Package etomica.normalmode

Class CoordinateDefinitionHSDimer

java.lang.Object

etomica.normalmode.CoordinateDefinition

etomica.normalmode.CoordinateDefinitionMolecule

etomica.normalmode.CoordinateDefinitionHSDimer

All Implemented Interfaces:

java.io.Serializable

public class CoordinateDefinitionHSDimer
extends CoordinateDefinitionMolecule
implements java.io.Serializable

CoordinateDefinition implementation for HS Dimer. 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 and 2 rotational displacements.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	CoordinateDefinitionHSDimer.IntegerFunction

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

CoordinateDefinition.BasisCell, CoordinateDefinition.SiteSource

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

CoordinateDefinitionMolecule.MoleculeSiteSource

Field Summary

Fields

Modifier and Type	Field	Description
protected MoleculeChildAtomAction	atomGroupAction
protected Vector[][]	axes
protected Vector	axis
protected Configuration	configuration
protected double[]	cosTheta
protected IOrientation	orientation
protected CoordinateDefinitionHSDimer.IntegerFunction	orientationSelector

Fields inherited from class etomica.normalmode.CoordinateDefinition

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

Fields inherited from class etomica.normalmode.CoordinateDefinitionMolecule

inflate, initVolume, moleculeSiteManager, positionDefinition, rScale, sim, u, work1

Constructor Summary

Constructors

Constructor	Description
CoordinateDefinitionHSDimer(Simulation sim, Box box, Primitive primitive, Basis basis, 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.
IOrientation	getMoleculeOrientation(IMolecule molecule)	return the initial Orientation of the molecule
void	initializeCoordinates(int[] nCells)
void	setConfiguration(Configuration configuration)
void	setOrientations(Vector[][] newAxes, double[] newTheta, CoordinateDefinitionHSDimer.IntegerFunction newOrientationSelector)
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.
void	setToUMoleculei(int moleculei, double[] newU)

Methods inherited from class etomica.normalmode.CoordinateDefinition

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

Methods inherited from class etomica.normalmode.CoordinateDefinitionMolecule

getLatticePosition, getPositionDefinition, initNominalU, setInitVolume, setPositionDefinition

Methods inherited from class java.lang.Object

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

Field Detail

axes

protected Vector[][] axes

orientation

protected final IOrientation orientation

orientationSelector

protected CoordinateDefinitionHSDimer.IntegerFunction orientationSelector

axis

protected final Vector axis

configuration

protected Configuration configuration

atomGroupAction

protected final MoleculeChildAtomAction atomGroupAction

cosTheta

protected double[] cosTheta

Constructor Detail

CoordinateDefinitionHSDimer

public CoordinateDefinitionHSDimer(Simulation sim,
                                   Box box,
                                   Primitive primitive,
                                   Basis basis,
                                   Space _space)

Method Detail

initializeCoordinates

public void initializeCoordinates(int[] nCells)

Overrides:

initializeCoordinates in class CoordinateDefinitionMolecule

setConfiguration

public void setConfiguration(Configuration configuration)

setOrientations

public void setOrientations(Vector[][] newAxes,
                            double[] newTheta,
                            CoordinateDefinitionHSDimer.IntegerFunction newOrientationSelector)

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.

Overrides:

calcU in class CoordinateDefinitionMolecule

Parameters:

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

getMoleculeOrientation

public IOrientation getMoleculeOrientation(IMolecule molecule)

return the initial Orientation of the molecule

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()

Overrides:

setToU in class CoordinateDefinitionMolecule

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.

setToUMoleculei

public void setToUMoleculei(int moleculei,
                            double[] newU)