Package etomica.space

Class BoundaryDeformablePeriodic

java.lang.Object

etomica.space.Boundary

etomica.space.BoundaryDeformablePeriodic

Direct Known Subclasses:

BoundaryDeformableLattice, BoundaryDeformablePeriodicSwitch

public class BoundaryDeformablePeriodic
extends Boundary

Boundary shaped as an arbitrary parallelepiped. Applicable only for a 2D or 3D spaces.

Field Summary

Fields

Modifier and Type	Field	Description
protected Vector[]	transformVectors
protected double	truncationRadius
protected double[]	tV2

Fields inherited from class etomica.space.Boundary

box, eventManager, inflateEvent, shape, space

Constructor Summary

Constructors

Constructor	Description
BoundaryDeformablePeriodic(Space _space)	Make a cubic boundary with edges of length equal to the default boxSize and periodic in every direction.
BoundaryDeformablePeriodic(Space space, double boxSize)	Make a cubic boundary of specified edge length and periodicity.
BoundaryDeformablePeriodic(Space space, Vector[] vex)	Make a parallelepiped boundary of specified shape and periodicity.

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).
void	deform(Tensor deformationTensor)	Applies the given deformation tensor to the boundary in its current shape.
Tensor	getBoundaryTensor()	Returns the boundary tensor that fully describes the shape of the boundary.
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	getEdgeVector(int d)	Returns the vector that defines the edge of this boundary for the given dimension.
IndexIteratorSizable	getIndexIterator()
boolean	getPeriodicity(int i)	Returns true if the boundary is periodic in the given direction (as defined by the getEdgeVector method).
double	getTruncationRadius()
double[][]	imageOrigins(int nShells)	Set of vectors describing the displacements needed to translate the central image to all of the periodic images.
void	nearestImage(Vector dr)	The nearest image is the pair of atom images that are closest when all periodic-boundary images are considered.
void	setAsCube(double edgeLength)	Sets the shape of the boundary to a cube with edges equal to the given value.
void	setAsRectangular(Vector vector)	Sets the shape of the boundary as a rectangular parallelepiped (or parallelogram) with edge lengths given by the elements of the given vector.
void	setBoxSize(Vector v)	Scales each boundary edge so that its length equals the corresponding value in the given vector.
void	setDimensions(Tensor t)	Sets the boundary tensor to equal the given tensor.
void	setEdgeVector(int i, Vector v)
void	setEdgeVectors(Vector[] vectors)
void	setTruncationRadius(double newTruncationRadius)
protected void	testTransformVector(Vector v)	We test the given vector (v) to see if 0.5*v would be transformed by any of our existing transformVectors.
protected void	update()
double	volume()

Methods inherited from class etomica.space.Boundary

getBox, getCenter, getEventManager, getPeriodicity, getShape, setBox

Methods inherited from class java.lang.Object

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

Field Detail

transformVectors

protected Vector[] transformVectors

tV2

protected double[] tV2

truncationRadius

protected double truncationRadius

Constructor Detail

BoundaryDeformablePeriodic

public BoundaryDeformablePeriodic(Space _space)

Make a cubic boundary with edges of length equal to the default boxSize and periodic in every direction.

BoundaryDeformablePeriodic

public BoundaryDeformablePeriodic(Space space,
                                  double boxSize)

Make a cubic boundary of specified edge length and periodicity.

BoundaryDeformablePeriodic

public BoundaryDeformablePeriodic(Space space,
                                  Vector[] vex)

Make a parallelepiped boundary of specified shape and periodicity.

Parameters:

space - the governing space

vex - array of vectors specifying directions for the parallelepiped edges

Throws:

java.lang.IllegalArgumentException - if the dimension of space is not 2 or 3

java.lang.IllegalArgumentException - if the vex.length is not equal to the dimension of the space

Method Detail

getBoxSize

public Vector getBoxSize()

Returns the length of the sides of a rectangular box oriented in the lab frame and in which the boundary is inscribed.

Specified by:

getBoxSize in class Boundary

Returns:

the box size

getBoundaryTensor

public Tensor getBoundaryTensor()

Returns the boundary tensor that fully describes the shape of the boundary. Each column of the tensor is an edge vector of the boundary. Manipulation of the returned tensor does not affect the state of the boundary. Shape-changing methods (e.g., deform()) must be used to affect the boundary shape.

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

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

deform

public void deform(Tensor deformationTensor)

Applies the given deformation tensor to the boundary in its current shape.

Throws:

java.lang.IllegalArgumentException - if the spatial dimension of the tensor is inconsistent with the dimension of the boundary

setAsRectangular

public void setAsRectangular(Vector vector)

Sets the shape of the boundary as a rectangular parallelepiped (or parallelogram) with edge lengths given by the elements of the given vector. To keep the edge lengths unchanged while deforming into a rectangular shape, call this method with getDimensions() as its argument.

Throws:

java.lang.IllegalArgumentException - if the spatial dimension of the vector is inconsistent with the dimension of the boundary

setAsCube

public void setAsCube(double edgeLength)

Sets the shape of the boundary to a cube with edges equal to the given value.

setBoxSize

public void setBoxSize(Vector v)

Scales each boundary edge so that its length equals the corresponding value in the given vector. Deformation of boundary is otherwise unchanged.

Specified by:

setBoxSize in class Boundary

Parameters:

v - the box's new size

setEdgeVector

public void setEdgeVector(int i,
                          Vector v)

setEdgeVectors

public void setEdgeVectors(Vector[] vectors)

setDimensions

public void setDimensions(Tensor t)

Sets the boundary tensor to equal the given tensor.

volume

public double volume()

Overrides:

volume in class Boundary

Returns:

the volume enclosed by the boundary

setTruncationRadius

public void setTruncationRadius(double newTruncationRadius)

getTruncationRadius

public double getTruncationRadius()

update

protected void update()

testTransformVector

protected void testTransformVector(Vector v)

We test the given vector (v) to see if 0.5*v would be transformed by any of our existing transformVectors. If so, then we don't need to keep v as an additional transform vector. We also check to see if vectors that would be transformed could be within our truncation radius (if given). If no vector transformed by only v would be within the truncation radius, then v is not included as a new transform vector.

getEdgeVector

public Vector getEdgeVector(int d)

Description copied from class: Boundary

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.

Specified by:

getEdgeVector in class Boundary

Parameters:

d - the dimension of the desired edge vector

Returns:

the edge vector

getPeriodicity

public boolean getPeriodicity(int i)

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:

i - the dimension of the desired periodicity

Returns:

the periodicity of dimension d

getIndexIterator

public IndexIteratorSizable getIndexIterator()

Specified by:

getIndexIterator in class Boundary

imageOrigins

public double[][] imageOrigins(int nShells)

Description copied from class: Boundary

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.

Specified by:

imageOrigins in class Boundary

Parameters:

nShells - the number of shells of images to be computed