CoordinateDefinitionNitrogen

java.lang.Object
- etomica.normalmode.CoordinateDefinition
- - etomica.normalmode.CoordinateDefinitionMolecule
  - - etomica.models.nitrogen.CoordinateDefinitionNitrogen

All Implemented Interfaces:

java.io.Serializable
```
public class CoordinateDefinitionNitrogen
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 CoordinateDefinitionNitrogen.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

Nested Classes
Modifier and Type	Class	Description
`protected static class`	`CoordinateDefinitionNitrogen.OrientationAgentSource`

Field Summary

Fields
Modifier and Type	Field	Description
`protected MoleculeChildAtomAction`	`atomGroupAction`
`protected MoleculeChildAtomAction`	`atomGroupActionTranslate`
`protected Vector`	`axis`
`protected Configuration`	`configuration`
`boolean`	`isAlpha`
`boolean`	`isBeta`
`boolean`	`isBetaHCP`
`boolean`	`isBetaLatticeSum`
`boolean`	`isDoLatticeSum`
`boolean`	`isGamma`
`protected MoleculeAgentManager<Vector[]>`	`orientationManager`
`protected Vector`	`orientVector`
`protected Vector[]`	`positionVector`
`protected IRandom`	`random`
`protected RotationTensor3D`	`rotationTensor`
`int`	`rotDim`
`protected Tensor3D`	`tensor`
`protected AtomActionTranslateBy`	`translateBy`
`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
`CoordinateDefinitionNitrogen(Simulation sim, Box box, Primitive primitive, Basis basis, Space _space)`
`CoordinateDefinitionNitrogen(Simulation sim, Box box, Primitive primitive, Basis basis, Space _space, int rotDim)`

Method Summary

All Methods Instance Methods Concrete Methods
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)`
`Tensor[]`	`getXzOrientationTensor()`
`Tensor[]`	`getyOrientationTensor()`
`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
`void`	`setBetaPositionAndOrientation(IMoleculeList molecules)`
`void`	`setConfiguration(Configuration configuration)`
`void`	`setIsAlpha()`
`void`	`setIsBeta()`
`void`	`setIsBetaHCP()`
`void`	`setIsBetaLatticeSum()`
`void`	`setIsDoLatticeSum()`
`void`	`setIsGamma()`
`void`	`setNominalReference(IMoleculeList molecules)`
`void`	`setOrientationVectorAlpha(Space space)`
`void`	`setOrientationVectorBeta(Space space)`
`void`	`setOrientationVectorBetaInitial(Space space)`
`void`	`setOrientationVectorBetaLatticeSum(Space space, double density, double[][] param)`
`void`	`setOrientationVectorGamma(Space space)`
`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, 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
```

orientVector
```
protected final Vector orientVector
```

atomGroupAction

protected final MoleculeChildAtomAction atomGroupAction

isAlpha
```
public boolean isAlpha
```

isGamma
```
public boolean isGamma
```

isBeta
```
public boolean isBeta
```

isBetaHCP
```
public boolean isBetaHCP
```

isBetaLatticeSum
```
public boolean isBetaLatticeSum
```

isDoLatticeSum
```
public boolean isDoLatticeSum
```

rotDim
```
public int rotDim
```

positionVector
```
protected Vector[] positionVector
```

configuration
```
protected Configuration configuration
```

orientationManager

protected MoleculeAgentManager<Vector[]> orientationManager

translateBy

protected AtomActionTranslateBy translateBy

atomGroupActionTranslate

protected MoleculeChildAtomAction atomGroupActionTranslate

random
```
protected IRandom random
```

Constructor Detail

CoordinateDefinitionNitrogen

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

CoordinateDefinitionNitrogen

public CoordinateDefinitionNitrogen(Simulation sim,
                                    Box box,
                                    Primitive primitive,
                                    Basis basis,
                                    Space _space,
                                    int rotDim)

Method Detail
- initializeCoordinates
```
public void initializeCoordinates(int[] nCells)
```
  Overrides:
  
  initializeCoordinates in class CoordinateDefinitionMolecule
- setBetaPositionAndOrientation
```
public void setBetaPositionAndOrientation(IMoleculeList molecules)
```
- setNominalReference
```
public void setNominalReference(IMoleculeList molecules)
```
- setConfiguration
```
public void setConfiguration(Configuration configuration)
```
- setOrientationVectorGamma
```
public void setOrientationVectorGamma(Space space)
```
- setOrientationVectorAlpha
```
public void setOrientationVectorAlpha(Space space)
```
- setOrientationVectorBetaInitial
```
public void setOrientationVectorBetaInitial(Space space)
```
- setOrientationVectorBeta
```
public void setOrientationVectorBeta(Space space)
```
- setOrientationVectorBetaLatticeSum
```
public void setOrientationVectorBetaLatticeSum(Space space,
                                               double density,
                                               double[][] param)
```
- getXzOrientationTensor
```
public Tensor[] getXzOrientationTensor()
```
- getyOrientationTensor
```
public Tensor[] getyOrientationTensor()
```
- 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()
```
- setIsBeta
```
public void setIsBeta()
```
- setIsBetaHCP
```
public void setIsBetaHCP()
```
- setIsBetaLatticeSum
```
public void setIsBetaLatticeSum()
```
- setIsDoLatticeSum
```
public void setIsDoLatticeSum()
```
- 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.
- setToUMoleculei
```
public void setToUMoleculei(int moleculei,
                            double[] newU)
```

Class CoordinateDefinitionNitrogen

Nested Class Summary

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

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

Field Summary

Fields inherited from class etomica.normalmode.CoordinateDefinition

Fields inherited from class etomica.normalmode.CoordinateDefinitionMolecule

Constructor Summary

Method Summary

Methods inherited from class etomica.normalmode.CoordinateDefinition

Methods inherited from class etomica.normalmode.CoordinateDefinitionMolecule

Methods inherited from class java.lang.Object

Field Detail

rotationTensor

xzOrientationTensor

yOrientationTensor

tensor

axis

orientVector

atomGroupAction

isAlpha

isGamma

isBeta

isBetaHCP

isBetaLatticeSum

isDoLatticeSum

rotDim

positionVector

configuration

orientationManager

translateBy

atomGroupActionTranslate

random

Constructor Detail

CoordinateDefinitionNitrogen

CoordinateDefinitionNitrogen

Method Detail

initializeCoordinates

setBetaPositionAndOrientation

setNominalReference

setConfiguration

setOrientationVectorGamma

setOrientationVectorAlpha

setOrientationVectorBetaInitial

setOrientationVectorBeta

setOrientationVectorBetaLatticeSum

getXzOrientationTensor

getyOrientationTensor

calcU

initNominalU

setIsGamma

setIsAlpha

setIsBeta

setIsBetaHCP

setIsBetaLatticeSum

setIsDoLatticeSum

getMoleculeOrientation

setToU

setToUMoleculei