Package etomica.space

Class Boundary

java.lang.Object

etomica.space.Boundary

Direct Known Subclasses:

BoundaryDeformablePeriodic, BoundaryRectangular, BoundaryTruncatedOctahedron

public abstract class Boundary
extends java.lang.Object

Parent class of boundary objects that describe the size and periodic nature of the box boundaries. Each Box has its own instance of this class. It may be referenced by a coordinate pair when computing distances between atoms, or by a cell iterator when generating neighbor lists. It is also used by objects that enforce periodic images.

The boundary is responsible for firing inflate events when the boundary dimensions change.

Field Summary

Fields

Modifier and Type	Field	Description
protected Box	box
protected BoundaryEventManager	eventManager
protected BoundaryEvent	inflateEvent
protected Polytope	shape
protected Space	space

Constructor Summary

Constructors

Constructor	Description
Boundary(Space space, Polytope shape)	Subclasses must invoke this constructor and provide a Space instance that can be used to generate Vectors, and a Polytope that defines the shape and volume of the boundary region.

Method Summary

Modifier and Type	Method	Description
abstract 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).
Box	getBox()
abstract Vector	getBoxSize()	Returns the length of the sides of a rectangular box oriented in the lab frame and in which the boundary is inscribed.
Vector	getCenter()
abstract Vector	getEdgeVector(int d)	Returns the vector that defines the edge of this boundary for the given dimension.
BoundaryEventManager	getEventManager()
abstract IndexIteratorSizable	getIndexIterator()
boolean[]	getPeriodicity()
abstract boolean	getPeriodicity(int d)	Returns true if the boundary is periodic in the given direction (as defined by the getEdgeVector method).
Polytope	getShape()
abstract double[][]	imageOrigins(int nShells)	Set of vectors describing the displacements needed to translate the central image to all of the periodic images.
abstract void	nearestImage(Vector dr)	The nearest image is the pair of atom images that are closest when all periodic-boundary images are considered.
void	setBox(Box newBox)	Sets the box that holds the boundary.
abstract void	setBoxSize(Vector v)	Scales the boundary dimensions such that the boundary's would be inscribed within a rectangle of the of the given size.
double	volume()

Methods inherited from class java.lang.Object

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

Field Detail

shape

protected final Polytope shape

space

protected final Space space

box

protected Box box

inflateEvent

protected BoundaryEvent inflateEvent

eventManager

protected BoundaryEventManager eventManager

Constructor Detail

Boundary

public Boundary(Space space,
                Polytope shape)

Subclasses must invoke this constructor and provide a Space instance that can be used to generate Vectors, and a Polytope that defines the shape and volume of the boundary region. Both are final.

Method Detail

getBox

public Box getBox()

Returns:

the boundary's Box. Might be null if the boundary is not associated with a box.

setBox

public void setBox(Box newBox)

Sets the box that holds the boundary. If no box holds the boundary, the box should be set to null.

Parameters:

newBox - the box that holds the boundary

getShape

public Polytope getShape()

volume

public double volume()

Returns:

the volume enclosed by the boundary

getCenter

public Vector getCenter()

Returns:

the center point (origin) of the boundary

getEventManager

public BoundaryEventManager getEventManager()

Returns:

the event manager, which fires notifications about changes to this boundary to any added listener.

getIndexIterator

public abstract IndexIteratorSizable getIndexIterator()

imageOrigins

public abstract double[][] imageOrigins(int nShells)

Set of vectors describing the displacements needed to translate the central image to all of the periodic images. The first index specifies each periodic image, while the second index indicates the xyz components of the translation vector.

Parameters:

nShells - the number of shells of images to be computed

centralImage

public abstract 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).

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

nearestImage

public abstract void nearestImage(Vector dr)

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.

Parameters:

dr - the vector to be transformed

getBoxSize

public abstract Vector getBoxSize()

Returns the length of the sides of a rectangular box oriented in the lab frame and in which the boundary is inscribed. For a rectangular boundary, this is simply the length of the boundary in each direction. Each element of the returned vector gives in that coordinate direction the maximum distance from one point on the boundary to another.

Manipulation of this copy will not cause any change to the boundary's dimensions.

Returns:

the box size

setBoxSize

public abstract void setBoxSize(Vector v)

Scales the boundary dimensions such that the boundary's would be inscribed within a rectangle of the of the given size. For a rectangular boundary, this simply sets the boundary length in each dimension. Specific interpretation of the given values for non-rectangular shapes depends on the subclass.

Parameters:

v - the box's new size

getEdgeVector

public abstract Vector getEdgeVector(int d)

Returns the vector that defines the edge of this boundary for the given dimension. All vectors returned by this method can be considered to originate from one corner.

Parameters:

d - the dimension of the desired edge vector

Returns:

the edge vector

getPeriodicity

public abstract boolean getPeriodicity(int d)

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

Parameters:

d - the dimension of the desired periodicity

Returns:

the periodicity of dimension d

getPeriodicity

public boolean[] getPeriodicity()