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

#include <IonicNoblePurkinje.hpp>

Inheritance diagram for IonicNoblePurkinje:

Collaboration diagram for IonicNoblePurkinje:

Public Member Functions
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...

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	showMe ()
	Display information about the model. More...

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...

virtual 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...

	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...

Private Attributes
Real	M_gi
	Solves the ionic model. More...

Real	M_vNa

Real	M_vK

Real	M_Cm

Real	M_Itot

Type definitions
typedef ElectroIonicModel	super

typedef std::shared_ptr< VectorEpetra >	vectorPtr_Type

typedef std::shared_ptr< VectorElemental >	elvecPtr_Type

typedef RegionMesh< LinearTetra >	mesh_Type

Constructors & Destructor
	IonicNoblePurkinje ()
	Constructor. More...

	IonicNoblePurkinje (Teuchos::ParameterList &parameterList)

	IonicNoblePurkinje (const IonicNoblePurkinje &model)

virtual	~IonicNoblePurkinje ()
	Destructor. More...

Overloads
IonicNoblePurkinje &	operator= (const IonicNoblePurkinje &model)
	Operator. More...

Setters and getters
const Real &	gi () const

const Real &	Cm () const

const Real &	vK () const

const Real &	vNa () const

const Real &	Itotal () const

void	setgi (const Real &p)

void	setCm (const Real &p)

void	setvNa (const Real &p)

void	setvK (const Real &p)

static Real	GeneralFunctionAlphaAndBeta (const Real &V, const Real &C1, const Real &C2, const Real &C3, const Real &C4, const Real &C5, const Real &V_0)

static Real	mInf (const Real &V)

static Real	hInf (const Real &V)

static Real	nInf (const Real &V)

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

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 58 of file IonicNoblePurkinje.hpp.

Member Typedef Documentation

◆ super

typedef ElectroIonicModel super

Definition at line 64 of file IonicNoblePurkinje.hpp.

◆ vectorPtr_Type

typedef std::shared_ptr<VectorEpetra> vectorPtr_Type

Definition at line 65 of file IonicNoblePurkinje.hpp.

◆ elvecPtr_Type

typedef std::shared_ptr<VectorElemental> elvecPtr_Type

Definition at line 66 of file IonicNoblePurkinje.hpp.

◆ mesh_Type

typedef RegionMesh<LinearTetra> mesh_Type

Definition at line 67 of file IonicNoblePurkinje.hpp.

Constructor & Destructor Documentation

◆ IonicNoblePurkinje() [1/3]

IonicNoblePurkinje ( )

Constructor.

Constructors.

Definition at line 50 of file IonicNoblePurkinje.cpp.

◆ IonicNoblePurkinje() [2/3]

IonicNoblePurkinje ( Teuchos::ParameterList & parameterList )

Parameters

Epetra	communicator
list	of parameters in an xml file

Definition at line 65 of file IonicNoblePurkinje.cpp.

◆ IonicNoblePurkinje() [3/3]

IonicNoblePurkinje ( const IonicNoblePurkinje & model )

Parameters

IonicNoblePurkinje object

Definition at line 76 of file IonicNoblePurkinje.cpp.

◆ ~IonicNoblePurkinje()

virtual ~IonicNoblePurkinje ( )

inlinevirtual

Destructor.

Definition at line 89 of file IonicNoblePurkinje.hpp.

Member Function Documentation

◆ operator=()

IonicNoblePurkinje & operator= ( const IonicNoblePurkinje & model )

Operator.

Definition at line 93 of file IonicNoblePurkinje.cpp.

◆ gi()

const Real& gi ( ) const

inline

Definition at line 104 of file IonicNoblePurkinje.hpp.

◆ Cm()

const Real& Cm ( ) const

inline

Definition at line 110 of file IonicNoblePurkinje.hpp.

◆ vK()

const Real& vK ( ) const

inline

Definition at line 115 of file IonicNoblePurkinje.hpp.

◆ vNa()

const Real& vNa ( ) const

inline

Definition at line 120 of file IonicNoblePurkinje.hpp.

◆ Itotal()

const Real& Itotal ( ) const

inline

Definition at line 125 of file IonicNoblePurkinje.hpp.

◆ setgi()

void setgi ( const Real & p )

inline

Definition at line 131 of file IonicNoblePurkinje.hpp.

◆ setCm()

void setCm ( const Real & p )

inline

Definition at line 137 of file IonicNoblePurkinje.hpp.

◆ setvNa()

void setvNa ( const Real & p )

inline

Definition at line 142 of file IonicNoblePurkinje.hpp.

◆ setvK()

void setvK ( const Real & p )

inline

Definition at line 147 of file IonicNoblePurkinje.hpp.

◆ GeneralFunctionAlphaAndBeta()

static Real GeneralFunctionAlphaAndBeta	(	const Real &	V,
		const Real &	C1,
		const Real &	C2,
		const Real &	C3,
		const Real &	C4,
		const Real &	C5,
		const Real &	V_0
	)

inlinestatic

Definition at line 153 of file IonicNoblePurkinje.hpp.

◆ mInf()

static Real mInf ( const Real & V )

inlinestatic

Definition at line 166 of file IonicNoblePurkinje.hpp.

◆ hInf()

static Real hInf ( const Real & V )

inlinestatic

Definition at line 174 of file IonicNoblePurkinje.hpp.

◆ nInf()

static Real nInf ( const Real & V )

inlinestatic

Definition at line 182 of file IonicNoblePurkinje.hpp.

◆ computeGatingRhs()

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

virtual

Methods.

Implements ElectroIonicModel.

Definition at line 111 of file IonicNoblePurkinje.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

v	vector of state variables including the voltage (with n elements)
rhs	vector of right hand side state variables including the voltage (with n elements)

Implements ElectroIonicModel.

Definition at line 132 of file IonicNoblePurkinje.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

v	vector of state variables including the voltage (with n elements)

Implements ElectroIonicModel.

Definition at line 160 of file IonicNoblePurkinje.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

v	vector of state variables
dt	time step of the simulation

Reimplemented from ElectroIonicModel.

Definition at line 188 of file IonicNoblePurkinje.cpp.

◆ showMe()

void showMe ( )

virtual

Display information about the model.

Implements ElectroIonicModel.

Definition at line 214 of file IonicNoblePurkinje.cpp.

Field Documentation

◆ M_gi

Real M_gi

private

Solves the ionic model.

Model Parameters Chemical kinetics parameters

Definition at line 216 of file IonicNoblePurkinje.hpp.

◆ M_vNa

Real M_vNa

private

Definition at line 217 of file IonicNoblePurkinje.hpp.

◆ M_vK

Real M_vK

private

Definition at line 218 of file IonicNoblePurkinje.hpp.

◆ M_Cm

Real M_Cm

private

Definition at line 219 of file IonicNoblePurkinje.hpp.

◆ M_Itot

Real M_Itot

private

Definition at line 220 of file IonicNoblePurkinje.hpp.

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

Public Member Functions

Private Attributes

Type definitions

Constructors & Destructor

Overloads

Setters and getters

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ super

◆ vectorPtr_Type

◆ elvecPtr_Type

◆ mesh_Type

Constructor & Destructor Documentation

◆ IonicNoblePurkinje() [1/3]

◆ IonicNoblePurkinje() [2/3]

◆ IonicNoblePurkinje() [3/3]

◆ ~IonicNoblePurkinje()

Member Function Documentation

◆ operator=()

◆ gi()

◆ Cm()

◆ vK()

◆ vNa()

◆ Itotal()

◆ setgi()

◆ setCm()

◆ setvNa()

◆ setvK()

◆ GeneralFunctionAlphaAndBeta()

◆ mInf()

◆ hInf()

◆ nInf()

◆ computeGatingRhs()

◆ computeRhs()

◆ computeLocalPotentialRhs()

◆ computeGatingVariablesWithRushLarsen()

◆ showMe()

Field Documentation

◆ M_gi

◆ M_vNa

◆ M_vK

◆ M_Cm

◆ M_Itot