Aliev-Panfilov ionic model. More...

#include <ionic_aliev_panfilov.h>

Inheritance diagram for AlievPanfilov:

Classes
class	Parameters
	Model parameters class. More...

Public Member Functions
	AlievPanfilov ()
	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 = "AP"
	Model label.

static const InitialStates	initial_X = {{"V", -80.0}, {"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 = 1.0e-2
	Corresponding to parameter a in Aliev-Panfilov paper [1].

double	a = 2.0e-3
	Corresponding to parameter epsilon0 in Aliev-Panfilov paper [1].

double	b = 0.15
	Corresponding to parameter a in Aliev-Panfilov paper [1].

double	c = 8.0
	Corresponding to parameter k in Aliev-Panfilov paper [1].

double	mu1 = 0.20
	[1].

double	mu2 = 0.30
	[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

Aliev-Panfilov ionic model.

Reference: Aliev, Panfilov. A simple two-variable model of cardiac excitation. Chaos, Solitons and Fractals (1996).

Constructor & Destructor Documentation

◆ AlievPanfilov()

AlievPanfilov::AlievPanfilov ( )

inline

Constructor.

Member Function Documentation

◆ distribute_parameters()

void AlievPanfilov::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 AlievPanfilov::get_calcium_index ( ) const

inlineoverridevirtual

Get the calcium proxy index.

Implements IonicModel.

◆ get_parameters()

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

inlineoverridevirtual

Construct an instance of model parameters.

Reimplemented from IonicModel.

◆ getf()

Vector< double > AlievPanfilov::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 > AlievPanfilov::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 AlievPanfilov::read_parameters ( const IonicModelParameters & params )

overridevirtual

Read model parameters from a parameter object.

Reimplemented from IonicModel.

◆ update_g()

virtual void AlievPanfilov::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 AlievPanfilov::a = 2.0e-3

protected

Corresponding to parameter epsilon0 in Aliev-Panfilov paper [1].

◆ alpha

double AlievPanfilov::alpha = 1.0e-2

protected

Corresponding to parameter a in Aliev-Panfilov paper [1].

◆ b

double AlievPanfilov::b = 0.15

protected

Corresponding to parameter a in Aliev-Panfilov paper [1].

◆ c

double AlievPanfilov::c = 8.0

protected

Corresponding to parameter k in Aliev-Panfilov paper [1].

◆ calcium_index

constexpr unsigned int AlievPanfilov::calcium_index = 1

staticconstexpr

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

◆ initial_X

const InitialStates AlievPanfilov::initial_X = {{"V", -80.0}, {"w", 1.0e-3}}

inlinestatic

State variables.

◆ initial_Xg

const InitialStates AlievPanfilov::initial_Xg = {}

inlinestatic

Gating variables.

◆ label

const std::string AlievPanfilov::label = "AP"

inlinestatic

Model label.

◆ mu1

double AlievPanfilov::mu1 = 0.20

protected

[1].

◆ mu2

double AlievPanfilov::mu2 = 0.30

protected

[1].

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

solver/ionic_aliev_panfilov.h
solver/ionic_aliev_panfilov.cpp

Classes

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ AlievPanfilov()

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

◆ mu1

◆ mu2