FitzHugh-Nagumo model. More...

#include <FitzhughNagumo.h>

Inheritance diagram for Nektar::CellModelFitzHughNagumo:

Public Member Functions
	CellModelFitzHughNagumo (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)

	~CellModelFitzHughNagumo () override

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
void	v_Update (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time) override

void	v_GenerateSummary (SummaryList &s) override

void	v_SetInitialConditions () override

Protected Member Functions inherited from Nektar::CellModel
virtual void	v_Update (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)=0

virtual void	v_GenerateSummary (SummaryList &s)=0

virtual std::string	v_GetCellVarName (size_t idx)

virtual void	v_SetInitialConditions ()=0

void	LoadCellModel ()

Private Attributes
NekDouble	m_beta

NekDouble	m_epsilon

Array< OneD, NekDouble >	m_uuu
	Temporary space for storing \(u^3\) when computing reaction term. More...

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

FitzHugh-Nagumo model.

Definition at line 43 of file FitzhughNagumo.h.

Constructor & Destructor Documentation

◆ CellModelFitzHughNagumo()

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

Definition at line 51 of file FitzhughNagumo.cpp.

    : CellModel(pSession, pField)
{
    pSession->LoadParameter("beta", m_beta, 0.0);
    pSession->LoadParameter("epsilon", m_epsilon, 1.0);
 
    m_uuu = Array<OneD, NekDouble>(m_nq, 0.0);
 
    m_nvar = 2;
    m_concentrations.push_back(1);
}

References m_beta, Nektar::CellModel::m_concentrations, m_epsilon, Nektar::CellModel::m_nq, Nektar::CellModel::m_nvar, and m_uuu.

◆ ~CellModelFitzHughNagumo()

Nektar::CellModelFitzHughNagumo::~CellModelFitzHughNagumo ( )

inlineoverride

Definition at line 62 of file FitzhughNagumo.h.

63 {

64 }

Member Function Documentation

◆ create()

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

inlinestatic

Creates an instance of this class.

Definition at line 47 of file FitzhughNagumo.h.

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

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

◆ v_GenerateSummary()

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

overrideprotectedvirtual

Implements Nektar::CellModel.

Definition at line 97 of file FitzhughNagumo.cpp.

{
    SolverUtils::AddSummaryItem(s, "Cell model", "FitzHugh-Nagumo");
    SolverUtils::AddSummaryItem(s, "Cell model beta", m_beta);
}

References Nektar::SolverUtils::AddSummaryItem(), and m_beta.

◆ v_SetInitialConditions()

void Nektar::CellModelFitzHughNagumo::v_SetInitialConditions ( )

overrideprotectedvirtual

Implements Nektar::CellModel.

Definition at line 106 of file FitzhughNagumo.cpp.

{
    Vmath::Fill(m_nq, 0.0, m_cellSol[0], 1);
    Vmath::Fill(m_nq, 0.0, m_cellSol[1], 1);
}

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

◆ v_Update()

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

overrideprotectedvirtual

Implements Nektar::CellModel.

Definition at line 65 of file FitzhughNagumo.cpp.

{
    NekDouble m_gamma = 0.5;
 
    // compute u^2: m_u = u*u
    Vmath::Vmul(m_nq, &inarray[0][0], 1, &inarray[0][0], 1, &m_uuu[0], 1);
 
    // compute u^3: m_u = u*u*u
    Vmath::Vmul(m_nq, &inarray[0][0], 1, &m_uuu[0], 1, &m_uuu[0], 1);
 
    // For u: (1/m_epsilon)*( u*-u*u*u/3 - v )
    // physfield = u - (1.0/3.0)*u*u*u
    Vmath::Svtvp(m_nq, (-1.0 / 3.0), &m_uuu[0], 1, &inarray[0][0], 1,
                 &outarray[0][0], 1);
 
    Vmath::Vsub(m_nq, &inarray[1][0], 1, &outarray[0][0], 1, &outarray[0][0],
                1);
    Vmath::Smul(m_nq, -1.0 / m_epsilon, &outarray[0][0], 1, &outarray[0][0], 1);
 
    // For v: m_epsilon*( u + m_beta - m_gamma*v )
    Vmath::Svtvp(m_nq, -1.0 * m_gamma, &inarray[1][0], 1, &inarray[0][0], 1,
                 &outarray[1][0], 1);
    Vmath::Sadd(m_nq, m_beta, &outarray[1][0], 1, &outarray[1][0], 1);
    Vmath::Smul(m_nq, m_epsilon, &outarray[1][0], 1, &outarray[1][0], 1);
}

References m_beta, m_epsilon, Nektar::CellModel::m_nq, m_uuu, Vmath::Sadd(), Vmath::Smul(), Vmath::Svtvp(), Vmath::Vmul(), and Vmath::Vsub().

Member Data Documentation

◆ className

std::string Nektar::CellModelFitzHughNagumo::className

static

Initial value:

=
    GetCellModelFactory().RegisterCreatorFunction(
        "FitzHughNagumo", CellModelFitzHughNagumo::create,
        "Phenomological model of squid nerve cell.")

Name of class.

Registers the class with the Factory.

Definition at line 56 of file FitzhughNagumo.h.

◆ m_beta

NekDouble Nektar::CellModelFitzHughNagumo::m_beta

private

Definition at line 76 of file FitzhughNagumo.h.

Referenced by CellModelFitzHughNagumo(), v_GenerateSummary(), and v_Update().

◆ m_epsilon

NekDouble Nektar::CellModelFitzHughNagumo::m_epsilon

private

Definition at line 77 of file FitzhughNagumo.h.

Referenced by CellModelFitzHughNagumo(), and v_Update().

◆ m_uuu

Array<OneD, NekDouble> Nektar::CellModelFitzHughNagumo::m_uuu

private

Temporary space for storing \(u^3\) when computing reaction term.

Definition at line 80 of file FitzhughNagumo.h.

Referenced by CellModelFitzHughNagumo(), and v_Update().

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CellModelFitzHughNagumo()

◆ ~CellModelFitzHughNagumo()

Member Function Documentation

◆ create()

◆ v_GenerateSummary()

◆ v_SetInitialConditions()

◆ v_Update()

Member Data Documentation

◆ className

◆ m_beta

◆ m_epsilon

◆ m_uuu