JavaGenes, NASA Ames. Written largely by Al Globus

gov.nasa.javaGenes.forceFields
Class MMEFreferenceRMS

java.lang.Object
  extended bygov.nasa.javaGenes.core.FitnessFunction
      extended bygov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
          extended bygov.nasa.javaGenes.forceFields.MMEFreferenceRMS
All Implemented Interfaces:
java.io.Serializable
Direct Known Subclasses:
MMEFreferenceTanimoto

public class MMEFreferenceRMS
extends ManyMoleculesEnergyFitness

the first cluster in the ManyMultiBodiesForOneEnergy is used to calulate differences from

See Also:
Serialized Form

Field Summary
protected  double energyRangeDivideBy
           
protected  double referenceEnergy
           
protected  DoubleInterval referenceEnergyUncertainty
           
protected  double targetReferenceEnergy
           
 
Fields inherited from class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
doPerAtomEnergies, energies, filename, molecules, originalEnergyInterval, potential, scaleTo
 
Fields inherited from class gov.nasa.javaGenes.core.FitnessFunction
name
 
Constructor Summary
MMEFreferenceRMS(Potential p, ManyMultiBodiesForOneEnergy m, boolean inDoPerAtomEnergies)
           
MMEFreferenceRMS(Potential p, ManyMultiBodiesForOneEnergy m, double inEnergyRangeDivideBy, double referenceEnergy)
           
MMEFreferenceRMS(Potential p, ManyMultiBodiesForOneEnergy m, double inEnergyRangeDivideBy, double inReferenceEnergy, double referenceEnergyLowerBound, double referenceEnergyUpperBound, boolean inDoPerAtomEnergies)
           
 
Method Summary
protected  double calculateDelta(double energy, double target)
           
protected  double calculateDistance(double energyToCheck, double targetEnergy)
           
 
Methods inherited from class gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
add, addEnergy, addToEnergies, calculateEnergy, evaluateFitness, getEnergy, getEnergyInterval, getFilename, getMultiBodiesForOneEnergy, multiplyEnergiesBy, report, scaleEnergiesTo, setEnergy, setFilename, toString
 
Methods inherited from class gov.nasa.javaGenes.core.FitnessFunction
bestDouble, getFunction, getName, getNameArray, isNewFunction, makeFiles, numberOfObjectives, setName, worstDouble
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

referenceEnergy

protected double referenceEnergy

referenceEnergyUncertainty

protected DoubleInterval referenceEnergyUncertainty

energyRangeDivideBy

protected double energyRangeDivideBy

targetReferenceEnergy

protected double targetReferenceEnergy
Constructor Detail

MMEFreferenceRMS

public MMEFreferenceRMS(Potential p,
                        ManyMultiBodiesForOneEnergy m,
                        double inEnergyRangeDivideBy,
                        double inReferenceEnergy,
                        double referenceEnergyLowerBound,
                        double referenceEnergyUpperBound,
                        boolean inDoPerAtomEnergies)

MMEFreferenceRMS

public MMEFreferenceRMS(Potential p,
                        ManyMultiBodiesForOneEnergy m,
                        double inEnergyRangeDivideBy,
                        double referenceEnergy)

MMEFreferenceRMS

public MMEFreferenceRMS(Potential p,
                        ManyMultiBodiesForOneEnergy m,
                        boolean inDoPerAtomEnergies)
Method Detail

calculateDistance

protected double calculateDistance(double energyToCheck,
                                   double targetEnergy)
Overrides:
calculateDistance in class ManyMoleculesEnergyFitness

calculateDelta

protected double calculateDelta(double energy,
                                double target)

JavaGenes, NASA Ames. Written largely by Al Globus