Package etomica.config

Class ConfigurationLatticeWithPlane

java.lang.Object

etomica.config.ConfigurationLattice

etomica.config.ConfigurationLatticeWithPlane

All Implemented Interfaces:

Configuration

public class ConfigurationLatticeWithPlane
extends ConfigurationLattice

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.

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/interfaces inherited from class etomica.config.ConfigurationLattice

ConfigurationLattice.MyLattice

Field Summary

Fields inherited from class etomica.config.ConfigurationLattice

atomActionTranslateTo, boundaryPadding, indexIterator, lattice, myLat, positionDefinition, rescalingToFitVolume, space

Constructor Summary

Constructors

Constructor	Description
ConfigurationLatticeWithPlane(SpaceLattice lattice, Plane plane, Space space)	Constructs class using instance of IndexIteratorRectangular as the default index iterator.

Method Summary

Modifier and Type	Method	Description
void	addSpecies(ISpecies newSpecies)
float	getSpeciesAllocation(ISpecies sp)	Sets the initial allocation of the species on the left side of the plane.
void	initializeCoordinates(Box box)	Places the molecules in the given box on the positions of the lattice.
void	removeSpecies(ISpecies remSpecies)
void	setSpeciesAllocation(ISpecies sp, float pct)	Sets the initial allocation of the species on the left side of the plane.

Methods inherited from class etomica.config.ConfigurationLattice

calculateLatticeDimensions, getBoundaryPadding, getLatticeMemento, initializeCoordinates, isRescalingToFitVolume, setBoundaryPadding, setRescalingToFitVolume

Methods inherited from class java.lang.Object

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

Constructor Detail

ConfigurationLatticeWithPlane

public ConfigurationLatticeWithPlane(SpaceLattice lattice,
                                     Plane plane,
                                     Space space)

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

Method Detail

addSpecies

public void addSpecies(ISpecies newSpecies)

Parameters:

newSpecies - : species that will need to be configured

removeSpecies

public void removeSpecies(ISpecies remSpecies)

Parameters:

remSpecies - : species that should be removed from configuration

setSpeciesAllocation

public void setSpeciesAllocation(ISpecies sp,
                                 float pct)

Sets the initial allocation of the species on the left side of the plane. The remaining molecules in the species will be initially allocated to the right side of the plane.

Parameters:

sp - : Species to set allocation for

pct - : Percentage of species to initially allocate on the left side of the plane (0.0 <= pct <= 1.0)

getSpeciesAllocation

public float getSpeciesAllocation(ISpecies sp)

Sets the initial allocation of the species on the left side of the plane. The remaining molecules in the species will be initially allocated to the right side of the plane.

Parameters:

sp - : Species to set allocation for

initializeCoordinates

public void initializeCoordinates(Box box)

Places the molecules in the given box on the positions of the lattice. The molecules must be of a species added with addSpecies() or they will not be displayed.

Specified by:

initializeCoordinates in interface Configuration

Overrides:

initializeCoordinates in class ConfigurationLattice