Aliev Panfilov model. More...

#include <AlievPanfilov.h>

Inheritance diagram for Nektar::CellModelAlievPanfilov:

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

	~CellModelAlievPanfilov () 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_a
	Trigger parameter a. More...

NekDouble	m_k
	Scaling parameter k. More...

NekDouble	m_mu1
	Restitution parameter \(\mu_1\). More...

NekDouble	m_mu2
	Restitution parameter \(\mu_2\). More...

NekDouble	m_eps
	Restitution parameter \(\epsilon\). More...

Array< OneD, NekDouble >	m_uu
	Temporary space for storing \(u^2\) when computing reaction term. More...

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

Array< OneD, NekDouble >	m_tmp1
	Workspace for computing reaction term. More...

Array< OneD, NekDouble >	m_tmp2
	Workspace for 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

Aliev Panfilov model.

Definition at line 43 of file AlievPanfilov.h.

Constructor & Destructor Documentation

◆ CellModelAlievPanfilov()

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

Definition at line 51 of file AlievPanfilov.cpp.

    : CellModel(pSession, pField)
{
    pSession->LoadParameter("k", m_k, 0.0);
    pSession->LoadParameter("a", m_a, 0.0);
    pSession->LoadParameter("mu1", m_mu1, 0.0);
    pSession->LoadParameter("mu2", m_mu2, 0.0);
    pSession->LoadParameter("eps", m_eps, 0.0);
 
    m_uu   = Array<OneD, NekDouble>(m_nq, 0.0);
    m_uuu  = Array<OneD, NekDouble>(m_nq, 0.0);
    m_tmp1 = Array<OneD, NekDouble>(m_nq, 0.0);
    m_tmp2 = Array<OneD, NekDouble>(m_nq, 0.0);
 
    m_nvar = 2;
    m_concentrations.push_back(1);
}

References m_a, Nektar::CellModel::m_concentrations, m_eps, m_k, m_mu1, m_mu2, Nektar::CellModel::m_nq, Nektar::CellModel::m_nvar, m_tmp1, m_tmp2, m_uu, and m_uuu.

◆ ~CellModelAlievPanfilov()

Nektar::CellModelAlievPanfilov::~CellModelAlievPanfilov ( )

inlineoverride

Definition at line 61 of file AlievPanfilov.h.

62 {

63 }

Member Function Documentation

◆ create()

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

inlinestatic

Creates an instance of this class.

Definition at line 47 of file AlievPanfilov.h.

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

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

◆ v_GenerateSummary()

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

overrideprotectedvirtual

Implements Nektar::CellModel.

Definition at line 186 of file AlievPanfilov.cpp.

{
    SolverUtils::AddSummaryItem(s, "Cell model", "Aliev-Panfilov");
    SolverUtils::AddSummaryItem(s, "k", m_k);
    SolverUtils::AddSummaryItem(s, "a", m_a);
    SolverUtils::AddSummaryItem(s, "eps", m_eps);
    SolverUtils::AddSummaryItem(s, "mu1", m_mu1);
    SolverUtils::AddSummaryItem(s, "mu2", m_mu2);
}

References Nektar::SolverUtils::AddSummaryItem(), m_a, m_eps, m_k, m_mu1, and m_mu2.

◆ v_SetInitialConditions()

void Nektar::CellModelAlievPanfilov::v_SetInitialConditions ( )

overrideprotectedvirtual

Implements Nektar::CellModel.

Definition at line 199 of file AlievPanfilov.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::CellModelAlievPanfilov::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 71 of file AlievPanfilov.cpp.

{
    // inarray[0] holds initial physical u values throughout
    // inarray[1] holds initial physical v values throughout
 
    // compute u^2: m_u = u*u
    Vmath::Vmul(m_nq, &inarray[0][0], 1, &inarray[0][0], 1, &m_uu[0], 1);
 
    // compute u^3: m_u = u*u*u
    Vmath::Vmul(m_nq, &inarray[0][0], 1, &m_uu[0], 1, &m_uuu[0], 1);
 
    // --------------------------------------
    // Compute reaction term f(u,v)
    // --------------------------------------
    //        if (m_spatialParameters->Exists("a"))
    //        {
    //          Vmath::Vmul(m_nq,
    //          &m_spatialParameters->GetData("a")->GetPhys()[0], 1,
    //                           &inarray[0][0], 1, &m_tmp1[0], 1);
    //
    //          Vmath::Vvtvm(m_nq,
    //          &m_spatialParameters->GetData("a")->GetPhys()[0], 1,
    //                           &m_uu[0], 1, &m_tmp1[0], 1, &m_tmp1[0], 1);
    //
    //          Vmath::Svtvm(m_nq, -1.0, &m_uu[0], 1, &m_tmp1[0], 1, &m_tmp1[0],
    //          1);
    //        }
    //        else
    //        {
    // Ru = au
    Vmath::Smul(m_nq, m_a, &inarray[0][0], 1, &m_tmp1[0], 1);
    // Ru = (-1-a)u*u + au
    Vmath::Svtvp(m_nq, (-1.0 - m_a), &m_uu[0], 1, &m_tmp1[0], 1, &m_tmp1[0], 1);
    //        }
    // Ru = u*u*u - (1+a)u*u + au
    Vmath::Vadd(m_nq, &m_uuu[0], 1, &m_tmp1[0], 1, &m_tmp1[0], 1);
    // Ru = k(u*u*u - (1+a)u*u + au)
    //        if (m_spatialParameters->Exists("k"))
    //        {
    //          Vmath::Vmul(m_nq,
    //          &m_spatialParameters->GetData("k")->GetPhys()[0], 1,
    //                          &m_tmp1[0], 1, &m_tmp1[0], 1);
    //        }
    //        else
    //        {
    Vmath::Smul(m_nq, m_k, &m_tmp1[0], 1, &m_tmp1[0], 1);
    //        }
 
    // Ru = k(u*u*u - (1+a)u*u + au) + I_stim
    Vmath::Vadd(m_nq, &outarray[0][0], 1, &m_tmp1[0], 1, &outarray[0][0], 1);
 
    // Ru = k(u*u*u - (1+a)u*u + au) + uv + I_stim
    Vmath::Vvtvp(m_nq, &inarray[0][0], 1, &inarray[1][0], 1, &m_tmp1[0], 1,
                 &outarray[0][0], 1);
    // Ru = -k(u*u*u - (1+a)u*u + au) - uv - I_stim
    Vmath::Neg(m_nq, &outarray[0][0], 1);
 
    // --------------------------------------
    // Compute reaction term g(u,v)
    // --------------------------------------
    // tmp2 = mu2 + u
    Vmath::Sadd(m_nq, m_mu2, &inarray[0][0], 1, &m_tmp2[0], 1);
 
    // tmp2 = v/(mu2 + u)
    Vmath::Vdiv(m_nq, &inarray[1][0], 1, &m_tmp2[0], 1, &m_tmp2[0], 1);
 
    // tmp2 = mu1*v/(mu2 + u)
    Vmath::Smul(m_nq, m_mu1, &m_tmp2[0], 1, &m_tmp2[0], 1);
 
    // tmp1 = Eps + mu1*v/(mu2+u)
    Vmath::Sadd(m_nq, m_eps, &m_tmp2[0], 1, &m_tmp2[0], 1);
 
    // tmp1 = (-a-1) + u
    //        if (m_spatialParameters->Exists("a"))
    //        {
    //          Vmath::Vsub(m_nq, &inarray[0][0], 1,
    //                          &m_spatialParameters->GetData("a")->GetPhys()[0],
    //                          1, &m_tmp1[0], 1);
    //
    //          Vmath::Sadd(m_nq, -1.0, &inarray[0][0], 1, &m_tmp1[0], 1);
    //        }
    //        else
    //        {
    Vmath::Sadd(m_nq, (-m_a - 1), &inarray[0][0], 1, &m_tmp1[0], 1);
    //        }
 
    // tmp1 = k(u-a-1)
    //        if (m_spatialParameters->Exists("k"))
    //        {
    //          Vmath::Vmul(m_nq,
    //          &m_spatialParameters->GetData("k")->GetPhys()[0], 1,
    //                          &m_tmp1[0], 1, &m_tmp1[0], 1);
    //        }
    //        else
    //        {
    Vmath::Smul(m_nq, m_k, &m_tmp1[0], 1, &m_tmp1[0], 1);
    //        }
 
    // tmp1 = ku(u-a-1) + v
    Vmath::Vvtvp(m_nq, &inarray[0][0], 1, &m_tmp1[0], 1, &inarray[1][0], 1,
                 &m_tmp1[0], 1);
 
    // tmp1 = -ku(u-a-1)-v
    Vmath::Neg(m_nq, &m_tmp1[0], 1);
 
    // outarray = [Eps + mu1*v/(mu2+u)] * [-ku(u-a-1)-v]
    Vmath::Vmul(m_nq, &m_tmp1[0], 1, &m_tmp2[0], 1, &outarray[1][0], 1);
}

References m_a, m_eps, m_k, m_mu1, m_mu2, Nektar::CellModel::m_nq, m_tmp1, m_tmp2, m_uu, m_uuu, Vmath::Neg(), Vmath::Sadd(), Vmath::Smul(), Vmath::Svtvp(), Vmath::Vadd(), Vmath::Vdiv(), Vmath::Vmul(), and Vmath::Vvtvp().

Member Data Documentation

◆ className

std::string Nektar::CellModelAlievPanfilov::className

static

Initial value:

=
    GetCellModelFactory().RegisterCreatorFunction(
        "AlievPanfilov", CellModelAlievPanfilov::create,
        "Phenomological model of canine cardiac electrophysiology.")

Name of class.

Registers the class with the Factory.

Definition at line 56 of file AlievPanfilov.h.

◆ m_a

NekDouble Nektar::CellModelAlievPanfilov::m_a

private

Trigger parameter a.

Definition at line 76 of file AlievPanfilov.h.

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

◆ m_eps

NekDouble Nektar::CellModelAlievPanfilov::m_eps

private

Restitution parameter \(\epsilon\).

Definition at line 84 of file AlievPanfilov.h.

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

◆ m_k

NekDouble Nektar::CellModelAlievPanfilov::m_k

private

Scaling parameter k.

Definition at line 78 of file AlievPanfilov.h.

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

◆ m_mu1

NekDouble Nektar::CellModelAlievPanfilov::m_mu1

private

Restitution parameter \(\mu_1\).

Definition at line 80 of file AlievPanfilov.h.

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

◆ m_mu2

NekDouble Nektar::CellModelAlievPanfilov::m_mu2

private

Restitution parameter \(\mu_2\).

Definition at line 82 of file AlievPanfilov.h.

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

◆ m_tmp1

Array<OneD, NekDouble> Nektar::CellModelAlievPanfilov::m_tmp1

private

Workspace for computing reaction term.

Definition at line 91 of file AlievPanfilov.h.

Referenced by CellModelAlievPanfilov(), and v_Update().

◆ m_tmp2

Array<OneD, NekDouble> Nektar::CellModelAlievPanfilov::m_tmp2

private

Workspace for computing reaction term.

Definition at line 93 of file AlievPanfilov.h.

Referenced by CellModelAlievPanfilov(), and v_Update().

◆ m_uu

Array<OneD, NekDouble> Nektar::CellModelAlievPanfilov::m_uu

private

Temporary space for storing \(u^2\) when computing reaction term.

Definition at line 87 of file AlievPanfilov.h.

Referenced by CellModelAlievPanfilov(), and v_Update().

◆ m_uuu

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

private

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

Definition at line 89 of file AlievPanfilov.h.

Referenced by CellModelAlievPanfilov(), 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

◆ CellModelAlievPanfilov()

◆ ~CellModelAlievPanfilov()

Member Function Documentation

◆ create()

◆ v_GenerateSummary()

◆ v_SetInitialConditions()

◆ v_Update()

Member Data Documentation

◆ className

◆ m_a

◆ m_eps

◆ m_k

◆ m_mu1

◆ m_mu2

◆ m_tmp1

◆ m_tmp2

◆ m_uu

◆ m_uuu