Package etomica.integrator

Class IntegratorVelocityVerlet

java.lang.Object

etomica.integrator.Integrator

etomica.integrator.IntegratorBox

etomica.integrator.IntegratorMD

etomica.integrator.IntegratorVelocityVerlet

All Implemented Interfaces:

AtomLeafAgentManager.AgentSource<Vector>, BoxEventListener

Direct Known Subclasses:

IntegratorFixedWall, IntegratorImageHarmonicMD, IntegratorImageMultistepMD, IntegratorMDHarmonicMC, IntegratorVelocityVerletSAM

public class IntegratorVelocityVerlet
extends IntegratorMD
implements AtomLeafAgentManager.AgentSource<Vector>

Nested Class Summary

Nested classes/interfaces inherited from class etomica.integrator.Integrator

Integrator.Forcible, Integrator.Torquable

Nested classes/interfaces inherited from class etomica.integrator.IntegratorMD

IntegratorMD.ThermostatType, IntegratorMD.VectorSource

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomLeafAgentManager<Vector>	agentManager
protected IteratorDirective	allAtoms
protected PotentialCalculationForceSum	forceSum
protected Tensor	pressureTensor
protected Tensor	workTensor

Fields inherited from class etomica.integrator.Integrator

eventManager, initialized, interval, stepCount

Fields inherited from class etomica.integrator.IntegratorBox

box, currentPotentialEnergy, isothermal, meterPE, potentialMaster, space, temperature

Fields inherited from class etomica.integrator.IntegratorMD

alwaysScaleMomenta, atomActionRandomizeVelocity, currentKineticEnergy, currentTime, integratorMC, mcSteps, meterKE, meterTemperature, momentum, nAccepted, nRejected, oldEnergy, oldPositionAgentManager, oldPotentialEnergy, random, temperatureVec, thermostat, thermostatCount, thermostatInterval, thermostatNoDrift, thermostatting, timeStep

Constructor Summary

Constructors

Constructor	Description
IntegratorVelocityVerlet(PotentialMaster potentialMaster, IRandom random, double timeStep, double temperature, Box box)
IntegratorVelocityVerlet(Simulation sim, PotentialMaster potentialMaster, Box box)

Method Summary

Modifier and Type	Method	Description
protected void	doStepInternal()	Performs the elementary integration step, such as a molecular dynamics time step, or a Monte Carlo trial.
AtomLeafAgentManager<Vector>	getAgentManager()
PotentialCalculationForceSum	getForceSum()
Tensor	getPressureTensor()	Returns the pressure tensor based on the forces calculated during the last time step.
Vector	makeAgent(IAtom a, Box agentBox)	Returns an agent for the given Atom.
void	releaseAgent(Vector agent, IAtom atom, Box agentBox)	This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements.
void	reset()	Performs superclass reset actions and recalculated currentPotentialEnergy
void	setForceSum(PotentialCalculationForceSum pc)

Methods inherited from class etomica.integrator.Integrator

doStep, getEventInterval, getEventManager, getStepCount, isInitialized, setEventInterval

Methods inherited from class etomica.integrator.IntegratorBox

getBox, getMeterPotentialEnergy, getPotentialEnergy, getPotentialMaster, getTemperature, getTemperatureDimension, isIsothermal, setBox, setMeterPotentialEnergy

Methods inherited from class etomica.integrator.IntegratorMD

boxAtomLeafIndexChanged, boxGlobalAtomLeafIndexChanged, boxMoleculeAdded, boxMoleculeIndexChanged, boxMoleculeRemoved, boxNumberMolecules, doThermostat, doThermostatInternal, getAlwaysScaleRandomizedMomenta, getCurrentTime, getHybridAcceptance, getIntegratorMC, getKineticEnergy, getMeterTemperature, getThermostat, getThermostatInterval, getTimeStep, isThermostatNoDrift, randomizeMomenta, randomizeMomentum, randomizeTotalKE, resetHybridAcceptance, resetStepCount, scaleMomenta, scaleMomenta, setAlwaysScaleRandomizedMomenta, setIntegratorMC, setIsothermal, setMeterTemperature, setTemperature, setThermostat, setThermostatInterval, setThermostatNoDrift, setTimeStep, setup, shiftMomenta

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

forceSum

protected PotentialCalculationForceSum forceSum

allAtoms

protected final IteratorDirective allAtoms

pressureTensor

protected final Tensor pressureTensor

workTensor

protected final Tensor workTensor

agentManager

protected AtomLeafAgentManager<Vector> agentManager

Constructor Detail

IntegratorVelocityVerlet

public IntegratorVelocityVerlet(Simulation sim,
                                PotentialMaster potentialMaster,
                                Box box)

IntegratorVelocityVerlet

public IntegratorVelocityVerlet(PotentialMaster potentialMaster,
                                IRandom random,
                                double timeStep,
                                double temperature,
                                Box box)

Method Detail

getForceSum

public PotentialCalculationForceSum getForceSum()

getAgentManager

public AtomLeafAgentManager<Vector> getAgentManager()

setForceSum

public void setForceSum(PotentialCalculationForceSum pc)

doStepInternal

protected void doStepInternal()

Description copied from class: Integrator

Performs the elementary integration step, such as a molecular dynamics time step, or a Monte Carlo trial.

Overrides:

doStepInternal in class IntegratorMD

getPressureTensor

public Tensor getPressureTensor()

Returns the pressure tensor based on the forces calculated during the last time step.

reset

public void reset()

Description copied from class: IntegratorBox

Performs superclass reset actions and recalculated currentPotentialEnergy

Overrides:

reset in class IntegratorMD

makeAgent

public Vector makeAgent(IAtom a,
                        Box agentBox)

Description copied from interface: AtomLeafAgentManager.AgentSource

Returns an agent for the given Atom. The agentBox is provided for convenience for agent sources that handle multiple boxes.

Specified by:

makeAgent in interface AtomLeafAgentManager.AgentSource<Vector>

agentBox - TODO

releaseAgent

public void releaseAgent(Vector agent,
                         IAtom atom,
                         Box agentBox)

Description copied from interface: AtomLeafAgentManager.AgentSource

This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements. The agentBox is provided for convenience for agent sources that handle multiple boxes.

Specified by:

releaseAgent in interface AtomLeafAgentManager.AgentSource<Vector>