broadwick.stochastic.algorithms

Class GillespieSimple

java.lang.Object

broadwick.stochastic.StochasticSimulator

broadwick.stochastic.algorithms.GillespieSimple

public class GillespieSimple
extends StochasticSimulator

Implementation of Gillespie's Direct method. It is a simple Monte-Carlo algorithm which draws from a from Gillspie derived distribution a reaction that will fire and a time at which the reaction will fire.

For reference see Daniel T. Gillespie., A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions, J.Comp.Phys. 22, 403 (1976)

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	changed
private static RNG	GENERATOR

Fields inherited from class broadwick.stochastic.StochasticSimulator

reverseTime

Constructor Summary

Constructors

Constructor and Description
GillespieSimple(AmountManager amountManager, TransitionKernel transitionKernel) Implementation of Gillespie's Direct method.
GillespieSimple(AmountManager amountManager, TransitionKernel transitionKernel, boolean reverseTime) Implementation of Gillespie's Direct method.

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.
private SimulationEvent	directMCReaction() obtains a random (but following a specific distribution) reaction as described by the direct method in chapter 5A page 417ff.
protected double	directMCTau(double sum) obtains a random (but following a specific distribution) timestep as described by the direct method in chapter 5A page 417ff.
String	getName() Gets the name of the algorithm.
private boolean	isThetaEventInCurrentStep(double tau) Determine of there is a theta event in the current time step, taking into account possible reverse time jumps.
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.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

Field Detail

changed

private boolean changed

GENERATOR

private static final RNG GENERATOR

Constructor Detail

GillespieSimple

public GillespieSimple(AmountManager amountManager,
                       TransitionKernel transitionKernel)

Implementation of Gillespie's Direct method.

Parameters:

amountManager - the amount manager used in the simulator.

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

GillespieSimple

public GillespieSimple(AmountManager amountManager,
                       TransitionKernel transitionKernel,
                       boolean reverseTime)

Implementation of Gillespie's Direct method.

Parameters:

amountManager - the amount manager used in the simulator.

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

reverseTime - true if we wish to go backwards in time.

Method Detail

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.

isThetaEventInCurrentStep

private boolean isThetaEventInCurrentStep(double tau)

Determine of there is a theta event in the current time step, taking into account possible reverse time jumps.

Parameters:

tau - the time interval (will be negative for reverse time).

Returns:

true if a theta event is found.

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.

directMCReaction

private SimulationEvent directMCReaction()

obtains a random (but following a specific distribution) reaction as described by the direct method in chapter 5A page 417ff.

Returns:

the simulation event selected.

directMCTau

protected final double directMCTau(double sum)

obtains a random (but following a specific distribution) timestep as described by the direct method in chapter 5A page 417ff.

Parameters:

sum - sum of the propensities

Returns:

tau