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
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.Simulator |
addObserver, getAmount, getNet, getNextThetaEvent, getPropensity, getPropensityCalculator, getTime, getVolume, isInterpolateTheta, registerNewTheta, setInterpolateTheta, start, start |
AbstractTauLeapingPropensityBoundSimulator
public AbstractTauLeapingPropensityBoundSimulator(Network net)