JavaGenes, NASA Ames. Written largely by Al Globus

Package gov.nasa.javaGenes.forceFields

Class Summary
Allele Used to control a single double value in a chromosome.
AlleleSetup  
AlleleTemplate a two-dimensional array of alleles.
AlleleTemplateTest  
AlleleTest  
AssumedParameters  
AssumedParametersTest  
AtomicSpecies For a multibody atomic potential, this class is used to indicate what atomic element a body has.
Bodies Holds a set of bodies for a multibody potential to find the energy of
BodiesTest  
Body This is used as a superclass by OneBody, TwoBody, and ThreeBody
Chromosome Implement the representation of a two-dimensional array of double.
ChromosomeArrayCrossover  
ChromosomeCrossover Implements a uniform crossover operator where the value of each double in the child has an equal probability of coming from the father or the mother
ChromosomeDistanceFitness fitness is the distance from a target chromosome.
ChromosomeIndividual  
ChromosomeIntervalCrossover Implements a form of crossover were each allele in the child is a function of a random number and values in the mother and father.
ChromosomeIntervalCrossoverTest  
ChromosomeMutation Mutates some fraction of the alleles with a random number chosen from a Gaussian distribution
ChromosomeMutationTest  
ChromosomeParameters  
ChromosomeParameterValues  
ChromosomePopulation  
ChromosomeReporter  
ChromosomeXoverWithMutation  
ChromosomeXoverWithMutationTest  
FirstClusterLowestEnergyFitnessFunction  
FirstClusterLowestEnergyFitnessFunctionTest  
ForceFitnessRMS  
ForceFitnessRMSTest  
ForceFitnessTanimoto  
FunctionalForm  
GetLengthsAndAngles  
Immigrant  
Immigrants  
ImmigrantsTest  
ImmigrantTest  
LowestToHighestEnergyFitness  
LowestToHighestEnergyFitnessTest  
LowestToHighestEnergyGradualFitness  
LowestToHighestEnergyGradualFitnessTest  
Main  
MakeDimer  
MakeDimerPair  
MakeSiFMolecules requires SiF4.mol, Si2F6.mol, and Si3F8.mol to be in current directory.
MakeThreeBodyXyz  
MakeTrimer  
ManyMoleculesEnergyFitness  
ManyMoleculesEnergyFitnessRatio  
ManyMoleculesEnergyFitnessTanimotoDistance  
ManyMultiBodiesForOneEnergy  
MMEFreferenceRMS the first cluster in the ManyMultiBodiesForOneEnergy is used to calulate differences from
MMEFreferenceRMSTest  
MMEFreferenceTanimoto  
MultiBodiesForOneEnergy  
MultiBodiesForOneEnergyTest  
MultiBody  
Mutation3Parents Mutates all alleles with a random number chosen from a Gaussian distribution with the standard deviation taken by the difference in two of the children
OneBody represents a single body in a multibody potential.
Potential this classes used to find energy of a multibody system given a particular Chromosome for the potential parameters.
PotentialEnergyFitness fitness function based on RMS distance of potential energies between the target and candidate Chromosome
PotentialEnergyTestCase  
PutPotentialEnergiesAndForces  
RunChromosome run a genetic algorithm with a Chromosome (two-dimensional array) representation
SecondBody represents the second body and relevant parameters of a three-body.
Species superclass for objects representing the species of the body for many body problems.
Species2IndexMap used to convert a Species object to a array index for fast processing.
StillingerWeber Implements Thomas A.
StillingerWeberEnergies  
StillingerWeberPartialSiF  
StillingerWeberPrintEnergiesAndForces  
StillingerWeberSi  
StillingerWeberSiF  
StillingerWeberSiFTest  
StillingerWeberSiTest  
StillingerWeberTest  
Tersoff Implements the Tersoff potential.
TersoffTest  
ThirdBody represents the last body and relevant parameters of a three-body.
ThreeBody  
ThreeBodyTest  
TwoBody  
TwoBodyTest  
 


JavaGenes, NASA Ames. Written largely by Al Globus