MeterProfileByAtoms

java.lang.Object
- etomica.data.meter.MeterProfileByAtoms

All Implemented Interfaces:

DataSourceIndependent, IDataSource, IEtomicaDataSource, java.io.Serializable
```
public class MeterProfileByAtoms
extends java.lang.Object
implements IEtomicaDataSource, DataSourceIndependent, java.io.Serializable
```
Meter that takes a (scalar) Meter and records its property as a 1-dimensional function of position in the simulation volume. The measured property must be a quantity that can be associated with a single molecule. The position coordinate lies along one dimension (x,y,z). Data is averaged in each bin as sum(values)/numAtoms So, bins that don't have atoms will have an average of NaN. The averaging is done within this class, so use of an AccumulatorAverage is not needed. The data returned by this class /is/ the average. To reset the average, this class' reset method should be called.

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`protected IBox`	`box`
`protected DataFunction`	`data`
`protected IEtomicaDataInfo`	`dataInfo`
`protected DataSourceMolecular`	`meter` Meter that defines the property being profiled.
`protected int[]`	`nAtoms`
`protected IVectorMutable`	`position`
`protected int`	`profileDim` Vector describing the orientation of the profile.
`protected ISpecies`	`species`
`protected DataTag`	`tag`
`protected DataSourceUniform`	`xDataSource`
`protected double[]`	`y`

Constructor Summary

Constructors
Constructor and Description

MeterProfileByAtoms(ISpace space)
Default constructor sets profile along the y-axis, with 100 histogram points.

Constructors
Constructor and Description
`MeterProfileByAtoms(ISpace space)` Default constructor sets profile along the y-axis, with 100 histogram points.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`IBox`	`getBox()`
`IData`	`getData()` Returns the profile for the current configuration.
`IEtomicaDataInfo`	`getDataInfo()`
`DataSourceMolecular`	`getDataSource()` The meter that defines the profiled quantity
`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.
`IAtomPositionDefinition`	`getPositionDefinition()`
`int`	`getProfileDim()` Accessor method for vector describing the direction along which the profile is measured.
`ISpecies`	`getSpecies()`
`DataTag`	`getTag()`
`void`	`reset()`
`void`	`setBox(IBox box)`
`void`	`setDataSource(DataSourceMolecular m)` Accessor method for the meter that defines the profiled quantity.
`void`	`setPositionDefinition(IAtomPositionDefinition positionDefinition)`
`void`	`setProfileDim(int dim)` Accessor method for vector describing the direction along which the profile is measured.
`void`	`setSpecies(ISpecies newSpecies)`

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

- Field Detail
  - box
```
protected IBox box
```
  - xDataSource
```
protected DataSourceUniform xDataSource
```
  - data
```
protected DataFunction data
```
  - y
```
protected double[] y
```
  - nAtoms
```
protected int[] nAtoms
```
  - dataInfo
```
protected IEtomicaDataInfo dataInfo
```
  - profileDim
```
protected int profileDim
```
    Vector describing the orientation of the profile. For example, (1,0) is along the x-axis.
  - position
```
protected final IVectorMutable position
```
  - meter
```
protected DataSourceMolecular meter
```
    Meter that defines the property being profiled.
  - tag
```
protected final DataTag tag
```
  - species
```
protected ISpecies species
```
- Constructor Detail
  - MeterProfileByAtoms
```
public MeterProfileByAtoms(ISpace space)
```
    Default constructor sets profile along the y-axis, with 100 histogram points.
- Method Detail
  - getDataInfo
```
public IEtomicaDataInfo getDataInfo()
```
    Specified by:
    
    getDataInfo in interface IEtomicaDataSource
  - getTag
```
public DataTag getTag()
```
    Specified by:
    
    getTag in interface IEtomicaDataSource
  - getDataSource
```
public DataSourceMolecular getDataSource()
```
    The meter that defines the profiled quantity
  - setDataSource
```
public void setDataSource(DataSourceMolecular m)
```
    Accessor method for the meter that defines the profiled quantity.
  - getProfileDim
```
public int getProfileDim()
```
    Accessor method for vector describing the direction along which the profile is measured. Each atom position is dotted along this vector to obtain its profile abscissa value.
  - setProfileDim
```
public void setProfileDim(int dim)
```
    Accessor method for vector describing the direction along which the profile is measured. Each atom position is dotted along this vector to obtain its profile abscissa value. The given vector is converted to a unit vector, if not already.
  - getData
```
public IData getData()
```
    Returns the profile for the current configuration.
    
    Specified by:
    
    getData in interface IDataSource
    
    Returns:
    
    the data given by this source
  - 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
  - getBox
```
public IBox getBox()
```
    Returns:
    
    Returns the box.
  - setBox
```
public void setBox(IBox box)
```
    Parameters:
    
    box - The box to set.
  - getSpecies
```
public ISpecies getSpecies()
```
  - setSpecies
```
public void setSpecies(ISpecies newSpecies)
```
  - reset
```
public void reset()
```
  - setPositionDefinition
```
public void setPositionDefinition(IAtomPositionDefinition positionDefinition)
```
  - getPositionDefinition
```
public IAtomPositionDefinition getPositionDefinition()
```

Class MeterProfileByAtoms

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

box

xDataSource

data

y

nAtoms

dataInfo

profileDim

position

meter

tag

species

Constructor Detail

MeterProfileByAtoms

Method Detail

getDataInfo

getTag

getDataSource

setDataSource

getProfileDim

setProfileDim

getData

getIndependentData

getIndependentDataInfo

getIndependentArrayDimension

getIndependentTag

getBox

setBox

getSpecies

setSpecies

reset

setPositionDefinition

getPositionDefinition