AbstractOdeSolver (Snifflib API)

java.lang.Object
- java.lang.Thread
- - com.mockturtlesolutions.snifflib.integration.AbstractOdeSolver

All Implemented Interfaces:

Reportable, OdeSolution, java.lang.Runnable

Direct Known Subclasses:

AbstractOdeUpdater, DefaultOdeSolver
```
public abstract class AbstractOdeSolver
extends java.lang.Thread
implements OdeSolution
```
General Ode numerical integrator. This defualt solver implements the Euler method. In order to solve a particular ODE one should exTend the class by overriding the getDeriv method (public double getDeriv()). The following code shows how this is done. public class logistic exTends odesolve { public double getDeriv() { //Return dYdt = 0.1*Y return 1*(1-this.ynow/1)*this.ynow; } } Note to programmers: To implement a different numerical method one would override the update method (public void update()).

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

class AbstractOdeSolver.Interp1D
Interp1D is an inner class used to interpolate to TSPAN points.
- Nested classes/interfaces inherited from class java.lang.Thread
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Nested Classes
Modifier and Type	Class and Description
`class`	`AbstractOdeSolver.Interp1D` Interp1D is an inner class used to interpolate to TSPAN points.

Field Summary

Fields
Modifier and Type	Field and Description
`protected InterpolationQueue`	`interpQ`
`protected int`	`iter`
`protected Ode`	`ode`
`protected OdeSet`	`options`
`protected int`	`Progress`
`protected DefaultReporter`	`reporter`
`protected AbstractOdeUpdater`	`stepintegrator`
`protected DblMatrix`	`T`
`protected DblMatrix`	`tnew`
`protected DblMatrix`	`tnow`
`protected DblMatrix`	`Y`
`protected DblMatrix`	`ynew`
`protected DblMatrix`	`ynow`

Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors
Constructor and Description
`AbstractOdeSolver()` Sets up the default ODE problem.
`AbstractOdeSolver(AbstractOdeUpdater stepper)` Constructor that accepts an already constructed step updater.
`AbstractOdeSolver(Ode problem)`
`AbstractOdeSolver(Ode problem, OdeSet opts)`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`forwardTimePoints()` Sets the TimePoints options of this solver's step integrator the same as this solver's.
`DblMatrix`	`getDesiredAccuracy(DblMatrix Yold, DblMatrix Ynow, DblMatrix dT)` Standard methods for determining a desired accuracy for a solution of a single integration step.
`Ode`	`getOde()`
`OdeSet`	`getOptions()`
`Reporter`	`getReporter()`
`int`	`getStatus()`
`DblMatrix`	`getT()`
`DblMatrix`	`getY()`
`boolean`	`isRunning()`
`void`	`run()` Calls the solve method in a separate thread.
`void`	`setOde(Ode problem)`
`void`	`setOptions(OdeSet opts)`
`void`	`setReporter(Reporter F)`
`abstract void`	`solve()`
`void`	`trimToTimePoints()`

Methods inherited from class java.lang.Thread
activeCount, checkAccess, clone, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, toString, yield

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - options
```
protected OdeSet options
```
  - ode
```
protected Ode ode
```
  - iter
```
protected int iter
```
  - tnow
```
protected DblMatrix tnow
```
  - ynow
```
protected DblMatrix ynow
```
  - tnew
```
protected DblMatrix tnew
```
  - ynew
```
protected DblMatrix ynew
```
  - Progress
```
protected int Progress
```
  - T
```
protected DblMatrix T
```
  - Y
```
protected DblMatrix Y
```
  - reporter
```
protected DefaultReporter reporter
```
  - stepintegrator
```
protected AbstractOdeUpdater stepintegrator
```
  - interpQ
```
protected InterpolationQueue interpQ
```
- Constructor Detail
  - AbstractOdeSolver
```
public AbstractOdeSolver()
```
    Sets up the default ODE problem.
  - AbstractOdeSolver
```
public AbstractOdeSolver(Ode problem)
```
  - AbstractOdeSolver
```
public AbstractOdeSolver(Ode problem,
                 OdeSet opts)
```
  - AbstractOdeSolver
```
public AbstractOdeSolver(AbstractOdeUpdater stepper)
```
    Constructor that accepts an already constructed step updater.
- Method Detail
  - getDesiredAccuracy
```
public DblMatrix getDesiredAccuracy(DblMatrix Yold,
                           DblMatrix Ynow,
                           DblMatrix dT)
```
    Standard methods for determining a desired accuracy for a solution of a single integration step. The scalings are always multiplied by Options.RelTol. The value of OdeSet.Options.YscaleMethod will determine which method is used. To make the desired accuracies a more stringent component-wise error the result can be multiplied by the timestep (dT). Some care should be taken when doing this however, since it can affect the accuracy of new time step guesses. Interested users can refer to the discussion on p 712 of Press et al Numerical Recipes in Fortran. Usually the IntervalIntegrator being used will do the increment-wise error conversions and make the appropriate adjustments automatically without the user needing to intervene.
  - setReporter
```
public void setReporter(Reporter F)
```
  - getReporter
```
public Reporter getReporter()
```
  - getStatus
```
public int getStatus()
```
  - isRunning
```
public boolean isRunning()
```
  - solve
```
public abstract void solve()
                    throws SnifflibIntegrationException
```
    Specified by:
    
    solve in interface OdeSolution
    
    Throws:
    
    SnifflibIntegrationException
  - run
```
public void run()
```
    Calls the solve method in a separate thread.
    
    Specified by:
    
    run in interface java.lang.Runnable
    
    Overrides:
    
    run in class java.lang.Thread
  - forwardTimePoints
```
public void forwardTimePoints()
```
    Sets the TimePoints options of this solver's step integrator the same as this solver's. This allows the step integrator to make calls to trimToTimePoints so that only essential output are retained in working memory.
  - trimToTimePoints
```
public void trimToTimePoints()
```
  - getT
```
public DblMatrix getT()
```
    Specified by:
    
    getT in interface OdeSolution
  - getY
```
public DblMatrix getY()
```
    Specified by:
    
    getY in interface OdeSolution
  - setOde
```
public void setOde(Ode problem)
```
    Specified by:
    
    setOde in interface OdeSolution
  - getOde
```
public Ode getOde()
```
    Specified by:
    
    getOde in interface OdeSolution
  - setOptions
```
public void setOptions(OdeSet opts)
```
    Specified by:
    
    setOptions in interface OdeSolution
  - getOptions
```
public OdeSet getOptions()
```
    Specified by:
    
    getOptions in interface OdeSolution

Class AbstractOdeSolver

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Field Summary

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

options

ode

iter

tnow

ynow

tnew

ynew

Progress

T

Y

reporter

stepintegrator

interpQ

Constructor Detail

AbstractOdeSolver

AbstractOdeSolver

AbstractOdeSolver

AbstractOdeSolver

Method Detail

getDesiredAccuracy

setReporter

getReporter

getStatus

isRunning

solve

run

forwardTimePoints

trimToTimePoints

getT

getY

setOde

getOde

setOptions

getOptions