#include <AbstractBackwardEulerCardiacCell.hpp>

Inheritance diagram for AbstractBackwardEulerCardiacCell< SIZE >:

Collaboration diagram for AbstractBackwardEulerCardiacCell< SIZE >:

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)

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 tStart)=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)

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

template<unsigned SIZE>
class AbstractBackwardEulerCardiacCell< SIZE >

This is the base class for cardiac cells solved using a (decoupled) backward Euler approach (see http://dx.doi.org/10.1109/TBME.2006.879425).

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 67 of file AbstractBackwardEulerCardiacCell.hpp.

Constructor & Destructor Documentation

template<unsigned SIZE>

AbstractBackwardEulerCardiacCell< SIZE >::AbstractBackwardEulerCardiacCell	(	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:

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 208 of file AbstractBackwardEulerCardiacCell.hpp.

template<unsigned SIZE>

AbstractBackwardEulerCardiacCell< SIZE >::~AbstractBackwardEulerCardiacCell ( )

virtual

Virtual destructor

Definition at line 219 of file AbstractBackwardEulerCardiacCell.hpp.

Member Function Documentation

template<unsigned SIZE>

OdeSolution AbstractBackwardEulerCardiacCell< SIZE >::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 223 of file AbstractBackwardEulerCardiacCell.hpp.

References OdeSolution::rGetSolutions(), OdeSolution::rGetTimes(), OdeSolution::SetNumberOfTimeSteps(), and OdeSolution::SetOdeSystemInformation().

template<unsigned SIZE>

void AbstractBackwardEulerCardiacCell< SIZE >::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.

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 275 of file AbstractBackwardEulerCardiacCell.hpp.

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>

virtual void AbstractBackwardEulerCardiacCell< SIZE >::ComputeOneStepExceptVoltage ( double tStart )

protectedpure 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< 0u >::Compute(), AbstractBackwardEulerCardiacCell< 0u >::ComputeExceptVoltage(), and AbstractBackwardEulerCardiacCell< 0u >::SolveAndUpdateState().

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>

void AbstractBackwardEulerCardiacCell< SIZE >::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 170 of file AbstractBackwardEulerCardiacCell.hpp.

References NEVER_REACHED.

template<unsigned SIZE>

template<class Archive >

void AbstractBackwardEulerCardiacCell< SIZE >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Archive the member variables.

Parameters

archive
version

Definition at line 79 of file AbstractBackwardEulerCardiacCell.hpp.

template<unsigned SIZE>

void AbstractBackwardEulerCardiacCell< SIZE >::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 301 of file AbstractBackwardEulerCardiacCell.hpp.

References TimeStepper::AdvanceOneTimeStep(), TimeStepper::GetTime(), and TimeStepper::IsTimeAtEnd().

template<unsigned SIZE>

virtual void AbstractBackwardEulerCardiacCell< SIZE >::UpdateTransmembranePotential ( double time )

protectedpure 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< 0u >::Compute(), and AbstractBackwardEulerCardiacCell< 0u >::SolveAndUpdateState().

Friends And Related Function Documentation

template<unsigned SIZE>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 71 of file AbstractBackwardEulerCardiacCell.hpp.

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

heart/src/odes/AbstractBackwardEulerCardiacCell.hpp

Public Member Functions

Protected Member Functions

Private Member Functions

Friends

Additional Inherited Members

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 >