com.mockturtlesolutions.snifflib.integration

Class Ode

java.lang.Object

com.mockturtlesolutions.snifflib.functions.AbstractFunction

com.mockturtlesolutions.snifflib.functions.MultiMultiFunction

com.mockturtlesolutions.snifflib.integration.Ode

All Implemented Interfaces:

NamedParameters, VectorValued

Direct Known Subclasses:

Exponential, Logistic

public abstract class Ode
extends MultiMultiFunction
implements NamedParameters, VectorValued

The getDeriv() and related methods do not accept input arguments. This intentional simplification was utilized so that more complicated calling sequences would not have to be implemented. In particular the inputs to a derivative RHS are logically divided into time and variable components. The inventiveness of function calls, vectorization of calls during Jacobian calculations etc is relegated to the ODE solver rather than requiring the user to implement various method invocations.

Field Summary

Fields

Modifier and Type	Field and Description
protected DblParamSet	Param
protected DblMatrix	T
protected java.util.HashMap	variableNames
protected DblMatrix	Y

Fields inherited from class com.mockturtlesolutions.snifflib.functions.AbstractFunction

domainDimension, rangeDimension

Constructor Summary

Constructors

Constructor and Description
Ode()

Method Summary

Methods

Modifier and Type	Method and Description
abstract java.lang.String	about() Gives some information about this ODE.
abstract int	dimension() Returns the number of intrinsic state variables.
int	domainDimension() The domain dimension is always equal to the number of intrinsic state variables plus one to account for time as a variable.
abstract OdeSet	getDefaultOptions() By providing a default OdeSet an ODE can provide for it's own default parameters.
abstract DblMatrix	getDeriv()
DblMatrix	getDerivChk() Returns the current derivative (or rhs) but also checks for reasonableness of the answer.
DblMatrix	getEvents()
DblMatrix	getJacobn()
DblMatrix	getJacobnPattern()
DblMatrix	getParam(java.lang.String name)
DblMatrix	getT()
DblMatrix	getValue()
DblMatrix	getValueAt(DblMatrix X) This is provided for compatability with the AbstractFunction.
DblMatrix	getValueAt(DblMatrix[] X) This is provided for compatability with the AbstractFunction.
DblMatrix	getVar(DblMatrix W, java.lang.String name) Gets the column of the input matrix according to the current variable name mapping.
DblMatrix	getVar(java.lang.String name) Gets the column of the Y field according to the current variable name mapping.
java.lang.String[]	getVariableNames() Gets the current variable names
DblMatrix	getY()
boolean	hasParameter(java.lang.String name)
java.lang.String[]	parameterSet()
int	rangeDimension() Returns the dimension of the lhs of a system of ODE's.
void	replaceParams(DblParamSet X)
void	setParam(java.lang.String name, DblMatrix value)
void	setT(DblMatrix T) This sets the T pointer of the model to the input DblMatrix.
void	setVar(DblMatrix W, java.lang.String name, DblMatrix V) Sets the column of the input matrix according to the current variable name mapping.
void	setVar(java.lang.String name, DblMatrix val) Change the current values of the state variables according to the current variable name mapping.
void	setVariableNames(java.lang.String[] s)
void	setY(DblMatrix Y) This sets the Y pointer of the model to the input DblMatrix.

Methods inherited from class com.mockturtlesolutions.snifflib.functions.MultiMultiFunction

plotOver

Methods inherited from class com.mockturtlesolutions.snifflib.functions.AbstractFunction

plotOver

Methods inherited from class java.lang.Object

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

Field Detail

Param

protected DblParamSet Param

T

protected DblMatrix T

Y

protected DblMatrix Y

variableNames

protected java.util.HashMap variableNames

Constructor Detail

Ode

public Ode()

Method Detail

getVar

public DblMatrix getVar(java.lang.String name)

Gets the column of the Y field according to the current variable name mapping.

getVar

public DblMatrix getVar(DblMatrix W,
               java.lang.String name)

Gets the column of the input matrix according to the current variable name mapping.

setVar

public void setVar(java.lang.String name,
          DblMatrix val)

Change the current values of the state variables according to the current variable name mapping. This is probably very rarely needed.

setVar

public void setVar(DblMatrix W,
          java.lang.String name,
          DblMatrix V)

Sets the column of the input matrix according to the current variable name mapping.

getVariableNames

public java.lang.String[] getVariableNames()

Gets the current variable names

setVariableNames

public void setVariableNames(java.lang.String[] s)

dimension

public abstract int dimension()

Returns the number of intrinsic state variables. Each equation in the system of differential equations corresponds to an intrinsic state variable. Note, there may be other variables such as forcing variables but these are not included.

rangeDimension

public int rangeDimension()

Returns the dimension of the lhs of a system of ODE's. The range dimension is always equal to the number of intrinsic state variables.

Overrides:

rangeDimension in class AbstractFunction

domainDimension

public int domainDimension()

The domain dimension is always equal to the number of intrinsic state variables plus one to account for time as a variable.

Overrides:

domainDimension in class AbstractFunction

setT

public void setT(DblMatrix T)

This sets the T pointer of the model to the input DblMatrix.

setY

public void setY(DblMatrix Y)

This sets the Y pointer of the model to the input DblMatrix.

getT

public DblMatrix getT()

getY

public DblMatrix getY()

hasParameter

public boolean hasParameter(java.lang.String name)

Specified by:

hasParameter in interface NamedParameters

getParam

public DblMatrix getParam(java.lang.String name)

Specified by:

getParam in interface NamedParameters

setParam

public void setParam(java.lang.String name,
            DblMatrix value)

Specified by:

setParam in interface NamedParameters

replaceParams

public void replaceParams(DblParamSet X)

Specified by:

replaceParams in interface NamedParameters

parameterSet

public java.lang.String[] parameterSet()

Specified by:

parameterSet in interface NamedParameters

getDerivChk

public DblMatrix getDerivChk()

Returns the current derivative (or rhs) but also checks for reasonableness of the answer.

getDeriv

public abstract DblMatrix getDeriv()

getJacobn

public DblMatrix getJacobn()

getJacobnPattern

public DblMatrix getJacobnPattern()

getEvents

public DblMatrix getEvents()

getValue

public DblMatrix getValue()

Specified by:

getValue in interface VectorValued

getValueAt

public DblMatrix getValueAt(DblMatrix X)

This is provided for compatability with the AbstractFunction. The first input is assumed to represent the time while the remaining values are assumed to be values of the state variables.

Specified by:

getValueAt in class AbstractFunction

getValueAt

public DblMatrix getValueAt(DblMatrix[] X)

This is provided for compatability with the AbstractFunction. The first input is assumed to represent the time while the remaining values are assumed to be values of the state variables.

Specified by:

getValueAt in class AbstractFunction

getDefaultOptions

public abstract OdeSet getDefaultOptions()

By providing a default OdeSet an ODE can provide for it's own default parameters. Users should over-ride this method to provide specific options.

about

public abstract java.lang.String about()

Gives some information about this ODE.