Package etomica.normalmode

Class DataSourceFE

java.lang.Object

etomica.normalmode.DataSourceFE

All Implemented Interfaces:

DataSourceIndependent, IDataSource

public class DataSourceFE
extends java.lang.Object
implements IDataSource, DataSourceIndependent

Free energy data source that computes free energy differences based on overlap sampling performed by an MCMoveOverlapListener.

Field Summary

Fields

Modifier and Type	Field	Description
protected DataFunction	data
protected DataFunction.DataInfoFunction	dataInfo
protected boolean	doAvgDef
protected boolean	doSubtractComb
protected MCMoveOverlapListener	mcMoveOverlapMeter
protected DataTag	tag
protected DataDoubleArray	xData
protected DataDoubleArray.DataInfoDoubleArray	xDataInfo
protected DataTag	xTag

Constructor Summary

Constructors

Constructor	Description
DataSourceFE(MCMoveOverlapListener mcMoveOverlapMeter)

Method Summary

Modifier and Type	Method	Description
IData	getData()
IDataInfo	getDataInfo()
int	getIndependentArrayDimension()	Returns the number of independent data dimensions
DataDoubleArray	getIndependentData(int i)	Returns the X data for the given dimension
DataDoubleArray.DataInfoDoubleArray	getIndependentDataInfo(int i)	Returns the DataInfo for the given dimension
DataTag	getIndependentTag()	Returns the tag associated with this DataSource.
DataTag	getTag()
void	setAvgDef(boolean doAvgDef)
void	setSubtractComb(boolean doSubtractComb)	If true, the free energy differences will not include the combinatoric contributions (they will be the free energy of defect formation).

Methods inherited from class java.lang.Object

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

Field Detail

mcMoveOverlapMeter

protected final MCMoveOverlapListener mcMoveOverlapMeter

data

protected DataFunction data

dataInfo

protected DataFunction.DataInfoFunction dataInfo

xData

protected DataDoubleArray xData

xDataInfo

protected DataDoubleArray.DataInfoDoubleArray xDataInfo

tag

protected final DataTag tag

xTag

protected final DataTag xTag

doSubtractComb

protected boolean doSubtractComb

doAvgDef

protected boolean doAvgDef

Constructor Detail

DataSourceFE

public DataSourceFE(MCMoveOverlapListener mcMoveOverlapMeter)

Method Detail

setSubtractComb

public void setSubtractComb(boolean doSubtractComb)

If true, the free energy differences will not include the combinatoric contributions (they will be the free energy of defect formation). http://dx.doi.org/10.1073/pnas.1211784109

setAvgDef

public void setAvgDef(boolean doAvgDef)

getData

public IData getData()

Specified by:

getData in interface IDataSource

Returns:

the data given by this source

getTag

public DataTag getTag()

Specified by:

getTag in interface IDataSource

Returns:

a tag that uniquely identifies the IDataInfo

getDataInfo

public IDataInfo getDataInfo()

Specified by:

getDataInfo in interface IDataSource

getIndependentData

public DataDoubleArray getIndependentData(int i)

Description copied from interface: DataSourceIndependent

Returns the X data for the given dimension

Specified by:

getIndependentData in interface DataSourceIndependent

getIndependentDataInfo

public DataDoubleArray.DataInfoDoubleArray getIndependentDataInfo(int i)

Description copied from interface: DataSourceIndependent

Returns the DataInfo for the given dimension

Specified by:

getIndependentDataInfo in interface DataSourceIndependent

getIndependentArrayDimension

public int getIndependentArrayDimension()

Description copied from interface: DataSourceIndependent

Returns the number of independent data dimensions

Specified by:

getIndependentArrayDimension in interface DataSourceIndependent

getIndependentTag

public DataTag getIndependentTag()

Description copied from interface: DataSourceIndependent

Returns the tag associated with this DataSource.

Specified by:

getIndependentTag in interface DataSourceIndependent