MeterFlux

java.lang.Object
- etomica.modules.rosmosis.MeterFlux

All Implemented Interfaces:

MoleculeAgentManager.MoleculeAgentSource, IDataSource, IEtomicaDataSource
```
public class MeterFlux
extends java.lang.Object
implements IEtomicaDataSource, MoleculeAgentManager.MoleculeAgentSource
```
Meter to measure flux across a boundary or boundaries. If an atom is on one side of the boundary at one time and on the other side of the boundary the next time, then the meter counts that as a crossing. Each boundary can have a coefficient, such that flow into one region through boundaries on either side can be considered "positive" flux. If an IntegratorMD is used, flux will be given in terms of crossings per area per time. Otherwise, flux will be given in terms of crossings per area per step.

Field Summary

Fields
Modifier and Type	Field and Description
`protected MoleculeAgentManager`	`agentManager`
`protected double[]`	`boundaries`
`protected int[]`	`boundaryCoefficients`
`protected IBox`	`box`
`protected DataDouble`	`data`
`protected DataDouble.DataInfoDouble`	`dataInfo`
`protected int`	`dim`
`protected IntegratorBox`	`integrator`
`protected long`	`oldStep`
`protected double`	`oldTime`
`protected IAtomPositionDefinition`	`positionDefinition`
`protected ISimulation`	`sim`
`protected ISpecies[]`	`species`
`protected DataTag`	`tag`

Constructor Summary

Constructors
Constructor and Description

MeterFlux(ISimulation sim, ISpace _space)

Constructors
Constructor and Description
`MeterFlux(ISimulation sim, ISpace _space)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`double[]`	`getBoundaries()`
`IBox`	`getBox()`
`IData`	`getData()`
`IEtomicaDataInfo`	`getDataInfo()`
`int`	`getDim()`
`java.lang.Class`	`getMoleculeAgentClass()` Returns the Class of the agent.
`ISpecies[]`	`getSpecies()`
`DataTag`	`getTag()`
`java.lang.Object`	`makeAgent(IMolecule a)` Returns an agent for the given Atom.
`void`	`releaseAgent(java.lang.Object agent, IMolecule atom)` This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements
`void`	`setBoundaries(int newDim, double[] newBoundaries, int[] newBoundaryCoefficients)`
`void`	`setBox(IBox newBox)`
`void`	`setIntegrator(IntegratorBox newIntegrator)`
`void`	`setSpecies(ISpecies[] newSpecies)`

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

Field Detail

sim
```
protected final ISimulation sim
```

data
```
protected final DataDouble data
```

dataInfo

protected DataDouble.DataInfoDouble dataInfo

tag
```
protected final DataTag tag
```

species
```
protected ISpecies[] species
```

box
```
protected IBox box
```

boundaries
```
protected double[] boundaries
```

boundaryCoefficients
```
protected int[] boundaryCoefficients
```

dim
```
protected int dim
```

agentManager

protected MoleculeAgentManager agentManager

integrator
```
protected IntegratorBox integrator
```

oldTime
```
protected double oldTime
```

oldStep
```
protected long oldStep
```

positionDefinition

protected IAtomPositionDefinition positionDefinition

Constructor Detail

MeterFlux

public MeterFlux(ISimulation sim,
                 ISpace _space)

Method Detail
- setBoundaries
```
public void setBoundaries(int newDim,
                          double[] newBoundaries,
                          int[] newBoundaryCoefficients)
```
- getDim
```
public int getDim()
```
- getBoundaries
```
public double[] getBoundaries()
```
- setSpecies
```
public void setSpecies(ISpecies[] newSpecies)
```
- getSpecies
```
public ISpecies[] getSpecies()
```
- setBox
```
public void setBox(IBox newBox)
```
- getBox
```
public IBox getBox()
```
- setIntegrator
```
public void setIntegrator(IntegratorBox newIntegrator)
```
- getData
```
public IData getData()
```
  Specified by:
  
  getData in interface IDataSource
  
  Returns:
  
  the data given by this source
- getDataInfo
```
public IEtomicaDataInfo getDataInfo()
```
  Specified by:
  
  getDataInfo in interface IEtomicaDataSource
- getTag
```
public DataTag getTag()
```
  Specified by:
  
  getTag in interface IEtomicaDataSource
- getMoleculeAgentClass
```
public java.lang.Class getMoleculeAgentClass()
```
  Description copied from interface: etomica.atom.MoleculeAgentManager.MoleculeAgentSource
  
  Returns the Class of the agent. This is used to create an array of the appropriate Class.
  
  Specified by:
  
  getMoleculeAgentClass in interface MoleculeAgentManager.MoleculeAgentSource
- makeAgent
```
public java.lang.Object makeAgent(IMolecule a)
```
  Description copied from interface: etomica.atom.MoleculeAgentManager.MoleculeAgentSource
  
  Returns an agent for the given Atom.
  
  Specified by:
  
  makeAgent in interface MoleculeAgentManager.MoleculeAgentSource
- releaseAgent
```
public void releaseAgent(java.lang.Object agent,
                         IMolecule atom)
```
  Description copied from interface: etomica.atom.MoleculeAgentManager.MoleculeAgentSource
  
  This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements
  
  Specified by:
  
  releaseAgent in interface MoleculeAgentManager.MoleculeAgentSource

Class MeterFlux

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

sim

data

dataInfo

tag

species

box

boundaries

boundaryCoefficients

dim

agentManager

integrator

oldTime

oldStep

positionDefinition

Constructor Detail

MeterFlux

Method Detail

setBoundaries

getDim

getBoundaries

setSpecies

getSpecies

setBox

getBox

setIntegrator

getData

getDataInfo

getTag

getMoleculeAgentClass

makeAgent

releaseAgent