Package org.jmol.minimize.forcefield
Class CalculationsUFF
- java.lang.Object
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- org.jmol.minimize.forcefield.Calculations
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- org.jmol.minimize.forcefield.CalculationsUFF
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class CalculationsUFF extends Calculations
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Field Summary
Fields Modifier and Type Field Description (package private) Calculation
angleCalc
(package private) Calculation
bondCalc
(package private) static double
KCAL22
(package private) static double
KCAL332
(package private) static double
KCAL44
(package private) static double
KCAL6
(package private) static double
KCAL644
(package private) Calculation
oopCalc
(package private) static int
PAR_D
(package private) static int
PAR_HARD
(package private) static int
PAR_R
(package private) static int
PAR_RADIUS
(package private) static int
PAR_THETA
(package private) static int
PAR_U
(package private) static int
PAR_V
(package private) static int
PAR_X
(package private) static int
PAR_XI
(package private) static int
PAR_Z
(package private) static int
PAR_ZETA
(package private) Calculation
torsionCalc
(package private) Calculation
vdwCalc
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Fields inherited from class org.jmol.minimize.forcefield.Calculations
ac, angleCount, bondCount, CALC_ANGLE, CALC_DISTANCE, CALC_ES, CALC_MAX, CALC_OOP, CALC_STRETCH_BEND, CALC_TORSION, CALC_VDW, calculations, da, db, dc, dd, DEG_TO_RAD, ff, ffParams, gradients, ia, ib, ic, id, isPreliminary, KCAL_TO_KJ, logData, logging, loggingEnabled, minAngles, minAtoms, minBonds, minTorsions, parA, parB, parC, RAD_TO_DEG, silent, torsionCount, v1, v2, v3
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Constructor Summary
Constructors Constructor Description CalculationsUFF(ForceField ff, java.util.Map<java.lang.Object,java.lang.Object> ffParams, MinAtom[] minAtoms, MinBond[] minBonds, MinAngle[] minAngles, MinTorsion[] minTorsions, MinPosition[] minPositions, javajs.util.Lst<MMConstraint> constraints)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) static double
calculateR0(double ri, double rj, double chiI, double chiJ, double bondorder)
(package private) double
compute(int iType, java.lang.Object[] dataIn)
(package private) java.lang.String
getDebugHeader(int iType)
protected java.lang.Object
getParameterObj(MinObject o)
(package private) java.lang.String
getUnits()
private static boolean
isInvertible(int n)
(package private) boolean
setupCalculations()
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Methods inherited from class org.jmol.minimize.forcefield.Calculations
addForce, addForces, appendLogData, energyAngle, energyBond, energyES, energyOOP, energyStrBnd, energyStretchBend, energyTorsion, energyVDW, getAtomList, getConstraintList, getDebugFooter, getDebugHeader2, getDebugLine, getDebugLineC, getLogData, getParameter, isLinear, pairSearch, setAngleVariables, setConstraints, setCoords, setLoggingEnabled, setOopVariables, setPairVariables, setPreliminary, setSilent, setTorsionVariables
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Field Detail
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KCAL332
static final double KCAL332
- See Also:
- Constant Field Values
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KCAL644
static final double KCAL644
- See Also:
- Constant Field Values
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KCAL6
static final double KCAL6
- See Also:
- Constant Field Values
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KCAL22
static final double KCAL22
- See Also:
- Constant Field Values
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KCAL44
static final double KCAL44
- See Also:
- Constant Field Values
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PAR_R
static final int PAR_R
- See Also:
- Constant Field Values
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PAR_THETA
static final int PAR_THETA
- See Also:
- Constant Field Values
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PAR_X
static final int PAR_X
- See Also:
- Constant Field Values
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PAR_D
static final int PAR_D
- See Also:
- Constant Field Values
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PAR_ZETA
static final int PAR_ZETA
- See Also:
- Constant Field Values
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PAR_Z
static final int PAR_Z
- See Also:
- Constant Field Values
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PAR_V
static final int PAR_V
- See Also:
- Constant Field Values
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PAR_U
static final int PAR_U
- See Also:
- Constant Field Values
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PAR_XI
static final int PAR_XI
- See Also:
- Constant Field Values
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PAR_HARD
static final int PAR_HARD
- See Also:
- Constant Field Values
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PAR_RADIUS
static final int PAR_RADIUS
- See Also:
- Constant Field Values
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bondCalc
Calculation bondCalc
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angleCalc
Calculation angleCalc
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torsionCalc
Calculation torsionCalc
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oopCalc
Calculation oopCalc
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vdwCalc
Calculation vdwCalc
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Constructor Detail
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CalculationsUFF
CalculationsUFF(ForceField ff, java.util.Map<java.lang.Object,java.lang.Object> ffParams, MinAtom[] minAtoms, MinBond[] minBonds, MinAngle[] minAngles, MinTorsion[] minTorsions, MinPosition[] minPositions, javajs.util.Lst<MMConstraint> constraints)
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Method Detail
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getUnits
java.lang.String getUnits()
- Specified by:
getUnits
in classCalculations
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setupCalculations
boolean setupCalculations()
- Specified by:
setupCalculations
in classCalculations
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isInvertible
private static boolean isInvertible(int n)
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calculateR0
static double calculateR0(double ri, double rj, double chiI, double chiJ, double bondorder)
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compute
double compute(int iType, java.lang.Object[] dataIn)
- Specified by:
compute
in classCalculations
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getDebugHeader
java.lang.String getDebugHeader(int iType)
- Specified by:
getDebugHeader
in classCalculations
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getParameterObj
protected java.lang.Object getParameterObj(MinObject o)
- Specified by:
getParameterObj
in classCalculations
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