Package etomica.normalmode

Class CoordinateDefinitionLeaf

java.lang.Object

etomica.normalmode.CoordinateDefinition

etomica.normalmode.CoordinateDefinitionLeaf

All Implemented Interfaces:

java.io.Serializable

Direct Known Subclasses:

CoordinateDefinitionLeafSuperBox

public class CoordinateDefinitionLeaf
extends CoordinateDefinition
implements java.io.Serializable

CoordinateDefinition implementation for monatomic molecules that are simply leaf atoms. The class simply takes the u values to be real space displacements from the nominal positions.

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class etomica.normalmode.CoordinateDefinition

CoordinateDefinition.BasisCell, CoordinateDefinition.SiteSource

Field Summary

Fields

Modifier and Type	Field	Description
protected double[]	u
protected Vector	workVector

Fields inherited from class etomica.normalmode.CoordinateDefinition

atomActionTranslateTo, basis, box, cells, coordinateDim, lattice, primitive, siteManager, space

Constructor Summary

Constructors

Constructor	Description
CoordinateDefinitionLeaf(Box box, Primitive primitive, Basis basis, Space space)
CoordinateDefinitionLeaf(Box box, Primitive primitive, Space space)

Method Summary

Modifier and Type	Method	Description
double[]	calcU(IMoleculeList atoms)	Assigns the given array u to be the current position of the atom minus its lattice position
void	initNominalU(IMoleculeList molecules)	Initializes the CoordinateDefinition for the given molecule and associates the molecule with the given index.
void	setToU(IMoleculeList atoms, double[] newU)	Sets the position of the atom to be its lattice position plus the offset u

Methods inherited from class etomica.normalmode.CoordinateDefinition

calcT, getBasis, getBasisCells, getBox, getCoordinateDim, getLatticePosition, getPrimitive, getSiteManager, initializeCoordinates

Methods inherited from class java.lang.Object

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

Field Detail

workVector

protected final Vector workVector

u

protected final double[] u

Constructor Detail

CoordinateDefinitionLeaf

public CoordinateDefinitionLeaf(Box box,
                                Primitive primitive,
                                Space space)

CoordinateDefinitionLeaf

public CoordinateDefinitionLeaf(Box box,
                                Primitive primitive,
                                Basis basis,
                                Space space)

Method Detail

calcU

public double[] calcU(IMoleculeList atoms)

Assigns the given array u to be the current position of the atom minus its lattice position

Specified by:

calcU in class CoordinateDefinition

Parameters:

atoms - The molecules of interest, which should be those forming a unit cell of the lattice

initNominalU

public void initNominalU(IMoleculeList molecules)

Description copied from class: CoordinateDefinition

Initializes the CoordinateDefinition for the given molecule and associates the molecule with the given index. Typically this will be called when the molecule is in a nominal position and orientation, and the generalized coordinates for the molecule will be defined with respect to this nominal case.

Specified by:

initNominalU in class CoordinateDefinition

setToU

public void setToU(IMoleculeList atoms,
                   double[] newU)

Sets the position of the atom to be its lattice position plus the offset u

Specified by:

setToU in class CoordinateDefinition

Parameters:

atoms - The molecules of interest

newU - The generalized coordinate that defines the position and orientation to which the molecules will be set by this method.