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