Package org.simulator.math.odes

Class RungeKutta_EventSolver

java.lang.Object

org.simulator.math.odes.AbstractDESSolver

org.simulator.math.odes.RungeKutta_EventSolver

All Implemented Interfaces:

Serializable, Cloneable, DelayValueHolder, DESSolver

public class RungeKutta_EventSolver
extends AbstractDESSolver

Runge-Kutta method.

Since:

0.9

Version:

$Rev$

Author:

Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected double[]	kHelp	Helper variable for the k values.
protected double[][]	kVals	Stores temporary results for the fourth-order Runge-Kutta method.

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

clonedSolver, PROGRESS

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

CONTINUE, RESET_DERIVATIVES, RESET_STATE, STOP

Constructor Summary

Constructors

Constructor	Description
RungeKutta_EventSolver()	default constructor
RungeKutta_EventSolver(double stepSize)
RungeKutta_EventSolver(double stepSize, boolean nonnegative)
RungeKutta_EventSolver(RungeKutta_EventSolver rkEventSolver)	clone constructor

Method Summary

Modifier and Type	Method	Description
RungeKutta_EventSolver	clone()
double[]	computeChange(DESystem DES, double[] yTemp, double t, double h, double[] change, boolean steadyState)	Computes the change for a given system at the current time with the current setting for the integration step size.
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.
protected boolean	hasSolverEventProcessing()

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, setStepSize, setUnstableFlag, solve, solve, solve, solve, steadystate

Methods inherited from class java.lang.Object

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

Field Detail

kVals

protected transient double[][] kVals

Stores temporary results for the fourth-order Runge-Kutta method.

kHelp

protected transient double[] kHelp

Helper variable for the k values.

Constructor Detail

RungeKutta_EventSolver

public RungeKutta_EventSolver()

default constructor

RungeKutta_EventSolver

public RungeKutta_EventSolver(double stepSize)

Parameters:

stepSize -

RungeKutta_EventSolver

public RungeKutta_EventSolver(double stepSize,
                              boolean nonnegative)

Parameters:

stepSize -

nonnegative - the nonnegative flag of the super class

See Also:

AbstractDESSolver

RungeKutta_EventSolver

public RungeKutta_EventSolver(RungeKutta_EventSolver rkEventSolver)

clone constructor

Parameters:

rkEventSolver -

Method Detail

computeChange

public double[] computeChange(DESystem DES,
                              double[] yTemp,
                              double t,
                              double h,
                              double[] change,
                              boolean steadyState)
                       throws org.apache.commons.math.ode.DerivativeException

Description copied from class: AbstractDESSolver

Computes the change for a given system at the current time with the current setting for the integration step size.

Specified by:

computeChange in class AbstractDESSolver

Parameters:

DES - The system to be simulated.

yTemp - The current state of the system.

t - The current simulation time.

h - The current integration step size.

change - The vector for the resulting change of the system.

Returns:

The change.

Throws:

org.apache.commons.math.ode.DerivativeException

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.

clone

public RungeKutta_EventSolver clone()

Specified by:

clone in interface DESSolver

Specified by:

clone in class AbstractDESSolver

Returns:

the cloned solver

hasSolverEventProcessing

protected boolean hasSolverEventProcessing()

Specified by:

hasSolverEventProcessing in class AbstractDESSolver

Returns:

Does the solver do the event processing itself?

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