PNWaterGCPM

java.lang.Object
- etomica.potential.PotentialMolecular
- - etomica.models.water.PNWaterGCPM

All Implemented Interfaces:

IPotential, IPotentialMolecular, PotentialPolarizable

Direct Known Subclasses:

P2HardAssociationGCPMReference, PNWaterGCPMThreeSite
```
public class PNWaterGCPM
extends PotentialMolecular
implements PotentialPolarizable
```
GCPM Water potential class. This class assumes assumes no periodic boundaries exist. The polarization energy is solved for using matrix inversion rather than iteration, so this class may not be suitable for large systems.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class PNWaterGCPM.Component

class PNWaterGCPM.PNWaterGCPMCached

Nested Classes
Modifier and Type	Class	Description
`static class`	`PNWaterGCPM.Component`
`class`	`PNWaterGCPM.PNWaterGCPMCached`

Field Summary

Fields
Modifier and Type	Field	Description
`protected Jama.Matrix[]`	`A`
`protected double`	`alphaPol`
`boolean`	`berr`
`protected Boundary`	`boundary`
`protected double`	`chargeH`
`protected double`	`chargeM`
`protected PNWaterGCPM.Component`	`component`
`protected Vector`	`comWi`
`protected Vector`	`comWj`
`protected double`	`core`
`protected double`	`epsilon`
`protected Jama.Matrix[]`	`Eq`
`protected double`	`gamma`
`protected double`	`massH`
`protected double`	`massO`
`protected MoleculePair`	`pair`
`protected double[][]`	`pairPolarization`
`protected Vector`	`rijVector`
`protected Vector`	`shift`
`protected double`	`sigma`
`protected double`	`sigmaH`
`protected double`	`sigmaM`
`protected double`	`sqrtHMsigmas`
`protected double`	`sqrtPiHMsigmas`
`protected double`	`sqrtPiMMsigmas`
`protected Tensor`	`Tij`
`protected double`	`totalMass`
`protected Tensor`	`Tunit`
`protected Vector`	`work`

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

Constructor Summary

Constructors
Constructor Description

PNWaterGCPM(Space space)

Constructors
Constructor	Description
`PNWaterGCPM(Space space)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`energy(IMoleculeList molecules)`	Returns the interaction energy between the given molecules.
`double`	`erfc(double x)`
`double`	`getLastPolarizationEnergy()`	Returns the polarization energy from the last call to energy(AtomSet).
`double`	`getNonPolarizationEnergy(IMoleculeList atoms)`	This returns the pairwise-additive portion of the GCPM potential for a pair of atoms (dispersion + fixed-charge electrostatics)
`double`	`getPolarizationEnergy(IMoleculeList molecules)`	This returns the polarizable portion of the GCPM potential for any number of atoms.
`double`	`getRange()`	Returns the range over which the potential applies.
`PNWaterGCPM.PNWaterGCPMCached`	`makeCachedPairPolarization()`
`void`	`setBox(Box box)`	Informs the potential of the box on which it acts.
`void`	`setComponent(PNWaterGCPM.Component comp)`

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
  - pair
```
protected final MoleculePair pair
```
  - sigma
```
protected final double sigma
```
  - epsilon
```
protected final double epsilon
```
  - gamma
```
protected final double gamma
```
  - chargeH
```
protected final double chargeH
```
  - chargeM
```
protected final double chargeM
```
  - core
```
protected final double core
```
  - rijVector
```
protected final Vector rijVector
```
  - work
```
protected final Vector work
```
  - shift
```
protected final Vector shift
```
  - Tunit
```
protected final Tensor Tunit
```
  - Tij
```
protected final Tensor Tij
```
  - sigmaM
```
protected final double sigmaM
```
  - sigmaH
```
protected final double sigmaH
```
  - sqrtHMsigmas
```
protected final double sqrtHMsigmas
```
  - massH
```
protected final double massH
```
  - massO
```
protected final double massO
```
  - totalMass
```
protected final double totalMass
```
  - sqrtPiHMsigmas
```
protected final double sqrtPiHMsigmas
```
  - sqrtPiMMsigmas
```
protected final double sqrtPiMMsigmas
```
  - alphaPol
```
protected final double alphaPol
```
  - pairPolarization
```
protected final double[][] pairPolarization
```
  - boundary
```
protected Boundary boundary
```
  - Eq
```
protected Jama.Matrix[] Eq
```
  - A
```
protected Jama.Matrix[] A
```
  - comWi
```
protected Vector comWi
```
  - comWj
```
protected Vector comWj
```
  - component
```
protected PNWaterGCPM.Component component
```
  - berr
```
public boolean berr
```
- Constructor Detail
  - PNWaterGCPM
```
public PNWaterGCPM(Space space)
```
- Method Detail
  - setComponent
```
public void setComponent(PNWaterGCPM.Component comp)
```
  - erfc
```
public double erfc(double x)
```
  - energy
```
public double energy(IMoleculeList molecules)
```
    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
  - makeCachedPairPolarization
```
public PNWaterGCPM.PNWaterGCPMCached makeCachedPairPolarization()
```
  - getNonPolarizationEnergy
```
public double getNonPolarizationEnergy(IMoleculeList atoms)
```
    This returns the pairwise-additive portion of the GCPM potential for a pair of atoms (dispersion + fixed-charge electrostatics)
  - getPolarizationEnergy
```
public double getPolarizationEnergy(IMoleculeList molecules)
```
    This returns the polarizable portion of the GCPM potential for any number of atoms.
    
    Specified by:
    
    getPolarizationEnergy in interface PotentialPolarizable
  - getLastPolarizationEnergy
```
public double getLastPolarizationEnergy()
```
    Description copied from interface: PotentialPolarizable
    
    Returns the polarization energy from the last call to energy(AtomSet).
    
    Specified by:
    
    getLastPolarizationEnergy in interface PotentialPolarizable
    
    Returns:
  - getRange
```
public final 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
  - 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

Class PNWaterGCPM

Nested Class Summary

Field Summary

Fields inherited from class etomica.potential.PotentialMolecular

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from class etomica.potential.PotentialMolecular

Field Detail

pair

sigma

epsilon

gamma

chargeH

chargeM

core

rijVector

work

shift

Tunit

Tij

sigmaM

sigmaH

sqrtHMsigmas

massH

massO

totalMass

sqrtPiHMsigmas

sqrtPiMMsigmas

alphaPol

pairPolarization

boundary

Eq

A

comWi

comWj

component

berr

Constructor Detail

PNWaterGCPM

Method Detail

setComponent

erfc

energy

makeCachedPairPolarization

getNonPolarizationEnergy

getPolarizationEnergy

getLastPolarizationEnergy

getRange

setBox