org.jmol.minimize.forcefield
Class ForceField
public abstract
class
ForceField
extends Object
int atomCount
int bondCount
BitSet bsFixed
private double[][] coordSaved
private double criterion
private int currentStep
private double dE
private double e0
static final int EANGLE
static final int EBOND
static final int EELECTROSTATIC
static final int ENERGY
static final int EOOP
static final int ESTRBND
static final int ETORSION
static final int EVDW
private int stepMax
public ForceField()
private void clearForces()
public boolean detectExplosion()
double energyAngle(boolean gradients)
double energyBond(boolean gradients)
double energyES(boolean gradients)
public double energyFull(boolean gradients, boolean isSilent)
double energyOOP(boolean gradients)
double energyStrBnd(boolean gradients)
double energyTorsion(boolean gradients)
double energyVDW(boolean gradients)
public String getAtomList(String title)
public abstract Vector getAtomTypes()
public int getCurrentStep()
private double getDE(
MinAtom atom, int terms, int i, double delta)
private double getEnergy(int terms, boolean gradients)
public double getEnergy()
public double getEnergyDiff()
protected abstract Hashtable getFFParameters()
public String getLogData()
double getNormalizedDE()
private String getUnits()
private void linearSearch()
private void restoreCoordinates()
private void saveCoordinates()
private void setForcesUsingNumericalDerivative(
MinAtom atom, int terms)
public boolean setup()
public void steepestDescentInitialize(int stepMax, double criterion)
public boolean steepestDescentTakeNSteps(int n)