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