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. 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 NekDouble &pTime=0.0, 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 NekDouble &pTime=0.0, 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	SetSteps (const int steps)

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 std::string &s1, const std::string &s2)
	Perform a case-insensitive string comparison. More...

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)
	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)
	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)

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)
	Initialises EquationSystem class members. More...

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

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	EvaluateFunctionExp (std::string pFieldName, Array< OneD, NekDouble > &pArray, const std::string &pFunctionName, const NekDouble &pTime=0.0, const int domain=0)

SOLVER_UTILS_EXPORT void	EvaluateFunctionFld (std::string pFieldName, Array< OneD, NekDouble > &pArray, const std::string &pFunctionName, const NekDouble &pTime=0.0, const int domain=0)

SOLVER_UTILS_EXPORT void	EvaluateFunctionPts (std::string pFieldName, Array< OneD, NekDouble > &pArray, const std::string &pFunctionName, const NekDouble &pTime=0.0, const int domain=0)

SOLVER_UTILS_EXPORT void	LoadPts (std::string funcFilename, std::string filename, Nektar::LibUtilities::PtsFieldSharedPtr &outPts)

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_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_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...

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...

std::map< std::string, FieldUtils::Interpolator >	m_interpolators
	Map of interpolator objects. More...

std::map< std::string, std::pair< std::string, LibUtilities::PtsFieldSharedPtr > >	m_loadedPtsFields
	pts fields we already read from disk: {funcFilename: (filename, ptsfield)} More...

std::map< std::string, std::pair< std::string, loadedFldField > >	m_loadedFldFields

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...

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, 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...

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 327 of file BidomainRoth.cpp.

 {
 
 }

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

protected

Constructor.

Definition at line 59 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.

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

     {
         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 339 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 378 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

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

protectedvirtual

Prints a summary of the model parameters.

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 473 of file BidomainRoth.cpp.

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

 {
     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 69 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 459 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

friend class MemoryManager< BidomainRoth >

friend

Definition at line 51 of file BidomainRoth.h.

Member Data Documentation

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.

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().