CEPS: AbstractIonicModel Class Reference

Detailed Description

Represents a ionic model for a group of cells, i.e. multiple systems of ODEs.

Ionic models are ODE systems with several state variables plus the transmembrane voltage $v_\mathrm{m}$ .

The evolution function can be generally splitted into a linear part and a non linear part .

The computeRates method, which must be defined in derived classes must compute the a and b terms accordingly.

The units of the model may be different of CEPS units. In this case, override the conversion methods.

Definition at line 53 of file AbstractIonicModel.hpp.

#include <AbstractIonicModel.hpp>

Inheritance diagram for AbstractIonicModel:

[legend]

Public Member Functions
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 void	getInitialCondition (CepsReal v, CepsReal y) const =0
	Sets initial values of state variables and transmembrane voltage for a single point. Arrays y,dty must be preallocated with size m_nStateVars. More...

virtual void	computeRates (CepsReal t, CepsReal y, CepsReal v, CepsReal dtyL, CepsReal dtyNL, CepsReal dtv, DegreeOfFreedom dof) const =0
	Get the linear and non linear part of the evolution function f. Also computes the ionic current. 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...

virtual CepsReal	convertCurrentFromCepsUnit (const CepsReal &i) const
	Convert current from ionic model units to ceps units (uA per cm2). Does nothing by default. More...

virtual CepsReal	convertCmFromCepsUnit (const CepsReal &cm) const
	Convert capacitance from ceps units (uF/cm2) to ionic model units. Does nothing by default. More...

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

Constructor & Destructor Documentation

◆ ~AbstractIonicModel()

AbstractIonicModel::~AbstractIonicModel ( )

virtual

Destructor.

Definition at line 32 of file AbstractIonicModel.cpp.

◆ AbstractIonicModel()

AbstractIonicModel::AbstractIonicModel	(	Unknown *	u,
		const CepsSet< CepsAttribute > &	attrs = `{}`
	)

protected

Called only by derived classes.

Definition at line 157 of file AbstractIonicModel.cpp.

Member Function Documentation

◆ addStimulation()

void AbstractIonicModel::addStimulation ( ScalarSourceTerm * stim )

Links the model to a stimulation function, needed for computation of _ki.

Definition at line 78 of file AbstractIonicModel.cpp.

◆ computeRates()

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

pure virtual

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

Implemented in ORdmD16, MS03, BR77, TTP06, MS03Modified, CRN98, and AP95.

◆ convertCmFromCepsUnit()

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

virtual

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

Reimplemented in MS03, CRN98, AP95, and BR77.

Definition at line 138 of file AbstractIonicModel.cpp.

◆ convertCmToCepsUnit()

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

virtual

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

Reimplemented in MS03, CRN98, AP95, and BR77.

Definition at line 132 of file AbstractIonicModel.cpp.

◆ convertCurrentFromCepsUnit()

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

virtual

Convert current from ionic model units to ceps units (uA per cm2). Does nothing by default.

Reimplemented in BR77, MS03, CRN98, and AP95.

Definition at line 126 of file AbstractIonicModel.cpp.

◆ convertDtvToCepsUnit()

CepsReal AbstractIonicModel::convertDtvToCepsUnit ( const CepsReal & dtv ) const

virtual

Convert current from ionic model units to ceps units (mV ms-1). Does nothing by default.

Reimplemented in MS03, and AP95.

Definition at line 120 of file AbstractIonicModel.cpp.

◆ convertVoltageFromCepsUnit()

CepsReal AbstractIonicModel::convertVoltageFromCepsUnit ( const CepsReal & v ) const

virtual

Convert voltage from ceps units (mV) to ionic model units. Does nothing by default.

Reimplemented in MS03, and AP95.

Definition at line 114 of file AbstractIonicModel.cpp.

◆ convertVoltageToCepsUnit()

CepsReal AbstractIonicModel::convertVoltageToCepsUnit ( const CepsReal & v ) const

virtual

Convert voltage from ionic model units to ceps units (mV). Does nothing by default.

Reimplemented in MS03, and AP95.

Definition at line 108 of file AbstractIonicModel.cpp.

◆ gaussian()

CepsReal AbstractIonicModel::gaussian	(	CepsReal	x,
		CepsReal	c,
		CepsReal	s
	)		const

protected

Function often used in rates evaluations.

Definition at line 191 of file AbstractIonicModel.cpp.

◆ getCm()

ScalarField< DegreeOfFreedom > * AbstractIonicModel::getCm ( ) const

Link to Cm coefficient of PDE.

Definition at line 52 of file AbstractIonicModel.cpp.

◆ getCmInternal()

CepsReal AbstractIonicModel::getCmInternal	(	CepsReal	t,
		DegreeOfFreedom *	dof
	)		const

protected

Get either the value of cm on dof, or the default value from the paper.

Definition at line 176 of file AbstractIonicModel.cpp.

◆ getInitialCondition()

virtual void AbstractIonicModel::getInitialCondition	(	CepsReal *	v,
		CepsReal *	y
	)		const

pure virtual

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

Implemented in TTP06, ORdmD16, MS03, CRN98, BR77, and AP95.

◆ getLinkedSolver()

IonicSolver * AbstractIonicModel::getLinkedSolver ( ) const

Get link to solver.

Definition at line 150 of file AbstractIonicModel.cpp.

◆ getName()

CepsString AbstractIonicModel::getName ( ) const

Name of the solver for info display.

Definition at line 40 of file AbstractIonicModel.cpp.

◆ getNbStateVariables()

CepsUInt AbstractIonicModel::getNbStateVariables ( ) const

virtual

The number of state variables, except transmembrane voltage.

Definition at line 93 of file AbstractIonicModel.cpp.

◆ getPaperCm()

CepsReal AbstractIonicModel::getPaperCm ( CepsBool cepsUnit ) const

Get the original value of Cm used in paper.

Definition at line 64 of file AbstractIonicModel.cpp.

◆ getPaperStim()

CepsReal AbstractIonicModel::getPaperStim ( ) const

Get the original amplitude of stimulation, converted into ceps units.

Definition at line 72 of file AbstractIonicModel.cpp.

◆ getStateVariableName()

CepsString AbstractIonicModel::getStateVariableName ( CepsUInt i ) const

Gives the name of the i-th state variable.

Definition at line 99 of file AbstractIonicModel.cpp.

◆ getStimulation()

CepsReal AbstractIonicModel::getStimulation	(	DegreeOfFreedom *	x,
		CepsReal	t
	)		const

Get the sum of all stimulations at time t and dof x.

Definition at line 84 of file AbstractIonicModel.cpp.

◆ getUnknown()

Unknown * AbstractIonicModel::getUnknown ( ) const

The unknown object of the transmembrane voltage.

Returns

Definition at line 46 of file AbstractIonicModel.cpp.

◆ setCm()

void AbstractIonicModel::setCm ( ScalarField< DegreeOfFreedom > * cm )

Link to Cm coefficient of PDE.

Definition at line 58 of file AbstractIonicModel.cpp.

◆ setLinkedSolver()

void AbstractIonicModel::setLinkedSolver ( IonicSolver * solver )

Links instance to solver.

Definition at line 144 of file AbstractIonicModel.cpp.

◆ sigmoid()

CepsReal AbstractIonicModel::sigmoid	(	CepsReal	x,
		CepsReal	c,
		CepsReal	k
	)		const

protected

Function often used in rates evaluations.

Definition at line 185 of file AbstractIonicModel.cpp.

◆ uOverExpm1u()

CepsReal AbstractIonicModel::uOverExpm1u ( CepsReal u ) const

protected

Functions u/(1-exp(u)) that returns 2 (from expansion around 0)

Definition at line 197 of file AbstractIonicModel.cpp.

Field Documentation

◆ m_cm

ScalarField<DegreeOfFreedom>* AbstractIonicModel::m_cm

protected

Link to coef Cm of the PDE, for unit conversion.

Definition at line 196 of file AbstractIonicModel.hpp.

◆ m_constants

CepsReal* AbstractIonicModel::m_constants

protected

Constant parameters of the model, from inputs.

Definition at line 194 of file AbstractIonicModel.hpp.

◆ m_dconstants

CepsReal* AbstractIonicModel::m_dconstants

protected

Constant parameters of the model, computed from others.

Definition at line 195 of file AbstractIonicModel.hpp.

◆ m_name

CepsString AbstractIonicModel::m_name

protected

A label for display.

Definition at line 202 of file AbstractIonicModel.hpp.

◆ m_nStateVars

CepsUInt AbstractIonicModel::m_nStateVars

protected

Dimensionality of the ODE system, -1 for vm.

Definition at line 200 of file AbstractIonicModel.hpp.

◆ m_paperCm

CepsReal AbstractIonicModel::m_paperCm

protected

Original value of Cm.

Definition at line 197 of file AbstractIonicModel.hpp.

◆ m_paperStim

CepsReal AbstractIonicModel::m_paperStim

protected

Original stim amplitude.

Definition at line 198 of file AbstractIonicModel.hpp.

◆ m_solver

IonicSolver* AbstractIonicModel::m_solver

protected

Link to solver, set when solver is created.

Definition at line 203 of file AbstractIonicModel.hpp.

◆ m_stateVarNames

CepsVector<CepsString> AbstractIonicModel::m_stateVarNames

protected

Names of state variables.

Definition at line 201 of file AbstractIonicModel.hpp.

◆ m_stims

CepsVector<ScalarSourceTerm*> AbstractIonicModel::m_stims

protected

Link to excitations.

Definition at line 199 of file AbstractIonicModel.hpp.

◆ m_unknown

Unknown* AbstractIonicModel::m_unknown

protected

Pointer on unknown on which the model applies.

Definition at line 193 of file AbstractIonicModel.hpp.

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

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

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

◆ ~AbstractIonicModel()

◆ AbstractIonicModel()

Member Function Documentation

◆ addStimulation()

◆ computeRates()

◆ convertCmFromCepsUnit()

◆ convertCmToCepsUnit()

◆ convertCurrentFromCepsUnit()

◆ convertDtvToCepsUnit()

◆ convertVoltageFromCepsUnit()

◆ convertVoltageToCepsUnit()

◆ gaussian()

◆ getCm()

◆ getCmInternal()

◆ getInitialCondition()

◆ getLinkedSolver()

◆ getName()

◆ getNbStateVariables()

◆ getPaperCm()

◆ getPaperStim()

◆ getStateVariableName()

◆ getStimulation()

◆ getUnknown()

◆ setCm()

◆ setLinkedSolver()

◆ sigmoid()

◆ uOverExpm1u()

Field Documentation

◆ m_cm

◆ m_constants

◆ m_dconstants

◆ m_name

◆ m_nStateVars

◆ m_paperCm

◆ m_paperStim

◆ m_solver

◆ m_stateVarNames

◆ m_stims

◆ m_unknown