org.jmol.minimize.forcefield

Class ForceField

public abstract class ForceField extends Object

Field Summary
intatomCount
MinAtom[]atoms
intbondCount
MinBond[]bonds
BitSetbsFixed
Calculationscalc
double[][]coordSaved
doublecriterion
intcurrentStep
doubledE
doublee0
static intEANGLE
static intEBOND
static intEELECTROSTATIC
static intENERGY
static intEOOP
static intESTRBND
static intETORSION
static intEVDW
intstepMax
Viewerviewer
Constructor Summary
ForceField()
Method Summary
voidclearForces()
booleandetectExplosion()
doubleenergyAngle(boolean gradients)
doubleenergyBond(boolean gradients)
doubleenergyES(boolean gradients)
doubleenergyFull(boolean gradients, boolean isSilent)
doubleenergyOOP(boolean gradients)
doubleenergyStrBnd(boolean gradients)
doubleenergyTorsion(boolean gradients)
doubleenergyVDW(boolean gradients)
StringgetAtomList(String title)
abstract VectorgetAtomTypes()
intgetCurrentStep()
doublegetDE(MinAtom atom, int terms, int i, double delta)
doublegetEnergy(int terms, boolean gradients)
doublegetEnergy()
doublegetEnergyDiff()
protected abstract HashtablegetFFParameters()
StringgetLogData()
doublegetNormalizedDE()
StringgetUnits()
voidlinearSearch()
voidrestoreCoordinates()
voidsaveCoordinates()
voidsetConstraints(Minimizer m)
voidsetForcesUsingNumericalDerivative(MinAtom atom, int terms)
voidsetModel(Minimizer m)
booleansetup()
voidsteepestDescentInitialize(int stepMax, double criterion)
booleansteepestDescentTakeNSteps(int n)

Field Detail

atomCount

int atomCount

atoms

MinAtom[] atoms

bondCount

int bondCount

bonds

MinBond[] bonds

bsFixed

BitSet bsFixed

calc

Calculations calc

coordSaved

private double[][] coordSaved

criterion

private double criterion

currentStep

private int currentStep

dE

private double dE

e0

private double e0

EANGLE

static final int EANGLE

EBOND

static final int EBOND

EELECTROSTATIC

static final int EELECTROSTATIC

ENERGY

static final int ENERGY

EOOP

static final int EOOP

ESTRBND

static final int ESTRBND

ETORSION

static final int ETORSION

EVDW

static final int EVDW

stepMax

private int stepMax

viewer

Viewer viewer

Constructor Detail

ForceField

public ForceField()

Method Detail

clearForces

private void clearForces()

detectExplosion

public boolean detectExplosion()

energyAngle

double energyAngle(boolean gradients)

energyBond

double energyBond(boolean gradients)

energyES

double energyES(boolean gradients)

energyFull

public double energyFull(boolean gradients, boolean isSilent)

energyOOP

double energyOOP(boolean gradients)

energyStrBnd

double energyStrBnd(boolean gradients)

energyTorsion

double energyTorsion(boolean gradients)

energyVDW

double energyVDW(boolean gradients)

getAtomList

public String getAtomList(String title)

getAtomTypes

public abstract Vector getAtomTypes()

getCurrentStep

public int getCurrentStep()

getDE

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

getEnergy

private double getEnergy(int terms, boolean gradients)

getEnergy

public double getEnergy()

getEnergyDiff

public double getEnergyDiff()

getFFParameters

protected abstract Hashtable getFFParameters()

getLogData

public String getLogData()

getNormalizedDE

double getNormalizedDE()

getUnits

private String getUnits()

linearSearch

private void linearSearch()

restoreCoordinates

private void restoreCoordinates()

saveCoordinates

private void saveCoordinates()

setConstraints

public void setConstraints(Minimizer m)

setForcesUsingNumericalDerivative

private void setForcesUsingNumericalDerivative(MinAtom atom, int terms)

setModel

public void setModel(Minimizer m)

setup

public boolean setup()

steepestDescentInitialize

public void steepestDescentInitialize(int stepMax, double criterion)

steepestDescentTakeNSteps

public boolean steepestDescentTakeNSteps(int n)