ConfigurationMembraneWater

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

All Implemented Interfaces:: Configuration

public class ConfigurationMembraneWater
extends java.lang.Object
implements Configuration

Field Summary

Fields
Modifier and Type	Field	Description
`protected int`	`membraneDim`
`protected double`	`membraneTotalThickness`
`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`	`speciesSolute1`
`protected ISpecies`	`speciesSolute2`
`protected ISpecies`	`speciesSolvent`

Constructor Summary

Constructors
Constructor Description

ConfigurationMembraneWater(Simulation sim, Space _space)

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

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`getMembraneDim()`	The dimension of the membrane (0=x, 1=y, 2=z).
`double`	`getMembraneThickness()`	Returns the thickness (angstroms) of each layer of the membrane (see getNumMembraneLayers)
`int`	`getMembraneWidth()`	Returns the width of the membrane.
`int`	`getNumMembraneLayers()`	Returns the number of membrane layers.
`double`	`getSoluteMoleFraction()`	Returns the mole fraction of solutes within the solute chamber.
`double`	`getSolutionChamberDensity()`	Returns the number density of the solution chamber
`double`	`getSolventChamberDensity()`	Returns the number density of the solvent chamber
`ISpecies`	`getSpeciesMembrane()`
`ISpecies`	`getSpeciesSolute1()`
`ISpecies`	`getSpeciesSolute2()`
`ISpecies`	`getSpeciesSolvent()`
`void`	`initializeCoordinates(Box box)`	Defines the placement of the molecules.
`void`	`setMembraneDim(int newMembraneDim)`
`void`	`setMembraneThickness(double newMembraneThickness)`
`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`	`setSpeciesSolute1(ISpecies newSpeciesSolute1)`
`void`	`setSpeciesSolute2(ISpecies newSpeciesSolute2)`
`void`	`setSpeciesSolvent(ISpecies newSpeciesSolvent)`

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

- Field Detail
  - speciesSolute1
```
protected ISpecies speciesSolute1
```
  - speciesSolute2
```
protected ISpecies speciesSolute2
```
  - speciesSolvent
```
protected ISpecies speciesSolvent
```
  - speciesMembrane
```
protected ISpecies speciesMembrane
```
  - membraneTotalThickness
```
protected double membraneTotalThickness
```
  - 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
  - ConfigurationMembraneWater
```
public ConfigurationMembraneWater(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
  - getMembraneThickness
```
public double getMembraneThickness()
```
    Returns the thickness (angstroms) of each layer of the membrane (see getNumMembraneLayers)
  - setMembraneThickness
```
public void setMembraneThickness(double newMembraneThickness)
```
  - getNumMembraneLayers
```
public int getNumMembraneLayers()
```
    Returns the number of membrane layers. If the membrane is in the yz plane, then this is then number of layers in the x direction. layers=2 means 1 unit cell.
  - setNumMembraneLayers
```
public void setNumMembraneLayers(int newNumMembraneLayers)
```
  - getMembraneWidth
```
public int getMembraneWidth()
```
    Returns the width of the membrane. If the membrane is in the yz plane, this is the number of lattice cells in the y direction and z direction. membraneWidth = 2 means 2x2 cells.
  - setMembraneWidth
```
public void setMembraneWidth(int newMembraneWidth)
```
  - getSolventChamberDensity
```
public double getSolventChamberDensity()
```
    Returns the number density of the solvent chamber
  - setSolventChamberDensity
```
public void setSolventChamberDensity(double newSolventChamberDensity)
```
  - getSolutionChamberDensity
```
public double getSolutionChamberDensity()
```
    Returns the number density of the solution chamber
  - setSolutionChamberDensity
```
public void setSolutionChamberDensity(double newSolutionChamberDensity)
```
  - getSoluteMoleFraction
```
public double getSoluteMoleFraction()
```
    Returns the mole fraction of solutes within the solute chamber.
  - setSoluteMoleFraction
```
public void setSoluteMoleFraction(double newSoluteMoleFraction)
```
  - getMembraneDim
```
public int getMembraneDim()
```
    The dimension of the membrane (0=x, 1=y, 2=z). x means that the membrane exists in the yz plane.
  - setMembraneDim
```
public void setMembraneDim(int newMembraneDim)
```
  - getSpeciesSolute1
```
public ISpecies getSpeciesSolute1()
```
  - setSpeciesSolute1
```
public void setSpeciesSolute1(ISpecies newSpeciesSolute1)
```
  - getSpeciesSolute2
```
public ISpecies getSpeciesSolute2()
```
  - setSpeciesSolute2
```
public void setSpeciesSolute2(ISpecies newSpeciesSolute2)
```
  - getSpeciesSolvent
```
public ISpecies getSpeciesSolvent()
```
  - setSpeciesSolvent
```
public void setSpeciesSolvent(ISpecies newSpeciesSolvent)
```
  - getSpeciesMembrane
```
public ISpecies getSpeciesMembrane()
```
  - setSpeciesMembrane
```
public void setSpeciesMembrane(ISpecies newSpeciesMembrane)
```

Class ConfigurationMembraneWater

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

speciesSolute1

speciesSolute2

speciesSolvent

speciesMembrane

membraneTotalThickness

numMembraneLayers

membraneWidth

solventChamberDensity

solutionChamberDensity

soluteMoleFraction

membraneDim

sim

positionDefinition

Constructor Detail

ConfigurationMembraneWater

Method Detail

initializeCoordinates

getMembraneThickness

setMembraneThickness

getNumMembraneLayers

setNumMembraneLayers

getMembraneWidth

setMembraneWidth

getSolventChamberDensity

setSolventChamberDensity

getSolutionChamberDensity

setSolutionChamberDensity

getSoluteMoleFraction

setSoluteMoleFraction

getMembraneDim

setMembraneDim

getSpeciesSolute1

setSpeciesSolute1

getSpeciesSolute2

setSpeciesSolute2

getSpeciesSolvent

setSpeciesSolvent

getSpeciesMembrane

setSpeciesMembrane