#include <IonicFitzHughNagumo.hpp>

Inheritance diagram for IonicFitzHughNagumo:

Collaboration diagram for IonicFitzHughNagumo:

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

	IonicFitzHughNagumo (Teuchos::ParameterList &parameterList)

	IonicFitzHughNagumo (const IonicFitzHughNagumo &model)

virtual	~IonicFitzHughNagumo ()
	Destructor. More...

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

Setters and getters
Real	M_G
	Model Parameters. More...

Real	M_Vth

Real	M_Vp

Real	M_Eta1

Real	M_Eta2

Real	M_Eta3

Real	M_Eta

Real	M_Gamma

const Real &	G () const

const Real &	Vth () const

const Real &	Vp () const

const Real &	Eta1 () const

const Real &	Eta2 () const

const Real &	Eta3 () const

const Real &	Eta () const

const Real &	Gamma () const

void	setG (const Real &G)

void	setVth (const Real &Vth)

void	setVp (const Real &Vp)

void	setEta1 (const Real &Eta1)

void	setEta2 (const Real &Eta2)

void	setEta3 (const Real &Eta3)

void	setup (Teuchos::ParameterList &parameterList)
	Methods. More...

void	computeGatingRhs (const std::vector< Real > &v, std::vector< Real > &rhs)
	A new ionic model must have the following 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...

void	computeRhs (const VectorSmall< 2 > &v, VectorSmall< 2 > &rhs)

Real	computeLocalPotentialRhs (const std::vector< Real > &v)
	This methods contains the actual evaluation of the rhs of the voltage equation only (0D version) More...

matrix_Type	getJac (const vector_Type &v, Real h=1.0e-8)
	This methods computes the Jacobian numerically. More...

std::vector< std::vector< Real > >	getJac (const std::vector< Real > &v, Real h=1.0e-8)
	This methods computes the Jacobian numerically. More...

MatrixSmall< 2, 2 >	getJac (const VectorSmall< 2 > &v, Real h=1.0e-8)

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 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

Definition at line 73 of file IonicFitzHughNagumo.hpp.

Constructor & Destructor Documentation

◆ IonicFitzHughNagumo() [1/3]

IonicFitzHughNagumo ( )

Constructor.

Constructors.

Definition at line 45 of file IonicFitzHughNagumo.cpp.

◆ IonicFitzHughNagumo() [2/3]

IonicFitzHughNagumo ( Teuchos::ParameterList & parameterList )

Parameters

Epetra	communicator
list	of parameters in an xml file

Definition at line 61 of file IonicFitzHughNagumo.cpp.

◆ IonicFitzHughNagumo() [3/3]

IonicFitzHughNagumo ( const IonicFitzHughNagumo & model )

Parameters

IonicFitzHughNagumo object

Definition at line 70 of file IonicFitzHughNagumo.cpp.

◆ ~IonicFitzHughNagumo()

virtual ~IonicFitzHughNagumo ( )

inlinevirtual

Destructor.

Definition at line 94 of file IonicFitzHughNagumo.hpp.

Member Function Documentation

◆ operator=()

IonicFitzHughNagumo & operator= ( const IonicFitzHughNagumo & model )

Operator.

Definition at line 88 of file IonicFitzHughNagumo.cpp.

◆ G()

const Real& G ( ) const

inline

Definition at line 109 of file IonicFitzHughNagumo.hpp.

◆ Vth()

const Real& Vth ( ) const

inline

Definition at line 113 of file IonicFitzHughNagumo.hpp.

◆ Vp()

const Real& Vp ( ) const

inline

Definition at line 117 of file IonicFitzHughNagumo.hpp.

◆ Eta1()

const Real& Eta1 ( ) const

inline

Definition at line 121 of file IonicFitzHughNagumo.hpp.

◆ Eta2()

const Real& Eta2 ( ) const

inline

Definition at line 125 of file IonicFitzHughNagumo.hpp.

◆ Eta3()

const Real& Eta3 ( ) const

inline

Definition at line 129 of file IonicFitzHughNagumo.hpp.

◆ Eta()

const Real& Eta ( ) const

inline

Definition at line 133 of file IonicFitzHughNagumo.hpp.

◆ Gamma()

const Real& Gamma ( ) const

inline

Definition at line 137 of file IonicFitzHughNagumo.hpp.

◆ setG()

void setG ( const Real & G )

inline

Definition at line 142 of file IonicFitzHughNagumo.hpp.

◆ setVth()

void setVth ( const Real & Vth )

inline

Definition at line 146 of file IonicFitzHughNagumo.hpp.

◆ setVp()

void setVp ( const Real & Vp )

inline

Definition at line 150 of file IonicFitzHughNagumo.hpp.

◆ setEta1()

void setEta1 ( const Real & Eta1 )

inline

Definition at line 155 of file IonicFitzHughNagumo.hpp.

◆ setEta2()

void setEta2 ( const Real & Eta2 )

inline

Definition at line 159 of file IonicFitzHughNagumo.hpp.

◆ setEta3()

void setEta3 ( const Real & Eta3 )

inline

Definition at line 165 of file IonicFitzHughNagumo.hpp.

◆ setup()

void setup ( Teuchos::ParameterList & parameterList )

virtual

Methods.

Reimplemented from ElectroIonicModel.

Definition at line 109 of file IonicFitzHughNagumo.cpp.

◆ computeGatingRhs()

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

virtual

A new ionic model must have the following methods ///.

This methods contains the actual evaluation of the rhs of all state variables except for the voltage equation (0D version)

Parameters

v	vector of state variables including the voltage (with n elements)
rhs	vector of right hand side state variables excluding the voltage (with n-1 elements)

Implements ElectroIonicModel.

Definition at line 123 of file IonicFitzHughNagumo.cpp.

◆ computeRhs() [1/2]

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 IonicFitzHughNagumo.cpp.

◆ computeRhs() [2/2]

void computeRhs	(	const VectorSmall< 2 > &	v,
		VectorSmall< 2 > &	rhs
	)

Definition at line 142 of file IonicFitzHughNagumo.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 152 of file IonicFitzHughNagumo.cpp.

◆ getJac() [1/3]

matrix_Type getJac	(	const vector_Type &	v,
		Real	h = `1.0e-8`
	)

virtual

This methods computes the Jacobian numerically.

Parameters

v	vector of pointers to the state variables vectors
h	differentiation step

Reimplemented from ElectroIonicModel.

Definition at line 179 of file IonicFitzHughNagumo.cpp.

◆ getJac() [2/3]

std::vector< std::vector< Real > > getJac	(	const std::vector< Real > &	v,
		Real	h = `1.0e-8`
	)

virtual

This methods computes the Jacobian numerically.

Parameters

v	vector of the state variables
h	differentiation step

Reimplemented from ElectroIonicModel.

Definition at line 157 of file IonicFitzHughNagumo.cpp.

◆ getJac() [3/3]

MatrixSmall< 2, 2 > getJac	(	const VectorSmall< 2 > &	v,
		Real	h = `1.0e-8`
	)

Definition at line 168 of file IonicFitzHughNagumo.cpp.

◆ showMe()

void showMe ( )

virtual

Display information about the model.

Implements ElectroIonicModel.

Definition at line 211 of file IonicFitzHughNagumo.cpp.

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Field Documentation

◆ M_G

Real M_G

private

Model Parameters.

Chemical kinetics parameters

Definition at line 195 of file IonicFitzHughNagumo.hpp.

◆ M_Vth

Real M_Vth

private

Definition at line 196 of file IonicFitzHughNagumo.hpp.

◆ M_Vp

Real M_Vp

private

Definition at line 197 of file IonicFitzHughNagumo.hpp.

◆ M_Eta1

Real M_Eta1

private

Definition at line 198 of file IonicFitzHughNagumo.hpp.

◆ M_Eta2

Real M_Eta2

private

Definition at line 199 of file IonicFitzHughNagumo.hpp.

◆ M_Eta3

Real M_Eta3

private

Definition at line 200 of file IonicFitzHughNagumo.hpp.

◆ M_Eta

Real M_Eta

private

Definition at line 201 of file IonicFitzHughNagumo.hpp.

◆ M_Gamma

Real M_Gamma

private

Definition at line 202 of file IonicFitzHughNagumo.hpp.

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

Constructors & Destructor

Overloads

Setters and getters

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ IonicFitzHughNagumo() [1/3]

◆ IonicFitzHughNagumo() [2/3]

◆ IonicFitzHughNagumo() [3/3]

◆ ~IonicFitzHughNagumo()

Member Function Documentation

◆ operator=()

◆ G()

◆ Vth()

◆ Vp()

◆ Eta1()

◆ Eta2()

◆ Eta3()

◆ Eta()

◆ Gamma()

◆ setG()

◆ setVth()

◆ setVp()

◆ setEta1()

◆ setEta2()

◆ setEta3()

◆ setup()

◆ computeGatingRhs()

◆ computeRhs() [1/2]

◆ computeRhs() [2/2]

◆ computeLocalPotentialRhs()

◆ getJac() [1/3]

◆ getJac() [2/3]

◆ getJac() [3/3]

◆ showMe()

Field Documentation

◆ M_G

◆ M_Vth

◆ M_Vp

◆ M_Eta1

◆ M_Eta2

◆ M_Eta3

◆ M_Eta

◆ M_Gamma