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Nektar::PulseWaveSystem Class Reference

Base class for unsteady solvers. More...

#include <PulseWaveSystem.h>

Inheritance diagram for Nektar::PulseWaveSystem:
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Public Member Functions

virtual ~PulseWaveSystem ()
 Destructor. More...
 
int GetNdomains ()
 
Array< OneD,
MultiRegions::ExpListSharedPtr > 		UpdateVessels (void)
 
void CalcCharacteristicVariables (int omega)
 
- Public Member Functions inherited from Nektar::SolverUtils::UnsteadySystem
virtual SOLVER_UTILS_EXPORT ~UnsteadySystem ()
 Destructor. More...
 
SOLVER_UTILS_EXPORT NekDouble GetTimeStep (const Array< OneD, const Array< OneD, NekDouble > > &inarray)
 Calculate the larger time-step mantaining the problem stable. More...
 
- Public Member Functions inherited from Nektar::SolverUtils::EquationSystem
virtual SOLVER_UTILS_EXPORT ~EquationSystem ()
 Destructor. More...
 
SOLVER_UTILS_EXPORT void SetUpTraceNormals (void)
 
SOLVER_UTILS_EXPORT void InitObject ()
 Initialises the members of this object. More...
 
SOLVER_UTILS_EXPORT void DoInitialise ()
 Perform any initialisation necessary before solving the problem. More...
 
SOLVER_UTILS_EXPORT void DoSolve ()
 Solve the problem. More...
 
SOLVER_UTILS_EXPORT void TransCoeffToPhys ()
 Transform from coefficient to physical space. More...
 
SOLVER_UTILS_EXPORT void TransPhysToCoeff ()
 Transform from physical to coefficient space. More...
 
SOLVER_UTILS_EXPORT void Output ()
 Perform output operations after solve. More...
 
SOLVER_UTILS_EXPORT NekDouble LinfError (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray)
 Linf error computation. More...
 
SOLVER_UTILS_EXPORT std::string GetSessionName ()
 Get Session name. More...
 
template<class T >
boost::shared_ptr< T > as ()
 
SOLVER_UTILS_EXPORT void ResetSessionName (std::string newname)
 Reset Session name. More...
 
SOLVER_UTILS_EXPORT
LibUtilities::SessionReaderSharedPtr 		GetSession ()
 Get Session name. More...
 
SOLVER_UTILS_EXPORT
MultiRegions::ExpListSharedPtr 		GetPressure ()
 Get pressure field if available. More...
 
SOLVER_UTILS_EXPORT void PrintSummary (std::ostream &out)
 Print a summary of parameters and solver characteristics. More...
 
SOLVER_UTILS_EXPORT void SetLambda (NekDouble lambda)
 Set parameter m_lambda. More...
 
SOLVER_UTILS_EXPORT void EvaluateFunction (Array< OneD, Array< OneD, NekDouble > > &pArray, std::string pFunctionName, const NekDouble pTime=0.0, const int domain=0)
 Evaluates a function as specified in the session file. More...
 
SOLVER_UTILS_EXPORT void EvaluateFunction (std::vector< std::string > pFieldNames, Array< OneD, Array< OneD, NekDouble > > &pFields, const std::string &pName, const NekDouble &pTime=0.0, const int domain=0)
 Populate given fields with the function from session. More...
 
SOLVER_UTILS_EXPORT void EvaluateFunction (std::vector< std::string > pFieldNames, Array< OneD, MultiRegions::ExpListSharedPtr > &pFields, const std::string &pName, const NekDouble &pTime=0.0, const int domain=0)
 Populate given fields with the function from session. More...
 
SOLVER_UTILS_EXPORT void EvaluateFunction (std::string pFieldName, Array< OneD, NekDouble > &pArray, const std::string &pFunctionName, const NekDouble &pTime=0.0, const int domain=0)
 
SOLVER_UTILS_EXPORT std::string DescribeFunction (std::string pFieldName, const std::string &pFunctionName, const int domain)
 Provide a description of a function for a given field name. More...
 
SOLVER_UTILS_EXPORT void InitialiseBaseFlow (Array< OneD, Array< OneD, NekDouble > > &base)
 Perform initialisation of the base flow. More...
 
SOLVER_UTILS_EXPORT void SetInitialConditions (NekDouble initialtime=0.0, bool dumpInitialConditions=true, const int domain=0)
 Initialise the data in the dependent fields. More...
 
SOLVER_UTILS_EXPORT void EvaluateExactSolution (int field, Array< OneD, NekDouble > &outfield, const NekDouble time)
 Evaluates an exact solution. More...
 
SOLVER_UTILS_EXPORT NekDouble L2Error (unsigned int field, const Array< OneD, NekDouble > &exactsoln, bool Normalised=false)
 Compute the L2 error between fields and a given exact solution. More...
 
SOLVER_UTILS_EXPORT NekDouble L2Error (unsigned int field, bool Normalised=false)
 Compute the L2 error of the fields. More...
 
SOLVER_UTILS_EXPORT Array
< OneD, NekDouble > 		ErrorExtraPoints (unsigned int field)
 Compute error (L2 and L_inf) over an larger set of quadrature points return [L2 Linf]. More...
 
SOLVER_UTILS_EXPORT void WeakAdvectionGreensDivergenceForm (const Array< OneD, Array< OneD, NekDouble > > &F, Array< OneD, NekDouble > &outarray)
 Compute the inner product $ (\nabla \phi \cdot F) $. More...
 
SOLVER_UTILS_EXPORT void WeakAdvectionDivergenceForm (const Array< OneD, Array< OneD, NekDouble > > &F, Array< OneD, NekDouble > &outarray)
 Compute the inner product $ (\phi, \nabla \cdot F) $. More...
 
SOLVER_UTILS_EXPORT void WeakAdvectionNonConservativeForm (const Array< OneD, Array< OneD, NekDouble > > &V, const Array< OneD, const NekDouble > &u, Array< OneD, NekDouble > &outarray, bool UseContCoeffs=false)
 Compute the inner product $ (\phi, V\cdot \nabla u) $. More...
 
f SOLVER_UTILS_EXPORT void AdvectionNonConservativeForm (const Array< OneD, Array< OneD, NekDouble > > &V, const Array< OneD, const NekDouble > &u, Array< OneD, NekDouble > &outarray, Array< OneD, NekDouble > &wk=NullNekDouble1DArray)
 Compute the non-conservative advection. More...
 
SOLVER_UTILS_EXPORT void WeakDGAdvection (const Array< OneD, Array< OneD, NekDouble > > &InField, Array< OneD, Array< OneD, NekDouble > > &OutField, bool NumericalFluxIncludesNormal=true, bool InFieldIsInPhysSpace=false, int nvariables=0)
 Calculate the weak discontinuous Galerkin advection. More...
 
SOLVER_UTILS_EXPORT void WeakDGDiffusion (const Array< OneD, Array< OneD, NekDouble > > &InField, Array< OneD, Array< OneD, NekDouble > > &OutField, bool NumericalFluxIncludesNormal=true, bool InFieldIsInPhysSpace=false)
 Calculate weak DG Diffusion in the LDG form. More...
 
SOLVER_UTILS_EXPORT void Checkpoint_Output (const int n)
 Write checkpoint file of m_fields. More...
 
SOLVER_UTILS_EXPORT void Checkpoint_Output (const int n, MultiRegions::ExpListSharedPtr &field, std::vector< Array< OneD, NekDouble > > &fieldcoeffs, std::vector< std::string > &variables)
 Write checkpoint file of custom data fields. More...
 
SOLVER_UTILS_EXPORT void Checkpoint_BaseFlow (const int n)
 Write base flow file of m_fields. More...
 
SOLVER_UTILS_EXPORT void WriteFld (const std::string &outname)
 Write field data to the given filename. More...
 
SOLVER_UTILS_EXPORT void WriteFld (const std::string &outname, MultiRegions::ExpListSharedPtr &field, std::vector< Array< OneD, NekDouble > > &fieldcoeffs, std::vector< std::string > &variables)
 Write input fields to the given filename. More...
 
SOLVER_UTILS_EXPORT void ImportFld (const std::string &infile, Array< OneD, MultiRegions::ExpListSharedPtr > &pFields)
 Input field data from the given file. More...
 
SOLVER_UTILS_EXPORT void ImportFldToMultiDomains (const std::string &infile, Array< OneD, MultiRegions::ExpListSharedPtr > &pFields, const int ndomains)
 Input field data from the given file to multiple domains. More...
 
SOLVER_UTILS_EXPORT void ImportFld (const std::string &infile, std::vector< std::string > &fieldStr, Array< OneD, Array< OneD, NekDouble > > &coeffs)
 Output a field. Input field data into array from the given file. More...
 
SOLVER_UTILS_EXPORT void ImportFld (const std::string &infile, MultiRegions::ExpListSharedPtr &pField, std::string &pFieldName)
 Output a field. Input field data into ExpList from the given file. More...
 
SOLVER_UTILS_EXPORT void ScanForHistoryPoints ()
 Builds map of which element holds each history point. More...
 
SOLVER_UTILS_EXPORT void WriteHistoryData (std::ostream &out)
 Probe each history point and write to file. More...
 
SOLVER_UTILS_EXPORT void SessionSummary (SummaryList &vSummary)
 Write out a session summary. More...
 
SOLVER_UTILS_EXPORT Array
< OneD,
MultiRegions::ExpListSharedPtr > & 		UpdateFields ()
 
SOLVER_UTILS_EXPORT
LibUtilities::FieldMetaDataMap & 		UpdateFieldMetaDataMap ()
 Get hold of FieldInfoMap so it can be updated. More...
 
SOLVER_UTILS_EXPORT NekDouble GetFinalTime ()
 Return final time. More...
 
SOLVER_UTILS_EXPORT int GetNcoeffs ()
 
SOLVER_UTILS_EXPORT int GetNcoeffs (const int eid)
 
SOLVER_UTILS_EXPORT int GetNumExpModes ()
 
SOLVER_UTILS_EXPORT const
Array< OneD, int > 		GetNumExpModesPerExp ()
 
SOLVER_UTILS_EXPORT int GetNvariables ()
 
SOLVER_UTILS_EXPORT const
std::string 		GetVariable (unsigned int i)
 
SOLVER_UTILS_EXPORT int GetTraceTotPoints ()
 
SOLVER_UTILS_EXPORT int GetTraceNpoints ()
 
SOLVER_UTILS_EXPORT int GetExpSize ()
 
SOLVER_UTILS_EXPORT int GetPhys_Offset (int n)
 
SOLVER_UTILS_EXPORT int GetCoeff_Offset (int n)
 
SOLVER_UTILS_EXPORT int GetTotPoints ()
 
SOLVER_UTILS_EXPORT int GetTotPoints (int n)
 
SOLVER_UTILS_EXPORT int GetNpoints ()
 
SOLVER_UTILS_EXPORT int GetNumElmVelocity ()
 
SOLVER_UTILS_EXPORT int GetSteps ()
 
SOLVER_UTILS_EXPORT NekDouble GetTimeStep ()
 
SOLVER_UTILS_EXPORT void CopyFromPhysField (const int i, Array< OneD, NekDouble > &output)
 
SOLVER_UTILS_EXPORT void CopyToPhysField (const int i, Array< OneD, NekDouble > &output)
 
SOLVER_UTILS_EXPORT void SetSteps (const int steps)
 
SOLVER_UTILS_EXPORT void ZeroPhysFields ()
 
SOLVER_UTILS_EXPORT void FwdTransFields ()
 
SOLVER_UTILS_EXPORT void GetFluxVector (const int i, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &flux)
 
SOLVER_UTILS_EXPORT void GetFluxVector (const int i, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &fluxX, Array< OneD, Array< OneD, NekDouble > > &fluxY)
 
SOLVER_UTILS_EXPORT void GetFluxVector (const int i, const int j, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &flux)
 
SOLVER_UTILS_EXPORT void NumericalFlux (Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numflux)
 
SOLVER_UTILS_EXPORT void NumericalFlux (Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numfluxX, Array< OneD, Array< OneD, NekDouble > > &numfluxY)
 
SOLVER_UTILS_EXPORT void NumFluxforScalar (const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &uflux)
 
SOLVER_UTILS_EXPORT void NumFluxforVector (const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &qfield, Array< OneD, Array< OneD, NekDouble > > &qflux)
 
SOLVER_UTILS_EXPORT void SetModifiedBasis (const bool modbasis)
 
SOLVER_UTILS_EXPORT int NoCaseStringCompare (const string &s1, const string &s2)
 Perform a case-insensitive string comparison. More...
 
SOLVER_UTILS_EXPORT int GetCheckpointNumber ()
 
SOLVER_UTILS_EXPORT void SetCheckpointNumber (int num)
 
SOLVER_UTILS_EXPORT int GetCheckpointSteps ()
 
SOLVER_UTILS_EXPORT void SetCheckpointSteps (int num)
 
SOLVER_UTILS_EXPORT void SetTime (const NekDouble time)
 
SOLVER_UTILS_EXPORT void SetInitialStep (const int step)
 
SOLVER_UTILS_EXPORT void SetBoundaryConditions (NekDouble time)
 Evaluates the boundary conditions at the given time. More...
 
virtual SOLVER_UTILS_EXPORT bool v_NegatedOp ()
 Virtual function to identify if operator is negated in DoSolve. More...
 

Protected Member Functions

 PulseWaveSystem (const LibUtilities::SessionReaderSharedPtr &m_session)
 Initialises PulseWaveSystem class members. More...
 
virtual void v_InitObject ()
 
virtual void v_DoInitialise ()
 Sets up initial conditions. More...
 
virtual void v_DoSolve ()
 Solves an unsteady problem. More...
 
void LinkSubdomains (Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &fields)
 Links the subdomains. More...
 
void BifurcationRiemann (Array< OneD, NekDouble > &Au, Array< OneD, NekDouble > &uu, Array< OneD, NekDouble > &beta, Array< OneD, NekDouble > &A_0)
 Riemann Problem for Bifurcation. More...
 
void MergingRiemann (Array< OneD, NekDouble > &Au, Array< OneD, NekDouble > &uu, Array< OneD, NekDouble > &beta, Array< OneD, NekDouble > &A_0)
 Riemann Problem for Merging Flow. More...
 
void JunctionRiemann (Array< OneD, NekDouble > &Au, Array< OneD, NekDouble > &uu, Array< OneD, NekDouble > &beta, Array< OneD, NekDouble > &A_0)
 Riemann Problem for Junction. More...
 
virtual void v_Output (void)
 
void CheckPoint_Output (const int n)
 
NekDouble v_L2Error (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray, bool Normalised=false)
 Compute the L2 error between fields and a given exact solution. More...
 
NekDouble v_LinfError (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray)
 Compute the L_inf error between fields and a given exact solution. More...
 
void WriteVessels (const std::string &outname)
 Write input fields to the given filename. More...
 
void EnforceInterfaceConditions (const Array< OneD, const Array< OneD, NekDouble > > &fields)
 
- Protected Member Functions inherited from Nektar::SolverUtils::UnsteadySystem
SOLVER_UTILS_EXPORT UnsteadySystem (const LibUtilities::SessionReaderSharedPtr &pSession)
 Initialises UnsteadySystem class members. More...
 
SOLVER_UTILS_EXPORT NekDouble MaxTimeStepEstimator ()
 Get the maximum timestep estimator for cfl control. More...
 
virtual SOLVER_UTILS_EXPORT void v_GenerateSummary (SummaryList &s)
 Print a summary of time stepping parameters. More...
 
virtual SOLVER_UTILS_EXPORT void v_AppendOutput1D (Array< OneD, Array< OneD, NekDouble > > &solution1D)
 Print the solution at each solution point in a txt file. More...
 
virtual SOLVER_UTILS_EXPORT void v_NumericalFlux (Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numflux)
 
virtual SOLVER_UTILS_EXPORT void v_NumericalFlux (Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numfluxX, Array< OneD, Array< OneD, NekDouble > > &numfluxY)
 
virtual SOLVER_UTILS_EXPORT void v_NumFluxforScalar (const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &uflux)
 
virtual SOLVER_UTILS_EXPORT void v_NumFluxforVector (const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &qfield, Array< OneD, Array< OneD, NekDouble > > &qflux)
 
virtual SOLVER_UTILS_EXPORT
NekDouble 		v_GetTimeStep (const Array< OneD, const Array< OneD, NekDouble > > &inarray)
 Return the timestep to be used for the next step in the time-marching loop. More...
 
virtual SOLVER_UTILS_EXPORT bool v_PreIntegrate (int step)
 
virtual SOLVER_UTILS_EXPORT bool v_PostIntegrate (int step)
 
virtual SOLVER_UTILS_EXPORT bool v_SteadyStateCheck (int step)
 
SOLVER_UTILS_EXPORT void CheckForRestartTime (NekDouble &time)
 
SOLVER_UTILS_EXPORT void SVVVarDiffCoeff (const Array< OneD, Array< OneD, NekDouble > > vel, StdRegions::VarCoeffMap &varCoeffMap)
 Evaluate the SVV diffusion coefficient according to Moura's paper where it should proportional to h time velocity. More...
 
- Protected Member Functions inherited from Nektar::SolverUtils::EquationSystem
SOLVER_UTILS_EXPORT EquationSystem (const LibUtilities::SessionReaderSharedPtr &pSession)
 Initialises EquationSystem class members. More...
 
int nocase_cmp (const string &s1, const string &s2)
 
virtual SOLVER_UTILS_EXPORT void v_TransCoeffToPhys ()
 Virtual function for transformation to physical space. More...
 
virtual SOLVER_UTILS_EXPORT void v_TransPhysToCoeff ()
 Virtual function for transformation to coefficient space. More...
 
virtual SOLVER_UTILS_EXPORT void v_SetInitialConditions (NekDouble initialtime=0.0, bool dumpInitialConditions=true, const int domain=0)
 
virtual SOLVER_UTILS_EXPORT void v_EvaluateExactSolution (unsigned int field, Array< OneD, NekDouble > &outfield, const NekDouble time)
 
SOLVER_UTILS_EXPORT void SetUpBaseFields (SpatialDomains::MeshGraphSharedPtr &mesh)
 
SOLVER_UTILS_EXPORT void ImportFldBase (std::string pInfile, SpatialDomains::MeshGraphSharedPtr pGraph)
 
virtual SOLVER_UTILS_EXPORT
MultiRegions::ExpListSharedPtr 		v_GetPressure (void)
 
virtual SOLVER_UTILS_EXPORT void v_ExtraFldOutput (std::vector< Array< OneD, NekDouble > > &fieldcoeffs, std::vector< std::string > &variables)
 

Protected Attributes

Array< OneD,
MultiRegions::ExpListSharedPtr > 		m_vessels
 
int m_nDomains
 
int m_currentDomain
 
int m_nVariables
 
UpwindTypePulse m_upwindTypePulse
 
Array< OneD, int > m_fieldPhysOffset
 
NekDouble m_rho
 
NekDouble m_pext
 
NekDouble m_C
 
NekDouble m_RT
 
NekDouble m_pout
 
Array< OneD, Array< OneD,
NekDouble > > 		m_A_0
 
Array< OneD, Array< OneD,
NekDouble > > 		m_A_0_trace
 
Array< OneD, Array< OneD,
NekDouble > > 		m_beta
 
Array< OneD, Array< OneD,
NekDouble > > 		m_beta_trace
 
Array< OneD, Array< OneD,
NekDouble > > 		m_trace_fwd_normal
 
std::vector< std::vector
< InterfacePointShPtr > > 		m_vesselJcts
 
std::vector< std::vector
< InterfacePointShPtr > > 		m_bifurcations
 
std::vector< std::vector
< InterfacePointShPtr > > 		m_mergingJcts
 
- Protected Attributes inherited from Nektar::SolverUtils::UnsteadySystem
int m_infosteps
 Number of time steps between outputting status information. More...
 
LibUtilities::TimeIntegrationWrapperSharedPtr m_intScheme
 Wrapper to the time integration scheme. More...
 
LibUtilities::TimeIntegrationSchemeOperators m_ode
 The time integration scheme operators to use. More...
 
LibUtilities::TimeIntegrationSolutionSharedPtr m_intSoln
 
NekDouble m_epsilon
 
bool m_explicitDiffusion
 Indicates if explicit or implicit treatment of diffusion is used. More...
 
bool m_explicitAdvection
 Indicates if explicit or implicit treatment of advection is used. More...
 
bool m_explicitReaction
 Indicates if explicit or implicit treatment of reaction is used. More...
 
bool m_homoInitialFwd
 Flag to determine if simulation should start in homogeneous forward transformed state. More...
 
std::vector< int > m_intVariables
 
std::vector< FilterSharedPtr > m_filters
 
- Protected Attributes inherited from Nektar::SolverUtils::EquationSystem
LibUtilities::CommSharedPtr m_comm
 Communicator. More...
 
LibUtilities::SessionReaderSharedPtr m_session
 The session reader. More...
 
LibUtilities::FieldIOSharedPtr m_fld
 Field input/output. More...
 
map< std::string, Array< OneD,
Array< OneD, float > > > 		m_interpWeights
 Map of the interpolation weights for a specific filename. More...
 
map< std::string, Array< OneD,
Array< OneD, unsigned int > > > 		m_interpInds
 Map of the interpolation indices for a specific filename. More...
 
Array< OneD,
MultiRegions::ExpListSharedPtr > 		m_fields
 Array holding all dependent variables. More...
 
Array< OneD,
MultiRegions::ExpListSharedPtr > 		m_base
 Base fields. More...
 
Array< OneD,
MultiRegions::ExpListSharedPtr > 		m_derivedfields
 Array holding all dependent variables. More...
 
SpatialDomains::BoundaryConditionsSharedPtr m_boundaryConditions
 Pointer to boundary conditions object. More...
 
SpatialDomains::MeshGraphSharedPtr m_graph
 Pointer to graph defining mesh. More...
 
std::string m_sessionName
 Name of the session. More...
 
NekDouble m_time
 Current time of simulation. More...
 
int m_initialStep
 Number of the step where the simulation should begin. More...
 
NekDouble m_fintime
 Finish time of the simulation. More...
 
NekDouble m_timestep
 Time step size. More...
 
NekDouble m_lambda
 Lambda constant in real system if one required. More...
 
std::set< std::string > m_loadedFields
 
NekDouble m_checktime
 Time between checkpoints. More...
 
int m_nchk
 Number of checkpoints written so far. More...
 
int m_steps
 Number of steps to take. More...
 
int m_checksteps
 Number of steps between checkpoints. More...
 
int m_spacedim
 Spatial dimension (>= expansion dim). More...
 
int m_expdim
 Expansion dimension. More...
 
bool m_singleMode
 Flag to determine if single homogeneous mode is used. More...
 
bool m_halfMode
 Flag to determine if half homogeneous mode is used. More...
 
bool m_multipleModes
 Flag to determine if use multiple homogenenous modes are used. More...
 
bool m_useFFT
 Flag to determine if FFT is used for homogeneous transform. More...
 
bool m_homogen_dealiasing
 Flag to determine if dealiasing is used for homogeneous simulations. More...
 
bool m_specHP_dealiasing
 Flag to determine if dealisising is usde for the Spectral/hp element discretisation. More...
 
enum MultiRegions::ProjectionType m_projectionType
 Type of projection; e.g continuous or discontinuous. More...
 
Array< OneD, Array< OneD,
NekDouble > > 		m_traceNormals
 Array holding trace normals for DG simulations in the forwards direction. More...
 
Array< OneD, Array< OneD,
Array< OneD, NekDouble > > > 		m_gradtan
 1 x nvariable x nq More...
 
Array< OneD, Array< OneD,
Array< OneD, NekDouble > > > 		m_tanbasis
 2 x m_spacedim x nq More...
 
Array< OneD, bool > m_checkIfSystemSingular
 Flag to indicate if the fields should be checked for singularity. More...
 
LibUtilities::FieldMetaDataMap m_fieldMetaDataMap
 Map to identify relevant solver info to dump in output fields. More...
 
int m_NumQuadPointsError
 Number of Quadrature points used to work out the error. More...
 
enum HomogeneousType m_HomogeneousType
 
NekDouble m_LhomX
 physical length in X direction (if homogeneous) More...
 
NekDouble m_LhomY
 physical length in Y direction (if homogeneous) More...
 
NekDouble m_LhomZ
 physical length in Z direction (if homogeneous) More...
 
int m_npointsX
 number of points in X direction (if homogeneous) More...
 
int m_npointsY
 number of points in Y direction (if homogeneous) More...
 
int m_npointsZ
 number of points in Z direction (if homogeneous) More...
 
int m_HomoDirec
 number of homogenous directions More...
 
int m_NumMode
 Mode to use in case of single mode analysis. More...
 

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)
 

Additional Inherited Members

- Public Attributes inherited from Nektar::SolverUtils::UnsteadySystem
NekDouble m_cflSafetyFactor
 CFL safety factor (comprise between 0 to 1). More...
 
- Protected Types inherited from Nektar::SolverUtils::EquationSystem
enum  HomogeneousType { eHomogeneous1D, eHomogeneous2D, eHomogeneous3D, eNotHomogeneous }
 Parameter for homogeneous expansions. More...
 

Detailed Description

Base class for unsteady solvers.

Initialises the arterial subdomains in m_vessels and sets up all domain-linking conditions (bifurcations, 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 86 of file PulseWaveSystem.h.

Constructor & Destructor Documentation

Nektar::PulseWaveSystem::~PulseWaveSystem ( )
virtual

Destructor.

Destructor

Definition at line 72 of file PulseWaveSystem.cpp.

73  {
74  }
Nektar::PulseWaveSystem::PulseWaveSystem ( const LibUtilities::SessionReaderSharedPtr &  m_session)
protected

Initialises PulseWaveSystem class members.

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

Parameters
m_SessionSession object to read parameters from.

Definition at line 64 of file PulseWaveSystem.cpp.

65  : UnsteadySystem(m_session)
66  {
67  }
Nektar::SolverUtils::UnsteadySystem::UnsteadySystem
SOLVER_UTILS_EXPORT UnsteadySystem(const LibUtilities::SessionReaderSharedPtr &pSession)
Initialises UnsteadySystem class members.
Definition: UnsteadySystem.cpp:65
Nektar::SolverUtils::EquationSystem::m_session
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Definition: EquationSystem.h:452

Member Function Documentation

void Nektar::PulseWaveSystem::BifurcationRiemann ( Array< OneD, NekDouble > &  Au,
Array< OneD, NekDouble > &  uu,
Array< OneD, NekDouble > &  beta,
Array< OneD, NekDouble > &  A_0 
)
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 652 of file PulseWaveSystem.cpp.

References ASSERTL0, and m_rho.

Referenced by EnforceInterfaceConditions().

654  {
655  NekDouble rho = m_rho;
656  Array<OneD, NekDouble> W(3);
657  Array<OneD, NekDouble> W_Au(3);
658  Array<OneD, NekDouble> P_Au(3);
659  Array<OneD, NekDouble> f(6);
660  Array<OneD, NekDouble> g(6);
661  Array<OneD, NekDouble> tmp(6);
662  Array<OneD, Array<OneD, NekDouble> > inv_J(6);
663  for (int i=0; i<6; i++)
664  {
665  inv_J[i] = Array<OneD, NekDouble> (6);
666  }
667  NekDouble k = 0.0;
668  NekDouble k1 = 0.0;
669  NekDouble k2 = 0.0;
670  NekDouble k3 = 0.0;
671 
672  int proceed = 1;
673  int iter = 0;
674  int MAX_ITER = 7;
675 
676  // Calculated from input
677  W[0] = uu[0] + 4*sqrt(beta[0]/(2*rho))*(sqrt(sqrt(Au[0])) - sqrt(sqrt(A_0[0])));
678  W[1] = uu[1] - 4*sqrt(beta[1]/(2*rho))*(sqrt(sqrt(Au[1])) - sqrt(sqrt(A_0[1])));
679  W[2] = uu[2] - 4*sqrt(beta[2]/(2*rho))*(sqrt(sqrt(Au[2])) - sqrt(sqrt(A_0[2])));
680 
681  // Tolerances for the algorithm
682  NekDouble Tol = 1.0e-10;
683 
684  // Newton Iteration
685  while ((proceed) && (iter < MAX_ITER))
686  {
687  iter = iter+1;
688 
689  // Calculate the constraint vector, six equations:
690  // 3 characteristic variables, mass conservation,
691  // total pressure
692  W_Au[0] = 4*sqrt(beta[0]/(2*rho))*(sqrt(sqrt(Au[0])) - sqrt(sqrt(A_0[0])));
693  W_Au[1] = 4*sqrt(beta[1]/(2*rho))*(sqrt(sqrt(Au[1])) - sqrt(sqrt(A_0[1])));
694  W_Au[2] = 4*sqrt(beta[2]/(2*rho))*(sqrt(sqrt(Au[2])) - sqrt(sqrt(A_0[2])));
695 
696  P_Au[0] = beta[0]*(sqrt(Au[0]) - sqrt(A_0[0]));
697  P_Au[1] = beta[1]*(sqrt(Au[1]) - sqrt(A_0[1]));
698  P_Au[2] = beta[2]*(sqrt(Au[2]) - sqrt(A_0[2]));
699 
700  f[0] = uu[0] + W_Au[0] - W[0];
701  f[1] = uu[1] - W_Au[1] - W[1];
702  f[2] = uu[2] - W_Au[2] - W[2];
703  f[3] = Au[0]*uu[0] - Au[1]*uu[1] - Au[2]*uu[2];
704  f[4] = uu[0]*uu[0] + 2.0/rho*P_Au[0] - uu[1]*uu[1] - 2.0/rho*P_Au[1];
705  f[5] = uu[0]*uu[0] + 2.0/rho*P_Au[0] - uu[2]*uu[2] - 2.0/rho*P_Au[2];
706 
707  // Calculate the wave speed at each vessel
708  NekDouble c1 = sqrt(beta[0]/(2*rho))*sqrt(sqrt(Au[0]));
709  NekDouble c2 = sqrt(beta[1]/(2*rho))*sqrt(sqrt(Au[1]));
710  NekDouble c3 = sqrt(beta[2]/(2*rho))*sqrt(sqrt(Au[2]));
711 
712  // Inverse Jacobian matrix J(x[n])^(-1), is
713  // already inverted here analytically
714  k = c1*Au[1]*c3+Au[0]*c3*c2+Au[2]*c1*c2;
715  k1 = (c1-uu[0])*k;
716  inv_J[0][0] = (-c2*uu[0]*c3*Au[0]+Au[2]*c2*c1*c1+Au[1]*c1*c1*c3)/k1;
717  inv_J[0][1] = Au[1]*(c2-uu[1])*c1*c3/k1;
718  inv_J[0][2] = Au[2]*(c3-uu[2])*c1*c2/k1;
719  inv_J[0][3] = c1*c2*c3/k1;
720  inv_J[0][4] = -0.5*c1*Au[1]*c3/k1;
721  inv_J[0][5] = -0.5*Au[2]*c1*c2/k1;
722 
723  k2 = (c2+uu[1])*k;
724  inv_J[1][0] = Au[0]*(c1+uu[0])*c2*c3/k2;
725  inv_J[1][1] = (c1*uu[1]*c3*Au[1]+Au[2]*c1*c2*c2+c3*c2*c2*Au[0])/k2;
726  inv_J[1][2] = -Au[2]*(c3-uu[2])*c1*c2/k2;
727  inv_J[1][3] = -c1*c2*c3/k2;
728  inv_J[1][4] = -0.5*(c1*Au[2]+Au[0]*c3)*c2/k2;
729  inv_J[1][5] = 0.5*Au[2]*c1*c2/k2;
730 
731  k3 = (c3+uu[2])*k;
732  inv_J[2][0] = Au[0]*(c1+uu[0])*c2*c3/k3;
733  inv_J[2][1] = -Au[1]*(c2-uu[1])*c1*c3/k3;
734  inv_J[2][2] = (c1*c2*uu[2]*Au[2]+c1*Au[1]*c3*c3+c2*c3*c3*Au[0])/k3;
735  inv_J[2][3] = -c1*c2*c3/k3;
736  inv_J[2][4] = 0.5*c1*Au[1]*c3/k3;
737  inv_J[2][5] = -0.5*(Au[1]*c1+c2*Au[0])*c3/k3;
738 
739  inv_J[3][0] = Au[0]*(Au[0]*c3*c2-uu[0]*c3*Au[1]-uu[0]*c2*Au[2])/k1;
740  inv_J[3][1] = -Au[0]*Au[1]*(c2-uu[1])*c3/k1;
741  inv_J[3][2] = -Au[0]*Au[2]*(c3-uu[2])*c2/k1;
742  inv_J[3][3] = -Au[0]*c3*c2/k1;
743  inv_J[3][4] = 0.5*Au[0]*Au[1]*c3/k1;
744  inv_J[3][5] = 0.5*Au[0]*c2*Au[2]/k1;
745 
746  inv_J[4][0] = Au[0]*Au[1]*(c1+uu[0])*c3/k2;
747  inv_J[4][1] = -Au[1]*(c1*Au[1]*c3+c1*uu[1]*Au[2]+c3*uu[1]*Au[0])/k2;
748  inv_J[4][2] = -Au[2]*Au[1]*(c3-uu[2])*c1/k2;
749  inv_J[4][3] = -c1*Au[1]*c3/k2;
750  inv_J[4][4] = -0.5*Au[1]*(c1*Au[2]+Au[0]*c3)/k2;
751  inv_J[4][5] = 0.5*Au[2]*Au[1]*c1/k2;
752 
753  inv_J[5][0] = Au[0]*Au[2]*(c1+uu[0])*c2/k3;
754  inv_J[5][1] = -Au[2]*Au[1]*(c2-uu[1])*c1/k3;
755  inv_J[5][2] = -Au[2]*(Au[2]*c1*c2+c1*uu[2]*Au[1]+c2*uu[2]*Au[0])/k3;
756  inv_J[5][3] = -Au[2]*c1*c2/k3;
757  inv_J[5][4] = 0.5*Au[2]*Au[1]*c1/k3;
758  inv_J[5][5] = -0.5*Au[2]*(Au[1]*c1+c2*Au[0])/k3;
759 
760 
761  // Solve the system by multiplying the Jacobian with the vector f:
762  // g = (inv_J)*f
763  for (int j=0; j<6; j++)
764  {
765  tmp[j] =0.0;
766  g[j] = 0.0;
767  }
768 
769  for (int j=0; j<6; j++)
770  {
771  for (int i=0; i<6; i++)
772  {
773  tmp[j] = inv_J[j][i]*f[i];
774  g[j] += tmp[j];
775  }
776  }
777 
778  // Update the solution: x_new = x_old - dx
779  uu[0] = uu[0] - g[0];
780  uu[1] = uu[1] - g[1];
781  uu[2] = uu[2] - g[2];
782  Au[0] = Au[0] - g[3];
783  Au[1] = Au[1] - g[4];
784  Au[2] = Au[2] - g[5];
785 
786  // Check if the error of the solution is smaller than Tol
787  if ((g[0]*g[0] + g[1]*g[1] + g[2]*g[2] + g[3]*g[3]+ g[4]*g[4] + g[5]*g[5]) < Tol)
788  {
789  proceed = 0;
790  }
791 
792  // Check if solver converges
793  if (iter >= MAX_ITER)
794  {
795  ASSERTL0(false,"Riemann solver for Bifurcation did not converge");
796  }
797  }
798  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:161
Nektar::NekDouble
double NekDouble
Definition: NektarUnivTypeDefs.hpp:44
void Nektar::PulseWaveSystem::CalcCharacteristicVariables ( int  omega)

Definition at line 1291 of file PulseWaveSystem.cpp.

References m_beta, m_rho, m_vessels, Vmath::Smul(), Vmath::Vadd(), Vmath::Vmul(), Vmath::Vsqrt(), and Vmath::Vsub().

1292  {
1293  int nq = m_vessels[omega]->GetTotPoints();
1294  Array<OneD, NekDouble> A = m_vessels[omega]->UpdatePhys();
1295  Array<OneD, NekDouble> u = m_vessels[omega+1]->UpdatePhys();
1296  Array<OneD, NekDouble> c(nq);
1297 
1298  //Calc 4*c
1299  Vmath::Vsqrt(nq,A,1,c,1);
1300  Vmath::Vmul(nq,m_beta[omega],1,c,1,c,1);
1301  Vmath::Smul(nq,16.0/(2*m_rho),c,1,c,1);
1302  Vmath::Vsqrt(nq,c,1,c,1);
1303 
1304  // Characteristics
1305  Vmath::Vadd(nq,u,1,c,1,A,1);
1306  Vmath::Vsub(nq,u,1,c,1,u,1);
1307  }
Vmath::Vsqrt
void Vsqrt(int n, const T *x, const int incx, T *y, const int incy)
sqrt y = sqrt(x)
Definition: Vmath.cpp:394
Vmath::Smul
void Smul(int n, const T alpha, const T *x, const int incx, T *y, const int incy)
Scalar multiply y = alpha*y.
Definition: Vmath.cpp:199
Vmath::Vsub
void Vsub(int n, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
Subtract vector z = x-y.
Definition: Vmath.cpp:329
Nektar::PulseWaveSystem::m_beta
Array< OneD, Array< OneD, NekDouble > > m_beta
Definition: PulseWaveSystem.h:121
Nektar::PulseWaveSystem::m_vessels
Array< OneD, MultiRegions::ExpListSharedPtr > m_vessels
Definition: PulseWaveSystem.h:105
Vmath::Vadd
void Vadd(int n, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
Add vector z = x+y.
Definition: Vmath.cpp:285
Vmath::Vmul
void Vmul(int n, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
Multiply vector z = x*y.
Definition: Vmath.cpp:169
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 1098 of file PulseWaveSystem.cpp.

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

Referenced by v_DoSolve().

1099  {
1100  std::stringstream outname;
1101  outname << m_sessionName << "_" << n << ".chk";
1102 
1103  WriteVessels(outname.str());
1104  }
Nektar::SolverUtils::EquationSystem::m_sessionName
std::string m_sessionName
Name of the session.
Definition: EquationSystem.h:470
Nektar::PulseWaveSystem::WriteVessels
void WriteVessels(const std::string &outname)
Write input fields to the given filename.
Definition: PulseWaveSystem.cpp:1111
void Nektar::PulseWaveSystem::EnforceInterfaceConditions ( const Array< OneD, const Array< OneD, NekDouble > > &  fields)
protected

Definition at line 563 of file PulseWaveSystem.cpp.

References BifurcationRiemann(), FillDataFromInterfacePoint(), JunctionRiemann(), m_bifurcations, m_mergingJcts, m_nVariables, m_vesselJcts, m_vessels, and MergingRiemann().

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

564  {
565  int dom, bcpos;
566  Array<OneD, NekDouble> Au(3),uu(3),beta(3),A_0(3);
567 
568 
569  // Enfore Bifurcations;
570  for(int n = 0; n < m_bifurcations.size(); ++n)
571  {
572  FillDataFromInterfacePoint(m_bifurcations[n][0],fields,
573  Au[0],uu[0],beta[0],A_0[0]);
574  FillDataFromInterfacePoint(m_bifurcations[n][1],fields,
575  Au[1],uu[1],beta[1],A_0[1]);
576  FillDataFromInterfacePoint(m_bifurcations[n][2],fields,
577  Au[2],uu[2],beta[2],A_0[2]);
578 
579  // Solve the Riemann problem for a bifurcation
580  BifurcationRiemann(Au, uu, beta, A_0);
581 
582  // Store the values into the right positions:
583  for(int i = 0; i < 3; ++i)
584  {
585  dom = m_bifurcations[n][i]->m_domain;
586  bcpos = m_bifurcations[n][i]->m_bcPosition;
587  m_vessels[dom*m_nVariables] ->UpdateBndCondExpansion(bcpos)->UpdatePhys()[0] = Au[i];
588  m_vessels[dom*m_nVariables+1]->UpdateBndCondExpansion(bcpos)->UpdatePhys()[0] = uu[i];
589  }
590  }
591 
592  // Enfore Bifurcations;
593  for(int n = 0; n < m_mergingJcts.size(); ++n)
594  {
595  // Merged vessel
596  FillDataFromInterfacePoint(m_mergingJcts[n][0],fields,
597  Au[0],uu[0],beta[0],A_0[0]);
598  FillDataFromInterfacePoint(m_mergingJcts[n][1],fields,
599  Au[1],uu[1],beta[1],A_0[1]);
600  FillDataFromInterfacePoint(m_mergingJcts[n][2],fields,
601  Au[2],uu[2],beta[2],A_0[2]);
602 
603  // Solve the Riemann problem for a merging vessel
604  MergingRiemann(Au, uu, beta, A_0);
605 
606  // Store the values into the right positions:
607  for(int i = 0; i < 3; ++i)
608  {
609  int dom = m_mergingJcts[n][i]->m_domain;
610  int bcpos = m_mergingJcts[n][i]->m_bcPosition;
611  m_vessels[dom*m_nVariables] ->UpdateBndCondExpansion(bcpos)->UpdatePhys()[0] = Au[i];
612  m_vessels[dom*m_nVariables+1]->UpdateBndCondExpansion(bcpos)->UpdatePhys()[0] = uu[i];
613  }
614  }
615 
616  for(int n = 0; n < m_vesselJcts.size(); ++n)
617  {
618 
619  FillDataFromInterfacePoint(m_vesselJcts[n][0],fields,
620  Au[0],uu[0],beta[0],A_0[0]);
621  FillDataFromInterfacePoint(m_vesselJcts[n][1],fields,
622  Au[1],uu[1],beta[1],A_0[1]);
623 
624  JunctionRiemann(Au, uu, beta, A_0);
625 
626  // Store the values into the right positions:
627  for(int i = 0; i < 2; ++i)
628  {
629  int dom = m_vesselJcts[n][i]->m_domain;
630  int bcpos = m_vesselJcts[n][i]->m_bcPosition;
631  m_vessels[dom*m_nVariables] ->UpdateBndCondExpansion(bcpos)->UpdatePhys()[0] = Au[i];
632  m_vessels[dom*m_nVariables+1]->UpdateBndCondExpansion(bcpos)->UpdatePhys()[0] = uu[i];
633  //cout<<"Au: "<<Au[i]<<endl;
634  //cout<<"uu: "<<uu[i]<<endl;
635  //cout<<endl;
636  }
637 
638  }
639  }
Nektar::PulseWaveSystem::BifurcationRiemann
void BifurcationRiemann(Array< OneD, NekDouble > &Au, Array< OneD, NekDouble > &uu, Array< OneD, NekDouble > &beta, Array< OneD, NekDouble > &A_0)
Riemann Problem for Bifurcation.
Definition: PulseWaveSystem.cpp:652
Nektar::PulseWaveSystem::m_vesselJcts
std::vector< std::vector< InterfacePointShPtr > > m_vesselJcts
Definition: PulseWaveSystem.h:126
Nektar::PulseWaveSystem::MergingRiemann
void MergingRiemann(Array< OneD, NekDouble > &Au, Array< OneD, NekDouble > &uu, Array< OneD, NekDouble > &beta, Array< OneD, NekDouble > &A_0)
Riemann Problem for Merging Flow.
Definition: PulseWaveSystem.cpp:811
Nektar::PulseWaveSystem::m_bifurcations
std::vector< std::vector< InterfacePointShPtr > > m_bifurcations
Definition: PulseWaveSystem.h:127
Nektar::PulseWaveSystem::FillDataFromInterfacePoint
void FillDataFromInterfacePoint(InterfacePointShPtr &I, const Array< OneD, const Array< OneD, NekDouble > > &field, NekDouble &A, NekDouble &u, NekDouble &beta, NekDouble &A_0)
Definition: PulseWaveSystem.cpp:537
Nektar::PulseWaveSystem::JunctionRiemann
void JunctionRiemann(Array< OneD, NekDouble > &Au, Array< OneD, NekDouble > &uu, Array< OneD, NekDouble > &beta, Array< OneD, NekDouble > &A_0)
Riemann Problem for Junction.
Definition: PulseWaveSystem.cpp:968
Nektar::PulseWaveSystem::m_vessels
Array< OneD, MultiRegions::ExpListSharedPtr > m_vessels
Definition: PulseWaveSystem.h:105
Nektar::PulseWaveSystem::m_mergingJcts
std::vector< std::vector< InterfacePointShPtr > > m_mergingJcts
Definition: PulseWaveSystem.h:128
void Nektar::PulseWaveSystem::FillDataFromInterfacePoint ( InterfacePointShPtr &  I,
const Array< OneD, const Array< OneD, NekDouble > > &  field,
NekDouble &  A,
NekDouble &  u,
NekDouble &  beta,
NekDouble &  A_0 
)
private

Definition at line 537 of file PulseWaveSystem.cpp.

References m_A_0_trace, m_beta_trace, m_fieldPhysOffset, m_nVariables, m_vessels, and Nektar::NekMeshUtils::vert.

Referenced by EnforceInterfaceConditions().

541  {
542  int omega, traceId, eid, vert, phys_offset, vesselID;
543 
544 
545  // Parent vessel
546  omega = I->m_domain;
547  traceId = I->m_traceId;
548  eid = I->m_elmt;
549  vert = I->m_elmtVert;
550  vesselID = omega*m_nVariables;
551 
552  phys_offset = m_vessels[vesselID]->GetPhys_Offset(eid);
553 
554  m_vessels[vesselID]->GetExp(eid)->
555  GetVertexPhysVals(vert, fields[0]+m_fieldPhysOffset[omega]+phys_offset, A);
556  m_vessels[vesselID]->GetExp(eid)->
557  GetVertexPhysVals(vert, fields[1]+m_fieldPhysOffset[omega]+phys_offset, u);
558 
559  beta = m_beta_trace[omega][traceId];
560  A_0 = m_A_0_trace [omega][traceId];
561  }
Nektar::PulseWaveSystem::m_fieldPhysOffset
Array< OneD, int > m_fieldPhysOffset
Definition: PulseWaveSystem.h:111
Nektar::PulseWaveSystem::m_beta_trace
Array< OneD, Array< OneD, NekDouble > > m_beta_trace
Definition: PulseWaveSystem.h:122
Nektar::PulseWaveSystem::m_A_0_trace
Array< OneD, Array< OneD, NekDouble > > m_A_0_trace
Definition: PulseWaveSystem.h:120
Nektar::PulseWaveSystem::m_vessels
Array< OneD, MultiRegions::ExpListSharedPtr > m_vessels
Definition: PulseWaveSystem.h:105
int Nektar::PulseWaveSystem::GetNdomains ( )
inline

Definition at line 92 of file PulseWaveSystem.h.

93  {
94  return m_nDomains;
95  }
void Nektar::PulseWaveSystem::JunctionRiemann ( Array< OneD, NekDouble > &  Au,
Array< OneD, NekDouble > &  uu,
Array< OneD, NekDouble > &  beta,
Array< OneD, NekDouble > &  A_0 
)
protected

Riemann Problem for Junction.

Solves the Riemann problem at an interdomain junction 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 968 of file PulseWaveSystem.cpp.

References ASSERTL0, and m_rho.

Referenced by EnforceInterfaceConditions().

970  {
971  NekDouble rho = m_rho;
972  Array<OneD, NekDouble> W(2);
973  Array<OneD, NekDouble> W_Au(2);
974  Array<OneD, NekDouble> P_Au(2);
975  Array<OneD, NekDouble> f(4);
976  Array<OneD, NekDouble> g(4);
977  Array<OneD, NekDouble> tmp(4);
978  Array<OneD, Array<OneD, NekDouble> > inv_J(4);
979  for (int i=0; i<4; i++)
980  {
981  inv_J[i] = Array<OneD, NekDouble> (4);
982  }
983  NekDouble k = 0.0;
984  NekDouble k1 = 0.0;
985  NekDouble k2 = 0.0;
986 
987  int proceed = 1;
988  int iter = 0;
989  int MAX_ITER = 7;
990  NekDouble Tol = 1.0e-10;
991 
992  // Calculated from input
993  W[0] = uu[0] + 4*sqrt(beta[0]/(2*rho))*(sqrt(sqrt(Au[0])) - sqrt(sqrt(A_0[0])));
994  W[1] = uu[1] - 4*sqrt(beta[1]/(2*rho))*(sqrt(sqrt(Au[1])) - sqrt(sqrt(A_0[1])));
995 
996  while((proceed) && (iter < MAX_ITER))
997  {
998  iter = iter+1;
999 
1000  // Calculate the constraint vector, 4 equations:
1001  // 2 characteristic variables, mass conservation,
1002  // total pressure
1003  W_Au[0] = 4*sqrt(beta[0]/(2*rho))*(sqrt(sqrt(Au[0])) - sqrt(sqrt(A_0[0])));
1004  W_Au[1] = 4*sqrt(beta[1]/(2*rho))*(sqrt(sqrt(Au[1])) - sqrt(sqrt(A_0[1])));
1005 
1006  P_Au[0] = beta[0]*(sqrt(Au[0]) - sqrt(A_0[0]));
1007  P_Au[1] = beta[1]*(sqrt(Au[1]) - sqrt(A_0[1]));
1008 
1009  f[0] = uu[0] + W_Au[0] - W[0];
1010  f[1] = uu[1] - W_Au[1] - W[1];
1011  f[2] = Au[0]*uu[0] - Au[1]*uu[1];
1012  f[3] = uu[0]*uu[0] + 2.0/rho*P_Au[0] - uu[1]*uu[1] - 2.0/rho*P_Au[1];
1013 
1014  // Calculate the wave speed at each vessel
1015  NekDouble cl = sqrt(beta[0]/(2*rho))*sqrt(sqrt(Au[0]));
1016  NekDouble cr = sqrt(beta[1]/(2*rho))*sqrt(sqrt(Au[1]));
1017 
1018  // Inverse Jacobian matrix J(x[n])^(-1), is already inverted here analytically
1019  k = (cl*Au[1]+Au[0]*cr);
1020  k1 = (cl-uu[0])*k;
1021  inv_J[0][0] = (Au[1]*cl*cl-cr*uu[0]*Au[0])/k1;
1022  inv_J[0][1] = Au[1]*(cr-uu[1])*cl/k1;
1023  inv_J[0][2] = cl*cr/k1;
1024  inv_J[0][3] = -0.5*cl*Au[1]/k1;
1025 
1026  k2 = (cr+uu[1])*k;
1027  inv_J[1][0] = Au[0]*(cl+uu[0])*cr/k2;
1028  inv_J[1][1] = (cl*uu[1]*Au[1]+cr*cr*Au[0])/k2;
1029  inv_J[1][2] = -cl*cr/k2;
1030  inv_J[1][3] = -0.5*Au[0]*cr/k2;
1031 
1032  inv_J[2][0] = Au[0]*(Au[0]*cr-uu[0]*Au[1])/k1;
1033  inv_J[2][1] = -Au[0]*Au[1]*(cr-uu[1])/k1;
1034  inv_J[2][2] = -Au[0]*cr/k1;
1035  inv_J[2][3] = 0.5*Au[1]*Au[0]/k1;
1036 
1037  inv_J[3][0] = Au[0]*Au[1]*(cl+uu[0])/k2;
1038  inv_J[3][1] = -Au[1]*(cl*Au[1]+uu[1]*Au[0])/k2;
1039  inv_J[3][2] = -cl*Au[1]/k2;
1040  inv_J[3][3] = -0.5*Au[1]*Au[0]/k2;
1041 
1042  // Solve the system by multiplying the Jacobian with the vector f:
1043  // g = (inv_J)*f
1044  for (int j=0; j<4; j++)
1045  {
1046  tmp[j] =0.0;
1047  g[j] = 0.0;
1048  }
1049 
1050  for (int j=0; j<4; j++)
1051  {
1052  for (int i=0; i<4; i++)
1053  {
1054  tmp[j] = inv_J[j][i]*f[i];
1055  g[j] += tmp[j];
1056  }
1057  }
1058 
1059  // Update solution: x_new = x_old - dx
1060  uu[0] -= g[0];
1061  uu[1] -= g[1];
1062  Au[0] -= g[2];
1063  Au[1] -= g[3];
1064 
1065  // Check if the error of the solution is smaller than Tol.
1066  if((g[0]*g[0] + g[1]*g[1] + g[2]*g[2] + g[3]*g[3]) < Tol)
1067  proceed = 0;
1068  }
1069 
1070  if(iter >= MAX_ITER)
1071  {
1072  ASSERTL0(false,"Riemann solver for Junction did not converge");
1073  }
1074  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:161
Nektar::NekDouble
double NekDouble
Definition: NektarUnivTypeDefs.hpp:44
void Nektar::PulseWaveSystem::LinkSubdomains ( Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &  fields)
protected

Links the subdomains.

void Nektar::PulseWaveSystem::MergingRiemann ( Array< OneD, NekDouble > &  Au,
Array< OneD, NekDouble > &  uu,
Array< OneD, NekDouble > &  beta,
Array< OneD, NekDouble > &  A_0 
)
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 811 of file PulseWaveSystem.cpp.

References ASSERTL0, and m_rho.

Referenced by EnforceInterfaceConditions().

812  {
813  NekDouble rho = m_rho;
814  Array<OneD, NekDouble> W(3);
815  Array<OneD, NekDouble> W_Au(3);
816  Array<OneD, NekDouble> P_Au(3);
817  Array<OneD, NekDouble> f(6);
818  Array<OneD, NekDouble> g(6);
819  Array<OneD, NekDouble> tmp(6);
820  Array<OneD, Array<OneD, NekDouble> > inv_J(6);
821 
822  for (int i=0; i<6; i++)
823  {
824  inv_J[i] = Array<OneD, NekDouble> (6);
825  }
826 
827  NekDouble k = 0.0;
828  NekDouble k1 = 0.0;
829  NekDouble k2 = 0.0;
830  NekDouble k3 = 0.0;
831 
832  int proceed = 1;
833  int iter = 0;
834  int MAX_ITER = 7;
835 
836  // Calculated from input
837  W[0] = uu[0] - 4*sqrt(beta[0]/(2*rho))*(sqrt(sqrt(Au[0])) - sqrt(sqrt(A_0[0])));
838  W[1] = uu[1] + 4*sqrt(beta[1]/(2*rho))*(sqrt(sqrt(Au[1])) - sqrt(sqrt(A_0[1])));
839  W[2] = uu[2] + 4*sqrt(beta[2]/(2*rho))*(sqrt(sqrt(Au[2])) - sqrt(sqrt(A_0[2])));
840 
841  // Tolerances for the algorithm
842  NekDouble Tol = 1.0e-10;
843 
844  // Newton Iteration
845  while ((proceed) && (iter < MAX_ITER))
846  {
847  iter = iter+1;
848 
849  // Calculate the constraint vector, six equations:
850  // 3 characteristic variables, mass conservation,
851  // total pressure
852  W_Au[0] = 4*sqrt(beta[0]/(2*rho))*(sqrt(sqrt(Au[0])) - sqrt(sqrt(A_0[0])));
853  W_Au[1] = 4*sqrt(beta[1]/(2*rho))*(sqrt(sqrt(Au[1])) - sqrt(sqrt(A_0[1])));
854  W_Au[2] = 4*sqrt(beta[2]/(2*rho))*(sqrt(sqrt(Au[2])) - sqrt(sqrt(A_0[2])));
855 
856  P_Au[0] = beta[0]*(sqrt(Au[0]) - sqrt(A_0[0]));
857  P_Au[1] = beta[1]*(sqrt(Au[1]) - sqrt(A_0[1]));
858  P_Au[2] = beta[2]*(sqrt(Au[2]) - sqrt(A_0[2]));
859 
860  f[0] = uu[0] - W_Au[0] - W[0];
861  f[1] = uu[1] + W_Au[1] - W[1];
862  f[2] = uu[2] + W_Au[2] - W[2];
863  f[3] = Au[0]*uu[0] - Au[1]*uu[1] - Au[2]*uu[2];
864  f[4] = uu[0]*uu[0] + 2.0/rho*P_Au[0] - uu[1]*uu[1] - 2.0/rho*P_Au[1];
865  f[5] = uu[0]*uu[0] + 2.0/rho*P_Au[0] - uu[2]*uu[2] - 2.0/rho*P_Au[2];
866 
867  // Calculate the wave speed at each vessel
868  NekDouble c1 = sqrt(beta[0]/(2*rho))*sqrt(sqrt(Au[0]));
869  NekDouble c2 = sqrt(beta[1]/(2*rho))*sqrt(sqrt(Au[1]));
870  NekDouble c3 = sqrt(beta[2]/(2*rho))*sqrt(sqrt(Au[2]));
871 
872  // Inverse Jacobian matrix J(x[n])^(-1), is already inverted here analytically
873  k = c1*Au[1]*c3+Au[0]*c3*c2+Au[2]*c1*c2;
874  k1 = (c1+uu[0])*k;
875  inv_J[0][0] = (c2*uu[0]*c3*Au[0]+Au[2]*c2*c1*c1+Au[1]*c1*c1*c3)/k1;
876  inv_J[0][1] = Au[1]*(c2+uu[1])*c1*c3/k1;
877  inv_J[0][2] = Au[2]*(c3+uu[2])*c1*c2/k1;
878  inv_J[0][3] = c1*c2*c3/k1;
879  inv_J[0][4] = 0.5*Au[1]*c1*c3/k1;
880  inv_J[0][5] = 0.5*Au[2]*c1*c2/k1;
881 
882  k2 = (c2-uu[1])*k;
883  inv_J[1][0] = Au[0]*(c1-uu[0])*c2*c3/k2;
884  inv_J[1][1] = (-c1*uu[1]*c3*Au[1]+Au[2]*c1*c2*c2+c3*c2*c2*Au[0])/k2;
885  inv_J[1][2] = -Au[2]*(c3+uu[2])*c1*c2/k2;
886  inv_J[1][3] = -c1*c2*c3/k2;
887  inv_J[1][4] = 0.5*(c1*Au[2]+Au[0]*c3)*c2/k2;
888  inv_J[1][5] = -0.5*Au[2]*c1*c2/k2;
889 
890  k3 = (c3-uu[2])*k;
891  inv_J[2][0] = Au[0]*(c1-uu[0])*c2*c3/k3;
892  inv_J[2][1] = -Au[1]*(c2+uu[1])*c1*c3/k3;
893  inv_J[2][2] = -(c1*uu[2]*c2*Au[2]-Au[1]*c1*c3*c3-c2*c3*c3*Au[0])/k3;
894  inv_J[2][3] = -c1*c2*c3/k3;
895  inv_J[2][4] = -0.5*Au[1]*c1*c3/k3;
896  inv_J[2][5] = 0.5*(Au[1]*c1+Au[0]*c2)*c3/k3;
897 
898  inv_J[3][0] = -Au[0]*(Au[0]*c3*c2+uu[0]*c3*Au[1]+uu[0]*c2*Au[2])/k1;
899  inv_J[3][1] = Au[0]*Au[1]*(c2+uu[1])*c3/k1;
900  inv_J[3][2] = Au[0]*Au[2]*(c3+uu[2])*c2/k1;
901  inv_J[3][3] = Au[0]*c3*c2/k1;
902  inv_J[3][4] = 0.5*Au[0]*Au[1]*c3/k1;
903  inv_J[3][5] = 0.5*Au[0]*c2*Au[2]/k1;
904 
905  inv_J[4][0] = -Au[0]*Au[1]*(c1-uu[0])*c3/k2;
906  inv_J[4][1] = Au[1]*(Au[1]*c1*c3-c1*uu[1]*Au[2]-c3*uu[1]*Au[0])/k2;
907  inv_J[4][2] = Au[2]*Au[1]*(c3+uu[2])*c1/k2;
908  inv_J[4][3] = Au[1]*c1*c3/k2;
909  inv_J[4][4] = -0.5*Au[1]*(c1*Au[2]+Au[0]*c3)/k2;
910  inv_J[4][5] = 0.5*Au[2]*Au[1]*c1/k2;
911 
912  inv_J[5][0] = -Au[0]*Au[2]*(c1-uu[0])*c2/k3;
913  inv_J[5][1] = Au[2]*Au[1]*(c2+uu[1])*c1/k3;
914  inv_J[5][2] = Au[2]*(Au[2]*c1*c2-c1*uu[2]*Au[1]-c2*uu[2]*Au[0])/k3;
915  inv_J[5][3] = Au[2]*c1*c2/k3;
916  inv_J[5][4] = 0.5*Au[2]*Au[1]*c1/k3;
917  inv_J[5][5] = -0.5*Au[2]*(Au[1]*c1+Au[0]*c2)/k3;
918 
919  // Solve the system by multiplying the Jacobian with the vector f:
920  // g = (inv_J)*f
921  for (int j=0; j<6; j++)
922  {
923  tmp[j] =0.0;
924  g[j] = 0.0;
925  }
926 
927  for (int j=0; j<6; j++)
928  {
929  for (int i=0; i<6; i++)
930  {
931  tmp[j] = inv_J[j][i]*f[i];
932  g[j] += tmp[j];
933  }
934  }
935 
936  // Update the solution: x_new = x_old - dx
937  uu[0] = uu[0] - g[0];
938  uu[1] = uu[1] - g[1];
939  uu[2] = uu[2] - g[2];
940  Au[0] = Au[0] - g[3];
941  Au[1] = Au[1] - g[4];
942  Au[2] = Au[2] - g[5];
943 
944  // Check if the error of the solution is smaller than Tol
945  if ((g[0]*g[0] + g[1]*g[1] + g[2]*g[2] + g[3]*g[3]+ g[4]*g[4] + g[5]*g[5]) < Tol)
946  {
947  proceed = 0;
948  }
949 
950  // Check if solver converges
951  if (iter >= MAX_ITER)
952  {
953  ASSERTL0(false,"Riemann solver for Merging Flow did not converge");
954  }
955 
956  }
957  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:161
Nektar::NekDouble
double NekDouble
Definition: NektarUnivTypeDefs.hpp:44
void Nektar::PulseWaveSystem::SetUpDomainInterfaces ( void  )
private

Definition at line 262 of file PulseWaveSystem.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, Nektar::SpatialDomains::eDirichlet, Nektar::SpatialDomains::eNotDefined, ErrorUtil::ewarning, Nektar::iterator, m_bifurcations, m_mergingJcts, m_nDomains, m_nVariables, m_vesselJcts, m_vessels, and NEKERROR.

Referenced by v_InitObject().

263  {
264  map<int,std::vector<InterfacePointShPtr> > VidToDomain;
265  map<int,std::vector<InterfacePointShPtr> >::iterator iter;
266 
267  // loop over domain and find out if we have any undefined
268  // boundary conditions representing interfaces. If so make a
269  // map based around vid and storing the domains that are
270  // part of interfaces.
271  for(int omega = 0; omega < m_nDomains; ++omega)
272  {
273  int vesselID = omega*m_nVariables;
274 
275  for(int i = 0; i < 2; ++i)
276  {
277  if(m_vessels[vesselID]->GetBndConditions()[i]->GetBoundaryConditionType() == SpatialDomains::eNotDefined)
278  {
279  // Get Vid of interface
280  int vid = m_vessels[vesselID]->UpdateBndCondExpansion(i)->GetExp(0)->GetGeom()->GetVid(0);
281  cout<<"Shared vertex id: "<<vid<<endl;
282  MultiRegions::ExpListSharedPtr trace = m_vessels[vesselID]->GetTrace();
283  InterfacePointShPtr Ipt;
284 
285  bool finish = false;
286  // find which elmt, the lcoal vertex and the data offset of point
287  for(int n = 0; n < m_vessels[vesselID]->GetExpSize(); ++n)
288  {
289  for(int p = 0; p < 2; ++p)
290  {
291  if(m_vessels[vesselID]->GetTraceMap()->GetElmtToTrace()[n][p]->as<LocalRegions::Expansion>()->GetGeom()->GetVid(0) == vid)
292  {
293  int eid = m_vessels[vesselID]->GetTraceMap()->GetElmtToTrace()[n][p]->GetElmtId();
294 
295  int tid = m_vessels[vesselID]->GetTrace()->GetCoeff_Offset(eid);
296  Ipt = MemoryManager<InterfacePoint>::AllocateSharedPtr(vid,omega,n,p,tid,i);
297 
298  cout<<"Global Vid of interface point: "<<vid<<endl;
299  cout<<"Domain interface point belongs to: "<<omega<<endl;
300  cout<<"Element id of vertex: "<<n<<endl;
301  cout<<"Vertex id within local element: "<<p<<endl;
302  cout<<"Element id within the trace: "<<tid<<endl;
303  cout<<"Position of boundary condition in region: "<<i<<endl;
304 
305  finish = true;
306  break;
307  }
308  }
309  if(finish == true)
310  {
311  break;
312  }
313  }
314 
315  VidToDomain[vid].push_back(Ipt);
316 
317  // finally reset boundary condition to Dirichlet
318  m_vessels[vesselID]->GetBndConditions()[i]
319  ->SetBoundaryConditionType(SpatialDomains::eDirichlet);
320 
321  m_vessels[vesselID+1]->GetBndConditions()[i]
322  ->SetBoundaryConditionType(SpatialDomains::eDirichlet);
323  }
324  }
325  }
326 
327  // loop over map and set up Interface information;
328  for(iter = VidToDomain.begin(); iter != VidToDomain.end(); ++iter)
329  {
330  if(iter->second.size() == 2) // Vessel jump interface
331  {
332  m_vesselJcts.push_back(iter->second);
333  }
334  else if(iter->second.size() == 3) // Bifurcation or Merging junction.
335  {
336  int nbeg = 0;
337  int nend = 0;
338 
339  // Determine if bifurcation or merging junction
340  // through number of elemnt vertices that meet at
341  // junction. Only one vertex using a m_elmtVert=1
342  // indicates a bifurcation
343  for(int i = 0; i < 3; ++i)
344  {
345  if(iter->second[i]->m_elmtVert == 0)
346  {
347  nbeg += 1;
348  }
349  else
350  {
351  nend += 1;
352  }
353  }
354 
355  // Set up Bifurcation information
356  if(nbeg == 2)
357  {
358  // ensure first InterfacePoint is parent
359  if(iter->second[0]->m_elmtVert == 1) //m_elmtVert: Vertex id in local element
360  {
361  m_bifurcations.push_back(iter->second);
362  }
363  else
364  {
365  //order points according to Riemann solver convention
366  InterfacePointShPtr I;
367  //find merging vessel
368  if(iter->second[1]->m_elmtVert == 1)
369  {
370  I = iter->second[0];
371  iter->second[0] = iter->second[1];
372  iter->second[1] = I;
373  }
374  else if (iter->second[2]->m_elmtVert == 1)
375  {
376  I = iter->second[0];
377  iter->second[0] = iter->second[2];
378  iter->second[2] = I;
379  }
380  NEKERROR(ErrorUtil::ewarning,"This routine has not been checked");
381  }
382  }
383  else
384  {
385  // ensure last InterfacePoint is merged vessel
386  if(iter->second[0]->m_elmtVert == 0)
387  {
388  m_mergingJcts.push_back(iter->second);
389  }
390  else
391  {
392  //order points according to Riemann solver convention
393  InterfacePointShPtr I;
394  //find merging vessel
395  if(iter->second[1]->m_elmtVert == 0)
396  {
397  I = iter->second[0];
398  iter->second[0] = iter->second[1];
399  iter->second[1] = I;
400  }
401  else if (iter->second[2]->m_elmtVert == 0)
402  {
403  I = iter->second[0];
404  iter->second[0] = iter->second[2];
405  iter->second[2] = I;
406  }
407  NEKERROR(ErrorUtil::ewarning,"This routine has not been checked");
408  }
409  }
410 
411  }
412  else
413  {
414  ASSERTL0(false,"Unknown junction type");
415  }
416  }
417  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:161
NEKERROR
#define NEKERROR(type, msg)
Assert Level 0 – Fundamental assert which is used whether in FULLDEBUG, DEBUG or OPT compilation mod...
Definition: ErrorUtil.hpp:158
Nektar::MemoryManager::AllocateSharedPtr
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
Definition: NekMemoryManager.hpp:235
Nektar::PulseWaveSystem::m_vesselJcts
std::vector< std::vector< InterfacePointShPtr > > m_vesselJcts
Definition: PulseWaveSystem.h:126
Nektar::PulseWaveSystem::m_bifurcations
std::vector< std::vector< InterfacePointShPtr > > m_bifurcations
Definition: PulseWaveSystem.h:127
Nektar::MultiRegions::ExpListSharedPtr
boost::shared_ptr< ExpList > ExpListSharedPtr
Shared pointer to an ExpList object.
Definition: LocTraceToTraceMap.h:56
Nektar::iterator
StandardMatrixTag boost::call_traits< LhsDataType >::const_reference rhs typedef NekMatrix< LhsDataType, StandardMatrixTag >::iterator iterator
Definition: MatrixOperations.cpp:96
Nektar::PulseWaveSystem::m_vessels
Array< OneD, MultiRegions::ExpListSharedPtr > m_vessels
Definition: PulseWaveSystem.h:105
Nektar::PulseWaveSystem::m_mergingJcts
std::vector< std::vector< InterfacePointShPtr > > m_mergingJcts
Definition: PulseWaveSystem.h:128
Nektar::InterfacePointShPtr
boost::shared_ptr< InterfacePoint > InterfacePointShPtr
Definition: PulseWaveSystem.h:83
Array<OneD, MultiRegions::ExpListSharedPtr> Nektar::PulseWaveSystem::UpdateVessels ( void  )
inline

Definition at line 97 of file PulseWaveSystem.h.

98  {
99  return m_vessels;
100  }
Nektar::PulseWaveSystem::m_vessels
Array< OneD, MultiRegions::ExpListSharedPtr > m_vessels
Definition: PulseWaveSystem.h:105
void Nektar::PulseWaveSystem::v_DoInitialise ( void  )
protectedvirtual

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 427 of file PulseWaveSystem.cpp.

References Nektar::SolverUtils::EquationSystem::m_fields, m_nDomains, m_nVariables, Nektar::SolverUtils::EquationSystem::m_session, m_vessels, and Nektar::SolverUtils::EquationSystem::SetInitialConditions().

428  {
429 
430  if (m_session->GetComm()->GetRank() == 0)
431  {
432  cout << "Initial Conditions:" << endl;
433  }
434 
435  /* Loop over all subdomains to initialize all with the Initial
436  * Conditions read from the inputfile*/
437  for (int omega = 0; omega < m_nDomains; omega++)
438  {
439  m_fields[0] = m_vessels[m_nVariables*omega];
440  m_fields[1] = m_vessels[m_nVariables*omega+1];
441 
442  if (m_session->GetComm()->GetRank() == 0)
443  {
444  cout << "Subdomain = " <<omega<<endl;
445  }
446 
447  SetInitialConditions(0.0,0,omega);
448  }
449  // Reset to first definition
450  m_fields[0] = m_vessels[0];
451  m_fields[1] = m_vessels[1];
452 
453  }
Nektar::SolverUtils::EquationSystem::m_fields
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
Definition: EquationSystem.h:460
Nektar::SolverUtils::EquationSystem::m_session
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Definition: EquationSystem.h:452
Nektar::SolverUtils::EquationSystem::SetInitialConditions
SOLVER_UTILS_EXPORT void SetInitialConditions(NekDouble initialtime=0.0, bool dumpInitialConditions=true, const int domain=0)
Initialise the data in the dependent fields.
Definition: EquationSystem.h:786
Nektar::PulseWaveSystem::m_vessels
Array< OneD, MultiRegions::ExpListSharedPtr > m_vessels
Definition: PulseWaveSystem.h:105
void Nektar::PulseWaveSystem::v_DoSolve ( void  )
protectedvirtual

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 independentl 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

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 472 of file PulseWaveSystem.cpp.

References CheckPoint_Output(), Nektar::SolverUtils::EquationSystem::m_checksteps, Nektar::SolverUtils::EquationSystem::m_fields, Nektar::SolverUtils::UnsteadySystem::m_infosteps, Nektar::SolverUtils::UnsteadySystem::m_intScheme, Nektar::SolverUtils::UnsteadySystem::m_intSoln, m_nDomains, m_nVariables, Nektar::SolverUtils::UnsteadySystem::m_ode, Nektar::SolverUtils::EquationSystem::m_session, Nektar::SolverUtils::EquationSystem::m_steps, Nektar::SolverUtils::EquationSystem::m_time, Nektar::SolverUtils::EquationSystem::m_timestep, m_vessels, Nektar::Timer::Start(), Nektar::Timer::Stop(), Nektar::Timer::TimePerTest(), and Vmath::Vcopy().

473  {
474  NekDouble IntegrationTime = 0.0;
475  int i,n,nchk = 1;
476 
477  Array<OneD, Array<OneD,NekDouble> > fields(m_nVariables);
478 
479  for(int i = 0; i < m_nVariables; ++i)
480  {
481  fields[i] = m_vessels[i]->UpdatePhys();
482  m_fields[i]->SetPhysState(false);
483  }
484 
485  m_intSoln = m_intScheme->InitializeScheme(
486  m_timestep,fields,m_time,m_ode);
487 
488  // Time loop
489  for(n = 0; n < m_steps; ++n)
490  {
491  Timer timer;
492  timer.Start();
493  fields = m_intScheme->TimeIntegrate(n,m_timestep,m_intSoln,m_ode);
494  //cout<<"integration: "<<fields[0][fields[0].num_elements()-1]<<endl;
495  m_time += m_timestep;
496  timer.Stop();
497  IntegrationTime += timer.TimePerTest(1);
498 
499  // Write out status information.
500  if(m_session->GetComm()->GetRank() == 0 && !((n+1)%m_infosteps))
501  {
502  cout << "Steps: " << n+1
503  << "\t Time: " << m_time
504  << "\t Time-step: " << m_timestep << "\t" << endl;
505  }
506 
507  // Transform data if needed
508  if(!((n+1)%m_checksteps))
509  {
510  for (i = 0; i < m_nVariables; ++i)
511  {
512  int cnt = 0;
513  for (int omega = 0; omega < m_nDomains; omega++)
514  {
515  m_vessels[omega*m_nVariables+i]->FwdTrans(fields[i]+cnt,
516  m_vessels[omega*m_nVariables+i]->UpdateCoeffs());
517  cnt += m_vessels[omega*m_nVariables+i]->GetTotPoints();
518  }
519  }
520  CheckPoint_Output(nchk++);
521  }
522 
523  }//end of timeintegration
524 
525  //Copy Array To Vessel Phys Fields
526  for(int i = 0; i < m_nVariables; ++i)
527  {
528  Vmath::Vcopy(fields[i].num_elements(), fields[i],1,m_vessels[i]->UpdatePhys(),1);
529  }
530 
531  cout <<"Time-integration timing : "
532  << IntegrationTime << " s" << endl << endl;
533  }
Nektar::PulseWaveSystem::CheckPoint_Output
void CheckPoint_Output(const int n)
Definition: PulseWaveSystem.cpp:1098
Nektar::SolverUtils::EquationSystem::m_time
NekDouble m_time
Current time of simulation.
Definition: EquationSystem.h:472
Nektar::SolverUtils::UnsteadySystem::m_ode
LibUtilities::TimeIntegrationSchemeOperators m_ode
The time integration scheme operators to use.
Definition: UnsteadySystem.h:67
Nektar::SolverUtils::EquationSystem::m_timestep
NekDouble m_timestep
Time step size.
Definition: EquationSystem.h:478
Nektar::SolverUtils::EquationSystem::m_checksteps
int m_checksteps
Number of steps between checkpoints.
Definition: EquationSystem.h:490
Nektar::SolverUtils::EquationSystem::m_steps
int m_steps
Number of steps to take.
Definition: EquationSystem.h:488
Nektar::Timer::Stop
void Stop()
Definition: Timer.cpp:62
Nektar::NekDouble
double NekDouble
Definition: NektarUnivTypeDefs.hpp:44
Nektar::SolverUtils::EquationSystem::m_fields
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
Definition: EquationSystem.h:460
Nektar::SolverUtils::EquationSystem::m_session
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Definition: EquationSystem.h:452
Nektar::SolverUtils::UnsteadySystem::m_intScheme
LibUtilities::TimeIntegrationWrapperSharedPtr m_intScheme
Wrapper to the time integration scheme.
Definition: UnsteadySystem.h:65
Nektar::SolverUtils::UnsteadySystem::m_infosteps
int m_infosteps
Number of time steps between outputting status information.
Definition: UnsteadySystem.h:63
Nektar::Timer::Start
void Start()
Definition: Timer.cpp:51
Nektar::Timer::TimePerTest
NekDouble TimePerTest(unsigned int n)
Returns amount of seconds per iteration in a test with n iterations.
Definition: Timer.cpp:108
Vmath::Vcopy
void Vcopy(int n, const T *x, const int incx, T *y, const int incy)
Definition: Vmath.cpp:1047
Nektar::PulseWaveSystem::m_vessels
Array< OneD, MultiRegions::ExpListSharedPtr > m_vessels
Definition: PulseWaveSystem.h:105
Nektar::SolverUtils::UnsteadySystem::m_intSoln
LibUtilities::TimeIntegrationSolutionSharedPtr m_intSoln
Definition: UnsteadySystem.h:69
void Nektar::PulseWaveSystem::v_InitObject ( )
protectedvirtual

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

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

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

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

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Reimplemented in Nektar::PulseWavePropagation, and Nektar::PulseWaveSystemOutput.

Definition at line 85 of file PulseWaveSystem.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, Nektar::MultiRegions::eDiscontinuous, Nektar::SolverUtils::EquationSystem::EvaluateFunction(), Nektar::SolverUtils::EquationSystem::GetTraceTotPoints(), m_A_0, m_A_0_trace, m_beta, m_beta_trace, Nektar::SolverUtils::EquationSystem::m_checksteps, m_fieldPhysOffset, Nektar::SolverUtils::EquationSystem::m_fields, Nektar::SolverUtils::EquationSystem::m_fintime, Nektar::SolverUtils::EquationSystem::m_graph, Nektar::SolverUtils::UnsteadySystem::m_infosteps, m_nDomains, Nektar::SolverUtils::EquationSystem::m_NumQuadPointsError, m_nVariables, m_pext, Nektar::SolverUtils::EquationSystem::m_projectionType, m_rho, Nektar::SolverUtils::EquationSystem::m_session, Nektar::SolverUtils::EquationSystem::m_steps, Nektar::SolverUtils::EquationSystem::m_time, Nektar::SolverUtils::EquationSystem::m_timestep, m_trace_fwd_normal, m_upwindTypePulse, m_vessels, SetUpDomainInterfaces(), Nektar::SIZE_UpwindTypePulse, Nektar::UpwindTypeMapPulse, and Nektar::SolverUtils::EquationSystem::ZeroPhysFields().

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

86  {
87  // Initialise base class
88  UnsteadySystem::v_InitObject();
89 
90  // Read the geometry and the expansion information
91  m_nDomains = m_graph->GetDomain().size();
92 
93  // Determine projectiontype
94  ASSERTL0(m_session->MatchSolverInfo("Projection","DisContinuous"),"Pulse solver only set up for Discontinuous projections");
95  m_projectionType = MultiRegions::eDiscontinuous;
96  ASSERTL0(m_graph->GetMeshDimension() == 1,"Pulse wave solver only set up for expansion dimension equal to 1");
97 
98  int i;
99  m_nVariables = m_session->GetVariables().size();
100 
101  m_fields = Array<OneD, MultiRegions::ExpListSharedPtr> (m_nVariables);
102  m_vessels = Array<OneD, MultiRegions::ExpListSharedPtr> (m_nVariables*m_nDomains);
103 
104  const std::vector<SpatialDomains::CompositeMap> domain = m_graph->GetDomain();
105 
106  SpatialDomains::BoundaryConditions Allbcs(m_session, m_graph);
107 
108  // Set up domains and put geometry to be only one space dimension.
109  int cnt = 0;
110  bool SetToOneSpaceDimension = true;
111 
112  if(m_session->DefinesCmdLineArgument("SetToOneSpaceDimension"))
113  {
114  std::string cmdline = m_session->GetCmdLineArgument<std::string>("SetToOneSpaceDimension");
115  if(boost::to_upper_copy(cmdline) == "FALSE")
116  {
117  SetToOneSpaceDimension = false;
118  }
119  }
120 
121  for(i = 0 ; i < m_nDomains; ++i)
122  {
123  for(int j = 0; j < m_nVariables; ++j)
124  {
125  m_vessels[cnt++] = MemoryManager<MultiRegions::DisContField1D>
126  ::AllocateSharedPtr(m_session, m_graph, domain[i],
127  Allbcs,
128  m_session->GetVariable(j),
129  SetToOneSpaceDimension);
130  }
131  }
132 
133  // Reset coeff and phys space to be continuous over all domains
134  int totcoeffs = 0;
135  int totphys = 0;
136  m_fieldPhysOffset = Array<OneD, int>(m_nDomains+1,0);
137  for(i = 0; i < m_nDomains; ++i)
138  {
139  totcoeffs += m_vessels[i*m_nVariables]->GetNcoeffs();
140 
141  m_fieldPhysOffset[i] = totphys;
142  totphys += m_vessels[i*m_nVariables]->GetTotPoints();
143  }
144  m_fieldPhysOffset[m_nDomains] = totphys;
145 
146  for(int n = 0; n < m_nVariables; ++n)
147  {
148  Array<OneD, NekDouble> coeffs(totcoeffs,0.0);
149  Array<OneD, NekDouble> phys(totphys,0.0);
150  Array<OneD, NekDouble> tmpcoeffs,tmpphys;
151 
152  m_vessels[n]->SetCoeffsArray(coeffs);
153  m_vessels[n]->SetPhysArray(phys);
154 
155  int cnt = m_vessels[n]->GetNcoeffs();
156  int cnt1 = m_vessels[n]->GetTotPoints();
157 
158  for(i = 1; i < m_nDomains; ++i)
159  {
160  m_vessels[i*m_nVariables+n]->SetCoeffsArray(tmpcoeffs = coeffs + cnt);
161  m_vessels[i*m_nVariables+n]->SetPhysArray (tmpphys = phys + cnt1);
162  cnt += m_vessels[i*m_nVariables+n]->GetNcoeffs();
163  cnt1 += m_vessels[i*m_nVariables+n]->GetTotPoints();
164  }
165  }
166 
167  // Set Default Parameter
168  m_session->LoadParameter("Time", m_time, 0.0);
169  m_session->LoadParameter("TimeStep", m_timestep, 0.01);
170  m_session->LoadParameter("NumSteps", m_steps, 0);
171  m_session->LoadParameter("IO_CheckSteps", m_checksteps, m_steps);
172  m_session->LoadParameter("FinTime", m_fintime, 0);
173  m_session->LoadParameter("NumQuadPointsError", m_NumQuadPointsError, 0);
174 
175  m_fields[0] = m_vessels[0];
176  m_fields[1] = m_vessels[1];
177 
178  // Zero all physical fields initially.
179  ZeroPhysFields();
180 
181  // If Discontinuous Galerkin determine upwinding method to use
182  for (int i = 0; i < (int)SIZE_UpwindTypePulse; ++i)
183  {
184  bool match;
185  m_session->MatchSolverInfo("UPWINDTYPEPULSE", UpwindTypeMapPulse[i], match, false);
186  if (match)
187  {
188  m_upwindTypePulse = (UpwindTypePulse) i;
189  break;
190  }
191  }
192  // Load solver- specific parameters
193  m_session->LoadParameter("IO_InfoSteps", m_infosteps, 0);
194  // Load blood density
195  m_session->LoadParameter("rho", m_rho, 0.5);
196  // Load external pressure
197  m_session->LoadParameter("pext", m_pext, 0.0);
198 
199  int nq = 0;
200  /**
201  * Gets the Material Properties of each arterial segment
202  * specified in the inputfile from section MaterialProperties
203  * Also gets the Area at static equilibrium A_0 specified in the
204  * inputfile.
205  *
206  * Having found these points also extract the values at the
207  * trace points and the normal direction consistent with the
208  * left adjacent definition of Fwd and Bwd
209  */
210  m_beta = Array<OneD, Array<OneD, NekDouble> >(m_nDomains);
211  m_beta_trace = Array<OneD, Array<OneD, NekDouble> >(m_nDomains);
212  m_A_0 = Array<OneD, Array<OneD, NekDouble> >(m_nDomains);
213  m_A_0_trace = Array<OneD, Array<OneD, NekDouble> >(m_nDomains);
214  m_trace_fwd_normal = Array<OneD, Array<OneD, NekDouble> >(m_nDomains);
215 
216  for (int omega = 0; omega < m_nDomains; omega++)
217  {
218  nq = m_vessels[2*omega]->GetNpoints();
219  m_fields[0] = m_vessels[2*omega];
220 
221  m_beta[omega] = Array<OneD, NekDouble>(nq);
222  EvaluateFunction("beta", m_beta[omega], "MaterialProperties", m_time, omega);
223 
224  m_A_0[omega] = Array<OneD, NekDouble>(nq);
225  EvaluateFunction("A_0", m_A_0[omega], "A_0", m_time, omega);
226 
227  int nqTrace = GetTraceTotPoints();
228 
229  m_beta_trace[omega] = Array<OneD, NekDouble>(nqTrace);
230  m_fields[0]->ExtractTracePhys(m_beta[omega],m_beta_trace[omega]);
231 
232  m_A_0_trace[omega] = Array<OneD, NekDouble>(nqTrace);
233  m_fields[0]->ExtractTracePhys(m_A_0[omega],m_A_0_trace[omega]);
234 
235 
236  if(SetToOneSpaceDimension)
237  {
238  m_trace_fwd_normal[omega] = Array<OneD, NekDouble>(nqTrace,0.0);
239 
240  MultiRegions::ExpListSharedPtr trace = m_fields[0]->GetTrace();
241  int nelmt_trace = trace->GetExpSize();
242 
243  Array<OneD, Array<OneD, NekDouble> > normals(nelmt_trace);
244 
245  for(int i = 0 ; i < nelmt_trace; ++i)
246  {
247  normals[i] = m_trace_fwd_normal[omega]+i;
248  }
249 
250  // need to set to 1 for consistency since boundary
251  // conditions may not have coordim=1
252  trace->GetExp(0)->GetGeom()->SetCoordim(1);
253 
254  trace->GetNormals(normals);
255  }
256  }
257 
258  SetUpDomainInterfaces();
259 
260  }
Nektar::PulseWaveSystem::m_fieldPhysOffset
Array< OneD, int > m_fieldPhysOffset
Definition: PulseWaveSystem.h:111
Nektar::PulseWaveSystem::m_beta_trace
Array< OneD, Array< OneD, NekDouble > > m_beta_trace
Definition: PulseWaveSystem.h:122
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:161
Nektar::PulseWaveSystem::m_upwindTypePulse
UpwindTypePulse m_upwindTypePulse
Definition: PulseWaveSystem.h:109
Nektar::MemoryManager::AllocateSharedPtr
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
Definition: NekMemoryManager.hpp:235
Nektar::SolverUtils::EquationSystem::m_time
NekDouble m_time
Current time of simulation.
Definition: EquationSystem.h:472
Nektar::SolverUtils::EquationSystem::m_timestep
NekDouble m_timestep
Time step size.
Definition: EquationSystem.h:478
Nektar::SolverUtils::EquationSystem::m_projectionType
enum MultiRegions::ProjectionType m_projectionType
Type of projection; e.g continuous or discontinuous.
Definition: EquationSystem.h:514
Nektar::UpwindTypeMapPulse
const char *const UpwindTypeMapPulse[]
Definition: PulseWaveSystem.h:53
Nektar::PulseWaveSystem::m_trace_fwd_normal
Array< OneD, Array< OneD, NekDouble > > m_trace_fwd_normal
Definition: PulseWaveSystem.h:123
Nektar::SolverUtils::EquationSystem::m_checksteps
int m_checksteps
Number of steps between checkpoints.
Definition: EquationSystem.h:490
Nektar::PulseWaveSystem::m_A_0_trace
Array< OneD, Array< OneD, NekDouble > > m_A_0_trace
Definition: PulseWaveSystem.h:120
Nektar::SolverUtils::EquationSystem::m_fintime
NekDouble m_fintime
Finish time of the simulation.
Definition: EquationSystem.h:476
Nektar::SolverUtils::EquationSystem::m_steps
int m_steps
Number of steps to take.
Definition: EquationSystem.h:488
Nektar::PulseWaveSystem::m_A_0
Array< OneD, Array< OneD, NekDouble > > m_A_0
Definition: PulseWaveSystem.h:119
Nektar::MultiRegions::ExpListSharedPtr
boost::shared_ptr< ExpList > ExpListSharedPtr
Shared pointer to an ExpList object.
Definition: LocTraceToTraceMap.h:56
Nektar::SIZE_UpwindTypePulse
Length of enum list.
Definition: PulseWaveSystem.h:50
Nektar::SolverUtils::EquationSystem::EvaluateFunction
SOLVER_UTILS_EXPORT void EvaluateFunction(Array< OneD, Array< OneD, NekDouble > > &pArray, std::string pFunctionName, const NekDouble pTime=0.0, const int domain=0)
Evaluates a function as specified in the session file.
Definition: EquationSystem.cpp:690
Nektar::SolverUtils::EquationSystem::GetTraceTotPoints
SOLVER_UTILS_EXPORT int GetTraceTotPoints()
Definition: EquationSystem.h:843
Nektar::PulseWaveSystem::m_beta
Array< OneD, Array< OneD, NekDouble > > m_beta
Definition: PulseWaveSystem.h:121
Nektar::SolverUtils::EquationSystem::m_fields
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
Definition: EquationSystem.h:460
Nektar::SolverUtils::EquationSystem::m_session
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Definition: EquationSystem.h:452
Nektar::SolverUtils::EquationSystem::ZeroPhysFields
SOLVER_UTILS_EXPORT void ZeroPhysFields()
Definition: EquationSystem.cpp:1523
Nektar::SolverUtils::UnsteadySystem::m_infosteps
int m_infosteps
Number of time steps between outputting status information.
Definition: UnsteadySystem.h:63
Nektar::SolverUtils::EquationSystem::m_graph
SpatialDomains::MeshGraphSharedPtr m_graph
Pointer to graph defining mesh.
Definition: EquationSystem.h:468
Nektar::SolverUtils::EquationSystem::m_NumQuadPointsError
int m_NumQuadPointsError
Number of Quadrature points used to work out the error.
Definition: EquationSystem.h:527
Nektar::PulseWaveSystem::m_vessels
Array< OneD, MultiRegions::ExpListSharedPtr > m_vessels
Definition: PulseWaveSystem.h:105
NekDouble Nektar::PulseWaveSystem::v_L2Error ( unsigned int  field,
const Array< OneD, NekDouble > &  exactsoln = NullNekDouble1DArray,
bool  Normalised = false 
)
protectedvirtual

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

Reimplemented from Nektar::SolverUtils::EquationSystem.

Definition at line 1157 of file PulseWaveSystem.cpp.

References ASSERTL0, Nektar::SolverUtils::EquationSystem::EvaluateFunction(), Nektar::SolverUtils::EquationSystem::GetNpoints(), Nektar::SolverUtils::EquationSystem::m_comm, m_nDomains, Nektar::SolverUtils::EquationSystem::m_NumQuadPointsError, m_nVariables, Nektar::SolverUtils::EquationSystem::m_session, Nektar::SolverUtils::EquationSystem::m_time, m_vessels, and Nektar::LibUtilities::ReduceSum.

1160  {
1161  NekDouble L2error = 0.0;
1162  NekDouble L2error_dom;
1163  NekDouble Vol = 0.0;
1164 
1165  if(m_NumQuadPointsError == 0)
1166  {
1167  for (int omega = 0; omega < m_nDomains; omega++)
1168  {
1169  int vesselid = field + omega*m_nVariables;
1170 
1171  if(m_vessels[vesselid]->GetPhysState() == false)
1172  {
1173  m_vessels[vesselid]->BwdTrans(m_vessels[vesselid]->GetCoeffs(),
1174  m_vessels[vesselid]->UpdatePhys());
1175  }
1176 
1177  if(exactsoln.num_elements())
1178  {
1179  L2error_dom = m_vessels[vesselid]->L2(
1180  m_vessels[vesselid]->GetPhys(),
1181  exactsoln);
1182  }
1183  else if (m_session->DefinesFunction("ExactSolution"))
1184  {
1185  Array<OneD, NekDouble> exactsoln(m_vessels[vesselid]->GetNpoints());
1186 
1187  LibUtilities::EquationSharedPtr vEqu
1188  = m_session->GetFunction("ExactSolution",field,omega);
1189  EvaluateFunction(m_session->GetVariable(field),exactsoln,"ExactSolution",
1190  m_time);
1191 
1192  L2error_dom = m_vessels[vesselid]->L2(
1193  m_vessels[vesselid]->GetPhys(),
1194  exactsoln);
1195 
1196  }
1197  else
1198  {
1199  L2error_dom = m_vessels[vesselid]->L2(
1200  m_vessels[vesselid]->GetPhys());
1201  }
1202 
1203  L2error += L2error_dom*L2error_dom;
1204 
1205  if(Normalised == true)
1206  {
1207  Array<OneD, NekDouble> one(m_vessels[vesselid]->GetNpoints(), 1.0);
1208 
1209  Vol += m_vessels[vesselid]->PhysIntegral(one);
1210  }
1211 
1212  }
1213  }
1214  else
1215  {
1216  ASSERTL0(false,"Not set up");
1217  }
1218 
1219 
1220  if(Normalised == true)
1221  {
1222  m_comm->AllReduce(Vol, LibUtilities::ReduceSum);
1223 
1224  L2error = sqrt(L2error/Vol);
1225  }
1226  else
1227  {
1228  L2error = sqrt(L2error);
1229  }
1230 
1231  return L2error;
1232  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:161
Nektar::SolverUtils::EquationSystem::m_time
NekDouble m_time
Current time of simulation.
Definition: EquationSystem.h:472
Nektar::SolverUtils::EquationSystem::m_comm
LibUtilities::CommSharedPtr m_comm
Communicator.
Definition: EquationSystem.h:450
Nektar::NekDouble
double NekDouble
Definition: NektarUnivTypeDefs.hpp:44
Nektar::SolverUtils::EquationSystem::EvaluateFunction
SOLVER_UTILS_EXPORT void EvaluateFunction(Array< OneD, Array< OneD, NekDouble > > &pArray, std::string pFunctionName, const NekDouble pTime=0.0, const int domain=0)
Evaluates a function as specified in the session file.
Definition: EquationSystem.cpp:690
Nektar::LibUtilities::EquationSharedPtr
boost::shared_ptr< Equation > EquationSharedPtr
Definition: SessionReader.h:100
Nektar::SolverUtils::EquationSystem::GetNpoints
SOLVER_UTILS_EXPORT int GetNpoints()
Definition: EquationSystem.h:878
Nektar::SolverUtils::EquationSystem::m_session
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Definition: EquationSystem.h:452
Nektar::SolverUtils::EquationSystem::m_NumQuadPointsError
int m_NumQuadPointsError
Number of Quadrature points used to work out the error.
Definition: EquationSystem.h:527
Nektar::PulseWaveSystem::m_vessels
Array< OneD, MultiRegions::ExpListSharedPtr > m_vessels
Definition: PulseWaveSystem.h:105
NekDouble Nektar::PulseWaveSystem::v_LinfError ( unsigned int  field,
const Array< OneD, NekDouble > &  exactsoln = NullNekDouble1DArray 
)
protectedvirtual

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

Compute the error in the L_inf-norm

Parameters
fieldThe field to compare.
exactsolnThe exact solution to compare with.
Returns
Error in the L_inft-norm.

Reimplemented from Nektar::SolverUtils::EquationSystem.

Definition at line 1241 of file PulseWaveSystem.cpp.

References ASSERTL0, Nektar::SolverUtils::EquationSystem::EvaluateFunction(), Nektar::SolverUtils::EquationSystem::GetNpoints(), m_nDomains, Nektar::SolverUtils::EquationSystem::m_NumQuadPointsError, m_nVariables, Nektar::SolverUtils::EquationSystem::m_session, Nektar::SolverUtils::EquationSystem::m_time, and m_vessels.

1243  {
1244  NekDouble LinferrorDom, Linferror = -1.0;
1245 
1246  for (int omega = 0; omega < m_nDomains; omega++)
1247  {
1248  int vesselid = field + omega*m_nVariables;
1249 
1250  if(m_NumQuadPointsError == 0)
1251  {
1252  if(m_vessels[vesselid]->GetPhysState() == false)
1253  {
1254  m_vessels[vesselid]->BwdTrans(m_vessels[vesselid]->GetCoeffs(),
1255  m_vessels[vesselid]->UpdatePhys());
1256  }
1257 
1258  if(exactsoln.num_elements())
1259  {
1260  LinferrorDom = m_vessels[vesselid]->Linf(
1261  m_vessels[vesselid]->GetPhys(),
1262  exactsoln);
1263  }
1264  else if (m_session->DefinesFunction("ExactSolution"))
1265  {
1266  Array<OneD, NekDouble> exactsoln(m_vessels[vesselid]->GetNpoints());
1267 
1268  EvaluateFunction(m_session->GetVariable(field),exactsoln,"ExactSolution",
1269  m_time);
1270 
1271  LinferrorDom = m_vessels[vesselid]->Linf(
1272  m_vessels[vesselid]->GetPhys(),
1273  exactsoln);
1274  }
1275  else
1276  {
1277  LinferrorDom = 0.0;
1278  }
1279 
1280  Linferror = (Linferror > LinferrorDom)? Linferror:LinferrorDom;
1281 
1282  }
1283  else
1284  {
1285  ASSERTL0(false,"ErrorExtraPoints not allowed for this solver");
1286  }
1287  }
1288  return Linferror;
1289  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:161
Nektar::SolverUtils::EquationSystem::m_time
NekDouble m_time
Current time of simulation.
Definition: EquationSystem.h:472
Nektar::NekDouble
double NekDouble
Definition: NektarUnivTypeDefs.hpp:44
Nektar::SolverUtils::EquationSystem::EvaluateFunction
SOLVER_UTILS_EXPORT void EvaluateFunction(Array< OneD, Array< OneD, NekDouble > > &pArray, std::string pFunctionName, const NekDouble pTime=0.0, const int domain=0)
Evaluates a function as specified in the session file.
Definition: EquationSystem.cpp:690
Nektar::SolverUtils::EquationSystem::GetNpoints
SOLVER_UTILS_EXPORT int GetNpoints()
Definition: EquationSystem.h:878
Nektar::SolverUtils::EquationSystem::m_session
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Definition: EquationSystem.h:452
Nektar::SolverUtils::EquationSystem::m_NumQuadPointsError
int m_NumQuadPointsError
Number of Quadrature points used to work out the error.
Definition: EquationSystem.h:527
Nektar::PulseWaveSystem::m_vessels
Array< OneD, MultiRegions::ExpListSharedPtr > m_vessels
Definition: PulseWaveSystem.h:105
void Nektar::PulseWaveSystem::v_Output ( void  )
protectedvirtual

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 1082 of file PulseWaveSystem.cpp.

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

1083  {
1084  /**
1085  * Write the field data to file. The file is named according to the session
1086  * name with the extension .fld appended.
1087  */
1088  std::string outname = m_sessionName + ".fld";
1089 
1090  WriteVessels(outname);
1091  }
Nektar::SolverUtils::EquationSystem::m_sessionName
std::string m_sessionName
Name of the session.
Definition: EquationSystem.h:470
Nektar::PulseWaveSystem::WriteVessels
void WriteVessels(const std::string &outname)
Write input fields to the given filename.
Definition: PulseWaveSystem.cpp:1111
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
outnameFilename to write to.

Definition at line 1111 of file PulseWaveSystem.cpp.

References Nektar::SolverUtils::EquationSystem::m_fieldMetaDataMap, m_nDomains, m_nVariables, Nektar::SolverUtils::EquationSystem::m_session, Nektar::SolverUtils::EquationSystem::m_time, m_vessels, and Nektar::LibUtilities::Write().

Referenced by CheckPoint_Output(), and v_Output().

1112  {
1113 
1114  std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef;
1115  std::vector<std::string> variables = m_session->GetVariables();
1116 
1117  for(int n = 0; n < m_nDomains; ++n)
1118  {
1119  m_vessels[n*m_nVariables]->GetFieldDefinitions(FieldDef);
1120  }
1121 
1122  std::vector<std::vector<NekDouble> > FieldData(FieldDef.size());
1123 
1124  int nFieldDefPerDomain = FieldDef.size()/m_nDomains;
1125  int cnt;
1126  // Copy Data into FieldData and set variable
1127  for(int n = 0; n < m_nDomains; ++n)
1128  {
1129  for(int j = 0; j < m_nVariables; ++j)
1130  {
1131  for(int i = 0; i < nFieldDefPerDomain; ++i)
1132  {
1133  cnt = n*nFieldDefPerDomain+i;
1134  FieldDef[cnt]->m_fields.push_back(variables[j]);
1135  m_vessels[n*m_nVariables]->AppendFieldData(FieldDef[cnt], FieldData[cnt], m_vessels[n*m_nVariables+j]->UpdateCoeffs());
1136  }
1137  }
1138  }
1139 
1140  // Update time in field info if required
1141  if(m_fieldMetaDataMap.find("Time") != m_fieldMetaDataMap.end())
1142  {
1143  m_fieldMetaDataMap["Time"] = boost::lexical_cast<std::string>(m_time);
1144  }
1145 
1146  //LibUtilities::CombineFields(FieldDef, FieldData);
1147 
1148  LibUtilities::Write(outname, FieldDef, FieldData, m_fieldMetaDataMap);
1149  }
Nektar::SolverUtils::EquationSystem::m_time
NekDouble m_time
Current time of simulation.
Definition: EquationSystem.h:472
Nektar::SolverUtils::EquationSystem::m_fieldMetaDataMap
LibUtilities::FieldMetaDataMap m_fieldMetaDataMap
Map to identify relevant solver info to dump in output fields.
Definition: EquationSystem.h:524
Nektar::SolverUtils::EquationSystem::m_session
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Definition: EquationSystem.h:452
Nektar::LibUtilities::Write
void Write(const std::string &outFile, std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble > > &fielddata, const FieldMetaDataMap &fieldinfomap)
Write a field file in serial only.
Definition: FieldIO.cpp:81
Nektar::PulseWaveSystem::m_vessels
Array< OneD, MultiRegions::ExpListSharedPtr > m_vessels
Definition: PulseWaveSystem.h:105

Member Data Documentation

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

Definition at line 119 of file PulseWaveSystem.h.

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

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

Definition at line 120 of file PulseWaveSystem.h.

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

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

Definition at line 121 of file PulseWaveSystem.h.

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

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

Definition at line 122 of file PulseWaveSystem.h.

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

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

Definition at line 127 of file PulseWaveSystem.h.

Referenced by EnforceInterfaceConditions(), and SetUpDomainInterfaces().

NekDouble Nektar::PulseWaveSystem::m_C
protected

Definition at line 115 of file PulseWaveSystem.h.

int Nektar::PulseWaveSystem::m_currentDomain
protected

Definition at line 107 of file PulseWaveSystem.h.

Referenced by Nektar::PulseWavePropagation::DoOdeRhs(), Nektar::PulseWavePropagation::v_GetFluxVector(), and Nektar::PulseWavePropagation::v_NumericalFlux().

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

Definition at line 111 of file PulseWaveSystem.h.

Referenced by FillDataFromInterfacePoint(), and v_InitObject().

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

Definition at line 128 of file PulseWaveSystem.h.

Referenced by EnforceInterfaceConditions(), and SetUpDomainInterfaces().

int Nektar::PulseWaveSystem::m_nDomains
protected

Definition at line 106 of file PulseWaveSystem.h.

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

int Nektar::PulseWaveSystem::m_nVariables
protected

Definition at line 108 of file PulseWaveSystem.h.

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

NekDouble Nektar::PulseWaveSystem::m_pext
protected

Definition at line 113 of file PulseWaveSystem.h.

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

NekDouble Nektar::PulseWaveSystem::m_pout
protected

Definition at line 117 of file PulseWaveSystem.h.

NekDouble Nektar::PulseWaveSystem::m_rho
protected

Definition at line 112 of file PulseWaveSystem.h.

Referenced by BifurcationRiemann(), CalcCharacteristicVariables(), JunctionRiemann(), MergingRiemann(), Nektar::PulseWavePropagation::RiemannSolverUpwind(), Nektar::PulseWavePropagation::v_GetFluxVector(), and v_InitObject().

NekDouble Nektar::PulseWaveSystem::m_RT
protected

Definition at line 116 of file PulseWaveSystem.h.

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

Definition at line 123 of file PulseWaveSystem.h.

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

UpwindTypePulse Nektar::PulseWaveSystem::m_upwindTypePulse
protected

Definition at line 109 of file PulseWaveSystem.h.

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

std::vector<std::vector<InterfacePointShPtr> > Nektar::PulseWaveSystem::m_vesselJcts
protected

Definition at line 126 of file PulseWaveSystem.h.

Referenced by EnforceInterfaceConditions(), and SetUpDomainInterfaces().

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

Definition at line 105 of file PulseWaveSystem.h.

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

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