Description

The StatePropagatorData::Element takes part in the simulator run, as it might have to save a valid state at the right moment during the integration. Placing the StatePropagatorData::Element correctly is the duty of the simulator builder - this might be automatized later if we have enough meta-data of the variables (i.e., if StatePropagatorData knows at which time the variables currently are, and can decide when a valid state (full-time step of all variables) is reached. The StatePropagatorData::Element is also a client of both the trajectory signaller and writer - it will save a state for later writeout during the simulator step if it knows that trajectory writing will occur later in the step, and it knows how to write to file given a file pointer by the TrajectoryElement. It is also responsible to store the state for checkpointing.

Public Member Functions
	Element (StatePropagatorData statePropagatorData, FILE fplog, const t_commrec cr, int nstxout, int nstvout, int nstfout, int nstxout_compressed, bool canMoleculesBeDistributedOverPBC, bool writeFinalConfiguration, std::string finalConfigurationFilename, const t_inputrec inputrec, const gmx_mtop_t &globalTop)
	Constructor.

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

void	elementSetup () override
	Backup starting velocities. More...

void	elementTeardown () override
	No element teardown needed.

void	setFreeEnergyPerturbationData (FreeEnergyPerturbationData *freeEnergyPerturbationData)
	Set free energy data.

void	saveCheckpointState (std::optional< WriteCheckpointData > checkpointData, const t_commrec *cr) override
	ICheckpointHelperClient write checkpoint implementation.

void	restoreCheckpointState (std::optional< ReadCheckpointData > checkpointData, const t_commrec *cr) override
	ICheckpointHelperClient read checkpoint implementation.

const std::string &	clientID () override
	ICheckpointHelperClient key implementation.

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

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

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

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

Public Member Functions inherited from gmx::ILastStepSignallerClient
virtual	~ILastStepSignallerClient ()=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)
	Factory method implementation. More...

Additional Inherited Members
Protected Member Functions inherited from gmx::ITrajectoryWriterClient
virtual void	trajectoryWriterSetup (gmx_mdoutf *outf)=0
	Setup method with valid output pointer.

Member Function Documentation

void gmx::StatePropagatorData::Element::elementSetup ( )

overridevirtual

Backup starting velocities.

This is only needed for vv, where the first (velocity) half step is only used to compute the constraint virial, but the velocities need to be reset after. TODO: There must be a more elegant solution to this!

Implements gmx::ISimulatorElement.

ISimulatorElement * gmx::StatePropagatorData::Element::getElementPointerImpl	(	LegacySimulatorData *	legacySimulatorData,
		ModularSimulatorAlgorithmBuilderHelper *	builderHelper,
		StatePropagatorData *	statePropagatorData,
		EnergyData *	energyData,
		FreeEnergyPerturbationData *	freeEnergyPerturbationData,
		GlobalCommunicationHelper *	globalCommunicationHelper,
		ObservablesReducer *	observablesReducer
	)

static

Factory method implementation.

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

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

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

overridevirtual

Register run function for step / time.

This needs to be called during the integration part of the simulator, at the moment at which the state is at a full time step. Positioning this element is the responsibility of the programmer writing the integration algorithm! If the current step is a trajectory writing step, StatePropagatorData will save a backup for later writeout.

This is also the place at which the current state becomes the previous state.

Parameters

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

Implements gmx::ISimulatorElement.

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

src/gromacs/modularsimulator/statepropagatordata.h
src/gromacs/modularsimulator/statepropagatordata.cpp

Description

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Member Function Documentation