P2EAM

java.lang.Object
- etomica.potential.Potential
- - etomica.potential.Potential2
  - - etomica.eam.P2EAM

All Implemented Interfaces:

IPotential, IPotentialAtomic, PotentialSoft
```
public class P2EAM
extends Potential2
implements PotentialSoft
```
EAM (Embedded Atom Method) potential that pretends to be a pair potential. Since it is only pretending, the methods must be called in a somewhat different manner. The different structure should result in higher performance, as compared to PotentialEAM.
To compute the energy, the P1EAM inner class should also be added to the potential master. The energy method should be called for all interacting pairs and then summed with the result of calling energy1.
To compute the gradient, the energy method should be called for all pairs. Then call prepForGradient. Then the gradient method should be called for all pairs and summed appropriately. To speed things up, disableEnergy may be called.

Field Summary

Fields
Modifier and Type	Field	Description
`protected double`	`a`
`protected double`	`a2`
`protected Boundary`	`boundary`
`protected double`	`Ceps`
`protected Vector`	`dr`
`protected boolean`	`energyDisabled`
`protected double`	`eps`
`protected Vector[]`	`gradient`
`protected double`	`m2`
`protected double`	`n2`
`protected double`	`rc12`
`protected double`	`rc22`
`protected double[]`	`rho`
`protected Vector`	`rhograd`

Fields inherited from class etomica.potential.Potential
space

Constructor Summary

Constructors
Constructor Description

P2EAM(Space space, double n, double m, double eps, double a, double C, double rc1, double rc2)

Constructors
Constructor	Description
`P2EAM(Space space, double n, double m, double eps, double a, double C, double rc1, double rc2)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`disableEnergy()`
`void`	`enableEnergy()`
`double`	`energy(IAtomList atoms)`	Returns the interaction energy between the given atoms.
`double`	`energy1()`
`double`	`getRange()`	Returns the range over which the potential applies.
`Vector[]`	`gradient(IAtomList atoms)`	Returns the gradient of the potential as it applies to each atom in the given AtomSet, indicating how the energy would change as the position of the first atom is varied.
`Vector[]`	`gradient(IAtomList atoms, Tensor pressureTensor)`	Returns the same gradient as gradient(AtomSet) and also adds in the contribution of the AtomSet to the pressureTensor.
`IntegratorListenerMD`	`makeIntegratorListener(PotentialMaster potentialMaster, Box box)`	Creates and returns an integrator listener that makes the integrator's force sum work properly by running an energy calculation first.
`void`	`prepForGradient()`
`void`	`reset()`
`void`	`setBox(Box box)`	Informs the potential of the box on which it acts.
`void`	`setCutoff(double rc1, double rc2)`
`double`	`virial(IAtomList atoms)`

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
  - n2
```
protected double n2
```
  - m2
```
protected double m2
```
  - eps
```
protected double eps
```
  - a
```
protected double a
```
  - a2
```
protected double a2
```
  - Ceps
```
protected double Ceps
```
  - rc12
```
protected double rc12
```
  - rc22
```
protected double rc22
```
  - boundary
```
protected Boundary boundary
```
  - dr
```
protected final Vector dr
```
  - gradient
```
protected Vector[] gradient
```
  - rhograd
```
protected Vector rhograd
```
  - rho
```
protected double[] rho
```
  - energyDisabled
```
protected boolean energyDisabled
```
- Constructor Detail
  - P2EAM
```
public P2EAM(Space space,
             double n,
             double m,
             double eps,
             double a,
             double C,
             double rc1,
             double rc2)
```
- 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
  - setCutoff
```
public void setCutoff(double rc1,
                      double rc2)
```
  - disableEnergy
```
public void disableEnergy()
```
  - enableEnergy
```
public void enableEnergy()
```
  - reset
```
public void reset()
```
  - prepForGradient
```
public void prepForGradient()
```
  - energy
```
public double energy(IAtomList atoms)
```
    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
  - energy1
```
public double energy1()
```
  - 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
  - virial
```
public double virial(IAtomList atoms)
```
    Specified by:
    
    virial in interface PotentialSoft
  - gradient
```
public Vector[] gradient(IAtomList atoms)
```
    Description copied from interface: PotentialSoft
    
    Returns the gradient of the potential as it applies to each atom in the given AtomSet, indicating how the energy would change as the position of the first atom is varied. The method is allowed to return an array of Vectors with fewer elements than the number of atoms in the AtomSet.
    
    Specified by:
    
    gradient in interface PotentialSoft
    
    Returns:
  - gradient
```
public Vector[] gradient(IAtomList atoms,
                         Tensor pressureTensor)
```
    Description copied from interface: PotentialSoft
    
    Returns the same gradient as gradient(AtomSet) and also adds in the contribution of the AtomSet to the pressureTensor. Their contribution is added to the given Tensor. This combined method exists for computational efficiency. Calculating the pressureTensor is generally trivial once the gradient is known but often requires intermediate information.
    
    Specified by:
    
    gradient in interface PotentialSoft
  - makeIntegratorListener
```
public IntegratorListenerMD makeIntegratorListener(PotentialMaster potentialMaster,
                                                   Box box)
```
    Creates and returns an integrator listener that makes the integrator's force sum work properly by running an energy calculation first.
    
    Parameters:
    
    potentialMaster -
    
    box -
    
    Returns:
    
    the listener

Class P2EAM

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

n2

m2

eps

a

a2

Ceps

rc12

rc22

boundary

dr

gradient

rhograd

rho

energyDisabled

Constructor Detail

P2EAM

Method Detail

getRange

setCutoff

disableEnergy

enableEnergy

reset

prepForGradient

energy

energy1

setBox

virial

gradient

gradient

makeIntegratorListener