Base class for unsteady solvers. More...

#include <PulseWaveSystem.h>

Inheritance diagram for Nektar::PulseWaveSystem:

Public Member Functions
int	GetNdomains ()

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

Public Member Functions inherited from Nektar::SolverUtils::UnsteadySystem
SOLVER_UTILS_EXPORT	~UnsteadySystem () override=default
	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 NekDouble	GetTimeStep ()

SOLVER_UTILS_EXPORT void	SetTimeStep (const NekDouble timestep)

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 NekDouble	H1Error (unsigned int field, const Array< OneD, NekDouble > &exactsoln, bool Normalised=false)
	Compute the H1 error between fields and a given exact solution. 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	GetTime ()
	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 void	SetSteps (const int steps)

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 Array< OneD, NekDouble > &	UpdatePhysField (const int i)

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...

Public Member Functions inherited from Nektar::SolverUtils::ALEHelper
virtual	~ALEHelper ()=default

virtual SOLVER_UTILS_EXPORT void	v_ALEInitObject (int spaceDim, Array< OneD, MultiRegions::ExpListSharedPtr > &fields)

SOLVER_UTILS_EXPORT void	InitObject (int spaceDim, Array< OneD, MultiRegions::ExpListSharedPtr > &fields)

virtual SOLVER_UTILS_EXPORT void	v_UpdateGridVelocity (const NekDouble &time)

virtual SOLVER_UTILS_EXPORT void	v_ALEPreMultiplyMass (Array< OneD, Array< OneD, NekDouble > > &fields)

SOLVER_UTILS_EXPORT void	ALEDoElmtInvMass (Array< OneD, Array< OneD, NekDouble > > &traceNormals, Array< OneD, Array< OneD, NekDouble > > &fields, NekDouble time)
	Update m_fields with u^n by multiplying by inverse mass matrix. That's then used in e.g. checkpoint output and L^2 error calculation. More...

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

SOLVER_UTILS_EXPORT void	MoveMesh (const NekDouble &time, Array< OneD, Array< OneD, NekDouble > > &traceNormals)

const Array< OneD, const Array< OneD, NekDouble > > &	GetGridVelocity ()

SOLVER_UTILS_EXPORT const Array< OneD, const Array< OneD, NekDouble > > &	GetGridVelocityTrace ()

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

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

	~PulseWaveSystem () override=default

void	v_InitObject (bool DeclareField=false) override

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

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...

void	v_Output (void) override

void	CheckPoint_Output (const int n)

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...

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...

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

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...

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

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 NekDouble	v_H1Error (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray, bool Normalised=false)
	Virtual function for the H_1 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
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

std::map< int, std::vector< int > >	m_domainToFilterIDs

std::map< int, int >	m_filterToVesselID

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_movingFrameData
	Moving reference frame status in the inertial frame X, Y, Z, Theta_x, Theta_y, Theta_z, U, V, W, Omega_x, Omega_y, Omega_z, A_x, A_y, A_z, DOmega_x, DOmega_y, DOmega_z, pivot_x, pivot_y, pivot_z. More...

std::vector< std::string >	m_strFrameData
	variable name in m_movingFrameData 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...

Protected Attributes inherited from Nektar::SolverUtils::ALEHelper
Array< OneD, MultiRegions::ExpListSharedPtr >	m_fieldsALE

Array< OneD, Array< OneD, NekDouble > >	m_gridVelocity

Array< OneD, Array< OneD, NekDouble > >	m_gridVelocityTrace

std::vector< ALEBaseShPtr >	m_ALEs

bool	m_ALESolver = false

bool	m_ImplicitALESolver = false

NekDouble	m_prevStageTime = 0.0

int	m_spaceDim

Private Member Functions
void	SetUpDomainInterfaces (void)

void	FillDataFromInterfacePoint (InterfacePointShPtr &I, const Array< OneD, const Array< OneD, NekDouble > > &field, NekDouble &A, NekDouble &u, NekDouble &beta, NekDouble &A_0, NekDouble &alpha)

void	GetCommArray (std::map< int, LibUtilities::CommSharedPtr > &retval)
	Set and retrn a series of communicators for each partition. More...

void	SetUpDomainInterfaceBCs (SpatialDomains::BoundaryConditions &AllBcs, std::map< int, LibUtilities::CommSharedPtr > &domComm)

Private Attributes
Gs::gs_data *	m_intComm
	Communicator for interfaces. More...

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

static std::string	cmdSetStartChkNum

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

Base class for unsteady solvers.

Initialises the arterial subdomains in m_vessels and sets up all domain-linking conditions (bifurcations, intefaces/junctions, merging flows). Detects the network structure and assigns boundary conditons. Also provides the underlying timestepping framework for pulse wave solvers including the general timestepping routines.

Definition at line 77 of file PulseWaveSystem.h.

Constructor & Destructor Documentation

◆ PulseWaveSystem()

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

protected

Initialises PulseWaveSystem class members.

Processes SolverInfo parameters from the session file and sets up timestepping-specific code.

Parameters

m_Session Session object to read parameters from.

Definition at line 64 of file PulseWaveSystem.cpp.

    : UnsteadySystem(pSession, pGraph)
{
}

◆ ~PulseWaveSystem()

Nektar::PulseWaveSystem::~PulseWaveSystem ( )

overrideprotecteddefault

Member Function Documentation

◆ BifurcationRiemann()

void Nektar::PulseWaveSystem::BifurcationRiemann	(	Array< OneD, NekDouble > &	Au,
		Array< OneD, NekDouble > &	uu,
		Array< OneD, NekDouble > &	beta,
		Array< OneD, NekDouble > &	A_0,
		Array< OneD, NekDouble > &	alpha
	)

protected

Riemann Problem for Bifurcation.

Solves the Riemann problem at a bifurcation by assuming subsonic flow at both sides of the boundary and by applying conservation of mass and continuity of the total pressure \( \frac{p}{rho} + \frac{u^{2}}{2}. \) The other 3 missing equations come from the characteristic variables. For further information see "Pulse WavePropagation in the human vascular system" Section 3.4.4

Definition at line 1589 of file PulseWaveSystem.cpp.

{
 
    NekDouble rho = m_rho;
    Array<OneD, NekDouble> W(3);
    Array<OneD, NekDouble> P_Au(3);
    Array<OneD, NekDouble> W_Au(3);
    NekMatrix<NekDouble> invJ(6, 6);
    NekVector<NekDouble> f(6);
    NekVector<NekDouble> dx(6);
 
    int proceed  = 1;
    int iter     = 0;
    int MAX_ITER = 100;
 
    // Forward characteristic
    m_pressureArea->GetW1(W[0], uu[0], beta[0], Au[0], A_0[0], alpha[0]);
 
    // Backward characteristics
    for (size_t i = 1; i < 3; ++i)
    {
        m_pressureArea->GetW2(W[i], uu[i], beta[i], Au[i], A_0[i], alpha[i]);
    }
 
    // Tolerances for the algorithm
    NekDouble Tol = 1.0E-10;
 
    // Newton Iteration
    while ((proceed) && (iter < MAX_ITER))
    {
        LibUtilities::Timer time_BifurcationRiemann;
        time_BifurcationRiemann.Start();
        iter += 1;
 
        /*
         * We solve the six constraint equations via a multivariate Newton
         * iteration. Equations are:
         * 1. Forward characteristic:          W1(A_L,  U_L)  = W1(Au_L,
         * Uu_L)
         * 2. Backward characteristic 1:       W2(A_R1, U_R1) = W2(Au_R1,
         * Uu_R1)
         * 3. Backward characteristic 2:       W2(A_R2, U_R2) = W2(Au_R2,
         * Uu_R2)
         * 4. Conservation of mass:            Au_L * Uu_L    = Au_R1 *
         * Uu_R1 + Au_R2 * Uu_R2
         * 5. Continuity of total pressure 1:  rho * Uu_L  * Uu_L  / 2 +
         * p(Au_L) = rho * Uu_R1 * Uu_R1 / 2 + p(Au_R1)
         * 6. Continuity of total pressure 2:  rho * Uu_L  * Uu_L  / 2 +
         * p(Au_L) = rho * Uu_R2 * Uu_R2 / 2 + p(Au_R2)
         */
        for (size_t i = 0; i < 3; ++i)
        {
            m_pressureArea->GetPressure(P_Au[i], beta[i], Au[i], A_0[i], 0, 0,
                                        alpha[i]);
        }
 
        m_pressureArea->GetW1(W_Au[0], uu[0], beta[0], Au[0], A_0[0], alpha[0]);
        m_pressureArea->GetW2(W_Au[1], uu[1], beta[1], Au[1], A_0[1], alpha[1]);
        m_pressureArea->GetW2(W_Au[2], uu[2], beta[2], Au[2], A_0[2], alpha[2]);
 
        // Constraint equations set to zero
        f[0] = W_Au[0] - W[0];
        f[1] = W_Au[1] - W[1];
        f[2] = W_Au[2] - W[2];
        f[3] = Au[0] * uu[0] - Au[1] * uu[1] - Au[2] * uu[2];
        f[4] = uu[0] * uu[0] + 2 * P_Au[0] / rho - uu[1] * uu[1] -
               2 * P_Au[1] / rho;
        f[5] = uu[0] * uu[0] + 2 * P_Au[0] / rho - uu[2] * uu[2] -
               2 * P_Au[2] / rho;
 
        // Inverse Jacobian for x + dx = x - J^(-1) * f(x)
        m_pressureArea->GetJacobianInverse(invJ, Au, uu, beta, A_0, alpha,
                                           "Bifurcation");
 
        Multiply(dx, invJ, f);
 
        // Update the solution: x_new = x_old - dx
        for (int i = 0; i < 3; ++i)
        {
            uu[i] -= dx[i];
            Au[i] -= dx[i + 3];
        }
 
        // Check if the error of the solution is smaller than Tol
        if (Dot(dx, dx) < Tol)
        {
            proceed = 0;
        }
 
        // Check if solver converges
        if (iter >= MAX_ITER)
        {
            ASSERTL0(false, "Riemann solver for Bifurcation did not converge.");
        }
        time_BifurcationRiemann.Stop();
        time_BifurcationRiemann.AccumulateRegion(
            "PulseWaveSystem::Bifurcation Riemann", 2);
    }
}

References Nektar::LibUtilities::Timer::AccumulateRegion(), ASSERTL0, Nektar::LibUtilities::beta, Nektar::Dot(), m_pressureArea, m_rho, Nektar::Multiply(), Nektar::LibUtilities::Timer::Start(), and Nektar::LibUtilities::Timer::Stop().

Referenced by EnforceInterfaceConditions().

◆ CheckPoint_Output()

void Nektar::PulseWaveSystem::CheckPoint_Output ( const int n )

protected

Writes the .fld file at the end of the simulation. Similar to the normal v_Output however the Multidomain output has to be prepared.

Definition at line 1919 of file PulseWaveSystem.cpp.

{
    std::stringstream outname;
    outname << m_sessionName << "_" << n << ".chk";
 
    WriteVessels(outname.str());
}

References Nektar::SolverUtils::EquationSystem::m_sessionName, and WriteVessels().

Referenced by v_DoSolve().

◆ EnforceInterfaceConditions()

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

protected

Definition at line 1445 of file PulseWaveSystem.cpp.

{
    LibUtilities::Timer time_EnforceInterfaceConditions;
    time_EnforceInterfaceConditions.Start();
    int dom, bcpos;
 
    int totif =
        m_bifurcations.size() + m_mergingJcts.size() + m_vesselIntfcs.size();
 
    Array<OneD, NekDouble> Aut, Au(3 * totif, 0.0);
    Array<OneD, NekDouble> uut, uu(3 * totif, 0.0);
    Array<OneD, NekDouble> betat, beta(3 * totif, 0.0);
    Array<OneD, NekDouble> A_0t, A_0(3 * totif, 0.0);
    Array<OneD, NekDouble> alphat, alpha(3 * totif, 0.0);
 
    // Bifurcations Data:
    size_t cnt = 0;
    for (size_t n = 0; n < m_bifurcations.size(); ++n, ++cnt)
    {
        for (size_t i = 0; i < m_bifurcations[n].size(); ++i)
        {
            size_t l = m_bifurcations[n][i]->m_riemannOrd;
            FillDataFromInterfacePoint(
                m_bifurcations[n][i], fields, Au[l + 3 * cnt], uu[l + 3 * cnt],
                beta[l + 3 * cnt], A_0[l + 3 * cnt], alpha[l + 3 * cnt]);
        }
    }
 
    // Enforce Merging vessles Data:
    for (size_t n = 0; n < m_mergingJcts.size(); ++n, ++cnt)
    {
        // Merged vessel
        for (size_t i = 0; i < m_mergingJcts.size(); ++i)
        {
            int l = m_mergingJcts[n][i]->m_riemannOrd;
            FillDataFromInterfacePoint(
                m_mergingJcts[n][i], fields, Au[l + 3 * cnt], uu[l + 3 * cnt],
                beta[l + 3 * cnt], A_0[l + 3 * cnt], alpha[l + 3 * cnt]);
        }
    }
 
    // Enforce interface junction between two vessesls
    for (size_t n = 0; n < m_vesselIntfcs.size(); ++n, ++cnt)
    {
        for (size_t i = 0; i < m_vesselIntfcs[n].size(); ++i)
        {
            int l = m_vesselIntfcs[n][i]->m_riemannOrd;
            FillDataFromInterfacePoint(
                m_vesselIntfcs[n][i], fields, Au[l + 3 * cnt], uu[l + 3 * cnt],
                beta[l + 3 * cnt], A_0[l + 3 * cnt], alpha[l + 3 * cnt]);
        }
    }
 
    // Gather data if running in parallel
    Gs::Gather(Au, Gs::gs_add, m_intComm);
    Gs::Gather(uu, Gs::gs_add, m_intComm);
    Gs::Gather(beta, Gs::gs_add, m_intComm);
    Gs::Gather(A_0, Gs::gs_add, m_intComm);
    Gs::Gather(alpha, Gs::gs_add, m_intComm);
 
    // Enforce Bifurcations:
    cnt = 0;
    for (size_t n = 0; n < m_bifurcations.size(); ++n, ++cnt)
    {
        // Solve the Riemann problem for a bifurcation
        BifurcationRiemann(Aut = Au + 3 * cnt, uut = uu + 3 * cnt,
                           betat = beta + 3 * cnt, A_0t = A_0 + 3 * cnt,
                           alphat = alpha + 3 * cnt);
 
        // Store the values into the right positions:
        for (size_t i = 0; i < m_bifurcations[n].size(); ++i)
        {
            dom   = m_bifurcations[n][i]->m_domain;
            bcpos = m_bifurcations[n][i]->m_bcPosition;
            int l = m_bifurcations[n][i]->m_riemannOrd;
            m_vessels[dom * m_nVariables]
                ->UpdateBndCondExpansion(bcpos)
                ->UpdatePhys()[0] = Au[l + 3 * cnt];
            m_vessels[dom * m_nVariables + 1]
                ->UpdateBndCondExpansion(bcpos)
                ->UpdatePhys()[0] = uu[l + 3 * cnt];
        }
    }
 
    // Enforce Merging vessles;
    for (size_t n = 0; n < m_mergingJcts.size(); ++n, ++cnt)
    {
        // Solve the Riemann problem for a merging vessel
        MergingRiemann(Aut = Au + 3 * cnt, uut = uu + 3 * cnt,
                       betat = beta + 3 * cnt, A_0t = A_0 + 3 * cnt,
                       alphat = alpha + 3 * cnt);
 
        // Store the values into the right positions:
        for (size_t i = 0; i < m_mergingJcts[n].size(); ++i)
        {
            int dom   = m_mergingJcts[n][i]->m_domain;
            int bcpos = m_mergingJcts[n][i]->m_bcPosition;
            int l     = m_mergingJcts[n][i]->m_riemannOrd;
            m_vessels[dom * m_nVariables]
                ->UpdateBndCondExpansion(bcpos)
                ->UpdatePhys()[0] = Au[l + 3 * cnt];
            m_vessels[dom * m_nVariables + 1]
                ->UpdateBndCondExpansion(bcpos)
                ->UpdatePhys()[0] = uu[l + 3 * cnt];
        }
    }
 
    // Enforce interface junction between two vessesls
    for (size_t n = 0; n < m_vesselIntfcs.size(); ++n, ++cnt)
    {
        InterfaceRiemann(Aut = Au + 3 * cnt, uut = uu + 3 * cnt,
                         betat = beta + 3 * cnt, A_0t = A_0 + 3 * cnt,
                         alphat = alpha + 3 * cnt);
 
        // Store the values into the right positions:
        for (size_t i = 0; i < m_vesselIntfcs[n].size(); ++i)
        {
            int dom   = m_vesselIntfcs[n][i]->m_domain;
            int bcpos = m_vesselIntfcs[n][i]->m_bcPosition;
            int l     = m_vesselIntfcs[n][i]->m_riemannOrd;
            m_vessels[dom * m_nVariables]
                ->UpdateBndCondExpansion(bcpos)
                ->UpdatePhys()[0] = Au[l + 3 * cnt];
            m_vessels[dom * m_nVariables + 1]
                ->UpdateBndCondExpansion(bcpos)
                ->UpdatePhys()[0] = uu[l + 3 * cnt];
        }
    }
    time_EnforceInterfaceConditions.Stop();
    time_EnforceInterfaceConditions.AccumulateRegion(
        "PulseWaveSystem::EnforceInterfaceConditions", 1);
}

References Nektar::LibUtilities::Timer::AccumulateRegion(), Nektar::LibUtilities::beta, BifurcationRiemann(), FillDataFromInterfacePoint(), Gs::Gather(), Gs::gs_add, InterfaceRiemann(), m_bifurcations, m_intComm, m_mergingJcts, m_nVariables, m_vesselIntfcs, m_vessels, MergingRiemann(), Nektar::LibUtilities::Timer::Start(), and Nektar::LibUtilities::Timer::Stop().

Referenced by Nektar::PulseWavePropagation::DoOdeRhs().

◆ FillDataFromInterfacePoint()

void Nektar::PulseWaveSystem::FillDataFromInterfacePoint	(	InterfacePointShPtr &	I,
		const Array< OneD, const Array< OneD, NekDouble > > &	field,
		NekDouble &	A,
		NekDouble &	u,
		NekDouble &	beta,
		NekDouble &	A_0,
		NekDouble &	alpha
	)

private

Definition at line 1413 of file PulseWaveSystem.cpp.

{
    LibUtilities::Timer time_FillDataFromInterfacePoint;
    time_FillDataFromInterfacePoint.Start();
 
    int omega       = I->m_domain;
    int traceId     = I->m_traceId;
    int eid         = I->m_elmt;
    int vert        = I->m_elmtVert;
    int vesselID    = omega * m_nVariables;
    int phys_offset = m_vessels[vesselID]->GetPhys_Offset(eid);
    LocalRegions::ExpansionSharedPtr dumExp;
    Array<OneD, NekDouble> Tmp(1);
 
    m_vessels[vesselID]->GetExp(eid)->GetTracePhysVals(
        vert, dumExp, fields[0] + m_fieldPhysOffset[omega] + phys_offset, Tmp);
    A = Tmp[0];
    m_vessels[vesselID]->GetExp(eid)->GetTracePhysVals(
        vert, dumExp, fields[1] + m_fieldPhysOffset[omega] + phys_offset, Tmp);
    u = Tmp[0];
 
    beta  = m_beta_trace[omega][traceId];
    A_0   = m_A_0_trace[omega][traceId];
    alpha = m_alpha_trace[omega][traceId];
    time_FillDataFromInterfacePoint.Stop();
    time_FillDataFromInterfacePoint.AccumulateRegion(
        "PulseWaveSystem::FillDataFromInterfacePoint", 2);
}

References Nektar::LibUtilities::Timer::AccumulateRegion(), Nektar::LibUtilities::beta, m_A_0_trace, m_alpha_trace, m_beta_trace, m_fieldPhysOffset, m_nVariables, m_vessels, Nektar::LibUtilities::Timer::Start(), and Nektar::LibUtilities::Timer::Stop().

Referenced by EnforceInterfaceConditions().

◆ GetCommArray()

void Nektar::PulseWaveSystem::GetCommArray ( std::map< int, LibUtilities::CommSharedPtr > & retval )

private

Set and retrn a series of communicators for each partition.

Definition at line 347 of file PulseWaveSystem.cpp.

{
 
    // set up defualt serial communicator
    std::string def("default");
    char *argv = new char[def.length() + 1];
    std::strcpy(argv, def.c_str());
    LibUtilities::CommSharedPtr serialComm =
        MemoryManager<LibUtilities::CommSerial>::AllocateSharedPtr(1, &argv);
 
    size_t nprocs = m_comm->GetSize();
 
    if (nprocs == 1) // serial case
    {
        for (auto &d : m_domain)
        {
            // serial communicator
            retval[d.first] = serialComm;
            // fill out m_domOrder set for serial case
            m_domOrder.push_back(d.first);
        }
    }
    else // parallel case
    {
        size_t rank = m_comm->GetRank();
 
        // Fill array with domain details
        size_t dmax = 0;
        for (auto &d : m_domain)
        {
            dmax = ((size_t)d.first > dmax) ? d.first : dmax;
        }
        dmax += 1;
 
        // get domain maximum id + 1;
        m_comm->AllReduce(dmax, LibUtilities::ReduceMax);
 
        Array<OneD, int> commtmp(dmax, 0);
        for (auto &d : m_domain)
        {
            commtmp[d.first] = 1;
        }
 
        // identfy which domains are split between two procs
        m_comm->AllReduce(commtmp, LibUtilities::ReduceSum);
 
        Array<OneD, bool> DoneCreate(nprocs, false);
 
        // setup communicators for domain partitions greater than 2
        for (size_t d = 0; d < dmax; ++d)
        {
            // set up communicator for cases where more than 2 procs
            // share domain
            if (commtmp[d] > 2)
            {
                LibUtilities::CommSharedPtr newcomm;
                int flag = 0;
                // set flag to 10 if d is on this processors domain
                for (auto &d1 : m_domain)
                {
                    if ((size_t)d1.first == d)
                    {
                        flag = 10;
                    }
                }
 
                newcomm = m_comm->CommCreateIf(flag);
 
                // set up communicator if domain on this processor
                for (auto &d1 : m_domain)
                {
                    if ((size_t)d1.first == d)
                    {
                        retval[d] = newcomm;
                    }
                }
 
                // turn off commtmp flag since should now be setup
                commtmp[d] = -1;
            }
        }
 
        // we now should have a list of the number of each
        // domains/vessel that is split over two processors
 
        // set up serial communicators for domains on only one
        // processor and set up map of domains that require parallel
        // communicator and number of processors in parallel
 
        // communicator
        std::map<int, int> SharedProc;
        Array<OneD, int> commtmp1(dmax, 0);
 
        for (auto &d : m_domain)
        {
            if (commtmp[d.first] == 1) // set to serial communicator
            {
                retval[d.first] = serialComm;
            }
            else if (commtmp[d.first] == 2) // shared by 2 procs
            {
                SharedProc[d.first] = 1;
                commtmp1[d.first]   = rank;
            }
            else // do nothing
            {
            }
        }
 
        // find the maximum number of communicator on all processors
        size_t nShrProc = SharedProc.size();
        int commMax     = nShrProc;
        m_comm->AllReduce(commMax, LibUtilities::ReduceMax);
 
        // find out processor id of each communicator by adding rank
        // and then subtracting local rank
 
        m_comm->AllReduce(commtmp1, LibUtilities::ReduceSum);
 
        // reset SharedProc to hold shared proc id.
        for (auto &d : SharedProc)
        {
            SharedProc[d.first] = commtmp1[d.first] - rank;
        }
 
        // now work out a comm ordering;
        Array<OneD, int> procs(2);
        int commcall = 0;
        std::map<int, std::pair<int, int>> CreateComm;
 
        bool search = true;
        Array<OneD, int> setdone(3);
 
        while (search)
        {
            size_t dorank = 0;      // search index over processors
            std::set<int> proclist; // has proc been identified for a comm at
            // this level
            int flag = 100; // colour for communicators in this search level
 
            while (dorank < nprocs)
            {
                int sharedproc = -1;
                int ncomms     = 0;
 
                if (DoneCreate[dorank] == false)
                {
                    // check to see if proc even has a shared domain
                    ncomms = (rank == dorank) ? nShrProc : 0;
                    m_comm->AllReduce(ncomms, LibUtilities::ReduceMax);
 
                    // set DoneCreate to true if n comms required on
                    // proc
                    DoneCreate[dorank] = (ncomms == 0) ? true : false;
                }
 
                // requires communicator and needs to create one.
                if (ncomms)
                {
                    bool doneCreateOnDoRank     = false;
                    bool doneCreateOnSharedProc = false;
                    bool createdComm            = false;
 
                    // check not already callng communicator on
                    // this processor for this search sweep
                    if ((proclist.count(dorank) == 0))
                    {
 
                        // give all processors rank id of shared proc
                        if (rank == dorank)
                        {
                            for (auto &d : SharedProc)
                            {
                                if (CreateComm.count(d.first) == 0)
                                {
                                    sharedproc = SharedProc[d.first];
                                    break;
                                }
                            }
 
                            ASSERTL1(sharedproc != -1,
                                     "Failed to fine a new "
                                     "processor to set up another "
                                     "communicator");
 
                            if (proclist.count(sharedproc) == 0)
                            {
                                // save all communicators on this for
                                // split comm setup
                                for (auto &d : SharedProc)
                                {
                                    if (d.second == sharedproc)
                                    {
                                        CreateComm[d.first] =
                                            std::pair<int, int>(commcall,
                                                                flag + d.first);
                                        createdComm = true;
                                    }
                                }
                            }
 
                            // set bool to mark as done on dorank
                            if (CreateComm.size() == nShrProc)
                            {
                                doneCreateOnDoRank = true;
                            }
                        }
                        else
                        {
                            sharedproc = -1;
                        }
 
                        m_comm->AllReduce(sharedproc, LibUtilities::ReduceMax);
                        ASSERTL1(
                            sharedproc < nprocs,
                            "Error in obtaining rank "
                            "shared by domain. Sharedproc value is greater "
                            "than number of procs");
 
                        if (proclist.count(sharedproc) == 0)
                        {
                            if ((int)rank == sharedproc)
                            {
                                // save all communicators on this for
                                // split comm setup
                                for (auto &d : SharedProc)
                                {
                                    if (d.second == (int)dorank)
                                    {
                                        CreateComm[d.first] =
                                            std::pair<int, int>(commcall,
                                                                flag + d.first);
                                        createdComm = true;
                                    }
                                }
 
                                if (CreateComm.size() == nShrProc)
                                {
                                    doneCreateOnSharedProc = true;
                                }
                            }
                        }
                    }
 
                    // mark DoneCreate as if complete
                    setdone[0] = (doneCreateOnDoRank) ? 1 : 0;
                    setdone[1] = (doneCreateOnSharedProc) ? 1 : 0;
                    setdone[2] = (createdComm) ? 1 : 0;
                    m_comm->AllReduce(setdone, LibUtilities::ReduceMax);
                    DoneCreate[dorank] = (bool)setdone[0];
                    if (sharedproc != -1)
                    {
                        DoneCreate[sharedproc] = (bool)setdone[1];
                    }
                    if (setdone[2]) // created new communicator
                    {
                        proclist.insert(dorank);
                        proclist.insert(sharedproc);
                    }
                }
 
                dorank++;
            }
 
            // have we found all comms on all processors.
            size_t i;
            for (i = 0; i < nprocs; ++i)
            {
                if (DoneCreate[i] == false)
                {
                    break;
                }
            }
 
            if (i == nprocs)
            {
                search = false;
            }
            else
            {
                commcall++;
                ASSERTL0(commcall < 4 * commMax,
                         "Failed to find sub communicators "
                         "pattern in 4*commMax searches");
            }
        }
 
        ASSERTL1(CreateComm.size() == nShrProc,
                 "Have not created communicators for all shared procs");
 
        // determine maxmimum number of CreateComm size
        size_t maxCreateComm = CreateComm.size();
        m_comm->AllReduce(maxCreateComm, LibUtilities::ReduceMax);
 
        // loop over CreateComm list
        for (size_t i = 0; i < maxCreateComm; ++i)
        {
            LibUtilities::CommSharedPtr newcomm;
            int flag = 0;
 
            for (auto &d : CreateComm)
            {
                if (d.second.first == (int)i)
                {
                    flag = d.second.second;
                }
            }
 
            newcomm = m_comm->CommCreateIf(flag);
 
            for (auto &d : CreateComm)
            {
                if (d.second.first == (int)i)
                {
                    retval[d.first] = newcomm;
                }
            }
        }
 
        // Finally need to re-order domain list so that we call the
        // communicators in a non-locking manner. This is done by
        // uniquely numbering each shared proc/comm interface and
        // ensuring the domains are ordered so that we call this
        // numbering in an increasing order
 
        Array<OneD, NekDouble> numShared(nprocs, 0.0);
        // determine the number of communicators on this rank where
        // the share proc has a higher rank id
        numShared[rank] = nShrProc;
        m_comm->AllReduce(numShared, LibUtilities::ReduceSum);
        int totShared = (int)Vmath::Vsum(nprocs, numShared, 1);
 
        if (totShared)
        {
            size_t cnt = 0;
            Array<OneD, NekDouble> numOffset(nprocs, 0.0);
            for (auto &s : SharedProc)
            {
                if (s.second > (int)rank)
                {
                    cnt++;
                }
            }
 
            numOffset[rank] = cnt;
            m_comm->AllReduce(numOffset, LibUtilities::ReduceMax);
 
            // make numShared into a cumulative list
            for (size_t i = 1; i < nprocs; ++i)
            {
                numShared[i] += numShared[i - 1];
                numOffset[i] += numOffset[i - 1];
            }
            for (size_t i = nprocs - 1; i > 0; --i)
            {
                numShared[i] = numShared[i - 1];
                numOffset[i] = numOffset[i - 1];
            }
            numShared[0] = 0;
            numOffset[0] = 0;
 
            Array<OneD, NekDouble> shareddom(totShared, -1.0);
            cnt = 0; // collect a list of domains that each shared commm is
            // attached to
            for (auto &s : SharedProc)
            {
                shareddom[numShared[rank] + cnt] = s.first;
                ++cnt;
            }
            m_comm->AllReduce(shareddom, LibUtilities::ReduceMax);
 
            // define a numbering scheme
            Array<OneD, NekDouble> sharedid(totShared, -1.0);
            cnt         = 0;
            size_t cnt1 = 0;
            for (auto &s : SharedProc)
            {
                if (s.second > (int)rank)
                {
                    sharedid[numShared[rank] + cnt] = numOffset[rank] + cnt1;
 
                    // find shared proc offset by matching the domain ids.
                    size_t j;
                    for (j = 0; j < maxCreateComm; ++j)
                    {
                        if ((numShared[s.second] + j < totShared) &&
                            (shareddom[numShared[s.second] + j] == s.first))
                        {
                            break;
                        }
                    }
 
                    sharedid[numShared[s.second] + j] = numOffset[rank] + cnt1;
                    cnt1++;
                }
                cnt++;
            }
 
            // now communicate ids to all procesors.
            m_comm->AllReduce(sharedid, LibUtilities::ReduceMax);
 
            if (rank == 0)
            {
                for (size_t i = 0; i < (size_t)totShared; ++i)
                {
                    ASSERTL1(sharedid[i] != -1.0,
                             "Failed to number shared proc uniquely");
                }
            }
 
            cnt = 0;
            int maxoffset =
                (int)Vmath::Vmax(nShrProc, &sharedid[numShared[rank]], 1);
            m_comm->AllReduce(maxoffset, LibUtilities::ReduceMax);
            maxoffset++;
 
            // make a map relating the order of the SharedProc to the domain
            // id
            std::map<int, int> ShrToDom;
            cnt = 0;
            for (auto &s : SharedProc)
            {
                ShrToDom[cnt] = s.first;
                ++cnt;
            }
 
            // Set up a set the domain ids listed in the ordering of
            // the SharedProc unique numbering
            std::set<int> doneDom;
            for (size_t i = 0; i < nShrProc; ++i)
            {
                int minId =
                    Vmath::Imin(nShrProc, &sharedid[numShared[rank]], 1);
                sharedid[numShared[rank] + minId] += maxoffset;
 
                m_domOrder.push_back(ShrToDom[minId]);
                doneDom.insert(ShrToDom[minId]);
            }
 
            // add all the other
            for (auto &d : m_domain)
            {
                if (doneDom.count(d.first) == 0)
                {
                    m_domOrder.push_back(d.first);
                }
            }
        }
    }
}

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, ASSERTL1, Nektar::UnitTests::d(), Vmath::Imin(), Nektar::SolverUtils::EquationSystem::m_comm, m_domain, m_domOrder, Nektar::LibUtilities::ReduceMax, Nektar::LibUtilities::ReduceSum, Vmath::Vmax(), and Vmath::Vsum().

Referenced by v_InitObject().

◆ GetNdomains()

int Nektar::PulseWaveSystem::GetNdomains ( )

inline

Definition at line 80 of file PulseWaveSystem.h.

    {
        return m_nDomains;
    }

References m_nDomains.

◆ InterfaceRiemann()

void Nektar::PulseWaveSystem::InterfaceRiemann	(	Array< OneD, NekDouble > &	Au,
		Array< OneD, NekDouble > &	uu,
		Array< OneD, NekDouble > &	beta,
		Array< OneD, NekDouble > &	A_0,
		Array< OneD, NekDouble > &	alpha
	)

protected

Riemann Problem for Interface/Junction.

Solves the Riemann problem at an interdomain junction/Interface by assuming subsonic flow at both sides of the boundary and by applying conservation of mass and continuity of the total pressure \( \frac{p}{rho} + \frac{u^{2}}{2}. \) The other 2 missing equations come from the characteristic variables. For further information see "Pulse WavePropagation in the human vascular system" Section 3.4.

Definition at line 1816 of file PulseWaveSystem.cpp.

{
 
    NekDouble rho = m_rho;
    Array<OneD, NekDouble> W(2);
    Array<OneD, NekDouble> W_Au(2);
    Array<OneD, NekDouble> P_Au(2);
    NekMatrix<NekDouble> invJ(4, 4);
    NekVector<NekDouble> f(4);
    NekVector<NekDouble> dx(4);
 
    int proceed   = 1;
    int iter      = 0;
    int MAX_ITER  = 15;
    NekDouble Tol = 1.0E-10;
 
    // Forward and backward characteristics
    m_pressureArea->GetW1(W[0], uu[0], beta[0], Au[0], A_0[0], alpha[0]);
    m_pressureArea->GetW2(W[1], uu[1], beta[1], Au[1], A_0[1], alpha[1]);
 
    while ((proceed) && (iter < MAX_ITER))
    {
        LibUtilities::Timer time_InterfaceRiemann;
        time_InterfaceRiemann.Start();
        iter += 1;
 
        /*
         * We solve the four constraint equations via a multivariate Newton
         * iteration. Equations are:
         * 1. Forward characteristic:        W1(A_L, U_L) = W1(Au_L, Uu_L)
         * 2. Backward characteristic:       W2(A_R, U_R) = W2(Au_R, Uu_R)
         * 3. Conservation of mass:          Au_L * Uu_L = Au_R * Uu_R
         * 4. Continuity of total pressure:  rho * Uu_L * Uu_L / 2 + p(Au_L)
         * = rho * Uu_R * Uu_R / 2 + p(Au_R)
         */
        for (size_t i = 0; i < 2; ++i)
        {
            m_pressureArea->GetPressure(P_Au[i], beta[i], Au[i], A_0[i], 0, 0,
                                        alpha[i]);
        }
 
        m_pressureArea->GetW1(W_Au[0], uu[0], beta[0], Au[0], A_0[0], alpha[0]);
        m_pressureArea->GetW2(W_Au[1], uu[1], beta[1], Au[1], A_0[1], alpha[1]);
 
        // Constraint equations set to zero
        f[0] = W_Au[0] - W[0];
        f[1] = W_Au[1] - W[1];
        f[2] = Au[0] * uu[0] - Au[1] * uu[1];
        f[3] = uu[0] * uu[0] + 2 * P_Au[0] / rho - uu[1] * uu[1] -
               2 * P_Au[1] / rho;
 
        // Inverse Jacobian for x + dx = x - J^(-1) * f(x)
        m_pressureArea->GetJacobianInverse(invJ, Au, uu, beta, A_0, alpha,
                                           "Interface");
 
        Multiply(dx, invJ, f);
 
        // Update solution: x_new = x_old - dx
        for (size_t i = 0; i < 2; ++i)
        {
            uu[i] -= dx[i];
            Au[i] -= dx[i + 2];
        }
 
        // Check if the error of the solution is smaller than Tol.
        if (Dot(dx, dx) < Tol)
        {
            proceed = 0;
        }
        time_InterfaceRiemann.Stop();
        time_InterfaceRiemann.AccumulateRegion(
            "PulseWaveSystem::InterfaceRiemann", 2);
    }
 
    if (iter >= MAX_ITER)
    {
        ASSERTL0(false, "Riemann solver for Interface did not converge");
    }
}

References Nektar::LibUtilities::Timer::AccumulateRegion(), ASSERTL0, Nektar::LibUtilities::beta, Nektar::Dot(), m_pressureArea, m_rho, Nektar::Multiply(), Nektar::LibUtilities::Timer::Start(), and Nektar::LibUtilities::Timer::Stop().

Referenced by EnforceInterfaceConditions().

◆ LinkSubdomains()

void Nektar::PulseWaveSystem::LinkSubdomains ( Array< OneD, Array< OneD, Array< OneD, NekDouble > > > & fields )

protected

Links the subdomains.

◆ MergingRiemann()

void Nektar::PulseWaveSystem::MergingRiemann	(	Array< OneD, NekDouble > &	Au,
		Array< OneD, NekDouble > &	uu,
		Array< OneD, NekDouble > &	beta,
		Array< OneD, NekDouble > &	A_0,
		Array< OneD, NekDouble > &	alpha
	)

protected

Riemann Problem for Merging Flow.

Solves the Riemann problem at an merging flow condition by assuming subsonic flow at both sides of the boundary and by applying conservation of mass and continuity of the total pressure \( \frac{p}{rho} + \frac{u^{2}}{2}. \) The other 3 missing equations come from the characteristic variables. For further information see "Pulse WavePropagation in the human vascular system" Section 3.4.4

Definition at line 1702 of file PulseWaveSystem.cpp.

{
 
    NekDouble rho = m_rho;
    Array<OneD, NekDouble> W(3);
    Array<OneD, NekDouble> W_Au(3);
    Array<OneD, NekDouble> P_Au(3);
    NekMatrix<NekDouble> invJ(6, 6);
    NekVector<NekDouble> f(6);
    NekVector<NekDouble> dx(6);
 
    int proceed  = 1;
    int iter     = 0;
    int MAX_ITER = 15;
 
    // Backward characteristic
    m_pressureArea->GetW2(W[0], uu[0], beta[0], Au[0], A_0[0], alpha[0]);
 
    // Forward characteristics
    for (size_t i = 1; i < 3; ++i)
    {
        m_pressureArea->GetW1(W[i], uu[i], beta[i], Au[i], A_0[i], alpha[i]);
    }
 
    // Tolerances for the algorithm
    NekDouble Tol = 1.0E-10;
 
    // Newton Iteration
    while ((proceed) && (iter < MAX_ITER))
    {
        LibUtilities::Timer time_MergingRiemann;
        time_MergingRiemann.Start();
        iter += 1;
 
        /*
         * We solve the six constraint equations via a multivariate Newton
         * iteration. Equations are:
         * 1. Backward characteristic:          W2(A_R,  U_R)  = W1(Au_R,
         * Uu_R)
         * 2. Forward characteristic 1:         W1(A_L1, U_L1) = W1(Au_L1,
         * Uu_R1)
         * 3. Forward characteristic 2:         W1(A_L2, U_L2) = W1(Au_L2,
         * Uu_L2)
         * 4. Conservation of mass:             Au_R * Uu_R    = Au_L1 *
         * Uu_L1 + Au_L2 * Uu_L2
         * 5. Continuity of total pressure 1:  rho * Uu_R  * Uu_R  / 2 +
         * p(Au_R) = rho * Uu_L1 * Uu_L1 / 2 + p(Au_L1)
         * 6. Continuity of total pressure 2:  rho * Uu_R  * Uu_R  / 2 +
         * p(Au_R) = rho * Uu_L2 * Uu_L2 / 2 + p(Au_L2)
         */
        for (size_t i = 0; i < 3; ++i)
        {
            m_pressureArea->GetPressure(P_Au[i], beta[i], Au[i], A_0[i], 0, 0,
                                        alpha[i]);
        }
 
        m_pressureArea->GetW2(W_Au[0], uu[0], beta[0], Au[0], A_0[0], alpha[0]);
        m_pressureArea->GetW1(W_Au[1], uu[1], beta[1], Au[1], A_0[1], alpha[1]);
        m_pressureArea->GetW1(W_Au[2], uu[2], beta[2], Au[2], A_0[2], alpha[2]);
 
        // Constraint equations set to zero
        f[0] = W_Au[0] - W[0];
        f[1] = W_Au[1] - W[1];
        f[2] = W_Au[2] - W[2];
        f[3] = Au[0] * uu[0] - Au[1] * uu[1] - Au[2] * uu[2];
        f[4] = uu[0] * uu[0] + 2 * P_Au[0] / rho - uu[1] * uu[1] -
               2 * P_Au[1] / rho;
        f[5] = uu[0] * uu[0] + 2 * P_Au[0] / rho - uu[2] * uu[2] -
               2 * P_Au[2] / rho;
 
        // Inverse Jacobian for x + dx = x - J^(-1) * f(x)
        m_pressureArea->GetJacobianInverse(invJ, Au, uu, beta, A_0, alpha,
                                           "Merge");
 
        Multiply(dx, invJ, f);
 
        // Update the solution: x_new = x_old - dx
        for (size_t i = 0; i < 3; ++i)
        {
            uu[i] -= dx[i];
            Au[i] -= dx[i + 3];
        }
 
        // Check if the error of the solution is smaller than Tol
        if (Dot(dx, dx) < Tol)
        {
            proceed = 0;
        }
 
        // Check if solver converges
        if (iter >= MAX_ITER)
        {
            ASSERTL0(false, "Riemann solver for Merging Flow did not converge");
        }
        time_MergingRiemann.Stop();
        time_MergingRiemann.AccumulateRegion("PulseWaveSystem::MergingRiemann",
                                             2);
    }
}

References Nektar::LibUtilities::Timer::AccumulateRegion(), ASSERTL0, Nektar::LibUtilities::beta, Nektar::Dot(), m_pressureArea, m_rho, Nektar::Multiply(), Nektar::LibUtilities::Timer::Start(), and Nektar::LibUtilities::Timer::Stop().

Referenced by EnforceInterfaceConditions().

◆ SetUpDomainInterfaceBCs()

void Nektar::PulseWaveSystem::SetUpDomainInterfaceBCs	(	SpatialDomains::BoundaryConditions &	AllBcs,
		std::map< int, LibUtilities::CommSharedPtr > &	domComm
	)

private

Definition at line 1074 of file PulseWaveSystem.cpp.

{
 
    const SpatialDomains::BoundaryRegionCollection &bregions =
        Allbcs.GetBoundaryRegions();
 
    /* Loop over domain and find out if we have any undefined
     * boundary conditions representing interfaces. If so make a
     * map based around vid and storing the domains that are
     * part of interfaces.
     */
    int numNewBc = 1;
    for (auto &d : m_domOrder)
    {
 
        std::map<int, SpatialDomains::GeometrySharedPtr> domvids;
 
        // Loop over each domain and find which vids are only touched
        // by one element
        for (auto &compIt : m_domain[d])
        {
            for (size_t j = 0; j < compIt.second->m_geomVec.size(); ++j)
            {
 
                // get hold of vids of each segment
                for (size_t p = 0; p < 2; ++p)
                {
                    SpatialDomains::GeometrySharedPtr vert =
                        compIt.second->m_geomVec[j]->GetVertex(p);
                    int vid = vert->GetGlobalID();
 
                    // if vid has already been added remove it otherwise add
                    // into set
                    if (domvids.count(vid))
                    {
                        domvids.erase(vid);
                    }
                    else
                    {
                        domvids[vid] = vert;
                    }
                }
            }
        }
 
        ASSERTL1(domvids.size() == 2, "Failed to find two end points "
                                      "of a domain (domvids = " +
                                          std::to_string(domvids.size()) + ")");
 
        size_t nprocs = domComm[d]->GetSize();
 
        if (nprocs > 1) // Remove parallel interfaces
        {
            size_t rank = domComm[d]->GetRank();
            Array<OneD, int> nvids(nprocs, 0);
            nvids[rank] = domvids.size();
            domComm[d]->AllReduce(nvids, LibUtilities::ReduceSum);
 
            size_t totvids = Vmath::Vsum(nprocs, nvids, 1);
 
            Array<OneD, int> locids(totvids, -1);
 
            size_t cnt = 0;
            for (size_t i = 0; i < rank; ++i)
            {
                cnt += nvids[i];
            }
 
            for (auto &i : domvids)
            {
                locids[cnt++] = i.first;
            }
 
            // collect lcoal vids on this domain on all processor
            domComm[d]->AllReduce(locids, LibUtilities::ReduceMax);
 
            std::set<int> chkvids;
            for (size_t i = 0; i < totvids; ++i)
            {
                if (chkvids.count(locids[i]))
                {
                    // if this id is on local domain then remove
                    if (domvids.count(locids[i]))
                    {
                        domvids.erase(locids[i]);
                    }
                }
                else
                {
                    chkvids.insert(locids[i]);
                }
            }
        }
 
        // Finally check if remaining domvids are already declared, if
        // not add them
 
        // Erase from domvids any existing BCs
        for (auto &it : bregions)
        {
            for (auto &bregionIt : *it.second)
            {
                // can assume that all regions only contain one point in 1D
                // Really do not need loop above
                int id = bregionIt.second->m_geomVec[0]->GetGlobalID();
 
                if (domvids.count(id))
                {
                    domvids.erase(id);
                }
            }
        }
 
        // Finally add interface conditions to Allbcs
        std::vector<std::string> variables = m_session->GetVariables();
 
        // determine the maxmimum bregion index
        int maxbregind = 0;
        for (auto &b : bregions)
        {
            maxbregind = (maxbregind > b.first) ? maxbregind : b.first;
        }
 
        for (auto &b : domvids)
        {
            SpatialDomains::BoundaryRegionShPtr breg(
                MemoryManager<
                    SpatialDomains::BoundaryRegion>::AllocateSharedPtr());
 
            // Set up Composite (GemetryVector) to contain vertex and put
            // into bRegion
            SpatialDomains::CompositeSharedPtr gvec =
                MemoryManager<SpatialDomains::Composite>::AllocateSharedPtr();
            gvec->m_geomVec.push_back(b.second);
            (*breg)[b.first] = gvec;
 
            Allbcs.AddBoundaryRegions(maxbregind + numNewBc, breg);
 
            SpatialDomains::BoundaryConditionMapShPtr bCondition =
                MemoryManager<
                    SpatialDomains::BoundaryConditionMap>::AllocateSharedPtr();
 
            std::string userDefined = "Interface";
            // Set up just boundary condition for this variable.
            SpatialDomains::BoundaryConditionShPtr DirichletInterface(
                MemoryManager<SpatialDomains::DirichletBoundaryCondition>::
                    AllocateSharedPtr(m_session, "0", userDefined));
 
            for (size_t i = 0; i < variables.size(); ++i)
            {
                (*bCondition)[variables[i]] = DirichletInterface;
            }
 
            Allbcs.AddBoundaryConditions(maxbregind + numNewBc, bCondition);
            ++numNewBc;
        }
    }
}

References Nektar::SpatialDomains::BoundaryConditions::AddBoundaryConditions(), Nektar::SpatialDomains::BoundaryConditions::AddBoundaryRegions(), Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL1, Nektar::UnitTests::d(), Nektar::SpatialDomains::BoundaryConditions::GetBoundaryRegions(), m_domain, m_domOrder, Nektar::SolverUtils::EquationSystem::m_session, CellMLToNektar.cellml_metadata::p, Nektar::LibUtilities::ReduceMax, Nektar::LibUtilities::ReduceSum, and Vmath::Vsum().

Referenced by v_InitObject().

◆ SetUpDomainInterfaces()

void Nektar::PulseWaveSystem::SetUpDomainInterfaces ( void )

private

Definition at line 799 of file PulseWaveSystem.cpp.

{
    std::map<int, std::vector<InterfacePointShPtr>> VidToDomain;
 
    // First set up domain to determine how many vertices meet at a
    // vertex.  This allows us to
 
    /* Loop over domain and find out if we have any undefined
     * boundary conditions representing interfaces. If so make a
     * map based around vid and storing the domains that are
     * part of interfaces.
     */
    for (size_t omega = 0; omega < m_nDomains; ++omega)
    {
        size_t vesselID = omega * m_nVariables;
 
        for (size_t i = 0; i < (m_vessels[vesselID]->GetBndConditions()).size();
             ++i)
        {
            if (m_vessels[vesselID]->GetBndConditions()[i]->GetUserDefined() ==
                "Interface")
            {
                // Get Vid of interface
                int vid = m_vessels[vesselID]
                              ->UpdateBndCondExpansion(i)
                              ->GetExp(0)
                              ->GetGeom()
                              ->GetVid(0);
 
                MultiRegions::ExpListSharedPtr trace =
                    m_vessels[vesselID]->GetTrace();
                InterfacePointShPtr Ipt;
 
                bool finish = false;
                // find which elmt, the local vertex and the data
                // offset of point
                size_t nExp = m_vessels[vesselID]->GetExpSize();
                for (size_t n = 0; n < nExp; ++n)
                {
                    for (size_t p = 0; p < 2; ++p)
                    {
 
                        if (m_vessels[vesselID]
                                ->GetTraceMap()
                                ->GetElmtToTrace()[n][p]
                                ->as<LocalRegions::Expansion>()
                                ->GetGeom()
                                ->GetVid(0) == vid)
                        {
                            int eid = m_vessels[vesselID]
                                          ->GetTraceMap()
                                          ->GetElmtToTrace()[n][p]
                                          ->GetElmtId();
 
                            int tid = m_vessels[vesselID]
                                          ->GetTrace()
                                          ->GetCoeff_Offset(eid);
 
                            Ipt = MemoryManager<
                                InterfacePoint>::AllocateSharedPtr(vid, omega,
                                                                   n, p, tid,
                                                                   i);
 
                            finish = true;
                            break;
                        }
                    }
                    if (finish == true)
                    {
                        break;
                    }
                }
 
                VidToDomain[vid].push_back(Ipt);
            }
        }
    }
 
    // Set up comms for parallel cases
    std::map<int, int> domId;
 
    size_t cnt = 0;
    for (auto &d : m_domain)
    {
        domId[cnt] = d.first;
        ++cnt;
    }
    ASSERTL1(domId.size() == m_nDomains, "Number of domains do not match");
 
    Gs::gs_data *gscomm;
    int nvid2dom = VidToDomain.size();
    Array<OneD, long> tmp(nvid2dom);
    Array<OneD, NekDouble> nvid(nvid2dom, 0.0);
 
    cnt = 0;
    for (auto &v : VidToDomain)
    {
        tmp[cnt] = v.first + 1;
        for (size_t i = 0; i < v.second.size(); ++i)
        {
            nvid[cnt] += 1.0;
        }
        cnt++;
    }
 
    const bool verbose = m_session->DefinesCmdLineArgument("verbose");
 
    gscomm = Gs::Init(tmp, m_comm->GetRowComm(), verbose);
    Gs::Gather(nvid, Gs::gs_add, gscomm);
 
    // Loop over domains and identify how many vessels at a
    // bifurcation use the beginning of the element at the
    // junction. This distinguishes a bifurcation and merging junction
    // since we implicitly assume elements are ordered left ot right
    // and so at a bifurcation we have two elements meeting this point
    // at the first vertex
    Array<OneD, NekDouble> nbeg(nvid2dom, 0.0);
    cnt = 0;
    for (auto &v : VidToDomain)
    {
        if (nvid[cnt] == 3.0)
        {
            for (size_t i = 0; i < v.second.size(); ++i)
            {
                // for bifurcations and merging junctions store how
                // many points at interface are at the beginning or
                // end
                if (v.second[i]->m_elmtVert == 0)
                {
                    nbeg[cnt] += 1.0;
                }
            }
        }
        ++cnt;
    }
    Gs::Gather(nbeg, Gs::gs_add, gscomm);
 
    // Finally determine the maximum domain id between the two vessels
    // at an interfaces or the maximum domain id of the daughter
    // vessels for a bifurcation or the two parent id's for a merging
    // junction
    Array<OneD, NekDouble> dom(VidToDomain.size(), 0.0);
    cnt = 0;
    for (auto &v : VidToDomain)
    {
        if (nvid[cnt] == 2.0)
        {
            // store the domain id of the two domains
            for (size_t i = 0; i < v.second.size(); ++i)
            {
                dom[cnt] =
                    std::max(dom[cnt], (NekDouble)domId[v.second[i]->m_domain]);
            }
        }
        else if (nvid[cnt] == 3.0)
        {
            // store the domain id of the two daughter vessels if a
            // bifurcation or the two parent vessels if a merging
            // junction
 
            int val = (nbeg[cnt] == 2.0) ? 0 : 1;
 
            for (size_t i = 0; i < v.second.size(); ++i)
            {
                if (v.second[i]->m_elmtVert == val)
                {
                    dom[cnt] = std::max(
                        dom[cnt], (NekDouble)domId[v.second[i]->m_domain]);
                }
            }
        }
        ++cnt;
    }
    Gs::Gather(dom, Gs::gs_max, gscomm);
 
    // loop over map and set up Interface information;
    int v = 0;
    for (auto &iter : VidToDomain)
    {
        ASSERTL1(nvid[v] != 1.0, "Found an interface wth only "
                                 "one domain which should not happen");
 
        if (nvid[v] == 2.0) // Vessel jump interface
        {
            for (size_t i = 0; i < iter.second.size(); ++i)
            {
                if (domId[iter.second[i]->m_domain] == dom[v])
                {
                    iter.second[i]->m_riemannOrd = 1;
                }
                else
                {
                    iter.second[i]->m_riemannOrd = 0;
                }
            }
            m_vesselIntfcs.push_back(iter.second);
        }
        else if (nvid[v] == 3.0) // Bifurcation or Merging junction.
        {
            // Set up Bifurcation information
            int val = (nbeg[v] == 2.0) ? 1 : 0;
 
            for (size_t i = 0; i < iter.second.size(); ++i)
            {
                if (iter.second[i]->m_elmtVert == val)
                {
                    iter.second[i]->m_riemannOrd = 0;
                }
                else
                {
                    if (domId[iter.second[i]->m_domain] == dom[v])
                    {
                        iter.second[i]->m_riemannOrd = 2;
                    }
                    else
                    {
                        iter.second[i]->m_riemannOrd = 1;
                    }
                }
            }
 
            if (nbeg[v] == 2.0)
            {
                m_bifurcations.push_back(iter.second);
            }
            else
            {
                m_mergingJcts.push_back(iter.second);
            }
        }
        else
        {
            ASSERTL0(false, "Unknown junction type");
        }
        ++v; // incrementing loop over vertices
    }
 
    // finally set up a communicator for interface data collection
    Array<OneD, long> tmp1(3 * nvid2dom);
    if (nvid2dom)
    {
        Vmath::Zero(3 * nvid2dom, tmp1, 1);
    }
 
    cnt = 0;
    for (size_t n = 0; n < m_bifurcations.size(); ++n, ++cnt)
    {
        size_t vid = m_bifurcations[n][0]->m_vid;
        for (size_t i = 0; i < 3; ++i)
        {
            tmp1[3 * cnt + i] = (NekDouble)(3 * vid + i + 1);
        }
    }
 
    for (size_t n = 0; n < m_mergingJcts.size(); ++n, ++cnt)
    {
        size_t vid = m_mergingJcts[n][0]->m_vid;
        for (size_t i = 0; i < 3; ++i)
        {
            tmp1[3 * cnt + i] = (NekDouble)(3 * vid + i + 1);
        }
    }
 
    for (size_t n = 0; n < m_vesselIntfcs.size(); ++n, ++cnt)
    {
        size_t vid = m_vesselIntfcs[n][0]->m_vid;
        for (size_t i = 0; i < 3; ++i)
        {
            tmp1[3 * cnt + i] = (NekDouble)(3 * vid + i + 1);
        }
    }
 
    m_intComm = Gs::Init(tmp1, m_comm->GetRowComm(), verbose);
}

References ASSERTL0, ASSERTL1, Nektar::UnitTests::d(), Gs::Gather(), Gs::gs_add, Gs::gs_max, Gs::Init(), m_bifurcations, Nektar::SolverUtils::EquationSystem::m_comm, m_domain, m_intComm, m_mergingJcts, m_nDomains, m_nVariables, Nektar::SolverUtils::EquationSystem::m_session, m_vesselIntfcs, m_vessels, CellMLToNektar.cellml_metadata::p, and Vmath::Zero().

Referenced by v_InitObject().

◆ UpdateVessels()

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

inline

Definition at line 85 of file PulseWaveSystem.h.

    {
        return m_vessels;
    }

References m_vessels.

◆ v_DoInitialise()

void Nektar::PulseWaveSystem::v_DoInitialise ( bool dumpInitialConditions = false )

overrideprotectedvirtual

Sets up initial conditions.

Initialisation routine for multiple subdomain case. Sets the initial conditions for all arterial subdomains read from the inputfile. Sets the material properties and the A_0 area for all subdomains and fills the domain-linking boundary conditions with the initial values of their domain.

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 1242 of file PulseWaveSystem.cpp.

{
    if (m_session->GetComm()->GetRank() == 0)
    {
        std::cout << "Initial Conditions: " << std::endl;
    }
 
    /* Loop over all subdomains to initialize all with the Initial
     * Conditions read from the inputfile*/
    int omega = 0;
    for (auto &d : m_domOrder)
    {
        for (size_t i = 0; i < m_nVariables; ++i)
        {
            m_fields[i] = m_vessels[m_nVariables * omega + i];
        }
 
        if (m_session->GetComm()->GetRank() == 0)
        {
            std::cout << "Subdomain: " << omega << std::endl;
        }
 
        SetInitialConditions(0.0, false, d);
        omega++;
    }
 
    // Reset  variables to first vessels
    for (size_t i = 0; i < m_nVariables; ++i)
    {
        m_fields[i] = m_vessels[i];
    }
 
    // Update filters.
    for (auto &d : m_domainToFilterIDs)
    {
        Array<OneD, MultiRegions::ExpListSharedPtr> filterFields(m_nVariables);
 
        int vesselID = m_filterToVesselID[d.second[0]];
        for (size_t j = 0; j < m_nVariables; ++j)
        {
            filterFields[j] = m_vessels[vesselID + j];
        }
 
        // loop over filters in domain
        for (auto &f : d.second)
        {
            m_filters[f].second->Update(filterFields, m_time);
        }
    }
}

References Nektar::UnitTests::d(), m_domainToFilterIDs, m_domOrder, Nektar::SolverUtils::EquationSystem::m_fields, Nektar::SolverUtils::UnsteadySystem::m_filters, m_filterToVesselID, m_nVariables, Nektar::SolverUtils::EquationSystem::m_session, Nektar::SolverUtils::EquationSystem::m_time, m_vessels, and Nektar::SolverUtils::EquationSystem::SetInitialConditions().

◆ v_DoSolve()

void Nektar::PulseWaveSystem::v_DoSolve ( void )

overrideprotectedvirtual

Solves an unsteady problem.

NEEDS Updating:

DoSolve routine for PulseWavePropagation with multiple subdomains taken from UnsteadySystem and modified for multidomain case. Initialises the time integration scheme (as specified in the session file), and perform the time integration. Within the timestepping loop the following is done: 1. Link all arterial segments according to the network structure, solve the Riemann problem between different arterial segments and assign the values to the boundary conditions (LinkSubdomains) 2. Every arterial segment is solved independently for this timestep. This is done by handing the solution vector \( \mathbf{u} \) and the right hand side m_ode, which is the PulseWavePropagation class in this example over to the time integration scheme

if(m_session->GetComm()->GetRank() == 0) { cout << "Time-integration timing: " << IntegrationTime << " s" << endl << endl; }

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 1311 of file PulseWaveSystem.cpp.

{
    size_t i;
    int n;
    int nchk = 1;
 
    Array<OneD, Array<OneD, NekDouble>> fields(m_nVariables);
 
    for (i = 0; i < m_nVariables; ++i)
    {
        fields[i] = m_vessels[i]->UpdatePhys();
        m_fields[i]->SetPhysState(false);
    }
 
    m_intScheme->InitializeScheme(m_timestep, fields, m_time, m_ode);
 
    // Time loop
    for (n = 0; n < m_steps; ++n)
    {
        LibUtilities::Timer time_v_IntStep;
        time_v_IntStep.Start();
        fields = m_intScheme->TimeIntegrate(n, m_timestep);
        m_time += m_timestep;
        time_v_IntStep.Stop();
        time_v_IntStep.AccumulateRegion("PulseWaveSystem::TimeIntegrationStep",
                                        0);
        // Write out status information.
        if (m_infosteps && !((n + 1) % m_infosteps) &&
            m_session->GetComm()->GetRank() == 0)
        {
            std::cout << "Steps: " << n + 1 << "\t Time: " << m_time
                      << "\t Time-step: " << m_timestep << "\t" << std::endl;
        }
 
        // Copy Array To Vessel Phys Fields
        for (size_t i = 0; i < m_nVariables; ++i)
        {
            Vmath::Vcopy(fields[i].size(), fields[i], 1,
                         m_vessels[i]->UpdatePhys(), 1);
        }
 
        // Transform data if needed
        if (m_checksteps && !((n + 1) % m_checksteps))
        {
            for (i = 0; i < m_nVariables; ++i)
            {
                for (size_t omega = 0; omega < m_nDomains; omega++)
                {
                    unsigned int offset = omega * m_nVariables + i;
                    m_vessels[offset]->FwdTrans(
                        fields[i] + m_fieldPhysOffset[omega],
                        m_vessels[offset]->UpdateCoeffs());
                }
            }
            CheckPoint_Output(nchk++);
        }
 
        // Update filters.
        for (auto &d : m_domainToFilterIDs)
        {
            Array<OneD, MultiRegions::ExpListSharedPtr> filterFields(
                m_nVariables);
            int vesselID = m_filterToVesselID[d.second[0]];
            for (size_t j = 0; j < m_nVariables; ++j)
            {
                filterFields[j] = m_vessels[vesselID + j];
            }
 
            // loop over filters in domain
            for (auto &f : d.second)
            {
                m_filters[f].second->Update(filterFields, m_time);
            }
        }
 
    } // end of timeintegration
 
    /**  if(m_session->GetComm()->GetRank() == 0)
         {
         cout << "Time-integration timing: " << IntegrationTime << " s" <<
         endl
         << endl;
         } **/
 
    // Finalise filters.
    for (auto &d : m_domainToFilterIDs)
    {
        Array<OneD, MultiRegions::ExpListSharedPtr> filterFields(m_nVariables);
        int vesselID = m_filterToVesselID[d.second[0]];
        for (size_t j = 0; j < m_nVariables; ++j)
        {
            filterFields[j] = m_vessels[vesselID + j];
        }
 
        // loop over filters in domain
        for (auto &f : d.second)
        {
            m_filters[f].second->Finalise(filterFields, m_time);
        }
    }
}

◆ v_InitObject()

void Nektar::PulseWaveSystem::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::SolverUtils::UnsteadySystem.

Definition at line 80 of file PulseWaveSystem.cpp.

{
    // Initialise base class
    UnsteadySystem::v_InitObject(DeclareField);
 
    // Read the geometry and the expansion information
    m_domain   = m_graph->GetDomain();
    m_nDomains = m_domain.size();
 
    // Determine projectiontype
    ASSERTL0(m_session->MatchSolverInfo("Projection", "DisContinuous"),
             "Pulse solver only set up for Discontinuous projections");
    m_projectionType = MultiRegions::eDiscontinuous;
    ASSERTL0(
        m_graph->GetMeshDimension() == 1,
        "Pulse wave solver only set up for expansion dimension equal to 1");
 
    size_t i;
    m_nVariables = m_session->GetVariables().size();
 
    m_fields = Array<OneD, MultiRegions::ExpListSharedPtr>(m_nVariables);
    m_vessels =
        Array<OneD, MultiRegions::ExpListSharedPtr>(m_nVariables * m_nDomains);
 
    /* If the PressureArea property is not specified, default to the Beta
     * law; it's the most well known and this way previous examples that did
     * not specify the tube law will still work.
     */
    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);
    }
 
    m_pressure = Array<OneD, Array<OneD, NekDouble>>(m_nDomains);
 
    m_PWV = Array<OneD, Array<OneD, NekDouble>>(m_nDomains);
    m_W1  = Array<OneD, Array<OneD, NekDouble>>(m_nDomains);
    m_W2  = Array<OneD, Array<OneD, NekDouble>>(m_nDomains);
 
    SpatialDomains::BoundaryConditions Allbcs(m_session, m_graph);
 
    // get parallel communicators as required
    std::map<int, LibUtilities::CommSharedPtr> domComm;
    GetCommArray(domComm);
 
    SetUpDomainInterfaceBCs(Allbcs, domComm);
 
    // set up a list of the domain to filter ids
    auto filterMap    = m_session->GetFilters();
    unsigned int fcnt = 0;
    for (auto &x : filterMap)
    {
        ASSERTL0(x.domain != -1, "Filter needs DOMAIN attribute when "
                                 "applied to PulseWaveSolver.")
        m_domainToFilterIDs[x.domain].push_back(fcnt);
        ++fcnt;
    }
 
    // Set up domains and put geometry to be only one space dimension.
    size_t cnt = 0;
    // currently I believe we have to set to one space dimension on
    // constuction since the advection terms are set to differentiate
    // with respect to x (or the lcoal ordinate) not as an arc length
    // derivative. So will not get consistent answers wtihout this
    bool SetToOneSpaceDimension = true;
 
    for (auto &d : m_domOrder)
    {
        // need to check if we have filters on this domain and if so
        // set them up without SetToOneSpaceDimension if so we can
        // initialisatio them (i.e. history points)
        if (m_domainToFilterIDs.count(d))
        {
            // make temporary expansion list to not settig to one space
            // dimension
            Array<OneD, MultiRegions::ExpListSharedPtr> filterFields(
                m_nVariables);
            for (size_t j = 0; j < m_nVariables; ++j)
            {
                filterFields[j] = MemoryManager<MultiRegions::DisContField>::
                    AllocateSharedPtr(m_session, m_graph, m_domain[d], Allbcs,
                                      m_session->GetVariable(j), domComm[d],
                                      false);
            }
 
            // intiialise filters with temporary expansion lsits
            for (auto &x : m_domainToFilterIDs[d])
            {
                m_filters[x].second->SetUpdateOnInitialise(false);
                m_filters[x].second->Initialise(filterFields, m_time);
                m_filters[x].second->SetUpdateOnInitialise(true);
 
                // save vessel start id for update
                m_filterToVesselID[x] = cnt;
            }
        }
 
        for (size_t j = 0; j < m_nVariables; ++j)
        {
            m_vessels[cnt++] =
                MemoryManager<MultiRegions::DisContField>::AllocateSharedPtr(
                    m_session, m_graph, m_domain[d], Allbcs,
                    m_session->GetVariable(j), domComm[d],
                    SetToOneSpaceDimension);
        }
    }
 
    // Reset coeff and phys space to be continuous over all domains
    int totcoeffs     = 0;
    int totphys       = 0;
    m_fieldPhysOffset = Array<OneD, int>(m_nDomains + 1, 0);
    for (i = 0; i < m_nDomains; ++i)
    {
        totcoeffs += m_vessels[i * m_nVariables]->GetNcoeffs();
 
        m_fieldPhysOffset[i] = totphys;
        totphys += m_vessels[i * m_nVariables]->GetTotPoints();
    }
    m_fieldPhysOffset[m_nDomains] = totphys;
 
    for (size_t n = 0; n < m_nVariables; ++n)
    {
        Array<OneD, NekDouble> coeffs(totcoeffs, 0.0);
        Array<OneD, NekDouble> phys(totphys, 0.0);
        Array<OneD, NekDouble> tmpcoeffs, tmpphys;
 
        m_vessels[n]->SetCoeffsArray(coeffs);
        m_vessels[n]->SetPhysArray(phys);
 
        int cnt  = m_vessels[n]->GetNcoeffs();
        int cnt1 = m_vessels[n]->GetTotPoints();
 
        for (i = 1; i < m_nDomains; ++i)
        {
            m_vessels[i * m_nVariables + n]->SetCoeffsArray(tmpcoeffs =
                                                                coeffs + cnt);
            m_vessels[i * m_nVariables + n]->SetPhysArray(tmpphys =
                                                              phys + cnt1);
            cnt += m_vessels[i * m_nVariables + n]->GetNcoeffs();
            cnt1 += m_vessels[i * m_nVariables + n]->GetTotPoints();
        }
    }
 
    // If Discontinuous Galerkin determine upwinding method to use
    for (size_t i = 0; i < SIZE_UpwindTypePulse; ++i)
    {
        bool match;
        m_session->MatchSolverInfo("UPWINDTYPEPULSE", UpwindTypeMapPulse[i],
                                   match, false);
        if (match)
        {
            m_upwindTypePulse = (UpwindTypePulse)i;
            break;
        }
    }
 
    // Load blood density and external pressure
    m_session->LoadParameter("rho", m_rho, 0.5);
    m_session->LoadParameter("pext", m_pext, 0.0);
 
    int nq = 0;
    /*
     *  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
     */
    m_beta             = Array<OneD, Array<OneD, NekDouble>>(m_nDomains);
    m_beta_trace       = Array<OneD, Array<OneD, NekDouble>>(m_nDomains);
    m_gamma            = Array<OneD, Array<OneD, NekDouble>>(m_nDomains);
    m_alpha            = Array<OneD, Array<OneD, NekDouble>>(m_nDomains);
    m_alpha_trace      = Array<OneD, Array<OneD, NekDouble>>(m_nDomains);
    m_A_0              = Array<OneD, Array<OneD, NekDouble>>(m_nDomains);
    m_A_0_trace        = Array<OneD, Array<OneD, NekDouble>>(m_nDomains);
    m_trace_fwd_normal = Array<OneD, Array<OneD, NekDouble>>(m_nDomains);
 
    int omega = 0;
    for (auto &d : m_domOrder)
    {
        nq          = m_vessels[2 * omega]->GetNpoints();
        m_fields[0] = m_vessels[2 * omega];
 
        m_beta[omega] = Array<OneD, NekDouble>(nq);
        GetFunction("MaterialProperties")
            ->Evaluate("beta", m_beta[omega], m_time, d);
 
        // If the input file doesn't specify viscoelasticity, set it to zero.
        m_gamma[omega] = Array<OneD, NekDouble>(nq);
 
        if (m_session->DefinesFunction("Viscoelasticity"))
        {
            GetFunction("Viscoelasticity")
                ->Evaluate("gamma", m_gamma[omega], m_time, d);
        }
        else
        {
            for (int j = 0; j < nq; ++j)
            {
                m_gamma[omega][j] = 0;
            }
        }
 
        /* If the input file doesn't specify strain-stiffening, set it to
         * 0.5 for elastic behaviour.
         */
        m_alpha[omega] = Array<OneD, NekDouble>(nq);
 
        if (m_session->DefinesFunction("StrainStiffening"))
        {
            GetFunction("StrainStiffening")
                ->Evaluate("alpha", m_alpha[omega], m_time, d);
        }
        else
        {
            for (int j = 0; j < nq; ++j)
            {
                m_alpha[omega][j] = 0.5;
            }
        }
 
        m_A_0[omega] = Array<OneD, NekDouble>(nq);
        GetFunction("A_0")->Evaluate("A_0", m_A_0[omega], m_time, d);
 
        int nqTrace = GetTraceTotPoints();
 
        m_beta_trace[omega] = Array<OneD, NekDouble>(nqTrace);
        m_fields[0]->ExtractTracePhys(m_beta[omega], m_beta_trace[omega]);
 
        m_A_0_trace[omega] = Array<OneD, NekDouble>(nqTrace);
        m_fields[0]->ExtractTracePhys(m_A_0[omega], m_A_0_trace[omega]);
 
        m_alpha_trace[omega] = Array<OneD, NekDouble>(nqTrace);
        m_fields[0]->ExtractTracePhys(m_alpha[omega], m_alpha_trace[omega]);
 
        m_trace_fwd_normal[omega] = Array<OneD, NekDouble>(nqTrace, 0.0);
 
        MultiRegions::ExpListSharedPtr trace = m_fields[0]->GetTrace();
        int nelmt_trace                      = trace->GetExpSize();
 
        Array<OneD, Array<OneD, NekDouble>> normals(nelmt_trace);
 
        for (int i = 0; i < nelmt_trace; ++i)
        {
            normals[i] = m_trace_fwd_normal[omega] + i;
        }
 
        // need to set to 1 for consistency since boundary
        // conditions may not have coordim = 1
        trace->GetExp(0)->GetGeom()->SetCoordim(1);
 
        trace->GetNormals(normals);
        omega++;
    }
 
    SetUpDomainInterfaces();
}

Referenced by Nektar::PulseWavePropagation::v_InitObject().

◆ v_L2Error()

NekDouble Nektar::PulseWaveSystem::v_L2Error	(	unsigned int	field,
		const Array< OneD, NekDouble > &	exactsoln = `NullNekDouble1DArray`,
		bool	Normalised = `false`
	)

overrideprotectedvirtual

Compute the L2 error between fields and a given exact solution.

Reimplemented from Nektar::SolverUtils::EquationSystem.

Definition at line 2025 of file PulseWaveSystem.cpp.

{
    NekDouble L2error = 0.0;
    NekDouble L2error_dom;
    NekDouble Vol = 0.0;
 
    if (m_NumQuadPointsError == 0)
    {
        for (size_t omega = 0; omega < m_nDomains; omega++)
        {
            size_t vesselid = field + omega * m_nVariables;
 
            // since exactsoln is passed for just the first field size we
            // need to reset it each domain
            Array<OneD, NekDouble> exactsoln(m_vessels[vesselid]->GetNpoints());
            m_fields[field] = m_vessels[omega * m_nVariables];
            EvaluateExactSolution(field, exactsoln, m_time);
 
            if (m_vessels[vesselid]->GetPhysState() == false)
            {
                m_vessels[vesselid]->BwdTrans(
                    m_vessels[vesselid]->GetCoeffs(),
                    m_vessels[vesselid]->UpdatePhys());
            }
 
            if (exactsoln.size())
            {
                L2error_dom = m_vessels[vesselid]->L2(
                    m_vessels[vesselid]->GetPhys(), exactsoln);
            }
            else if (m_session->DefinesFunction("ExactSolution"))
            {
                Array<OneD, NekDouble> exactsoln(
                    m_vessels[vesselid]->GetNpoints());
 
                LibUtilities::EquationSharedPtr vEqu =
                    m_session->GetFunction("ExactSolution", field, omega);
                GetFunction("ExactSolution")
                    ->Evaluate(m_session->GetVariable(field), exactsoln,
                               m_time);
 
                L2error_dom = m_vessels[vesselid]->L2(
                    m_vessels[vesselid]->GetPhys(), exactsoln);
            }
            else
            {
                L2error_dom =
                    m_vessels[vesselid]->L2(m_vessels[vesselid]->GetPhys());
            }
 
            if (m_vessels[vesselid]->GetComm()->GetRank())
            {
                // ensure domains are only summed on local root of
                // domain
                L2error_dom = 0.0;
            }
 
            L2error += L2error_dom * L2error_dom;
 
            if (Normalised == true)
            {
                Array<OneD, NekDouble> one(m_vessels[vesselid]->GetNpoints(),
                                           1.0);
 
                Vol += m_vessels[vesselid]->Integral(one);
            }
        }
    }
    else
    {
        ASSERTL0(false, "Not set up");
    }
 
    m_comm->AllReduce(L2error, LibUtilities::ReduceSum);
 
    if (Normalised == true)
    {
        m_comm->AllReduce(Vol, LibUtilities::ReduceSum);
 
        L2error = sqrt(L2error / Vol);
    }
    else
    {
        L2error = sqrt(L2error);
    }
 
    return L2error;
}

◆ v_LinfError()

NekDouble Nektar::PulseWaveSystem::v_LinfError	(	unsigned int	field,
		const Array< OneD, NekDouble > &	exact = `NullNekDouble1DArray`
	)

overrideprotectedvirtual

Compute the L_inf error between fields and a given exact solution.

Compute the error in the L_inf-norm

Parameters

field	The field to compare.
exactsoln	The exact solution to compare with.

Returns: Error in the L_inft-norm.

Reimplemented from Nektar::SolverUtils::EquationSystem.

Definition at line 2122 of file PulseWaveSystem.cpp.

{
    NekDouble LinferrorDom, Linferror = -1.0;
 
    for (size_t omega = 0; omega < m_nDomains; ++omega)
    {
        size_t vesselid = field + omega * m_nVariables;
 
        // since exactsoln is passed for just the first field size we need
        // to reset it each domain
        Array<OneD, NekDouble> exactsoln(m_vessels[vesselid]->GetNpoints());
        m_fields[field] = m_vessels[omega * m_nVariables];
        EvaluateExactSolution(field, exactsoln, m_time);
 
        if (m_NumQuadPointsError == 0)
        {
            if (m_vessels[vesselid]->GetPhysState() == false)
            {
                m_vessels[vesselid]->BwdTrans(
                    m_vessels[vesselid]->GetCoeffs(),
                    m_vessels[vesselid]->UpdatePhys());
            }
 
            if (exactsoln.size())
            {
                LinferrorDom = m_vessels[vesselid]->Linf(
                    m_vessels[vesselid]->GetPhys(), exactsoln);
            }
            else if (m_session->DefinesFunction("ExactSolution"))
            {
                Array<OneD, NekDouble> exactsoln(
                    m_vessels[vesselid]->GetNpoints());
 
                GetFunction("ExactSolution")
                    ->Evaluate(m_session->GetVariable(field), exactsoln,
                               m_time);
 
                LinferrorDom = m_vessels[vesselid]->Linf(
                    m_vessels[vesselid]->GetPhys(), exactsoln);
            }
            else
            {
                LinferrorDom = 0.0;
            }
 
            Linferror = (Linferror > LinferrorDom) ? Linferror : LinferrorDom;
        }
        else
        {
            ASSERTL0(false, "ErrorExtraPoints not allowed for this solver");
        }
    }
    m_comm->AllReduce(Linferror, LibUtilities::ReduceMax);
    return Linferror;
}

◆ v_Output()

void Nektar::PulseWaveSystem::v_Output ( void )

overrideprotectedvirtual

Writes the .fld file at the end of the simulation. Similar to the normal v_Output however the Multidomain output has to be prepared.

Write the field data to file. The file is named according to the session name with the extension .fld appended.

Reimplemented from Nektar::SolverUtils::EquationSystem.

Definition at line 1904 of file PulseWaveSystem.cpp.

{
    /**
     * Write the field data to file. The file is named according to the
     * session name with the extension .fld appended.
     */
    std::string outname = m_sessionName + ".fld";
 
    WriteVessels(outname);
}

References Nektar::SolverUtils::EquationSystem::m_sessionName, and WriteVessels().

◆ WriteVessels()

void Nektar::PulseWaveSystem::WriteVessels ( const std::string & outname )

protected

Write input fields to the given filename.

Writes the field data to a file with the given filename.

Parameters

outname Filename to write to.

Definition at line 1931 of file PulseWaveSystem.cpp.

{
    std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef;
    std::vector<std::string> variables = m_session->GetVariables();
 
    for (size_t n = 0; n < m_nDomains; ++n)
    {
        m_vessels[n * m_nVariables]->GetFieldDefinitions(FieldDef);
    }
 
    std::vector<std::vector<NekDouble>> FieldData(FieldDef.size());
 
    size_t nFieldDefPerDomain = FieldDef.size() / m_nDomains;
    size_t cnt;
 
    // Copy Data into FieldData and set variable
    for (size_t n = 0; n < m_nDomains; ++n)
    {
        // Outputs area and velocity
        for (size_t j = 0; j < m_nVariables; ++j)
        {
            for (size_t i = 0; i < nFieldDefPerDomain; ++i)
            {
                cnt = n * nFieldDefPerDomain + i;
 
                FieldDef[cnt]->m_fields.push_back(variables[j]);
 
                m_vessels[n * m_nVariables]->AppendFieldData(
                    FieldDef[cnt], FieldData[cnt],
                    m_vessels[n * m_nVariables + j]->UpdateCoeffs());
            }
        }
 
        // Outputs pressure
        Array<OneD, NekDouble> PFwd(m_vessels[n * m_nVariables]->GetNcoeffs());
 
        m_vessels[n * m_nVariables]->FwdTransLocalElmt(m_pressure[n], PFwd);
 
        for (size_t i = 0; i < nFieldDefPerDomain; ++i)
        {
            cnt = n * nFieldDefPerDomain + i;
 
            FieldDef[cnt]->m_fields.push_back("P");
 
            m_vessels[n * m_nVariables]->AppendFieldData(FieldDef[cnt],
                                                         FieldData[cnt], PFwd);
        }
 
        if (extraFields)
        {
            Array<OneD, NekDouble> PWVFwd(
                m_vessels[n * m_nVariables]->GetNcoeffs());
            Array<OneD, NekDouble> W1Fwd(
                m_vessels[n * m_nVariables]->GetNcoeffs());
            Array<OneD, NekDouble> W2Fwd(
                m_vessels[n * m_nVariables]->GetNcoeffs());
 
            m_vessels[n * m_nVariables]->FwdTransLocalElmt(m_PWV[n], PWVFwd);
            m_vessels[n * m_nVariables]->FwdTransLocalElmt(m_W1[n], W1Fwd);
            m_vessels[n * m_nVariables]->FwdTransLocalElmt(m_W2[n], W2Fwd);
 
            for (size_t i = 0; i < nFieldDefPerDomain; ++i)
            {
                cnt = n * nFieldDefPerDomain + i;
 
                FieldDef[cnt]->m_fields.push_back("c");
                FieldDef[cnt]->m_fields.push_back("W1");
                FieldDef[cnt]->m_fields.push_back("W2");
 
                m_vessels[n * m_nVariables]->AppendFieldData(
                    FieldDef[cnt], FieldData[cnt], PWVFwd);
                m_vessels[n * m_nVariables]->AppendFieldData(
                    FieldDef[cnt], FieldData[cnt], W1Fwd);
                m_vessels[n * m_nVariables]->AppendFieldData(
                    FieldDef[cnt], FieldData[cnt], W2Fwd);
            }
        }
    }
 
    // Update time in field info if required
    if (m_fieldMetaDataMap.find("Time") != m_fieldMetaDataMap.end())
    {
        m_fieldMetaDataMap["Time"] = boost::lexical_cast<std::string>(m_time);
    }
 
    m_fld->Write(outname, FieldDef, FieldData, m_fieldMetaDataMap);
}

References extraFields, Nektar::SolverUtils::EquationSystem::GetNcoeffs(), Nektar::SolverUtils::EquationSystem::m_fieldMetaDataMap, Nektar::SolverUtils::EquationSystem::m_fld, m_nDomains, m_nVariables, m_pressure, m_PWV, Nektar::SolverUtils::EquationSystem::m_session, Nektar::SolverUtils::EquationSystem::m_time, m_vessels, m_W1, and m_W2.

Referenced by CheckPoint_Output(), and v_Output().

Member Data Documentation

◆ extraFields

bool Nektar::PulseWaveSystem::extraFields = false

protected

Definition at line 124 of file PulseWaveSystem.h.

Referenced by Nektar::PulseWavePropagation::GetFluxVector(), and WriteVessels().

◆ m_A_0

Array<OneD, Array<OneD, NekDouble> > Nektar::PulseWaveSystem::m_A_0

protected

Definition at line 105 of file PulseWaveSystem.h.

Referenced by Nektar::PulseWavePropagation::GetFluxVector(), Nektar::PulseWavePropagation::SetPulseWaveBoundaryConditions(), and v_InitObject().

◆ m_A_0_trace

Array<OneD, Array<OneD, NekDouble> > Nektar::PulseWaveSystem::m_A_0_trace

protected

Definition at line 106 of file PulseWaveSystem.h.

Referenced by FillDataFromInterfacePoint(), Nektar::PulseWavePropagation::GetA0(), and v_InitObject().

◆ m_alpha

Array<OneD, Array<OneD, NekDouble> > Nektar::PulseWaveSystem::m_alpha

protected

Definition at line 110 of file PulseWaveSystem.h.

Referenced by Nektar::PulseWavePropagation::GetFluxVector(), Nektar::PulseWavePropagation::SetPulseWaveBoundaryConditions(), and v_InitObject().

◆ m_alpha_trace

Array<OneD, Array<OneD, NekDouble> > Nektar::PulseWaveSystem::m_alpha_trace

protected

Definition at line 111 of file PulseWaveSystem.h.

Referenced by FillDataFromInterfacePoint(), Nektar::PulseWavePropagation::GetAlpha(), and v_InitObject().

◆ m_beta

Array<OneD, Array<OneD, NekDouble> > Nektar::PulseWaveSystem::m_beta

protected

Definition at line 107 of file PulseWaveSystem.h.

Referenced by Nektar::PulseWavePropagation::GetFluxVector(), Nektar::PulseWavePropagation::SetPulseWaveBoundaryConditions(), and v_InitObject().

◆ m_beta_trace

Array<OneD, Array<OneD, NekDouble> > Nektar::PulseWaveSystem::m_beta_trace

protected

Definition at line 108 of file PulseWaveSystem.h.

Referenced by FillDataFromInterfacePoint(), Nektar::PulseWavePropagation::GetBeta(), and v_InitObject().

◆ m_bifurcations

std::vector<std::vector<InterfacePointShPtr> > Nektar::PulseWaveSystem::m_bifurcations

protected

Definition at line 130 of file PulseWaveSystem.h.

Referenced by EnforceInterfaceConditions(), and SetUpDomainInterfaces().

◆ m_C

NekDouble Nektar::PulseWaveSystem::m_C

protected

Definition at line 101 of file PulseWaveSystem.h.

◆ m_currentDomain

size_t Nektar::PulseWaveSystem::m_currentDomain

protected

Definition at line 93 of file PulseWaveSystem.h.

Referenced by Nektar::PulseWavePropagation::DoOdeRhs(), Nektar::PulseWavePropagation::GetA0(), Nektar::PulseWavePropagation::GetAlpha(), Nektar::PulseWavePropagation::GetBeta(), Nektar::PulseWavePropagation::GetFluxVector(), and Nektar::PulseWavePropagation::GetN().

◆ m_domain

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

protected

Definition at line 115 of file PulseWaveSystem.h.

Referenced by GetCommArray(), SetUpDomainInterfaceBCs(), SetUpDomainInterfaces(), and v_InitObject().

◆ m_domainToFilterIDs

std::map<int, std::vector<int> > Nektar::PulseWaveSystem::m_domainToFilterIDs

protected

Definition at line 117 of file PulseWaveSystem.h.

Referenced by v_DoInitialise(), v_DoSolve(), and v_InitObject().

◆ m_domOrder

std::vector<int> Nektar::PulseWaveSystem::m_domOrder

protected

Definition at line 116 of file PulseWaveSystem.h.

Referenced by GetCommArray(), SetUpDomainInterfaceBCs(), v_DoInitialise(), and v_InitObject().

◆ m_fieldPhysOffset

Array<OneD, int> Nektar::PulseWaveSystem::m_fieldPhysOffset

protected

Definition at line 97 of file PulseWaveSystem.h.

Referenced by FillDataFromInterfacePoint(), v_DoSolve(), and v_InitObject().

◆ m_filterToVesselID

std::map<int, int> Nektar::PulseWaveSystem::m_filterToVesselID

protected

Definition at line 118 of file PulseWaveSystem.h.

Referenced by v_DoInitialise(), v_DoSolve(), and v_InitObject().

◆ m_gamma

Array<OneD, Array<OneD, NekDouble> > Nektar::PulseWaveSystem::m_gamma

protected

Definition at line 109 of file PulseWaveSystem.h.

Referenced by Nektar::PulseWavePropagation::GetFluxVector(), and v_InitObject().

◆ m_intComm

Gs::gs_data* Nektar::PulseWaveSystem::m_intComm

private

Communicator for interfaces.

Definition at line 196 of file PulseWaveSystem.h.

Referenced by EnforceInterfaceConditions(), and SetUpDomainInterfaces().

◆ m_mergingJcts

std::vector<std::vector<InterfacePointShPtr> > Nektar::PulseWaveSystem::m_mergingJcts

protected

Definition at line 131 of file PulseWaveSystem.h.

Referenced by EnforceInterfaceConditions(), and SetUpDomainInterfaces().

◆ m_nDomains

size_t Nektar::PulseWaveSystem::m_nDomains

protected

Definition at line 92 of file PulseWaveSystem.h.

Referenced by Nektar::PulseWavePropagation::DoOdeRhs(), Nektar::PulseWavePropagation::GetDomains(), GetNdomains(), Nektar::PulseWavePropagation::SetPulseWaveBoundaryConditions(), SetUpDomainInterfaces(), v_DoSolve(), v_InitObject(), v_L2Error(), v_LinfError(), and WriteVessels().

◆ m_nVariables

size_t Nektar::PulseWaveSystem::m_nVariables

protected

Definition at line 94 of file PulseWaveSystem.h.

Referenced by Nektar::PulseWavePropagation::DoOdeProjection(), Nektar::PulseWavePropagation::DoOdeRhs(), EnforceInterfaceConditions(), FillDataFromInterfacePoint(), Nektar::PulseWavePropagation::GetFluxVector(), SetUpDomainInterfaces(), v_DoInitialise(), v_DoSolve(), v_InitObject(), v_L2Error(), v_LinfError(), and WriteVessels().

◆ m_pext

NekDouble Nektar::PulseWaveSystem::m_pext

protected

Definition at line 99 of file PulseWaveSystem.h.

Referenced by v_InitObject().

◆ m_pout

NekDouble Nektar::PulseWaveSystem::m_pout

protected

Definition at line 103 of file PulseWaveSystem.h.

◆ m_pressure

Array<OneD, Array<OneD, NekDouble> > Nektar::PulseWaveSystem::m_pressure

protected

Definition at line 120 of file PulseWaveSystem.h.

Referenced by Nektar::PulseWavePropagation::GetFluxVector(), v_InitObject(), and WriteVessels().

◆ m_pressureArea

PulseWavePressureAreaSharedPtr Nektar::PulseWaveSystem::m_pressureArea

protected

Definition at line 121 of file PulseWaveSystem.h.

Referenced by BifurcationRiemann(), Nektar::PulseWavePropagation::GetFluxVector(), InterfaceRiemann(), MergingRiemann(), Nektar::PulseWavePropagation::SetPulseWaveBoundaryConditions(), Nektar::PulseWavePropagation::v_InitObject(), and v_InitObject().

◆ m_PWV

Array<OneD, Array<OneD, NekDouble> > Nektar::PulseWaveSystem::m_PWV

protected

Definition at line 125 of file PulseWaveSystem.h.

Referenced by Nektar::PulseWavePropagation::GetFluxVector(), v_InitObject(), and WriteVessels().

◆ m_rho

NekDouble Nektar::PulseWaveSystem::m_rho

protected

Definition at line 98 of file PulseWaveSystem.h.

Referenced by BifurcationRiemann(), Nektar::PulseWavePropagation::GetFluxVector(), Nektar::PulseWavePropagation::GetRho(), InterfaceRiemann(), MergingRiemann(), and v_InitObject().

◆ m_RT

NekDouble Nektar::PulseWaveSystem::m_RT

protected

Definition at line 102 of file PulseWaveSystem.h.

◆ m_trace_fwd_normal

Array<OneD, Array<OneD, NekDouble> > Nektar::PulseWaveSystem::m_trace_fwd_normal

protected

Definition at line 112 of file PulseWaveSystem.h.

Referenced by Nektar::PulseWavePropagation::GetN(), and v_InitObject().

◆ m_upwindTypePulse

UpwindTypePulse Nektar::PulseWaveSystem::m_upwindTypePulse

protected

Definition at line 95 of file PulseWaveSystem.h.

Referenced by Nektar::PulseWavePropagation::v_InitObject(), and v_InitObject().

◆ m_vesselIntfcs

std::vector<std::vector<InterfacePointShPtr> > Nektar::PulseWaveSystem::m_vesselIntfcs

protected

Definition at line 129 of file PulseWaveSystem.h.

Referenced by EnforceInterfaceConditions(), and SetUpDomainInterfaces().

◆ m_vessels

Array<OneD, MultiRegions::ExpListSharedPtr> Nektar::PulseWaveSystem::m_vessels

protected

Definition at line 91 of file PulseWaveSystem.h.

Referenced by Nektar::PulseWavePropagation::DoOdeRhs(), EnforceInterfaceConditions(), FillDataFromInterfacePoint(), Nektar::PulseWavePropagation::GetFluxVector(), Nektar::PulseWavePropagation::SetPulseWaveBoundaryConditions(), SetUpDomainInterfaces(), UpdateVessels(), v_DoInitialise(), v_DoSolve(), Nektar::PulseWavePropagation::v_InitObject(), v_InitObject(), v_L2Error(), v_LinfError(), and WriteVessels().

◆ m_W1

Array<OneD, Array<OneD, NekDouble> > Nektar::PulseWaveSystem::m_W1

protected

Definition at line 126 of file PulseWaveSystem.h.

Referenced by Nektar::PulseWavePropagation::GetFluxVector(), v_InitObject(), and WriteVessels().

◆ m_W2

Array<OneD, Array<OneD, NekDouble> > Nektar::PulseWaveSystem::m_W2

protected

Definition at line 127 of file PulseWaveSystem.h.

Referenced by Nektar::PulseWavePropagation::GetFluxVector(), v_InitObject(), and WriteVessels().

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PulseWaveSystem()

◆ ~PulseWaveSystem()

Member Function Documentation

◆ BifurcationRiemann()

◆ CheckPoint_Output()

◆ EnforceInterfaceConditions()

◆ FillDataFromInterfacePoint()

◆ GetCommArray()

◆ GetNdomains()

◆ InterfaceRiemann()

◆ LinkSubdomains()

◆ MergingRiemann()

◆ SetUpDomainInterfaceBCs()

◆ SetUpDomainInterfaces()

◆ UpdateVessels()

◆ v_DoInitialise()

◆ v_DoSolve()

◆ v_InitObject()

◆ v_L2Error()

◆ v_LinfError()

◆ v_Output()

◆ WriteVessels()

Member Data Documentation

◆ extraFields

◆ m_A_0

◆ m_A_0_trace

◆ m_alpha

◆ m_alpha_trace

◆ m_beta

◆ m_beta_trace

◆ m_bifurcations

◆ m_C

◆ m_currentDomain

◆ m_domain

◆ m_domainToFilterIDs

◆ m_domOrder

◆ m_fieldPhysOffset

◆ m_filterToVesselID

◆ m_gamma

◆ m_intComm

◆ m_mergingJcts

◆ m_nDomains

◆ m_nVariables

◆ m_pext

◆ m_pout

◆ m_pressure

◆ m_pressureArea

◆ m_PWV

◆ m_rho

◆ m_RT

◆ m_trace_fwd_normal

◆ m_upwindTypePulse

◆ m_vesselIntfcs

◆ m_vessels

◆ m_W1

◆ m_W2