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36 * \brief Defines a velocity-scaling temperature coupling element for
37 * the modular simulator
39 * \author Pascal Merz <pascal.merz@me.com>
40 * \ingroup module_modularsimulator
45 #include "velocityscalingtemperaturecoupling.h"
49 #include "gromacs/domdec/domdec_network.h"
50 #include "gromacs/math/units.h"
51 #include "gromacs/math/vec.h"
52 #include "gromacs/mdlib/coupling.h"
53 #include "gromacs/mdlib/stat.h"
54 #include "gromacs/mdtypes/checkpointdata.h"
55 #include "gromacs/mdtypes/commrec.h"
56 #include "gromacs/mdtypes/group.h"
57 #include "gromacs/mdtypes/inputrec.h"
58 #include "gromacs/utility/fatalerror.h"
59 #include "gromacs/utility/strconvert.h"
61 #include "modularsimulator.h"
62 #include "simulatoralgorithm.h"
68 * \brief Data used by the concrete temperature coupling implementations
70 struct TemperatureCouplingData
72 //! The coupling time step - simulation time step x nstcouple_
73 const double couplingTimeStep;
74 //! Coupling temperature per group
75 ArrayRef<const real> referenceTemperature;
76 //! Coupling time per group
77 ArrayRef<const real> couplingTime;
78 //! Number of degrees of freedom per group
79 ArrayRef<const real> numDegreesOfFreedom;
80 //! Work exerted by thermostat per group
81 ArrayRef<const double> temperatureCouplingIntegral;
85 * \brief Interface for temperature coupling implementations
87 class ITemperatureCouplingImpl
90 //! Allow access to the scaling vectors
91 virtual void connectWithPropagator(const PropagatorConnection& connectionData,
92 int numTemperatureGroups) = 0;
94 /*! \brief Make a temperature control step
96 * \param step The current step
97 * \param temperatureGroup The current temperature group
98 * \param currentKineticEnergy The kinetic energy of the temperature group
99 * \param currentTemperature The temperature of the temperature group
100 * \param temperatureCouplingData Access to general temperature coupling data
102 * \return The temperature coupling integral for the current temperature group
104 [[nodiscard]] virtual real apply(Step step,
105 int temperatureGroup,
106 real currentKineticEnergy,
107 real currentTemperature,
108 const TemperatureCouplingData& temperatureCouplingData) = 0;
110 //! Write private data to checkpoint
111 virtual void writeCheckpoint(std::optional<WriteCheckpointData> checkpointData,
112 const t_commrec* cr) = 0;
113 //! Read private data from checkpoint
114 virtual void readCheckpoint(std::optional<ReadCheckpointData> checkpointData, const t_commrec* cr) = 0;
116 //! Update the reference temperature and update and return the temperature coupling integral
117 virtual real updateReferenceTemperatureAndIntegral(int temperatureGroup,
119 ReferenceTemperatureChangeAlgorithm algorithm,
120 const TemperatureCouplingData& temperatureCouplingData) = 0;
122 //! Standard virtual destructor
123 virtual ~ITemperatureCouplingImpl() = default;
127 * \brief Implements v-rescale temperature coupling
129 class VRescaleTemperatureCoupling final : public ITemperatureCouplingImpl
132 //! Apply the v-rescale temperature control
133 real apply(Step step,
134 int temperatureGroup,
135 real currentKineticEnergy,
136 real gmx_unused currentTemperature,
137 const TemperatureCouplingData& temperatureCouplingData) override
139 if (!(temperatureCouplingData.couplingTime[temperatureGroup] >= 0
140 && temperatureCouplingData.numDegreesOfFreedom[temperatureGroup] > 0
141 && currentKineticEnergy > 0))
143 lambdaStartVelocities_[temperatureGroup] = 1.0;
144 return temperatureCouplingData.temperatureCouplingIntegral[temperatureGroup];
147 const real referenceKineticEnergy =
148 0.5 * temperatureCouplingData.referenceTemperature[temperatureGroup] * gmx::c_boltz
149 * temperatureCouplingData.numDegreesOfFreedom[temperatureGroup];
151 const real newKineticEnergy =
152 vrescale_resamplekin(currentKineticEnergy,
153 referenceKineticEnergy,
154 temperatureCouplingData.numDegreesOfFreedom[temperatureGroup],
155 temperatureCouplingData.couplingTime[temperatureGroup]
156 / temperatureCouplingData.couplingTimeStep,
160 // Analytically newKineticEnergy >= 0, but we check for rounding errors
161 if (newKineticEnergy <= 0)
163 lambdaStartVelocities_[temperatureGroup] = 0.0;
167 lambdaStartVelocities_[temperatureGroup] = std::sqrt(newKineticEnergy / currentKineticEnergy);
173 "TC: group %d: Ekr %g, Ek %g, Ek_new %g, Lambda: %g\n",
175 referenceKineticEnergy,
176 currentKineticEnergy,
178 lambdaStartVelocities_[temperatureGroup]);
181 return temperatureCouplingData.temperatureCouplingIntegral[temperatureGroup]
182 - (newKineticEnergy - currentKineticEnergy);
185 //! Connect with propagator - v-rescale only scales start step velocities
186 void connectWithPropagator(const PropagatorConnection& connectionData, int numTemperatureGroups) override
188 GMX_RELEASE_ASSERT(connectionData.hasStartVelocityScaling(),
189 "V-Rescale requires start velocity scaling.");
190 connectionData.setNumVelocityScalingVariables(numTemperatureGroups, ScaleVelocities::PreStepOnly);
191 lambdaStartVelocities_ = connectionData.getViewOnStartVelocityScaling();
194 //! No data to write to checkpoint
195 void writeCheckpoint(std::optional<WriteCheckpointData> gmx_unused checkpointData,
196 const t_commrec gmx_unused* cr) override
199 //! No data to read from checkpoints
200 void readCheckpoint(std::optional<ReadCheckpointData> gmx_unused checkpointData,
201 const t_commrec gmx_unused* cr) override
205 //! No changes needed
206 real updateReferenceTemperatureAndIntegral(int temperatureGroup,
207 real gmx_unused newTemperature,
208 ReferenceTemperatureChangeAlgorithm gmx_unused algorithm,
209 const TemperatureCouplingData& temperatureCouplingData) override
211 return temperatureCouplingData.temperatureCouplingIntegral[temperatureGroup];
215 VRescaleTemperatureCoupling(int64_t seed) : seed_(seed) {}
221 //! View on the scaling factor of the propagator (pre-step velocities)
222 ArrayRef<real> lambdaStartVelocities_;
226 * \brief Implements Berendsen temperature coupling
228 class BerendsenTemperatureCoupling final : public ITemperatureCouplingImpl
231 //! Apply the v-rescale temperature control
232 real apply(Step gmx_unused step,
233 int temperatureGroup,
234 real currentKineticEnergy,
235 real currentTemperature,
236 const TemperatureCouplingData& temperatureCouplingData) override
238 if (!(temperatureCouplingData.couplingTime[temperatureGroup] >= 0
239 && temperatureCouplingData.numDegreesOfFreedom[temperatureGroup] > 0
240 && currentKineticEnergy > 0))
242 lambdaStartVelocities_[temperatureGroup] = 1.0;
243 return temperatureCouplingData.temperatureCouplingIntegral[temperatureGroup];
248 + (temperatureCouplingData.couplingTimeStep
249 / temperatureCouplingData.couplingTime[temperatureGroup])
250 * (temperatureCouplingData.referenceTemperature[temperatureGroup] / currentTemperature
252 lambdaStartVelocities_[temperatureGroup] =
253 std::max<real>(std::min<real>(lambda, 1.25_real), 0.8_real);
257 "TC: group %d: T: %g, Lambda: %g\n",
260 lambdaStartVelocities_[temperatureGroup]);
262 return temperatureCouplingData.temperatureCouplingIntegral[temperatureGroup]
263 - (lambdaStartVelocities_[temperatureGroup] * lambdaStartVelocities_[temperatureGroup]
264 - 1) * currentKineticEnergy;
267 //! Connect with propagator - Berendsen only scales start step velocities
268 void connectWithPropagator(const PropagatorConnection& connectionData, int numTemperatureGroups) override
270 GMX_RELEASE_ASSERT(connectionData.hasStartVelocityScaling(),
271 "Berendsen T-coupling requires start velocity scaling.");
272 connectionData.setNumVelocityScalingVariables(numTemperatureGroups, ScaleVelocities::PreStepOnly);
273 lambdaStartVelocities_ = connectionData.getViewOnStartVelocityScaling();
276 //! No data to write to checkpoint
277 void writeCheckpoint(std::optional<WriteCheckpointData> gmx_unused checkpointData,
278 const t_commrec gmx_unused* cr) override
281 //! No data to read from checkpoints
282 void readCheckpoint(std::optional<ReadCheckpointData> gmx_unused checkpointData,
283 const t_commrec gmx_unused* cr) override
287 //! No changes needed
288 real updateReferenceTemperatureAndIntegral(int temperatureGroup,
289 real gmx_unused newTemperature,
290 ReferenceTemperatureChangeAlgorithm gmx_unused algorithm,
291 const TemperatureCouplingData& temperatureCouplingData) override
293 return temperatureCouplingData.temperatureCouplingIntegral[temperatureGroup];
297 //! View on the scaling factor of the propagator (pre-step velocities)
298 ArrayRef<real> lambdaStartVelocities_;
301 // Prepare NoseHooverTemperatureCoupling checkpoint data
305 * \brief Enum describing the contents NoseHoover writes to modular checkpoint
307 * When changing the checkpoint content, add a new element just above Count, and adjust the
308 * checkpoint functionality.
310 enum class NHCheckpointVersion
312 Base, //!< First version of modular checkpointing
313 Count //!< Number of entries. Add new versions right above this!
315 constexpr auto c_nhCurrentVersion = NHCheckpointVersion(int(NHCheckpointVersion::Count) - 1);
319 * \brief Implements the Nose-Hoover temperature coupling
321 class NoseHooverTemperatureCoupling final : public ITemperatureCouplingImpl
324 //! Calculate the current value of the temperature coupling integral
325 real integral(int temperatureGroup, real numDegreesOfFreedom, real referenceTemperature)
327 return 0.5 * c_boltz * numDegreesOfFreedom
328 * (xiVelocities_[temperatureGroup] * xiVelocities_[temperatureGroup])
329 / invXiMass_[temperatureGroup]
330 + numDegreesOfFreedom * xi_[temperatureGroup] * c_boltz * referenceTemperature;
333 //! Apply the Nose-Hoover temperature control
334 real apply(Step gmx_unused step,
335 int temperatureGroup,
336 real currentKineticEnergy,
337 real currentTemperature,
338 const TemperatureCouplingData& thermostatData) override
340 return applyLeapFrog(
341 step, temperatureGroup, currentKineticEnergy, currentTemperature, thermostatData);
344 /*! \brief Apply for leap-frog
346 * This is called after the force calculation, before coordinate update
348 * We expect system to be at x(t), v(t-dt/2), f(t), T(t-dt/2)
349 * Internal variables are at xi(t-dt), v_xi(t-dt)
350 * Force on xi is calculated at time of system temperature
351 * After calling this, we will have xi(t), v_xi(t)
352 * The thermostat integral returned is a function of xi and v_xi,
353 * and hence at time t.
355 * This performs an update of the thermostat variables calculated as
356 * a_xi(t-dt/2) = (T_sys(t-dt/2) - T_ref) / mass_xi;
357 * v_xi(t) = v_xi(t-dt) + dt_xi * a_xi(t-dt/2);
358 * xi(t) = xi(t-dt) + dt_xi * (v_xi(t-dt) + v_xi(t))/2;
360 * This will be followed by leap-frog integration of coordinates, calculated as
361 * v(t-dt/2) *= - 0.5 * dt * v_xi(t); // scale previous velocities
362 * v(t+dt/2) = update_leapfrog_v(v(t-dt/2), f(t)); // do whatever LF does
363 * v(t+dt/2) *= 1 / (1 + 0.5 * dt * v_xi(t)) // scale new velocities
364 * x(t+dt) = update_leapfrog_x(x(t), v(t+dt/2)); // do whatever LF does
366 real applyLeapFrog(Step gmx_unused step,
367 int temperatureGroup,
368 real currentKineticEnergy,
369 real currentTemperature,
370 const TemperatureCouplingData& thermostatData)
372 if (!(thermostatData.couplingTime[temperatureGroup] >= 0
373 && thermostatData.numDegreesOfFreedom[temperatureGroup] > 0 && currentKineticEnergy > 0))
375 lambdaStartVelocities_[temperatureGroup] = 1.0;
376 lambdaEndVelocities_[temperatureGroup] = 1.0;
377 return thermostatData.temperatureCouplingIntegral[temperatureGroup];
380 const auto oldXiVelocity = xiVelocities_[temperatureGroup];
381 const auto xiAcceleration =
382 invXiMass_[temperatureGroup]
383 * (currentTemperature - thermostatData.referenceTemperature[temperatureGroup]);
384 xiVelocities_[temperatureGroup] += thermostatData.couplingTimeStep * xiAcceleration;
385 xi_[temperatureGroup] += thermostatData.couplingTimeStep
386 * (oldXiVelocity + xiVelocities_[temperatureGroup]) * 0.5;
387 lambdaStartVelocities_[temperatureGroup] =
388 (1 - 0.5 * thermostatData.couplingTimeStep * xiVelocities_[temperatureGroup]);
389 lambdaEndVelocities_[temperatureGroup] =
390 1. / (1 + 0.5 * thermostatData.couplingTimeStep * xiVelocities_[temperatureGroup]);
392 // Current value of the thermostat integral
393 return integral(temperatureGroup,
394 thermostatData.numDegreesOfFreedom[temperatureGroup],
395 thermostatData.referenceTemperature[temperatureGroup]);
398 //! Connect with propagator - Nose-Hoover scales start and end step velocities
399 void connectWithPropagator(const PropagatorConnection& connectionData, int numTemperatureGroups) override
402 connectionData.hasStartVelocityScaling() && connectionData.hasEndVelocityScaling(),
403 "Nose-Hoover T-coupling requires both start and end velocity scaling.");
404 connectionData.setNumVelocityScalingVariables(numTemperatureGroups,
405 ScaleVelocities::PreStepAndPostStep);
406 lambdaStartVelocities_ = connectionData.getViewOnStartVelocityScaling();
407 lambdaEndVelocities_ = connectionData.getViewOnEndVelocityScaling();
411 NoseHooverTemperatureCoupling(int numTemperatureGroups,
412 ArrayRef<const real> referenceTemperature,
413 ArrayRef<const real> couplingTime)
415 xi_.resize(numTemperatureGroups, 0.0);
416 xiVelocities_.resize(numTemperatureGroups, 0.0);
417 invXiMass_.resize(numTemperatureGroups, 0.0);
418 for (auto temperatureGroup = 0; temperatureGroup < numTemperatureGroups; ++temperatureGroup)
420 if (referenceTemperature[temperatureGroup] > 0 && couplingTime[temperatureGroup] > 0)
422 // Note: This mass definition is equal to legacy md
423 // legacy md-vv divides the mass by ndof * kB
424 invXiMass_[temperatureGroup] = 1.0
425 / (gmx::square(couplingTime[temperatureGroup] / M_2PI)
426 * referenceTemperature[temperatureGroup]);
431 //! Helper function to read from / write to CheckpointData
432 template<CheckpointDataOperation operation>
433 void doCheckpointData(CheckpointData<operation>* checkpointData)
435 checkpointVersion(checkpointData, "Nose-Hoover version", c_nhCurrentVersion);
436 checkpointData->arrayRef("xi", makeCheckpointArrayRef<operation>(xi_));
437 checkpointData->arrayRef("xi velocities", makeCheckpointArrayRef<operation>(xiVelocities_));
440 //! Write thermostat dof to checkpoint
441 void writeCheckpoint(std::optional<WriteCheckpointData> checkpointData, const t_commrec* cr) override
445 doCheckpointData(&checkpointData.value());
448 //! Read thermostat dof from checkpoint
449 void readCheckpoint(std::optional<ReadCheckpointData> checkpointData, const t_commrec* cr) override
453 doCheckpointData(&checkpointData.value());
455 if (haveDDAtomOrdering(*cr))
457 dd_bcast(cr->dd, xi_.size() * sizeof(real), xi_.data());
458 dd_bcast(cr->dd, xiVelocities_.size() * sizeof(real), xiVelocities_.data());
463 real updateReferenceTemperatureAndIntegral(int temperatureGroup,
464 real gmx_unused newTemperature,
465 ReferenceTemperatureChangeAlgorithm gmx_unused algorithm,
466 const TemperatureCouplingData& temperatureCouplingData) override
468 // Currently, we don't know about any temperature change algorithms, so we assert this never gets called
470 "NoseHooverTemperatureCoupling: Unknown ReferenceTemperatureChangeAlgorithm.");
471 const bool newTemperatureIsValid =
472 (newTemperature > 0 && temperatureCouplingData.couplingTime[temperatureGroup] > 0
473 && temperatureCouplingData.numDegreesOfFreedom[temperatureGroup] > 0);
474 const bool oldTemperatureIsValid =
475 (temperatureCouplingData.referenceTemperature[temperatureGroup] > 0
476 && temperatureCouplingData.couplingTime[temperatureGroup] > 0
477 && temperatureCouplingData.numDegreesOfFreedom[temperatureGroup] > 0);
478 GMX_RELEASE_ASSERT(newTemperatureIsValid == oldTemperatureIsValid,
479 "Cannot turn temperature coupling on / off during simulation run.");
480 if (oldTemperatureIsValid && newTemperatureIsValid)
482 invXiMass_[temperatureGroup] *=
483 (temperatureCouplingData.referenceTemperature[temperatureGroup] / newTemperature);
484 xiVelocities_[temperatureGroup] *= std::sqrt(
485 newTemperature / temperatureCouplingData.referenceTemperature[temperatureGroup]);
487 return integral(temperatureGroup,
488 temperatureCouplingData.numDegreesOfFreedom[temperatureGroup],
493 //! The thermostat degree of freedom
494 std::vector<real> xi_;
495 //! Velocity of the thermostat dof
496 std::vector<real> xiVelocities_;
497 //! Inverse mass of the thermostat dof
498 std::vector<real> invXiMass_;
500 //! View on the scaling factor of the propagator (pre-step velocities)
501 ArrayRef<real> lambdaStartVelocities_;
502 //! View on the scaling factor of the propagator (post-step velocities)
503 ArrayRef<real> lambdaEndVelocities_;
506 VelocityScalingTemperatureCoupling::VelocityScalingTemperatureCoupling(
509 UseFullStepKE useFullStepKE,
510 ReportPreviousStepConservedEnergy reportPreviousConservedEnergy,
512 int numTemperatureGroups,
513 double couplingTimeStep,
514 const real* referenceTemperature,
515 const real* couplingTime,
516 const real* numDegreesOfFreedom,
517 EnergyData* energyData,
518 TemperatureCoupling couplingType) :
519 nstcouple_(nstcouple),
521 useFullStepKE_(useFullStepKE),
522 reportPreviousConservedEnergy_(reportPreviousConservedEnergy),
523 numTemperatureGroups_(numTemperatureGroups),
524 couplingTimeStep_(couplingTimeStep),
525 referenceTemperature_(referenceTemperature, referenceTemperature + numTemperatureGroups),
526 couplingTime_(couplingTime, couplingTime + numTemperatureGroups),
527 numDegreesOfFreedom_(numDegreesOfFreedom, numDegreesOfFreedom + numTemperatureGroups),
528 temperatureCouplingIntegral_(numTemperatureGroups, 0.0),
529 energyData_(energyData),
530 nextEnergyCalculationStep_(-1)
532 if (couplingType == TemperatureCoupling::VRescale)
534 temperatureCouplingImpl_ = std::make_unique<VRescaleTemperatureCoupling>(seed);
536 else if (couplingType == TemperatureCoupling::Berendsen)
538 temperatureCouplingImpl_ = std::make_unique<BerendsenTemperatureCoupling>();
540 else if (couplingType == TemperatureCoupling::NoseHoover)
542 temperatureCouplingImpl_ = std::make_unique<NoseHooverTemperatureCoupling>(
543 numTemperatureGroups_, referenceTemperature_, couplingTime_);
547 throw NotImplementedError("Temperature coupling " + std::string(enumValueToString(couplingType))
548 + " is not implemented for modular simulator.");
550 energyData->addConservedEnergyContribution([this](Step gmx_used_in_debug step, Time /*unused*/) {
551 GMX_ASSERT(conservedEnergyContributionStep_ == step,
552 "VelocityScalingTemperatureCoupling conserved energy step mismatch.");
553 return conservedEnergyContribution_;
557 void VelocityScalingTemperatureCoupling::connectWithMatchingPropagator(const PropagatorConnection& connectionData,
558 const PropagatorTag& propagatorTag)
560 if (connectionData.tag == propagatorTag)
562 temperatureCouplingImpl_->connectWithPropagator(connectionData, numTemperatureGroups_);
563 propagatorCallback_ = connectionData.getVelocityScalingCallback();
567 void VelocityScalingTemperatureCoupling::elementSetup()
569 if (!propagatorCallback_)
571 throw MissingElementConnectionError(
572 "Velocity scaling temperature coupling was not connected to a propagator.\n"
573 "Connection to a propagator element is needed to scale the velocities.\n"
574 "Use connectWithMatchingPropagator(...) before building the "
575 "ModularSimulatorAlgorithm "
580 void VelocityScalingTemperatureCoupling::scheduleTask(Step step,
581 Time gmx_unused time,
582 const RegisterRunFunction& registerRunFunction)
584 /* The thermostat will need a valid kinetic energy when it is running.
585 * Currently, computeGlobalCommunicationPeriod() is making sure this
587 * TODO: Once we're switching to a new global communication scheme, we
588 * will want the thermostat to signal that global reduction
589 * of the kinetic energy is needed.
592 if (step == nextEnergyCalculationStep_
593 && reportPreviousConservedEnergy_ == ReportPreviousStepConservedEnergy::Yes)
595 // add conserved energy before we do T-coupling
596 registerRunFunction([this, step]() {
597 conservedEnergyContribution_ = conservedEnergyContribution();
598 conservedEnergyContributionStep_ = step;
601 if (do_per_step(step + nstcouple_ + offset_, nstcouple_))
603 // do T-coupling this step
604 registerRunFunction([this, step]() { setLambda(step); });
606 // Let propagator know that we want to do T-coupling
607 propagatorCallback_(step);
609 if (step == nextEnergyCalculationStep_
610 && reportPreviousConservedEnergy_ == ReportPreviousStepConservedEnergy::No)
612 // add conserved energy after we did T-coupling
613 registerRunFunction([this, step]() {
614 conservedEnergyContribution_ = conservedEnergyContribution();
615 conservedEnergyContributionStep_ = step;
620 void VelocityScalingTemperatureCoupling::setLambda(Step step)
622 const auto* ekind = energyData_->ekindata();
623 TemperatureCouplingData thermostatData = {
624 couplingTimeStep_, referenceTemperature_, couplingTime_, numDegreesOfFreedom_, temperatureCouplingIntegral_
627 for (int temperatureGroup = 0; (temperatureGroup < numTemperatureGroups_); temperatureGroup++)
629 const real currentKineticEnergy = useFullStepKE_ == UseFullStepKE::Yes
630 ? trace(ekind->tcstat[temperatureGroup].ekinf)
631 : trace(ekind->tcstat[temperatureGroup].ekinh);
632 const real currentTemperature = useFullStepKE_ == UseFullStepKE::Yes
633 ? ekind->tcstat[temperatureGroup].T
634 : ekind->tcstat[temperatureGroup].Th;
636 temperatureCouplingIntegral_[temperatureGroup] = temperatureCouplingImpl_->apply(
637 step, temperatureGroup, currentKineticEnergy, currentTemperature, thermostatData);
641 void VelocityScalingTemperatureCoupling::updateReferenceTemperature(ArrayRef<const real> temperatures,
642 ReferenceTemperatureChangeAlgorithm algorithm)
644 TemperatureCouplingData thermostatData = {
645 couplingTimeStep_, referenceTemperature_, couplingTime_, numDegreesOfFreedom_, temperatureCouplingIntegral_
647 for (int temperatureGroup = 0; (temperatureGroup < numTemperatureGroups_); temperatureGroup++)
649 temperatureCouplingIntegral_[temperatureGroup] =
650 temperatureCouplingImpl_->updateReferenceTemperatureAndIntegral(
651 temperatureGroup, temperatures[temperatureGroup], algorithm, thermostatData);
653 // Currently, we don't know about any temperature change algorithms, so we assert this never gets called
655 "VelocityScalingTemperatureCoupling: Unknown ReferenceTemperatureChangeAlgorithm.");
656 std::copy(temperatures.begin(), temperatures.end(), referenceTemperature_.begin());
662 * \brief Enum describing the contents VelocityScalingTemperatureCoupling writes to modular checkpoint
664 * When changing the checkpoint content, add a new element just above Count, and adjust the
665 * checkpoint functionality.
667 enum class CheckpointVersion
669 Base, //!< First version of modular checkpointing
670 Count //!< Number of entries. Add new versions right above this!
672 constexpr auto c_currentVersion = CheckpointVersion(int(CheckpointVersion::Count) - 1);
675 template<CheckpointDataOperation operation>
676 void VelocityScalingTemperatureCoupling::doCheckpointData(CheckpointData<operation>* checkpointData)
678 checkpointVersion(checkpointData, "VRescaleThermostat version", c_currentVersion);
680 checkpointData->arrayRef("thermostat integral",
681 makeCheckpointArrayRef<operation>(temperatureCouplingIntegral_));
684 void VelocityScalingTemperatureCoupling::saveCheckpointState(std::optional<WriteCheckpointData> checkpointData,
689 doCheckpointData<CheckpointDataOperation::Write>(&checkpointData.value());
691 temperatureCouplingImpl_->writeCheckpoint(
693 ? std::make_optional(checkpointData->subCheckpointData("thermostat impl"))
698 void VelocityScalingTemperatureCoupling::restoreCheckpointState(std::optional<ReadCheckpointData> checkpointData,
703 doCheckpointData<CheckpointDataOperation::Read>(&checkpointData.value());
705 if (haveDDAtomOrdering(*cr))
708 ssize(temperatureCouplingIntegral_) * int(sizeof(double)),
709 temperatureCouplingIntegral_.data());
711 temperatureCouplingImpl_->readCheckpoint(
713 ? std::make_optional(checkpointData->subCheckpointData("thermostat impl"))
718 const std::string& VelocityScalingTemperatureCoupling::clientID()
723 real VelocityScalingTemperatureCoupling::conservedEnergyContribution() const
725 return std::accumulate(temperatureCouplingIntegral_.begin(), temperatureCouplingIntegral_.end(), 0.0);
728 std::optional<SignallerCallback> VelocityScalingTemperatureCoupling::registerEnergyCallback(EnergySignallerEvent event)
730 if (event == EnergySignallerEvent::EnergyCalculationStep)
732 return [this](Step step, Time /*unused*/) { nextEnergyCalculationStep_ = step; };
737 ISimulatorElement* VelocityScalingTemperatureCoupling::getElementPointerImpl(
738 LegacySimulatorData* legacySimulatorData,
739 ModularSimulatorAlgorithmBuilderHelper* builderHelper,
740 StatePropagatorData gmx_unused* statePropagatorData,
741 EnergyData* energyData,
742 FreeEnergyPerturbationData gmx_unused* freeEnergyPerturbationData,
743 GlobalCommunicationHelper gmx_unused* globalCommunicationHelper,
744 ObservablesReducer* /*observablesReducer*/,
746 UseFullStepKE useFullStepKE,
747 ReportPreviousStepConservedEnergy reportPreviousStepConservedEnergy,
748 const PropagatorTag& propagatorTag)
750 // Element is now owned by the caller of this method, who will handle lifetime (see ModularSimulatorAlgorithm)
751 auto* element = builderHelper->storeElement(std::make_unique<VelocityScalingTemperatureCoupling>(
752 legacySimulatorData->inputrec->nsttcouple,
755 reportPreviousStepConservedEnergy,
756 legacySimulatorData->inputrec->ld_seed,
757 legacySimulatorData->inputrec->opts.ngtc,
758 legacySimulatorData->inputrec->delta_t * legacySimulatorData->inputrec->nsttcouple,
759 legacySimulatorData->inputrec->opts.ref_t,
760 legacySimulatorData->inputrec->opts.tau_t,
761 legacySimulatorData->inputrec->opts.nrdf,
763 legacySimulatorData->inputrec->etc));
764 auto* thermostat = static_cast<VelocityScalingTemperatureCoupling*>(element);
765 // Capturing pointer is safe because lifetime is handled by caller
766 builderHelper->registerTemperaturePressureControl(
767 [thermostat, propagatorTag](const PropagatorConnection& connection) {
768 thermostat->connectWithMatchingPropagator(connection, propagatorTag);
770 builderHelper->registerReferenceTemperatureUpdate(
771 [thermostat](ArrayRef<const real> temperatures, ReferenceTemperatureChangeAlgorithm algorithm) {
772 thermostat->updateReferenceTemperature(temperatures, algorithm);