AbstractCvodeCell Class Reference

#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 (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)
bool	GetMinimalReset ()
	Get whether we want to run with minimal reset or not (no reinitialisation of the solver if variables change)
bool	GetForceReset ()
	Get whether we will force a solver reset on every call to Solve()
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_Vector Y)
std::string	DumpState (const std::string &rMessage, N_Vector Y, 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::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::~AbstractCvodeCell ( )

virtual

Free the state variables, if they have been set.

Definition at line 59 of file AbstractCvodeCell.cpp.

Member Function Documentation

Compute()

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

Implements AbstractCardiacCellInterface.

Definition at line 102 of file AbstractCvodeCell.cpp.

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

ComputeExceptVoltage()

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 116 of file AbstractCvodeCell.cpp.

References GetVoltage(), SetVoltage(), AbstractCardiacCellInterface::SetVoltageDerivativeToZero(), SolveAndUpdateState(), and AbstractParameterisedSystem< N_Vector >::VerifyStateVariables().

Referenced by AbstractCardiacTissue< SPACE_DIM >::SetConductivityModifier().

GetAnyVariable()

double AbstractCvodeCell::GetAnyVariable ( const std::string &  rName, double  time = 0.0  )

virtual

This just calls the method AbstractCvodeSystem::GetAnyVariable

It is here (despite being inherited) because we seem to need to specify explicitly which method in the parent classes we intend to implement to take care of the pure definition in AbstractCardiacCellInterface.

Parameters

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

Returns

value of the variable at that time

Implements AbstractCardiacCellInterface.

Definition at line 187 of file AbstractCvodeCell.cpp.

References AbstractParameterisedSystem< N_Vector >::GetAnyVariable().

GetNumberOfParameters()

unsigned AbstractCvodeCell::GetNumberOfParameters ( ) const

virtual

This just returns the number of parameters in the cell model.

It is here because we seem to need to specify explicitly which method in the parent classes we intend to implement to take care of the pure definition in AbstractCardiacCellInterface

Returns

the number of parameters

Implements AbstractCardiacCellInterface.

Definition at line 148 of file AbstractCvodeCell.cpp.

References AbstractUntemplatedParameterisedSystem::GetNumberOfParameters().

GetNumberOfStateVariables()

unsigned AbstractCvodeCell::GetNumberOfStateVariables ( ) const

virtual

This just returns the number of state variables in the cell model.

It is here because we seem to need to specify explicitly which method in the parent classes we intend to implement to take care of the pure definition in AbstractCardiacCellInterface

Returns

the number of state variables

Implements AbstractCardiacCellInterface.

Definition at line 143 of file AbstractCvodeCell.cpp.

References AbstractUntemplatedParameterisedSystem::GetNumberOfStateVariables().

Referenced by GetStdVecStateVariables().

GetParameter() [1/2]

double AbstractCvodeCell::GetParameter ( const std::string &  rParameterName )

virtual

This just calls AbstractCvodeSystem::GetParameter

It is here (despite being inherited) because we seem to need to specify explicitly which method in the parent classes we intend to implement to take care of the pure definition in AbstractCardiacCellInterface.

Parameters

rParameterName

the name of a parameter to get the value of,

Returns

the parameter's value.

Implements AbstractCardiacCellInterface.

Definition at line 192 of file AbstractCvodeCell.cpp.

References AbstractParameterisedSystem< N_Vector >::GetParameter().

GetParameter() [2/2]

double AbstractCvodeCell::GetParameter ( unsigned  parameterIndex )

virtual

This is just here to show there is an alternative to the above!

It just calls the base class method.

Parameters

parameterIndex

the index of the parameter vector entry to return

Returns

the parameter value

Implements AbstractCardiacCellInterface.

Definition at line 197 of file AbstractCvodeCell.cpp.

References AbstractParameterisedSystem< N_Vector >::GetParameter().

GetStdVecStateVariables()

std::vector< double > AbstractCvodeCell::GetStdVecStateVariables ( )

virtual

This just returns the state variables in the cell model.

It is here (despite being inherited) because we seem to need to specify explicitly which method in the parent classes we intend to implement to take care of the pure definition in AbstractCardiacCellInterface.

Returns

the state variables

Implements AbstractCardiacCellInterface.

Definition at line 153 of file AbstractCvodeCell.cpp.

References CopyToStdVector(), GetNumberOfStateVariables(), and AbstractParameterisedSystem< N_Vector >::rGetStateVariables().

GetTimestep()

double AbstractCvodeCell::GetTimestep

(

)

Returns

The maximum timestep that is used by CVODE with this cell.

Definition at line 87 of file AbstractCvodeCell.cpp.

References mMaxDt.

GetVoltage()

double AbstractCvodeCell::GetVoltage ( )

virtual

Returns

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

Implements AbstractCardiacCellInterface.

Definition at line 63 of file AbstractCvodeCell.cpp.

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

Referenced by ComputeExceptVoltage().

rGetStateVariableNames()

const std::vector< std::string > & AbstractCvodeCell::rGetStateVariableNames ( ) const

virtual

Just calls AbstractCvodeSystem::rGetStateVariableNames().

It is here (despite being inherited) because we seem to need to specify explicitly which method in the parent classes we intend to implement to take care of the pure definition in AbstractCardiacCellInterface.

Returns

the state variable names in the cell's ODE system.

Implements AbstractCardiacCellInterface.

Definition at line 160 of file AbstractCvodeCell.cpp.

References AbstractUntemplatedParameterisedSystem::rGetStateVariableNames().

serialize()

template<class Archive >

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

inlineprivate

Archive the member variables.

Parameters

archive
version

Definition at line 90 of file AbstractCvodeCell.hpp.

References mMaxDt.

SetMaxTimestep()

void AbstractCvodeCell::SetMaxTimestep

(

double

maxDt

)

Set the maximum timestep to use for simulating this cell.

Parameters

maxDt

the maximum timestep

Definition at line 77 of file AbstractCvodeCell.cpp.

References SetTimestep().

SetParameter()

void AbstractCvodeCell::SetParameter ( const std::string &  rParameterName, double  value  )

virtual

This just calls AbstractCvodeSystem::SetParameter

It is here (despite being inherited) because we seem to need to specify explicitly which method in the parent classes we intend to implement to take care of the pure definition in AbstractCardiacCellInterface.

Parameters

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

Implements AbstractCardiacCellInterface.

Definition at line 202 of file AbstractCvodeCell.cpp.

References AbstractParameterisedSystem< N_Vector >::SetParameter().

Referenced by AbstractCvodeCellWithDataClamp::TurnOffDataClamp(), and AbstractCvodeCellWithDataClamp::TurnOnDataClamp().

SetStateVariable() [1/2]

void AbstractCvodeCell::SetStateVariable ( const std::string &  rName, double  newValue  )

virtual

This just calls the method AbstractCvodeSystem::SetStateVariable

It is here (despite being inherited) because we seem to need to specify explicitly which method in the parent classes we intend to implement to take care of the pure definition in AbstractCardiacCellInterface.

Parameters

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

Implements AbstractCardiacCellInterface.

Definition at line 182 of file AbstractCvodeCell.cpp.

References AbstractParameterisedSystem< N_Vector >::SetStateVariable().

SetStateVariable() [2/2]

void AbstractCvodeCell::SetStateVariable ( unsigned  index, double  newValue  )

virtual

This just calls the method AbstractCvodeSystem::SetStateVariable

It is here (despite being inherited) because we seem to need to specify explicitly which method in the parent classes we intend to implement to take care of the pure definition in AbstractCardiacCellInterface.

Parameters

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

Implements AbstractCardiacCellInterface.

Definition at line 177 of file AbstractCvodeCell.cpp.

References AbstractParameterisedSystem< N_Vector >::SetStateVariable().

SetStateVariables() [1/2]

void AbstractCvodeCell::SetStateVariables

(

const N_Vector &

rVariables

)

This is also needed now just to show there is an alternative to the above method!

Parameters

rVariables

the state variables (to take a copy of).

Definition at line 172 of file AbstractCvodeCell.cpp.

References AbstractParameterisedSystem< N_Vector >::SetStateVariables().

SetStateVariables() [2/2]

void AbstractCvodeCell::SetStateVariables ( const std::vector< double > &  rVariables )

virtual

This just sets the state variables in the cell model.

It is here (despite being inherited) because we seem to need to specify explicitly which method in the parent classes we intend to implement to take care of the pure definition in AbstractCardiacCellInterface.

Parameters

rVariables

the state variables (to take a copy of).

Implements AbstractCardiacCellInterface.

Definition at line 165 of file AbstractCvodeCell.cpp.

References DeleteVector(), MakeNVector(), and AbstractParameterisedSystem< N_Vector >::SetStateVariables().

SetTimestep()

void AbstractCvodeCell::SetTimestep ( double  maxDt )

virtual

Set the maximum timestep to use for simulating this cell.

As CVODE adaptively alters the timestep used, this method just sets the maximum timestep allowed (despite its name). It is required as our base class AbstractCardiacCellInterface declares it as a pure virtual method. Users using this class directly should call SetMaxTimestep instead of this method, for clearer code.

Parameters

maxDt

the maximum timestep

Implements AbstractCardiacCellInterface.

Definition at line 82 of file AbstractCvodeCell.cpp.

References mMaxDt.

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

SetVoltage()

void AbstractCvodeCell::SetVoltage ( double  voltage )

virtual

Set the transmembrane potential

Parameters

voltage

new value

Implements AbstractCardiacCellInterface.

Definition at line 69 of file AbstractCvodeCell.cpp.

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

Referenced by ComputeExceptVoltage().

SetVoltageDerivativeToZero()

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 134 of file AbstractCvodeCell.cpp.

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

SolveAndUpdateState()

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 93 of file AbstractCvodeCell.cpp.

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

Referenced by ComputeExceptVoltage().

Friends And Related Symbol Documentation

boost::serialization::access

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 82 of file AbstractCvodeCell.hpp.

Member Data Documentation

mMaxDt

double AbstractCvodeCell::mMaxDt

protected

The maximum timestep to use.

Definition at line 100 of file AbstractCvodeCell.hpp.

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

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

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