CEPS: AP95 Class Reference

Detailed Description

Aliev-Panfilov ionic model.

https://doi.org/10.1016/0960-0779(95)00089-5

Definition at line 40 of file AP95.hpp.

#include <AP95.hpp>

Inheritance diagram for AP95:

Public Member Functions
	AP95 (Unknown u, const CepsSet< CepsAttribute > &attrs={}, InputParameters params=nullptr)
	Constructor (sets constants) More...

virtual	~AP95 ()=default
	Destructor. More...

void	getInitialCondition (CepsReal v, CepsReal y) const final
	Sets initial values of state variables and transmembrane voltage for a single point. Arrays y,dty must be preallocated with size m_nStateVars. More...

void	computeRates (CepsReal t, CepsReal y, CepsReal v, CepsReal dtyL, CepsReal dtyNL, CepsReal dtv, DegreeOfFreedom dof) const final
	Get the linear and non linear part of the evolution function f. Also computes the ionic current. More...

CepsReal	convertVoltageToCepsUnit (const CepsReal &u) const override
	Convert from no unit to mV. More...

CepsReal	convertVoltageFromCepsUnit (const CepsReal &u) const override
	Convert from mV to no unit. More...

CepsReal	convertDtvToCepsUnit (const CepsReal &i) const override
	Convert from s-1 to uA per cm2. More...

CepsReal	convertCurrentFromCepsUnit (const CepsReal &i) const override
	Convert from uA per cm2 to s-1. More...

CepsReal	convertCmFromCepsUnit (const CepsReal &cm) const override
	Convert capacitance from ceps units (uF/cm2) to ionic model units. More...

CepsReal	convertCmToCepsUnit (const CepsReal &cm) const override
	Convert capacitance from ionic model units to ceps units (uF/cm2). More...

Public Member Functions inherited from AbstractIonicModel
virtual	~AbstractIonicModel ()
	Destructor. More...

CepsString	getName () const
	Name of the solver for info display. More...

Unknown *	getUnknown () const
	The unknown object of the transmembrane voltage. More...

ScalarField< DegreeOfFreedom > *	getCm () const
	Link to Cm coefficient of PDE. More...

void	setCm (ScalarField< DegreeOfFreedom > *)
	Link to Cm coefficient of PDE. More...

CepsReal	getPaperCm (CepsBool cepsUnit) const
	Get the original value of Cm used in paper. More...

CepsReal	getPaperStim () const
	Get the original amplitude of stimulation, converted into ceps units. More...

void	addStimulation (ScalarSourceTerm *stim)
	Links the model to a stimulation function, needed for computation of _ki. More...

CepsReal	getStimulation (DegreeOfFreedom *x, CepsReal t) const
	Get the sum of all stimulations at time t and dof x. More...

virtual CepsUInt	getNbStateVariables () const
	The number of state variables, except transmembrane voltage. More...

CepsString	getStateVariableName (CepsUInt i) const
	Gives the name of the i-th state variable. More...

void	setLinkedSolver (IonicSolver *solver)
	Links instance to solver. More...

IonicSolver *	getLinkedSolver () const
	Get link to solver. More...

Public Member Functions inherited from ceps::HoldsAttributes
	HoldsAttributes (const CepsSet< CepsAttribute > &attributes)
	Constructor with any number of attributes. More...

	HoldsAttributes (const CepsVector< CepsAttribute > &attributes)
	Constructor with any number of attributes. More...

	HoldsAttributes (CepsAttribute *attributes, const CepsUInt &n)
	Constructor with any number of attributes. More...

	HoldsAttributes ()=default
	Default constructor. More...

	HoldsAttributes (const HoldsAttributes &)=default
	Assignement operator. More...

	HoldsAttributes (HoldsAttributes &&) noexcept=default
	Copy constructor. More...

virtual	~HoldsAttributes ()=default
	Destructor. More...

HoldsAttributes &	operator= (const HoldsAttributes &)=default
	Assignment operator. More...

HoldsAttributes &	operator= (HoldsAttributes &&) noexcept=default
	Assignment operator. More...

CepsUInt	getNumberOfAttributes () const
	Returns number of attributes of the entity. More...

CepsSet< CepsAttribute > &	getAttributes ()
	Returns the attributes of the entity. More...

const CepsSet< CepsAttribute > &	getAttributes () const
	Returns the attributes of the entity, const version. More...

void	setAttributes (const CepsVector< CepsAttribute > &attributes)
	Sets the attributes of the entity. More...

void	setAttributes (const CepsSet< CepsAttribute > &attributes)
	Sets the attributes of the entity. More...

void	setAttributes (const CepsAttribute *attributes, const CepsUInt &n)
	Sets the attributes of the entity. More...

template<class _It >
void	setAttributes (_It first, _It last)
	Sets the attributes of the entity. More...

void	addAttribute (const CepsAttribute &name)
	Adds an attribute to the entity. More...

void	addAttributes (const CepsVector< CepsAttribute > &attributes)
	Adds several attributes to the entity. More...

void	addAttributes (const CepsSet< CepsAttribute > &attributes)
	Adds several attributes to the entity. More...

void	addAttributes (const CepsAttribute *attributes, const CepsUInt &n)
	Adds several attributes to the entity. More...

template<class _It >
void	addAttributes (_It first, _It last)
	Adds several attributes to the entity. More...

void	removeAttribute (const CepsAttribute &name)
	Removes an attribute from the entity. More...

void	removeAttributes (const CepsSet< CepsAttribute > &attributes)
	Removes several attributes from the entity. More...

void	removeAttributes (const CepsVector< CepsAttribute > &attributes)
	Removes several attributes from the entity. More...

void	removeAttributes (const CepsAttribute *attributes, const CepsUInt &n)
	Removes several attributes from the entity. More...

template<class _It >
void	removeAttributes (_It first, _It last)
	Removes several attributes from the entity. More...

void	clearAttributes ()
	Removes all attributes from the entity. More...

CepsBool	hasAttribute (const CepsAttribute &name) const
	Tells if the entity has the attribute in argument. More...

CepsBool	hasAllAttributes (const CepsVector< CepsAttribute > &attributes) const
	Tells if the entity has all the attributes in argument. More...

CepsBool	hasAllAttributes (const CepsAttribute *attributes, const CepsUInt &n) const
	Tells if the entity has all the attributes in argument. More...

template<class _It >
CepsBool	hasAllAttributes (_It first, _It last) const
	Tells if the entity has all the attributes in argument. More...

CepsBool	hasOneOfAttributes (const CepsSet< CepsAttribute > &attributes) const
	Tells if the entity has one of the attributes in argument. More...

CepsBool	hasOneOfAttributes (const CepsVector< CepsAttribute > &attributes) const
	Tells if the entity has one of the attributes in argument. More...

CepsBool	hasOneOfAttributes (const CepsAttribute *attributes, const CepsUInt &n) const
	Tells if the entity has one of the attributes in argument. More...

template<class _It >
CepsBool	hasOneOfAttributes (_It first, _It last) const
	Tells if the entity has one of the attributes in argument. More...

CepsBool	hasUniversalAttribute () const
	Detect if the current entity has the attribute universal. More...

void	reset ()
	Equivalent to HoldsAttributes::clear() More...

Protected Member Functions
void	setupWithParameters (InputParameters p, FunctionDictionary dico)
	Sets the constants and the space dependant parameters from text inputs. More...

Protected Member Functions inherited from AbstractIonicModel
	AbstractIonicModel (Unknown *u, const CepsSet< CepsAttribute > &attrs={})
	Called only by derived classes. More...

CepsReal	getCmInternal (CepsReal t, DegreeOfFreedom *dof) const
	Get either the value of cm on dof, or the default value from the paper. More...

CepsReal	sigmoid (CepsReal x, CepsReal c, CepsReal k) const
	Function often used in rates evaluations. More...

CepsReal	gaussian (CepsReal x, CepsReal c, CepsReal s) const
	Function often used in rates evaluations. More...

CepsReal	uOverExpm1u (CepsReal u) const
	Functions u/(1-exp(u)) that returns 2 (from expansion around 0) More...

Protected Attributes
CepsReal	m_vMin
	lower bound of voltage normalization interval More...

CepsReal	m_vMax
	upper bound of voltage normalization interval More...

CepsReal	m_cellSurface
	surface of a cell used for unit scaling. Default is surface of a cylinder (r=10um,l=100um) More...

Protected Attributes inherited from AbstractIonicModel
Unknown *	m_unknown
	Pointer on unknown on which the model applies. More...

CepsReal *	m_constants
	Constant parameters of the model, from inputs. More...

CepsReal *	m_dconstants
	Constant parameters of the model, computed from others. More...

ScalarField< DegreeOfFreedom > *	m_cm
	Link to coef Cm of the PDE, for unit conversion. More...

CepsReal	m_paperCm
	Original value of Cm. More...

CepsReal	m_paperStim
	Original stim amplitude. More...

CepsVector< ScalarSourceTerm * >	m_stims
	Link to excitations. More...

CepsUInt	m_nStateVars
	Dimensionality of the ODE system, -1 for vm. More...

CepsVector< CepsString >	m_stateVarNames
	Names of state variables. More...

CepsString	m_name
	A label for display. More...

IonicSolver *	m_solver
	Link to solver, set when solver is created. More...

Protected Attributes inherited from ceps::HoldsAttributes
CepsSet< CepsAttribute >	m_attributes
	The attributes held by the entity. More...

Static Protected Attributes
static constexpr const CepsInt	_h = 0
	indexing alias More...

static constexpr const CepsInt	_k = 0
	indexing alias More...

static constexpr const CepsInt	_a = 1
	indexing alias More...

static constexpr const CepsInt	_mu1 = 2
	indexing alias More...

static constexpr const CepsInt	_mu2 = 3
	indexing alias More...

static constexpr const CepsInt	_eps0 = 4
	indexing alias More...

Constructor & Destructor Documentation

◆ AP95()

AP95::AP95	(	Unknown *	u,
		const CepsSet< CepsAttribute > &	attrs = `{}`,
		InputParameters *	params = `nullptr`
	)

Constructor (sets constants)

Definition at line 32 of file AP95.cpp.

◆ ~AP95()

virtual AP95::~AP95 ( )

virtualdefault

Destructor.

Member Function Documentation

◆ computeRates()

void AP95::computeRates	(	CepsReal	t,
		CepsReal *	y,
		CepsReal *	v,
		CepsReal *	dtyL,
		CepsReal *	dtyNL,
		CepsReal *	dtv,
		DegreeOfFreedom *	dof
	)		const

finalvirtual

Get the linear and non linear part of the evolution function f. Also computes the ionic current.

Parameters

[in]	t	time
[in]	y	value of state variables at time
[in]	v	value of transmembrane voltage at time
[out]	dtyL	will be filled with the linear part of the derivative
[out]	dtyNL	the non linear part of the derivative
[out]	dtv	value of ionic current at time
[in]	dof	degree of freedom, in case some coefficients depend on space

Implements AbstractIonicModel.

Definition at line 76 of file AP95.cpp.

◆ convertCmFromCepsUnit()

CepsReal AP95::convertCmFromCepsUnit ( const CepsReal & cm ) const

overridevirtual

Convert capacitance from ceps units (uF/cm2) to ionic model units.

Reimplemented from AbstractIonicModel.

Definition at line 128 of file AP95.cpp.

◆ convertCmToCepsUnit()

CepsReal AP95::convertCmToCepsUnit ( const CepsReal & cm ) const

overridevirtual

Convert capacitance from ionic model units to ceps units (uF/cm2).

Reimplemented from AbstractIonicModel.

Definition at line 134 of file AP95.cpp.

◆ convertCurrentFromCepsUnit()

CepsReal AP95::convertCurrentFromCepsUnit ( const CepsReal & i ) const

overridevirtual

Convert from uA per cm2 to s-1.

Reimplemented from AbstractIonicModel.

Definition at line 116 of file AP95.cpp.

◆ convertDtvToCepsUnit()

CepsReal AP95::convertDtvToCepsUnit ( const CepsReal & i ) const

overridevirtual

Convert from s-1 to uA per cm2.

Reimplemented from AbstractIonicModel.

Definition at line 122 of file AP95.cpp.

◆ convertVoltageFromCepsUnit()

CepsReal AP95::convertVoltageFromCepsUnit ( const CepsReal & u ) const

overridevirtual

Convert from mV to no unit.

Reimplemented from AbstractIonicModel.

Definition at line 110 of file AP95.cpp.

◆ convertVoltageToCepsUnit()

CepsReal AP95::convertVoltageToCepsUnit ( const CepsReal & u ) const

overridevirtual

Convert from no unit to mV.

Reimplemented from AbstractIonicModel.

Definition at line 104 of file AP95.cpp.

◆ getInitialCondition()

void AP95::getInitialCondition	(	CepsReal *	v,
		CepsReal *	y
	)		const

finalvirtual

Sets initial values of state variables and transmembrane voltage for a single point. Arrays y,dty must be preallocated with size m_nStateVars.

Implements AbstractIonicModel.

Definition at line 69 of file AP95.cpp.

◆ setupWithParameters()

void AP95::setupWithParameters	(	InputParameters *	p,
		FunctionDictionary *	dico
	)

protected

Sets the constants and the space dependant parameters from text inputs.

Definition at line 140 of file AP95.cpp.

Field Documentation

◆ _a

constexpr const CepsInt AP95::_a = 1

staticconstexprprotected

indexing alias

Definition at line 114 of file AP95.hpp.

◆ _eps0

constexpr const CepsInt AP95::_eps0 = 4

staticconstexprprotected

indexing alias

Definition at line 117 of file AP95.hpp.

◆ _h

constexpr const CepsInt AP95::_h = 0

staticconstexprprotected

indexing alias

Definition at line 110 of file AP95.hpp.

◆ _k

constexpr const CepsInt AP95::_k = 0

staticconstexprprotected

indexing alias

Definition at line 113 of file AP95.hpp.

◆ _mu1

constexpr const CepsInt AP95::_mu1 = 2

staticconstexprprotected

indexing alias

Definition at line 115 of file AP95.hpp.

◆ _mu2

constexpr const CepsInt AP95::_mu2 = 3

staticconstexprprotected

indexing alias

Definition at line 116 of file AP95.hpp.

◆ m_cellSurface

CepsReal AP95::m_cellSurface

protected

surface of a cell used for unit scaling. Default is surface of a cylinder (r=10um,l=100um)

Definition at line 107 of file AP95.hpp.

◆ m_vMax

CepsReal AP95::m_vMax

protected

upper bound of voltage normalization interval

Definition at line 106 of file AP95.hpp.

◆ m_vMin

CepsReal AP95::m_vMin

protected

lower bound of voltage normalization interval

Definition at line 105 of file AP95.hpp.

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

/builds/xxjFYZX3/0/carmen/ceps/src/ode/ionicModels/AP95.hpp
/builds/xxjFYZX3/0/carmen/ceps/src/ode/ionicModels/AP95.cpp

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Constructor & Destructor Documentation

◆ AP95()

◆ ~AP95()

Member Function Documentation

◆ computeRates()

◆ convertCmFromCepsUnit()

◆ convertCmToCepsUnit()

◆ convertCurrentFromCepsUnit()

◆ convertDtvToCepsUnit()

◆ convertVoltageFromCepsUnit()

◆ convertVoltageToCepsUnit()

◆ getInitialCondition()

◆ setupWithParameters()

Field Documentation

◆ _a

◆ _eps0

◆ _h

◆ _k

◆ _mu1

◆ _mu2

◆ m_cellSurface

◆ m_vMax

◆ m_vMin