meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol
Class FiniteExcludedVolEnergyElement

java.lang.Object
  meshi.energy.EnergyElement
      meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyElement
          meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement

public class FiniteExcludedVolEnergyElement
extends NonBondedEnergyElement

Field Summary

double	ALPHA ALPHA is the transition zone (in Ang) where the energy change in the forth power 0.0 to 1.0.
protected Atom	atom1
protected Atom	atom2
double	BETA
double	C C is the parameter of EV = C*(d-sigma)^4 in the range [0,sigma]
protected double	dEdD
protected double	dEdX
protected double	dEdY
protected double	dEdZ
protected double	dis
protected Distance	distance
protected DistanceMatrix	distanceMatrix
protected double	DMinusSig
protected double	DMinusSig3
protected double	DMinusSig4
protected double	dx
protected double	dy
protected double	dz
protected double	energy
protected boolean	frozen
protected double	invWCDMinusSig4PlusBETA
protected double	localSigma
protected double[][]	parameters
protected double	Rfac
protected double	rMax
protected double	sigma
protected double	WC
protected double	WCDMinusSig3
protected double	WCDMinusSig4
protected double	weight

Fields inherited from class meshi.energy.EnergyElement

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

Constructor Summary

FiniteExcludedVolEnergyElement()

FiniteExcludedVolEnergyElement(DistanceMatrix distanceMatrix, double Rfac, double weight, double[][] parameters)

Method Summary

double	evaluate()
void	set(java.lang.Object obj)
protected void	setAtoms()
java.lang.String	toString()

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

ALPHA

public final double ALPHA

ALPHA is the transition zone (in Ang) where the energy change in the forth power 0.0 to 1.0.

See Also:

Constant Field Values

BETA

public final double BETA

See Also:

Constant Field Values

C

public final double C

C is the parameter of EV = C*(d-sigma)^4 in the range [0,sigma]

See Also:

Constant Field Values

distanceMatrix

protected DistanceMatrix distanceMatrix

atom1

protected Atom atom1

atom2

protected Atom atom2

distance

protected Distance distance

sigma

protected double sigma

Rfac

protected double Rfac

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

parameters

protected double[][] parameters

DMinusSig

protected double DMinusSig

localSigma

protected double localSigma

dis

protected double dis

dx

protected double dx

dy

protected double dy

dz

protected double dz

DMinusSig3

protected double DMinusSig3

DMinusSig4

protected double DMinusSig4

WC

protected double WC

WCDMinusSig3

protected double WCDMinusSig3

WCDMinusSig4

protected double WCDMinusSig4

invWCDMinusSig4PlusBETA

protected double invWCDMinusSig4PlusBETA

Constructor Detail

FiniteExcludedVolEnergyElement

public FiniteExcludedVolEnergyElement()

FiniteExcludedVolEnergyElement

public FiniteExcludedVolEnergyElement(DistanceMatrix distanceMatrix,
                                      double Rfac,
                                      double weight,
                                      double[][] parameters)

Method Detail

setAtoms

protected void setAtoms()

Specified by:

setAtoms in class EnergyElement

set

public void set(java.lang.Object obj)

Specified by:

set in class NonBondedEnergyElement

evaluate

public double evaluate()

Specified by:

evaluate in class EnergyElement

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object