src/gromacs/modularsimulator/energydata.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
   7  * top-level source directory and at http://www.gromacs.org.
   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 microstate for 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 "energydata.h"
  45
  46 #include "gromacs/gmxlib/network.h"
  47 #include "gromacs/math/vec.h"
  48 #include "gromacs/mdlib/compute_io.h"
  49 #include "gromacs/mdlib/coupling.h"
  50 #include "gromacs/mdlib/enerdata_utils.h"
  51 #include "gromacs/mdlib/energyoutput.h"
  52 #include "gromacs/mdlib/mdatoms.h"
  53 #include "gromacs/mdlib/mdoutf.h"
  54 #include "gromacs/mdlib/stat.h"
  55 #include "gromacs/mdlib/update.h"
  56 #include "gromacs/mdrunutility/handlerestart.h"
  57 #include "gromacs/mdtypes/checkpointdata.h"
  58 #include "gromacs/mdtypes/commrec.h"
  59 #include "gromacs/mdtypes/enerdata.h"
  60 #include "gromacs/mdtypes/energyhistory.h"
  61 #include "gromacs/mdtypes/inputrec.h"
  62 #include "gromacs/mdtypes/mdatom.h"
  63 #include "gromacs/mdtypes/observableshistory.h"
  64 #include "gromacs/mdtypes/pullhistory.h"
  65 #include "gromacs/topology/topology.h"
  66
  67 #include "freeenergyperturbationdata.h"
  68 #include "modularsimulator.h"
  69 #include "parrinellorahmanbarostat.h"
  70 #include "simulatoralgorithm.h"
  71 #include "statepropagatordata.h"
  72 #include "velocityscalingtemperaturecoupling.h"
  73
  74 struct pull_t;
  75 class t_state;
  76
  77 namespace gmx
  78 {
  79 class Awh;
  80
  81 EnergyData::EnergyData(StatePropagatorData*        statePropagatorData,
  82                        FreeEnergyPerturbationData* freeEnergyPerturbationData,
  83                        const gmx_mtop_t*           globalTopology,
  84                        const t_inputrec*           inputrec,
  85                        const MDAtoms*              mdAtoms,
  86                        gmx_enerdata_t*             enerd,
  87                        gmx_ekindata_t*             ekind,
  88                        const Constraints*          constr,
  89                        FILE*                       fplog,
  90                        t_fcdata*                   fcd,
  91                        const MdModulesNotifier&    mdModulesNotifier,
  92                        bool                        isMasterRank,
  93                        ObservablesHistory*         observablesHistory,
  94                        StartingBehavior            startingBehavior,
  95                        bool                        simulationsShareState) :
  96     element_(std::make_unique<Element>(this, isMasterRank)),
  97     isMasterRank_(isMasterRank),
  98     forceVirialStep_(-1),
  99     shakeVirialStep_(-1),
 100     totalVirialStep_(-1),
 101     pressureStep_(-1),
 102     needToSumEkinhOld_(false),
 103     hasReadEkinFromCheckpoint_(false),
 104     startingBehavior_(startingBehavior),
 105     statePropagatorData_(statePropagatorData),
 106     freeEnergyPerturbationData_(freeEnergyPerturbationData),
 107     velocityScalingTemperatureCoupling_(nullptr),
 108     parrinelloRahmanBarostat_(nullptr),
 109     inputrec_(inputrec),
 110     top_global_(globalTopology),
 111     mdAtoms_(mdAtoms),
 112     enerd_(enerd),
 113     ekind_(ekind),
 114     constr_(constr),
 115     fplog_(fplog),
 116     fcd_(fcd),
 117     mdModulesNotifier_(mdModulesNotifier),
 118     groups_(&globalTopology->groups),
 119     observablesHistory_(observablesHistory),
 120     simulationsShareState_(simulationsShareState)
 121 {
 122     clear_mat(forceVirial_);
 123     clear_mat(shakeVirial_);
 124     clear_mat(totalVirial_);
 125     clear_mat(pressure_);
 126     clear_rvec(muTot_);
 127
 128     init_ekinstate(&ekinstate_, inputrec_);
 129     observablesHistory_->energyHistory = std::make_unique<energyhistory_t>();
 130 }
 131
 132 void EnergyData::Element::scheduleTask(Step step, Time time, const RegisterRunFunction& registerRunFunction)
 133 {
 134     if (!isMasterRank_)
 135     {
 136         return;
 137     }
 138     auto writeEnergy                 = energyWritingStep_ == step;
 139     auto isEnergyCalculationStep     = energyCalculationStep_ == step;
 140     auto isFreeEnergyCalculationStep = freeEnergyCalculationStep_ == step;
 141     if (isEnergyCalculationStep || writeEnergy)
 142     {
 143         registerRunFunction([this, time, isEnergyCalculationStep, isFreeEnergyCalculationStep]() {
 144             energyData_->doStep(time, isEnergyCalculationStep, isFreeEnergyCalculationStep);
 145         });
 146     }
 147     else
 148     {
 149         registerRunFunction([this]() { energyData_->energyOutput_->recordNonEnergyStep(); });
 150     }
 151 }
 152
 153 void EnergyData::teardown()
 154 {
 155     if (inputrec_->nstcalcenergy > 0 && isMasterRank_)
 156     {
 157         energyOutput_->printEnergyConservation(fplog_, inputrec_->simulation_part, EI_MD(inputrec_->eI));
 158         energyOutput_->printAverages(fplog_, groups_);
 159     }
 160 }
 161
 162 void EnergyData::Element::trajectoryWriterSetup(gmx_mdoutf* outf)
 163 {
 164     energyData_->setup(outf);
 165 }
 166
 167 void EnergyData::setup(gmx_mdoutf* outf)
 168 {
 169     pull_t* pull_work = nullptr;
 170     energyOutput_     = std::make_unique<EnergyOutput>(mdoutf_get_fp_ene(outf),
 171                                                    *top_global_,
 172                                                    *inputrec_,
 173                                                    pull_work,
 174                                                    mdoutf_get_fp_dhdl(outf),
 175                                                    false,
 176                                                    startingBehavior_,
 177                                                    simulationsShareState_,
 178                                                    mdModulesNotifier_);
 179
 180     if (!isMasterRank_)
 181     {
 182         return;
 183     }
 184
 185     initializeEnergyHistory(startingBehavior_, observablesHistory_, energyOutput_.get());
 186
 187     // TODO: This probably doesn't really belong here...
 188     //       but we have all we need in this element,
 189     //       so we'll leave it here for now!
 190     double io = compute_io(inputrec_, top_global_->natoms, *groups_, energyOutput_->numEnergyTerms(), 1);
 191     if ((io > 2000) && isMasterRank_)
 192     {
 193         fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 194     }
 195     if (!inputrec_->bContinuation)
 196     {
 197         real temp = enerd_->term[F_TEMP];
 198         if (inputrec_->eI != IntegrationAlgorithm::VV)
 199         {
 200             /* Result of Ekin averaged over velocities of -half
 201              * and +half step, while we only have -half step here.
 202              */
 203             temp *= 2;
 204         }
 205         fprintf(fplog_, "Initial temperature: %g K\n", temp);
 206     }
 207 }
 208
 209 std::optional<ITrajectoryWriterCallback> EnergyData::Element::registerTrajectoryWriterCallback(TrajectoryEvent event)
 210 {
 211     if (event == TrajectoryEvent::EnergyWritingStep && isMasterRank_)
 212     {
 213         return [this](gmx_mdoutf* mdoutf, Step step, Time time, bool writeTrajectory, bool writeLog) {
 214             energyData_->write(mdoutf, step, time, writeTrajectory, writeLog);
 215         };
 216     }
 217     return std::nullopt;
 218 }
 219
 220 std::optional<SignallerCallback> EnergyData::Element::registerTrajectorySignallerCallback(gmx::TrajectoryEvent event)
 221 {
 222     if (event == TrajectoryEvent::EnergyWritingStep && isMasterRank_)
 223     {
 224         return [this](Step step, Time /*unused*/) { energyWritingStep_ = step; };
 225     }
 226     return std::nullopt;
 227 }
 228
 229 std::optional<SignallerCallback> EnergyData::Element::registerEnergyCallback(EnergySignallerEvent event)
 230 {
 231     if (event == EnergySignallerEvent::EnergyCalculationStep && isMasterRank_)
 232     {
 233         return [this](Step step, Time /*unused*/) { energyCalculationStep_ = step; };
 234     }
 235     if (event == EnergySignallerEvent::FreeEnergyCalculationStep && isMasterRank_)
 236     {
 237         return [this](Step step, Time /*unused*/) { freeEnergyCalculationStep_ = step; };
 238     }
 239     return std::nullopt;
 240 }
 241
 242 void EnergyData::doStep(Time time, bool isEnergyCalculationStep, bool isFreeEnergyCalculationStep)
 243 {
 244     enerd_->term[F_ETOT] = enerd_->term[F_EPOT] + enerd_->term[F_EKIN];
 245     if (freeEnergyPerturbationData_)
 246     {
 247         accumulateKineticLambdaComponents(
 248                 enerd_, freeEnergyPerturbationData_->constLambdaView(), *inputrec_->fepvals);
 249     }
 250     if (integratorHasConservedEnergyQuantity(inputrec_))
 251     {
 252         enerd_->term[F_ECONSERVED] =
 253                 enerd_->term[F_ETOT]
 254                 + (velocityScalingTemperatureCoupling_
 255                            ? velocityScalingTemperatureCoupling_->conservedEnergyContribution()
 256                            : 0)
 257                 + (parrinelloRahmanBarostat_ ? parrinelloRahmanBarostat_->conservedEnergyContribution() : 0);
 258     }
 259     matrix nullMatrix = {};
 260     energyOutput_->addDataAtEnergyStep(
 261             isFreeEnergyCalculationStep,
 262             isEnergyCalculationStep,
 263             time,
 264             mdAtoms_->mdatoms()->tmass,
 265             enerd_,
 266             inputrec_->fepvals.get(),
 267             inputrec_->expandedvals.get(),
 268             statePropagatorData_->constPreviousBox(),
 269             PTCouplingArrays({ parrinelloRahmanBarostat_ ? parrinelloRahmanBarostat_->boxVelocities() : nullMatrix,
 270                                {},
 271                                {},
 272                                {},
 273                                {} }),
 274             freeEnergyPerturbationData_ ? freeEnergyPerturbationData_->currentFEPState() : 0,
 275             shakeVirial_,
 276             forceVirial_,
 277             totalVirial_,
 278             pressure_,
 279             ekind_,
 280             muTot_,
 281             constr_);
 282 }
 283
 284 void EnergyData::write(gmx_mdoutf* outf, Step step, Time time, bool writeTrajectory, bool writeLog)
 285 {
 286     if (writeLog)
 287     {
 288         energyOutput_->printHeader(fplog_, step, time);
 289     }
 290
 291     bool do_dr = do_per_step(step, inputrec_->nstdisreout);
 292     bool do_or = do_per_step(step, inputrec_->nstorireout);
 293
 294     // energyOutput_->printAnnealingTemperatures(writeLog ? fplog_ : nullptr, groups_, &(inputrec_->opts));
 295     Awh* awh = nullptr;
 296     energyOutput_->printStepToEnergyFile(
 297             mdoutf_get_fp_ene(outf), writeTrajectory, do_dr, do_or, writeLog ? fplog_ : nullptr, step, time, fcd_, awh);
 298 }
 299
 300 void EnergyData::addToForceVirial(const tensor virial, Step step)
 301 {
 302     if (step > forceVirialStep_)
 303     {
 304         forceVirialStep_ = step;
 305         clear_mat(forceVirial_);
 306     }
 307     m_add(forceVirial_, virial, forceVirial_);
 308 }
 309
 310 void EnergyData::addToConstraintVirial(const tensor virial, Step step)
 311 {
 312     if (step > shakeVirialStep_)
 313     {
 314         shakeVirialStep_ = step;
 315         clear_mat(shakeVirial_);
 316     }
 317     m_add(shakeVirial_, virial, shakeVirial_);
 318 }
 319
 320 rvec* EnergyData::forceVirial(Step gmx_unused step)
 321 {
 322     if (step > forceVirialStep_)
 323     {
 324         forceVirialStep_ = step;
 325         clear_mat(forceVirial_);
 326     }
 327     GMX_ASSERT(step >= forceVirialStep_ || forceVirialStep_ == -1,
 328                "Asked for force virial of previous step.");
 329     return forceVirial_;
 330 }
 331
 332 rvec* EnergyData::constraintVirial(Step gmx_unused step)
 333 {
 334     if (step > shakeVirialStep_)
 335     {
 336         shakeVirialStep_ = step;
 337         clear_mat(shakeVirial_);
 338     }
 339     GMX_ASSERT(step >= shakeVirialStep_ || shakeVirialStep_ == -1,
 340                "Asked for constraint virial of previous step.");
 341     return shakeVirial_;
 342 }
 343
 344 rvec* EnergyData::totalVirial(Step gmx_unused step)
 345 {
 346     if (step > totalVirialStep_)
 347     {
 348         totalVirialStep_ = step;
 349         clear_mat(totalVirial_);
 350     }
 351     GMX_ASSERT(step >= totalVirialStep_ || totalVirialStep_ == -1,
 352                "Asked for total virial of previous step.");
 353     return totalVirial_;
 354 }
 355
 356 rvec* EnergyData::pressure(Step gmx_unused step)
 357 {
 358     if (step > pressureStep_)
 359     {
 360         pressureStep_ = step;
 361         clear_mat(pressure_);
 362     }
 363     GMX_ASSERT(step >= pressureStep_ || pressureStep_ == -1, "Asked for pressure of previous step.");
 364     return pressure_;
 365 }
 366
 367 real* EnergyData::muTot()
 368 {
 369     return muTot_;
 370 }
 371
 372 gmx_enerdata_t* EnergyData::enerdata()
 373 {
 374     return enerd_;
 375 }
 376
 377 gmx_ekindata_t* EnergyData::ekindata()
 378 {
 379     return ekind_;
 380 }
 381
 382 bool* EnergyData::needToSumEkinhOld()
 383 {
 384     return &needToSumEkinhOld_;
 385 }
 386
 387 bool EnergyData::hasReadEkinFromCheckpoint() const
 388 {
 389     return hasReadEkinFromCheckpoint_;
 390 }
 391
 392 namespace
 393 {
 394 /*!
 395  * \brief Enum describing the contents EnergyData::Element writes to modular checkpoint
 396  *
 397  * When changing the checkpoint content, add a new element just above Count, and adjust the
 398  * checkpoint functionality.
 399  */
 400 enum class CheckpointVersion
 401 {
 402     Base, //!< First version of modular checkpointing
 403     Count //!< Number of entries. Add new versions right above this!
 404 };
 405 constexpr auto c_currentVersion = CheckpointVersion(int(CheckpointVersion::Count) - 1);
 406 } // namespace
 407
 408 template<CheckpointDataOperation operation>
 409 void EnergyData::Element::doCheckpointData(CheckpointData<operation>* checkpointData)
 410 {
 411     checkpointVersion(checkpointData, "EnergyData version", c_currentVersion);
 412
 413     energyData_->observablesHistory_->energyHistory->doCheckpoint<operation>(
 414             checkpointData->subCheckpointData("energy history"));
 415     energyData_->ekinstate_.doCheckpoint<operation>(checkpointData->subCheckpointData("ekinstate"));
 416 }
 417
 418 void EnergyData::Element::saveCheckpointState(std::optional<WriteCheckpointData> checkpointData,
 419                                               const t_commrec*                   cr)
 420 {
 421     if (MASTER(cr))
 422     {
 423         if (energyData_->needToSumEkinhOld_)
 424         {
 425             energyData_->ekinstate_.bUpToDate = false;
 426         }
 427         else
 428         {
 429             update_ekinstate(&energyData_->ekinstate_, energyData_->ekind_);
 430             energyData_->ekinstate_.bUpToDate = true;
 431         }
 432         energyData_->energyOutput_->fillEnergyHistory(
 433                 energyData_->observablesHistory_->energyHistory.get());
 434         doCheckpointData<CheckpointDataOperation::Write>(&checkpointData.value());
 435     }
 436 }
 437
 438 void EnergyData::Element::restoreCheckpointState(std::optional<ReadCheckpointData> checkpointData,
 439                                                  const t_commrec*                  cr)
 440 {
 441     if (MASTER(cr))
 442     {
 443         doCheckpointData<CheckpointDataOperation::Read>(&checkpointData.value());
 444     }
 445     energyData_->hasReadEkinFromCheckpoint_ = MASTER(cr) ? energyData_->ekinstate_.bUpToDate : false;
 446     if (PAR(cr))
 447     {
 448         gmx_bcast(sizeof(hasReadEkinFromCheckpoint_),
 449                   &energyData_->hasReadEkinFromCheckpoint_,
 450                   cr->mpi_comm_mygroup);
 451     }
 452     if (energyData_->hasReadEkinFromCheckpoint_)
 453     {
 454         // this takes care of broadcasting from master to agents
 455         restore_ekinstate_from_state(cr, energyData_->ekind_, &energyData_->ekinstate_);
 456     }
 457 }
 458
 459 const std::string& EnergyData::Element::clientID()
 460 {
 461     return identifier_;
 462 }
 463
 464 void EnergyData::initializeEnergyHistory(StartingBehavior    startingBehavior,
 465                                          ObservablesHistory* observablesHistory,
 466                                          EnergyOutput*       energyOutput)
 467 {
 468     if (startingBehavior != StartingBehavior::NewSimulation)
 469     {
 470         /* Restore from energy history if appending to output files */
 471         if (startingBehavior == StartingBehavior::RestartWithAppending)
 472         {
 473             /* If no history is available (because a checkpoint is from before
 474              * it was written) make a new one later, otherwise restore it.
 475              */
 476             if (observablesHistory->energyHistory)
 477             {
 478                 energyOutput->restoreFromEnergyHistory(*observablesHistory->energyHistory);
 479             }
 480         }
 481         else if (observablesHistory->energyHistory)
 482         {
 483             /* We might have read an energy history from checkpoint.
 484              * As we are not appending, we want to restart the statistics.
 485              * Free the allocated memory and reset the counts.
 486              */
 487             observablesHistory->energyHistory = {};
 488             /* We might have read a pull history from checkpoint.
 489              * We will still want to keep the statistics, so that the files
 490              * can be joined and still be meaningful.
 491              * This means that observablesHistory_->pullHistory
 492              * should not be reset.
 493              */
 494         }
 495     }
 496     if (!observablesHistory->energyHistory)
 497     {
 498         observablesHistory->energyHistory = std::make_unique<energyhistory_t>();
 499     }
 500     if (!observablesHistory->pullHistory)
 501     {
 502         observablesHistory->pullHistory = std::make_unique<PullHistory>();
 503     }
 504     /* Set the initial energy history */
 505     energyOutput->fillEnergyHistory(observablesHistory->energyHistory.get());
 506 }
 507
 508 void EnergyData::setVelocityScalingTemperatureCoupling(const VelocityScalingTemperatureCoupling* velocityScalingTemperatureCoupling)
 509 {
 510     velocityScalingTemperatureCoupling_ = velocityScalingTemperatureCoupling;
 511 }
 512
 513 void EnergyData::setParrinelloRahamnBarostat(const gmx::ParrinelloRahmanBarostat* parrinelloRahmanBarostat)
 514 {
 515     parrinelloRahmanBarostat_ = parrinelloRahmanBarostat;
 516 }
 517
 518 EnergyData::Element* EnergyData::element()
 519 {
 520     return element_.get();
 521 }
 522
 523 EnergyData::Element::Element(EnergyData* energyData, bool isMasterRank) :
 524     energyData_(energyData),
 525     isMasterRank_(isMasterRank),
 526     energyWritingStep_(-1),
 527     energyCalculationStep_(-1),
 528     freeEnergyCalculationStep_(-1)
 529 {
 530 }
 531
 532 ISimulatorElement* EnergyData::Element::getElementPointerImpl(
 533         LegacySimulatorData gmx_unused*        legacySimulatorData,
 534         ModularSimulatorAlgorithmBuilderHelper gmx_unused* builderHelper,
 535         StatePropagatorData gmx_unused* statePropagatorData,
 536         EnergyData*                     energyData,
 537         FreeEnergyPerturbationData gmx_unused* freeEnergyPerturbationData,
 538         GlobalCommunicationHelper gmx_unused* globalCommunicationHelper)
 539 {
 540     return energyData->element();
 541 }
 542
 543 } // namespace gmx