Package etomica.integrator

Class IntegratorGear4

java.lang.Object

etomica.integrator.Integrator

etomica.integrator.IntegratorBox

etomica.integrator.IntegratorMD

etomica.integrator.IntegratorGear4

All Implemented Interfaces:

AtomLeafAgentManager.AgentSource<IntegratorGear4.Agent>, BoxEventListener

public class IntegratorGear4
extends IntegratorMD
implements AtomLeafAgentManager.AgentSource<IntegratorGear4.Agent>

Gear 4th-order predictor-corrector integrator.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	IntegratorGear4.Agent

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<IntegratorGear4.Agent>	agentManager
protected AtomLeafAgentManager<Vector>	forces

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
IntegratorGear4(PotentialMaster potentialMaster, IRandom random, double timeStep, double temperature, Box box)
IntegratorGear4(Simulation sim, PotentialMaster potentialMaster, Box box)

Method Summary

Modifier and Type	Method	Description
protected void	calculateForces()
protected void	corrector()
protected void	doStepInternal()	Performs the elementary integration step, such as a molecular dynamics time step, or a Monte Carlo trial.
IntegratorGear4.Agent	makeAgent(IAtom a, Box agentBox)	Returns an agent for the given Atom.
protected void	predictor()
void	releaseAgent(IntegratorGear4.Agent 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	setTimeStep(double dt)

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, setup, shiftMomenta

Methods inherited from class java.lang.Object

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

Field Detail

agentManager

protected AtomLeafAgentManager<IntegratorGear4.Agent> agentManager

forces

protected AtomLeafAgentManager<Vector> forces

Constructor Detail

IntegratorGear4

public IntegratorGear4(Simulation sim,
                       PotentialMaster potentialMaster,
                       Box box)

IntegratorGear4

public IntegratorGear4(PotentialMaster potentialMaster,
                       IRandom random,
                       double timeStep,
                       double temperature,
                       Box box)

Method Detail

setTimeStep

public void setTimeStep(double dt)

Overrides:

setTimeStep in class IntegratorMD

Parameters:

dt - the new integration time step

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

calculateForces

protected void calculateForces()

corrector

protected void corrector()

predictor

protected void predictor()

reset

public void reset()

Description copied from class: IntegratorBox

Performs superclass reset actions and recalculated currentPotentialEnergy

Overrides:

reset in class IntegratorMD

makeAgent

public IntegratorGear4.Agent 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<IntegratorGear4.Agent>

agentBox - TODO

releaseAgent

public void releaseAgent(IntegratorGear4.Agent 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<IntegratorGear4.Agent>