#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< double >	GetStdVecStateVariables ()

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< double >	GetStateVariables ()

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< double >	GetInitialConditions () 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< double >	ComputeDerivedQuantities (double time, const std::vector< double > &rState)

std::vector< double >	ComputeDerivedQuantitiesFromCurrentState (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< double >	mStateVariables

std::vector< double >	mParameters

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

pSolver	unused
pIntracellularStimulus	unused

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

tStart	unused
tEnd	unused

Reimplemented from AbstractCardiacCell.

Definition at line 62 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

time	unused
rY	unused
rDY	unused

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

pStateVariables unused

Returns: zero

Implements AbstractCardiacCellInterface.

Definition at line 57 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 66 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:

heart/src/odes/ionicmodels/FakeBathCell.hpp
heart/src/odes/ionicmodels/FakeBathCell.cpp

Public Member Functions

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation