org.jmol.minimize.forcefield
Class ForceField
java.lang.Object
org.jmol.minimize.forcefield.ForceField
- Direct Known Subclasses:
- ForceFieldUFF
public abstract class ForceField
- extends Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
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
atomCount
int atomCount
bondCount
int bondCount
atoms
MinAtom[] atoms
bonds
MinBond[] bonds
bsFixed
BitSet bsFixed
minimizer
Minimizer minimizer
ForceField
public ForceField()
getUnits
private String getUnits()
getAtomTypes
public abstract List getAtomTypes()
getFFParameters
protected abstract Hashtable getFFParameters()
setModel
public void setModel(Minimizer m)
setConstraints
public void setConstraints(Minimizer m)
setup
public boolean setup()
steepestDescentInitialize
public void steepestDescentInitialize(int stepMax,
double criterion)
clearForces
private void clearForces()
steepestDescentTakeNSteps
public boolean steepestDescentTakeNSteps(int n)
getEnergy
private double getEnergy(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)
energyStrBnd
double energyStrBnd(boolean gradients)
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()