#include <AbstractRushLarsenCardiacCell.hpp>

Inheritance diagram for AbstractRushLarsenCardiacCell:

Collaboration diagram for AbstractRushLarsenCardiacCell:

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

virtual	~AbstractRushLarsenCardiacCell ()

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

void	ComputeExceptVoltage (double tStart, double tEnd)

void	SolveAndUpdateState (double tStart, double tEnd)

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 (const std::vector< double > &rDY, const std::vector< double > &rAlphaOrTau, const std::vector< double > &rBetaOrInf)=0

void	UpdateTransmembranePotential (const std::vector< double > &rDY)

virtual void	EvaluateEquations (double time, std::vector< double > &rDY, std::vector< double > &rAlphaOrTau, std::vector< double > &rBetaOrInf)=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)

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

Additional Inherited Members
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 is the base class for cardiac cells solved using the Rush-Larsen method. It is based on code contributed by Megan Lewis, University of Saskatchewan

The basic approach to solving such models is:

Compute alpha & beta values for gating variables, and derivatives for other state variables.
Update the transmembrane potential, either from solving an external PDE, or using a forward Euler step.
Update any eligible gating variables (or similar) with Rush-Larsen scheme.
Update the remaining state variables using a forward Euler step.

Definition at line 58 of file AbstractRushLarsenCardiacCell.hpp.

Constructor & Destructor Documentation

AbstractRushLarsenCardiacCell::AbstractRushLarsenCardiacCell	(	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 45 of file AbstractRushLarsenCardiacCell.cpp.

AbstractRushLarsenCardiacCell::~AbstractRushLarsenCardiacCell ( )

virtual

Virtual destructor

Definition at line 54 of file AbstractRushLarsenCardiacCell.cpp.

Member Function Documentation

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

virtual

Simulates this cell's behaviour between the time interval [tStart, tEnd], with timestep mDt. Uses a forward Euler step to update the transmembrane potential at each timestep.

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 57 of file AbstractRushLarsenCardiacCell.cpp.

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

void AbstractRushLarsenCardiacCell::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 106 of file AbstractRushLarsenCardiacCell.cpp.

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

virtual void AbstractRushLarsenCardiacCell::ComputeOneStepExceptVoltage	(	const std::vector< double > &	rDY,
		const std::vector< double > &	rAlphaOrTau,
		const std::vector< double > &	rBetaOrInf
	)

protectedpure virtual

Update the values of elligible gating variables using the Rush-Larsen method, and of other non-V variables using forward Euler, for a single timestep.

Note: This method must be provided by subclasses.

Parameters

rDY	vector containing dy/dt values
rAlphaOrTau	vector containing alpha or tau values, depending on the formulation
rBetaOrInf	vector containing beta or inf values, depending on the formulation

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

virtual void AbstractRushLarsenCardiacCell::EvaluateEquations	(	double	time,
		std::vector< double > &	rDY,
		std::vector< double > &	rAlphaOrTau,
		std::vector< double > &	rBetaOrInf
	)

protectedpure virtual

Compute dy/dt and alpha and beta values.

Note: This method must be provided by subclasses.

Parameters

time	start of this timestep
rDY	vector to fill in with dy/dt values
rAlphaOrTau	vector to fill in with alpha or tau values, depending on the formulation
rBetaOrInf	vector to fill in with beta or inf values, depending on the formulation

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

void AbstractRushLarsenCardiacCell::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 142 of file AbstractRushLarsenCardiacCell.hpp.

References NEVER_REACHED.

template<class Archive >

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

inlineprivate

Archive the member variables.

Parameters

archive
version

Definition at line 70 of file AbstractRushLarsenCardiacCell.hpp.

void AbstractRushLarsenCardiacCell::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 130 of file AbstractRushLarsenCardiacCell.cpp.

References TimeStepper::AdvanceOneTimeStep(), ComputeOneStepExceptVoltage(), EvaluateEquations(), TimeStepper::GetTime(), TimeStepper::IsTimeAtEnd(), AbstractCardiacCell::mDt, AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, UpdateTransmembranePotential(), and AbstractParameterisedSystem< std::vector< double > >::VerifyStateVariables().

void AbstractRushLarsenCardiacCell::UpdateTransmembranePotential ( const std::vector< double > & rDY )

protected

Perform a forward Euler step to update the transmembrane potential.

Parameters

rDY	vector containing dy/dt values

Definition at line 149 of file AbstractRushLarsenCardiacCell.cpp.

References AbstractCardiacCellInterface::GetVoltageIndex(), AbstractCardiacCell::mDt, and AbstractParameterisedSystem< std::vector< double > >::rGetStateVariables().

Referenced by Compute(), and SolveAndUpdateState().

Friends And Related Function Documentation

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 62 of file AbstractRushLarsenCardiacCell.hpp.

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

heart/src/odes/AbstractRushLarsenCardiacCell.hpp
heart/src/odes/AbstractRushLarsenCardiacCell.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation