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
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   8  *
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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         // Define the tags and offsets for MTTK pressure scaling
 197         const MttkPropagatorConnectionDetails mttkPropagatorConnectionDetails = {
 198             PropagatorTag("ScaleMTTKXPre"),  PropagatorTag("ScaleMTTKXPost"),  Offset(0),
 199             PropagatorTag("ScaleMTTKVPre1"), PropagatorTag("ScaleMTTKVPost1"), Offset(1),
 200             PropagatorTag("ScaleMTTKVPre2"), PropagatorTag("ScaleMTTKVPost2"), Offset(0)
 201         };
 202
 203         builder->add<ForceElement>();
 204         // Propagate velocities from t-dt/2 to t
 205         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 206         {
 207             builder->add<Propagator<IntegrationStage::ScaleVelocities>>(
 208                     PropagatorTag("ScaleMTTKVPre1"));
 209         }
 210         builder->add<Propagator<IntegrationStage::VelocitiesOnly>>(
 211                 PropagatorTag("VelocityHalfStep1"),
 212                 TimeStep(0.5 * legacySimulatorData_->inputrec->delta_t));
 213         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 214         {
 215             builder->add<Propagator<IntegrationStage::ScaleVelocities>>(
 216                     PropagatorTag("ScaleMTTKVPost1"));
 217         }
 218         if (legacySimulatorData_->constr)
 219         {
 220             builder->add<ConstraintsElement<ConstraintVariable::Velocities>>();
 221         }
 222         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
 223
 224         // Propagate extended system variables from t-dt/2 to t
 225         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 226         {
 227             builder->add<MttkElement>(
 228                     Offset(-1), scheduleTrotterFirstHalfOnInitStep, mttkPropagatorConnectionDetails);
 229         }
 230         if (legacySimulatorData_->inputrec->etc == TemperatureCoupling::NoseHoover)
 231         {
 232             builder->add<NoseHooverChainsElement>(NhcUsage::System,
 233                                                   Offset(-1),
 234                                                   UseFullStepKE::Yes,
 235                                                   scheduleTrotterFirstHalfOnInitStep,
 236                                                   PropagatorTag("ScaleNHC"));
 237             builder->add<Propagator<IntegrationStage::ScaleVelocities>>(PropagatorTag("ScaleNHC"));
 238         }
 239         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 240         {
 241             builder->add<NoseHooverChainsElement>(NhcUsage::Barostat,
 242                                                   Offset(-1),
 243                                                   UseFullStepKE::Yes,
 244                                                   scheduleTrotterFirstHalfOnInitStep,
 245                                                   mttkPropagatorConnectionDetails);
 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>(NhcUsage::Barostat,
 254                                                   Offset(0),
 255                                                   UseFullStepKE::Yes,
 256                                                   ScheduleOnInitStep::Yes,
 257                                                   mttkPropagatorConnectionDetails);
 258         }
 259         if (legacySimulatorData_->inputrec->etc == TemperatureCoupling::NoseHoover)
 260         {
 261             builder->add<NoseHooverChainsElement>(NhcUsage::System,
 262                                                   Offset(0),
 263                                                   UseFullStepKE::Yes,
 264                                                   ScheduleOnInitStep::Yes,
 265                                                   PropagatorTag("VelocityHalfStep2"));
 266         }
 267         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 268         {
 269             builder->add<MttkElement>(Offset(0), ScheduleOnInitStep::Yes, mttkPropagatorConnectionDetails);
 270             builder->add<Propagator<IntegrationStage::ScaleVelocities>>(
 271                     PropagatorTag("ScaleMTTKVPre2"));
 272         }
 273
 274         // Propagate velocities from t to t+dt/2
 275         builder->add<Propagator<IntegrationStage::VelocitiesOnly>>(
 276                 PropagatorTag("VelocityHalfStep2"),
 277                 TimeStep(0.5 * legacySimulatorData_->inputrec->delta_t));
 278         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 279         {
 280             builder->add<Propagator<IntegrationStage::ScaleVelocities>>(
 281                     PropagatorTag("ScaleMTTKVPost2"));
 282             builder->add<Propagator<IntegrationStage::ScalePositions>>(
 283                     PropagatorTag("ScaleMTTKXPre"));
 284         }
 285         // Propagate positions from t to t+dt
 286         builder->add<Propagator<IntegrationStage::PositionsOnly>>(
 287                 PropagatorTag("PositionFullStep"), TimeStep(legacySimulatorData_->inputrec->delta_t));
 288         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 289         {
 290             builder->add<Propagator<IntegrationStage::ScalePositions>>(
 291                     PropagatorTag("ScaleMTTKXPost"));
 292         }
 293         if (legacySimulatorData_->constr)
 294         {
 295             builder->add<ConstraintsElement<ConstraintVariable::Positions>>();
 296         }
 297         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
 298
 299         // Propagate box from t to t+dt
 300         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 301         {
 302             builder->add<MttkBoxScaling>(mttkPropagatorConnectionDetails);
 303         }
 304         else if (legacySimulatorData_->inputrec->epc == PressureCoupling::CRescale)
 305         {
 306             // Legacy implementation allows combination of C-Rescale with Trotter Nose-Hoover
 307             builder->add<FirstOrderPressureCoupling>(0, ReportPreviousStepConservedEnergy::Yes);
 308         }
 309     }
 310     else
 311     {
 312         gmx_fatal(FARGS, "Integrator not implemented for the modular simulator.");
 313     }
 314     builder->add<EnergyData::Element>();
 315 }
 316
 317 bool ModularSimulator::isInputCompatible(bool                             exitOnFailure,
 318                                          const t_inputrec*                inputrec,
 319                                          bool                             doRerun,
 320                                          const gmx_mtop_t&                globalTopology,
 321                                          const gmx_multisim_t*            ms,
 322                                          const ReplicaExchangeParameters& replExParams,
 323                                          const t_fcdata*                  fcd,
 324                                          bool                             doEssentialDynamics,
 325                                          bool                             doMembed)
 326 {
 327     auto conditionalAssert = [exitOnFailure](bool condition, const char* message) {
 328         if (exitOnFailure)
 329         {
 330             GMX_RELEASE_ASSERT(condition, message);
 331         }
 332         return condition;
 333     };
 334
 335     // GMX_USE_MODULAR_SIMULATOR allows to use modular simulator also for non-standard uses,
 336     // such as the leap-frog integrator
 337     const auto modularSimulatorExplicitlyTurnedOn = (getenv("GMX_USE_MODULAR_SIMULATOR") != nullptr);
 338     // GMX_USE_MODULAR_SIMULATOR allows to use disable modular simulator for all uses,
 339     // including the velocity-verlet integrator used by default
 340     const auto modularSimulatorExplicitlyTurnedOff = (getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
 341
 342     GMX_RELEASE_ASSERT(
 343             !(modularSimulatorExplicitlyTurnedOn && modularSimulatorExplicitlyTurnedOff),
 344             "Cannot have both GMX_USE_MODULAR_SIMULATOR=ON and GMX_DISABLE_MODULAR_SIMULATOR=ON. "
 345             "Unset one of the two environment variables to explicitly chose which simulator to "
 346             "use, "
 347             "or unset both to recover default behavior.");
 348
 349     GMX_RELEASE_ASSERT(
 350             !(modularSimulatorExplicitlyTurnedOff && inputrec->eI == IntegrationAlgorithm::VV
 351               && inputrec->epc == PressureCoupling::ParrinelloRahman),
 352             "Cannot use a Parrinello-Rahman barostat with md-vv and "
 353             "GMX_DISABLE_MODULAR_SIMULATOR=ON, "
 354             "as the Parrinello-Rahman barostat is not implemented in the legacy simulator. Unset "
 355             "GMX_DISABLE_MODULAR_SIMULATOR or use a different pressure control algorithm.");
 356
 357     bool isInputCompatible = conditionalAssert(
 358             inputrec->eI == IntegrationAlgorithm::MD || inputrec->eI == IntegrationAlgorithm::VV,
 359             "Only integrators md and md-vv are supported by the modular simulator.");
 360     isInputCompatible = isInputCompatible
 361                         && conditionalAssert(inputrec->eI != IntegrationAlgorithm::MD
 362                                                      || modularSimulatorExplicitlyTurnedOn,
 363                                              "Set GMX_USE_MODULAR_SIMULATOR=ON to use the modular "
 364                                              "simulator with integrator md.");
 365     isInputCompatible =
 366             isInputCompatible
 367             && conditionalAssert(
 368                     !inputrec->useMts,
 369                     "Multiple time stepping is not supported by the modular simulator.");
 370     isInputCompatible =
 371             isInputCompatible
 372             && conditionalAssert(!doRerun, "Rerun is not supported by the modular simulator.");
 373     isInputCompatible =
 374             isInputCompatible
 375             && conditionalAssert(inputrec->efep == FreeEnergyPerturbationType::No
 376                                          || inputrec->efep == FreeEnergyPerturbationType::Yes
 377                                          || inputrec->efep == FreeEnergyPerturbationType::SlowGrowth,
 378                                  "Expanded ensemble free energy calculation is not "
 379                                  "supported by the modular simulator.");
 380     isInputCompatible = isInputCompatible
 381                         && conditionalAssert(!inputrec->bPull,
 382                                              "Pulling is not supported by the modular simulator.");
 383     isInputCompatible =
 384             isInputCompatible
 385             && conditionalAssert(inputrec->cos_accel == 0.0,
 386                                  "Acceleration is not supported by the modular simulator.");
 387     isInputCompatible =
 388             isInputCompatible
 389             && conditionalAssert(!inputrecFrozenAtoms(inputrec),
 390                                  "Freeze groups are not supported by the modular simulator.");
 391     isInputCompatible =
 392             isInputCompatible
 393             && conditionalAssert(
 394                     inputrec->deform[XX][XX] == 0.0 && inputrec->deform[XX][YY] == 0.0
 395                             && inputrec->deform[XX][ZZ] == 0.0 && inputrec->deform[YY][XX] == 0.0
 396                             && inputrec->deform[YY][YY] == 0.0 && inputrec->deform[YY][ZZ] == 0.0
 397                             && inputrec->deform[ZZ][XX] == 0.0 && inputrec->deform[ZZ][YY] == 0.0
 398                             && inputrec->deform[ZZ][ZZ] == 0.0,
 399                     "Deformation is not supported by the modular simulator.");
 400     isInputCompatible =
 401             isInputCompatible
 402             && conditionalAssert(gmx_mtop_interaction_count(globalTopology, IF_VSITE) == 0,
 403                                  "Virtual sites are not supported by the modular simulator.");
 404     isInputCompatible = isInputCompatible
 405                         && conditionalAssert(!inputrec->bDoAwh,
 406                                              "AWH is not supported by the modular simulator.");
 407     isInputCompatible =
 408             isInputCompatible
 409             && conditionalAssert(gmx_mtop_ftype_count(globalTopology, F_DISRES) == 0,
 410                                  "Distance restraints are not supported by the modular simulator.");
 411     isInputCompatible =
 412             isInputCompatible
 413             && conditionalAssert(
 414                     gmx_mtop_ftype_count(globalTopology, F_ORIRES) == 0,
 415                     "Orientation restraints are not supported by the modular simulator.");
 416     isInputCompatible =
 417             isInputCompatible
 418             && conditionalAssert(ms == nullptr,
 419                                  "Multi-sim are not supported by the modular simulator.");
 420     isInputCompatible =
 421             isInputCompatible
 422             && conditionalAssert(replExParams.exchangeInterval == 0,
 423                                  "Replica exchange is not supported by the modular simulator.");
 424
 425     int numEnsembleRestraintSystems;
 426     if (fcd)
 427     {
 428         numEnsembleRestraintSystems = fcd->disres->nsystems;
 429     }
 430     else
 431     {
 432         auto* distantRestraintEnsembleEnvVar = getenv("GMX_DISRE_ENSEMBLE_SIZE");
 433         numEnsembleRestraintSystems =
 434                 (ms != nullptr && distantRestraintEnsembleEnvVar != nullptr)
 435                         ? static_cast<int>(strtol(distantRestraintEnsembleEnvVar, nullptr, 10))
 436                         : 0;
 437     }
 438     isInputCompatible =
 439             isInputCompatible
 440             && conditionalAssert(numEnsembleRestraintSystems <= 1,
 441                                  "Ensemble restraints are not supported by the modular simulator.");
 442     isInputCompatible =
 443             isInputCompatible
 444             && conditionalAssert(!doSimulatedAnnealing(inputrec),
 445                                  "Simulated annealing is not supported by the modular simulator.");
 446     isInputCompatible =
 447             isInputCompatible
 448             && conditionalAssert(!inputrec->bSimTemp,
 449                                  "Simulated tempering is not supported by the modular simulator.");
 450     isInputCompatible = isInputCompatible
 451                         && conditionalAssert(!inputrec->bExpanded,
 452                                              "Expanded ensemble simulations are not supported by "
 453                                              "the modular simulator.");
 454     isInputCompatible =
 455             isInputCompatible
 456             && conditionalAssert(!doEssentialDynamics,
 457                                  "Essential dynamics is not supported by the modular simulator.");
 458     isInputCompatible = isInputCompatible
 459                         && conditionalAssert(inputrec->eSwapCoords == SwapType::No,
 460                                              "Ion / water position swapping is not supported by "
 461                                              "the modular simulator.");
 462     isInputCompatible =
 463             isInputCompatible
 464             && conditionalAssert(!inputrec->bIMD,
 465                                  "Interactive MD is not supported by the modular simulator.");
 466     isInputCompatible =
 467             isInputCompatible
 468             && conditionalAssert(!doMembed,
 469                                  "Membrane embedding is not supported by the modular simulator.");
 470     // TODO: Change this to the boolean passed when we merge the user interface change for the GPU update.
 471     isInputCompatible =
 472             isInputCompatible
 473             && conditionalAssert(
 474                     getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") == nullptr,
 475                     "Integration on the GPU is not supported by the modular simulator.");
 476     // Modular simulator is centered around NS updates
 477     // TODO: think how to handle nstlist == 0
 478     isInputCompatible = isInputCompatible
 479                         && conditionalAssert(inputrec->nstlist != 0,
 480                                              "Simulations without neighbor list update are not "
 481                                              "supported by the modular simulator.");
 482     isInputCompatible = isInputCompatible
 483                         && conditionalAssert(!GMX_FAHCORE,
 484                                              "GMX_FAHCORE not supported by the modular simulator.");
 485     if (!isInputCompatible
 486         && (inputrec->eI == IntegrationAlgorithm::VV && inputrec->epc == PressureCoupling::ParrinelloRahman))
 487     {
 488         gmx_fatal(FARGS,
 489                   "Requested Parrinello-Rahman barostat with md-vv. This combination is only "
 490                   "available in the modular simulator. Some other selected options are, however, "
 491                   "only available in the legacy simulator. Use a different pressure control "
 492                   "algorithm.");
 493     }
 494     return isInputCompatible;
 495 }
 496
 497 ModularSimulator::ModularSimulator(std::unique_ptr<LegacySimulatorData>      legacySimulatorData,
 498                                    std::unique_ptr<ReadCheckpointDataHolder> checkpointDataHolder) :
 499     legacySimulatorData_(std::move(legacySimulatorData)),
 500     checkpointDataHolder_(std::move(checkpointDataHolder))
 501 {
 502     checkInputForDisabledFunctionality();
 503 }
 504
 505 void ModularSimulator::checkInputForDisabledFunctionality()
 506 {
 507     isInputCompatible(true,
 508                       legacySimulatorData_->inputrec,
 509                       legacySimulatorData_->mdrunOptions.rerun,
 510                       legacySimulatorData_->top_global,
 511                       legacySimulatorData_->ms,
 512                       legacySimulatorData_->replExParams,
 513                       legacySimulatorData_->fr->fcdata.get(),
 514                       opt2bSet("-ei", legacySimulatorData_->nfile, legacySimulatorData_->fnm),
 515                       legacySimulatorData_->membed != nullptr);
 516     if (legacySimulatorData_->observablesHistory->edsamHistory)
 517     {
 518         gmx_fatal(FARGS,
 519                   "The checkpoint is from a run with essential dynamics sampling, "
 520                   "but the current run did not specify the -ei option. "
 521                   "Either specify the -ei option to mdrun, or do not use this checkpoint file.");
 522     }
 523 }
 524
 525 void ModularSimulator::readCheckpointToTrxFrame(t_trxframe*               fr,
 526                                                 ReadCheckpointDataHolder* readCheckpointDataHolder,
 527                                                 const CheckpointHeaderContents& checkpointHeaderContents)
 528 {
 529     GMX_RELEASE_ASSERT(checkpointHeaderContents.isModularSimulatorCheckpoint,
 530                        "ModularSimulator::readCheckpointToTrxFrame can only read checkpoints "
 531                        "written by modular simulator.");
 532     fr->bStep = true;
 533     fr->step = int64_to_int(checkpointHeaderContents.step, "conversion of checkpoint to trajectory");
 534     fr->bTime = true;
 535     fr->time  = checkpointHeaderContents.t;
 536
 537     fr->bAtoms = false;
 538
 539     StatePropagatorData::readCheckpointToTrxFrame(
 540             fr, readCheckpointDataHolder->checkpointData(StatePropagatorData::checkpointID()));
 541     if (readCheckpointDataHolder->keyExists(FreeEnergyPerturbationData::checkpointID()))
 542     {
 543         FreeEnergyPerturbationData::readCheckpointToTrxFrame(
 544                 fr, readCheckpointDataHolder->checkpointData(FreeEnergyPerturbationData::checkpointID()));
 545     }
 546     else
 547     {
 548         FreeEnergyPerturbationData::readCheckpointToTrxFrame(fr, std::nullopt);
 549     }
 550 }
 551
 552 } // namespace gmx