#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	SetMaxTimestep (double maxDt)

void	SetTimestep (double maxDt)

double	GetTimestep ()

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)

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)

void	SetFixedVoltage (double voltage)

virtual void	SetStretch (double stretch)

virtual double	GetIntracellularCalciumConcentration ()

Public Member Functions inherited from AbstractCvodeSystem
	AbstractCvodeSystem (unsigned numberOfStateVariables)

virtual	~AbstractCvodeSystem ()

virtual void	EvaluateYDerivatives (realtype time, const N_Vector y, N_Vector ydot)=0

virtual void	EvaluateAnalyticJacobian (long int N, realtype time, N_Vector y, N_Vector ydot, CHASTE_CVODE_DENSE_MATRIX jacobian, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3)

void	SetForceReset (bool autoReset)

void	SetMinimalReset (bool minimalReset)

void	ResetSolver ()

OdeSolution	Solve (realtype tStart, realtype tEnd, realtype maxDt, realtype tSamp)

void	Solve (realtype tStart, realtype tEnd, realtype maxDt)

void	SetMaxSteps (long int numSteps)

long int	GetMaxSteps ()

void	SetTolerances (double relTol=1e-5, double absTol=1e-7)

double	GetRelativeTolerance ()

double	GetAbsoluteTolerance ()

double	GetLastStepSize ()

bool	GetUseAnalyticJacobian () const

bool	HasAnalyticJacobian () const

void	ForceUseOfNumericalJacobian (bool useNumericalJacobian=true)

Public Member Functions inherited from AbstractParameterisedSystem< N_Vector >
	AbstractParameterisedSystem (unsigned numberOfStateVariables)

N_Vector &	rGetStateVariables ()

N_Vector	GetStateVariables ()

void	SetStateVariables (const N_Vector &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 N_Vector &rInitialConditions)

void	SetDefaultInitialCondition (unsigned index, double initialCondition)

N_Vector	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, N_Vector *pDerivedQuantities=NULL)

double	GetAnyVariable (const std::string &rName, double time=0.0, N_Vector *pDerivedQuantities=NULL)

void	SetAnyVariable (unsigned index, double value)

void	SetAnyVariable (const std::string &rName, double value)

virtual N_Vector	ComputeDerivedQuantities (double time, const N_Vector &rState)

N_Vector	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 Attributes
double	mMaxDt

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 AbstractCvodeSystem
bool	mHasAnalyticJacobian

bool	mUseAnalyticJacobian

double	mRelTol

double	mAbsTol

void *	mpCvodeMem

long int	mMaxSteps

double	mLastInternalStepSize

Protected Attributes inherited from AbstractParameterisedSystem< N_Vector >
N_Vector	mStateVariables

N_Vector	mParameters

Protected Attributes inherited from AbstractUntemplatedParameterisedSystem
unsigned	mNumberOfStateVariables

boost::shared_ptr < AbstractOdeSystemInformation >	mpSystemInfo

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from AbstractCvodeSystem
void	Init ()

Protected Member Functions inherited from AbstractParameterisedSystem< N_Vector >
std::string	DumpState (const std::string &rMessage)

std::string	DumpState (const std::string &rMessage, N_VectorY)

std::string	DumpState (const std::string &rMessage, N_VectorY, double time)

void	CheckParametersOnLoad (const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames)

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 tSamp, 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 HeartConfig printing time step)

Returns: solution object

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

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

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

Public Member Functions

Protected Attributes

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation