fern.simulation.algorithm

Class AbstractTauLeapingPropensityBoundSimulator

java.lang.Object

fern.simulation.Simulator

fern.simulation.algorithm.GillespieEnhanced

fern.simulation.algorithm.AbstractBaseTauLeaping

fern.simulation.algorithm.AbstractTauLeapingPropensityBoundSimulator

Direct Known Subclasses:

TauLeapingAbsoluteBoundSimulator, TauLeapingRelativeBoundSimulator

public abstract class AbstractTauLeapingPropensityBoundSimulator
extends AbstractBaseTauLeaping

There are some possibilities to bind the expected change of the propensities by a value epsilon in order to fulfill the leap condition. This base class provides mathematics for binding it directly by examining the actual propensities.

Daniel T. Gillespie, Approximate accelerated stochastic simulation of chemically reacting systems, Journal of chemical physics vol 115, nr 4 (2001); Cao et al., Efficient step size selection for the tau-leaping simulation method, Journal of chemical physics 124, 044109 (2006)

Author:

Florian Erhard

Nested Class Summary

Nested classes/interfaces inherited from class fern.simulation.Simulator

Simulator.FireType

Constructor Summary

Constructors

Constructor and Description
AbstractTauLeapingPropensityBoundSimulator(Network net)

Method Summary

Methods inherited from class fern.simulation.algorithm.AbstractBaseTauLeaping

getEpsilon, getLangevinThreshold, getName, getNCritical, getNumSimpleCalls, getUseSimpleFactor, isVerbose, performStep, setEpsilon, setLangevinThreshold, setNCritical, setNumSimpleCalls, setUseSimpleFactor, setVerbose

Methods inherited from class fern.simulation.algorithm.GillespieEnhanced

initialize, isEfficientlyAdaptSum, reinitialize, setAmount, setEfficientlyAdaptSum, setVolume

Methods inherited from class fern.simulation.Simulator

addObserver, getAmount, getNet, getNextThetaEvent, getPropensity, getPropensityCalculator, getTime, getVolume, initializePropensities, isInterpolateTheta, postRun, preRun, registerNewTheta, run, setInterpolateTheta, setStochasticSeed, start, start

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractTauLeapingPropensityBoundSimulator

public AbstractTauLeapingPropensityBoundSimulator(Network net)