#include <gromacs/modularsimulator/energydata.h>

Description

Data class managing energies.

The EnergyData owns the EnergyObject, the tensors for the different virials and the pressure as well as the total dipole vector. It has a member class which is part of the simulator loop and and is responsible for saving energy data and writing it to trajectory.

The EnergyData offers an interface to add virial contributions, but also allows access to the raw pointers to tensor data, the dipole vector, and the legacy energy data structures.

The EnergyData owns an object of type EnergyData::Element, which takes part in the simulation loop, allowing to record and output energies during the simulation.

Classes
class	Element
	Element for EnergyData. More...

Public Member Functions
	EnergyData (StatePropagatorData statePropagatorData, FreeEnergyPerturbationData freeEnergyPerturbationData, const gmx_mtop_t &globalTopology, const t_inputrec inputrec, const MDAtoms mdAtoms, gmx_enerdata_t enerd, gmx_ekindata_t ekind, const Constraints constr, FILE fplog, t_fcdata fcd, const MDModulesNotifiers &mdModulesNotifiers, bool isMainRank, ObservablesHistory observablesHistory, StartingBehavior startingBehavior, bool simulationsShareHamiltonian, pull_t *pullWork)
	Constructor.

void	teardown ()
	Final output. More...

void	addToForceVirial (const tensor virial, Step step)
	Add contribution to force virial. More...

void	addToConstraintVirial (const tensor virial, Step step)
	Add contribution to constraint virial. More...

rvec *	forceVirial (Step step)
	Get pointer to force virial tensor. More...

rvec *	constraintVirial (Step step)
	Get pointer to constraint virial tensor. More...

rvec *	totalVirial (Step step)
	Get pointer to total virial tensor. More...

rvec *	pressure (Step step)
	Get pointer to pressure tensor. More...

real *	muTot ()
	Get pointer to mu_tot. More...

gmx_enerdata_t *	enerdata ()
	Get pointer to energy structure. More...

const gmx_enerdata_t *	enerdata () const
	Get const pointer to energy structure. More...

gmx_ekindata_t *	ekindata ()
	Get pointer to kinetic energy structure. More...

bool *	needToSumEkinhOld ()
	Get pointer to needToSumEkinhOld. More...

bool	hasReadEkinFromCheckpoint () const
	Whether kinetic energy was read from checkpoint. More...

void	addConservedEnergyContribution (EnergyContribution &&energyContribution)
	Add conserved energy contribution. More...

void	setParrinelloRahmanBoxVelocities (std::function< const rvec *()> &&parrinelloRahmanBoxVelocities)
	set Parrinello-Rahman barostat More...

void	updateKineticEnergy ()
	Request (local) kinetic energy update.

Element *	element ()
	Get pointer to element (whose lifetime is managed by this)

Static Public Member Functions
static void	initializeEnergyHistory (StartingBehavior startingBehavior, ObservablesHistory observablesHistory, EnergyOutput energyOutput)
	Initialize energy history. More...

Member Function Documentation

void gmx::EnergyData::addConservedEnergyContribution ( EnergyContribution && energyContribution )

Add conserved energy contribution.

This allows other elements to register callbacks for contributions to the conserved energy term.

void gmx::EnergyData::addToConstraintVirial	(	const tensor	virial,
		Step	step
	)

Add contribution to constraint virial.

This automatically resets the tensor if the step is higher than the current step, starting the tensor calculation for a new step at zero. Otherwise, it adds the new contribution to the existing virial.

void gmx::EnergyData::addToForceVirial	(	const tensor	virial,
		Step	step
	)

Add contribution to force virial.

This automatically resets the tensor if the step is higher than the current step, starting the tensor calculation for a new step at zero. Otherwise, it adds the new contribution to the existing virial.

rvec * gmx::EnergyData::constraintVirial ( Step step )

Get pointer to constraint virial tensor.

Allows access to the raw pointer to the tensor.

gmx_ekindata_t * gmx::EnergyData::ekindata ( )

Get pointer to kinetic energy structure.

gmx_enerdata_t * gmx::EnergyData::enerdata ( )

Get pointer to energy structure.

const gmx_enerdata_t * gmx::EnergyData::enerdata ( ) const

Get const pointer to energy structure.

rvec * gmx::EnergyData::forceVirial ( Step step )

Get pointer to force virial tensor.

Allows access to the raw pointer to the tensor.

bool gmx::EnergyData::hasReadEkinFromCheckpoint ( ) const

Whether kinetic energy was read from checkpoint.

This is needed by the compute globals element TODO: Remove this when moving global reduction to client system (#3421)

void gmx::EnergyData::initializeEnergyHistory	(	StartingBehavior	startingBehavior,
		ObservablesHistory *	observablesHistory,
		EnergyOutput *	energyOutput
	)

static

Initialize energy history.

Kept as a static function to allow usage from legacy code

Todo:: Make member function once legacy use is not needed anymore

real * gmx::EnergyData::muTot ( )

Get pointer to mu_tot.

Allows access to the raw pointer to the dipole vector.

bool * gmx::EnergyData::needToSumEkinhOld ( )

Get pointer to needToSumEkinhOld.

rvec * gmx::EnergyData::pressure ( Step step )

Get pointer to pressure tensor.

Allows access to the raw pointer to the tensor.

void gmx::EnergyData::setParrinelloRahmanBoxVelocities ( std::function< const rvec *()> && parrinelloRahmanBoxVelocities )

set Parrinello-Rahman barostat

This allows to set a pointer to the Parrinello-Rahman barostat used to print the box velocities.

void gmx::EnergyData::teardown ( )

Final output.

Prints the averages to log. This is called from ModularSimulatorAlgorithm.

See Also: ModularSimulatorAlgorithm::teardown

rvec * gmx::EnergyData::totalVirial ( Step step )

Get pointer to total virial tensor.

Allows access to the raw pointer to the tensor.

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

src/gromacs/modularsimulator/energydata.h
src/gromacs/modularsimulator/energydata.cpp

Description

Classes

Public Member Functions

Static Public Member Functions

Member Function Documentation