fern.simulation.algorithm

Class GillespieEnhanced

java.lang.Object

fern.simulation.Simulator

fern.simulation.algorithm.GillespieEnhanced

Direct Known Subclasses:

AbstractBaseTauLeaping, CompositionRejection

public class GillespieEnhanced
extends Simulator

This is an enhanced version of the original Direct method developed by Gillespie. Just like the algorithm of Gibson and Bruck it uses a dependency graph to know what propensities have to be recalculated.

Take care with the option efficientlyAdaptSum: if it is true, it is possible that the sum become numerically unstable and the simulation fails, but especially for sparse networks it should be much more efficient.

For references see Daniel T. Gillespie., A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions, J.Comp.Phys. 22, 403 (1976) and M.A.Gibson and J.Bruck, Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels, J.Phys.Chem.A., Vol 104, no 9, 2000

Author:

Florian Erhard

See Also:

GillespieSimple, DependencyGraph

Nested Class Summary

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

Simulator.FireType

Constructor Summary

Constructors

Constructor and Description
GillespieEnhanced(Network net)

Method Summary

Modifier and Type	Method and Description
String	getName() Gets the name of the algorithm.
void	initialize() Initializes the algorithm: set t=0reset the AmountManagerrecalculate the propensities Gets called at the very beginning of start
boolean	isEfficientlyAdaptSum()
void	performStep(SimulationController control) Performs one simulation step.
void	reinitialize() Reset propensities when a event has been executed.
void	setAmount(int species, long amount) Sets the amount of the given species.
void	setEfficientlyAdaptSum(boolean efficientlyAdaptSum)
void	setVolume(double volume) Sets the volume of the reaction network.

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

GillespieEnhanced

public GillespieEnhanced(Network net)

Method Detail

initialize

public void initialize()

Description copied from class: Simulator

Initializes the algorithm:

• set t=0
• reset the AmountManager
• recalculate the propensities

Gets called at the very beginning of start

Overrides:

initialize in class Simulator

reinitialize

public void reinitialize()

Description copied from class: Simulator

Reset propensities when a event has been executed.

Specified by:

reinitialize in class Simulator

performStep

public void performStep(SimulationController control)

Description copied from class: Simulator

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 Simulator

Parameters:

control - the simulators controller

setVolume

public void setVolume(double volume)

Description copied from class: Simulator

Sets the volume of the reaction network.

Overrides:

setVolume in class Simulator

Parameters:

volume - the volume

setAmount

public void setAmount(int species,
                      long amount)

Description copied from class: Simulator

Sets the amount of the given species. Propensities have to be recalculated!

Overrides:

setAmount in class Simulator

Parameters:

species - species index

amount - amount of species

See Also:

AmountManager.setAmount(int, long)

getName

public String getName()

Description copied from class: Simulator

Gets the name of the algorithm.

Specified by:

getName in class Simulator

Returns:

name of the algorithm

isEfficientlyAdaptSum

public boolean isEfficientlyAdaptSum()

setEfficientlyAdaptSum

public void setEfficientlyAdaptSum(boolean efficientlyAdaptSum)