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. 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 >
boost::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	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 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. More...

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. More...

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. More...

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. More...

SOLVER_UTILS_EXPORT void	InitialiseBaseFlow (Array< OneD, Array< OneD, NekDouble > > &base)
	Perform initialisation of the base flow. 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	WeakAdvectionGreensDivergenceForm (const Array< OneD, Array< OneD, NekDouble > > &F, Array< OneD, NekDouble > &outarray)
	Compute the inner product $(\nabla \phi \cdot F)$ . More...

SOLVER_UTILS_EXPORT void	WeakAdvectionDivergenceForm (const Array< OneD, Array< OneD, NekDouble > > &F, Array< OneD, NekDouble > &outarray)
	Compute the inner product $(\phi, \nabla \cdot F)$ . More...

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 $(\phi, V\cdot \nabla u)$ . More...

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. More...

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. More...

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. 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	ScanForHistoryPoints ()
	Builds map of which element holds each history point. More...

SOLVER_UTILS_EXPORT void	WriteHistoryData (std::ostream &out)
	Probe each history point and write to 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	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. More...

virtual SOLVER_UTILS_EXPORT bool	v_NegatedOp ()
	Virtual function to identify if operator is negated in DoSolve. More...

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

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

Protected Member Functions
	Monodomain (const LibUtilities::SessionReaderSharedPtr &pSession)
	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 and . 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)
	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 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. 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_SteadyStateCheck (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. More...

int	nocase_cmp (const string &s1, const string &s2)

SOLVER_UTILS_EXPORT void	SetBoundaryConditions (NekDouble time)
	Evaluates the boundary conditions at the given time. 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)

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. More...

std::vector< StimulusSharedPtr >	m_stimulus

StdRegions::VarCoeffMap	m_vardiff
	Variable diffusivity. More...

NekDouble	m_chi

NekDouble	m_capMembrane

NekDouble	m_stimDuration
	Stimulus current. More...

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). 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...

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...

std::vector< int >	m_intVariables

std::vector< FilterSharedPtr >	m_filters

Protected Attributes inherited from Nektar::SolverUtils::EquationSystem
LibUtilities::CommSharedPtr	m_comm
	Communicator. More...

LibUtilities::SessionReaderSharedPtr	m_session
	The session reader. More...

LibUtilities::FieldIOSharedPtr	m_fld
	Field input/output. More...

map< std::string, Array< OneD, Array< OneD, float > > >	m_interpWeights
	Map of the interpolation weights for a specific filename. More...

map< std::string, Array< OneD, Array< OneD, unsigned int > > >	m_interpInds
	Map of the interpolation indices for a specific filename. More...

Array< OneD, MultiRegions::ExpListSharedPtr >	m_fields
	Array holding all dependent variables. More...

Array< OneD, MultiRegions::ExpListSharedPtr >	m_base
	Base fields. More...

Array< OneD, MultiRegions::ExpListSharedPtr >	m_derivedfields
	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...

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_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, Array< OneD, Array< OneD, NekDouble > > >	m_gradtan
	1 x nvariable x nq More...

Array< OneD, Array< OneD, Array< OneD, NekDouble > > >	m_tanbasis
	2 x m_spacedim x nq 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...

int	m_NumMode
	Mode to use in case of single mode analysis. More...

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 315 of file Monodomain.cpp.

     {
 
     }

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

protected

Constructor.

Definition at line 71 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.

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

         {
             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 327 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 368 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

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

protectedvirtual

Prints a summary of the model parameters.

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 401 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 81 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;
                 }
             }
         }
         else
         {
             // Otherwise apply isotropic conductivity value (o_max) to
             // diagonal components of tensor
             NekDouble o_max = m_session->GetParameter("o_max");
             for (int i = 0; i < nVarDiffCmpts; ++i)
             {
                 Vmath::Smul(nq,o_max,
                                 m_vardiff[varCoeffEnum[i]], 1,
                                 m_vardiff[varCoeffEnum[i]], 1);
             }
         }
 
         // 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);
             }
             if (x->first == "CellHistoryPoints")
             {
                 boost::shared_ptr<FilterCellHistoryPoints> c
                     = boost::dynamic_pointer_cast<FilterCellHistoryPoints>(
                                                                 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 387 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