ConfigurationCatalysis

java.lang.Object
- etomica.modules.catalysis.ConfigurationCatalysis

All Implemented Interfaces:

Configuration
```
public class ConfigurationCatalysis
extends java.lang.Object
implements Configuration
```
Configuration for catalysis module. Places molecules within the box on an FCC lattice, and the surface atoms at the bottom of the box in a hexagonal lattice.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class ConfigurationCatalysis.BasisOrthorhombicHexagonal3D

Nested Classes
Modifier and Type	Class	Description
`static class`	`ConfigurationCatalysis.BasisOrthorhombicHexagonal3D`

Field Summary

Fields
Modifier and Type	Field	Description
`protected AtomLeafAgentManager`	`agentManager`
`protected double`	`cellSizeX`
`protected double`	`cellSizeZ`
`protected ConformationChainZigZag[]`	`conformation`
`protected Vector`	`moleculeOffset`
`protected int`	`nCellsX`
`protected int`	`nCellsZ`
`protected int`	`nCO`
`protected int`	`nO2`
`protected PotentialMasterList`	`potentialMaster`
`protected Simulation`	`sim`
`protected Space`	`space`
`protected ISpecies`	`speciesC`
`protected ISpecies`	`speciesO`
`protected ISpecies`	`speciesSurface`
`protected double`	`yOffset`

Constructor Summary

Constructors
Constructor	Description
`ConfigurationCatalysis(Simulation sim, Space space, ISpecies speciesSurface, ISpecies speciesC, ISpecies speciesO, AtomLeafAgentManager agentManager)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`getCellSizeX()`
`double`	`getCellSizeZ()`
`Vector`	`getMoleculeOffset()`
`int`	`getNCellsX()`
`int`	`getNCellsZ()`
`int`	`getNumCO()`
`int`	`getNumO2()`
`double`	`getSurfaceYOffset()`
`void`	`initializeCoordinates(Box box)`	Defines the placement of the molecules.
`void`	`setCellSizeX(double cellSizeX)`
`void`	`setCellSizeZ(double cellSizeZ)`
`void`	`setMoleculeOffset(Vector newMoleculeOffset)`
`void`	`setNCellsX(int cellsX)`
`void`	`setNCellsZ(int cellsZ)`
`void`	`setNumCO(int newNumCO)`
`void`	`setNumO2(int newNumO2)`
`void`	`setSurfaceYOffset(double newYOffset)`

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

Field Detail

space
```
protected final Space space
```

sim
```
protected final Simulation sim
```

speciesSurface

protected final ISpecies speciesSurface

speciesO
```
protected final ISpecies speciesO
```

speciesC
```
protected final ISpecies speciesC
```

nCO
```
protected int nCO
```

nO2
```
protected int nO2
```

agentManager

protected final AtomLeafAgentManager agentManager

cellSizeX
```
protected double cellSizeX
```

cellSizeZ
```
protected double cellSizeZ
```

nCellsX
```
protected int nCellsX
```

nCellsZ
```
protected int nCellsZ
```

yOffset
```
protected double yOffset
```

moleculeOffset
```
protected final Vector moleculeOffset
```

conformation

protected ConformationChainZigZag[] conformation

potentialMaster

protected PotentialMasterList potentialMaster

Constructor Detail

ConfigurationCatalysis

public ConfigurationCatalysis(Simulation sim,
                              Space space,
                              ISpecies speciesSurface,
                              ISpecies speciesC,
                              ISpecies speciesO,
                              AtomLeafAgentManager agentManager)

Method Detail
- setMoleculeOffset
```
public void setMoleculeOffset(Vector newMoleculeOffset)
```
- getMoleculeOffset
```
public Vector getMoleculeOffset()
```
- 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
- setNumCO
```
public void setNumCO(int newNumCO)
```
- setNumO2
```
public void setNumO2(int newNumO2)
```
- getNumCO
```
public int getNumCO()
```
- getNumO2
```
public int getNumO2()
```
- getSurfaceYOffset
```
public double getSurfaceYOffset()
```
- setSurfaceYOffset
```
public void setSurfaceYOffset(double newYOffset)
```
- getCellSizeX
```
public double getCellSizeX()
```
- setCellSizeX
```
public void setCellSizeX(double cellSizeX)
```
- getCellSizeZ
```
public double getCellSizeZ()
```
- setCellSizeZ
```
public void setCellSizeZ(double cellSizeZ)
```
- getNCellsX
```
public int getNCellsX()
```
- setNCellsX
```
public void setNCellsX(int cellsX)
```
- getNCellsZ
```
public int getNCellsZ()
```
- setNCellsZ
```
public void setNCellsZ(int cellsZ)
```

Class ConfigurationCatalysis

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

space

sim

speciesSurface

speciesO

speciesC

nCO

nO2

agentManager

cellSizeX

cellSizeZ

nCellsX

nCellsZ

yOffset

moleculeOffset

conformation

potentialMaster

Constructor Detail

ConfigurationCatalysis

Method Detail

setMoleculeOffset

getMoleculeOffset

initializeCoordinates

setNumCO

setNumO2

getNumCO

getNumO2

getSurfaceYOffset

setSurfaceYOffset

getCellSizeX

setCellSizeX

getCellSizeZ

setCellSizeZ

getNCellsX

setNCellsX

getNCellsZ

setNCellsZ