AbstractGeneralizedRushLarsenCardiacCell Class Reference

#include <AbstractGeneralizedRushLarsenCardiacCell.hpp>

Inherits AbstractCardiacCell.

Collaboration diagram for AbstractGeneralizedRushLarsenCardiacCell:
Collaboration graph
[legend]

List of all members.

Public Member Functions

 AbstractGeneralizedRushLarsenCardiacCell (unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
virtual ~AbstractGeneralizedRushLarsenCardiacCell ()
OdeSolution Compute (double tStart, double tEnd, double tSamp=0.0)
void ComputeExceptVoltage (double tStart, double tEnd)
void SolveAndUpdateState (double tStart, double tEnd)

Protected Member Functions

virtual void ComputeOneStepExceptVoltage (double time)=0
virtual void UpdateTransmembranePotential (double time)=0

Protected Attributes

std::vector< double > mPartialF
std::vector< double > mEvalF
std::vector< double > mYInit

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

Detailed Description

This is the base class for cardiac cells solved using the GRL methods (GRL1 and GRL2). Modified from AbstractRushLarsenCardiacCell.hpp

Definition at line 59 of file AbstractGeneralizedRushLarsenCardiacCell.hpp.

Constructor & Destructor Documentation

AbstractGeneralizedRushLarsenCardiacCell::AbstractGeneralizedRushLarsenCardiacCell ( unsigned  numberOfStateVariables,
unsigned  voltageIndex,
boost::shared_ptr< AbstractStimulusFunction >  pIntracellularStimulus 
)

Standard constructor for a cell.

Parameters:
numberOfStateVariables the size of the ODE system
voltageIndex the index of the variable representing the transmembrane potential within the state variable vector
pIntracellularStimulus the intracellular stimulus function

Some notes for future reference:

  • 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 53 of file AbstractGeneralizedRushLarsenCardiacCell.cpp.

References mEvalF, mPartialF, and mYInit.

AbstractGeneralizedRushLarsenCardiacCell::~AbstractGeneralizedRushLarsenCardiacCell (  )  [virtual]

Virtual destructor

Definition at line 66 of file AbstractGeneralizedRushLarsenCardiacCell.cpp.

Member Function Documentation

OdeSolution AbstractGeneralizedRushLarsenCardiacCell::Compute ( double  tStart,
double  tEnd,
double  tSamp = 0.0 
) [virtual]

Simulates this cell's behaviour between the time interval [tStart, tEnd], with timestep mDt.

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

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 mDt)
Returns:
the values of each state variable, at intervals of tSamp.

Reimplemented from AbstractCardiacCell.

Definition at line 69 of file AbstractGeneralizedRushLarsenCardiacCell.cpp.

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

void AbstractGeneralizedRushLarsenCardiacCell::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, but the other state variables are updated.

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

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

Reimplemented from AbstractCardiacCell.

Definition at line 109 of file AbstractGeneralizedRushLarsenCardiacCell.cpp.

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

virtual void AbstractGeneralizedRushLarsenCardiacCell::ComputeOneStepExceptVoltage ( double  time  )  [protected, pure virtual]

Update the values of all variables except the transmembrane potential using a GRL method.

Parameters:
time the current simulation time

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

void AbstractGeneralizedRushLarsenCardiacCell::EvaluateYDerivatives ( double  time,
const std::vector< double > &  rY,
std::vector< double > &  rDY 
) [inline, private, virtual]

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

Parameters:
time 
rY 
rDY 

Implements AbstractOdeSystem.

Definition at line 142 of file AbstractGeneralizedRushLarsenCardiacCell.hpp.

References NEVER_REACHED.

template<class Archive >
void AbstractGeneralizedRushLarsenCardiacCell::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, private]

Archive the member variables.

Parameters:
archive 
version 

Reimplemented from AbstractCardiacCell.

Definition at line 71 of file AbstractGeneralizedRushLarsenCardiacCell.hpp.

void AbstractGeneralizedRushLarsenCardiacCell::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:
tStart beginning of the time interval to simulate
tEnd end of the time interval to simulate

Reimplemented from AbstractCardiacCell.

Definition at line 128 of file AbstractGeneralizedRushLarsenCardiacCell.cpp.

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

virtual void AbstractGeneralizedRushLarsenCardiacCell::UpdateTransmembranePotential ( double  time  )  [protected, pure virtual]

Perform a forward Euler step to update the transmembrane potential.

Parameters:
time the current simulation time

Referenced by Compute(), and SolveAndUpdateState().

Friends And Related Function Documentation

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractCardiacCell.

Definition at line 63 of file AbstractGeneralizedRushLarsenCardiacCell.hpp.

Member Data Documentation

std::vector<double> AbstractGeneralizedRushLarsenCardiacCell::mEvalF [protected]

The derivatives, working memory for use by subclasses.

Definition at line 167 of file AbstractGeneralizedRushLarsenCardiacCell.hpp.

Referenced by AbstractGeneralizedRushLarsenCardiacCell().

std::vector<double> AbstractGeneralizedRushLarsenCardiacCell::mPartialF [protected]

The diagonal of the Jacobian, working memory for use by subclasses.

Definition at line 164 of file AbstractGeneralizedRushLarsenCardiacCell.hpp.

Referenced by AbstractGeneralizedRushLarsenCardiacCell().

std::vector<double> AbstractGeneralizedRushLarsenCardiacCell::mYInit [protected]

The state at the beginning of the current step, working memory for use by subclasses.

Definition at line 170 of file AbstractGeneralizedRushLarsenCardiacCell.hpp.

Referenced by AbstractGeneralizedRushLarsenCardiacCell().

The documentation for this class was generated from the following files:
Generated by  doxygen 1.6.2