Package org.jmol.minimize.forcefield
Class ForceField
java.lang.Object
org.jmol.minimize.forcefield.ForceField
- Direct Known Subclasses:
ForceFieldMMFF
,ForceFieldUFF
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
(package private) javajs.util.BS
(package private) Calculations
private double[][]
private double
(package private) int
private double
private double
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) MinAngle[]
(package private) int
(package private) MinAtom[]
(package private) int
(package private) MinBond[]
(package private) Minimizer
(package private) MinPosition[]
(package private) MinTorsion[]
static final int
static final int
static final int
static final int
private int
static final int
static final int
static final int
(package private) double
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionabstract void
clear()
private void
boolean
(package private) double
energyAngle
(boolean gradients) (package private) double
energyBond
(boolean gradients) (package private) double
energyES
(boolean gradients) double
energyFull
(boolean gradients, boolean isSilent) (package private) double
energyOOP
(boolean gradients) (package private) double
energyStretchBend
(boolean gradients) (package private) double
energyTorsion
(boolean gradients) (package private) double
energyVDW
(boolean gradients) getAtomList
(String title) protected BufferedReader
getBufferedReader
(String resourceName) int
private double
private double
getEnergies
(int terms, boolean gradients) Get the energy of a given type or types.double
double
(package private) double
private void
void
private void
private void
void
private void
setForcesUsingNumericalDerivative
(MinAtom atom, int terms) abstract boolean
setModel
(javajs.util.BS bsElements, int elemnoMax) protected void
void
steepestDescentInitialize
(int stepMax, double criterion, double trustRadius) boolean
steepestDescentTakeNSteps
(int n) private float
float
toUserUnits
(double energy)
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Field Details
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ENERGY
static final int ENERGY- See Also:
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EBOND
static final int EBOND- See Also:
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EANGLE
static final int EANGLE- See Also:
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ESTRBND
static final int ESTRBND- See Also:
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ETORSION
static final int ETORSION- See Also:
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EOOP
static final int EOOP- See Also:
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EVDW
static final int EVDW- See Also:
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EELECTROSTATIC
static final int EELECTROSTATIC- See Also:
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ABI_IJ
public static final int ABI_IJ- See Also:
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ABI_JK
public static final int ABI_JK- See Also:
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TBI_AB
public static final int TBI_AB- See Also:
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TBI_BC
public static final int TBI_BC- See Also:
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TBI_CD
public static final int TBI_CD- See Also:
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R3
public static final int R3- See Also:
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R4
public static final int R4- See Also:
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R5
public static final int R5- See Also:
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Raromatic
public static final int Raromatic- See Also:
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name
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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
javajs.util.BS bsFixed -
trustRadius
double trustRadius -
minimizer
Minimizer minimizer
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Constructor Details
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ForceField
public ForceField()
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Method Details
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clear
public abstract void clear() -
setModel
public abstract boolean setModel(javajs.util.BS bsElements, int elemnoMax) throws JmolAsyncException - Throws:
JmolAsyncException
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setModelFields
protected void setModelFields() -
setConstraints
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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
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setForcesUsingNumericalDerivative
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getDE
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energyFull
public double energyFull(boolean gradients, boolean isSilent) -
energyStretchBend
double energyStretchBend(boolean gradients) - Parameters:
gradients
-- Returns:
- energy
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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
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getEnergyDiff
public double getEnergyDiff() -
getLogData
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getNormalizedDE
double getNormalizedDE() -
toUserUnits
public float toUserUnits(double energy) -
toUnits
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log
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getBufferedReader
- Throws:
IOException
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