PNWaterGCPMReactionField

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

All Implemented Interfaces:

IPotential, IPotentialMolecular, PotentialPolarizable
```
public class PNWaterGCPMReactionField
extends PotentialMolecular
implements PotentialPolarizable
```
GCPM Water potential class including Reaction Field Method. The polarization energy is solved for using matrix inversion rather than iteration, so this class may not be suitable for large systems.

Field Summary

Fields
Modifier and Type	Field	Description
`protected Jama.Matrix[]`	`A`
`protected double`	`alphaPol`
`protected Boundary`	`boundary`
`protected Box`	`box`
`protected double`	`chargeH`
`protected double`	`chargeM`
`protected Vector`	`comH11r`
`protected Vector`	`comH12r`
`protected Vector`	`comH21r`
`protected Vector`	`comH22r`
`protected Vector`	`comHi1r`
`protected Vector`	`comHi2r`
`protected Vector`	`comHj1r`
`protected Vector`	`comHj2r`
`protected Vector`	`comM1r`
`protected Vector`	`comM2r`
`protected Vector`	`comMir`
`protected Vector`	`comMjr`
`protected Vector`	`comW1`
`protected Vector`	`comW2`
`protected Vector`	`comWi`
`protected Vector`	`comWj`
`protected double`	`core`
`protected Vector`	`dipoleMoment1`
`protected Vector`	`dipoleMoment2`
`static boolean`	`dodebug`
`protected double`	`epsilon`
`protected Jama.Matrix[]`	`Eq`
`protected double`	`gamma`
`protected Vector`	`iDipoleMoment`
`protected Vector`	`jDipoleMoment`
`protected double`	`massH`
`protected double`	`massO`
`protected Vector`	`myRq`
`protected double`	`myRqFactor`
`protected MoleculePair`	`pair`
`protected Vector`	`r12Vector`
`protected Vector`	`rijVector`
`protected Jama.Matrix[]`	`Rq`
`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 double`	`UpolAtkins`
`protected Vector`	`work`

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

Constructor Summary

Constructors
Constructor Description

PNWaterGCPMReactionField(Space space)

Constructors
Constructor	Description
`PNWaterGCPMReactionField(Space space)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`energy(IMoleculeList atoms)`	Returns the interaction energy between the given molecules.
`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 atoms)`	This returns the polarizable portion of the GCPM potential for any number of atoms.
`double`	`getRange()`	Returns the range over which the potential applies.
`void`	`initRqFactor()`
`void`	`setBox(Box box)`	Informs the potential of the box on which it acts.
`void`	`setCutOffDistance(double a)`
`void`	`setDodebug(boolean a)`
`void`	`setRho(double c)`
`void`	`setTemperature(double t)`

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
```

boundary
```
protected Boundary boundary
```

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
```

Eq
```
protected Jama.Matrix[] Eq
```

Rq
```
protected Jama.Matrix[] Rq
```

A
```
protected Jama.Matrix[] A
```

comW1
```
protected Vector comW1
```

comW2
```
protected Vector comW2
```

comWi
```
protected Vector comWi
```

comWj
```
protected Vector comWj
```

comH11r
```
protected Vector comH11r
```

comH12r
```
protected Vector comH12r
```

comM1r
```
protected Vector comM1r
```

comH21r
```
protected Vector comH21r
```

comH22r
```
protected Vector comH22r
```

comM2r
```
protected Vector comM2r
```

comHi1r
```
protected Vector comHi1r
```

comHi2r
```
protected Vector comHi2r
```

comMir
```
protected Vector comMir
```

comHj1r
```
protected Vector comHj1r
```

comHj2r
```
protected Vector comHj2r
```

comMjr
```
protected Vector comMjr
```

r12Vector
```
protected final Vector r12Vector
```

rijVector
```
protected final Vector rijVector
```

work
```
protected final Vector work
```

shift
```
protected final Vector shift
```

dipoleMoment1
```
protected final Vector dipoleMoment1
```

dipoleMoment2
```
protected final Vector dipoleMoment2
```

iDipoleMoment
```
protected final Vector iDipoleMoment
```

jDipoleMoment
```
protected final Vector jDipoleMoment
```

myRq
```
protected final Vector myRq
```

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
```

UpolAtkins
```
protected double UpolAtkins
```

myRqFactor
```
protected double myRqFactor
```

box
```
protected Box box
```

dodebug
```
public static boolean dodebug
```

Constructor Detail

PNWaterGCPMReactionField

public PNWaterGCPMReactionField(Space space)

Method Detail
- energy
```
public double energy(IMoleculeList atoms)
```
  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
- 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 atoms)
```
  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
- setCutOffDistance
```
public void setCutOffDistance(double a)
```
- setTemperature
```
public void setTemperature(double t)
```
- setRho
```
public void setRho(double c)
```
- initRqFactor
```
public void initRqFactor()
```
- 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
- setDodebug
```
public void setDodebug(boolean a)
```

Class PNWaterGCPMReactionField

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

boundary

sigma

epsilon

gamma

chargeH

chargeM

core

Eq

Rq

A

comW1

comW2

comWi

comWj

comH11r

comH12r

comM1r

comH21r

comH22r

comM2r

comHi1r

comHi2r

comMir

comHj1r

comHj2r

comMjr

r12Vector

rijVector

work

shift

dipoleMoment1

dipoleMoment2

iDipoleMoment

jDipoleMoment

myRq

Tunit

Tij

sigmaM

sigmaH

sqrtHMsigmas

massH

massO

totalMass

sqrtPiHMsigmas

sqrtPiMMsigmas

alphaPol

UpolAtkins

myRqFactor

box

dodebug

Constructor Detail

PNWaterGCPMReactionField

Method Detail

energy

getNonPolarizationEnergy

getPolarizationEnergy

getLastPolarizationEnergy

getRange

setCutOffDistance

setTemperature

setRho

initRqFactor

setBox

setDodebug