Package etomica.virial.simulations

Class SimulationVirialOverlap2

java.lang.Object

etomica.simulation.Simulation

etomica.virial.simulations.SimulationVirialOverlap2

public class SimulationVirialOverlap2
extends Simulation

Simulation implementing the overlap-sampling approach to evaluating a cluster diagram.

Field Summary

Fields

Modifier and Type	Field	Description
protected DataPumpListener[]	accumulatorPumps
AccumulatorRatioAverageCovarianceFull[]	accumulators
AccumulatorAverageCovariance	blockAccumulator
protected long	blockSize
BoxCluster[]	box
protected double[]	boxLengths
protected boolean	doWiggle
DataProcessorVirialOverlap[]	dpVirialOverlap
DataVirialOverlap	dvo
protected ClusterAbstract[]	extraTargetClusters
protected boolean	initialized
IntegratorOverlap	integratorOS
IntegratorMC[]	integrators
MCMoveBoxStep[]	mcMoveRotate
MCMoveBoxStep[]	mcMoveTranslate
MCMoveBoxStep[]	mcMoveWiggle
MeterVirial[]	meters
protected int[]	nMolecules
protected int	numAlpha
int	numExtraTargetClusters
double	refPref
protected ClusterWeight[]	sampleClusters
protected ISpecies[]	species
protected HistogramSimple	targHist
protected HistogramNotSoSimple	targPiHist
protected double	temperature
protected ClusterAbstract[]	valueClusters

Fields inherited from class etomica.simulation.Simulation

eventManager, random, seeds, space

Constructor Summary

Constructors

Constructor	Description
SimulationVirialOverlap2(Space aSpace, ISpecies[] species, int[] nMolecules, double temperature, ClusterAbstract[] aValueClusters, ClusterAbstract[] extraTargetClusters, ClusterWeight[] aSampleClusters, boolean doWiggle)
SimulationVirialOverlap2(Space aSpace, ISpecies[] species, int[] nMolecules, double temperature, ClusterAbstract[] aValueClusters, ClusterWeight[] aSampleClusters, boolean doWiggle)
SimulationVirialOverlap2(Space aSpace, ISpecies[] species, int[] nMolecules, double temperature, ClusterAbstract refCluster, ClusterAbstract targetCluster)	This constructor will create your simulation class, but you may call set methods before using it.
SimulationVirialOverlap2(Space aSpace, ISpecies species, double temperature, ClusterAbstract[] aValueClusters, ClusterWeight[] aSampleClusters, boolean doWiggle)
SimulationVirialOverlap2(Space aSpace, ISpecies species, double temperature, ClusterAbstract refCluster, ClusterAbstract targetCluster)
SimulationVirialOverlap2(Space aSpace, ISpecies species, double temperature, ClusterAbstract refCluster, ClusterAbstract targetCluster, boolean doWiggle)
SimulationVirialOverlap2(Space aSpace, ISpecies species, int nMolecules, double temperature, ClusterAbstract refCluster, ClusterAbstract targetCluster)	This constructor will create your simulation class, but you may call set methods before using it.

Method Summary

Modifier and Type	Method	Description
IntegratorListener	addProgressListener(double HSB, long interval)	Causes a progress report (coefficient value and uncertainty) 10 times during the course of the simulation.
IntegratorListener	addProgressListener(double HSB, long interval, boolean full)	Causes a progress report (coefficient value and uncertainty) 10 times during the course of the simulation.
void	equilibrate(java.lang.String fileName, long initSteps)
void	equilibrate(java.lang.String fileName, long initSteps, boolean runBlocking)
double[]	findUmbrellaWeights(java.lang.String uWeightsFileName, long uSteps)
boolean	getDoWiggle()
ClusterAbstract[]	getExtraTargetClusters()
Integrator	getIntegrator()
int	getNumAlpha()	Returns the number of alpha values used for the production stage of the simulation
ClusterWeight[]	getSampleClusters()
void	init()
protected void	initBlockAccumulator()
void	initRefPref(java.lang.String fileName, long initSteps)
void	initRefPref(java.lang.String fileName, long initSteps, boolean runBlocking)
void	printResults(double refIntegral)
void	printResults(double refIntegral, java.lang.String[] extraNames)
void	printTargetHistogram()	Prints out the target histogram of maximum separation distances as set up by setupTargetHistogram().
protected void	readBoxRestart(java.io.BufferedReader br, int iBox)
long	readRestart(java.lang.String restartFilename, boolean readRef)
void	setAccumulatorBlockSize(long newBlockSize)
void	setBoxLengths(double refLength, double targetLength)
void	setDoWiggle(boolean newDoWiggle)
void	setExtraTargetClusters(ClusterAbstract[] extraTargetClusters)
void	setNumAlpha(int newNumAlpha)	Sets the number of alpha values used for the production stage of the simulation.
void	setRefPref(double newRefPref)
void	setRefPref(double refPrefCenter, double span)
void	setSampleClusters(ClusterWeight[] sampleClusters)
void	setupTargetHistogram(long interval)	Sets up a histogram for the target system that measures how often maximum separation distances are visited.
void	setWriteRestart(java.lang.String restartFilename, boolean writeRef)
protected void	writeBoxRestart(java.io.FileWriter fw, int iBox)

Methods inherited from class java.lang.Object

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

Methods inherited from class etomica.simulation.Simulation

addBox, addSpecies, box, getBox, getBoxCount, getBoxes, getController, getEventManager, getRandom, getRandomSeeds, getSpace, getSpecies, getSpeciesCount, getSpeciesList, makeBox, makeBox, makeUniqueElementSymbol, removeBox, setRandom, species

Field Detail

accumulators

public final AccumulatorRatioAverageCovarianceFull[] accumulators

box

public final BoxCluster[] box

integrators

public final IntegratorMC[] integrators

meters

public final MeterVirial[] meters

dpVirialOverlap

public final DataProcessorVirialOverlap[] dpVirialOverlap

species

protected final ISpecies[] species

temperature

protected final double temperature

valueClusters

protected final ClusterAbstract[] valueClusters

nMolecules

protected final int[] nMolecules

sampleClusters

protected final ClusterWeight[] sampleClusters

dvo

public DataVirialOverlap dvo

blockAccumulator

public AccumulatorAverageCovariance blockAccumulator

mcMoveRotate

public MCMoveBoxStep[] mcMoveRotate

mcMoveTranslate

public MCMoveBoxStep[] mcMoveTranslate

mcMoveWiggle

public MCMoveBoxStep[] mcMoveWiggle

numExtraTargetClusters

public int numExtraTargetClusters

integratorOS

public IntegratorOverlap integratorOS

refPref

public double refPref

initialized

protected boolean initialized

doWiggle

protected boolean doWiggle

extraTargetClusters

protected ClusterAbstract[] extraTargetClusters

accumulatorPumps

protected DataPumpListener[] accumulatorPumps

blockSize

protected long blockSize

numAlpha

protected int numAlpha

targHist

protected HistogramSimple targHist

targPiHist

protected HistogramNotSoSimple targPiHist

boxLengths

protected double[] boxLengths

Constructor Detail

SimulationVirialOverlap2

public SimulationVirialOverlap2(Space aSpace,
                                ISpecies species,
                                int nMolecules,
                                double temperature,
                                ClusterAbstract refCluster,
                                ClusterAbstract targetCluster)

This constructor will create your simulation class, but you may call set methods before using it. When you are done calling set methods, you must call init() before using it.

SimulationVirialOverlap2

public SimulationVirialOverlap2(Space aSpace,
                                ISpecies[] species,
                                int[] nMolecules,
                                double temperature,
                                ClusterAbstract refCluster,
                                ClusterAbstract targetCluster)

This constructor will create your simulation class, but you may call set methods before using it. When you are done calling set methods, you must call init() before using it.

SimulationVirialOverlap2

public SimulationVirialOverlap2(Space aSpace,
                                ISpecies species,
                                double temperature,
                                ClusterAbstract refCluster,
                                ClusterAbstract targetCluster)

SimulationVirialOverlap2

public SimulationVirialOverlap2(Space aSpace,
                                ISpecies species,
                                double temperature,
                                ClusterAbstract refCluster,
                                ClusterAbstract targetCluster,
                                boolean doWiggle)

SimulationVirialOverlap2

public SimulationVirialOverlap2(Space aSpace,
                                ISpecies species,
                                double temperature,
                                ClusterAbstract[] aValueClusters,
                                ClusterWeight[] aSampleClusters,
                                boolean doWiggle)

SimulationVirialOverlap2

public SimulationVirialOverlap2(Space aSpace,
                                ISpecies[] species,
                                int[] nMolecules,
                                double temperature,
                                ClusterAbstract[] aValueClusters,
                                ClusterWeight[] aSampleClusters,
                                boolean doWiggle)

SimulationVirialOverlap2

public SimulationVirialOverlap2(Space aSpace,
                                ISpecies[] species,
                                int[] nMolecules,
                                double temperature,
                                ClusterAbstract[] aValueClusters,
                                ClusterAbstract[] extraTargetClusters,
                                ClusterWeight[] aSampleClusters,
                                boolean doWiggle)

Method Detail

getDoWiggle

public boolean getDoWiggle()

setDoWiggle

public void setDoWiggle(boolean newDoWiggle)

getExtraTargetClusters

public ClusterAbstract[] getExtraTargetClusters()

setExtraTargetClusters

public void setExtraTargetClusters(ClusterAbstract[] extraTargetClusters)

getSampleClusters

public ClusterWeight[] getSampleClusters()

setSampleClusters

public void setSampleClusters(ClusterWeight[] sampleClusters)

setBoxLengths

public void setBoxLengths(double refLength,
                          double targetLength)

init

public void init()

setAccumulatorBlockSize

public void setAccumulatorBlockSize(long newBlockSize)

setRefPref

public void setRefPref(double refPrefCenter,
                       double span)

getNumAlpha

public int getNumAlpha()

Returns the number of alpha values used for the production stage of the simulation

setNumAlpha

public void setNumAlpha(int newNumAlpha)

Sets the number of alpha values used for the production stage of the simulation. The default value (1) is sufficient most of the time.

initBlockAccumulator

protected void initBlockAccumulator()

setRefPref

public void setRefPref(double newRefPref)

addProgressListener

public IntegratorListener addProgressListener(double HSB,
                                              long interval)

Causes a progress report (coefficient value and uncertainty) 10 times during the course of the simulation. The listener is returned.

addProgressListener

public IntegratorListener addProgressListener(double HSB,
                                              long interval,
                                              boolean full)

Causes a progress report (coefficient value and uncertainty) 10 times during the course of the simulation. With full=true, the full output (as would be printed at the end of the simulation) is printed. The listener is returned.

setupTargetHistogram

public void setupTargetHistogram(long interval)

Sets up a histogram for the target system that measures how often maximum separation distances are visited. The histogram is printed out 10 times during the simulation and may also be printed at the end of the simulation via printTargetHistogram().

printTargetHistogram

public void printTargetHistogram()

Prints out the target histogram of maximum separation distances as set up by setupTargetHistogram().

findUmbrellaWeights

public double[] findUmbrellaWeights(java.lang.String uWeightsFileName,
                                    long uSteps)

initRefPref

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

initRefPref

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

readBoxRestart

protected void readBoxRestart(java.io.BufferedReader br,
                              int iBox)
                       throws java.io.IOException

Throws:

java.io.IOException

readRestart

public long readRestart(java.lang.String restartFilename,
                        boolean readRef)

equilibrate

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

equilibrate

public void equilibrate(java.lang.String fileName,
                        long initSteps,
                        boolean runBlocking)

writeBoxRestart

protected void writeBoxRestart(java.io.FileWriter fw,
                               int iBox)
                        throws java.io.IOException

Throws:

java.io.IOException

setWriteRestart

public void setWriteRestart(java.lang.String restartFilename,
                            boolean writeRef)

printResults

public void printResults(double refIntegral)

printResults

public void printResults(double refIntegral,
                         java.lang.String[] extraNames)

getIntegrator

public Integrator getIntegrator()

Overrides:

getIntegrator in class Simulation

Returns:

the Simulation's primary integrator. If the controller holds multiple integrators, the first is returned. If the first integrator holds sub-integrators, the top-level integrator is still returned. This method assumes the controller holds an ActivityIntegrate. Returns null if no integrator is found.