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