A model for cardiac conduction. More...

#include <BidomainRoth.h>

Inheritance diagram for Nektar::BidomainRoth:

Collaboration diagram for Nektar::BidomainRoth:

Public Member Functions
virtual	~BidomainRoth ()
	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 SolverUtils::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
	BidomainRoth (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_vardiffi
StdRegions::VarCoeffMap	m_vardiffe
StdRegions::VarCoeffMap	m_vardiffie
NekDouble	m_chi
NekDouble	m_capMembrane
NekDouble	m_stimDuration
	Stimulus current.

Friends
class	MemoryManager< BidomainRoth >

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.

Definition at line 48 of file BidomainRoth.h.

Constructor & Destructor Documentation

Nektar::BidomainRoth::~BidomainRoth ( )

virtual

Desctructor.

Definition at line 325 of file BidomainRoth.cpp.

{
}

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

protected

Constructor.

Definition at line 57 of file BidomainRoth.cpp.

    : UnsteadySystem(pSession)
{
}

Member Function Documentation

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

inlinestatic

Creates an instance of this class.

Definition at line 54 of file BidomainRoth.h.

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

void Nektar::BidomainRoth::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 337 of file BidomainRoth.cpp.

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

Referenced by v_InitObject().

{
    int nq          = m_fields[0]->GetNpoints();
    StdRegions::ConstFactorMap factorsHelmholtz;
    // lambda = \Delta t
    factorsHelmholtz[StdRegions::eFactorLambda] 
                    = 1.0/lambda*m_chi*m_capMembrane;
    // ------------------------------
    // Solve Helmholtz problem for Vm
    // ------------------------------
    // Multiply 1.0/timestep
    //Vmath::Vadd(nq, inarray[0], 1, ggrad, 1, m_fields[0]->UpdatePhys(), 1);
    Vmath::Smul(nq, -factorsHelmholtz[StdRegions::eFactorLambda], inarray[0], 1,
                                    m_fields[0]->UpdatePhys(), 1);
    // Solve a system of equations with Helmholtz solver and transform
    // back into physical space.
    m_fields[0]->HelmSolve(m_fields[0]->GetPhys(),
                           m_fields[0]->UpdateCoeffs(), NullFlagList,
                           factorsHelmholtz, m_vardiffe);
    m_fields[0]->BwdTrans( m_fields[0]->GetCoeffs(),
                           m_fields[0]->UpdatePhys());
    m_fields[0]->SetPhysState(true);
    // Copy the solution vector (required as m_fields must be set).
    outarray[0] = m_fields[0]->GetPhys();
}

void Nektar::BidomainRoth::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 376 of file BidomainRoth.cpp.

References Nektar::StdRegions::eFactorLambda, Nektar::StdRegions::eVarCoeffD00, Nektar::StdRegions::eVarCoeffD11, Nektar::StdRegions::eVarCoeffD22, m_cell, Nektar::SolverUtils::EquationSystem::m_fields, Nektar::SolverUtils::EquationSystem::m_session, m_stimulus, m_vardiffi, m_vardiffie, Nektar::NullFlagList, Vmath::Smul(), Vmath::Vadd(), and Vmath::Vmul().

Referenced by v_InitObject().

{
    int nq          = m_fields[0]->GetNpoints();
    // 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);
    }
    Array<OneD, NekDouble> ggrad0(nq), ggrad1(nq), ggrad2(nq), ggrad(nq);
    StdRegions::ConstFactorMap factorsPoisson;
    factorsPoisson[StdRegions::eFactorLambda] = 0.0;
    // ----------------------------
    // Compute \nabla g_i \nabla Vm
    // ----------------------------
    m_fields[0]->PhysDeriv(inarray[0], ggrad0, ggrad1, ggrad2);
    m_fields[0]->PhysDeriv(0, ggrad0, ggrad0);
    m_fields[0]->PhysDeriv(1, ggrad1, ggrad1);
    m_fields[0]->PhysDeriv(2, ggrad2, ggrad2);
    if (m_session->DefinesFunction("IntracellularAnisotropicConductivity") &&
        m_session->DefinesFunction("ExtracellularAnisotropicConductivity"))
    {
        Vmath::Vmul(nq, m_vardiffi[StdRegions::eVarCoeffD00], 1, ggrad0,
                1, ggrad0, 1);
        Vmath::Vmul(nq, m_vardiffi[StdRegions::eVarCoeffD11], 1, ggrad1,
                1, ggrad1, 1);
        Vmath::Vmul(nq, m_vardiffi[StdRegions::eVarCoeffD22], 1, ggrad2,
                1, ggrad2, 1);
    }
    // Add partial derivatives together
    Vmath::Vadd(nq, ggrad0, 1, ggrad1, 1, ggrad, 1);
    Vmath::Vadd(nq, ggrad2, 1, ggrad, 1, ggrad, 1);
    Vmath::Smul(nq, -1.0, ggrad, 1, m_fields[1]->UpdatePhys(), 1);
    // ----------------------------
    // Solve Poisson problem for Ve
    // ----------------------------
    m_fields[1]->HelmSolve(m_fields[1]->GetPhys(),
            m_fields[1]->UpdateCoeffs(), NullFlagList, factorsPoisson,
            m_vardiffie);
    m_fields[1]->BwdTrans(m_fields[1]->GetCoeffs(),
            m_fields[1]->UpdatePhys());
    m_fields[1]->SetPhysState(true);
    // ------------------------------
    // Compute Laplacian of Ve (forcing term)
    // ------------------------------
    m_fields[1]->PhysDeriv(m_fields[1]->GetPhys(), ggrad0, ggrad1, ggrad2);
    m_fields[1]->PhysDeriv(0, ggrad0, ggrad0);
    m_fields[1]->PhysDeriv(1, ggrad1, ggrad1);
    m_fields[1]->PhysDeriv(2, ggrad2, ggrad2);
    if (m_session->DefinesFunction("IntracellularAnisotropicConductivity") &&
        m_session->DefinesFunction("ExtracellularAnisotropicConductivity"))
    {
        Vmath::Vmul(nq, m_vardiffi[StdRegions::eVarCoeffD00], 1, ggrad0,
                1, ggrad0, 1);
        Vmath::Vmul(nq, m_vardiffi[StdRegions::eVarCoeffD11], 1, ggrad1,
                1, ggrad1, 1);
        Vmath::Vmul(nq, m_vardiffi[StdRegions::eVarCoeffD22], 1, ggrad2,
                1, ggrad2, 1);
    }
    // Add partial derivatives together
    Vmath::Vadd(nq, ggrad0, 1, ggrad1, 1, ggrad, 1);
    Vmath::Vadd(nq, ggrad2, 1, ggrad, 1, ggrad, 1);
    Vmath::Vadd(nq, ggrad, 1, outarray[0], 1, outarray[0], 1);
}

void Nektar::BidomainRoth::LoadStimuli ( )

private

Referenced by v_InitObject().

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

protectedvirtual

Prints a summary of the model parameters.

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 471 of file BidomainRoth.cpp.

References m_cell.

{
    UnsteadySystem::v_GenerateSummary(s);
    m_cell->GenerateSummary(s);
}

void Nektar::BidomainRoth::v_InitObject ( )

protectedvirtual

Init object for UnsteadySystem class.

Initialization object for UnsteadySystem class.

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 67 of file BidomainRoth.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();
    // 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_vardiffi[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 1.0);
                m_vardiffe[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 1.0);
                m_vardiffie[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 1.0);
            }
            else
            {
                m_vardiffi[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 0.0);
                m_vardiffe[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 0.0);
                m_vardiffie[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("ExtracellularAnisotropicConductivity"))
    {
        if (m_session->DefinesCmdLineArgument("verbose"))
        {
            cout << "Loading Extracellular 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(
                                        "ExtracellularAnisotropicConductivity",
                                        aniso_var[j]),
                     "Function 'AnisotropicConductivity' not correctly "
                     "defined.");
            EvaluateFunction(aniso_var[j], vTemp_j,
                             "ExtracellularAnisotropicConductivity");
            // Loop through rows of D
            for (int i = 0; i < j + 1; ++i)
            {
                ASSERTL0(m_session->DefinesFunction(
                                    "ExtracellularAnisotropicConductivity",
                                    aniso_var[i]),
                         "Function 'ExtracellularAnisotropicConductivity' not "
                         "correctly defined.");
                EvaluateFunction(aniso_var[i], vTemp_i,
                                 "ExtracellularAnisotropicConductivity");
                Vmath::Vmul(nq, vTemp_i, 1, vTemp_j, 1,
                                m_vardiffe[varCoeffEnum[k]], 1);
                Vmath::Smul(nq, o_max-o_min,
                                m_vardiffe[varCoeffEnum[k]], 1,
                                m_vardiffe[varCoeffEnum[k]], 1);
                if (i == j)
                {
                    Vmath::Sadd(nq, o_min,
                                    m_vardiffe[varCoeffEnum[k]], 1,
                                    m_vardiffe[varCoeffEnum[k]], 1);
                }
            }
        }
    }
    // 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("IntracellularAnisotropicConductivity"))
    {
        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(
                                        "IntracellularAnisotropicConductivity",
                                        aniso_var[j]),
                     "Function 'IntracellularAnisotropicConductivity' not "
                     "correctly defined.");
            EvaluateFunction(aniso_var[j], vTemp_j,
                             "IntracellularAnisotropicConductivity");
            // Loop through rows of D
            for (int i = 0; i < j + 1; ++i)
            {
                ASSERTL0(m_session->DefinesFunction(
                                    "IntracellularAnisotropicConductivity",
                                    aniso_var[i]),
                         "Function 'IntracellularAnisotropicConductivity' not "
                         "correctly defined.");
                EvaluateFunction(aniso_var[i], vTemp_i,
                                 "IntracellularAnisotropicConductivity");
                Vmath::Vmul(nq, vTemp_i, 1, vTemp_j, 1,
                                m_vardiffi[varCoeffEnum[k]], 1);
                Vmath::Smul(nq, o_max-o_min,
                                m_vardiffi[varCoeffEnum[k]], 1,
                                m_vardiffi[varCoeffEnum[k]], 1);
                if (i == j)
                {
                    Vmath::Sadd(nq, o_min,
                                    m_vardiffi[varCoeffEnum[k]], 1,
                                    m_vardiffi[varCoeffEnum[k]], 1);
                }
                Vmath::Vadd(nq, m_vardiffe[varCoeffEnum[k]], 1,
                                m_vardiffi[varCoeffEnum[k]], 1,
                                m_vardiffie[varCoeffEnum[k]], 1);
                ++k;
            }
        }
    }
    // 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_vardiffi[varCoeffEnum[k]],
                                             m_fields[0]->UpdateCoeffs());
            std::stringstream filenamei;
            filenamei << "IConductivity_" << varCoeffString[k] << ".fld";
            WriteFld(filenamei.str());
            // Transform variable coefficient and write out to file.
            m_fields[0]->FwdTrans_IterPerExp(m_vardiffe[varCoeffEnum[k]],
                                             m_fields[0]->UpdateCoeffs());
            std::stringstream filenamee;
            filenamee << "EConductivity_" << varCoeffString[k] << ".fld";
            WriteFld(filenamee.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 (&BidomainRoth::DoImplicitSolve, this);
    }
    m_ode.DefineOdeRhs(&BidomainRoth::DoOdeRhs, this);
}

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

protectedvirtual

Sets a custom initial condition.

Reimplemented from Nektar::SolverUtils::EquationSystem.

Definition at line 457 of file BidomainRoth.cpp.

References m_cell.

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

Friends And Related Function Documentation

friend class MemoryManager< BidomainRoth >

friend

Definition at line 51 of file BidomainRoth.h.

Member Data Documentation

string Nektar::BidomainRoth::className

static

Initial value:

 GetEquationSystemFactory().RegisterCreatorFunction(
            "BidomainRoth",
            BidomainRoth::create,
            "Bidomain Roth model of cardiac electrophysiology.")

Name of class.

Registers the class with the Factory.

Definition at line 64 of file BidomainRoth.h.

NekDouble Nektar::BidomainRoth::m_capMembrane

private

Definition at line 108 of file BidomainRoth.h.

Referenced by DoImplicitSolve(), and v_InitObject().

CellModelSharedPtr Nektar::BidomainRoth::m_cell

private

Cell model.

Definition at line 99 of file BidomainRoth.h.

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