broadwick.stochastic.algorithms

Class TauLeaping

java.lang.Object

broadwick.stochastic.StochasticSimulator

broadwick.stochastic.algorithms.AbstractTauLeapingBase

broadwick.stochastic.algorithms.TauLeaping

public class TauLeaping
extends AbstractTauLeapingBase

Implementation of the tau-leaping algorithm that makes an approximation to the stochastic ODE by picking a reasonable time-step and then performing all the reactions that occur in this step. It is faster than the Gillespie algorithm for large population sizes.

Field Summary

Fields inherited from class broadwick.stochastic.algorithms.AbstractTauLeapingBase

GENERATOR

Fields inherited from class broadwick.stochastic.StochasticSimulator

reverseTime

Constructor Summary

Constructors

Constructor and Description
TauLeaping(AmountManager amountManager, TransitionKernel transitionKernel) Create the tau-leaping object.

Method Summary

Modifier and Type	Method and Description
private double	calculateRTotal() Calculate the h's described in (14) page 413 and the sum a (26) page 418.
String	getName() Gets the name of the algorithm.
void	performStep() Performs one simulation step.
void	reinitialize() Reset propensities when a event has been executed.
void	setRngSeed(int seed) Seed the RNG if required.

Methods inherited from class broadwick.stochastic.algorithms.AbstractTauLeapingBase

isThetaEventInCurrentStep, updateStates

Methods inherited from class broadwick.stochastic.StochasticSimulator

addObserver, doEvent, doEvent, doThetaEvent, getDefaultObserver, getNextThetaEventTime, init, registerNewTheta, run, run

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TauLeaping

public TauLeaping(AmountManager amountManager,
                  TransitionKernel transitionKernel)

Create the tau-leaping object.

Parameters:

amountManager - the amount manager used in the simulator.

transitionKernel - the transition kernel to be used with the stochastic solver.

Method Detail

getName

public final String getName()

Description copied from class: StochasticSimulator

Gets the name of the algorithm.

Specified by:

getName in class StochasticSimulator

Returns:

name of the algorithm

setRngSeed

public final void setRngSeed(int seed)

Description copied from class: StochasticSimulator

Seed the RNG if required.

Specified by:

setRngSeed in class StochasticSimulator

Parameters:

seed - the RNG seed.

reinitialize

public final void reinitialize()

Description copied from class: StochasticSimulator

Reset propensities when a event has been executed.

Specified by:

reinitialize in class StochasticSimulator

performStep

public final void performStep()

Description copied from class: StochasticSimulator

Performs one simulation step. Between steps the terminating condition is checked. The simulators controller is passed, if an extending class wants to check it within one step. Implementing algorithms cannot be sure that the propensities are correct at the beginning of a step (e.g. if the volume changed). They should override Simulator#setAmount(int, long) and Simulator#setVolume(double) if they need correct values!

Specified by:

performStep in class StochasticSimulator

calculateRTotal

private double calculateRTotal()

Calculate the h's described in (14) page 413 and the sum a (26) page 418.

Returns:

the sum of the probabilities of all events.