Package org.simulator.math.odes

Class GraggBulirschStoerSolver

java.lang.Object

org.simulator.math.odes.AbstractDESSolver

org.simulator.math.odes.AdaptiveStepsizeIntegrator

org.simulator.math.odes.FirstOrderSolver

org.simulator.math.odes.GraggBulirschStoerSolver

All Implemented Interfaces:

Serializable, Cloneable, DelayValueHolder, DESSolver

public class GraggBulirschStoerSolver
extends FirstOrderSolver

This class is a wrapper for the Gragg-Bulirsch-Stoer solver in the Apache Math Library.

Since:

0.9

Version:

$Rev$

Author:

Roland Keller

See Also:

Serialized Form

Field Summary

Fields inherited from class org.simulator.math.odes.AbstractDESSolver

clonedSolver, PROGRESS

Fields inherited from class org.simulator.math.odes.AdaptiveStepsizeIntegrator

absTol, relTol

Fields inherited from interface org.apache.commons.math.ode.events.EventHandler

CONTINUE, RESET_DERIVATIVES, RESET_STATE, STOP

Fields inherited from class org.simulator.math.odes.FirstOrderSolver

integrator

Constructor Summary

Constructors

Constructor	Description
GraggBulirschStoerSolver()	default constructor
GraggBulirschStoerSolver(double stepSize)
GraggBulirschStoerSolver(double stepSize, boolean nonnegative)
GraggBulirschStoerSolver(GraggBulirschStoerSolver solver)	clone constructor

Method Summary

Modifier and Type	Method	Description
GraggBulirschStoerSolver	clone()
protected void	createIntegrator()	initialization function of the integrator
int	getKiSAOterm()	For details about the Kinetic Simulation Algorithm Ontology (KiSAO) see http://biomodels.net/kisao/.
String	getName()	This gives a human-readable name of this solver that can be displayed in a graphical user interface.

Methods inherited from class org.simulator.math.odes.AbstractDESSolver

additionalResults, addPropertyChangeListener, computeDelayedValue, computeSteadyState, eventOccurred, firePropertyChange, g, getSerialversionuid, getStepSize, inBetweenSteps, initResultMatrix, initResultMatrix, initResultMatrix, isIncludeIntermediates, isNonnegative, isUnstable, processEvents, processEventsAndRules, processRules, removePropertyChangeListener, reset, resetState, setIncludeIntermediates, setNonnegative, setUnstableFlag, solve, solve, solve, solve, steadystate

Methods inherited from class org.simulator.math.odes.AdaptiveStepsizeIntegrator

getAbsTol, getRelTol, setAbsTol, setRelTol

Methods inherited from class org.simulator.math.odes.FirstOrderSolver

computeChange, getIntegrator, hasSolverEventProcessing, setStepSize

Methods inherited from class java.lang.Object

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

Constructor Detail

GraggBulirschStoerSolver

public GraggBulirschStoerSolver()

default constructor

GraggBulirschStoerSolver

public GraggBulirschStoerSolver(double stepSize)

Parameters:

stepSize -

GraggBulirschStoerSolver

public GraggBulirschStoerSolver(double stepSize,
                                boolean nonnegative)

Parameters:

stepSize - the nonnegative flag of the super class

nonnegative -

See Also:

AbstractDESSolver

GraggBulirschStoerSolver

public GraggBulirschStoerSolver(GraggBulirschStoerSolver solver)

clone constructor

Parameters:

solver -

Method Detail

clone

public GraggBulirschStoerSolver clone()

Specified by:

clone in interface DESSolver

Specified by:

clone in class FirstOrderSolver

Returns:

the cloned solver

createIntegrator

protected void createIntegrator()

Description copied from class: FirstOrderSolver

initialization function of the integrator

Specified by:

createIntegrator in class FirstOrderSolver

getName

public String getName()

Description copied from class: AbstractDESSolver

This gives a human-readable name of this solver that can be displayed in a graphical user interface.

Specified by:

getName in class AbstractDESSolver

Returns:

A name that describes the underlying algorithm.

getKiSAOterm

public int getKiSAOterm()

Description copied from interface: DESSolver

For details about the Kinetic Simulation Algorithm Ontology (KiSAO) see http://biomodels.net/kisao/.

Returns:

the KiSAO term of the algorithm