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java.lang.Objectfern.simulation.Simulator
fern.simulation.algorithm.GillespieEnhanced
fern.simulation.algorithm.AbstractBaseTauLeaping
public abstract class AbstractBaseTauLeaping
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)
GillespieEnhanced
Nested Class Summary |
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Nested classes/interfaces inherited from class fern.simulation.Simulator |
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Simulator.FireType |
Constructor Summary | |
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AbstractBaseTauLeaping(Network net)
Create the simulator for a given network. |
Method Summary | |
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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 |
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 |
void |
setVerbose(boolean verbose)
Sets if each step is to print to stdout. |
Methods inherited from class fern.simulation.algorithm.GillespieEnhanced |
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initialize, isEfficientlyAdaptSum, reinitialize, setAmount, setEfficientlyAdaptSum, setVolume |
Methods inherited from class fern.simulation.Simulator |
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addObserver, getAmount, getNet, getNextThetaEvent, getPropensity, getPropensityCalculator, getTime, getVolume, isInterpolateTheta, registerNewTheta, setInterpolateTheta, start, start |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public AbstractBaseTauLeaping(Network net)
net
- the simulation networkMethod Detail |
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public void performStep(SimulationController control)
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.
performStep
in class GillespieEnhanced
control
- the simulators controllerpublic double getLangevinThreshold()
public void setLangevinThreshold(double langevinThreshold)
langevinThreshold
- the langevinThreshold to setpublic double getUseSimpleFactor()
public void setUseSimpleFactor(double useSimpleFactor)
useSimpleFactor
- the useSimpleFactor to setpublic int getNumSimpleCalls()
public void setNumSimpleCalls(int numSimpleCalls)
numSimpleCalls
- the numSimpleCalls to setpublic int getNCritical()
public void setNCritical(int critical)
critical
- the nCritical to setpublic double getEpsilon()
public void setEpsilon(double epsilon)
epsilon
- the epsilon to setpublic boolean isVerbose()
public void setVerbose(boolean verbose)
verbose
- verbosepublic String getName()
getName
in class GillespieEnhanced
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