#include <PulseWavePropagation.h>

Inheritance diagram for Nektar::PulseWavePropagation:

Public Member Functions
virtual	~PulseWavePropagation ()

Array< OneD, NekDouble > &	GetA0 ()

Array< OneD, NekDouble > &	GetBeta ()

Array< OneD, NekDouble > &	GetAlpha ()

Array< OneD, NekDouble > &	GetN ()

NekDouble	GetRho ()

NekDouble	GetDomains ()

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

int	GetNdomains ()

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

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...

SOLVER_UTILS_EXPORT void	SteadyStateResidual (int step, Array< OneD, NekDouble > &L2)

SOLVER_UTILS_EXPORT LibUtilities::TimeIntegrationSchemeSharedPtr &	GetTimeIntegrationScheme ()
	Returns the time integration scheme. More...

SOLVER_UTILS_EXPORT LibUtilities::TimeIntegrationSchemeOperators &	GetTimeIntegrationSchemeOperators ()
	Returns the time integration scheme operators. More...

Public Member Functions inherited from Nektar::SolverUtils::EquationSystem
virtual SOLVER_UTILS_EXPORT	~EquationSystem ()
	Destructor. More...

SOLVER_UTILS_EXPORT void	InitObject (bool DeclareField=true)
	Initialises the members of this object. More...

SOLVER_UTILS_EXPORT void	DoInitialise (bool dumpInitialConditions=true)
	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 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 NekDouble	LinfError (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray)
	Linf error computation. 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, const Array< OneD, const NekDouble > &input)

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 int	GetInfoSteps ()

SOLVER_UTILS_EXPORT void	SetInfoSteps (int num)

SOLVER_UTILS_EXPORT void	SetIterationNumberPIT (int num)

SOLVER_UTILS_EXPORT void	SetWindowNumberPIT (int num)

SOLVER_UTILS_EXPORT Array< OneD, const Array< OneD, NekDouble > >	GetTraceNormals ()

SOLVER_UTILS_EXPORT void	SetTime (const NekDouble time)

SOLVER_UTILS_EXPORT void	SetTimeStep (const NekDouble timestep)

SOLVER_UTILS_EXPORT void	SetInitialStep (const int step)

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

SOLVER_UTILS_EXPORT bool	NegatedOp ()
	Identify if operator is negated in DoSolve. More...

SOLVER_UTILS_EXPORT bool	ParallelInTime ()
	Check if solver use Parallel-in-Time. More...

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

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

Static Public Attributes inherited from Nektar::SolverUtils::UnsteadySystem
static std::string	cmdSetStartTime

static std::string	cmdSetStartChkNum

Protected Member Functions
	PulseWavePropagation (const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &pGraph)

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 (bool DeclareField=false) override

void	GetFluxVector (const Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &flux)
	DG Pulse Wave Propagation routines: More...

virtual void	v_GenerateSummary (SolverUtils::SummaryList &s) override

Protected Member Functions inherited from Nektar::PulseWaveSystem
	PulseWaveSystem (const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &pGraph)
	Initialises PulseWaveSystem class members. More...

virtual void	v_InitObject (bool DeclareField=false) override

virtual void	v_DoInitialise (bool dumpInitialConditions=false) override
	Sets up initial conditions. More...

virtual void	v_DoSolve () override
	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, Array< OneD, NekDouble > &alpha)
	Riemann Problem for Bifurcation. More...

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

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

virtual void	v_Output (void) override

void	CheckPoint_Output (const int n)

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

virtual NekDouble	v_LinfError (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray) override
	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, const SpatialDomains::MeshGraphSharedPtr &pGraph)
	Initialises UnsteadySystem class members. More...

virtual SOLVER_UTILS_EXPORT void	v_InitObject (bool DeclareField=true) override
	Init object for UnsteadySystem class. More...

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

virtual SOLVER_UTILS_EXPORT void	v_PrintStatusInformation (const int step, const NekDouble cpuTime)
	Print Status Information. More...

virtual SOLVER_UTILS_EXPORT void	v_PrintSummaryStatistics (const NekDouble intTime)
	Print Summary Statistics. More...

virtual SOLVER_UTILS_EXPORT void	v_DoInitialise (bool dumpInitialConditions=true) override
	Sets up initial conditions. More...

virtual SOLVER_UTILS_EXPORT void	v_GenerateSummary (SummaryList &s) override
	Print a summary of time stepping parameters. 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 ()

virtual SOLVER_UTILS_EXPORT void	v_SteadyStateResidual (int step, Array< OneD, NekDouble > &L2)

virtual SOLVER_UTILS_EXPORT bool	v_UpdateTimeStepCheck ()

SOLVER_UTILS_EXPORT NekDouble	MaxTimeStepEstimator ()
	Get the maximum timestep estimator for cfl control. More...

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...

SOLVER_UTILS_EXPORT void	DoDummyProjection (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)
	Perform dummy projection. 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 void	v_InitObject (bool DeclareFeld=true)
	Initialisation object for EquationSystem. More...

virtual SOLVER_UTILS_EXPORT void	v_DoInitialise (bool dumpInitialConditions=true)
	Virtual function for initialisation implementation. More...

virtual SOLVER_UTILS_EXPORT void	v_DoSolve ()
	Virtual function for solve implementation. 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_GenerateSummary (SummaryList &l)
	Virtual function for generating summary information. 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)

virtual SOLVER_UTILS_EXPORT void	v_Output (void)

virtual SOLVER_UTILS_EXPORT MultiRegions::ExpListSharedPtr	v_GetPressure (void)

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

virtual SOLVER_UTILS_EXPORT void	v_ExtraFldOutput (std::vector< Array< OneD, NekDouble > > &fieldcoeffs, std::vector< std::string > &variables)

Protected Attributes
SolverUtils::RiemannSolverSharedPtr	m_riemannSolver

SolverUtils::AdvectionSharedPtr	m_advObject

Array< OneD, PulseWaveBoundarySharedPtr >	m_Boundary

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

size_t	m_nDomains

size_t	m_currentDomain

size_t	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_gamma

Array< OneD, Array< OneD, NekDouble > >	m_alpha

Array< OneD, Array< OneD, NekDouble > >	m_alpha_trace

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

std::map< int, SpatialDomains::CompositeMap >	m_domain

std::vector< int >	m_domOrder

Array< OneD, Array< OneD, NekDouble > >	m_pressure

PulseWavePressureAreaSharedPtr	m_pressureArea

bool	extraFields = false

Array< OneD, Array< OneD, NekDouble > >	m_PWV

Array< OneD, Array< OneD, NekDouble > >	m_W1

Array< OneD, Array< OneD, NekDouble > >	m_W2

std::vector< std::vector< InterfacePointShPtr > >	m_vesselIntfcs

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

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

Protected Attributes inherited from Nektar::SolverUtils::UnsteadySystem
LibUtilities::TimeIntegrationSchemeSharedPtr	m_intScheme
	Wrapper to the time integration scheme. More...

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

Array< OneD, Array< OneD, NekDouble > >	m_previousSolution
	Storage for previous solution for steady-state check. More...

std::vector< int >	m_intVariables

NekDouble	m_cflSafetyFactor
	CFL safety factor (comprise between 0 to 1). More...

NekDouble	m_CFLGrowth
	CFL growth rate. More...

NekDouble	m_CFLEnd
	Maximun cfl in cfl growth. More...

int	m_abortSteps
	Number of steps between checks for abort conditions. More...

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...

int	m_steadyStateSteps
	Check for steady state at step interval. More...

NekDouble	m_steadyStateTol
	Tolerance to which steady state should be evaluated at. More...

int	m_filtersInfosteps
	Number of time steps between outputting filters information. More...

std::vector< std::pair< std::string, FilterSharedPtr > >	m_filters

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

std::ofstream	m_errFile

NekDouble	m_epsilon
	Diffusion coefficient. More...

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

bool	m_verbose

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...

NekDouble	m_lastCheckTime

NekDouble	m_TimeIncrementFactor

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_infosteps
	Number of time steps between outputting status information. More...

int	m_iterPIT = 0
	Number of parallel-in-time time iteration. More...

int	m_windowPIT = 0
	Index of windows for parallel-in-time time iteration. 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...

Array< OneD, NekDouble >	m_movingFrameVelsxyz
	Moving frame of reference velocities. More...

Array< OneD, NekDouble >	m_movingFrameTheta
	Moving frame of reference angles with respect to the. More...

boost::numeric::ublas::matrix< NekDouble >	m_movingFrameProjMat
	Projection matrix for transformation between inertial and moving. 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
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 []

static std::string	projectionTypeLookupIds []

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 50 of file PulseWavePropagation.h.

Constructor & Destructor Documentation

◆ ~PulseWavePropagation()

Nektar::PulseWavePropagation::~PulseWavePropagation ( )

virtual

Definition at line 138 of file PulseWavePropagation.cpp.

139{

140}

◆ PulseWavePropagation()

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

protected

Definition at line 65 of file PulseWavePropagation.cpp.

    : PulseWaveSystem(pSession, pGraph)
{
}

Member Function Documentation

◆ create()

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

inlinestatic

Creates an instance of this class.

Definition at line 56 of file PulseWavePropagation.h.

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

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

◆ DoOdeProjection()

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 203 of file PulseWavePropagation.cpp.

{
    boost::ignore_unused(time);
 
    // Just copy over array
    if (inarray != outarray)
    {
        for (size_t i = 0; i < m_nVariables; ++i)
        {
            Vmath::Vcopy(inarray[i].size(), inarray[i], 1, outarray[i], 1);
        }
    }
}

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

Referenced by v_InitObject().

◆ DoOdeRhs()

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, m_advObject->Advect will be called

Definition at line 150 of file PulseWavePropagation.cpp.

{
    size_t i;
 
    Array<OneD, Array<OneD, NekDouble>> physarray(m_nVariables);
 
    // Dummy array for WeakDG advection
    Array<OneD, Array<OneD, NekDouble>> advVel(m_spacedim);
 
    // Output array for advection
    Array<OneD, Array<OneD, NekDouble>> out(m_nVariables);
 
    size_t 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 evaluation in all domains
    for (size_t omega = 0; omega < m_nDomains; ++omega)
    {
        LibUtilities::Timer timer;
        m_currentDomain = omega;
        size_t nq       = m_vessels[omega * m_nVariables]->GetTotPoints();
 
        timer.Start();
        for (i = 0; i < m_nVariables; ++i)
        {
            physarray[i] = inarray[i] + cnt;
            out[i]       = outarray[i] + cnt;
        }
 
        for (i = 0; i < m_nVariables; ++i)
        {
            m_fields[i] = m_vessels[omega * m_nVariables + i];
        }
 
        m_advObject->Advect(m_nVariables, m_fields, advVel, physarray, out,
                            time);
        for (i = 0; i < m_nVariables; ++i)
        {
            Vmath::Neg(nq, out[i], 1);
        }
        timer.Stop();
        timer.AccumulateRegion("PulseWavePropagation:_DoOdeRHS", 1);
        cnt += nq;
    }
}

References Nektar::LibUtilities::Timer::AccumulateRegion(), Nektar::PulseWaveSystem::EnforceInterfaceConditions(), m_advObject, Nektar::PulseWaveSystem::m_currentDomain, Nektar::SolverUtils::EquationSystem::m_fields, Nektar::PulseWaveSystem::m_nDomains, Nektar::PulseWaveSystem::m_nVariables, Nektar::SolverUtils::EquationSystem::m_spacedim, Nektar::PulseWaveSystem::m_vessels, Vmath::Neg(), SetPulseWaveBoundaryConditions(), Nektar::LibUtilities::Timer::Start(), and Nektar::LibUtilities::Timer::Stop().

Referenced by v_InitObject().

◆ GetA0()

Array< OneD, NekDouble > & Nektar::PulseWavePropagation::GetA0 ( )

Definition at line 390 of file PulseWavePropagation.cpp.

{
    return m_A_0_trace[m_currentDomain];
}

References Nektar::PulseWaveSystem::m_A_0_trace, and Nektar::PulseWaveSystem::m_currentDomain.

Referenced by v_InitObject().

◆ GetAlpha()

Array< OneD, NekDouble > & Nektar::PulseWavePropagation::GetAlpha ( )

Definition at line 400 of file PulseWavePropagation.cpp.

{
    return m_alpha_trace[m_currentDomain];
}

References Nektar::PulseWaveSystem::m_alpha_trace, and Nektar::PulseWaveSystem::m_currentDomain.

Referenced by v_InitObject().

◆ GetBeta()

Array< OneD, NekDouble > & Nektar::PulseWavePropagation::GetBeta ( )

Definition at line 395 of file PulseWavePropagation.cpp.

{
    return m_beta_trace[m_currentDomain];
}

References Nektar::PulseWaveSystem::m_beta_trace, and Nektar::PulseWaveSystem::m_currentDomain.

Referenced by v_InitObject().

◆ GetDomains()

NekDouble Nektar::PulseWavePropagation::GetDomains ( )

Definition at line 415 of file PulseWavePropagation.cpp.

{
    return m_nDomains;
}

References Nektar::PulseWaveSystem::m_nDomains.

Referenced by v_InitObject().

◆ GetFluxVector()

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

protected

DG Pulse Wave Propagation routines:

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 $\mathbf{U} = [A,u]^T$ physfield[0] = A physfield[1] = u flux[0] = F[0] = A*u flux[1] = F[1] = u^2/2 + p/rho

Definition at line 314 of file PulseWavePropagation.cpp.

{
    size_t nq = m_vessels[m_currentDomain * m_nVariables]->GetTotPoints();
    NekDouble domain   = m_currentDomain;
    m_pressure[domain] = Array<OneD, NekDouble>(nq);
    Array<OneD, NekDouble> dAUdx(nq);
    NekDouble viscoelasticGradient = 0.0;
 
    LibUtilities::Timer timer;
 
    for (size_t j = 0; j < nq; ++j)
    {
        timer.Start();
        flux[0][0][j] = physfield[0][j] * physfield[1][j];
        timer.Stop();
        timer.AccumulateRegion("PulseWavePropagation:GetFluxVector-flux", 3);
    }
 
    // d/dx of AU, for the viscoelastic tube law and extra fields
    m_fields[0]->PhysDeriv(flux[0][0], dAUdx);
 
    for (size_t j = 0; j < nq; ++j)
    {
        if ((j == 0) || (j == nq - 1))
        {
            viscoelasticGradient = dAUdx[j];
        }
        else
        {
            viscoelasticGradient = (dAUdx[j] + dAUdx[j + 1]) / 2;
        }
 
        m_pressureArea->GetPressure(m_pressure[domain][j], m_beta[domain][j],
                                    physfield[0][j], m_A_0[domain][j],
                                    viscoelasticGradient, m_gamma[domain][j],
                                    m_alpha[domain][j]);
 
        flux[1][0][j] = physfield[1][j] * physfield[1][j] / 2 +
                        m_pressure[domain][j] / m_rho;
    }
 
    m_session->MatchSolverInfo("OutputExtraFields", "True", extraFields, true);
 
    if (extraFields)
    {
        /*
        Calculates wave speed and characteristic variables.
 
        Ideally this should be moved to PulseWaveSystem, but it's easiest to
        implement here.
        */
        size_t counter = 0;
 
        m_PWV[domain] = Array<OneD, NekDouble>(nq);
        m_W1[domain]  = Array<OneD, NekDouble>(nq);
        m_W2[domain]  = Array<OneD, NekDouble>(nq);
 
        for (size_t j = 0; j < nq; ++j)
        {
            m_pressureArea->GetC(m_PWV[domain][j], m_beta[domain][j],
                                 physfield[0][counter + j], m_A_0[domain][j],
                                 m_alpha[domain][j]);
            m_pressureArea->GetW1(m_W1[domain][j], physfield[1][counter + j],
                                  m_beta[domain][j], physfield[0][counter + j],
                                  m_A_0[domain][j], m_alpha[domain][j]);
            m_pressureArea->GetW2(m_W2[domain][j], physfield[1][counter + j],
                                  m_beta[domain][j], physfield[0][counter + j],
                                  m_A_0[domain][j], m_alpha[domain][j]);
        }
 
        counter += nq;
    }
}

Referenced by v_InitObject().

◆ GetN()

Array< OneD, NekDouble > & Nektar::PulseWavePropagation::GetN ( )

Definition at line 405 of file PulseWavePropagation.cpp.

{
    return m_trace_fwd_normal[m_currentDomain];
}

References Nektar::PulseWaveSystem::m_currentDomain, and Nektar::PulseWaveSystem::m_trace_fwd_normal.

Referenced by v_InitObject().

◆ GetRho()

NekDouble Nektar::PulseWavePropagation::GetRho ( )

Definition at line 410 of file PulseWavePropagation.cpp.

{
    return m_rho;
}

References Nektar::PulseWaveSystem::m_rho.

Referenced by v_InitObject().

◆ SetPulseWaveBoundaryConditions()

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 224 of file PulseWavePropagation.cpp.

{
    boost::ignore_unused(outarray);
 
    size_t omega;
 
    Array<OneD, MultiRegions::ExpListSharedPtr> vessel(2);
 
    size_t 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];
            vessel[1] = m_vessels[2 * omega + 1];
 
            for (size_t j = 0; j < 2; ++j)
            {
                std::string BCType;
 
                if (j < vessel[0]->GetBndConditions().size())
                {
                    BCType = vessel[0]->GetBndConditions()[j]->GetUserDefined();
                }
 
                // if no condition given define it to be NoUserDefined
                if (BCType.empty() || BCType == "Interface")
                {
                    BCType = "NoUserDefined";
                }
 
                m_Boundary[2 * omega + j] = GetBoundaryFactory().CreateInstance(
                    BCType, m_vessels, m_session, m_pressureArea);
 
                // turn on time dependent BCs
                if (BCType == "Q-inflow")
                {
                    vessel[0]->GetBndConditions()[j]->SetIsTimeDependent(true);
                }
                else if (BCType == "A-inflow")
                {
                    vessel[0]->GetBndConditions()[j]->SetIsTimeDependent(true);
                }
                else if (BCType == "U-inflow")
                {
                    vessel[1]->GetBndConditions()[j]->SetIsTimeDependent(true);
                }
                else if (BCType == "RCR-terminal")
                {
                    vessel[0]->GetBndConditions()[j]->SetIsTimeDependent(true);
                }
            }
        }
    }
 
    SetBoundaryConditions(time);
 
    // Loop over all vessels and set boundary conditions
    LibUtilities::Timer timer;
    for (omega = 0; omega < m_nDomains; ++omega)
    {
        timer.Start();
        for (size_t n = 0; n < 2; ++n)
        {
            m_Boundary[2 * omega + n]->DoBoundary(
                inarray, m_A_0, m_beta, m_alpha, time, omega, offset, n);
        }
 
        offset += m_vessels[2 * omega]->GetTotPoints();
        timer.Stop();
        timer.AccumulateRegion("PulseWavePropagation:_SetBCs", 1);
    }
}

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

Referenced by DoOdeRhs().

◆ v_GenerateSummary()

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

overrideprotectedvirtual

Print summary routine, calls virtual routine reimplemented in UnsteadySystem

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 424 of file PulseWavePropagation.cpp.

{
    PulseWaveSystem::v_GenerateSummary(s);
}

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

◆ v_InitObject()

void Nektar::PulseWavePropagation::v_InitObject ( bool DeclareField = false )

overrideprotectedvirtual

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

Reimplemented from Nektar::PulseWaveSystem.

Definition at line 72 of file PulseWavePropagation.cpp.

{
    boost::ignore_unused(DeclareField);
 
    // Will set up an array of vessels/fields in PulseWaveSystem::v_InitObject
    // so set DeclareField to false so that the fields are not set up in
    // EquationSystem unnecessarily. Note the number of fields in Equation
    // system is related to the number of variables. The number of vessels is
    // therefore held in PulwWaveSystem.
    PulseWaveSystem::v_InitObject(false);
 
    if (m_session->DefinesSolverInfo("PressureArea"))
    {
        m_pressureArea = GetPressureAreaFactory().CreateInstance(
            m_session->GetSolverInfo("PressureArea"), m_vessels, m_session);
    }
    else
    {
        m_pressureArea = GetPressureAreaFactory().CreateInstance(
            "Beta", m_vessels, m_session);
    }
 
    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.");
    }
 
    // Create advection object
    string advName;
    string riemName;
    switch (m_upwindTypePulse)
    {
        case eUpwindPulse:
        {
            advName  = "WeakDG";
            riemName = "UpwindPulse";
        }
        break;
        default:
        {
            ASSERTL0(false, "populate switch statement for upwind flux");
        }
        break;
    }
    m_advObject =
        SolverUtils::GetAdvectionFactory().CreateInstance(advName, advName);
    m_advObject->SetFluxVector(&PulseWavePropagation::GetFluxVector, this);
    m_riemannSolver = SolverUtils::GetRiemannSolverFactory().CreateInstance(
        riemName, m_session);
    m_riemannSolver->SetScalar("A0", &PulseWavePropagation::GetA0, this);
    m_riemannSolver->SetScalar("beta", &PulseWavePropagation::GetBeta, this);
    m_riemannSolver->SetScalar("alpha", &PulseWavePropagation::GetAlpha, this);
    m_riemannSolver->SetScalar("N", &PulseWavePropagation::GetN, this);
    m_riemannSolver->SetParam("rho", &PulseWavePropagation::GetRho, this);
    m_riemannSolver->SetParam("domains", &PulseWavePropagation::GetDomains,
                              this);
 
    m_advObject->SetRiemannSolver(m_riemannSolver);
    m_advObject->InitObject(m_session, m_fields);
}

References ASSERTL0, Nektar::LibUtilities::NekFactory< tKey, tBase, tParam >::CreateInstance(), Nektar::LibUtilities::TimeIntegrationSchemeOperators::DefineOdeRhs(), Nektar::LibUtilities::TimeIntegrationSchemeOperators::DefineProjection(), DoOdeProjection(), DoOdeRhs(), Nektar::eUpwindPulse, GetA0(), Nektar::SolverUtils::GetAdvectionFactory(), GetAlpha(), GetBeta(), GetDomains(), GetFluxVector(), GetN(), Nektar::GetPressureAreaFactory(), GetRho(), Nektar::SolverUtils::GetRiemannSolverFactory(), m_advObject, Nektar::SolverUtils::UnsteadySystem::m_explicitAdvection, Nektar::SolverUtils::EquationSystem::m_fields, Nektar::SolverUtils::UnsteadySystem::m_ode, Nektar::PulseWaveSystem::m_pressureArea, m_riemannSolver, Nektar::SolverUtils::EquationSystem::m_session, Nektar::PulseWaveSystem::m_upwindTypePulse, Nektar::PulseWaveSystem::m_vessels, and Nektar::PulseWaveSystem::v_InitObject().

Friends And Related Function Documentation

◆ MemoryManager< PulseWavePropagation >

friend class MemoryManager< PulseWavePropagation >

friend

Definition at line 1 of file PulseWavePropagation.h.

Member Data Documentation

◆ className

string Nektar::PulseWavePropagation::className

static

Initial value:

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

Name of class.

Definition at line 68 of file PulseWavePropagation.h.

◆ m_advObject

SolverUtils::AdvectionSharedPtr Nektar::PulseWavePropagation::m_advObject

protected

Definition at line 103 of file PulseWavePropagation.h.

Referenced by DoOdeRhs(), and v_InitObject().

◆ m_Boundary

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

protected

Definition at line 105 of file PulseWavePropagation.h.

Referenced by SetPulseWaveBoundaryConditions().

◆ m_riemannSolver

SolverUtils::RiemannSolverSharedPtr Nektar::PulseWavePropagation::m_riemannSolver

protected

Definition at line 102 of file PulseWavePropagation.h.

Referenced by v_InitObject().

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ~PulseWavePropagation()

◆ PulseWavePropagation()

Member Function Documentation

◆ create()

◆ DoOdeProjection()

◆ DoOdeRhs()

◆ GetA0()

◆ GetAlpha()

◆ GetBeta()

◆ GetDomains()

◆ GetFluxVector()

◆ GetN()

◆ GetRho()

◆ SetPulseWaveBoundaryConditions()

◆ v_GenerateSummary()

◆ v_InitObject()

Friends And Related Function Documentation

◆ MemoryManager< PulseWavePropagation >

Member Data Documentation

◆ className

◆ m_advObject

◆ m_Boundary

◆ m_riemannSolver