etomica.config

Class ConfigurationLattice

java.lang.Object

etomica.config.ConfigurationLattice

All Implemented Interfaces:

Configuration, java.io.Serializable

Direct Known Subclasses:

ConfigurationLatticeWithPlane, ConfigurationZincblende

public class ConfigurationLattice
extends java.lang.Object
implements Configuration, java.io.Serializable

Constructs configuration that has the molecules placed on the sites of a lattice. Molecules are placed sequentially on the sites of the lattice in an order specified by an index iterator set at construction.

Iteration over the indexes yields integer arrays, and with each iteration the array is passed to the site method of the lattice which returns the position for placement of the next molecule. Each array index is iterated to a maximum value determined by the number of molecules to be placed, the dimensions of the box in which they are placed, and the lattice constants of the lattice. If there are not enough molecules to fill the lattice, they will be distributed as evenly as possible.

An instance of this class may be configured to place atoms such that they uniformly fill the volume of the box. It will attempt this by scaling the lattice constants of the configuration in an appropriate way. Success in getting a good spatial distribution may vary.

An instance can also be configured to remember the indices used to get lattice position for each molecule that is placed. This can be useful if it is desired to associate each molecule with a lattice site.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ConfigurationLattice.MyLattice Used to store the state of a lattice.

Field Summary

Fields

Modifier and Type	Field and Description
protected MoleculeActionTranslateTo	atomActionTranslateTo
protected double	boundaryPadding
protected IndexIteratorSizable	indexIterator
protected SpaceLattice	lattice
protected ConfigurationLattice.MyLattice	myLat
protected IAtomPositionDefinition	positionDefinition
protected boolean	rescalingToFitVolume
protected ISpace	space

Constructor Summary

Constructors

Constructor and Description
ConfigurationLattice(SpaceLattice lattice, IndexIteratorSizable indexIterator, ISpace space) Construct class that will place atoms on sites of the given lattice, proceeding in the order resulting from iteration through the given index iterator.
ConfigurationLattice(SpaceLattice lattice, ISpace space) Constructs class using instance of IndexIteratorRectangular as the default index iterator.

Method Summary

Modifier and Type	Method and Description
protected int[]	calculateLatticeDimensions(int nCells, IVector shape)
double	getBoundaryPadding()
SpaceLattice	getLatticeMemento() Returns a lattice with positions the same as those used in the most recent use of initializeCoordinates.
void	initializeCoordinates(IBox box) Places the molecules in the given box on the positions of the lattice.
void	initializeCoordinates(IBox box, ISpecies species)
boolean	isRescalingToFitVolume() Returns the resizeLatticeToFitVolume flag.
void	setBoundaryPadding(double newBoundaryPadding)
void	setRescalingToFitVolume(boolean resizeLatticeToFitVolume) Sets the resizeLatticeToFitVolume flag, which if true indicates that the primitive vectors should be resized to fit the dimensions of the box.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

lattice

protected final SpaceLattice lattice

indexIterator

protected final IndexIteratorSizable indexIterator

rescalingToFitVolume

protected boolean rescalingToFitVolume

atomActionTranslateTo

protected final MoleculeActionTranslateTo atomActionTranslateTo

myLat

protected ConfigurationLattice.MyLattice myLat

boundaryPadding

protected double boundaryPadding

space

protected final ISpace space

positionDefinition

protected IAtomPositionDefinition positionDefinition

Constructor Detail

ConfigurationLattice

public ConfigurationLattice(SpaceLattice lattice,
                            ISpace space)

Constructs class using instance of IndexIteratorRectangular as the default index iterator.

ConfigurationLattice

public ConfigurationLattice(SpaceLattice lattice,
                            IndexIteratorSizable indexIterator,
                            ISpace space)

Construct class that will place atoms on sites of the given lattice, proceeding in the order resulting from iteration through the given index iterator.

Method Detail

setBoundaryPadding

public void setBoundaryPadding(double newBoundaryPadding)

getBoundaryPadding

public double getBoundaryPadding()

initializeCoordinates

public void initializeCoordinates(IBox box)

Places the molecules in the given box on the positions of the lattice.

Specified by:

initializeCoordinates in interface Configuration

initializeCoordinates

public void initializeCoordinates(IBox box,
                                  ISpecies species)

calculateLatticeDimensions

protected int[] calculateLatticeDimensions(int nCells,
                                           IVector shape)

getLatticeMemento

public SpaceLattice getLatticeMemento()

Returns a lattice with positions the same as those used in the most recent use of initializeCoordinates. Includes any scaling or translation applied to fill the space, and thus will not necessarily be the same positions as specified by the lattice given at construction.

isRescalingToFitVolume

public boolean isRescalingToFitVolume()

Returns the resizeLatticeToFitVolume flag.

Returns:

boolean

setRescalingToFitVolume

public void setRescalingToFitVolume(boolean resizeLatticeToFitVolume)

Sets the resizeLatticeToFitVolume flag, which if true indicates that the primitive vectors should be resized to fit the dimensions of the box. Default is true.

Parameters:

resizeLatticeToFitVolume - The resizeLatticeToFitVolume to set