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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  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/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 "pullelement.h"
  88 #include "simulatoralgorithm.h"
  89 #include "statepropagatordata.h"
  90 #include "velocityscalingtemperaturecoupling.h"
  91
  92 namespace gmx
  93 {
  94 void ModularSimulator::run()
  95 {
  96     GMX_LOG(legacySimulatorData_->mdlog.info)
  97             .asParagraph()
  98             .appendText("Using the modular simulator.");
  99
 100     ModularSimulatorAlgorithmBuilder algorithmBuilder(compat::make_not_null(legacySimulatorData_),
 101                                                       std::move(checkpointDataHolder_));
 102     addIntegrationElements(&algorithmBuilder);
 103     auto algorithm = algorithmBuilder.build();
 104
 105     while (const auto* task = algorithm.getNextTask())
 106     {
 107         // execute task
 108         (*task)();
 109     }
 110 }
 111
 112 void ModularSimulator::addIntegrationElements(ModularSimulatorAlgorithmBuilder* builder)
 113 {
 114     const bool isTrotter = inputrecNvtTrotter(legacySimulatorData_->inputrec)
 115                            || inputrecNptTrotter(legacySimulatorData_->inputrec)
 116                            || inputrecNphTrotter(legacySimulatorData_->inputrec);
 117     if (legacySimulatorData_->inputrec->eI == IntegrationAlgorithm::MD)
 118     {
 119         // The leap frog integration algorithm
 120         builder->add<ForceElement>();
 121         builder->add<StatePropagatorData::Element>();
 122         if (legacySimulatorData_->inputrec->etc == TemperatureCoupling::VRescale
 123             || legacySimulatorData_->inputrec->etc == TemperatureCoupling::Berendsen
 124             || legacySimulatorData_->inputrec->etc == TemperatureCoupling::NoseHoover)
 125         {
 126             builder->add<VelocityScalingTemperatureCoupling>(Offset(-1),
 127                                                              UseFullStepKE::No,
 128                                                              ReportPreviousStepConservedEnergy::No,
 129                                                              PropagatorTag("LeapFrogPropagator"));
 130         }
 131         builder->add<Propagator<IntegrationStage::LeapFrog>>(
 132                 PropagatorTag("LeapFrogPropagator"), TimeStep(legacySimulatorData_->inputrec->delta_t));
 133         if (legacySimulatorData_->constr)
 134         {
 135             builder->add<ConstraintsElement<ConstraintVariable::Positions>>();
 136         }
 137
 138         if (legacySimulatorData_->inputrec->bPull)
 139         {
 140             builder->add<PullElement>();
 141         }
 142
 143         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>>();
 144         if (legacySimulatorData_->inputrec->epc == PressureCoupling::ParrinelloRahman)
 145         {
 146             builder->add<ParrinelloRahmanBarostat>(Offset(-1), PropagatorTag("LeapFrogPropagator"));
 147         }
 148         else if (legacySimulatorData_->inputrec->epc == PressureCoupling::Berendsen
 149                  || legacySimulatorData_->inputrec->epc == PressureCoupling::CRescale)
 150         {
 151             builder->add<FirstOrderPressureCoupling>(0, ReportPreviousStepConservedEnergy::No);
 152         }
 153     }
 154     else if (legacySimulatorData_->inputrec->eI == IntegrationAlgorithm::VV && !isTrotter)
 155     {
 156         // The velocity verlet integration algorithm
 157         builder->add<ForceElement>();
 158         builder->add<Propagator<IntegrationStage::VelocitiesOnly>>(
 159                 PropagatorTag("VelocityHalfStep"), TimeStep(0.5 * legacySimulatorData_->inputrec->delta_t));
 160         if (legacySimulatorData_->constr)
 161         {
 162             builder->add<ConstraintsElement<ConstraintVariable::Velocities>>();
 163         }
 164         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
 165         // Here, we have x / v / f at the full time step
 166         builder->add<StatePropagatorData::Element>();
 167         if (legacySimulatorData_->inputrec->bExpanded)
 168         {
 169             builder->add<ExpandedEnsembleElement>();
 170         }
 171         if (legacySimulatorData_->inputrec->etc == TemperatureCoupling::VRescale
 172             || legacySimulatorData_->inputrec->etc == TemperatureCoupling::Berendsen)
 173         {
 174             builder->add<VelocityScalingTemperatureCoupling>(
 175                     Offset(0),
 176                     UseFullStepKE::Yes,
 177                     ReportPreviousStepConservedEnergy::Yes,
 178                     PropagatorTag("VelocityHalfAndPositionFullStep"));
 179         }
 180         else if (ETC_ANDERSEN(legacySimulatorData_->inputrec->etc))
 181         {
 182             builder->add<AndersenTemperatureCoupling>();
 183         }
 184         builder->add<Propagator<IntegrationStage::VelocityVerletPositionsAndVelocities>>(
 185                 PropagatorTag("VelocityHalfAndPositionFullStep"),
 186                 TimeStep(legacySimulatorData_->inputrec->delta_t));
 187         if (legacySimulatorData_->constr)
 188         {
 189             builder->add<ConstraintsElement<ConstraintVariable::Positions>>();
 190         }
 191
 192         if (legacySimulatorData_->inputrec->bPull)
 193         {
 194             builder->add<PullElement>();
 195         }
 196
 197         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
 198         if (legacySimulatorData_->inputrec->epc == PressureCoupling::ParrinelloRahman)
 199         {
 200             builder->add<ParrinelloRahmanBarostat>(Offset(-1), PropagatorTag("VelocityHalfStep"));
 201         }
 202         else if (legacySimulatorData_->inputrec->epc == PressureCoupling::Berendsen
 203                  || legacySimulatorData_->inputrec->epc == PressureCoupling::CRescale)
 204         {
 205             builder->add<FirstOrderPressureCoupling>(0, ReportPreviousStepConservedEnergy::Yes);
 206         }
 207     }
 208     else if (legacySimulatorData_->inputrec->eI == IntegrationAlgorithm::VV && isTrotter)
 209     {
 210         // For a new simulation, avoid the first Trotter half step
 211         const auto scheduleTrotterFirstHalfOnInitStep =
 212                 ((legacySimulatorData_->startingBehavior == StartingBehavior::NewSimulation)
 213                          ? ScheduleOnInitStep::No
 214                          : ScheduleOnInitStep::Yes);
 215         // Define the tags and offsets for MTTK pressure scaling
 216         const MttkPropagatorConnectionDetails mttkPropagatorConnectionDetails = {
 217             PropagatorTag("ScaleMTTKXPre"),  PropagatorTag("ScaleMTTKXPost"),  Offset(0),
 218             PropagatorTag("ScaleMTTKVPre1"), PropagatorTag("ScaleMTTKVPost1"), Offset(1),
 219             PropagatorTag("ScaleMTTKVPre2"), PropagatorTag("ScaleMTTKVPost2"), Offset(0)
 220         };
 221
 222         builder->add<ForceElement>();
 223         // Propagate velocities from t-dt/2 to t
 224         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 225         {
 226             builder->add<Propagator<IntegrationStage::ScaleVelocities>>(
 227                     PropagatorTag("ScaleMTTKVPre1"));
 228         }
 229         builder->add<Propagator<IntegrationStage::VelocitiesOnly>>(
 230                 PropagatorTag("VelocityHalfStep1"),
 231                 TimeStep(0.5 * legacySimulatorData_->inputrec->delta_t));
 232         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 233         {
 234             builder->add<Propagator<IntegrationStage::ScaleVelocities>>(
 235                     PropagatorTag("ScaleMTTKVPost1"));
 236         }
 237         if (legacySimulatorData_->constr)
 238         {
 239             builder->add<ConstraintsElement<ConstraintVariable::Velocities>>();
 240         }
 241         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
 242
 243         // Propagate extended system variables from t-dt/2 to t
 244         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 245         {
 246             builder->add<MttkElement>(
 247                     Offset(-1), scheduleTrotterFirstHalfOnInitStep, mttkPropagatorConnectionDetails);
 248         }
 249         if (legacySimulatorData_->inputrec->etc == TemperatureCoupling::NoseHoover)
 250         {
 251             builder->add<NoseHooverChainsElement>(NhcUsage::System,
 252                                                   Offset(-1),
 253                                                   UseFullStepKE::Yes,
 254                                                   scheduleTrotterFirstHalfOnInitStep,
 255                                                   PropagatorTag("ScaleNHC"));
 256             builder->add<Propagator<IntegrationStage::ScaleVelocities>>(PropagatorTag("ScaleNHC"));
 257         }
 258         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 259         {
 260             builder->add<NoseHooverChainsElement>(NhcUsage::Barostat,
 261                                                   Offset(-1),
 262                                                   UseFullStepKE::Yes,
 263                                                   scheduleTrotterFirstHalfOnInitStep,
 264                                                   mttkPropagatorConnectionDetails);
 265         }
 266         // We have a full state at time t here
 267         builder->add<StatePropagatorData::Element>();
 268         if (legacySimulatorData_->inputrec->bExpanded)
 269         {
 270             builder->add<ExpandedEnsembleElement>();
 271         }
 272
 273         // Propagate extended system variables from t to t+dt/2
 274         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 275         {
 276             builder->add<NoseHooverChainsElement>(NhcUsage::Barostat,
 277                                                   Offset(0),
 278                                                   UseFullStepKE::Yes,
 279                                                   ScheduleOnInitStep::Yes,
 280                                                   mttkPropagatorConnectionDetails);
 281         }
 282         if (legacySimulatorData_->inputrec->etc == TemperatureCoupling::NoseHoover)
 283         {
 284             builder->add<NoseHooverChainsElement>(NhcUsage::System,
 285                                                   Offset(0),
 286                                                   UseFullStepKE::Yes,
 287                                                   ScheduleOnInitStep::Yes,
 288                                                   PropagatorTag("VelocityHalfStep2"));
 289         }
 290         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 291         {
 292             builder->add<MttkElement>(Offset(0), ScheduleOnInitStep::Yes, mttkPropagatorConnectionDetails);
 293             builder->add<Propagator<IntegrationStage::ScaleVelocities>>(
 294                     PropagatorTag("ScaleMTTKVPre2"));
 295         }
 296
 297         // Propagate velocities from t to t+dt/2
 298         builder->add<Propagator<IntegrationStage::VelocitiesOnly>>(
 299                 PropagatorTag("VelocityHalfStep2"),
 300                 TimeStep(0.5 * legacySimulatorData_->inputrec->delta_t));
 301         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 302         {
 303             builder->add<Propagator<IntegrationStage::ScaleVelocities>>(
 304                     PropagatorTag("ScaleMTTKVPost2"));
 305             builder->add<Propagator<IntegrationStage::ScalePositions>>(
 306                     PropagatorTag("ScaleMTTKXPre"));
 307         }
 308         // Propagate positions from t to t+dt
 309         builder->add<Propagator<IntegrationStage::PositionsOnly>>(
 310                 PropagatorTag("PositionFullStep"), TimeStep(legacySimulatorData_->inputrec->delta_t));
 311         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 312         {
 313             builder->add<Propagator<IntegrationStage::ScalePositions>>(
 314                     PropagatorTag("ScaleMTTKXPost"));
 315         }
 316         if (legacySimulatorData_->constr)
 317         {
 318             builder->add<ConstraintsElement<ConstraintVariable::Positions>>();
 319         }
 320
 321         if (legacySimulatorData_->inputrec->bPull)
 322         {
 323             builder->add<PullElement>();
 324         }
 325
 326         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
 327
 328         // Propagate box from t to t+dt
 329         if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
 330         {
 331             builder->add<MttkBoxScaling>(mttkPropagatorConnectionDetails);
 332         }
 333         else if (legacySimulatorData_->inputrec->epc == PressureCoupling::CRescale)
 334         {
 335             // Legacy implementation allows combination of C-Rescale with Trotter Nose-Hoover
 336             builder->add<FirstOrderPressureCoupling>(0, ReportPreviousStepConservedEnergy::Yes);
 337         }
 338     }
 339     else
 340     {
 341         gmx_fatal(FARGS, "Integrator not implemented for the modular simulator.");
 342     }
 343     builder->add<EnergyData::Element>();
 344 }
 345
 346 bool ModularSimulator::isInputCompatible(bool                             exitOnFailure,
 347                                          const t_inputrec*                inputrec,
 348                                          bool                             doRerun,
 349                                          const gmx_mtop_t&                globalTopology,
 350                                          const gmx_multisim_t*            ms,
 351                                          const ReplicaExchangeParameters& replExParams,
 352                                          const t_fcdata*                  fcd,
 353                                          bool                             doEssentialDynamics,
 354                                          bool                             doMembed)
 355 {
 356     auto conditionalAssert = [exitOnFailure](bool condition, const char* message) {
 357         if (exitOnFailure)
 358         {
 359             GMX_RELEASE_ASSERT(condition, message);
 360         }
 361         return condition;
 362     };
 363
 364     // GMX_USE_MODULAR_SIMULATOR allows to use modular simulator also for non-standard uses,
 365     // such as the leap-frog integrator
 366     const auto modularSimulatorExplicitlyTurnedOn = (getenv("GMX_USE_MODULAR_SIMULATOR") != nullptr);
 367     // GMX_USE_MODULAR_SIMULATOR allows to use disable modular simulator for all uses,
 368     // including the velocity-verlet integrator used by default
 369     const auto modularSimulatorExplicitlyTurnedOff = (getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
 370
 371     GMX_RELEASE_ASSERT(
 372             !(modularSimulatorExplicitlyTurnedOn && modularSimulatorExplicitlyTurnedOff),
 373             "Cannot have both GMX_USE_MODULAR_SIMULATOR=ON and GMX_DISABLE_MODULAR_SIMULATOR=ON. "
 374             "Unset one of the two environment variables to explicitly chose which simulator to "
 375             "use, "
 376             "or unset both to recover default behavior.");
 377
 378     GMX_RELEASE_ASSERT(
 379             !(modularSimulatorExplicitlyTurnedOff && inputrec->eI == IntegrationAlgorithm::VV
 380               && inputrec->epc == PressureCoupling::ParrinelloRahman),
 381             "Cannot use a Parrinello-Rahman barostat with md-vv and "
 382             "GMX_DISABLE_MODULAR_SIMULATOR=ON, "
 383             "as the Parrinello-Rahman barostat is not implemented in the legacy simulator. Unset "
 384             "GMX_DISABLE_MODULAR_SIMULATOR or use a different pressure control algorithm.");
 385
 386     bool isInputCompatible = conditionalAssert(
 387             inputrec->eI == IntegrationAlgorithm::MD || inputrec->eI == IntegrationAlgorithm::VV,
 388             "Only integrators md and md-vv are supported by the modular simulator.");
 389     isInputCompatible = isInputCompatible
 390                         && conditionalAssert(inputrec->eI != IntegrationAlgorithm::MD
 391                                                      || modularSimulatorExplicitlyTurnedOn,
 392                                              "Set GMX_USE_MODULAR_SIMULATOR=ON to use the modular "
 393                                              "simulator with integrator md.");
 394     isInputCompatible =
 395             isInputCompatible
 396             && conditionalAssert(
 397                     !inputrec->useMts,
 398                     "Multiple time stepping is not supported by the modular simulator.");
 399     isInputCompatible =
 400             isInputCompatible
 401             && conditionalAssert(!doRerun, "Rerun is not supported by the modular simulator.");
 402     isInputCompatible =
 403             isInputCompatible
 404             && conditionalAssert(!inputrec->useConstantAcceleration && inputrec->cos_accel == 0.0,
 405                                  "Acceleration is not supported by the modular simulator.");
 406     isInputCompatible =
 407             isInputCompatible
 408             && conditionalAssert(!inputrecFrozenAtoms(inputrec),
 409                                  "Freeze groups are not supported by the modular simulator.");
 410     isInputCompatible =
 411             isInputCompatible
 412             && conditionalAssert(
 413                     inputrec->deform[XX][XX] == 0.0 && inputrec->deform[XX][YY] == 0.0
 414                             && inputrec->deform[XX][ZZ] == 0.0 && inputrec->deform[YY][XX] == 0.0
 415                             && inputrec->deform[YY][YY] == 0.0 && inputrec->deform[YY][ZZ] == 0.0
 416                             && inputrec->deform[ZZ][XX] == 0.0 && inputrec->deform[ZZ][YY] == 0.0
 417                             && inputrec->deform[ZZ][ZZ] == 0.0,
 418                     "Deformation is not supported by the modular simulator.");
 419     isInputCompatible =
 420             isInputCompatible
 421             && conditionalAssert(gmx_mtop_interaction_count(globalTopology, IF_VSITE) == 0,
 422                                  "Virtual sites are not supported by the modular simulator.");
 423     isInputCompatible = isInputCompatible
 424                         && conditionalAssert(!inputrec->bDoAwh,
 425                                              "AWH is not supported by the modular simulator.");
 426     isInputCompatible =
 427             isInputCompatible
 428             && conditionalAssert(gmx_mtop_ftype_count(globalTopology, F_DISRES) == 0,
 429                                  "Distance restraints are not supported by the modular simulator.");
 430     isInputCompatible =
 431             isInputCompatible
 432             && conditionalAssert(
 433                     gmx_mtop_ftype_count(globalTopology, F_ORIRES) == 0,
 434                     "Orientation restraints are not supported by the modular simulator.");
 435     isInputCompatible =
 436             isInputCompatible
 437             && conditionalAssert(ms == nullptr,
 438                                  "Multi-sim are not supported by the modular simulator.");
 439     isInputCompatible =
 440             isInputCompatible
 441             && conditionalAssert(replExParams.exchangeInterval == 0,
 442                                  "Replica exchange is not supported by the modular simulator.");
 443
 444     int numEnsembleRestraintSystems;
 445     if (fcd)
 446     {
 447         numEnsembleRestraintSystems = fcd->disres->nsystems;
 448     }
 449     else
 450     {
 451         auto* distantRestraintEnsembleEnvVar = getenv("GMX_DISRE_ENSEMBLE_SIZE");
 452         numEnsembleRestraintSystems =
 453                 (ms != nullptr && distantRestraintEnsembleEnvVar != nullptr)
 454                         ? static_cast<int>(strtol(distantRestraintEnsembleEnvVar, nullptr, 10))
 455                         : 0;
 456     }
 457     isInputCompatible =
 458             isInputCompatible
 459             && conditionalAssert(numEnsembleRestraintSystems <= 1,
 460                                  "Ensemble restraints are not supported by the modular simulator.");
 461     isInputCompatible =
 462             isInputCompatible
 463             && conditionalAssert(!doSimulatedAnnealing(inputrec),
 464                                  "Simulated annealing is not supported by the modular simulator.");
 465     isInputCompatible =
 466             isInputCompatible
 467             && conditionalAssert(!inputrec->bSimTemp,
 468                                  "Simulated tempering is not supported by the modular simulator.");
 469     isInputCompatible =
 470             isInputCompatible
 471             && conditionalAssert(!doEssentialDynamics,
 472                                  "Essential dynamics is not supported by the modular simulator.");
 473     isInputCompatible = isInputCompatible
 474                         && conditionalAssert(inputrec->eSwapCoords == SwapType::No,
 475                                              "Ion / water position swapping is not supported by "
 476                                              "the modular simulator.");
 477     isInputCompatible =
 478             isInputCompatible
 479             && conditionalAssert(!inputrec->bIMD,
 480                                  "Interactive MD is not supported by the modular simulator.");
 481     isInputCompatible =
 482             isInputCompatible
 483             && conditionalAssert(!doMembed,
 484                                  "Membrane embedding is not supported by the modular simulator.");
 485     // TODO: Change this to the boolean passed when we merge the user interface change for the GPU update.
 486     isInputCompatible =
 487             isInputCompatible
 488             && conditionalAssert(
 489                     getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") == nullptr,
 490                     "Integration on the GPU is not supported by the modular simulator.");
 491     // Modular simulator is centered around NS updates
 492     // TODO: think how to handle nstlist == 0
 493     isInputCompatible = isInputCompatible
 494                         && conditionalAssert(inputrec->nstlist != 0,
 495                                              "Simulations without neighbor list update are not "
 496                                              "supported by the modular simulator.");
 497     isInputCompatible = isInputCompatible
 498                         && conditionalAssert(!GMX_FAHCORE,
 499                                              "GMX_FAHCORE not supported by the modular simulator.");
 500     if (!isInputCompatible
 501         && (inputrec->eI == IntegrationAlgorithm::VV && inputrec->epc == PressureCoupling::ParrinelloRahman))
 502     {
 503         gmx_fatal(FARGS,
 504                   "Requested Parrinello-Rahman barostat with md-vv. This combination is only "
 505                   "available in the modular simulator. Some other selected options are, however, "
 506                   "only available in the legacy simulator. Use a different pressure control "
 507                   "algorithm.");
 508     }
 509     return isInputCompatible;
 510 }
 511
 512 ModularSimulator::ModularSimulator(std::unique_ptr<LegacySimulatorData>      legacySimulatorData,
 513                                    std::unique_ptr<ReadCheckpointDataHolder> checkpointDataHolder) :
 514     legacySimulatorData_(std::move(legacySimulatorData)),
 515     checkpointDataHolder_(std::move(checkpointDataHolder))
 516 {
 517     checkInputForDisabledFunctionality();
 518 }
 519
 520 void ModularSimulator::checkInputForDisabledFunctionality()
 521 {
 522     isInputCompatible(true,
 523                       legacySimulatorData_->inputrec,
 524                       legacySimulatorData_->mdrunOptions.rerun,
 525                       legacySimulatorData_->top_global,
 526                       legacySimulatorData_->ms,
 527                       legacySimulatorData_->replExParams,
 528                       legacySimulatorData_->fr->fcdata.get(),
 529                       opt2bSet("-ei", legacySimulatorData_->nfile, legacySimulatorData_->fnm),
 530                       legacySimulatorData_->membed != nullptr);
 531     if (legacySimulatorData_->observablesHistory->edsamHistory)
 532     {
 533         gmx_fatal(FARGS,
 534                   "The checkpoint is from a run with essential dynamics sampling, "
 535                   "but the current run did not specify the -ei option. "
 536                   "Either specify the -ei option to mdrun, or do not use this checkpoint file.");
 537     }
 538 }
 539
 540 void ModularSimulator::readCheckpointToTrxFrame(t_trxframe*               fr,
 541                                                 ReadCheckpointDataHolder* readCheckpointDataHolder,
 542                                                 const CheckpointHeaderContents& checkpointHeaderContents)
 543 {
 544     GMX_RELEASE_ASSERT(checkpointHeaderContents.isModularSimulatorCheckpoint,
 545                        "ModularSimulator::readCheckpointToTrxFrame can only read checkpoints "
 546                        "written by modular simulator.");
 547     fr->bStep = true;
 548     fr->step = int64_to_int(checkpointHeaderContents.step, "conversion of checkpoint to trajectory");
 549     fr->bTime = true;
 550     fr->time  = checkpointHeaderContents.t;
 551
 552     fr->bAtoms = false;
 553
 554     StatePropagatorData::readCheckpointToTrxFrame(
 555             fr, readCheckpointDataHolder->checkpointData(StatePropagatorData::checkpointID()));
 556     if (readCheckpointDataHolder->keyExists(FreeEnergyPerturbationData::checkpointID()))
 557     {
 558         FreeEnergyPerturbationData::readCheckpointToTrxFrame(
 559                 fr, readCheckpointDataHolder->checkpointData(FreeEnergyPerturbationData::checkpointID()));
 560     }
 561     else
 562     {
 563         FreeEnergyPerturbationData::readCheckpointToTrxFrame(fr, std::nullopt);
 564     }
 565 }
 566
 567 } // namespace gmx