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36 * \brief Defines the microstate for the modular simulator
38 * \author Pascal Merz <pascal.merz@me.com>
39 * \ingroup module_modularsimulator
44 #include "energydata.h"
46 #include "gromacs/gmxlib/network.h"
47 #include "gromacs/math/vec.h"
48 #include "gromacs/mdlib/compute_io.h"
49 #include "gromacs/mdlib/enerdata_utils.h"
50 #include "gromacs/mdlib/energyoutput.h"
51 #include "gromacs/mdlib/mdatoms.h"
52 #include "gromacs/mdlib/mdoutf.h"
53 #include "gromacs/mdlib/stat.h"
54 #include "gromacs/mdlib/update.h"
55 #include "gromacs/mdtypes/commrec.h"
56 #include "gromacs/mdtypes/enerdata.h"
57 #include "gromacs/mdtypes/energyhistory.h"
58 #include "gromacs/mdtypes/inputrec.h"
59 #include "gromacs/mdtypes/mdatom.h"
60 #include "gromacs/mdtypes/observableshistory.h"
61 #include "gromacs/mdtypes/pullhistory.h"
62 #include "gromacs/topology/topology.h"
64 #include "freeenergyperturbationdata.h"
65 #include "modularsimulator.h"
66 #include "simulatoralgorithm.h"
67 #include "statepropagatordata.h"
76 EnergyData::EnergyData(StatePropagatorData* statePropagatorData,
77 FreeEnergyPerturbationData* freeEnergyPerturbationData,
78 const gmx_mtop_t& globalTopology,
79 const t_inputrec* inputrec,
80 const MDAtoms* mdAtoms,
81 gmx_enerdata_t* enerd,
82 gmx_ekindata_t* ekind,
83 const Constraints* constr,
86 const MdModulesNotifier& mdModulesNotifier,
88 ObservablesHistory* observablesHistory,
89 StartingBehavior startingBehavior,
90 bool simulationsShareState) :
91 element_(std::make_unique<Element>(this, isMasterRank)),
92 isMasterRank_(isMasterRank),
97 needToSumEkinhOld_(false),
98 hasReadEkinFromCheckpoint_(false),
99 startingBehavior_(startingBehavior),
100 statePropagatorData_(statePropagatorData),
101 freeEnergyPerturbationData_(freeEnergyPerturbationData),
103 top_global_(globalTopology),
110 mdModulesNotifier_(mdModulesNotifier),
111 groups_(&globalTopology.groups),
112 observablesHistory_(observablesHistory),
113 simulationsShareState_(simulationsShareState)
115 clear_mat(forceVirial_);
116 clear_mat(shakeVirial_);
117 clear_mat(totalVirial_);
118 clear_mat(pressure_);
121 init_ekinstate(&ekinstate_, inputrec_);
122 observablesHistory_->energyHistory = std::make_unique<energyhistory_t>();
125 void EnergyData::Element::scheduleTask(Step step, Time time, const RegisterRunFunction& registerRunFunction)
131 auto writeEnergy = energyWritingStep_ == step;
132 auto isEnergyCalculationStep = energyCalculationStep_ == step;
133 auto isFreeEnergyCalculationStep = freeEnergyCalculationStep_ == step;
134 if (isEnergyCalculationStep || writeEnergy)
136 registerRunFunction([this, step, time, isEnergyCalculationStep, isFreeEnergyCalculationStep]() {
137 energyData_->doStep(step, time, isEnergyCalculationStep, isFreeEnergyCalculationStep);
142 registerRunFunction([this]() { energyData_->energyOutput_->recordNonEnergyStep(); });
146 void EnergyData::teardown()
148 if (inputrec_->nstcalcenergy > 0 && isMasterRank_)
150 energyOutput_->printEnergyConservation(fplog_, inputrec_->simulation_part, EI_MD(inputrec_->eI));
151 energyOutput_->printAverages(fplog_, groups_);
155 void EnergyData::Element::trajectoryWriterSetup(gmx_mdoutf* outf)
157 energyData_->setup(outf);
160 void EnergyData::setup(gmx_mdoutf* outf)
162 pull_t* pull_work = nullptr;
163 energyOutput_ = std::make_unique<EnergyOutput>(mdoutf_get_fp_ene(outf),
167 mdoutf_get_fp_dhdl(outf),
170 simulationsShareState_,
178 initializeEnergyHistory(startingBehavior_, observablesHistory_, energyOutput_.get());
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_)
186 fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
188 if (!inputrec_->bContinuation)
190 real temp = enerd_->term[F_TEMP];
191 if (inputrec_->eI != IntegrationAlgorithm::VV)
193 /* Result of Ekin averaged over velocities of -half
194 * and +half step, while we only have -half step here.
198 fprintf(fplog_, "Initial temperature: %g K\n", temp);
202 std::optional<ITrajectoryWriterCallback> EnergyData::Element::registerTrajectoryWriterCallback(TrajectoryEvent event)
204 if (event == TrajectoryEvent::EnergyWritingStep && isMasterRank_)
206 return [this](gmx_mdoutf* mdoutf, Step step, Time time, bool writeTrajectory, bool writeLog) {
207 energyData_->write(mdoutf, step, time, writeTrajectory, writeLog);
213 std::optional<SignallerCallback> EnergyData::Element::registerTrajectorySignallerCallback(gmx::TrajectoryEvent event)
215 if (event == TrajectoryEvent::EnergyWritingStep && isMasterRank_)
217 return [this](Step step, Time /*unused*/) { energyWritingStep_ = step; };
222 std::optional<SignallerCallback> EnergyData::Element::registerEnergyCallback(EnergySignallerEvent event)
224 if (event == EnergySignallerEvent::EnergyCalculationStep && isMasterRank_)
226 return [this](Step step, Time /*unused*/) { energyCalculationStep_ = step; };
228 if (event == EnergySignallerEvent::FreeEnergyCalculationStep && isMasterRank_)
230 return [this](Step step, Time /*unused*/) { freeEnergyCalculationStep_ = step; };
235 void EnergyData::doStep(Step step, Time time, bool isEnergyCalculationStep, bool isFreeEnergyCalculationStep)
237 enerd_->term[F_ETOT] = enerd_->term[F_EPOT] + enerd_->term[F_EKIN];
238 if (freeEnergyPerturbationData_)
240 accumulateKineticLambdaComponents(
241 enerd_, freeEnergyPerturbationData_->constLambdaView(), *inputrec_->fepvals);
243 if (integratorHasConservedEnergyQuantity(inputrec_))
245 enerd_->term[F_ECONSERVED] = enerd_->term[F_ETOT];
246 for (const auto& energyContibution : conservedEnergyContributions_)
248 enerd_->term[F_ECONSERVED] += energyContibution(step, time);
251 matrix nullMatrix = {};
252 energyOutput_->addDataAtEnergyStep(
253 isFreeEnergyCalculationStep,
254 isEnergyCalculationStep,
256 mdAtoms_->mdatoms()->tmass,
258 inputrec_->fepvals.get(),
259 inputrec_->expandedvals.get(),
260 statePropagatorData_->constPreviousBox(),
261 PTCouplingArrays({ parrinelloRahmanBoxVelocities_ ? parrinelloRahmanBoxVelocities_() : nullMatrix,
266 freeEnergyPerturbationData_ ? freeEnergyPerturbationData_->currentFEPState() : 0,
276 void EnergyData::write(gmx_mdoutf* outf, Step step, Time time, bool writeTrajectory, bool writeLog)
280 energyOutput_->printHeader(fplog_, step, time);
283 bool do_dr = do_per_step(step, inputrec_->nstdisreout);
284 bool do_or = do_per_step(step, inputrec_->nstorireout);
286 // energyOutput_->printAnnealingTemperatures(writeLog ? fplog_ : nullptr, groups_, &(inputrec_->opts));
288 energyOutput_->printStepToEnergyFile(
289 mdoutf_get_fp_ene(outf), writeTrajectory, do_dr, do_or, writeLog ? fplog_ : nullptr, step, time, fcd_, awh);
292 void EnergyData::addToForceVirial(const tensor virial, Step step)
294 if (step > forceVirialStep_)
296 forceVirialStep_ = step;
297 clear_mat(forceVirial_);
299 m_add(forceVirial_, virial, forceVirial_);
302 void EnergyData::addToConstraintVirial(const tensor virial, Step step)
304 if (step > shakeVirialStep_)
306 shakeVirialStep_ = step;
307 clear_mat(shakeVirial_);
309 m_add(shakeVirial_, virial, shakeVirial_);
312 rvec* EnergyData::forceVirial(Step gmx_unused step)
314 if (step > forceVirialStep_)
316 forceVirialStep_ = step;
317 clear_mat(forceVirial_);
319 GMX_ASSERT(step >= forceVirialStep_ || forceVirialStep_ == -1,
320 "Asked for force virial of previous step.");
324 rvec* EnergyData::constraintVirial(Step gmx_unused step)
326 if (step > shakeVirialStep_)
328 shakeVirialStep_ = step;
329 clear_mat(shakeVirial_);
331 GMX_ASSERT(step >= shakeVirialStep_ || shakeVirialStep_ == -1,
332 "Asked for constraint virial of previous step.");
336 rvec* EnergyData::totalVirial(Step gmx_unused step)
338 if (step > totalVirialStep_)
340 totalVirialStep_ = step;
341 clear_mat(totalVirial_);
343 GMX_ASSERT(step >= totalVirialStep_ || totalVirialStep_ == -1,
344 "Asked for total virial of previous step.");
348 rvec* EnergyData::pressure(Step gmx_unused step)
350 if (step > pressureStep_)
352 pressureStep_ = step;
353 clear_mat(pressure_);
355 GMX_ASSERT(step >= pressureStep_ || pressureStep_ == -1, "Asked for pressure of previous step.");
359 real* EnergyData::muTot()
364 gmx_enerdata_t* EnergyData::enerdata()
369 gmx_ekindata_t* EnergyData::ekindata()
374 bool* EnergyData::needToSumEkinhOld()
376 return &needToSumEkinhOld_;
379 bool EnergyData::hasReadEkinFromCheckpoint() const
381 return hasReadEkinFromCheckpoint_;
387 * \brief Enum describing the contents EnergyData::Element writes to modular checkpoint
389 * When changing the checkpoint content, add a new element just above Count, and adjust the
390 * checkpoint functionality.
392 enum class CheckpointVersion
394 Base, //!< First version of modular checkpointing
395 Count //!< Number of entries. Add new versions right above this!
397 constexpr auto c_currentVersion = CheckpointVersion(int(CheckpointVersion::Count) - 1);
400 template<CheckpointDataOperation operation>
401 void EnergyData::Element::doCheckpointData(CheckpointData<operation>* checkpointData)
403 checkpointVersion(checkpointData, "EnergyData version", c_currentVersion);
405 energyData_->observablesHistory_->energyHistory->doCheckpoint<operation>(
406 checkpointData->subCheckpointData("energy history"));
407 energyData_->ekinstate_.doCheckpoint<operation>(checkpointData->subCheckpointData("ekinstate"));
410 void EnergyData::Element::saveCheckpointState(std::optional<WriteCheckpointData> checkpointData,
415 if (energyData_->needToSumEkinhOld_)
417 energyData_->ekinstate_.bUpToDate = false;
421 update_ekinstate(&energyData_->ekinstate_, energyData_->ekind_);
422 energyData_->ekinstate_.bUpToDate = true;
424 energyData_->energyOutput_->fillEnergyHistory(
425 energyData_->observablesHistory_->energyHistory.get());
426 doCheckpointData<CheckpointDataOperation::Write>(&checkpointData.value());
430 void EnergyData::Element::restoreCheckpointState(std::optional<ReadCheckpointData> checkpointData,
435 doCheckpointData<CheckpointDataOperation::Read>(&checkpointData.value());
437 energyData_->hasReadEkinFromCheckpoint_ = MASTER(cr) ? energyData_->ekinstate_.bUpToDate : false;
440 gmx_bcast(sizeof(hasReadEkinFromCheckpoint_),
441 &energyData_->hasReadEkinFromCheckpoint_,
442 cr->mpi_comm_mygroup);
444 if (energyData_->hasReadEkinFromCheckpoint_)
446 // this takes care of broadcasting from master to agents
447 restore_ekinstate_from_state(cr, energyData_->ekind_, &energyData_->ekinstate_);
451 const std::string& EnergyData::Element::clientID()
456 void EnergyData::initializeEnergyHistory(StartingBehavior startingBehavior,
457 ObservablesHistory* observablesHistory,
458 EnergyOutput* energyOutput)
460 if (startingBehavior != StartingBehavior::NewSimulation)
462 /* Restore from energy history if appending to output files */
463 if (startingBehavior == StartingBehavior::RestartWithAppending)
465 /* If no history is available (because a checkpoint is from before
466 * it was written) make a new one later, otherwise restore it.
468 if (observablesHistory->energyHistory)
470 energyOutput->restoreFromEnergyHistory(*observablesHistory->energyHistory);
473 else if (observablesHistory->energyHistory)
475 /* We might have read an energy history from checkpoint.
476 * As we are not appending, we want to restart the statistics.
477 * Free the allocated memory and reset the counts.
479 observablesHistory->energyHistory = {};
480 /* We might have read a pull history from checkpoint.
481 * We will still want to keep the statistics, so that the files
482 * can be joined and still be meaningful.
483 * This means that observablesHistory_->pullHistory
484 * should not be reset.
488 if (!observablesHistory->energyHistory)
490 observablesHistory->energyHistory = std::make_unique<energyhistory_t>();
492 if (!observablesHistory->pullHistory)
494 observablesHistory->pullHistory = std::make_unique<PullHistory>();
496 /* Set the initial energy history */
497 energyOutput->fillEnergyHistory(observablesHistory->energyHistory.get());
500 void EnergyData::addConservedEnergyContribution(EnergyContribution&& energyContribution)
502 conservedEnergyContributions_.emplace_back(std::move(energyContribution));
505 void EnergyData::setParrinelloRahmanBoxVelocities(std::function<const rvec*()>&& parrinelloRahmanBoxVelocities)
507 GMX_RELEASE_ASSERT(!parrinelloRahmanBoxVelocities_,
508 "Received a second callback to the Parrinello-Rahman velocities");
509 parrinelloRahmanBoxVelocities_ = parrinelloRahmanBoxVelocities;
512 EnergyData::Element* EnergyData::element()
514 return element_.get();
517 EnergyData::Element::Element(EnergyData* energyData, bool isMasterRank) :
518 energyData_(energyData),
519 isMasterRank_(isMasterRank),
520 energyWritingStep_(-1),
521 energyCalculationStep_(-1),
522 freeEnergyCalculationStep_(-1)
526 ISimulatorElement* EnergyData::Element::getElementPointerImpl(
527 LegacySimulatorData gmx_unused* legacySimulatorData,
528 ModularSimulatorAlgorithmBuilderHelper gmx_unused* builderHelper,
529 StatePropagatorData gmx_unused* statePropagatorData,
530 EnergyData* energyData,
531 FreeEnergyPerturbationData gmx_unused* freeEnergyPerturbationData,
532 GlobalCommunicationHelper gmx_unused* globalCommunicationHelper)
534 return energyData->element();