Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
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#include <FakeBathCell.hpp>
Public Member Functions | |
FakeBathCell (boost::shared_ptr< AbstractIvpOdeSolver > pSolver, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus) | |
~FakeBathCell () | |
void | EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY) |
double | GetIIonic (const std::vector< double > *pStateVariables=NULL) |
void | ComputeExceptVoltage (double tStart, double tEnd) |
double | GetIntracellularCalciumConcentration () |
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) |
virtual void | SolveAndUpdateState (double tStart, double tEnd) |
virtual OdeSolution | Compute (double tStart, double tEnd, double tSamp=0.0) |
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 () |
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) |
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 |
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 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) |
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 |
This class represents a fake cell for use within the bath of a bidomain simulation.
Definition at line 52 of file FakeBathCell.hpp.
FakeBathCell::FakeBathCell | ( | boost::shared_ptr< AbstractIvpOdeSolver > | pSolver, |
boost::shared_ptr< AbstractStimulusFunction > | pIntracellularStimulus | ||
) |
Constructor uses the same signature as normal cells, for convenience.
pSolver | unused |
pIntracellularStimulus | unused |
Definition at line 39 of file FakeBathCell.cpp.
References AbstractCardiacCell::Init(), OdeSystemInformation< ODE_SYSTEM >::Instance(), and AbstractUntemplatedParameterisedSystem::mpSystemInfo.
FakeBathCell::~FakeBathCell | ( | ) |
Destructor; does nothing.
Definition at line 47 of file FakeBathCell.cpp.
There isn't really a cell here, so we override this method to do nothing.
tStart | unused |
tEnd | unused |
Reimplemented from AbstractCardiacCell.
Definition at line 63 of file FakeBathCell.cpp.
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virtual |
This method is pure in a base class, so we need it, but we never use it. It has an empty body.
time | unused |
rY | unused |
rDY | unused |
Implements AbstractOdeSystem.
Definition at line 52 of file FakeBathCell.cpp.
References NEVER_REACHED.
Fake cells have no transmembrane currents, so this method always returns 0.
pStateVariables | unused |
Implements AbstractCardiacCellInterface.
Definition at line 58 of file FakeBathCell.cpp.
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virtual |
There is really no calcium here, so we override this method to return a dummy value (0) Implementing this with a dummy implementation is needed by mechanics
Reimplemented from AbstractCardiacCellInterface.
Definition at line 67 of file FakeBathCell.cpp.
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inlineprivate |
Archive this cell. Just calls the base class version.
archive | |
version |
Definition at line 64 of file FakeBathCell.hpp.
References AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables.
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friend |
Needed for serialization.
Definition at line 56 of file FakeBathCell.hpp.