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

#include <IonicAlievPanfilov.hpp>

Inheritance diagram for IonicAlievPanfilov:

Collaboration diagram for IonicAlievPanfilov:

Private Attributes
Real	M_mu1
	Solves the ionic model. More...

Real	M_mu2

Real	M_epsilon

Real	M_k

Real	M_a

Type definitions
typedef ElectroIonicModel	super

typedef std::shared_ptr< VectorEpetra >	vectorPtr_Type

typedef RegionMesh< LinearTetra >	mesh_Type

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

	IonicAlievPanfilov (Teuchos::ParameterList &parameterList)

	IonicAlievPanfilov (const IonicAlievPanfilov &model)

virtual	~IonicAlievPanfilov ()
	Destructor. More...

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

Setters and getters
const Real &	Mu1 () const

const Real &	Mu2 () const

const Real &	K () const

const Real &	A () const

const Real &	Epsilon () const

void	setMu1 (const Real &mu1)

void	setMu2 (const Real &mu2)

void	setK (const Real &k)

void	setA (const Real &a)

void	setEpsilon (const Real &epsilon)

void	setup (Teuchos::ParameterList &parameterList)
	setup the parameters of the ionic model from an xml file More...

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...

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...

virtual void	computeGatingVariablesWithRushLarsen (std::vector< Real > &, const Real)
	This methods contains the actual evaluation of the rhs of the voltage equation only (0D version) 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...

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 58 of file IonicAlievPanfilov.hpp.

Member Typedef Documentation

◆ super

typedef ElectroIonicModel super

Definition at line 64 of file IonicAlievPanfilov.hpp.

◆ vectorPtr_Type

typedef std::shared_ptr<VectorEpetra> vectorPtr_Type

Definition at line 65 of file IonicAlievPanfilov.hpp.

◆ mesh_Type

typedef RegionMesh<LinearTetra> mesh_Type

Definition at line 66 of file IonicAlievPanfilov.hpp.

Constructor & Destructor Documentation

◆ IonicAlievPanfilov() [1/3]

IonicAlievPanfilov ( )

Constructor.

IonicModel - This class implements an ionic model.

Constructors

Definition at line 51 of file IonicAlievPanfilov.cpp.

◆ IonicAlievPanfilov() [2/3]

IonicAlievPanfilov ( Teuchos::ParameterList & parameterList )

Parameters

Epetra	communicator
list	of parameters in an xml file

Definition at line 63 of file IonicAlievPanfilov.cpp.

◆ IonicAlievPanfilov() [3/3]

IonicAlievPanfilov ( const IonicAlievPanfilov & model )

Parameters

IonicAlievPanfilov object

Definition at line 72 of file IonicAlievPanfilov.cpp.

◆ ~IonicAlievPanfilov()

virtual ~IonicAlievPanfilov ( )

inlinevirtual

Destructor.

Definition at line 88 of file IonicAlievPanfilov.hpp.

Member Function Documentation

◆ operator=()

IonicAlievPanfilov & operator= ( const IonicAlievPanfilov & model )

Operator.

Definition at line 88 of file IonicAlievPanfilov.cpp.

◆ Mu1()

const Real& Mu1 ( ) const

inline

Definition at line 103 of file IonicAlievPanfilov.hpp.

◆ Mu2()

const Real& Mu2 ( ) const

inline

Definition at line 107 of file IonicAlievPanfilov.hpp.

◆ K()

const Real& K ( ) const

inline

Definition at line 111 of file IonicAlievPanfilov.hpp.

◆ A()

const Real& A ( ) const

inline

Definition at line 115 of file IonicAlievPanfilov.hpp.

◆ Epsilon()

const Real& Epsilon ( ) const

inline

Definition at line 119 of file IonicAlievPanfilov.hpp.

◆ setMu1()

void setMu1 ( const Real & mu1 )

inline

Definition at line 124 of file IonicAlievPanfilov.hpp.

◆ setMu2()

void setMu2 ( const Real & mu2 )

inline

Definition at line 128 of file IonicAlievPanfilov.hpp.

◆ setK()

void setK ( const Real & k )

inline

Definition at line 132 of file IonicAlievPanfilov.hpp.

◆ setA()

void setA ( const Real & a )

inline

Definition at line 136 of file IonicAlievPanfilov.hpp.

◆ setEpsilon()

void setEpsilon ( const Real & epsilon )

inline

Definition at line 140 of file IonicAlievPanfilov.hpp.

◆ setup()

void setup ( Teuchos::ParameterList & parameterList )

virtual

setup the parameters of the ionic model from an xml file

Parameters

parameterList Teuchos parameter list

Reimplemented from ElectroIonicModel.

Definition at line 102 of file IonicAlievPanfilov.cpp.

◆ computeGatingRhs()

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

virtual

Methods.

Implements ElectroIonicModel.

Definition at line 114 of file IonicAlievPanfilov.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 125 of file IonicAlievPanfilov.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 138 of file IonicAlievPanfilov.cpp.

◆ showMe()

void showMe ( )

virtual

Display information about the model.

Implements ElectroIonicModel.

Definition at line 144 of file IonicAlievPanfilov.cpp.

Field Documentation

◆ M_mu1

Real M_mu1

private

Solves the ionic model.

Model Parameters Chemical kinetics parameters

Definition at line 183 of file IonicAlievPanfilov.hpp.

◆ M_mu2

Real M_mu2

private

Definition at line 184 of file IonicAlievPanfilov.hpp.

◆ M_epsilon

Real M_epsilon

private

Definition at line 185 of file IonicAlievPanfilov.hpp.

◆ M_k

Real M_k

private

Definition at line 186 of file IonicAlievPanfilov.hpp.

◆ M_a

Real M_a

private

Definition at line 187 of file IonicAlievPanfilov.hpp.

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

Private Attributes

Type definitions

Constructors & Destructor

Overloads

Setters and getters

Methods

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ super

◆ vectorPtr_Type

◆ mesh_Type

Constructor & Destructor Documentation

◆ IonicAlievPanfilov() [1/3]

◆ IonicAlievPanfilov() [2/3]

◆ IonicAlievPanfilov() [3/3]

◆ ~IonicAlievPanfilov()

Member Function Documentation

◆ operator=()

◆ Mu1()

◆ Mu2()

◆ K()

◆ A()

◆ Epsilon()

◆ setMu1()

◆ setMu2()

◆ setK()

◆ setA()

◆ setEpsilon()

◆ setup()

◆ computeGatingRhs()

◆ computeRhs()

◆ computeLocalPotentialRhs()

◆ showMe()

Field Documentation

◆ M_mu1

◆ M_mu2

◆ M_epsilon

◆ M_k

◆ M_a