#include <FentonKarma.h>

Inheritance diagram for Nektar::FentonKarma:

Public Member Functions
	FentonKarma (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
	Constructor. More...

virtual	~FentonKarma ()
	Destructor. More...

Public Member Functions inherited from Nektar::CellModel
	CellModel (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)

virtual	~CellModel ()

void	Initialise ()
	Initialise the cell model storage and set initial conditions. More...

void	TimeIntegrate (const Array< OneD, const Array< OneD, NekDouble >> &inarray, Array< OneD, Array< OneD, NekDouble >> &outarray, const NekDouble time)
	Time integrate the cell model by one PDE timestep. More...

void	Update (const Array< OneD, const Array< OneD, NekDouble >> &inarray, Array< OneD, Array< OneD, NekDouble >> &outarray, const NekDouble time)
	Compute the derivatives of cell model variables. More...

void	GenerateSummary (SummaryList &s)
	Print a summary of the cell model. More...

size_t	GetNumCellVariables ()

std::string	GetCellVarName (size_t idx)

Array< OneD, NekDouble >	GetCellSolutionCoeffs (size_t idx)

Array< OneD, NekDouble >	GetCellSolution (size_t idx)

Static Public Member Functions
static CellModelSharedPtr	create (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
	Creates an instance of this class. More...

Static Public Attributes
static std::string	className
	Name of class. More...

Protected Member Functions
virtual void	v_Update (const Array< OneD, const Array< OneD, NekDouble >> &inarray, Array< OneD, Array< OneD, NekDouble >> &outarray, const NekDouble time) override
	Computes the reaction terms $f(u,v)$ and $g(u,v)$. More...

virtual void	v_GenerateSummary (SummaryList &s) override
	Prints a summary of the model parameters. More...

virtual void	v_SetInitialConditions () override

virtual std::string	v_GetCellVarName (size_t idx) override

Protected Member Functions inherited from Nektar::CellModel
void	LoadCellModel ()

Private Types
enum	Variants { eBR , eMBR , eMLR1 , eGP , eCF1 , eCF2a , eCF2b , eCF2c , eCF3a , eCF3b , eFC2002Set1a , eFC2002Set1b , eFC2002Set1c , eFC2002Set1d , eFC2002Set1e , eFC2002Set2 , eFC2002Set4a , eFC2002Set4b , eFC2002Set4c , eFC2002Set4d , eFC2002Set5 , eFC2002Set6 , eFC2002Set7 , eFC2002Set8 , eFC2002Set9 , eLawson , eCAF }

Private Attributes
NekDouble	C_m

NekDouble	V_0

NekDouble	V_fi

NekDouble	u_fi

NekDouble	u_c

NekDouble	u_v

NekDouble	u_r

NekDouble	g_fi_max

NekDouble	tau_d

NekDouble	tau_v1_minus

NekDouble	tau_v2_minus

NekDouble	tau_v_plus

NekDouble	tau_0

NekDouble	tau_r

NekDouble	tau_si

NekDouble	tau_y_plus

NekDouble	tau_y_minus

NekDouble	u_csi

NekDouble	k1

NekDouble	k2

NekDouble	tau_w_minus

NekDouble	tau_w_plus

bool	isCF3

enum Variants	model_variant

Static Private Attributes
static std::string	lookupIds []

static std::string	def

Additional Inherited Members
Protected Attributes inherited from Nektar::CellModel
LibUtilities::SessionReaderSharedPtr	m_session
	Session. More...

MultiRegions::ExpListSharedPtr	m_field
	Transmembrane potential field from PDE system. More...

size_t	m_nq
	Number of physical points. More...

size_t	m_nvar
	Number of variables in cell model (inc. transmembrane voltage) More...

NekDouble	m_lastTime
	Timestep for pde model. More...

size_t	m_substeps
	Number of substeps to take. More...

Array< OneD, Array< OneD, NekDouble > >	m_cellSol
	Cell model solution variables. More...

Array< OneD, Array< OneD, NekDouble > >	m_wsp
	Cell model integration workspace. More...

bool	m_useNodal
	Flag indicating whether nodal projection in use. More...

StdRegions::StdNodalTriExpSharedPtr	m_nodalTri
	StdNodalTri for cell model calculations. More...

StdRegions::StdNodalTetExpSharedPtr	m_nodalTet

Array< OneD, Array< OneD, NekDouble > >	m_nodalTmp
	Temporary array for nodal projection. More...

std::vector< int >	m_concentrations
	Indices of cell model variables which are concentrations. More...

std::vector< int >	m_gates
	Indices of cell model variables which are gates. More...

Array< OneD, Array< OneD, NekDouble > >	m_gates_tau
	Storage for gate tau values. More...

Detailed Description

Definition at line 42 of file FentonKarma.h.

Member Enumeration Documentation

◆ Variants

enum Nektar::FentonKarma::Variants

private

Enumerator
eBR
eMBR
eMLR1
eGP
eCF1
eCF2a
eCF2b
eCF2c
eCF3a
eCF3b
eFC2002Set1a
eFC2002Set1b
eFC2002Set1c
eFC2002Set1d
eFC2002Set1e
eFC2002Set2
eFC2002Set4a
eFC2002Set4b
eFC2002Set4c
eFC2002Set4d
eFC2002Set5
eFC2002Set6
eFC2002Set7
eFC2002Set8
eFC2002Set9
eLawson
eCAF

Definition at line 103 of file FentonKarma.h.

     {
         eBR,
         eMBR,
         eMLR1,
         eGP,
         eCF1,
         eCF2a,
         eCF2b,
         eCF2c,
         eCF3a,
         eCF3b,
         eFC2002Set1a,
         eFC2002Set1b,
         eFC2002Set1c,
         eFC2002Set1d,
         eFC2002Set1e,
         eFC2002Set2,
         eFC2002Set4a,
         eFC2002Set4b,
         eFC2002Set4c,
         eFC2002Set4d,
         eFC2002Set5,
         eFC2002Set6,
         eFC2002Set7,
         eFC2002Set8,
         eFC2002Set9,
         eLawson,
         eCAF
     };

Constructor & Destructor Documentation

◆ FentonKarma()

Nektar::FentonKarma::FentonKarma	(	const LibUtilities::SessionReaderSharedPtr &	pSession,
		const MultiRegions::ExpListSharedPtr &	pField
	)

Constructor.

Initialise Fenton-Karma model parameters. k1 is k in the original model. k2 is an additional parameter introduced in Cherry&Fenton 2004. u_r and u_fi are introduced by Cherry&Fenton 2004 and is the same as u_c in the original model.

Definition at line 122 of file FentonKarma.cpp.

     : CellModel(pSession, pField)
 {
     model_variant = pSession->GetSolverInfoAsEnum<FentonKarma::Variants>(
         "CellModelVariant");
  
     C_m  = 1; // picoF
     V_0  = -85;
     V_fi = 15;
  
     switch (model_variant)
     {
         case eBR: // (Fenton, Karma, Chaos 8(1), 1998)
             g_fi_max     = 4;
             tau_r        = 33.33;
             tau_si       = 29;
             tau_0        = 12.5;
             tau_v_plus   = 3.33;
             tau_v1_minus = 1250;
             tau_v2_minus = 19.6;
             tau_w_plus   = 870;
             tau_w_minus  = 41;
             u_c          = 0.13;
             u_v          = 0.04;
             u_r          = 0.13;
             u_fi         = 0.13;
             u_csi        = 0.85;
             k1           = 10;
             k2           = 0.0;
             break;
         case eMBR: // (Fenton, Karma, Chaos 8(1), 1998)
             g_fi_max     = 4;
             tau_r        = 50;
             tau_si       = 44.84;
             tau_0        = 8.3;
             tau_v_plus   = 3.33;
             tau_v1_minus = 1000;
             tau_v2_minus = 19.2;
             tau_w_plus   = 667;
             tau_w_minus  = 11;
             u_c          = 0.13;
             u_v          = 0.04;
             u_r          = 0.13;
             u_fi         = 0.13;
             u_csi        = 0.85;
             k1           = 10;
             k2           = 0.0;
             break;
         case eMLR1: // (Fenton, Karma, Chaos 8(1), 1998)
             g_fi_max     = 5.8;
             tau_r        = 130;
             tau_si       = 127;
             tau_0        = 12.5;
             tau_v_plus   = 10;
             tau_v1_minus = 18.2;
             tau_v2_minus = 18.2;
             tau_w_plus   = 1020;
             tau_w_minus  = 80;
             u_c          = 0.13;
             u_v          = 0.0;
             u_r          = 0.13;
             u_fi         = 0.13;
             u_csi        = 0.85;
             k1           = 10;
             k2           = 0.0;
             break;
         case eGP: // (Fenton, Karma, Chaos 8(1), 1998)
             g_fi_max     = 8.7;
             tau_r        = 25;
             tau_si       = 22.22;
             tau_0        = 12.5;
             tau_v_plus   = 10;
             tau_v1_minus = 333;
             tau_v2_minus = 40;
             tau_w_plus   = 1000;
             tau_w_minus  = 65;
             u_c          = 0.13;
             u_v          = 0.025;
             u_r          = 0.13;
             u_fi         = 0.13;
             u_csi        = 0.85;
             k1           = 10;
             k2           = 0.0;
             break;
         case eCF1: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
             g_fi_max     = 6.6666;
             tau_r        = 12.5;
             tau_si       = 10;
             tau_0        = 1.5;
             tau_v_plus   = 10;
             tau_v1_minus = 350;
             tau_v2_minus = 80;
             tau_w_plus   = 562;
             tau_w_minus  = 48.5;
             u_c          = 0.25;
             u_v          = 0.001;
             u_r          = 0.25;
             u_fi         = 0.15;
             u_csi        = 0.2;
             k1           = 15;
             k2           = 0;
             break;
         case eCF2a: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
             g_fi_max     = 6.6666;
             tau_r        = 31;
             tau_si       = 26.5;
             tau_0        = 1.5;
             tau_v_plus   = 10;
             tau_v1_minus = 20;
             tau_v2_minus = 20;
             tau_w_plus   = 800;
             tau_w_minus  = 45;
             u_c          = 0.25;
             u_v          = 0.05;
             u_r          = 0.6;
             u_fi         = 0.11;
             u_csi        = 0.7;
             k1           = 10;
             k2           = 1;
             break;
         case eCF2b: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
             g_fi_max     = 6.6666;
             tau_r        = 31;
             tau_si       = 26.5;
             tau_0        = 1.5;
             tau_v_plus   = 10;
             tau_v1_minus = 100;
             tau_v2_minus = 20;
             tau_w_plus   = 800;
             tau_w_minus  = 45;
             u_c          = 0.25;
             u_v          = 0.05;
             u_r          = 0.6;
             u_fi         = 0.11;
             u_csi        = 0.7;
             k1           = 10;
             k2           = 1;
             break;
         case eCF2c: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
             g_fi_max     = 6.6666;
             tau_r        = 31;
             tau_si       = 26.5;
             tau_0        = 1.5;
             tau_v_plus   = 10;
             tau_v1_minus = 150;
             tau_v2_minus = 20;
             tau_w_plus   = 800;
             tau_w_minus  = 45;
             u_c          = 0.25;
             u_v          = 0.05;
             u_r          = 0.6;
             u_fi         = 0.11;
             u_csi        = 0.7;
             k1           = 10;
             k2           = 1;
             break;
         case eCF3a: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
             g_fi_max     = 13.3333;
             tau_r        = 38;
             tau_si       = 127;
             tau_0        = 8.3;
             tau_v_plus   = 3.33;
             tau_v1_minus = 45;
             tau_v2_minus = 300;
             tau_w_plus   = 600;
             tau_w_minus  = 40;
             tau_y_plus   = 1000;
             tau_y_minus  = 230;
             u_c          = 0.25;
             u_v          = 0.5;
             u_r          = 0.25;
             u_fi         = 0.25;
             u_csi        = 0.7;
             k1           = 60;
             k2           = 0;
             break;
         case eCF3b: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
             g_fi_max     = 13.3333;
             tau_r        = 38;
             tau_si       = 127;
             tau_0        = 8.3;
             tau_v_plus   = 3.33;
             tau_v1_minus = 20;
             tau_v2_minus = 300;
             tau_w_plus   = 600;
             tau_w_minus  = 40;
             tau_y_plus   = 1000;
             tau_y_minus  = 230;
             u_c          = 0.25;
             u_v          = 0.5;
             u_r          = 0.25;
             u_fi         = 0.25;
             u_csi        = 0.7;
             k1           = 60;
             k2           = 0;
             break;
         case eFC2002Set1a:           // (Fenton, Cherry, Chaos 12(852), 2002)
             g_fi_max     = 1 / 0.41; // 2.44 - Fig 1A
             tau_r        = 50;
             tau_si       = 45;
             tau_0        = 1 / 0.12; // 8.33
             tau_v_plus   = 3.33;
             tau_v1_minus = 1000;
             tau_v2_minus = 19.6;
             tau_w_plus   = 667;
             tau_w_minus  = 11;
             u_c          = 0.13;
             u_v          = 0.055;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 0.85;
             k1           = 10;
             k2           = 0;
             break;
         case eFC2002Set1b:            // (Fenton, Cherry, Chaos 12(852), 2002)
             g_fi_max     = 1 / 0.392; // 2.55 - Fig 1B
             tau_r        = 50;
             tau_si       = 45;
             tau_0        = 1 / 0.12; // 8.33
             tau_v_plus   = 3.33;
             tau_v1_minus = 1000;
             tau_v2_minus = 19.6;
             tau_w_plus   = 667;
             tau_w_minus  = 11;
             u_c          = 0.13;
             u_v          = 0.055;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 0.85;
             k1           = 10;
             k2           = 0;
             break;
         case eFC2002Set1c:            // (Fenton, Cherry, Chaos 12(852), 2002)
             g_fi_max     = 1 / 0.381; // 2.62 - Fig 1C
             tau_r        = 50;
             tau_si       = 45;
             tau_0        = 1 / 0.12; // 8.33
             tau_v_plus   = 3.33;
             tau_v1_minus = 1000;
             tau_v2_minus = 19.6;
             tau_w_plus   = 667;
             tau_w_minus  = 11;
             u_c          = 0.13;
             u_v          = 0.055;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 0.85;
             k1           = 10;
             k2           = 0;
             break;
         case eFC2002Set1d:           // (Fenton, Cherry, Chaos 12(852), 2002)
             g_fi_max     = 1 / 0.36; // 2.77 - Fig 1D
             tau_r        = 50;
             tau_si       = 45;
             tau_0        = 1 / 0.12; // 8.33
             tau_v_plus   = 3.33;
             tau_v1_minus = 1000;
             tau_v2_minus = 19.6;
             tau_w_plus   = 667;
             tau_w_minus  = 11;
             u_c          = 0.13;
             u_v          = 0.055;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 0.85;
             k1           = 10;
             k2           = 0;
             break;
         case eFC2002Set1e:           // (Fenton, Cherry, Chaos 12(852), 2002)
             g_fi_max     = 1 / 0.25; // 4 - Fig 1E
             tau_r        = 50;
             tau_si       = 45;
             tau_0        = 1 / 0.12; // 8.33
             tau_v_plus   = 3.33;
             tau_v1_minus = 1000;
             tau_v2_minus = 19.6;
             tau_w_plus   = 667;
             tau_w_minus  = 11;
             u_c          = 0.13;
             u_v          = 0.055;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 0.85;
             k1           = 10;
             k2           = 0;
             break;
         case eFC2002Set2: // (Fenton, Cherry, Chaos 12(852), 2002)
             g_fi_max     = 4;
             tau_r        = 190;
             tau_si       = 100000;
             tau_0        = 10;
             tau_v_plus   = 10;
             tau_v1_minus = 10;
             tau_v2_minus = 10;
             tau_w_plus   = 100000;
             tau_w_minus  = 100000;
             u_c          = 0.13;
             u_v          = 100;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 100;
             k1           = 10;
             k2           = 0;
             break;
         case eFC2002Set4a: // (Fenton, Cherry, Chaos 12(852), 2002)
             g_fi_max     = 1.0 / 0.407;
             tau_r        = 34;
             tau_si       = 26.5;
             tau_0        = 9;
             tau_v_plus   = 3.33;
             tau_v1_minus = 5;    // Opposite convention
             tau_v2_minus = 15.6; // to the paper
             tau_w_plus   = 350;
             tau_w_minus  = 80;
             u_c          = 0.15;
             u_v          = 0.04;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 0.45;
             k1           = 15;
             k2           = 0;
             break;
         case eFC2002Set4b: // (Fenton, Cherry, Chaos 12(852), 2002)
             g_fi_max     = 1.0 / 0.41;
             tau_r        = 34;
             tau_si       = 26.5;
             tau_0        = 9;
             tau_v_plus   = 3.33;
             tau_v1_minus = 5;    // Opposite convention
             tau_v2_minus = 15.6; // to the paper
             tau_w_plus   = 350;
             tau_w_minus  = 80;
             u_c          = 0.15;
             u_v          = 0.04;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 0.45;
             k1           = 15;
             k2           = 0;
             break;
         case eFC2002Set4c: // (Fenton, Cherry, Chaos 12(852), 2002)
             g_fi_max     = 1.0 / 0.405;
             tau_r        = 34;
             tau_si       = 26.5;
             tau_0        = 9;
             tau_v_plus   = 3.33;
             tau_v1_minus = 5;    // Opposite convention
             tau_v2_minus = 15.6; // to the paper
             tau_w_plus   = 350;
             tau_w_minus  = 80;
             u_c          = 0.15;
             u_v          = 0.04;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 0.45;
             k1           = 15;
             k2           = 0;
             break;
         case eFC2002Set4d: // (Fenton, Cherry, Chaos 12(852), 2002)
             g_fi_max     = 1.0 / 0.4;
             tau_r        = 34;
             tau_si       = 26.5;
             tau_0        = 9;
             tau_v_plus   = 3.33;
             tau_v1_minus = 5;    // Opposite convention
             tau_v2_minus = 15.6; // to the paper
             tau_w_plus   = 350;
             tau_w_minus  = 80;
             u_c          = 0.15;
             u_v          = 0.04;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 0.45;
             k1           = 15;
             k2           = 0;
             break;
         case eFC2002Set5: // (Fenton, Cherry, Chaos 12(852), 2002)
             g_fi_max     = 2.76;
             tau_r        = 33.33;
             tau_si       = 29;
             tau_0        = 5;
             tau_v_plus   = 3.33;
             tau_v1_minus = 2;  // Opposite convention
             tau_v2_minus = 12; // to the paper
             tau_w_plus   = 1000;
             tau_w_minus  = 100;
             u_c          = 0.13;
             u_v          = 0.14;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 0.70;
             k1           = 15;
             k2           = 0;
             break;
         case eFC2002Set6: // (Fenton, Cherry, Chaos 12(852), 2002)
             g_fi_max     = 2.53;
             tau_r        = 33.33;
             tau_si       = 29;
             tau_0        = 9;
             tau_v_plus   = 3.33;
             tau_v1_minus = 8; // Opposite convention
             tau_v2_minus = 9; // to the paper
             tau_w_plus   = 250;
             tau_w_minus  = 60;
             u_c          = 0.13;
             u_v          = 0.04;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 0.50;
             k1           = 15;
             k2           = 0;
             break;
         case eFC2002Set7: // (Fenton, Cherry, Chaos 12(852), 2002)
             g_fi_max     = 4;
             tau_r        = 100;
             tau_si       = 100000;
             tau_0        = 12;
             tau_v_plus   = 10;
             tau_v1_minus = 7; // Opposite convention
             tau_v2_minus = 7; // to the paper
             tau_w_plus   = 100000;
             tau_w_minus  = 100000;
             u_c          = 0.13;
             u_v          = 100;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 100;
             k1           = 10;
             k2           = 0;
             break;
         case eFC2002Set8: // (Fenton, Cherry, Chaos 12(852), 2002)
             g_fi_max     = 2.2;
             tau_r        = 33.25;
             tau_si       = 29;
             tau_0        = 12.5;
             tau_v_plus   = 13.03;
             tau_v1_minus = 1250; // Opposite convention
             tau_v2_minus = 19.6; // to the paper
             tau_w_plus   = 800;
             tau_w_minus  = 40;
             u_c          = 0.13;
             u_v          = 0.04;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 0.85;
             k1           = 10;
             k2           = 0;
             break;
         case eFC2002Set9: // (Fenton, Cherry, Chaos 12(852), 2002)
             g_fi_max     = 4;
             tau_r        = 28;
             tau_si       = 29;
             tau_0        = 12.5;
             tau_v_plus   = 3.33;
             tau_v1_minus = 2;  // Opposite convention
             tau_v2_minus = 15; // to the paper
             tau_w_plus   = 670;
             tau_w_minus  = 61;
             u_c          = 0.13;
             u_v          = 0.05;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 0.45;
             k1           = 10;
             k2           = 0;
             break;
         case eLawson: // (Lawson, Front. Physiol, 2018)
             g_fi_max     = 3;
             tau_r        = 1 / 0.02;
             tau_si       = 1 / 0.0223;
             tau_0        = 1 / 0.12;
             tau_v_plus   = 3.33;
             tau_v1_minus = 1000;
             tau_v2_minus = 19.6;
             tau_w_plus   = 667;
             tau_w_minus  = 11;
             u_c          = 0.13;
             u_v          = 0.055;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 0.85;
             k1           = 10;
             k2           = 0;
             break;
         case eCAF:
             g_fi_max     = 8;
             tau_r        = 70;
             tau_si       = 114;
             tau_0        = 32.5; // 8.33
             tau_v_plus   = 5.75;
             tau_v1_minus = 60;
             tau_v2_minus = 82.5;
             tau_w_plus   = 300;
             tau_w_minus  = 400;
             u_c          = 0.16;
             u_v          = 0.04;
             u_r          = u_c;
             u_fi         = u_c;
             u_csi        = 0.85;
             k1           = 10;
             k2           = 0;
             break;
     }
  
     tau_d = C_m / g_fi_max;
  
     isCF3 = (model_variant == eCF3a || model_variant == eCF3b);
  
     // List gates and concentrations
     m_gates.push_back(1);
     m_gates.push_back(2);
     m_nvar = 3;
  
     // Cherry-Fenton 2004 Model 3 has extra gating variable
     if (isCF3)
     {
         m_gates.push_back(3);
         m_nvar = 4;
     }
  
     ASSERTL0(!isCF3, "Cherry-Fenton model 3 not implemented yet.");
 }

References ASSERTL0, C_m, eBR, eCAF, eCF1, eCF2a, eCF2b, eCF2c, eCF3a, eCF3b, eFC2002Set1a, eFC2002Set1b, eFC2002Set1c, eFC2002Set1d, eFC2002Set1e, eFC2002Set2, eFC2002Set4a, eFC2002Set4b, eFC2002Set4c, eFC2002Set4d, eFC2002Set5, eFC2002Set6, eFC2002Set7, eFC2002Set8, eFC2002Set9, eGP, eLawson, eMBR, eMLR1, g_fi_max, isCF3, k1, k2, Nektar::CellModel::m_gates, Nektar::CellModel::m_nvar, model_variant, tau_0, tau_d, tau_r, tau_si, tau_v1_minus, tau_v2_minus, tau_v_plus, tau_w_minus, tau_w_plus, tau_y_minus, tau_y_plus, u_c, u_csi, u_fi, u_r, u_v, V_0, and V_fi.

◆ ~FentonKarma()

Nektar::FentonKarma::~FentonKarma ( )

virtual

Destructor.

Definition at line 649 of file FentonKarma.cpp.

650 {

651 }

Member Function Documentation

◆ create()

static CellModelSharedPtr Nektar::FentonKarma::create	(	const LibUtilities::SessionReaderSharedPtr &	pSession,
		const MultiRegions::ExpListSharedPtr &	pField
	)

inlinestatic

Creates an instance of this class.

Definition at line 46 of file FentonKarma.h.

     {
         return MemoryManager<FentonKarma>::AllocateSharedPtr(pSession, pField);
     }

References Nektar::MemoryManager< DataType >::AllocateSharedPtr().

◆ v_GenerateSummary()

void Nektar::FentonKarma::v_GenerateSummary ( SummaryList & s )

overrideprotectedvirtual

Prints a summary of the model parameters.

Implements Nektar::CellModel.

Definition at line 732 of file FentonKarma.cpp.

 {
     SolverUtils::AddSummaryItem(s, "Cell model", "Fenton Karma");
     SolverUtils::AddSummaryItem(s, "Cell model var.", lookupIds[model_variant]);
 }

References Nektar::SolverUtils::AddSummaryItem(), lookupIds, and model_variant.

◆ v_GetCellVarName()

std::string Nektar::FentonKarma::v_GetCellVarName ( size_t idx )

overrideprotectedvirtual

Reimplemented from Nektar::CellModel.

Definition at line 749 of file FentonKarma.cpp.

 {
     switch (idx)
     {
         case 0:
             return "u";
         case 1:
             return "v";
         case 2:
             return "w";
         case 3:
             return "y";
         default:
             return "unknown";
     }
 }

◆ v_SetInitialConditions()

void Nektar::FentonKarma::v_SetInitialConditions ( )

overrideprotectedvirtual

Implements Nektar::CellModel.

Definition at line 738 of file FentonKarma.cpp.

 {
     Vmath::Fill(m_nq, 0.0, m_cellSol[0], 1);
     Vmath::Fill(m_nq, 1.0, m_cellSol[1], 1);
     Vmath::Fill(m_nq, 1.0, m_cellSol[2], 1);
     if (isCF3)
     {
         Vmath::Fill(m_nq, 0.1, m_cellSol[2], 1);
     }
 }

References Vmath::Fill(), isCF3, Nektar::CellModel::m_cellSol, and Nektar::CellModel::m_nq.

◆ v_Update()

void Nektar::FentonKarma::v_Update	(	const Array< OneD, const Array< OneD, NekDouble >> &	inarray,
		Array< OneD, Array< OneD, NekDouble >> &	outarray,
		const NekDouble	time
	)

overrideprotectedvirtual

Computes the reaction terms $f(u,v)$ and $g(u,v)$.

Implements Nektar::CellModel.

Definition at line 653 of file FentonKarma.cpp.

 {
     boost::ignore_unused(time);
     ASSERTL0(inarray.get() != outarray.get(),
              "Must have different arrays for input and output.");
  
     // Variables
     //  0   u    membrane potential
     //  1   v    v gate
     //  2   w    w gate
  
     // Declare pointers
     const NekDouble *u = &inarray[0][0];
     const NekDouble *v = &inarray[1][0];
     const NekDouble *w = &inarray[2][0];
     const NekDouble *y = isCF3 ? &inarray[3][0] : 0;
     NekDouble *u_new   = &outarray[0][0];
     NekDouble *v_new   = &outarray[1][0];
     NekDouble *w_new   = &outarray[2][0];
     // NekDouble *y_new   = isCF3 ? &outarray[3][0] : 0;
     NekDouble *v_tau = &m_gates_tau[0][0];
     NekDouble *w_tau = &m_gates_tau[1][0];
     // NekDouble *y_tau   = isCF3 ? &m_gates_tau[2][0] : 0;
  
     // Temporary variables
     NekDouble J_fi, J_so, J_si, h1, h2, h3, alpha, beta;
  
     double V;
     // Compute rates for each point in domain
     for (size_t i = 0; i < m_nq; ++i)
     {
         // *u is dimensional
         // V is non-dimensional for what follows
         V = (*u - V_0) / (V_fi - V_0);
  
         // Heavyside functions
         h1 = (V < u_c) ? 0.0 : 1.0;
         h2 = (V < u_v) ? 0.0 : 1.0;
         h3 = (V < u_r) ? 0.0 : 1.0;
  
         // w-gate
         alpha  = (1 - h1) / tau_w_minus;
         beta   = h1 / tau_w_plus;
         *w_tau = 1.0 / (alpha + beta);
         *w_new = alpha * (*w_tau);
  
         // v-gate
         alpha  = (1 - h1) / (h2 * tau_v1_minus + (1 - h2) * tau_v2_minus);
         beta   = h1 / tau_v_plus;
         *v_tau = 1.0 / (alpha + beta);
         *v_new = alpha * (*v_tau);
  
         // y-gate
         if (isCF3)
         {
             // TODO: implementation for y_tau and y_new
         }
  
         // J_fi
         J_fi = -(*v) * h1 * (1 - V) * (V - u_c) / tau_d;
  
         // J_so
         // added extra (1-k2*v) term from Cherry&Fenton 2004
         J_so = V * (1 - h3) * (1 - k2 * (*v)) / tau_0 +
                (isCF3 ? h3 * V * (*y) / tau_r : h3 / tau_r);
  
         // J_si
         J_si = -(*w) * (1 + tanh(k1 * (V - u_csi))) / (2.0 * tau_si);
  
         // u
         *u_new = -J_fi - J_so - J_si;
         *u_new *= C_m * (V_fi - V_0);
  
         ++u, ++v, ++w, ++u_new, ++v_new, ++w_new, ++v_tau, ++w_tau;
     }
 }

References ASSERTL0, Nektar::LibUtilities::beta, C_m, isCF3, k1, k2, Nektar::CellModel::m_gates_tau, Nektar::CellModel::m_nq, tau_0, tau_d, tau_r, tau_si, tau_v1_minus, tau_v2_minus, tau_v_plus, tau_w_minus, tau_w_plus, u_c, u_csi, u_r, u_v, V_0, and V_fi.

Member Data Documentation

◆ C_m

NekDouble Nektar::FentonKarma::C_m

private

Definition at line 78 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ className

std::string Nektar::FentonKarma::className

static

Initial value:

=
    GetCellModelFactory().RegisterCreatorFunction(
        "FentonKarma", FentonKarma::create, "Phenomenological Model.")

Name of class.

Definition at line 54 of file FentonKarma.h.

◆ def

std::string Nektar::FentonKarma::def

staticprivate

Initial value:

=
    LibUtilities::SessionReader::RegisterDefaultSolverInfo("CellModelVariant",
                                                           "BR")

Definition at line 136 of file FentonKarma.h.

◆ g_fi_max

NekDouble Nektar::FentonKarma::g_fi_max

private

Definition at line 85 of file FentonKarma.h.

Referenced by FentonKarma().

◆ isCF3

bool Nektar::FentonKarma::isCF3

private

Definition at line 101 of file FentonKarma.h.

Referenced by FentonKarma(), v_SetInitialConditions(), and v_Update().

◆ k1

NekDouble Nektar::FentonKarma::k1

private

Definition at line 96 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ k2

NekDouble Nektar::FentonKarma::k2

private

Definition at line 97 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ lookupIds

std::string Nektar::FentonKarma::lookupIds

staticprivate

Definition at line 135 of file FentonKarma.h.

Referenced by v_GenerateSummary().

◆ model_variant

enum Variants Nektar::FentonKarma::model_variant

private

Definition at line 101 of file FentonKarma.h.

Referenced by FentonKarma(), and v_GenerateSummary().

◆ tau_0

NekDouble Nektar::FentonKarma::tau_0

private

Definition at line 90 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_d

NekDouble Nektar::FentonKarma::tau_d

private

Definition at line 86 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_r

NekDouble Nektar::FentonKarma::tau_r

private

Definition at line 91 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_si

NekDouble Nektar::FentonKarma::tau_si

private

Definition at line 92 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_v1_minus

NekDouble Nektar::FentonKarma::tau_v1_minus

private

Definition at line 87 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_v2_minus

NekDouble Nektar::FentonKarma::tau_v2_minus

private

Definition at line 88 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_v_plus

NekDouble Nektar::FentonKarma::tau_v_plus

private

Definition at line 89 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_w_minus

NekDouble Nektar::FentonKarma::tau_w_minus

private

Definition at line 98 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_w_plus

NekDouble Nektar::FentonKarma::tau_w_plus

private

Definition at line 99 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_y_minus

NekDouble Nektar::FentonKarma::tau_y_minus

private

Definition at line 94 of file FentonKarma.h.

Referenced by FentonKarma().

◆ tau_y_plus

NekDouble Nektar::FentonKarma::tau_y_plus

private

Definition at line 93 of file FentonKarma.h.

Referenced by FentonKarma().

◆ u_c

NekDouble Nektar::FentonKarma::u_c

private

Definition at line 82 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ u_csi

NekDouble Nektar::FentonKarma::u_csi

private

Definition at line 95 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ u_fi

NekDouble Nektar::FentonKarma::u_fi

private

Definition at line 81 of file FentonKarma.h.

Referenced by FentonKarma().

◆ u_r

NekDouble Nektar::FentonKarma::u_r

private

Definition at line 84 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ u_v

NekDouble Nektar::FentonKarma::u_v

private

Definition at line 83 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ V_0

NekDouble Nektar::FentonKarma::V_0

private

Definition at line 79 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ V_fi

NekDouble Nektar::FentonKarma::V_fi

private

Definition at line 80 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Private Types

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ Variants

Constructor & Destructor Documentation

◆ FentonKarma()

◆ ~FentonKarma()

Member Function Documentation

◆ create()

◆ v_GenerateSummary()

◆ v_GetCellVarName()

◆ v_SetInitialConditions()

◆ v_Update()

Member Data Documentation

◆ C_m

◆ className

◆ def

◆ g_fi_max

◆ isCF3

◆ k1

◆ k2

◆ lookupIds

◆ model_variant

◆ tau_0

◆ tau_d

◆ tau_r

◆ tau_si

◆ tau_v1_minus

◆ tau_v2_minus

◆ tau_v_plus

◆ tau_w_minus

◆ tau_w_plus

◆ tau_y_minus

◆ tau_y_plus

◆ u_c

◆ u_csi

◆ u_fi

◆ u_r

◆ u_v

◆ V_0

◆ V_fi