meshi.energy.hydrogenBondsAngle
Class AbstractPunishAngleEnergyElement

java.lang.Object
  meshi.energy.EnergyElement
      meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyElement
          meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement

Direct Known Subclasses:

HbondsPunishHOCAngleEnergyElement, HBondsPunishOHNAngleEnergyElement

public abstract class AbstractPunishAngleEnergyElement
extends NonBondedEnergyElement

Created by IntelliJ IDEA. User: amilev Date: 13/03/2006 Time: 10:49:48 implements the main code for energyElements of energy terms that punish angles of Hydrogen Bonds

Field Summary

protected double	a1
protected double	a2
protected Angle	angle
protected double	angleEnergy
protected double	angleValue
protected double	angleValue2
protected Atom	atom1
protected Atom	atom2
protected double	b1
protected double	b2
protected double	c1
protected double	c2
protected double	dAngleEnergyDAngle
protected double	dAngleEnergyDxHAtom
protected double	dAngleEnergyDxOAtom
protected double	dAngleEnergyDxTheidAtom
protected double	dAngleEnergyDyHAtom
protected double	dAngleEnergyDyOAtom
protected double	dAngleEnergyDyTheidAtom
protected double	dAngleEnergyDzHAtom
protected double	dAngleEnergyDzOAtom
protected double	dAngleEnergyDzTheidAtom
protected double	dDistanceEnergy_Ddistance
protected double	dDistanceEnergyDx
protected double	dDistanceEnergyDxHAtom
protected double	dDistanceEnergyDxOAtom
protected double	dDistanceEnergyDy
protected double	dDistanceEnergyDyHAtom
protected double	dDistanceEnergyDyOAtom
protected double	dDistanceEnergyDz
protected double	dDistanceEnergyDzHAtom
protected double	dDistanceEnergyDzOAtom
protected double	deDxHAtom
protected double	deDxOAtom
protected double	deDxTheidAtom
protected double	deDyHAtom
protected double	deDyOAtom
protected double	deDyTheidAtom
protected double	deDzHAtom
protected double	deDzOAtom
protected double	deDzTheidAtom
protected Distance	distance
protected double	distanceEnergy
protected DistanceMatrix	distanceMatrix
protected double	distanceValue
protected double	distanceValue2
protected double	energy
protected Atom	hAtom
protected int	hFactor
protected Atom	oAtom
protected int	oFactor
protected Atom	theirdAtom
protected double	weight
protected double	X_ANGLE
protected double	X_ANGLE2
protected double	X_MAX
protected double	X_MAX2
protected double	y1X_Angle2

Fields inherited from class meshi.energy.EnergyElement

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

Constructor Summary

AbstractPunishAngleEnergyElement(DistanceMatrix distanceMatrix, double weight)

AbstractPunishAngleEnergyElement(DistanceMatrix distanceMatrix, double weight, double xMax)

AbstractPunishAngleEnergyElement(DistanceMatrix distanceMatrix, double weight, double xMax, double maxAngle)

Method Summary

abstract java.lang.String	comment()
double	evaluate() energy calculation and atom forces updating.
double	evaluate(double weight)
void	set(java.lang.Object obj)
abstract boolean	setAngle()
protected void	setAtoms()
abstract void	setDAngleEnergyDatoms()
abstract void	setTheirdAtom()
void	updateAtoms()
void	updateAtoms(double weight)
double	updateEnergy() energy and dirivarives calculation.
abstract void	updateTheirdAtom()
abstract void	updateTheirdAtom(double weight)

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, toString, wait, wait, wait

Field Detail

oAtom

protected Atom oAtom

hAtom

protected Atom hAtom

atom1

protected Atom atom1

atom2

protected Atom atom2

theirdAtom

protected Atom theirdAtom

dDistanceEnergy_Ddistance

protected double dDistanceEnergy_Ddistance

distanceEnergy

protected double distanceEnergy

distance

protected Distance distance

distanceMatrix

protected DistanceMatrix distanceMatrix

distanceValue

protected double distanceValue

distanceValue2

protected double distanceValue2

X_MAX

protected double X_MAX

X_MAX2

protected double X_MAX2

X_ANGLE

protected double X_ANGLE

X_ANGLE2

protected double X_ANGLE2

c1

protected double c1

a1

protected double a1

b1

protected double b1

c2

protected double c2

a2

protected double a2

b2

protected double b2

y1X_Angle2

protected double y1X_Angle2

weight

protected double weight

dDistanceEnergyDx

protected double dDistanceEnergyDx

dDistanceEnergyDy

protected double dDistanceEnergyDy

dDistanceEnergyDz

protected double dDistanceEnergyDz

dDistanceEnergyDxOAtom

protected double dDistanceEnergyDxOAtom

dDistanceEnergyDyOAtom

protected double dDistanceEnergyDyOAtom

dDistanceEnergyDzOAtom

protected double dDistanceEnergyDzOAtom

dDistanceEnergyDxHAtom

protected double dDistanceEnergyDxHAtom

dDistanceEnergyDyHAtom

protected double dDistanceEnergyDyHAtom

dDistanceEnergyDzHAtom

protected double dDistanceEnergyDzHAtom

energy

protected double energy

angleEnergy

protected double angleEnergy

dAngleEnergyDxOAtom

protected double dAngleEnergyDxOAtom

dAngleEnergyDyOAtom

protected double dAngleEnergyDyOAtom

dAngleEnergyDzOAtom

protected double dAngleEnergyDzOAtom

dAngleEnergyDxHAtom

protected double dAngleEnergyDxHAtom

dAngleEnergyDyHAtom

protected double dAngleEnergyDyHAtom

dAngleEnergyDzHAtom

protected double dAngleEnergyDzHAtom

dAngleEnergyDxTheidAtom

protected double dAngleEnergyDxTheidAtom

dAngleEnergyDyTheidAtom

protected double dAngleEnergyDyTheidAtom

dAngleEnergyDzTheidAtom

protected double dAngleEnergyDzTheidAtom

oFactor

protected int oFactor

hFactor

protected int hFactor

deDxOAtom

protected double deDxOAtom

deDyOAtom

protected double deDyOAtom

deDzOAtom

protected double deDzOAtom

deDxHAtom

protected double deDxHAtom

deDyHAtom

protected double deDyHAtom

deDzHAtom

protected double deDzHAtom

deDxTheidAtom

protected double deDxTheidAtom

deDyTheidAtom

protected double deDyTheidAtom

deDzTheidAtom

protected double deDzTheidAtom

angle

protected Angle angle

angleValue

protected double angleValue

angleValue2

protected double angleValue2

dAngleEnergyDAngle

protected double dAngleEnergyDAngle

Constructor Detail

AbstractPunishAngleEnergyElement

public AbstractPunishAngleEnergyElement(DistanceMatrix distanceMatrix,
                                        double weight)

AbstractPunishAngleEnergyElement

public AbstractPunishAngleEnergyElement(DistanceMatrix distanceMatrix,
                                        double weight,
                                        double xMax)

AbstractPunishAngleEnergyElement

public AbstractPunishAngleEnergyElement(DistanceMatrix distanceMatrix,
                                        double weight,
                                        double xMax,
                                        double maxAngle)

Method Detail

comment

public abstract java.lang.String comment()

setTheirdAtom

public abstract void setTheirdAtom()

set

public void set(java.lang.Object obj)

Specified by:

set in class NonBondedEnergyElement

evaluate

public double evaluate()

energy calculation and atom forces updating.

Specified by:

evaluate in class EnergyElement

evaluate

public double evaluate(double weight)

setAngle

public abstract boolean setAngle()

setDAngleEnergyDatoms

public abstract void setDAngleEnergyDatoms()

updateEnergy

public double updateEnergy()

energy and dirivarives calculation.

updateAtoms

public void updateAtoms()

updateAtoms

public void updateAtoms(double weight)

updateTheirdAtom

public abstract void updateTheirdAtom(double weight)

updateTheirdAtom

public abstract void updateTheirdAtom()

setAtoms

protected void setAtoms()

Specified by:

setAtoms in class EnergyElement