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