AbstractGeneralizedRushLarsenCardiacCell Class Reference

#include <AbstractGeneralizedRushLarsenCardiacCell.hpp>

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)
Protected Member Functions
virtual void	ComputeOneStepExceptVoltage (double time)=0
virtual void	UpdateTransmembranePotential (double time)=0
Protected Attributes
std::vector< double >	mPartialF
std::vector< double >	mEvalF
std::vector< double >	mYInit
bool	mHasAnalyticJacobian
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 ) [protected, pure 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
	)			`[inline, private, virtual]`

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
	)			`[inline, private]`

Archive the member variables.

Parameters:

	archive
	version

Reimplemented from AbstractCardiacCell.

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 ) [protected, pure 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.

Reimplemented from AbstractCardiacCell.

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

AbstractGeneralizedRushLarsenCardiacCell Class Reference

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