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
   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.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  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/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>(-1, UseFullStepKE::No,
 115                                                              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, RegisterWithThermostat::False,
 137                 RegisterWithBarostat::True);
 138         if (legacySimulatorData_->constr)
 139         {
 140             builder->add<ConstraintsElement<ConstraintVariable::Velocities>>();
 141         }
 142         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
 143         builder->add<StatePropagatorData::Element>();
 144         if (legacySimulatorData_->inputrec->etc == etcVRESCALE
 145             || legacySimulatorData_->inputrec->etc == etcBERENDSEN)
 146         {
 147             builder->add<VelocityScalingTemperatureCoupling>(
 148                     0, UseFullStepKE::Yes, ReportPreviousStepConservedEnergy::Yes);
 149         }
 150         builder->add<Propagator<IntegrationStep::VelocityVerletPositionsAndVelocities>>(
 151                 legacySimulatorData_->inputrec->delta_t, RegisterWithThermostat::True,
 152                 RegisterWithBarostat::False);
 153         if (legacySimulatorData_->constr)
 154         {
 155             builder->add<ConstraintsElement<ConstraintVariable::Positions>>();
 156         }
 157         builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
 158         builder->add<EnergyData::Element>();
 159         if (legacySimulatorData_->inputrec->epc == epcPARRINELLORAHMAN)
 160         {
 161             builder->add<ParrinelloRahmanBarostat>(-1);
 162         }
 163     }
 164     else
 165     {
 166         gmx_fatal(FARGS, "Integrator not implemented for the modular simulator.");
 167     }
 168 }
 169
 170 bool ModularSimulator::isInputCompatible(bool                             exitOnFailure,
 171                                          const t_inputrec*                inputrec,
 172                                          bool                             doRerun,
 173                                          const gmx_mtop_t&                globalTopology,
 174                                          const gmx_multisim_t*            ms,
 175                                          const ReplicaExchangeParameters& replExParams,
 176                                          const t_fcdata*                  fcd,
 177                                          bool                             doEssentialDynamics,
 178                                          bool                             doMembed)
 179 {
 180     auto conditionalAssert = [exitOnFailure](bool condition, const char* message) {
 181         if (exitOnFailure)
 182         {
 183             GMX_RELEASE_ASSERT(condition, message);
 184         }
 185         return condition;
 186     };
 187
 188     // GMX_USE_MODULAR_SIMULATOR allows to use modular simulator also for non-standard uses,
 189     // such as the leap-frog integrator
 190     const auto modularSimulatorExplicitlyTurnedOn = (getenv("GMX_USE_MODULAR_SIMULATOR") != nullptr);
 191     // GMX_USE_MODULAR_SIMULATOR allows to use disable modular simulator for all uses,
 192     // including the velocity-verlet integrator used by default
 193     const auto modularSimulatorExplicitlyTurnedOff = (getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
 194
 195     GMX_RELEASE_ASSERT(
 196             !(modularSimulatorExplicitlyTurnedOn && modularSimulatorExplicitlyTurnedOff),
 197             "Cannot have both GMX_USE_MODULAR_SIMULATOR=ON and GMX_DISABLE_MODULAR_SIMULATOR=ON. "
 198             "Unset one of the two environment variables to explicitly chose which simulator to "
 199             "use, "
 200             "or unset both to recover default behavior.");
 201
 202     GMX_RELEASE_ASSERT(
 203             !(modularSimulatorExplicitlyTurnedOff && inputrec->eI == eiVV
 204               && inputrec->epc == epcPARRINELLORAHMAN),
 205             "Cannot use a Parrinello-Rahman barostat with md-vv and "
 206             "GMX_DISABLE_MODULAR_SIMULATOR=ON, "
 207             "as the Parrinello-Rahman barostat is not implemented in the legacy simulator. Unset "
 208             "GMX_DISABLE_MODULAR_SIMULATOR or use a different pressure control algorithm.");
 209
 210     bool isInputCompatible = conditionalAssert(
 211             inputrec->eI == eiMD || inputrec->eI == eiVV,
 212             "Only integrators md and md-vv are supported by the modular simulator.");
 213     isInputCompatible = isInputCompatible
 214                         && conditionalAssert(inputrec->eI != eiMD || modularSimulatorExplicitlyTurnedOn,
 215                                              "Set GMX_USE_MODULAR_SIMULATOR=ON to use the modular "
 216                                              "simulator with integrator md.");
 217     isInputCompatible =
 218             isInputCompatible
 219             && conditionalAssert(!doRerun, "Rerun is not supported by the modular simulator.");
 220     isInputCompatible = isInputCompatible
 221                         && conditionalAssert(inputrec->etc == etcNO || inputrec->etc == etcVRESCALE
 222                                                      || inputrec->etc == etcBERENDSEN,
 223                                              "Only v-rescale and Berendsen thermostat are "
 224                                              "supported by the modular simulator.");
 225     isInputCompatible =
 226             isInputCompatible
 227             && conditionalAssert(
 228                        inputrec->epc == epcNO || inputrec->epc == epcPARRINELLORAHMAN,
 229                        "Only Parrinello-Rahman barostat is supported by the modular simulator.");
 230     isInputCompatible =
 231             isInputCompatible
 232             && conditionalAssert(
 233                        !(inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec)
 234                          || inputrecNvtTrotter(inputrec)),
 235                        "Legacy Trotter decomposition is not supported by the modular simulator.");
 236     isInputCompatible = isInputCompatible
 237                         && conditionalAssert(inputrec->efep == efepNO || inputrec->efep == efepYES
 238                                                      || inputrec->efep == efepSLOWGROWTH,
 239                                              "Expanded ensemble free energy calculation is not "
 240                                              "supported by the modular simulator.");
 241     isInputCompatible = isInputCompatible
 242                         && conditionalAssert(!inputrec->bPull,
 243                                              "Pulling is not supported by the modular simulator.");
 244     isInputCompatible =
 245             isInputCompatible
 246             && conditionalAssert(inputrec->opts.ngacc == 1 && inputrec->opts.acc[0][XX] == 0.0
 247                                          && inputrec->opts.acc[0][YY] == 0.0
 248                                          && inputrec->opts.acc[0][ZZ] == 0.0 && inputrec->cos_accel == 0.0,
 249                                  "Acceleration is not supported by the modular simulator.");
 250     isInputCompatible =
 251             isInputCompatible
 252             && conditionalAssert(inputrec->opts.ngfrz == 1 && inputrec->opts.nFreeze[0][XX] == 0
 253                                          && inputrec->opts.nFreeze[0][YY] == 0
 254                                          && inputrec->opts.nFreeze[0][ZZ] == 0,
 255                                  "Freeze groups are not supported by the modular simulator.");
 256     isInputCompatible =
 257             isInputCompatible
 258             && conditionalAssert(
 259                        inputrec->deform[XX][XX] == 0.0 && inputrec->deform[XX][YY] == 0.0
 260                                && inputrec->deform[XX][ZZ] == 0.0 && inputrec->deform[YY][XX] == 0.0
 261                                && inputrec->deform[YY][YY] == 0.0 && inputrec->deform[YY][ZZ] == 0.0
 262                                && inputrec->deform[ZZ][XX] == 0.0 && inputrec->deform[ZZ][YY] == 0.0
 263                                && inputrec->deform[ZZ][ZZ] == 0.0,
 264                        "Deformation is not supported by the modular simulator.");
 265     isInputCompatible =
 266             isInputCompatible
 267             && conditionalAssert(gmx_mtop_interaction_count(globalTopology, IF_VSITE) == 0,
 268                                  "Virtual sites are not supported by the modular simulator.");
 269     isInputCompatible = isInputCompatible
 270                         && conditionalAssert(!inputrec->bDoAwh,
 271                                              "AWH is not supported by the modular simulator.");
 272     isInputCompatible =
 273             isInputCompatible
 274             && conditionalAssert(gmx_mtop_ftype_count(globalTopology, F_DISRES) == 0,
 275                                  "Distance restraints are not supported by the modular simulator.");
 276     isInputCompatible =
 277             isInputCompatible
 278             && conditionalAssert(
 279                        gmx_mtop_ftype_count(globalTopology, F_ORIRES) == 0,
 280                        "Orientation restraints are not supported by the modular simulator.");
 281     isInputCompatible =
 282             isInputCompatible
 283             && conditionalAssert(ms == nullptr,
 284                                  "Multi-sim are not supported by the modular simulator.");
 285     isInputCompatible =
 286             isInputCompatible
 287             && conditionalAssert(replExParams.exchangeInterval == 0,
 288                                  "Replica exchange is not supported by the modular simulator.");
 289
 290     int numEnsembleRestraintSystems;
 291     if (fcd)
 292     {
 293         numEnsembleRestraintSystems = fcd->disres->nsystems;
 294     }
 295     else
 296     {
 297         auto distantRestraintEnsembleEnvVar = getenv("GMX_DISRE_ENSEMBLE_SIZE");
 298         numEnsembleRestraintSystems =
 299                 (ms != nullptr && distantRestraintEnsembleEnvVar != nullptr)
 300                         ? static_cast<int>(strtol(distantRestraintEnsembleEnvVar, nullptr, 10))
 301                         : 0;
 302     }
 303     isInputCompatible =
 304             isInputCompatible
 305             && conditionalAssert(numEnsembleRestraintSystems <= 1,
 306                                  "Ensemble restraints are not supported by the modular simulator.");
 307     isInputCompatible =
 308             isInputCompatible
 309             && conditionalAssert(!doSimulatedAnnealing(inputrec),
 310                                  "Simulated annealing is not supported by the modular simulator.");
 311     isInputCompatible =
 312             isInputCompatible
 313             && conditionalAssert(!inputrec->bSimTemp,
 314                                  "Simulated tempering is not supported by the modular simulator.");
 315     isInputCompatible = isInputCompatible
 316                         && conditionalAssert(!inputrec->bExpanded,
 317                                              "Expanded ensemble simulations are not supported by "
 318                                              "the modular simulator.");
 319     isInputCompatible =
 320             isInputCompatible
 321             && conditionalAssert(!doEssentialDynamics,
 322                                  "Essential dynamics is not supported by the modular simulator.");
 323     isInputCompatible = isInputCompatible
 324                         && conditionalAssert(inputrec->eSwapCoords == eswapNO,
 325                                              "Ion / water position swapping is not supported by "
 326                                              "the modular simulator.");
 327     isInputCompatible =
 328             isInputCompatible
 329             && conditionalAssert(!inputrec->bIMD,
 330                                  "Interactive MD is not supported by the modular simulator.");
 331     isInputCompatible =
 332             isInputCompatible
 333             && conditionalAssert(!doMembed,
 334                                  "Membrane embedding is not supported by the modular simulator.");
 335     // TODO: Change this to the boolean passed when we merge the user interface change for the GPU update.
 336     isInputCompatible =
 337             isInputCompatible
 338             && conditionalAssert(
 339                        getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") == nullptr,
 340                        "Integration on the GPU is not supported by the modular simulator.");
 341     // Modular simulator is centered around NS updates
 342     // TODO: think how to handle nstlist == 0
 343     isInputCompatible = isInputCompatible
 344                         && conditionalAssert(inputrec->nstlist != 0,
 345                                              "Simulations without neighbor list update are not "
 346                                              "supported by the modular simulator.");
 347     isInputCompatible = isInputCompatible
 348                         && conditionalAssert(!GMX_FAHCORE,
 349                                              "GMX_FAHCORE not supported by the modular simulator.");
 350
 351     return isInputCompatible;
 352 }
 353
 354 ModularSimulator::ModularSimulator(std::unique_ptr<LegacySimulatorData>      legacySimulatorData,
 355                                    std::unique_ptr<ReadCheckpointDataHolder> checkpointDataHolder) :
 356     legacySimulatorData_(std::move(legacySimulatorData)),
 357     checkpointDataHolder_(std::move(checkpointDataHolder))
 358 {
 359     checkInputForDisabledFunctionality();
 360 }
 361
 362 void ModularSimulator::checkInputForDisabledFunctionality()
 363 {
 364     isInputCompatible(true, legacySimulatorData_->inputrec, legacySimulatorData_->mdrunOptions.rerun,
 365                       *legacySimulatorData_->top_global, legacySimulatorData_->ms,
 366                       legacySimulatorData_->replExParams, legacySimulatorData_->fr->fcdata.get(),
 367                       opt2bSet("-ei", legacySimulatorData_->nfile, legacySimulatorData_->fnm),
 368                       legacySimulatorData_->membed != nullptr);
 369     if (legacySimulatorData_->observablesHistory->edsamHistory)
 370     {
 371         gmx_fatal(FARGS,
 372                   "The checkpoint is from a run with essential dynamics sampling, "
 373                   "but the current run did not specify the -ei option. "
 374                   "Either specify the -ei option to mdrun, or do not use this checkpoint file.");
 375     }
 376 }
 377
 378 } // namespace gmx