FitzHugh-Nagumo ionic model. More...

#include <ionic_fitzhugh_nagumo.h>

Inheritance diagram for FitzHughNagumo:

Classes
class	Parameters
	Model parameters class. More...

Public Member Functions
	FitzHughNagumo ()
	Constructor.

virtual std::unique_ptr< IonicModelParameters >	get_parameters () const override
	Construct an instance of model parameters.

virtual void	read_parameters (const IonicModelParameters &params) override
	Read model parameters from a parameter object.

virtual void	distribute_parameters (const CmMod &cm_mod, const cmType &cm) override
	Distribute model parameters to all parallel processes.

virtual unsigned int	get_calcium_index () const override
	Get the calcium proxy index.

Public Member Functions inherited from IonicModel
	IonicModel (const InitialStates &initial_X_, const InitialStates &initial_Xg_, const double Vrest_)
	Constructor.

	IonicModel (const InitialStates &initial_X_, const InitialStates &initial_Xg_, const double Vrest_, const double Vscale_, const double Tscale_, const double Voffset_)
	Constructor with scaling factors.

virtual	~IonicModel ()=default
	Virtual destructor.

void	init (Vector< double > &X, Vector< double > &Xg) const
	Setup model initial conditions.

void	integ (const odeType &ode_solver_params, const int zone_id, const double t, const double dt, const double Istim, const double Ksac, Vector< double > &X, Vector< double > &Xg) const
	Integrate over one time step.

unsigned int	nX () const
	Get the number of state variables.

unsigned int	nG () const
	Get the number of gating variables.

virtual std::vector< std::pair< std::string, int > >	get_output_variables () const
	Get a list of state variables to export to VTU.

std::vector< outputType >	get_registered_outputs () const
	Get output variable information for output registration.

Static Public Attributes
static const std::string	label = "FN"
	Model label.

static const InitialStates	initial_X = {{"V", 1.0e-3}, {"w", 1.0e-3}}
	State variables.

static const InitialStates	initial_Xg = {}
	Gating variables.

static constexpr unsigned int	calcium_index = 1

Protected Member Functions
virtual void	update_g (const unsigned int zone_id, const double dt, const Vector< double > &X, Vector< double > &Xg) const override

virtual Vector< double >	getf (const unsigned int zone_id, const Vector< double > &X, const Vector< double > &Xg, const double I_stim, const double I_sac) const override
	Model right-hand side.

virtual Array< double >	getj (const unsigned int zone_id, const Vector< double > &X, const Vector< double > &Xg, const double Ksac) const override
	Model jacobian.

Protected Member Functions inherited from IonicModel
void	integ_fe (const unsigned int zone_id, Vector< double > &X, Vector< double > &Xg, const double Ts, const double Ti, const double Istim, const double Ksac) const
	Integrate the model with the forward Euler method.

void	integ_rk (const unsigned int zone_id, Vector< double > &X, Vector< double > &Xg, const double Ts, const double Ti, const double Istim, const double Ksac) const
	Integrate the model with the fourth-order explicit Runge-Kutta method.

void	integ_cn2 (const unsigned int zone_id, Vector< double > &X, Vector< double > &Xg, const double Ts, const double Ti, const double Istim, const double Ksac, const unsigned int max_iter, const double rtol, const double atol) const
	Integrate the model with the Crank-Nicolson method.

Protected Attributes
Model parameters
double	alpha = -0.50
	[1].

double	a = 0.0
	[1].

double	b = -0.60
	[1].

double	c = 50.0
	[1].

Protected Attributes inherited from IonicModel
InitialStates	initial_X
	Initial states.

InitialStates	initial_Xg
	Initial gating variables.

const double	Vrest

const double	Vscale
	Voltage scaling [mV].

const double	Tscale
	Time scaling [ms].

const double	Voffset
	Voltage offset parameter [mV].

Additional Inherited Members
Public Types inherited from IonicModel
using	InitialStates = std::vector< std::pair< std::string, double > >

Detailed Description

FitzHugh-Nagumo ionic model.

References:

FitzHugh, Impulses and physiological states in theoretical models of nerve membrane. Biophysical Journal (1961)
Nagumo, Arimoto, Yoshizawa. An active pulse transmission line simulating nerve axon. Proceedings of the IRE (1962).

Constructor & Destructor Documentation

◆ FitzHughNagumo()

FitzHughNagumo::FitzHughNagumo ( )

inline

Constructor.

Member Function Documentation

◆ distribute_parameters()

void FitzHughNagumo::distribute_parameters	(	const CmMod &	cm_mod,
		const cmType &	cm
	)

overridevirtual

Distribute model parameters to all parallel processes.

Reimplemented from IonicModel.

◆ get_calcium_index()

virtual unsigned int FitzHughNagumo::get_calcium_index ( ) const

inlineoverridevirtual

Get the calcium proxy index.

Implements IonicModel.

◆ get_parameters()

virtual std::unique_ptr< IonicModelParameters > FitzHughNagumo::get_parameters ( ) const

inlineoverridevirtual

Construct an instance of model parameters.

Reimplemented from IonicModel.

◆ getf()

Vector< double > FitzHughNagumo::getf	(	const unsigned int	zone_id,
		const Vector< double > &	X,
		const Vector< double > &	Xg,
		const double	I_stim,
		const double	I_sac
	)		const

overrideprotectedvirtual

Model right-hand side.

Implements IonicModel.

◆ getj()

Array< double > FitzHughNagumo::getj	(	const unsigned int	zone_id,
		const Vector< double > &	X,
		const Vector< double > &	Xg,
		const double	Ksac
	)		const

overrideprotectedvirtual

Model jacobian.

Reimplemented from IonicModel.

◆ read_parameters()

void FitzHughNagumo::read_parameters ( const IonicModelParameters & params )

overridevirtual

Read model parameters from a parameter object.

Reimplemented from IonicModel.

◆ update_g()

virtual void FitzHughNagumo::update_g	(	const unsigned int	zone_id,
		const double	dt,
		const Vector< double > &	X,
		Vector< double > &	Xg
	)		const

inlineoverrideprotectedvirtual

Update variable with analytical solution. This model has none, so this method does nothing.

Implements IonicModel.

Member Data Documentation

◆ a

double FitzHughNagumo::a = 0.0

protected

[1].

◆ alpha

double FitzHughNagumo::alpha = -0.50

protected

[1].

◆ b

double FitzHughNagumo::b = -0.60

protected

[1].

◆ c

double FitzHughNagumo::c = 50.0

protected

[1].

◆ calcium_index

constexpr unsigned int FitzHughNagumo::calcium_index = 1

staticconstexpr

Index of the recovery variable (w), used as calcium proxy for electromechanical coupling.

◆ initial_X

const InitialStates FitzHughNagumo::initial_X = {{"V", 1.0e-3}, {"w", 1.0e-3}}

inlinestatic

State variables.

◆ initial_Xg

const InitialStates FitzHughNagumo::initial_Xg = {}

inlinestatic

Gating variables.

◆ label

const std::string FitzHughNagumo::label = "FN"

inlinestatic

Model label.

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

solver/ionic_fitzhugh_nagumo.h
solver/ionic_fitzhugh_nagumo.cpp

Classes

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FitzHughNagumo()

Member Function Documentation

◆ distribute_parameters()

◆ get_calcium_index()

◆ get_parameters()

◆ getf()

◆ getj()

◆ read_parameters()

◆ update_g()

Member Data Documentation

◆ a

◆ alpha

◆ b

◆ c

◆ calcium_index

◆ initial_X

◆ initial_Xg

◆ label