src/gromacs/modularsimulator/energydata.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  *
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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_->printAverages(fplog_, groups_);
 158     }
 159 }
 160
 161 void EnergyData::Element::trajectoryWriterSetup(gmx_mdoutf* outf)
 162 {
 163     energyData_->setup(outf);
 164 }
 165
 166 void EnergyData::setup(gmx_mdoutf* outf)
 167 {
 168     pull_t* pull_work = nullptr;
 169     energyOutput_     = std::make_unique<EnergyOutput>(
 170             mdoutf_get_fp_ene(outf), top_global_, inputrec_, pull_work, mdoutf_get_fp_dhdl(outf),
 171             false, startingBehavior_, simulationsShareState_, mdModulesNotifier_);
 172
 173     if (!isMasterRank_)
 174     {
 175         return;
 176     }
 177
 178     initializeEnergyHistory(startingBehavior_, observablesHistory_, energyOutput_.get());
 179
 180     // TODO: This probably doesn't really belong here...
 181     //       but we have all we need in this element,
 182     //       so we'll leave it here for now!
 183     double io = compute_io(inputrec_, top_global_->natoms, *groups_, energyOutput_->numEnergyTerms(), 1);
 184     if ((io > 2000) && isMasterRank_)
 185     {
 186         fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 187     }
 188     if (!inputrec_->bContinuation)
 189     {
 190         real temp = enerd_->term[F_TEMP];
 191         if (inputrec_->eI != eiVV)
 192         {
 193             /* Result of Ekin averaged over velocities of -half
 194              * and +half step, while we only have -half step here.
 195              */
 196             temp *= 2;
 197         }
 198         fprintf(fplog_, "Initial temperature: %g K\n", temp);
 199     }
 200 }
 201
 202 std::optional<ITrajectoryWriterCallback> EnergyData::Element::registerTrajectoryWriterCallback(TrajectoryEvent event)
 203 {
 204     if (event == TrajectoryEvent::EnergyWritingStep && isMasterRank_)
 205     {
 206         return [this](gmx_mdoutf* mdoutf, Step step, Time time, bool writeTrajectory, bool writeLog) {
 207             energyData_->write(mdoutf, step, time, writeTrajectory, writeLog);
 208         };
 209     }
 210     return std::nullopt;
 211 }
 212
 213 std::optional<SignallerCallback> EnergyData::Element::registerTrajectorySignallerCallback(gmx::TrajectoryEvent event)
 214 {
 215     if (event == TrajectoryEvent::EnergyWritingStep && isMasterRank_)
 216     {
 217         return [this](Step step, Time /*unused*/) { energyWritingStep_ = step; };
 218     }
 219     return std::nullopt;
 220 }
 221
 222 std::optional<SignallerCallback> EnergyData::Element::registerEnergyCallback(EnergySignallerEvent event)
 223 {
 224     if (event == EnergySignallerEvent::EnergyCalculationStep && isMasterRank_)
 225     {
 226         return [this](Step step, Time /*unused*/) { energyCalculationStep_ = step; };
 227     }
 228     if (event == EnergySignallerEvent::FreeEnergyCalculationStep && isMasterRank_)
 229     {
 230         return [this](Step step, Time /*unused*/) { freeEnergyCalculationStep_ = step; };
 231     }
 232     return std::nullopt;
 233 }
 234
 235 void EnergyData::doStep(Time time, bool isEnergyCalculationStep, bool isFreeEnergyCalculationStep)
 236 {
 237     enerd_->term[F_ETOT] = enerd_->term[F_EPOT] + enerd_->term[F_EKIN];
 238     if (freeEnergyPerturbationData_)
 239     {
 240         accumulateKineticLambdaComponents(enerd_, freeEnergyPerturbationData_->constLambdaView(),
 241                                           *inputrec_->fepvals);
 242     }
 243     if (integratorHasConservedEnergyQuantity(inputrec_))
 244     {
 245         enerd_->term[F_ECONSERVED] =
 246                 enerd_->term[F_ETOT]
 247                 + (velocityScalingTemperatureCoupling_
 248                            ? velocityScalingTemperatureCoupling_->conservedEnergyContribution()
 249                            : 0)
 250                 + (parrinelloRahmanBarostat_ ? parrinelloRahmanBarostat_->conservedEnergyContribution() : 0);
 251     }
 252     matrix nullMatrix = {};
 253     energyOutput_->addDataAtEnergyStep(
 254             isFreeEnergyCalculationStep, isEnergyCalculationStep, time, mdAtoms_->mdatoms()->tmass, enerd_,
 255             inputrec_->fepvals, inputrec_->expandedvals, statePropagatorData_->constPreviousBox(),
 256             PTCouplingArrays({ parrinelloRahmanBarostat_ ? parrinelloRahmanBarostat_->boxVelocities() : nullMatrix,
 257                                {},
 258                                {},
 259                                {},
 260                                {} }),
 261             freeEnergyPerturbationData_ ? freeEnergyPerturbationData_->currentFEPState() : 0,
 262             shakeVirial_, forceVirial_, totalVirial_, pressure_, ekind_, muTot_, constr_);
 263 }
 264
 265 void EnergyData::write(gmx_mdoutf* outf, Step step, Time time, bool writeTrajectory, bool writeLog)
 266 {
 267     if (writeLog)
 268     {
 269         energyOutput_->printHeader(fplog_, step, time);
 270     }
 271
 272     bool do_dr = do_per_step(step, inputrec_->nstdisreout);
 273     bool do_or = do_per_step(step, inputrec_->nstorireout);
 274
 275     // energyOutput_->printAnnealingTemperatures(writeLog ? fplog_ : nullptr, groups_, &(inputrec_->opts));
 276     Awh* awh = nullptr;
 277     energyOutput_->printStepToEnergyFile(mdoutf_get_fp_ene(outf), writeTrajectory, do_dr, do_or,
 278                                          writeLog ? fplog_ : nullptr, step, time, fcd_, awh);
 279 }
 280
 281 void EnergyData::addToForceVirial(const tensor virial, Step step)
 282 {
 283     if (step > forceVirialStep_)
 284     {
 285         forceVirialStep_ = step;
 286         clear_mat(forceVirial_);
 287     }
 288     m_add(forceVirial_, virial, forceVirial_);
 289 }
 290
 291 void EnergyData::addToConstraintVirial(const tensor virial, Step step)
 292 {
 293     if (step > shakeVirialStep_)
 294     {
 295         shakeVirialStep_ = step;
 296         clear_mat(shakeVirial_);
 297     }
 298     m_add(shakeVirial_, virial, shakeVirial_);
 299 }
 300
 301 rvec* EnergyData::forceVirial(Step gmx_unused step)
 302 {
 303     if (step > forceVirialStep_)
 304     {
 305         forceVirialStep_ = step;
 306         clear_mat(forceVirial_);
 307     }
 308     GMX_ASSERT(step >= forceVirialStep_ || forceVirialStep_ == -1,
 309                "Asked for force virial of previous step.");
 310     return forceVirial_;
 311 }
 312
 313 rvec* EnergyData::constraintVirial(Step gmx_unused step)
 314 {
 315     if (step > shakeVirialStep_)
 316     {
 317         shakeVirialStep_ = step;
 318         clear_mat(shakeVirial_);
 319     }
 320     GMX_ASSERT(step >= shakeVirialStep_ || shakeVirialStep_ == -1,
 321                "Asked for constraint virial of previous step.");
 322     return shakeVirial_;
 323 }
 324
 325 rvec* EnergyData::totalVirial(Step gmx_unused step)
 326 {
 327     if (step > totalVirialStep_)
 328     {
 329         totalVirialStep_ = step;
 330         clear_mat(totalVirial_);
 331     }
 332     GMX_ASSERT(step >= totalVirialStep_ || totalVirialStep_ == -1,
 333                "Asked for total virial of previous step.");
 334     return totalVirial_;
 335 }
 336
 337 rvec* EnergyData::pressure(Step gmx_unused step)
 338 {
 339     if (step > pressureStep_)
 340     {
 341         pressureStep_ = step;
 342         clear_mat(pressure_);
 343     }
 344     GMX_ASSERT(step >= pressureStep_ || pressureStep_ == -1,
 345                "Asked for pressure of previous step.");
 346     return pressure_;
 347 }
 348
 349 real* EnergyData::muTot()
 350 {
 351     return muTot_;
 352 }
 353
 354 gmx_enerdata_t* EnergyData::enerdata()
 355 {
 356     return enerd_;
 357 }
 358
 359 gmx_ekindata_t* EnergyData::ekindata()
 360 {
 361     return ekind_;
 362 }
 363
 364 bool* EnergyData::needToSumEkinhOld()
 365 {
 366     return &needToSumEkinhOld_;
 367 }
 368
 369 bool EnergyData::hasReadEkinFromCheckpoint() const
 370 {
 371     return hasReadEkinFromCheckpoint_;
 372 }
 373
 374 namespace
 375 {
 376 /*!
 377  * \brief Enum describing the contents EnergyData::Element writes to modular checkpoint
 378  *
 379  * When changing the checkpoint content, add a new element just above Count, and adjust the
 380  * checkpoint functionality.
 381  */
 382 enum class CheckpointVersion
 383 {
 384     Base, //!< First version of modular checkpointing
 385     Count //!< Number of entries. Add new versions right above this!
 386 };
 387 constexpr auto c_currentVersion = CheckpointVersion(int(CheckpointVersion::Count) - 1);
 388 } // namespace
 389
 390 template<CheckpointDataOperation operation>
 391 void EnergyData::Element::doCheckpointData(CheckpointData<operation>* checkpointData)
 392 {
 393     checkpointVersion(checkpointData, "EnergyData version", c_currentVersion);
 394
 395     energyData_->observablesHistory_->energyHistory->doCheckpoint<operation>(
 396             checkpointData->subCheckpointData("energy history"));
 397     energyData_->ekinstate_.doCheckpoint<operation>(checkpointData->subCheckpointData("ekinstate"));
 398 }
 399
 400 void EnergyData::Element::saveCheckpointState(std::optional<WriteCheckpointData> checkpointData,
 401                                               const t_commrec*                   cr)
 402 {
 403     if (MASTER(cr))
 404     {
 405         if (energyData_->needToSumEkinhOld_)
 406         {
 407             energyData_->ekinstate_.bUpToDate = false;
 408         }
 409         else
 410         {
 411             update_ekinstate(&energyData_->ekinstate_, energyData_->ekind_);
 412             energyData_->ekinstate_.bUpToDate = true;
 413         }
 414         energyData_->energyOutput_->fillEnergyHistory(
 415                 energyData_->observablesHistory_->energyHistory.get());
 416         doCheckpointData<CheckpointDataOperation::Write>(&checkpointData.value());
 417     }
 418 }
 419
 420 void EnergyData::Element::restoreCheckpointState(std::optional<ReadCheckpointData> checkpointData,
 421                                                  const t_commrec*                  cr)
 422 {
 423     if (MASTER(cr))
 424     {
 425         doCheckpointData<CheckpointDataOperation::Read>(&checkpointData.value());
 426     }
 427     energyData_->hasReadEkinFromCheckpoint_ = MASTER(cr) ? energyData_->ekinstate_.bUpToDate : false;
 428     if (PAR(cr))
 429     {
 430         gmx_bcast(sizeof(hasReadEkinFromCheckpoint_), &energyData_->hasReadEkinFromCheckpoint_,
 431                   cr->mpi_comm_mygroup);
 432     }
 433     if (energyData_->hasReadEkinFromCheckpoint_)
 434     {
 435         // this takes care of broadcasting from master to agents
 436         restore_ekinstate_from_state(cr, energyData_->ekind_, &energyData_->ekinstate_);
 437     }
 438 }
 439
 440 const std::string& EnergyData::Element::clientID()
 441 {
 442     return identifier_;
 443 }
 444
 445 void EnergyData::initializeEnergyHistory(StartingBehavior    startingBehavior,
 446                                          ObservablesHistory* observablesHistory,
 447                                          EnergyOutput*       energyOutput)
 448 {
 449     if (startingBehavior != StartingBehavior::NewSimulation)
 450     {
 451         /* Restore from energy history if appending to output files */
 452         if (startingBehavior == StartingBehavior::RestartWithAppending)
 453         {
 454             /* If no history is available (because a checkpoint is from before
 455              * it was written) make a new one later, otherwise restore it.
 456              */
 457             if (observablesHistory->energyHistory)
 458             {
 459                 energyOutput->restoreFromEnergyHistory(*observablesHistory->energyHistory);
 460             }
 461         }
 462         else if (observablesHistory->energyHistory)
 463         {
 464             /* We might have read an energy history from checkpoint.
 465              * As we are not appending, we want to restart the statistics.
 466              * Free the allocated memory and reset the counts.
 467              */
 468             observablesHistory->energyHistory = {};
 469             /* We might have read a pull history from checkpoint.
 470              * We will still want to keep the statistics, so that the files
 471              * can be joined and still be meaningful.
 472              * This means that observablesHistory_->pullHistory
 473              * should not be reset.
 474              */
 475         }
 476     }
 477     if (!observablesHistory->energyHistory)
 478     {
 479         observablesHistory->energyHistory = std::make_unique<energyhistory_t>();
 480     }
 481     if (!observablesHistory->pullHistory)
 482     {
 483         observablesHistory->pullHistory = std::make_unique<PullHistory>();
 484     }
 485     /* Set the initial energy history */
 486     energyOutput->fillEnergyHistory(observablesHistory->energyHistory.get());
 487 }
 488
 489 void EnergyData::setVelocityScalingTemperatureCoupling(const VelocityScalingTemperatureCoupling* velocityScalingTemperatureCoupling)
 490 {
 491     velocityScalingTemperatureCoupling_ = velocityScalingTemperatureCoupling;
 492 }
 493
 494 void EnergyData::setParrinelloRahamnBarostat(const gmx::ParrinelloRahmanBarostat* parrinelloRahmanBarostat)
 495 {
 496     parrinelloRahmanBarostat_ = parrinelloRahmanBarostat;
 497 }
 498
 499 EnergyData::Element* EnergyData::element()
 500 {
 501     return element_.get();
 502 }
 503
 504 EnergyData::Element::Element(EnergyData* energyData, bool isMasterRank) :
 505     energyData_(energyData),
 506     isMasterRank_(isMasterRank),
 507     energyWritingStep_(-1),
 508     energyCalculationStep_(-1),
 509     freeEnergyCalculationStep_(-1)
 510 {
 511 }
 512
 513 ISimulatorElement* EnergyData::Element::getElementPointerImpl(
 514         LegacySimulatorData gmx_unused*        legacySimulatorData,
 515         ModularSimulatorAlgorithmBuilderHelper gmx_unused* builderHelper,
 516         StatePropagatorData gmx_unused* statePropagatorData,
 517         EnergyData*                     energyData,
 518         FreeEnergyPerturbationData gmx_unused* freeEnergyPerturbationData,
 519         GlobalCommunicationHelper gmx_unused* globalCommunicationHelper)
 520 {
 521     return energyData->element();
 522 }
 523
 524 } // namespace gmx