AbstractCvodeCell Class Reference

#include <AbstractCvodeCell.hpp>

Inherits AbstractCardiacCellInterface, and AbstractCvodeSystem.

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)
Private Attributes
double	mMaxDt

Detailed Description

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

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 doesn't work for us.

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

Note that a call to Solve will initialise the CVODE solver, and free its working memory when done. There is thus a non-trivial overhead involved.

Todo:: #890 Add an option to just initialise once, and assume subsequent Solve calls are continuing from where we left off.

Definition at line 59 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 41 of file AbstractCvodeCell.cpp.

AbstractCvodeCell::~AbstractCvodeCell ( ) [virtual]

Free the state variables, if they have been set.

Definition at line 52 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)

Implements AbstractCardiacCellInterface.

Definition at line 84 of file AbstractCvodeCell.cpp.

References DOUBLE_UNSET, HeartConfig::GetPrintingTimeStep(), HeartConfig::Instance(), mMaxDt, SetTimestep(), and AbstractCvodeSystem::Solve().

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

Simulates this cell's behaviour between the time interval [tStart, tEnd], but does not update the voltage.

Parameters:

	tStart	beginning of the time interval to simulate
	tEnd	end of the time interval to simulate

Implements AbstractCardiacCellInterface.

Definition at line 98 of file AbstractCvodeCell.cpp.

References EXCEPTION.

double AbstractCvodeCell::GetVoltage ( ) [virtual]

Get the current value of the transmembrane potential, as given in our state variable vector.

Implements AbstractCardiacCellInterface.

Definition at line 56 of file AbstractCvodeCell.cpp.

References AbstractParameterisedSystem< N_Vector >::GetAnyVariable(), AbstractParameterisedSystem< N_Vector >::mStateVariables, and AbstractCardiacCellInterface::mVoltageIndex.

void AbstractCvodeCell::SetTimestep ( double maxDt ) [virtual]

Set the maximum timestep to use for simulating this cell.

Parameters:

maxDt

the maximum timestep

Implements AbstractCardiacCellInterface.

Definition at line 69 of file AbstractCvodeCell.cpp.

References mMaxDt.

Referenced by Compute(), and SolveAndUpdateState().

void AbstractCvodeCell::SetVoltage ( double voltage ) [virtual]

Set the transmembrane potential

Parameters:

voltage

new value

Implements AbstractCardiacCellInterface.

Definition at line 62 of file AbstractCvodeCell.cpp.

References AbstractParameterisedSystem< N_Vector >::mStateVariables, AbstractCardiacCellInterface::mVoltageIndex, and AbstractParameterisedSystem< N_Vector >::SetAnyVariable().

void AbstractCvodeCell::SetVoltageDerivativeToZero ( bool clamp = true ) [virtual]

Set whether to clamp the voltage by setting its derivative to zero. We need to ensure CVODE is re-initialised if this setting changes.

Parameters:

clamp

whether to clamp

Reimplemented from AbstractCardiacCellInterface.

Definition at line 104 of file AbstractCvodeCell.cpp.

References AbstractCardiacCellInterface::mSetVoltageDerivativeToZero, and AbstractCvodeSystem::ResetSolver().

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

Simulate this cell's behaviour between the time interval [tStart, tEnd], updating the internal state variable values.

The maximum time step to use is given by mMaxDt, which defaults to HeartConfig::Instance()->GetPrintingTimeStep() if unset.

Parameters:

	tStart	beginning of the time interval to simulate
	tEnd	end of the time interval to simulate

Implements AbstractCardiacCellInterface.

Definition at line 75 of file AbstractCvodeCell.cpp.

References DOUBLE_UNSET, HeartConfig::Instance(), mMaxDt, SetTimestep(), and AbstractCvodeSystem::Solve().

Member Data Documentation

double AbstractCvodeCell::mMaxDt [private]

The maximum timestep to use.

Definition at line 63 of file AbstractCvodeCell.hpp.

Referenced by Compute(), SetTimestep(), and SolveAndUpdateState().

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

heart/src/odes/AbstractCvodeCell.hpp
heart/src/odes/AbstractCvodeCell.cpp

AbstractCvodeCell Class Reference

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation