#include <AbstractGeneralizedRushLarsenCardiacCell.hpp>

Inheritance diagram for AbstractGeneralizedRushLarsenCardiacCell:

Collaboration diagram for AbstractGeneralizedRushLarsenCardiacCell:

Public Member Functions
	AbstractGeneralizedRushLarsenCardiacCell (unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)

virtual	~AbstractGeneralizedRushLarsenCardiacCell ()

OdeSolution	Compute (double tStart, double tEnd, double tSamp=0.0)

void	ComputeExceptVoltage (double tStart, double tEnd)

void	SolveAndUpdateState (double tStart, double tEnd)

bool	HasAnalyticJacobian () const

void	ForceUseOfNumericalJacobian (bool useNumericalJacobian=true)

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)

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 ()

virtual double	GetIIonic (const std::vector< double > *pStateVariables=NULL)=0

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)

virtual double	GetIntracellularCalciumConcentration ()

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

Protected Member Functions
virtual void	ComputeOneStepExceptVoltage (double time)=0

virtual void	UpdateTransmembranePotential (double time)=0

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
std::vector< double >	mPartialF

std::vector< double >	mEvalF

std::vector< double >	mYInit

bool	mHasAnalyticJacobian

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

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

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

Friends
class	boost::serialization::access

Detailed Description

This is the base class for cardiac cells solved using the GRL methods (GRL1 and GRL2). Modified from AbstractRushLarsenCardiacCell.hpp

Definition at line 59 of file AbstractGeneralizedRushLarsenCardiacCell.hpp.

Constructor & Destructor Documentation

AbstractGeneralizedRushLarsenCardiacCell::AbstractGeneralizedRushLarsenCardiacCell	(	unsigned	numberOfStateVariables,
		unsigned	voltageIndex,
		boost::shared_ptr< AbstractStimulusFunction >	pIntracellularStimulus
	)

Standard constructor for a cell.

Parameters

numberOfStateVariables	the size of the ODE system
voltageIndex	the index of the variable representing the transmembrane potential within the state variable vector
pIntracellularStimulus	the intracellular stimulus function

Some notes for future reference:

It's a pity that inheriting from AbstractCardiacCell forces us to store a null pointer (for the unused ODE solver) in every instance. We may want to revisit this design decision at a later date.

Definition at line 53 of file AbstractGeneralizedRushLarsenCardiacCell.cpp.

References mEvalF, mPartialF, and mYInit.

AbstractGeneralizedRushLarsenCardiacCell::~AbstractGeneralizedRushLarsenCardiacCell ( )

virtual

Virtual destructor

Definition at line 67 of file AbstractGeneralizedRushLarsenCardiacCell.cpp.

Member Function Documentation

OdeSolution AbstractGeneralizedRushLarsenCardiacCell::Compute	(	double	tStart,
		double	tEnd,
		double	tSamp = `0.0`
	)

virtual

Simulates this cell's behaviour between the time interval [tStart, tEnd], with timestep mDt.

The length of the time interval must be a multiple of the timestep.

Parameters

tStart	beginning of the time interval to simulate
tEnd	end of the time interval to simulate
tSamp	sampling interval for returned results (defaults to mDt)

Returns: the values of each state variable, at intervals of tSamp.

Reimplemented from AbstractCardiacCell.

Definition at line 70 of file AbstractGeneralizedRushLarsenCardiacCell.cpp.

References ComputeOneStepExceptVoltage(), AbstractCardiacCellInterface::GetVoltageIndex(), AbstractCardiacCell::mDt, AbstractUntemplatedParameterisedSystem::mpSystemInfo, OdeSolution::rGetSolutions(), AbstractParameterisedSystem< std::vector< double > >::rGetStateVariables(), OdeSolution::rGetTimes(), OdeSolution::SetNumberOfTimeSteps(), OdeSolution::SetOdeSystemInformation(), UpdateTransmembranePotential(), and AbstractParameterisedSystem< std::vector< double > >::VerifyStateVariables().

void AbstractGeneralizedRushLarsenCardiacCell::ComputeExceptVoltage	(	double	tStart,
		double	tEnd
	)

virtual

Simulates this cell's behaviour between the time interval [tStart, tEnd], with timestep mDt. The transmembrane potential is kept fixed throughout, but the other state variables are updated.

The length of the time interval must be a multiple of the timestep.

Parameters

tStart	beginning of the time interval to simulate
tEnd	end of the time interval to simulate

Reimplemented from AbstractCardiacCell.

Definition at line 115 of file AbstractGeneralizedRushLarsenCardiacCell.cpp.

References TimeStepper::AdvanceOneTimeStep(), ComputeOneStepExceptVoltage(), TimeStepper::GetTime(), TimeStepper::IsTimeAtEnd(), AbstractCardiacCell::mDt, AbstractCardiacCellInterface::SetVoltageDerivativeToZero(), and AbstractParameterisedSystem< std::vector< double > >::VerifyStateVariables().

virtual void AbstractGeneralizedRushLarsenCardiacCell::ComputeOneStepExceptVoltage ( double time )

protectedpure virtual

Update the values of all variables except the transmembrane potential using a GRL method.

Parameters

time	the current simulation time

Referenced by Compute(), ComputeExceptVoltage(), and SolveAndUpdateState().

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

inlineprivatevirtual

This function should never be called - the cell class incorporates its own solver.

Parameters

time
rY
rDY

Implements AbstractOdeSystem.

Definition at line 157 of file AbstractGeneralizedRushLarsenCardiacCell.hpp.

References NEVER_REACHED.

void AbstractGeneralizedRushLarsenCardiacCell::ForceUseOfNumericalJacobian ( bool useNumericalJacobian = true )

Force the use of a numerical Jacobian, even if an analytic form is provided. This is needed for a handful of troublesome models.

Parameters

useNumericalJacobian Whether to use a numerical instead of the analytic Jacobian.

Definition at line 159 of file AbstractGeneralizedRushLarsenCardiacCell.cpp.

References EXCEPTION, and AbstractOdeSystem::mUseAnalyticJacobian.

bool AbstractGeneralizedRushLarsenCardiacCell::HasAnalyticJacobian ( ) const

Returns: whether the ODE system has an analytic Jacobian (mHasAnalyticJacobian).

Definition at line 154 of file AbstractGeneralizedRushLarsenCardiacCell.cpp.

References mHasAnalyticJacobian.

template<class Archive >

void AbstractGeneralizedRushLarsenCardiacCell::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Archive the member variables.

Parameters

archive
version

Definition at line 71 of file AbstractGeneralizedRushLarsenCardiacCell.hpp.

void AbstractGeneralizedRushLarsenCardiacCell::SolveAndUpdateState	(	double	tStart,
		double	tEnd
	)

virtual

Simulate this cell's behaviour between the time interval [tStart, tEnd], with timestemp mDt, updating the internal state variable values.

Parameters

tStart	beginning of the time interval to simulate
tEnd	end of the time interval to simulate

Reimplemented from AbstractCardiacCell.

Definition at line 134 of file AbstractGeneralizedRushLarsenCardiacCell.cpp.

References TimeStepper::AdvanceOneTimeStep(), ComputeOneStepExceptVoltage(), TimeStepper::GetTime(), AbstractCardiacCellInterface::GetVoltageIndex(), TimeStepper::IsTimeAtEnd(), AbstractCardiacCell::mDt, AbstractParameterisedSystem< std::vector< double > >::rGetStateVariables(), UpdateTransmembranePotential(), and AbstractParameterisedSystem< std::vector< double > >::VerifyStateVariables().

virtual void AbstractGeneralizedRushLarsenCardiacCell::UpdateTransmembranePotential ( double time )

protectedpure virtual

Perform a forward Euler step to update the transmembrane potential.

Parameters

time	the current simulation time

Referenced by Compute(), and SolveAndUpdateState().

Friends And Related Function Documentation

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 63 of file AbstractGeneralizedRushLarsenCardiacCell.hpp.

Member Data Documentation

std::vector<double> AbstractGeneralizedRushLarsenCardiacCell::mEvalF

protected

The derivatives, working memory for use by subclasses.

Definition at line 182 of file AbstractGeneralizedRushLarsenCardiacCell.hpp.

Referenced by AbstractGeneralizedRushLarsenCardiacCell().

bool AbstractGeneralizedRushLarsenCardiacCell::mHasAnalyticJacobian

protected

Whether we have an analytic Jacobian.

Definition at line 188 of file AbstractGeneralizedRushLarsenCardiacCell.hpp.

Referenced by HasAnalyticJacobian().

std::vector<double> AbstractGeneralizedRushLarsenCardiacCell::mPartialF

protected

The diagonal of the Jacobian, working memory for use by subclasses.

Definition at line 179 of file AbstractGeneralizedRushLarsenCardiacCell.hpp.

Referenced by AbstractGeneralizedRushLarsenCardiacCell().

std::vector<double> AbstractGeneralizedRushLarsenCardiacCell::mYInit

protected

The state at the beginning of the current step, working memory for use by subclasses.

Definition at line 185 of file AbstractGeneralizedRushLarsenCardiacCell.hpp.

Referenced by AbstractGeneralizedRushLarsenCardiacCell().

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

heart/src/odes/AbstractGeneralizedRushLarsenCardiacCell.hpp
heart/src/odes/AbstractGeneralizedRushLarsenCardiacCell.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation