#include <PulseWavePropagation.h>

Inheritance diagram for Nektar::PulseWavePropagation:

Collaboration diagram for Nektar::PulseWavePropagation:

Public Member Functions
virtual	~PulseWavePropagation ()

Public Member Functions inherited from Nektar::PulseWaveSystem
virtual	~PulseWaveSystem ()
	Destructor. More...

int	GetNdomains ()

Array< OneD, MultiRegions::ExpListSharedPtr >	UpdateVessels (void)

void	CalcCharacteristicVariables (int omega)

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 EquationSystemSharedPtr	create (const LibUtilities::SessionReaderSharedPtr &pSession)
	Creates an instance of this class. More...

Static Public Attributes
static std::string	className = GetEquationSystemFactory().RegisterCreatorFunction("PulseWavePropagation", PulseWavePropagation::create, "Pulse Wave Propagation equation.")
	Name of class. More...

Protected Member Functions
	PulseWavePropagation (const LibUtilities::SessionReaderSharedPtr &pSession)

void	DoOdeRhs (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)

void	DoOdeProjection (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)

void	SetPulseWaveBoundaryConditions (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)

virtual void	v_InitObject ()

virtual void	v_GetFluxVector (const int i, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &flux)

virtual void	v_NumericalFlux (Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numflux)
	DG Pulse Wave Propagation routines: Numerical Flux at interelemental boundaries. More...

void	RiemannSolverUpwind (NekDouble AL, NekDouble uL, NekDouble AR, NekDouble uR, NekDouble &Aflux, NekDouble &uflux, NekDouble A_0, NekDouble beta, NekDouble n)
	Upwinding Riemann solver for interelemental boundaries. More...

virtual void	v_GenerateSummary (SolverUtils::SummaryList &s)

Protected Member Functions inherited from Nektar::PulseWaveSystem
	PulseWaveSystem (const LibUtilities::SessionReaderSharedPtr &m_session)
	Initialises PulseWaveSystem class members. More...

virtual void	v_DoInitialise ()
	Sets up initial conditions. More...

virtual void	v_DoSolve ()
	Solves an unsteady problem. More...

void	LinkSubdomains (Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &fields)
	Links the subdomains. More...

void	BifurcationRiemann (Array< OneD, NekDouble > &Au, Array< OneD, NekDouble > &uu, Array< OneD, NekDouble > &beta, Array< OneD, NekDouble > &A_0)
	Riemann Problem for Bifurcation. More...

void	MergingRiemann (Array< OneD, NekDouble > &Au, Array< OneD, NekDouble > &uu, Array< OneD, NekDouble > &beta, Array< OneD, NekDouble > &A_0)
	Riemann Problem for Merging Flow. More...

void	JunctionRiemann (Array< OneD, NekDouble > &Au, Array< OneD, NekDouble > &uu, Array< OneD, NekDouble > &beta, Array< OneD, NekDouble > &A_0)
	Riemann Problem for Junction. More...

virtual void	v_Output (void)

void	CheckPoint_Output (const int n)

NekDouble	v_L2Error (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray, bool Normalised=false)
	Compute the L2 error between fields and a given exact solution. More...

NekDouble	v_LinfError (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray)
	Compute the L_inf error between fields and a given exact solution. More...

void	WriteVessels (const std::string &outname)
	Write input fields to the given filename. More...

void	EnforceInterfaceConditions (const Array< OneD, const Array< OneD, NekDouble > > &fields)

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_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 > > &numfluxX, Array< OneD, Array< OneD, NekDouble > > &numfluxY)

virtual SOLVER_UTILS_EXPORT void	v_NumFluxforScalar (const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &uflux)

virtual SOLVER_UTILS_EXPORT void	v_NumFluxforVector (const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &qfield, Array< OneD, Array< OneD, NekDouble > > &qflux)

virtual SOLVER_UTILS_EXPORT NekDouble	v_GetTimeStep (const Array< OneD, const Array< OneD, NekDouble > > &inarray)
	Return the timestep to be used for the next step in the time-marching loop. More...

virtual SOLVER_UTILS_EXPORT bool	v_PreIntegrate (int step)

virtual SOLVER_UTILS_EXPORT bool	v_PostIntegrate (int step)

virtual SOLVER_UTILS_EXPORT bool	v_SteadyStateCheck (int step)

SOLVER_UTILS_EXPORT void	CheckForRestartTime (NekDouble &time)

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 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_SetInitialConditions (NekDouble initialtime=0.0, bool dumpInitialConditions=true, const int domain=0)

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

SOLVER_UTILS_EXPORT void	SetUpBaseFields (SpatialDomains::MeshGraphSharedPtr &mesh)

SOLVER_UTILS_EXPORT void	ImportFldBase (std::string pInfile, SpatialDomains::MeshGraphSharedPtr pGraph)

virtual SOLVER_UTILS_EXPORT 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
Array< OneD, PulseWaveBoundarySharedPtr >	m_Boundary

PulseWavePressureAreaSharedPtr	m_pressureArea

Protected Attributes inherited from Nektar::PulseWaveSystem
Array< OneD, MultiRegions::ExpListSharedPtr >	m_vessels

int	m_nDomains

int	m_currentDomain

int	m_nVariables

UpwindTypePulse	m_upwindTypePulse

Array< OneD, int >	m_fieldPhysOffset

NekDouble	m_rho

NekDouble	m_pext

NekDouble	m_C

NekDouble	m_RT

NekDouble	m_pout

Array< OneD, Array< OneD, NekDouble > >	m_A_0

Array< OneD, Array< OneD, NekDouble > >	m_A_0_trace

Array< OneD, Array< OneD, NekDouble > >	m_beta

Array< OneD, Array< OneD, NekDouble > >	m_beta_trace

Array< OneD, Array< OneD, NekDouble > >	m_trace_fwd_normal

std::vector< std::vector < InterfacePointShPtr > >	m_vesselJcts

std::vector< std::vector < InterfacePointShPtr > >	m_bifurcations

std::vector< std::vector < InterfacePointShPtr > >	m_mergingJcts

Protected Attributes inherited from Nektar::SolverUtils::UnsteadySystem
int	m_infosteps
	Number of time steps between outputting status information. More...

LibUtilities::TimeIntegrationWrapperSharedPtr	m_intScheme
	Wrapper to the time integration scheme. More...

LibUtilities::TimeIntegrationSchemeOperators	m_ode
	The time integration scheme operators to use. More...

LibUtilities::TimeIntegrationSolutionSharedPtr	m_intSoln

NekDouble	m_epsilon

bool	m_explicitDiffusion
	Indicates if explicit or implicit treatment of diffusion is used. More...

bool	m_explicitAdvection
	Indicates if explicit or implicit treatment of advection is used. More...

bool	m_explicitReaction
	Indicates if explicit or implicit treatment of reaction is used. More...

bool	m_homoInitialFwd
	Flag to determine if simulation should start in homogeneous forward transformed state. More...

std::vector< int >	m_intVariables

std::vector< FilterSharedPtr >	m_filters

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

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

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

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

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

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

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

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

SpatialDomains::BoundaryConditionsSharedPtr	m_boundaryConditions
	Pointer to boundary conditions object. More...

SpatialDomains::MeshGraphSharedPtr	m_graph
	Pointer to graph defining mesh. More...

std::string	m_sessionName
	Name of the session. More...

NekDouble	m_time
	Current time of simulation. More...

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...

std::set< std::string >	m_loadedFields

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...

Friends
class	MemoryManager< PulseWavePropagation >

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...

Detailed Description

Set up the routines based on the weak formulation from "Computational Modelling of 1D blood flow with variable mechanical properties" by S. J. Sherwin et al. The weak formulation (1) reads: $\sum_{e=1}^{N_{el}} \left[ \left( \frac{\partial \mathbf{U}^{\delta} }{\partial t} , \mathbf{\psi}^{\delta} \right)_{\Omega_e} - \left( \frac{\partial \mathbf{F(\mathbf{U})}^{\delta} } {\partial x}, \mathbf{\psi}^{\delta} \right)_{\Omega_e} + \left[ \mathbf{\psi}^{\delta} \cdot \{ \mathbf{F}^u - \mathbf{F}(\mathbf{U}^{\delta}) \} \right]_{x_e^l}^{x_eû} \right] = 0$

Definition at line 47 of file PulseWavePropagation.h.

Constructor & Destructor Documentation

Nektar::PulseWavePropagation::~PulseWavePropagation ( )

virtual

Definition at line 80 of file PulseWavePropagation.cpp.

81 {

82 }

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

protected

Definition at line 57 of file PulseWavePropagation.cpp.

     : PulseWaveSystem(pSession)
     {
     }

Member Function Documentation

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

inlinestatic

Creates an instance of this class.

Definition at line 53 of file PulseWavePropagation.h.

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

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

void Nektar::PulseWavePropagation::DoOdeProjection	(	const Array< OneD, const Array< OneD, NekDouble > > &	inarray,
		Array< OneD, Array< OneD, NekDouble > > &	outarray,
		const NekDouble	time
	)

protected

Definition at line 147 of file PulseWavePropagation.cpp.

References Nektar::PulseWaveSystem::m_nVariables, and Vmath::Vcopy().

Referenced by v_InitObject().

     {
         // Just copy over array
         for(int i = 0; i < m_nVariables; ++i)
         {
             Vmath::Vcopy(inarray[i].num_elements(),inarray[i],1,outarray[i],1);
         }
     }

void Nektar::PulseWavePropagation::DoOdeRhs	(	const Array< OneD, const Array< OneD, NekDouble > > &	inarray,
		Array< OneD, Array< OneD, NekDouble > > &	outarray,
		const NekDouble	time
	)

protected

Computes the right hand side of (1). The RHS is everything except the term that contains the time derivative $\frac{\partial \mathbf{U}}{\partial t}$ . In case of a Discontinuous Galerkin projection, the routine WeakDGAdvection will be called which then calls v_GetFluxVector and v_NumericalFlux implemented in the PulseWavePropagation class.

Definition at line 94 of file PulseWavePropagation.cpp.

References Nektar::PulseWaveSystem::EnforceInterfaceConditions(), Nektar::PulseWaveSystem::m_currentDomain, Nektar::SolverUtils::EquationSystem::m_fields, Nektar::PulseWaveSystem::m_nDomains, Nektar::PulseWaveSystem::m_nVariables, Nektar::PulseWaveSystem::m_vessels, Vmath::Neg(), SetPulseWaveBoundaryConditions(), and Nektar::SolverUtils::EquationSystem::WeakDGAdvection().

Referenced by v_InitObject().

     {
         int i;
             
         Array<OneD, Array<OneD, NekDouble> > physarray(m_nVariables);
         Array<OneD, Array<OneD, NekDouble> > modarray (m_nVariables);
     
     Array<OneD, NekDouble> tmpArray;
 
         int cnt = 0;
 
         // Set up Inflow and Outflow boundary conditions. 
         SetPulseWaveBoundaryConditions(inarray, outarray, time);
     
         // Set up any interface conditions and write into boundary condition
         EnforceInterfaceConditions(inarray);
         
         // do advection evauation in all domains
         for(int omega=0; omega < m_nDomains; ++omega)
         {
             m_currentDomain = omega;
             int nq = m_vessels[omega*m_nVariables]->GetTotPoints();
             int ncoeffs = m_vessels[omega*m_nVariables]->GetNcoeffs();
             
             for (i = 0; i < m_nVariables; ++i)
             {
                 physarray[i] = inarray[i]+cnt;
                 modarray[i]  = Array<OneD, NekDouble>(ncoeffs);
             }
 
             for(i = 0; i < m_nVariables; ++i)
             {
                 m_fields[i] = m_vessels[omega*m_nVariables+ i];
             }
             
             WeakDGAdvection(physarray, modarray, true, true);
             
             for(i = 0; i < m_nVariables; ++i)
             {
                 Vmath::Neg(ncoeffs,modarray[i],1);
             }     
             
             for(i = 0; i < m_nVariables; ++i)
             {
                 m_vessels[omega*m_nVariables+i]->MultiplyByElmtInvMass(modarray[i],modarray[i]);
                 m_vessels[omega*m_nVariables+i]->BwdTrans(modarray[i],tmpArray = outarray[i]+cnt);
             }
             cnt += nq;
         }
     }

void Nektar::PulseWavePropagation::RiemannSolverUpwind	(	NekDouble	AL,
		NekDouble	uL,
		NekDouble	AR,
		NekDouble	uR,
		NekDouble &	Aflux,
		NekDouble &	uflux,
		NekDouble	A_0,
		NekDouble	beta,
		NekDouble	n
	)

protected

Upwinding Riemann solver for interelemental boundaries.

Riemann solver for upwinding at an interface between two elements. Uses the characteristic variables for calculating the upwinded state $(A_u,u_u)$ from the left $(A_L,u_L)$ and right state $(A_R,u_R)$ . Returns the upwinded flux ${F}^u$ needed for the weak formulation (1). Details can be found in "Pulse wave propagation in the human vascular system", section 3.3

Definition at line 338 of file PulseWavePropagation.cpp.

References ASSERTL1, Nektar::PulseWaveSystem::m_pext, and Nektar::PulseWaveSystem::m_rho.

Referenced by v_NumericalFlux().

     {
         Array<OneD, NekDouble> W(2);
         Array<OneD, NekDouble> upwindedphysfield(2);
         NekDouble cL = 0.0;
         NekDouble cR = 0.0;
         NekDouble rho = m_rho; 
         NekDouble pext = m_pext; 
         NekDouble p = 0.0;
         NekDouble p_t = 0.0;
         
         // Compute the wave speeds. The use of the normal here allows
         // for the definition of the characteristics to be inverted
         // (and hence the left and right state) if n is in the -ve
         // x-direction. This means we end up with the positive
         // defintion of the flux which has to therefore be multiplied
         // by the normal at the end of the methods This is a bit of a
         // mind twister but is efficient from a coding perspective.
         cL = sqrt(beta*sqrt(AL)/(2*rho))*n;
         cR = sqrt(beta*sqrt(AR)/(2*rho))*n;
 
         ASSERTL1(fabs(cL+cR) > fabs(uL+uR),"Conditions are not sub-sonic");
 
         // If upwinding from left and right for subsonic domain
         // then know characteristics immediately
         W[0] = uL + 4*cL;
         W[1] = uR - 4*cR;
 
         // Calculate conservative variables from characteristics
         NekDouble w0mw1 = 0.25*(W[0]-W[1]);
         NekDouble fac = rho/(2*beta);
         w0mw1 *= w0mw1; // squared
         w0mw1 *= w0mw1; // fourth power
         fac *= fac;     // squared
         upwindedphysfield[0]= w0mw1*fac;
         upwindedphysfield[1]= 0.5*(W[0] + W[1]);
 
         // Compute the fluxes multipled by the normal. 
         Aflux = upwindedphysfield[0] * upwindedphysfield[1]*n;
         p = pext + beta*(sqrt(upwindedphysfield[0]) - sqrt(A_0));
         p_t = 0.5*(upwindedphysfield[1]*upwindedphysfield[1]) + p/rho;              
         uflux =  p_t*n;
     }    

void Nektar::PulseWavePropagation::SetPulseWaveBoundaryConditions	(	const Array< OneD, const Array< OneD, NekDouble > > &	inarray,
		Array< OneD, Array< OneD, NekDouble > > &	outarray,
		const NekDouble	time
	)

protected

Does the projection between ... space and the ... space. Also checks for Q-inflow boundary conditions at the inflow of the current arterial segment and applies the Q-inflow if specified

Definition at line 164 of file PulseWavePropagation.cpp.

References Nektar::LibUtilities::NekFactory< tKey, tBase, >::CreateInstance(), Nektar::GetBoundaryFactory(), Nektar::PulseWaveSystem::m_A_0, Nektar::PulseWaveSystem::m_beta, m_Boundary, Nektar::PulseWaveSystem::m_nDomains, m_pressureArea, Nektar::SolverUtils::EquationSystem::m_session, Nektar::PulseWaveSystem::m_vessels, and Nektar::SolverUtils::EquationSystem::SetBoundaryConditions().

Referenced by DoOdeRhs().

     {
         int omega;
         
         Array<OneD, MultiRegions::ExpListSharedPtr>     vessel(2);
 
         int offset=0; 
 
         //This will be moved to the RCR boundary condition once factory is setup
     if (time == 0)
         {
             m_Boundary = Array<OneD,PulseWaveBoundarySharedPtr>(2*m_nDomains);
 
             for(omega = 0; omega < m_nDomains; ++omega)
             {
                 vessel[0] = m_vessels[2*omega];
 
                 for(int j = 0; j < 2; ++j)
                 {   
                     std::string BCType =vessel[0]->GetBndConditions()[j]->GetUserDefined();
                     if(BCType.empty()) // if not condition given define it to be NoUserDefined
                     {
                         BCType = "NoUserDefined";
                     }
 
                     m_Boundary[2*omega+j]=GetBoundaryFactory().CreateInstance(BCType,m_vessels,m_session,m_pressureArea);
                     
                     // turn on time depedent BCs 
                     if(BCType == "Q-inflow")
                     {
                         vessel[0]->GetBndConditions()[j]->SetIsTimeDependent(true);
                     }
                     else if(BCType == "RCR-terminal")
                     {
                         vessel[0]->GetBndConditions()[j]->SetIsTimeDependent(true);
                     }
                 }
             }
 
         }
 
         SetBoundaryConditions(time);
 
         // Loop over all vessesls and set boundary conditions
         for(omega = 0; omega < m_nDomains; ++omega)
         {
             for(int n = 0; n < 2; ++n)
             {   
                 m_Boundary[2*omega+n]->DoBoundary(inarray,m_A_0,m_beta,time,omega,offset,n);
             }
             offset += m_vessels[2*omega]->GetTotPoints();
         }
 
     }

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

protectedvirtual

Print summary routine, calls virtual routine reimplemented in UnsteadySystem

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 392 of file PulseWavePropagation.cpp.

References Nektar::SolverUtils::UnsteadySystem::v_GenerateSummary().

     {
         PulseWaveSystem::v_GenerateSummary(s);
     }

void Nektar::PulseWavePropagation::v_GetFluxVector	(	const int	i,
		Array< OneD, Array< OneD, NekDouble > > &	physfield,
		Array< OneD, Array< OneD, NekDouble > > &	flux
	)

protectedvirtual

Calculates the second term of the weak form (1): $\left( \frac{\partial \mathbf{F(\mathbf{U})}^{\delta} }{\partial x}, \mathbf{\psi}^{\delta} \right)_{\Omega_e}$ The variables of the system are ${U} = [A,u]^T$ physfield[0] = A physfield[1] = u flux[0] = F[0] = A*u flux[1] = F[1] = u^2/2 + p/rho p-A-relationship: p = p_ext + beta*(sqrt(A)-sqrt(A_0))

Reimplemented from Nektar::SolverUtils::EquationSystem.

Definition at line 234 of file PulseWavePropagation.cpp.

References ASSERTL0, Nektar::PulseWaveSystem::m_A_0, Nektar::PulseWaveSystem::m_beta, Nektar::PulseWaveSystem::m_currentDomain, Nektar::PulseWaveSystem::m_nVariables, Nektar::PulseWaveSystem::m_pext, Nektar::PulseWaveSystem::m_rho, and Nektar::PulseWaveSystem::m_vessels.

     {
         int nq = m_vessels[m_currentDomain*m_nVariables]->GetTotPoints();
         NekDouble p = 0.0;
         NekDouble p_t = 0.0;
     
         switch (i)
         {
         case 0:   // Flux for A equation
             {
                 for (int j = 0; j < nq; j++)
                 {
                     flux[0][j] = physfield[0][j]*physfield[1][j]; 
                 }
             }
             break;
         case 1:  // Flux for u equation
             {
                 for (int j = 0; j < nq; j++)
                 {
                     ASSERTL0(physfield[0][j]>=0,"Negative A not allowed.");
 
                     p = m_pext + m_beta[m_currentDomain][j]*
                         (sqrt(physfield[0][j]) - sqrt(m_A_0[m_currentDomain][j]));
 
                     p_t = (physfield[1][j]*physfield[1][j])/2 + p/m_rho;
                     flux[0][j] =  p_t;
                 }
             }
             break;
         default:
             ASSERTL0(false,"GetFluxVector: illegal vector index");
             break;
         }
     }

void Nektar::PulseWavePropagation::v_InitObject ( )

protectedvirtual

Initialisation routine for multidomain solver. Sets up the expansions for every arterial segment (m_vessels) and for one complete field m_outfield which is needed to write the postprocessing output. Also determines which upwind strategy is used (currently only upwinding scheme available) and reads blodd flow specific parameters from the inputfile

Gets the Material Properties of each arterial segment
specified in the inputfile from section MaterialProperties

Also gets the Area at static equilibrium A_0 specified in the inputfile.

Having found these points also extract the values at the trace points and the normal direction consistent with the left adjacent definition of Fwd and Bwd

Reimplemented from Nektar::PulseWaveSystem.

Definition at line 62 of file PulseWavePropagation.cpp.

References ASSERTL0, Nektar::LibUtilities::NekFactory< tKey, tBase, >::CreateInstance(), Nektar::LibUtilities::TimeIntegrationSchemeOperators::DefineOdeRhs(), Nektar::LibUtilities::TimeIntegrationSchemeOperators::DefineProjection(), DoOdeProjection(), DoOdeRhs(), Nektar::GetPressureAreaFactory(), Nektar::SolverUtils::UnsteadySystem::m_explicitAdvection, Nektar::SolverUtils::UnsteadySystem::m_ode, m_pressureArea, Nektar::SolverUtils::EquationSystem::m_session, Nektar::PulseWaveSystem::m_vessels, and Nektar::PulseWaveSystem::v_InitObject().

     {
         PulseWaveSystem::v_InitObject();
     
         m_pressureArea=GetPressureAreaFactory().CreateInstance("Lymphatic",m_vessels,m_session);
         m_pressureArea->DoPressure();
     
         if (m_explicitAdvection)
         {
             m_ode.DefineOdeRhs       (&PulseWavePropagation::DoOdeRhs, this);
             m_ode.DefineProjection   (&PulseWavePropagation::DoOdeProjection, this);
         }
         else
         {
             ASSERTL0(false, "Implicit Pulse Wave Propagation not set up.");
         }
     }

void Nektar::PulseWavePropagation::v_NumericalFlux	(	Array< OneD, Array< OneD, NekDouble > > &	physfield,
		Array< OneD, Array< OneD, NekDouble > > &	numflux
	)

protectedvirtual

DG Pulse Wave Propagation routines: Numerical Flux at interelemental boundaries.

Calculates the third term of the weak form (1): numerical flux at boundary $\left[ \mathbf{\psi}^{\delta} \cdot \{ \mathbf{F}^u - \mathbf{F}(\mathbf{U}^{\delta}) \} \right]_{x_e^l}^{x_eû}$

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 278 of file PulseWavePropagation.cpp.

References ASSERTL0, Nektar::eUpwindPulse, Nektar::SolverUtils::EquationSystem::GetTraceTotPoints(), Nektar::PulseWaveSystem::m_A_0_trace, Nektar::PulseWaveSystem::m_beta_trace, Nektar::PulseWaveSystem::m_currentDomain, Nektar::PulseWaveSystem::m_nVariables, Nektar::PulseWaveSystem::m_trace_fwd_normal, Nektar::PulseWaveSystem::m_upwindTypePulse, Nektar::PulseWaveSystem::m_vessels, and RiemannSolverUpwind().

     {       
         int i;
         int nTracePts = GetTraceTotPoints();
         
         Array<OneD, Array<OneD, NekDouble> > Fwd(m_nVariables);
         Array<OneD, Array<OneD, NekDouble> > Bwd(m_nVariables);
         
         for (i = 0; i < m_nVariables; ++i)
         {
             Fwd[i] = Array<OneD, NekDouble>(nTracePts);
             Bwd[i] = Array<OneD, NekDouble>(nTracePts);
         }
     
         // Get the physical values at the trace
         for (i = 0; i < m_nVariables; ++i)
         {
             m_vessels[m_currentDomain*m_nVariables+ i]->
                 GetFwdBwdTracePhys(physfield[i],Fwd[i],Bwd[i]);
         }
         
         // Solve the upwinding Riemann problem within one arterial
         // segment by calling the upwinding Riemann solver implemented
         // in this file
         NekDouble Aflux, uflux;
         for (i = 0; i < nTracePts; ++i)
         {
             switch(m_upwindTypePulse)
             {
             case eUpwindPulse:
                 {
                     RiemannSolverUpwind(Fwd[0][i],Fwd[1][i],Bwd[0][i],Bwd[1][i],
                                         Aflux, uflux, m_A_0_trace[m_currentDomain][i],
                                         m_beta_trace[m_currentDomain][i],
                                         m_trace_fwd_normal[m_currentDomain][i]);
                 }
                 break;
             default:
                 {
                     ASSERTL0(false,"populate switch statement for upwind flux");
                 }
                 break;
             }
             numflux[0][i] = Aflux;
             numflux[1][i] = uflux;
         }
     }

Friends And Related Function Documentation

friend class MemoryManager< PulseWavePropagation >

friend

Definition at line 50 of file PulseWavePropagation.h.

Member Data Documentation

string Nektar::PulseWavePropagation::className = GetEquationSystemFactory().RegisterCreatorFunction("PulseWavePropagation", PulseWavePropagation::create, "Pulse Wave Propagation equation.")

static

Name of class.

Definition at line 61 of file PulseWavePropagation.h.

Array<OneD, PulseWaveBoundarySharedPtr> Nektar::PulseWavePropagation::m_Boundary

protected

Definition at line 95 of file PulseWavePropagation.h.

Referenced by SetPulseWaveBoundaryConditions().

PulseWavePressureAreaSharedPtr Nektar::PulseWavePropagation::m_pressureArea

protected

Definition at line 97 of file PulseWavePropagation.h.

Referenced by SetPulseWaveBoundaryConditions(), and v_InitObject().

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Friends

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Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation