meshi.energy.simpleEnergyTerms.bond
Class BondEnergy

java.lang.Object
  meshi.energy.AbstractEnergy
      meshi.energy.simpleEnergyTerms.SimpleEnergyTerm
          meshi.energy.simpleEnergyTerms.bond.BondEnergy

All Implemented Interfaces:

Attributable, Updateable

public class BondEnergy
extends SimpleEnergyTerm

Bond energy term. Has the general form Eb = SIGMAi(Ki(Di-D0i)^2) where Di is the distance between the two bonded atoms, D0i is their expected average distance (depends on their types) and Ki is a force constant that again, depends on the atom types.
This class is used for both calculating the bond-energy term of an energy function and for updating the forces on each atom accordingly. It is assumed that the list of bonds is constant during the simulation. That is no bonds are made or broken.

Nested Class Summary

Nested classes/interfaces inherited from class meshi.energy.AbstractEnergy

AbstractEnergy.UpdateableList

Field Summary

protected DistanceMatrix

distanceMatrix The constructor associates any bond with its parameters.

Fields inherited from class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm

elementsList, parametersList

Fields inherited from class meshi.energy.AbstractEnergy

comment, filter, INFINITY, NaN, on, updateableResources, weight

Constructor Summary

BondEnergy()

BondEnergy(AtomPairList bondList, DistanceMatrix distanceMatrix, BondParametersList parametersList, double weight)

Method Summary

EnergyElement	createElement(java.lang.Object baseElement, Parameters parameters)
void	removeBadBonds(double farAway)

Methods inherited from class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm

createElementsList, elementsList, evaluate, evaluateAtoms, test

Methods inherited from class meshi.energy.AbstractEnergy

addAttribute, comment, getAttribute, handleMissingParameters, isOn, off, on, toArray, toArray, toArray, toArray, toString, update

Methods inherited from class java.lang.Object

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

Field Detail

distanceMatrix

protected DistanceMatrix distanceMatrix

The constructor associates any bond with its parameters.

Constructor Detail

BondEnergy

public BondEnergy()

BondEnergy

public BondEnergy(AtomPairList bondList,
                  DistanceMatrix distanceMatrix,
                  BondParametersList parametersList,
                  double weight)

Method Detail

createElement

public EnergyElement createElement(java.lang.Object baseElement,
                                   Parameters parameters)

Specified by:

createElement in class SimpleEnergyTerm

removeBadBonds

public void removeBadBonds(double farAway)