Chaste  Release::2018.1
FakeBathCell Class Reference

#include <FakeBathCell.hpp>

+ Inheritance diagram for FakeBathCell:
+ Collaboration diagram for FakeBathCell:

Public Member Functions

 FakeBathCell (boost::shared_ptr< AbstractIvpOdeSolver > pSolver, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
 
 ~FakeBathCell ()
 
void EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)
 
double GetIIonic (const std::vector< double > *pStateVariables=NULL)
 
void ComputeExceptVoltage (double tStart, double tEnd)
 
double GetIntracellularCalciumConcentration ()
 
- Public Member Functions inherited from AbstractCardiacCell
 AbstractCardiacCell (boost::shared_ptr< AbstractIvpOdeSolver > pOdeSolver, unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
 
virtual ~AbstractCardiacCell ()
 
void Init ()
 
void SetTimestep (double dt)
 
virtual void SolveAndUpdateState (double tStart, double tEnd)
 
virtual OdeSolution Compute (double tStart, double tEnd, double tSamp=0.0)
 
void SetVoltage (double voltage)
 
double GetVoltage ()
 
unsigned GetNumberOfStateVariables () const
 
unsigned GetNumberOfParameters () const
 
std::vector< doubleGetStdVecStateVariables ()
 
const std::vector< std::string > & rGetStateVariableNames () const
 
void SetStateVariables (const std::vector< double > &rVariables)
 
void SetStateVariable (unsigned index, double newValue)
 
void SetStateVariable (const std::string &rName, double newValue)
 
double GetAnyVariable (const std::string &rName, double time=0.0)
 
double GetParameter (const std::string &rParameterName)
 
double GetParameter (unsigned parameterIndex)
 
void SetParameter (const std::string &rParameterName, double value)
 
virtual void SetState (CellModelState state)
 
virtual void SetSlowValues (const std::vector< double > &rSlowValues)
 
virtual void GetSlowValues (std::vector< double > &rSlowValues)
 
virtual bool IsFastOnly ()
 
virtual void AdjustOutOfRangeSlowValues (std::vector< double > &rSlowValues)
 
virtual unsigned GetNumSlowValues ()
 
- Public Member Functions inherited from AbstractCardiacCellInterface
 AbstractCardiacCellInterface (boost::shared_ptr< AbstractIvpOdeSolver > pOdeSolver, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
 
virtual ~AbstractCardiacCellInterface ()
 
unsigned GetVoltageIndex ()
 
void SetStimulusFunction (boost::shared_ptr< AbstractStimulusFunction > pStimulus)
 
double GetStimulus (double time)
 
void SetIntracellularStimulusFunction (boost::shared_ptr< AbstractStimulusFunction > pStimulus)
 
double GetIntracellularStimulus (double time)
 
double GetIntracellularAreaStimulus (double time)
 
void SetUsedInTissueSimulation (bool tissue=true)
 
virtual boost::shared_ptr
< RegularStimulus
UseCellMLDefaultStimulus ()
 
bool HasCellMLDefaultStimulus ()
 
virtual
AbstractLookupTableCollection
GetLookupTableCollection ()
 
boost::shared_ptr
< AbstractStimulusFunction
GetStimulusFunction ()
 
const boost::shared_ptr
< AbstractStimulusFunction
GetStimulusFunction () const
 
const boost::shared_ptr
< AbstractIvpOdeSolver
GetSolver () const
 
void SetSolver (boost::shared_ptr< AbstractIvpOdeSolver > pSolver)
 
virtual void SetVoltageDerivativeToZero (bool clamp=true)
 
void SetFixedVoltage (double voltage)
 
virtual void SetStretch (double stretch)
 
- Public Member Functions inherited from AbstractOdeSystem
 AbstractOdeSystem (unsigned numberOfStateVariables)
 
virtual ~AbstractOdeSystem ()
 
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
AbstractOdeSystemInformation
GetSystemInformation () 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
 

Private Member Functions

template<class Archive >
void serialize (Archive &archive, const unsigned int version)
 

Friends

class boost::serialization::access
 

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 AbstractCardiacCell
double mDt
 
- Protected Attributes inherited from AbstractCardiacCellInterface
unsigned mVoltageIndex
 
boost::shared_ptr
< AbstractIvpOdeSolver
mpOdeSolver
 
boost::shared_ptr
< AbstractStimulusFunction
mpIntracellularStimulus
 
bool mSetVoltageDerivativeToZero
 
bool mIsUsedInTissue
 
bool mHasDefaultStimulusFromCellML
 
double mFixedVoltage
 
- 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
< AbstractOdeSystemInformation
mpSystemInfo
 

Detailed Description

This class represents a fake cell for use within the bath of a bidomain simulation.

Note
Note that only a portion of the normal functionality of a cardiac cell is actually redefined in this class. If further calls to cardiac cells are later added to the simulation process, additional overrides may need to be added here.

Definition at line 52 of file FakeBathCell.hpp.

Constructor & Destructor Documentation

FakeBathCell::FakeBathCell ( boost::shared_ptr< AbstractIvpOdeSolver pSolver,
boost::shared_ptr< AbstractStimulusFunction pIntracellularStimulus 
)

Constructor uses the same signature as normal cells, for convenience.

Parameters
pSolverunused
pIntracellularStimulusunused

Definition at line 39 of file FakeBathCell.cpp.

References AbstractCardiacCell::Init(), OdeSystemInformation< ODE_SYSTEM >::Instance(), and AbstractUntemplatedParameterisedSystem::mpSystemInfo.

FakeBathCell::~FakeBathCell ( )

Destructor; does nothing.

Definition at line 47 of file FakeBathCell.cpp.

Member Function Documentation

void FakeBathCell::ComputeExceptVoltage ( double  tStart,
double  tEnd 
)
virtual

There isn't really a cell here, so we override this method to do nothing.

Parameters
tStartunused
tEndunused

Reimplemented from AbstractCardiacCell.

Definition at line 63 of file FakeBathCell.cpp.

void FakeBathCell::EvaluateYDerivatives ( double  time,
const std::vector< double > &  rY,
std::vector< double > &  rDY 
)
virtual

This method is pure in a base class, so we need it, but we never use it. It has an empty body.

Parameters
timeunused
rYunused
rDYunused

Implements AbstractOdeSystem.

Definition at line 52 of file FakeBathCell.cpp.

References NEVER_REACHED.

double FakeBathCell::GetIIonic ( const std::vector< double > *  pStateVariables = NULL)
virtual

Fake cells have no transmembrane currents, so this method always returns 0.

Parameters
pStateVariablesunused
Returns
zero

Implements AbstractCardiacCellInterface.

Definition at line 58 of file FakeBathCell.cpp.

double FakeBathCell::GetIntracellularCalciumConcentration ( )
virtual

There is really no calcium here, so we override this method to return a dummy value (0) Implementing this with a dummy implementation is needed by mechanics

Returns
always zero

Reimplemented from AbstractCardiacCellInterface.

Definition at line 67 of file FakeBathCell.cpp.

template<class Archive >
void FakeBathCell::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

Archive this cell. Just calls the base class version.

Parameters
archive
version

Definition at line 64 of file FakeBathCell.hpp.

References AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables.

Friends And Related Function Documentation

friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 56 of file FakeBathCell.hpp.


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