Package etomica.normalmode

Class CoordinateDefinitionMolecule

java.lang.Object

etomica.normalmode.CoordinateDefinition

etomica.normalmode.CoordinateDefinitionMolecule

All Implemented Interfaces:

java.io.Serializable

Direct Known Subclasses:

CoordinateDefinitionHSDimer, CoordinateDefinitionNitrogen, CoordinateDefinitionNitrogenSuperBox

public class CoordinateDefinitionMolecule
extends CoordinateDefinition
implements java.io.Serializable

CoordinateDefinition implementation for molecules. The class takes the first space.D values of u to be real space displacements of the molecule center of mass from its nominal position. Subclasses should add additional u values for intramolecular degrees of freedom.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
protected static class	CoordinateDefinitionMolecule.MoleculeSiteSource

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

CoordinateDefinition.BasisCell, CoordinateDefinition.SiteSource

Field Summary

Fields

Modifier and Type	Field	Description
protected BoxInflate	inflate
protected Vector	initVolume
protected MoleculeAgentManager<Vector>	moleculeSiteManager
protected IMoleculePositionDefinition	positionDefinition
protected double	rScale
protected Simulation	sim
protected double[]	u
protected Vector	work1

Fields inherited from class etomica.normalmode.CoordinateDefinition

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

Constructor Summary

Constructors

Constructor	Description
CoordinateDefinitionMolecule(Simulation sim, Box box, Primitive primitive, int orientationDim, Basis basis, Space space)
CoordinateDefinitionMolecule(Simulation sim, Box box, Primitive primitive, int orientationDim, Space space)

Method Summary

Modifier and Type	Method	Description
double[]	calcU(IMoleculeList molecules)	Calculates the generalized coordinates for the given molecules in their current position and orientation.
Vector	getLatticePosition(IMolecule molecule)
IMoleculePositionDefinition	getPositionDefinition()
void	initializeCoordinates(int[] nCells)
void	initNominalU(IMoleculeList molecules)	Override if nominal U is more than the lattice position of the molecule
void	setInitVolume(Vector initV)
void	setPositionDefinition(IMoleculePositionDefinition positionDefinition)
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 etomica.normalmode.CoordinateDefinition

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

Methods inherited from class java.lang.Object

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

Field Detail

sim

protected final Simulation sim

moleculeSiteManager

protected MoleculeAgentManager<Vector> moleculeSiteManager

work1

protected final Vector work1

u

protected final double[] u

positionDefinition

protected IMoleculePositionDefinition positionDefinition

rScale

protected double rScale

initVolume

protected Vector initVolume

inflate

protected final BoxInflate inflate

Constructor Detail

CoordinateDefinitionMolecule

public CoordinateDefinitionMolecule(Simulation sim,
                                    Box box,
                                    Primitive primitive,
                                    int orientationDim,
                                    Space space)

CoordinateDefinitionMolecule

public CoordinateDefinitionMolecule(Simulation sim,
                                    Box box,
                                    Primitive primitive,
                                    int orientationDim,
                                    Basis basis,
                                    Space space)

Method Detail

initializeCoordinates

public void initializeCoordinates(int[] nCells)

Overrides:

initializeCoordinates in class CoordinateDefinition

calcU

public double[] calcU(IMoleculeList molecules)

Description copied from class: CoordinateDefinition

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

Specified by:

calcU in class CoordinateDefinition

Parameters:

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

initNominalU

public void initNominalU(IMoleculeList molecules)

Override if nominal U is more than the lattice position of the molecule

Specified by:

initNominalU in class CoordinateDefinition

setToU

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

Description copied from class: CoordinateDefinition

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()

Specified by:

setToU in class CoordinateDefinition

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.

getLatticePosition

public Vector getLatticePosition(IMolecule molecule)

setPositionDefinition

public void setPositionDefinition(IMoleculePositionDefinition positionDefinition)

getPositionDefinition

public IMoleculePositionDefinition getPositionDefinition()

setInitVolume

public void setInitVolume(Vector initV)