Package org.evoludo.simulator.modules

Class ATBT.ODE

Object

Model

ODE

RungeKutta

ODE

All Implemented Interfaces:

Discrete, CLOProvider

Enclosing class:

ATBT

public class ATBT.ODE
extends RungeKutta

Provide ODE implementation for asymmetric 2×2 games with environmental feedback.

Nested Class Summary

Nested classes/interfaces inherited from class ODE

ODE.HasDE, ODE.HasODE, ODE.InitType

Field Summary

Fields

Modifier and Type	Field	Description
protected Module	module	Convenience variable: module associated with this model (useful for single species).

Fields inherited from class ODE

cloAdjustedDynamics, cloDEAccuracy, cloDEdt, cloInit, cloTimeReversed, initType, monoStop

Fields inherited from class Model

cloSamples, cloTimeRelax, cloTimeStep, cloTimeStop, connect, converged, engine, fixData, isMultispecies, logger, mode, nSamples, nSpecies, nStatisticsFailed, nStatisticsSamples, rng, species, statisticsSampleNew, time, timeRelax, timeStep, timeStop

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	ODE(EvoLudo engine)	Constructs a new ODE solver taylored for the integration of asymmetric 2×2 games with environmental feedback.

Method Summary

Modifier and Type	Method	Description
protected void	getDerivatives(double t, double[] state, double[] fitness, double[] change)	Calculate the rates of change for all species in state at time given the fitness fitness and returned in change.
boolean	permitsTimeReversal()	Checks if time reversal is permitted.

Methods inherited from class RungeKutta

check, deStep, getAutoDt, reset, setAutoDt, unload

Methods inherited from class ODE

checkConvergence, collectCLO, encodeState, getAccuracy, getDt, getFitnessData, getFitnessHistogramData, getInitialTraits, getInitialTraits, getMaxFitness, getMaxScore, getMeanFitness, getMeanFitness, getMeanTraits, getMeanTraits, getMinFitness, getMinScore, getMonoScore, getNMean, getNMean, getStatus, getTraitData, init, isDensity, isMonomorphic, isTimeReversed, load, next, normalizeState, parse, restoreState, setAccuracy, setAdjustedDynamics, setDt, setInitialTraits, setInitialTraits, setTimeReversed, update, updateBest, updateBestResponse, updateEcology, updateImitate, updateImitateBetter, updateProportional, updateThermal

Methods inherited from class Model

debugStep, getCounter, getFitnessNameAt, getFixationData, getLogger, getMeanFitnessAt, getMeanName, getMeanNames, getMeanTraitAt, getMode, getNextHalt, getNSamples, getNSpecies, getNStatisticsFailed, getNStatisticsSamples, getScoreNameAt, getSpecies, getTime, getTimeRelax, getTimeStep, getTimeStop, getTraitNameAt, getType, hasConverged, initStatisticsFailed, initStatisticsSample, isConnected, isContinuous, isDE, isIBS, isODE, isPDE, isRelaxing, isSDE, isType, permitsDebugStep, permitsMode, permitsSampleStatistics, permitsUpdateStatistics, readStatisticsSample, relax, requestMode, resetStatisticsSample, setMode, setNSamples, setTimeRelax, setTimeStep, setTimeStop, useScheduling

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface CLOProvider

adjustCLO

Field Details

module

protected Module module

Convenience variable: module associated with this model (useful for single species).

Constructor Details

ODE

protected ODE(EvoLudo engine)

Constructs a new ODE solver taylored for the integration of asymmetric 2×2 games with environmental feedback.

Parameters:

engine - the pacemaker for running the model

Method Details

permitsTimeReversal

public boolean permitsTimeReversal()

Checks if time reversal is permitted. By default returns false. Only few models are capable of time reversal.

ODE and SDE models return true by default.

Ecological feedback is unable to deal with time reversal.

Overrides:

permitsTimeReversal in class ODE

Returns:

true if time reversal permissible.

See Also:

• Model.setTimeReversed(boolean)

getDerivatives

protected void getDerivatives(double t,
 double[] state,
 double[] fitness,
 double[] change)

Description copied from class: ODE

Calculate the rates of change for all species in state at time given the fitness fitness and returned in change. For replicator models the dynamics depends on the selected type of player updating, see PlayerUpdate.Type, while for modules with variable population sizes (density based or with vaccant 'space' (reproductive opportunities)) the fitness denotes the rate of reproduction moderated by the available 'space'.

IMPORTANT: parallel processing for PDE's in JRE requires this method to be thread safe.

Note: adding synchronized to this method would seem to make sense but this results in a deadlock for multiple threads in PDE's and JRE. However, apparently not needed as javascript and java yield the exact same results (after 15k generations!)

Overrides:

getDerivatives in class ODE

Parameters:

t - the time at which to calculate the derivative

state - the array of frequencies/densities denoting the state population

fitness - the array of fitness values of types in population

change - the array to return the rate of change of each type in the population

See Also:

• ODE.updateBest(Module, double[], double[], int, int, double[])
• ODE.updateBestResponse(Module, double[], double[], int, int, double[])
• ODE.updateEcology(Module, double[], double[], int, int, double[])
• ODE.updateImitate(Module, double[], double[], int, int, double[])
• ODE.updateThermal(Module, double[], double[], int, int, double[])