Chaste  Release::2017.1
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AbstractBackwardEulerCardiacCell< SIZE > Class Template Referenceabstract

#include <AbstractBackwardEulerCardiacCell.hpp>

+ Inheritance diagram for AbstractBackwardEulerCardiacCell< SIZE >:
+ Collaboration diagram for AbstractBackwardEulerCardiacCell< SIZE >:

Public Member Functions

 AbstractBackwardEulerCardiacCell (unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
 
virtual ~AbstractBackwardEulerCardiacCell ()
 
virtual void ComputeResidual (double time, const double rCurrentGuess[SIZE], double rResidual[SIZE])=0
 
virtual void ComputeJacobian (double time, const double rCurrentGuess[SIZE], double rJacobian[SIZE][SIZE])=0
 
OdeSolution Compute (double tStart, double tEnd, double tSamp=0.0)
 
void ComputeExceptVoltage (double tStart, double tEnd)
 
void SolveAndUpdateState (double tStart, double tEnd)
 
- Public Member Functions inherited from AbstractCardiacCell
 AbstractCardiacCell (boost::shared_ptr< AbstractIvpOdeSolver > pOdeSolver, unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
 
virtual ~AbstractCardiacCell ()
 
void Init ()
 
void SetTimestep (double dt)
 
void SetVoltage (double voltage)
 
double GetVoltage ()
 
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 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)
 
virtual void SetState (CellModelState state)
 
virtual void SetSlowValues (const std::vector< double > &rSlowValues)
 
virtual void GetSlowValues (std::vector< double > &rSlowValues)
 
virtual bool IsFastOnly ()
 
virtual void AdjustOutOfRangeSlowValues (std::vector< double > &rSlowValues)
 
virtual unsigned GetNumSlowValues ()
 
- 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)
 
virtual void SetVoltageDerivativeToZero (bool clamp=true)
 
void SetFixedVoltage (double voltage)
 
virtual void SetStretch (double stretch)
 
virtual double GetIntracellularCalciumConcentration ()
 
- Public Member Functions inherited from AbstractOdeSystem
 AbstractOdeSystem (unsigned numberOfStateVariables)
 
virtual ~AbstractOdeSystem ()
 
virtual bool CalculateStoppingEvent (double time, const std::vector< double > &rY)
 
virtual double CalculateRootFunction (double time, const std::vector< double > &rY)
 
bool GetUseAnalyticJacobian ()
 
const std::vector< double > & rGetConstStateVariables () const
 
- Public Member Functions inherited from AbstractParameterisedSystem< std::vector< double > >
 AbstractParameterisedSystem (unsigned numberOfStateVariables)
 
std::vector< double > & rGetStateVariables ()
 
std::vector< double > GetStateVariables ()
 
void SetStateVariables (const std::vector< double > &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 std::vector< double > &rInitialConditions)
 
void SetDefaultInitialCondition (unsigned index, double initialCondition)
 
std::vector< double > 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, std::vector< double > *pDerivedQuantities=NULL)
 
double GetAnyVariable (const std::string &rName, double time=0.0, std::vector< double > *pDerivedQuantities=NULL)
 
void SetAnyVariable (unsigned index, double value)
 
void SetAnyVariable (const std::string &rName, double value)
 
virtual std::vector< double > ComputeDerivedQuantities (double time, const std::vector< double > &rState)
 
std::vector< double > 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

virtual void ComputeOneStepExceptVoltage (double tStart)=0
 
virtual void UpdateTransmembranePotential (double time)=0
 
- Protected Member Functions inherited from AbstractParameterisedSystem< std::vector< double > >
std::string DumpState (const std::string &rMessage)
 
std::string DumpState (const std::string &rMessage, std::vector< double >Y)
 
std::string DumpState (const std::string &rMessage, std::vector< double >Y, double time)
 
void CheckParametersOnLoad (const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames)
 

Private Member Functions

template<class Archive >
void serialize (Archive &archive, const unsigned int version)
 
void EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)
 

Friends

class boost::serialization::access
 

Additional Inherited Members

- Protected Attributes inherited from AbstractCardiacCell
double mDt
 
- 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 AbstractOdeSystem
bool mUseAnalyticJacobian
 
- Protected Attributes inherited from AbstractParameterisedSystem< std::vector< double > >
std::vector< double > mStateVariables
 
std::vector< double > mParameters
 
- Protected Attributes inherited from AbstractUntemplatedParameterisedSystem
unsigned mNumberOfStateVariables
 
boost::shared_ptr< AbstractOdeSystemInformation > mpSystemInfo
 

Detailed Description

template<unsigned SIZE>
class AbstractBackwardEulerCardiacCell< SIZE >

This is the base class for cardiac cells solved using a (decoupled) backward Euler approach (see http://dx.doi.org/10.1109/TBME.2006.879425).

The basic approach to solving such models is:

  • Update the transmembrane potential, either from solving an external PDE, or using a forward Euler step.
  • Update any gating variables (or similar) using a backward euler step. Suitable ODEs can be written in the form $du/dt = g(V) + h(V)*u$. The update expression is then $u_n = ( u_{n-1} + g(V_n)*dt ) / ( 1 - h(V_n)*dt )$.
  • Update the remaining state variables using Newton's method to solve the nonlinear system $U_n - U_{n-1} = dt*F(U_n, V_n)$. The template parameter to the class specifies the size of this nonlinear system.

Definition at line 67 of file AbstractBackwardEulerCardiacCell.hpp.

Constructor & Destructor Documentation

template<unsigned SIZE>
AbstractBackwardEulerCardiacCell< SIZE >::AbstractBackwardEulerCardiacCell ( unsigned  numberOfStateVariables,
unsigned  voltageIndex,
boost::shared_ptr< AbstractStimulusFunction >  pIntracellularStimulus 
)

Standard constructor for a cell.

Parameters
numberOfStateVariablesthe size of the ODE system
voltageIndexthe index of the variable representing the transmembrane potential within the state variable vector
pIntracellularStimulusthe intracellular stimulus function

Some notes for future reference:

  • We may want to remove the timestep from this class, and instead pass it to the Compute* methods, especially if variable timestepping is to be used.
  • It's a pity that inheriting from AbstractCardiacCell forces us to store a null pointer (for the unused ODE solver) in every instance. We may want to revisit this design decision at a later date.

Definition at line 208 of file AbstractBackwardEulerCardiacCell.hpp.

Referenced by AbstractBackwardEulerCardiacCell< SIZE >::serialize().

template<unsigned SIZE>
AbstractBackwardEulerCardiacCell< SIZE >::~AbstractBackwardEulerCardiacCell ( )
virtual

Virtual destructor

Definition at line 219 of file AbstractBackwardEulerCardiacCell.hpp.

Referenced by AbstractBackwardEulerCardiacCell< SIZE >::serialize().

Member Function Documentation

template<unsigned SIZE>
OdeSolution AbstractBackwardEulerCardiacCell< SIZE >::Compute ( double  tStart,
double  tEnd,
double  tSamp = 0.0 
)
virtual

Simulates this cell's behaviour between the time interval [tStart, tEnd], with timestep mDt. Uses a forward Euler step to update the transmembrane potential at each timestep.

The length of the time interval must be a multiple of the timestep.

Parameters
tStartbeginning of the time interval to simulate
tEndend of the time interval to simulate
tSampsampling interval for returned results (defaults to mDt)
Returns
the values of each state variable, at intervals of tSamp.

Reimplemented from AbstractCardiacCell.

Definition at line 223 of file AbstractBackwardEulerCardiacCell.hpp.

References AbstractBackwardEulerCardiacCell< SIZE >::ComputeOneStepExceptVoltage(), AbstractCardiacCell::mDt, AbstractUntemplatedParameterisedSystem::mpSystemInfo, OdeSolution::rGetSolutions(), AbstractParameterisedSystem< std::vector< double > >::rGetStateVariables(), OdeSolution::rGetTimes(), OdeSolution::SetNumberOfTimeSteps(), OdeSolution::SetOdeSystemInformation(), AbstractBackwardEulerCardiacCell< SIZE >::UpdateTransmembranePotential(), and AbstractParameterisedSystem< std::vector< double > >::VerifyStateVariables().

Referenced by AbstractBackwardEulerCardiacCell< SIZE >::serialize().

template<unsigned SIZE>
void AbstractBackwardEulerCardiacCell< SIZE >::ComputeExceptVoltage ( double  tStart,
double  tEnd 
)
virtual

Simulates this cell's behaviour between the time interval [tStart, tEnd], with timestep mDt. The transmembrane potential is kept fixed throughout.

The length of the time interval must be a multiple of the timestep.

Parameters
tStartbeginning of the time interval to simulate
tEndend of the time interval to simulate

Reimplemented from AbstractCardiacCell.

Definition at line 275 of file AbstractBackwardEulerCardiacCell.hpp.

References AbstractBackwardEulerCardiacCell< SIZE >::ComputeOneStepExceptVoltage(), AbstractCardiacCell::mDt, and AbstractParameterisedSystem< std::vector< double > >::VerifyStateVariables().

Referenced by AbstractBackwardEulerCardiacCell< SIZE >::serialize().

template<unsigned SIZE>
virtual void AbstractBackwardEulerCardiacCell< SIZE >::ComputeJacobian ( double  time,
const double  rCurrentGuess[SIZE],
double  rJacobian[SIZE][SIZE] 
)
pure virtual

Compute the Jacobian matrix for the nonlinear system portion of the cell model.

Parameters
timethe current time
rCurrentGuessthe current guess for $U_n$
rJacobianto be filled in with the Jacobian matrix

Referenced by AbstractBackwardEulerCardiacCell< SIZE >::serialize().

template<unsigned SIZE>
virtual void AbstractBackwardEulerCardiacCell< SIZE >::ComputeOneStepExceptVoltage ( double  tStart)
protectedpure virtual

Compute the values of all state variables, except the voltage, using backward Euler, for one timestep from tStart.

Note
This method must be provided by subclasses.
Parameters
tStartstart of this timestep

Referenced by AbstractBackwardEulerCardiacCell< SIZE >::Compute(), AbstractBackwardEulerCardiacCell< 0u >::Compute(), AbstractBackwardEulerCardiacCell< SIZE >::ComputeExceptVoltage(), AbstractBackwardEulerCardiacCell< 0u >::ComputeExceptVoltage(), AbstractBackwardEulerCardiacCell< SIZE >::EvaluateYDerivatives(), AbstractBackwardEulerCardiacCell< 0u >::EvaluateYDerivatives(), AbstractBackwardEulerCardiacCell< SIZE >::SolveAndUpdateState(), and AbstractBackwardEulerCardiacCell< 0u >::SolveAndUpdateState().

template<unsigned SIZE>
virtual void AbstractBackwardEulerCardiacCell< SIZE >::ComputeResidual ( double  time,
const double  rCurrentGuess[SIZE],
double  rResidual[SIZE] 
)
pure virtual

Compute the residual of the nonlinear system portion of the cell model.

Parameters
timethe current time
rCurrentGuessthe current guess for $U_n$
rResidualto be filled in with the residual vector

Referenced by AbstractBackwardEulerCardiacCell< SIZE >::serialize().

template<unsigned SIZE>
void AbstractBackwardEulerCardiacCell< SIZE >::EvaluateYDerivatives ( double  time,
const std::vector< double > &  rY,
std::vector< double > &  rDY 
)
inlineprivatevirtual

This function should never be called - the cell class incorporates its own solver.

Parameters
time
rY
rDY

Implements AbstractOdeSystem.

Definition at line 170 of file AbstractBackwardEulerCardiacCell.hpp.

References AbstractBackwardEulerCardiacCell< SIZE >::ComputeOneStepExceptVoltage(), NEVER_REACHED, and AbstractBackwardEulerCardiacCell< SIZE >::UpdateTransmembranePotential().

template<unsigned SIZE>
template<class Archive >
void AbstractBackwardEulerCardiacCell< SIZE >::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

Archive the member variables.

Parameters
archive
version

Definition at line 79 of file AbstractBackwardEulerCardiacCell.hpp.

References AbstractBackwardEulerCardiacCell< SIZE >::AbstractBackwardEulerCardiacCell(), AbstractBackwardEulerCardiacCell< SIZE >::Compute(), AbstractBackwardEulerCardiacCell< SIZE >::ComputeExceptVoltage(), AbstractBackwardEulerCardiacCell< SIZE >::ComputeJacobian(), AbstractBackwardEulerCardiacCell< SIZE >::ComputeResidual(), AbstractBackwardEulerCardiacCell< SIZE >::SolveAndUpdateState(), and AbstractBackwardEulerCardiacCell< SIZE >::~AbstractBackwardEulerCardiacCell().

template<unsigned SIZE>
void AbstractBackwardEulerCardiacCell< SIZE >::SolveAndUpdateState ( double  tStart,
double  tEnd 
)
virtual

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

Parameters
tStartbeginning of the time interval to simulate
tEndend of the time interval to simulate

Reimplemented from AbstractCardiacCell.

Definition at line 301 of file AbstractBackwardEulerCardiacCell.hpp.

References TimeStepper::AdvanceOneTimeStep(), AbstractBackwardEulerCardiacCell< SIZE >::ComputeOneStepExceptVoltage(), TimeStepper::GetTime(), TimeStepper::IsTimeAtEnd(), AbstractCardiacCell::mDt, AbstractBackwardEulerCardiacCell< SIZE >::UpdateTransmembranePotential(), and AbstractParameterisedSystem< std::vector< double > >::VerifyStateVariables().

Referenced by AbstractBackwardEulerCardiacCell< SIZE >::serialize().

template<unsigned SIZE>
virtual void AbstractBackwardEulerCardiacCell< SIZE >::UpdateTransmembranePotential ( double  time)
protectedpure virtual

Perform a forward Euler step to update the transmembrane potential.

Note
This method must be provided by subclasses.
Parameters
timestart of this timestep

Referenced by AbstractBackwardEulerCardiacCell< SIZE >::Compute(), AbstractBackwardEulerCardiacCell< 0u >::Compute(), AbstractBackwardEulerCardiacCell< SIZE >::EvaluateYDerivatives(), AbstractBackwardEulerCardiacCell< 0u >::EvaluateYDerivatives(), AbstractBackwardEulerCardiacCell< SIZE >::SolveAndUpdateState(), and AbstractBackwardEulerCardiacCell< 0u >::SolveAndUpdateState().

Friends And Related Function Documentation

template<unsigned SIZE>
friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 71 of file AbstractBackwardEulerCardiacCell.hpp.

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