JavaGenes, NASA Ames. Written largely by Al Globus

gov.nasa.javaGenes.forceFields
Class StillingerWeberSiF

java.lang.Object
  extended bygov.nasa.javaGenes.forceFields.Potential
      extended bygov.nasa.javaGenes.forceFields.StillingerWeber
          extended bygov.nasa.javaGenes.forceFields.StillingerWeberSiF
All Implemented Interfaces:
java.io.Serializable
Direct Known Subclasses:
StillingerWeberPartialSiF

public class StillingerWeberSiF
extends StillingerWeber

See Also:
Serialized Form

Nested Class Summary
 
Nested classes inherited from class gov.nasa.javaGenes.forceFields.StillingerWeber
StillingerWeber.ChromosomeParametersData
 
Field Summary
protected  double energyUnitErgPerAtom
           
protected  double energyUnitKcalPerMol
           
 
Fields inherited from class gov.nasa.javaGenes.forceFields.StillingerWeber
a_index, A_index, a1_index, a2_index, alleles, alleleSetup, alpha_index, angleInterval, B_index, beta_index, bondLengthInterval, C_index, chromosome, cutoffInterval, cutoffs, delta_index, exponentInterval, factorInterval, flourineThreeBodyParametersIncrement, gamma_index, lambda_index, m_index, NotApplicable, numberOfThreeBodyParameters, numberOfTwoBodyParameters, p_index, q_index, setupComplete, specialThreeBodyParametersIncrement, theta0_index
 
Fields inherited from class gov.nasa.javaGenes.forceFields.Potential
STILLINGER_WEBER, TERSOFF
 
Constructor Summary
protected StillingerWeberSiF()
           
  StillingerWeberSiF(DoubleInterval factorInterval, DoubleInterval exponentInterval, DoubleInterval cutoffInterval)
           
 
Method Summary
 void addFFF(int index)
           
 void addThreeBody(java.lang.String name, int index)
           
 void addTwoBody(java.lang.String name, int index)
           
protected  void formSetup()
           
protected  double getEnergy(ThreeBody threeBody)
           
protected  double getEnergy(TwoBody pair)
           
 double getForce(TwoBody pair)
           
static double getLengthScale()
           
protected  void need(java.lang.String name, int index)
           
 void setCutoff(ThreeBody threeBody, double value)
          value is in angstoms
 void setCutoff(ThreeBody threeBody, double a1_value, double a2_value)
          values are in angstoms
 void setCutoff(TwoBody pair, double value)
          value is in angstoms
protected  void setupChromosomeFromPaper(java.lang.String name)
           
 
Methods inherited from class gov.nasa.javaGenes.forceFields.StillingerWeber
addSpecialThreeBody, addToArraySizes, calculateForce, calculateTwoBodyEnergy, canModel, cutoff, getAlleles, getChromosome, getChromosomeArraySizes, getCutoff, getCutoff, getCutoffTerm, getEnergy, getEnergy, getSpeciesIndex, getValue, hasThreeBody, hasTwoBody, lengthTerm, mustModel, mustModel, mustModel, need, noThreeTermParameters, setBondLengthInterval, setChromosome, setCutoff, setCutoffInterval, setExponentInterval, setFactorInterval, setIndices, setupAllelesAndChromosome, setupChromosomeFromPaper, setValue
 
Methods inherited from class gov.nasa.javaGenes.forceFields.Potential
getEnergy, getEnergy, toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

energyUnitKcalPerMol

protected double energyUnitKcalPerMol

energyUnitErgPerAtom

protected double energyUnitErgPerAtom
Constructor Detail

StillingerWeberSiF

protected StillingerWeberSiF()

StillingerWeberSiF

public StillingerWeberSiF(DoubleInterval factorInterval,
                          DoubleInterval exponentInterval,
                          DoubleInterval cutoffInterval)
Method Detail

getLengthScale

public static double getLengthScale()

getEnergy

protected double getEnergy(TwoBody pair)
Overrides:
getEnergy in class StillingerWeber

getForce

public double getForce(TwoBody pair)
Overrides:
getForce in class StillingerWeber

getEnergy

protected double getEnergy(ThreeBody threeBody)
Overrides:
getEnergy in class StillingerWeber

setCutoff

public void setCutoff(TwoBody pair,
                      double value)
Description copied from class: StillingerWeber
value is in angstoms

Overrides:
setCutoff in class StillingerWeber

setCutoff

public void setCutoff(ThreeBody threeBody,
                      double value)
Description copied from class: StillingerWeber
value is in angstoms

Overrides:
setCutoff in class StillingerWeber

setCutoff

public void setCutoff(ThreeBody threeBody,
                      double a1_value,
                      double a2_value)
Description copied from class: StillingerWeber
values are in angstoms

Overrides:
setCutoff in class StillingerWeber

formSetup

protected void formSetup()
Overrides:
formSetup in class StillingerWeber

need

protected void need(java.lang.String name,
                    int index)

addTwoBody

public void addTwoBody(java.lang.String name,
                       int index)
Overrides:
addTwoBody in class StillingerWeber

addThreeBody

public void addThreeBody(java.lang.String name,
                         int index)
Overrides:
addThreeBody in class StillingerWeber

addFFF

public void addFFF(int index)

setupChromosomeFromPaper

protected void setupChromosomeFromPaper(java.lang.String name)

JavaGenes, NASA Ames. Written largely by Al Globus