Package etomica.normalmode

Class CoordinateDefinition

java.lang.Object

etomica.normalmode.CoordinateDefinition

Direct Known Subclasses:

CoordinateDefinitionLeaf, CoordinateDefinitionMolecule, CoordinateDefinitionMoleculeVolumeFluctuation

public abstract class CoordinateDefinition
extends java.lang.Object

An abstract class that defines the real-space generalized coordinates that are summed (over molecules) to form collective coordinates (from which normal coordinates are determined). Typically these generalized coordinates are given by the displacement of the molecule from its nominal lattice position. For non-spherical molecules it will also include elements related to the orientation. This class provides methods to compute the k-dependent collective generalized coordinates, obtained by Fourier-summing the generalized coordinates over the atoms in a box.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	CoordinateDefinition.BasisCell
protected static class	CoordinateDefinition.SiteSource

Field Summary

Fields

Modifier and Type	Field	Description
protected MoleculeActionTranslateTo	atomActionTranslateTo
protected Basis	basis
protected Box	box
protected CoordinateDefinition.BasisCell[]	cells
protected int	coordinateDim
protected BravaisLatticeCrystal	lattice
protected Primitive	primitive
protected AtomLeafAgentManager<Vector>	siteManager
protected Space	space

Constructor Summary

Constructors

Constructor	Description
CoordinateDefinition(Box box, int coordinateDim, Primitive primitive, Basis basis, Space _space)
CoordinateDefinition(Box box, int coordinateDim, Primitive primitive, Space _space)

Method Summary

Modifier and Type	Method	Description
void	calcT(Vector k, double[] realT, double[] imaginaryT)	Calculates the complex "T vector", which is collective coordinate given by the Fourier sum (over atoms) of the generalized coordinate vector.
abstract double[]	calcU(IMoleculeList molecules)	Calculates the generalized coordinates for the given molecules in their current position and orientation.
Basis	getBasis()
CoordinateDefinition.BasisCell[]	getBasisCells()
Box	getBox()
int	getCoordinateDim()	Returns the number of generalized coordinates associated with each molecule.
Vector	getLatticePosition(IAtom atom)
Primitive	getPrimitive()
AtomLeafAgentManager<Vector>	getSiteManager()
void	initializeCoordinates(int[] nCells)
protected abstract void	initNominalU(IMoleculeList molecules)	Initializes the CoordinateDefinition for the given molecule and associates the molecule with the given index.
abstract void	setToU(IMoleculeList molecules, double[] newU)	Set all the molecules in a cell to a position and orientation that corresponds to the given generalized coordinate.

Methods inherited from class java.lang.Object

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

Field Detail

coordinateDim

protected final int coordinateDim

box

protected final Box box

siteManager

protected AtomLeafAgentManager<Vector> siteManager

lattice

protected final BravaisLatticeCrystal lattice

primitive

protected final Primitive primitive

basis

protected final Basis basis

atomActionTranslateTo

protected final MoleculeActionTranslateTo atomActionTranslateTo

cells

protected CoordinateDefinition.BasisCell[] cells

space

protected final Space space

Constructor Detail

CoordinateDefinition

public CoordinateDefinition(Box box,
                            int coordinateDim,
                            Primitive primitive,
                            Space _space)

CoordinateDefinition

public CoordinateDefinition(Box box,
                            int coordinateDim,
                            Primitive primitive,
                            Basis basis,
                            Space _space)

Method Detail

initializeCoordinates

public void initializeCoordinates(int[] nCells)

getCoordinateDim

public int getCoordinateDim()

Returns the number of generalized coordinates associated with each molecule. If no orientational coordinates are involved, this value is typically equal to the space dimension.

calcU

public abstract double[] calcU(IMoleculeList molecules)

Calculates the generalized coordinates for the given molecules in their current position and orientation. The result is stored in the |u| field.

Parameters:

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

initNominalU

protected abstract void initNominalU(IMoleculeList molecules)

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.

setToU

public abstract void setToU(IMoleculeList molecules,
                            double[] newU)

Set all the molecules in a cell to a position and orientation that corresponds to the given generalized coordinate. |u| must be of length getCoordinateDim()

Parameters:

molecules - The molecules of interest

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

calcT

public void calcT(Vector k,
                  double[] realT,
                  double[] imaginaryT)

Calculates the complex "T vector", which is collective coordinate given by the Fourier sum (over atoms) of the generalized coordinate vector.

Parameters:

k - the wave vector

realT - outputs the real component of the T vector

imaginaryT - outputs the imaginary component of the T vector

getBox

public Box getBox()

getLatticePosition

public Vector getLatticePosition(IAtom atom)

getBasisCells

public CoordinateDefinition.BasisCell[] getBasisCells()

getPrimitive

public Primitive getPrimitive()

getBasis

public Basis getBasis()

getSiteManager

public AtomLeafAgentManager<Vector> getSiteManager()