P2MoleculeSoftTruncatedSwitched

java.lang.Object
- etomica.potential.PotentialMolecular
- - etomica.potential.P2MoleculeSoftTruncatedSwitched

All Implemented Interfaces:

IPotential, IPotentialMolecular, IPotentialMolecularTorque, PotentialMolecularSoft
```
public class P2MoleculeSoftTruncatedSwitched
extends PotentialMolecular
implements IPotentialMolecularTorque
```
Wraps a soft-spherical potential to apply a truncation to it. The energy is switched from fully-on to 0 over a short range (i.e. from 0.95*rC to rC).

Field Summary

Fields
Modifier and Type	Field	Description
`protected Boundary`	`boundary`
`protected Vector`	`dr`
`protected Vector[][]`	`gradientAndTorque`
`protected IPotentialMolecularTorque`	`potential`
`protected double`	`r2Cutoff`
`protected double`	`r2Switch`
`protected double`	`rCutoff`
`protected double`	`switchFac`
`protected int`	`taperOrder`

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

Constructor Summary

Constructors
Constructor	Description
`P2MoleculeSoftTruncatedSwitched(IPotentialMolecularTorque potential, double truncationRadius, Space _space)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`energy(IMoleculeList atoms)`	Returns the interaction energy between the given molecules.
`protected double`	`getdFdr(double r)`
`protected double`	`getF(double r)`
`double`	`getRange()`	Returns the truncation radius.
`double`	`getSwitchFac()`
`double`	`getTruncationRadius()`	Accessor method for the radial cutoff distance.
`Dimension`	`getTruncationRadiusDimension()`	Returns the dimension (length) of the radial cutoff distance.
`IPotentialMolecularTorque`	`getWrappedPotential()`	Returns the wrapped potential.
`Vector[]`	`gradient(IMoleculeList 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(IMoleculeList atoms, Tensor pressureTensor)`	Returns the same gradient as gradient(IMoleculeList) and also adds in the contribution of the molecules to the pressureTensor.
`Vector[][]`	`gradientAndTorque(IMoleculeList atoms)`
`static void`	`main(java.lang.String[] args)`
`void`	`setBox(Box newBox)`	Informs the potential of the box on which it acts.
`void`	`setSwitchFac(double newSwitchFac)`
`void`	`setTruncationRadius(double rCut)`	Mutator method for the radial cutoff distance.
`double`	`virial(IMoleculeList 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.PotentialMolecular
nBody

- Field Detail
  - rCutoff
```
protected double rCutoff
```
  - r2Cutoff
```
protected double r2Cutoff
```
  - potential
```
protected final IPotentialMolecularTorque potential
```
  - dr
```
protected final Vector dr
```
  - boundary
```
protected Boundary boundary
```
  - gradientAndTorque
```
protected final Vector[][] gradientAndTorque
```
  - taperOrder
```
protected int taperOrder
```
  - switchFac
```
protected double switchFac
```
  - r2Switch
```
protected double r2Switch
```
- Constructor Detail
  - P2MoleculeSoftTruncatedSwitched
```
public P2MoleculeSoftTruncatedSwitched(IPotentialMolecularTorque potential,
                                       double truncationRadius,
                                       Space _space)
```
- Method Detail
  - getWrappedPotential
```
public IPotentialMolecularTorque getWrappedPotential()
```
    Returns the wrapped potential.
  - setTruncationRadius
```
public void setTruncationRadius(double rCut)
```
    Mutator method for the radial cutoff distance.
  - getSwitchFac
```
public double getSwitchFac()
```
  - setSwitchFac
```
public void setSwitchFac(double newSwitchFac)
```
  - getTruncationRadius
```
public double getTruncationRadius()
```
    Accessor method for the radial cutoff distance.
  - getRange
```
public double getRange()
```
    Returns the truncation radius.
    
    Specified by:
    
    getRange in interface IPotential
    
    Specified by:
    
    getRange in class PotentialMolecular
  - gradientAndTorque
```
public Vector[][] gradientAndTorque(IMoleculeList atoms)
```
    Specified by:
    
    gradientAndTorque in interface IPotentialMolecularTorque
  - getF
```
protected double getF(double r)
```
  - getdFdr
```
protected double getdFdr(double r)
```
  - main
```
public static void main(java.lang.String[] args)
```
  - gradient
```
public Vector[] gradient(IMoleculeList atoms)
```
    Description copied from interface: PotentialMolecularSoft
    
    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 molecules in the IMoleculeList.
    
    Specified by:
    
    gradient in interface PotentialMolecularSoft
  - gradient
```
public Vector[] gradient(IMoleculeList atoms,
                         Tensor pressureTensor)
```
    Description copied from interface: PotentialMolecularSoft
    
    Returns the same gradient as gradient(IMoleculeList) and also adds in the contribution of the molecules 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 PotentialMolecularSoft
  - 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
  - virial
```
public double virial(IMoleculeList atoms)
```
    Specified by:
    
    virial in interface PotentialMolecularSoft
  - getTruncationRadiusDimension
```
public Dimension getTruncationRadiusDimension()
```
    Returns the dimension (length) of the radial cutoff distance.
  - setBox
```
public void setBox(Box newBox)
```
    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

Class P2MoleculeSoftTruncatedSwitched

Field Summary

Fields inherited from class etomica.potential.PotentialMolecular

Constructor Summary

Method Summary

Methods inherited from interface etomica.potential.IPotential

Methods inherited from class java.lang.Object

Methods inherited from class etomica.potential.PotentialMolecular

Field Detail

rCutoff

r2Cutoff

potential

dr

boundary

gradientAndTorque

taperOrder

switchFac

r2Switch

Constructor Detail

P2MoleculeSoftTruncatedSwitched

Method Detail

getWrappedPotential

setTruncationRadius

getSwitchFac

setSwitchFac

getTruncationRadius

getRange

gradientAndTorque

getF

getdFdr

main

gradient

gradient

energy

virial

getTruncationRadiusDimension

setBox