Package etomica.data

Class AccumulatorAverageCovariance

java.lang.Object

etomica.data.DataProcessor

etomica.data.DataProcessorForked

etomica.data.DataAccumulator

etomica.data.AccumulatorAverage

etomica.data.AccumulatorAverageFixed

etomica.data.AccumulatorAverageCovariance

All Implemented Interfaces:

DataPipe, DataPipeForked, IDataSink, IDataSource

Direct Known Subclasses:

AccumulatorRatioAverageCovariance, AccumulatorRatioAverageCovarianceFull

public class AccumulatorAverageCovariance
extends AccumulatorAverageFixed

Class that does the work of AccumulatorAverageFixed and also calculates the covariance of the incoming data values (the covariance of each value with each other value, as well as itself (which is actually its standard deviation)) as well as the covariance of the block averages of the different data quantities.

Nested Class Summary

Nested classes/interfaces inherited from class etomica.data.AccumulatorAverage

AccumulatorAverage.StatType

Field Summary

Fields

Modifier and Type	Field	Description
static AccumulatorAverage.StatType	BLOCK_COVARIANCE
protected DataDoubleArray	blockCovariance
protected DataDoubleArray	blockCovSum
protected DataDoubleArray	covariance
static AccumulatorAverage.StatType	COVARIANCE
protected DataDoubleArray	covSum
protected boolean	fullCovariance

Fields inherited from class etomica.data.AccumulatorAverage

average, AVERAGE, BLOCK_CORRELATION, blockCorrelation, blockCountDown, blockSize, count, dataGroup, doIncludeACInError, error, ERROR, MOST_RECENT, mostRecent, STANDARD_DEVIATION, standardDeviation

Fields inherited from class etomica.data.AccumulatorAverageFixed

blockDataSink, blockFilename, blockVarSum, correlationSum, currentBlockAvg, firstBlock, mostRecentBlock, negativeChop, numSavedBlockData, sanityCheckBC, savedBlockData, sumSquare, work, work2

Fields inherited from class etomica.data.DataAccumulator

active, hasUnpushedData, pushInterval, putCount

Fields inherited from class etomica.data.DataProcessor

dataInfo, dataSink, tag

Constructor Summary

Constructors

Constructor	Description
AccumulatorAverageCovariance()
AccumulatorAverageCovariance(boolean fullCovariance)
AccumulatorAverageCovariance(long blockSize)
AccumulatorAverageCovariance(long blockSize, boolean fullCovariance)

Method Summary

Modifier and Type	Method	Description
boolean	addData(IData data)	Add the given values to the sums and block sums.
protected void	doBlockSum()	Performs the block sum after blockSize calls to addData.
IData	getData()
IDataInfo	processDataInfo(IDataInfo incomingDataInfo)	Prepares the accumulator for input data.
void	reset()	Resets all sums to zero.
static AccumulatorAverage.StatType[]	statChoices()

Methods inherited from class etomica.data.AccumulatorAverage

addDataSink, doIncludeACInError, getBlockCount, getBlockSize, getData, getSampleCount, getTag, setBlockSize, setIncludeACInError

Methods inherited from class etomica.data.AccumulatorAverageFixed

getBlockDataSink, getDoStrictBlockData, putDataInfo, readBlockData, setBlockDataSink, setWriteBlocks, writeBlockData

Methods inherited from class etomica.data.DataAccumulator

getPushInterval, isActive, processData, setActive, setPushInterval, toString

Methods inherited from interface etomica.data.DataPipe

getTag

Methods inherited from class etomica.data.DataProcessor

getDataInfo, getTag, putData

Methods inherited from class etomica.data.DataProcessorForked

addDataSink, getDataSink, getDataSinks, removeDataSink, setDataSink, setDataSinks

Methods inherited from interface etomica.data.IDataSink

putData

Methods inherited from interface etomica.data.IDataSource

getDataInfo, getTag

Methods inherited from class java.lang.Object

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

Field Detail

COVARIANCE

public static final AccumulatorAverage.StatType COVARIANCE

BLOCK_COVARIANCE

public static final AccumulatorAverage.StatType BLOCK_COVARIANCE

covSum

protected DataDoubleArray covSum

blockCovSum

protected DataDoubleArray blockCovSum

covariance

protected DataDoubleArray covariance

blockCovariance

protected DataDoubleArray blockCovariance

fullCovariance

protected final boolean fullCovariance

Constructor Detail

AccumulatorAverageCovariance

public AccumulatorAverageCovariance()

AccumulatorAverageCovariance

public AccumulatorAverageCovariance(boolean fullCovariance)

Parameters:

fullCovariance - enables calculation of covariance for each pair of data values. With fullCovariance off, covariance is computed between the first data value and all others.

AccumulatorAverageCovariance

public AccumulatorAverageCovariance(long blockSize)

AccumulatorAverageCovariance

public AccumulatorAverageCovariance(long blockSize,
                                    boolean fullCovariance)

Method Detail

addData

public boolean addData(IData data)

Description copied from class: AccumulatorAverageFixed

Add the given values to the sums and block sums. If any of the given data values is NaN, method returns with no effect on accumulation sums.

Overrides:

addData in class AccumulatorAverageFixed

Parameters:

data - data to be added.

Returns:

true if data are not NaN.

doBlockSum

protected void doBlockSum()

Description copied from class: AccumulatorAverageFixed

Performs the block sum after blockSize calls to addData.

Overrides:

doBlockSum in class AccumulatorAverageFixed

getData

public IData getData()

Specified by:

getData in interface IDataSource

Overrides:

getData in class AccumulatorAverageFixed

Returns:

the data given by this source

reset

public void reset()

Description copied from class: AccumulatorAverage

Resets all sums to zero. All statistics are cleared.

Overrides:

reset in class AccumulatorAverageFixed

processDataInfo

public IDataInfo processDataInfo(IDataInfo incomingDataInfo)

Description copied from class: AccumulatorAverage

Prepares the accumulator for input data. Discards any previous contributions to statistics.

Overrides:

processDataInfo in class AccumulatorAverageFixed

Parameters:

incomingDataInfo - the DataInfo instance for the data that will be given to addData

Returns:

dataInfo object for the output of this accumulator.

statChoices

public static AccumulatorAverage.StatType[] statChoices()