Chaste  Release::2017.1
AbstractOdeSystemWithAnalyticJacobian Class Referenceabstract

#include <AbstractOdeSystemWithAnalyticJacobian.hpp>

+ Inheritance diagram for AbstractOdeSystemWithAnalyticJacobian:
+ Collaboration diagram for AbstractOdeSystemWithAnalyticJacobian:

Public Member Functions

 AbstractOdeSystemWithAnalyticJacobian (unsigned numberOfStateVariables=0)
 
virtual void AnalyticJacobian (const std::vector< double > &rSolutionGuess, double **jacobian, double time, double timeStep)=0
 
- Public Member Functions inherited from AbstractOdeSystem
 AbstractOdeSystem (unsigned numberOfStateVariables)
 
virtual ~AbstractOdeSystem ()
 
virtual void EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)=0
 
virtual bool CalculateStoppingEvent (double time, const std::vector< double > &rY)
 
virtual double CalculateRootFunction (double time, const std::vector< double > &rY)
 
bool GetUseAnalyticJacobian ()
 
const std::vector< double > & rGetConstStateVariables () const
 
- Public Member Functions inherited from AbstractParameterisedSystem< std::vector< double > >
 AbstractParameterisedSystem (unsigned numberOfStateVariables)
 
std::vector< double > & rGetStateVariables ()
 
std::vector< doubleGetStateVariables ()
 
void SetStateVariables (const std::vector< double > &rStateVariables)
 
double GetStateVariable (unsigned index) const
 
double GetStateVariable (const std::string &rName) const
 
void SetStateVariable (unsigned index, double newValue)
 
void SetStateVariable (const std::string &rName, double newValue)
 
virtual void VerifyStateVariables ()
 
void SetDefaultInitialConditions (const std::vector< double > &rInitialConditions)
 
void SetDefaultInitialCondition (unsigned index, double initialCondition)
 
std::vector< doubleGetInitialConditions () const
 
void ResetToInitialConditions ()
 
double GetParameter (unsigned index) const
 
double GetParameter (const std::string &rName) const
 
void SetParameter (const std::string &rName, double value)
 
void SetParameter (unsigned index, double value)
 
double GetAnyVariable (unsigned index, double time=0.0, std::vector< double > *pDerivedQuantities=NULL)
 
double GetAnyVariable (const std::string &rName, double time=0.0, std::vector< double > *pDerivedQuantities=NULL)
 
void SetAnyVariable (unsigned index, double value)
 
void SetAnyVariable (const std::string &rName, double value)
 
virtual std::vector< doubleComputeDerivedQuantities (double time, const std::vector< double > &rState)
 
std::vector< doubleComputeDerivedQuantitiesFromCurrentState (double time)
 
- Public Member Functions inherited from AbstractUntemplatedParameterisedSystem
 AbstractUntemplatedParameterisedSystem (unsigned numberOfStateVariables)
 
virtual ~AbstractUntemplatedParameterisedSystem ()
 
boost::shared_ptr< const AbstractOdeSystemInformationGetSystemInformation () const
 
std::string GetSystemName () const
 
unsigned GetNumberOfAttributes () const
 
bool HasAttribute (const std::string &rName) const
 
double GetAttribute (const std::string &rName) const
 
unsigned GetNumberOfStateVariables () const
 
const std::vector< std::string > & rGetStateVariableNames () const
 
const std::vector< std::string > & rGetStateVariableUnits () const
 
unsigned GetStateVariableIndex (const std::string &rName) const
 
bool HasStateVariable (const std::string &rName) const
 
std::string GetStateVariableUnits (unsigned index) const
 
unsigned GetNumberOfParameters () const
 
const std::vector< std::string > & rGetParameterNames () const
 
const std::vector< std::string > & rGetParameterUnits () const
 
unsigned GetParameterIndex (const std::string &rName) const
 
bool HasParameter (const std::string &rName) const
 
std::string GetParameterUnits (unsigned index) const
 
unsigned GetNumberOfDerivedQuantities () const
 
const std::vector< std::string > & rGetDerivedQuantityNames () const
 
const std::vector< std::string > & rGetDerivedQuantityUnits () const
 
unsigned GetDerivedQuantityIndex (const std::string &rName) const
 
bool HasDerivedQuantity (const std::string &rName) const
 
std::string GetDerivedQuantityUnits (unsigned index) const
 
unsigned GetAnyVariableIndex (const std::string &rName) const
 
bool HasAnyVariable (const std::string &rName) const
 
std::string GetAnyVariableUnits (unsigned index) const
 
std::string GetAnyVariableUnits (const std::string &rName) const
 

Additional Inherited Members

- Protected Member Functions inherited from AbstractParameterisedSystem< std::vector< double > >
std::string DumpState (const std::string &rMessage)
 
std::string DumpState (const std::string &rMessage, std::vector< double >Y)
 
std::string DumpState (const std::string &rMessage, std::vector< double >Y, double time)
 
void CheckParametersOnLoad (const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames)
 
- Protected Attributes inherited from AbstractOdeSystem
bool mUseAnalyticJacobian
 
- Protected Attributes inherited from AbstractParameterisedSystem< std::vector< double > >
std::vector< doublemStateVariables
 
std::vector< doublemParameters
 
- Protected Attributes inherited from AbstractUntemplatedParameterisedSystem
unsigned mNumberOfStateVariables
 
boost::shared_ptr< AbstractOdeSystemInformationmpSystemInfo
 

Detailed Description

Abstract analytic Jacobian class.

Represents an ODE system with an analytic Jacobian available, which can be computed using the method AnalyticJacobian.

Definition at line 49 of file AbstractOdeSystemWithAnalyticJacobian.hpp.

Constructor & Destructor Documentation

AbstractOdeSystemWithAnalyticJacobian::AbstractOdeSystemWithAnalyticJacobian ( unsigned  numberOfStateVariables = 0)
inline

Constructor.

Parameters
numberOfStateVariablesthe number of state variables in the ODE system (defaults to 0)

Definition at line 58 of file AbstractOdeSystemWithAnalyticJacobian.hpp.

References AnalyticJacobian(), and AbstractOdeSystem::mUseAnalyticJacobian.

Member Function Documentation

virtual void AbstractOdeSystemWithAnalyticJacobian::AnalyticJacobian ( const std::vector< double > &  rSolutionGuess,
double **  jacobian,
double  time,
double  timeStep 
)
pure virtual

Compute the analytic Jacobian matrix of the ODE system.

Parameters
rSolutionGuessthe current guess at the solution for this time step
jacobianwill be filled in with the Jacobian matrix entries
timethe current simulation time
timeStepthe time step in use by the integrator at present

Implemented in TysonNovak2001OdeSystem.

Referenced by AbstractOdeSystemWithAnalyticJacobian(), and BackwardEulerIvpOdeSolver::ComputeJacobian().


The documentation for this class was generated from the following file: