fern.simulation.algorithm
Class TauLeapingSpeciesPopulationBoundSimulator

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.TauLeapingSpeciesPopulationBoundSimulator

public class TauLeapingSpeciesPopulationBoundSimulator
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. Here it is bound indirectly by the reactant species of each reaction which gives the same leaps in a more efficient manner.

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
TauLeapingSpeciesPopulationBoundSimulator(Network net)
           
 
Method Summary
 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, isInterpolateTheta, registerNewTheta, setInterpolateTheta, start, start
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

TauLeapingSpeciesPopulationBoundSimulator

public TauLeapingSpeciesPopulationBoundSimulator(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