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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <FitzHughNagumo1961OdeSystem.hpp>
Public Member Functions | |
FitzHughNagumo1961OdeSystem (boost::shared_ptr< AbstractIvpOdeSolver > pOdeSolver, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus) | |
~FitzHughNagumo1961OdeSystem () | |
void | EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY) |
double | GetIIonic (const std::vector< double > *pStateVariables=NULL) |
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AbstractCardiacCell (boost::shared_ptr< AbstractIvpOdeSolver > pOdeSolver, unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus) | |
virtual | ~AbstractCardiacCell () |
void | Init () |
void | SetTimestep (double dt) |
virtual void | SolveAndUpdateState (double tStart, double tEnd) |
virtual OdeSolution | Compute (double tStart, double tEnd, double tSamp=0.0) |
virtual void | ComputeExceptVoltage (double tStart, double tEnd) |
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 () |
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AbstractCardiacCellInterface (boost::shared_ptr< AbstractIvpOdeSolver > pOdeSolver, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus) | |
virtual | ~AbstractCardiacCellInterface () |
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 () |
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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 |
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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) |
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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 |
Static Private Attributes | |
static const double | mAlpha = -0.08 |
static const double | mGamma = 3.00 |
static const double | mEpsilon = 0.005 |
Additional Inherited Members | |
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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) |
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double | mDt |
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unsigned | mVoltageIndex |
boost::shared_ptr< AbstractIvpOdeSolver > | mpOdeSolver |
boost::shared_ptr< AbstractStimulusFunction > | mpIntracellularStimulus |
bool | mSetVoltageDerivativeToZero |
bool | mIsUsedInTissue |
bool | mHasDefaultStimulusFromCellML |
double | mFixedVoltage |
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bool | mUseAnalyticJacobian |
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std::vector< double > | mStateVariables |
std::vector< double > | mParameters |
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unsigned | mNumberOfStateVariables |
boost::shared_ptr< AbstractOdeSystemInformation > | mpSystemInfo |
Represents the FitzHugh-Nagumo system of ODEs.
Definition at line 45 of file FitzHughNagumo1961OdeSystem.hpp.
FitzHughNagumo1961OdeSystem::FitzHughNagumo1961OdeSystem | ( | boost::shared_ptr< AbstractIvpOdeSolver > | pOdeSolver, |
boost::shared_ptr< AbstractStimulusFunction > | pIntracellularStimulus | ||
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Constructor
pOdeSolver | is a pointer to the ODE solver |
pIntracellularStimulus | is a pointer to the intracellular stimulus |
Definition at line 47 of file FitzHughNagumo1961OdeSystem.cpp.
References AbstractCardiacCell::Init(), OdeSystemInformation< ODE_SYSTEM >::Instance(), and AbstractUntemplatedParameterisedSystem::mpSystemInfo.
FitzHughNagumo1961OdeSystem::~FitzHughNagumo1961OdeSystem | ( | void | ) |
Destructor
Definition at line 57 of file FitzHughNagumo1961OdeSystem.cpp.
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virtual |
Compute the RHS of the FitHugh-Nagumo system of ODEs
time | the current time, in milliseconds |
rY | current values of the state variables |
rDY | to be filled in with derivatives |
Implements AbstractOdeSystem.
Definition at line 61 of file FitzHughNagumo1961OdeSystem.cpp.
References AbstractCardiacCellInterface::GetIntracellularAreaStimulus(), mAlpha, mEpsilon, mGamma, and AbstractCardiacCellInterface::mSetVoltageDerivativeToZero.
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virtual |
Calculates the ionic current.
pStateVariables | optionally can be supplied to evaluate the ionic current at the given state; by default the cell's internal state will be used. |
Implements AbstractCardiacCellInterface.
Definition at line 83 of file FitzHughNagumo1961OdeSystem.cpp.
References mAlpha, AbstractParameterisedSystem< std::vector< double > >::mStateVariables, and AbstractCardiacCellInterface::mVoltageIndex.
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staticprivate |
Constant parameter alpha
Definition at line 48 of file FitzHughNagumo1961OdeSystem.hpp.
Referenced by EvaluateYDerivatives(), and GetIIonic().
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staticprivate |
Constant parameter epsilon
Definition at line 50 of file FitzHughNagumo1961OdeSystem.hpp.
Referenced by EvaluateYDerivatives().
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staticprivate |
Constant parameter gamma
Definition at line 49 of file FitzHughNagumo1961OdeSystem.hpp.
Referenced by EvaluateYDerivatives().