fern.simulation.algorithm

Class TauLeapingAbsoluteBoundSimulator

java.lang.Object

fern.simulation.Simulator

fern.simulation.algorithm.GillespieEnhanced

fern.simulation.algorithm.AbstractBaseTauLeaping

fern.simulation.algorithm.AbstractTauLeapingPropensityBoundSimulator

fern.simulation.algorithm.TauLeapingAbsoluteBoundSimulator

public class TauLeapingAbsoluteBoundSimulator
extends AbstractTauLeapingPropensityBoundSimulator

There are some possibilities to bind the expected change of the propensities by a value epsilon in order to fulfill the leap condition. Here the expected change is bound to the sum of all 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
TauLeapingAbsoluteBoundSimulator(Network net)

Method Summary

Modifier and Type	Method and Description
String	getName() Returns the name of this simulator

Methods inherited from class fern.simulation.algorithm.AbstractBaseTauLeaping

getEpsilon, getLangevinThreshold, 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

TauLeapingAbsoluteBoundSimulator

public TauLeapingAbsoluteBoundSimulator(Network net)

Method Detail

getName

public String getName()

Description copied from class: AbstractBaseTauLeaping

Returns the name of this simulator

Overrides:

getName in class AbstractBaseTauLeaping

Returns:

simulator name