Package etomica.potential

Class P2ReactionFieldDipole

java.lang.Object

etomica.potential.PotentialMolecular

etomica.potential.P2ReactionFieldDipole

All Implemented Interfaces:

IPotential, IPotentialMolecular, IPotentialMolecularSecondDerivative, IPotentialMolecularTorque, PotentialMolecularSoft

public class P2ReactionFieldDipole
extends PotentialMolecular
implements PotentialMolecularSoft, IPotentialMolecularSecondDerivative

Potential to implement the reaction field treatment of electrostatic interactions. In this approach, the long range electrostatic interactions are modeled via a dielectric continuum with dielectric constant epsilon. The net effect is that molecules within a specified cutoff distance interact with an effective pair potential that is otherwise independent of their separation distance.

In conjunction with this two-body potential, a zero-body potential must also be added to the PotentialMaster. The zero-body potential is provided by the method makeP0.

Field Summary

Fields

Modifier and Type	Field	Description
protected Vector3D[]	a
protected Boundary	boundary
protected Vector	cavityDipole
protected double	cutoff
protected double	cutoff2
protected DipoleSource	dipoleSource
protected Vector	dr
protected double	epsilon
protected double	fac
protected Vector[][]	gradientAndTorque
protected Vector	iDipole
protected IMoleculePositionDefinition	positionDefinition
protected Tensor[]	secondDerivative

Fields inherited from class etomica.potential.PotentialMolecular

nBody, space

Constructor Summary

Constructors

Constructor	Description
P2ReactionFieldDipole(Space space, IMoleculePositionDefinition positionDefinition)

Method Summary

Modifier and Type	Method	Description
double	energy(IMoleculeList molecules)	Returns the interaction energy between the given molecules.
double	getDielectric()
DipoleSource	getDipoleSource()	The DipoleSource returns the dipole vector of a given molecule.
double	getRange()	The radius of the sphere within which molecules contribute to the reaction field of a given molecule.
Vector[]	gradient(IMoleculeList molecules)	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 molecules, Tensor pressureTensor)	Returns the same gradient as gradient(IMoleculeList) and also adds in the contribution of the molecules to the pressureTensor.
Vector[][]	gradientAndTorque(IMoleculeList molecules)
IPotentialMolecular	makeP0()
Tensor[]	secondDerivative(IMoleculeList molecules)
void	setBox(Box box)	Informs the potential of the box on which it acts.
void	setDielectric(double newDielectric)
void	setDipoleSource(DipoleSource newDipoleSource)
void	setRange(double newRange)
double	virial(IMoleculeList molecules)

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

positionDefinition

protected final IMoleculePositionDefinition positionDefinition

iDipole

protected final Vector iDipole

cavityDipole

protected final Vector cavityDipole

dr

protected final Vector dr

gradientAndTorque

protected final Vector[][] gradientAndTorque

secondDerivative

protected final Tensor[] secondDerivative

a

protected final Vector3D[] a

dipoleSource

protected DipoleSource dipoleSource

boundary

protected Boundary boundary

cutoff2

protected double cutoff2

cutoff

protected double cutoff

epsilon

protected double epsilon

fac

protected double fac

Constructor Detail

P2ReactionFieldDipole

public P2ReactionFieldDipole(Space space,
                             IMoleculePositionDefinition positionDefinition)

Parameters:

space - defines the dimensionality of the simulation

positionDefinition - defines the location of a molecule

Method Detail

getDipoleSource

public DipoleSource getDipoleSource()

The DipoleSource returns the dipole vector of a given molecule.

Returns:

the dipole source used by this object.

setDipoleSource

public void setDipoleSource(DipoleSource newDipoleSource)

Parameters:

newDipoleSource - the DipoleSource to set

getRange

public double getRange()

The radius of the sphere within which molecules contribute to the reaction field of a given molecule. This value should match the truncation radius for electrostatic interactions.

Specified by:

getRange in interface IPotential

Specified by:

getRange in class PotentialMolecular

Returns:

the cutoff radius of the reactionField.

setRange

public void setRange(double newRange)

Parameters:

newRange - the new cutoff radius of the reactionField.

getDielectric

public double getDielectric()

Returns:

the dielectric constant of the medium surrounding the cavity.

setDielectric

public void setDielectric(double newDielectric)

Parameters:

newDielectric - the new value of the dielectric constant of the medium surrounding the cavity.

setBox

public void setBox(Box box)

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

energy

public double energy(IMoleculeList molecules)

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

gradientAndTorque

public Vector[][] gradientAndTorque(IMoleculeList molecules)

Specified by:

gradientAndTorque in interface IPotentialMolecularTorque

secondDerivative

public Tensor[] secondDerivative(IMoleculeList molecules)

Specified by:

secondDerivative in interface IPotentialMolecularSecondDerivative

gradient

public Vector[] gradient(IMoleculeList molecules)

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 molecules,
                         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

virial

public double virial(IMoleculeList molecules)

Specified by:

virial in interface PotentialMolecularSoft

makeP0

public IPotentialMolecular makeP0()

Returns:

a 0-body potential that should be added along with this potential.