BR77 Class Reference

Detailed Description

Beeler Reuter (1977) ionic model.

Reference:

Reconstruction of the action potential of ventricular myocardial fibres, Beeler, G.W. and Reuter, H. 1977 Journal of Physiology , 268, 177-210. PubMed ID: 874889

CellML model: https://models.physiomeproject.org/e/23a/beeler_reuter_1977.cellml/view

Units of currents and capacity are in uA and uF per mm2 !

Definition at line 49 of file BR77.hpp.

#include <BR77.hpp>

Inheritance diagram for BR77:

Public Member Functions
	BR77 (Unknown *u, AbstractPdeProblem *pb, const CepsSet< CepsAttribute > &attrs={}, InputParameters *params=nullptr)
	Constructor (sets constants) More...
	~BR77 ()=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 override
	Get the linear and non linear part of the evolution function f. Also computes the ionic current. More...
CepsReal	convertCurrentFromCepsUnit (const CepsReal &v) const final
	Convert from muA per cm2 to muA per mm2. More...
CepsReal	convertCmFromCepsUnit (const CepsReal &cm) const final
	Convert capacitance from ceps units (uF/cm2) to ionic model units. Does nothing by default. More...
CepsReal	convertCmToCepsUnit (const CepsReal &cm) const final
	Convert capacitance from ionic model units to ceps units (uF/cm2). Does nothing by default. 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...
virtual CepsReal	convertVoltageFromCepsUnit (const CepsReal &v) const
	Convert voltage from ceps units (mV) to ionic model units. Does nothing by default. More...
virtual CepsReal	convertVoltageToCepsUnit (const CepsReal &v) const
	Convert voltage from ionic model units to ceps units (mV). Does nothing by default. More...
virtual CepsReal	convertDtvToCepsUnit (const CepsReal &dtv) const
	Convert current from ionic model units to ceps units (mV ms-1). Does nothing by default. 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, AbstractPdeProblem *pb)
	Sets the constants and the space dependant parameters from text inputs. More...
virtual CepsReal	getINa (CepsReal *y, CepsReal gNaCa, CepsReal gNa, CepsReal v) const
	Returns the iNa current. 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
ScalarField< DegreeOfFreedom > *	m_gNa
	This parameter may vary with space. More...
ScalarField< DegreeOfFreedom > *	m_gNaCa
	This parameter may vary with space. 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	_gS = 0
	Index alias. More...
static constexpr const CepsInt	_ENa = 1
	Index alias. More...
static constexpr const CepsInt	_m = 0
	Index alias. More...
static constexpr const CepsInt	_h = 1
	Index alias. More...
static constexpr const CepsInt	_j = 2
	Index alias. More...
static constexpr const CepsInt	_CaI = 3
	Index alias. More...
static constexpr const CepsInt	_d = 4
	Index alias. More...
static constexpr const CepsInt	_f = 5
	Index alias. More...
static constexpr const CepsInt	_x1 = 6
	Index alias. More...

Constructor & Destructor Documentation

BR77()

BR77::BR77	(	Unknown *	u,
		AbstractPdeProblem *	pb,
		const CepsSet< CepsAttribute > &	attrs = {},
		InputParameters *	params = nullptr
	)

Constructor (sets constants)

Definition at line 33 of file BR77.cpp.

~BR77()

BR77::~BR77 ( )

default

Destructor.

Member Function Documentation

computeRates()

void BR77::computeRates ( CepsReal  t, CepsReal *  y, CepsReal *  v, CepsReal *  dtyL, CepsReal *  dtyNL, CepsReal *  dtv, DegreeOfFreedom *  dof  ) const

overridevirtual

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

(1+std::exp(-0.082*(v+22.5)));

Implements AbstractIonicModel.

Definition at line 107 of file BR77.cpp.

convertCmFromCepsUnit()

CepsReal BR77::convertCmFromCepsUnit ( const CepsReal &  cm ) const

finalvirtual

Convert capacitance from ceps units (uF/cm2) to ionic model units. Does nothing by default.

Reimplemented from AbstractIonicModel.

Definition at line 201 of file BR77.cpp.

convertCmToCepsUnit()

CepsReal BR77::convertCmToCepsUnit ( const CepsReal &  cm ) const

finalvirtual

Convert capacitance from ionic model units to ceps units (uF/cm2). Does nothing by default.

Reimplemented from AbstractIonicModel.

Definition at line 195 of file BR77.cpp.

convertCurrentFromCepsUnit()

CepsReal BR77::convertCurrentFromCepsUnit ( const CepsReal &  v ) const

finalvirtual

Convert from muA per cm2 to muA per mm2.

Reimplemented from AbstractIonicModel.

Definition at line 189 of file BR77.cpp.

getINa()

CepsReal BR77::getINa ( CepsReal *  y, CepsReal  gNaCa, CepsReal  gNa, CepsReal  v  ) const

protectedvirtual

Returns the iNa current.

Reimplemented in BR77Modified.

Definition at line 222 of file BR77.cpp.

getInitialCondition()

void BR77::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 94 of file BR77.cpp.

setupWithParameters()

void BR77::setupWithParameters ( InputParameters *  p, FunctionDictionary *  dico, AbstractPdeProblem *  pb  )

protected

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

Definition at line 207 of file BR77.cpp.

Field Documentation

_CaI

constexpr const CepsInt BR77::_CaI = 3

staticconstexprprotected

Index alias.

Definition at line 117 of file BR77.hpp.

_d

constexpr const CepsInt BR77::_d = 4

staticconstexprprotected

Index alias.

Definition at line 118 of file BR77.hpp.

_ENa

constexpr const CepsInt BR77::_ENa = 1

staticconstexprprotected

Index alias.

Definition at line 111 of file BR77.hpp.

_f

constexpr const CepsInt BR77::_f = 5

staticconstexprprotected

Index alias.

Definition at line 119 of file BR77.hpp.

_gS

constexpr const CepsInt BR77::_gS = 0

staticconstexprprotected

Index alias.

Definition at line 110 of file BR77.hpp.

_h

constexpr const CepsInt BR77::_h = 1

staticconstexprprotected

Index alias.

Definition at line 115 of file BR77.hpp.

_j

constexpr const CepsInt BR77::_j = 2

staticconstexprprotected

Index alias.

Definition at line 116 of file BR77.hpp.

_m

constexpr const CepsInt BR77::_m = 0

staticconstexprprotected

Index alias.

Definition at line 114 of file BR77.hpp.

_x1

constexpr const CepsInt BR77::_x1 = 6

staticconstexprprotected

Index alias.

Definition at line 120 of file BR77.hpp.

m_gNa

ScalarField<DegreeOfFreedom>* BR77::m_gNa

protected

This parameter may vary with space.

Definition at line 106 of file BR77.hpp.

m_gNaCa

ScalarField<DegreeOfFreedom>* BR77::m_gNaCa

protected

This parameter may vary with space.

Definition at line 107 of file BR77.hpp.

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

• /builds/xxjFYZX3/0/carmen/ceps/src/ode/ionicModels/BR77.hpp
• /builds/xxjFYZX3/0/carmen/ceps/src/ode/ionicModels/BR77.cpp