Package etomica.normalmode

Class IntegratorHarmonic

java.lang.Object

etomica.integrator.Integrator

etomica.integrator.IntegratorBox

etomica.integrator.IntegratorMD

etomica.normalmode.IntegratorHarmonic

All Implemented Interfaces:

BoxEventListener

public class IntegratorHarmonic
extends IntegratorMD

Integrator that is used for the harmonic osciallating system

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 int	eValNum
protected boolean	isRejectable
protected double	lastEnergy
protected boolean	oneEVal
protected boolean	oneWV
protected double[][]	Qi
protected double[][]	Qr
protected double	temperature
protected double[]	u
protected int	waveVectorNum

Fields inherited from class etomica.integrator.Integrator

eventManager, initialized, interval, stepCount

Fields inherited from class etomica.integrator.IntegratorBox

box, currentPotentialEnergy, isothermal, meterPE, potentialMaster, space

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
IntegratorHarmonic(IRandom random, double timeStep, double temperature, Box box, CoordinateDefinition coordDef, Vector[] waveVectors)

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.
void	doThermostat()	Invokes thermostat, modifying velocities according to specified temperature and algorithm of thermostat specified via setThermostat.
CoordinateDefinition	getCoordinateDefinition()
int	getEValNum()
int	getWaveVectorNum()
Vector[]	getWaveVectors()
boolean	isOneEVal()
boolean	isOneWV()
void	setEigenVectors(double[][][] newEigenVectors)
void	setEValNum(int valNum)
void	setOmegaSquared(double[][] omega2, double[] coeff)
void	setOneEVal(boolean oneEVal)
void	setOneWV(boolean b)
void	setTemperature(double newTemperature)
void	setWaveVectorCoefficients(double[] newWaveVectorCoefficients)
void	setWaveVectorNum(int waveVectorNum)
void	setWaveVectors(Vector[] newWaveVectors)

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, doThermostatInternal, getAlwaysScaleRandomizedMomenta, getCurrentTime, getHybridAcceptance, getIntegratorMC, getKineticEnergy, getMeterTemperature, getThermostat, getThermostatInterval, getTimeStep, isThermostatNoDrift, randomizeMomenta, randomizeMomentum, randomizeTotalKE, reset, resetHybridAcceptance, resetStepCount, scaleMomenta, scaleMomenta, setAlwaysScaleRandomizedMomenta, setIntegratorMC, setIsothermal, setMeterTemperature, 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

u

protected double[] u

Qr

protected double[][] Qr

Qi

protected double[][] Qi

lastEnergy

protected double lastEnergy

temperature

protected double temperature

isRejectable

protected boolean isRejectable

oneWV

protected boolean oneWV

oneEVal

protected boolean oneEVal

waveVectorNum

protected int waveVectorNum

eValNum

protected int eValNum

Constructor Detail

IntegratorHarmonic

public IntegratorHarmonic(IRandom random,
                          double timeStep,
                          double temperature,
                          Box box,
                          CoordinateDefinition coordDef,
                          Vector[] waveVectors)

Method Detail

getCoordinateDefinition

public CoordinateDefinition getCoordinateDefinition()

getWaveVectors

public Vector[] getWaveVectors()

setWaveVectors

public void setWaveVectors(Vector[] newWaveVectors)

setOmegaSquared

public void setOmegaSquared(double[][] omega2,
                            double[] coeff)

setWaveVectorCoefficients

public void setWaveVectorCoefficients(double[] newWaveVectorCoefficients)

setEigenVectors

public void setEigenVectors(double[][][] newEigenVectors)

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

setTemperature

public void setTemperature(double newTemperature)

Overrides:

setTemperature in class IntegratorMD

Parameters:

newTemperature - the new temperature

doThermostat

public void doThermostat()

Description copied from class: IntegratorMD

Invokes thermostat, modifying velocities according to specified temperature and algorithm of thermostat specified via setThermostat.

Overrides:

doThermostat in class IntegratorMD

isOneWV

public boolean isOneWV()

setOneWV

public void setOneWV(boolean b)

getWaveVectorNum

public int getWaveVectorNum()

setWaveVectorNum

public void setWaveVectorNum(int waveVectorNum)

getEValNum

public int getEValNum()

isOneEVal

public boolean isOneEVal()

setOneEVal

public void setOneEVal(boolean oneEVal)

setEValNum

public void setEValNum(int valNum)