Package etomica.normalmode

Class SimOverlapModule

java.lang.Object

etomica.normalmode.SimOverlapModule

public class SimOverlapModule
extends java.lang.Object

Overlap sampling "module" to calculate free energy difference.

Field Summary

Fields

Modifier and Type	Field	Description
protected DataPumpListener[]	accumulatorPumps
protected Controller	controller
protected DataOverlap	dataOverlap
protected IntegratorOverlap	integratorOverlap
protected Integrator[]	integrators
protected MeterOverlap[]	meters
protected int	referenceDataInterval
protected int	targetDataInterval

Constructor Summary

Constructors

Constructor	Description
SimOverlapModule(Box boxReference, Box boxTarget, Integrator integratorReference, Integrator integratorTarget, IAPIPotential potentialReference, IAPIPotential potentialTarget, double temperature)

Method Summary

Modifier and Type	Method	Description
void	equilibrate(long initSteps)
double	getAlphaCenter()
DataOverlap	getDataOverlap()
IntegratorOverlap	getIntegratorOverlap()
int	getReferenceDataInterval()
int	getTargetDataInterval()
void	initRefPref(java.lang.String fileName, long initSteps)
void	setAlpha(double refPrefCenter, double span)
void	setIntegratorOverlap(IntegratorOverlap integratorOverlap)
void	setReferenceDataInterval(int newReferenceDataInterval)
void	setTargetDataInterval(int newTargetDataInterval)

Methods inherited from class java.lang.Object

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

Field Detail

integratorOverlap

protected IntegratorOverlap integratorOverlap

dataOverlap

protected DataOverlap dataOverlap

integrators

protected Integrator[] integrators

accumulatorPumps

protected DataPumpListener[] accumulatorPumps

meters

protected MeterOverlap[] meters

controller

protected Controller controller

targetDataInterval

protected int targetDataInterval

referenceDataInterval

protected int referenceDataInterval

Constructor Detail

SimOverlapModule

public SimOverlapModule(Box boxReference,
                        Box boxTarget,
                        Integrator integratorReference,
                        Integrator integratorTarget,
                        IAPIPotential potentialReference,
                        IAPIPotential potentialTarget,
                        double temperature)

Method Detail

setTargetDataInterval

public void setTargetDataInterval(int newTargetDataInterval)

getTargetDataInterval

public int getTargetDataInterval()

setReferenceDataInterval

public void setReferenceDataInterval(int newReferenceDataInterval)

getReferenceDataInterval

public int getReferenceDataInterval()

getIntegratorOverlap

public IntegratorOverlap getIntegratorOverlap()

setIntegratorOverlap

public void setIntegratorOverlap(IntegratorOverlap integratorOverlap)

getDataOverlap

public DataOverlap getDataOverlap()

getAlphaCenter

public double getAlphaCenter()

setAlpha

public void setAlpha(double refPrefCenter,
                     double span)

initRefPref

public void initRefPref(java.lang.String fileName,
                        long initSteps)

equilibrate

public void equilibrate(long initSteps)