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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/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"
67 #include "freeenergyperturbationdata.h"
68 #include "modularsimulator.h"
69 #include "parrinellorahmanbarostat.h"
70 #include "simulatoralgorithm.h"
71 #include "statepropagatordata.h"
72 #include "velocityscalingtemperaturecoupling.h"
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,
91 const MdModulesNotifier& mdModulesNotifier,
93 ObservablesHistory* observablesHistory,
94 StartingBehavior startingBehavior,
95 bool simulationsShareState) :
96 element_(std::make_unique<Element>(this, isMasterRank)),
97 isMasterRank_(isMasterRank),
100 totalVirialStep_(-1),
102 needToSumEkinhOld_(false),
103 hasReadEkinFromCheckpoint_(false),
104 startingBehavior_(startingBehavior),
105 statePropagatorData_(statePropagatorData),
106 freeEnergyPerturbationData_(freeEnergyPerturbationData),
107 velocityScalingTemperatureCoupling_(nullptr),
108 parrinelloRahmanBarostat_(nullptr),
110 top_global_(globalTopology),
117 mdModulesNotifier_(mdModulesNotifier),
118 groups_(&globalTopology->groups),
119 observablesHistory_(observablesHistory),
120 simulationsShareState_(simulationsShareState)
122 clear_mat(forceVirial_);
123 clear_mat(shakeVirial_);
124 clear_mat(totalVirial_);
125 clear_mat(pressure_);
128 init_ekinstate(&ekinstate_, inputrec_);
129 observablesHistory_->energyHistory = std::make_unique<energyhistory_t>();
132 void EnergyData::Element::scheduleTask(Step step, Time time, const RegisterRunFunction& registerRunFunction)
138 auto writeEnergy = energyWritingStep_ == step;
139 auto isEnergyCalculationStep = energyCalculationStep_ == step;
140 auto isFreeEnergyCalculationStep = freeEnergyCalculationStep_ == step;
141 if (isEnergyCalculationStep || writeEnergy)
143 registerRunFunction([this, time, isEnergyCalculationStep, isFreeEnergyCalculationStep]() {
144 energyData_->doStep(time, isEnergyCalculationStep, isFreeEnergyCalculationStep);
149 registerRunFunction([this]() { energyData_->energyOutput_->recordNonEnergyStep(); });
153 void EnergyData::teardown()
155 if (inputrec_->nstcalcenergy > 0 && isMasterRank_)
157 energyOutput_->printAverages(fplog_, groups_);
161 void EnergyData::Element::trajectoryWriterSetup(gmx_mdoutf* outf)
163 energyData_->setup(outf);
166 void EnergyData::setup(gmx_mdoutf* outf)
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_);
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 != eiVV)
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(Time time, bool isEnergyCalculationStep, bool isFreeEnergyCalculationStep)
237 enerd_->term[F_ETOT] = enerd_->term[F_EPOT] + enerd_->term[F_EKIN];
238 if (freeEnergyPerturbationData_)
240 accumulateKineticLambdaComponents(enerd_, freeEnergyPerturbationData_->constLambdaView(),
241 *inputrec_->fepvals);
243 if (integratorHasConservedEnergyQuantity(inputrec_))
245 enerd_->term[F_ECONSERVED] =
247 + (velocityScalingTemperatureCoupling_
248 ? velocityScalingTemperatureCoupling_->conservedEnergyContribution()
250 + (parrinelloRahmanBarostat_ ? parrinelloRahmanBarostat_->conservedEnergyContribution() : 0);
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,
261 freeEnergyPerturbationData_ ? freeEnergyPerturbationData_->currentFEPState() : 0,
262 shakeVirial_, forceVirial_, totalVirial_, pressure_, ekind_, muTot_, constr_);
265 void EnergyData::write(gmx_mdoutf* outf, Step step, Time time, bool writeTrajectory, bool writeLog)
269 energyOutput_->printHeader(fplog_, step, time);
272 bool do_dr = do_per_step(step, inputrec_->nstdisreout);
273 bool do_or = do_per_step(step, inputrec_->nstorireout);
275 // energyOutput_->printAnnealingTemperatures(writeLog ? fplog_ : nullptr, groups_, &(inputrec_->opts));
277 energyOutput_->printStepToEnergyFile(mdoutf_get_fp_ene(outf), writeTrajectory, do_dr, do_or,
278 writeLog ? fplog_ : nullptr, step, time, fcd_, awh);
281 void EnergyData::addToForceVirial(const tensor virial, Step step)
283 if (step > forceVirialStep_)
285 forceVirialStep_ = step;
286 clear_mat(forceVirial_);
288 m_add(forceVirial_, virial, forceVirial_);
291 void EnergyData::addToConstraintVirial(const tensor virial, Step step)
293 if (step > shakeVirialStep_)
295 shakeVirialStep_ = step;
296 clear_mat(shakeVirial_);
298 m_add(shakeVirial_, virial, shakeVirial_);
301 rvec* EnergyData::forceVirial(Step gmx_unused step)
303 if (step > forceVirialStep_)
305 forceVirialStep_ = step;
306 clear_mat(forceVirial_);
308 GMX_ASSERT(step >= forceVirialStep_ || forceVirialStep_ == -1,
309 "Asked for force virial of previous step.");
313 rvec* EnergyData::constraintVirial(Step gmx_unused step)
315 if (step > shakeVirialStep_)
317 shakeVirialStep_ = step;
318 clear_mat(shakeVirial_);
320 GMX_ASSERT(step >= shakeVirialStep_ || shakeVirialStep_ == -1,
321 "Asked for constraint virial of previous step.");
325 rvec* EnergyData::totalVirial(Step gmx_unused step)
327 if (step > totalVirialStep_)
329 totalVirialStep_ = step;
330 clear_mat(totalVirial_);
332 GMX_ASSERT(step >= totalVirialStep_ || totalVirialStep_ == -1,
333 "Asked for total virial of previous step.");
337 rvec* EnergyData::pressure(Step gmx_unused step)
339 if (step > pressureStep_)
341 pressureStep_ = step;
342 clear_mat(pressure_);
344 GMX_ASSERT(step >= pressureStep_ || pressureStep_ == -1,
345 "Asked for pressure of previous step.");
349 real* EnergyData::muTot()
354 gmx_enerdata_t* EnergyData::enerdata()
359 gmx_ekindata_t* EnergyData::ekindata()
364 bool* EnergyData::needToSumEkinhOld()
366 return &needToSumEkinhOld_;
369 bool EnergyData::hasReadEkinFromCheckpoint() const
371 return hasReadEkinFromCheckpoint_;
377 * \brief Enum describing the contents EnergyData::Element writes to modular checkpoint
379 * When changing the checkpoint content, add a new element just above Count, and adjust the
380 * checkpoint functionality.
382 enum class CheckpointVersion
384 Base, //!< First version of modular checkpointing
385 Count //!< Number of entries. Add new versions right above this!
387 constexpr auto c_currentVersion = CheckpointVersion(int(CheckpointVersion::Count) - 1);
390 template<CheckpointDataOperation operation>
391 void EnergyData::Element::doCheckpointData(CheckpointData<operation>* checkpointData)
393 checkpointVersion(checkpointData, "EnergyData version", c_currentVersion);
395 energyData_->observablesHistory_->energyHistory->doCheckpoint<operation>(
396 checkpointData->subCheckpointData("energy history"));
397 energyData_->ekinstate_.doCheckpoint<operation>(checkpointData->subCheckpointData("ekinstate"));
400 void EnergyData::Element::saveCheckpointState(std::optional<WriteCheckpointData> checkpointData,
405 if (energyData_->needToSumEkinhOld_)
407 energyData_->ekinstate_.bUpToDate = false;
411 update_ekinstate(&energyData_->ekinstate_, energyData_->ekind_);
412 energyData_->ekinstate_.bUpToDate = true;
414 energyData_->energyOutput_->fillEnergyHistory(
415 energyData_->observablesHistory_->energyHistory.get());
416 doCheckpointData<CheckpointDataOperation::Write>(&checkpointData.value());
420 void EnergyData::Element::restoreCheckpointState(std::optional<ReadCheckpointData> checkpointData,
425 doCheckpointData<CheckpointDataOperation::Read>(&checkpointData.value());
427 energyData_->hasReadEkinFromCheckpoint_ = MASTER(cr) ? energyData_->ekinstate_.bUpToDate : false;
430 gmx_bcast(sizeof(hasReadEkinFromCheckpoint_), &energyData_->hasReadEkinFromCheckpoint_,
431 cr->mpi_comm_mygroup);
433 if (energyData_->hasReadEkinFromCheckpoint_)
435 // this takes care of broadcasting from master to agents
436 restore_ekinstate_from_state(cr, energyData_->ekind_, &energyData_->ekinstate_);
440 const std::string& EnergyData::Element::clientID()
445 void EnergyData::initializeEnergyHistory(StartingBehavior startingBehavior,
446 ObservablesHistory* observablesHistory,
447 EnergyOutput* energyOutput)
449 if (startingBehavior != StartingBehavior::NewSimulation)
451 /* Restore from energy history if appending to output files */
452 if (startingBehavior == StartingBehavior::RestartWithAppending)
454 /* If no history is available (because a checkpoint is from before
455 * it was written) make a new one later, otherwise restore it.
457 if (observablesHistory->energyHistory)
459 energyOutput->restoreFromEnergyHistory(*observablesHistory->energyHistory);
462 else if (observablesHistory->energyHistory)
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.
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.
477 if (!observablesHistory->energyHistory)
479 observablesHistory->energyHistory = std::make_unique<energyhistory_t>();
481 if (!observablesHistory->pullHistory)
483 observablesHistory->pullHistory = std::make_unique<PullHistory>();
485 /* Set the initial energy history */
486 energyOutput->fillEnergyHistory(observablesHistory->energyHistory.get());
489 void EnergyData::setVelocityScalingTemperatureCoupling(const VelocityScalingTemperatureCoupling* velocityScalingTemperatureCoupling)
491 velocityScalingTemperatureCoupling_ = velocityScalingTemperatureCoupling;
494 void EnergyData::setParrinelloRahamnBarostat(const gmx::ParrinelloRahmanBarostat* parrinelloRahmanBarostat)
496 parrinelloRahmanBarostat_ = parrinelloRahmanBarostat;
499 EnergyData::Element* EnergyData::element()
501 return element_.get();
504 EnergyData::Element::Element(EnergyData* energyData, bool isMasterRank) :
505 energyData_(energyData),
506 isMasterRank_(isMasterRank),
507 energyWritingStep_(-1),
508 energyCalculationStep_(-1),
509 freeEnergyCalculationStep_(-1)
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)
521 return energyData->element();