Package etomica.modules.sam

Class ConfigurationSAM

java.lang.Object

etomica.modules.sam.ConfigurationSAM

All Implemented Interfaces:

Configuration

public class ConfigurationSAM
extends java.lang.Object
implements Configuration

Field Summary

Fields

Modifier and Type	Field	Description
protected Basis	basisMolecules
protected Basis	basisSurface
protected double	cellSizeX
protected double	cellSizeZ
protected ConformationChainZigZag[]	conformation
protected Vector	moleculeOffset
protected int	nCellsX
protected int	nCellsZ
protected PotentialMasterList	potentialMaster
protected Simulation	sim
protected Space	space
protected ISpecies	speciesMolecules
protected ISpecies	speciesSurface
protected double	yOffset

Constructor Summary

Constructors

Constructor	Description
ConfigurationSAM(Simulation sim, Space space, ISpecies speciesMolecules, ISpecies speciesSurface, PotentialMasterList potentialMaster)

Method Summary

Modifier and Type	Method	Description
Basis	getBasisMolecules()
Basis	getBasisSurface()
double	getCellSizeX()
double	getCellSizeZ()
ConformationChainZigZag	getConformation(int iChain)
Vector	getMoleculeOffset()
int	getNCellsX()
int	getNCellsZ()
double	getSurfaceYOffset()
void	initializeCoordinates(Box box)	Defines the placement of the molecules.
void	setBasisMolecules(Basis basisMolecules)
void	setBasisSurface(Basis basisSurface)
void	setCellSizeX(double cellSizeX)
void	setCellSizeZ(double cellSizeZ)
void	setConformation(int iChain, ConformationChainZigZag newConformation)
void	setMoleculeOffset(Vector newMoleculeOffset)
void	setNCellsX(int cellsX)
void	setNCellsZ(int cellsZ)
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

speciesMolecules

protected final ISpecies speciesMolecules

speciesSurface

protected final ISpecies speciesSurface

cellSizeX

protected double cellSizeX

cellSizeZ

protected double cellSizeZ

nCellsX

protected int nCellsX

nCellsZ

protected int nCellsZ

basisMolecules

protected Basis basisMolecules

basisSurface

protected Basis basisSurface

yOffset

protected double yOffset

moleculeOffset

protected final Vector moleculeOffset

conformation

protected ConformationChainZigZag[] conformation

potentialMaster

protected PotentialMasterList potentialMaster

Constructor Detail

ConfigurationSAM

public ConfigurationSAM(Simulation sim,
                        Space space,
                        ISpecies speciesMolecules,
                        ISpecies speciesSurface,
                        PotentialMasterList potentialMaster)

Method Detail

getConformation

public ConformationChainZigZag getConformation(int iChain)

setConformation

public void setConformation(int iChain,
                            ConformationChainZigZag newConformation)

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

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)

getBasisMolecules

public Basis getBasisMolecules()

setBasisMolecules

public void setBasisMolecules(Basis basisMolecules)

getBasisSurface

public Basis getBasisSurface()

setBasisSurface

public void setBasisSurface(Basis basisSurface)