fern.simulation.algorithm

Class GibsonBruckSimulator

java.lang.Object

fern.simulation.Simulator

fern.simulation.algorithm.GibsonBruckSimulator

public class GibsonBruckSimulator
extends Simulator

Implementation of the algorithm of Gibson and Bruck. They made two major improvements to Gillespie's Direct method (GillespieSimple):

1. using a dependency graph
2. using a indexed priority queue

The first describes, which propensities have to be recalculates after some reaction has fired, the latter puts an end to the time consuming search for the Direct which fires after one firing. The priority queue just yields the next reaction to fire (from which the name "Next reaction method" is derived). The priority queue holds for each reaction the time of its next firing.

In order to do that the perspective of viewing the simulators time has to be changed from relative to absolute. As a consequence, a new random number has to be drawn for each reaction whose propensity has changed by a firing. To avoid this inefficient permanent discarding of random numbers (drawing a random number is a time expensive operation) Gibson and Bruck developed a method for reusing unused random numbers.

One pitfall remains: What happens, when a propensity decreases to 0 and after a time ceases to be 0. Then the propensity from the pre-0 state can be reused which is tricky to implement. Some implementations (including Dizzy) just draw a new random number which is always valid but slow. Actually may these extra random numbers spoil the whole improvement of the indexed priority queue in certain networks and it would be faster to use the Direct method with the dependency graph (as in GillespieEnhanced ).

For reference see 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, GillespieEnhanced, DependencyGraph, IndexedPriorityQueue

Nested Class Summary

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

Simulator.FireType

Constructor Summary

Constructors

Constructor and Description
GibsonBruckSimulator(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
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	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

GibsonBruckSimulator

public GibsonBruckSimulator(Network net)

Method Detail

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

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

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

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)