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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  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/mdlib/update.h"
  61 #include "gromacs/mdrun/replicaexchange.h"
  62 #include "gromacs/mdrun/shellfc.h"
  63 #include "gromacs/mdrunutility/handlerestart.h"
  64 #include "gromacs/mdrunutility/printtime.h"
  65 #include "gromacs/mdtypes/commrec.h"
  66 #include "gromacs/mdtypes/fcdata.h"
  67 #include "gromacs/mdtypes/forcerec.h"
  68 #include "gromacs/mdtypes/inputrec.h"
  69 #include "gromacs/mdtypes/mdatom.h"
  70 #include "gromacs/mdtypes/mdrunoptions.h"
  71 #include "gromacs/mdtypes/observableshistory.h"
  72 #include "gromacs/nbnxm/nbnxm.h"
  73 #include "gromacs/topology/mtop_util.h"
  74 #include "gromacs/topology/topology.h"
  75 #include "gromacs/trajectory/trajectoryframe.h"
  76 #include "gromacs/utility/fatalerror.h"
  77 #include "gromacs/utility/int64_to_int.h"
  78
  79 #include "computeglobalselement.h"
  80 #include "constraintelement.h"
  81 #include "forceelement.h"
  82 #include "parrinellorahmanbarostat.h"
  83 #include "simulatoralgorithm.h"
  84 #include "statepropagatordata.h"
  85 #include "velocityscalingtemperaturecoupling.h"
  86
  87 namespace gmx
  88 {
  89 void ModularSimulator::run()
  90 {
  91     GMX_LOG(legacySimulatorData_->mdlog.info)
  92             .asParagraph()
  93             .appendText("Using the modular simulator.");
  94
  95     ModularSimulatorAlgorithmBuilder algorithmBuilder(compat::make_not_null(legacySimulatorData_),
  96                                                       std::move(checkpointDataHolder_));
  97     addIntegrationElements(&algorithmBuilder);
  98     auto algorithm = algorithmBuilder.build();
  99
 100     while (const auto* task = algorithm.getNextTask())
 101     {
 102         // execute task
 103         (*task)();
 104     }
 105 }
 106
 107 void ModularSimulator::addIntegrationElements(ModularSimulatorAlgorithmBuilder* builder)
 108 {
 109     if (legacySimulatorData_->inputrec->eI == IntegrationAlgorithm::MD)
 110     {
 111         // The leap frog integration algorithm
 112         builder->add<ForceElement>();
 113         builder->add<StatePropagatorData::Element>();
 114         if (legacySimulatorData_->inputrec->etc == TemperatureCoupling::VRescale
 115             || legacySimulatorData_->inputrec->etc == TemperatureCoupling::Berendsen)
 116         {
 117             builder->add<VelocityScalingTemperatureCoupling>(
 118                     -1, UseFullStepKE::No, ReportPreviousStepConservedEnergy::No);
 119         }
 120         builder->add<Propagator<IntegrationStep::LeapFrog>>(legacySimulatorData_->inputrec->delta_t,
 121                                                             RegisterWithThermostat::True,
 122                                                             RegisterWithBarostat::True);
 123         if (legacySimulatorData_->constr)
 124         {
 125             builder->add<ConstraintsElement<ConstraintVariable::Positions>>();
 126         }
 127         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>>();
 128         builder->add<EnergyData::Element>();
 129         if (legacySimulatorData_->inputrec->epc == PressureCoupling::ParrinelloRahman)
 130         {
 131             builder->add<ParrinelloRahmanBarostat>(-1);
 132         }
 133     }
 134     else if (legacySimulatorData_->inputrec->eI == IntegrationAlgorithm::VV)
 135     {
 136         // The velocity verlet integration algorithm
 137         builder->add<ForceElement>();
 138         builder->add<Propagator<IntegrationStep::VelocitiesOnly>>(
 139                 0.5 * legacySimulatorData_->inputrec->delta_t,
 140                 RegisterWithThermostat::False,
 141                 RegisterWithBarostat::True);
 142         if (legacySimulatorData_->constr)
 143         {
 144             builder->add<ConstraintsElement<ConstraintVariable::Velocities>>();
 145         }
 146         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
 147         builder->add<StatePropagatorData::Element>();
 148         if (legacySimulatorData_->inputrec->etc == TemperatureCoupling::VRescale
 149             || legacySimulatorData_->inputrec->etc == TemperatureCoupling::Berendsen)
 150         {
 151             builder->add<VelocityScalingTemperatureCoupling>(
 152                     0, UseFullStepKE::Yes, ReportPreviousStepConservedEnergy::Yes);
 153         }
 154         builder->add<Propagator<IntegrationStep::VelocityVerletPositionsAndVelocities>>(
 155                 legacySimulatorData_->inputrec->delta_t,
 156                 RegisterWithThermostat::True,
 157                 RegisterWithBarostat::False);
 158         if (legacySimulatorData_->constr)
 159         {
 160             builder->add<ConstraintsElement<ConstraintVariable::Positions>>();
 161         }
 162         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
 163         builder->add<EnergyData::Element>();
 164         if (legacySimulatorData_->inputrec->epc == PressureCoupling::ParrinelloRahman)
 165         {
 166             builder->add<ParrinelloRahmanBarostat>(-1);
 167         }
 168     }
 169     else
 170     {
 171         gmx_fatal(FARGS, "Integrator not implemented for the modular simulator.");
 172     }
 173 }
 174
 175 bool ModularSimulator::isInputCompatible(bool                             exitOnFailure,
 176                                          const t_inputrec*                inputrec,
 177                                          bool                             doRerun,
 178                                          const gmx_mtop_t&                globalTopology,
 179                                          const gmx_multisim_t*            ms,
 180                                          const ReplicaExchangeParameters& replExParams,
 181                                          const t_fcdata*                  fcd,
 182                                          bool                             doEssentialDynamics,
 183                                          bool                             doMembed)
 184 {
 185     auto conditionalAssert = [exitOnFailure](bool condition, const char* message) {
 186         if (exitOnFailure)
 187         {
 188             GMX_RELEASE_ASSERT(condition, message);
 189         }
 190         return condition;
 191     };
 192
 193     // GMX_USE_MODULAR_SIMULATOR allows to use modular simulator also for non-standard uses,
 194     // such as the leap-frog integrator
 195     const auto modularSimulatorExplicitlyTurnedOn = (getenv("GMX_USE_MODULAR_SIMULATOR") != nullptr);
 196     // GMX_USE_MODULAR_SIMULATOR allows to use disable modular simulator for all uses,
 197     // including the velocity-verlet integrator used by default
 198     const auto modularSimulatorExplicitlyTurnedOff = (getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
 199
 200     GMX_RELEASE_ASSERT(
 201             !(modularSimulatorExplicitlyTurnedOn && modularSimulatorExplicitlyTurnedOff),
 202             "Cannot have both GMX_USE_MODULAR_SIMULATOR=ON and GMX_DISABLE_MODULAR_SIMULATOR=ON. "
 203             "Unset one of the two environment variables to explicitly chose which simulator to "
 204             "use, "
 205             "or unset both to recover default behavior.");
 206
 207     GMX_RELEASE_ASSERT(
 208             !(modularSimulatorExplicitlyTurnedOff && inputrec->eI == IntegrationAlgorithm::VV
 209               && inputrec->epc == PressureCoupling::ParrinelloRahman),
 210             "Cannot use a Parrinello-Rahman barostat with md-vv and "
 211             "GMX_DISABLE_MODULAR_SIMULATOR=ON, "
 212             "as the Parrinello-Rahman barostat is not implemented in the legacy simulator. Unset "
 213             "GMX_DISABLE_MODULAR_SIMULATOR or use a different pressure control algorithm.");
 214
 215     bool isInputCompatible = conditionalAssert(
 216             inputrec->eI == IntegrationAlgorithm::MD || inputrec->eI == IntegrationAlgorithm::VV,
 217             "Only integrators md and md-vv are supported by the modular simulator.");
 218     isInputCompatible = isInputCompatible
 219                         && conditionalAssert(inputrec->eI != IntegrationAlgorithm::MD
 220                                                      || modularSimulatorExplicitlyTurnedOn,
 221                                              "Set GMX_USE_MODULAR_SIMULATOR=ON to use the modular "
 222                                              "simulator with integrator md.");
 223     isInputCompatible =
 224             isInputCompatible
 225             && conditionalAssert(
 226                        !inputrec->useMts,
 227                        "Multiple time stepping is not supported by the modular simulator.");
 228     isInputCompatible =
 229             isInputCompatible
 230             && conditionalAssert(!doRerun, "Rerun is not supported by the modular simulator.");
 231     isInputCompatible = isInputCompatible
 232                         && conditionalAssert(inputrec->etc == TemperatureCoupling::No
 233                                                      || inputrec->etc == TemperatureCoupling::VRescale
 234                                                      || inputrec->etc == TemperatureCoupling::Berendsen,
 235                                              "Only v-rescale and Berendsen thermostat are "
 236                                              "supported by the modular simulator.");
 237     isInputCompatible =
 238             isInputCompatible
 239             && conditionalAssert(
 240                        inputrec->epc == PressureCoupling::No
 241                                || inputrec->epc == PressureCoupling::ParrinelloRahman,
 242                        "Only Parrinello-Rahman barostat is supported by the modular simulator.");
 243     isInputCompatible =
 244             isInputCompatible
 245             && conditionalAssert(
 246                        !(inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec)
 247                          || inputrecNvtTrotter(inputrec)),
 248                        "Legacy Trotter decomposition is not supported by the modular simulator.");
 249     isInputCompatible =
 250             isInputCompatible
 251             && conditionalAssert(inputrec->efep == FreeEnergyPerturbationType::No
 252                                          || inputrec->efep == FreeEnergyPerturbationType::Yes
 253                                          || inputrec->efep == FreeEnergyPerturbationType::SlowGrowth,
 254                                  "Expanded ensemble free energy calculation is not "
 255                                  "supported by the modular simulator.");
 256     isInputCompatible = isInputCompatible
 257                         && conditionalAssert(!inputrec->bPull,
 258                                              "Pulling is not supported by the modular simulator.");
 259     isInputCompatible =
 260             isInputCompatible
 261             && conditionalAssert(inputrec->cos_accel == 0.0,
 262                                  "Acceleration is not supported by the modular simulator.");
 263     isInputCompatible =
 264             isInputCompatible
 265             && conditionalAssert(!inputrecFrozenAtoms(inputrec),
 266                                  "Freeze groups are not supported by the modular simulator.");
 267     isInputCompatible =
 268             isInputCompatible
 269             && conditionalAssert(
 270                        inputrec->deform[XX][XX] == 0.0 && inputrec->deform[XX][YY] == 0.0
 271                                && inputrec->deform[XX][ZZ] == 0.0 && inputrec->deform[YY][XX] == 0.0
 272                                && inputrec->deform[YY][YY] == 0.0 && inputrec->deform[YY][ZZ] == 0.0
 273                                && inputrec->deform[ZZ][XX] == 0.0 && inputrec->deform[ZZ][YY] == 0.0
 274                                && inputrec->deform[ZZ][ZZ] == 0.0,
 275                        "Deformation is not supported by the modular simulator.");
 276     isInputCompatible =
 277             isInputCompatible
 278             && conditionalAssert(gmx_mtop_interaction_count(globalTopology, IF_VSITE) == 0,
 279                                  "Virtual sites are not supported by the modular simulator.");
 280     isInputCompatible = isInputCompatible
 281                         && conditionalAssert(!inputrec->bDoAwh,
 282                                              "AWH is not supported by the modular simulator.");
 283     isInputCompatible =
 284             isInputCompatible
 285             && conditionalAssert(gmx_mtop_ftype_count(globalTopology, F_DISRES) == 0,
 286                                  "Distance restraints are not supported by the modular simulator.");
 287     isInputCompatible =
 288             isInputCompatible
 289             && conditionalAssert(
 290                        gmx_mtop_ftype_count(globalTopology, F_ORIRES) == 0,
 291                        "Orientation restraints are not supported by the modular simulator.");
 292     isInputCompatible =
 293             isInputCompatible
 294             && conditionalAssert(ms == nullptr,
 295                                  "Multi-sim are not supported by the modular simulator.");
 296     isInputCompatible =
 297             isInputCompatible
 298             && conditionalAssert(replExParams.exchangeInterval == 0,
 299                                  "Replica exchange is not supported by the modular simulator.");
 300
 301     int numEnsembleRestraintSystems;
 302     if (fcd)
 303     {
 304         numEnsembleRestraintSystems = fcd->disres->nsystems;
 305     }
 306     else
 307     {
 308         auto distantRestraintEnsembleEnvVar = getenv("GMX_DISRE_ENSEMBLE_SIZE");
 309         numEnsembleRestraintSystems =
 310                 (ms != nullptr && distantRestraintEnsembleEnvVar != nullptr)
 311                         ? static_cast<int>(strtol(distantRestraintEnsembleEnvVar, nullptr, 10))
 312                         : 0;
 313     }
 314     isInputCompatible =
 315             isInputCompatible
 316             && conditionalAssert(numEnsembleRestraintSystems <= 1,
 317                                  "Ensemble restraints are not supported by the modular simulator.");
 318     isInputCompatible =
 319             isInputCompatible
 320             && conditionalAssert(!doSimulatedAnnealing(inputrec),
 321                                  "Simulated annealing is not supported by the modular simulator.");
 322     isInputCompatible =
 323             isInputCompatible
 324             && conditionalAssert(!inputrec->bSimTemp,
 325                                  "Simulated tempering is not supported by the modular simulator.");
 326     isInputCompatible = isInputCompatible
 327                         && conditionalAssert(!inputrec->bExpanded,
 328                                              "Expanded ensemble simulations are not supported by "
 329                                              "the modular simulator.");
 330     isInputCompatible =
 331             isInputCompatible
 332             && conditionalAssert(!doEssentialDynamics,
 333                                  "Essential dynamics is not supported by the modular simulator.");
 334     isInputCompatible = isInputCompatible
 335                         && conditionalAssert(inputrec->eSwapCoords == SwapType::No,
 336                                              "Ion / water position swapping is not supported by "
 337                                              "the modular simulator.");
 338     isInputCompatible =
 339             isInputCompatible
 340             && conditionalAssert(!inputrec->bIMD,
 341                                  "Interactive MD is not supported by the modular simulator.");
 342     isInputCompatible =
 343             isInputCompatible
 344             && conditionalAssert(!doMembed,
 345                                  "Membrane embedding is not supported by the modular simulator.");
 346     // TODO: Change this to the boolean passed when we merge the user interface change for the GPU update.
 347     isInputCompatible =
 348             isInputCompatible
 349             && conditionalAssert(
 350                        getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") == nullptr,
 351                        "Integration on the GPU is not supported by the modular simulator.");
 352     // Modular simulator is centered around NS updates
 353     // TODO: think how to handle nstlist == 0
 354     isInputCompatible = isInputCompatible
 355                         && conditionalAssert(inputrec->nstlist != 0,
 356                                              "Simulations without neighbor list update are not "
 357                                              "supported by the modular simulator.");
 358     isInputCompatible = isInputCompatible
 359                         && conditionalAssert(!GMX_FAHCORE,
 360                                              "GMX_FAHCORE not supported by the modular simulator.");
 361     GMX_RELEASE_ASSERT(
 362             isInputCompatible
 363                     || !(inputrec->eI == IntegrationAlgorithm::VV
 364                          && inputrec->epc == PressureCoupling::ParrinelloRahman),
 365             "Requested Parrinello-Rahman barostat with md-vv, but other options are not compatible "
 366             "with the modular simulator. The Parrinello-Rahman barostat is not implemented for "
 367             "md-vv in the legacy simulator. Use a different pressure control algorithm.");
 368
 369     return isInputCompatible;
 370 }
 371
 372 ModularSimulator::ModularSimulator(std::unique_ptr<LegacySimulatorData>      legacySimulatorData,
 373                                    std::unique_ptr<ReadCheckpointDataHolder> checkpointDataHolder) :
 374     legacySimulatorData_(std::move(legacySimulatorData)),
 375     checkpointDataHolder_(std::move(checkpointDataHolder))
 376 {
 377     checkInputForDisabledFunctionality();
 378 }
 379
 380 void ModularSimulator::checkInputForDisabledFunctionality()
 381 {
 382     isInputCompatible(true,
 383                       legacySimulatorData_->inputrec,
 384                       legacySimulatorData_->mdrunOptions.rerun,
 385                       *legacySimulatorData_->top_global,
 386                       legacySimulatorData_->ms,
 387                       legacySimulatorData_->replExParams,
 388                       legacySimulatorData_->fr->fcdata.get(),
 389                       opt2bSet("-ei", legacySimulatorData_->nfile, legacySimulatorData_->fnm),
 390                       legacySimulatorData_->membed != nullptr);
 391     if (legacySimulatorData_->observablesHistory->edsamHistory)
 392     {
 393         gmx_fatal(FARGS,
 394                   "The checkpoint is from a run with essential dynamics sampling, "
 395                   "but the current run did not specify the -ei option. "
 396                   "Either specify the -ei option to mdrun, or do not use this checkpoint file.");
 397     }
 398 }
 399
 400 void ModularSimulator::readCheckpointToTrxFrame(t_trxframe*               fr,
 401                                                 ReadCheckpointDataHolder* readCheckpointDataHolder,
 402                                                 const CheckpointHeaderContents& checkpointHeaderContents)
 403 {
 404     GMX_RELEASE_ASSERT(checkpointHeaderContents.isModularSimulatorCheckpoint,
 405                        "ModularSimulator::readCheckpointToTrxFrame can only read checkpoints "
 406                        "written by modular simulator.");
 407     fr->bStep = true;
 408     fr->step = int64_to_int(checkpointHeaderContents.step, "conversion of checkpoint to trajectory");
 409     fr->bTime = true;
 410     fr->time  = checkpointHeaderContents.t;
 411
 412     fr->bAtoms = false;
 413
 414     StatePropagatorData::readCheckpointToTrxFrame(
 415             fr, readCheckpointDataHolder->checkpointData(StatePropagatorData::checkpointID()));
 416     if (readCheckpointDataHolder->keyExists(FreeEnergyPerturbationData::checkpointID()))
 417     {
 418         FreeEnergyPerturbationData::readCheckpointToTrxFrame(
 419                 fr, readCheckpointDataHolder->checkpointData(FreeEnergyPerturbationData::checkpointID()));
 420     }
 421     else
 422     {
 423         FreeEnergyPerturbationData::readCheckpointToTrxFrame(fr, std::nullopt);
 424     }
 425 }
 426
 427 } // namespace gmx