Package etomica.integrator

Class IntegratorVelocityVerletShake

java.lang.Object

etomica.integrator.Integrator

etomica.integrator.IntegratorBox

etomica.integrator.IntegratorMD

etomica.integrator.IntegratorVelocityVerletShake

All Implemented Interfaces:

BoxEventListener, SpeciesAgentManager.AgentSource

Direct Known Subclasses:

IntegratorVelocityVerletRattle

public class IntegratorVelocityVerletShake
extends IntegratorMD
implements SpeciesAgentManager.AgentSource

Integrator implementing SHAKE algorithm.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	IntegratorVelocityVerletShake.BondConstraints

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 Vector	dr
protected Vector[]	drOld
protected PotentialCalculationForceSum	forceSum
protected int	maxIterations
protected boolean[][]	moved
int	printInterval
protected SpeciesAgentManager	shakeAgentManager
protected double	shakeTol
protected Vector	temp

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
IntegratorVelocityVerletShake(Simulation sim, PotentialMaster potentialMaster, Box box)
IntegratorVelocityVerletShake(Simulation sim, PotentialMaster potentialMaster, IRandom random, double timeStep, double temperature, 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.
IntegratorVelocityVerletShake.BondConstraints	getBondConstratins(ISpecies species)
int	getMaxIterations()
SpeciesAgentManager	getShakeAgentManager()
double	getShakeTolerance()
java.lang.Object	makeAgent(ISpecies a)	Returns an agent for the given AtomType.
void	releaseAgent(java.lang.Object agent, ISpecies atom)	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	setBondConstraints(ISpecies species, int[][] bondedAtoms, double[] bondLengths)
void	setForceSum(PotentialCalculationForceSum pc)
void	setMaxIterations(int newMaxIterations)
void	setShakeTolerance(double newShakeTol)

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

shakeAgentManager

protected final SpeciesAgentManager shakeAgentManager

agentManager

protected AtomLeafAgentManager<Vector> agentManager

dr

protected final Vector dr

shakeTol

protected double shakeTol

maxIterations

protected int maxIterations

moved

protected boolean[][] moved

drOld

protected Vector[] drOld

temp

protected final Vector temp

printInterval

public int printInterval

Constructor Detail

IntegratorVelocityVerletShake

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

IntegratorVelocityVerletShake

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

Method Detail

setForceSum

public void setForceSum(PotentialCalculationForceSum pc)

setBondConstraints

public void setBondConstraints(ISpecies species,
                               int[][] bondedAtoms,
                               double[] bondLengths)

getBondConstratins

public IntegratorVelocityVerletShake.BondConstraints getBondConstratins(ISpecies species)

getShakeAgentManager

public SpeciesAgentManager getShakeAgentManager()

setShakeTolerance

public void setShakeTolerance(double newShakeTol)

getShakeTolerance

public double getShakeTolerance()

getMaxIterations

public int getMaxIterations()

setMaxIterations

public void setMaxIterations(int newMaxIterations)

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

reset

public void reset()

Description copied from class: IntegratorBox

Performs superclass reset actions and recalculated currentPotentialEnergy

Overrides:

reset in class IntegratorMD

makeAgent

public final java.lang.Object makeAgent(ISpecies a)

Description copied from interface: SpeciesAgentManager.AgentSource

Returns an agent for the given AtomType.

Specified by:

makeAgent in interface SpeciesAgentManager.AgentSource

releaseAgent

public void releaseAgent(java.lang.Object agent,
                         ISpecies atom)

Description copied from interface: SpeciesAgentManager.AgentSource

This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements.

Specified by:

releaseAgent in interface SpeciesAgentManager.AgentSource