fern.simulation.algorithm

Class AbstractBaseTauLeaping

java.lang.Object

fern.simulation.Simulator

fern.simulation.algorithm.GillespieEnhanced

fern.simulation.algorithm.AbstractBaseTauLeaping

Direct Known Subclasses:

AbstractTauLeapingPropensityBoundSimulator, TauLeapingSpeciesPopulationBoundSimulator

public abstract class AbstractBaseTauLeaping
extends GillespieEnhanced

Base class for all tau leaping procedures (which are different in the methods choosing the timestep candidates for critical and noncritical reactions). It extends GillespieEnhanced because it uses the SSP algorithm, when the timestep candidate is to small.

Each tau leaping algorithm only works with an AbstractKineticConstantPropensityCalculator and only if the highest order of a reaction is maximal 3.

For references see 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

See Also:

GillespieEnhanced

Nested Class Summary

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

Simulator.FireType

Constructor Summary

Constructors

Constructor and Description
AbstractBaseTauLeaping(Network net) Create the simulator for a given network.

Method Summary

Modifier and Type	Method and Description
double	getEpsilon() The epsilon is an error control parameter and bounds the expected change of the propensity functions by epsilon * a_sum.
double	getLangevinThreshold() The Langevin threshold determines, when the normal distribution is used as an approximation for the poisson distribution.
String	getName() Returns the name of this simulator
int	getNCritical() The nCritical determines, when a reaction is called critical.
int	getNumSimpleCalls() The numSimpleCalls determines, how often the SSA is called, when tau leaping is abandoned.
double	getUseSimpleFactor() The useSimpleFactor determines, when the tau leaping is abandoned and the SSA method is used (if tau < useSimpleFactor / a_0).
boolean	isVerbose() Gets if each step is to print to stdout.
void	performStep(SimulationController control) Performs a tau leaping step.
void	setEpsilon(double epsilon) The epsilon is an error control parameter and bounds the expected change of the propensity functions by epsilon * a_sum.
void	setLangevinThreshold(double langevinThreshold) The Langevin threshold determines, when the normal distribution is used as an approximation for the poisson distribution.
void	setNCritical(int critical) The nCritical determines, when a reaction is called critical.
void	setNumSimpleCalls(int numSimpleCalls) The numSimpleCalls determines, how often the SSA is called, when tau leaping is abandoned.
void	setUseSimpleFactor(double useSimpleFactor) The useSimpleFactor determines, when the tau leaping is abandoned and the SSA method is used (if tau < useSimpleFactor / a_0).The default value is 10.
void	setVerbose(boolean verbose) Sets if each step is to print to stdout.

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

AbstractBaseTauLeaping

public AbstractBaseTauLeaping(Network net)

Create the simulator for a given network.

Parameters:

net - the simulation network

Method Detail

performStep

public void performStep(SimulationController control)

Performs a tau leaping step. First, critical reactions (that could exhaust one of its reactants) are idenfied. The threshold for criticals can be controlled by the field nCriticals. Second, a candidate timestep is chosen for noncritical reactions. If this timestep is to little (controlled by useSimpleFactor), numSimpleCalls steps from the SSP-Algorithm GillespieEnhanced are perform. Otherwise a second timestep candidate is drawn for the criticals (such that only one critical reaction is firing and only once in this leap). The smaller candidate is then used as tau.

Overrides:

performStep in class GillespieEnhanced

Parameters:

control - the simulators controller

getLangevinThreshold

public double getLangevinThreshold()

The Langevin threshold determines, when the normal distribution is used as an approximation for the poisson distribution. The default value is Infinity (no approximation).

Returns:

the langevinThreshold

setLangevinThreshold

public void setLangevinThreshold(double langevinThreshold)

The Langevin threshold determines, when the normal distribution is used as an approximation for the poisson distribution. The default value is Infinity (no approximation).

Parameters:

langevinThreshold - the langevinThreshold to set

getUseSimpleFactor

public double getUseSimpleFactor()

The useSimpleFactor determines, when the tau leaping is abandoned and the SSA method is used (if tau < useSimpleFactor / a_0). The default value is 10.

Returns:

the useSimpleFactor

setUseSimpleFactor

public void setUseSimpleFactor(double useSimpleFactor)

The useSimpleFactor determines, when the tau leaping is abandoned and the SSA method is used (if tau < useSimpleFactor / a_0).The default value is 10.

Parameters:

useSimpleFactor - the useSimpleFactor to set

getNumSimpleCalls

public int getNumSimpleCalls()

The numSimpleCalls determines, how often the SSA is called, when tau leaping is abandoned. The default value is 100.

Returns:

the numSimpleCalls

setNumSimpleCalls

public void setNumSimpleCalls(int numSimpleCalls)

The numSimpleCalls determines, how often the SSA is called, when tau leaping is abandoned. The default value is 100.

Parameters:

numSimpleCalls - the numSimpleCalls to set

getNCritical

public int getNCritical()

The nCritical determines, when a reaction is called critical. It is critical, when the maximum number, a reaction can fire before exhausting one of its reactants is less than nCritical. The default value is 10.

Returns:

the nCritical

setNCritical

public void setNCritical(int critical)

The nCritical determines, when a reaction is called critical. It is critical, when the maximum number, a reaction can fire before exhausting one of its reactants is less than nCritical. The default value is 10.

Parameters:

critical - the nCritical to set

getEpsilon

public double getEpsilon()

The epsilon is an error control parameter and bounds the expected change of the propensity functions by epsilon * a_sum. It has to be 0 < epsilon << 1. The default value is 0.03.

Returns:

the epsilon

setEpsilon

public void setEpsilon(double epsilon)

The epsilon is an error control parameter and bounds the expected change of the propensity functions by epsilon * a_sum. It has to be 0 < epsilon << 1. The default value is 0.03.

Parameters:

epsilon - the epsilon to set

isVerbose

public boolean isVerbose()

Gets if each step is to print to stdout.

Returns:

verbose

setVerbose

public void setVerbose(boolean verbose)

Sets if each step is to print to stdout.

Parameters:

verbose - verbose

getName

public String getName()

Returns the name of this simulator

Overrides:

getName in class GillespieEnhanced

Returns:

simulator name