Package org.jmol.minimize.forcefield
Class ForceField
- java.lang.Object
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- org.jmol.minimize.forcefield.ForceField
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- Direct Known Subclasses:
ForceFieldMMFF
,ForceFieldUFF
public abstract class ForceField extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description static int
ABI_IJ
static int
ABI_JK
(package private) javajs.util.BS
bsFixed
(package private) Calculations
calc
private double[][]
coordSaved
private double
criterion
(package private) int
currentStep
private double
dE
private double
e0
(package private) static int
EANGLE
(package private) static int
EBOND
(package private) static int
EELECTROSTATIC
(package private) static int
ENERGY
(package private) static int
EOOP
(package private) static int
ESTRBND
(package private) static int
ETORSION
(package private) static int
EVDW
(package private) MinAngle[]
minAngles
(package private) int
minAtomCount
(package private) MinAtom[]
minAtoms
(package private) int
minBondCount
(package private) MinBond[]
minBonds
(package private) Minimizer
minimizer
(package private) MinPosition[]
minPositions
(package private) MinTorsion[]
minTorsions
java.lang.String
name
static int
R3
static int
R4
static int
R5
static int
Raromatic
private int
stepMax
static int
TBI_AB
static int
TBI_BC
static int
TBI_CD
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Constructor Summary
Constructors Constructor Description ForceField()
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description abstract void
clear()
private void
clearForces()
boolean
detectExplosion()
(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)
java.lang.String
getAtomList(java.lang.String title)
protected java.io.BufferedReader
getBufferedReader(java.lang.String resourceName)
int
getCurrentStep()
private double
getDE(MinAtom atom, int terms, int i, double delta)
private double
getEnergies(int terms, boolean gradients)
Get the energy of a given type or types.double
getEnergy()
double
getEnergyDiff()
java.lang.String
getLogData()
(package private) double
getNormalizedDE()
private void
linearSearch()
void
log(java.lang.String s)
private void
restoreCoordinates()
private void
saveCoordinates()
void
setConstraints(Minimizer m)
private void
setForcesUsingNumericalDerivative(MinAtom atom, int terms)
abstract boolean
setModel(javajs.util.BS bsElements, int elemnoMax)
protected void
setModelFields()
void
steepestDescentInitialize(int stepMax, double criterion)
boolean
steepestDescentTakeNSteps(int n)
private float
toUnits(double energy, java.lang.String units)
float
toUserUnits(double energy)
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Field Detail
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ENERGY
static final int ENERGY
- See Also:
- Constant Field Values
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EBOND
static final int EBOND
- See Also:
- Constant Field Values
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EANGLE
static final int EANGLE
- See Also:
- Constant Field Values
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ESTRBND
static final int ESTRBND
- See Also:
- Constant Field Values
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ETORSION
static final int ETORSION
- See Also:
- Constant Field Values
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EOOP
static final int EOOP
- See Also:
- Constant Field Values
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EVDW
static final int EVDW
- See Also:
- Constant Field Values
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EELECTROSTATIC
static final int EELECTROSTATIC
- See Also:
- Constant Field Values
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ABI_IJ
public static final int ABI_IJ
- See Also:
- Constant Field Values
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ABI_JK
public static final int ABI_JK
- See Also:
- Constant Field Values
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TBI_AB
public static final int TBI_AB
- See Also:
- Constant Field Values
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TBI_BC
public static final int TBI_BC
- See Also:
- Constant Field Values
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TBI_CD
public static final int TBI_CD
- See Also:
- Constant Field Values
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R3
public static final int R3
- See Also:
- Constant Field Values
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R4
public static final int R4
- See Also:
- Constant Field Values
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R5
public static final int R5
- See Also:
- Constant Field Values
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Raromatic
public static final int Raromatic
- See Also:
- Constant Field Values
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name
public java.lang.String name
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calc
Calculations calc
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criterion
private double criterion
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e0
private double e0
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dE
private double dE
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currentStep
int currentStep
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stepMax
private int stepMax
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coordSaved
private double[][] coordSaved
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minAtomCount
int minAtomCount
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minBondCount
int minBondCount
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minAtoms
MinAtom[] minAtoms
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minBonds
MinBond[] minBonds
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minAngles
MinAngle[] minAngles
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minTorsions
MinTorsion[] minTorsions
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minPositions
MinPosition[] minPositions
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bsFixed
javajs.util.BS bsFixed
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minimizer
Minimizer minimizer
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Method Detail
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clear
public abstract void clear()
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setModel
public abstract boolean setModel(javajs.util.BS bsElements, int elemnoMax) throws JmolAsyncException
- Throws:
JmolAsyncException
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setModelFields
protected void setModelFields()
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setConstraints
public void setConstraints(Minimizer m)
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steepestDescentInitialize
public void steepestDescentInitialize(int stepMax, double criterion)
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clearForces
private void clearForces()
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steepestDescentTakeNSteps
public boolean steepestDescentTakeNSteps(int n)
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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
private void setForcesUsingNumericalDerivative(MinAtom atom, int terms)
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getDE
private double getDE(MinAtom atom, int terms, int i, double delta)
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energyFull
public double energyFull(boolean gradients, boolean isSilent)
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energyStretchBend
double energyStretchBend(boolean gradients)
- Parameters:
gradients
-- Returns:
- energy
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energyBond
double energyBond(boolean gradients)
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energyAngle
double energyAngle(boolean gradients)
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energyTorsion
double energyTorsion(boolean gradients)
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energyOOP
double energyOOP(boolean gradients)
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energyVDW
double energyVDW(boolean gradients)
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energyES
double energyES(boolean gradients)
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linearSearch
private void linearSearch()
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saveCoordinates
private void saveCoordinates()
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restoreCoordinates
private void restoreCoordinates()
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detectExplosion
public boolean detectExplosion()
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getCurrentStep
public int getCurrentStep()
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getEnergy
public double getEnergy()
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getAtomList
public java.lang.String getAtomList(java.lang.String title)
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getEnergyDiff
public double getEnergyDiff()
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getLogData
public java.lang.String getLogData()
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getNormalizedDE
double getNormalizedDE()
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toUserUnits
public float toUserUnits(double energy)
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toUnits
private float toUnits(double energy, java.lang.String units)
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log
public void log(java.lang.String s)
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getBufferedReader
protected java.io.BufferedReader getBufferedReader(java.lang.String resourceName) throws java.io.IOException
- Throws:
java.io.IOException
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