A model for cardiac conduction. More...

#include <MMFDiffusion.h>

Inheritance diagram for Nektar::MMFDiffusion:

Public Member Functions
virtual	~MMFDiffusion ()
	Desctructor. More...

Public Member Functions inherited from Nektar::SolverUtils::MMFSystem
SOLVER_UTILS_EXPORT	MMFSystem (const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &pGraph)

virtual SOLVER_UTILS_EXPORT	~MMFSystem ()

SOLVER_UTILS_EXPORT void	MMFInitObject (const Array< OneD, const Array< OneD, NekDouble >> &Anisotropy, const int TangentXelem=-1)

SOLVER_UTILS_EXPORT void	CopyBoundaryTrace (const Array< OneD, const NekDouble > &Fwd, Array< OneD, NekDouble > &Bwd, const BoundaryCopyType BDCopyType, const int var=0, const std::string btype="NoUserDefined")

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...

Public Attributes
TestType	m_TestType

Public Attributes inherited from Nektar::SolverUtils::MMFSystem
NekDouble	m_pi

int	m_shapedim

SurfaceType	m_surfaceType

UpwindType	m_upwindType

TestMaxwellType	m_TestMaxwellType

PolType	m_PolType

IncType	m_IncType

Array< OneD, NekDouble >	m_MMFfactors

Public Attributes inherited from Nektar::SolverUtils::UnsteadySystem
NekDouble	m_cflSafetyFactor
	CFL safety factor (comprise between 0 to 1). More...

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

Protected Member Functions
	MMFDiffusion (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...

void	TestPlaneProblem (const NekDouble time, Array< OneD, NekDouble > &outfield)

void	TestCubeProblem (const NekDouble time, Array< OneD, NekDouble > &outfield)

void	Morphogenesis (const NekDouble time, unsigned int field, Array< OneD, NekDouble > &outfield)

Array< OneD, NekDouble >	PlanePhiWave ()

virtual void	v_SetInitialConditions (NekDouble initialtime, bool dumpInitialConditions, const int domain)
	Sets a custom initial condition. More...

virtual void	v_GenerateSummary (SolverUtils::SummaryList &s)
	Prints a summary of the model parameters. More...

virtual void	v_EvaluateExactSolution (unsigned int field, Array< OneD, NekDouble > &outfield, const NekDouble time)

Protected Member Functions inherited from Nektar::SolverUtils::MMFSystem
void	SetUpMovingFrames (const Array< OneD, const Array< OneD, NekDouble >> &Anisotropy, const int TangentXelem)

void	CheckMovingFrames (const Array< OneD, const Array< OneD, NekDouble >> &movingframes)

SOLVER_UTILS_EXPORT void	ComputencdotMF ()

SOLVER_UTILS_EXPORT void	ComputeDivCurlMF ()

SOLVER_UTILS_EXPORT void	ComputeMFtrace ()

SOLVER_UTILS_EXPORT void	VectorDotProd (const Array< OneD, const Array< OneD, NekDouble >> &v1, const Array< OneD, const Array< OneD, NekDouble >> &v2, Array< OneD, NekDouble > &v3)

SOLVER_UTILS_EXPORT void	VectorCrossProd (const Array< OneD, const Array< OneD, NekDouble >> &v1, const Array< OneD, const Array< OneD, NekDouble >> &v2, Array< OneD, Array< OneD, NekDouble >> &v3)

SOLVER_UTILS_EXPORT void	VectorCrossProd (const Array< OneD, NekDouble > &v1, const Array< OneD, NekDouble > &v2, Array< OneD, NekDouble > &v3)

SOLVER_UTILS_EXPORT void	ComputeCurl (const Array< OneD, const Array< OneD, NekDouble >> &inarray, Array< OneD, Array< OneD, NekDouble >> &outarray)

SOLVER_UTILS_EXPORT Array< OneD, NekDouble >	CartesianToMovingframes (const Array< OneD, const Array< OneD, NekDouble >> &uvec, unsigned int field)

SOLVER_UTILS_EXPORT void	DeriveCrossProductMF (Array< OneD, Array< OneD, NekDouble >> &CrossProductMF)

SOLVER_UTILS_EXPORT void	ComputeNtimesMF ()

SOLVER_UTILS_EXPORT void	ComputeNtimesFz (const int dir, const Array< OneD, Array< OneD, NekDouble >> &Fwd, const Array< OneD, Array< OneD, NekDouble >> &Bwd, const Array< OneD, const NekDouble > &imFwd, const Array< OneD, const NekDouble > &imBwd, Array< OneD, NekDouble > &outarrayFwd, Array< OneD, NekDouble > &outarrayBwd)

SOLVER_UTILS_EXPORT void	ComputeNtimesF12 (const Array< OneD, Array< OneD, NekDouble >> &Fwd, const Array< OneD, Array< OneD, NekDouble >> &Bwd, const Array< OneD, const NekDouble > &im1Fwd, const Array< OneD, const NekDouble > &im1Bwd, const Array< OneD, const NekDouble > &im2Fwd, const Array< OneD, const NekDouble > &im2Bwd, Array< OneD, NekDouble > &outarrayFwd, Array< OneD, NekDouble > &outarrayBwd)

SOLVER_UTILS_EXPORT void	ComputeNtimestimesdFz (const int dir, const Array< OneD, Array< OneD, NekDouble >> &Fwd, const Array< OneD, Array< OneD, NekDouble >> &Bwd, const Array< OneD, const NekDouble > &imFwd, const Array< OneD, const NekDouble > &imBwd, Array< OneD, NekDouble > &outarrayFwd, Array< OneD, NekDouble > &outarrayBwd)

SOLVER_UTILS_EXPORT void	ComputeNtimestimesdF12 (const Array< OneD, Array< OneD, NekDouble >> &Fwd, const Array< OneD, Array< OneD, NekDouble >> &Bwd, const Array< OneD, const NekDouble > &im1Fwd, const Array< OneD, const NekDouble > &im1Bwd, const Array< OneD, const NekDouble > &im2Fwd, const Array< OneD, const NekDouble > &im2Bwd, Array< OneD, NekDouble > &outarrayFwd, Array< OneD, NekDouble > &outarrayBwd)

SOLVER_UTILS_EXPORT void	CartesianToSpherical (const NekDouble x0j, const NekDouble x1j, const NekDouble x2j, NekDouble &sin_varphi, NekDouble &cos_varphi, NekDouble &sin_theta, NekDouble &cos_theta)

SOLVER_UTILS_EXPORT void	ComputeZimYim (Array< OneD, Array< OneD, NekDouble >> &epsvec, Array< OneD, Array< OneD, NekDouble >> &muvec)

SOLVER_UTILS_EXPORT void	AdddedtMaxwell (const Array< OneD, const Array< OneD, NekDouble >> &physarray, Array< OneD, Array< OneD, NekDouble >> &outarray)

SOLVER_UTILS_EXPORT void	GetMaxwellFluxVector (const int var, const Array< OneD, const Array< OneD, NekDouble >> &physfield, Array< OneD, Array< OneD, NekDouble >> &flux)

SOLVER_UTILS_EXPORT void	GetMaxwellFlux1D (const int var, const Array< OneD, const Array< OneD, NekDouble >> &physfield, Array< OneD, Array< OneD, NekDouble >> &flux)

SOLVER_UTILS_EXPORT void	GetMaxwellFlux2D (const int var, const Array< OneD, const Array< OneD, NekDouble >> &physfield, Array< OneD, Array< OneD, NekDouble >> &flux)

SOLVER_UTILS_EXPORT void	LaxFriedrichMaxwellFlux1D (Array< OneD, Array< OneD, NekDouble >> &physfield, Array< OneD, Array< OneD, NekDouble >> &numfluxFwd, Array< OneD, Array< OneD, NekDouble >> &numfluxBwd)

SOLVER_UTILS_EXPORT void	UpwindMaxwellFlux1D (Array< OneD, Array< OneD, NekDouble >> &physfield, Array< OneD, Array< OneD, NekDouble >> &numfluxFwd, Array< OneD, Array< OneD, NekDouble >> &numfluxBwd)

SOLVER_UTILS_EXPORT void	AverageMaxwellFlux1D (Array< OneD, Array< OneD, NekDouble >> &physfield, Array< OneD, Array< OneD, NekDouble >> &numfluxFwd, Array< OneD, Array< OneD, NekDouble >> &numfluxBwd)

SOLVER_UTILS_EXPORT void	NumericalMaxwellFlux (Array< OneD, Array< OneD, NekDouble >> &physfield, Array< OneD, Array< OneD, NekDouble >> &numfluxFwd, Array< OneD, Array< OneD, NekDouble >> &numfluxBwd, const NekDouble time=0.0)

SOLVER_UTILS_EXPORT void	NumericalMaxwellFluxTM (Array< OneD, Array< OneD, NekDouble >> &physfield, Array< OneD, Array< OneD, NekDouble >> &numfluxFwd, Array< OneD, Array< OneD, NekDouble >> &numfluxBwd, const NekDouble time)

SOLVER_UTILS_EXPORT void	NumericalMaxwellFluxTE (Array< OneD, Array< OneD, NekDouble >> &physfield, Array< OneD, Array< OneD, NekDouble >> &numfluxFwd, Array< OneD, Array< OneD, NekDouble >> &numfluxBwd, const NekDouble time)

SOLVER_UTILS_EXPORT Array< OneD, NekDouble >	GetIncidentField (const int var, const NekDouble time)

SOLVER_UTILS_EXPORT void	Computedemdxicdote ()

SOLVER_UTILS_EXPORT NekDouble	AvgInt (const Array< OneD, const NekDouble > &inarray)

SOLVER_UTILS_EXPORT NekDouble	AvgAbsInt (const Array< OneD, const NekDouble > &inarray)

SOLVER_UTILS_EXPORT NekDouble	AbsIntegral (const Array< OneD, const NekDouble > &inarray)

SOLVER_UTILS_EXPORT NekDouble	RootMeanSquare (const Array< OneD, const NekDouble > &inarray)

SOLVER_UTILS_EXPORT NekDouble	VectorAvgMagnitude (const Array< OneD, const Array< OneD, NekDouble >> &inarray)

SOLVER_UTILS_EXPORT void	GramSchumitz (const Array< OneD, const Array< OneD, NekDouble >> &v1, const Array< OneD, const Array< OneD, NekDouble >> &v2, Array< OneD, Array< OneD, NekDouble >> &outarray, bool KeepTheMagnitude=true)

SOLVER_UTILS_EXPORT void	BubbleSort (Array< OneD, NekDouble > &refarray, Array< OneD, NekDouble > &sortarray)

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_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)

Protected Attributes
InitWaveType	m_InitWaveType

NekDouble	m_InitPtx

NekDouble	m_InitPty

NekDouble	m_InitPtz

Protected Attributes inherited from Nektar::SolverUtils::MMFSystem
NekDouble	m_alpha

NekDouble	m_Incfreq

int	m_SmoothFactor

NekDouble	m_SFinit

Array< OneD, Array< OneD, NekDouble > >	m_movingframes

Array< OneD, Array< OneD, NekDouble > >	m_surfaceNormal

Array< OneD, Array< OneD, NekDouble > >	m_ncdotMFFwd

Array< OneD, Array< OneD, NekDouble > >	m_ncdotMFBwd

Array< OneD, Array< OneD, NekDouble > >	m_nperpcdotMFFwd

Array< OneD, Array< OneD, NekDouble > >	m_nperpcdotMFBwd

Array< OneD, Array< OneD, NekDouble > >	m_DivMF

Array< OneD, Array< OneD, Array< OneD, NekDouble > > >	m_CurlMF

Array< OneD, Array< OneD, Array< OneD, NekDouble > > >	m_MFtraceFwd

Array< OneD, Array< OneD, Array< OneD, NekDouble > > >	m_MFtraceBwd

Array< OneD, Array< OneD, Array< OneD, NekDouble > > >	m_ntimesMFFwd

Array< OneD, Array< OneD, Array< OneD, NekDouble > > >	m_ntimesMFBwd

Array< OneD, Array< OneD, Array< OneD, NekDouble > > >	m_ntimes_ntimesMFFwd

Array< OneD, Array< OneD, Array< OneD, NekDouble > > >	m_ntimes_ntimesMFBwd

Array< OneD, Array< OneD, NekDouble > >	m_ZimFwd

Array< OneD, Array< OneD, NekDouble > >	m_ZimBwd

Array< OneD, Array< OneD, NekDouble > >	m_YimFwd

Array< OneD, Array< OneD, NekDouble > >	m_YimBwd

Array< OneD, Array< OneD, NekDouble > >	m_epsvec

Array< OneD, Array< OneD, NekDouble > >	m_muvec

Array< OneD, Array< OneD, NekDouble > >	m_negepsvecminus1

Array< OneD, Array< OneD, NekDouble > >	m_negmuvecminus1

Array< OneD, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > >	m_dedxi_cdot_e

SpatialDomains::GeomMMF	m_MMFdir

Array< OneD, NekDouble >	m_MFlength

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...

Private Attributes
StdRegions::VarCoeffMap	m_varcoeff
	Variable diffusivity. More...

Array< OneD, NekDouble >	m_epsilon

Array< OneD, NekDouble >	m_epsu

Friends
class	MemoryManager< MMFDiffusion >

Additional Inherited Members
Protected Types inherited from Nektar::SolverUtils::EquationSystem
enum	HomogeneousType { eHomogeneous1D, eHomogeneous2D, eHomogeneous3D, eNotHomogeneous }
	Parameter for homogeneous expansions. More...

Static Protected Attributes inherited from Nektar::SolverUtils::EquationSystem
static std::string	equationSystemTypeLookupIds []

Detailed Description

A model for cardiac conduction.

Definition at line 91 of file MMFDiffusion.h.

Constructor & Destructor Documentation

◆ ~MMFDiffusion()

Nektar::MMFDiffusion::~MMFDiffusion ( )

virtual

Desctructor.

Definition at line 195 of file MMFDiffusion.cpp.

196 {

197 }

◆ MMFDiffusion()

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

protected

Constructor.

Definition at line 58 of file MMFDiffusion.cpp.

       : UnsteadySystem(pSession, pGraph),
     MMFSystem(pSession, pGraph)
     {
     }

Member Function Documentation

◆ create()

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

inlinestatic

Creates an instance of this class.

Definition at line 97 of file MMFDiffusion.h.

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

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

◆ DoImplicitSolve()

void Nektar::MMFDiffusion::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.

OdeRhs

Parameters

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

Definition at line 206 of file MMFDiffusion.cpp.

References Nektar::StdRegions::eFactorLambda, Nektar::StdRegions::eFactorTau, m_epsu, Nektar::SolverUtils::EquationSystem::m_fields, m_varcoeff, Nektar::NullFlagList, Nektar::SolverUtils::EquationSystem::SetBoundaryConditions(), and Vmath::Smul().

Referenced by v_InitObject().

     {
         int nvariables  = inarray.num_elements();
         int nq          = m_fields[0]->GetNpoints();
 
 
         StdRegions::ConstFactorMap factors;
     factors[StdRegions::eFactorTau]    = 1.0;
 
         Array<OneD, Array< OneD, NekDouble> > F(nvariables);
     factors[StdRegions::eFactorLambda] = 1.0/lambda;
         F[0] = Array<OneD, NekDouble> (nq*nvariables);
 
         for (int n = 1; n < nvariables; ++n)
         {
             F[n] = F[n-1] + nq;
             //cout << "F["<< n<<"=" << F[n][1] <<endl;
         }
 
         // 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
     SetBoundaryConditions(time);
 
         for (int i = 0; i < nvariables; ++i)
         {
       factors[StdRegions::eFactorLambda] = 1.0/lambda/m_epsu[i];
 
       // Multiply 1.0/timestep
       Vmath::Smul(nq, -factors[StdRegions::eFactorLambda],inarray[i], 1, F[i], 1);
 
            /* for (int k = 0; k < 15; ++k)
                 cout << "inarray["<<i << "]"<< k<<"=" << inarray[i][k]<<endl;*/
       // Solve a system of equations with Helmholtz solver and transform
       // back into physical space.
       m_fields[i]->HelmSolve(F[i], m_fields[i]->UpdateCoeffs(),NullFlagList, factors, m_varcoeff);
 
       m_fields[i]->BwdTrans(m_fields[i]->GetCoeffs(), outarray[i]);
            /* Array<OneD, NekDouble> coefarray = m_fields[i]->GetCoeffs();
             for (int k = 0; k < 15; ++k)
                 cout << "inarray["<< k<<"=" << coefarray[k]<<endl;*/
         }
        /* for (int kk = 0; kk < 15; ++kk)
             cout << "inarray["<< kk<<"=" << m_varcoeff[StdRegions::eVarCoeffMF3Mag][kk]<<endl;*/
 
 
     }

◆ DoOdeRhs()

void Nektar::MMFDiffusion::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 263 of file MMFDiffusion.cpp.

References Nektar::eFHNAlievPanf, Nektar::eFHNRogers, Nektar::eFHNStandard, Nektar::eTestCube, Nektar::eTestLinearSphere, Nektar::eTestNonlinearSphere, Nektar::eTestPlane, Nektar::SolverUtils::EquationSystem::GetTotPoints(), m_epsilon, Nektar::SolverUtils::EquationSystem::m_fields, Nektar::SolverUtils::MMFSystem::m_pi, m_TestType, Vmath::Neg(), Vmath::Sadd(), Vmath::Smul(), Vmath::Svtvm(), Vmath::Svtvp(), Vmath::Vadd(), Vmath::Vdiv(), and Vmath::Vmul().

Referenced by v_InitObject().

     {
         int nq = GetTotPoints();
 
         switch(m_TestType)
         {
     case eTestPlane:
       {
 
         Array<OneD, NekDouble> x(nq);
         Array<OneD, NekDouble> y(nq);
         Array<OneD, NekDouble> z(nq);
 
         m_fields[0]->GetCoords(x,y,z);
 
         for(int k=0; k<nq; k++)
           {
         outarray[0][k] = (m_epsilon[0]+m_epsilon[1]-1.0)*m_pi*m_pi*exp(-1.0*m_pi*m_pi*time)*sin(m_pi*x[k])*cos(m_pi*y[k]);
           }
       }
       break;
 
     case eTestCube:
       {
 
         Array<OneD, NekDouble> x(nq);
         Array<OneD, NekDouble> y(nq);
         Array<OneD, NekDouble> z(nq);
 
         m_fields[0]->GetCoords(x,y,z);
 
         for(int k=0; k<nq; k++)
           {
         outarray[0][k] = (m_epsilon[0]+m_epsilon[1]+m_epsilon[2]-1.0)*m_pi*m_pi*exp(-1.0*m_pi*m_pi*time)*sin(m_pi*x[k])*sin(m_pi*y[k])*sin(m_pi*z[k]);
 
           }
 
       }
       break;
 
         case eTestLinearSphere:
         {
       Array<OneD, NekDouble> temp(nq);
 
       NekDouble A = 2.0;
       NekDouble B = 5.0;
 
       NekDouble m_a, m_b, m_c, m_d;
       m_a = B-1.0;
       m_b = A*A;
       m_c = -1.0*B;
       m_d = -1.0*A*A;
 
       temp = Array<OneD, NekDouble>(nq,0.0);
       Vmath::Svtvp(nq,m_a,&inarray[0][0],1,&temp[0],1,&temp[0],1);
       Vmath::Svtvp(nq,m_b,&inarray[1][0],1,&temp[0],1,&outarray[0][0],1);
 
       temp = Array<OneD, NekDouble>(nq,0.0);
       Vmath::Svtvp(nq,m_c,&inarray[0][0],1,&temp[0],1,&temp[0],1);
       Vmath::Svtvp(nq,m_d,&inarray[1][0],1,&temp[0],1,&outarray[1][0],1);
     }
         break;
 
     case eTestNonlinearSphere:
       {
         NekDouble A = 2.0;
         NekDouble B = 5.0;
 
         Array<OneD, NekDouble> Aonevec(nq,A);
 
         // cube = phys0*phys0*phy1
         Array<OneD, NekDouble> cube(nq);
         Vmath::Vmul(nq,&inarray[0][0],1,&inarray[0][0],1,&cube[0],1);
         Vmath::Vmul(nq,&inarray[1][0],1,&cube[0],1,&cube[0],1);
 
         // outarray[0] = A - B*phy0 + phy0*phy0*phy1 - phy0
         NekDouble coeff = -1.0*B - 1.0;
         Array<OneD, NekDouble> tmp(nq);
         Vmath::Svtvp(nq,coeff,&inarray[0][0],1,&cube[0],1,&tmp[0],1);
         Vmath::Vadd(nq,&Aonevec[0],1,&tmp[0],1,&outarray[0][0],1);
 
         // outarray[1] = B*phys0 - phy0*phy0*phy1
         Vmath::Svtvm(nq,B,&inarray[0][0],1,&cube[0],1,&outarray[1][0],1);
 
       }
       break;
 
     case eFHNStandard:
     {
       // \phi - \phi^3/3 - \psi
       NekDouble a = 0.12;
       NekDouble b = 0.011;
       NekDouble c1 = 0.175;
       NekDouble c2 = 0.03;
       NekDouble d = 0.55;
 
       Array<OneD, NekDouble> tmp(nq);
 
       // Reaction for \phi = c1 \phi ( \phi - a)*(1 - \phi) - c2 v
       Vmath::Smul(nq, -1.0*c1, inarray[0], 1, outarray[0], 1);
       Vmath::Sadd(nq, -1.0*a, inarray[0], 1, tmp, 1);
       Vmath::Vmul(nq, tmp, 1, inarray[0], 1, outarray[0], 1);
       Vmath::Sadd(nq, -1.0, inarray[0], 1, tmp, 1);
       Vmath::Vmul(nq, tmp, 1, outarray[0], 1, outarray[0], 1);
 
       Vmath::Smul(nq, -1.0*c2, inarray[1], 1, tmp, 1);
       Vmath::Vadd(nq, tmp, 1, outarray[0], 1, outarray[0], 1);
 
 
       // Reaction for \psi = b (\phi - d \psi )
       Vmath::Svtvp(nq, -1.0*d, inarray[1], 1, inarray[0], 1, outarray[1], 1);
       Vmath::Smul(nq, b, outarray[1], 1, outarray[1], 1);
     }
     break;
 
       case eFHNRogers:
     {
       NekDouble a = 0.13;
       NekDouble b = 0.013;
       NekDouble c1 = 0.26;
       NekDouble c2 = 0.1;
       NekDouble d = 1.0;
 
       Array<OneD, NekDouble> tmp(nq);
 
       // Reaction for \phi = c1 \phi ( \phi - a)*(1 - \phi) - c2 u v
       Vmath::Smul(nq, -1.0*c1, inarray[0], 1, outarray[0], 1);
       Vmath::Sadd(nq, -1.0*a, inarray[0], 1, tmp, 1);
       Vmath::Vmul(nq, tmp, 1, outarray[0], 1, outarray[0], 1);
       Vmath::Sadd(nq, -1.0, inarray[0], 1, tmp, 1);
       Vmath::Vmul(nq, tmp, 1, outarray[0], 1, outarray[0], 1);
 
       Vmath::Vmul(nq, inarray[0], 1, inarray[1], 1, tmp, 1);
       Vmath::Smul(nq, -1.0*c2, tmp, 1, tmp, 1);
       Vmath::Vadd(nq, tmp, 1, outarray[0], 1, outarray[0], 1);
 
       // Reaction for \psi = b (\phi - d \psi )
       Vmath::Svtvp(nq, -1.0*d, inarray[1], 1, inarray[0], 1, outarray[1], 1);
       Vmath::Smul(nq, b, outarray[1], 1, outarray[1], 1);
     }
     break;
 
       case eFHNAlievPanf:
     {
 
       NekDouble a = 0.15;
       NekDouble c1 = 8.0;
       NekDouble c2 = 1.0;
       NekDouble c0 = 0.002;
       NekDouble mu1 = 0.2;
       NekDouble mu2 = 0.3;
 
       Array<OneD, NekDouble> tmp(nq);
 
       // Reaction for \phi = c1 \phi ( \phi - a)*(1 - \phi) - c2 u v
       Vmath::Smul(nq, -1.0*c1, inarray[0], 1, outarray[0], 1);
       Vmath::Sadd(nq, -1.0*a, inarray[0], 1, tmp, 1);
       Vmath::Vmul(nq, tmp, 1, outarray[0], 1, outarray[0], 1);
       Vmath::Sadd(nq, -1.0, inarray[0], 1, tmp, 1);
       Vmath::Vmul(nq, tmp, 1, outarray[0], 1, outarray[0], 1);
 
       Vmath::Vmul(nq, inarray[0], 1, inarray[1], 1, tmp, 1);
       Vmath::Smul(nq, -1.0*c2, tmp, 1, tmp, 1);
       Vmath::Vadd(nq, tmp, 1, outarray[0], 1, outarray[0], 1);
 
       // Reaction for \psi = (c0 + (\mu1 \psi/(\mu2+\phi) ) )*(-\psi - c1 * \phi*(\phi - a - 1) )
 
       Vmath::Smul(nq, mu1, inarray[1], 1, outarray[1], 1);
       Vmath::Sadd(nq, mu2, inarray[0], 1, tmp, 1);
       Vmath::Vdiv(nq, outarray[1], 1, tmp, 1, outarray[1], 1);
       Vmath::Sadd(nq, c0, outarray[1], 1, outarray[1], 1);
 
       Vmath::Sadd(nq, (-a-1.0), inarray[0], 1, tmp, 1);
       Vmath::Vmul(nq, inarray[0], 1, tmp, 1, tmp, 1);
       Vmath::Smul(nq, c1, tmp, 1, tmp, 1);
       Vmath::Vadd(nq, inarray[1], 1, tmp, 1, tmp, 1);
       Vmath::Neg(nq, tmp, 1);
 
       Vmath::Vmul(nq, tmp, 1, outarray[1], 1, outarray[1], 1);
     }
     break;
 
     default:
       break;
     }
     }

◆ Morphogenesis()

void Nektar::MMFDiffusion::Morphogenesis	(	const NekDouble	time,
		unsigned int	field,
		Array< OneD, NekDouble > &	outfield
	)

protected

Definition at line 580 of file MMFDiffusion.cpp.

References Nektar::SolverUtils::EquationSystem::GetTotPoints(), Nektar::SolverUtils::EquationSystem::m_fields, m_mu, and Nektar::SolverUtils::MMFSystem::m_pi.

Referenced by v_EvaluateExactSolution(), and v_SetInitialConditions().

   {
         int nq  = GetTotPoints();
 
         int i, m, n, ind;
         NekDouble a_n, d_n, gamma_n;
         NekDouble A_mn, C_mn, theta, phi,radius;
 
         std::complex<double> Spericharmonic, delta_n, temp;
     std::complex<double> varphi0, varphi1;
         std::complex<double> B_mn, D_mn;
 
         // Set some parameter values
         int Maxn = 6;
         int Maxm = 2*Maxn-1;
 
         NekDouble A = 2.0;
         NekDouble B = 5.0;
 
         NekDouble m_mu = 0.001;
         NekDouble m_nu = 0.002;
 
         NekDouble m_a, m_b, m_c, m_d;
 
         m_a = B-1.0;
         m_b = A*A;
         m_c = -1.0*B;
         m_d = -1.0*A*A;
 
         Array<OneD, Array<OneD, NekDouble> > Ainit(Maxn);
         Array<OneD, Array<OneD, NekDouble> > Binit(Maxn);
 
         for (i = 0; i < Maxn; ++i)
         {
             Ainit[i] = Array<OneD, NekDouble>(Maxm, 0.0);
             Binit[i] = Array<OneD, NekDouble>(Maxm, 0.0);
         }
 
         Ainit[5][0] = -0.5839;
         Ainit[5][1] = -0.8436;
         Ainit[5][2] = -0.4764;
         Ainit[5][3] = 0.6475;
         Ainit[5][4] = 0.1886;
         Ainit[5][5] = 0.8709;
         Ainit[5][6] = -0.8338;
         Ainit[5][7] = 0.1795;
         Ainit[5][8] = -0.7873;
         Ainit[5][9] = 0.8842;
         Ainit[5][10] = 0.2943;
 
         Binit[5][0] = -0.6263;
         Binit[5][1] = 0.9803;
         Binit[5][2] = 0.7222;
         Binit[5][3] = 0.5945;
         Binit[5][4] = 0.6026;
         Binit[5][5] = -0.2076;
         Binit[5][6] = 0.4556;
         Binit[5][7] = 0.6024;
         Binit[5][8] = 0.9695;
         Binit[5][9] = -0.4936;
         Binit[5][10] = 0.1098;
 
         Array<OneD, NekDouble> u(nq);
         Array<OneD, NekDouble> v(nq);
         Array<OneD, NekDouble> x(nq);
         Array<OneD, NekDouble> y(nq);
         Array<OneD, NekDouble> z(nq);
 
         m_fields[0]->GetCoords(x,y,z);
         for (int i = 0; i < nq; ++i)
         {
       radius = sqrt(x[i]*x[i] + y[i]*y[i] + z[i]*z[i]) ;
 
       // theta is in [0, pi]
       theta = asin( z[i]/radius ) + 0.5*m_pi;
 
       // phi is in [0, 2*pi]
       phi = atan2( y[i], x[i] ) + m_pi;
 
       varphi0 = 0.0*varphi0;
       varphi1 = 0.0*varphi1;
       for (n = 0; n < Maxn; ++n)
         {
           // Set up parameters
           a_n = m_a - m_mu*( n*(n+1)/radius/radius );
           d_n = m_d - m_nu*( n*(n+1)/radius/radius );
 
           gamma_n = 0.5*( a_n + d_n );
 
           temp = ( a_n + d_n )*( a_n + d_n ) - 4.0*( a_n*d_n - m_b*m_c );
           delta_n = 0.5*sqrt( temp );
 
           for (m = -n; m <=n; ++m)
         {
           ind = m + n;
           A_mn = Ainit[n][ind];
           C_mn = Binit[n][ind];
 
           B_mn = ( (a_n - gamma_n)*Ainit[n][ind] + m_b*Binit[n][ind])/delta_n;
           D_mn = ( m_c*Ainit[n][ind] + (d_n - gamma_n)*Binit[n][ind])/delta_n;
 
           Spericharmonic = boost::math::spherical_harmonic(n, m, theta, phi);
           varphi0 += exp(gamma_n*time)*(A_mn*cosh(delta_n*time) + B_mn*sinh(delta_n*time))*Spericharmonic;
           varphi1 += exp(gamma_n*time)*(C_mn*cosh(delta_n*time) + D_mn*sinh(delta_n*time))*Spericharmonic;
                }
         }
 
       u[i] = varphi0.real();
       v[i] = varphi1.real();
     }
 
         switch (field)
       {
         case 0:
       {
             outfield = u;
       }
       break;
 
         case 1:
       {
             outfield = v;
       }
       break;
         }
     }

◆ PlanePhiWave()

Array< OneD, NekDouble > Nektar::MMFDiffusion::PlanePhiWave ( )

protected

Definition at line 710 of file MMFDiffusion.cpp.

References Nektar::eBothEnds, Nektar::eCenter, Nektar::eLeft, Nektar::eLeftBottomCorner, Nektar::ePoint, Nektar::eSpiralDock, Nektar::SolverUtils::EquationSystem::GetTotPoints(), Nektar::SolverUtils::EquationSystem::m_fields, m_InitPtx, m_InitPty, m_InitPtz, m_InitWaveType, Nektar::LibUtilities::rad(), Vmath::Vmax(), and Vmath::Vmin().

Referenced by v_SetInitialConditions().

   {
     int nq  = GetTotPoints();
     Array<OneD, NekDouble> outarray(nq,0.0);
 
     Array<OneD, NekDouble> x(nq);
     Array<OneD, NekDouble> y(nq);
     Array<OneD, NekDouble> z(nq);
 
     m_fields[0]->GetCoords(x,y,z);
 
     NekDouble xmin, ymin, xmax;
 
     xmin = Vmath::Vmin(nq, x, 1);
     xmax = Vmath::Vmax(nq, x, 1);
     ymin = Vmath::Vmin(nq, y, 1);
 
     NekDouble xp, yp, xp2;
     for (int i=0; i<nq; i++)
       {
     switch(m_InitWaveType)
       {
       case eLeft:
         {
           NekDouble radiusofinit = 4.0;
           NekDouble frontstiff = 0.1;
 
           xp = x[i] - xmin;
           outarray[i] = 1.0/( 1.0 + exp( ( xp - radiusofinit)/frontstiff ) );
         }
         break;
 
       case eBothEnds:
         {
           NekDouble radiusofinit = 3.0;
           NekDouble frontstiff = 0.1;
 
           xp = x[i] - xmin;
           xp2 = x[i] - xmax;
 
           outarray[i] = 1.0/( 1.0 + exp( ( sqrt(xp*xp) - radiusofinit)/frontstiff ) ) + 1.0/( 1.0 + exp( ( sqrt(xp2*xp2) - radiusofinit)/frontstiff ) );
         }
         break;
 
       case eCenter:
         {
           NekDouble radiusofinit = 6.0;
           NekDouble frontstiff = 0.1;
 
           // NekDouble xc = 0.5*(Vmath::Vmax(nq, x, 1) + Vmath::Vmin(nq, x, 1));
 
           xp = x[i] - xmin;
           outarray[i] =1.0/( 1.0 + exp( ( xp - radiusofinit)/frontstiff ) );
         }
         break;
 
       case eLeftBottomCorner:
         {
           NekDouble radiusofinit = 6.0;
           NekDouble frontstiff = 0.1;
           NekDouble bs = 2.0;
 
           xp = x[i] - xmin;
           yp = y[i] - ymin;
           outarray[i] = 1.0/( 1.0 + exp( ( sqrt(xp*xp+yp*yp)/bs - radiusofinit)/frontstiff ) );
         }
         break;
 
       case ePoint:
         {
           NekDouble xloc, yloc, zloc, rad;
           NekDouble radiusofinit = 10.0;
 
           xloc = x[i]-m_InitPtx;
           yloc = y[i]-m_InitPty;
           zloc = z[i]-m_InitPtz;
 
           rad = sqrt(xloc*xloc + yloc*yloc + zloc*zloc);
 
           xloc = xloc/radiusofinit;
           yloc = yloc/radiusofinit;
           zloc = zloc/radiusofinit;
 
           if(rad<radiusofinit)
         {
           outarray[i] = exp( -(1.0/2.0)*( xloc*xloc + yloc*yloc + zloc*zloc) ) ;
         }
 
           else
         {
           outarray[i] = 0.0;
         }
         }
         break;
 
       case eSpiralDock:
         {
           NekDouble radiusofinit = 3.0;
           NekDouble frontstiff = 0.1;
           xp = x[i] - 4.0;
           yp = y[i];
           outarray[i] = (1.0/(1.0+exp(2.0*yp)))*(1.0/(1.0+exp(-2.0*xp)))*( 1.0/( 1.0 + exp( ( xp - radiusofinit)/frontstiff ) ) );
         }
         break;
 
       default:
         break;
       }
 
       }
 
     return outarray;
   }

◆ TestCubeProblem()

void Nektar::MMFDiffusion::TestCubeProblem	(	const NekDouble	time,
		Array< OneD, NekDouble > &	outfield
	)

protected

Definition at line 560 of file MMFDiffusion.cpp.

References Nektar::SolverUtils::EquationSystem::GetTotPoints(), Nektar::SolverUtils::EquationSystem::m_fields, and Nektar::SolverUtils::MMFSystem::m_pi.

Referenced by v_EvaluateExactSolution(), and v_SetInitialConditions().

   {
         int nq  = GetTotPoints();
 
         Array<OneD, NekDouble> x(nq);
         Array<OneD, NekDouble> y(nq);
         Array<OneD, NekDouble> z(nq);
 
         m_fields[0]->GetCoords(x,y,z);
 
         outfield = Array<OneD, NekDouble> (nq);
     for (int k=0; k<nq; k++)
       {
         outfield[k] = exp(-1.0*m_pi*m_pi*time)*sin(m_pi*x[k])*sin(m_pi*y[k])*sin(m_pi*z[k]);
       }
   }

◆ TestPlaneProblem()

void Nektar::MMFDiffusion::TestPlaneProblem	(	const NekDouble	time,
		Array< OneD, NekDouble > &	outfield
	)

protected

Definition at line 540 of file MMFDiffusion.cpp.

References Nektar::SolverUtils::EquationSystem::GetTotPoints(), Nektar::SolverUtils::EquationSystem::m_fields, and Nektar::SolverUtils::MMFSystem::m_pi.

Referenced by v_EvaluateExactSolution(), and v_SetInitialConditions().

   {
         int nq  = GetTotPoints();
 
         Array<OneD, NekDouble> x(nq);
         Array<OneD, NekDouble> y(nq);
         Array<OneD, NekDouble> z(nq);
 
         m_fields[0]->GetCoords(x,y,z);
 
         outfield = Array<OneD, NekDouble> (nq);
     for (int k=0; k<nq; k++)
       {
         outfield[k] = exp(-1.0*m_pi*m_pi*time)*sin(m_pi*x[k])*cos(m_pi*y[k]);
 
       }
   }

◆ v_EvaluateExactSolution()

void Nektar::MMFDiffusion::v_EvaluateExactSolution	(	unsigned int	field,
		Array< OneD, NekDouble > &	outfield,
		const NekDouble	time
	)

protectedvirtual

Reimplemented from Nektar::SolverUtils::EquationSystem.

Definition at line 824 of file MMFDiffusion.cpp.

References Nektar::eFHNAlievPanf, Nektar::eFHNRogers, Nektar::eFHNStandard, Nektar::eTestCube, Nektar::eTestLinearSphere, Nektar::eTestNonlinearSphere, Nektar::eTestPlane, Nektar::SolverUtils::EquationSystem::GetTotPoints(), m_TestType, Morphogenesis(), TestCubeProblem(), TestPlaneProblem(), and Nektar::SolverUtils::EquationSystem::v_EvaluateExactSolution().

   {
     switch(m_TestType)
       {
       case eTestPlane:
     {
       TestPlaneProblem(time,outfield);
     }
     break;
 
       case eTestCube:
     {
       TestCubeProblem(time,outfield);
     }
     break;
 
       case eTestLinearSphere:
       case eTestNonlinearSphere:
         {
       Morphogenesis(time, field, outfield);
         }
         break;
 
       case eFHNStandard:
       case eFHNRogers:
       case eFHNAlievPanf:
     {
       int nq  = GetTotPoints();
       outfield = Array<OneD, NekDouble>(nq, 0.0);
     }
         /* Falls through. */
       default:
         {
       EquationSystem::v_EvaluateExactSolution(field,outfield,time);
         }
         break;
       }
   }

◆ v_GenerateSummary()

void Nektar::MMFDiffusion::v_GenerateSummary ( SolverUtils::SummaryList & s )

protectedvirtual

Prints a summary of the model parameters.

Reimplemented from Nektar::SolverUtils::MMFSystem.

Definition at line 865 of file MMFDiffusion.cpp.

References Nektar::SolverUtils::AddSummaryItem(), Nektar::eTestLinearSphere, m_epsilon, m_epsu, m_TestType, Nektar::TestTypeMap, and Nektar::SolverUtils::MMFSystem::v_GenerateSummary().

     {
         MMFSystem::v_GenerateSummary(s);
     SolverUtils::AddSummaryItem(s, "TestType", TestTypeMap[m_TestType]);
     SolverUtils::AddSummaryItem(s, "epsilon0", m_epsilon[0]);
     SolverUtils::AddSummaryItem(s, "epsilon1", m_epsilon[1]);
     SolverUtils::AddSummaryItem(s, "epsilon2", m_epsilon[2]);
     if(m_TestType==eTestLinearSphere)
       {
         SolverUtils::AddSummaryItem(s, "epsilon for u", m_epsu[0]);
         SolverUtils::AddSummaryItem(s, "epsilon for v", m_epsu[1]);
       }
     }

◆ v_InitObject()

void Nektar::MMFDiffusion::v_InitObject ( )

protectedvirtual

Init object for UnsteadySystem class.

Initialization object for UnsteadySystem class.

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 66 of file MMFDiffusion.cpp.

     {
       UnsteadySystem::v_InitObject();
 
       int nq = m_fields[0]->GetNpoints();
       int nvar  =  m_fields.num_elements();
       int MFdim = 3;
 
       // Diffusivity coefficient for e^j
       m_epsilon = Array<OneD, NekDouble>(MFdim);
       m_session->LoadParameter("epsilon0", m_epsilon[0],  1.0);
       m_session->LoadParameter("epsilon1", m_epsilon[1],  1.0);
       m_session->LoadParameter("epsilon2", m_epsilon[2],  1.0);
 
       // Diffusivity coefficient for u^j
       m_epsu = Array<OneD, NekDouble>(nvar+1);
       m_session->LoadParameter("epsu0", m_epsu[0],  1.0);
       m_session->LoadParameter("epsu1", m_epsu[1],  1.0);
 
       m_session->LoadParameter("InitPtx", m_InitPtx, 0.0);
       m_session->LoadParameter("InitPty", m_InitPty, 0.0);
       m_session->LoadParameter("InitPtz", m_InitPtz, 0.0);
 
       int shapedim = m_fields[0]->GetShapeDimension();
       Array<OneD, Array<OneD, NekDouble> > Anisotropy(shapedim);
       for(int j=0; j<shapedim; ++j)
     {
       Anisotropy[j] = Array<OneD, NekDouble>(nq,1.0);
       Vmath::Fill(nq, sqrt(m_epsilon[j]), &Anisotropy[j][0], 1);
 
     }
 
       MMFSystem::MMFInitObject(Anisotropy);
 
       // Define ProblemType
       if(m_session->DefinesSolverInfo("TESTTYPE"))
         {
       std::string TestTypeStr = m_session->GetSolverInfo("TESTTYPE");
       int i;
       for(i = 0; i < (int) SIZE_TestType; ++i)
             {
           if(boost::iequals(TestTypeMap[i],TestTypeStr))
                 {
           m_TestType = (TestType)i;
           break;
                 }
             }
         }
       else
         {
       m_TestType = (TestType)0;
         }
 
         if(m_session->DefinesSolverInfo("INITWAVETYPE"))
       {
             std::string InitWaveTypeStr = m_session->GetSolverInfo("INITWAVETYPE");
             for(int i = 0; i < (int) SIZE_TestType; ++i)
             {
                 if(boost::iequals(InitWaveTypeMap[i],InitWaveTypeStr))
                 {
                     m_InitWaveType = (InitWaveType)i;
                     break;
                 }
             }
       }
         else
       {
             m_InitWaveType = (InitWaveType)0;
       }
 
 
       StdRegions::VarCoeffType MMFCoeffs[15] = {StdRegions::eVarCoeffMF1x,
                            StdRegions::eVarCoeffMF1y,
                            StdRegions::eVarCoeffMF1z,
                            StdRegions::eVarCoeffMF1Div,
                            StdRegions::eVarCoeffMF1Mag,
                            StdRegions::eVarCoeffMF2x,
                            StdRegions::eVarCoeffMF2y,
                            StdRegions::eVarCoeffMF2z,
                            StdRegions::eVarCoeffMF2Div,
                            StdRegions::eVarCoeffMF2Mag,
                            StdRegions::eVarCoeffMF3x,
                            StdRegions::eVarCoeffMF3y,
                            StdRegions::eVarCoeffMF3z,
                            StdRegions::eVarCoeffMF3Div,
                            StdRegions::eVarCoeffMF3Mag};
 
       int indx;
       Array<OneD, NekDouble> tmp(nq);
     for (int k=0; k<MFdim; ++k)
       {
         // For Moving Frames
         indx = 5*k;
 
         for (int j=0; j<m_spacedim; ++j)
           {
         m_varcoeff[MMFCoeffs[indx+j]] = Array<OneD, NekDouble>(nq, 0.0);
         Vmath::Vcopy(nq, &m_movingframes[k][j*nq], 1, &m_varcoeff[MMFCoeffs[indx+j]][0], 1);
           }
 
         // m_DivMF
         m_varcoeff[MMFCoeffs[indx+3]] = Array<OneD, NekDouble>(nq, 0.0);
         Vmath::Vcopy(nq, &m_DivMF[k][0], 1, &m_varcoeff[MMFCoeffs[indx+3]][0], 1);
 
         // \| e^k \|
         m_varcoeff[MMFCoeffs[indx+4]] = Array<OneD, NekDouble>(nq,0.0);
         tmp = Array<OneD, NekDouble>(nq,0.0);
         for (int i=0; i<m_spacedim; ++i)
           {
         Vmath::Vvtvp(nq, &m_movingframes[k][i*nq], 1, &m_movingframes[k][i*nq], 1, &tmp[0], 1, &tmp[0], 1);
           }
 
         Vmath::Vcopy(nq, &tmp[0], 1, &m_varcoeff[MMFCoeffs[indx+4]][0], 1);
 
 
       }
 
 
       if (!m_explicitDiffusion)
         {
       m_ode.DefineImplicitSolve (&MMFDiffusion::DoImplicitSolve, this);
         }
 
       m_ode.DefineOdeRhs(&MMFDiffusion::DoOdeRhs, this);
     }

◆ v_SetInitialConditions()

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

protectedvirtual

Sets a custom initial condition.

Reimplemented from Nektar::SolverUtils::EquationSystem.

Definition at line 457 of file MMFDiffusion.cpp.

References Nektar::eFHNAlievPanf, Nektar::eFHNRogers, Nektar::eFHNStandard, Nektar::eTestCube, Nektar::eTestLinearSphere, Nektar::eTestNonlinearSphere, Nektar::eTestPlane, Nektar::SolverUtils::EquationSystem::GetTotPoints(), Nektar::SolverUtils::EquationSystem::m_fields, Nektar::SolverUtils::EquationSystem::m_sessionName, m_TestType, Morphogenesis(), PlanePhiWave(), TestCubeProblem(), TestPlaneProblem(), Nektar::SolverUtils::EquationSystem::v_SetInitialConditions(), Nektar::SolverUtils::EquationSystem::WriteFld(), and Vmath::Zero().

     {
         boost::ignore_unused(domain);
 
       int nq  = GetTotPoints();
 
       switch(m_TestType)
         {
         case eTestPlane:
       {
         Array<OneD, NekDouble> u(nq);
 
         TestPlaneProblem(initialtime,u);
         m_fields[0]->SetPhys(u);
 
       }
       break;
 
         case eTestCube:
       {
         Array<OneD, NekDouble> u(nq);
 
         TestCubeProblem(initialtime,u);
         m_fields[0]->SetPhys(u);
           /*for (int k=0; k<nq; ++k)
           {
               //for (int j=0; j<m_spacedim; ++j)
               //{
               cout << "_varcoeff" << u[k] <<endl;
               // }
           }*/
 
       }
       break;
 
         case eTestLinearSphere:
     case eTestNonlinearSphere:
       {
         Array<OneD, NekDouble> u(nq);
         Array<OneD, NekDouble> v(nq);
 
         Morphogenesis(initialtime,0,u);
         Morphogenesis(initialtime,1,v);
 
         m_fields[0]->SetPhys(u);
         m_fields[1]->SetPhys(v);
       }
       break;
 
     case eFHNStandard:
     case eFHNRogers:
     case eFHNAlievPanf:
       {
         Array<OneD, NekDouble> Zero(nq,0.0);
         m_fields[0]->SetPhys(PlanePhiWave());
         m_fields[1]->SetPhys(Zero);
       }
       break;
 
         default:
         {
             EquationSystem::v_SetInitialConditions(initialtime,false);
         }
         break;
         }
 
       // forward transform to fill the modal coeffs
       for(int i = 0; i < m_fields.num_elements(); ++i)
     {
       m_fields[i]->SetPhysState(true);
       m_fields[i]->FwdTrans(m_fields[i]->GetPhys(),m_fields[i]->UpdateCoeffs());
     }
 
         if(dumpInitialConditions)
         {
             std::string outname = m_sessionName + "_initial.chk";
             WriteFld(outname);
         }
     }

Friends And Related Function Documentation

◆ MemoryManager< MMFDiffusion >

friend class MemoryManager< MMFDiffusion >

friend

Definition at line 94 of file MMFDiffusion.h.

Member Data Documentation

◆ className

string Nektar::MMFDiffusion::className

static

Initial value:

= SolverUtils::GetEquationSystemFactory().
    RegisterCreatorFunction("MMFDiffusion",
                MMFDiffusion::create,
                "MMFDiffusion equation.")

Name of class.

Definition at line 107 of file MMFDiffusion.h.

◆ m_epsilon

Array<OneD, NekDouble> Nektar::MMFDiffusion::m_epsilon

private

Definition at line 168 of file MMFDiffusion.h.

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

◆ m_epsu

Array<OneD, NekDouble> Nektar::MMFDiffusion::m_epsu

private

Definition at line 169 of file MMFDiffusion.h.

Referenced by DoImplicitSolve(), v_GenerateSummary(), and v_InitObject().

◆ m_InitPtx

NekDouble Nektar::MMFDiffusion::m_InitPtx

protected

Definition at line 162 of file MMFDiffusion.h.

Referenced by PlanePhiWave(), and v_InitObject().

◆ m_InitPty

NekDouble Nektar::MMFDiffusion::m_InitPty

protected

Definition at line 162 of file MMFDiffusion.h.

Referenced by PlanePhiWave(), and v_InitObject().

◆ m_InitPtz

NekDouble Nektar::MMFDiffusion::m_InitPtz

protected

Definition at line 162 of file MMFDiffusion.h.

Referenced by PlanePhiWave(), and v_InitObject().

◆ m_InitWaveType

InitWaveType Nektar::MMFDiffusion::m_InitWaveType

protected

Definition at line 119 of file MMFDiffusion.h.

Referenced by PlanePhiWave(), and v_InitObject().

◆ m_TestType

TestType Nektar::MMFDiffusion::m_TestType

Definition at line 109 of file MMFDiffusion.h.

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

◆ m_varcoeff

StdRegions::VarCoeffMap Nektar::MMFDiffusion::m_varcoeff

private

Variable diffusivity.

Definition at line 166 of file MMFDiffusion.h.

Referenced by DoImplicitSolve(), and v_InitObject().

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ~MMFDiffusion()

◆ MMFDiffusion()

Member Function Documentation

◆ create()

◆ DoImplicitSolve()

◆ DoOdeRhs()

◆ Morphogenesis()

◆ PlanePhiWave()

◆ TestCubeProblem()

◆ TestPlaneProblem()

◆ v_EvaluateExactSolution()

◆ v_GenerateSummary()

◆ v_InitObject()

◆ v_SetInitialConditions()

Friends And Related Function Documentation

◆ MemoryManager< MMFDiffusion >

Member Data Documentation

◆ className

◆ m_epsilon

◆ m_epsu

◆ m_InitPtx

◆ m_InitPty

◆ m_InitPtz

◆ m_InitWaveType

◆ m_TestType

◆ m_varcoeff