IonicModel - This class implements the Hodgkin-Huxley model. More...

#include <IonicHodgkinHuxley.hpp>

Inheritance diagram for IonicHodgkinHuxley:

Collaboration diagram for IonicHodgkinHuxley:

Private Attributes
Real	M_gNa
	Model Parameters. More...

Real	M_gK

Real	M_gL

Real	M_vNa

Real	M_vK

Real	M_vL

Type definitions
typedef ElectroIonicModel	super

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

	IonicHodgkinHuxley (Teuchos::ParameterList &parameterList)

	IonicHodgkinHuxley (const IonicHodgkinHuxley &model)

virtual	~IonicHodgkinHuxley ()
	Destructor. More...

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

Setters and getters
const Real &	gNa () const

const Real &	gK () const

const Real &	gL () const

const Real &	vL () const

const Real &	vK () const

const Real &	vNa () const

void	setGNa (const Real &p)

void	setGK (const Real &p)

void	setGL (const Real &p)

void	setVL (const Real &p)

void	setVNa (const Real &p)

void	setVK (const Real &p)

Methods
void	computeGatingRhs (const std::vector< Real > &v, std::vector< Real > &rhs)
	Compute the rhs of the gating variables a single node or for the 0D case. More...

Real	computeLocalPotentialRhs (const std::vector< Real > &v)
	compute the rhs of the potential equation on a single node or for the 0D case More...

void	computeRhs (const std::vector< Real > &v, std::vector< Real > &rhs)
	Compute the rhs on a single node or for the 0D case. More...

void	computeGatingVariablesWithRushLarsen (std::vector< Real > &v, const Real dt)
	compute the rhs of the gating variables with the RushLarsen scheme 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	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...

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 the Hodgkin-Huxley model.

Definition at line 57 of file IonicHodgkinHuxley.hpp.

Member Typedef Documentation

◆ super

typedef ElectroIonicModel super

Definition at line 63 of file IonicHodgkinHuxley.hpp.

Constructor & Destructor Documentation

◆ IonicHodgkinHuxley() [1/3]

IonicHodgkinHuxley ( )

Constructor.

Definition at line 45 of file IonicHodgkinHuxley.cpp.

◆ IonicHodgkinHuxley() [2/3]

IonicHodgkinHuxley ( Teuchos::ParameterList & parameterList )

Parameters

list	of parameters in an xml file

Definition at line 61 of file IonicHodgkinHuxley.cpp.

◆ IonicHodgkinHuxley() [3/3]

IonicHodgkinHuxley ( const IonicHodgkinHuxley & model )

Parameters

IonicHodgkinHuxley object

Definition at line 77 of file IonicHodgkinHuxley.cpp.

◆ ~IonicHodgkinHuxley()

virtual ~IonicHodgkinHuxley ( )

inlinevirtual

Destructor.

Definition at line 85 of file IonicHodgkinHuxley.hpp.

Member Function Documentation

◆ operator=()

IonicHodgkinHuxley & operator= ( const IonicHodgkinHuxley & model )

Operator.

Definition at line 97 of file IonicHodgkinHuxley.cpp.

◆ gNa()

const Real& gNa ( ) const

inline

Definition at line 100 of file IonicHodgkinHuxley.hpp.

◆ gK()

const Real& gK ( ) const

inline

Definition at line 105 of file IonicHodgkinHuxley.hpp.

◆ gL()

const Real& gL ( ) const

inline

Definition at line 110 of file IonicHodgkinHuxley.hpp.

◆ vL()

const Real& vL ( ) const

inline

Definition at line 116 of file IonicHodgkinHuxley.hpp.

◆ vK()

const Real& vK ( ) const

inline

Definition at line 121 of file IonicHodgkinHuxley.hpp.

◆ vNa()

const Real& vNa ( ) const

inline

Definition at line 126 of file IonicHodgkinHuxley.hpp.

◆ setGNa()

void setGNa ( const Real & p )

inline

Definition at line 134 of file IonicHodgkinHuxley.hpp.

◆ setGK()

void setGK ( const Real & p )

inline

Definition at line 139 of file IonicHodgkinHuxley.hpp.

◆ setGL()

void setGL ( const Real & p )

inline

Definition at line 144 of file IonicHodgkinHuxley.hpp.

◆ setVL()

void setVL ( const Real & p )

inline

Definition at line 149 of file IonicHodgkinHuxley.hpp.

◆ setVNa()

void setVNa ( const Real & p )

inline

Definition at line 154 of file IonicHodgkinHuxley.hpp.

◆ setVK()

void setVK ( const Real & p )

inline

Definition at line 159 of file IonicHodgkinHuxley.hpp.

◆ computeGatingRhs()

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

virtual

Compute the rhs of the gating variables a single node or for the 0D case.

Methods.

Parameters

v	vector with the variables (V, M, N, H)
rhs	vector where we will insert the rhs of the equations of the gating variables

Implements ElectroIonicModel.

Definition at line 118 of file IonicHodgkinHuxley.cpp.

◆ computeLocalPotentialRhs()

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

virtual

compute the rhs of the potential equation on a single node or for the 0D case

Parameters

v	vector with the variables (V, M, N, H)

Implements ElectroIonicModel.

Definition at line 151 of file IonicHodgkinHuxley.cpp.

◆ computeRhs()

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

virtual

Compute the rhs on a single node or for the 0D case.

Parameters

v	vector with the variables (V, M, N, H)
rhs	vector where we will insert the rhs of the equations

Implements ElectroIonicModel.

Definition at line 139 of file IonicHodgkinHuxley.cpp.

◆ computeGatingVariablesWithRushLarsen()

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

virtual

compute the rhs of the gating variables with the RushLarsen scheme

Parameters

v	vector with the variables (V, M, N, H)
dt	timestep

Reimplemented from ElectroIonicModel.

Definition at line 166 of file IonicHodgkinHuxley.cpp.

◆ showMe()

void showMe ( )

virtual

Display information about the model.

Implements ElectroIonicModel.

Definition at line 194 of file IonicHodgkinHuxley.cpp.

Field Documentation

◆ M_gNa

Real M_gNa

private

Model Parameters.

Chemical kinetics parameters

Definition at line 205 of file IonicHodgkinHuxley.hpp.

◆ M_gK

Real M_gK

private

Definition at line 206 of file IonicHodgkinHuxley.hpp.

◆ M_gL

Real M_gL

private

Definition at line 207 of file IonicHodgkinHuxley.hpp.

◆ M_vNa

Real M_vNa

private

Definition at line 208 of file IonicHodgkinHuxley.hpp.

◆ M_vK

Real M_vK

private

Definition at line 209 of file IonicHodgkinHuxley.hpp.

◆ M_vL

Real M_vL

private

Definition at line 210 of file IonicHodgkinHuxley.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

Constructor & Destructor Documentation

◆ IonicHodgkinHuxley() [1/3]

◆ IonicHodgkinHuxley() [2/3]

◆ IonicHodgkinHuxley() [3/3]

◆ ~IonicHodgkinHuxley()

Member Function Documentation

◆ operator=()

◆ gNa()

◆ gK()

◆ gL()

◆ vL()

◆ vK()

◆ vNa()

◆ setGNa()

◆ setGK()

◆ setGL()

◆ setVL()

◆ setVNa()

◆ setVK()

◆ computeGatingRhs()

◆ computeLocalPotentialRhs()

◆ computeRhs()

◆ computeGatingVariablesWithRushLarsen()

◆ showMe()

Field Documentation

◆ M_gNa

◆ M_gK

◆ M_gL

◆ M_vNa

◆ M_vK

◆ M_vL