P2SquareWellBonding

java.lang.Object
- etomica.potential.Potential
- - etomica.potential.Potential2
  - - etomica.modules.catalysis.P2SquareWellBonding

All Implemented Interfaces:

IPotential, IPotentialAtomic, PotentialHard
```
public class P2SquareWellBonding
extends Potential2
implements PotentialHard, IPotentialAtomic
```
Basic square-well potential. Energy is infinite if spheres overlap, is -epsilon if less than lambda*sigma and not overlapping, and is zero otherwise. Core diameter describes size of hard core; lambda is multiplier to get range of well. Suitable for use in space of any dimension. Can be used with negative value for epsilon to produce square-shoulder potential.

Field Summary

Fields
Modifier and Type	Field	Description
`protected AtomLeafAgentManager`	`agentManager`
`protected Boundary`	`boundary`
`protected double`	`coreDiameter`
`protected double`	`coreDiameterSquared`
`protected Vector`	`dr`
`protected Vector`	`dv`
`protected double`	`epsilon`
`protected double`	`epsilonBarrier`
`protected double`	`epsilonBonding`
`protected double`	`lambda`
`protected double`	`lastCollisionVirial`
`protected double`	`lastCollisionVirialr2`
`protected Tensor`	`lastCollisionVirialTensor`
`protected double`	`lastEnergyChange`
`protected double`	`minOCOr2`
`protected int`	`nSurfaceSites`
`protected double`	`wellDiameter`
`protected double`	`wellDiameterSquared`

Fields inherited from class etomica.potential.Potential
space

Constructor Summary

Constructors
Constructor	Description
`P2SquareWellBonding(Space space, AtomLeafAgentManager agentManager, double coreDiameter, double lambda, double epsilon, int nSurfaceSites, double epsilonBarrier, double epsilonBonding, double minOCOr)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`bump(IAtomList pair, double falseTime)`	Implements collision dynamics between two square-well atoms.
`double`	`collisionTime(IAtomList pair, double falseTime)`	Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
`double`	`energy(IAtomList pair)`	Returns the interaction energy between the given atoms.
`double`	`energyChange()`	returns change in potential energy due to the last collision
`double`	`getBarrier()`
`double`	`getCoreDiameter()`	Accessor method for core diameter.
`Dimension`	`getCoreDiameterDimension()`
`double`	`getEpsilon()`	Accessor method for depth of well
`double`	`getEpsilonBonding()`
`Dimension`	`getEpsilonDimension()`
`double`	`getLambda()`	Accessor method for well-diameter multiplier.
`Dimension`	`getLambdaDimension()`
`int`	`getNumSurfaceSites()`
`double`	`getRange()`	Returns the range over which the potential applies.
`double`	`lastCollisionVirial()`	Value of the virial from the most recent collision.
`Tensor`	`lastCollisionVirialTensor()`	Value of the virial from the most recent collision, decomposed into it tensoral elements.
`void`	`setBarrier(double newBarrier)`
`void`	`setBox(Box box)`	Informs the potential of the box on which it acts.
`void`	`setCoreDiameter(double c)`	Accessor method for core diameter.
`void`	`setEpsilon(double eps)`	Accessor method for depth of well
`void`	`setEpsilonBonding(double newEpsilonBonding)`
`void`	`setLambda(double lam)`	Accessor method for well-diameter multiplier.
`void`	`setNumSurfaceSites(int newNumSurfaceSites)`

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.Potential
nBody

- Field Detail
  - coreDiameter
```
protected double coreDiameter
```
  - coreDiameterSquared
```
protected double coreDiameterSquared
```
  - wellDiameter
```
protected double wellDiameter
```
  - wellDiameterSquared
```
protected double wellDiameterSquared
```
  - lambda
```
protected double lambda
```
  - epsilon
```
protected double epsilon
```
  - lastCollisionVirial
```
protected double lastCollisionVirial
```
  - lastCollisionVirialr2
```
protected double lastCollisionVirialr2
```
  - lastCollisionVirialTensor
```
protected Tensor lastCollisionVirialTensor
```
  - lastEnergyChange
```
protected double lastEnergyChange
```
  - dv
```
protected Vector dv
```
  - agentManager
```
protected final AtomLeafAgentManager agentManager
```
  - dr
```
protected final Vector dr
```
  - boundary
```
protected Boundary boundary
```
  - nSurfaceSites
```
protected int nSurfaceSites
```
  - epsilonBarrier
```
protected double epsilonBarrier
```
  - epsilonBonding
```
protected double epsilonBonding
```
  - minOCOr2
```
protected final double minOCOr2
```
- Constructor Detail
  - P2SquareWellBonding
```
public P2SquareWellBonding(Space space,
                           AtomLeafAgentManager agentManager,
                           double coreDiameter,
                           double lambda,
                           double epsilon,
                           int nSurfaceSites,
                           double epsilonBarrier,
                           double epsilonBonding,
                           double minOCOr)
```
- Method Detail
  - 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 Potential
  - bump
```
public void bump(IAtomList pair,
                 double falseTime)
```
    Implements collision dynamics between two square-well atoms. Includes all possibilities involving collision of hard cores, and collision of wells both approaching and diverging
    
    Specified by:
    
    bump in interface PotentialHard
  - lastCollisionVirial
```
public double lastCollisionVirial()
```
    Description copied from interface: PotentialHard
    
    Value of the virial from the most recent collision.
    
    Specified by:
    
    lastCollisionVirial in interface PotentialHard
    
    Returns:
    
    double virial value
  - lastCollisionVirialTensor
```
public Tensor lastCollisionVirialTensor()
```
    Description copied from interface: PotentialHard
    
    Value of the virial from the most recent collision, decomposed into it tensoral elements.
    
    Specified by:
    
    lastCollisionVirialTensor in interface PotentialHard
    
    Returns:
    
    Tensor
  - collisionTime
```
public double collisionTime(IAtomList pair,
                            double falseTime)
```
    Computes next time of collision of two square-well atoms, assuming free-flight kinematics. Collision may occur when cores collides, or when wells first encounter each other on approach, or when they edge of the wells are reached as atoms diverge.
    
    Specified by:
    
    collisionTime in interface PotentialHard
  - energy
```
public double energy(IAtomList pair)
```
    Description copied from class: Potential
    
    Returns the interaction energy between the given atoms. There might be 0, 1, 2 or more atoms in the AtomSet.
    
    Specified by:
    
    energy in interface IPotentialAtomic
    
    Specified by:
    
    energy in class Potential
  - energyChange
```
public double energyChange()
```
    Description copied from interface: PotentialHard
    
    returns change in potential energy due to the last collision
    
    Specified by:
    
    energyChange in interface PotentialHard
  - getCoreDiameter
```
public double getCoreDiameter()
```
    Accessor method for core diameter.
  - setCoreDiameter
```
public void setCoreDiameter(double c)
```
    Accessor method for core diameter. Well diameter is defined as a multiple (lambda) of this, and is updated when core diameter is changed
  - getCoreDiameterDimension
```
public Dimension getCoreDiameterDimension()
```
  - getLambda
```
public double getLambda()
```
    Accessor method for well-diameter multiplier.
  - setLambda
```
public void setLambda(double lam)
```
    Accessor method for well-diameter multiplier. Well diameter is defined as this multiple of core diameter, and is updated when this is changed
  - getLambdaDimension
```
public Dimension getLambdaDimension()
```
  - getEpsilon
```
public double getEpsilon()
```
    Accessor method for depth of well
  - setEpsilon
```
public void setEpsilon(double eps)
```
    Accessor method for depth of well
  - getEpsilonDimension
```
public Dimension getEpsilonDimension()
```
  - getNumSurfaceSites
```
public int getNumSurfaceSites()
```
  - setNumSurfaceSites
```
public void setNumSurfaceSites(int newNumSurfaceSites)
```
  - getBarrier
```
public double getBarrier()
```
  - setBarrier
```
public void setBarrier(double newBarrier)
```
  - getEpsilonBonding
```
public double getEpsilonBonding()
```
  - setEpsilonBonding
```
public void setEpsilonBonding(double newEpsilonBonding)
```
  - setBox
```
public void setBox(Box box)
```
    Description copied from class: Potential
    
    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 Potential

Class P2SquareWellBonding

Field Summary

Fields inherited from class etomica.potential.Potential

Constructor Summary

Method Summary

Methods inherited from interface etomica.potential.IPotential

Methods inherited from class java.lang.Object

Methods inherited from class etomica.potential.Potential

Field Detail

coreDiameter

coreDiameterSquared

wellDiameter

wellDiameterSquared

lambda

epsilon

lastCollisionVirial

lastCollisionVirialr2

lastCollisionVirialTensor

lastEnergyChange

dv

agentManager

dr

boundary

nSurfaceSites

epsilonBarrier

epsilonBonding

minOCOr2

Constructor Detail

P2SquareWellBonding

Method Detail

getRange

bump

lastCollisionVirial

lastCollisionVirialTensor

collisionTime

energy

energyChange

getCoreDiameter

setCoreDiameter

getCoreDiameterDimension

getLambda

setLambda

getLambdaDimension

getEpsilon

setEpsilon

getEpsilonDimension

getNumSurfaceSites

setNumSurfaceSites

getBarrier

setBarrier

getEpsilonBonding

setEpsilonBonding

setBox