Field Detail

• ENERGY

  static final int ENERGY

  See Also:

  Constant Field Values

• EBOND

  static final int EBOND

  See Also:

  Constant Field Values

• EANGLE

  static final int EANGLE

  See Also:

  Constant Field Values

• ESTRBND

  static final int ESTRBND

  See Also:

  Constant Field Values

• ETORSION

  static final int ETORSION

  See Also:

  Constant Field Values

• EOOP

  static final int EOOP

  See Also:

  Constant Field Values

• EVDW

  static final int EVDW

  See Also:

  Constant Field Values

• EELECTROSTATIC

  static final int EELECTROSTATIC

  See Also:

  Constant Field Values

• ABI_IJ

  public static final int ABI_IJ

  See Also:

  Constant Field Values

• ABI_JK

  public static final int ABI_JK

  See Also:

  Constant Field Values

• TBI_AB

  public static final int TBI_AB

  See Also:

  Constant Field Values

• TBI_BC

  public static final int TBI_BC

  See Also:

  Constant Field Values

• TBI_CD

  public static final int TBI_CD

  See Also:

  Constant Field Values

• R3

  public static final int R3

  See Also:

  Constant Field Values

• R4

  public static final int R4

  See Also:

  Constant Field Values

• R5

  public static final int R5

  See Also:

  Constant Field Values

• Raromatic

  public static final int Raromatic

  See Also:

  Constant Field Values

• name

  public java.lang.String name

• calc

  Calculations calc

• criterion

  private double criterion

• e0

  private double e0

• dE

  private double dE

• currentStep

  int currentStep

• stepMax

  private int stepMax

• coordSaved

  private double[][] coordSaved

• minAtomCount

  int minAtomCount

• minBondCount

  int minBondCount

• minAtoms

  MinAtom[] minAtoms

• minBonds

  MinBond[] minBonds

• minAngles

  MinAngle[] minAngles

• minTorsions

  MinTorsion[] minTorsions

• minPositions

  MinPosition[] minPositions

• bsFixed

  BS bsFixed

• minimizer

  Minimizer minimizer

Constructor Detail

• ForceField

  public ForceField()

Method Detail

• clear

  public abstract void clear()

• setModel

  public abstract boolean setModel​(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)

• clearForces

  private void clearForces()

• steepestDescentTakeNSteps

  public boolean steepestDescentTakeNSteps​(int n)

• getEnergies

  private double getEnergies​(int terms,
                             boolean gradients)

• 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 java.lang.String getAtomList​(java.lang.String title)

• getEnergyDiff

  public double getEnergyDiff()

• getLogData

  public java.lang.String getLogData()

• getNormalizedDE

  double getNormalizedDE()

• toUserUnits

  public float toUserUnits​(double energy)

• toUnits

  private float toUnits​(double energy,
                        java.lang.String units)

• log

  public void log​(java.lang.String s)

• getBufferedReader

  protected java.io.BufferedReader getBufferedReader​(java.lang.String resourceName)
                                              throws java.io.IOException

  Throws:

  java.io.IOException