P2SquareWellBondingCO

java.lang.Object
- etomica.potential.Potential
- - etomica.potential.Potential2
  - - etomica.potential.Potential2HardSpherical
    - - etomica.modules.catalysis.P2SquareWellBondingCO

All Implemented Interfaces:

IPotential, IPotentialAtomic, Potential2Spherical, PotentialHard
```
public class P2SquareWellBondingCO
extends Potential2HardSpherical
```
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 double`	`coreDiameter`
`protected double`	`coreDiameterSquared`
`protected Vector`	`drOO`
`protected Vector`	`dv`
`protected Vector`	`dvOO`
`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`	`minOOr2`
`protected int`	`nSurfaceSites`
`protected P2SquareWellSurface`	`potentialCS`
`protected double`	`wellDiameter`
`protected double`	`wellDiameterSquared`

Fields inherited from class etomica.potential.Potential
space

Fields inherited from class etomica.potential.Potential2HardSpherical
boundary, dr

Constructor Summary

Constructors
Constructor	Description
`P2SquareWellBondingCO(Space space, AtomLeafAgentManager agentManager, double coreDiameter, double lambda, double epsilon, int nSurfaceSites, double epsilonBarrier, double epsilonBonding, double minOOr)`

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)`	Energy of the pair as given by the u(double) method, with application of any PotentialTruncation that may be defined for the potential.
`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`	`setCoreDiameter(double c)`	Accessor method for core diameter.
`void`	`setCSPotential(P2SquareWellSurface newPotentialCS)`
`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)`
`double`	`u(double r2)`	The pair energy u(r^2) with no truncation applied.

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

Methods inherited from class etomica.potential.Potential2HardSpherical
setBox

- 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 final Tensor lastCollisionVirialTensor
```
  - lastEnergyChange
```
protected double lastEnergyChange
```
  - dv
```
protected final Vector dv
```
  - dvOO
```
protected final Vector dvOO
```
  - drOO
```
protected final Vector drOO
```
  - agentManager
```
protected final AtomLeafAgentManager agentManager
```
  - nSurfaceSites
```
protected int nSurfaceSites
```
  - epsilonBarrier
```
protected double epsilonBarrier
```
  - epsilonBonding
```
protected double epsilonBonding
```
  - minOOr2
```
protected final double minOOr2
```
  - potentialCS
```
protected P2SquareWellSurface potentialCS
```
- Constructor Detail
  - P2SquareWellBondingCO
```
public P2SquareWellBondingCO(Space space,
                             AtomLeafAgentManager agentManager,
                             double coreDiameter,
                             double lambda,
                             double epsilon,
                             int nSurfaceSites,
                             double epsilonBarrier,
                             double epsilonBonding,
                             double minOOr)
```
- 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
  - lastCollisionVirial
```
public double lastCollisionVirial()
```
    Description copied from interface: PotentialHard
    
    Value of the virial from the most recent collision.
    
    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.
    
    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.
  - energy
```
public double energy(IAtomList pair)
```
    Description copied from class: Potential2HardSpherical
    
    Energy of the pair as given by the u(double) method, with application of any PotentialTruncation that may be defined for the potential. This does not take into account any false positioning that the Integrator may be using.
    
    Specified by:
    
    energy in interface IPotentialAtomic
    
    Overrides:
    
    energy in class Potential2HardSpherical
  - u
```
public double u(double r2)
```
    Description copied from class: Potential2HardSpherical
    
    The pair energy u(r^2) with no truncation applied.
    
    Specified by:
    
    u in interface Potential2Spherical
    
    Specified by:
    
    u in class Potential2HardSpherical
    
    Parameters:
    
    r2 - the square of the distance between the particles.
  - energyChange
```
public double energyChange()
```
    Description copied from interface: PotentialHard
    
    returns change in potential energy due to the last collision
  - 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()
```
  - getBarrier
```
public double getBarrier()
```
  - setBarrier
```
public void setBarrier(double newBarrier)
```
  - getEpsilonBonding
```
public double getEpsilonBonding()
```
  - setEpsilonBonding
```
public void setEpsilonBonding(double newEpsilonBonding)
```
  - getNumSurfaceSites
```
public int getNumSurfaceSites()
```
  - setNumSurfaceSites
```
public void setNumSurfaceSites(int newNumSurfaceSites)
```
  - setCSPotential
```
public void setCSPotential(P2SquareWellSurface newPotentialCS)
```

Class P2SquareWellBondingCO

Field Summary

Fields inherited from class etomica.potential.Potential

Fields inherited from class etomica.potential.Potential2HardSpherical

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

Methods inherited from class etomica.potential.Potential2HardSpherical

Field Detail

coreDiameter

coreDiameterSquared

wellDiameter

wellDiameterSquared

lambda

epsilon

lastCollisionVirial

lastCollisionVirialr2

lastCollisionVirialTensor

lastEnergyChange

dv

dvOO

drOO

agentManager

nSurfaceSites

epsilonBarrier

epsilonBonding

minOOr2

potentialCS

Constructor Detail

P2SquareWellBondingCO

Method Detail

getRange

bump

lastCollisionVirial

lastCollisionVirialTensor

collisionTime

energy

u

energyChange

getCoreDiameter

setCoreDiameter

getCoreDiameterDimension

getLambda

setLambda

getLambdaDimension

getEpsilon

setEpsilon

getEpsilonDimension

getBarrier

setBarrier

getEpsilonBonding

setEpsilonBonding

getNumSurfaceSites

setNumSurfaceSites

setCSPotential