#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)

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 (bool DeclareField=true)
	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 Array< OneD, const Array< OneD, NekDouble > >	GetTraceNormals ()

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, 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)

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)

Protected Member Functions inherited from Nektar::PulseWaveSystem
	PulseWaveSystem (const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &pGraph)
	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, 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)

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, 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_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 ()

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

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...

virtual SOLVER_UTILS_EXPORT bool	UpdateTimeStepCheck ()

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_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)

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
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

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_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
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::TimeIntegrationSchemeSharedPtr	m_intScheme
	Wrapper to the time integration scheme. More...

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

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...

NekDouble	m_steadyStateRes = 1.0

NekDouble	m_steadyStateRes0 = 1.0

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...

NekDouble	m_TimeIntegLambda = 0.0
	coefff of spacial derivatives(rhs or m_F in GLM) in calculating the residual of the whole equation(used in unsteady time integrations) More...

bool	m_flagImplicitItsStatistics

bool	m_flagImplicitSolver = false

Array< OneD, NekDouble >	m_magnitdEstimat
	estimate the magnitude of each conserved varibles More...

Array< OneD, NekDouble >	m_locTimeStep
	local time step(notice only for jfnk other see m_cflSafetyFactor) More...

NekDouble	m_inArrayNorm = -1.0

int	m_TotLinItePerStep = 0

int	m_StagesPerStep = 1

bool	m_flagUpdatePreconMat

int	m_maxLinItePerNewton

int	m_TotNewtonIts = 0

int	m_TotLinIts = 0

int	m_TotImpStages = 0

bool	m_CalcPhysicalAV = true
	flag to update artificial viscosity More...

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

bool	m_verbose

bool	m_root

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_timestepMax = -1.0
	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_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
Public Attributes inherited from Nektar::SolverUtils::UnsteadySystem
NekDouble	m_cflSafetyFactor
	CFL safety factor (comprise between 0 to 1). More...

NekDouble	m_cflNonAcoustic

NekDouble	m_CFLGrowth
	CFL growth rate. More...

NekDouble	m_CFLEnd
	maximun cfl in cfl growth More...

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

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 136 of file PulseWavePropagation.cpp.

137 {

138 }

◆ 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 201 of file PulseWavePropagation.cpp.

 {
     // Just copy over array
     for (int 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 148 of file PulseWavePropagation.cpp.

 {
     int 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);
  
     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 evaluation in all domains
     for (int omega = 0; omega < m_nDomains; ++omega)
     {
         LibUtilities::Timer timer;
         m_currentDomain = omega;
         int 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 381 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 391 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 386 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 406 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 305 of file PulseWavePropagation.cpp.

 {
     int 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 (int 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 (int 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.
         */
         int counter = 0;
  
         m_PWV[domain] = Array<OneD, NekDouble>(nq);
         m_W1[domain]  = Array<OneD, NekDouble>(nq);
         m_W2[domain]  = Array<OneD, NekDouble>(nq);
  
         for (int 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 396 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 401 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 217 of file PulseWavePropagation.cpp.

 {
     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];
             vessel[1] = m_vessels[2 * omega + 1];
  
             for (int 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 (int 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 )

protectedvirtual

Print summary routine, calls virtual routine reimplemented in UnsteadySystem

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 415 of file PulseWavePropagation.cpp.

 {
     PulseWaveSystem::v_GenerateSummary(s);
 }

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

◆ v_InitObject()

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

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

Reimplemented from Nektar::PulseWaveSystem.

Definition at line 72 of file PulseWavePropagation.cpp.

 {
     // 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