#include <AbstractCvodeCellWithDataClamp.hpp>

Inheritance diagram for AbstractCvodeCellWithDataClamp:

Collaboration diagram for AbstractCvodeCellWithDataClamp:

Public Member Functions
	AbstractCvodeCellWithDataClamp (boost::shared_ptr< AbstractIvpOdeSolver > pSolver, unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)

virtual	~AbstractCvodeCellWithDataClamp ()

void	SetExperimentalData (std::vector< double > experimentalTimes, std::vector< double > experimentalVoltages)

void	TurnOffDataClamp ()

void	TurnOnDataClamp (double conductance=100)

Public Member Functions inherited from AbstractCvodeCell
	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 Member Functions
double	GetExperimentalVoltageAtTimeT (const double &rTime)

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)

Protected Attributes
bool	mDataClampIsOn

Protected Attributes inherited from AbstractCvodeCell
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)

Private Attributes
std::vector< double >	mExperimentalTimes

std::vector< double >	mExperimentalVoltages

bool	mDataAvailable

Friends
class	TestCvodeCellsWithDataClamp

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.

This subclass of AbstractCvodeCell contains methods used by systems that have had an 'artificial' data clamp current introduced into the dV/dt equation. These are generated by PyCML with ConvertCellModel using the option '–cvode-data-clamp'.

Definition at line 51 of file AbstractCvodeCellWithDataClamp.hpp.

Constructor & Destructor Documentation

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

Constructor

Parameters

pSolver	UNUSED for CVODE cells.
numberOfStateVariables	Number of ODEs in the system.
voltageIndex	The index of the variable which represents membrane voltage.
pIntracellularStimulus	The intracellular stimulus function.

Definition at line 49 of file AbstractCvodeCellWithDataClamp.cpp.

AbstractCvodeCellWithDataClamp::~AbstractCvodeCellWithDataClamp ( )

virtual

Destructor: free any memory we've used.

Definition at line 59 of file AbstractCvodeCellWithDataClamp.cpp.

Member Function Documentation

double AbstractCvodeCellWithDataClamp::GetExperimentalVoltageAtTimeT ( const double & rTime )

protected

Linear interpolation method to work out the voltage at any given time the ODE solver requests.

Parameters

rTime The time in the data trace at which to return the voltage (linearly interpolated).

Returns: The voltage at rTime.

Definition at line 73 of file AbstractCvodeCellWithDataClamp.cpp.

References DOUBLE_UNSET, EXCEPTION, mDataClampIsOn, mExperimentalTimes, and mExperimentalVoltages.

template<class Archive >

void AbstractCvodeCellWithDataClamp::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Archive the member variables.

Parameters

archive
version

Definition at line 67 of file AbstractCvodeCellWithDataClamp.hpp.

References mDataAvailable, mDataClampIsOn, mExperimentalTimes, and mExperimentalVoltages.

void AbstractCvodeCellWithDataClamp::SetExperimentalData	(	std::vector< double >	experimentalTimes,
		std::vector< double >	experimentalVoltages
	)

Provide experimental data. Must be called before TurnOnDataClamp().

Parameters

experimentalTimes	a vector of times - must be monotonically increasing, but can have variable intervals.
experimentalVoltages	a vector of voltages recorded at these times.

These two vectors must be the same length.

Definition at line 63 of file AbstractCvodeCellWithDataClamp.cpp.

References mDataAvailable, mExperimentalTimes, and mExperimentalVoltages.

void AbstractCvodeCellWithDataClamp::TurnOffDataClamp ( )

Switch off the data clamping current

Definition at line 113 of file AbstractCvodeCellWithDataClamp.cpp.

References mDataClampIsOn, and AbstractCvodeCell::SetParameter().

void AbstractCvodeCellWithDataClamp::TurnOnDataClamp ( double conductance = 100 )

Switch on the data clamping current

Parameters

conductance The conductance of the data clamping current - don't yet know best number to set this to.

Definition at line 119 of file AbstractCvodeCellWithDataClamp.cpp.