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Private Attributes
IonicFox Class Reference

IonicModel - This class implements an ionic model. More...

#include <IonicFox.hpp>

+ Inheritance diagram for IonicFox:
+ Collaboration diagram for IonicFox:

Private Attributes

Real M_ACap
 Cell Geometry Parameters (4) More...
 
Real M_VMyo
 
Real M_Vsr
 
Real M_Vup
 
Real M_NaO
 Standard Ionic Concentrations (5) More...
 
Real M_CaO
 
Real M_K0
 
Real M_NaIn
 
Real M_KIn
 
Real M_CmdnTot
 Buffering Parameters (4) More...
 
Real M_CsqnTot
 
Real M_KmCmdn
 
Real M_KmCsqn
 
Real M_Cm
 Membrane Current Parameters (24) More...
 
Real M_F
 
Real M_T
 
Real M_R
 
Real M_GNa
 
Real M_GKp
 
Real M_kNaCa
 
Real M_KmNa
 
Real M_KmCa
 
Real M_kSat
 
Real M_eta
 
Real M_INaK
 
Real M_KmNai
 
Real M_KmK0
 
Real M_GK1
 
Real M_GKr
 
Real M_GKs
 
Real M_Gt0
 
Real M_IpCa
 
Real M_KmPCa
 
Real M_GCab
 
Real M_GNab
 
Real M_KmK1
 
Real M_KmfCa
 
Real M_KmUp
 SR Parameters (1) More...
 
Real M_PCa
 L-type Ca2+ Channel Parameters (6) More...
 
Real M_PCaK
 
Real M_Prel
 
Real M_Pleak
 
Real M_ICaHalf
 
Real M_KmpCa
 

Type definitions

typedef ElectroIonicModel super
 
typedef std::shared_ptr< VectorEpetra > vectorPtr_Type
 
typedef RegionMesh< LinearTetra > mesh_Type
 

Constructors & Destructor

 IonicFox ()
 Constructor. More...
 
 IonicFox (Teuchos::ParameterList &parameterList)
 
 IonicFox (const IonicFox &model)
 
virtual ~IonicFox ()
 Destructor. More...
 

Overloads

IonicFox & operator= (const IonicFox &model)
 Operator. More...
 

Setters and getters

const Real & areaCap () const
 
void setACap (const Real &areaCap)
 
const Real & volMyo () const
 
void setVMyo (const Real &volMyo)
 
const Real & volSR () const
 
void setVsr (const Real &volSR)
 
const Real & volUp () const
 
void setVup (const Real &volUp)
 
const Real & concNa0 () const
 
void setNa0 (const Real &concNa0)
 
const Real & concCa0 () const
 
void setCa0 (const Real &concCa0)
 
const Real & concK0 () const
 
void setK0 (const Real &concK0)
 
const Real & concNaIn () const
 
void setNaIn (const Real &concNaIn)
 
const Real & concKIn () const
 
void setKIn (const Real &concKIn)
 
const Real & cmdnTot () const
 
void setCmdnTot (const Real &cmdnTot)
 
const Real & csqnTot () const
 
void setCsqnTot (const Real &csqnTot)
 
const Real & constmCmdn () const
 
void setKmCmdn (const Real &constmCmdn)
 
const Real & constmCsqn () const
 
void setKmCsqn (const Real &constmCsqn)
 
const Real & capMem () const
 
void setCapMem (const Real &capMem)
 
const Real & farad () const
 
void setFarad (const Real &farad)
 
const Real & temp () const
 
void setTemp (const Real &temp)
 
const Real & gasConst () const
 
void setR (const Real &gasConst)
 
const Real & maxCondNa () const
 
void setGNa (const Real &maxCondNa)
 
const Real & maxCondKp () const
 
void setGkp (const Real &maxCondKp)
 
const Real & maxCondK1 () const
 
void setGk1 (const Real &maxCondK1)
 
const Real & maxCondKr () const
 
void setGkr (const Real &maxCondKr)
 
const Real & maxCondKs () const
 
void setGks (const Real &maxCondKs)
 
const Real & maxCondt0 () const
 
void setGkt0 (const Real &maxCondt0)
 
const Real & kNaCa () const
 
void setKNaCa (const Real &kNaCa)
 
const Real & constmfCa () const
 
void setKmfCa (const Real &constmfCa)
 
const Real & constmK1 () const
 
void setKmK1 (const Real &constmK1)
 
const Real & constmNa () const
 
void setKmNa (const Real &constmNa)
 
const Real & constmCa () const
 
void setKmCa (const Real &constmCa)
 
const Real & kSat () const
 
void setKSat (const Real &kSat)
 
const Real & eta () const
 
void setEta (const Real &eta)
 
const Real & courNaK () const
 
void setINaK (const Real &courNaK)
 
const Real & constmNai () const
 
void setKmNai (const Real &constmNai)
 
const Real & constmK0 () const
 
void setKmK0 (const Real &constmK0)
 
const Real & permCa () const
 
void setPnsCa (const Real &permCa)
 
const Real & constmpCa () const
 
void setKmpCa (const Real &constmpCa)
 
const Real & courpCa () const
 
void setIpCa (const Real &courpCa)
 
const Real & maxCondCab () const
 
void setGCab (const Real &maxCondCab)
 
const Real & maxCondNab () const
 
void setGNab (const Real &maxCondNab)
 
const Real & constmUp () const
 
void setKmUp (const Real &constmUp)
 
const Real & permCaK () const
 
void setPCaK (const Real &permCaK)
 
const Real & permrel () const
 
void setPrel (const Real &permrel)
 
const Real & permleak () const
 
void setPleak (const Real &permleak)
 
const Real & courCaHalf () const
 
void setICaHalf (const Real &courCaHalf)
 

Methods

void computeGatingRhs (const std::vector< Real > &v, std::vector< Real > &rhs)
 Methods. More...
 
void computeRhs (const std::vector< Real > &v, std::vector< Real > &rhs)
 This methods contains the actual evaluation of the rhs of all state variablesin the model (0D version) More...
 
Real computeLocalPotentialRhs (const std::vector< Real > &v)
 This methods contains the actual evaluation of the rhs of the voltage equation only (0D version) More...
 
std::vector< Real > computeLocalGatingRhs (const std::vector< Real > &v)
 
void computeGatingVariablesWithRushLarsen (std::vector< Real > &v, const Real dt)
 This methods contains the actual evaluation of the rhs of the voltage equation only (0D version) More...
 
void computeNonGatingRhs (const std::vector< Real > &v, std::vector< Real > &rhs)
 In the case this method is improperly used, it should use this default implementation. More...
 
std::vector< Real > computeLocalSubSysCaRhs (const std::vector< Real > &v)
 Ca2+ Subsystem. More...
 
std::vector< Real > fastINa (const std::vector< Real > &v)
 Ionic Currents (Luo and Rudy) More...
 
std::vector< Real > rapidIK (const std::vector< Real > &v)
 
std::vector< Real > transOutIK (const std::vector< Real > &v)
 
std::vector< Real > slowIK (const std::vector< Real > &v)
 
std::vector< Real > timeDIK (const std::vector< Real > &v)
 
Real timeIIK1 (const std::vector< Real > &v)
 
Real plaIKp (const std::vector< Real > &v)
 
Real exINaCa (const std::vector< Real > &v)
 
Real pumpINaK (const std::vector< Real > &v)
 
Real pumpIpCa (const std::vector< Real > &v)
 
Real backICab (const std::vector< Real > &v)
 
Real backINab (const std::vector< Real > &v)
 
void showMe ()
 Display information about the model. More...
 

Additional Inherited Members

- Public Types inherited from ElectroIonicModel
typedef VectorEpetra vector_Type
 
typedef std::shared_ptr< VectorEpetra > vectorPtr_Type
 
typedef std::shared_ptr< VectorElemental > elvecPtr_Type
 
typedef RegionMesh< LinearTetra > mesh_Type
 
typedef MatrixEpetra< Real > matrix_Type
 
typedef std::shared_ptr< matrix_Type > matrixPtr_Type
 
typedef FESpace< mesh_Type, MapEpetra > feSpace_Type
 
typedef std::shared_ptr< feSpace_Type > feSpacePtr_Type
 
typedef std::function< Real(const Real &t, const Real &x, const Real &y, const Real &z, const ID &i) > function_Type
 
typedef FactorySingleton< Factory< ElectroIonicModel, std::string > > IonicModelFactory
 
- Public Member Functions inherited from ElectroIonicModel
virtual matrix_Type getJac (const vector_Type &v, Real h=1.0e-8)
 This methods computes the Jacobian numerically. More...
 
virtual std::vector< std::vector< Real > > getJac (const std::vector< Real > &v, Real h=1.0e-8)
 This methods computes the Jacobian numerically. More...
 
virtual void computeGatingRhs (const std::vector< vectorPtr_Type > &v, std::vector< vectorPtr_Type > &rhs)
 This methods computes the right hand side of the gating variables in the 3D case. More...
 
virtual void computeNonGatingRhs (const std::vector< vectorPtr_Type > &v, std::vector< vectorPtr_Type > &rhs)
 This methods computes the right hand side of the state variables that are not gating variables in the 3D case. More...
 
virtual void computeGatingVariablesWithRushLarsen (std::vector< vectorPtr_Type > &v, const Real dt)
 Compute the new value of the gating variables in 3D with the Rush Larsen method specified in the 0D version of the ionic model. More...
 
virtual void computeRhs (const std::vector< vectorPtr_Type > &v, std::vector< vectorPtr_Type > &rhs)
 Compute the right hand side of the ionic model in 3D. More...
 
virtual void computePotentialRhsICI (const std::vector< vectorPtr_Type > &v, std::vector< vectorPtr_Type > &rhs, matrix_Type &massMatrix)
 Compute the right hand side of the voltage equation linearly interpolating the ionic currents. More...
 
virtual void computePotentialRhsSVI (const std::vector< vectorPtr_Type > &v, std::vector< vectorPtr_Type > &rhs, FESpace< mesh_Type, MapEpetra > &uFESpace)
 Compute the right hand side of the voltage equation using SVI. More...
 
virtual void computePotentialRhsSVI (const std::vector< vectorPtr_Type > &v, std::vector< vectorPtr_Type > &rhs, FESpace< mesh_Type, MapEpetra > &uFESpace, const QuadratureRule &qr)
 Compute the right hand side of the voltage equation using SVI specifying the quadrature rule. More...
 
virtual void initialize (std::vector< Real > &v)
 Initialize the ionic model with a given vector of state variable (0D version) More...
 
virtual void initialize (std::vector< vectorPtr_Type > &v)
 Initialize the ionic model in 3D with a given vector of state variable vector pointers. More...
 
 ElectroIonicModel ()
 Empty Constructor. More...
 
 ElectroIonicModel (int n)
 Constructor. More...
 
 ElectroIonicModel (int n, int g)
 Constructor. More...
 
 ElectroIonicModel (const ElectroIonicModel &Ionic)
 Copy Constructor. More...
 
virtual ~ElectroIonicModel ()
 Destructor. More...
 
virtual void setup (Teuchos::ParameterList &parameterList)
 setup the parameters of the ionic model from an xml file More...
 
const short int Size () const
 returns the number of equations of the ionic model More...
 
const short int numberOfGatingVariables () const
 returns the number of gating variables in the ionic model More...
 
const Real membraneCapacitance () const
 returns the value of the membrane capacitance in the model More...
 
const Real appliedCurrent () const
 returns the value of the applied current in the model/point More...
 
vectorPtr_Type appliedCurrentPtr ()
 returns the pointer to the applied current FE vector in the 3D case More...
 
const std::vector< Real > restingConditions () const
 returns the vector with the resting values of the variables in the ionic model More...
 
const function_Type pacaingProtocol () const
 returns the function describing the pacing protocol for the ionic model More...
 
void setMembraneCapacitance (const Real p)
 set the membrane capacitance in the ionic model More...
 
void setAppliedCurrent (const Real p)
 set the applied current in the ionic model/point More...
 
void setAppliedCurrentPtr (const vectorPtr_Type p)
 set the pointer to the applied current in the 3D ionic model More...
 
void setAppliedCurrent (const vector_Type &p)
 set the pointer to the applied current in the 3D ionic model More...
 
void setAppliedCurrentFromFunction (function_Type &f, feSpacePtr_Type feSpacePtr, Real time=0.0)
 Interpolate the function f on the FE space feSpacePtr at time time. More...
 
void setAppliedCurrentFromElectroStimulus (ElectroStimulus &stimulus, feSpacePtr_Type feSpacePtr, Real time=0.0)
 Interpolate the function of the electro stimulus. More...
 
void setPacingProtocol (function_Type pacingProtocol)
 Set the pacing protocol as boost function. More...
 
void setRestingCondtions (Real value, int j)
 Set component of the resting conditions. More...
 
void setRestingCondtions (std::vector< Real > &restingConditions)
 Set resting conditions. More...
 
void addAppliedCurrent (Real &rhs)
 Simple wrapper to add the applied current. More...
 
void addAppliedCurrent (std::vector< Real > &rhs)
 Simple wrapper to add the applied current. More...
 
ElectroIonicModel & operator= (const ElectroIonicModel &Ionic)
 Assignment operator. More...
 
- Protected Attributes inherited from ElectroIonicModel
short int M_numberOfEquations
 
short int M_numberOfGatingVariables
 
std::vector< Real > M_restingConditions
 
Real M_membraneCapacitance
 
Real M_appliedCurrent
 
vectorPtr_Type M_appliedCurrentPtr
 
function_Type M_pacingProtocol
 

Detailed Description

IonicModel - This class implements an ionic model.

Definition at line 61 of file IonicFox.hpp.

Member Typedef Documentation

◆ super

typedef ElectroIonicModel super

Definition at line 67 of file IonicFox.hpp.

◆ vectorPtr_Type

typedef std::shared_ptr<VectorEpetra> vectorPtr_Type

Definition at line 68 of file IonicFox.hpp.

◆ mesh_Type

typedef RegionMesh<LinearTetra> mesh_Type

Definition at line 69 of file IonicFox.hpp.

Constructor & Destructor Documentation

◆ IonicFox() [1/3]

IonicFox ( )

Constructor.

Constructors.

Definition at line 51 of file IonicFox.cpp.

◆ IonicFox() [2/3]

IonicFox ( Teuchos::ParameterList &  parameterList)
Parameters
Epetracommunicator
listof parameters in an xml file

Definition at line 112 of file IonicFox.cpp.

◆ IonicFox() [3/3]

IonicFox ( const IonicFox &  model)
Parameters
IonicFoxobject

Definition at line 160 of file IonicFox.cpp.

◆ ~IonicFox()

virtual ~IonicFox ( )
inlinevirtual

Destructor.

Definition at line 92 of file IonicFox.hpp.

Member Function Documentation

◆ operator=()

IonicFox & operator= ( const IonicFox &  model)

Operator.

Definition at line 214 of file IonicFox.cpp.

◆ areaCap()

const Real& areaCap ( ) const
inline

Definition at line 106 of file IonicFox.hpp.

◆ setACap()

void setACap ( const Real &  areaCap)
inline

Definition at line 110 of file IonicFox.hpp.

◆ volMyo()

const Real& volMyo ( ) const
inline

Definition at line 115 of file IonicFox.hpp.

◆ setVMyo()

void setVMyo ( const Real &  volMyo)
inline

Definition at line 119 of file IonicFox.hpp.

◆ volSR()

const Real& volSR ( ) const
inline

Definition at line 124 of file IonicFox.hpp.

◆ setVsr()

void setVsr ( const Real &  volSR)
inline

Definition at line 128 of file IonicFox.hpp.

◆ volUp()

const Real& volUp ( ) const
inline

Definition at line 133 of file IonicFox.hpp.

◆ setVup()

void setVup ( const Real &  volUp)
inline

Definition at line 138 of file IonicFox.hpp.

◆ concNa0()

const Real& concNa0 ( ) const
inline

Definition at line 143 of file IonicFox.hpp.

◆ setNa0()

void setNa0 ( const Real &  concNa0)
inline

Definition at line 147 of file IonicFox.hpp.

◆ concCa0()

const Real& concCa0 ( ) const
inline

Definition at line 152 of file IonicFox.hpp.

◆ setCa0()

void setCa0 ( const Real &  concCa0)
inline

Definition at line 156 of file IonicFox.hpp.

◆ concK0()

const Real& concK0 ( ) const
inline

Definition at line 161 of file IonicFox.hpp.

◆ setK0()

void setK0 ( const Real &  concK0)
inline

Definition at line 165 of file IonicFox.hpp.

◆ concNaIn()

const Real& concNaIn ( ) const
inline

Definition at line 170 of file IonicFox.hpp.

◆ setNaIn()

void setNaIn ( const Real &  concNaIn)
inline

Definition at line 174 of file IonicFox.hpp.

◆ concKIn()

const Real& concKIn ( ) const
inline

Definition at line 179 of file IonicFox.hpp.

◆ setKIn()

void setKIn ( const Real &  concKIn)
inline

Definition at line 183 of file IonicFox.hpp.

◆ cmdnTot()

const Real& cmdnTot ( ) const
inline

Definition at line 188 of file IonicFox.hpp.

◆ setCmdnTot()

void setCmdnTot ( const Real &  cmdnTot)
inline

Definition at line 192 of file IonicFox.hpp.

◆ csqnTot()

const Real& csqnTot ( ) const
inline

Definition at line 197 of file IonicFox.hpp.

◆ setCsqnTot()

void setCsqnTot ( const Real &  csqnTot)
inline

Definition at line 201 of file IonicFox.hpp.

◆ constmCmdn()

const Real& constmCmdn ( ) const
inline

Definition at line 206 of file IonicFox.hpp.

◆ setKmCmdn()

void setKmCmdn ( const Real &  constmCmdn)
inline

Definition at line 210 of file IonicFox.hpp.

◆ constmCsqn()

const Real& constmCsqn ( ) const
inline

Definition at line 215 of file IonicFox.hpp.

◆ setKmCsqn()

void setKmCsqn ( const Real &  constmCsqn)
inline

Definition at line 219 of file IonicFox.hpp.

◆ capMem()

const Real& capMem ( ) const
inline

Definition at line 224 of file IonicFox.hpp.

◆ setCapMem()

void setCapMem ( const Real &  capMem)
inline

Definition at line 228 of file IonicFox.hpp.

◆ farad()

const Real& farad ( ) const
inline

Definition at line 233 of file IonicFox.hpp.

◆ setFarad()

void setFarad ( const Real &  farad)
inline

Definition at line 237 of file IonicFox.hpp.

◆ temp()

const Real& temp ( ) const
inline

Definition at line 242 of file IonicFox.hpp.

◆ setTemp()

void setTemp ( const Real &  temp)
inline

Definition at line 246 of file IonicFox.hpp.

◆ gasConst()

const Real& gasConst ( ) const
inline

Definition at line 251 of file IonicFox.hpp.

◆ setR()

void setR ( const Real &  gasConst)
inline

Definition at line 255 of file IonicFox.hpp.

◆ maxCondNa()

const Real& maxCondNa ( ) const
inline

Definition at line 260 of file IonicFox.hpp.

◆ setGNa()

void setGNa ( const Real &  maxCondNa)
inline

Definition at line 264 of file IonicFox.hpp.

◆ maxCondKp()

const Real& maxCondKp ( ) const
inline

Definition at line 269 of file IonicFox.hpp.

◆ setGkp()

void setGkp ( const Real &  maxCondKp)
inline

Definition at line 273 of file IonicFox.hpp.

◆ maxCondK1()

const Real& maxCondK1 ( ) const
inline

Definition at line 278 of file IonicFox.hpp.

◆ setGk1()

void setGk1 ( const Real &  maxCondK1)
inline

Definition at line 282 of file IonicFox.hpp.

◆ maxCondKr()

const Real& maxCondKr ( ) const
inline

Definition at line 287 of file IonicFox.hpp.

◆ setGkr()

void setGkr ( const Real &  maxCondKr)
inline

Definition at line 291 of file IonicFox.hpp.

◆ maxCondKs()

const Real& maxCondKs ( ) const
inline

Definition at line 296 of file IonicFox.hpp.

◆ setGks()

void setGks ( const Real &  maxCondKs)
inline

Definition at line 300 of file IonicFox.hpp.

◆ maxCondt0()

const Real& maxCondt0 ( ) const
inline

Definition at line 305 of file IonicFox.hpp.

◆ setGkt0()

void setGkt0 ( const Real &  maxCondt0)
inline

Definition at line 309 of file IonicFox.hpp.

◆ kNaCa()

const Real& kNaCa ( ) const
inline

Definition at line 314 of file IonicFox.hpp.

◆ setKNaCa()

void setKNaCa ( const Real &  kNaCa)
inline

Definition at line 318 of file IonicFox.hpp.

◆ constmfCa()

const Real& constmfCa ( ) const
inline

Definition at line 323 of file IonicFox.hpp.

◆ setKmfCa()

void setKmfCa ( const Real &  constmfCa)
inline

Definition at line 327 of file IonicFox.hpp.

◆ constmK1()

const Real& constmK1 ( ) const
inline

Definition at line 332 of file IonicFox.hpp.

◆ setKmK1()

void setKmK1 ( const Real &  constmK1)
inline

Definition at line 336 of file IonicFox.hpp.

◆ constmNa()

const Real& constmNa ( ) const
inline

Definition at line 341 of file IonicFox.hpp.

◆ setKmNa()

void setKmNa ( const Real &  constmNa)
inline

Definition at line 345 of file IonicFox.hpp.

◆ constmCa()

const Real& constmCa ( ) const
inline

Definition at line 350 of file IonicFox.hpp.

◆ setKmCa()

void setKmCa ( const Real &  constmCa)
inline

Definition at line 354 of file IonicFox.hpp.

◆ kSat()

const Real& kSat ( ) const
inline

Definition at line 359 of file IonicFox.hpp.

◆ setKSat()

void setKSat ( const Real &  kSat)
inline

Definition at line 363 of file IonicFox.hpp.

◆ eta()

const Real& eta ( ) const
inline

Definition at line 368 of file IonicFox.hpp.

◆ setEta()

void setEta ( const Real &  eta)
inline

Definition at line 372 of file IonicFox.hpp.

◆ courNaK()

const Real& courNaK ( ) const
inline

Definition at line 377 of file IonicFox.hpp.

◆ setINaK()

void setINaK ( const Real &  courNaK)
inline

Definition at line 381 of file IonicFox.hpp.

◆ constmNai()

const Real& constmNai ( ) const
inline

Definition at line 386 of file IonicFox.hpp.

◆ setKmNai()

void setKmNai ( const Real &  constmNai)
inline

Definition at line 390 of file IonicFox.hpp.

◆ constmK0()

const Real& constmK0 ( ) const
inline

Definition at line 395 of file IonicFox.hpp.

◆ setKmK0()

void setKmK0 ( const Real &  constmK0)
inline

Definition at line 399 of file IonicFox.hpp.

◆ permCa()

const Real& permCa ( ) const
inline

Definition at line 404 of file IonicFox.hpp.

◆ setPnsCa()

void setPnsCa ( const Real &  permCa)
inline

Definition at line 408 of file IonicFox.hpp.

◆ constmpCa()

const Real& constmpCa ( ) const
inline

Definition at line 413 of file IonicFox.hpp.

◆ setKmpCa()

void setKmpCa ( const Real &  constmpCa)
inline

Definition at line 417 of file IonicFox.hpp.

◆ courpCa()

const Real& courpCa ( ) const
inline

Definition at line 422 of file IonicFox.hpp.

◆ setIpCa()

void setIpCa ( const Real &  courpCa)
inline

Definition at line 426 of file IonicFox.hpp.

◆ maxCondCab()

const Real& maxCondCab ( ) const
inline

Definition at line 431 of file IonicFox.hpp.

◆ setGCab()

void setGCab ( const Real &  maxCondCab)
inline

Definition at line 435 of file IonicFox.hpp.

◆ maxCondNab()

const Real& maxCondNab ( ) const
inline

Definition at line 440 of file IonicFox.hpp.

◆ setGNab()

void setGNab ( const Real &  maxCondNab)
inline

Definition at line 444 of file IonicFox.hpp.

◆ constmUp()

const Real& constmUp ( ) const
inline

Definition at line 449 of file IonicFox.hpp.

◆ setKmUp()

void setKmUp ( const Real &  constmUp)
inline

Definition at line 453 of file IonicFox.hpp.

◆ permCaK()

const Real& permCaK ( ) const
inline

Definition at line 458 of file IonicFox.hpp.

◆ setPCaK()

void setPCaK ( const Real &  permCaK)
inline

Definition at line 462 of file IonicFox.hpp.

◆ permrel()

const Real& permrel ( ) const
inline

Definition at line 467 of file IonicFox.hpp.

◆ setPrel()

void setPrel ( const Real &  permrel)
inline

Definition at line 471 of file IonicFox.hpp.

◆ permleak()

const Real& permleak ( ) const
inline

Definition at line 476 of file IonicFox.hpp.

◆ setPleak()

void setPleak ( const Real &  permleak)
inline

Definition at line 480 of file IonicFox.hpp.

◆ courCaHalf()

const Real& courCaHalf ( ) const
inline

Definition at line 485 of file IonicFox.hpp.

◆ setICaHalf()

void setICaHalf ( const Real &  courCaHalf)
inline

Definition at line 489 of file IonicFox.hpp.

◆ computeGatingRhs()

void computeGatingRhs ( const std::vector< Real > &  v,
std::vector< Real > &  rhs 
)
virtual

Methods.

Implements ElectroIonicModel.

Definition at line 272 of file IonicFox.cpp.

◆ computeRhs()

void computeRhs ( const std::vector< Real > &  v,
std::vector< Real > &  rhs 
)
virtual

This methods contains the actual evaluation of the rhs of all state variablesin the model (0D version)

Although this method can just wrap the computeGatingRhs ( const std::vector<Real>& v, std::vector<Real>& rhs ) and the computeLocalPotentialRhs ( const std::vector<Real>& v ) methods, for efficiency it may be better to duplicate the code.

Parameters
vvector of state variables including the voltage (with n elements)
rhsvector of right hand side state variables including the voltage (with n elements)

Implements ElectroIonicModel.

Definition at line 282 of file IonicFox.cpp.

◆ computeLocalPotentialRhs()

Real computeLocalPotentialRhs ( const std::vector< Real > &  v)
virtual

This methods contains the actual evaluation of the rhs of the voltage equation only (0D version)

Parameters
vvector of state variables including the voltage (with n elements)

Implements ElectroIonicModel.

Definition at line 313 of file IonicFox.cpp.

◆ computeLocalGatingRhs()

std::vector< Real > computeLocalGatingRhs ( const std::vector< Real > &  v)

Definition at line 330 of file IonicFox.cpp.

◆ computeGatingVariablesWithRushLarsen()

void computeGatingVariablesWithRushLarsen ( std::vector< Real > &  ,
const Real   
)
virtual

This methods contains the actual evaluation of the rhs of the voltage equation only (0D version)

Overload this method in order to solve the ionic model with the Rush-Larsen method in the monodomain solver

Parameters
vvector of state variables
dttime step of the simulation

Reimplemented from ElectroIonicModel.

Definition at line 359 of file IonicFox.cpp.

◆ computeNonGatingRhs()

void computeNonGatingRhs ( const std::vector< Real > &  v,
std::vector< Real > &  rhs 
)
virtual

In the case this method is improperly used, it should use this default implementation.

This method should be used together with the Rush-Larsen time advancing scheme

Parameters
vvector of state variables including the voltage (with n elements)
rhsvector of right hand side state variables excluding the voltage and the gating variables (with n-g-1 elements)

Reimplemented from ElectroIonicModel.

Definition at line 302 of file IonicFox.cpp.

◆ computeLocalSubSysCaRhs()

std::vector< Real > computeLocalSubSysCaRhs ( const std::vector< Real > &  v)

Ca2+ Subsystem.

Definition at line 404 of file IonicFox.cpp.

◆ fastINa()

std::vector< Real > fastINa ( const std::vector< Real > &  v)

Ionic Currents (Luo and Rudy)

Definition at line 463 of file IonicFox.cpp.

◆ rapidIK()

std::vector< Real > rapidIK ( const std::vector< Real > &  v)

Definition at line 495 of file IonicFox.cpp.

◆ transOutIK()

std::vector< Real > transOutIK ( const std::vector< Real > &  v)

Definition at line 539 of file IonicFox.cpp.

◆ slowIK()

std::vector< Real > slowIK ( const std::vector< Real > &  v)

Definition at line 517 of file IonicFox.cpp.

◆ timeDIK()

std::vector<Real> timeDIK ( const std::vector< Real > &  v)

◆ timeIIK1()

Real timeIIK1 ( const std::vector< Real > &  v)

Definition at line 565 of file IonicFox.cpp.

◆ plaIKp()

Real plaIKp ( const std::vector< Real > &  v)

Definition at line 578 of file IonicFox.cpp.

◆ exINaCa()

Real exINaCa ( const std::vector< Real > &  v)

Definition at line 589 of file IonicFox.cpp.

◆ pumpINaK()

Real pumpINaK ( const std::vector< Real > &  v)

Definition at line 602 of file IonicFox.cpp.

◆ pumpIpCa()

Real pumpIpCa ( const std::vector< Real > &  v)

Definition at line 614 of file IonicFox.cpp.

◆ backICab()

Real backICab ( const std::vector< Real > &  v)

Definition at line 620 of file IonicFox.cpp.

◆ backINab()

Real backINab ( const std::vector< Real > &  v)

Definition at line 631 of file IonicFox.cpp.

◆ showMe()

void showMe ( )
virtual

Display information about the model.

Implements ElectroIonicModel.

Definition at line 640 of file IonicFox.cpp.

+ Here is the caller graph for this function:

Field Documentation

◆ M_ACap

Real M_ACap
private

Cell Geometry Parameters (4)

Definition at line 550 of file IonicFox.hpp.

◆ M_VMyo

Real M_VMyo
private

Definition at line 551 of file IonicFox.hpp.

◆ M_Vsr

Real M_Vsr
private

Definition at line 552 of file IonicFox.hpp.

◆ M_Vup

Real M_Vup
private

Definition at line 553 of file IonicFox.hpp.

◆ M_NaO

Real M_NaO
private

Standard Ionic Concentrations (5)

Definition at line 557 of file IonicFox.hpp.

◆ M_CaO

Real M_CaO
private

Definition at line 558 of file IonicFox.hpp.

◆ M_K0

Real M_K0
private

Definition at line 559 of file IonicFox.hpp.

◆ M_NaIn

Real M_NaIn
private

Definition at line 560 of file IonicFox.hpp.

◆ M_KIn

Real M_KIn
private

Definition at line 561 of file IonicFox.hpp.

◆ M_CmdnTot

Real M_CmdnTot
private

Buffering Parameters (4)

Definition at line 565 of file IonicFox.hpp.

◆ M_CsqnTot

Real M_CsqnTot
private

Definition at line 566 of file IonicFox.hpp.

◆ M_KmCmdn

Real M_KmCmdn
private

Definition at line 567 of file IonicFox.hpp.

◆ M_KmCsqn

Real M_KmCsqn
private

Definition at line 568 of file IonicFox.hpp.

◆ M_Cm

Real M_Cm
private

Membrane Current Parameters (24)

Definition at line 572 of file IonicFox.hpp.

◆ M_F

Real M_F
private

Definition at line 573 of file IonicFox.hpp.

◆ M_T

Real M_T
private

Definition at line 574 of file IonicFox.hpp.

◆ M_R

Real M_R
private

Definition at line 575 of file IonicFox.hpp.

◆ M_GNa

Real M_GNa
private

Definition at line 576 of file IonicFox.hpp.

◆ M_GKp

Real M_GKp
private

Definition at line 577 of file IonicFox.hpp.

◆ M_kNaCa

Real M_kNaCa
private

Definition at line 578 of file IonicFox.hpp.

◆ M_KmNa

Real M_KmNa
private

Definition at line 579 of file IonicFox.hpp.

◆ M_KmCa

Real M_KmCa
private

Definition at line 580 of file IonicFox.hpp.

◆ M_kSat

Real M_kSat
private

Definition at line 581 of file IonicFox.hpp.

◆ M_eta

Real M_eta
private

Definition at line 582 of file IonicFox.hpp.

◆ M_INaK

Real M_INaK
private

Definition at line 583 of file IonicFox.hpp.

◆ M_KmNai

Real M_KmNai
private

Definition at line 584 of file IonicFox.hpp.

◆ M_KmK0

Real M_KmK0
private

Definition at line 585 of file IonicFox.hpp.

◆ M_GK1

Real M_GK1
private

Definition at line 586 of file IonicFox.hpp.

◆ M_GKr

Real M_GKr
private

Definition at line 587 of file IonicFox.hpp.

◆ M_GKs

Real M_GKs
private

Definition at line 588 of file IonicFox.hpp.

◆ M_Gt0

Real M_Gt0
private

Definition at line 589 of file IonicFox.hpp.

◆ M_IpCa

Real M_IpCa
private

Definition at line 590 of file IonicFox.hpp.

◆ M_KmPCa

Real M_KmPCa
private

Definition at line 591 of file IonicFox.hpp.

◆ M_GCab

Real M_GCab
private

Definition at line 592 of file IonicFox.hpp.

◆ M_GNab

Real M_GNab
private

Definition at line 593 of file IonicFox.hpp.

◆ M_KmK1

Real M_KmK1
private

Definition at line 594 of file IonicFox.hpp.

◆ M_KmfCa

Real M_KmfCa
private

Definition at line 595 of file IonicFox.hpp.

◆ M_KmUp

Real M_KmUp
private

SR Parameters (1)

Definition at line 599 of file IonicFox.hpp.

◆ M_PCa

Real M_PCa
private

L-type Ca2+ Channel Parameters (6)

Definition at line 603 of file IonicFox.hpp.

◆ M_PCaK

Real M_PCaK
private

Definition at line 604 of file IonicFox.hpp.

◆ M_Prel

Real M_Prel
private

Definition at line 605 of file IonicFox.hpp.

◆ M_Pleak

Real M_Pleak
private

Definition at line 606 of file IonicFox.hpp.

◆ M_ICaHalf

Real M_ICaHalf
private

Definition at line 607 of file IonicFox.hpp.

◆ M_KmpCa

Real M_KmpCa
private

Definition at line 608 of file IonicFox.hpp.

The documentation for this class was generated from the following files: