meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics
Class CoulombElectrostaticEnergyElement

java.lang.Object
  meshi.energy.EnergyElement
      meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyElement
          meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement

public class CoulombElectrostaticEnergyElement
extends NonBondedEnergyElement

This object represents Electrostatic Energy between two Atoms. It updates the energy according to the change in their distance and position.

Field Summary

static double	ALPHA
protected Atom	atom1
protected int	atom1Number
protected Atom	atom2
protected int	atom2Number
protected double[]	charges
protected double	contact
protected double	dCdD
protected double	dCdX
protected double	dCdY
protected double	dCdZ
protected double	dEdD
protected double	dEdX
protected double	dEdY
protected double	dEdZ
protected double	dielectricConstant
protected DistanceMatrix	distanceMatrix
protected double	energy
private int	FIRST
protected boolean	frozen
static double	MAX_ENERGY
protected double	q1
protected double	q2
protected double	rMax
private int	SECOND
protected double	weight

Fields inherited from class meshi.energy.EnergyElement

atoms, dFormatSrt, dFormatStd, DX, relativeDiffTolerance, VERY_SMALL, XYZ

Constructor Summary

CoulombElectrostaticEnergyElement()
default constructor

CoulombElectrostaticEnergyElement(DistanceMatrix distanceMatrix, double weight, double dielectricConstant, double[] charges)
constructor

Method Summary

double	contact()
double	contact(double weight)
double	contactAtoms(double weight)
double	dEdXAtom(int index)
double	dEdYAtom(int index)
double	dEdZAtom(int index)
double	evaluate() evaluate - 1) Invokes updateEnergy() - updates the energy, 2) Invokes updateAtoms() - updates the atoms' position.
void	set(java.lang.Object obj) Sets the relevant charge values for each atom in an atom pair.
protected void	setAtoms() setAtoms
java.lang.String	toString() toString
void	updateAtoms() Updates the atoms position
double	updateEnergy() Updates the energy

Methods inherited from class meshi.energy.EnergyElement

atoms, evaluateAtoms, frozen, test, updateFrozen

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

MAX_ENERGY

public static final double MAX_ENERGY

See Also:

Constant Field Values

ALPHA

public static final double ALPHA

See Also:

Constant Field Values

distanceMatrix

protected DistanceMatrix distanceMatrix

atom1

protected Atom atom1

atom2

protected Atom atom2

atom1Number

protected int atom1Number

atom2Number

protected int atom2Number

dielectricConstant

protected double dielectricConstant

q1

protected double q1

q2

protected double q2

frozen

protected boolean frozen

dEdD

protected double dEdD

dEdX

protected double dEdX

dEdY

protected double dEdY

dEdZ

protected double dEdZ

energy

protected double energy

weight

protected double weight

rMax

protected double rMax

contact

protected double contact

dCdD

protected double dCdD

dCdX

protected double dCdX

dCdY

protected double dCdY

dCdZ

protected double dCdZ

FIRST

private final int FIRST

See Also:

Constant Field Values

SECOND

private final int SECOND

See Also:

Constant Field Values

charges

protected double[] charges

Constructor Detail

CoulombElectrostaticEnergyElement

public CoulombElectrostaticEnergyElement()

default constructor

CoulombElectrostaticEnergyElement

public CoulombElectrostaticEnergyElement(DistanceMatrix distanceMatrix,
                                         double weight,
                                         double dielectricConstant,
                                         double[] charges)

constructor

Parameters:

distanceMatrix -

weight -

dielectricConstant -

charges -

Method Detail

setAtoms

protected void setAtoms()

setAtoms

Specified by:

setAtoms in class EnergyElement

set

public void set(java.lang.Object obj)

Sets the relevant charge values for each atom in an atom pair. The data is taken from the parameter list.

Specified by:

set in class NonBondedEnergyElement

Parameters:

obj - an AtomPair

evaluate

public double evaluate()

evaluate - 1) Invokes updateEnergy() - updates the energy, 2) Invokes updateAtoms() - updates the atoms' position.

Specified by:

evaluate in class EnergyElement

Returns:

double - energy*weight

updateEnergy

public double updateEnergy()

Updates the energy

Returns:

double - energy*weight

updateAtoms

public void updateAtoms()

Updates the atoms position

contactAtoms

public double contactAtoms(double weight)

Parameters:

weight -

Returns:

double

dEdXAtom

public double dEdXAtom(int index)

Parameters:

index -

Returns:

double

dEdYAtom

public double dEdYAtom(int index)

Parameters:

index -

Returns:

double

dEdZAtom

public double dEdZAtom(int index)

Parameters:

index -

Returns:

double

contact

public double contact(double weight)

Parameters:

weight -

Returns:

double

contact

public double contact()

Returns:

double

toString

public java.lang.String toString()

toString

Overrides:

toString in class java.lang.Object

Returns:

String