src/gromacs/modularsimulator/modularsimulator.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2019,2020, 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 == eiMD)
 110     {
 111         // The leap frog integration algorithm
 112         builder->add<ForceElement>();
 113         builder->add<StatePropagatorData::Element>();
 114         if (legacySimulatorData_->inputrec->etc == etcVRESCALE
 115             || legacySimulatorData_->inputrec->etc == etcBERENDSEN)
 116         {
 117             builder->add<VelocityScalingTemperatureCoupling>(-1, UseFullStepKE::No,
 118                                                              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 == epcPARRINELLORAHMAN)
 130         {
 131             builder->add<ParrinelloRahmanBarostat>(-1);
 132         }
 133     }
 134     else if (legacySimulatorData_->inputrec->eI == eiVV)
 135     {
 136         // The velocity verlet integration algorithm
 137         builder->add<ForceElement>();
 138         builder->add<Propagator<IntegrationStep::VelocitiesOnly>>(
 139                 0.5 * legacySimulatorData_->inputrec->delta_t, RegisterWithThermostat::False,
 140                 RegisterWithBarostat::True);
 141         if (legacySimulatorData_->constr)
 142         {
 143             builder->add<ConstraintsElement<ConstraintVariable::Velocities>>();
 144         }
 145         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
 146         builder->add<StatePropagatorData::Element>();
 147         if (legacySimulatorData_->inputrec->etc == etcVRESCALE
 148             || legacySimulatorData_->inputrec->etc == etcBERENDSEN)
 149         {
 150             builder->add<VelocityScalingTemperatureCoupling>(
 151                     0, UseFullStepKE::Yes, ReportPreviousStepConservedEnergy::Yes);
 152         }
 153         builder->add<Propagator<IntegrationStep::VelocityVerletPositionsAndVelocities>>(
 154                 legacySimulatorData_->inputrec->delta_t, RegisterWithThermostat::True,
 155                 RegisterWithBarostat::False);
 156         if (legacySimulatorData_->constr)
 157         {
 158             builder->add<ConstraintsElement<ConstraintVariable::Positions>>();
 159         }
 160         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
 161         builder->add<EnergyData::Element>();
 162         if (legacySimulatorData_->inputrec->epc == epcPARRINELLORAHMAN)
 163         {
 164             builder->add<ParrinelloRahmanBarostat>(-1);
 165         }
 166     }
 167     else
 168     {
 169         gmx_fatal(FARGS, "Integrator not implemented for the modular simulator.");
 170     }
 171 }
 172
 173 bool ModularSimulator::isInputCompatible(bool                             exitOnFailure,
 174                                          const t_inputrec*                inputrec,
 175                                          bool                             doRerun,
 176                                          const gmx_mtop_t&                globalTopology,
 177                                          const gmx_multisim_t*            ms,
 178                                          const ReplicaExchangeParameters& replExParams,
 179                                          const t_fcdata*                  fcd,
 180                                          bool                             doEssentialDynamics,
 181                                          bool                             doMembed)
 182 {
 183     auto conditionalAssert = [exitOnFailure](bool condition, const char* message) {
 184         if (exitOnFailure)
 185         {
 186             GMX_RELEASE_ASSERT(condition, message);
 187         }
 188         return condition;
 189     };
 190
 191     // GMX_USE_MODULAR_SIMULATOR allows to use modular simulator also for non-standard uses,
 192     // such as the leap-frog integrator
 193     const auto modularSimulatorExplicitlyTurnedOn = (getenv("GMX_USE_MODULAR_SIMULATOR") != nullptr);
 194     // GMX_USE_MODULAR_SIMULATOR allows to use disable modular simulator for all uses,
 195     // including the velocity-verlet integrator used by default
 196     const auto modularSimulatorExplicitlyTurnedOff = (getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
 197
 198     GMX_RELEASE_ASSERT(
 199             !(modularSimulatorExplicitlyTurnedOn && modularSimulatorExplicitlyTurnedOff),
 200             "Cannot have both GMX_USE_MODULAR_SIMULATOR=ON and GMX_DISABLE_MODULAR_SIMULATOR=ON. "
 201             "Unset one of the two environment variables to explicitly chose which simulator to "
 202             "use, "
 203             "or unset both to recover default behavior.");
 204
 205     GMX_RELEASE_ASSERT(
 206             !(modularSimulatorExplicitlyTurnedOff && inputrec->eI == eiVV
 207               && inputrec->epc == epcPARRINELLORAHMAN),
 208             "Cannot use a Parrinello-Rahman barostat with md-vv and "
 209             "GMX_DISABLE_MODULAR_SIMULATOR=ON, "
 210             "as the Parrinello-Rahman barostat is not implemented in the legacy simulator. Unset "
 211             "GMX_DISABLE_MODULAR_SIMULATOR or use a different pressure control algorithm.");
 212
 213     bool isInputCompatible = conditionalAssert(
 214             inputrec->eI == eiMD || inputrec->eI == eiVV,
 215             "Only integrators md and md-vv are supported by the modular simulator.");
 216     isInputCompatible = isInputCompatible
 217                         && conditionalAssert(inputrec->eI != eiMD || modularSimulatorExplicitlyTurnedOn,
 218                                              "Set GMX_USE_MODULAR_SIMULATOR=ON to use the modular "
 219                                              "simulator with integrator md.");
 220     isInputCompatible =
 221             isInputCompatible
 222             && conditionalAssert(
 223                        !inputrec->useMts,
 224                        "Multiple time stepping is not supported by the modular simulator.");
 225     isInputCompatible =
 226             isInputCompatible
 227             && conditionalAssert(!doRerun, "Rerun is not supported by the modular simulator.");
 228     isInputCompatible = isInputCompatible
 229                         && conditionalAssert(inputrec->etc == etcNO || inputrec->etc == etcVRESCALE
 230                                                      || inputrec->etc == etcBERENDSEN,
 231                                              "Only v-rescale and Berendsen thermostat are "
 232                                              "supported by the modular simulator.");
 233     isInputCompatible =
 234             isInputCompatible
 235             && conditionalAssert(
 236                        inputrec->epc == epcNO || inputrec->epc == epcPARRINELLORAHMAN,
 237                        "Only Parrinello-Rahman barostat is supported by the modular simulator.");
 238     isInputCompatible =
 239             isInputCompatible
 240             && conditionalAssert(
 241                        !(inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec)
 242                          || inputrecNvtTrotter(inputrec)),
 243                        "Legacy Trotter decomposition is not supported by the modular simulator.");
 244     isInputCompatible = isInputCompatible
 245                         && conditionalAssert(inputrec->efep == efepNO || inputrec->efep == efepYES
 246                                                      || inputrec->efep == efepSLOWGROWTH,
 247                                              "Expanded ensemble free energy calculation is not "
 248                                              "supported by the modular simulator.");
 249     isInputCompatible = isInputCompatible
 250                         && conditionalAssert(!inputrec->bPull,
 251                                              "Pulling is not supported by the modular simulator.");
 252     isInputCompatible =
 253             isInputCompatible
 254             && conditionalAssert(inputrec->opts.ngacc == 1 && inputrec->opts.acc[0][XX] == 0.0
 255                                          && inputrec->opts.acc[0][YY] == 0.0
 256                                          && inputrec->opts.acc[0][ZZ] == 0.0 && inputrec->cos_accel == 0.0,
 257                                  "Acceleration is not supported by the modular simulator.");
 258     isInputCompatible =
 259             isInputCompatible
 260             && conditionalAssert(inputrec->opts.ngfrz == 1 && inputrec->opts.nFreeze[0][XX] == 0
 261                                          && inputrec->opts.nFreeze[0][YY] == 0
 262                                          && inputrec->opts.nFreeze[0][ZZ] == 0,
 263                                  "Freeze groups are not supported by the modular simulator.");
 264     isInputCompatible =
 265             isInputCompatible
 266             && conditionalAssert(
 267                        inputrec->deform[XX][XX] == 0.0 && inputrec->deform[XX][YY] == 0.0
 268                                && inputrec->deform[XX][ZZ] == 0.0 && inputrec->deform[YY][XX] == 0.0
 269                                && inputrec->deform[YY][YY] == 0.0 && inputrec->deform[YY][ZZ] == 0.0
 270                                && inputrec->deform[ZZ][XX] == 0.0 && inputrec->deform[ZZ][YY] == 0.0
 271                                && inputrec->deform[ZZ][ZZ] == 0.0,
 272                        "Deformation is not supported by the modular simulator.");
 273     isInputCompatible =
 274             isInputCompatible
 275             && conditionalAssert(gmx_mtop_interaction_count(globalTopology, IF_VSITE) == 0,
 276                                  "Virtual sites are not supported by the modular simulator.");
 277     isInputCompatible = isInputCompatible
 278                         && conditionalAssert(!inputrec->bDoAwh,
 279                                              "AWH is not supported by the modular simulator.");
 280     isInputCompatible =
 281             isInputCompatible
 282             && conditionalAssert(gmx_mtop_ftype_count(globalTopology, F_DISRES) == 0,
 283                                  "Distance restraints are not supported by the modular simulator.");
 284     isInputCompatible =
 285             isInputCompatible
 286             && conditionalAssert(
 287                        gmx_mtop_ftype_count(globalTopology, F_ORIRES) == 0,
 288                        "Orientation restraints are not supported by the modular simulator.");
 289     isInputCompatible =
 290             isInputCompatible
 291             && conditionalAssert(ms == nullptr,
 292                                  "Multi-sim are not supported by the modular simulator.");
 293     isInputCompatible =
 294             isInputCompatible
 295             && conditionalAssert(replExParams.exchangeInterval == 0,
 296                                  "Replica exchange is not supported by the modular simulator.");
 297
 298     int numEnsembleRestraintSystems;
 299     if (fcd)
 300     {
 301         numEnsembleRestraintSystems = fcd->disres->nsystems;
 302     }
 303     else
 304     {
 305         auto distantRestraintEnsembleEnvVar = getenv("GMX_DISRE_ENSEMBLE_SIZE");
 306         numEnsembleRestraintSystems =
 307                 (ms != nullptr && distantRestraintEnsembleEnvVar != nullptr)
 308                         ? static_cast<int>(strtol(distantRestraintEnsembleEnvVar, nullptr, 10))
 309                         : 0;
 310     }
 311     isInputCompatible =
 312             isInputCompatible
 313             && conditionalAssert(numEnsembleRestraintSystems <= 1,
 314                                  "Ensemble restraints are not supported by the modular simulator.");
 315     isInputCompatible =
 316             isInputCompatible
 317             && conditionalAssert(!doSimulatedAnnealing(inputrec),
 318                                  "Simulated annealing is not supported by the modular simulator.");
 319     isInputCompatible =
 320             isInputCompatible
 321             && conditionalAssert(!inputrec->bSimTemp,
 322                                  "Simulated tempering is not supported by the modular simulator.");
 323     isInputCompatible = isInputCompatible
 324                         && conditionalAssert(!inputrec->bExpanded,
 325                                              "Expanded ensemble simulations are not supported by "
 326                                              "the modular simulator.");
 327     isInputCompatible =
 328             isInputCompatible
 329             && conditionalAssert(!doEssentialDynamics,
 330                                  "Essential dynamics is not supported by the modular simulator.");
 331     isInputCompatible = isInputCompatible
 332                         && conditionalAssert(inputrec->eSwapCoords == eswapNO,
 333                                              "Ion / water position swapping is not supported by "
 334                                              "the modular simulator.");
 335     isInputCompatible =
 336             isInputCompatible
 337             && conditionalAssert(!inputrec->bIMD,
 338                                  "Interactive MD is not supported by the modular simulator.");
 339     isInputCompatible =
 340             isInputCompatible
 341             && conditionalAssert(!doMembed,
 342                                  "Membrane embedding is not supported by the modular simulator.");
 343     // TODO: Change this to the boolean passed when we merge the user interface change for the GPU update.
 344     isInputCompatible =
 345             isInputCompatible
 346             && conditionalAssert(
 347                        getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") == nullptr,
 348                        "Integration on the GPU is not supported by the modular simulator.");
 349     // Modular simulator is centered around NS updates
 350     // TODO: think how to handle nstlist == 0
 351     isInputCompatible = isInputCompatible
 352                         && conditionalAssert(inputrec->nstlist != 0,
 353                                              "Simulations without neighbor list update are not "
 354                                              "supported by the modular simulator.");
 355     isInputCompatible = isInputCompatible
 356                         && conditionalAssert(!GMX_FAHCORE,
 357                                              "GMX_FAHCORE not supported by the modular simulator.");
 358     GMX_RELEASE_ASSERT(
 359             isInputCompatible || !(inputrec->eI == eiVV && inputrec->epc == epcPARRINELLORAHMAN),
 360             "Requested Parrinello-Rahman barostat with md-vv, but other options are not compatible "
 361             "with the modular simulator. The Parrinello-Rahman barostat is not implemented for "
 362             "md-vv in the legacy simulator. Use a different pressure control algorithm.");
 363
 364     return isInputCompatible;
 365 }
 366
 367 ModularSimulator::ModularSimulator(std::unique_ptr<LegacySimulatorData>      legacySimulatorData,
 368                                    std::unique_ptr<ReadCheckpointDataHolder> checkpointDataHolder) :
 369     legacySimulatorData_(std::move(legacySimulatorData)),
 370     checkpointDataHolder_(std::move(checkpointDataHolder))
 371 {
 372     checkInputForDisabledFunctionality();
 373 }
 374
 375 void ModularSimulator::checkInputForDisabledFunctionality()
 376 {
 377     isInputCompatible(true, legacySimulatorData_->inputrec, legacySimulatorData_->mdrunOptions.rerun,
 378                       *legacySimulatorData_->top_global, legacySimulatorData_->ms,
 379                       legacySimulatorData_->replExParams, legacySimulatorData_->fr->fcdata.get(),
 380                       opt2bSet("-ei", legacySimulatorData_->nfile, legacySimulatorData_->fnm),
 381                       legacySimulatorData_->membed != nullptr);
 382     if (legacySimulatorData_->observablesHistory->edsamHistory)
 383     {
 384         gmx_fatal(FARGS,
 385                   "The checkpoint is from a run with essential dynamics sampling, "
 386                   "but the current run did not specify the -ei option. "
 387                   "Either specify the -ei option to mdrun, or do not use this checkpoint file.");
 388     }
 389 }
 390
 391 void ModularSimulator::readCheckpointToTrxFrame(t_trxframe*               fr,
 392                                                 ReadCheckpointDataHolder* readCheckpointDataHolder,
 393                                                 const CheckpointHeaderContents& checkpointHeaderContents)
 394 {
 395     GMX_RELEASE_ASSERT(checkpointHeaderContents.isModularSimulatorCheckpoint,
 396                        "ModularSimulator::readCheckpointToTrxFrame can only read checkpoints "
 397                        "written by modular simulator.");
 398     fr->bStep = true;
 399     fr->step =
 400             int64_to_int(checkpointHeaderContents.step, "conversion of checkpoint to trajectory");
 401     fr->bTime = true;
 402     fr->time  = checkpointHeaderContents.t;
 403
 404     fr->bAtoms = false;
 405
 406     StatePropagatorData::readCheckpointToTrxFrame(
 407             fr, readCheckpointDataHolder->checkpointData(StatePropagatorData::checkpointID()));
 408     if (readCheckpointDataHolder->keyExists(FreeEnergyPerturbationData::checkpointID()))
 409     {
 410         FreeEnergyPerturbationData::readCheckpointToTrxFrame(
 411                 fr, readCheckpointDataHolder->checkpointData(FreeEnergyPerturbationData::checkpointID()));
 412     }
 413     else
 414     {
 415         FreeEnergyPerturbationData::readCheckpointToTrxFrame(fr, std::nullopt);
 416     }
 417 }
 418
 419 } // namespace gmx