Package etomica.models.nitrogen

Class MeterTargetTPMolecule

java.lang.Object

etomica.models.nitrogen.MeterTargetTPMolecule

All Implemented Interfaces:

IDataSource

public class MeterTargetTPMolecule
extends java.lang.Object
implements IDataSource

For molecular model, e.g., diatomic Nitrogen model, with 5 d.o.f. or even molecular model with 6 d.o.f. d.o.f. = degrees of freedom. Meter that measures the overlap averages for perturbing from a solid at one temperature into other the system at other temperatures. The atoms are scaled back toward their lattice sites by a factor of Tp/T0, where T0 is the simulation temperature and Tp is the temperature being perturbed into. For the purposes of the overlap average, the lower temperature is considered the reference. ep/(e0 + alpha*ep) if Tp > T0 e0/(ep + alpha*e0) if T0 > Tp

Field Summary

Fields

Modifier and Type	Field	Description
protected double[][]	alpha
protected double[]	alphaCenter
protected double	alphaSpan
protected CoordinateDefinitionNitrogen	coordinateDefinition
protected DataDoubleArray	data
protected DataDoubleArray.DataInfoDoubleArray	dataInfo
protected java.io.FileWriter	fw
protected boolean	isBetaPhase
protected double	latticeEnergy
protected MeterPotentialEnergy	meterPotential
protected int	numAlpha
protected double[]	otherTemperatures
protected PotentialMaster	potentialMaster
protected Box	pretendBox
protected ISpecies	species
protected DataTag	tag
protected double	temperature

Constructor Summary

Constructors

Constructor	Description
MeterTargetTPMolecule(PotentialMaster potentialMaster, ISpecies species, Simulation sim, CoordinateDefinitionNitrogen coordinateDefinition)

Method Summary

Modifier and Type	Method	Description
void	closeFW()	Closes file with overlap data.
double[]	getAlpha(int iTemp)
CoordinateDefinitionNitrogen	getCoordinateDefinition()
IData	getData()
IDataInfo	getDataInfo()
double	getLatticeEnergy()
double[]	getOtherTemperatures()
DataTag	getTag()
double	getTemperature()
protected void	initAlpha()
boolean	isBetaPhase()
void	openFW(java.lang.String filename)	Writes collected overlap data (for the "middle" alpha) to a file.
void	setAlpha(double[] newAlpha)
void	setAlphaSpan(double newAlphaSpan)
void	setBetaPhase(boolean isBetaPhase)
void	setLatticeEnergy(double latticeEnergy)
void	setNumAlpha(int newNumAlpha)
void	setOtherTemperatures(double[] otherTemperatures)
void	setTemperature(double temperature)

Methods inherited from class java.lang.Object

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

Field Detail

meterPotential

protected final MeterPotentialEnergy meterPotential

potentialMaster

protected final PotentialMaster potentialMaster

latticeEnergy

protected double latticeEnergy

temperature

protected double temperature

otherTemperatures

protected double[] otherTemperatures

dataInfo

protected DataDoubleArray.DataInfoDoubleArray dataInfo

data

protected DataDoubleArray data

tag

protected final DataTag tag

pretendBox

protected final Box pretendBox

coordinateDefinition

protected final CoordinateDefinitionNitrogen coordinateDefinition

species

protected final ISpecies species

alpha

protected double[][] alpha

alphaCenter

protected double[] alphaCenter

alphaSpan

protected double alphaSpan

numAlpha

protected int numAlpha

fw

protected java.io.FileWriter fw

isBetaPhase

protected boolean isBetaPhase

Constructor Detail

MeterTargetTPMolecule

public MeterTargetTPMolecule(PotentialMaster potentialMaster,
                             ISpecies species,
                             Simulation sim,
                             CoordinateDefinitionNitrogen coordinateDefinition)

Method Detail

getDataInfo

public IDataInfo getDataInfo()

Specified by:

getDataInfo in interface IDataSource

getTag

public DataTag getTag()

Specified by:

getTag in interface IDataSource

Returns:

a tag that uniquely identifies the IDataInfo

getData

public IData getData()

Specified by:

getData in interface IDataSource

Returns:

the data given by this source

openFW

public void openFW(java.lang.String filename)

Writes collected overlap data (for the "middle" alpha) to a file. Only data for the first perturbed temperature is written.

closeFW

public void closeFW()

Closes file with overlap data.

getLatticeEnergy

public double getLatticeEnergy()

setLatticeEnergy

public void setLatticeEnergy(double latticeEnergy)

getTemperature

public double getTemperature()

setTemperature

public void setTemperature(double temperature)

getOtherTemperatures

public double[] getOtherTemperatures()

setOtherTemperatures

public void setOtherTemperatures(double[] otherTemperatures)

initAlpha

protected void initAlpha()

getAlpha

public double[] getAlpha(int iTemp)

setAlpha

public void setAlpha(double[] newAlpha)

setAlphaSpan

public void setAlphaSpan(double newAlphaSpan)

setNumAlpha

public void setNumAlpha(int newNumAlpha)

isBetaPhase

public boolean isBetaPhase()

setBetaPhase

public void setBetaPhase(boolean isBetaPhase)

getCoordinateDefinition

public CoordinateDefinitionNitrogen getCoordinateDefinition()