Class ForceField

java.lang.Object
org.jmol.minimize.forcefield.ForceField
Direct Known Subclasses:
ForceFieldMMFF, ForceFieldUFF

public abstract class ForceField extends Object
  • Field Details

  • Constructor Details

    • ForceField

      public ForceField()
  • Method Details

    • clear

      public abstract void clear()
    • setModel

      public abstract boolean setModel(javajs.util.BS bsElements, int elemnoMax) throws JmolAsyncException
      Throws:
      JmolAsyncException
    • setModelFields

      protected void setModelFields()
    • setConstraints

      public void setConstraints(Minimizer m)
    • steepestDescentInitialize

      public void steepestDescentInitialize(int stepMax, double criterion, double trustRadius)
    • clearForces

      private void clearForces()
    • steepestDescentTakeNSteps

      public boolean steepestDescentTakeNSteps(int n)
    • getEnergies

      private double getEnergies(int terms, boolean gradients)
      Get the energy of a given type or types. Note: gradients is always false
      Parameters:
      terms -
      gradients - ignored (false)
      Returns:
      energy
    • setForcesUsingNumericalDerivative

      private void setForcesUsingNumericalDerivative(MinAtom atom, int terms)
    • getDE

      private double getDE(MinAtom atom, int terms, int i, double delta)
    • energyFull

      public double energyFull(boolean gradients, boolean isSilent)
    • energyStretchBend

      double energyStretchBend(boolean gradients)
      Parameters:
      gradients -
      Returns:
      energy
    • energyBond

      double energyBond(boolean gradients)
    • energyAngle

      double energyAngle(boolean gradients)
    • energyTorsion

      double energyTorsion(boolean gradients)
    • energyOOP

      double energyOOP(boolean gradients)
    • energyVDW

      double energyVDW(boolean gradients)
    • energyES

      double energyES(boolean gradients)
    • linearSearch

      private void linearSearch()
    • saveCoordinates

      private void saveCoordinates()
    • restoreCoordinates

      private void restoreCoordinates()
    • detectExplosion

      public boolean detectExplosion()
    • getCurrentStep

      public int getCurrentStep()
    • getEnergy

      public double getEnergy()
    • getAtomList

      public String getAtomList(String title)
    • getEnergyDiff

      public double getEnergyDiff()
    • getLogData

      public String getLogData()
    • getNormalizedDE

      double getNormalizedDE()
    • toUserUnits

      public float toUserUnits(double energy)
    • toUnits

      private float toUnits(double energy, String units)
    • log

      public void log(String s)
    • getBufferedReader

      protected BufferedReader getBufferedReader(String resourceName) throws IOException
      Throws:
      IOException