Package etomica.modules.rosmosis

Class MeterFlux

java.lang.Object

etomica.modules.rosmosis.MeterFlux

All Implemented Interfaces:

IDataSource, MoleculeAgentManager.MoleculeAgentSource<Vector>

public class MeterFlux
extends java.lang.Object
implements IDataSource, MoleculeAgentManager.MoleculeAgentSource<Vector>

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	Description
protected MoleculeAgentManager<Vector>	agentManager
protected double[]	boundaries
protected int[]	boundaryCoefficients
protected Box	box
protected DataDouble	data
protected DataDouble.DataInfoDouble	dataInfo
protected int	dim
protected IntegratorBox	integrator
protected long	oldStep
protected double	oldTime
protected IMoleculePositionDefinition	positionDefinition
protected Simulation	sim
protected ISpecies[]	species
protected DataTag	tag

Constructor Summary

Constructors

Constructor	Description
MeterFlux(Simulation sim, Space _space)

Method Summary

Modifier and Type	Method	Description
double[]	getBoundaries()
Box	getBox()
IData	getData()
IDataInfo	getDataInfo()
int	getDim()
ISpecies[]	getSpecies()
DataTag	getTag()
Vector	makeAgent(IMolecule a)	Returns an agent for the given Atom.
void	releaseAgent(Vector 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(Box 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 Simulation sim

data

protected final DataDouble data

dataInfo

protected DataDouble.DataInfoDouble dataInfo

tag

protected final DataTag tag

species

protected ISpecies[] species

box

protected Box box

boundaries

protected double[] boundaries

boundaryCoefficients

protected int[] boundaryCoefficients

dim

protected int dim

agentManager

protected MoleculeAgentManager<Vector> agentManager

integrator

protected IntegratorBox integrator

oldTime

protected double oldTime

oldStep

protected long oldStep

positionDefinition

protected IMoleculePositionDefinition positionDefinition

Constructor Detail

MeterFlux

public MeterFlux(Simulation sim,
                 Space _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(Box newBox)

getBox

public Box 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 IDataInfo getDataInfo()

Specified by:

getDataInfo in interface IDataSource

getTag

public DataTag getTag()

Specified by:

getTag in interface IDataSource

Returns:

a tag that uniquely identifies the IDataInfo

makeAgent

public Vector makeAgent(IMolecule a)

Description copied from interface: MoleculeAgentManager.MoleculeAgentSource

Returns an agent for the given Atom.

Specified by:

makeAgent in interface MoleculeAgentManager.MoleculeAgentSource<Vector>

releaseAgent

public void releaseAgent(Vector agent,
                         IMolecule atom)

Description copied from interface: 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<Vector>