputCompatible =
 399             isInputCompatible
 400             && conditionalAssert(
 401                     inputrec->deform[XX][XX] == 0.0 && inputrec->deform[XX][YY] == 0.0
 402                             && inputrec->deform[XX][ZZ] == 0.0 && inputrec->deform[YY][XX] == 0.0
 403                             && inputrec->deform[YY][YY] == 0.0 && inputrec->deform[YY][ZZ] == 0.0
 404                             && inputrec->deform[ZZ][XX] == 0.0 && inputrec->deform[ZZ][YY] == 0.0
 405                             && inputrec->deform[ZZ][ZZ] == 0.0,
 406                     "Deformation is not supported by the modular simulator.");
 407     isInputCompatible =
 408             isInputCompatible
 409             && conditionalAssert(gmx_mtop_interaction_count(globalTopology, IF_VSITE) == 0,
 410                                  "Virtual sites are not supported by the modular simulator.");
 411     isInputCompatible = isInputCompatible
 412                         && conditionalAssert(!inputrec->bDoAwh,
 413                                              "AWH is not supported by the modular simulator.");
 414     isInputCompatible =
 415             isInputCompatible
 416             && conditionalAssert(gmx_mtop_ftype_count(globalTopology, F_DISRES) == 0,
 417                                  "Distance restraints are not supported by the modular simulator.");
 418     isInputCompatible =
 419             isInputCompatible
 420             && conditionalAssert(
 421                     gmx_mtop_ftype_count(globalTopology, F_ORIRES) == 0,
 422                     "Orientation restraints are not supported by the modular simulator.");
 423     isInputCompatible =
 424             isInputCompatible
 425             && conditionalAssert(ms == nullptr,
 426                                  "Multi-sim are not supported by the modular simulator.");
 427     isInputCompatible =
 428             isInputCompatible
 429             && conditionalAssert(replExParams.exchangeInterval == 0,
 430                                  "Replica exchange is not supported by the modular simulator.");
 431
 432     int numEnsembleRestraintSystems;
 433     if (fcd)
 434     {
 435         numEnsembleRestraintSystems = fcd->disres->nsystems;
 436     }
 437     else
 438     {
 439         auto* distantRestraintEnsembleEnvVar = getenv("GMX_DISRE_ENSEMBLE_SIZE");
 440         numEnsembleRestraintSystems =
 441                 (ms != nullptr && distantRestraintEnsembleEnvVar != nullptr)
 442                         ? static_cast<int>(strtol(distantRestraintEnsembleEnvVar, nullptr, 10))
 443                         : 0;
 444     }
 445     isInputCompatible =
 446             isInputCompatible
 447             && conditionalAssert(numEnsembleRestraintSystems <= 1,
 448                                  "Ensemble restraints are not supported by the modular simulator.");
 449     isInputCompatible =
 450             isInputCompatible
 451             && conditionalAssert(!doSimulatedAnnealing(inputrec),
 452                                  "Simulated annealing is not supported by the modular simulator.");
 453     isInputCompatible =
 454             isInputCompatible
 455             && conditionalAssert(!inputrec->bSimTemp,
 456                                  "Simulated tempering is not supported by the modular simulator.");
 457     isInputCompatible = isInputCompatible
 458                         && conditionalAssert(!inputrec->bExpanded,
 459                                              "Expanded ensemble simulations are not supported by "
 460                                              "the modular simulator.");
 461     isInputCompatible =
 462             isInputCompatible
 463             && conditionalAssert(!doEssentialDynamics,
 464                                  "Essential dynamics is not supported by the modular simulator.");
 465     isInputCompatible = isInputCompatible
 466                         && conditionalAssert(inputrec->eSwapCoords == SwapType::No,
 467                                              "Ion / water position swapping is not supported by "
 468                                              "the modular simulator.");
 469     isInputCompatible =
 470             isInputCompatible
 471             && conditionalAssert(!inputrec->bIMD,
 472                                  "Interactive MD is not supported by the modular simulator.");
 473     isInputCompatible =
 474             isInputCompatible
 475             && conditionalAssert(!doMembed,
 476                                  "Membrane embedding is not supported by the modular simulator.");
 477     // TODO: Change this to the boolean passed when we merge the user interface change for the GPU update.
 478     isInputCompatible =
 479             isInputCompatible
 480             && conditionalAssert(
 481                     getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") == nullptr,
 482                     "Integration on the GPU is not supported by the modular simulator.");
 483     // Modular simulator is centered around NS updates
 484     // TODO: think how to handle nstlist == 0
 485     isInputCompatible = isInputCompatible
 486                         && conditionalAssert(inputrec->nstlist != 0,
 487                                              "Simulations without neighbor list update are not "
 488                                              "supported by the modular simulator.");
 489     isInputCompatible = isInputCompatible
 490                         && conditionalAssert(!GMX_FAHCORE,
 491                                              "GMX_FAHCORE not supported by the modular simulator.");
 492     if (!isInputCompatible
 493         && (inputrec->eI == IntegrationAlgorithm::VV && inputrec->epc == PressureCoupling::ParrinelloRahman))
 494     {
 495         gmx_fatal(FARGS,
 496                   "Requested Parrinello-Rahman barostat with md-vv. This combination is only "
 497                   "available in the modular simulator. Some other selected options are, however, "
 498                   "only available in the legacy simulator. Use a different pressure control "
 499                   "algorithm.");
 500     }
 501     return isInputCompatible;
 502 }
 503
 504 ModularSimulator::ModularSimulator(std::unique_ptr<LegacySimulatorData>      legacySimulatorData,
 505                                    std::unique_ptr<ReadCheckpointDataHolder> checkpointDataHolder) :
 506     legacySimulatorData_(std::move(legacySimulatorData)),
 507     checkpointDataHolder_(std::move(checkpointDataHolder))
 508 {
 509     checkInputForDisabledFunctionality();
 510 }
 511
 512 void ModularSimulator::checkInputForDisabledFunctionality()
 513 {
 514     isInputCompatible(true,
 515                       legacySimulatorData_->inputrec,
 516                       legacySimulatorData_->mdrunOptions.rerun,
 517                       legacySimulatorData_->top_global,
 518                       legacySimulatorData_->ms,
 519                       legacySimulatorData_->replExParams,
 520                       legacySimulatorData_->fr->fcdata.get(),
 521                       opt2bSet("-ei", legacySimulatorData_->nfile, legacySimulatorData_->fnm),
 522                       legacySimulatorData_->membed != nullptr);
 523     if (legacySimulatorData_->observablesHistory->edsamHistory)
 524     {
 525         gmx_fatal(FARGS,
 526                   "The checkpoint is from a run with essential dynamics sampling, "
 527                   "but the current run did not specify the -ei option. "
 528                   "Either specify the -ei option to mdrun, or do not use this checkpoint file.");
 529     }
 530 }
 531
 532 void ModularSimulator::readCheckpointToTrxFrame(t_trxframe*               fr,
 533                                                 ReadCheckpointDataHolder* readCheckpointDataHolder,
 534                                                 const CheckpointHeaderContents& checkpointHeaderContents)
 535 {
 536     GMX_RELEASE_ASSERT(checkpointHeaderContents.isModularSimulatorCheckpoint,
 537                        "ModularSimulator::readCheckpointToTrxFrame can only read checkpoints "
 538                        "written by modular simulator.");
 539     fr->bStep = true;
 540     fr->step = int64_to_int(checkpointHeaderContents.step, "conversion of checkpoint to trajectory");
 541     fr->bTime = true;
 542     fr->time  = checkpointHeaderContents.t;
 543
 544     fr->bAtoms = false;
 545
 546     StatePropagatorData::readCheckpointToTrxFrame(
 547             fr, readCheckpointDataHolder->checkpointData(StatePropagatorData::checkpointID()));
 548     if (readCheckpointDataHolder->keyExists(FreeEnergyPerturbationData::checkpointID()))
 549     {
 550         FreeEnergyPerturbationData::readCheckpointToTrxFrame(
 551                 fr, readCheckpointDataHolder->checkpointData(FreeEnergyPerturbationData::checkpointID()));
 552     }
 553     else
 554     {
 555         FreeEnergyPerturbationData::readCheckpointToTrxFrame(fr, std::nullopt);
 556     }
 557 }
 558
 559 } // namespace gmx