P2SquareWellRobust

java.lang.Object
- etomica.potential.Potential
- - etomica.potential.Potential2
  - - etomica.potential.Potential2HardSpherical
    - - etomica.potential.P2SquareWellRobust

All Implemented Interfaces:

AtomLeafAgentManager.AgentSource<AtomArrayList>, IPotential, IPotentialAtomic, Potential2Spherical, PotentialHard
```
public class P2SquareWellRobust
extends Potential2HardSpherical
implements AtomLeafAgentManager.AgentSource<AtomArrayList>
```
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. This implementation keeps track of which atom pairs are in the well, avoiding numerical roundoff issues after a collision and avoiding any need to bump atoms apart or together after capture and escape. If a simulation component moves atoms around externally, this class will become confused and fail. If such movement is necessary, consider using P2SquareWell instead.

Field Summary

Fields
Modifier and Type	Field	Description
`protected AtomType[]`	`atomTypes`
`protected java.util.Map<Box,AtomLeafAgentManager<AtomArrayList>>`	`boxWellManager`
`protected double`	`coreDiameter`
`protected double`	`coreDiameterSquared`
`protected Vector`	`dv`
`protected double`	`epsilon`
`protected boolean`	`ignoreOverlap`
`protected double`	`lambda`
`protected double`	`lastCollisionVirial`
`protected double`	`lastCollisionVirialr2`
`protected Tensor`	`lastCollisionVirialTensor`
`protected double`	`lastEnergyChange`
`protected PotentialMasterList`	`potentialMaster`
`protected boolean`	`suppressMakeAgent`
`protected double`	`wellDiameter`
`protected double`	`wellDiameterSquared`
`protected AtomLeafAgentManager<AtomArrayList>`	`wellManager`

Fields inherited from class etomica.potential.Potential
space

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

Constructor Summary

Constructors
Constructor	Description
`P2SquareWellRobust(Space space)`
`P2SquareWellRobust(Space space, double coreDiameter, double lambda, double epsilon, boolean ignoreOverlap)`

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`	`energyChange()`	returns change in potential energy due to the last collision
`double`	`getCoreDiameter()`	Accessor method for core diameter.
`Dimension`	`getCoreDiameterDimension()`
`double`	`getEpsilon()`	Accessor method for depth of well
`Dimension`	`getEpsilonDimension()`
`double`	`getLambda()`	Accessor method for well-diameter multiplier.
`Dimension`	`getLambdaDimension()`
`double`	`getRange()`	Returns the range over which the potential applies.
`protected void`	`handleNewAtomNbr(IAtom a, AtomLeafAgentManager<AtomArrayList> agentManager, NeighborListManager nbrListManager, AtomArrayList iList)`
`protected void`	`handleNewAtomNoNbr(IAtom a, AtomLeafAgentManager<AtomArrayList> agentManager, IAtomList leafList, AtomArrayList iList)`
`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.
`AtomArrayList`	`makeAgent(IAtom atom, Box agentBox)`	Returns an agent for the given Atom.
`AtomLeafAgentManager<AtomArrayList>`	`makeAgent(Box box)`
`void`	`releaseAgent(AtomArrayList iList, IAtom atom, Box agentBox)`	This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements.
`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`	`setLambda(double lam)`	Accessor method for well-diameter multiplier.
`void`	`setPotentialMaster(PotentialMasterList potentialMaster, AtomType[] types)`	Informs the square-well class what the potential master is (if neighbor listing is used) and the types of atoms interacting with this potential.
`double`	`u(double r2)`	Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.

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
energy

- Field Detail
  - ignoreOverlap
```
protected final boolean ignoreOverlap
```
  - boxWellManager
```
protected final java.util.Map<Box,AtomLeafAgentManager<AtomArrayList>> boxWellManager
```
  - 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
```
  - wellManager
```
protected AtomLeafAgentManager<AtomArrayList> wellManager
```
  - potentialMaster
```
protected PotentialMasterList potentialMaster
```
  - atomTypes
```
protected AtomType[] atomTypes
```
  - suppressMakeAgent
```
protected boolean suppressMakeAgent
```
- Constructor Detail
  - P2SquareWellRobust
```
public P2SquareWellRobust(Space space)
```
  - P2SquareWellRobust
```
public P2SquareWellRobust(Space space,
                          double coreDiameter,
                          double lambda,
                          double epsilon,
                          boolean ignoreOverlap)
```
- Method Detail
  - setPotentialMaster
```
public void setPotentialMaster(PotentialMasterList potentialMaster,
                               AtomType[] types)
```
    Informs the square-well class what the potential master is (if neighbor listing is used) and the types of atoms interacting with this potential. This helps the potential construct a list of atom pairs that are in the well (atoms that do not interact with this potential will be excluded from the list). If neighbor listing is not used, null should be passed. If this method is not called (or if null is passed for both parameters), then the potential will construct a list including all atom pairs (even those that do not interact with this potential). Also, for a large system, the potential must check all pairs (even pairs with large distances).
    
    Parameters:
    
    potentialMaster -
    
    types -
  - 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
  - u
```
public double u(double r2)
```
    Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
    
    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
    
    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()
```
  - 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
    
    Overrides:
    
    setBox in class Potential2HardSpherical
  - handleNewAtomNbr
```
protected void handleNewAtomNbr(IAtom a,
                                AtomLeafAgentManager<AtomArrayList> agentManager,
                                NeighborListManager nbrListManager,
                                AtomArrayList iList)
```
  - handleNewAtomNoNbr
```
protected void handleNewAtomNoNbr(IAtom a,
                                  AtomLeafAgentManager<AtomArrayList> agentManager,
                                  IAtomList leafList,
                                  AtomArrayList iList)
```
  - makeAgent
```
public AtomLeafAgentManager<AtomArrayList> makeAgent(Box box)
```
  - makeAgent
```
public AtomArrayList makeAgent(IAtom atom,
                               Box agentBox)
```
    Description copied from interface: AtomLeafAgentManager.AgentSource
    
    Returns an agent for the given Atom. The agentBox is provided for convenience for agent sources that handle multiple boxes.
    
    Specified by:
    
    makeAgent in interface AtomLeafAgentManager.AgentSource<AtomArrayList>
    
    agentBox - TODO
  - releaseAgent
```
public void releaseAgent(AtomArrayList iList,
                         IAtom atom,
                         Box agentBox)
```
    Description copied from interface: AtomLeafAgentManager.AgentSource
    
    This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements. The agentBox is provided for convenience for agent sources that handle multiple boxes.
    
    Specified by:
    
    releaseAgent in interface AtomLeafAgentManager.AgentSource<AtomArrayList>

Class P2SquareWellRobust

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

ignoreOverlap

boxWellManager

coreDiameter

coreDiameterSquared

wellDiameter

wellDiameterSquared

lambda

epsilon

lastCollisionVirial

lastCollisionVirialr2

lastCollisionVirialTensor

lastEnergyChange

dv

wellManager

potentialMaster

atomTypes

suppressMakeAgent

Constructor Detail

P2SquareWellRobust

P2SquareWellRobust

Method Detail

setPotentialMaster

getRange

bump

lastCollisionVirial

lastCollisionVirialTensor

collisionTime

u

energyChange

getCoreDiameter

setCoreDiameter

getCoreDiameterDimension

getLambda

setLambda

getLambdaDimension

getEpsilon

setEpsilon

getEpsilonDimension

setBox

handleNewAtomNbr

handleNewAtomNoNbr

makeAgent

makeAgent

releaseAgent