Package etomica.freeenergy.npath

Class IntegratorMDHarmonicMC

java.lang.Object

etomica.integrator.Integrator

etomica.integrator.IntegratorBox

etomica.integrator.IntegratorMD

etomica.integrator.IntegratorVelocityVerlet

etomica.freeenergy.npath.IntegratorMDHarmonicMC

All Implemented Interfaces:

AtomLeafAgentManager.AgentSource<Vector>, BoxEventListener

public class IntegratorMDHarmonicMC
extends IntegratorVelocityVerlet

Created by andrew on 4/30/17.

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 Boundary	boundary
protected double	chiSum
protected Vector	dr
protected Vector[]	drAll
protected Vector	drTmp
protected Vector	dv
protected Vector	dvTmp
protected boolean	firstTrial
protected Vector	fTot
protected int	nAttempted
protected P1ImageHarmonic	p1
protected Vector	vTot

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

Fields inherited from class etomica.integrator.IntegratorVelocityVerlet

agentManager, allAtoms, forceSum, pressureTensor, workTensor

Constructor Summary

Constructors

Constructor	Description
IntegratorMDHarmonicMC(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.
double	getAcceptanceProbability()
void	resetAcceptance()
void	setP1Harmonic(P1ImageHarmonic p1)

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 etomica.integrator.IntegratorVelocityVerlet

getAgentManager, getForceSum, getPressureTensor, makeAgent, releaseAgent, reset, setForceSum

Methods inherited from class java.lang.Object

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

Field Detail

dr

protected final Vector dr

drTmp

protected final Vector drTmp

dv

protected final Vector dv

dvTmp

protected final Vector dvTmp

fTot

protected final Vector fTot

vTot

protected final Vector vTot

p1

protected P1ImageHarmonic p1

boundary

protected Boundary boundary

drAll

protected Vector[] drAll

firstTrial

protected boolean firstTrial

nAttempted

protected int nAttempted

chiSum

protected double chiSum

Constructor Detail

IntegratorMDHarmonicMC

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

Method Detail

setP1Harmonic

public void setP1Harmonic(P1ImageHarmonic p1)

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 IntegratorVelocityVerlet

resetAcceptance

public void resetAcceptance()

getAcceptanceProbability

public double getAcceptanceProbability()