Package etomica.integrator

Class IntegratorVerlet

java.lang.Object

etomica.integrator.Integrator

etomica.integrator.IntegratorBox

etomica.integrator.IntegratorMD

etomica.integrator.IntegratorVerlet

All Implemented Interfaces:

AtomLeafAgentManager.AgentSource<IntegratorVerlet.Agent>, BoxEventListener

public final class IntegratorVerlet
extends IntegratorMD
implements AtomLeafAgentManager.AgentSource<IntegratorVerlet.Agent>

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	IntegratorVerlet.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<IntegratorVerlet.Agent>	agentManager
protected PotentialCalculationForcePressureSum	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
IntegratorVerlet(PotentialMaster potentialMaster, IRandom random, double timeStep, double temperature, Box box)
IntegratorVerlet(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.
Tensor	getPressureTensor()	Returns the pressure tensor based on the forces calculated during the last time step.
IntegratorVerlet.Agent	makeAgent(IAtom a, Box agentBox)	Returns an agent for the given Atom.
protected void	randomizeMomenta()	Updates MrLast appropriately after randomizing momenta as part of the Andersen thermostat.
protected void	randomizeMomentum(IAtomKinetic atom)	Updates MrLast appropriately after randomizing momentum as part of the Andersen thermostat.
void	releaseAgent(IntegratorVerlet.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 t)
protected void	updateMrLast()

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, 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

forceSum

protected final PotentialCalculationForcePressureSum forceSum

pressureTensor

protected final Tensor pressureTensor

workTensor

protected final Tensor workTensor

agentManager

protected AtomLeafAgentManager<IntegratorVerlet.Agent> agentManager

Constructor Detail

IntegratorVerlet

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

IntegratorVerlet

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

Method Detail

setTimeStep

public final void setTimeStep(double t)

Overrides:

setTimeStep in class IntegratorMD

Parameters:

t - 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

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

updateMrLast

protected void updateMrLast()

randomizeMomenta

protected void randomizeMomenta()

Updates MrLast appropriately after randomizing momenta as part of the Andersen thermostat.

Overrides:

randomizeMomenta in class IntegratorMD

randomizeMomentum

protected void randomizeMomentum(IAtomKinetic atom)

Updates MrLast appropriately after randomizing momentum as part of the Andersen thermostat.

Overrides:

randomizeMomentum in class IntegratorMD

Parameters:

atom - whose momenta is be randomized

makeAgent

public final IntegratorVerlet.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<IntegratorVerlet.Agent>

agentBox - TODO

releaseAgent

public void releaseAgent(IntegratorVerlet.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<IntegratorVerlet.Agent>