#include <IonicGoldbeter.hpp>

Inheritance diagram for IonicGoldbeter:

Collaboration diagram for IonicGoldbeter:

Private Attributes
Real	M_nu1
	Model Parameters. More...

Real	M_nu2

Real	M_nu3

Real	M_nu4

Real	M_nu5

Real	M_k1

Real	M_k2

Real	M_k3

Real	M_k4

Type definitions
typedef ElectroIonicModel	super

typedef std::shared_ptr< VectorEpetra >	vectorPtr_Type

typedef RegionMesh< LinearTetra >	mesh_Type

Constructors & Destructor
	IonicGoldbeter ()
	Constructor. More...

	IonicGoldbeter (Teuchos::ParameterList &parameterList)

	IonicGoldbeter (const IonicGoldbeter &model)

virtual	~IonicGoldbeter ()
	Destructor. More...

Overloads
IonicGoldbeter &	operator= (const IonicGoldbeter &model)
	Operator. More...

Setters and getters
const Real &	Nu1 () const

const Real &	Nu2 () const

const Real &	Nu3 () const

const Real &	Nu4 () const

const Real &	Nu5 () const

const Real &	K1 () const

const Real &	K2 () const

const Real &	K3 () const

const Real &	K4 () const

void	setNu1 (const Real &nu1)

void	setNu2 (const Real &nu2)

void	setNu3 (const Real &nu3)

void	setNu4 (const Real &nu4)

void	setNu5 (const Real &nu5)

void	setK1 (const Real &k1)

void	setK2 (const Real &k2)

void	setK3 (const Real &k3)

void	setK4 (const Real &k4)

Methods
void	computeGatingRhs (const std::vector< Real > &v, std::vector< Real > &rhs)
	Methods. More...

void	computeRhs (const std::vector< Real > &v, std::vector< Real > &rhs)
	This methods contains the actual evaluation of the rhs of all state variablesin the model (0D version) More...

Real	computeLocalPotentialRhs (const std::vector< Real > &v)
	This methods contains the actual evaluation of the rhs of the voltage equation only (0D version) More...

void	showMe ()
	Display information about the model. More...

Additional Inherited Members
Public Types inherited from ElectroIonicModel
typedef VectorEpetra	vector_Type

typedef std::shared_ptr< VectorEpetra >	vectorPtr_Type

typedef std::shared_ptr< VectorElemental >	elvecPtr_Type

typedef RegionMesh< LinearTetra >	mesh_Type

typedef MatrixEpetra< Real >	matrix_Type

typedef std::shared_ptr< matrix_Type >	matrixPtr_Type

typedef FESpace< mesh_Type, MapEpetra >	feSpace_Type

typedef std::shared_ptr< feSpace_Type >	feSpacePtr_Type

typedef std::function< Real(const Real &t, const Real &x, const Real &y, const Real &z, const ID &i) >	function_Type

typedef FactorySingleton< Factory< ElectroIonicModel, std::string > >	IonicModelFactory

Public Member Functions inherited from ElectroIonicModel
virtual matrix_Type	getJac (const vector_Type &v, Real h=1.0e-8)
	This methods computes the Jacobian numerically. More...

virtual std::vector< std::vector< Real > >	getJac (const std::vector< Real > &v, Real h=1.0e-8)
	This methods computes the Jacobian numerically. More...

virtual void	computeGatingRhs (const std::vector< vectorPtr_Type > &v, std::vector< vectorPtr_Type > &rhs)
	This methods computes the right hand side of the gating variables in the 3D case. More...

virtual void	computeNonGatingRhs (const std::vector< vectorPtr_Type > &v, std::vector< vectorPtr_Type > &rhs)
	This methods computes the right hand side of the state variables that are not gating variables in the 3D case. More...

virtual void	computeGatingVariablesWithRushLarsen (std::vector< vectorPtr_Type > &v, const Real dt)
	Compute the new value of the gating variables in 3D with the Rush Larsen method specified in the 0D version of the ionic model. More...

virtual void	computeRhs (const std::vector< vectorPtr_Type > &v, std::vector< vectorPtr_Type > &rhs)
	Compute the right hand side of the ionic model in 3D. More...

virtual void	computePotentialRhsICI (const std::vector< vectorPtr_Type > &v, std::vector< vectorPtr_Type > &rhs, matrix_Type &massMatrix)
	Compute the right hand side of the voltage equation linearly interpolating the ionic currents. More...

virtual void	computePotentialRhsSVI (const std::vector< vectorPtr_Type > &v, std::vector< vectorPtr_Type > &rhs, FESpace< mesh_Type, MapEpetra > &uFESpace)
	Compute the right hand side of the voltage equation using SVI. More...

virtual void	computePotentialRhsSVI (const std::vector< vectorPtr_Type > &v, std::vector< vectorPtr_Type > &rhs, FESpace< mesh_Type, MapEpetra > &uFESpace, const QuadratureRule &qr)
	Compute the right hand side of the voltage equation using SVI specifying the quadrature rule. More...

virtual void	initialize (std::vector< Real > &v)
	Initialize the ionic model with a given vector of state variable (0D version) More...

virtual void	initialize (std::vector< vectorPtr_Type > &v)
	Initialize the ionic model in 3D with a given vector of state variable vector pointers. More...

virtual void	computeGatingVariablesWithRushLarsen (std::vector< Real > &, const Real)
	This methods contains the actual evaluation of the rhs of the voltage equation only (0D version) More...

virtual void	computeNonGatingRhs (const std::vector< Real > &v, std::vector< Real > &rhs)
	In the case this method is improperly used, it should use this default implementation. More...

	ElectroIonicModel ()
	Empty Constructor. More...

	ElectroIonicModel (int n)
	Constructor. More...

	ElectroIonicModel (int n, int g)
	Constructor. More...

	ElectroIonicModel (const ElectroIonicModel &Ionic)
	Copy Constructor. More...

virtual	~ElectroIonicModel ()
	Destructor. More...

virtual void	setup (Teuchos::ParameterList &parameterList)
	setup the parameters of the ionic model from an xml file More...

const short int	Size () const
	returns the number of equations of the ionic model More...

const short int	numberOfGatingVariables () const
	returns the number of gating variables in the ionic model More...

const Real	membraneCapacitance () const
	returns the value of the membrane capacitance in the model More...

const Real	appliedCurrent () const
	returns the value of the applied current in the model/point More...

vectorPtr_Type	appliedCurrentPtr ()
	returns the pointer to the applied current FE vector in the 3D case More...

const std::vector< Real >	restingConditions () const
	returns the vector with the resting values of the variables in the ionic model More...

const function_Type	pacaingProtocol () const
	returns the function describing the pacing protocol for the ionic model More...

void	setMembraneCapacitance (const Real p)
	set the membrane capacitance in the ionic model More...

void	setAppliedCurrent (const Real p)
	set the applied current in the ionic model/point More...

void	setAppliedCurrentPtr (const vectorPtr_Type p)
	set the pointer to the applied current in the 3D ionic model More...

void	setAppliedCurrent (const vector_Type &p)
	set the pointer to the applied current in the 3D ionic model More...

void	setAppliedCurrentFromFunction (function_Type &f, feSpacePtr_Type feSpacePtr, Real time=0.0)
	Interpolate the function f on the FE space feSpacePtr at time time. More...

void	setAppliedCurrentFromElectroStimulus (ElectroStimulus &stimulus, feSpacePtr_Type feSpacePtr, Real time=0.0)
	Interpolate the function of the electro stimulus. More...

void	setPacingProtocol (function_Type pacingProtocol)
	Set the pacing protocol as boost function. More...

void	setRestingCondtions (Real value, int j)
	Set component of the resting conditions. More...

void	setRestingCondtions (std::vector< Real > &restingConditions)
	Set resting conditions. More...

void	addAppliedCurrent (Real &rhs)
	Simple wrapper to add the applied current. More...

void	addAppliedCurrent (std::vector< Real > &rhs)
	Simple wrapper to add the applied current. More...

ElectroIonicModel &	operator= (const ElectroIonicModel &Ionic)
	Assignment operator. More...

Protected Attributes inherited from ElectroIonicModel
short int	M_numberOfEquations

short int	M_numberOfGatingVariables

std::vector< Real >	M_restingConditions

Real	M_membraneCapacitance

Real	M_appliedCurrent

vectorPtr_Type	M_appliedCurrentPtr

function_Type	M_pacingProtocol

Detailed Description

Definition at line 62 of file IonicGoldbeter.hpp.

Member Typedef Documentation

◆ super

typedef ElectroIonicModel super

Definition at line 68 of file IonicGoldbeter.hpp.

◆ vectorPtr_Type

typedef std::shared_ptr<VectorEpetra> vectorPtr_Type

Definition at line 69 of file IonicGoldbeter.hpp.

◆ mesh_Type

typedef RegionMesh<LinearTetra> mesh_Type

Definition at line 70 of file IonicGoldbeter.hpp.

Constructor & Destructor Documentation

◆ IonicGoldbeter() [1/3]

IonicGoldbeter ( )

Constructor.

Constructors.

Definition at line 54 of file IonicGoldbeter.cpp.

◆ IonicGoldbeter() [2/3]

IonicGoldbeter ( Teuchos::ParameterList & parameterList )

Parameters

Epetra	communicator
list	of parameters in an xml file

Definition at line 71 of file IonicGoldbeter.cpp.

◆ IonicGoldbeter() [3/3]

IonicGoldbeter ( const IonicGoldbeter & model )

Parameters

IntracellularCalciumGoldbeter object

Definition at line 86 of file IonicGoldbeter.cpp.

◆ ~IonicGoldbeter()

virtual ~IonicGoldbeter ( )

inlinevirtual

Destructor.

Definition at line 92 of file IonicGoldbeter.hpp.

Member Function Documentation

◆ operator=()

IonicGoldbeter & operator= ( const IonicGoldbeter & model )

Operator.

Definition at line 106 of file IonicGoldbeter.cpp.

◆ Nu1()

const Real& Nu1 ( ) const

inline

Definition at line 107 of file IonicGoldbeter.hpp.

◆ Nu2()

const Real& Nu2 ( ) const

inline

Definition at line 111 of file IonicGoldbeter.hpp.

◆ Nu3()

const Real& Nu3 ( ) const

inline

Definition at line 115 of file IonicGoldbeter.hpp.

◆ Nu4()

const Real& Nu4 ( ) const

inline

Definition at line 119 of file IonicGoldbeter.hpp.

◆ Nu5()

const Real& Nu5 ( ) const

inline

Definition at line 123 of file IonicGoldbeter.hpp.

◆ K1()

const Real& K1 ( ) const

inline

Definition at line 127 of file IonicGoldbeter.hpp.

◆ K2()

const Real& K2 ( ) const

inline

Definition at line 131 of file IonicGoldbeter.hpp.

◆ K3()

const Real& K3 ( ) const

inline

Definition at line 135 of file IonicGoldbeter.hpp.

◆ K4()

const Real& K4 ( ) const

inline

Definition at line 139 of file IonicGoldbeter.hpp.

◆ setNu1()

void setNu1 ( const Real & nu1 )

inline

Definition at line 144 of file IonicGoldbeter.hpp.

◆ setNu2()

void setNu2 ( const Real & nu2 )

inline

Definition at line 148 of file IonicGoldbeter.hpp.

◆ setNu3()

void setNu3 ( const Real & nu3 )

inline

Definition at line 152 of file IonicGoldbeter.hpp.

◆ setNu4()

void setNu4 ( const Real & nu4 )

inline

Definition at line 156 of file IonicGoldbeter.hpp.

◆ setNu5()

void setNu5 ( const Real & nu5 )

inline

Definition at line 160 of file IonicGoldbeter.hpp.

◆ setK1()

void setK1 ( const Real & k1 )

inline

Definition at line 164 of file IonicGoldbeter.hpp.

◆ setK2()

void setK2 ( const Real & k2 )

inline

Definition at line 168 of file IonicGoldbeter.hpp.

◆ setK3()

void setK3 ( const Real & k3 )

inline

Definition at line 172 of file IonicGoldbeter.hpp.

◆ setK4()

void setK4 ( const Real & k4 )

inline

Definition at line 176 of file IonicGoldbeter.hpp.

◆ computeGatingRhs()

void computeGatingRhs	(	const std::vector< Real > &	v,
		std::vector< Real > &	rhs
	)

virtual

Methods.

Implements ElectroIonicModel.

Definition at line 129 of file IonicGoldbeter.cpp.

◆ computeRhs()

void computeRhs	(	const std::vector< Real > &	v,
		std::vector< Real > &	rhs
	)

virtual

This methods contains the actual evaluation of the rhs of all state variablesin the model (0D version)

Although this method can just wrap the computeGatingRhs ( const std::vector<Real>& v, std::vector<Real>& rhs ) and the computeLocalPotentialRhs ( const std::vector<Real>& v ) methods, for efficiency it may be better to duplicate the code.

Parameters

v	vector of state variables including the voltage (with n elements)
rhs	vector of right hand side state variables including the voltage (with n elements)

Implements ElectroIonicModel.

Definition at line 141 of file IonicGoldbeter.cpp.

◆ computeLocalPotentialRhs()

Real computeLocalPotentialRhs ( const std::vector< Real > & v )

virtual

This methods contains the actual evaluation of the rhs of the voltage equation only (0D version)

Parameters

v	vector of state variables including the voltage (with n elements)

Implements ElectroIonicModel.

Definition at line 156 of file IonicGoldbeter.cpp.

◆ showMe()

void showMe ( )

virtual

Display information about the model.

Implements ElectroIonicModel.

Definition at line 165 of file IonicGoldbeter.cpp.

Here is the caller graph for this function:

Field Documentation

◆ M_nu1

Real M_nu1

private

Model Parameters.

Chemical kinetics parameters

Definition at line 212 of file IonicGoldbeter.hpp.

◆ M_nu2

Real M_nu2

private

Definition at line 213 of file IonicGoldbeter.hpp.

◆ M_nu3

Real M_nu3

private

Definition at line 214 of file IonicGoldbeter.hpp.

◆ M_nu4

Real M_nu4

private

Definition at line 215 of file IonicGoldbeter.hpp.

◆ M_nu5

Real M_nu5

private

Definition at line 216 of file IonicGoldbeter.hpp.

◆ M_k1

Real M_k1

private

Definition at line 217 of file IonicGoldbeter.hpp.

◆ M_k2

Real M_k2

private

Definition at line 218 of file IonicGoldbeter.hpp.

◆ M_k3

Real M_k3

private

Definition at line 219 of file IonicGoldbeter.hpp.

◆ M_k4

Real M_k4

private

Definition at line 220 of file IonicGoldbeter.hpp.

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

Private Attributes

Type definitions

Constructors & Destructor

Overloads

Setters and getters

Methods

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ super

◆ vectorPtr_Type

◆ mesh_Type

Constructor & Destructor Documentation

◆ IonicGoldbeter() [1/3]

◆ IonicGoldbeter() [2/3]

◆ IonicGoldbeter() [3/3]

◆ ~IonicGoldbeter()

Member Function Documentation

◆ operator=()

◆ Nu1()

◆ Nu2()

◆ Nu3()

◆ Nu4()

◆ Nu5()

◆ K1()

◆ K2()

◆ K3()

◆ K4()

◆ setNu1()

◆ setNu2()

◆ setNu3()

◆ setNu4()

◆ setNu5()

◆ setK1()

◆ setK2()

◆ setK3()

◆ setK4()

◆ computeGatingRhs()

◆ computeRhs()

◆ computeLocalPotentialRhs()

◆ showMe()

Field Documentation

◆ M_nu1

◆ M_nu2

◆ M_nu3

◆ M_nu4

◆ M_nu5

◆ M_k1

◆ M_k2

◆ M_k3

◆ M_k4