AbstractBackwardEulerCardiacCell< SIZE > Class Template Reference

#include <AbstractBackwardEulerCardiacCell.hpp>

Inheritance diagram for AbstractBackwardEulerCardiacCell< SIZE >:

Collaboration diagram for AbstractBackwardEulerCardiacCell< SIZE >:

List of all members.

Public Member Functions

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

virtual ~AbstractBackwardEulerCardiacCell ()

virtual void ComputeResidual (double time, const double rCurrentGuess[SIZE], double rResidual[SIZE])=0

virtual void ComputeJacobian (double time, const double rCurrentGuess[SIZE], double rJacobian[SIZE][SIZE])=0

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

void ComputeExceptVoltage (double tStart, double tEnd)

void SolveAndUpdateState (double tStart, double tEnd)

Protected Member Functions

virtual void ComputeOneStepExceptVoltage (double tStart)=0

virtual void UpdateTransmembranePotential (double time)=0

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

template<unsigned SIZE>
class AbstractBackwardEulerCardiacCell< SIZE >

This is the base class for cardiac cells solved using a (decoupled) backward Euler approach.

The basic approach to solving such models is:

Update the transmembrane potential, either from solving an external PDE, or using a forward Euler step.
Update any gating variables (or similar) using a backward euler step. Suitable ODEs can be written in the form . The update expression is then $u_n = ( u_{n-1} + g(V_n)*dt ) / ( 1 - h(V_n)*dt )$ .
Update the remaining state variables using Newton's method to solve the nonlinear system $U_n - U_{n-1} = dt*F(U_n, V_n)$ . The template parameter to the class specifies the size of this nonlinear system.

Definition at line 60 of file AbstractBackwardEulerCardiacCell.hpp.

Constructor & Destructor Documentation

template<unsigned SIZE>

AbstractBackwardEulerCardiacCell< SIZE >::AbstractBackwardEulerCardiacCell	(	unsigned	numberOfStateVariables,
		unsigned	voltageIndex,
		boost::shared_ptr< AbstractStimulusFunction >	pIntracellularStimulus
	)			`[inline]`

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:

We may want to remove the timestep from this class, and instead pass it to the Compute* methods, especially if variable timestepping is to be used.
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 198 of file AbstractBackwardEulerCardiacCell.hpp.

template<unsigned SIZE>

AbstractBackwardEulerCardiacCell< SIZE >::~AbstractBackwardEulerCardiacCell ( ) [inline, virtual]

Virtual destructor

Definition at line 209 of file AbstractBackwardEulerCardiacCell.hpp.

Member Function Documentation

template<unsigned SIZE>

template<class Archive>

void AbstractBackwardEulerCardiacCell< SIZE >::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Archive the member variables.

Parameters:

	archive
	version

Reimplemented from AbstractCardiacCell.

Definition at line 72 of file AbstractBackwardEulerCardiacCell.hpp.

template<unsigned SIZE>

virtual void AbstractBackwardEulerCardiacCell< SIZE >::ComputeResidual	(	double	time,
		const double	rCurrentGuess[SIZE],
		double	rResidual[SIZE]
	)			`[pure virtual]`

Compute the residual of the nonlinear system portion of the cell model.

Parameters:

	time	the current time
	rCurrentGuess	the current guess for
	rResidual	to be filled in with the residual vector

template<unsigned SIZE>

virtual void AbstractBackwardEulerCardiacCell< SIZE >::ComputeJacobian	(	double	time,
		const double	rCurrentGuess[SIZE],
		double	rJacobian[SIZE][SIZE]
	)			`[pure virtual]`

Compute the Jacobian matrix for the nonlinear system portion of the cell model.

Parameters:

	time	the current time
	rCurrentGuess	the current guess for
	rJacobian	to be filled in with the Jacobian matrix

template<unsigned SIZE>

OdeSolution AbstractBackwardEulerCardiacCell< SIZE >::Compute	(	double	tStart,
		double	tEnd,
		double	tSamp = `0.0`
	)			`[inline, 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 213 of file AbstractBackwardEulerCardiacCell.hpp.

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

template<unsigned SIZE>

void AbstractBackwardEulerCardiacCell< SIZE >::ComputeExceptVoltage	(	double	tStart,
		double	tEnd
	)			`[inline, virtual]`

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

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 265 of file AbstractBackwardEulerCardiacCell.hpp.

References AbstractBackwardEulerCardiacCell< SIZE >::ComputeOneStepExceptVoltage(), AbstractCardiacCell::mDt, and AbstractCardiacCell::VerifyStateVariables().

template<unsigned SIZE>

void AbstractBackwardEulerCardiacCell< SIZE >::SolveAndUpdateState	(	double	tStart,
		double	tEnd
	)			`[inline, 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 291 of file AbstractBackwardEulerCardiacCell.hpp.

References TimeStepper::AdvanceOneTimeStep(), AbstractBackwardEulerCardiacCell< SIZE >::ComputeOneStepExceptVoltage(), TimeStepper::GetTime(), TimeStepper::IsTimeAtEnd(), AbstractCardiacCell::mDt, AbstractBackwardEulerCardiacCell< SIZE >::UpdateTransmembranePotential(), and AbstractCardiacCell::VerifyStateVariables().

template<unsigned SIZE>

void AbstractBackwardEulerCardiacCell< SIZE >::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 163 of file AbstractBackwardEulerCardiacCell.hpp.

References NEVER_REACHED.

template<unsigned SIZE>

virtual void AbstractBackwardEulerCardiacCell< SIZE >::ComputeOneStepExceptVoltage ( double tStart ) [protected, pure virtual]

Compute the values of all state variables, except the voltage, using backward Euler, for one timestep from tStart.

Note:: This method must be provided by subclasses.

Parameters:

tStart

start of this timestep

Referenced by AbstractBackwardEulerCardiacCell< SIZE >::Compute(), AbstractBackwardEulerCardiacCell< SIZE >::ComputeExceptVoltage(), and AbstractBackwardEulerCardiacCell< SIZE >::SolveAndUpdateState().

template<unsigned SIZE>

virtual void AbstractBackwardEulerCardiacCell< SIZE >::UpdateTransmembranePotential ( double time ) [protected, pure virtual]

Perform a forward Euler step to update the transmembrane potential.

Note:: This method must be provided by subclasses.

Parameters:

time

start of this timestep

Referenced by AbstractBackwardEulerCardiacCell< SIZE >::Compute(), and AbstractBackwardEulerCardiacCell< SIZE >::SolveAndUpdateState().

Friends And Related Function Documentation

template<unsigned SIZE>

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractCardiacCell.

Definition at line 64 of file AbstractBackwardEulerCardiacCell.hpp.

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

heart/src/odes/AbstractBackwardEulerCardiacCell.hpp


Public Member Functions
	AbstractBackwardEulerCardiacCell (unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
virtual	~AbstractBackwardEulerCardiacCell ()
virtual void	ComputeResidual (double time, const double rCurrentGuess[SIZE], double rResidual[SIZE])=0
virtual void	ComputeJacobian (double time, const double rCurrentGuess[SIZE], double rJacobian[SIZE][SIZE])=0
OdeSolution	Compute (double tStart, double tEnd, double tSamp=0.0)
void	ComputeExceptVoltage (double tStart, double tEnd)
void	SolveAndUpdateState (double tStart, double tEnd)
Protected Member Functions
virtual void	ComputeOneStepExceptVoltage (double tStart)=0
virtual void	UpdateTransmembranePotential (double time)=0
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

AbstractBackwardEulerCardiacCell< SIZE > Class Template Reference

Public Member Functions

Protected Member Functions

Private Member Functions

Friends

Detailed Description

template<unsigned SIZE> class AbstractBackwardEulerCardiacCell< SIZE >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

template<unsigned SIZE>
class AbstractBackwardEulerCardiacCell< SIZE >