CEPS: MS03Modified Class Reference

Detailed Description

Mitchell-Schaeffer ionic model, with modification to keep ionic current bounded.

Reference: Eq 2.15 and 2.16 of A. Davidovic PhD, 2016 Multiscale mathematical modelling of structural heterogeneities in cardiac electrophysiology

Also, if TMV is outside a parametrized interval [a,b] with a<0 and b>1, the dtv function is replaced by a sigmoid arc with C1 connexion at a and b.

If v>=b: $\tilde{i_\mathrm{ion}}(v) = i_\mathrm{ion}(b)(1+\tanh(k_b(v_b)))$ with computed to match the derivative at v=b.

Definition at line 146 of file MS03.hpp.

#include <MS03.hpp>

Inheritance diagram for MS03Modified:

[legend]

Public Member Functions
	MS03Modified (Unknown u, const CepsSet< CepsAttribute > &attrs={}, InputParameters params=nullptr)
	Constructor (sets constants) More...

virtual	~MS03Modified ()=default
	Destructor. 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...

Public Member Functions inherited from MS03
	MS03 (Unknown u, const CepsSet< CepsAttribute > &attrs={}, InputParameters params=nullptr)
	Constructor (sets constants) More...

virtual	~MS03 ()=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...

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 MS03
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_etaGate
	Slope in smooth transition hinfty. More...

Protected Attributes inherited from MS03
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...

CepsReal	m_vInit
	Initial condition for v. More...

CepsReal	m_hInit
	Initial condition for h. 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	_etaGate = 5
	indexing alias More...

static constexpr const CepsInt	_vA = 6
	indexing alias More...

static constexpr const CepsInt	_vB = 7
	indexing alias More...

Static Protected Attributes inherited from MS03
static constexpr const CepsInt	_h = 0
	indexing alias More...

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

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

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

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

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

Constructor & Destructor Documentation

◆ MS03Modified()

MS03Modified::MS03Modified	(	Unknown *	u,
		const CepsSet< CepsAttribute > &	attrs = `{}`,
		InputParameters *	params = `nullptr`
	)

Constructor (sets constants)

Definition at line 174 of file MS03.cpp.

◆ ~MS03Modified()

virtual MS03Modified::~MS03Modified ( )

virtualdefault

Destructor.

Member Function Documentation

◆ computeRates()

void MS03Modified::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

Reimplemented from MS03.

Definition at line 207 of file MS03.cpp.

◆ setupWithParameters()

void MS03Modified::setupWithParameters	(	InputParameters *	p,
		FunctionDictionary *	dico
	)

protected

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

Definition at line 263 of file MS03.cpp.

Field Documentation

◆ _etaGate

constexpr const CepsInt MS03Modified::_etaGate = 5

staticconstexprprotected

indexing alias

Definition at line 183 of file MS03.hpp.

◆ _vA

constexpr const CepsInt MS03Modified::_vA = 6

staticconstexprprotected

indexing alias

Definition at line 184 of file MS03.hpp.

◆ _vB

constexpr const CepsInt MS03Modified::_vB = 7

staticconstexprprotected

indexing alias

Definition at line 185 of file MS03.hpp.

◆ m_etaGate

CepsReal MS03Modified::m_etaGate

protected

Slope in smooth transition hinfty.

Definition at line 182 of file MS03.hpp.

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

/builds/xxjFYZX3/0/carmen/ceps/src/ode/ionicModels/MS03.hpp
/builds/xxjFYZX3/0/carmen/ceps/src/ode/ionicModels/MS03.cpp

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Constructor & Destructor Documentation

◆ MS03Modified()

◆ ~MS03Modified()

Member Function Documentation

◆ computeRates()

◆ setupWithParameters()

Field Documentation

◆ _etaGate

◆ _vA

◆ _vB

◆ m_etaGate