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JavaGenes, NASA Ames. Written largely by Al Globus | |||||||||
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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 |
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JavaGenes, NASA Ames. Written largely by Al Globus | |||||||||
PREV PACKAGE NEXT PACKAGE | FRAMES NO FRAMES |