ConfigurationMembrane

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

All Implemented Interfaces:: Configuration

public class ConfigurationMembrane
extends java.lang.Object
implements Configuration

Field Summary

Fields
Modifier and Type	Field	Description
`protected int`	`membraneDim`
`protected double`	`membraneThicknessPerLayer`
`protected int`	`membraneWidth`
`protected int`	`numMembraneLayers`
`protected IMoleculePositionDefinition`	`positionDefinition`
`protected Simulation`	`sim`
`protected double`	`soluteMoleFraction`
`protected double`	`solutionChamberDensity`
`protected double`	`solventChamberDensity`
`protected ISpecies`	`speciesMembrane`
`protected ISpecies`	`speciesSolute`
`protected ISpecies`	`speciesSolvent`

Constructor Summary

Constructors
Constructor Description

ConfigurationMembrane(Simulation sim, Space _space)

Constructors
Constructor	Description
`ConfigurationMembrane(Simulation sim, Space _space)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`getMembraneDim()`
`double`	`getMembraneThicknessPerLayer()`
`int`	`getMembraneWidth()`
`int`	`getNumMembraneLayers()`
`double`	`getSoluteMoleFraction()`
`double`	`getSolutionChamberDensity()`
`double`	`getSolventChamberDensity()`
`ISpecies`	`getSpeciesMembrane()`
`ISpecies`	`getSpeciesSolute()`
`ISpecies`	`getSpeciesSolvent()`
`void`	`initializeCoordinates(Box box)`	Defines the placement of the molecules.
`void`	`setMembraneDim(int newMembraneDim)`
`void`	`setMembraneThicknessPerLayer(double newMembraneWidth)`
`void`	`setMembraneWidth(int newMembraneWidth)`
`void`	`setNumMembraneLayers(int newNumMembraneLayers)`
`void`	`setSoluteMoleFraction(double newSoluteMoleFraction)`
`void`	`setSolutionChamberDensity(double newSolutionChamberDensity)`
`void`	`setSolventChamberDensity(double newSolventChamberDensity)`
`void`	`setSpeciesMembrane(ISpecies newSpeciesMembrane)`
`void`	`setSpeciesSolute(ISpecies newSpeciesSolute)`
`void`	`setSpeciesSolvent(ISpecies newSpeciesSolvent)`

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

Field Detail

speciesSolute
```
protected ISpecies speciesSolute
```

speciesSolvent
```
protected ISpecies speciesSolvent
```

speciesMembrane
```
protected ISpecies speciesMembrane
```

membraneThicknessPerLayer

protected double membraneThicknessPerLayer

numMembraneLayers
```
protected int numMembraneLayers
```

membraneWidth
```
protected int membraneWidth
```

solventChamberDensity
```
protected double solventChamberDensity
```

solutionChamberDensity

protected double solutionChamberDensity

soluteMoleFraction
```
protected double soluteMoleFraction
```

membraneDim
```
protected int membraneDim
```

sim
```
protected final Simulation sim
```

positionDefinition

protected IMoleculePositionDefinition positionDefinition

Constructor Detail

ConfigurationMembrane

public ConfigurationMembrane(Simulation sim,
                             Space _space)

Method Detail

initializeCoordinates
```
public void initializeCoordinates(Box box)
```
Description copied from interface: Configuration

Defines the placement of the molecules. Atoms in all lists are considered for placement. Subclasses define the specific algorithm for placement, and for interpretation of the different lists. Some subclasses will simply place all atoms as if they are in a single list, while others will place atoms in different lists in different ways, for example to form a lattice appropriate to a compound (i.e., a solid-box mixture).

Specified by:

initializeCoordinates in interface Configuration

getMembraneThicknessPerLayer

public double getMembraneThicknessPerLayer()

setMembraneThicknessPerLayer

public void setMembraneThicknessPerLayer(double newMembraneWidth)

getNumMembraneLayers
```
public int getNumMembraneLayers()
```

setNumMembraneLayers

public void setNumMembraneLayers(int newNumMembraneLayers)

getMembraneWidth
```
public int getMembraneWidth()
```

setMembraneWidth

public void setMembraneWidth(int newMembraneWidth)

getSolventChamberDensity

public double getSolventChamberDensity()

setSolventChamberDensity

public void setSolventChamberDensity(double newSolventChamberDensity)

getSolutionChamberDensity

public double getSolutionChamberDensity()

setSolutionChamberDensity

public void setSolutionChamberDensity(double newSolutionChamberDensity)

getSoluteMoleFraction

public double getSoluteMoleFraction()

setSoluteMoleFraction

public void setSoluteMoleFraction(double newSoluteMoleFraction)

getMembraneDim
```
public int getMembraneDim()
```

setMembraneDim

public void setMembraneDim(int newMembraneDim)

getSpeciesSolute
```
public ISpecies getSpeciesSolute()
```

setSpeciesSolute

public void setSpeciesSolute(ISpecies newSpeciesSolute)

getSpeciesSolvent

public ISpecies getSpeciesSolvent()

setSpeciesSolvent

public void setSpeciesSolvent(ISpecies newSpeciesSolvent)

getSpeciesMembrane

public ISpecies getSpeciesMembrane()

setSpeciesMembrane

public void setSpeciesMembrane(ISpecies newSpeciesMembrane)

Class ConfigurationMembrane

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

speciesSolute

speciesSolvent

speciesMembrane

membraneThicknessPerLayer

numMembraneLayers

membraneWidth

solventChamberDensity

solutionChamberDensity

soluteMoleFraction

membraneDim

sim

positionDefinition

Constructor Detail

ConfigurationMembrane

Method Detail

initializeCoordinates

getMembraneThicknessPerLayer

setMembraneThicknessPerLayer

getNumMembraneLayers

setNumMembraneLayers

getMembraneWidth

setMembraneWidth

getSolventChamberDensity

setSolventChamberDensity

getSolutionChamberDensity

setSolutionChamberDensity

getSoluteMoleFraction

setSoluteMoleFraction

getMembraneDim

setMembraneDim

getSpeciesSolute

setSpeciesSolute

getSpeciesSolvent

setSpeciesSolvent

getSpeciesMembrane

setSpeciesMembrane