Description

Element propagating the Nose-Hoover chains.

This propagates the Nose-Hoover chain degrees of freedom, and transmits the scaling factor to a connected propagator.

Public Member Functions
	NoseHooverChainsElement (int nstcouple, int offset, NhcUsage nhcUsage, UseFullStepKE useFullStepKE, double propagationTimeStep, ScheduleOnInitStep scheduleOnInitStep, Step initStep, EnergyData energyData, NoseHooverChainsData noseHooverChainData, MttkData *mttkData)
	Constructor.

void	scheduleTask (Step step, Time time, const RegisterRunFunction &registerRunFunction) override
	Register run function for step / time. More...

void	elementSetup () override
	Sanity check at setup time.

void	elementTeardown () override
	No element teardown needed.

void	connectWithPropagator (const PropagatorConnection &connectionData, const PropagatorTag &propagatorTag)
	Connect this to propagator.

Public Member Functions inherited from gmx::ISimulatorElement
virtual	~ISimulatorElement ()=default
	Standard virtual destructor.

Static Public Member Functions
static ISimulatorElement *	getElementPointerImpl (LegacySimulatorData legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper builderHelper, StatePropagatorData statePropagatorData, EnergyData energyData, FreeEnergyPerturbationData freeEnergyPerturbationData, GlobalCommunicationHelper globalCommunicationHelper, ObservablesReducer *observablesReducer, NhcUsage nhcUsage, Offset offset, UseFullStepKE useFullStepKE, ScheduleOnInitStep scheduleOnInitStep, const MttkPropagatorConnectionDetails &mttkPropagatorConnectionDetails)
	Factory method implementation (no propagator connection) More...

static ISimulatorElement *	getElementPointerImpl (LegacySimulatorData legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper builderHelper, StatePropagatorData statePropagatorData, EnergyData energyData, FreeEnergyPerturbationData freeEnergyPerturbationData, GlobalCommunicationHelper globalCommunicationHelper, ObservablesReducer *observablesReducer, NhcUsage nhcUsage, Offset offset, UseFullStepKE useFullStepKE, ScheduleOnInitStep scheduleOnInitStep, const PropagatorTag &propagatorTag)
	Factory method implementation (including propagator connection) More...

Member Function Documentation

static ISimulatorElement* gmx::NoseHooverChainsElement::getElementPointerImpl	(	LegacySimulatorData *	legacySimulatorData,
		ModularSimulatorAlgorithmBuilderHelper *	builderHelper,
		StatePropagatorData *	statePropagatorData,
		EnergyData *	energyData,
		FreeEnergyPerturbationData *	freeEnergyPerturbationData,
		GlobalCommunicationHelper *	globalCommunicationHelper,
		ObservablesReducer *	observablesReducer,
		NhcUsage	nhcUsage,
		Offset	offset,
		UseFullStepKE	useFullStepKE,
		ScheduleOnInitStep	scheduleOnInitStep,
		const MttkPropagatorConnectionDetails &	mttkPropagatorConnectionDetails
	)

static

Factory method implementation (no propagator connection)

This signature is used to connect a Nose-Hoover chain to a barostat

Parameters

legacySimulatorData	Pointer allowing access to simulator level data
builderHelper	ModularSimulatorAlgorithmBuilder helper object
statePropagatorData	Pointer to the `StatePropagatorData` object
energyData	Pointer to the `EnergyData` object
freeEnergyPerturbationData	Pointer to the `FreeEnergyPerturbationData` object
globalCommunicationHelper	Pointer to the `GlobalCommunicationHelper` object
observablesReducer	Pointer to the `ObservablesReducer` object
nhcUsage	What the NHC is connected to - system or barostat
offset	The step offset at which the thermostat is applied
useFullStepKE	Whether full step or half step KE is used
scheduleOnInitStep	Whether the element is scheduled on the initial step
mttkPropagatorConnectionDetails	Connection information for the MTTK barostat

Returns: Pointer to the element to be added. Element needs to have been stored using storeElement

static ISimulatorElement* gmx::NoseHooverChainsElement::getElementPointerImpl	(	LegacySimulatorData *	legacySimulatorData,
		ModularSimulatorAlgorithmBuilderHelper *	builderHelper,
		StatePropagatorData *	statePropagatorData,
		EnergyData *	energyData,
		FreeEnergyPerturbationData *	freeEnergyPerturbationData,
		GlobalCommunicationHelper *	globalCommunicationHelper,
		ObservablesReducer *	observablesReducer,
		NhcUsage	nhcUsage,
		Offset	offset,
		UseFullStepKE	useFullStepKE,
		ScheduleOnInitStep	scheduleOnInitStep,
		const PropagatorTag &	propagatorTag
	)

static

Factory method implementation (including propagator connection)

Parameters

legacySimulatorData	Pointer allowing access to simulator level data
builderHelper	ModularSimulatorAlgorithmBuilder helper object
statePropagatorData	Pointer to the `StatePropagatorData` object
energyData	Pointer to the `EnergyData` object
freeEnergyPerturbationData	Pointer to the `FreeEnergyPerturbationData` object
globalCommunicationHelper	Pointer to the `GlobalCommunicationHelper` object
observablesReducer	Pointer to the `ObservablesReducer` object
nhcUsage	What the NHC is connected to - system or barostat
offset	The step offset at which the thermostat is applied
useFullStepKE	Whether full step or half step KE is used
scheduleOnInitStep	Whether the element is scheduled on the initial step
propagatorTag	Tag of the propagator to connect to

Returns: Pointer to the element to be added. Element needs to have been stored using storeElement

void gmx::NoseHooverChainsElement::scheduleTask	(	Step	step,
		Time	time,
		const RegisterRunFunction &	registerRunFunction
	)

overridevirtual

Register run function for step / time.

Parameters

step	The step number
time	The time
registerRunFunction	Function allowing to register a run function

The documentation for this class was generated from the following files: