#include <AbstractCardiacCell.hpp>

Inheritance diagram for AbstractCardiacCell:

Collaboration diagram for AbstractCardiacCell:

Public Member Functions
	AbstractCardiacCell (boost::shared_ptr< AbstractIvpOdeSolver > pOdeSolver, unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
virtual	~AbstractCardiacCell ()
void	Init ()
void	SetTimestep (double dt)
virtual void	SolveAndUpdateState (double tStart, double tEnd)
virtual OdeSolution	Compute (double tStart, double tEnd, double tSamp=0.0)
virtual void	ComputeExceptVoltage (double tStart, double tEnd)
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)
void	SetParameter (unsigned parameterIndex, 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 ()
Protected Attributes
double	mDt
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
void	CheckForArchiveFix ()
Friends
class	boost::serialization::access

Detailed Description

This is the base class for ode-based cardiac cell models.

It is essentially a cardiac-specific wrapper for ODE systems providing an interface which can interact with the stimulus classes and the voltage in a mono/bidomain simulation.

Concrete classes can be autogenerated from CellML files by the PyCml package, and will automatically inherit from this class.

Definition at line 74 of file AbstractCardiacCell.hpp.

Constructor & Destructor Documentation

AbstractCardiacCell::AbstractCardiacCell	(	boost::shared_ptr< AbstractIvpOdeSolver >	pOdeSolver,
		unsigned	numberOfStateVariables,
		unsigned	voltageIndex,
		boost::shared_ptr< AbstractStimulusFunction >	pIntracellularStimulus
	)

Create a new cardiac cell. The state variables of the cell will be set to AbstractOdeSystemInformation::GetInitialConditions(). Note that calls to SetDefaultInitialConditions() on a particular instance of this class will not modify its state variables. You can modify them directly with rGetStateVariables().

Parameters:

pOdeSolver	the ODE solver to use when simulating this cell
numberOfStateVariables	the size of the ODE system modelling this cell
voltageIndex	the index of the transmembrane potential within the vector of state variables
pIntracellularStimulus	the intracellular stimulus current

Definition at line 43 of file AbstractCardiacCell.cpp.

References AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables.

AbstractCardiacCell::~AbstractCardiacCell ( ) [virtual]

Virtual destructor

Definition at line 55 of file AbstractCardiacCell.cpp.

Member Function Documentation

void AbstractCardiacCell::AdjustOutOfRangeSlowValues ( std::vector< double > & rSlowValues ) [virtual]

In a multiscale simulation a cut-down cell model can be run:

fast values are calculated according to the CellML definition
slow values are interpolated on synchronisation time-steps. There's a chance that linear interpolation/extrapolation may push some gating variable out of the range [0, 1]. This method alters any values which are out-of-range.

Note:: This must be implemented by fast/slow cardiac cell subclasses.

Parameters:

rSlowValues A vector of the slow values for a particular cell after they have been interpolated from nearby coarse cells

Definition at line 225 of file AbstractCardiacCell.cpp.

References EXCEPTION.

void AbstractCardiacCell::CheckForArchiveFix ( ) [private]

The Luo-Rudy 1991 model saved in previous Chaste versions had a different ordering of state variables. If we're loading that model, we'll need to permute the state vector. This can't (easily) be done in the LR91 code itself, since that is auto-generated!

Definition at line 174 of file AbstractCardiacCell.cpp.

References GetNumberOfStateVariables(), AbstractParameterisedSystem< std::vector< double > >::mParameters, AbstractParameterisedSystem< std::vector< double > >::mStateVariables, and AbstractUntemplatedParameterisedSystem::rGetParameterNames().

Referenced by serialize().

OdeSolution AbstractCardiacCell::Compute	(	double	tStart,
		double	tEnd,
		double	tSamp = `0.0`
	)		`[virtual]`

Simulates this cell's behaviour between the time interval [tStart, tEnd], with timestep mDt, and return state variable values.

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)

void AbstractCardiacCell::ComputeExceptVoltage	(	double	tStart,
		double	tEnd
	)		`[virtual]`

double AbstractCardiacCell::GetAnyVariable	(	const std::string &	rName,
		double	time = `0.0`
	)		`[virtual]`

void AbstractCardiacCell::serialize	(	Archive &	archive,
		const unsigned int	version
	)		`[inline, private]`

void AbstractCardiacCell::SetParameter	(	const std::string &	rParameterName,
		double	value
	)		`[virtual]`

rParameterName	the parameter name to set the value of,
value	value to set it to.

void AbstractCardiacCell::SetParameter	(	unsigned	parameterIndex,
		double	value
	)		`[virtual]`

parameterIndex	the parameter to set the value of,
value	value to set it to.

void AbstractCardiacCell::SetStateVariable	(	unsigned	index,
		double	newValue
	)		`[virtual]`

index	index of the state variable to be set
newValue	new value of the state variable

rName	name of the state variable to be set
newValue	new value of the state variable

archive
version

void AbstractCardiacCell::SolveAndUpdateState	(	double	tStart,
		double	tEnd
	)		`[virtual]`

Public Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation