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