P2Nitrogen

java.lang.Object
- etomica.potential.PotentialMolecular
- - etomica.models.nitrogen.P2Nitrogen

All Implemented Interfaces:

IPotential, IPotentialMolecular, IPotentialMolecularTorque, PotentialMolecularSoft
```
public class P2Nitrogen
extends PotentialMolecular
implements IPotentialMolecularTorque
```
P2 6-point potential for Nitrogen. Reference paper: Etters RD. et al, Phys. Rev B 33(12) 1986

Field Summary

Fields
Modifier and Type	Field	Description
`protected double`	`A1`
`protected double`	`A2`
`protected double`	`alpha1`
`protected double`	`alpha2`
`protected double`	`B1`
`protected Boundary`	`boundary`
`protected double[]`	`C`
`protected double`	`chargeP1`
`protected double`	`chargeP1P1`
`protected double`	`chargeP1P2`
`protected double`	`chargeP2`
`protected double`	`chargeP2P2`
`protected Vector`	`com1`
`protected Vector`	`com2`
`protected Vector`	`dr1`
`protected Vector`	`dr2`
`protected Vector`	`duWork`
`protected boolean`	`enablePBC`
`protected Vector[]`	`gradient`
`protected Vector[][]`	`gradientAndTorque`
`protected Tensor`	`identity`
`protected double[][]`	`q`
`protected double`	`R0`
`protected double`	`R1`
`protected double`	`r2`
`protected double`	`rC`
`protected Vector[][]`	`secDerXr`
`protected Vector`	`shift`
`protected DataTensor`	`tensorWork`
`protected Vector[]`	`torque`
`protected Vector`	`tWork`
`protected Vector`	`vectorR`
`protected Vector`	`work`
`protected double[][]`	`workdTorq`
`protected Vector[]`	`workTorqVec`
`protected Vector[]`	`workVec`

Fields inherited from class etomica.potential.PotentialMolecular
nBody, space

Constructor Summary

Constructors
Constructor Description

P2Nitrogen(Space space, double rC)

Constructors
Constructor	Description
`P2Nitrogen(Space space, double rC)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`doGradientNoShift(Vector v1, Vector v2, double cc)`
`protected void`	`doGradientShift(Vector v1, Vector v2, double cc)`
`void`	`doSecDerXrNoShift(Vector v1, Vector v2, double cc)`
`void`	`doSecDerXrRotRotNoShift(Vector v1, Vector v2, double cc)`
`void`	`doSecDerXrRotRotWShift(Vector v1, Vector v2, double cc)`
`void`	`doSecDerXrWShift(Vector v1, Vector v2, double cc)`
`double`	`energy(IMoleculeList pair)`	Returns the interaction energy between the given molecules.
`double`	`getRange()`	Returns the range over which the potential applies.
`Vector[]`	`gradient(IMoleculeList pair)`	Returns the gradient of the potential as it applies to each atom in the given AtomSet, indicating how the energy would change as the position of the first atom is varied.
`Vector[]`	`gradient(IMoleculeList atoms, Tensor pressureTensor)`	Returns the same gradient as gradient(IMoleculeList) and also adds in the contribution of the molecules to the pressureTensor.
`Vector[][]`	`gradientAndTorque(IMoleculeList pair)`
`boolean`	`isEnablePBC()`
`DataTensor`	`secondDerivative(IMoleculeList pair)`
`Vector[][]`	`secondDerivativeXr(IMoleculeList pair)`
`Tensor`	`secondDerivativeXrRotRot(IMoleculeList pair)`
`void`	`setBox(Box box)`	Informs the potential of the box on which it acts.
`void`	`setEnablePBC(boolean enablePBC)`
`void`	`setRange(double rC)`
`double`	`virial(IMoleculeList pair)`

Methods inherited from interface etomica.potential.IPotential
nBody

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from class etomica.potential.PotentialMolecular
nBody

Field Detail

gradient
```
protected final Vector[] gradient
```

torque
```
protected final Vector[] torque
```

workVec
```
protected final Vector[] workVec
```

workTorqVec
```
protected final Vector[] workTorqVec
```

workdTorq
```
protected final double[][] workdTorq
```

q
```
protected final double[][] q
```

gradientAndTorque

protected final Vector[][] gradientAndTorque

secDerXr
```
protected final Vector[][] secDerXr
```

boundary
```
protected Boundary boundary
```

tensorWork
```
protected DataTensor tensorWork
```

chargeP1
```
protected final double chargeP1
```

chargeP2
```
protected final double chargeP2
```

chargeP1P1
```
protected final double chargeP1P1
```

chargeP1P2
```
protected final double chargeP1P2
```

chargeP2P2
```
protected final double chargeP2P2
```

A1
```
protected final double A1
```

alpha1
```
protected final double alpha1
```
See Also:

Constant Field Values

B1
```
protected final double B1
```

A2
```
protected final double A2
```

alpha2
```
protected final double alpha2
```
See Also:

Constant Field Values

R0
```
protected final double R0
```
See Also:

Constant Field Values

R1
```
protected final double R1
```
See Also:

Constant Field Values

C
```
protected double[] C
```

work
```
protected final Vector work
```

shift
```
protected final Vector shift
```

duWork
```
protected final Vector duWork
```

tWork
```
protected final Vector tWork
```

dr1
```
protected final Vector dr1
```

dr2
```
protected final Vector dr2
```

com1
```
protected final Vector com1
```

com2
```
protected final Vector com2
```

vectorR
```
protected final Vector vectorR
```

rC
```
protected double rC
```

r2
```
protected double r2
```

enablePBC
```
protected boolean enablePBC
```

identity
```
protected final Tensor identity
```

Constructor Detail

P2Nitrogen

public P2Nitrogen(Space space,
                  double rC)

Method Detail
- setRange
```
public void setRange(double rC)
```
- setBox
```
public void setBox(Box box)
```
  Description copied from class: PotentialMolecular
  
  Informs the potential of the box on which it acts. Typically this requires at least that it update the nearestImageTransformer of its coordinatePair (if it uses one), e.g.: cPair.setNearestImageTransformer(box.boundary());
  
  Specified by:
  
  setBox in interface IPotential
  
  Specified by:
  
  setBox in class PotentialMolecular
- energy
```
public double energy(IMoleculeList pair)
```
  Description copied from class: PotentialMolecular
  
  Returns the interaction energy between the given molecules. There might be 0, 1, 2 or more atoms in the IMoleculeList.
  
  Specified by:
  
  energy in interface IPotentialMolecular
  
  Specified by:
  
  energy in class PotentialMolecular
- virial
```
public double virial(IMoleculeList pair)
```
  Specified by:
  
  virial in interface PotentialMolecularSoft
- gradient
```
public Vector[] gradient(IMoleculeList pair)
```
  Description copied from interface: PotentialMolecularSoft
  
  Returns the gradient of the potential as it applies to each atom in the given AtomSet, indicating how the energy would change as the position of the first atom is varied. The method is allowed to return an array of Vectors with fewer elements than the number of molecules in the IMoleculeList.
  
  Specified by:
  
  gradient in interface PotentialMolecularSoft
- gradientAndTorque
```
public Vector[][] gradientAndTorque(IMoleculeList pair)
```
  Specified by:
  
  gradientAndTorque in interface IPotentialMolecularTorque
- doGradientShift
```
protected void doGradientShift(Vector v1,
                               Vector v2,
                               double cc)
```
- doGradientNoShift
```
protected void doGradientNoShift(Vector v1,
                                 Vector v2,
                                 double cc)
```
- secondDerivative
```
public DataTensor secondDerivative(IMoleculeList pair)
```
- secondDerivativeXr
```
public Vector[][] secondDerivativeXr(IMoleculeList pair)
```
- doSecDerXrNoShift
```
public void doSecDerXrNoShift(Vector v1,
                              Vector v2,
                              double cc)
```
- doSecDerXrWShift
```
public void doSecDerXrWShift(Vector v1,
                             Vector v2,
                             double cc)
```
- secondDerivativeXrRotRot
```
public Tensor secondDerivativeXrRotRot(IMoleculeList pair)
```
- doSecDerXrRotRotNoShift
```
public void doSecDerXrRotRotNoShift(Vector v1,
                                    Vector v2,
                                    double cc)
```
- doSecDerXrRotRotWShift
```
public void doSecDerXrRotRotWShift(Vector v1,
                                   Vector v2,
                                   double cc)
```
- gradient
```
public Vector[] gradient(IMoleculeList atoms,
                         Tensor pressureTensor)
```
  Description copied from interface: PotentialMolecularSoft
  
  Returns the same gradient as gradient(IMoleculeList) and also adds in the contribution of the molecules to the pressureTensor. Their contribution is added to the given Tensor. This combined method exists for computational efficiency. Calculating the pressureTensor is generally trivial once the gradient is known but often requires intermediate information.
  
  Specified by:
  
  gradient in interface PotentialMolecularSoft
- isEnablePBC
```
public boolean isEnablePBC()
```
- setEnablePBC
```
public void setEnablePBC(boolean enablePBC)
```
- getRange
```
public double getRange()
```
  Description copied from interface: IPotential
  
  Returns the range over which the potential applies. IAtoms with a greater separation do not interact.
  
  Specified by:
  
  getRange in interface IPotential
  
  Specified by:
  
  getRange in class PotentialMolecular

Class P2Nitrogen

Field Summary

Fields inherited from class etomica.potential.PotentialMolecular

Constructor Summary

Method Summary

Methods inherited from interface etomica.potential.IPotential

Methods inherited from class java.lang.Object

Methods inherited from class etomica.potential.PotentialMolecular

Field Detail

gradient

torque

workVec

workTorqVec

workdTorq

q

gradientAndTorque

secDerXr

boundary

tensorWork

chargeP1

chargeP2

chargeP1P1

chargeP1P2

chargeP2P2

A1

alpha1

B1

A2

alpha2

R0

R1

C

work

shift

duWork

tWork

dr1

dr2

com1

com2

vectorR

rC

r2

enablePBC

identity

Constructor Detail

P2Nitrogen

Method Detail

setRange

setBox

energy

virial

gradient

gradientAndTorque

doGradientShift

doGradientNoShift

secondDerivative

secondDerivativeXr

doSecDerXrNoShift

doSecDerXrWShift

secondDerivativeXrRotRot

doSecDerXrRotRotNoShift

doSecDerXrRotRotWShift

gradient

isEnablePBC

setEnablePBC

getRange