AbstractCardiacCellInterface(boost::shared_ptr< AbstractIvpOdeSolver > pOdeSolver, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus) | AbstractCardiacCellInterface | |
AbstractCvodeCell(boost::shared_ptr< AbstractIvpOdeSolver > pSolver, unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus) | AbstractCvodeCell | |
AbstractCvodeCellWithDataClamp(boost::shared_ptr< AbstractIvpOdeSolver > pSolver, unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus) | AbstractCvodeCellWithDataClamp | |
AbstractCvodeSystem(unsigned numberOfStateVariables) | AbstractCvodeSystem | |
AbstractParameterisedSystem(unsigned numberOfStateVariables) | AbstractParameterisedSystem< N_Vector > | |
AbstractUntemplatedParameterisedSystem(unsigned numberOfStateVariables) | AbstractUntemplatedParameterisedSystem | |
boost::serialization::access | AbstractCvodeCellWithDataClamp | friend |
CheckParametersOnLoad(const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames) | AbstractParameterisedSystem< N_Vector > | protected |
Compute(double tStart, double tEnd, double tSamp=0.0) | AbstractCvodeCell | virtual |
ComputeDerivedQuantities(double time, const N_Vector &rState) | AbstractParameterisedSystem< N_Vector > | virtual |
ComputeDerivedQuantitiesFromCurrentState(double time) | AbstractParameterisedSystem< N_Vector > | |
ComputeExceptVoltage(double tStart, double tEnd) | AbstractCvodeCell | virtual |
CvodeError(int flag, const char *msg, const double &rTime, const double &rStartTime, const double &rEndTime) | AbstractCvodeSystem | private |
DumpState(const std::string &rMessage) | AbstractParameterisedSystem< N_Vector > | protected |
DumpState(const std::string &rMessage, N_Vector Y) | AbstractParameterisedSystem< N_Vector > | protected |
DumpState(const std::string &rMessage, N_Vector Y, double time) | AbstractParameterisedSystem< N_Vector > | protected |
EvaluateAnalyticJacobian(realtype time, N_Vector y, N_Vector ydot, CHASTE_CVODE_DENSE_MATRIX jacobian, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3) | AbstractCvodeSystem | inlinevirtual |
EvaluateYDerivatives(realtype time, const N_Vector y, N_Vector ydot)=0 | AbstractCvodeSystem | pure virtual |
ForceUseOfNumericalJacobian(bool useNumericalJacobian=true) | AbstractCvodeSystem | |
FreeCvodeMemory() | AbstractCvodeSystem | private |
GetAbsoluteTolerance() | AbstractCvodeSystem | |
GetAnyVariable(const std::string &rName, double time=0.0) | AbstractCvodeCell | virtual |
AbstractCvodeSystem::GetAnyVariable(unsigned index, double time=0.0, N_Vector *pDerivedQuantities=NULL) | AbstractParameterisedSystem< N_Vector > | |
AbstractCvodeSystem::GetAnyVariable(const std::string &rName, double time=0.0, N_Vector *pDerivedQuantities=NULL) | AbstractParameterisedSystem< N_Vector > | |
GetAnyVariableIndex(const std::string &rName) const | AbstractUntemplatedParameterisedSystem | |
GetAnyVariableUnits(unsigned index) const | AbstractUntemplatedParameterisedSystem | |
GetAnyVariableUnits(const std::string &rName) const | AbstractUntemplatedParameterisedSystem | |
GetAttribute(const std::string &rName) const | AbstractUntemplatedParameterisedSystem | |
GetDerivedQuantityIndex(const std::string &rName) const | AbstractUntemplatedParameterisedSystem | |
GetDerivedQuantityUnits(unsigned index) const | AbstractUntemplatedParameterisedSystem | |
GetExperimentalVoltageAtTimeT(const double &rTime) | AbstractCvodeCellWithDataClamp | protected |
GetForceReset() | AbstractCvodeSystem | |
GetIIonic(const std::vector< double > *pStateVariables=NULL)=0 | AbstractCardiacCellInterface | pure virtual |
GetInitialConditions() const | AbstractParameterisedSystem< N_Vector > | |
GetIntracellularAreaStimulus(double time) | AbstractCardiacCellInterface | |
GetIntracellularCalciumConcentration() | AbstractCardiacCellInterface | virtual |
GetIntracellularStimulus(double time) | AbstractCardiacCellInterface | |
GetLastStepSize() | AbstractCvodeSystem | |
GetLookupTableCollection() | AbstractCardiacCellInterface | inlinevirtual |
GetMaxSteps() | AbstractCvodeSystem | |
GetMinimalReset() | AbstractCvodeSystem | |
GetNumberOfAttributes() const | AbstractUntemplatedParameterisedSystem | |
GetNumberOfDerivedQuantities() const | AbstractUntemplatedParameterisedSystem | |
GetNumberOfParameters() const | AbstractCvodeCell | virtual |
GetNumberOfStateVariables() const | AbstractCvodeCell | virtual |
GetParameter(const std::string &rParameterName) | AbstractCvodeCell | virtual |
GetParameter(unsigned parameterIndex) | AbstractCvodeCell | virtual |
AbstractCvodeSystem::GetParameter(unsigned index) const | AbstractParameterisedSystem< N_Vector > | |
AbstractCvodeSystem::GetParameter(const std::string &rName) const | AbstractParameterisedSystem< N_Vector > | |
GetParameterIndex(const std::string &rName) const | AbstractUntemplatedParameterisedSystem | |
GetParameterUnits(unsigned index) const | AbstractUntemplatedParameterisedSystem | |
GetRelativeTolerance() | AbstractCvodeSystem | |
GetSolver() const | AbstractCardiacCellInterface | |
GetStateMessage(const std::string &rMessage, N_Vector Y) | AbstractParameterisedSystem< N_Vector > | private |
GetStateVariable(unsigned index) const | AbstractParameterisedSystem< N_Vector > | |
GetStateVariable(const std::string &rName) const | AbstractParameterisedSystem< N_Vector > | |
GetStateVariableIndex(const std::string &rName) const | AbstractUntemplatedParameterisedSystem | |
GetStateVariables() | AbstractParameterisedSystem< N_Vector > | |
GetStateVariableUnits(unsigned index) const | AbstractUntemplatedParameterisedSystem | |
GetStdVecStateVariables() | AbstractCvodeCell | virtual |
GetStimulus(double time) | AbstractCardiacCellInterface | |
GetStimulusFunction() | AbstractCardiacCellInterface | |
GetStimulusFunction() const | AbstractCardiacCellInterface | |
GetSystemInformation() const | AbstractUntemplatedParameterisedSystem | |
GetSystemName() const | AbstractUntemplatedParameterisedSystem | |
GetTimestep() | AbstractCvodeCell | |
GetUseAnalyticJacobian() const | AbstractCvodeSystem | |
GetVoltage() | AbstractCvodeCell | virtual |
GetVoltageIndex() | AbstractCardiacCellInterface | |
HasAnalyticJacobian() const | AbstractCvodeSystem | |
HasAnyVariable(const std::string &rName) const | AbstractUntemplatedParameterisedSystem | |
HasAttribute(const std::string &rName) const | AbstractUntemplatedParameterisedSystem | |
HasCellMLDefaultStimulus() | AbstractCardiacCellInterface | |
HasDerivedQuantity(const std::string &rName) const | AbstractUntemplatedParameterisedSystem | |
HasParameter(const std::string &rName) const | AbstractUntemplatedParameterisedSystem | |
HasStateVariable(const std::string &rName) const | AbstractUntemplatedParameterisedSystem | |
Init() | AbstractCvodeSystem | protected |
load(Archive &archive, const unsigned int version) | AbstractCvodeSystem | inlineprivate |
mAbsTol | AbstractCvodeSystem | protected |
mDataAvailable | AbstractCvodeCellWithDataClamp | private |
mDataClampIsOn | AbstractCvodeCellWithDataClamp | protected |
mExperimentalTimes | AbstractCvodeCellWithDataClamp | private |
mExperimentalVoltages | AbstractCvodeCellWithDataClamp | private |
mFixedVoltage | AbstractCardiacCellInterface | protected |
mForceMinimalReset | AbstractCvodeSystem | private |
mForceReset | AbstractCvodeSystem | private |
mHasAnalyticJacobian | AbstractCvodeSystem | protected |
mHasDefaultStimulusFromCellML | AbstractCardiacCellInterface | protected |
mIsUsedInTissue | AbstractCardiacCellInterface | protected |
mLastInternalStepSize | AbstractCvodeSystem | protected |
mLastSolutionState | AbstractCvodeSystem | private |
mLastSolutionTime | AbstractCvodeSystem | private |
mMaxDt | AbstractCvodeCell | protected |
mMaxSteps | AbstractCvodeSystem | protected |
mNumberOfStateVariables | AbstractUntemplatedParameterisedSystem | protected |
mParameters | AbstractParameterisedSystem< N_Vector > | protected |
mpCvodeMem | AbstractCvodeSystem | protected |
mpIntracellularStimulus | AbstractCardiacCellInterface | protected |
mpOdeSolver | AbstractCardiacCellInterface | protected |
mpSystemInfo | AbstractUntemplatedParameterisedSystem | protected |
mRelTol | AbstractCvodeSystem | protected |
mSetVoltageDerivativeToZero | AbstractCardiacCellInterface | protected |
mStateVariables | AbstractParameterisedSystem< N_Vector > | protected |
mUseAnalyticJacobian | AbstractCvodeSystem | protected |
mVoltageIndex | AbstractCardiacCellInterface | protected |
RecordStoppingPoint(double stopTime) | AbstractCvodeSystem | private |
ResetSolver() | AbstractCvodeSystem | |
ResetToInitialConditions() | AbstractParameterisedSystem< N_Vector > | virtual |
rGetDerivedQuantityNames() const | AbstractUntemplatedParameterisedSystem | |
rGetDerivedQuantityUnits() const | AbstractUntemplatedParameterisedSystem | |
rGetParameterNames() const | AbstractUntemplatedParameterisedSystem | |
rGetParameterUnits() const | AbstractUntemplatedParameterisedSystem | |
rGetStateVariableNames() const | AbstractCvodeCell | virtual |
rGetStateVariables() | AbstractParameterisedSystem< N_Vector > | |
rGetStateVariableUnits() const | AbstractUntemplatedParameterisedSystem | |
save(Archive &archive, const unsigned int version) const | AbstractCvodeSystem | inlineprivate |
serialize(Archive &archive, const unsigned int version) | AbstractCvodeCellWithDataClamp | inlineprivate |
SetAnyVariable(unsigned index, double value) | AbstractParameterisedSystem< N_Vector > | |
SetAnyVariable(const std::string &rName, double value) | AbstractParameterisedSystem< N_Vector > | |
SetDefaultInitialCondition(unsigned index, double initialCondition) | AbstractParameterisedSystem< N_Vector > | |
SetDefaultInitialConditions(const N_Vector &rInitialConditions) | AbstractParameterisedSystem< N_Vector > | |
SetExperimentalData(std::vector< double > experimentalTimes, std::vector< double > experimentalVoltages) | AbstractCvodeCellWithDataClamp | |
SetFixedVoltage(double voltage) | AbstractCardiacCellInterface | |
SetForceReset(bool autoReset) | AbstractCvodeSystem | |
SetIntracellularStimulusFunction(boost::shared_ptr< AbstractStimulusFunction > pStimulus) | AbstractCardiacCellInterface | |
SetMaxSteps(long int numSteps) | AbstractCvodeSystem | |
SetMaxTimestep(double maxDt) | AbstractCvodeCell | |
SetMinimalReset(bool minimalReset) | AbstractCvodeSystem | |
SetParameter(const std::string &rParameterName, double value) | AbstractCvodeCell | virtual |
AbstractCvodeSystem::SetParameter(unsigned index, double value) | AbstractParameterisedSystem< N_Vector > | |
SetSolver(boost::shared_ptr< AbstractIvpOdeSolver > pSolver) | AbstractCardiacCellInterface | |
SetStateVariable(unsigned index, double newValue) | AbstractCvodeCell | virtual |
SetStateVariable(const std::string &rName, double newValue) | AbstractCvodeCell | virtual |
SetStateVariables(const std::vector< double > &rVariables) | AbstractCvodeCell | virtual |
SetStateVariables(const N_Vector &rVariables) | AbstractCvodeCell | |
AbstractCvodeSystem::SetStateVariables(const N_Vector &rStateVariables) | AbstractParameterisedSystem< N_Vector > | |
SetStimulusFunction(boost::shared_ptr< AbstractStimulusFunction > pStimulus) | AbstractCardiacCellInterface | |
SetStretch(double stretch) | AbstractCardiacCellInterface | inlinevirtual |
SetTimestep(double maxDt) | AbstractCvodeCell | virtual |
SetTolerances(double relTol=1e-5, double absTol=1e-7) | AbstractCvodeSystem | |
SetupCvode(N_Vector initialConditions, realtype tStart, realtype maxDt) | AbstractCvodeSystem | private |
SetUsedInTissueSimulation(bool tissue=true) | AbstractCardiacCellInterface | |
SetVoltage(double voltage) | AbstractCvodeCell | virtual |
SetVoltageDerivativeToZero(bool clamp=true) | AbstractCvodeCell | virtual |
Solve(realtype tStart, realtype tEnd, realtype maxDt, realtype tSamp) | AbstractCvodeSystem | |
Solve(realtype tStart, realtype tEnd, realtype maxDt) | AbstractCvodeSystem | |
SolveAndUpdateState(double tStart, double tEnd) | AbstractCvodeCell | virtual |
TestCvodeCellsWithDataClamp | AbstractCvodeCellWithDataClamp | friend |
TurnOffDataClamp() | AbstractCvodeCellWithDataClamp | |
TurnOnDataClamp(double conductance=100) | AbstractCvodeCellWithDataClamp | |
UseCellMLDefaultStimulus() | AbstractCardiacCellInterface | virtual |
VerifyStateVariables() | AbstractParameterisedSystem< N_Vector > | inlinevirtual |
~AbstractCardiacCellInterface() | AbstractCardiacCellInterface | virtual |
~AbstractCvodeCell() | AbstractCvodeCell | virtual |
~AbstractCvodeCellWithDataClamp() | AbstractCvodeCellWithDataClamp | virtual |
~AbstractCvodeSystem() | AbstractCvodeSystem | virtual |
~AbstractUntemplatedParameterisedSystem() | AbstractUntemplatedParameterisedSystem | virtual |