fern.simulation.algorithm
Class AbstractTauLeapingPropensityBoundSimulator

java.lang.Object
  extended by fern.simulation.Simulator
      extended by fern.simulation.algorithm.GillespieEnhanced
          extended by fern.simulation.algorithm.AbstractBaseTauLeaping
              extended by 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
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, isInterpolateTheta, registerNewTheta, setInterpolateTheta, 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)