A model for cardiac conduction. More...

#include <Monodomain.h>

Inheritance diagram for Nektar::Monodomain:

Collaboration diagram for Nektar::Monodomain:

Public Member Functions
virtual	~Monodomain ()
	Desctructor.
Public Member Functions inherited from Nektar::SolverUtils::UnsteadySystem
virtual SOLVER_UTILS_EXPORT	~UnsteadySystem ()
	Destructor.
SOLVER_UTILS_EXPORT NekDouble	GetTimeStep (const Array< OneD, const Array< OneD, NekDouble > > &inarray)
	Calculate the larger time-step mantaining the problem stable.
Public Member Functions inherited from Nektar::SolverUtils::EquationSystem
virtual SOLVER_UTILS_EXPORT	~EquationSystem ()
	Destructor.
SOLVER_UTILS_EXPORT void	SetUpTraceNormals (void)
SOLVER_UTILS_EXPORT void	InitObject ()
	Initialises the members of this object.
SOLVER_UTILS_EXPORT void	DoInitialise ()
	Perform any initialisation necessary before solving the problem.
SOLVER_UTILS_EXPORT void	DoSolve ()
	Solve the problem.
SOLVER_UTILS_EXPORT void	TransCoeffToPhys ()
	Transform from coefficient to physical space.
SOLVER_UTILS_EXPORT void	TransPhysToCoeff ()
	Transform from physical to coefficient space.
SOLVER_UTILS_EXPORT void	Output ()
	Perform output operations after solve.
SOLVER_UTILS_EXPORT NekDouble	LinfError (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray)
	Linf error computation.
SOLVER_UTILS_EXPORT std::string	GetSessionName ()
	Get Session name.
template<class T >
boost::shared_ptr< T >	as ()
SOLVER_UTILS_EXPORT void	ResetSessionName (std::string newname)
	Reset Session name.
SOLVER_UTILS_EXPORT LibUtilities::SessionReaderSharedPtr	GetSession ()
	Get Session name.
SOLVER_UTILS_EXPORT MultiRegions::ExpListSharedPtr	GetPressure ()
	Get pressure field if available.
SOLVER_UTILS_EXPORT void	PrintSummary (std::ostream &out)
	Print a summary of parameters and solver characteristics.
SOLVER_UTILS_EXPORT void	SetLambda (NekDouble lambda)
	Set parameter m_lambda.
SOLVER_UTILS_EXPORT void	EvaluateFunction (Array< OneD, Array< OneD, NekDouble > > &pArray, std::string pFunctionName, const NekDouble pTime=0.0, const int domain=0)
	Evaluates a function as specified in the session file.
SOLVER_UTILS_EXPORT void	EvaluateFunction (std::vector< std::string > pFieldNames, Array< OneD, Array< OneD, NekDouble > > &pFields, const std::string &pName, const int domain=0)
	Populate given fields with the function from session.
SOLVER_UTILS_EXPORT void	EvaluateFunction (std::vector< std::string > pFieldNames, Array< OneD, MultiRegions::ExpListSharedPtr > &pFields, const std::string &pName, const int domain=0)
	Populate given fields with the function from session.
SOLVER_UTILS_EXPORT void	EvaluateFunction (std::string pFieldName, Array< OneD, NekDouble > &pArray, const std::string &pFunctionName, const NekDouble &pTime=0.0, const int domain=0)
SOLVER_UTILS_EXPORT std::string	DescribeFunction (std::string pFieldName, const std::string &pFunctionName, const int domain)
	Provide a description of a function for a given field name.
SOLVER_UTILS_EXPORT void	InitialiseBaseFlow (Array< OneD, Array< OneD, NekDouble > > &base)
	Perform initialisation of the base flow.
SOLVER_UTILS_EXPORT void	SetInitialConditions (NekDouble initialtime=0.0, bool dumpInitialConditions=true, const int domain=0)
	Initialise the data in the dependent fields.
SOLVER_UTILS_EXPORT void	EvaluateExactSolution (int field, Array< OneD, NekDouble > &outfield, const NekDouble time)
	Evaluates an exact solution.
SOLVER_UTILS_EXPORT NekDouble	L2Error (unsigned int field, const Array< OneD, NekDouble > &exactsoln, bool Normalised=false)
	Compute the L2 error between fields and a given exact solution.
SOLVER_UTILS_EXPORT NekDouble	L2Error (unsigned int field, bool Normalised=false)
	Compute the L2 error of the fields.
SOLVER_UTILS_EXPORT Array < OneD, NekDouble >	ErrorExtraPoints (unsigned int field)
	Compute error (L2 and L_inf) over an larger set of quadrature points return [L2 Linf].
SOLVER_UTILS_EXPORT void	WeakAdvectionGreensDivergenceForm (const Array< OneD, Array< OneD, NekDouble > > &F, Array< OneD, NekDouble > &outarray)
	Compute the inner product $(\nabla \phi \cdot F)$ .
SOLVER_UTILS_EXPORT void	WeakAdvectionDivergenceForm (const Array< OneD, Array< OneD, NekDouble > > &F, Array< OneD, NekDouble > &outarray)
	Compute the inner product $(\phi, \nabla \cdot F)$ .
SOLVER_UTILS_EXPORT void	WeakAdvectionNonConservativeForm (const Array< OneD, Array< OneD, NekDouble > > &V, const Array< OneD, const NekDouble > &u, Array< OneD, NekDouble > &outarray, bool UseContCoeffs=false)
	Compute the inner product $(\phi, V\cdot \nabla u)$ .
f SOLVER_UTILS_EXPORT void	AdvectionNonConservativeForm (const Array< OneD, Array< OneD, NekDouble > > &V, const Array< OneD, const NekDouble > &u, Array< OneD, NekDouble > &outarray, Array< OneD, NekDouble > &wk=NullNekDouble1DArray)
	Compute the non-conservative advection.
SOLVER_UTILS_EXPORT void	WeakDGAdvection (const Array< OneD, Array< OneD, NekDouble > > &InField, Array< OneD, Array< OneD, NekDouble > > &OutField, bool NumericalFluxIncludesNormal=true, bool InFieldIsInPhysSpace=false, int nvariables=0)
	Calculate the weak discontinuous Galerkin advection.
SOLVER_UTILS_EXPORT void	WeakDGDiffusion (const Array< OneD, Array< OneD, NekDouble > > &InField, Array< OneD, Array< OneD, NekDouble > > &OutField, bool NumericalFluxIncludesNormal=true, bool InFieldIsInPhysSpace=false)
	Calculate weak DG Diffusion in the LDG form.
SOLVER_UTILS_EXPORT void	Checkpoint_Output (const int n)
	Write checkpoint file of m_fields.
SOLVER_UTILS_EXPORT void	Checkpoint_Output (const int n, MultiRegions::ExpListSharedPtr &field, std::vector< Array< OneD, NekDouble > > &fieldcoeffs, std::vector< std::string > &variables)
	Write checkpoint file of custom data fields.
SOLVER_UTILS_EXPORT void	Checkpoint_BaseFlow (const int n)
	Write base flow file of m_fields.
SOLVER_UTILS_EXPORT void	WriteFld (const std::string &outname)
	Write field data to the given filename.
SOLVER_UTILS_EXPORT void	WriteFld (const std::string &outname, MultiRegions::ExpListSharedPtr &field, std::vector< Array< OneD, NekDouble > > &fieldcoeffs, std::vector< std::string > &variables)
	Write input fields to the given filename.
SOLVER_UTILS_EXPORT void	ImportFld (const std::string &infile, Array< OneD, MultiRegions::ExpListSharedPtr > &pFields)
	Input field data from the given file.
SOLVER_UTILS_EXPORT void	ImportFldToMultiDomains (const std::string &infile, Array< OneD, MultiRegions::ExpListSharedPtr > &pFields, const int ndomains)
	Input field data from the given file to multiple domains.
SOLVER_UTILS_EXPORT void	ImportFld (const std::string &infile, std::vector< std::string > &fieldStr, Array< OneD, Array< OneD, NekDouble > > &coeffs)
	Output a field. Input field data into array from the given file.
SOLVER_UTILS_EXPORT void	ImportFld (const std::string &infile, MultiRegions::ExpListSharedPtr &pField, std::string &pFieldName)
	Output a field. Input field data into ExpList from the given file.
SOLVER_UTILS_EXPORT void	ScanForHistoryPoints ()
	Builds map of which element holds each history point.
SOLVER_UTILS_EXPORT void	WriteHistoryData (std::ostream &out)
	Probe each history point and write to file.
SOLVER_UTILS_EXPORT void	SessionSummary (SummaryList &vSummary)
	Write out a session summary.
SOLVER_UTILS_EXPORT Array < OneD, MultiRegions::ExpListSharedPtr > &	UpdateFields ()
SOLVER_UTILS_EXPORT LibUtilities::FieldMetaDataMap &	UpdateFieldMetaDataMap ()
	Get hold of FieldInfoMap so it can be updated.
SOLVER_UTILS_EXPORT NekDouble	GetFinalTime ()
	Return final time.
SOLVER_UTILS_EXPORT int	GetNcoeffs ()
SOLVER_UTILS_EXPORT int	GetNcoeffs (const int eid)
SOLVER_UTILS_EXPORT int	GetNumExpModes ()
SOLVER_UTILS_EXPORT const Array< OneD, int >	GetNumExpModesPerExp ()
SOLVER_UTILS_EXPORT int	GetNvariables ()
SOLVER_UTILS_EXPORT const std::string	GetVariable (unsigned int i)
SOLVER_UTILS_EXPORT int	GetTraceTotPoints ()
SOLVER_UTILS_EXPORT int	GetTraceNpoints ()
SOLVER_UTILS_EXPORT int	GetExpSize ()
SOLVER_UTILS_EXPORT int	GetPhys_Offset (int n)
SOLVER_UTILS_EXPORT int	GetCoeff_Offset (int n)
SOLVER_UTILS_EXPORT int	GetTotPoints ()
SOLVER_UTILS_EXPORT int	GetTotPoints (int n)
SOLVER_UTILS_EXPORT int	GetNpoints ()
SOLVER_UTILS_EXPORT int	GetNumElmVelocity ()
SOLVER_UTILS_EXPORT int	GetSteps ()
SOLVER_UTILS_EXPORT NekDouble	GetTimeStep ()
SOLVER_UTILS_EXPORT void	CopyFromPhysField (const int i, Array< OneD, NekDouble > &output)
SOLVER_UTILS_EXPORT void	CopyToPhysField (const int i, Array< OneD, NekDouble > &output)
SOLVER_UTILS_EXPORT void	SetStepsToOne ()
SOLVER_UTILS_EXPORT void	ZeroPhysFields ()
SOLVER_UTILS_EXPORT void	FwdTransFields ()
SOLVER_UTILS_EXPORT void	GetFluxVector (const int i, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &flux)
SOLVER_UTILS_EXPORT void	GetFluxVector (const int i, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &fluxX, Array< OneD, Array< OneD, NekDouble > > &fluxY)
SOLVER_UTILS_EXPORT void	GetFluxVector (const int i, const int j, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &flux)
SOLVER_UTILS_EXPORT void	NumericalFlux (Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numflux)
SOLVER_UTILS_EXPORT void	NumericalFlux (Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numfluxX, Array< OneD, Array< OneD, NekDouble > > &numfluxY)
SOLVER_UTILS_EXPORT void	NumFluxforScalar (const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &uflux)
SOLVER_UTILS_EXPORT void	NumFluxforVector (const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &qfield, Array< OneD, Array< OneD, NekDouble > > &qflux)
SOLVER_UTILS_EXPORT void	SetModifiedBasis (const bool modbasis)
SOLVER_UTILS_EXPORT int	NoCaseStringCompare (const string &s1, const string &s2)
	Perform a case-insensitive string comparison.

Static Public Member Functions
static EquationSystemSharedPtr	create (const LibUtilities::SessionReaderSharedPtr &pSession)
	Creates an instance of this class.

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

Protected Member Functions
	Monodomain (const LibUtilities::SessionReaderSharedPtr &pSession)
	Constructor.
virtual void	v_InitObject ()
	Init object for UnsteadySystem class.
void	DoImplicitSolve (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, NekDouble time, NekDouble lambda)
	Solve for the diffusion term.
void	DoOdeRhs (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)
	Computes the reaction terms and .
virtual void	v_SetInitialConditions (NekDouble initialtime, bool dumpInitialConditions, const int domain)
	Sets a custom initial condition.
virtual void	v_GenerateSummary (SummaryList &s)
	Prints a summary of the model parameters.
Protected Member Functions inherited from Nektar::SolverUtils::UnsteadySystem
SOLVER_UTILS_EXPORT	UnsteadySystem (const LibUtilities::SessionReaderSharedPtr &pSession)
	Initialises UnsteadySystem class members.
SOLVER_UTILS_EXPORT NekDouble	MaxTimeStepEstimator ()
	Get the maximum timestep estimator for cfl control.
virtual SOLVER_UTILS_EXPORT void	v_DoSolve ()
	Solves an unsteady problem.
virtual SOLVER_UTILS_EXPORT void	v_DoInitialise ()
	Sets up initial conditions.
virtual SOLVER_UTILS_EXPORT void	v_AppendOutput1D (Array< OneD, Array< OneD, NekDouble > > &solution1D)
	Print the solution at each solution point in a txt file.
virtual SOLVER_UTILS_EXPORT void	v_NumericalFlux (Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numflux)
virtual SOLVER_UTILS_EXPORT void	v_NumericalFlux (Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numfluxX, Array< OneD, Array< OneD, NekDouble > > &numfluxY)
virtual SOLVER_UTILS_EXPORT void	v_NumFluxforScalar (const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &uflux)
virtual SOLVER_UTILS_EXPORT void	v_NumFluxforVector (const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &qfield, Array< OneD, Array< OneD, NekDouble > > &qflux)
virtual SOLVER_UTILS_EXPORT NekDouble	v_GetTimeStep (const Array< OneD, const Array< OneD, NekDouble > > &inarray)
	Return the timestep to be used for the next step in the time-marching loop.
virtual SOLVER_UTILS_EXPORT bool	v_PreIntegrate (int step)
virtual SOLVER_UTILS_EXPORT bool	v_PostIntegrate (int step)
SOLVER_UTILS_EXPORT void	CheckForRestartTime (NekDouble &time)
Protected Member Functions inherited from Nektar::SolverUtils::EquationSystem
SOLVER_UTILS_EXPORT	EquationSystem (const LibUtilities::SessionReaderSharedPtr &pSession)
	Initialises EquationSystem class members.
int	nocase_cmp (const string &s1, const string &s2)
SOLVER_UTILS_EXPORT void	SetBoundaryConditions (NekDouble time)
	Evaluates the boundary conditions at the given time.
virtual SOLVER_UTILS_EXPORT NekDouble	v_LinfError (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray)
	Virtual function for the L_inf error computation between fields and a given exact solution.
virtual SOLVER_UTILS_EXPORT NekDouble	v_L2Error (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray, bool Normalised=false)
	Virtual function for the L_2 error computation between fields and a given exact solution.
virtual SOLVER_UTILS_EXPORT void	v_TransCoeffToPhys ()
	Virtual function for transformation to physical space.
virtual SOLVER_UTILS_EXPORT void	v_TransPhysToCoeff ()
	Virtual function for transformation to coefficient space.
virtual SOLVER_UTILS_EXPORT void	v_EvaluateExactSolution (unsigned int field, Array< OneD, NekDouble > &outfield, const NekDouble time)
SOLVER_UTILS_EXPORT void	SetUpBaseFields (SpatialDomains::MeshGraphSharedPtr &mesh)
SOLVER_UTILS_EXPORT void	ImportFldBase (std::string pInfile, SpatialDomains::MeshGraphSharedPtr pGraph)
virtual SOLVER_UTILS_EXPORT void	v_Output (void)
virtual SOLVER_UTILS_EXPORT MultiRegions::ExpListSharedPtr	v_GetPressure (void)
virtual SOLVER_UTILS_EXPORT void	v_ExtraFldOutput (std::vector< Array< OneD, NekDouble > > &fieldcoeffs, std::vector< std::string > &variables)

Private Member Functions
void	LoadStimuli ()

Private Attributes
CellModelSharedPtr	m_cell
	Cell model.
std::vector< StimulusSharedPtr >	m_stimulus
StdRegions::VarCoeffMap	m_vardiff
	Variable diffusivity.
NekDouble	m_chi
NekDouble	m_capMembrane
NekDouble	m_stimDuration
	Stimulus current.

Friends
class	MemoryManager< Monodomain >

Additional Inherited Members
Public Attributes inherited from Nektar::SolverUtils::UnsteadySystem
NekDouble	m_cflSafetyFactor
	CFL safety factor (comprise between 0 to 1).
Protected Types inherited from Nektar::SolverUtils::EquationSystem
enum	HomogeneousType { eHomogeneous1D, eHomogeneous2D, eHomogeneous3D, eNotHomogeneous }
	Parameter for homogeneous expansions. More...
Protected Attributes inherited from Nektar::SolverUtils::UnsteadySystem
int	m_infosteps
	Number of time steps between outputting status information.
LibUtilities::TimeIntegrationWrapperSharedPtr	m_intScheme
	Wrapper to the time integration scheme.
LibUtilities::TimeIntegrationSchemeOperators	m_ode
	The time integration scheme operators to use.
LibUtilities::TimeIntegrationSolutionSharedPtr	m_intSoln
NekDouble	m_epsilon
bool	m_explicitDiffusion
	Indicates if explicit or implicit treatment of diffusion is used.
bool	m_explicitAdvection
	Indicates if explicit or implicit treatment of advection is used.
bool	m_explicitReaction
	Indicates if explicit or implicit treatment of reaction is used.
bool	m_homoInitialFwd
	Flag to determine if simulation should start in homogeneous forward transformed state.
std::vector< int >	m_intVariables
std::vector< FilterSharedPtr >	m_filters

Detailed Description

A model for cardiac conduction.

Base model of cardiac electrophysiology of the form

$\begin{align*} \frac{\partial u}{\partial t} = \nabla^2 u + J_{ion}, \end{align*}$

where the reaction term, $J_{ion}$ is defined by a specific cell model.

This implementation, at present, treats the reaction terms explicitly and the diffusive element implicitly.

Definition at line 50 of file Monodomain.h.

Constructor & Destructor Documentation

Nektar::Monodomain::~Monodomain ( )

virtual

Desctructor.

Definition at line 295 of file Monodomain.cpp.

    {
    }

Nektar::Monodomain::Monodomain ( const LibUtilities::SessionReaderSharedPtr & pSession )

protected

Constructor.

Definition at line 70 of file Monodomain.cpp.

        : UnsteadySystem(pSession)
    {
    }

Member Function Documentation

static EquationSystemSharedPtr Nektar::Monodomain::create ( const LibUtilities::SessionReaderSharedPtr & pSession )

inlinestatic

Creates an instance of this class.

Definition at line 56 of file Monodomain.h.

        {
            EquationSystemSharedPtr p = MemoryManager<Monodomain>::AllocateSharedPtr(pSession);
            p->InitObject();
            return p;
        }

void Nektar::Monodomain::DoImplicitSolve	(	const Array< OneD, const Array< OneD, NekDouble > > &	inarray,
		Array< OneD, Array< OneD, NekDouble > > &	outarray,
		NekDouble	time,
		NekDouble	lambda
	)

protected

Solve for the diffusion term.

Parameters

inarray	Input array.
outarray	Output array.
time	Current simulation time.
lambda	Timestep.

Definition at line 307 of file Monodomain.cpp.

References Nektar::StdRegions::eFactorLambda, m_capMembrane, m_chi, Nektar::SolverUtils::EquationSystem::m_fields, m_vardiff, Nektar::NullFlagList, and Vmath::Smul().

Referenced by v_InitObject().

    {
        int nvariables  = inarray.num_elements();
        int nq          = m_fields[0]->GetNpoints();
        StdRegions::ConstFactorMap factors;
        // lambda = \Delta t
        factors[StdRegions::eFactorLambda] = 1.0/lambda*m_chi*m_capMembrane;
        // We solve ( \nabla^2 - HHlambda ) Y[i] = rhs [i]
        // inarray = input: \hat{rhs} -> output: \hat{Y}
        // outarray = output: nabla^2 \hat{Y}
        // where \hat = modal coeffs
        for (int i = 0; i < nvariables; ++i)
        {
            // Multiply 1.0/timestep
            Vmath::Smul(nq, -factors[StdRegions::eFactorLambda], inarray[i], 1,
                                            m_fields[i]->UpdatePhys(), 1);
            // Solve a system of equations with Helmholtz solver and transform
            // back into physical space.
            m_fields[i]->HelmSolve(m_fields[i]->GetPhys(),
                                   m_fields[i]->UpdateCoeffs(), NullFlagList,
                                   factors, m_vardiff);
            m_fields[i]->BwdTrans( m_fields[i]->GetCoeffs(),
                                   m_fields[i]->UpdatePhys());
            m_fields[i]->SetPhysState(true);
            // Copy the solution vector (required as m_fields must be set).
            outarray[i] = m_fields[i]->GetPhys();
        }
    }

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

protected

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

Definition at line 348 of file Monodomain.cpp.

References m_cell, and m_stimulus.

Referenced by v_InitObject().

    {
        // Compute I_ion
        m_cell->TimeIntegrate(inarray, outarray, time);
        // Compute I_stim
        for (unsigned int i = 0; i < m_stimulus.size(); ++i)
        {   
            m_stimulus[i]->Update(outarray, time);
        }
    }

void Nektar::Monodomain::LoadStimuli ( )

private

Referenced by v_InitObject().

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

protectedvirtual

Prints a summary of the model parameters.

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 381 of file Monodomain.cpp.

References Nektar::SolverUtils::AddSummaryItem(), Nektar::LibUtilities::eFunctionTypeExpression, m_cell, and Nektar::SolverUtils::EquationSystem::m_session.

    {
        UnsteadySystem::v_GenerateSummary(s);
        if (m_session->DefinesFunction("d00") &&
            m_session->GetFunctionType("d00", "intensity") 
                    == LibUtilities::eFunctionTypeExpression)
        {
            AddSummaryItem(s, "Diffusivity-x",
                m_session->GetFunction("d00", "intensity")->GetExpression());
        }
        if (m_session->DefinesFunction("d11") &&
            m_session->GetFunctionType("d11", "intensity") 
                    == LibUtilities::eFunctionTypeExpression)
        {
            AddSummaryItem(s, "Diffusivity-y",
                m_session->GetFunction("d11", "intensity")->GetExpression());
        }
        if (m_session->DefinesFunction("d22") &&
            m_session->GetFunctionType("d22", "intensity") 
                    == LibUtilities::eFunctionTypeExpression)
        {
            AddSummaryItem(s, "Diffusivity-z",
                m_session->GetFunction("d22", "intensity")->GetExpression());
        }
        m_cell->GenerateSummary(s);
    }

void Nektar::Monodomain::v_InitObject ( )

protectedvirtual

Init object for UnsteadySystem class.

Initialization object for UnsteadySystem class.

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 80 of file Monodomain.cpp.

    {
        UnsteadySystem::v_InitObject();
        m_session->LoadParameter("Chi",        m_chi);
        m_session->LoadParameter("Cm",         m_capMembrane);
        std::string vCellModel;
        m_session->LoadSolverInfo("CELLMODEL", vCellModel, "");
        ASSERTL0(vCellModel != "", "Cell Model not specified.");
        m_cell = GetCellModelFactory().CreateInstance(
                                        vCellModel, m_session, m_fields[0]);
        m_intVariables.push_back(0);
        // Load variable coefficients
        StdRegions::VarCoeffType varCoeffEnum[6] = {
                StdRegions::eVarCoeffD00,
                StdRegions::eVarCoeffD01,
                StdRegions::eVarCoeffD11,
                StdRegions::eVarCoeffD02,
                StdRegions::eVarCoeffD12,
                StdRegions::eVarCoeffD22
        };
        std::string varCoeffString[6] = {"xx","xy","yy","xz","yz","zz"};
        std::string aniso_var[3] = {"fx", "fy", "fz"};
        const int nq            = m_fields[0]->GetNpoints();
        const int nVarDiffCmpts = m_spacedim * (m_spacedim + 1) / 2;
        // Allocate storage for variable coeffs and initialize to 1.
        for (int i = 0, k = 0; i < m_spacedim; ++i)
        {
            for (int j = 0; j < i+1; ++j)
            {
                if (i == j)
                {
                    m_vardiff[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 1.0);
                }
                else
                {
                    m_vardiff[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 0.0);
                }
                ++k;
            }
        }
        // Apply fibre map f \in [0,1], scale to conductivity range
        // [o_min,o_max], specified by the session parameters o_min and o_max
        if (m_session->DefinesFunction("AnisotropicConductivity"))
        {
            if (m_session->DefinesCmdLineArgument("verbose"))
            {
                cout << "Loading Anisotropic Fibre map." << endl;
            }
            NekDouble   o_min        = m_session->GetParameter("o_min");
            NekDouble   o_max        = m_session->GetParameter("o_max");
            int         k            = 0;
            Array<OneD, NekDouble> vTemp_i;
            Array<OneD, NekDouble> vTemp_j;
            /*
             * Diffusivity matrix D is upper triangular and defined as
             *    d_00   d_01  d_02
             *           d_11  d_12
             *                 d_22
             *
             * Given a principle fibre direction _f_ the diffusivity is given
             * by
             *    d_ij = { D_2 + (D_1 - D_2) f_i f_j   if i==j
             *           {       (D_1 - D_2) f_i f_j   if i!=j
             *
             * The vector _f_ is given in terms of the variables fx,fy,fz in the
             * function AnisotropicConductivity. The values of D_1 and D_2 are
             * the parameters o_max and o_min, respectively.
             */
            // Loop through columns of D
            for (int j = 0; j < m_spacedim; ++j)
            {
                ASSERTL0(m_session->DefinesFunction("AnisotropicConductivity",
                                                    aniso_var[j]),
                         "Function 'AnisotropicConductivity' not correctly "
                         "defined.");
                EvaluateFunction(aniso_var[j], vTemp_j,
                                 "AnisotropicConductivity");
                // Loop through rows of D
                for (int i = 0; i < j + 1; ++i)
                {
                    ASSERTL0(m_session->DefinesFunction(
                                        "AnisotropicConductivity",aniso_var[i]),
                             "Function 'AnisotropicConductivity' not correctly "
                             "defined.");
                    EvaluateFunction(aniso_var[i], vTemp_i,
                                     "AnisotropicConductivity");
                    Vmath::Vmul(nq, vTemp_i, 1, vTemp_j, 1,
                                    m_vardiff[varCoeffEnum[k]], 1);
                    Vmath::Smul(nq, o_max-o_min,
                                    m_vardiff[varCoeffEnum[k]], 1,
                                    m_vardiff[varCoeffEnum[k]], 1);
                    if (i == j)
                    {
                        Vmath::Sadd(nq, o_min,
                                        m_vardiff[varCoeffEnum[k]], 1,
                                        m_vardiff[varCoeffEnum[k]], 1);
                    }
                    ++k;
                }
            }
        }
        // Scale by scar map (range 0->1) derived from intensity map
        // (range d_min -> d_max)
        if (m_session->DefinesFunction("IsotropicConductivity"))
        {
            if (m_session->DefinesCmdLineArgument("verbose"))
            {
                cout << "Loading Isotropic Conductivity map." << endl;
            }
            const std::string varName  = "intensity";
            Array<OneD, NekDouble> vTemp;
            EvaluateFunction(varName, vTemp, "IsotropicConductivity");
            // If the d_min and d_max parameters are defined, then we need to
            // rescale the isotropic conductivity to convert from the source
            // domain (e.g. late-gad intensity) to conductivity
            if ( m_session->DefinesParameter("d_min") ||
                 m_session->DefinesParameter("d_max") ) {
                const NekDouble   f_min    = m_session->GetParameter("d_min");
                const NekDouble   f_max    = m_session->GetParameter("d_max");
                const NekDouble   scar_min = 0.0;
                const NekDouble   scar_max = 1.0;
                // Threshold based on d_min, d_max
                for (int j = 0; j < nq; ++j)
                {
                    vTemp[j] = (vTemp[j] < f_min ? f_min : vTemp[j]);
                    vTemp[j] = (vTemp[j] > f_max ? f_max : vTemp[j]);
                }
                // Rescale to s \in [0,1] (0 maps to d_max, 1 maps to d_min)
                Vmath::Sadd(nq, -f_min, vTemp, 1, vTemp, 1);
                Vmath::Smul(nq, -1.0/(f_max-f_min), vTemp, 1, vTemp, 1);
                Vmath::Sadd(nq, 1.0, vTemp, 1, vTemp, 1);
                Vmath::Smul(nq, scar_max - scar_min, vTemp, 1, vTemp, 1);
                Vmath::Sadd(nq, scar_min, vTemp, 1, vTemp, 1);
            }
            // Scale anisotropic conductivity values
            for (int i = 0; i < nVarDiffCmpts; ++i)
            {
                Vmath::Vmul(nq, vTemp, 1,
                                m_vardiff[varCoeffEnum[i]], 1,
                                m_vardiff[varCoeffEnum[i]], 1);
            }
        }
        // Write out conductivity values
        for (int j = 0, k = 0; j < m_spacedim; ++j)
        {
            // Loop through rows of D
            for (int i = 0; i < j + 1; ++i)
            {
                // Transform variable coefficient and write out to file.
                m_fields[0]->FwdTrans_IterPerExp(m_vardiff[varCoeffEnum[k]],
                                                 m_fields[0]->UpdateCoeffs());
                std::stringstream filename;
                filename << "Conductivity_" << varCoeffString[k] << ".fld";
                WriteFld(filename.str());
                ++k;
            }
        }
        // Search through the loaded filters and pass the cell model to any
        // CheckpointCellModel filters loaded.
        int k = 0;
        const LibUtilities::FilterMap& f = m_session->GetFilters();
        LibUtilities::FilterMap::const_iterator x;
        for (x = f.begin(); x != f.end(); ++x, ++k)
        {
            if (x->first == "CheckpointCellModel")
            {
                boost::shared_ptr<FilterCheckpointCellModel> c
                    = boost::dynamic_pointer_cast<FilterCheckpointCellModel>(
                                                                m_filters[k]);
                c->SetCellModel(m_cell);
            }
        }
        // Load stimuli
        m_stimulus = Stimulus::LoadStimuli(m_session, m_fields[0]);
        if (!m_explicitDiffusion)
        {
            m_ode.DefineImplicitSolve (&Monodomain::DoImplicitSolve, this);
        }
        m_ode.DefineOdeRhs(&Monodomain::DoOdeRhs, this);
    }

void Nektar::Monodomain::v_SetInitialConditions	(	NekDouble	initialtime,
		bool	dumpInitialConditions,
		const int	domain
	)

protectedvirtual

Sets a custom initial condition.

Reimplemented from Nektar::SolverUtils::EquationSystem.

Definition at line 367 of file Monodomain.cpp.

References m_cell.

    {
        EquationSystem::v_SetInitialConditions(initialtime,
                                               dumpInitialConditions,
                                               domain);
        m_cell->Initialise();
    }

Friends And Related Function Documentation

friend class MemoryManager< Monodomain >

friend

Definition at line 53 of file Monodomain.h.

Member Data Documentation

string Nektar::Monodomain::className

static

Initial value:

 GetEquationSystemFactory().RegisterCreatorFunction(
                "Monodomain",
                Monodomain::create,
                "Monodomain model of cardiac electrophysiology.")

Name of class.

Registers the class with the Factory.

Definition at line 65 of file Monodomain.h.

NekDouble Nektar::Monodomain::m_capMembrane

private

Definition at line 108 of file Monodomain.h.

Referenced by DoImplicitSolve(), and v_InitObject().

CellModelSharedPtr Nektar::Monodomain::m_cell

private

Cell model.

Definition at line 100 of file Monodomain.h.

Referenced by DoOdeRhs(), v_GenerateSummary(), v_InitObject(), and v_SetInitialConditions().

NekDouble Nektar::Monodomain::m_chi

private

Definition at line 107 of file Monodomain.h.

Referenced by DoImplicitSolve(), and v_InitObject().

NekDouble Nektar::Monodomain::m_stimDuration

private

Stimulus current.

Definition at line 111 of file Monodomain.h.

std::vector<StimulusSharedPtr> Nektar::Monodomain::m_stimulus

private

Definition at line 102 of file Monodomain.h.

Referenced by DoOdeRhs(), and v_InitObject().

StdRegions::VarCoeffMap Nektar::Monodomain::m_vardiff

private

Variable diffusivity.

Definition at line 105 of file Monodomain.h.

Referenced by DoImplicitSolve(), and v_InitObject().

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation