Aliev Panfilov model. More...

#include <AlievPanfilov.h>

Inheritance diagram for Nektar::CellModelAlievPanfilov:

Collaboration diagram for Nektar::CellModelAlievPanfilov:

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

virtual	~CellModelAlievPanfilov ()

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...

unsigned int	GetNumCellVariables ()

std::string	GetCellVarName (unsigned int idx)

Array< OneD, NekDouble >	GetCellSolutionCoeffs (unsigned int idx)

Array< OneD, NekDouble >	GetCellSolution (unsigned int 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)

virtual void	v_GenerateSummary (SummaryList &s)

virtual void	v_SetInitialConditions ()

Protected Member Functions inherited from Nektar::CellModel
virtual std::string	v_GetCellVarName (unsigned int idx)

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 when computing reaction term. More...

Array< OneD, NekDouble >	m_uuu
	Temporary space for storing 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...

int	m_nq
	Number of physical points. More...

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

NekDouble	m_lastTime
	Timestep for pde model. More...

int	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 44 of file AlievPanfilov.h.

Constructor & Destructor Documentation

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

Definition at line 53 of file AlievPanfilov.cpp.

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.

             : 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);
     }

virtual Nektar::CellModelAlievPanfilov::~CellModelAlievPanfilov ( )

inlinevirtual

Definition at line 61 of file AlievPanfilov.h.

61 {}

Member Function Documentation

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

inlinestatic

Creates an instance of this class.

Definition at line 48 of file AlievPanfilov.h.

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

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

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

protectedvirtual

Implements Nektar::CellModel.

Definition at line 186 of file AlievPanfilov.cpp.

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

     {
         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);
     }

void Nektar::CellModelAlievPanfilov::v_SetInitialConditions ( )

protectedvirtual

Implements Nektar::CellModel.

Definition at line 200 of file AlievPanfilov.cpp.

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

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

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

protectedvirtual

Implements Nektar::CellModel.

Definition at line 74 of file AlievPanfilov.cpp.

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().

     {
         // 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);
     }

Member Data Documentation

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 55 of file AlievPanfilov.h.

NekDouble Nektar::CellModelAlievPanfilov::m_a

private

Trigger parameter a.

Definition at line 75 of file AlievPanfilov.h.

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

NekDouble Nektar::CellModelAlievPanfilov::m_eps

private

Restitution parameter $\epsilon$ .

Definition at line 83 of file AlievPanfilov.h.