Nektar::BidomainRoth Class Reference

A model for cardiac conduction. More...

#include <BidomainRoth.h>

Inheritance diagram for Nektar::BidomainRoth:

Public Member Functions
virtual	~BidomainRoth ()
	Desctructor. More...
Public Member Functions inherited from Nektar::SolverUtils::UnsteadySystem
virtual SOLVER_UTILS_EXPORT	~UnsteadySystem ()
	Destructor. More...
SOLVER_UTILS_EXPORT NekDouble	GetTimeStep (const Array< OneD, const Array< OneD, NekDouble >> &inarray)
	Calculate the larger time-step mantaining the problem stable. More...
Public Member Functions inherited from Nektar::SolverUtils::EquationSystem
virtual SOLVER_UTILS_EXPORT	~EquationSystem ()
	Destructor. More...
SOLVER_UTILS_EXPORT void	SetUpTraceNormals (void)
SOLVER_UTILS_EXPORT void	InitObject ()
	Initialises the members of this object. More...
SOLVER_UTILS_EXPORT void	DoInitialise ()
	Perform any initialisation necessary before solving the problem. More...
SOLVER_UTILS_EXPORT void	DoSolve ()
	Solve the problem. More...
SOLVER_UTILS_EXPORT void	TransCoeffToPhys ()
	Transform from coefficient to physical space. More...
SOLVER_UTILS_EXPORT void	TransPhysToCoeff ()
	Transform from physical to coefficient space. More...
SOLVER_UTILS_EXPORT void	Output ()
	Perform output operations after solve. More...
SOLVER_UTILS_EXPORT NekDouble	LinfError (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray)
	Linf error computation. More...
SOLVER_UTILS_EXPORT std::string	GetSessionName ()
	Get Session name. More...
template<class T >
std::shared_ptr< T >	as ()
SOLVER_UTILS_EXPORT void	ResetSessionName (std::string newname)
	Reset Session name. More...
SOLVER_UTILS_EXPORT LibUtilities::SessionReaderSharedPtr	GetSession ()
	Get Session name. More...
SOLVER_UTILS_EXPORT MultiRegions::ExpListSharedPtr	GetPressure ()
	Get pressure field if available. More...
SOLVER_UTILS_EXPORT void	ExtraFldOutput (std::vector< Array< OneD, NekDouble > > &fieldcoeffs, std::vector< std::string > &variables)
SOLVER_UTILS_EXPORT void	PrintSummary (std::ostream &out)
	Print a summary of parameters and solver characteristics. More...
SOLVER_UTILS_EXPORT void	SetLambda (NekDouble lambda)
	Set parameter m_lambda. More...
SOLVER_UTILS_EXPORT SessionFunctionSharedPtr	GetFunction (std::string name, const MultiRegions::ExpListSharedPtr &field=MultiRegions::NullExpListSharedPtr, bool cache=false)
	Get a SessionFunction by name. More...
SOLVER_UTILS_EXPORT void	SetInitialConditions (NekDouble initialtime=0.0, bool dumpInitialConditions=true, const int domain=0)
	Initialise the data in the dependent fields. More...
SOLVER_UTILS_EXPORT void	EvaluateExactSolution (int field, Array< OneD, NekDouble > &outfield, const NekDouble time)
	Evaluates an exact solution. More...
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. More...
SOLVER_UTILS_EXPORT NekDouble	L2Error (unsigned int field, bool Normalised=false)
	Compute the L2 error of the fields. More...
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]. More...
SOLVER_UTILS_EXPORT void	Checkpoint_Output (const int n)
	Write checkpoint file of m_fields. More...
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. More...
SOLVER_UTILS_EXPORT void	Checkpoint_BaseFlow (const int n)
	Write base flow file of m_fields. More...
SOLVER_UTILS_EXPORT void	WriteFld (const std::string &outname)
	Write field data to the given filename. More...
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. More...
SOLVER_UTILS_EXPORT void	ImportFld (const std::string &infile, Array< OneD, MultiRegions::ExpListSharedPtr > &pFields)
	Input field data from the given file. More...
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. More...
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. More...
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. More...
SOLVER_UTILS_EXPORT void	SessionSummary (SummaryList &vSummary)
	Write out a session summary. More...
SOLVER_UTILS_EXPORT Array< OneD, MultiRegions::ExpListSharedPtr > &	UpdateFields ()
SOLVER_UTILS_EXPORT LibUtilities::FieldMetaDataMap &	UpdateFieldMetaDataMap ()
	Get hold of FieldInfoMap so it can be updated. More...
SOLVER_UTILS_EXPORT NekDouble	GetFinalTime ()
	Return final time. More...
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	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	SetSteps (const int steps)
SOLVER_UTILS_EXPORT void	ZeroPhysFields ()
SOLVER_UTILS_EXPORT void	FwdTransFields ()
SOLVER_UTILS_EXPORT void	SetModifiedBasis (const bool modbasis)
SOLVER_UTILS_EXPORT int	GetCheckpointNumber ()
SOLVER_UTILS_EXPORT void	SetCheckpointNumber (int num)
SOLVER_UTILS_EXPORT int	GetCheckpointSteps ()
SOLVER_UTILS_EXPORT void	SetCheckpointSteps (int num)
SOLVER_UTILS_EXPORT void	SetTime (const NekDouble time)
SOLVER_UTILS_EXPORT void	SetInitialStep (const int step)
SOLVER_UTILS_EXPORT void	SetBoundaryConditions (NekDouble time)
	Evaluates the boundary conditions at the given time. More...
virtual SOLVER_UTILS_EXPORT bool	v_NegatedOp ()
	Virtual function to identify if operator is negated in DoSolve. More...

Static Public Member Functions
static SolverUtils::EquationSystemSharedPtr	create (const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &pGraph)
	Creates an instance of this class. More...

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

Protected Member Functions
	BidomainRoth (const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &pGraph)
	Constructor. More...
virtual void	v_InitObject ()
	Init object for UnsteadySystem class. More...
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. More...
void	DoOdeRhs (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)
	Computes the reaction terms \(f(u,v)\) and \(g(u,v)\). More...
virtual void	v_SetInitialConditions (NekDouble initialtime, bool dumpInitialConditions, const int domain)
	Sets a custom initial condition. More...
virtual void	v_GenerateSummary (SummaryList &s)
	Prints a summary of the model parameters. More...
Protected Member Functions inherited from Nektar::SolverUtils::UnsteadySystem
SOLVER_UTILS_EXPORT	UnsteadySystem (const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &pGraph)
	Initialises UnsteadySystem class members. More...
SOLVER_UTILS_EXPORT NekDouble	MaxTimeStepEstimator ()
	Get the maximum timestep estimator for cfl control. More...
virtual SOLVER_UTILS_EXPORT void	v_DoSolve ()
	Solves an unsteady problem. More...
virtual SOLVER_UTILS_EXPORT void	v_DoInitialise ()
	Sets up initial conditions. More...
virtual SOLVER_UTILS_EXPORT void	v_AppendOutput1D (Array< OneD, Array< OneD, NekDouble >> &solution1D)
	Print the solution at each solution point in a txt file. More...
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. More...
virtual SOLVER_UTILS_EXPORT bool	v_PreIntegrate (int step)
virtual SOLVER_UTILS_EXPORT bool	v_PostIntegrate (int step)
virtual SOLVER_UTILS_EXPORT bool	v_RequireFwdTrans ()
SOLVER_UTILS_EXPORT void	CheckForRestartTime (NekDouble &time, int &nchk)
SOLVER_UTILS_EXPORT void	SVVVarDiffCoeff (const Array< OneD, Array< OneD, NekDouble >> vel, StdRegions::VarCoeffMap &varCoeffMap)
	Evaluate the SVV diffusion coefficient according to Moura's paper where it should proportional to h time velocity. More...
Protected Member Functions inherited from Nektar::SolverUtils::EquationSystem
SOLVER_UTILS_EXPORT	EquationSystem (const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &pGraph)
	Initialises EquationSystem class members. More...
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. More...
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. More...
virtual SOLVER_UTILS_EXPORT void	v_TransCoeffToPhys ()
	Virtual function for transformation to physical space. More...
virtual SOLVER_UTILS_EXPORT void	v_TransPhysToCoeff ()
	Virtual function for transformation to coefficient space. More...
virtual SOLVER_UTILS_EXPORT void	v_EvaluateExactSolution (unsigned int field, Array< OneD, NekDouble > &outfield, const NekDouble time)
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. More...
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. More...

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). More...
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. More...
int	m_abortSteps
	Number of steps between checks for abort conditions. More...
int	m_filtersInfosteps
	Number of time steps between outputting filters information. More...
int	m_nanSteps
LibUtilities::TimeIntegrationWrapperSharedPtr	m_intScheme
	Wrapper to the time integration scheme. More...
LibUtilities::TimeIntegrationSchemeOperators	m_ode
	The time integration scheme operators to use. More...
LibUtilities::TimeIntegrationSolutionSharedPtr	m_intSoln
NekDouble	m_epsilon
bool	m_explicitDiffusion
	Indicates if explicit or implicit treatment of diffusion is used. More...
bool	m_explicitAdvection
	Indicates if explicit or implicit treatment of advection is used. More...
bool	m_explicitReaction
	Indicates if explicit or implicit treatment of reaction is used. More...
bool	m_homoInitialFwd
	Flag to determine if simulation should start in homogeneous forward transformed state. More...
NekDouble	m_steadyStateTol
	Tolerance to which steady state should be evaluated at. More...
int	m_steadyStateSteps
	Check for steady state at step interval. More...
Array< OneD, Array< OneD, NekDouble > >	m_previousSolution
	Storage for previous solution for steady-state check. More...
std::ofstream	m_errFile
std::vector< int >	m_intVariables
std::vector< std::pair< std::string, FilterSharedPtr > >	m_filters
NekDouble	m_filterTimeWarning
	Number of time steps between outputting status information. More...
Protected Attributes inherited from Nektar::SolverUtils::EquationSystem
LibUtilities::CommSharedPtr	m_comm
	Communicator. More...
LibUtilities::SessionReaderSharedPtr	m_session
	The session reader. More...
std::map< std::string, SolverUtils::SessionFunctionSharedPtr >	m_sessionFunctions
	Map of known SessionFunctions. More...
LibUtilities::FieldIOSharedPtr	m_fld
	Field input/output. More...
Array< OneD, MultiRegions::ExpListSharedPtr >	m_fields
	Array holding all dependent variables. More...
SpatialDomains::BoundaryConditionsSharedPtr	m_boundaryConditions
	Pointer to boundary conditions object. More...
SpatialDomains::MeshGraphSharedPtr	m_graph
	Pointer to graph defining mesh. More...
std::string	m_sessionName
	Name of the session. More...
NekDouble	m_time
	Current time of simulation. More...
int	m_initialStep
	Number of the step where the simulation should begin. More...
NekDouble	m_fintime
	Finish time of the simulation. More...
NekDouble	m_timestep
	Time step size. More...
NekDouble	m_lambda
	Lambda constant in real system if one required. More...
NekDouble	m_checktime
	Time between checkpoints. More...
int	m_nchk
	Number of checkpoints written so far. More...
int	m_steps
	Number of steps to take. More...
int	m_checksteps
	Number of steps between checkpoints. More...
int	m_spacedim
	Spatial dimension (>= expansion dim). More...
int	m_expdim
	Expansion dimension. More...
bool	m_singleMode
	Flag to determine if single homogeneous mode is used. More...
bool	m_halfMode
	Flag to determine if half homogeneous mode is used. More...
bool	m_multipleModes
	Flag to determine if use multiple homogenenous modes are used. More...
bool	m_useFFT
	Flag to determine if FFT is used for homogeneous transform. More...
bool	m_homogen_dealiasing
	Flag to determine if dealiasing is used for homogeneous simulations. More...
bool	m_specHP_dealiasing
	Flag to determine if dealisising is usde for the Spectral/hp element discretisation. More...
enum MultiRegions::ProjectionType	m_projectionType
	Type of projection; e.g continuous or discontinuous. More...
Array< OneD, Array< OneD, NekDouble > >	m_traceNormals
	Array holding trace normals for DG simulations in the forwards direction. More...
Array< OneD, bool >	m_checkIfSystemSingular
	Flag to indicate if the fields should be checked for singularity. More...
LibUtilities::FieldMetaDataMap	m_fieldMetaDataMap
	Map to identify relevant solver info to dump in output fields. More...
int	m_NumQuadPointsError
	Number of Quadrature points used to work out the error. More...
enum HomogeneousType	m_HomogeneousType
NekDouble	m_LhomX
	physical length in X direction (if homogeneous) More...
NekDouble	m_LhomY
	physical length in Y direction (if homogeneous) More...
NekDouble	m_LhomZ
	physical length in Z direction (if homogeneous) More...
int	m_npointsX
	number of points in X direction (if homogeneous) More...
int	m_npointsY
	number of points in Y direction (if homogeneous) More...
int	m_npointsZ
	number of points in Z direction (if homogeneous) More...
int	m_HomoDirec
	number of homogenous directions More...
Static Protected Attributes inherited from Nektar::SolverUtils::EquationSystem
static std::string	equationSystemTypeLookupIds []

Detailed Description

A model for cardiac conduction.

Definition at line 47 of file BidomainRoth.h.

Constructor & Destructor Documentation

~BidomainRoth()

Nektar::BidomainRoth::~BidomainRoth ( )

virtual

Desctructor.

Definition at line 320 of file BidomainRoth.cpp.

{

}

BidomainRoth()

Nektar::BidomainRoth::BidomainRoth ( const LibUtilities::SessionReaderSharedPtr &  pSession, const SpatialDomains::MeshGraphSharedPtr &  pGraph  )

protected

Constructor.

Definition at line 58 of file BidomainRoth.cpp.

    : UnsteadySystem(pSession, pGraph)
{
}

Member Function Documentation

create()

static SolverUtils::EquationSystemSharedPtr Nektar::BidomainRoth::create ( const LibUtilities::SessionReaderSharedPtr &  pSession, const SpatialDomains::MeshGraphSharedPtr &  pGraph  )

inlinestatic

Creates an instance of this class.

Definition at line 53 of file BidomainRoth.h.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), and CellMLToNektar.cellml_metadata::p.

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

DoImplicitSolve()

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 332 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();
}

DoOdeRhs()

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 371 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);
}

LoadStimuli()

void Nektar::BidomainRoth::LoadStimuli ( )

private

v_GenerateSummary()

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

protectedvirtual

Prints a summary of the model parameters.

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 466 of file BidomainRoth.cpp.

References m_cell, and Nektar::SolverUtils::UnsteadySystem::v_GenerateSummary().

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

v_InitObject()

void Nektar::BidomainRoth::v_InitObject ( )

protectedvirtual

Init object for UnsteadySystem class.

Initialization object for UnsteadySystem class.

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 69 of file BidomainRoth.cpp.

References ASSERTL0, Nektar::LibUtilities::NekFactory< tKey, tBase, tParam >::CreateInstance(), Nektar::LibUtilities::TimeIntegrationSchemeOperators::DefineImplicitSolve(), Nektar::LibUtilities::TimeIntegrationSchemeOperators::DefineOdeRhs(), DoImplicitSolve(), DoOdeRhs(), Nektar::StdRegions::eVarCoeffD00, Nektar::StdRegions::eVarCoeffD01, Nektar::StdRegions::eVarCoeffD02, Nektar::StdRegions::eVarCoeffD11, Nektar::StdRegions::eVarCoeffD12, Nektar::StdRegions::eVarCoeffD22, Nektar::GetCellModelFactory(), Nektar::SolverUtils::EquationSystem::GetFunction(), Nektar::Stimulus::LoadStimuli(), m_capMembrane, m_cell, m_chi, Nektar::SolverUtils::UnsteadySystem::m_explicitDiffusion, Nektar::SolverUtils::EquationSystem::m_fields, Nektar::SolverUtils::UnsteadySystem::m_filters, Nektar::SolverUtils::UnsteadySystem::m_intVariables, Nektar::SolverUtils::UnsteadySystem::m_ode, Nektar::SolverUtils::EquationSystem::m_session, Nektar::SolverUtils::EquationSystem::m_spacedim, m_stimulus, m_vardiffe, m_vardiffi, m_vardiffie, Vmath::Sadd(), Nektar::FilterCheckpointCellModel::SetCellModel(), Vmath::Smul(), Nektar::SolverUtils::UnsteadySystem::v_InitObject(), Vmath::Vadd(), Vmath::Vmul(), and Nektar::SolverUtils::EquationSystem::WriteFld().

{
    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.");

            GetFunction("ExtracellularAnisotropicConductivity")->Evaluate(aniso_var[j], vTemp_j);

            // 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.");

                GetFunction("ExtracellularAnisotropicConductivity")->Evaluate(aniso_var[i], vTemp_i);

                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.");

            GetFunction("IntracellularAnisotropicConductivity")->Evaluate(aniso_var[j], vTemp_j);

            // 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.");
                GetFunction("IntracellularAnisotropicConductivity")->Evaluate(aniso_var[i], vTemp_i);

                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.
    for (auto &x : m_filters)
    {
        if (x.first == "CheckpointCellModel")
        {
            std::shared_ptr<FilterCheckpointCellModel> c
                = std::dynamic_pointer_cast<FilterCheckpointCellModel>(
                x.second);
            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);
}

v_SetInitialConditions()

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 452 of file BidomainRoth.cpp.

References m_cell, and Nektar::SolverUtils::EquationSystem::v_SetInitialConditions().

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

Friends And Related Function Documentation

MemoryManager< BidomainRoth >

friend class MemoryManager< BidomainRoth >

friend

Definition at line 50 of file BidomainRoth.h.

Member Data Documentation

className

string Nektar::BidomainRoth::className

static

Initial value:

= SolverUtils::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.

m_capMembrane

NekDouble Nektar::BidomainRoth::m_capMembrane

private

Definition at line 109 of file BidomainRoth.h.

Referenced by DoImplicitSolve(), and v_InitObject().

m_cell

CellModelSharedPtr Nektar::BidomainRoth::m_cell

private

Cell model.

Definition at line 100 of file BidomainRoth.h.

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

m_chi

NekDouble Nektar::BidomainRoth::m_chi

private

Definition at line 108 of file BidomainRoth.h.

Referenced by DoImplicitSolve(), and v_InitObject().

m_stimDuration

NekDouble Nektar::BidomainRoth::m_stimDuration

private

Stimulus current.

Definition at line 112 of file BidomainRoth.h.

m_stimulus

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

private

Definition at line 102 of file BidomainRoth.h.

Referenced by DoOdeRhs(), and v_InitObject().

m_vardiffe

StdRegions::VarCoeffMap Nektar::BidomainRoth::m_vardiffe

private

Definition at line 105 of file BidomainRoth.h.

Referenced by DoImplicitSolve(), and v_InitObject().

m_vardiffi

StdRegions::VarCoeffMap Nektar::BidomainRoth::m_vardiffi

private

Definition at line 104 of file BidomainRoth.h.

Referenced by DoOdeRhs(), and v_InitObject().

m_vardiffie

StdRegions::VarCoeffMap Nektar::BidomainRoth::m_vardiffie

private

Definition at line 106 of file BidomainRoth.h.

Referenced by DoOdeRhs(), and v_InitObject().