Package etomica.modules.rheology

Class IntegratorPolymer

java.lang.Object

etomica.integrator.Integrator

etomica.integrator.IntegratorBox

etomica.integrator.IntegratorMD

etomica.modules.rheology.IntegratorPolymer

All Implemented Interfaces:

BoxEventListener

public class IntegratorPolymer
extends IntegratorMD

Integrator for Brownian dynamics of a polymer in a flow field.

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 double	a
protected double	b
protected Vector	center
protected Vector	dr
protected Vector	drPrev
protected Vector	ds
protected double[]	fQ
protected double	omdth
protected Vector[]	r
protected Vector[]	s
protected double	shearRate
protected double	sqdt
protected Vector[]	W

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
IntegratorPolymer(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.
protected void	doThermostatInternal()	Fires the thermostat if the appropriate interval has been reached.
double	getA()
double	getB()
double	getShearRate()
double	getShearRateNumber()
void	setA(double newA)
void	setB(double newB)
void	setShearRateNumber(double newShearRate)
void	setTimeStep(double newTimeStep)

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, getAlwaysScaleRandomizedMomenta, getCurrentTime, getHybridAcceptance, getIntegratorMC, getKineticEnergy, getMeterTemperature, getThermostat, getThermostatInterval, getTimeStep, isThermostatNoDrift, randomizeMomenta, randomizeMomentum, randomizeTotalKE, reset, 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

drPrev

protected final Vector drPrev

dr

protected final Vector dr

ds

protected final Vector ds

center

protected final Vector center

omdth

protected double omdth

sqdt

protected double sqdt

shearRate

protected double shearRate

a

protected double a

b

protected double b

W

protected Vector[] W

s

protected Vector[] s

r

protected Vector[] r

fQ

protected double[] fQ

Constructor Detail

IntegratorPolymer

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

Method Detail

doThermostatInternal

protected void doThermostatInternal()

Description copied from class: IntegratorMD

Fires the thermostat if the appropriate interval has been reached.

Overrides:

doThermostatInternal in class IntegratorMD

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

setTimeStep

public void setTimeStep(double newTimeStep)

Overrides:

setTimeStep in class IntegratorMD

Parameters:

newTimeStep - the new integration time step

setShearRateNumber

public void setShearRateNumber(double newShearRate)

getShearRate

public double getShearRate()

getShearRateNumber

public double getShearRateNumber()

getA

public double getA()

setA

public void setA(double newA)

getB

public double getB()

setB

public void setB(double newB)