Nektar++
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Properties Friends Macros Pages
Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | List of all members
Nektar::PulseWaveSystem Class Reference

Base class for unsteady solvers. More...

#include <PulseWaveSystem.h>

Inheritance diagram for Nektar::PulseWaveSystem:
Inheritance graph
[legend]
Collaboration diagram for Nektar::PulseWaveSystem:
Collaboration graph
[legend]

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 std::string &s1, const std::string &s2)
 Perform a case-insensitive string comparison. More...
 
SOLVER_UTILS_EXPORT int GetCheckpointNumber ()
 
SOLVER_UTILS_EXPORT void SetCheckpointNumber (int num)
 
SOLVER_UTILS_EXPORT int GetCheckpointSteps ()
 
SOLVER_UTILS_EXPORT void SetCheckpointSteps (int num)
 
SOLVER_UTILS_EXPORT void SetTime (const NekDouble time)
 
SOLVER_UTILS_EXPORT void SetInitialStep (const int step)
 
SOLVER_UTILS_EXPORT void SetBoundaryConditions (NekDouble time)
 Evaluates the boundary conditions at the given time. More...
 
virtual SOLVER_UTILS_EXPORT bool v_NegatedOp ()
 Virtual function to identify if operator is negated in DoSolve. More...
 

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)
 
virtual SOLVER_UTILS_EXPORT bool v_RequireFwdTrans ()
 
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...
 
- Protected Member Functions inherited from Nektar::SolverUtils::EquationSystem
SOLVER_UTILS_EXPORT EquationSystem (const LibUtilities::SessionReaderSharedPtr &pSession)
 Initialises EquationSystem class members. More...
 
int nocase_cmp (const std::string &s1, const std::string &s2)
 
virtual SOLVER_UTILS_EXPORT void v_TransCoeffToPhys ()
 Virtual function for transformation to physical space. More...
 
virtual SOLVER_UTILS_EXPORT void v_TransPhysToCoeff ()
 Virtual function for transformation to coefficient space. More...
 
virtual SOLVER_UTILS_EXPORT void v_SetInitialConditions (NekDouble initialtime=0.0, bool dumpInitialConditions=true, const int domain=0)
 
virtual SOLVER_UTILS_EXPORT void v_EvaluateExactSolution (unsigned int field, Array< OneD, NekDouble > &outfield, const NekDouble time)
 
SOLVER_UTILS_EXPORT void EvaluateFunctionExp (std::string pFieldName, Array< OneD, NekDouble > &pArray, const std::string &pFunctionName, const NekDouble &pTime=0.0, const int domain=0)
 
SOLVER_UTILS_EXPORT void EvaluateFunctionFld (std::string pFieldName, Array< OneD, NekDouble > &pArray, const std::string &pFunctionName, const NekDouble &pTime=0.0, const int domain=0)
 
SOLVER_UTILS_EXPORT void EvaluateFunctionPts (std::string pFieldName, Array< OneD, NekDouble > &pArray, const std::string &pFunctionName, const NekDouble &pTime=0.0, const int domain=0)
 
SOLVER_UTILS_EXPORT void LoadPts (std::string funcFilename, std::string filename, Nektar::LibUtilities::PtsFieldSharedPtr &outPts)
 
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...
 
int m_nanSteps
 
LibUtilities::TimeIntegrationWrapperSharedPtr m_intScheme
 Wrapper to the time integration scheme. More...
 
LibUtilities::TimeIntegrationSchemeOperators m_ode
 The time integration scheme operators to use. More...
 
LibUtilities::TimeIntegrationSolutionSharedPtr m_intSoln
 
NekDouble m_epsilon
 
bool m_explicitDiffusion
 Indicates if explicit or implicit treatment of diffusion is used. More...
 
bool m_explicitAdvection
 Indicates if explicit or implicit treatment of advection is used. More...
 
bool m_explicitReaction
 Indicates if explicit or implicit treatment of reaction is used. More...
 
bool m_homoInitialFwd
 Flag to determine if simulation should start in homogeneous forward transformed state. More...
 
std::vector< int > m_intVariables
 
std::vector< FilterSharedPtr > m_filters
 
- Protected Attributes inherited from Nektar::SolverUtils::EquationSystem
LibUtilities::CommSharedPtr m_comm
 Communicator. More...
 
LibUtilities::SessionReaderSharedPtr m_session
 The session reader. More...
 
LibUtilities::FieldIOSharedPtr m_fld
 Field input/output. More...
 
std::map< std::string,
FieldUtils::Interpolator > 		m_interpolators
 Map of interpolator objects. More...
 
std::map< std::string,
std::pair< std::string,
LibUtilities::PtsFieldSharedPtr > > 		m_loadedPtsFields
 pts fields we already read from disk: {funcFilename: (filename, ptsfield)} More...
 
std::map< std::string,
std::pair< std::string,
loadedFldField > > 		m_loadedFldFields
 
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...
 
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...
 

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 73 of file PulseWaveSystem.cpp.

74  {
75  }
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 65 of file PulseWaveSystem.cpp.

66  : UnsteadySystem(m_session)
67  {
68  }
Nektar::SolverUtils::UnsteadySystem::UnsteadySystem
SOLVER_UTILS_EXPORT UnsteadySystem(const LibUtilities::SessionReaderSharedPtr &pSession)
Initialises UnsteadySystem class members.
Definition: UnsteadySystem.cpp:67
Nektar::SolverUtils::EquationSystem::m_session
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Definition: EquationSystem.h:460

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 653 of file PulseWaveSystem.cpp.

References ASSERTL0, and m_rho.

Referenced by EnforceInterfaceConditions().

655  {
656  NekDouble rho = m_rho;
657  Array<OneD, NekDouble> W(3);
658  Array<OneD, NekDouble> W_Au(3);
659  Array<OneD, NekDouble> P_Au(3);
660  Array<OneD, NekDouble> f(6);
661  Array<OneD, NekDouble> g(6);
662  Array<OneD, NekDouble> tmp(6);
663  Array<OneD, Array<OneD, NekDouble> > inv_J(6);
664  for (int i=0; i<6; i++)
665  {
666  inv_J[i] = Array<OneD, NekDouble> (6);
667  }
668  NekDouble k = 0.0;
669  NekDouble k1 = 0.0;
670  NekDouble k2 = 0.0;
671  NekDouble k3 = 0.0;
672 
673  int proceed = 1;
674  int iter = 0;
675  int MAX_ITER = 7;
676 
677  // Calculated from input
678  W[0] = uu[0] + 4*sqrt(beta[0]/(2*rho))*(sqrt(sqrt(Au[0])) - sqrt(sqrt(A_0[0])));
679  W[1] = uu[1] - 4*sqrt(beta[1]/(2*rho))*(sqrt(sqrt(Au[1])) - sqrt(sqrt(A_0[1])));
680  W[2] = uu[2] - 4*sqrt(beta[2]/(2*rho))*(sqrt(sqrt(Au[2])) - sqrt(sqrt(A_0[2])));
681 
682  // Tolerances for the algorithm
683  NekDouble Tol = 1.0e-10;
684 
685  // Newton Iteration
686  while ((proceed) && (iter < MAX_ITER))
687  {
688  iter = iter+1;
689 
690  // Calculate the constraint vector, six equations:
691  // 3 characteristic variables, mass conservation,
692  // total pressure
693  W_Au[0] = 4*sqrt(beta[0]/(2*rho))*(sqrt(sqrt(Au[0])) - sqrt(sqrt(A_0[0])));
694  W_Au[1] = 4*sqrt(beta[1]/(2*rho))*(sqrt(sqrt(Au[1])) - sqrt(sqrt(A_0[1])));
695  W_Au[2] = 4*sqrt(beta[2]/(2*rho))*(sqrt(sqrt(Au[2])) - sqrt(sqrt(A_0[2])));
696 
697  P_Au[0] = beta[0]*(sqrt(Au[0]) - sqrt(A_0[0]));
698  P_Au[1] = beta[1]*(sqrt(Au[1]) - sqrt(A_0[1]));
699  P_Au[2] = beta[2]*(sqrt(Au[2]) - sqrt(A_0[2]));
700 
701  f[0] = uu[0] + W_Au[0] - W[0];
702  f[1] = uu[1] - W_Au[1] - W[1];
703  f[2] = uu[2] - W_Au[2] - W[2];
704  f[3] = Au[0]*uu[0] - Au[1]*uu[1] - Au[2]*uu[2];
705  f[4] = uu[0]*uu[0] + 2.0/rho*P_Au[0] - uu[1]*uu[1] - 2.0/rho*P_Au[1];
706  f[5] = uu[0]*uu[0] + 2.0/rho*P_Au[0] - uu[2]*uu[2] - 2.0/rho*P_Au[2];
707 
708  // Calculate the wave speed at each vessel
709  NekDouble c1 = sqrt(beta[0]/(2*rho))*sqrt(sqrt(Au[0]));
710  NekDouble c2 = sqrt(beta[1]/(2*rho))*sqrt(sqrt(Au[1]));
711  NekDouble c3 = sqrt(beta[2]/(2*rho))*sqrt(sqrt(Au[2]));
712 
713  // Inverse Jacobian matrix J(x[n])^(-1), is
714  // already inverted here analytically
715  k = c1*Au[1]*c3+Au[0]*c3*c2+Au[2]*c1*c2;
716  k1 = (c1-uu[0])*k;
717  inv_J[0][0] = (-c2*uu[0]*c3*Au[0]+Au[2]*c2*c1*c1+Au[1]*c1*c1*c3)/k1;
718  inv_J[0][1] = Au[1]*(c2-uu[1])*c1*c3/k1;
719  inv_J[0][2] = Au[2]*(c3-uu[2])*c1*c2/k1;
720  inv_J[0][3] = c1*c2*c3/k1;
721  inv_J[0][4] = -0.5*c1*Au[1]*c3/k1;
722  inv_J[0][5] = -0.5*Au[2]*c1*c2/k1;
723 
724  k2 = (c2+uu[1])*k;
725  inv_J[1][0] = Au[0]*(c1+uu[0])*c2*c3/k2;
726  inv_J[1][1] = (c1*uu[1]*c3*Au[1]+Au[2]*c1*c2*c2+c3*c2*c2*Au[0])/k2;
727  inv_J[1][2] = -Au[2]*(c3-uu[2])*c1*c2/k2;
728  inv_J[1][3] = -c1*c2*c3/k2;
729  inv_J[1][4] = -0.5*(c1*Au[2]+Au[0]*c3)*c2/k2;
730  inv_J[1][5] = 0.5*Au[2]*c1*c2/k2;
731 
732  k3 = (c3+uu[2])*k;
733  inv_J[2][0] = Au[0]*(c1+uu[0])*c2*c3/k3;
734  inv_J[2][1] = -Au[1]*(c2-uu[1])*c1*c3/k3;
735  inv_J[2][2] = (c1*c2*uu[2]*Au[2]+c1*Au[1]*c3*c3+c2*c3*c3*Au[0])/k3;
736  inv_J[2][3] = -c1*c2*c3/k3;
737  inv_J[2][4] = 0.5*c1*Au[1]*c3/k3;
738  inv_J[2][5] = -0.5*(Au[1]*c1+c2*Au[0])*c3/k3;
739 
740  inv_J[3][0] = Au[0]*(Au[0]*c3*c2-uu[0]*c3*Au[1]-uu[0]*c2*Au[2])/k1;
741  inv_J[3][1] = -Au[0]*Au[1]*(c2-uu[1])*c3/k1;
742  inv_J[3][2] = -Au[0]*Au[2]*(c3-uu[2])*c2/k1;
743  inv_J[3][3] = -Au[0]*c3*c2/k1;
744  inv_J[3][4] = 0.5*Au[0]*Au[1]*c3/k1;
745  inv_J[3][5] = 0.5*Au[0]*c2*Au[2]/k1;
746 
747  inv_J[4][0] = Au[0]*Au[1]*(c1+uu[0])*c3/k2;
748  inv_J[4][1] = -Au[1]*(c1*Au[1]*c3+c1*uu[1]*Au[2]+c3*uu[1]*Au[0])/k2;
749  inv_J[4][2] = -Au[2]*Au[1]*(c3-uu[2])*c1/k2;
750  inv_J[4][3] = -c1*Au[1]*c3/k2;
751  inv_J[4][4] = -0.5*Au[1]*(c1*Au[2]+Au[0]*c3)/k2;
752  inv_J[4][5] = 0.5*Au[2]*Au[1]*c1/k2;
753 
754  inv_J[5][0] = Au[0]*Au[2]*(c1+uu[0])*c2/k3;
755  inv_J[5][1] = -Au[2]*Au[1]*(c2-uu[1])*c1/k3;
756  inv_J[5][2] = -Au[2]*(Au[2]*c1*c2+c1*uu[2]*Au[1]+c2*uu[2]*Au[0])/k3;
757  inv_J[5][3] = -Au[2]*c1*c2/k3;
758  inv_J[5][4] = 0.5*Au[2]*Au[1]*c1/k3;
759  inv_J[5][5] = -0.5*Au[2]*(Au[1]*c1+c2*Au[0])/k3;
760 
761 
762  // Solve the system by multiplying the Jacobian with the vector f:
763  // g = (inv_J)*f
764  for (int j=0; j<6; j++)
765  {
766  tmp[j] =0.0;
767  g[j] = 0.0;
768  }
769 
770  for (int j=0; j<6; j++)
771  {
772  for (int i=0; i<6; i++)
773  {
774  tmp[j] = inv_J[j][i]*f[i];
775  g[j] += tmp[j];
776  }
777  }
778 
779  // Update the solution: x_new = x_old - dx
780  uu[0] = uu[0] - g[0];
781  uu[1] = uu[1] - g[1];
782  uu[2] = uu[2] - g[2];
783  Au[0] = Au[0] - g[3];
784  Au[1] = Au[1] - g[4];
785  Au[2] = Au[2] - g[5];
786 
787  // Check if the error of the solution is smaller than Tol
788  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)
789  {
790  proceed = 0;
791  }
792 
793  // Check if solver converges
794  if (iter >= MAX_ITER)
795  {
796  ASSERTL0(false,"Riemann solver for Bifurcation did not converge");
797  }
798  }
799  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
Nektar::NekDouble
double NekDouble
Definition: NektarUnivTypeDefs.hpp:44
void Nektar::PulseWaveSystem::CalcCharacteristicVariables ( int  omega)

Definition at line 1292 of file PulseWaveSystem.cpp.

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

1293  {
1294  int nq = m_vessels[omega]->GetTotPoints();
1295  Array<OneD, NekDouble> A = m_vessels[omega]->UpdatePhys();
1296  Array<OneD, NekDouble> u = m_vessels[omega+1]->UpdatePhys();
1297  Array<OneD, NekDouble> c(nq);
1298 
1299  //Calc 4*c
1300  Vmath::Vsqrt(nq,A,1,c,1);
1301  Vmath::Vmul(nq,m_beta[omega],1,c,1,c,1);
1302  Vmath::Smul(nq,16.0/(2*m_rho),c,1,c,1);
1303  Vmath::Vsqrt(nq,c,1,c,1);
1304 
1305  // Characteristics
1306  Vmath::Vadd(nq,u,1,c,1,A,1);
1307  Vmath::Vsub(nq,u,1,c,1,u,1);
1308  }
Vmath::Vsqrt
void Vsqrt(int n, const T *x, const int incx, T *y, const int incy)
sqrt y = sqrt(x)
Definition: Vmath.cpp:408
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:213
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:343
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:299
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:183
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 1099 of file PulseWaveSystem.cpp.

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

Referenced by v_DoSolve().

1100  {
1101  std::stringstream outname;
1102  outname << m_sessionName << "_" << n << ".chk";
1103 
1104  WriteVessels(outname.str());
1105  }
Nektar::SolverUtils::EquationSystem::m_sessionName
std::string m_sessionName
Name of the session.
Definition: EquationSystem.h:480
Nektar::PulseWaveSystem::WriteVessels
void WriteVessels(const std::string &outname)
Write input fields to the given filename.
Definition: PulseWaveSystem.cpp:1112
void Nektar::PulseWaveSystem::EnforceInterfaceConditions ( const Array< OneD, const Array< OneD, NekDouble > > &  fields)
protected

Definition at line 564 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().

565  {
566  int dom, bcpos;
567  Array<OneD, NekDouble> Au(3),uu(3),beta(3),A_0(3);
568 
569 
570  // Enfore Bifurcations;
571  for(int n = 0; n < m_bifurcations.size(); ++n)
572  {
573  FillDataFromInterfacePoint(m_bifurcations[n][0],fields,
574  Au[0],uu[0],beta[0],A_0[0]);
575  FillDataFromInterfacePoint(m_bifurcations[n][1],fields,
576  Au[1],uu[1],beta[1],A_0[1]);
577  FillDataFromInterfacePoint(m_bifurcations[n][2],fields,
578  Au[2],uu[2],beta[2],A_0[2]);
579 
580  // Solve the Riemann problem for a bifurcation
581  BifurcationRiemann(Au, uu, beta, A_0);
582 
583  // Store the values into the right positions:
584  for(int i = 0; i < 3; ++i)
585  {
586  dom = m_bifurcations[n][i]->m_domain;
587  bcpos = m_bifurcations[n][i]->m_bcPosition;
588  m_vessels[dom*m_nVariables] ->UpdateBndCondExpansion(bcpos)->UpdatePhys()[0] = Au[i];
589  m_vessels[dom*m_nVariables+1]->UpdateBndCondExpansion(bcpos)->UpdatePhys()[0] = uu[i];
590  }
591  }
592 
593  // Enfore Bifurcations;
594  for(int n = 0; n < m_mergingJcts.size(); ++n)
595  {
596  // Merged vessel
597  FillDataFromInterfacePoint(m_mergingJcts[n][0],fields,
598  Au[0],uu[0],beta[0],A_0[0]);
599  FillDataFromInterfacePoint(m_mergingJcts[n][1],fields,
600  Au[1],uu[1],beta[1],A_0[1]);
601  FillDataFromInterfacePoint(m_mergingJcts[n][2],fields,
602  Au[2],uu[2],beta[2],A_0[2]);
603 
604  // Solve the Riemann problem for a merging vessel
605  MergingRiemann(Au, uu, beta, A_0);
606 
607  // Store the values into the right positions:
608  for(int i = 0; i < 3; ++i)
609  {
610  int dom = m_mergingJcts[n][i]->m_domain;
611  int bcpos = m_mergingJcts[n][i]->m_bcPosition;
612  m_vessels[dom*m_nVariables] ->UpdateBndCondExpansion(bcpos)->UpdatePhys()[0] = Au[i];
613  m_vessels[dom*m_nVariables+1]->UpdateBndCondExpansion(bcpos)->UpdatePhys()[0] = uu[i];
614  }
615  }
616 
617  for(int n = 0; n < m_vesselJcts.size(); ++n)
618  {
619 
620  FillDataFromInterfacePoint(m_vesselJcts[n][0],fields,
621  Au[0],uu[0],beta[0],A_0[0]);
622  FillDataFromInterfacePoint(m_vesselJcts[n][1],fields,
623  Au[1],uu[1],beta[1],A_0[1]);
624 
625  JunctionRiemann(Au, uu, beta, A_0);
626 
627  // Store the values into the right positions:
628  for(int i = 0; i < 2; ++i)
629  {
630  int dom = m_vesselJcts[n][i]->m_domain;
631  int bcpos = m_vesselJcts[n][i]->m_bcPosition;
632  m_vessels[dom*m_nVariables] ->UpdateBndCondExpansion(bcpos)->UpdatePhys()[0] = Au[i];
633  m_vessels[dom*m_nVariables+1]->UpdateBndCondExpansion(bcpos)->UpdatePhys()[0] = uu[i];
634  //cout<<"Au: "<<Au[i]<<endl;
635  //cout<<"uu: "<<uu[i]<<endl;
636  //cout<<endl;
637  }
638 
639  }
640  }
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:653
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:812
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:538
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:969
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 538 of file PulseWaveSystem.cpp.

References m_A_0_trace, m_beta_trace, m_fieldPhysOffset, m_nVariables, and m_vessels.

Referenced by EnforceInterfaceConditions().

542  {
543  int omega, traceId, eid, vert, phys_offset, vesselID;
544 
545 
546  // Parent vessel
547  omega = I->m_domain;
548  traceId = I->m_traceId;
549  eid = I->m_elmt;
550  vert = I->m_elmtVert;
551  vesselID = omega*m_nVariables;
552 
553  phys_offset = m_vessels[vesselID]->GetPhys_Offset(eid);
554 
555  m_vessels[vesselID]->GetExp(eid)->
556  GetVertexPhysVals(vert, fields[0]+m_fieldPhysOffset[omega]+phys_offset, A);
557  m_vessels[vesselID]->GetExp(eid)->
558  GetVertexPhysVals(vert, fields[1]+m_fieldPhysOffset[omega]+phys_offset, u);
559 
560  beta = m_beta_trace[omega][traceId];
561  A_0 = m_A_0_trace [omega][traceId];
562  }
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 969 of file PulseWaveSystem.cpp.

References ASSERTL0, and m_rho.

Referenced by EnforceInterfaceConditions().

971  {
972  NekDouble rho = m_rho;
973  Array<OneD, NekDouble> W(2);
974  Array<OneD, NekDouble> W_Au(2);
975  Array<OneD, NekDouble> P_Au(2);
976  Array<OneD, NekDouble> f(4);
977  Array<OneD, NekDouble> g(4);
978  Array<OneD, NekDouble> tmp(4);
979  Array<OneD, Array<OneD, NekDouble> > inv_J(4);
980  for (int i=0; i<4; i++)
981  {
982  inv_J[i] = Array<OneD, NekDouble> (4);
983  }
984  NekDouble k = 0.0;
985  NekDouble k1 = 0.0;
986  NekDouble k2 = 0.0;
987 
988  int proceed = 1;
989  int iter = 0;
990  int MAX_ITER = 7;
991  NekDouble Tol = 1.0e-10;
992 
993  // Calculated from input
994  W[0] = uu[0] + 4*sqrt(beta[0]/(2*rho))*(sqrt(sqrt(Au[0])) - sqrt(sqrt(A_0[0])));
995  W[1] = uu[1] - 4*sqrt(beta[1]/(2*rho))*(sqrt(sqrt(Au[1])) - sqrt(sqrt(A_0[1])));
996 
997  while((proceed) && (iter < MAX_ITER))
998  {
999  iter = iter+1;
1000 
1001  // Calculate the constraint vector, 4 equations:
1002  // 2 characteristic variables, mass conservation,
1003  // total pressure
1004  W_Au[0] = 4*sqrt(beta[0]/(2*rho))*(sqrt(sqrt(Au[0])) - sqrt(sqrt(A_0[0])));
1005  W_Au[1] = 4*sqrt(beta[1]/(2*rho))*(sqrt(sqrt(Au[1])) - sqrt(sqrt(A_0[1])));
1006 
1007  P_Au[0] = beta[0]*(sqrt(Au[0]) - sqrt(A_0[0]));
1008  P_Au[1] = beta[1]*(sqrt(Au[1]) - sqrt(A_0[1]));
1009 
1010  f[0] = uu[0] + W_Au[0] - W[0];
1011  f[1] = uu[1] - W_Au[1] - W[1];
1012  f[2] = Au[0]*uu[0] - Au[1]*uu[1];
1013  f[3] = uu[0]*uu[0] + 2.0/rho*P_Au[0] - uu[1]*uu[1] - 2.0/rho*P_Au[1];
1014 
1015  // Calculate the wave speed at each vessel
1016  NekDouble cl = sqrt(beta[0]/(2*rho))*sqrt(sqrt(Au[0]));
1017  NekDouble cr = sqrt(beta[1]/(2*rho))*sqrt(sqrt(Au[1]));
1018 
1019  // Inverse Jacobian matrix J(x[n])^(-1), is already inverted here analytically
1020  k = (cl*Au[1]+Au[0]*cr);
1021  k1 = (cl-uu[0])*k;
1022  inv_J[0][0] = (Au[1]*cl*cl-cr*uu[0]*Au[0])/k1;
1023  inv_J[0][1] = Au[1]*(cr-uu[1])*cl/k1;
1024  inv_J[0][2] = cl*cr/k1;
1025  inv_J[0][3] = -0.5*cl*Au[1]/k1;
1026 
1027  k2 = (cr+uu[1])*k;
1028  inv_J[1][0] = Au[0]*(cl+uu[0])*cr/k2;
1029  inv_J[1][1] = (cl*uu[1]*Au[1]+cr*cr*Au[0])/k2;
1030  inv_J[1][2] = -cl*cr/k2;
1031  inv_J[1][3] = -0.5*Au[0]*cr/k2;
1032 
1033  inv_J[2][0] = Au[0]*(Au[0]*cr-uu[0]*Au[1])/k1;
1034  inv_J[2][1] = -Au[0]*Au[1]*(cr-uu[1])/k1;
1035  inv_J[2][2] = -Au[0]*cr/k1;
1036  inv_J[2][3] = 0.5*Au[1]*Au[0]/k1;
1037 
1038  inv_J[3][0] = Au[0]*Au[1]*(cl+uu[0])/k2;
1039  inv_J[3][1] = -Au[1]*(cl*Au[1]+uu[1]*Au[0])/k2;
1040  inv_J[3][2] = -cl*Au[1]/k2;
1041  inv_J[3][3] = -0.5*Au[1]*Au[0]/k2;
1042 
1043  // Solve the system by multiplying the Jacobian with the vector f:
1044  // g = (inv_J)*f
1045  for (int j=0; j<4; j++)
1046  {
1047  tmp[j] =0.0;
1048  g[j] = 0.0;
1049  }
1050 
1051  for (int j=0; j<4; j++)
1052  {
1053  for (int i=0; i<4; i++)
1054  {
1055  tmp[j] = inv_J[j][i]*f[i];
1056  g[j] += tmp[j];
1057  }
1058  }
1059 
1060  // Update solution: x_new = x_old - dx
1061  uu[0] -= g[0];
1062  uu[1] -= g[1];
1063  Au[0] -= g[2];
1064  Au[1] -= g[3];
1065 
1066  // Check if the error of the solution is smaller than Tol.
1067  if((g[0]*g[0] + g[1]*g[1] + g[2]*g[2] + g[3]*g[3]) < Tol)
1068  proceed = 0;
1069  }
1070 
1071  if(iter >= MAX_ITER)
1072  {
1073  ASSERTL0(false,"Riemann solver for Junction did not converge");
1074  }
1075  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
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 812 of file PulseWaveSystem.cpp.

References ASSERTL0, and m_rho.

Referenced by EnforceInterfaceConditions().

813  {
814  NekDouble rho = m_rho;
815  Array<OneD, NekDouble> W(3);
816  Array<OneD, NekDouble> W_Au(3);
817  Array<OneD, NekDouble> P_Au(3);
818  Array<OneD, NekDouble> f(6);
819  Array<OneD, NekDouble> g(6);
820  Array<OneD, NekDouble> tmp(6);
821  Array<OneD, Array<OneD, NekDouble> > inv_J(6);
822 
823  for (int i=0; i<6; i++)
824  {
825  inv_J[i] = Array<OneD, NekDouble> (6);
826  }
827 
828  NekDouble k = 0.0;
829  NekDouble k1 = 0.0;
830  NekDouble k2 = 0.0;
831  NekDouble k3 = 0.0;
832 
833  int proceed = 1;
834  int iter = 0;
835  int MAX_ITER = 7;
836 
837  // Calculated from input
838  W[0] = uu[0] - 4*sqrt(beta[0]/(2*rho))*(sqrt(sqrt(Au[0])) - sqrt(sqrt(A_0[0])));
839  W[1] = uu[1] + 4*sqrt(beta[1]/(2*rho))*(sqrt(sqrt(Au[1])) - sqrt(sqrt(A_0[1])));
840  W[2] = uu[2] + 4*sqrt(beta[2]/(2*rho))*(sqrt(sqrt(Au[2])) - sqrt(sqrt(A_0[2])));
841 
842  // Tolerances for the algorithm
843  NekDouble Tol = 1.0e-10;
844 
845  // Newton Iteration
846  while ((proceed) && (iter < MAX_ITER))
847  {
848  iter = iter+1;
849 
850  // Calculate the constraint vector, six equations:
851  // 3 characteristic variables, mass conservation,
852  // total pressure
853  W_Au[0] = 4*sqrt(beta[0]/(2*rho))*(sqrt(sqrt(Au[0])) - sqrt(sqrt(A_0[0])));
854  W_Au[1] = 4*sqrt(beta[1]/(2*rho))*(sqrt(sqrt(Au[1])) - sqrt(sqrt(A_0[1])));
855  W_Au[2] = 4*sqrt(beta[2]/(2*rho))*(sqrt(sqrt(Au[2])) - sqrt(sqrt(A_0[2])));
856 
857  P_Au[0] = beta[0]*(sqrt(Au[0]) - sqrt(A_0[0]));
858  P_Au[1] = beta[1]*(sqrt(Au[1]) - sqrt(A_0[1]));
859  P_Au[2] = beta[2]*(sqrt(Au[2]) - sqrt(A_0[2]));
860 
861  f[0] = uu[0] - W_Au[0] - W[0];
862  f[1] = uu[1] + W_Au[1] - W[1];
863  f[2] = uu[2] + W_Au[2] - W[2];
864  f[3] = Au[0]*uu[0] - Au[1]*uu[1] - Au[2]*uu[2];
865  f[4] = uu[0]*uu[0] + 2.0/rho*P_Au[0] - uu[1]*uu[1] - 2.0/rho*P_Au[1];
866  f[5] = uu[0]*uu[0] + 2.0/rho*P_Au[0] - uu[2]*uu[2] - 2.0/rho*P_Au[2];
867 
868  // Calculate the wave speed at each vessel
869  NekDouble c1 = sqrt(beta[0]/(2*rho))*sqrt(sqrt(Au[0]));
870  NekDouble c2 = sqrt(beta[1]/(2*rho))*sqrt(sqrt(Au[1]));
871  NekDouble c3 = sqrt(beta[2]/(2*rho))*sqrt(sqrt(Au[2]));
872 
873  // Inverse Jacobian matrix J(x[n])^(-1), is already inverted here analytically
874  k = c1*Au[1]*c3+Au[0]*c3*c2+Au[2]*c1*c2;
875  k1 = (c1+uu[0])*k;
876  inv_J[0][0] = (c2*uu[0]*c3*Au[0]+Au[2]*c2*c1*c1+Au[1]*c1*c1*c3)/k1;
877  inv_J[0][1] = Au[1]*(c2+uu[1])*c1*c3/k1;
878  inv_J[0][2] = Au[2]*(c3+uu[2])*c1*c2/k1;
879  inv_J[0][3] = c1*c2*c3/k1;
880  inv_J[0][4] = 0.5*Au[1]*c1*c3/k1;
881  inv_J[0][5] = 0.5*Au[2]*c1*c2/k1;
882 
883  k2 = (c2-uu[1])*k;
884  inv_J[1][0] = Au[0]*(c1-uu[0])*c2*c3/k2;
885  inv_J[1][1] = (-c1*uu[1]*c3*Au[1]+Au[2]*c1*c2*c2+c3*c2*c2*Au[0])/k2;
886  inv_J[1][2] = -Au[2]*(c3+uu[2])*c1*c2/k2;
887  inv_J[1][3] = -c1*c2*c3/k2;
888  inv_J[1][4] = 0.5*(c1*Au[2]+Au[0]*c3)*c2/k2;
889  inv_J[1][5] = -0.5*Au[2]*c1*c2/k2;
890 
891  k3 = (c3-uu[2])*k;
892  inv_J[2][0] = Au[0]*(c1-uu[0])*c2*c3/k3;
893  inv_J[2][1] = -Au[1]*(c2+uu[1])*c1*c3/k3;
894  inv_J[2][2] = -(c1*uu[2]*c2*Au[2]-Au[1]*c1*c3*c3-c2*c3*c3*Au[0])/k3;
895  inv_J[2][3] = -c1*c2*c3/k3;
896  inv_J[2][4] = -0.5*Au[1]*c1*c3/k3;
897  inv_J[2][5] = 0.5*(Au[1]*c1+Au[0]*c2)*c3/k3;
898 
899  inv_J[3][0] = -Au[0]*(Au[0]*c3*c2+uu[0]*c3*Au[1]+uu[0]*c2*Au[2])/k1;
900  inv_J[3][1] = Au[0]*Au[1]*(c2+uu[1])*c3/k1;
901  inv_J[3][2] = Au[0]*Au[2]*(c3+uu[2])*c2/k1;
902  inv_J[3][3] = Au[0]*c3*c2/k1;
903  inv_J[3][4] = 0.5*Au[0]*Au[1]*c3/k1;
904  inv_J[3][5] = 0.5*Au[0]*c2*Au[2]/k1;
905 
906  inv_J[4][0] = -Au[0]*Au[1]*(c1-uu[0])*c3/k2;
907  inv_J[4][1] = Au[1]*(Au[1]*c1*c3-c1*uu[1]*Au[2]-c3*uu[1]*Au[0])/k2;
908  inv_J[4][2] = Au[2]*Au[1]*(c3+uu[2])*c1/k2;
909  inv_J[4][3] = Au[1]*c1*c3/k2;
910  inv_J[4][4] = -0.5*Au[1]*(c1*Au[2]+Au[0]*c3)/k2;
911  inv_J[4][5] = 0.5*Au[2]*Au[1]*c1/k2;
912 
913  inv_J[5][0] = -Au[0]*Au[2]*(c1-uu[0])*c2/k3;
914  inv_J[5][1] = Au[2]*Au[1]*(c2+uu[1])*c1/k3;
915  inv_J[5][2] = Au[2]*(Au[2]*c1*c2-c1*uu[2]*Au[1]-c2*uu[2]*Au[0])/k3;
916  inv_J[5][3] = Au[2]*c1*c2/k3;
917  inv_J[5][4] = 0.5*Au[2]*Au[1]*c1/k3;
918  inv_J[5][5] = -0.5*Au[2]*(Au[1]*c1+Au[0]*c2)/k3;
919 
920  // Solve the system by multiplying the Jacobian with the vector f:
921  // g = (inv_J)*f
922  for (int j=0; j<6; j++)
923  {
924  tmp[j] =0.0;
925  g[j] = 0.0;
926  }
927 
928  for (int j=0; j<6; j++)
929  {
930  for (int i=0; i<6; i++)
931  {
932  tmp[j] = inv_J[j][i]*f[i];
933  g[j] += tmp[j];
934  }
935  }
936 
937  // Update the solution: x_new = x_old - dx
938  uu[0] = uu[0] - g[0];
939  uu[1] = uu[1] - g[1];
940  uu[2] = uu[2] - g[2];
941  Au[0] = Au[0] - g[3];
942  Au[1] = Au[1] - g[4];
943  Au[2] = Au[2] - g[5];
944 
945  // Check if the error of the solution is smaller than Tol
946  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)
947  {
948  proceed = 0;
949  }
950 
951  // Check if solver converges
952  if (iter >= MAX_ITER)
953  {
954  ASSERTL0(false,"Riemann solver for Merging Flow did not converge");
955  }
956 
957  }
958  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
Nektar::NekDouble
double NekDouble
Definition: NektarUnivTypeDefs.hpp:44
void Nektar::PulseWaveSystem::SetUpDomainInterfaces ( void  )
private

Definition at line 263 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, NEKERROR, and CellMLToNektar.cellml_metadata::p.

Referenced by v_InitObject().

264  {
265  map<int,std::vector<InterfacePointShPtr> > VidToDomain;
266  map<int,std::vector<InterfacePointShPtr> >::iterator iter;
267 
268  // loop over domain and find out if we have any undefined
269  // boundary conditions representing interfaces. If so make a
270  // map based around vid and storing the domains that are
271  // part of interfaces.
272  for(int omega = 0; omega < m_nDomains; ++omega)
273  {
274  int vesselID = omega*m_nVariables;
275 
276  for(int i = 0; i < 2; ++i)
277  {
278  if(m_vessels[vesselID]->GetBndConditions()[i]->GetBoundaryConditionType() == SpatialDomains::eNotDefined)
279  {
280  // Get Vid of interface
281  int vid = m_vessels[vesselID]->UpdateBndCondExpansion(i)->GetExp(0)->GetGeom()->GetVid(0);
282  cout<<"Shared vertex id: "<<vid<<endl;
283  MultiRegions::ExpListSharedPtr trace = m_vessels[vesselID]->GetTrace();
284  InterfacePointShPtr Ipt;
285 
286  bool finish = false;
287  // find which elmt, the lcoal vertex and the data offset of point
288  for(int n = 0; n < m_vessels[vesselID]->GetExpSize(); ++n)
289  {
290  for(int p = 0; p < 2; ++p)
291  {
292  if(m_vessels[vesselID]->GetTraceMap()->GetElmtToTrace()[n][p]->as<LocalRegions::Expansion>()->GetGeom()->GetVid(0) == vid)
293  {
294  int eid = m_vessels[vesselID]->GetTraceMap()->GetElmtToTrace()[n][p]->GetElmtId();
295 
296  int tid = m_vessels[vesselID]->GetTrace()->GetCoeff_Offset(eid);
297  Ipt = MemoryManager<InterfacePoint>::AllocateSharedPtr(vid,omega,n,p,tid,i);
298 
299  cout<<"Global Vid of interface point: "<<vid<<endl;
300  cout<<"Domain interface point belongs to: "<<omega<<endl;
301  cout<<"Element id of vertex: "<<n<<endl;
302  cout<<"Vertex id within local element: "<<p<<endl;
303  cout<<"Element id within the trace: "<<tid<<endl;
304  cout<<"Position of boundary condition in region: "<<i<<endl;
305 
306  finish = true;
307  break;
308  }
309  }
310  if(finish == true)
311  {
312  break;
313  }
314  }
315 
316  VidToDomain[vid].push_back(Ipt);
317 
318  // finally reset boundary condition to Dirichlet
319  m_vessels[vesselID]->GetBndConditions()[i]
320  ->SetBoundaryConditionType(SpatialDomains::eDirichlet);
321 
322  m_vessels[vesselID+1]->GetBndConditions()[i]
323  ->SetBoundaryConditionType(SpatialDomains::eDirichlet);
324  }
325  }
326  }
327 
328  // loop over map and set up Interface information;
329  for(iter = VidToDomain.begin(); iter != VidToDomain.end(); ++iter)
330  {
331  if(iter->second.size() == 2) // Vessel jump interface
332  {
333  m_vesselJcts.push_back(iter->second);
334  }
335  else if(iter->second.size() == 3) // Bifurcation or Merging junction.
336  {
337  int nbeg = 0;
338  int nend = 0;
339 
340  // Determine if bifurcation or merging junction
341  // through number of elemnt vertices that meet at
342  // junction. Only one vertex using a m_elmtVert=1
343  // indicates a bifurcation
344  for(int i = 0; i < 3; ++i)
345  {
346  if(iter->second[i]->m_elmtVert == 0)
347  {
348  nbeg += 1;
349  }
350  else
351  {
352  nend += 1;
353  }
354  }
355 
356  // Set up Bifurcation information
357  if(nbeg == 2)
358  {
359  // ensure first InterfacePoint is parent
360  if(iter->second[0]->m_elmtVert == 1) //m_elmtVert: Vertex id in local element
361  {
362  m_bifurcations.push_back(iter->second);
363  }
364  else
365  {
366  //order points according to Riemann solver convention
367  InterfacePointShPtr I;
368  //find merging vessel
369  if(iter->second[1]->m_elmtVert == 1)
370  {
371  I = iter->second[0];
372  iter->second[0] = iter->second[1];
373  iter->second[1] = I;
374  }
375  else if (iter->second[2]->m_elmtVert == 1)
376  {
377  I = iter->second[0];
378  iter->second[0] = iter->second[2];
379  iter->second[2] = I;
380  }
381  NEKERROR(ErrorUtil::ewarning,"This routine has not been checked");
382  }
383  }
384  else
385  {
386  // ensure last InterfacePoint is merged vessel
387  if(iter->second[0]->m_elmtVert == 0)
388  {
389  m_mergingJcts.push_back(iter->second);
390  }
391  else
392  {
393  //order points according to Riemann solver convention
394  InterfacePointShPtr I;
395  //find merging vessel
396  if(iter->second[1]->m_elmtVert == 0)
397  {
398  I = iter->second[0];
399  iter->second[0] = iter->second[1];
400  iter->second[1] = I;
401  }
402  else if (iter->second[2]->m_elmtVert == 0)
403  {
404  I = iter->second[0];
405  iter->second[0] = iter->second[2];
406  iter->second[2] = I;
407  }
408  NEKERROR(ErrorUtil::ewarning,"This routine has not been checked");
409  }
410  }
411 
412  }
413  else
414  {
415  ASSERTL0(false,"Unknown junction type");
416  }
417  }
418  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
NEKERROR
#define NEKERROR(type, msg)
Assert Level 0 – Fundamental assert which is used whether in FULLDEBUG, DEBUG or OPT compilation mod...
Definition: ErrorUtil.hpp:191
Nektar::MemoryManager::AllocateSharedPtr
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
Definition: NekMemoryManager.hpp:235
CellMLToNektar.cellml_metadata.p
tuple p
Definition: cellml_metadata.py:350
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 428 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().

429  {
430 
431  if (m_session->GetComm()->GetRank() == 0)
432  {
433  cout << "Initial Conditions:" << endl;
434  }
435 
436  /* Loop over all subdomains to initialize all with the Initial
437  * Conditions read from the inputfile*/
438  for (int omega = 0; omega < m_nDomains; omega++)
439  {
440  m_fields[0] = m_vessels[m_nVariables*omega];
441  m_fields[1] = m_vessels[m_nVariables*omega+1];
442 
443  if (m_session->GetComm()->GetRank() == 0)
444  {
445  cout << "Subdomain = " <<omega<<endl;
446  }
447 
448  SetInitialConditions(0.0,0,omega);
449  }
450  // Reset to first definition
451  m_fields[0] = m_vessels[0];
452  m_fields[1] = m_vessels[1];
453 
454  }
Nektar::SolverUtils::EquationSystem::m_fields
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
Definition: EquationSystem.h:470
Nektar::SolverUtils::EquationSystem::m_session
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Definition: EquationSystem.h:460
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:820
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 473 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().

474  {
475  NekDouble IntegrationTime = 0.0;
476  int i,n,nchk = 1;
477 
478  Array<OneD, Array<OneD,NekDouble> > fields(m_nVariables);
479 
480  for(int i = 0; i < m_nVariables; ++i)
481  {
482  fields[i] = m_vessels[i]->UpdatePhys();
483  m_fields[i]->SetPhysState(false);
484  }
485 
486  m_intSoln = m_intScheme->InitializeScheme(
487  m_timestep,fields,m_time,m_ode);
488 
489  // Time loop
490  for(n = 0; n < m_steps; ++n)
491  {
492  Timer timer;
493  timer.Start();
494  fields = m_intScheme->TimeIntegrate(n,m_timestep,m_intSoln,m_ode);
495  //cout<<"integration: "<<fields[0][fields[0].num_elements()-1]<<endl;
496  m_time += m_timestep;
497  timer.Stop();
498  IntegrationTime += timer.TimePerTest(1);
499 
500  // Write out status information.
501  if(m_session->GetComm()->GetRank() == 0 && !((n+1)%m_infosteps))
502  {
503  cout << "Steps: " << n+1
504  << "\t Time: " << m_time
505  << "\t Time-step: " << m_timestep << "\t" << endl;
506  }
507 
508  // Transform data if needed
509  if(!((n+1)%m_checksteps))
510  {
511  for (i = 0; i < m_nVariables; ++i)
512  {
513  int cnt = 0;
514  for (int omega = 0; omega < m_nDomains; omega++)
515  {
516  m_vessels[omega*m_nVariables+i]->FwdTrans(fields[i]+cnt,
517  m_vessels[omega*m_nVariables+i]->UpdateCoeffs());
518  cnt += m_vessels[omega*m_nVariables+i]->GetTotPoints();
519  }
520  }
521  CheckPoint_Output(nchk++);
522  }
523 
524  }//end of timeintegration
525 
526  //Copy Array To Vessel Phys Fields
527  for(int i = 0; i < m_nVariables; ++i)
528  {
529  Vmath::Vcopy(fields[i].num_elements(), fields[i],1,m_vessels[i]->UpdatePhys(),1);
530  }
531 
532  cout <<"Time-integration timing : "
533  << IntegrationTime << " s" << endl << endl;
534  }
Nektar::PulseWaveSystem::CheckPoint_Output
void CheckPoint_Output(const int n)
Definition: PulseWaveSystem.cpp:1099
Nektar::SolverUtils::EquationSystem::m_time
NekDouble m_time
Current time of simulation.
Definition: EquationSystem.h:482
Nektar::SolverUtils::UnsteadySystem::m_ode
LibUtilities::TimeIntegrationSchemeOperators m_ode
The time integration scheme operators to use.
Definition: UnsteadySystem.h:69
Nektar::SolverUtils::EquationSystem::m_timestep
NekDouble m_timestep
Time step size.
Definition: EquationSystem.h:488
Nektar::SolverUtils::EquationSystem::m_checksteps
int m_checksteps
Number of steps between checkpoints.
Definition: EquationSystem.h:498
Nektar::SolverUtils::EquationSystem::m_steps
int m_steps
Number of steps to take.
Definition: EquationSystem.h:496
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:470
Nektar::SolverUtils::EquationSystem::m_session
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Definition: EquationSystem.h:460
Nektar::SolverUtils::UnsteadySystem::m_intScheme
LibUtilities::TimeIntegrationWrapperSharedPtr m_intScheme
Wrapper to the time integration scheme.
Definition: UnsteadySystem.h:67
Nektar::SolverUtils::UnsteadySystem::m_infosteps
int m_infosteps
Number of time steps between outputting status information.
Definition: UnsteadySystem.h:63
Vmath::Vcopy
void Vcopy(int n, const T *x, const int incx, T *y, const int incy)
Definition: Vmath.cpp:1061
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:71
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 86 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, Nektar::SolverUtils::UnsteadySystem::v_InitObject(), and Nektar::SolverUtils::EquationSystem::ZeroPhysFields().

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

87  {
88  // Initialise base class
89  UnsteadySystem::v_InitObject();
90 
91  // Read the geometry and the expansion information
92  m_nDomains = m_graph->GetDomain().size();
93 
94  // Determine projectiontype
95  ASSERTL0(m_session->MatchSolverInfo("Projection","DisContinuous"),"Pulse solver only set up for Discontinuous projections");
96  m_projectionType = MultiRegions::eDiscontinuous;
97  ASSERTL0(m_graph->GetMeshDimension() == 1,"Pulse wave solver only set up for expansion dimension equal to 1");
98 
99  int i;
100  m_nVariables = m_session->GetVariables().size();
101 
102  m_fields = Array<OneD, MultiRegions::ExpListSharedPtr> (m_nVariables);
103  m_vessels = Array<OneD, MultiRegions::ExpListSharedPtr> (m_nVariables*m_nDomains);
104 
105  const std::vector<SpatialDomains::CompositeMap> domain = m_graph->GetDomain();
106 
107  SpatialDomains::BoundaryConditions Allbcs(m_session, m_graph);
108 
109  // Set up domains and put geometry to be only one space dimension.
110  int cnt = 0;
111  bool SetToOneSpaceDimension = true;
112 
113  if(m_session->DefinesCmdLineArgument("SetToOneSpaceDimension"))
114  {
115  std::string cmdline = m_session->GetCmdLineArgument<std::string>("SetToOneSpaceDimension");
116  if(boost::to_upper_copy(cmdline) == "FALSE")
117  {
118  SetToOneSpaceDimension = false;
119  }
120  }
121 
122  for(i = 0 ; i < m_nDomains; ++i)
123  {
124  for(int j = 0; j < m_nVariables; ++j)
125  {
126  m_vessels[cnt++] = MemoryManager<MultiRegions::DisContField1D>
127  ::AllocateSharedPtr(m_session, m_graph, domain[i],
128  Allbcs,
129  m_session->GetVariable(j),
130  SetToOneSpaceDimension);
131  }
132  }
133 
134  // Reset coeff and phys space to be continuous over all domains
135  int totcoeffs = 0;
136  int totphys = 0;
137  m_fieldPhysOffset = Array<OneD, int>(m_nDomains+1,0);
138  for(i = 0; i < m_nDomains; ++i)
139  {
140  totcoeffs += m_vessels[i*m_nVariables]->GetNcoeffs();
141 
142  m_fieldPhysOffset[i] = totphys;
143  totphys += m_vessels[i*m_nVariables]->GetTotPoints();
144  }
145  m_fieldPhysOffset[m_nDomains] = totphys;
146 
147  for(int n = 0; n < m_nVariables; ++n)
148  {
149  Array<OneD, NekDouble> coeffs(totcoeffs,0.0);
150  Array<OneD, NekDouble> phys(totphys,0.0);
151  Array<OneD, NekDouble> tmpcoeffs,tmpphys;
152 
153  m_vessels[n]->SetCoeffsArray(coeffs);
154  m_vessels[n]->SetPhysArray(phys);
155 
156  int cnt = m_vessels[n]->GetNcoeffs();
157  int cnt1 = m_vessels[n]->GetTotPoints();
158 
159  for(i = 1; i < m_nDomains; ++i)
160  {
161  m_vessels[i*m_nVariables+n]->SetCoeffsArray(tmpcoeffs = coeffs + cnt);
162  m_vessels[i*m_nVariables+n]->SetPhysArray (tmpphys = phys + cnt1);
163  cnt += m_vessels[i*m_nVariables+n]->GetNcoeffs();
164  cnt1 += m_vessels[i*m_nVariables+n]->GetTotPoints();
165  }
166  }
167 
168  // Set Default Parameter
169  m_session->LoadParameter("Time", m_time, 0.0);
170  m_session->LoadParameter("TimeStep", m_timestep, 0.01);
171  m_session->LoadParameter("NumSteps", m_steps, 0);
172  m_session->LoadParameter("IO_CheckSteps", m_checksteps, m_steps);
173  m_session->LoadParameter("FinTime", m_fintime, 0);
174  m_session->LoadParameter("NumQuadPointsError", m_NumQuadPointsError, 0);
175 
176  m_fields[0] = m_vessels[0];
177  m_fields[1] = m_vessels[1];
178 
179  // Zero all physical fields initially.
180  ZeroPhysFields();
181 
182  // If Discontinuous Galerkin determine upwinding method to use
183  for (int i = 0; i < (int)SIZE_UpwindTypePulse; ++i)
184  {
185  bool match;
186  m_session->MatchSolverInfo("UPWINDTYPEPULSE", UpwindTypeMapPulse[i], match, false);
187  if (match)
188  {
189  m_upwindTypePulse = (UpwindTypePulse) i;
190  break;
191  }
192  }
193  // Load solver- specific parameters
194  m_session->LoadParameter("IO_InfoSteps", m_infosteps, 0);
195  // Load blood density
196  m_session->LoadParameter("rho", m_rho, 0.5);
197  // Load external pressure
198  m_session->LoadParameter("pext", m_pext, 0.0);
199 
200  int nq = 0;
201  /**
202  * Gets the Material Properties of each arterial segment
203  * specified in the inputfile from section MaterialProperties
204  * Also gets the Area at static equilibrium A_0 specified in the
205  * inputfile.
206  *
207  * Having found these points also extract the values at the
208  * trace points and the normal direction consistent with the
209  * left adjacent definition of Fwd and Bwd
210  */
211  m_beta = Array<OneD, Array<OneD, NekDouble> >(m_nDomains);
212  m_beta_trace = Array<OneD, Array<OneD, NekDouble> >(m_nDomains);
213  m_A_0 = Array<OneD, Array<OneD, NekDouble> >(m_nDomains);
214  m_A_0_trace = Array<OneD, Array<OneD, NekDouble> >(m_nDomains);
215  m_trace_fwd_normal = Array<OneD, Array<OneD, NekDouble> >(m_nDomains);
216 
217  for (int omega = 0; omega < m_nDomains; omega++)
218  {
219  nq = m_vessels[2*omega]->GetNpoints();
220  m_fields[0] = m_vessels[2*omega];
221 
222  m_beta[omega] = Array<OneD, NekDouble>(nq);
223  EvaluateFunction("beta", m_beta[omega], "MaterialProperties", m_time, omega);
224 
225  m_A_0[omega] = Array<OneD, NekDouble>(nq);
226  EvaluateFunction("A_0", m_A_0[omega], "A_0", m_time, omega);
227 
228  int nqTrace = GetTraceTotPoints();
229 
230  m_beta_trace[omega] = Array<OneD, NekDouble>(nqTrace);
231  m_fields[0]->ExtractTracePhys(m_beta[omega],m_beta_trace[omega]);
232 
233  m_A_0_trace[omega] = Array<OneD, NekDouble>(nqTrace);
234  m_fields[0]->ExtractTracePhys(m_A_0[omega],m_A_0_trace[omega]);
235 
236 
237  if(SetToOneSpaceDimension)
238  {
239  m_trace_fwd_normal[omega] = Array<OneD, NekDouble>(nqTrace,0.0);
240 
241  MultiRegions::ExpListSharedPtr trace = m_fields[0]->GetTrace();
242  int nelmt_trace = trace->GetExpSize();
243 
244  Array<OneD, Array<OneD, NekDouble> > normals(nelmt_trace);
245 
246  for(int i = 0 ; i < nelmt_trace; ++i)
247  {
248  normals[i] = m_trace_fwd_normal[omega]+i;
249  }
250 
251  // need to set to 1 for consistency since boundary
252  // conditions may not have coordim=1
253  trace->GetExp(0)->GetGeom()->SetCoordim(1);
254 
255  trace->GetNormals(normals);
256  }
257  }
258 
259  SetUpDomainInterfaces();
260 
261  }
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:198
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:482
Nektar::SolverUtils::EquationSystem::m_timestep
NekDouble m_timestep
Time step size.
Definition: EquationSystem.h:488
Nektar::SolverUtils::EquationSystem::m_projectionType
enum MultiRegions::ProjectionType m_projectionType
Type of projection; e.g continuous or discontinuous.
Definition: EquationSystem.h:522
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:498
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:486
Nektar::SolverUtils::EquationSystem::m_steps
int m_steps
Number of steps to take.
Definition: EquationSystem.h:496
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::UnsteadySystem::v_InitObject
virtual SOLVER_UTILS_EXPORT void v_InitObject()
Init object for UnsteadySystem class.
Definition: UnsteadySystem.cpp:78
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:688
Nektar::SolverUtils::EquationSystem::GetTraceTotPoints
SOLVER_UTILS_EXPORT int GetTraceTotPoints()
Definition: EquationSystem.h:877
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:470
Nektar::SolverUtils::EquationSystem::m_session
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Definition: EquationSystem.h:460
Nektar::SolverUtils::EquationSystem::ZeroPhysFields
SOLVER_UTILS_EXPORT void ZeroPhysFields()
Definition: EquationSystem.cpp:1696
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:478
Nektar::SolverUtils::EquationSystem::m_NumQuadPointsError
int m_NumQuadPointsError
Number of Quadrature points used to work out the error.
Definition: EquationSystem.h:535
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 1158 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.

1161  {
1162  NekDouble L2error = 0.0;
1163  NekDouble L2error_dom;
1164  NekDouble Vol = 0.0;
1165 
1166  if(m_NumQuadPointsError == 0)
1167  {
1168  for (int omega = 0; omega < m_nDomains; omega++)
1169  {
1170  int vesselid = field + omega*m_nVariables;
1171 
1172  if(m_vessels[vesselid]->GetPhysState() == false)
1173  {
1174  m_vessels[vesselid]->BwdTrans(m_vessels[vesselid]->GetCoeffs(),
1175  m_vessels[vesselid]->UpdatePhys());
1176  }
1177 
1178  if(exactsoln.num_elements())
1179  {
1180  L2error_dom = m_vessels[vesselid]->L2(
1181  m_vessels[vesselid]->GetPhys(),
1182  exactsoln);
1183  }
1184  else if (m_session->DefinesFunction("ExactSolution"))
1185  {
1186  Array<OneD, NekDouble> exactsoln(m_vessels[vesselid]->GetNpoints());
1187 
1188  LibUtilities::EquationSharedPtr vEqu
1189  = m_session->GetFunction("ExactSolution",field,omega);
1190  EvaluateFunction(m_session->GetVariable(field),exactsoln,"ExactSolution",
1191  m_time);
1192 
1193  L2error_dom = m_vessels[vesselid]->L2(
1194  m_vessels[vesselid]->GetPhys(),
1195  exactsoln);
1196 
1197  }
1198  else
1199  {
1200  L2error_dom = m_vessels[vesselid]->L2(
1201  m_vessels[vesselid]->GetPhys());
1202  }
1203 
1204  L2error += L2error_dom*L2error_dom;
1205 
1206  if(Normalised == true)
1207  {
1208  Array<OneD, NekDouble> one(m_vessels[vesselid]->GetNpoints(), 1.0);
1209 
1210  Vol += m_vessels[vesselid]->PhysIntegral(one);
1211  }
1212 
1213  }
1214  }
1215  else
1216  {
1217  ASSERTL0(false,"Not set up");
1218  }
1219 
1220 
1221  if(Normalised == true)
1222  {
1223  m_comm->AllReduce(Vol, LibUtilities::ReduceSum);
1224 
1225  L2error = sqrt(L2error/Vol);
1226  }
1227  else
1228  {
1229  L2error = sqrt(L2error);
1230  }
1231 
1232  return L2error;
1233  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
Nektar::SolverUtils::EquationSystem::m_time
NekDouble m_time
Current time of simulation.
Definition: EquationSystem.h:482
Nektar::SolverUtils::EquationSystem::m_comm
LibUtilities::CommSharedPtr m_comm
Communicator.
Definition: EquationSystem.h:458
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:688
Nektar::LibUtilities::EquationSharedPtr
boost::shared_ptr< Equation > EquationSharedPtr
Definition: SessionReader.h:100
Nektar::SolverUtils::EquationSystem::GetNpoints
SOLVER_UTILS_EXPORT int GetNpoints()
Definition: EquationSystem.h:912
Nektar::SolverUtils::EquationSystem::m_session
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Definition: EquationSystem.h:460
Nektar::SolverUtils::EquationSystem::m_NumQuadPointsError
int m_NumQuadPointsError
Number of Quadrature points used to work out the error.
Definition: EquationSystem.h:535
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 1242 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.

1244  {
1245  NekDouble LinferrorDom, Linferror = -1.0;
1246 
1247  for (int omega = 0; omega < m_nDomains; omega++)
1248  {
1249  int vesselid = field + omega*m_nVariables;
1250 
1251  if(m_NumQuadPointsError == 0)
1252  {
1253  if(m_vessels[vesselid]->GetPhysState() == false)
1254  {
1255  m_vessels[vesselid]->BwdTrans(m_vessels[vesselid]->GetCoeffs(),
1256  m_vessels[vesselid]->UpdatePhys());
1257  }
1258 
1259  if(exactsoln.num_elements())
1260  {
1261  LinferrorDom = m_vessels[vesselid]->Linf(
1262  m_vessels[vesselid]->GetPhys(),
1263  exactsoln);
1264  }
1265  else if (m_session->DefinesFunction("ExactSolution"))
1266  {
1267  Array<OneD, NekDouble> exactsoln(m_vessels[vesselid]->GetNpoints());
1268 
1269  EvaluateFunction(m_session->GetVariable(field),exactsoln,"ExactSolution",
1270  m_time);
1271 
1272  LinferrorDom = m_vessels[vesselid]->Linf(
1273  m_vessels[vesselid]->GetPhys(),
1274  exactsoln);
1275  }
1276  else
1277  {
1278  LinferrorDom = 0.0;
1279  }
1280 
1281  Linferror = (Linferror > LinferrorDom)? Linferror:LinferrorDom;
1282 
1283  }
1284  else
1285  {
1286  ASSERTL0(false,"ErrorExtraPoints not allowed for this solver");
1287  }
1288  }
1289  return Linferror;
1290  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
Nektar::SolverUtils::EquationSystem::m_time
NekDouble m_time
Current time of simulation.
Definition: EquationSystem.h:482
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:688
Nektar::SolverUtils::EquationSystem::GetNpoints
SOLVER_UTILS_EXPORT int GetNpoints()
Definition: EquationSystem.h:912
Nektar::SolverUtils::EquationSystem::m_session
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Definition: EquationSystem.h:460
Nektar::SolverUtils::EquationSystem::m_NumQuadPointsError
int m_NumQuadPointsError
Number of Quadrature points used to work out the error.
Definition: EquationSystem.h:535
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 1083 of file PulseWaveSystem.cpp.

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

1084  {
1085  /**
1086  * Write the field data to file. The file is named according to the session
1087  * name with the extension .fld appended.
1088  */
1089  std::string outname = m_sessionName + ".fld";
1090 
1091  WriteVessels(outname);
1092  }
Nektar::SolverUtils::EquationSystem::m_sessionName
std::string m_sessionName
Name of the session.
Definition: EquationSystem.h:480
Nektar::PulseWaveSystem::WriteVessels
void WriteVessels(const std::string &outname)
Write input fields to the given filename.
Definition: PulseWaveSystem.cpp:1112
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 1112 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().

1113  {
1114 
1115  std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef;
1116  std::vector<std::string> variables = m_session->GetVariables();
1117 
1118  for(int n = 0; n < m_nDomains; ++n)
1119  {
1120  m_vessels[n*m_nVariables]->GetFieldDefinitions(FieldDef);
1121  }
1122 
1123  std::vector<std::vector<NekDouble> > FieldData(FieldDef.size());
1124 
1125  int nFieldDefPerDomain = FieldDef.size()/m_nDomains;
1126  int cnt;
1127  // Copy Data into FieldData and set variable
1128  for(int n = 0; n < m_nDomains; ++n)
1129  {
1130  for(int j = 0; j < m_nVariables; ++j)
1131  {
1132  for(int i = 0; i < nFieldDefPerDomain; ++i)
1133  {
1134  cnt = n*nFieldDefPerDomain+i;
1135  FieldDef[cnt]->m_fields.push_back(variables[j]);
1136  m_vessels[n*m_nVariables]->AppendFieldData(FieldDef[cnt], FieldData[cnt], m_vessels[n*m_nVariables+j]->UpdateCoeffs());
1137  }
1138  }
1139  }
1140 
1141  // Update time in field info if required
1142  if(m_fieldMetaDataMap.find("Time") != m_fieldMetaDataMap.end())
1143  {
1144  m_fieldMetaDataMap["Time"] = boost::lexical_cast<std::string>(m_time);
1145  }
1146 
1147  //LibUtilities::CombineFields(FieldDef, FieldData);
1148 
1149  LibUtilities::Write(outname, FieldDef, FieldData, m_fieldMetaDataMap);
1150  }
Nektar::SolverUtils::EquationSystem::m_time
NekDouble m_time
Current time of simulation.
Definition: EquationSystem.h:482
Nektar::SolverUtils::EquationSystem::m_fieldMetaDataMap
LibUtilities::FieldMetaDataMap m_fieldMetaDataMap
Map to identify relevant solver info to dump in output fields.
Definition: EquationSystem.h:532
Nektar::LibUtilities::Write
void Write(const std::string &outFile, std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble > > &fielddata, const FieldMetaDataMap &fieldinfomap, const bool backup)
This function allows for data to be written to an FLD file when a session and/or communicator is not ...
Definition: FieldIO.cpp:235
Nektar::SolverUtils::EquationSystem::m_session
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Definition: EquationSystem.h:460
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().

Generated on Sat Nov 25 2017 16:18:45 for Nektar++ by   doxygen 1.8.8