Package etomica.models.nitrogen

Class CoordinateDefinitionNitrogenSuperBox

java.lang.Object

etomica.normalmode.CoordinateDefinition

etomica.normalmode.CoordinateDefinitionMolecule

etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox

All Implemented Interfaces:

java.io.Serializable

public class CoordinateDefinitionNitrogenSuperBox
extends CoordinateDefinitionMolecule
implements java.io.Serializable

CoordinateDefinition implementation for nitrogen molecule. 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
protected static class	CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource

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	axis
protected Configuration	configuration
protected int[][]	innersegment
boolean	isAlpha
boolean	isGamma
protected MoleculeAgentManager	orientationManager
protected IRandom	random
protected RotationTensor3D	rotationTensor
protected int[]	segment
protected ISpecies	speciesA
protected ISpecies	speciesB
protected Tensor3D	tensor
protected Tensor[]	xzOrientationTensor
protected Tensor[]	yOrientationTensor

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
CoordinateDefinitionNitrogenSuperBox(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.
Vector[]	getMoleculeOrientation(IMolecule molecule)
void	initializeCoordinates(int[] nCells)
void	initNominalU(IMoleculeList molecules)	Override if nominal U is more than the lattice position of the molecule Number of molecules equals to basis atoms initNomial is the method to define the initial orientation of the molecule
void	setConfiguration(Configuration configuration)
void	setGammaPositionAndOrientation(IMoleculeList molecules)
void	setIsAlpha()
void	setIsGamma()
void	setOrientationVectorAlpha(Space space)
void	setOrientationVectorGamma(Space space)
void	setSpecies(ISpecies speciesA, ISpecies speciesB)
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 etomica.normalmode.CoordinateDefinitionMolecule

getLatticePosition, getPositionDefinition, setInitVolume, setPositionDefinition

Methods inherited from class java.lang.Object

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

Field Detail

rotationTensor

protected final RotationTensor3D rotationTensor

xzOrientationTensor

protected final Tensor[] xzOrientationTensor

yOrientationTensor

protected final Tensor[] yOrientationTensor

tensor

protected final Tensor3D tensor

axis

protected final Vector axis

configuration

protected Configuration configuration

orientationManager

protected MoleculeAgentManager orientationManager

atomGroupAction

protected final MoleculeChildAtomAction atomGroupAction

isAlpha

public boolean isAlpha

isGamma

public boolean isGamma

random

protected IRandom random

speciesA

protected ISpecies speciesA

speciesB

protected ISpecies speciesB

segment

protected int[] segment

innersegment

protected int[][] innersegment

Constructor Detail

CoordinateDefinitionNitrogenSuperBox

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

Method Detail

initializeCoordinates

public void initializeCoordinates(int[] nCells)

Overrides:

initializeCoordinates in class CoordinateDefinitionMolecule

setGammaPositionAndOrientation

public void setGammaPositionAndOrientation(IMoleculeList molecules)

setConfiguration

public void setConfiguration(Configuration configuration)

setOrientationVectorGamma

public void setOrientationVectorGamma(Space space)

setOrientationVectorAlpha

public void setOrientationVectorAlpha(Space space)

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

initNominalU

public void initNominalU(IMoleculeList molecules)

Override if nominal U is more than the lattice position of the molecule Number of molecules equals to basis atoms initNomial is the method to define the initial orientation of the molecule

Overrides:

initNominalU in class CoordinateDefinitionMolecule

setIsGamma

public void setIsGamma()

setIsAlpha

public void setIsAlpha()

getMoleculeOrientation

public Vector[] getMoleculeOrientation(IMolecule 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.

setSpecies

public void setSpecies(ISpecies speciesA,
                       ISpecies speciesB)