#include <AbstractCvodeCell.hpp>

Inheritance diagram for AbstractCvodeCell:

Collaboration diagram for AbstractCvodeCell:

Public Member Functions
	AbstractCvodeCell (boost::shared_ptr< AbstractIvpOdeSolver > pSolver, unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
virtual	~AbstractCvodeCell ()
double	GetVoltage ()
void	SetVoltage (double voltage)
void	SetTimestep (double maxDt)
virtual void	SolveAndUpdateState (double tStart, double tEnd)
OdeSolution	Compute (double tStart, double tEnd, double tSamp=0.0)
void	ComputeExceptVoltage (double tStart, double tEnd)
void	SetVoltageDerivativeToZero (bool clamp=true)
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	SetStateVariables (const N_Vector &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)
Protected Attributes
double	mMaxDt
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access

Detailed Description

A cardiac cell that is designed to be simulated using CVODE. It uses CVODE's vector type natively via AbstractCvodeSystem.

Functionality is similar to that provided by AbstractCardiacCell and AbstractOdeSystem, but not identical. It also includes a direct interface to the CVODE solver, via the Solve methods, since the CvodeAdaptor class may be a bit slower.

Assumes that it will be solving stiff systems, so uses BDF/Newton.

Various methods in this class just call methods on AbstractCvodeSystem, to reduce compiler confusion when working with things in an inheritance tree.

Any single cell work should generally use this class rather than AbstractCardiacCell.

This class may also be faster for certain tissue problems (especially when using a relatively large PDE timestep (~0.1ms)). BUT it will come with a memory overhead as every node has to carry a CVODE solver object as it stores the internal state of the solver, not just the state variables as ForwardEuler solver does. So may not be appropriate for very large meshes.

Definition at line 78 of file AbstractCvodeCell.hpp.

Constructor & Destructor Documentation

AbstractCvodeCell::AbstractCvodeCell	(	boost::shared_ptr< AbstractIvpOdeSolver >	pSolver,
		unsigned	numberOfStateVariables,
		unsigned	voltageIndex,
		boost::shared_ptr< AbstractStimulusFunction >	pIntracellularStimulus
	)

Create a new cardiac cell.

Note:: subclasses must call Init() in their constructor after setting mpSystemInfo.

Parameters:

pSolver	not used for these cells (they're always solved with CVODE); may be empty
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 48 of file AbstractCvodeCell.cpp.

AbstractCvodeCell::~AbstractCvodeCell ( ) [virtual]

Free the state variables, if they have been set.

Definition at line 59 of file AbstractCvodeCell.cpp.

Member Function Documentation

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

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

The maximum time step to use will be taken as mMaxDt. If this is unset it is the same as the sampling interval, which defaults to HeartConfig::Instance()->GetPrintingTimeStep().

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 dt)

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

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

rName	variable name
time	the time at which to evaluate variable (only needed for derived quantities).

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

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

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

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

parameterIndex	the index of the parameter vector to alter
value	the value the parameter should take

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

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

archive
version

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

void AbstractCvodeCell::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