DataOverlap

java.lang.Object
- etomica.overlap.DataOverlap

All Implemented Interfaces:

IntegratorOverlap.ReferenceFracSource

Direct Known Subclasses:

DataOverlapCaching
```
public class DataOverlap
extends java.lang.Object
implements IntegratorOverlap.ReferenceFracSource
```
Utility class for overlap sampling. This class retrieves data from reference and target systems and calculates averages, ratios and uncertainties as well as corresponding quantities for the natural log. This class retrieves its information for a DataSourceOverlapAvg, which actually understands how to retrieve data from the reference or target systems.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`static interface`	`DataOverlap.DataSourceOverlapAvg`	Interface for a class capable of return the average and uncertainty for a particular value of alpha.
`static class`	`DataOverlap.DataSourceOverlapAvgCollapsing`	Implementation of DataSourceOverlapLogAvg that retrieves data from a splitter whose data is dumped into different AccumulatorAverageCollapsingLog instances.
`static class`	`DataOverlap.DataSourceOverlapAvgCollapsingSplit`
`static class`	`DataOverlap.DataSourceOverlapAvgSimple`	Implementation of DataSourceOverlapAvg that retrieves data from a single AccumulatorAverage
`static interface`	`DataOverlap.DataSourceOverlapLogAvg`	Interface for a class capable of return the average and uncertainty as well as the log of the average and the uncertainty in the log, for a particular value of alpha.

Field Summary

Fields
Modifier and Type	Field	Description
`protected AkimaSpline`	`akima`
`protected AlphaSource`	`alphaSource`
`boolean`	`dumpit`
`protected double[]`	`err`
`protected boolean`	`includeAntibiasErr`
`protected double[]`	`lnAlpha`
`protected double[]`	`lnAlphaDiff`
`protected double[]`	`lnRatio`
`protected static int`	`RATIO`
`protected static int`	`REF`
`protected DataOverlap.DataSourceOverlapAvg`	`refAvg`
`protected static int`	`TARGET`
`protected DataOverlap.DataSourceOverlapAvg`	`targetAvg`
`protected double[]`	`tmp`

Constructor Summary

Constructors
Constructor Description

DataOverlap(DataOverlap.DataSourceOverlapAvg refAvg, DataOverlap.DataSourceOverlapAvg targetAvg, AlphaSource alphaSource)

Constructors
Constructor	Description
`DataOverlap(DataOverlap.DataSourceOverlapAvg refAvg, DataOverlap.DataSourceOverlapAvg targetAvg, AlphaSource alphaSource)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`AlphaSource`	`getAlphaSource()`	Returns an object capable of returning the different alpha values being used.
`double`	`getAverage(int iAlpha)`	Returns the ratio of the reference to target overlap ratio reference/target for the given value alpha.
`double[]`	`getAverageAndError(boolean isReference, double iAlpha)`	Returns the average from the reference or target system (as specified) and its uncertainty for the given value of alpha
`double[]`	`getAverageAndError(double iAlpha)`	Returns the average ratio and its uncertainty for the given value of alpha
`protected double[]`	`getAverageAndError(int which, double iAlpha, boolean doLog)`
`double`	`getError(int iAlpha)`	Returns the error in the ratio of the reference to target overlap-to-virial ratios (which reduces to target/reference) for the given value of the Bennet parameter.
`double`	`getIdealRefFraction(double oldFrac)`	Returns the ideal fraction of time (or steps) spent in the reference system under the assumption that the current data while spending oldFrac amount of the calculation on the reference system.
`double[]`	`getLogAverageAndError(boolean isReference, double iAlpha)`	Returns the natural log of the average value from the reference or target system (as specified) and its uncertainty for the given value of alpha
`double[]`	`getLogAverageAndError(double iAlpha)`	Returns the natural log of the average ratio and its uncertainty for the given value of alpha
`double`	`getLogError(int iAlpha)`	Returns the uncertainty in the log of the average corresponding to the iAlpha value of alpha.
`double[]`	`getOverlapAverageAndError()`	Returns the ratio of the reference to target overlap-to-virial ratios (which reduces to reference/target) for the optimal value of the Bennett parameter.
`DataOverlap.DataSourceOverlapAvg`	`getRefSource()`	Returns object capable of retrieving data from the reference system.
`DataOverlap.DataSourceOverlapAvg`	`getTargetSource()`	Returns object capable of retrieving data from the target system.
`protected void`	`populateArrays(int which, boolean doLog)`
`void`	`setRefAvg(DataOverlap.DataSourceOverlapAvg newRefAvg)`
`void`	`setTargetAvg(DataOverlap.DataSourceOverlapAvg newTargetAvg)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - refAvg
```
protected DataOverlap.DataSourceOverlapAvg refAvg
```
  - targetAvg
```
protected DataOverlap.DataSourceOverlapAvg targetAvg
```
  - alphaSource
```
protected AlphaSource alphaSource
```
  - akima
```
protected AkimaSpline akima
```
  - lnAlpha
```
protected double[] lnAlpha
```
  - err
```
protected double[] err
```
  - lnAlphaDiff
```
protected double[] lnAlphaDiff
```
  - lnRatio
```
protected double[] lnRatio
```
  - tmp
```
protected double[] tmp
```
  - includeAntibiasErr
```
protected boolean includeAntibiasErr
```
  - REF
```
protected static final int REF
```
    See Also:
    
    Constant Field Values
  - TARGET
```
protected static final int TARGET
```
    See Also:
    
    Constant Field Values
  - RATIO
```
protected static final int RATIO
```
    See Also:
    
    Constant Field Values
  - dumpit
```
public boolean dumpit
```
- Constructor Detail
  - DataOverlap
```
public DataOverlap(DataOverlap.DataSourceOverlapAvg refAvg,
                   DataOverlap.DataSourceOverlapAvg targetAvg,
                   AlphaSource alphaSource)
```
- Method Detail
  - setRefAvg
```
public void setRefAvg(DataOverlap.DataSourceOverlapAvg newRefAvg)
```
  - setTargetAvg
```
public void setTargetAvg(DataOverlap.DataSourceOverlapAvg newTargetAvg)
```
  - getAlphaSource
```
public AlphaSource getAlphaSource()
```
    Returns an object capable of returning the different alpha values being used.
  - populateArrays
```
protected void populateArrays(int which,
                              boolean doLog)
```
  - getOverlapAverageAndError
```
public double[] getOverlapAverageAndError()
```
    Returns the ratio of the reference to target overlap-to-virial ratios (which reduces to reference/target) for the optimal value of the Bennett parameter. The optimal value is determined via interpolation of y=(ln(ratio) - ln(alpha)) vs. x=ln(alpha) and taking the x value where y=0. If there are at least 5 alpha values, Akima spline interpolation is used. With 1 alpha value, no interpolation is needed. With 3 alpha values, linear interpolation is used.
  - getLogAverageAndError
```
public double[] getLogAverageAndError(double iAlpha)
```
    Returns the natural log of the average ratio and its uncertainty for the given value of alpha
  - getLogAverageAndError
```
public double[] getLogAverageAndError(boolean isReference,
                                      double iAlpha)
```
    Returns the natural log of the average value from the reference or target system (as specified) and its uncertainty for the given value of alpha
  - getAverageAndError
```
public double[] getAverageAndError(double iAlpha)
```
    Returns the average ratio and its uncertainty for the given value of alpha
  - getAverageAndError
```
public double[] getAverageAndError(boolean isReference,
                                   double iAlpha)
```
    Returns the average from the reference or target system (as specified) and its uncertainty for the given value of alpha
  - getAverageAndError
```
protected double[] getAverageAndError(int which,
                                      double iAlpha,
                                      boolean doLog)
```
  - getIdealRefFraction
```
public double getIdealRefFraction(double oldFrac)
```
    Returns the ideal fraction of time (or steps) spent in the reference system under the assumption that the current data while spending oldFrac amount of the calculation on the reference system.
    
    Specified by:
    
    getIdealRefFraction in interface IntegratorOverlap.ReferenceFracSource
  - getRefSource
```
public DataOverlap.DataSourceOverlapAvg getRefSource()
```
    Returns object capable of retrieving data from the reference system.
  - getTargetSource
```
public DataOverlap.DataSourceOverlapAvg getTargetSource()
```
    Returns object capable of retrieving data from the target system.
  - getAverage
```
public double getAverage(int iAlpha)
```
    Returns the ratio of the reference to target overlap ratio reference/target for the given value alpha.
  - getLogError
```
public double getLogError(int iAlpha)
```
    Returns the uncertainty in the log of the average corresponding to the iAlpha value of alpha.
  - getError
```
public double getError(int iAlpha)
```
    Returns the error in the ratio of the reference to target overlap-to-virial ratios (which reduces to target/reference) for the given value of the Bennet parameter.

Class DataOverlap

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

refAvg

targetAvg

alphaSource

akima

lnAlpha

err

lnAlphaDiff

lnRatio

tmp

includeAntibiasErr

REF

TARGET

RATIO

dumpit

Constructor Detail

DataOverlap

Method Detail

setRefAvg

setTargetAvg

getAlphaSource

populateArrays

getOverlapAverageAndError

getLogAverageAndError

getLogAverageAndError

getAverageAndError

getAverageAndError

getAverageAndError

getIdealRefFraction

getRefSource

getTargetSource

getAverage

getLogError

getError