Package etomica.space

Class BoundaryRectangularPore

java.lang.Object

etomica.space.Boundary

etomica.space.BoundaryRectangular

etomica.space.BoundaryRectangularPore

public class BoundaryRectangularPore
extends BoundaryRectangular

Class for implementing pore periodic boundary conditions, in which one dimension is periodic. Selection of periodic dimension may be changed after construction.

Field Summary

Fields

Modifier and Type	Field	Description
protected Vector	dimensionsHalf
protected Vector	tempImage

Fields inherited from class etomica.space.Boundary

box, eventManager, inflateEvent, shape, space

Fields inherited from class etomica.space.BoundaryRectangular

dimensions, edgeVectors, shift0

Constructor Summary

Constructors

Constructor	Description
BoundaryRectangularPore(Space space)	Makes cubic volume with the x-dimension (index 0) not periodic.
BoundaryRectangularPore(Space space, int poreDim)	Makes cubic volume with the indicated dimension not periodic.
BoundaryRectangularPore(Space space, int poreDim, double boxSize)	Constructor for periodic boundary conditions with a pore in the given dimension.

Method Summary

Modifier and Type	Method	Description
Vector	centralImage(Vector r)	Determines the translation vector needed to apply a periodic-image transformation that moves the given point to an image point within the boundary (if it lies outside, in a direction subject to periodic imaging).
IndexIteratorSizable	getIndexIterator()
boolean	getPeriodicity(int d)	Returns true if the boundary is periodic in the given direction (as defined by the getEdgeVector method).
int	getPoreDim()	Returns index of periodic dimension.
void	nearestImage(Vector dr)	The nearest image is the pair of atom images that are closest when all periodic-boundary images are considered.
void	setPoreDim(int poreDim)	Sets the periodic dimension to that indicated by the given value (0 is x-dimension, 1 is y-dimension, etc.).
protected void	updateDimensions()

Methods inherited from class etomica.space.Boundary

getBox, getCenter, getEventManager, getPeriodicity, getShape, setBox

Methods inherited from class etomica.space.BoundaryRectangular

getBoxSize, getEdgeVector, imageOrigins, setBoxSize, volume

Methods inherited from class java.lang.Object

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

Field Detail

dimensionsHalf

protected final Vector dimensionsHalf

tempImage

protected final Vector tempImage

Constructor Detail

BoundaryRectangularPore

public BoundaryRectangularPore(Space space)

Makes cubic volume with the x-dimension (index 0) not periodic. Length of each box edge is given by default boxSize in given Simulation.

BoundaryRectangularPore

public BoundaryRectangularPore(Space space,
                               int poreDim)

Makes cubic volume with the indicated dimension not periodic. Length of each box edge is given by the default boxSize in the given Simulation.

Parameters:

poreDim - index indicating dimension that is not periodic (0 for x-dimension, 1 for y-dimension, etc.).

Throws:

java.lang.IllegalArgumentException - if not (0 <= slitDim < space.D).

BoundaryRectangularPore

public BoundaryRectangularPore(Space space,
                               int poreDim,
                               double boxSize)

Constructor for periodic boundary conditions with a pore in the given dimension.

Parameters:

space -

poreDim - pore dimension (in which PBC is not imposed).

Method Detail

setPoreDim

public void setPoreDim(int poreDim)

Sets the periodic dimension to that indicated by the given value (0 is x-dimension, 1 is y-dimension, etc.).

Throws:

java.lang.IllegalArgumentException - if not (0 <= slitDim < space.D).

getPoreDim

public int getPoreDim()

Returns index of periodic dimension.

updateDimensions

protected void updateDimensions()

Overrides:

updateDimensions in class BoundaryRectangular

nearestImage

public void nearestImage(Vector dr)

Description copied from class: Boundary

The nearest image is the pair of atom images that are closest when all periodic-boundary images are considered.

If the vector passed to this method is the displacement vector between two points, the vector will be transformed such that it corresponds to the vector between the nearest image of those two points.

Specified by:

nearestImage in class Boundary

Parameters:

dr - the vector to be transformed

centralImage

public Vector centralImage(Vector r)

Description copied from class: Boundary

Determines the translation vector needed to apply a periodic-image transformation that moves the given point to an image point within the boundary (if it lies outside, in a direction subject to periodic imaging).

Specified by:

centralImage in class Boundary

Parameters:

r - vector position of untransformed point; r is not changed by this method

Returns:

the displacement that must be applied to r to move it to its central-image location

getIndexIterator

public IndexIteratorSizable getIndexIterator()

Specified by:

getIndexIterator in class Boundary

getPeriodicity

public boolean getPeriodicity(int d)

Description copied from class: Boundary

Returns true if the boundary is periodic in the given direction (as defined by the getEdgeVector method).

Specified by:

getPeriodicity in class Boundary

Parameters:

d - the dimension of the desired periodicity

Returns:

the periodicity of dimension d