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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <NhsContractionModel.hpp>
Public Member Functions | |
NhsContractionModel () | |
void | SetStretchAndStretchRate (double lambda, double dlambdaDt) |
void | SetInputParameters (ContractionModelInputParameters &rInputParameters) |
void | SetIntracellularCalciumConcentration (double calciumConcentration) |
double | GetCalciumTroponinValue () |
void | EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY) |
double | GetActiveTension () |
double | GetNextActiveTension () |
bool | IsStretchDependent () |
bool | IsStretchRateDependent () |
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AbstractOdeBasedContractionModel (unsigned numStateVariables) | |
virtual void | RunDoNotUpdate (double startTime, double endTime, double timeStep) |
void | UpdateStateVariables () |
void | RunAndUpdate (double startTime, double endTime, double timeStep) |
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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 |
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AbstractContractionModel () | |
virtual | ~AbstractContractionModel () |
void | SetStretch (double stretch) |
Protected Member Functions | |
void | CalculateCalciumTrop50 () |
double | CalculateT0 (double z) |
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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) |
Protected Attributes | |
double | mLambda |
double | mDLambdaDt |
double | mCalciumI |
double | mCalciumTrop50 |
double | mK1 |
double | mK2 |
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std::vector< double > | mTemporaryStateVariables |
double | mTime |
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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 |
Static Protected Attributes | |
static const double | mKon = 100 |
static const double | mKrefoff = 0.2 |
static const double | mGamma = 2 |
static const double | mCalciumTroponinMax = 0.07 |
static const double | mAlphaR1 = 0.002 |
static const double | mAlphaR2 = 0.0017 |
static const double | mKZ = 0.15 |
static const unsigned | mNr = 3u |
static const double | mBeta1 = -4 |
static const double | mAlpha0 = 0.008 |
static const unsigned | mN = 3u |
static const double | mZp = 0.85 |
static const double | mCalcium50ref = 0.00105 |
static const double | mTref = 56.2 |
static const double | mBeta0 = 4.9 |
static const double | mA = 0.35 |
static const double | mA1 = -29 |
static const double | mA2 = 138 |
static const double | mA3 = 129 |
static const double | mAlpha1 = 0.03 |
static const double | mAlpha2 = 0.130 |
static const double | mAlpha3 = 0.625 |
Friends | |
class | TestContractionModels |
NHS (Niederer, Hunter, Smith) model of active tension in cardiac cells.
A system of ODEs which determines the active potential, given the intracellular calcium concentration, the stretch (lambda) of the cell, and the stretch rate (dlambda_dt) of the cell.
The state variables are, in order: Calcium_troponin, z, Q1, Q2, Q3
Reference: S.A. Niederer, N.P. Smith, P.J. Hunter, "New developments in a strongly coupled cardiac electro-mechanical model" Europace 7, S118-S127
The active tension is returned in KPa.
Definition at line 56 of file NhsContractionModel.hpp.
NhsContractionModel::NhsContractionModel | ( | ) |
Constructor. Initialises all state variables to zero, lambda to 1, dlambda_dt to 0 and intracellular calcium concentration to 0
Definition at line 96 of file NhsContractionModel.cpp.
References CalculateCalciumTrop50(), OdeSystemInformation< ODE_SYSTEM >::Instance(), mAlphaR2, mCalciumI, mDLambdaDt, mK1, mK2, mKZ, mLambda, mNr, AbstractUntemplatedParameterisedSystem::mpSystemInfo, mZp, and AbstractParameterisedSystem< std::vector< double > >::ResetToInitialConditions().
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Compute the calcium_trop50 concentration. This is a function of constants and lambda, so only needs to be called in the constructor or when lambda is set
Definition at line 72 of file NhsContractionModel.cpp.
References mBeta0, mBeta1, mCalcium50ref, mCalciumTrop50, mCalciumTroponinMax, mGamma, mKon, mKrefoff, and mLambda.
Referenced by NhsContractionModel(), and SetStretchAndStretchRate().
z |
Definition at line 82 of file NhsContractionModel.cpp.
References mAlpha0, mAlphaR1, mBeta0, mCalciumTrop50, mCalciumTroponinMax, mK1, mK2, mLambda, mN, and mTref.
Referenced by NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), EvaluateYDerivatives(), GetActiveTension(), and NhsModelWithBackwardSolver::GetNextActiveTension().
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virtual |
Evaluate the derivatives of the state variables
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 145 of file NhsContractionModel.cpp.
References CalculateT0(), EXCEPTION, mA, mA1, mA2, mA3, mAlpha0, mAlpha1, mAlpha2, mAlpha3, mAlphaR1, mAlphaR2, mCalciumI, mCalciumTrop50, mCalciumTroponinMax, mDLambdaDt, mGamma, mKon, mKrefoff, mKZ, mN, mNr, and mTref.
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Implements AbstractContractionModel.
Definition at line 203 of file NhsContractionModel.cpp.
References CalculateT0(), mA, and AbstractParameterisedSystem< std::vector< double > >::mStateVariables.
double NhsContractionModel::GetCalciumTroponinValue | ( | ) |
Definition at line 140 of file NhsContractionModel.cpp.
References AbstractParameterisedSystem< std::vector< double > >::mStateVariables.
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inlinevirtual |
Implements AbstractContractionModel.
Reimplemented in NhsModelWithBackwardSolver.
Definition at line 211 of file NhsContractionModel.hpp.
References EXCEPTION.
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inlinevirtual |
Implements AbstractContractionModel.
Definition at line 219 of file NhsContractionModel.hpp.
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inlinevirtual |
Implements AbstractContractionModel.
Definition at line 227 of file NhsContractionModel.hpp.
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Set the current intracellular calcium concentration
rInputParameters | input parameters (calcium, voltage, time, of which only calcium is used) |
Implements AbstractContractionModel.
Definition at line 127 of file NhsContractionModel.cpp.
References DOUBLE_UNSET, ContractionModelInputParameters_::intracellularCalciumConcentration, and mCalciumI.
void NhsContractionModel::SetIntracellularCalciumConcentration | ( | double | calciumConcentration | ) |
Directly set the intracellular calcium concentration.
calciumConcentration | calcium concentration. |
Definition at line 134 of file NhsContractionModel.cpp.
References mCalciumI.
Set the current stretch and the stretch rate of the cell/fibre
lambda | current stretch |
dlambdaDt | current stretch rate |
Implements AbstractContractionModel.
Definition at line 118 of file NhsContractionModel.cpp.
References CalculateCalciumTrop50(), mDLambdaDt, and mLambda.
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Definition at line 58 of file NhsContractionModel.hpp.
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See reference. Dimensionless
Definition at line 125 of file NhsContractionModel.hpp.
Referenced by NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), EvaluateYDerivatives(), GetActiveTension(), and NhsModelWithBackwardSolver::GetNextActiveTension().
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staticprotected |
See reference. Dimensionless
Definition at line 128 of file NhsContractionModel.hpp.
Referenced by EvaluateYDerivatives(), and NhsModelWithBackwardSolver::ImplicitSolveForQ().
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See reference. Dimensionless
Definition at line 131 of file NhsContractionModel.hpp.
Referenced by EvaluateYDerivatives(), and NhsModelWithBackwardSolver::ImplicitSolveForQ().
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staticprotected |
See reference. Dimensionless
Definition at line 134 of file NhsContractionModel.hpp.
Referenced by EvaluateYDerivatives(), and NhsModelWithBackwardSolver::ImplicitSolveForQ().
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See reference. (ms)^-1
Definition at line 107 of file NhsContractionModel.hpp.
Referenced by NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), CalculateT0(), and EvaluateYDerivatives().
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See reference. (ms)^-1
Definition at line 137 of file NhsContractionModel.hpp.
Referenced by EvaluateYDerivatives(), and NhsModelWithBackwardSolver::ImplicitSolveForQ().
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See reference. (ms)^-1
Definition at line 140 of file NhsContractionModel.hpp.
Referenced by EvaluateYDerivatives(), and NhsModelWithBackwardSolver::ImplicitSolveForQ().
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staticprotected |
See reference. (ms)^-1
Definition at line 143 of file NhsContractionModel.hpp.
Referenced by EvaluateYDerivatives(), and NhsModelWithBackwardSolver::ImplicitSolveForQ().
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See reference. (ms)^-1
Definition at line 92 of file NhsContractionModel.hpp.
Referenced by NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), CalculateT0(), and EvaluateYDerivatives().
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See reference. (ms)^-1
Definition at line 95 of file NhsContractionModel.hpp.
Referenced by NhsContractionModel(), NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), and EvaluateYDerivatives().
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See reference. Dimensionless
Definition at line 122 of file NhsContractionModel.hpp.
Referenced by CalculateCalciumTrop50(), and CalculateT0().
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See reference. Dimensionless
Definition at line 104 of file NhsContractionModel.hpp.
Referenced by CalculateCalciumTrop50().
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See reference. mMols
Definition at line 116 of file NhsContractionModel.hpp.
Referenced by CalculateCalciumTrop50().
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The intracellular calcium concentration. To be specified by the caller
Definition at line 66 of file NhsContractionModel.hpp.
Referenced by NhsContractionModel(), NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), EvaluateYDerivatives(), SetInputParameters(), and SetIntracellularCalciumConcentration().
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A parameter only dependent on constants and lambda, so updated whenever lambda is updated
Definition at line 70 of file NhsContractionModel.hpp.
Referenced by CalculateCalciumTrop50(), NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), CalculateT0(), and EvaluateYDerivatives().
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See reference. mMols
Definition at line 89 of file NhsContractionModel.hpp.
Referenced by CalculateCalciumTrop50(), NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), CalculateT0(), and EvaluateYDerivatives().
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The stretch rate. To be specified by the caller
Definition at line 64 of file NhsContractionModel.hpp.
Referenced by NhsContractionModel(), EvaluateYDerivatives(), NhsModelWithBackwardSolver::ImplicitSolveForQ(), and SetStretchAndStretchRate().
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See reference. Dimensionless
Definition at line 86 of file NhsContractionModel.hpp.
Referenced by CalculateCalciumTrop50(), NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), and EvaluateYDerivatives().
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A constant determined from the other constrants. Set up in the constructor
Definition at line 73 of file NhsContractionModel.hpp.
Referenced by NhsContractionModel(), and CalculateT0().
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A constant determined from the other constrants. Set up in the constructor
Definition at line 75 of file NhsContractionModel.hpp.
Referenced by NhsContractionModel(), and CalculateT0().
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See reference. (mMols)^-1 (ms)^-1
Definition at line 80 of file NhsContractionModel.hpp.
Referenced by CalculateCalciumTrop50(), NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), and EvaluateYDerivatives().
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See reference. (ms)^-1
Definition at line 83 of file NhsContractionModel.hpp.
Referenced by CalculateCalciumTrop50(), NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), and EvaluateYDerivatives().
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See reference. Dimensionless
Definition at line 98 of file NhsContractionModel.hpp.
Referenced by NhsContractionModel(), NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), and EvaluateYDerivatives().
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The stretch. To be specified by the caller
Definition at line 62 of file NhsContractionModel.hpp.
Referenced by NhsContractionModel(), CalculateCalciumTrop50(), CalculateT0(), and SetStretchAndStretchRate().
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See reference. Dimensionless
Definition at line 110 of file NhsContractionModel.hpp.
Referenced by NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), CalculateT0(), and EvaluateYDerivatives().
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See reference. Dimensionless
Definition at line 101 of file NhsContractionModel.hpp.
Referenced by NhsContractionModel(), NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), and EvaluateYDerivatives().
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See reference. kPa
Definition at line 119 of file NhsContractionModel.hpp.
Referenced by NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), CalculateT0(), and EvaluateYDerivatives().
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See reference. Dimensionless
Definition at line 113 of file NhsContractionModel.hpp.
Referenced by NhsContractionModel().