geneticAlgorithm.evaluationFunctions

Class BasicGrowthPsdEvaluator

java.lang.Object

geneticAlgorithm.evaluationFunctions.AbstractEvaluator

geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator

geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator

All Implemented Interfaces:

IEvaluation

public class BasicGrowthPsdEvaluator
extends AbstractPsdEvaluator

Author:

N. Ferrando, J. Alberdi-Rodriguez

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	BasicGrowthPsdEvaluator.Runner Inner class responsible to update the interface.

Field Summary

Fields

Modifier and Type	Field and Description
private BasicGrowthPsdEvaluator.Runner	currentRun Current thread, responsible to run many KMCs to compute a PSD.
private double	g2g1
private double	g3g0
private double	g3g1
private double	g3g2
private double	g3g4
private double	g4g0
private double	g4g1
private double	hierarchyFrobeniusRef
private BasicGrowthKmc	kmc
private int	kmcError
private PsdSignature2D	psd
private float[][]	sampledSurface
private boolean	searchEnergies
private int	simulationCount
private float	temperature Temperature of the simulation.

Constructor Summary

Constructors

Constructor and Description
BasicGrowthPsdEvaluator(BasicGrowthKmc kmc, int repeats, int measureInterval, int psdSizeX, int psdSizeY, java.util.Set flags, java.lang.String hierarchyEvaluator, java.lang.String evolutionarySearchType, float temperature)

Method Summary

Modifier and Type	Method and Description
protected double	calculateHierarchyError(Individual ind) Calculates the hierarchy error based on the rates of Cox et al.
protected double	calculateHierarchyErrorDiscrete(Individual ind) If the difference is lower than 1, error is not added; otherwise, error is added by one.
protected double	calculateHierarchyErrorFrobenius(Individual ind)
protected double	calculateHierarchyErrorFromReference(Individual ind) Calculates the hierarchy error based on the rates of Cox et al.
protected double	calculateHierarchyErrorOrder(Individual ind) Adds the error if the next condition is not fulfilled: E_f > E_b > E_a > E_d > E_e > E_c g(3) > g(5) > g(4) > g(0) > g(2) > g(1)
float[][]	calculatePsdFromIndividual(Individual ind)
void	dispose()
private double	getMaxIteration()
private double	getRate(double gene)
double[]	getRates5(double[] genes) Calculates rates from the genes.
int	getSimulationCount() Method thought to be called from the main interface updater.
float[][]	getSurface()
void	killThread()
void	setHierarchy(double[] genes) Sets the expected rates hierarchies, based on the objective rates (genes).
private double	stepFunction(double division)

Methods inherited from class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator

calculateFrobeniusNormErrorMatrix, evaluate, getCurrentDifference, getCurrentError, getCurrentIteration, getCurrentPopulation, getCurrentPsd, getCurrentSimulation, getIndividualCount, getMeasureInterval, getProgressPercent, getPsdSizeX, getPsdSizeY, getRepeats, hasKmcFailed, kmcHasFailed, resetKmcError, setCurrentPopulation, setCurrentSimulation, setExpectedSimulationTime, setPsd, setPsdSizeX, setPsdSizeY, setRepeats

Methods inherited from class geneticAlgorithm.evaluationFunctions.AbstractEvaluator

getWheight, setShowGraphics, setWheight, showGraphics

Methods inherited from class java.lang.Object

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

Field Detail

kmc

private BasicGrowthKmc kmc

g4g0

private double g4g0

g3g0

private double g3g0

g3g1

private double g3g1

g3g2

private double g3g2

g3g4

private double g3g4

g4g1

private double g4g1

g2g1

private double g2g1

hierarchyFrobeniusRef

private double hierarchyFrobeniusRef

searchEnergies

private boolean searchEnergies

psd

private PsdSignature2D psd

kmcError

private int kmcError

simulationCount

private int simulationCount

sampledSurface

private float[][] sampledSurface

temperature

private final float temperature

Temperature of the simulation. Useful when searching for energies.

currentRun

private BasicGrowthPsdEvaluator.Runner currentRun

Current thread, responsible to run many KMCs to compute a PSD.

Constructor Detail

BasicGrowthPsdEvaluator

public BasicGrowthPsdEvaluator(BasicGrowthKmc kmc,
                               int repeats,
                               int measureInterval,
                               int psdSizeX,
                               int psdSizeY,
                               java.util.Set flags,
                               java.lang.String hierarchyEvaluator,
                               java.lang.String evolutionarySearchType,
                               float temperature)

Method Detail

calculatePsdFromIndividual

public float[][] calculatePsdFromIndividual(Individual ind)

Specified by:

calculatePsdFromIndividual in class AbstractPsdEvaluator

killThread

public void killThread()

getSurface

public float[][] getSurface()

Specified by:

getSurface in interface IEvaluation

Overrides:

getSurface in class AbstractEvaluator

getSimulationCount

public int getSimulationCount()

Method thought to be called from the main interface updater.

Specified by:

getSimulationCount in interface IEvaluation

Overrides:

getSimulationCount in class AbstractPsdEvaluator

Returns:

number of the current simulation

setHierarchy

public void setHierarchy(double[] genes)

Sets the expected rates hierarchies, based on the objective rates (genes). Not implemented (only a copy of Ag)

Specified by:

setHierarchy in class AbstractPsdEvaluator

Parameters:

genes -

calculateHierarchyErrorDiscrete

protected double calculateHierarchyErrorDiscrete(Individual ind)

If the difference is lower than 1, error is not added; otherwise, error is added by one.

Specified by:

calculateHierarchyErrorDiscrete in class AbstractPsdEvaluator

Parameters:

ind -

Returns:

calculated error

stepFunction

private double stepFunction(double division)

calculateHierarchyErrorOrder

protected double calculateHierarchyErrorOrder(Individual ind)

Adds the error if the next condition is not fulfilled: E_f > E_b > E_a > E_d > E_e > E_c g(3) > g(5) > g(4) > g(0) > g(2) > g(1)

Parameters:

ind -

Returns:

calculated error

calculateHierarchyErrorFromReference

protected double calculateHierarchyErrorFromReference(Individual ind)

Calculates the hierarchy error based on the rates of Cox et al.

Specified by:

calculateHierarchyErrorFromReference in class AbstractPsdEvaluator

Parameters:

ind - Current individual

Returns:

normalised hierarchy error

calculateHierarchyErrorFrobenius

protected double calculateHierarchyErrorFrobenius(Individual ind)

calculateHierarchyError

protected double calculateHierarchyError(Individual ind)

Calculates the hierarchy error based on the rates of Cox et al.

Specified by:

calculateHierarchyError in class AbstractPsdEvaluator

Parameters:

ind - Current individual

Returns:

hierarchy error, at least 6.52e-2

dispose

public void dispose()

Specified by:

dispose in class AbstractEvaluator

getRates5

public double[] getRates5(double[] genes)

Calculates rates from the genes. Some of the rates are 0, the rest is calculated from the given genes. Ratio (energy type) | ratio index 0) E_d (0,j) Terrace to any 1) E_c (1,0) Edge to terrace 2) E_f (1,1) Edge to edge 3) E_a (1,2)=(1,3) Edge to kink or island 4) E_b (2,1)=(2,2)=(2,3) Kink to any (but terrace)

Parameters:

genes -

Returns:

rates

getRate

private double getRate(double gene)

getMaxIteration

private double getMaxIteration()