Nektar++
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Properties Friends Macros Pages
Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | List of all members
Nektar::MultiRegions::DisContField3D Class Reference

#include <DisContField3D.h>

Inheritance diagram for Nektar::MultiRegions::DisContField3D:
Inheritance graph
[legend]
Collaboration diagram for Nektar::MultiRegions::DisContField3D:
Collaboration graph
[legend]

Public Member Functions

 DisContField3D ()
 Default constructor. More...
 
 DisContField3D (const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &graph3D, const std::string &variable, const bool SetUpJustDG=true, const Collections::ImplementationType ImpType=Collections::eNoImpType)
 Constructs a global discontinuous field based on an input mesh with boundary conditions. More...
 
 DisContField3D (const DisContField3D &In, const SpatialDomains::MeshGraphSharedPtr &graph3D, const std::string &variable, const bool SetUpJustDG=false)
 
 DisContField3D (const DisContField3D &In)
 Constructs a global discontinuous field based on another discontinuous field. More...
 
virtual ~DisContField3D ()
 Destructor. More...
 
GlobalLinSysSharedPtr GetGlobalBndLinSys (const GlobalLinSysKey &mkey)
 
void EvaluateHDGPostProcessing (Array< OneD, NekDouble > &outarray)
 Evaluate HDG post-processing to increase polynomial order of solution. More...
 
bool GetLeftAdjacentFaces (int cnt)
 
- Public Member Functions inherited from Nektar::MultiRegions::ExpList3D
 ExpList3D ()
 Default constructor. More...
 
 ExpList3D (const ExpList3D &In)
 Copy constructor. More...
 
 ExpList3D (const ExpList3D &In, const std::vector< unsigned int > &eIDs, const bool DeclareCoeffPhysArrays=true, const Collections::ImplementationType ImpType=Collections::eNoImpType)
 Constructor copying only elements defined in eIds. More...
 
 ExpList3D (const LibUtilities::SessionReaderSharedPtr &pSession, const LibUtilities::BasisKey &TBa, const LibUtilities::BasisKey &TBb, const LibUtilities::BasisKey &TBc, const LibUtilities::BasisKey &HBa, const LibUtilities::BasisKey &HBb, const LibUtilities::BasisKey &HBc, const SpatialDomains::MeshGraphSharedPtr &graph3D, const LibUtilities::PointsType TetNb=LibUtilities::SIZE_PointsType, const Collections::ImplementationType ImpType=Collections::eNoImpType)
 
 ExpList3D (const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &graph3D, const std::string &variable="DefaultVar", const Collections::ImplementationType ImpType=Collections::eNoImpType)
 Sets up a list of local expansions based on an input mesh. More...
 
 ExpList3D (const SpatialDomains::ExpansionMap &expansions, const Collections::ImplementationType ImpType=Collections::eNoImpType)
 Sets up a list of local expansions based on an expansion vector. More...
 
virtual ~ExpList3D ()
 Destructor. More...
 
- Public Member Functions inherited from Nektar::MultiRegions::ExpList
 ExpList ()
 The default constructor. More...
 
 ExpList (const LibUtilities::SessionReaderSharedPtr &pSession)
 The default constructor. More...
 
 ExpList (const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &pGraph)
 The default constructor. More...
 
 ExpList (const ExpList &in, const std::vector< unsigned int > &eIDs, const bool DeclareCoeffPhysArrays=true)
 Constructor copying only elements defined in eIds. More...
 
 ExpList (const ExpList &in, const bool DeclareCoeffPhysArrays=true)
 The copy constructor. More...
 
virtual ~ExpList ()
 The default destructor. More...
 
int GetNcoeffs (void) const
 Returns the total number of local degrees of freedom $N_{\mathrm{eof}}=\sum_{e=1}^{{N_{\mathrm{el}}}}N^{e}_m$. More...
 
int GetNcoeffs (const int eid) const
 Returns the total number of local degrees of freedom for element eid. More...
 
ExpansionType GetExpType (void)
 Returns the type of the expansion. More...
 
void SetExpType (ExpansionType Type)
 Returns the type of the expansion. More...
 
int EvalBasisNumModesMax (void) const
 Evaulates the maximum number of modes in the elemental basis order over all elements. More...
 
const Array< OneD, int > EvalBasisNumModesMaxPerExp (void) const
 Returns the vector of the number of modes in the elemental basis order over all elements. More...
 
int GetTotPoints (void) const
 Returns the total number of quadrature points m_npoints $=Q_{\mathrm{tot}}$. More...
 
int GetTotPoints (const int eid) const
 Returns the total number of quadrature points for eid's element $=Q_{\mathrm{tot}}$. More...
 
int GetNpoints (void) const
 Returns the total number of quadrature points m_npoints $=Q_{\mathrm{tot}}$. More...
 
int Get1DScaledTotPoints (const NekDouble scale) const
 Returns the total number of qudature points scaled by the factor scale on each 1D direction. More...
 
void SetWaveSpace (const bool wavespace)
 Sets the wave space to the one of the possible configuration true or false. More...
 
void SetModifiedBasis (const bool modbasis)
 Set Modified Basis for the stability analysis. More...
 
void SetPhys (int i, NekDouble val)
 Set the i th value of m_phys to value val. More...
 
bool GetWaveSpace (void) const
 This function returns the third direction expansion condition, which can be in wave space (coefficient) or not It is stored in the variable m_WaveSpace. More...
 
void SetPhys (const Array< OneD, const NekDouble > &inarray)
 Fills the array m_phys. More...
 
void SetPhysArray (Array< OneD, NekDouble > &inarray)
 Sets the array m_phys. More...
 
void SetPhysState (const bool physState)
 This function manually sets whether the array of physical values $\boldsymbol{u}_l$ (implemented as m_phys) is filled or not. More...
 
bool GetPhysState (void) const
 This function indicates whether the array of physical values $\boldsymbol{u}_l$ (implemented as m_phys) is filled or not. More...
 
NekDouble PhysIntegral (void)
 This function integrates a function $f(\boldsymbol{x})$ over the domain consisting of all the elements of the expansion. More...
 
NekDouble PhysIntegral (const Array< OneD, const NekDouble > &inarray)
 This function integrates a function $f(\boldsymbol{x})$ over the domain consisting of all the elements of the expansion. More...
 
void IProductWRTBase_IterPerExp (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 This function calculates the inner product of a function $f(\boldsymbol{x})$ with respect to all {local} expansion modes $\phi_n^e(\boldsymbol{x})$. More...
 
void IProductWRTBase (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, CoeffState coeffstate=eLocal)
 
void IProductWRTDerivBase (const int dir, const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 This function calculates the inner product of a function $f(\boldsymbol{x})$ with respect to the derivative (in direction. More...
 
void IProductWRTDerivBase (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, NekDouble > &outarray)
 This function calculates the inner product of a function $f(\boldsymbol{x})$ with respect to the derivative (in direction. More...
 
void FwdTrans_IterPerExp (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 This function elementally evaluates the forward transformation of a function $u(\boldsymbol{x})$ onto the global spectral/hp expansion. More...
 
void FwdTrans (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, CoeffState coeffstate=eLocal)
 
void MultiplyByElmtInvMass (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 This function elementally mulplies the coefficient space of Sin my the elemental inverse of the mass matrix. More...
 
void MultiplyByInvMassMatrix (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, CoeffState coeffstate=eLocal)
 
void SmoothField (Array< OneD, NekDouble > &field)
 Smooth a field across elements. More...
 
void HelmSolve (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, const FlagList &flags, const StdRegions::ConstFactorMap &factors, const StdRegions::VarCoeffMap &varcoeff=StdRegions::NullVarCoeffMap, const Array< OneD, const NekDouble > &dirForcing=NullNekDouble1DArray, const bool PhysSpaceForcing=true)
 Solve helmholtz problem. More...
 
void LinearAdvectionDiffusionReactionSolve (const Array< OneD, Array< OneD, NekDouble > > &velocity, const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, const NekDouble lambda, CoeffState coeffstate=eLocal, const Array< OneD, const NekDouble > &dirForcing=NullNekDouble1DArray)
 Solve Advection Diffusion Reaction. More...
 
void LinearAdvectionReactionSolve (const Array< OneD, Array< OneD, NekDouble > > &velocity, const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, const NekDouble lambda, CoeffState coeffstate=eLocal, const Array< OneD, const NekDouble > &dirForcing=NullNekDouble1DArray)
 Solve Advection Diffusion Reaction. More...
 
void FwdTrans_BndConstrained (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 
void BwdTrans_IterPerExp (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 This function elementally evaluates the backward transformation of the global spectral/hp element expansion. More...
 
void BwdTrans (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, CoeffState coeffstate=eLocal)
 
void GetCoords (Array< OneD, NekDouble > &coord_0, Array< OneD, NekDouble > &coord_1=NullNekDouble1DArray, Array< OneD, NekDouble > &coord_2=NullNekDouble1DArray)
 This function calculates the coordinates of all the elemental quadrature points $\boldsymbol{x}_i$. More...
 
void HomogeneousFwdTrans (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, CoeffState coeffstate=eLocal, bool Shuff=true, bool UnShuff=true)
 
void HomogeneousBwdTrans (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, CoeffState coeffstate=eLocal, bool Shuff=true, bool UnShuff=true)
 
void DealiasedProd (const Array< OneD, NekDouble > &inarray1, const Array< OneD, NekDouble > &inarray2, Array< OneD, NekDouble > &outarray, CoeffState coeffstate=eLocal)
 
void DealiasedDotProd (const Array< OneD, Array< OneD, NekDouble > > &inarray1, const Array< OneD, Array< OneD, NekDouble > > &inarray2, Array< OneD, Array< OneD, NekDouble > > &outarray, CoeffState coeffstate=eLocal)
 
void GetBCValues (Array< OneD, NekDouble > &BndVals, const Array< OneD, NekDouble > &TotField, int BndID)
 
void NormVectorIProductWRTBase (Array< OneD, const NekDouble > &V1, Array< OneD, const NekDouble > &V2, Array< OneD, NekDouble > &outarray, int BndID)
 
void NormVectorIProductWRTBase (Array< OneD, Array< OneD, NekDouble > > &V, Array< OneD, NekDouble > &outarray)
 
void ApplyGeomInfo ()
 Apply geometry information to each expansion. More...
 
void Reset ()
 Reset geometry information and reset matrices. More...
 
void WriteTecplotHeader (std::ostream &outfile, std::string var="")
 
void WriteTecplotZone (std::ostream &outfile, int expansion=-1)
 
void WriteTecplotField (std::ostream &outfile, int expansion=-1)
 
void WriteTecplotConnectivity (std::ostream &outfile, int expansion=-1)
 
void WriteVtkHeader (std::ostream &outfile)
 
void WriteVtkFooter (std::ostream &outfile)
 
void WriteVtkPieceHeader (std::ostream &outfile, int expansion, int istrip=0)
 
void WriteVtkPieceFooter (std::ostream &outfile, int expansion)
 
void WriteVtkPieceData (std::ostream &outfile, int expansion, std::string var="v")
 
int GetCoordim (int eid)
 This function returns the dimension of the coordinates of the element eid. More...
 
void SetCoeff (int i, NekDouble val)
 Set the i th coefficiient in m_coeffs to value val. More...
 
void SetCoeffs (int i, NekDouble val)
 Set the i th coefficiient in m_coeffs to value val. More...
 
void SetCoeffsArray (Array< OneD, NekDouble > &inarray)
 Set the m_coeffs array to inarray. More...
 
const Array< OneD, const
NekDouble > & 
GetCoeffs () const
 This function returns (a reference to) the array $\boldsymbol{\hat{u}}_l$ (implemented as m_coeffs) containing all local expansion coefficients. More...
 
void ImposeDirichletConditions (Array< OneD, NekDouble > &outarray)
 Impose Dirichlet Boundary Conditions onto Array. More...
 
void FillBndCondFromField (void)
 Fill Bnd Condition expansion from the values stored in expansion. More...
 
void FillBndCondFromField (const int nreg)
 Fill Bnd Condition expansion in nreg from the values stored in expansion. More...
 
void LocalToGlobal (bool useComm=true)
 Gathers the global coefficients $\boldsymbol{\hat{u}}_g$ from the local coefficients $\boldsymbol{\hat{u}}_l$. More...
 
void LocalToGlobal (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, bool useComm=true)
 
void GlobalToLocal (void)
 Scatters from the global coefficients $\boldsymbol{\hat{u}}_g$ to the local coefficients $\boldsymbol{\hat{u}}_l$. More...
 
void GlobalToLocal (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 
NekDouble GetCoeff (int i)
 Get the i th value (coefficient) of m_coeffs. More...
 
NekDouble GetCoeffs (int i)
 Get the i th value (coefficient) of m_coeffs. More...
 
const Array< OneD, const
NekDouble > & 
GetPhys () const
 This function returns (a reference to) the array $\boldsymbol{u}_l$ (implemented as m_phys) containing the function $u^{\delta}(\boldsymbol{x})$ evaluated at the quadrature points. More...
 
NekDouble Linf (const Array< OneD, const NekDouble > &inarray, const Array< OneD, const NekDouble > &soln=NullNekDouble1DArray)
 This function calculates the $L_\infty$ error of the global spectral/hp element approximation. More...
 
NekDouble L2 (const Array< OneD, const NekDouble > &inarray, const Array< OneD, const NekDouble > &soln=NullNekDouble1DArray)
 This function calculates the $L_2$ error with respect to soln of the global spectral/hp element approximation. More...
 
NekDouble H1 (const Array< OneD, const NekDouble > &inarray, const Array< OneD, const NekDouble > &soln=NullNekDouble1DArray)
 Calculates the $H^1$ error of the global spectral/hp element approximation. More...
 
NekDouble Integral (const Array< OneD, const NekDouble > &inarray)
 
Array< OneD, const NekDoubleHomogeneousEnergy (void)
 This function calculates the energy associated with each one of the modesof a 3D homogeneous nD expansion. More...
 
void SetHomo1DSpecVanVisc (Array< OneD, NekDouble > visc)
 This function sets the Spectral Vanishing Viscosity in homogeneous1D expansion. More...
 
Array< OneD, const unsigned int > GetZIDs (void)
 This function returns a vector containing the wave numbers in z-direction associated with the 3D homogenous expansion. Required if a parellelisation is applied in the Fourier direction. More...
 
LibUtilities::TranspositionSharedPtr GetTransposition (void)
 This function returns the transposition class associaed with the homogeneous expansion. More...
 
NekDouble GetHomoLen (void)
 This function returns the Width of homogeneous direction associaed with the homogeneous expansion. More...
 
Array< OneD, const unsigned int > GetYIDs (void)
 This function returns a vector containing the wave numbers in y-direction associated with the 3D homogenous expansion. Required if a parellelisation is applied in the Fourier direction. More...
 
void PhysInterp1DScaled (const NekDouble scale, const Array< OneD, NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 This function interpolates the physical space points in inarray to outarray using the same points defined in the expansion but where the number of points are rescaled by 1DScale. More...
 
void PhysGalerkinProjection1DScaled (const NekDouble scale, const Array< OneD, NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 This function Galerkin projects the physical space points in inarray to outarray where inarray is assumed to be defined in the expansion but where the number of points are rescaled by 1DScale. More...
 
int GetExpSize (void)
 This function returns the number of elements in the expansion. More...
 
int GetNumElmts (void)
 This function returns the number of elements in the expansion which may be different for a homogeoenous extended expansionp. More...
 
const boost::shared_ptr
< LocalRegions::ExpansionVector
GetExp () const
 This function returns the vector of elements in the expansion. More...
 
LocalRegions::ExpansionSharedPtrGetExp (int n) const
 This function returns (a shared pointer to) the local elemental expansion of the $n^{\mathrm{th}}$ element. More...
 
LocalRegions::ExpansionSharedPtrGetExp (const Array< OneD, const NekDouble > &gloCoord)
 This function returns (a shared pointer to) the local elemental expansion containing the arbitrary point given by gloCoord. More...
 
int GetExpIndex (const Array< OneD, const NekDouble > &gloCoord, NekDouble tol=0.0, bool returnNearestElmt=false)
 
int GetExpIndex (const Array< OneD, const NekDouble > &gloCoords, Array< OneD, NekDouble > &locCoords, NekDouble tol=0.0, bool returnNearestElmt=false)
 
int GetCoeff_Offset (int n) const
 Get the start offset position for a global list of m_coeffs correspoinding to element n. More...
 
int GetPhys_Offset (int n) const
 Get the start offset position for a global list of m_phys correspoinding to element n. More...
 
Array< OneD, NekDouble > & UpdateCoeffs ()
 This function returns (a reference to) the array $\boldsymbol{\hat{u}}_l$ (implemented as m_coeffs) containing all local expansion coefficients. More...
 
Array< OneD, NekDouble > & UpdatePhys ()
 This function returns (a reference to) the array $\boldsymbol{u}_l$ (implemented as m_phys) containing the function $u^{\delta}(\boldsymbol{x})$ evaluated at the quadrature points. More...
 
void PhysDeriv (Direction edir, const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &out_d)
 
void PhysDeriv (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &out_d0, Array< OneD, NekDouble > &out_d1=NullNekDouble1DArray, Array< OneD, NekDouble > &out_d2=NullNekDouble1DArray)
 This function discretely evaluates the derivative of a function $f(\boldsymbol{x})$ on the domain consisting of all elements of the expansion. More...
 
void PhysDeriv (const int dir, const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &out_d)
 
void CurlCurl (Array< OneD, Array< OneD, NekDouble > > &Vel, Array< OneD, Array< OneD, NekDouble > > &Q)
 
const Array< OneD, const
boost::shared_ptr< ExpList > > & 
GetBndCondExpansions ()
 
boost::shared_ptr< ExpList > & UpdateBndCondExpansion (int i)
 
void Upwind (const Array< OneD, const Array< OneD, NekDouble > > &Vec, const Array< OneD, const NekDouble > &Fwd, const Array< OneD, const NekDouble > &Bwd, Array< OneD, NekDouble > &Upwind)
 
void Upwind (const Array< OneD, const NekDouble > &Vn, const Array< OneD, const NekDouble > &Fwd, const Array< OneD, const NekDouble > &Bwd, Array< OneD, NekDouble > &Upwind)
 
boost::shared_ptr< ExpList > & GetTrace ()
 
boost::shared_ptr
< AssemblyMapDG > & 
GetTraceMap (void)
 
const Array< OneD, const int > & GetTraceBndMap (void)
 
void GetNormals (Array< OneD, Array< OneD, NekDouble > > &normals)
 
void AddTraceIntegral (const Array< OneD, const NekDouble > &Fx, const Array< OneD, const NekDouble > &Fy, Array< OneD, NekDouble > &outarray)
 
void AddTraceIntegral (const Array< OneD, const NekDouble > &Fn, Array< OneD, NekDouble > &outarray)
 
void AddFwdBwdTraceIntegral (const Array< OneD, const NekDouble > &Fwd, const Array< OneD, const NekDouble > &Bwd, Array< OneD, NekDouble > &outarray)
 
void GetFwdBwdTracePhys (Array< OneD, NekDouble > &Fwd, Array< OneD, NekDouble > &Bwd)
 
void GetFwdBwdTracePhys (const Array< OneD, const NekDouble > &field, Array< OneD, NekDouble > &Fwd, Array< OneD, NekDouble > &Bwd)
 
const std::vector< bool > & GetLeftAdjacentFaces (void) const
 
void ExtractTracePhys (Array< OneD, NekDouble > &outarray)
 
void ExtractTracePhys (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 
const Array< OneD, const
SpatialDomains::BoundaryConditionShPtr > & 
GetBndConditions ()
 
Array< OneD,
SpatialDomains::BoundaryConditionShPtr > & 
UpdateBndConditions ()
 
void EvaluateBoundaryConditions (const NekDouble time=0.0, const std::string varName="", const NekDouble=NekConstants::kNekUnsetDouble, const NekDouble=NekConstants::kNekUnsetDouble)
 
void GeneralMatrixOp (const GlobalMatrixKey &gkey, const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, CoeffState coeffstate=eLocal)
 This function calculates the result of the multiplication of a matrix of type specified by mkey with a vector given by inarray. More...
 
void GeneralMatrixOp_IterPerExp (const GlobalMatrixKey &gkey, const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 
void SetUpPhysNormals ()
 
void GetBoundaryToElmtMap (Array< OneD, int > &ElmtID, Array< OneD, int > &EdgeID)
 
void GetBndElmtExpansion (int i, boost::shared_ptr< ExpList > &result, const bool DeclareCoeffPhysArrays=true)
 
void ExtractElmtToBndPhys (int i, Array< OneD, NekDouble > &elmt, Array< OneD, NekDouble > &boundary)
 
void ExtractPhysToBndElmt (int i, const Array< OneD, const NekDouble > &phys, Array< OneD, NekDouble > &bndElmt)
 
void ExtractPhysToBnd (int i, const Array< OneD, const NekDouble > &phys, Array< OneD, NekDouble > &bnd)
 
void GetBoundaryNormals (int i, Array< OneD, Array< OneD, NekDouble > > &normals)
 
void GeneralGetFieldDefinitions (std::vector< LibUtilities::FieldDefinitionsSharedPtr > &fielddef, int NumHomoDir=0, Array< OneD, LibUtilities::BasisSharedPtr > &HomoBasis=LibUtilities::NullBasisSharedPtr1DArray, std::vector< NekDouble > &HomoLen=LibUtilities::NullNekDoubleVector, bool homoStrips=false, std::vector< unsigned int > &HomoSIDs=LibUtilities::NullUnsignedIntVector, std::vector< unsigned int > &HomoZIDs=LibUtilities::NullUnsignedIntVector, std::vector< unsigned int > &HomoYIDs=LibUtilities::NullUnsignedIntVector)
 
const
NekOptimize::GlobalOptParamSharedPtr
GetGlobalOptParam (void)
 
std::map< int,
RobinBCInfoSharedPtr
GetRobinBCInfo ()
 
void GetPeriodicEntities (PeriodicMap &periodicVerts, PeriodicMap &periodicEdges, PeriodicMap &periodicFaces=NullPeriodicMap)
 
std::vector
< LibUtilities::FieldDefinitionsSharedPtr
GetFieldDefinitions ()
 
void GetFieldDefinitions (std::vector< LibUtilities::FieldDefinitionsSharedPtr > &fielddef)
 
void AppendFieldData (LibUtilities::FieldDefinitionsSharedPtr &fielddef, std::vector< NekDouble > &fielddata)
 Append the element data listed in elements fielddef->m_ElementIDs onto fielddata. More...
 
void AppendFieldData (LibUtilities::FieldDefinitionsSharedPtr &fielddef, std::vector< NekDouble > &fielddata, Array< OneD, NekDouble > &coeffs)
 Append the data in coeffs listed in elements fielddef->m_ElementIDs onto fielddata. More...
 
void ExtractElmtDataToCoeffs (LibUtilities::FieldDefinitionsSharedPtr &fielddef, std::vector< NekDouble > &fielddata, std::string &field, Array< OneD, NekDouble > &coeffs)
 Extract the data in fielddata into the coeffs using the basic ExpList Elemental expansions rather than planes in homogeneous case. More...
 
void ExtractCoeffsToCoeffs (const boost::shared_ptr< ExpList > &fromExpList, const Array< OneD, const NekDouble > &fromCoeffs, Array< OneD, NekDouble > &toCoeffs)
 Extract the data from fromField using fromExpList the coeffs using the basic ExpList Elemental expansions rather than planes in homogeneous case. More...
 
void ExtractDataToCoeffs (LibUtilities::FieldDefinitionsSharedPtr &fielddef, std::vector< NekDouble > &fielddata, std::string &field, Array< OneD, NekDouble > &coeffs)
 Extract the data in fielddata into the coeffs. More...
 
boost::shared_ptr< ExpListGetSharedThisPtr ()
 Returns a shared pointer to the current object. More...
 
boost::shared_ptr
< LibUtilities::SessionReader
GetSession () const
 Returns the session object. More...
 
boost::shared_ptr
< LibUtilities::Comm
GetComm ()
 Returns the comm object. More...
 
SpatialDomains::MeshGraphSharedPtr GetGraph ()
 
LibUtilities::BasisSharedPtr GetHomogeneousBasis (void)
 
boost::shared_ptr< ExpList > & GetPlane (int n)
 
void CreateCollections (Collections::ImplementationType ImpType=Collections::eNoImpType)
 Construct collections of elements containing a single element type and polynomial order from the list of expansions. More...
 
void ClearGlobalLinSysManager (void)
 

Public Attributes

Array< OneD, int > m_BCtoElmMap
 
Array< OneD, int > m_BCtoFaceMap
 
- Public Attributes inherited from Nektar::MultiRegions::ExpList
ExpansionType m_expType
 

Protected Member Functions

void SetUpDG (const std::string="DefaultVar")
 Set up all DG member variables and maps. More...
 
bool SameTypeOfBoundaryConditions (const DisContField3D &In)
 
void GenerateBoundaryConditionExpansion (const SpatialDomains::MeshGraphSharedPtr &graph3D, const SpatialDomains::BoundaryConditions &bcs, const std::string &variable)
 
void FindPeriodicFaces (const SpatialDomains::BoundaryConditions &bcs, const std::string &variable)
 Determine the periodic faces, edges and vertices for the given graph. More...
 
bool IsLeftAdjacentFace (const int n, const int e)
 
virtual void v_GetFwdBwdTracePhys (Array< OneD, NekDouble > &Fwd, Array< OneD, NekDouble > &Bwd)
 This method extracts the "forward" and "backward" trace data from the array field and puts the data into output vectors Fwd and Bwd. More...
 
virtual void v_GetFwdBwdTracePhys (const Array< OneD, const NekDouble > &field, Array< OneD, NekDouble > &Fwd, Array< OneD, NekDouble > &Bwd)
 
virtual const std::vector< bool > & v_GetLeftAdjacentFaces (void) const
 
virtual void v_ExtractTracePhys (Array< OneD, NekDouble > &outarray)
 
virtual void v_ExtractTracePhys (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 
virtual void v_AddTraceIntegral (const Array< OneD, const NekDouble > &Fn, Array< OneD, NekDouble > &outarray)
 Add trace contributions into elemental coefficient spaces. More...
 
virtual void v_AddFwdBwdTraceIntegral (const Array< OneD, const NekDouble > &Fwd, const Array< OneD, const NekDouble > &Bwd, Array< OneD, NekDouble > &outarray)
 Add trace contributions into elemental coefficient spaces. More...
 
virtual void v_HelmSolve (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, const FlagList &flags, const StdRegions::ConstFactorMap &factors, const StdRegions::VarCoeffMap &varcoeff, const Array< OneD, const NekDouble > &dirForcing, const bool PhysSpaceForcing)
 
virtual void v_GeneralMatrixOp (const GlobalMatrixKey &gkey, const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, CoeffState coeffstate=eLocal)
 Calculates the result of the multiplication of a global matrix of type specified by mkey with a vector given by inarray. More...
 
virtual void v_GetBoundaryToElmtMap (Array< OneD, int > &ElmtID, Array< OneD, int > &FaceID)
 Set up a list of elemeent IDs and edge IDs that link to the boundary conditions. More...
 
virtual void v_GetBndElmtExpansion (int i, boost::shared_ptr< ExpList > &result, const bool DeclareCoeffPhysArrays)
 
virtual void v_Reset ()
 Reset this field, so that geometry information can be updated. More...
 
virtual void v_GetPeriodicEntities (PeriodicMap &periodicVerts, PeriodicMap &periodicEdges, PeriodicMap &periodicFaces)
 
virtual ExpListSharedPtrv_GetTrace ()
 
virtual AssemblyMapDGSharedPtrv_GetTraceMap ()
 
virtual const Array< OneD,
const
MultiRegions::ExpListSharedPtr > & 
v_GetBndCondExpansions ()
 
virtual const Array< OneD,
const
SpatialDomains::BoundaryConditionShPtr > & 
v_GetBndConditions ()
 
virtual
MultiRegions::ExpListSharedPtr
v_UpdateBndCondExpansion (int i)
 
virtual Array< OneD,
SpatialDomains::BoundaryConditionShPtr > & 
v_UpdateBndConditions ()
 
virtual void v_EvaluateBoundaryConditions (const NekDouble time=0.0, const std::string varName="", const NekDouble x2_in=NekConstants::kNekUnsetDouble, const NekDouble x3_in=NekConstants::kNekUnsetDouble)
 This function evaluates the boundary conditions at a certain time-level. More...
 
virtual std::map< int,
RobinBCInfoSharedPtr
v_GetRobinBCInfo ()
 
- Protected Member Functions inherited from Nektar::MultiRegions::ExpList3D
virtual void v_SetUpPhysNormals ()
 Set up the normals on each expansion. More...
 
- Protected Member Functions inherited from Nektar::MultiRegions::ExpList
void SetCoeffPhysOffsets ()
 Definition of the total number of degrees of freedom and quadrature points and offsets to access data. More...
 
boost::shared_ptr< DNekMatGenGlobalMatrixFull (const GlobalLinSysKey &mkey, const boost::shared_ptr< AssemblyMapCG > &locToGloMap)
 
const DNekScalBlkMatSharedPtr GenBlockMatrix (const GlobalMatrixKey &gkey)
 This function assembles the block diagonal matrix of local matrices of the type mtype. More...
 
const DNekScalBlkMatSharedPtrGetBlockMatrix (const GlobalMatrixKey &gkey)
 
void MultiplyByBlockMatrix (const GlobalMatrixKey &gkey, const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 
boost::shared_ptr< GlobalMatrixGenGlobalMatrix (const GlobalMatrixKey &mkey, const boost::shared_ptr< AssemblyMapCG > &locToGloMap)
 Generates a global matrix from the given key and map. More...
 
void GlobalEigenSystem (const boost::shared_ptr< DNekMat > &Gmat, Array< OneD, NekDouble > &EigValsReal, Array< OneD, NekDouble > &EigValsImag, Array< OneD, NekDouble > &EigVecs=NullNekDouble1DArray)
 
boost::shared_ptr< GlobalLinSysGenGlobalLinSys (const GlobalLinSysKey &mkey, const boost::shared_ptr< AssemblyMapCG > &locToGloMap)
 This operation constructs the global linear system of type mkey. More...
 
boost::shared_ptr< GlobalLinSysGenGlobalBndLinSys (const GlobalLinSysKey &mkey, const AssemblyMapSharedPtr &locToGloMap)
 Generate a GlobalLinSys from information provided by the key "mkey" and the mapping provided in LocToGloBaseMap. More...
 
void ReadGlobalOptimizationParameters ()
 
virtual int v_GetNumElmts (void)
 
virtual void v_Upwind (const Array< OneD, const Array< OneD, NekDouble > > &Vec, const Array< OneD, const NekDouble > &Fwd, const Array< OneD, const NekDouble > &Bwd, Array< OneD, NekDouble > &Upwind)
 
virtual void v_Upwind (const Array< OneD, const NekDouble > &Vn, const Array< OneD, const NekDouble > &Fwd, const Array< OneD, const NekDouble > &Bwd, Array< OneD, NekDouble > &Upwind)
 
virtual const Array< OneD,
const int > & 
v_GetTraceBndMap ()
 
virtual void v_GetNormals (Array< OneD, Array< OneD, NekDouble > > &normals)
 
virtual void v_AddTraceIntegral (const Array< OneD, const NekDouble > &Fx, const Array< OneD, const NekDouble > &Fy, Array< OneD, NekDouble > &outarray)
 
virtual void v_MultiplyByInvMassMatrix (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, CoeffState coeffstate)
 
virtual void v_LinearAdvectionDiffusionReactionSolve (const Array< OneD, Array< OneD, NekDouble > > &velocity, const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, const NekDouble lambda, CoeffState coeffstate=eLocal, const Array< OneD, const NekDouble > &dirForcing=NullNekDouble1DArray)
 
virtual void v_LinearAdvectionReactionSolve (const Array< OneD, Array< OneD, NekDouble > > &velocity, const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, const NekDouble lambda, CoeffState coeffstate=eLocal, const Array< OneD, const NekDouble > &dirForcing=NullNekDouble1DArray)
 
virtual void v_ImposeDirichletConditions (Array< OneD, NekDouble > &outarray)
 
virtual void v_FillBndCondFromField ()
 
virtual void v_FillBndCondFromField (const int nreg)
 
virtual void v_LocalToGlobal (bool UseComm)
 
virtual void v_LocalToGlobal (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, bool UseComm)
 
virtual void v_GlobalToLocal (void)
 
virtual void v_GlobalToLocal (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 
virtual void v_BwdTrans (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, CoeffState coeffstate)
 
virtual void v_BwdTrans_IterPerExp (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 
virtual void v_FwdTrans (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, CoeffState coeffstate)
 
virtual void v_FwdTrans_IterPerExp (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 
virtual void v_SmoothField (Array< OneD, NekDouble > &field)
 
virtual void v_IProductWRTBase (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, CoeffState coeffstate)
 
virtual void v_IProductWRTBase_IterPerExp (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray)
 
virtual void v_GetCoords (Array< OneD, NekDouble > &coord_0, Array< OneD, NekDouble > &coord_1, Array< OneD, NekDouble > &coord_2=NullNekDouble1DArray)
 
virtual void v_PhysDeriv (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &out_d0, Array< OneD, NekDouble > &out_d1, Array< OneD, NekDouble > &out_d2)
 
virtual void v_PhysDeriv (const int dir, const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &out_d)
 
virtual void v_PhysDeriv (Direction edir, const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &out_d)
 
virtual void v_CurlCurl (Array< OneD, Array< OneD, NekDouble > > &Vel, Array< OneD, Array< OneD, NekDouble > > &Q)
 
virtual void v_HomogeneousFwdTrans (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, CoeffState coeffstate=eLocal, bool Shuff=true, bool UnShuff=true)
 
virtual void v_HomogeneousBwdTrans (const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, CoeffState coeffstate=eLocal, bool Shuff=true, bool UnShuff=true)
 
virtual void v_DealiasedProd (const Array< OneD, NekDouble > &inarray1, const Array< OneD, NekDouble > &inarray2, Array< OneD, NekDouble > &outarray, CoeffState coeffstate=eLocal)
 
virtual void v_DealiasedDotProd (const Array< OneD, Array< OneD, NekDouble > > &inarray1, const Array< OneD, Array< OneD, NekDouble > > &inarray2, Array< OneD, Array< OneD, NekDouble > > &outarray, CoeffState coeffstate=eLocal)
 
virtual void v_GetBCValues (Array< OneD, NekDouble > &BndVals, const Array< OneD, NekDouble > &TotField, int BndID)
 
virtual void v_NormVectorIProductWRTBase (Array< OneD, const NekDouble > &V1, Array< OneD, const NekDouble > &V2, Array< OneD, NekDouble > &outarray, int BndID)
 
virtual void v_NormVectorIProductWRTBase (Array< OneD, Array< OneD, NekDouble > > &V, Array< OneD, NekDouble > &outarray)
 
virtual void v_ExtractElmtToBndPhys (int i, Array< OneD, NekDouble > &elmt, Array< OneD, NekDouble > &boundary)
 
virtual void v_ExtractPhysToBndElmt (int i, const Array< OneD, const NekDouble > &phys, Array< OneD, NekDouble > &bndElmt)
 
virtual void v_ExtractPhysToBnd (int i, const Array< OneD, const NekDouble > &phys, Array< OneD, NekDouble > &bnd)
 
virtual void v_GetBoundaryNormals (int i, Array< OneD, Array< OneD, NekDouble > > &normals)
 
virtual std::vector
< LibUtilities::FieldDefinitionsSharedPtr
v_GetFieldDefinitions (void)
 
virtual void v_GetFieldDefinitions (std::vector< LibUtilities::FieldDefinitionsSharedPtr > &fielddef)
 
virtual void v_AppendFieldData (LibUtilities::FieldDefinitionsSharedPtr &fielddef, std::vector< NekDouble > &fielddata)
 
virtual void v_AppendFieldData (LibUtilities::FieldDefinitionsSharedPtr &fielddef, std::vector< NekDouble > &fielddata, Array< OneD, NekDouble > &coeffs)
 
virtual void v_ExtractDataToCoeffs (LibUtilities::FieldDefinitionsSharedPtr &fielddef, std::vector< NekDouble > &fielddata, std::string &field, Array< OneD, NekDouble > &coeffs)
 Extract data from raw field data into expansion list. More...
 
virtual void v_ExtractCoeffsToCoeffs (const boost::shared_ptr< ExpList > &fromExpList, const Array< OneD, const NekDouble > &fromCoeffs, Array< OneD, NekDouble > &toCoeffs)
 
virtual void v_WriteTecplotHeader (std::ostream &outfile, std::string var="")
 
virtual void v_WriteTecplotZone (std::ostream &outfile, int expansion)
 
virtual void v_WriteTecplotField (std::ostream &outfile, int expansion)
 
virtual void v_WriteTecplotConnectivity (std::ostream &outfile, int expansion)
 
virtual void v_WriteVtkPieceData (std::ostream &outfile, int expansion, std::string var)
 
virtual NekDouble v_L2 (const Array< OneD, const NekDouble > &phys, const Array< OneD, const NekDouble > &soln=NullNekDouble1DArray)
 
virtual NekDouble v_Integral (const Array< OneD, const NekDouble > &inarray)
 
virtual Array< OneD, const
NekDouble
v_HomogeneousEnergy (void)
 
virtual
LibUtilities::TranspositionSharedPtr 
v_GetTransposition (void)
 
virtual NekDouble v_GetHomoLen (void)
 
virtual Array< OneD, const
unsigned int > 
v_GetZIDs (void)
 
virtual Array< OneD, const
unsigned int > 
v_GetYIDs (void)
 
virtual void v_ClearGlobalLinSysManager (void)
 
void ExtractFileBCs (const std::string &fileName, LibUtilities::CommSharedPtr comm, const std::string &varName, const boost::shared_ptr< ExpList > locExpList)
 

Protected Attributes

Array< OneD,
MultiRegions::ExpListSharedPtr
m_bndCondExpansions
 An object which contains the discretised boundary conditions. More...
 
Array< OneD,
SpatialDomains::BoundaryConditionShPtr
m_bndConditions
 An array which contains the information about the boundary condition on the different boundary regions. More...
 
GlobalLinSysMapShPtr m_globalBndMat
 
ExpListSharedPtr m_trace
 
AssemblyMapDGSharedPtr m_traceMap
 
LocTraceToTraceMapSharedPtr m_locTraceToTraceMap
 Map of local trace (the points at the face of the element) to the trace space discretisation. More...
 
std::set< int > m_boundaryFaces
 A set storing the global IDs of any boundary faces. More...
 
PeriodicMap m_periodicFaces
 A map which identifies pairs of periodic faces. More...
 
PeriodicMap m_periodicEdges
 A map which identifies groups of periodic edges. More...
 
PeriodicMap m_periodicVerts
 A map which identifies groups of periodic vertices. More...
 
std::vector< bool > m_leftAdjacentFaces
 
std::vector< int > m_periodicFwdCopy
 A vector indicating degress of freedom which need to be copied from forwards to backwards space in case of a periodic boundary condition. More...
 
std::vector< int > m_periodicBwdCopy
 
- Protected Attributes inherited from Nektar::MultiRegions::ExpList
LibUtilities::CommSharedPtr m_comm
 Communicator. More...
 
LibUtilities::SessionReaderSharedPtr m_session
 Session. More...
 
SpatialDomains::MeshGraphSharedPtr m_graph
 Mesh associated with this expansion list. More...
 
int m_ncoeffs
 The total number of local degrees of freedom. m_ncoeffs $=N_{\mathrm{eof}}=\sum_{e=1}^{{N_{\mathrm{el}}}}N^{e}_l$. More...
 
int m_npoints
 
Array< OneD, NekDoublem_coeffs
 Concatenation of all local expansion coefficients. More...
 
Array< OneD, NekDoublem_phys
 The global expansion evaluated at the quadrature points. More...
 
bool m_physState
 The state of the array m_phys. More...
 
boost::shared_ptr
< LocalRegions::ExpansionVector
m_exp
 The list of local expansions. More...
 
Collections::CollectionVector m_collections
 
std::vector< int > m_coll_coeff_offset
 Offset of elemental data into the array m_coeffs. More...
 
std::vector< int > m_coll_phys_offset
 Offset of elemental data into the array m_phys. More...
 
Array< OneD, int > m_coeff_offset
 Offset of elemental data into the array m_coeffs. More...
 
Array< OneD, int > m_phys_offset
 Offset of elemental data into the array m_phys. More...
 
NekOptimize::GlobalOptParamSharedPtr m_globalOptParam
 
BlockMatrixMapShPtr m_blockMat
 
bool m_WaveSpace
 
boost::unordered_map< int, int > m_elmtToExpId
 Mapping from geometry ID of element to index inside m_exp. More...
 

Additional Inherited Members

- Static Protected Member Functions inherited from Nektar::MultiRegions::ExpList
static
SpatialDomains::BoundaryConditionShPtr 
GetBoundaryCondition (const SpatialDomains::BoundaryConditionCollection &collection, unsigned int index, const std::string &variable)
 

Detailed Description

Abstraction of a global discontinuous three-dimensional spectral/hp element expansion which approximates the solution of a set of partial differential equations.

Definition at line 55 of file DisContField3D.h.

Constructor & Destructor Documentation

Nektar::MultiRegions::DisContField3D::DisContField3D ( )

Default constructor.

Definition at line 66 of file DisContField3D.cpp.

66  :
67  ExpList3D (),
69  m_bndConditions (),
71  {
72  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_bndCondExpansions
An object which contains the discretised boundary conditions.
static ExpListSharedPtr NullExpListSharedPtr
Definition: ExpList.h:1477
Array< OneD, SpatialDomains::BoundaryConditionShPtr > m_bndConditions
An array which contains the information about the boundary condition on the different boundary region...
ExpList3D()
Default constructor.
Definition: ExpList3D.cpp:54
Nektar::MultiRegions::DisContField3D::DisContField3D ( const LibUtilities::SessionReaderSharedPtr pSession,
const SpatialDomains::MeshGraphSharedPtr graph3D,
const std::string &  variable,
const bool  SetUpJustDG = true,
const Collections::ImplementationType  ImpType = Collections::eNoImpType 
)

Constructs a global discontinuous field based on an input mesh with boundary conditions.

Definition at line 78 of file DisContField3D.cpp.

References Nektar::MultiRegions::ExpList::EvaluateBoundaryConditions(), FindPeriodicFaces(), GenerateBoundaryConditionExpansion(), Nektar::MultiRegions::ExpList::GetBoundaryToElmtMap(), m_bndCondExpansions, Nektar::MultiRegions::ExpList::m_session, and SetUpDG().

83  :
84  ExpList3D (pSession, graph3D, variable, ImpType),
86  m_bndConditions (),
88  {
89  // do not set up BCs if default variable
90  if (variable.compare("DefaultVar") != 0)
91  {
92  SpatialDomains::BoundaryConditions bcs(m_session, graph3D);
93 
94  GenerateBoundaryConditionExpansion(graph3D,bcs,variable);
95  EvaluateBoundaryConditions(0.0, variable);
96 
97  // Find periodic edges for this variable.
98  FindPeriodicFaces(bcs, variable);
99  }
100 
101  if(SetUpJustDG)
102  {
103  SetUpDG();
104  }
105  else
106  {
107  // Set element edges to point to Robin BC edges if required.
108  int i, cnt, f;
109  Array<OneD, int> ElmtID, FaceID;
110  GetBoundaryToElmtMap(ElmtID, FaceID);
111 
112  for(cnt = i = 0; i < m_bndCondExpansions.num_elements(); ++i)
113  {
115  locExpList = m_bndCondExpansions[i];
116 
117  for(f = 0; f < locExpList->GetExpSize(); ++f)
118  {
120  = (*m_exp)[ElmtID[cnt+f]]->
121  as<LocalRegions::Expansion3D>();
123  = locExpList->GetExp(f)->
124  as<LocalRegions::Expansion2D>();
125 
126  exp3d->SetFaceExp(FaceID[cnt+f],exp2d);
127  exp2d->SetAdjacentElementExp(FaceID[cnt+f],exp3d);
128  }
129  cnt += m_bndCondExpansions[i]->GetExpSize();
130  }
131  }
132  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_bndCondExpansions
An object which contains the discretised boundary conditions.
static ExpListSharedPtr NullExpListSharedPtr
Definition: ExpList.h:1477
void EvaluateBoundaryConditions(const NekDouble time=0.0, const std::string varName="", const NekDouble=NekConstants::kNekUnsetDouble, const NekDouble=NekConstants::kNekUnsetDouble)
Definition: ExpList.h:2233
void GetBoundaryToElmtMap(Array< OneD, int > &ElmtID, Array< OneD, int > &EdgeID)
Definition: ExpList.h:2286
void FindPeriodicFaces(const SpatialDomains::BoundaryConditions &bcs, const std::string &variable)
Determine the periodic faces, edges and vertices for the given graph.
boost::shared_ptr< Expansion3D > Expansion3DSharedPtr
Definition: Expansion2D.h:48
boost::shared_ptr< ExpList > ExpListSharedPtr
Shared pointer to an ExpList object.
void GenerateBoundaryConditionExpansion(const SpatialDomains::MeshGraphSharedPtr &graph3D, const SpatialDomains::BoundaryConditions &bcs, const std::string &variable)
LibUtilities::SessionReaderSharedPtr m_session
Session.
Definition: ExpList.h:969
void SetUpDG(const std::string="DefaultVar")
Set up all DG member variables and maps.
Array< OneD, SpatialDomains::BoundaryConditionShPtr > m_bndConditions
An array which contains the information about the boundary condition on the different boundary region...
ExpList3D()
Default constructor.
Definition: ExpList3D.cpp:54
boost::shared_ptr< Expansion2D > Expansion2DSharedPtr
Definition: Expansion1D.h:49
Nektar::MultiRegions::DisContField3D::DisContField3D ( const DisContField3D In,
const SpatialDomains::MeshGraphSharedPtr graph3D,
const std::string &  variable,
const bool  SetUpJustDG = false 
)

Definition at line 138 of file DisContField3D.cpp.

References Nektar::MultiRegions::ExpList::ApplyGeomInfo(), Nektar::MultiRegions::ExpList::EvaluateBoundaryConditions(), FindPeriodicFaces(), GenerateBoundaryConditionExpansion(), Nektar::MultiRegions::ExpList::GetBoundaryToElmtMap(), m_bndCondExpansions, m_globalBndMat, m_locTraceToTraceMap, m_periodicEdges, m_periodicFaces, m_periodicVerts, Nektar::MultiRegions::ExpList::m_session, m_trace, m_traceMap, SameTypeOfBoundaryConditions(), SetUpDG(), and Nektar::MultiRegions::ExpList::SetUpPhysNormals().

143  : ExpList3D(In),
145  {
146  SpatialDomains::BoundaryConditions bcs(m_session, graph3D);
147 
148  GenerateBoundaryConditionExpansion(graph3D,bcs,variable);
149  EvaluateBoundaryConditions(0.0, variable);
150  ApplyGeomInfo();
151 
153  {
154  // Find periodic edges for this variable.
155  FindPeriodicFaces(bcs, variable);
156 
157  if (SetUpJustDG)
158  {
159  SetUpDG(variable);
160  }
161  else
162  {
163  int i,cnt,f;
164  Array<OneD, int> ElmtID,FaceID;
165  GetBoundaryToElmtMap(ElmtID,FaceID);
166 
167  for(cnt = i = 0; i < m_bndCondExpansions.num_elements(); ++i)
168  {
170  locExpList = m_bndCondExpansions[i];
171 
172  for(f = 0; f < locExpList->GetExpSize(); ++f)
173  {
175  = (*m_exp)[ElmtID[cnt+f]]->
176  as<LocalRegions::Expansion3D>();
178  = locExpList->GetExp(f)->
179  as<LocalRegions::Expansion2D>();
180 
181  exp3d->SetFaceExp(FaceID[cnt+f],exp2d);
182  exp2d->SetAdjacentElementExp(FaceID[cnt+f],exp3d);
183  }
184 
185  cnt += m_bndCondExpansions[i]->GetExpSize();
186  }
188  }
189 
190  }
191  //else if we have the same boundary condition
192  else
193  {
194  m_globalBndMat = In.m_globalBndMat;
195  m_trace = In.m_trace;
196  m_traceMap = In.m_traceMap;
197  m_locTraceToTraceMap = In.m_locTraceToTraceMap;
198  m_periodicVerts = In.m_periodicVerts;
199  m_periodicEdges = In.m_periodicEdges;
200  m_periodicFaces = In.m_periodicFaces;
201 
202  if(SetUpJustDG)
203  {
204  }
205  else
206  {
207  int i,cnt,f;
208  Array<OneD, int> ElmtID,FaceID;
209  GetBoundaryToElmtMap(ElmtID,FaceID);
210 
211  for (cnt = i = 0;
212  i < m_bndCondExpansions.num_elements(); ++i)
213  {
215  locExpList = m_bndCondExpansions[i];
216 
217  for(f = 0; f < locExpList->GetExpSize(); ++f)
218  {
220  = (*m_exp)[ElmtID[cnt+f]]->
221  as<LocalRegions::Expansion3D>();
223  = locExpList->GetExp(f)->
224  as<LocalRegions::Expansion2D>();
225 
226  exp3d->SetFaceExp(FaceID[cnt+f], exp2d);
227  exp2d->SetAdjacentElementExp(FaceID[cnt+f], exp3d);
228  }
229 
230  cnt += m_bndCondExpansions[i]->GetExpSize();
231  }
232 
233  if (m_session->DefinesSolverInfo("PROJECTION"))
234  {
235  std::string ProjectStr =
236  m_session->GetSolverInfo("PROJECTION");
237  if (ProjectStr == "MixedCGDG" ||
238  ProjectStr == "Mixed_CG_Discontinuous")
239  {
240  SetUpDG(variable);
241  }
242  else
243  {
245  }
246  }
247  else
248  {
250  }
251  }
252  }
253  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_bndCondExpansions
An object which contains the discretised boundary conditions.
static ExpListSharedPtr NullExpListSharedPtr
Definition: ExpList.h:1477
void EvaluateBoundaryConditions(const NekDouble time=0.0, const std::string varName="", const NekDouble=NekConstants::kNekUnsetDouble, const NekDouble=NekConstants::kNekUnsetDouble)
Definition: ExpList.h:2233
PeriodicMap m_periodicFaces
A map which identifies pairs of periodic faces.
void GetBoundaryToElmtMap(Array< OneD, int > &ElmtID, Array< OneD, int > &EdgeID)
Definition: ExpList.h:2286
void ApplyGeomInfo()
Apply geometry information to each expansion.
Definition: ExpList.cpp:1524
void FindPeriodicFaces(const SpatialDomains::BoundaryConditions &bcs, const std::string &variable)
Determine the periodic faces, edges and vertices for the given graph.
boost::shared_ptr< Expansion3D > Expansion3DSharedPtr
Definition: Expansion2D.h:48
LocTraceToTraceMapSharedPtr m_locTraceToTraceMap
Map of local trace (the points at the face of the element) to the trace space discretisation.
boost::shared_ptr< ExpList > ExpListSharedPtr
Shared pointer to an ExpList object.
void GenerateBoundaryConditionExpansion(const SpatialDomains::MeshGraphSharedPtr &graph3D, const SpatialDomains::BoundaryConditions &bcs, const std::string &variable)
LibUtilities::SessionReaderSharedPtr m_session
Session.
Definition: ExpList.h:969
void SetUpDG(const std::string="DefaultVar")
Set up all DG member variables and maps.
bool SameTypeOfBoundaryConditions(const DisContField3D &In)
PeriodicMap m_periodicVerts
A map which identifies groups of periodic vertices.
ExpList3D()
Default constructor.
Definition: ExpList3D.cpp:54
PeriodicMap m_periodicEdges
A map which identifies groups of periodic edges.
boost::shared_ptr< Expansion2D > Expansion2DSharedPtr
Definition: Expansion1D.h:49
Nektar::MultiRegions::DisContField3D::DisContField3D ( const DisContField3D In)

Constructs a global discontinuous field based on another discontinuous field.

Definition at line 258 of file DisContField3D.cpp.

258  :
259  ExpList3D(In),
260  m_bndCondExpansions (In.m_bndCondExpansions),
261  m_bndConditions (In.m_bndConditions),
262  m_globalBndMat (In.m_globalBndMat),
263  m_trace (In.m_trace),
264  m_traceMap (In.m_traceMap),
265  m_locTraceToTraceMap (In.m_locTraceToTraceMap),
266  m_periodicFaces (In.m_periodicFaces),
267  m_periodicEdges (In.m_periodicEdges),
268  m_periodicVerts (In.m_periodicVerts)
269  {
270  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_bndCondExpansions
An object which contains the discretised boundary conditions.
PeriodicMap m_periodicFaces
A map which identifies pairs of periodic faces.
LocTraceToTraceMapSharedPtr m_locTraceToTraceMap
Map of local trace (the points at the face of the element) to the trace space discretisation.
PeriodicMap m_periodicVerts
A map which identifies groups of periodic vertices.
Array< OneD, SpatialDomains::BoundaryConditionShPtr > m_bndConditions
An array which contains the information about the boundary condition on the different boundary region...
ExpList3D()
Default constructor.
Definition: ExpList3D.cpp:54
PeriodicMap m_periodicEdges
A map which identifies groups of periodic edges.
Nektar::MultiRegions::DisContField3D::~DisContField3D ( )
virtual

Destructor.

Definition at line 275 of file DisContField3D.cpp.

276  {
277  }

Member Function Documentation

void Nektar::MultiRegions::DisContField3D::EvaluateHDGPostProcessing ( Array< OneD, NekDouble > &  outarray)

Evaluate HDG post-processing to increase polynomial order of solution.

This function takes the solution (assumed to be one order lower) in physical space, and postprocesses at the current polynomial order by solving the system:

\[ \begin{aligned} (\nabla w, \nabla u^*) &= (\nabla w, u), \\ \langle \nabla u^*, 1 \rangle &= \langle \nabla u, 1 \rangle \end{aligned} \]

where $ u $ corresponds with the current solution as stored inside m_coeffs.

Parameters
outarrayThe resulting field $ u^* $.

Definition at line 2270 of file DisContField3D.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, Nektar::LibUtilities::eGaussLobattoLegendre, Nektar::LibUtilities::eGaussRadauMAlpha1Beta0, Nektar::LibUtilities::eGaussRadauMAlpha2Beta0, Nektar::LibUtilities::eHexahedron, Nektar::StdRegions::eInvLaplacianWithUnityMean, Nektar::LibUtilities::eOrtho_A, Nektar::LibUtilities::eOrtho_B, Nektar::LibUtilities::eOrtho_C, Nektar::LibUtilities::ePrism, Nektar::LibUtilities::eTetrahedron, Nektar::eWrapper, Nektar::MultiRegions::ExpList::GetExpSize(), Nektar::NekVector< DataType >::GetPtr(), Nektar::StdRegions::StdExpansion::GetTotPoints(), Nektar::MultiRegions::ExpList::m_coeff_offset, Nektar::MultiRegions::ExpList::m_coeffs, m_trace, m_traceMap, Vmath::Vadd(), and Vmath::Vcopy().

2272  {
2273  int i,cnt,f,ncoeff_face;
2274  Array<OneD, NekDouble> force, out_tmp,qrhs,qrhs1;
2275  Array<OneD, Array< OneD, LocalRegions::ExpansionSharedPtr> >
2276  &elmtToTrace = m_traceMap->GetElmtToTrace();
2277 
2278  int nq_elmt, nm_elmt;
2279  int LocBndCoeffs = m_traceMap->GetNumLocalBndCoeffs();
2280  Array<OneD, NekDouble> loc_lambda(LocBndCoeffs), face_lambda;
2281  Array<OneD, NekDouble> tmp_coeffs;
2282  m_traceMap->GlobalToLocalBnd(m_trace->GetCoeffs(),loc_lambda);
2283 
2284  face_lambda = loc_lambda;
2285 
2286  // Calculate Q using standard DG formulation.
2287  for(i = cnt = 0; i < GetExpSize(); ++i)
2288  {
2290  (*m_exp)[i]->as<LocalRegions::Expansion3D>();
2291 
2292  nq_elmt = (*m_exp)[i]->GetTotPoints();
2293  nm_elmt = (*m_exp)[i]->GetNcoeffs();
2294  qrhs = Array<OneD, NekDouble>(nq_elmt);
2295  qrhs1 = Array<OneD, NekDouble>(nq_elmt);
2296  force = Array<OneD, NekDouble>(2*nm_elmt);
2297  out_tmp = force + nm_elmt;
2299 
2300  int num_points0 = (*m_exp)[i]->GetBasis(0)->GetNumPoints();
2301  int num_points1 = (*m_exp)[i]->GetBasis(1)->GetNumPoints();
2302  int num_points2 = (*m_exp)[i]->GetBasis(2)->GetNumPoints();
2303  int num_modes0 = (*m_exp)[i]->GetBasis(0)->GetNumModes();
2304  int num_modes1 = (*m_exp)[i]->GetBasis(1)->GetNumModes();
2305  int num_modes2 = (*m_exp)[i]->GetBasis(2)->GetNumModes();
2306 
2307  // Probably a better way of setting up lambda than this. Note
2308  // cannot use PutCoeffsInToElmts since lambda space is mapped
2309  // during the solve.
2310  int nFaces = (*m_exp)[i]->GetNfaces();
2311  Array<OneD, Array<OneD, NekDouble> > faceCoeffs(nFaces);
2312  for(f = 0; f < nFaces; ++f)
2313  {
2314  ncoeff_face = elmtToTrace[i][f]->GetNcoeffs();
2315  faceCoeffs[f] = Array<OneD, NekDouble>(ncoeff_face);
2316  Vmath::Vcopy(ncoeff_face, face_lambda, 1, faceCoeffs[f], 1);
2317  exp->SetFaceToGeomOrientation(f, faceCoeffs[f]);
2318  face_lambda = face_lambda + ncoeff_face;
2319  }
2320 
2321  //creating orthogonal expansion (checking if we have quads or triangles)
2322  LibUtilities::ShapeType shape = (*m_exp)[i]->DetShapeType();
2323  switch(shape)
2324  {
2326  {
2327  const LibUtilities::PointsKey PkeyH1(num_points0,LibUtilities::eGaussLobattoLegendre);
2328  const LibUtilities::PointsKey PkeyH2(num_points1,LibUtilities::eGaussLobattoLegendre);
2329  const LibUtilities::PointsKey PkeyH3(num_points2,LibUtilities::eGaussLobattoLegendre);
2330  LibUtilities::BasisKey BkeyH1(LibUtilities::eOrtho_A, num_modes0, PkeyH1);
2331  LibUtilities::BasisKey BkeyH2(LibUtilities::eOrtho_A, num_modes1, PkeyH2);
2332  LibUtilities::BasisKey BkeyH3(LibUtilities::eOrtho_A, num_modes2, PkeyH3);
2333  SpatialDomains::HexGeomSharedPtr hGeom = boost::dynamic_pointer_cast<SpatialDomains::HexGeom>((*m_exp)[i]->GetGeom());
2334  ppExp = MemoryManager<LocalRegions::HexExp>::AllocateSharedPtr(BkeyH1, BkeyH2, BkeyH3, hGeom);
2335  }
2336  break;
2338  {
2339  const LibUtilities::PointsKey PkeyT1(num_points0,LibUtilities::eGaussLobattoLegendre);
2340  const LibUtilities::PointsKey PkeyT2(num_points1,LibUtilities::eGaussRadauMAlpha1Beta0);
2341  const LibUtilities::PointsKey PkeyT3(num_points2,LibUtilities::eGaussRadauMAlpha2Beta0);
2342  LibUtilities::BasisKey BkeyT1(LibUtilities::eOrtho_A, num_modes0, PkeyT1);
2343  LibUtilities::BasisKey BkeyT2(LibUtilities::eOrtho_B, num_modes1, PkeyT2);
2344  LibUtilities::BasisKey BkeyT3(LibUtilities::eOrtho_C, num_modes2, PkeyT3);
2345  SpatialDomains::TetGeomSharedPtr tGeom = boost::dynamic_pointer_cast<SpatialDomains::TetGeom>((*m_exp)[i]->GetGeom());
2346  ppExp = MemoryManager<LocalRegions::TetExp>::AllocateSharedPtr(BkeyT1, BkeyT2, BkeyT3, tGeom);
2347  }
2348  break;
2349  case LibUtilities::ePrism:
2350  {
2351  const LibUtilities::PointsKey PkeyP1(num_points0,LibUtilities::eGaussLobattoLegendre);
2352  const LibUtilities::PointsKey PkeyP2(num_points1,LibUtilities::eGaussLobattoLegendre);
2353  const LibUtilities::PointsKey PkeyP3(num_points2,LibUtilities::eGaussRadauMAlpha1Beta0);
2354  LibUtilities::BasisKey BkeyP1(LibUtilities::eOrtho_A, num_modes0, PkeyP1);
2355  LibUtilities::BasisKey BkeyP2(LibUtilities::eOrtho_A, num_modes1, PkeyP2);
2356  LibUtilities::BasisKey BkeyP3(LibUtilities::eOrtho_B, num_modes2, PkeyP3);
2357  SpatialDomains::PrismGeomSharedPtr pGeom = boost::dynamic_pointer_cast<SpatialDomains::PrismGeom>((*m_exp)[i]->GetGeom());
2358  ppExp = MemoryManager<LocalRegions::PrismExp>::AllocateSharedPtr(BkeyP1, BkeyP2, BkeyP3, pGeom);
2359  }
2360  break;
2361  default:
2362  ASSERTL0(false, "Wrong shape type, HDG postprocessing is not implemented");
2363  };
2364 
2365 
2366  //DGDeriv
2367  // (d/dx w, q_0)
2368  (*m_exp)[i]->DGDeriv(
2369  0,tmp_coeffs = m_coeffs + m_coeff_offset[i],
2370  elmtToTrace[i], faceCoeffs, out_tmp);
2371  (*m_exp)[i]->BwdTrans(out_tmp,qrhs);
2372  ppExp->IProductWRTDerivBase(0,qrhs,force);
2373 
2374 
2375  // + (d/dy w, q_1)
2376  (*m_exp)[i]->DGDeriv(
2377  1,tmp_coeffs = m_coeffs + m_coeff_offset[i],
2378  elmtToTrace[i], faceCoeffs, out_tmp);
2379  (*m_exp)[i]->BwdTrans(out_tmp,qrhs);
2380  ppExp->IProductWRTDerivBase(1,qrhs,out_tmp);
2381 
2382  Vmath::Vadd(nm_elmt,force,1,out_tmp,1,force,1);
2383 
2384  // + (d/dz w, q_2)
2385  (*m_exp)[i]->DGDeriv(
2386  2,tmp_coeffs = m_coeffs + m_coeff_offset[i],
2387  elmtToTrace[i], faceCoeffs, out_tmp);
2388  (*m_exp)[i]->BwdTrans(out_tmp,qrhs);
2389  ppExp->IProductWRTDerivBase(2,qrhs,out_tmp);
2390 
2391  Vmath::Vadd(nm_elmt,force,1,out_tmp,1,force,1);
2392  // determine force[0] = (1,u)
2393  (*m_exp)[i]->BwdTrans(
2394  tmp_coeffs = m_coeffs + m_coeff_offset[i],qrhs);
2395  force[0] = (*m_exp)[i]->Integral(qrhs);
2396 
2397  // multiply by inverse Laplacian matrix
2398  // get matrix inverse
2399  LocalRegions::MatrixKey lapkey(StdRegions::eInvLaplacianWithUnityMean, ppExp->DetShapeType(), *ppExp);
2400  DNekScalMatSharedPtr lapsys = ppExp->GetLocMatrix(lapkey);
2401 
2402  NekVector<NekDouble> in (nm_elmt, force, eWrapper);
2403  NekVector<NekDouble> out(nm_elmt);
2404 
2405  out = (*lapsys)*in;
2406 
2407  // Transforming back to modified basis
2408  Array<OneD, NekDouble> work(nq_elmt);
2409  ppExp->BwdTrans(out.GetPtr(), work);
2410  (*m_exp)[i]->FwdTrans(work,
2411  tmp_coeffs = outarray + m_coeff_offset[i]);
2412  }
2413  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
boost::shared_ptr< HexGeom > HexGeomSharedPtr
Definition: HexGeom.h:110
Array< OneD, NekDouble > m_coeffs
Concatenation of all local expansion coefficients.
Definition: ExpList.h:998
int GetExpSize(void)
This function returns the number of elements in the expansion.
Definition: ExpList.h:2046
boost::shared_ptr< DNekScalMat > DNekScalMatSharedPtr
Gauss Radau pinned at x=-1, .
Definition: PointsType.h:59
Principle Orthogonal Functions .
Definition: BasisType.h:47
Array< OneD, int > m_coeff_offset
Offset of elemental data into the array m_coeffs.
Definition: ExpList.h:1047
boost::shared_ptr< Expansion3D > Expansion3DSharedPtr
Definition: Expansion2D.h:48
Principle Orthogonal Functions .
Definition: BasisType.h:48
Principle Orthogonal Functions .
Definition: BasisType.h:46
boost::shared_ptr< Expansion > ExpansionSharedPtr
Definition: Expansion.h:68
boost::shared_ptr< PrismGeom > PrismGeomSharedPtr
Definition: PrismGeom.h:109
Gauss Radau pinned at x=-1, .
Definition: PointsType.h:60
boost::shared_ptr< TetGeom > TetGeomSharedPtr
Definition: TetGeom.h:106
void Vcopy(int n, const T *x, const int incx, T *y, const int incy)
Definition: Vmath.cpp:1061
1D Gauss-Lobatto-Legendre quadrature points
Definition: PointsType.h:52
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
void Nektar::MultiRegions::DisContField3D::FindPeriodicFaces ( const SpatialDomains::BoundaryConditions bcs,
const std::string &  variable 
)
protected

Determine the periodic faces, edges and vertices for the given graph.

Parameters
bcsInformation about the boundary conditions.
variableSpecifies the field.

Definition at line 674 of file DisContField3D.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, ASSERTL1, Nektar::StdRegions::eBackwards, Nektar::StdRegions::eDir1BwdDir1_Dir2BwdDir2, Nektar::StdRegions::eDir1BwdDir1_Dir2FwdDir2, Nektar::StdRegions::eDir1BwdDir2_Dir2BwdDir1, Nektar::StdRegions::eDir1BwdDir2_Dir2FwdDir1, Nektar::StdRegions::eDir1FwdDir1_Dir2BwdDir2, Nektar::StdRegions::eDir1FwdDir1_Dir2FwdDir2, Nektar::StdRegions::eDir1FwdDir2_Dir2BwdDir1, Nektar::StdRegions::eDir1FwdDir2_Dir2FwdDir1, Nektar::StdRegions::eForwards, Nektar::StdRegions::eNoOrientation, Nektar::SpatialDomains::ePeriodic, Nektar::MultiRegions::ExpList::GetBoundaryCondition(), Nektar::SpatialDomains::BoundaryConditions::GetBoundaryConditions(), Nektar::SpatialDomains::BoundaryConditions::GetBoundaryRegions(), Nektar::SpatialDomains::QuadGeom::GetFaceOrientation(), Nektar::SpatialDomains::TriGeom::GetFaceOrientation(), Nektar::iterator, Nektar::MultiRegions::ExpList::m_graph, m_periodicEdges, m_periodicFaces, m_periodicVerts, Nektar::MultiRegions::ExpList::m_session, CellMLToNektar.cellml_metadata::p, Nektar::LibUtilities::ReduceSum, and Vmath::Vsum().

Referenced by DisContField3D().

677  {
679  = bcs.GetBoundaryRegions();
681  = bcs.GetBoundaryConditions();
683  = boost::dynamic_pointer_cast<
684  SpatialDomains::MeshGraph3D>(m_graph);
685  SpatialDomains::BoundaryRegionCollection::const_iterator it;
686 
688  m_session->GetComm()->GetRowComm();
690  m_session->GetCompositeOrdering();
691  LibUtilities::BndRegionOrdering bndRegOrder =
692  m_session->GetBndRegionOrdering();
694  m_graph->GetComposites();
695 
696  // perComps: Stores a unique collection of pairs of periodic
697  // composites (i.e. if composites 1 and 2 are periodic then this map
698  // will contain either the pair (1,2) or (2,1) but not both).
699  //
700  // The four maps allVerts, allCoord, allEdges and allOrient map a
701  // periodic face to a vector containing the vertex ids of the face;
702  // their coordinates; the edge ids of the face; and their
703  // orientation within that face respectively.
704  //
705  // Finally the three sets locVerts, locEdges and locFaces store any
706  // vertices, edges and faces that belong to a periodic composite and
707  // lie on this process.
708  map<int,int> perComps;
709  map<int,vector<int> > allVerts;
710  map<int,SpatialDomains::PointGeomVector> allCoord;
711  map<int,vector<int> > allEdges;
712  map<int,vector<StdRegions::Orientation> > allOrient;
713  set<int> locVerts;
714  set<int> locEdges;
715  set<int> locFaces;
716 
717  int region1ID, region2ID, i, j, k, cnt;
719 
720  // Set up a set of all local verts and edges.
721  for(i = 0; i < (*m_exp).size(); ++i)
722  {
723  for(j = 0; j < (*m_exp)[i]->GetNverts(); ++j)
724  {
725  int id = (*m_exp)[i]->GetGeom()->GetVid(j);
726  locVerts.insert(id);
727  }
728 
729  for(j = 0; j < (*m_exp)[i]->GetNedges(); ++j)
730  {
731  int id = (*m_exp)[i]->GetGeom()->GetEid(j);
732  locEdges.insert(id);
733  }
734  }
735 
736  // Begin by populating the perComps map. We loop over all periodic
737  // boundary conditions and determine the composite associated with
738  // it, then fill out the all* maps.
739  for (it = bregions.begin(); it != bregions.end(); ++it)
740  {
741  locBCond = GetBoundaryCondition(
742  bconditions, it->first, variable);
743 
744  if (locBCond->GetBoundaryConditionType()
746  {
747  continue;
748  }
749 
750  // Identify periodic boundary region IDs.
751  region1ID = it->first;
752  region2ID = boost::static_pointer_cast<
753  SpatialDomains::PeriodicBoundaryCondition>(
754  locBCond)->m_connectedBoundaryRegion;
755 
756  // Check the region only contains a single composite.
757  ASSERTL0(it->second->size() == 1,
758  "Boundary region "+boost::lexical_cast<string>(
759  region1ID)+" should only contain 1 composite.");
760 
761  // From this identify composites by looking at the original
762  // boundary region ordering. Note that in serial the mesh
763  // partitioner is not run, so this map will be empty and
764  // therefore needs to be populated by using the corresponding
765  // boundary region.
766  int cId1, cId2;
767  if (vComm->GetSize() == 1)
768  {
769  cId1 = it->second->begin()->first;
770  cId2 = bregions.find(region2ID)->second->begin()->first;
771  }
772  else
773  {
774  cId1 = bndRegOrder.find(region1ID)->second[0];
775  cId2 = bndRegOrder.find(region2ID)->second[0];
776  }
777 
778  SpatialDomains::Composite c = it->second->begin()->second;
779  vector<unsigned int> tmpOrder;
780 
781  // From the composite, we now construct the allVerts, allEdges
782  // and allCoord map so that they can be transferred across
783  // processors. We also populate the locFaces set to store a
784  // record of all faces local to this process.
785  for (i = 0; i < c->size(); ++i)
786  {
788  boost::dynamic_pointer_cast<
789  SpatialDomains::Geometry2D>((*c)[i]);
790  ASSERTL1(faceGeom, "Unable to cast to shared ptr");
791 
792  // Get geometry ID of this face and store in locFaces.
793  int faceId = (*c)[i]->GetGlobalID();
794  locFaces.insert(faceId);
795 
796  // In serial, mesh partitioning will not have occurred so
797  // need to fill composite ordering map manually.
798  if (vComm->GetSize() == 1)
799  {
800  tmpOrder.push_back((*c)[i]->GetGlobalID());
801  }
802 
803  // Loop over vertices and edges of the face to populate
804  // allVerts, allEdges and allCoord maps.
805  vector<int> vertList, edgeList;
807  vector<StdRegions::Orientation> orientVec;
808  for (j = 0; j < faceGeom->GetNumVerts(); ++j)
809  {
810  vertList .push_back(faceGeom->GetVid (j));
811  edgeList .push_back(faceGeom->GetEid (j));
812  coordVec .push_back(faceGeom->GetVertex(j));
813  orientVec.push_back(faceGeom->GetEorient(j));
814  }
815 
816  allVerts [faceId] = vertList;
817  allEdges [faceId] = edgeList;
818  allCoord [faceId] = coordVec;
819  allOrient[faceId] = orientVec;
820  }
821 
822  // In serial, record the composite ordering in compOrder for
823  // later in the routine.
824  if (vComm->GetSize() == 1)
825  {
826  compOrder[it->second->begin()->first] = tmpOrder;
827  }
828 
829  // See if we already have either region1 or region2 stored in
830  // perComps map already and do a sanity check to ensure regions
831  // are mutually periodic.
832  if (perComps.count(cId1) == 0)
833  {
834  if (perComps.count(cId2) == 0)
835  {
836  perComps[cId1] = cId2;
837  }
838  else
839  {
840  std::stringstream ss;
841  ss << "Boundary region " << cId2 << " should be "
842  << "periodic with " << perComps[cId2] << " but "
843  << "found " << cId1 << " instead!";
844  ASSERTL0(perComps[cId2] == cId1, ss.str());
845  }
846  }
847  else
848  {
849  std::stringstream ss;
850  ss << "Boundary region " << cId1 << " should be "
851  << "periodic with " << perComps[cId1] << " but "
852  << "found " << cId2 << " instead!";
853  ASSERTL0(perComps[cId1] == cId1, ss.str());
854  }
855  }
856 
857  // The next routines process local face lists to exchange vertices,
858  // edges and faces.
859  int n = vComm->GetSize();
860  int p = vComm->GetRank();
861  int totFaces;
862  Array<OneD, int> facecounts(n,0);
863  Array<OneD, int> vertcounts(n,0);
864  Array<OneD, int> faceoffset(n,0);
865  Array<OneD, int> vertoffset(n,0);
866 
867  // First exchange the number of faces on each process.
868  facecounts[p] = locFaces.size();
869  vComm->AllReduce(facecounts, LibUtilities::ReduceSum);
870 
871  // Set up an offset map to allow us to distribute face IDs to all
872  // processors.
873  faceoffset[0] = 0;
874  for (i = 1; i < n; ++i)
875  {
876  faceoffset[i] = faceoffset[i-1] + facecounts[i-1];
877  }
878 
879  // Calculate total number of faces.
880  totFaces = Vmath::Vsum(n, facecounts, 1);
881 
882  // faceIds holds face IDs for each periodic face. faceVerts holds
883  // the number of vertices in this face.
884  Array<OneD, int> faceIds (totFaces, 0);
885  Array<OneD, int> faceVerts(totFaces, 0);
886 
887  // Process p writes IDs of its faces into position faceoffset[p] of
888  // faceIds which allows us to perform an AllReduce to distribute
889  // information amongst processors.
890  set<int>::iterator sIt;
891  for (i = 0, sIt = locFaces.begin(); sIt != locFaces.end(); ++sIt)
892  {
893  faceIds [faceoffset[p] + i ] = *sIt;
894  faceVerts[faceoffset[p] + i++] = allVerts[*sIt].size();
895  }
896 
897  vComm->AllReduce(faceIds, LibUtilities::ReduceSum);
898  vComm->AllReduce(faceVerts, LibUtilities::ReduceSum);
899 
900  // procVerts holds number of vertices (and also edges since each
901  // face is 2D) on each process.
902  Array<OneD, int> procVerts(n,0);
903  int nTotVerts;
904 
905  // Note if there are no periodic faces at all calling Vsum will
906  // cause a segfault.
907  if (totFaces > 0)
908  {
909  // Calculate number of vertices on each processor.
910  nTotVerts = Vmath::Vsum(totFaces, faceVerts, 1);
911  }
912  else
913  {
914  nTotVerts = 0;
915  }
916 
917  for (i = 0; i < n; ++i)
918  {
919  if (facecounts[i] > 0)
920  {
921  procVerts[i] = Vmath::Vsum(
922  facecounts[i], faceVerts + faceoffset[i], 1);
923  }
924  else
925  {
926  procVerts[i] = 0;
927  }
928  }
929 
930  // vertoffset is defined in the same manner as edgeoffset
931  // beforehand.
932  vertoffset[0] = 0;
933  for (i = 1; i < n; ++i)
934  {
935  vertoffset[i] = vertoffset[i-1] + procVerts[i-1];
936  }
937 
938  // At this point we exchange all vertex IDs, edge IDs and vertex
939  // coordinates for each face. The coordinates are necessary because
940  // we need to calculate relative face orientations between periodic
941  // faces to determined edge and vertex connectivity.
942  Array<OneD, int> vertIds(nTotVerts, 0);
943  Array<OneD, int> edgeIds(nTotVerts, 0);
944  Array<OneD, int> edgeOrt(nTotVerts, 0);
945  Array<OneD, NekDouble> vertX (nTotVerts, 0.0);
946  Array<OneD, NekDouble> vertY (nTotVerts, 0.0);
947  Array<OneD, NekDouble> vertZ (nTotVerts, 0.0);
948 
949  for (cnt = 0, sIt = locFaces.begin();
950  sIt != locFaces.end(); ++sIt)
951  {
952  for (j = 0; j < allVerts[*sIt].size(); ++j)
953  {
954  int vertId = allVerts[*sIt][j];
955  vertIds[vertoffset[p] + cnt ] = vertId;
956  vertX [vertoffset[p] + cnt ] = (*allCoord[*sIt][j])(0);
957  vertY [vertoffset[p] + cnt ] = (*allCoord[*sIt][j])(1);
958  vertZ [vertoffset[p] + cnt ] = (*allCoord[*sIt][j])(2);
959  edgeIds[vertoffset[p] + cnt ] = allEdges [*sIt][j];
960  edgeOrt[vertoffset[p] + cnt++] = allOrient[*sIt][j];
961  }
962  }
963 
964  vComm->AllReduce(vertIds, LibUtilities::ReduceSum);
965  vComm->AllReduce(vertX, LibUtilities::ReduceSum);
966  vComm->AllReduce(vertY, LibUtilities::ReduceSum);
967  vComm->AllReduce(vertZ, LibUtilities::ReduceSum);
968  vComm->AllReduce(edgeIds, LibUtilities::ReduceSum);
969  vComm->AllReduce(edgeOrt, LibUtilities::ReduceSum);
970 
971  // Finally now we have all of this information, we construct maps
972  // which make accessing the information easier. These are
973  // conceptually the same as all* maps at the beginning of the
974  // routine, but now hold information for all periodic vertices.
975  map<int, vector<int> > vertMap;
976  map<int, vector<int> > edgeMap;
977  map<int, SpatialDomains::PointGeomVector> coordMap;
978 
979  // These final two maps are required for determining the relative
980  // orientation of periodic edges. vCoMap associates vertex IDs with
981  // their coordinates, and eIdMap maps an edge ID to the two vertices
982  // which construct it.
983  map<int, SpatialDomains::PointGeomSharedPtr> vCoMap;
984  map<int, pair<int, int> > eIdMap;
985 
986  for (cnt = i = 0; i < totFaces; ++i)
987  {
988  vector<int> edges(faceVerts[i]);
989  vector<int> verts(faceVerts[i]);
990  SpatialDomains::PointGeomVector coord(faceVerts[i]);
991 
992  // Keep track of cnt to enable correct edge vertices to be
993  // inserted into eIdMap.
994  int tmp = cnt;
995  for (j = 0; j < faceVerts[i]; ++j, ++cnt)
996  {
997  edges[j] = edgeIds[cnt];
998  verts[j] = vertIds[cnt];
1001  3, verts[j], vertX[cnt], vertY[cnt], vertZ[cnt]);
1002  vCoMap[vertIds[cnt]] = coord[j];
1003 
1004  // Try to insert edge into the eIdMap to avoid re-inserting.
1005  pair<map<int, pair<int, int> >::iterator, bool> testIns =
1006  eIdMap.insert(make_pair(
1007  edgeIds[cnt],
1008  make_pair(vertIds[tmp+j],
1009  vertIds[tmp+((j+1) % faceVerts[i])])));
1010 
1011  if (testIns.second == false)
1012  {
1013  continue;
1014  }
1015 
1016  // If the edge is reversed with respect to the face, then
1017  // swap the edges so that we have the original ordering of
1018  // the edge in the 3D element. This is necessary to properly
1019  // determine edge orientation.
1020  if ((StdRegions::Orientation)edgeOrt[cnt]
1022  {
1023  swap(testIns.first->second.first,
1024  testIns.first->second.second);
1025  }
1026  }
1027 
1028  vertMap [faceIds[i]] = verts;
1029  edgeMap [faceIds[i]] = edges;
1030  coordMap[faceIds[i]] = coord;
1031  }
1032 
1033  // Go through list of composites and figure out which edges are
1034  // parallel from original ordering in session file. This includes
1035  // composites which are not necessarily on this process.
1036  map<int,int>::iterator cIt, pIt;
1037  map<int,int>::const_iterator oIt;
1038 
1039  // Store temporary map of periodic vertices which will hold all
1040  // periodic vertices on the entire mesh so that doubly periodic
1041  // vertices/edges can be counted properly across partitions. Local
1042  // vertices/edges are copied into m_periodicVerts and
1043  // m_periodicEdges at the end of the function.
1044  PeriodicMap periodicVerts;
1045  PeriodicMap periodicEdges;
1046 
1047  // Construct two maps which determine how vertices and edges of
1048  // faces connect given a specific face orientation. The key of the
1049  // map is the number of vertices in the face, used to determine
1050  // difference between tris and quads.
1051  map<int, map<StdRegions::Orientation, vector<int> > > vmap;
1052  map<int, map<StdRegions::Orientation, vector<int> > > emap;
1053 
1054  map<StdRegions::Orientation, vector<int> > quadVertMap;
1055  quadVertMap[StdRegions::eDir1FwdDir1_Dir2FwdDir2] += 0,1,2,3;
1056  quadVertMap[StdRegions::eDir1FwdDir1_Dir2BwdDir2] += 3,2,1,0;
1057  quadVertMap[StdRegions::eDir1BwdDir1_Dir2FwdDir2] += 1,0,3,2;
1058  quadVertMap[StdRegions::eDir1BwdDir1_Dir2BwdDir2] += 2,3,0,1;
1059  quadVertMap[StdRegions::eDir1FwdDir2_Dir2FwdDir1] += 0,3,2,1;
1060  quadVertMap[StdRegions::eDir1FwdDir2_Dir2BwdDir1] += 1,2,3,0;
1061  quadVertMap[StdRegions::eDir1BwdDir2_Dir2FwdDir1] += 3,0,1,2;
1062  quadVertMap[StdRegions::eDir1BwdDir2_Dir2BwdDir1] += 2,1,0,3;
1063 
1064  map<StdRegions::Orientation, vector<int> > quadEdgeMap;
1065  quadEdgeMap[StdRegions::eDir1FwdDir1_Dir2FwdDir2] += 0,1,2,3;
1066  quadEdgeMap[StdRegions::eDir1FwdDir1_Dir2BwdDir2] += 2,1,0,3;
1067  quadEdgeMap[StdRegions::eDir1BwdDir1_Dir2FwdDir2] += 0,3,2,1;
1068  quadEdgeMap[StdRegions::eDir1BwdDir1_Dir2BwdDir2] += 2,3,0,1;
1069  quadEdgeMap[StdRegions::eDir1FwdDir2_Dir2FwdDir1] += 3,2,1,0;
1070  quadEdgeMap[StdRegions::eDir1FwdDir2_Dir2BwdDir1] += 1,2,3,0;
1071  quadEdgeMap[StdRegions::eDir1BwdDir2_Dir2FwdDir1] += 3,0,1,2;
1072  quadEdgeMap[StdRegions::eDir1BwdDir2_Dir2BwdDir1] += 1,0,3,2;
1073 
1074  map<StdRegions::Orientation, vector<int> > triVertMap;
1075  triVertMap[StdRegions::eDir1FwdDir1_Dir2FwdDir2] += 0,1,2;
1076  triVertMap[StdRegions::eDir1BwdDir1_Dir2FwdDir2] += 1,0,2;
1077 
1078  map<StdRegions::Orientation, vector<int> > triEdgeMap;
1079  triEdgeMap[StdRegions::eDir1FwdDir1_Dir2FwdDir2] += 0,1,2;
1080  triEdgeMap[StdRegions::eDir1BwdDir1_Dir2FwdDir2] += 0,2,1;
1081 
1082  vmap[3] = triVertMap;
1083  vmap[4] = quadVertMap;
1084  emap[3] = triEdgeMap;
1085  emap[4] = quadEdgeMap;
1086 
1087  map<int,int> allCompPairs;
1088 
1089  // Finally we have enough information to populate the periodic
1090  // vertex, edge and face maps. Begin by looping over all pairs of
1091  // periodic composites to determine pairs of periodic faces.
1092  for (cIt = perComps.begin(); cIt != perComps.end(); ++cIt)
1093  {
1095  const int id1 = cIt->first;
1096  const int id2 = cIt->second;
1097  std::string id1s = boost::lexical_cast<string>(id1);
1098  std::string id2s = boost::lexical_cast<string>(id2);
1099 
1100  if (compMap.count(id1) > 0)
1101  {
1102  c[0] = compMap[id1];
1103  }
1104 
1105  if (compMap.count(id2) > 0)
1106  {
1107  c[1] = compMap[id2];
1108  }
1109 
1110  ASSERTL0(c[0] || c[1],
1111  "Neither composite not found on this process!");
1112 
1113  // Loop over composite ordering to construct list of all
1114  // periodic faces, regardless of whether they are on this
1115  // process.
1116  map<int,int> compPairs;
1117 
1118  ASSERTL0(compOrder.count(id1) > 0,
1119  "Unable to find composite "+id1s+" in order map.");
1120  ASSERTL0(compOrder.count(id2) > 0,
1121  "Unable to find composite "+id2s+" in order map.");
1122  ASSERTL0(compOrder[id1].size() == compOrder[id2].size(),
1123  "Periodic composites "+id1s+" and "+id2s+
1124  " should have the same number of elements.");
1125  ASSERTL0(compOrder[id1].size() > 0,
1126  "Periodic composites "+id1s+" and "+id2s+
1127  " are empty!");
1128 
1129  // Look up composite ordering to determine pairs.
1130  for (i = 0; i < compOrder[id1].size(); ++i)
1131  {
1132  int eId1 = compOrder[id1][i];
1133  int eId2 = compOrder[id2][i];
1134 
1135  ASSERTL0(compPairs.count(eId1) == 0,
1136  "Already paired.");
1137 
1138  // Sanity check that the faces are mutually periodic.
1139  if (compPairs.count(eId2) != 0)
1140  {
1141  ASSERTL0(compPairs[eId2] == eId1, "Pairing incorrect");
1142  }
1143  compPairs[eId1] = eId2;
1144  }
1145 
1146  // Now that we have all pairs of periodic faces, loop over the
1147  // ones local to this process and populate face/edge/vertex
1148  // maps.
1149  for (pIt = compPairs.begin(); pIt != compPairs.end(); ++pIt)
1150  {
1151  int ids [2] = {pIt->first, pIt->second};
1152  bool local[2] = {locFaces.count(pIt->first) > 0,
1153  locFaces.count(pIt->second) > 0};
1154 
1155  ASSERTL0(coordMap.count(ids[0]) > 0 &&
1156  coordMap.count(ids[1]) > 0,
1157  "Unable to find face in coordinate map");
1158 
1159  allCompPairs[pIt->first ] = pIt->second;
1160  allCompPairs[pIt->second] = pIt->first;
1161 
1162  // Loop up coordinates of the faces, check they have the
1163  // same number of vertices.
1165  = { coordMap[ids[0]], coordMap[ids[1]] };
1166 
1167  ASSERTL0(tmpVec[0].size() == tmpVec[1].size(),
1168  "Two periodic faces have different number "
1169  "of vertices!");
1170 
1171  // o will store relative orientation of faces. Note that in
1172  // some transpose cases (Dir1FwdDir2_Dir2BwdDir1 and
1173  // Dir1BwdDir1_Dir2FwdDir1) it seems orientation will be
1174  // different going from face1->face2 instead of face2->face1
1175  // (check this).
1177 
1178  // Record periodic faces.
1179  for (i = 0; i < 2; ++i)
1180  {
1181  if (!local[i])
1182  {
1183  continue;
1184  }
1185 
1186  // Reference to the other face.
1187  int other = (i+1) % 2;
1188 
1189  // Calculate relative face orientation.
1190  if (tmpVec[0].size() == 3)
1191  {
1193  tmpVec[i], tmpVec[other]);
1194  }
1195  else
1196  {
1198  tmpVec[i], tmpVec[other]);
1199  }
1200 
1201  // Record face ID, orientation and whether other face is
1202  // local.
1203  PeriodicEntity ent(ids [other], o,
1204  local[other]);
1205  m_periodicFaces[ids[i]].push_back(ent);
1206  }
1207 
1208  int nFaceVerts = vertMap[ids[0]].size();
1209 
1210  // Determine periodic vertices.
1211  for (i = 0; i < 2; ++i)
1212  {
1213  int other = (i+1) % 2;
1214 
1215  // Calculate relative face orientation.
1216  if (tmpVec[0].size() == 3)
1217  {
1219  tmpVec[i], tmpVec[other]);
1220  }
1221  else
1222  {
1224  tmpVec[i], tmpVec[other]);
1225  }
1226 
1227  if (nFaceVerts == 3)
1228  {
1229  ASSERTL0(
1232  "Unsupported face orientation for face "+
1233  boost::lexical_cast<string>(ids[i]));
1234  }
1235 
1236  // Look up vertices for this face.
1237  vector<int> per1 = vertMap[ids[i]];
1238  vector<int> per2 = vertMap[ids[other]];
1239 
1240  // tmpMap will hold the pairs of vertices which are
1241  // periodic.
1242  map<int, pair<int, bool> > tmpMap;
1243  map<int, pair<int, bool> >::iterator mIt;
1244 
1245  // Use vmap to determine which vertices connect given
1246  // the orientation o.
1247  for (j = 0; j < nFaceVerts; ++j)
1248  {
1249  int v = vmap[nFaceVerts][o][j];
1250  tmpMap[per1[j]] = make_pair(
1251  per2[v], locVerts.count(per2[v]) > 0);
1252  }
1253 
1254  // Now loop over tmpMap to associate periodic vertices.
1255  for (mIt = tmpMap.begin(); mIt != tmpMap.end(); ++mIt)
1256  {
1257  PeriodicEntity ent2(mIt->second.first,
1259  mIt->second.second);
1260 
1261  // See if this vertex has been recorded already.
1262  PeriodicMap::iterator perIt = periodicVerts.find(
1263  mIt->first);
1264 
1265  if (perIt == periodicVerts.end())
1266  {
1267  // Vertex is new - just record this entity as
1268  // usual.
1269  periodicVerts[mIt->first].push_back(ent2);
1270  perIt = periodicVerts.find(mIt->first);
1271  }
1272  else
1273  {
1274  // Vertex is known - loop over the vertices
1275  // inside the record and potentially add vertex
1276  // mIt->second to the list.
1277  for (k = 0; k < perIt->second.size(); ++k)
1278  {
1279  if (perIt->second[k].id == mIt->second.first)
1280  {
1281  break;
1282  }
1283  }
1284 
1285  if (k == perIt->second.size())
1286  {
1287  perIt->second.push_back(ent2);
1288  }
1289  }
1290  }
1291  }
1292 
1293  // Determine periodic edges. Logic is the same as above,
1294  // and perhaps should be condensed to avoid replication.
1295  for (i = 0; i < 2; ++i)
1296  {
1297  int other = (i+1) % 2;
1298 
1299  if (tmpVec[0].size() == 3)
1300  {
1302  tmpVec[i], tmpVec[other]);
1303  }
1304  else
1305  {
1307  tmpVec[i], tmpVec[other]);
1308  }
1309 
1310  vector<int> per1 = edgeMap[ids[i]];
1311  vector<int> per2 = edgeMap[ids[other]];
1312 
1313  map<int, pair<int, bool> > tmpMap;
1314  map<int, pair<int, bool> >::iterator mIt;
1315 
1316  for (j = 0; j < nFaceVerts; ++j)
1317  {
1318  int e = emap[nFaceVerts][o][j];
1319  tmpMap[per1[j]] = make_pair(
1320  per2[e], locEdges.count(per2[e]) > 0);
1321  }
1322 
1323  for (mIt = tmpMap.begin(); mIt != tmpMap.end(); ++mIt)
1324  {
1325  // Note we assume orientation of edges is forwards -
1326  // this may be reversed later.
1327  PeriodicEntity ent2(mIt->second.first,
1329  mIt->second.second);
1330  PeriodicMap::iterator perIt = periodicEdges.find(
1331  mIt->first);
1332 
1333  if (perIt == periodicEdges.end())
1334  {
1335  periodicEdges[mIt->first].push_back(ent2);
1336  perIt = periodicEdges.find(mIt->first);
1337  }
1338  else
1339  {
1340  for (k = 0; k < perIt->second.size(); ++k)
1341  {
1342  if (perIt->second[k].id == mIt->second.first)
1343  {
1344  break;
1345  }
1346  }
1347 
1348  if (k == perIt->second.size())
1349  {
1350  perIt->second.push_back(ent2);
1351  }
1352  }
1353  }
1354  }
1355  }
1356  }
1357 
1358  Array<OneD, int> pairSizes(n, 0);
1359  pairSizes[p] = allCompPairs.size();
1360  vComm->AllReduce(pairSizes, LibUtilities::ReduceSum);
1361 
1362  int totPairSizes = Vmath::Vsum(n, pairSizes, 1);
1363 
1364  Array<OneD, int> pairOffsets(n, 0);
1365  pairOffsets[0] = 0;
1366 
1367  for (i = 1; i < n; ++i)
1368  {
1369  pairOffsets[i] = pairOffsets[i-1] + pairSizes[i-1];
1370  }
1371 
1372  Array<OneD, int> first (totPairSizes, 0);
1373  Array<OneD, int> second(totPairSizes, 0);
1374 
1375  cnt = pairOffsets[p];
1376 
1377  for (pIt = allCompPairs.begin(); pIt != allCompPairs.end(); ++pIt)
1378  {
1379  first [cnt ] = pIt->first;
1380  second[cnt++] = pIt->second;
1381  }
1382 
1383  vComm->AllReduce(first, LibUtilities::ReduceSum);
1384  vComm->AllReduce(second, LibUtilities::ReduceSum);
1385 
1386  allCompPairs.clear();
1387 
1388  for(cnt = 0; cnt < totPairSizes; ++cnt)
1389  {
1390  allCompPairs[first[cnt]] = second[cnt];
1391  }
1392 
1393  // Search for periodic vertices and edges which are not
1394  // in a periodic composite but lie in this process. First,
1395  // loop over all information we have from other
1396  // processors.
1397  for (cnt = i = 0; i < totFaces; ++i)
1398  {
1399  int faceId = faceIds[i];
1400 
1401  ASSERTL0(allCompPairs.count(faceId) > 0,
1402  "Unable to find matching periodic face.");
1403 
1404  int perFaceId = allCompPairs[faceId];
1405 
1406  for (j = 0; j < faceVerts[i]; ++j, ++cnt)
1407  {
1408  int vId = vertIds[cnt];
1409 
1410  PeriodicMap::iterator perId = periodicVerts.find(vId);
1411 
1412  if (perId == periodicVerts.end())
1413  {
1414 
1415  // This vertex is not included in the map. Figure out which
1416  // vertex it is supposed to be periodic with. perFaceId is
1417  // the face ID which is periodic with faceId. The logic is
1418  // much the same as the loop above.
1420  = { coordMap[faceId], coordMap[perFaceId] };
1421 
1422  int nFaceVerts = tmpVec[0].size();
1423  StdRegions::Orientation o = nFaceVerts == 3 ?
1425  tmpVec[0], tmpVec[1]) :
1426  SpatialDomains::QuadGeom::GetFaceOrientation(
1427  tmpVec[0], tmpVec[1]);
1428 
1429  // Use vmap to determine which vertex of the other face
1430  // should be periodic with this one.
1431  int perVertexId = vertMap[perFaceId][vmap[nFaceVerts][o][j]];
1432 
1433 
1434  PeriodicEntity ent(perVertexId,
1436  locVerts.count(perVertexId) > 0);
1437 
1438  periodicVerts[vId].push_back(ent);
1439  }
1440 
1441  int eId = edgeIds[cnt];
1442 
1443  perId = periodicEdges.find(eId);
1444 
1445  if (perId == periodicEdges.end())
1446  {
1447  // This edge is not included in the map. Figure
1448  // out which edge it is supposed to be periodic
1449  // with. perFaceId is the face ID which is
1450  // periodic with faceId. The logic is much the
1451  // same as the loop above.
1453  = { coordMap[faceId], coordMap[perFaceId] };
1454 
1455  int nFaceEdges = tmpVec[0].size();
1456  StdRegions::Orientation o = nFaceEdges == 3 ?
1458  tmpVec[0], tmpVec[1]) :
1459  SpatialDomains::QuadGeom::GetFaceOrientation(
1460  tmpVec[0], tmpVec[1]);
1461 
1462  // Use emap to determine which edge of the other
1463  // face should be periodic with this one.
1464  int perEdgeId = edgeMap[perFaceId][emap[nFaceEdges][o][j]];
1465 
1466 
1467  PeriodicEntity ent(perEdgeId,
1469  locEdges.count(perEdgeId) > 0);
1470 
1471  periodicEdges[eId].push_back(ent);
1472  }
1473  }
1474  }
1475 
1476  // Finally, we must loop over the periodicVerts and periodicEdges
1477  // map to complete connectivity information.
1478  PeriodicMap::iterator perIt, perIt2;
1479  for (perIt = periodicVerts.begin();
1480  perIt != periodicVerts.end(); ++perIt)
1481  {
1482  // For each vertex that is periodic with this one...
1483  for (i = 0; i < perIt->second.size(); ++i)
1484  {
1485  // Find the vertex in the periodicVerts map...
1486  perIt2 = periodicVerts.find(perIt->second[i].id);
1487  ASSERTL0(perIt2 != periodicVerts.end(),
1488  "Couldn't find periodic vertex.");
1489 
1490  // Now search through this vertex's list and make sure that
1491  // we have a record of any vertices which aren't in the
1492  // original list.
1493  for (j = 0; j < perIt2->second.size(); ++j)
1494  {
1495  if (perIt2->second[j].id == perIt->first)
1496  {
1497  continue;
1498  }
1499 
1500  for (k = 0; k < perIt->second.size(); ++k)
1501  {
1502  if (perIt2->second[j].id == perIt->second[k].id)
1503  {
1504  break;
1505  }
1506  }
1507 
1508  if (k == perIt->second.size())
1509  {
1510  perIt->second.push_back(perIt2->second[j]);
1511  }
1512  }
1513  }
1514  }
1515 
1516  for (perIt = periodicEdges.begin();
1517  perIt != periodicEdges.end(); ++perIt)
1518  {
1519  for (i = 0; i < perIt->second.size(); ++i)
1520  {
1521  perIt2 = periodicEdges.find(perIt->second[i].id);
1522  ASSERTL0(perIt2 != periodicEdges.end(),
1523  "Couldn't find periodic edge.");
1524 
1525  for (j = 0; j < perIt2->second.size(); ++j)
1526  {
1527  if (perIt2->second[j].id == perIt->first)
1528  {
1529  continue;
1530  }
1531 
1532  for (k = 0; k < perIt->second.size(); ++k)
1533  {
1534  if (perIt2->second[j].id == perIt->second[k].id)
1535  {
1536  break;
1537  }
1538  }
1539 
1540  if (k == perIt->second.size())
1541  {
1542  perIt->second.push_back(perIt2->second[j]);
1543  }
1544  }
1545  }
1546  }
1547 
1548  // Loop over periodic edges to determine relative edge orientations.
1549  for (perIt = periodicEdges.begin();
1550  perIt != periodicEdges.end(); perIt++)
1551  {
1552  // Find edge coordinates
1553  map<int, pair<int, int> >::iterator eIt
1554  = eIdMap.find(perIt->first);
1555  SpatialDomains::PointGeom v[2] = {
1556  *vCoMap[eIt->second.first],
1557  *vCoMap[eIt->second.second]
1558  };
1559 
1560  // Loop over each edge, and construct a vector that takes us
1561  // from one vertex to another. Use this to figure out which
1562  // vertex maps to which.
1563  for (i = 0; i < perIt->second.size(); ++i)
1564  {
1565  eIt = eIdMap.find(perIt->second[i].id);
1566 
1567  SpatialDomains::PointGeom w[2] = {
1568  *vCoMap[eIt->second.first],
1569  *vCoMap[eIt->second.second]
1570  };
1571 
1572  NekDouble cx = 0.5*(w[0](0)-v[0](0)+w[1](0)-v[1](0));
1573  NekDouble cy = 0.5*(w[0](1)-v[0](1)+w[1](1)-v[1](1));
1574  NekDouble cz = 0.5*(w[0](2)-v[0](2)+w[1](2)-v[1](2));
1575 
1576  int vMap[2] = {-1,-1};
1577  for (j = 0; j < 2; ++j)
1578  {
1579  NekDouble x = v[j](0);
1580  NekDouble y = v[j](1);
1581  NekDouble z = v[j](2);
1582  for (k = 0; k < 2; ++k)
1583  {
1584  NekDouble x1 = w[k](0)-cx;
1585  NekDouble y1 = w[k](1)-cy;
1586  NekDouble z1 = w[k](2)-cz;
1587 
1588  if (sqrt((x1-x)*(x1-x)+(y1-y)*(y1-y)+(z1-z)*(z1-z))
1589  < 1e-8)
1590  {
1591  vMap[k] = j;
1592  break;
1593  }
1594  }
1595  }
1596 
1597  // Sanity check the map.
1598  ASSERTL0(vMap[0] >= 0 && vMap[1] >= 0,
1599  "Unable to align periodic vertices.");
1600  ASSERTL0((vMap[0] == 0 || vMap[0] == 1) &&
1601  (vMap[1] == 0 || vMap[1] == 1) &&
1602  (vMap[0] != vMap[1]),
1603  "Unable to align periodic vertices.");
1604 
1605  // If 0 -> 0 then edges are aligned already; otherwise
1606  // reverse the orientation.
1607  if (vMap[0] != 0)
1608  {
1609  perIt->second[i].orient = StdRegions::eBackwards;
1610  }
1611  }
1612  }
1613 
1614  // Do one final loop over periodic vertices/edges to remove
1615  // non-local vertices/edges from map.
1616  for (perIt = periodicVerts.begin();
1617  perIt != periodicVerts.end(); ++perIt)
1618  {
1619  if (locVerts.count(perIt->first) > 0)
1620  {
1621  m_periodicVerts.insert(*perIt);
1622  }
1623  }
1624 
1625  for (perIt = periodicEdges.begin();
1626  perIt != periodicEdges.end(); ++perIt)
1627  {
1628  if (locEdges.count(perIt->first) > 0)
1629  {
1630  m_periodicEdges.insert(*perIt);
1631  }
1632  }
1633  }
boost::shared_ptr< MeshGraph3D > MeshGraph3DSharedPtr
Definition: MeshGraph3D.h:224
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
std::vector< PointGeomSharedPtr > PointGeomVector
Definition: Geometry3D.h:61
PeriodicMap m_periodicFaces
A map which identifies pairs of periodic faces.
std::map< int, std::vector< unsigned int > > BndRegionOrdering
Definition: MeshPartition.h:54
std::map< int, std::vector< unsigned int > > CompositeOrdering
Definition: MeshPartition.h:53
boost::shared_ptr< Comm > CommSharedPtr
Pointer to a Communicator object.
Definition: Comm.h:55
static StdRegions::Orientation GetFaceOrientation(const QuadGeom &face1, const QuadGeom &face2)
Get the orientation of face1.
Definition: QuadGeom.cpp:254
std::map< int, BoundaryRegionShPtr > BoundaryRegionCollection
Definition: Conditions.h:217
SpatialDomains::MeshGraphSharedPtr m_graph
Mesh associated with this expansion list.
Definition: ExpList.h:972
LibUtilities::SessionReaderSharedPtr m_session
Session.
Definition: ExpList.h:969
double NekDouble
std::map< int, BoundaryConditionMapShPtr > BoundaryConditionCollection
Definition: Conditions.h:226
boost::shared_ptr< GeometryVector > Composite
Definition: MeshGraph.h:114
std::map< int, std::vector< PeriodicEntity > > PeriodicMap
std::map< int, Composite > CompositeMap
Definition: MeshGraph.h:115
boost::shared_ptr< Geometry2D > Geometry2DSharedPtr
Definition: Geometry2D.h:59
StandardMatrixTag boost::call_traits< LhsDataType >::const_reference rhs typedef NekMatrix< LhsDataType, StandardMatrixTag >::iterator iterator
PeriodicMap m_periodicVerts
A map which identifies groups of periodic vertices.
static SpatialDomains::BoundaryConditionShPtr GetBoundaryCondition(const SpatialDomains::BoundaryConditionCollection &collection, unsigned int index, const std::string &variable)
Definition: ExpList.cpp:3059
static StdRegions::Orientation GetFaceOrientation(const TriGeom &face1, const TriGeom &face2)
Definition: TriGeom.cpp:237
boost::shared_ptr< BoundaryConditionBase > BoundaryConditionShPtr
Definition: Conditions.h:219
T Vsum(int n, const T *x, const int incx)
Subtract return sum(x)
Definition: Vmath.cpp:737
struct Nektar::MultiRegions::_PeriodicEntity PeriodicEntity
#define ASSERTL1(condition, msg)
Assert Level 1 – Debugging which is used whether in FULLDEBUG or DEBUG compilation mode...
Definition: ErrorUtil.hpp:228
PeriodicMap m_periodicEdges
A map which identifies groups of periodic edges.
void Nektar::MultiRegions::DisContField3D::GenerateBoundaryConditionExpansion ( const SpatialDomains::MeshGraphSharedPtr graph3D,
const SpatialDomains::BoundaryConditions bcs,
const std::string &  variable 
)
protected

According to their boundary region, the separate segmental boundary expansions are bundled together in an object of the class MultiRegions::ExpList2D.

Parameters
graph3DA mesh, containing information about the domain and the spectral/hp element expansion.
bcsAn entity containing information about the boundaries and boundary conditions.
variableAn optional parameter to indicate for which variable the boundary conditions should be discretised.

Definition at line 609 of file DisContField3D.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), Nektar::SpatialDomains::eDirichlet, Nektar::SpatialDomains::ePeriodic, Nektar::MultiRegions::ExpList::GetBoundaryCondition(), Nektar::SpatialDomains::BoundaryConditions::GetBoundaryConditions(), Nektar::SpatialDomains::BoundaryConditions::GetBoundaryRegions(), m_bndCondExpansions, m_bndConditions, Nektar::MultiRegions::ExpList::m_session, and Nektar::MultiRegions::ExpList::SetUpPhysNormals().

Referenced by DisContField3D().

613  {
614  int cnt = 0;
617 
619  bcs.GetBoundaryRegions();
620  const SpatialDomains::BoundaryConditionCollection &bconditions =
621  bcs.GetBoundaryConditions();
622  SpatialDomains::BoundaryRegionCollection::const_iterator it;
623 
624  // count the number of non-periodic boundary regions
625  for (it = bregions.begin(); it != bregions.end(); ++it)
626  {
627  SpatialDomains::BoundaryConditionShPtr boundaryCondition =
628  GetBoundaryCondition(bconditions, it->first, variable);
629  if (boundaryCondition->GetBoundaryConditionType() !=
631  {
632  cnt++;
633  }
634  }
635 
636  m_bndCondExpansions = Array<OneD,MultiRegions::ExpListSharedPtr>(cnt);
637  m_bndConditions = Array<OneD,SpatialDomains::BoundaryConditionShPtr>(cnt);
638 
639  cnt = 0;
640 
641  // list Dirichlet boundaries first
642  for (it = bregions.begin(); it != bregions.end(); ++it)
643  {
644  locBCond = GetBoundaryCondition(
645  bconditions, it->first, variable);
646 
647  if(locBCond->GetBoundaryConditionType()
649  {
651  ::AllocateSharedPtr(m_session, *(it->second),
652  graph3D, variable);
653 
654  // Set up normals on non-Dirichlet boundary conditions
655  if(locBCond->GetBoundaryConditionType() !=
657  {
659  }
660 
661  m_bndCondExpansions[cnt] = locExpList;
662  m_bndConditions[cnt++] = locBCond;
663  }
664  }
665  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_bndCondExpansions
An object which contains the discretised boundary conditions.
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
std::map< int, BoundaryRegionShPtr > BoundaryRegionCollection
Definition: Conditions.h:217
LibUtilities::SessionReaderSharedPtr m_session
Session.
Definition: ExpList.h:969
std::map< int, BoundaryConditionMapShPtr > BoundaryConditionCollection
Definition: Conditions.h:226
boost::shared_ptr< ExpList2D > ExpList2DSharedPtr
Shared pointer to an ExpList2D object.
Definition: ExpList2D.h:49
Array< OneD, SpatialDomains::BoundaryConditionShPtr > m_bndConditions
An array which contains the information about the boundary condition on the different boundary region...
static SpatialDomains::BoundaryConditionShPtr GetBoundaryCondition(const SpatialDomains::BoundaryConditionCollection &collection, unsigned int index, const std::string &variable)
Definition: ExpList.cpp:3059
boost::shared_ptr< BoundaryConditionBase > BoundaryConditionShPtr
Definition: Conditions.h:219
GlobalLinSysSharedPtr Nektar::MultiRegions::DisContField3D::GetGlobalBndLinSys ( const GlobalLinSysKey mkey)

Definition at line 279 of file DisContField3D.cpp.

References ASSERTL0, ASSERTL1, Nektar::StdRegions::eHybridDGHelmBndLam, Nektar::MultiRegions::ExpList::GenGlobalBndLinSys(), Nektar::MultiRegions::GlobalLinSysKey::GetGlobalSysSolnType(), Nektar::MultiRegions::GlobalMatrixKey::GetMatrixType(), Nektar::iterator, m_globalBndMat, and m_traceMap.

Referenced by v_HelmSolve().

281  {
282  ASSERTL0(mkey.GetMatrixType() == StdRegions::eHybridDGHelmBndLam,
283  "Routine currently only tested for HybridDGHelmholtz");
284  ASSERTL1(mkey.GetGlobalSysSolnType() ==
285  m_traceMap->GetGlobalSysSolnType(),
286  "The local to global map is not set up for the requested "
287  "solution type");
288 
289  GlobalLinSysSharedPtr glo_matrix;
290  GlobalLinSysMap::iterator matrixIter = m_globalBndMat->find(mkey);
291 
292  if (matrixIter == m_globalBndMat->end())
293  {
294  glo_matrix = GenGlobalBndLinSys(mkey, m_traceMap);
295  (*m_globalBndMat)[mkey] = glo_matrix;
296  }
297  else
298  {
299  glo_matrix = matrixIter->second;
300  }
301 
302  return glo_matrix;
303  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
boost::shared_ptr< GlobalLinSys > GenGlobalBndLinSys(const GlobalLinSysKey &mkey, const AssemblyMapSharedPtr &locToGloMap)
Generate a GlobalLinSys from information provided by the key "mkey" and the mapping provided in LocTo...
Definition: ExpList.cpp:1294
StandardMatrixTag boost::call_traits< LhsDataType >::const_reference rhs typedef NekMatrix< LhsDataType, StandardMatrixTag >::iterator iterator
boost::shared_ptr< GlobalLinSys > GlobalLinSysSharedPtr
Pointer to a GlobalLinSys object.
Definition: GlobalLinSys.h:52
#define ASSERTL1(condition, msg)
Assert Level 1 – Debugging which is used whether in FULLDEBUG or DEBUG compilation mode...
Definition: ErrorUtil.hpp:228
bool Nektar::MultiRegions::DisContField3D::GetLeftAdjacentFaces ( int  cnt)
inline

Definition at line 88 of file DisContField3D.h.

References m_leftAdjacentFaces.

89  {
90  return m_leftAdjacentFaces[cnt];
91  }
bool Nektar::MultiRegions::DisContField3D::IsLeftAdjacentFace ( const int  n,
const int  e 
)
protected

Definition at line 1635 of file DisContField3D.cpp.

References ASSERTL2, Nektar::iterator, m_boundaryFaces, Nektar::MultiRegions::ExpList::m_exp, m_periodicFaces, m_trace, and m_traceMap.

Referenced by SetUpDG().

1636  {
1637  set<int>::iterator it;
1639  m_traceMap->GetElmtToTrace()[n][e]->
1640  as<LocalRegions::Expansion2D>();
1641 
1642  int offset = m_trace->GetPhys_Offset(traceEl->GetElmtId());
1643 
1644  bool fwd = true;
1645  if (traceEl->GetLeftAdjacentElementFace () == -1 ||
1646  traceEl->GetRightAdjacentElementFace() == -1)
1647  {
1648  // Boundary edge (1 connected element). Do nothing in
1649  // serial.
1650  it = m_boundaryFaces.find(traceEl->GetElmtId());
1651 
1652  // If the edge does not have a boundary condition set on
1653  // it, then assume it is a partition edge.
1654  if (it == m_boundaryFaces.end())
1655  {
1656  int traceGeomId = traceEl->GetGeom2D()->GetGlobalID();
1658  traceGeomId);
1659 
1660  if (pIt != m_periodicFaces.end() && !pIt->second[0].isLocal)
1661  {
1662  fwd = traceGeomId == min(traceGeomId,pIt->second[0].id);
1663  }
1664  else
1665  {
1666  fwd = m_traceMap->
1667  GetTraceToUniversalMapUnique(offset) >= 0;
1668  }
1669  }
1670  }
1671  else if (traceEl->GetLeftAdjacentElementFace () != -1 &&
1672  traceEl->GetRightAdjacentElementFace() != -1)
1673  {
1674  // Non-boundary edge (2 connected elements).
1675  fwd = dynamic_cast<Nektar::StdRegions::StdExpansion*>
1676  (traceEl->GetLeftAdjacentElementExp().get()) ==
1677  (*m_exp)[n].get();
1678  }
1679  else
1680  {
1681  ASSERTL2(false, "Unconnected trace element!");
1682  }
1683 
1684  return fwd;
1685  }
std::set< int > m_boundaryFaces
A set storing the global IDs of any boundary faces.
PeriodicMap m_periodicFaces
A map which identifies pairs of periodic faces.
The base class for all shapes.
Definition: StdExpansion.h:69
boost::shared_ptr< LocalRegions::ExpansionVector > m_exp
The list of local expansions.
Definition: ExpList.h:1036
StandardMatrixTag boost::call_traits< LhsDataType >::const_reference rhs typedef NekMatrix< LhsDataType, StandardMatrixTag >::iterator iterator
#define ASSERTL2(condition, msg)
Assert Level 2 – Debugging which is used FULLDEBUG compilation mode. This level assert is designed t...
Definition: ErrorUtil.hpp:250
boost::shared_ptr< Expansion2D > Expansion2DSharedPtr
Definition: Expansion1D.h:49
bool Nektar::MultiRegions::DisContField3D::SameTypeOfBoundaryConditions ( const DisContField3D In)
protected

For each boundary region, checks that the types and number of boundary expansions in that region match.

Parameters
InContField3D to compare with.
Returns
true if boundary conditions match.

Definition at line 567 of file DisContField3D.cpp.

References Nektar::MultiRegions::ExpList::GetExpSize(), m_bndCondExpansions, m_bndConditions, Nektar::MultiRegions::ExpList::m_comm, and Nektar::LibUtilities::ReduceMin.

Referenced by Nektar::MultiRegions::ContField3D::ContField3D(), and DisContField3D().

569  {
570  int i;
571  bool returnval = true;
572 
573  for(i = 0; i < m_bndConditions.num_elements(); ++i)
574  {
575 
576  // check to see if boundary condition type is the same
577  // and there are the same number of boundary
578  // conditions in the boundary definition.
579  if((m_bndConditions[i]->GetBoundaryConditionType()
580  != In.m_bndConditions[i]->GetBoundaryConditionType())||
582  != In.m_bndCondExpansions[i]->GetExpSize()))
583  {
584  returnval = false;
585  break;
586  }
587  }
588 
589  // Compare with all other processes. Return true only if all
590  // processes report having the same boundary conditions.
591  int vSame = returnval ? 1 : 0;
592  m_comm->AllReduce(vSame, LibUtilities::ReduceMin);
593 
594  return (vSame == 1);
595  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_bndCondExpansions
An object which contains the discretised boundary conditions.
int GetExpSize(void)
This function returns the number of elements in the expansion.
Definition: ExpList.h:2046
LibUtilities::CommSharedPtr m_comm
Communicator.
Definition: ExpList.h:966
Array< OneD, SpatialDomains::BoundaryConditionShPtr > m_bndConditions
An array which contains the information about the boundary condition on the different boundary region...
void Nektar::MultiRegions::DisContField3D::SetUpDG ( const std::string  variable = "DefaultVar")
protected

Set up all DG member variables and maps.

Definition at line 308 of file DisContField3D.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL1, Nektar::StdRegions::eDir1BwdDir1_Dir2BwdDir2, Nektar::StdRegions::eDir1BwdDir1_Dir2FwdDir2, Nektar::StdRegions::eDir1BwdDir2_Dir2BwdDir1, Nektar::StdRegions::eDir1BwdDir2_Dir2FwdDir1, Nektar::StdRegions::eDir1FwdDir1_Dir2BwdDir2, Nektar::StdRegions::eDir1FwdDir2_Dir2BwdDir1, Nektar::StdRegions::eDir1FwdDir2_Dir2FwdDir1, Nektar::SpatialDomains::ePeriodic, Nektar::LocalRegions::Expansion3D::GetGeom3D(), Nektar::MultiRegions::_PeriodicEntity::id, IsLeftAdjacentFace(), Nektar::MultiRegions::_PeriodicEntity::isLocal, Nektar::iterator, m_bndCondExpansions, m_bndConditions, m_boundaryFaces, Nektar::MultiRegions::ExpList::m_exp, m_globalBndMat, Nektar::MultiRegions::ExpList::m_graph, m_leftAdjacentFaces, m_locTraceToTraceMap, m_periodicBwdCopy, m_periodicFaces, m_periodicFwdCopy, Nektar::MultiRegions::ExpList::m_session, m_trace, m_traceMap, Nektar::MultiRegions::NullExpListSharedPtr, Nektar::MultiRegions::_PeriodicEntity::orient, Nektar::LocalRegions::Expansion2D::SetAdjacentElementExp(), and Nektar::MultiRegions::ExpList::SetUpPhysNormals().

Referenced by DisContField3D(), and v_GetTrace().

309  {
311  {
312  return;
313  }
314 
315  ExpList2DSharedPtr trace;
316 
318  boost::dynamic_pointer_cast<SpatialDomains::MeshGraph3D>(
319  m_graph);
320 
321  // Set up matrix map
324 
325  // Set up Trace space
326  bool UseGenSegExp = true;
329  *m_exp,graph3D, m_periodicFaces, UseGenSegExp);
330 
331  m_trace = trace;
332 
334  m_session,graph3D,trace,*this,m_bndCondExpansions,
335  m_bndConditions, m_periodicFaces,variable);
336 
337  if (m_session->DefinesCmdLineArgument("verbose"))
338  {
339  m_traceMap->PrintStats(std::cout, variable);
340  }
341 
342  Array<OneD, Array<OneD, LocalRegions::ExpansionSharedPtr> >
343  &elmtToTrace = m_traceMap->GetElmtToTrace();
344 
345  // Scatter trace segments to 3D elements. For each element, we
346  // find the trace segment associated to each edge. The element
347  // then retains a pointer to the trace space segments, to ensure
348  // uniqueness of normals when retrieving from two adjoining
349  // elements which do not lie in a plane.
350  for (int i = 0; i < m_exp->size(); ++i)
351  {
352  for (int j = 0; j < (*m_exp)[i]->GetNfaces(); ++j)
353  {
355  (*m_exp)[i]->as<LocalRegions::Expansion3D>();
357  elmtToTrace[i][j]->as<LocalRegions::Expansion2D>();
358  exp3d->SetFaceExp (j, exp2d);
359  exp2d->SetAdjacentElementExp(j, exp3d);
360  }
361  }
362 
363  // Set up physical normals
365 
366  // Set up information for parallel jobs.
367  for (int i = 0; i < m_trace->GetExpSize(); ++i)
368  {
370  m_trace->GetExp(i)->as<LocalRegions::Expansion2D>();
371 
372  int offset = m_trace->GetPhys_Offset(i);
373  int traceGeomId = traceEl->GetGeom2D()->GetGlobalID();
375  traceGeomId);
376 
377  if (pIt != m_periodicFaces.end() && !pIt->second[0].isLocal)
378  {
379  if (traceGeomId != min(pIt->second[0].id, traceGeomId))
380  {
381  traceEl->GetLeftAdjacentElementExp()->NegateFaceNormal(
382  traceEl->GetLeftAdjacentElementFace());
383  }
384  }
385  else if (m_traceMap->GetTraceToUniversalMapUnique(offset) < 0)
386  {
387  traceEl->GetLeftAdjacentElementExp()->NegateFaceNormal(
388  traceEl->GetLeftAdjacentElementFace());
389  }
390  }
391 
392  int cnt, n, e;
393 
394  // Identify boundary faces
395  for(cnt = 0, n = 0; n < m_bndCondExpansions.num_elements(); ++n)
396  {
397  if (m_bndConditions[n]->GetBoundaryConditionType() !=
399  {
400  for(e = 0; e < m_bndCondExpansions[n]->GetExpSize(); ++e)
401  {
402  m_boundaryFaces.insert(
403  m_traceMap->GetBndCondTraceToGlobalTraceMap(cnt+e));
404  }
405  }
406  cnt += m_bndCondExpansions[n]->GetExpSize();
407  }
408 
409  // Set up information for periodic boundary conditions.
410  boost::unordered_map<int,pair<int,int> > perFaceToExpMap;
411  boost::unordered_map<int,pair<int,int> >::iterator it2;
412  cnt = 0;
414  for (int n = 0; n < m_exp->size(); ++n)
415  {
416  exp3d = (*m_exp)[n]->as<LocalRegions::Expansion3D>();
417  for (int e = 0; e < exp3d->GetNfaces(); ++e, ++cnt)
418  {
420  exp3d->GetGeom3D()->GetFid(e));
421 
422  if (it != m_periodicFaces.end())
423  {
424  perFaceToExpMap[it->first] = make_pair(n, e);
425  }
426  }
427  }
428 
429  // Set up left-adjacent face list.
430  m_leftAdjacentFaces.resize(cnt);
431  cnt = 0;
432  for (int i = 0; i < m_exp->size(); ++i)
433  {
434  for (int j = 0; j < (*m_exp)[i]->GetNfaces(); ++j, ++cnt)
435  {
437  }
438  }
439 
440  // Set up mapping to copy Fwd of periodic bcs to Bwd of other edge.
441  cnt = 0;
442  for (int n = 0; n < m_exp->size(); ++n)
443  {
444  exp3d = (*m_exp)[n]->as<LocalRegions::Expansion3D>();
445  for (int e = 0; e < exp3d->GetNfaces(); ++e, ++cnt)
446  {
447  int faceGeomId = exp3d->GetGeom3D()->GetFid(e);
448  int offset = m_trace->GetPhys_Offset(
449  elmtToTrace[n][e]->GetElmtId());
450 
451  // Check to see if this face is periodic.
452  PeriodicMap::iterator it = m_periodicFaces.find(faceGeomId);
453 
454  if (it != m_periodicFaces.end())
455  {
456  const PeriodicEntity &ent = it->second[0];
457  it2 = perFaceToExpMap.find(ent.id);
458 
459  if (it2 == perFaceToExpMap.end())
460  {
461  if (m_session->GetComm()->GetSize() > 1 &&
462  !ent.isLocal)
463  {
464  continue;
465  }
466  else
467  {
468  ASSERTL1(false, "Periodic edge not found!");
469  }
470  }
471 
473  "Periodic face in non-forward space?");
474 
475  int offset2 = m_trace->GetPhys_Offset(
476  elmtToTrace[it2->second.first][it2->second.second]->
477  GetElmtId());
478 
479  // Calculate relative orientations between faces to
480  // calculate copying map.
481  int nquad1 = elmtToTrace[n][e]->GetNumPoints(0);
482  int nquad2 = elmtToTrace[n][e]->GetNumPoints(1);
483 
484  vector<int> tmpBwd(nquad1*nquad2);
485  vector<int> tmpFwd(nquad1*nquad2);
486 
487  if (ent.orient == StdRegions::eDir1FwdDir2_Dir2FwdDir1 ||
488  ent.orient == StdRegions::eDir1BwdDir2_Dir2FwdDir1 ||
489  ent.orient == StdRegions::eDir1FwdDir2_Dir2BwdDir1 ||
491  {
492  for (int i = 0; i < nquad2; ++i)
493  {
494  for (int j = 0; j < nquad1; ++j)
495  {
496  tmpBwd[i*nquad1+j] = offset2 + i*nquad1+j;
497  tmpFwd[i*nquad1+j] = offset + j*nquad2+i;
498  }
499  }
500  }
501  else
502  {
503  for (int i = 0; i < nquad2; ++i)
504  {
505  for (int j = 0; j < nquad1; ++j)
506  {
507  tmpBwd[i*nquad1+j] = offset2 + i*nquad1+j;
508  tmpFwd[i*nquad1+j] = offset + i*nquad1+j;
509  }
510  }
511  }
512 
513  if (ent.orient == StdRegions::eDir1BwdDir1_Dir2FwdDir2 ||
514  ent.orient == StdRegions::eDir1BwdDir1_Dir2BwdDir2 ||
515  ent.orient == StdRegions::eDir1FwdDir2_Dir2BwdDir1 ||
517  {
518  // Reverse x direction
519  for (int i = 0; i < nquad2; ++i)
520  {
521  for (int j = 0; j < nquad1/2; ++j)
522  {
523  swap(tmpFwd[i*nquad1 + j],
524  tmpFwd[i*nquad1 + nquad1-j-1]);
525  }
526  }
527  }
528 
529  if (ent.orient == StdRegions::eDir1FwdDir1_Dir2BwdDir2 ||
530  ent.orient == StdRegions::eDir1BwdDir1_Dir2BwdDir2 ||
531  ent.orient == StdRegions::eDir1BwdDir2_Dir2FwdDir1 ||
533  {
534  // Reverse y direction
535  for (int j = 0; j < nquad1; ++j)
536  {
537  for (int i = 0; i < nquad2/2; ++i)
538  {
539  swap(tmpFwd[i*nquad1 + j],
540  tmpFwd[(nquad2-i-1)*nquad1 + j]);
541  }
542  }
543  }
544 
545  for (int i = 0; i < nquad1*nquad2; ++i)
546  {
547  m_periodicFwdCopy.push_back(tmpFwd[i]);
548  m_periodicBwdCopy.push_back(tmpBwd[i]);
549  }
550  }
551  }
552  }
553 
555  AllocateSharedPtr(*this, m_trace, elmtToTrace,
557 
558  }
boost::shared_ptr< MeshGraph3D > MeshGraph3DSharedPtr
Definition: MeshGraph3D.h:224
Array< OneD, MultiRegions::ExpListSharedPtr > m_bndCondExpansions
An object which contains the discretised boundary conditions.
static ExpListSharedPtr NullExpListSharedPtr
Definition: ExpList.h:1477
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
bool IsLeftAdjacentFace(const int n, const int e)
std::set< int > m_boundaryFaces
A set storing the global IDs of any boundary faces.
PeriodicMap m_periodicFaces
A map which identifies pairs of periodic faces.
std::vector< int > m_periodicFwdCopy
A vector indicating degress of freedom which need to be copied from forwards to backwards space in ca...
boost::shared_ptr< LocalRegions::ExpansionVector > m_exp
The list of local expansions.
Definition: ExpList.h:1036
boost::shared_ptr< Expansion3D > Expansion3DSharedPtr
Definition: Expansion2D.h:48
LocTraceToTraceMapSharedPtr m_locTraceToTraceMap
Map of local trace (the points at the face of the element) to the trace space discretisation.
SpatialDomains::MeshGraphSharedPtr m_graph
Mesh associated with this expansion list.
Definition: ExpList.h:972
LibUtilities::SessionReaderSharedPtr m_session
Session.
Definition: ExpList.h:969
boost::shared_ptr< ExpList2D > ExpList2DSharedPtr
Shared pointer to an ExpList2D object.
Definition: ExpList2D.h:49
StandardMatrixTag boost::call_traits< LhsDataType >::const_reference rhs typedef NekMatrix< LhsDataType, StandardMatrixTag >::iterator iterator
Array< OneD, SpatialDomains::BoundaryConditionShPtr > m_bndConditions
An array which contains the information about the boundary condition on the different boundary region...
struct Nektar::MultiRegions::_PeriodicEntity PeriodicEntity
#define ASSERTL1(condition, msg)
Assert Level 1 – Debugging which is used whether in FULLDEBUG or DEBUG compilation mode...
Definition: ErrorUtil.hpp:228
boost::shared_ptr< Expansion2D > Expansion2DSharedPtr
Definition: Expansion1D.h:49
void Nektar::MultiRegions::DisContField3D::v_AddFwdBwdTraceIntegral ( const Array< OneD, const NekDouble > &  Fwd,
const Array< OneD, const NekDouble > &  Bwd,
Array< OneD, NekDouble > &  outarray 
)
protectedvirtual

Add trace contributions into elemental coefficient spaces.

Given some quantity $ \vec{Fn} $, which conatins this routine calculates the integral

\[ \int_{\Omega^e} \vec{Fn}, \mathrm{d}S \]

and adds this to the coefficient space provided by outarray. The value of q is determined from the routine IsLeftAdjacentFace() which if true we use Fwd else we use Bwd

See also
Expansion3D::AddFaceNormBoundaryInt
Parameters
FwdThe trace quantities associated with left (fwd) adjancent elmt.
BwdThe trace quantities associated with right (bwd) adjacent elet.
outarrayResulting 3D coefficient space.

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 1884 of file DisContField3D.cpp.

References m_locTraceToTraceMap, and m_trace.

1888  {
1889  Array<OneD, NekDouble> Coeffs(m_trace->GetNcoeffs());
1890 
1891  m_trace->IProductWRTBase(Fwd,Coeffs);
1892  m_locTraceToTraceMap->AddTraceCoeffsToFieldCoeffs(0,Coeffs,outarray);
1893  m_trace->IProductWRTBase(Bwd,Coeffs);
1894  m_locTraceToTraceMap->AddTraceCoeffsToFieldCoeffs(1,Coeffs,outarray);
1895  }
LocTraceToTraceMapSharedPtr m_locTraceToTraceMap
Map of local trace (the points at the face of the element) to the trace space discretisation.
void Nektar::MultiRegions::DisContField3D::v_AddTraceIntegral ( const Array< OneD, const NekDouble > &  Fn,
Array< OneD, NekDouble > &  outarray 
)
protectedvirtual

Add trace contributions into elemental coefficient spaces.

Given some quantity $ \vec{Fn} $, which conatins this routine calculates the integral

\[ \int_{\Omega^e} \vec{Fn}, \mathrm{d}S \]

and adds this to the coefficient space provided by outarray.

See also
Expansion3D::AddFaceNormBoundaryInt
Parameters
FnThe trace quantities.
outarrayResulting 3D coefficient space.

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 1850 of file DisContField3D.cpp.

References m_locTraceToTraceMap, and m_trace.

1853  {
1854 
1855  Array<OneD, NekDouble> Fcoeffs(m_trace->GetNcoeffs());
1856  m_trace->IProductWRTBase(Fn, Fcoeffs);
1857 
1858  m_locTraceToTraceMap->AddTraceCoeffsToFieldCoeffs(Fcoeffs,
1859  outarray);
1860  }
LocTraceToTraceMapSharedPtr m_locTraceToTraceMap
Map of local trace (the points at the face of the element) to the trace space discretisation.
void Nektar::MultiRegions::DisContField3D::v_EvaluateBoundaryConditions ( const NekDouble  time = 0.0,
const std::string  varName = "",
const NekDouble  x2_in = NekConstants::kNekUnsetDouble,
const NekDouble  x3_in = NekConstants::kNekUnsetDouble 
)
protectedvirtual

This function evaluates the boundary conditions at a certain time-level.

Based on the boundary condition $g(\boldsymbol{x},t)$ evaluated at a given time-level t, this function transforms the boundary conditions onto the coefficients of the (one-dimensional) boundary expansion. Depending on the type of boundary conditions, these expansion coefficients are calculated in different ways:

  • Dirichlet boundary conditions
    In order to ensure global $C^0$ continuity of the spectral/hp approximation, the Dirichlet boundary conditions are projected onto the boundary expansion by means of a modified $C^0$ continuous Galerkin projection. This projection can be viewed as a collocation projection at the vertices, followed by an $L^2$ projection on the interior modes of the edges. The resulting coefficients $\boldsymbol{\hat{u}}^{\mathcal{D}}$ will be stored for the boundary expansion.
  • Neumann boundary conditions In the discrete Galerkin formulation of the problem to be solved, the Neumann boundary conditions appear as the set of surface integrals:

    \[\boldsymbol{\hat{g}}=\int_{\Gamma} \phi^e_n(\boldsymbol{x})g(\boldsymbol{x})d(\boldsymbol{x})\quad \forall n \]

    As a result, it are the coefficients $\boldsymbol{\hat{g}}$ that will be stored in the boundary expansion
Parameters
timeThe time at which the boundary conditions should be evaluated.
bndCondExpansionsList of boundary conditions.
bndConditionsInformation about the boundary conditions.

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 2447 of file DisContField3D.cpp.

References ASSERTL0, Nektar::SpatialDomains::eDirichlet, Nektar::SpatialDomains::eNeumann, Nektar::SpatialDomains::eRobin, Nektar::LibUtilities::Equation::Evaluate(), Nektar::MultiRegions::ExpList::ExtractFileBCs(), m_bndCondExpansions, m_bndConditions, Nektar::SpatialDomains::DirichletBoundaryCondition::m_filename, Nektar::SpatialDomains::NeumannBoundaryCondition::m_filename, Nektar::SpatialDomains::RobinBoundaryCondition::m_filename, and Vmath::Vmul().

2452  {
2453  int i;
2454  int npoints;
2455  int nbnd = m_bndCondExpansions.num_elements();
2456  MultiRegions::ExpListSharedPtr locExpList;
2457 
2458  for (i = 0; i < nbnd; ++i)
2459  {
2460  if (time == 0.0 || m_bndConditions[i]->IsTimeDependent())
2461  {
2462  locExpList = m_bndCondExpansions[i];
2463  npoints = locExpList->GetNpoints();
2464 
2465  Array<OneD, NekDouble> x0(npoints, 0.0);
2466  Array<OneD, NekDouble> x1(npoints, 0.0);
2467  Array<OneD, NekDouble> x2(npoints, 0.0);
2468  Array<OneD, NekDouble> valuesFile(npoints, 1.0), valuesExp(npoints, 1.0);
2469 
2470  locExpList->GetCoords(x0, x1, x2);
2471 
2472  if (m_bndConditions[i]->GetBoundaryConditionType()
2474  {
2475  SpatialDomains::DirichletBCShPtr bcPtr = boost::static_pointer_cast<
2476  SpatialDomains::DirichletBoundaryCondition>(
2477  m_bndConditions[i]);
2478  string filebcs = bcPtr->m_filename;
2479  string exprbcs = bcPtr->m_expr;
2480 
2481  if (filebcs != "")
2482  {
2483  ExtractFileBCs(filebcs, bcPtr->m_comm, varName, locExpList);
2484  valuesFile = locExpList->GetPhys();
2485  }
2486 
2487  if (exprbcs != "")
2488  {
2489  LibUtilities::Equation condition = boost::static_pointer_cast<SpatialDomains::
2490  DirichletBoundaryCondition >(
2491  m_bndConditions[i])->m_dirichletCondition;
2492 
2493  condition.Evaluate(x0, x1, x2, time, valuesExp);
2494  }
2495 
2496  Vmath::Vmul(npoints, valuesExp, 1, valuesFile, 1, locExpList->UpdatePhys(), 1);
2497 
2498  locExpList->FwdTrans_BndConstrained(
2499  locExpList->GetPhys(),
2500  locExpList->UpdateCoeffs());
2501  }
2502  else if (m_bndConditions[i]->GetBoundaryConditionType()
2504  {
2505  SpatialDomains::NeumannBCShPtr bcPtr = boost::static_pointer_cast<
2506  SpatialDomains::NeumannBoundaryCondition>(
2507  m_bndConditions[i]);
2508  string filebcs = bcPtr->m_filename;
2509 
2510  if (filebcs != "")
2511  {
2512  ExtractFileBCs(filebcs, bcPtr->m_comm, varName, locExpList);
2513  }
2514  else
2515  {
2516 
2517  LibUtilities::Equation condition = boost::
2518  static_pointer_cast<SpatialDomains::
2519  NeumannBoundaryCondition>(
2520  m_bndConditions[i])->m_neumannCondition;
2521 
2522  condition.Evaluate(x0, x1, x2, time,
2523  locExpList->UpdatePhys());
2524 
2525  locExpList->IProductWRTBase(locExpList->GetPhys(),
2526  locExpList->UpdateCoeffs());
2527  }
2528  }
2529  else if (m_bndConditions[i]->GetBoundaryConditionType()
2531  {
2532  SpatialDomains::RobinBCShPtr bcPtr = boost::static_pointer_cast<
2533  SpatialDomains::RobinBoundaryCondition>(
2534  m_bndConditions[i]);
2535  string filebcs = bcPtr->m_filename;
2536 
2537  if (filebcs != "")
2538  {
2539  ExtractFileBCs(filebcs, bcPtr->m_comm, varName, locExpList);
2540  }
2541  else
2542  {
2543  LibUtilities::Equation condition = boost::
2544  static_pointer_cast<SpatialDomains::
2545  RobinBoundaryCondition>(
2546  m_bndConditions[i])->m_robinFunction;
2547 
2548  condition.Evaluate(x0, x1, x2, time,
2549  locExpList->UpdatePhys());
2550 
2551  }
2552 
2553  locExpList->IProductWRTBase(locExpList->GetPhys(),
2554  locExpList->UpdateCoeffs());
2555 
2556  }
2557  else
2558  {
2559  ASSERTL0(false, "This type of BC not implemented yet");
2560  }
2561  }
2562  }
2563  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
void ExtractFileBCs(const std::string &fileName, LibUtilities::CommSharedPtr comm, const std::string &varName, const boost::shared_ptr< ExpList > locExpList)
Definition: ExpList.cpp:2011
Array< OneD, MultiRegions::ExpListSharedPtr > m_bndCondExpansions
An object which contains the discretised boundary conditions.
boost::shared_ptr< NeumannBoundaryCondition > NeumannBCShPtr
Definition: Conditions.h:221
boost::shared_ptr< DirichletBoundaryCondition > DirichletBCShPtr
Definition: Conditions.h:220
boost::shared_ptr< ExpList > ExpListSharedPtr
Shared pointer to an ExpList object.
Array< OneD, SpatialDomains::BoundaryConditionShPtr > m_bndConditions
An array which contains the information about the boundary condition on the different boundary region...
boost::shared_ptr< RobinBoundaryCondition > RobinBCShPtr
Definition: Conditions.h:222
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::MultiRegions::DisContField3D::v_ExtractTracePhys ( Array< OneD, NekDouble > &  outarray)
protectedvirtual

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 1806 of file DisContField3D.cpp.

References ASSERTL1, Nektar::MultiRegions::ExpList::m_phys, and Nektar::MultiRegions::ExpList::m_physState.

1808  {
1809  ASSERTL1(m_physState == true,
1810  "Field is not in physical space.");
1811 
1812  v_ExtractTracePhys(m_phys, outarray);
1813  }
virtual void v_ExtractTracePhys(Array< OneD, NekDouble > &outarray)
Array< OneD, NekDouble > m_phys
The global expansion evaluated at the quadrature points.
Definition: ExpList.h:1015
bool m_physState
The state of the array m_phys.
Definition: ExpList.h:1024
#define ASSERTL1(condition, msg)
Assert Level 1 – Debugging which is used whether in FULLDEBUG or DEBUG compilation mode...
Definition: ErrorUtil.hpp:228
void Nektar::MultiRegions::DisContField3D::v_ExtractTracePhys ( const Array< OneD, const NekDouble > &  inarray,
Array< OneD, NekDouble > &  outarray 
)
protectedvirtual

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 1815 of file DisContField3D.cpp.

References m_locTraceToTraceMap, m_traceMap, and Vmath::Zero().

1818  {
1819 
1820  Vmath::Zero(outarray.num_elements(), outarray, 1);
1821 
1822  Array<OneD, NekDouble> facevals(m_locTraceToTraceMap->GetNFwdLocTracePts());
1823  m_locTraceToTraceMap->FwdLocTracesFromField(inarray,facevals);
1824  m_locTraceToTraceMap->InterpLocFacesToTrace(0,facevals,outarray);
1825 
1826  // gather entries along parallel partitions which have
1827  // only filled in Fwd part on their own partition
1828  m_traceMap->UniversalTraceAssemble(outarray);
1829 
1830  }
LocTraceToTraceMapSharedPtr m_locTraceToTraceMap
Map of local trace (the points at the face of the element) to the trace space discretisation.
void Zero(int n, T *x, const int incx)
Zero vector.
Definition: Vmath.cpp:373
void Nektar::MultiRegions::DisContField3D::v_GeneralMatrixOp ( const GlobalMatrixKey gkey,
const Array< OneD, const NekDouble > &  inarray,
Array< OneD, NekDouble > &  outarray,
CoeffState  coeffstate = eLocal 
)
protectedvirtual

Calculates the result of the multiplication of a global matrix of type specified by mkey with a vector given by inarray.

Parameters
mkeyKey representing desired matrix multiplication.
inarrayInput vector.
outarrayResulting multiplication.

Reimplemented from Nektar::MultiRegions::ExpList.

Reimplemented in Nektar::MultiRegions::ContField3D.

Definition at line 2164 of file DisContField3D.cpp.

References Nektar::eWrapper, Nektar::MultiRegions::ExpList::GetBlockMatrix(), and m_traceMap.

2169  {
2170  int LocBndCoeffs = m_traceMap->GetNumLocalBndCoeffs();
2171  Array<OneD, NekDouble> loc_lambda(LocBndCoeffs);
2172  DNekVec LocLambda(LocBndCoeffs,loc_lambda,eWrapper);
2173  const DNekScalBlkMatSharedPtr& HDGHelm = GetBlockMatrix(gkey);
2174 
2175  m_traceMap->GlobalToLocalBnd(inarray, loc_lambda);
2176  LocLambda = (*HDGHelm) * LocLambda;
2177  m_traceMap->AssembleBnd(loc_lambda,outarray);
2178  }
const DNekScalBlkMatSharedPtr & GetBlockMatrix(const GlobalMatrixKey &gkey)
Definition: ExpList.cpp:914
boost::shared_ptr< DNekScalBlkMat > DNekScalBlkMatSharedPtr
Definition: NekTypeDefs.hpp:74
NekVector< NekDouble > DNekVec
Definition: NekTypeDefs.hpp:49
virtual const Array<OneD,const MultiRegions::ExpListSharedPtr>& Nektar::MultiRegions::DisContField3D::v_GetBndCondExpansions ( void  )
inlineprotectedvirtual

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 240 of file DisContField3D.h.

References m_bndCondExpansions.

241  {
242  return m_bndCondExpansions;
243  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_bndCondExpansions
An object which contains the discretised boundary conditions.
virtual const Array<OneD,const SpatialDomains::BoundaryConditionShPtr>& Nektar::MultiRegions::DisContField3D::v_GetBndConditions ( void  )
inlineprotectedvirtual

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 247 of file DisContField3D.h.

References m_bndConditions.

248  {
249  return m_bndConditions;
250  }
Array< OneD, SpatialDomains::BoundaryConditionShPtr > m_bndConditions
An array which contains the information about the boundary condition on the different boundary region...
void Nektar::MultiRegions::DisContField3D::v_GetBndElmtExpansion ( int  i,
boost::shared_ptr< ExpList > &  result,
const bool  DeclareCoeffPhysArrays 
)
protectedvirtual

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 1956 of file DisContField3D.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), Nektar::MultiRegions::ExpList::GetBoundaryToElmtMap(), Nektar::MultiRegions::ExpList::GetCoeff_Offset(), Nektar::MultiRegions::ExpList::GetCoeffs(), Nektar::MultiRegions::ExpList::GetExp(), Nektar::MultiRegions::ExpList::GetPhys(), Nektar::MultiRegions::ExpList::GetPhys_Offset(), m_bndCondExpansions, and Vmath::Vcopy().

1959  {
1960  int n, cnt, nq;
1961  int offsetOld, offsetNew;
1962  std::vector<unsigned int> eIDs;
1963 
1964  Array<OneD, int> ElmtID,EdgeID;
1965  GetBoundaryToElmtMap(ElmtID,EdgeID);
1966 
1967  // Skip other boundary regions
1968  for (cnt = n = 0; n < i; ++n)
1969  {
1970  cnt += m_bndCondExpansions[n]->GetExpSize();
1971  }
1972 
1973  // Populate eIDs with information from BoundaryToElmtMap
1974  for (n = 0; n < m_bndCondExpansions[i]->GetExpSize(); ++n)
1975  {
1976  eIDs.push_back(ElmtID[cnt+n]);
1977  }
1978 
1979  // Create expansion list
1980  result =
1982  (*this, eIDs, DeclareCoeffPhysArrays);
1983 
1984  // Copy phys and coeffs to new explist
1985  if (DeclareCoeffPhysArrays)
1986  {
1987  Array<OneD, NekDouble> tmp1, tmp2;
1988  for (n = 0; n < result->GetExpSize(); ++n)
1989  {
1990  nq = GetExp(ElmtID[cnt+n])->GetTotPoints();
1991  offsetOld = GetPhys_Offset(ElmtID[cnt+n]);
1992  offsetNew = result->GetPhys_Offset(n);
1993  Vmath::Vcopy(nq, tmp1 = GetPhys()+ offsetOld, 1,
1994  tmp2 = result->UpdatePhys()+ offsetNew, 1);
1995 
1996  nq = GetExp(ElmtID[cnt+n])->GetNcoeffs();
1997  offsetOld = GetCoeff_Offset(ElmtID[cnt+n]);
1998  offsetNew = result->GetCoeff_Offset(n);
1999  Vmath::Vcopy(nq, tmp1 = GetCoeffs()+ offsetOld, 1,
2000  tmp2 = result->UpdateCoeffs()+ offsetNew, 1);
2001  }
2002  }
2003  }
const Array< OneD, const NekDouble > & GetCoeffs() const
This function returns (a reference to) the array (implemented as m_coeffs) containing all local expa...
Definition: ExpList.h:1938
Array< OneD, MultiRegions::ExpListSharedPtr > m_bndCondExpansions
An object which contains the discretised boundary conditions.
int GetCoeff_Offset(int n) const
Get the start offset position for a global list of m_coeffs correspoinding to element n...
Definition: ExpList.h:2076
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
int GetPhys_Offset(int n) const
Get the start offset position for a global list of m_phys correspoinding to element n...
Definition: ExpList.h:2084
const boost::shared_ptr< LocalRegions::ExpansionVector > GetExp() const
This function returns the vector of elements in the expansion.
Definition: ExpList.h:2067
void GetBoundaryToElmtMap(Array< OneD, int > &ElmtID, Array< OneD, int > &EdgeID)
Definition: ExpList.h:2286
const Array< OneD, const NekDouble > & GetPhys() const
This function returns (a reference to) the array (implemented as m_phys) containing the function ev...
Definition: ExpList.h:2037
void Vcopy(int n, const T *x, const int incx, T *y, const int incy)
Definition: Vmath.cpp:1061
void Nektar::MultiRegions::DisContField3D::v_GetBoundaryToElmtMap ( Array< OneD, int > &  ElmtID,
Array< OneD, int > &  FaceID 
)
protectedvirtual

Set up a list of elemeent IDs and edge IDs that link to the boundary conditions.

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 1901 of file DisContField3D.cpp.

References Nektar::MultiRegions::ExpList::GetExpSize(), m_BCtoElmMap, m_BCtoFaceMap, m_bndCondExpansions, m_bndConditions, and Nektar::MultiRegions::ExpList::m_graph.

1904  {
1905  if (m_BCtoElmMap.num_elements() == 0)
1906  {
1907  map<int,int> globalIdMap;
1908  int i, n;
1909  int cnt;
1910  int nbcs = 0;
1911 
1913  boost::dynamic_pointer_cast<SpatialDomains::MeshGraph3D>(
1914  m_graph);
1915 
1916  // Populate global ID map (takes global geometry ID to local
1917  // expansion list ID).
1919  for (i = 0; i < GetExpSize(); ++i)
1920  {
1921  exp3d = (*m_exp)[i]->as<LocalRegions::Expansion3D>();
1922  globalIdMap[exp3d->GetGeom3D()->GetGlobalID()] = i;
1923  }
1924 
1925  // Determine number of boundary condition expansions.
1926  for(i = 0; i < m_bndConditions.num_elements(); ++i)
1927  {
1928  nbcs += m_bndCondExpansions[i]->GetExpSize();
1929  }
1930 
1931  // Initialize arrays
1932  m_BCtoElmMap = Array<OneD, int>(nbcs);
1933  m_BCtoFaceMap = Array<OneD, int>(nbcs);
1934 
1936  for(cnt = n = 0; n < m_bndCondExpansions.num_elements(); ++n)
1937  {
1938  for(i = 0; i < m_bndCondExpansions[n]->GetExpSize(); ++i, ++cnt)
1939  {
1940  exp2d = m_bndCondExpansions[n]->GetExp(i)->
1941  as<LocalRegions::Expansion2D>();
1942  // Use face to element map from MeshGraph3D.
1944  graph3D->GetElementsFromFace(exp2d->GetGeom2D());
1945 
1946  m_BCtoElmMap[cnt] = globalIdMap[(*tmp)[0]->
1947  m_Element->GetGlobalID()];
1948  m_BCtoFaceMap[cnt] = (*tmp)[0]->m_FaceIndx;
1949  }
1950  }
1951  }
1952  ElmtID = m_BCtoElmMap;
1953  FaceID = m_BCtoFaceMap;
1954  }
boost::shared_ptr< MeshGraph3D > MeshGraph3DSharedPtr
Definition: MeshGraph3D.h:224
boost::shared_ptr< ElementFaceVector > ElementFaceVectorSharedPtr
Definition: MeshGraph.h:138
Array< OneD, MultiRegions::ExpListSharedPtr > m_bndCondExpansions
An object which contains the discretised boundary conditions.
int GetExpSize(void)
This function returns the number of elements in the expansion.
Definition: ExpList.h:2046
boost::shared_ptr< Expansion3D > Expansion3DSharedPtr
Definition: Expansion2D.h:48
SpatialDomains::MeshGraphSharedPtr m_graph
Mesh associated with this expansion list.
Definition: ExpList.h:972
Array< OneD, SpatialDomains::BoundaryConditionShPtr > m_bndConditions
An array which contains the information about the boundary condition on the different boundary region...
boost::shared_ptr< Expansion2D > Expansion2DSharedPtr
Definition: Expansion1D.h:49
void Nektar::MultiRegions::DisContField3D::v_GetFwdBwdTracePhys ( Array< OneD, NekDouble > &  Fwd,
Array< OneD, NekDouble > &  Bwd 
)
protectedvirtual

This method extracts the "forward" and "backward" trace data from the array field and puts the data into output vectors Fwd and Bwd.

We first define the convention which defines "forwards" and "backwards". First an association is made between the face of each element and its corresponding face in the trace space using the mapping m_traceMap. The element can either be left-adjacent or right-adjacent to this trace face (see Expansion2D::GetLeftAdjacentElementExp). Boundary faces are always left-adjacent since left-adjacency is populated first.

If the element is left-adjacent we extract the face trace data from field into the forward trace space Fwd; otherwise, we place it in the backwards trace space Bwd. In this way, we form a unique set of trace normals since these are always extracted from left-adjacent elements.

Parameters
fieldis a NekDouble array which contains the 3D data from which we wish to extract the backward and forward orientated trace/face arrays.
Returns
Updates a NekDouble array Fwd and Bwd

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 1712 of file DisContField3D.cpp.

References Nektar::MultiRegions::ExpList::m_phys.

1714  {
1715  v_GetFwdBwdTracePhys(m_phys, Fwd, Bwd);
1716  }
virtual void v_GetFwdBwdTracePhys(Array< OneD, NekDouble > &Fwd, Array< OneD, NekDouble > &Bwd)
This method extracts the "forward" and "backward" trace data from the array field and puts the data i...
Array< OneD, NekDouble > m_phys
The global expansion evaluated at the quadrature points.
Definition: ExpList.h:1015
void Nektar::MultiRegions::DisContField3D::v_GetFwdBwdTracePhys ( const Array< OneD, const NekDouble > &  field,
Array< OneD, NekDouble > &  Fwd,
Array< OneD, NekDouble > &  Bwd 
)
protectedvirtual

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 1718 of file DisContField3D.cpp.

References ASSERTL0, Nektar::SpatialDomains::eDirichlet, Nektar::SpatialDomains::eNeumann, Nektar::SpatialDomains::eRobin, Nektar::MultiRegions::ExpList::GetPhys(), m_bndCondExpansions, m_bndConditions, m_locTraceToTraceMap, m_periodicBwdCopy, m_periodicFwdCopy, m_trace, m_traceMap, npts, Vmath::Vcopy(), and Vmath::Zero().

1722  {
1723  int n, cnt, npts, e;
1724 
1725  // Zero vectors.
1726  Vmath::Zero(Fwd.num_elements(), Fwd, 1);
1727  Vmath::Zero(Bwd.num_elements(), Bwd, 1);
1728 
1729  Array<OneD, NekDouble> facevals(m_locTraceToTraceMap->
1730  GetNLocTracePts());
1731  m_locTraceToTraceMap->LocTracesFromField(field,facevals);
1732  m_locTraceToTraceMap->InterpLocFacesToTrace(0, facevals, Fwd);
1733 
1734  Array<OneD, NekDouble> invals = facevals + m_locTraceToTraceMap->
1735  GetNFwdLocTracePts();
1736  m_locTraceToTraceMap->InterpLocFacesToTrace(1, invals, Bwd);
1737 
1738  // Fill boundary conditions into missing elements
1739  int id1, id2 = 0;
1740  cnt = 0;
1741 
1742  for(n = 0; n < m_bndCondExpansions.num_elements(); ++n)
1743  {
1744  if(m_bndConditions[n]->GetBoundaryConditionType() ==
1746  {
1747  for(e = 0; e < m_bndCondExpansions[n]->GetExpSize(); ++e)
1748  {
1749  npts = m_bndCondExpansions[n]->GetExp(e)->GetTotPoints();
1750  id1 = m_bndCondExpansions[n]->GetPhys_Offset(e);
1751  id2 = m_trace->GetPhys_Offset(
1752  m_traceMap->GetBndCondTraceToGlobalTraceMap(cnt+e));
1753  Vmath::Vcopy(npts,
1754  &(m_bndCondExpansions[n]->GetPhys())[id1], 1,
1755  &Bwd[id2], 1);
1756  }
1757 
1758  cnt += e;
1759  }
1760  else if (m_bndConditions[n]->GetBoundaryConditionType() ==
1762  m_bndConditions[n]->GetBoundaryConditionType() ==
1764  {
1765  for(e = 0; e < m_bndCondExpansions[n]->GetExpSize(); ++e)
1766  {
1767  npts = m_bndCondExpansions[n]->GetExp(e)->GetTotPoints();
1768  id1 = m_bndCondExpansions[n]->GetPhys_Offset(e);
1769  id2 = m_trace->GetPhys_Offset(
1770  m_traceMap->GetBndCondTraceToGlobalTraceMap(cnt+e));
1771 
1772  // Turning this off since we can have non-zero
1773  //Neumann in mixed CG-DG method
1774  //ASSERTL1((m_bndCondExpansions[n]->GetPhys())[id1]
1775  //== 0.0, "method not set up for non-zero
1776  //Neumann " "boundary condition");
1777 
1778  Vmath::Vcopy(npts,&Fwd[id2],1,&Bwd[id2],1);
1779  }
1780 
1781  cnt += e;
1782  }
1783  else
1784  {
1785  ASSERTL0(false, "Method only set up for Dirichlet, Neumann "
1786  "and Robin conditions.");
1787  }
1788  }
1789 
1790  // Copy any periodic boundary conditions.
1791  for (n = 0; n < m_periodicFwdCopy.size(); ++n)
1792  {
1793  Bwd[m_periodicBwdCopy[n]] = Fwd[m_periodicFwdCopy[n]];
1794  }
1795 
1796  // Do parallel exchange for forwards/backwards spaces.
1797  m_traceMap->UniversalTraceAssemble(Fwd);
1798  m_traceMap->UniversalTraceAssemble(Bwd);
1799  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
Array< OneD, MultiRegions::ExpListSharedPtr > m_bndCondExpansions
An object which contains the discretised boundary conditions.
std::vector< int > m_periodicFwdCopy
A vector indicating degress of freedom which need to be copied from forwards to backwards space in ca...
LocTraceToTraceMapSharedPtr m_locTraceToTraceMap
Map of local trace (the points at the face of the element) to the trace space discretisation.
static std::string npts
Definition: InputFld.cpp:43
const Array< OneD, const NekDouble > & GetPhys() const
This function returns (a reference to) the array (implemented as m_phys) containing the function ev...
Definition: ExpList.h:2037
Array< OneD, SpatialDomains::BoundaryConditionShPtr > m_bndConditions
An array which contains the information about the boundary condition on the different boundary region...
void Zero(int n, T *x, const int incx)
Zero vector.
Definition: Vmath.cpp:373
void Vcopy(int n, const T *x, const int incx, T *y, const int incy)
Definition: Vmath.cpp:1061
const vector< bool > & Nektar::MultiRegions::DisContField3D::v_GetLeftAdjacentFaces ( void  ) const
protectedvirtual

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 1801 of file DisContField3D.cpp.

References m_leftAdjacentFaces.

1802  {
1803  return m_leftAdjacentFaces;
1804  }
virtual void Nektar::MultiRegions::DisContField3D::v_GetPeriodicEntities ( PeriodicMap periodicVerts,
PeriodicMap periodicEdges,
PeriodicMap periodicFaces 
)
inlineprotectedvirtual

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 214 of file DisContField3D.h.

References m_periodicEdges, m_periodicFaces, and m_periodicVerts.

218  {
219  periodicVerts = m_periodicVerts;
220  periodicEdges = m_periodicEdges;
221  periodicFaces = m_periodicFaces;
222  }
PeriodicMap m_periodicFaces
A map which identifies pairs of periodic faces.
PeriodicMap m_periodicVerts
A map which identifies groups of periodic vertices.
PeriodicMap m_periodicEdges
A map which identifies groups of periodic edges.
map< int, RobinBCInfoSharedPtr > Nektar::MultiRegions::DisContField3D::v_GetRobinBCInfo ( void  )
protectedvirtual

Search through the edge expansions and identify which ones have Robin/Mixed type boundary conditions. If find a Robin boundary then store the edge id of the boundary condition and the array of points of the physical space boundary condition which are hold the boundary condition primitive variable coefficient at the quatrature points

Returns
std map containing the robin boundary condition info using a key of the element id

There is a next member to allow for more than one Robin boundary condition per element

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 2193 of file DisContField3D.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), Nektar::SpatialDomains::eRobin, Nektar::LibUtilities::Equation::Evaluate(), Nektar::MultiRegions::ExpList::GetBoundaryToElmtMap(), m_bndCondExpansions, and m_bndConditions.

2194  {
2195  int i,cnt;
2196  map<int, RobinBCInfoSharedPtr> returnval;
2197  Array<OneD, int> ElmtID,FaceID;
2198  GetBoundaryToElmtMap(ElmtID,FaceID);
2199 
2200  for(cnt = i = 0; i < m_bndCondExpansions.num_elements(); ++i)
2201  {
2202  MultiRegions::ExpListSharedPtr locExpList;
2203 
2204  if(m_bndConditions[i]->GetBoundaryConditionType() == SpatialDomains::eRobin)
2205  {
2206  int e,elmtid;
2207  Array<OneD, NekDouble> Array_tmp;
2208 
2209  locExpList = m_bndCondExpansions[i];
2210 
2211  int npoints = locExpList->GetNpoints();
2212  Array<OneD, NekDouble> x0(npoints, 0.0);
2213  Array<OneD, NekDouble> x1(npoints, 0.0);
2214  Array<OneD, NekDouble> x2(npoints, 0.0);
2215  Array<OneD, NekDouble> coeffphys(npoints);
2216 
2217  locExpList->GetCoords(x0, x1, x2);
2218 
2219  LibUtilities::Equation coeffeqn =
2220  boost::static_pointer_cast<
2221  SpatialDomains::RobinBoundaryCondition>
2222  (m_bndConditions[i])->m_robinPrimitiveCoeff;
2223 
2224  // evalaute coefficient
2225  coeffeqn.Evaluate(x0, x1, x2, 0.0, coeffphys);
2226 
2227  for(e = 0; e < locExpList->GetExpSize(); ++e)
2228  {
2229  RobinBCInfoSharedPtr rInfo =
2231  ::AllocateSharedPtr(FaceID[cnt+e],
2232  Array_tmp = coeffphys +
2233  locExpList->GetPhys_Offset(e));
2234 
2235  elmtid = ElmtID[cnt+e];
2236  // make link list if necessary
2237  if(returnval.count(elmtid) != 0)
2238  {
2239  rInfo->next = returnval.find(elmtid)->second;
2240  }
2241  returnval[elmtid] = rInfo;
2242  }
2243  }
2244  cnt += m_bndCondExpansions[i]->GetExpSize();
2245  }
2246 
2247  return returnval;
2248  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_bndCondExpansions
An object which contains the discretised boundary conditions.
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
boost::shared_ptr< RobinBCInfo > RobinBCInfoSharedPtr
void GetBoundaryToElmtMap(Array< OneD, int > &ElmtID, Array< OneD, int > &EdgeID)
Definition: ExpList.h:2286
boost::shared_ptr< ExpList > ExpListSharedPtr
Shared pointer to an ExpList object.
Array< OneD, SpatialDomains::BoundaryConditionShPtr > m_bndConditions
An array which contains the information about the boundary condition on the different boundary region...
virtual ExpListSharedPtr& Nektar::MultiRegions::DisContField3D::v_GetTrace ( )
inlineprotectedvirtual

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 224 of file DisContField3D.h.

References m_trace, Nektar::MultiRegions::NullExpListSharedPtr, and SetUpDG().

225  {
227  {
228  SetUpDG();
229  }
230 
231  return m_trace;
232  }
static ExpListSharedPtr NullExpListSharedPtr
Definition: ExpList.h:1477
void SetUpDG(const std::string="DefaultVar")
Set up all DG member variables and maps.
virtual AssemblyMapDGSharedPtr& Nektar::MultiRegions::DisContField3D::v_GetTraceMap ( void  )
inlineprotectedvirtual

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 234 of file DisContField3D.h.

References m_traceMap.

235  {
236  return m_traceMap;
237  }
void Nektar::MultiRegions::DisContField3D::v_HelmSolve ( const Array< OneD, const NekDouble > &  inarray,
Array< OneD, NekDouble > &  outarray,
const FlagList flags,
const StdRegions::ConstFactorMap factors,
const StdRegions::VarCoeffMap varcoeff,
const Array< OneD, const NekDouble > &  dirForcing,
const bool  PhysSpaceForcing 
)
protectedvirtual

Solving Helmholtz Equation in 3D

Reimplemented from Nektar::MultiRegions::ExpList.

Reimplemented in Nektar::MultiRegions::ContField3D.

Definition at line 2022 of file DisContField3D.cpp.

References Nektar::SpatialDomains::eDirichlet, Nektar::StdRegions::eHybridDGHelmBndLam, Nektar::StdRegions::eHybridDGLamToU, Nektar::StdRegions::eInvHybridDGHelmholtz, Nektar::eWrapper, Nektar::MultiRegions::ExpList::GetBlockMatrix(), Nektar::MultiRegions::ExpList::GetExpSize(), GetGlobalBndLinSys(), Nektar::MultiRegions::ExpList::GetNcoeffs(), Nektar::MultiRegions::ExpList::IProductWRTBase(), m_bndCondExpansions, m_bndConditions, Nektar::MultiRegions::ExpList::m_ncoeffs, m_trace, m_traceMap, Vmath::Neg(), Nektar::MultiRegions::NullAssemblyMapSharedPtr, Vmath::Smul(), Nektar::Transpose(), and Vmath::Zero().

2030  {
2031  int i,j,n,cnt,cnt1,nbndry;
2032  int nexp = GetExpSize();
2034 
2035  Array<OneD,NekDouble> f(m_ncoeffs);
2036  DNekVec F(m_ncoeffs,f,eWrapper);
2037  Array<OneD,NekDouble> e_f, e_l;
2038 
2039  //----------------------------------
2040  // Setup RHS Inner product
2041  //----------------------------------
2042  if(PhysSpaceForcing)
2043  {
2044  IProductWRTBase(inarray,f);
2045  Vmath::Neg(m_ncoeffs,f,1);
2046  }
2047  else
2048  {
2049  Vmath::Smul(m_ncoeffs,-1.0,inarray,1,f,1);
2050  }
2051 
2052  //----------------------------------
2053  // Solve continuous flux System
2054  //----------------------------------
2055  int GloBndDofs = m_traceMap->GetNumGlobalBndCoeffs();
2056  int NumDirichlet = m_traceMap->GetNumLocalDirBndCoeffs();
2057  int e_ncoeffs,id;
2058 
2059  // Retrieve block matrix of U^e
2060  GlobalMatrixKey HDGLamToUKey(StdRegions::eHybridDGLamToU,NullAssemblyMapSharedPtr,factors,varcoeff);
2061  const DNekScalBlkMatSharedPtr &HDGLamToU = GetBlockMatrix(HDGLamToUKey);
2062 
2063  // Retrieve global trace space storage, \Lambda, from trace expansion
2064  Array<OneD,NekDouble> BndSol = m_trace->UpdateCoeffs();
2065 
2066  // Create trace space forcing, F
2067  Array<OneD,NekDouble> BndRhs(GloBndDofs,0.0);
2068 
2069  // Zero \Lambda
2070  Vmath::Zero(GloBndDofs,BndSol,1);
2071 
2072  // Retrieve number of local trace space coefficients N_{\lambda},
2073  // and set up local elemental trace solution \lambda^e.
2074  int LocBndCoeffs = m_traceMap->GetNumLocalBndCoeffs();
2075  Array<OneD, NekDouble> loc_lambda(LocBndCoeffs);
2076  DNekVec LocLambda(LocBndCoeffs,loc_lambda,eWrapper);
2077 
2078  //----------------------------------
2079  // Evaluate Trace Forcing vector F
2080  // Kirby et al, 2010, P23, Step 5.
2081  //----------------------------------
2082  // Loop over all expansions in the domain
2083  for(cnt = cnt1 = n = 0; n < nexp; ++n)
2084  {
2085  nbndry = (*m_exp)[n]->NumDGBndryCoeffs();
2086 
2087  e_ncoeffs = (*m_exp)[n]->GetNcoeffs();
2088  e_f = f + cnt;
2089  e_l = loc_lambda + cnt1;
2090 
2091  // Local trace space \lambda^e
2092  DNekVec Floc (nbndry, e_l, eWrapper);
2093  // Local forcing f^e
2094  DNekVec ElmtFce (e_ncoeffs, e_f, eWrapper);
2095  // Compute local (U^e)^{\top} f^e
2096  Floc = Transpose(*(HDGLamToU->GetBlock(n,n)))*ElmtFce;
2097 
2098  cnt += e_ncoeffs;
2099  cnt1 += nbndry;
2100  }
2101 
2102  // Assemble local \lambda_e into global \Lambda
2103  m_traceMap->AssembleBnd(loc_lambda,BndRhs);
2104 
2105  // Copy Dirichlet boundary conditions and weak forcing into trace
2106  // space
2107  cnt = 0;
2108  for(i = 0; i < m_bndCondExpansions.num_elements(); ++i)
2109  {
2110  if(m_bndConditions[i]->GetBoundaryConditionType() == SpatialDomains::eDirichlet)
2111  {
2112  for(j = 0; j < (m_bndCondExpansions[i])->GetNcoeffs(); ++j)
2113  {
2114  id = m_traceMap->GetBndCondCoeffsToGlobalCoeffsMap(cnt++);
2115  BndSol[id] = m_bndCondExpansions[i]->GetCoeffs()[j];
2116  }
2117  }
2118  else
2119  {
2120  //Add weak boundary condition to trace forcing
2121  for(j = 0; j < (m_bndCondExpansions[i])->GetNcoeffs(); ++j)
2122  {
2123  id = m_traceMap->GetBndCondCoeffsToGlobalCoeffsMap(cnt++);
2124  BndRhs[id] += m_bndCondExpansions[i]->GetCoeffs()[j];
2125  }
2126  }
2127  }
2128 
2129  //----------------------------------
2130  // Solve trace problem: \Lambda = K^{-1} F
2131  // K is the HybridDGHelmBndLam matrix.
2132  //----------------------------------
2133  if(GloBndDofs - NumDirichlet > 0)
2134  {
2135  GlobalLinSysKey key(StdRegions::eHybridDGHelmBndLam,
2136  m_traceMap,factors,varcoeff);
2138  LinSys->Solve(BndRhs,BndSol,m_traceMap);
2139  }
2140 
2141  //----------------------------------
2142  // Internal element solves
2143  //----------------------------------
2144  GlobalMatrixKey invHDGhelmkey(StdRegions::eInvHybridDGHelmholtz,NullAssemblyMapSharedPtr,factors,varcoeff);
2145  const DNekScalBlkMatSharedPtr& InvHDGHelm = GetBlockMatrix(invHDGhelmkey);
2146  DNekVec out(m_ncoeffs,outarray,eWrapper);
2147  Vmath::Zero(m_ncoeffs,outarray,1);
2148 
2149  // get local trace solution from BndSol
2150  m_traceMap->GlobalToLocalBnd(BndSol,loc_lambda);
2151 
2152  // out = u_f + u_lam = (*InvHDGHelm)*f + (LamtoU)*Lam
2153  out = (*InvHDGHelm)*F + (*HDGLamToU)*LocLambda;
2154  }
const DNekScalBlkMatSharedPtr & GetBlockMatrix(const GlobalMatrixKey &gkey)
Definition: ExpList.cpp:914
GlobalLinSysSharedPtr GetGlobalBndLinSys(const GlobalLinSysKey &mkey)
Array< OneD, MultiRegions::ExpListSharedPtr > m_bndCondExpansions
An object which contains the discretised boundary conditions.
int GetExpSize(void)
This function returns the number of elements in the expansion.
Definition: ExpList.h:2046
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
int m_ncoeffs
The total number of local degrees of freedom. m_ncoeffs .
Definition: ExpList.h:976
boost::shared_ptr< DNekScalBlkMat > DNekScalBlkMatSharedPtr
Definition: NekTypeDefs.hpp:74
NekMatrix< InnerMatrixType, BlockMatrixTag > Transpose(NekMatrix< InnerMatrixType, BlockMatrixTag > &rhs)
void Neg(int n, T *x, const int incx)
Negate x = -x.
Definition: Vmath.cpp:396
static AssemblyMapSharedPtr NullAssemblyMapSharedPtr
Definition: AssemblyMap.h:55
NekVector< NekDouble > DNekVec
Definition: NekTypeDefs.hpp:49
void IProductWRTBase(const Array< OneD, const NekDouble > &inarray, Array< OneD, NekDouble > &outarray, CoeffState coeffstate=eLocal)
Definition: ExpList.h:1641
Array< OneD, SpatialDomains::BoundaryConditionShPtr > m_bndConditions
An array which contains the information about the boundary condition on the different boundary region...
int GetNcoeffs(void) const
Returns the total number of local degrees of freedom .
Definition: ExpList.h:1485
boost::shared_ptr< GlobalLinSys > GlobalLinSysSharedPtr
Pointer to a GlobalLinSys object.
Definition: GlobalLinSys.h:52
void Zero(int n, T *x, const int incx)
Zero vector.
Definition: Vmath.cpp:373
boost::shared_ptr< StdExpansion > StdExpansionSharedPtr
void Nektar::MultiRegions::DisContField3D::v_Reset ( )
protectedvirtual

Reset this field, so that geometry information can be updated.

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 2008 of file DisContField3D.cpp.

References m_bndCondExpansions, and Nektar::MultiRegions::ExpList::v_Reset().

2009  {
2010  ExpList::v_Reset();
2011 
2012  // Reset boundary condition expansions.
2013  for (int n = 0; n < m_bndCondExpansions.num_elements(); ++n)
2014  {
2015  m_bndCondExpansions[n]->Reset();
2016  }
2017  }
virtual void v_Reset()
Reset geometry information, metrics, matrix managers and geometry information.
Definition: ExpList.cpp:1537
Array< OneD, MultiRegions::ExpListSharedPtr > m_bndCondExpansions
An object which contains the discretised boundary conditions.
virtual MultiRegions::ExpListSharedPtr& Nektar::MultiRegions::DisContField3D::v_UpdateBndCondExpansion ( int  i)
inlineprotectedvirtual

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 253 of file DisContField3D.h.

254  {
255  return m_bndCondExpansions[i];
256  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_bndCondExpansions
An object which contains the discretised boundary conditions.
virtual Array<OneD, SpatialDomains::BoundaryConditionShPtr>& Nektar::MultiRegions::DisContField3D::v_UpdateBndConditions ( )
inlineprotectedvirtual

Reimplemented from Nektar::MultiRegions::ExpList.

Definition at line 259 of file DisContField3D.h.

References m_bndConditions.

260  {
261  return m_bndConditions;
262  }
Array< OneD, SpatialDomains::BoundaryConditionShPtr > m_bndConditions
An array which contains the information about the boundary condition on the different boundary region...

Member Data Documentation

Array<OneD, int> Nektar::MultiRegions::DisContField3D::m_BCtoElmMap

Definition at line 93 of file DisContField3D.h.

Referenced by v_GetBoundaryToElmtMap().

Array<OneD, int> Nektar::MultiRegions::DisContField3D::m_BCtoFaceMap

Definition at line 94 of file DisContField3D.h.

Referenced by v_GetBoundaryToElmtMap().

Array<OneD,MultiRegions::ExpListSharedPtr> Nektar::MultiRegions::DisContField3D::m_bndCondExpansions
protected
Array<OneD,SpatialDomains::BoundaryConditionShPtr> Nektar::MultiRegions::DisContField3D::m_bndConditions
protected
std::set<int> Nektar::MultiRegions::DisContField3D::m_boundaryFaces
protected

A set storing the global IDs of any boundary faces.

Definition at line 125 of file DisContField3D.h.

Referenced by IsLeftAdjacentFace(), and SetUpDG().

GlobalLinSysMapShPtr Nektar::MultiRegions::DisContField3D::m_globalBndMat
protected

Definition at line 115 of file DisContField3D.h.

Referenced by DisContField3D(), GetGlobalBndLinSys(), and SetUpDG().

std::vector<bool> Nektar::MultiRegions::DisContField3D::m_leftAdjacentFaces
protected

Definition at line 146 of file DisContField3D.h.

Referenced by GetLeftAdjacentFaces(), SetUpDG(), and v_GetLeftAdjacentFaces().

LocTraceToTraceMapSharedPtr Nektar::MultiRegions::DisContField3D::m_locTraceToTraceMap
protected

Map of local trace (the points at the face of the element) to the trace space discretisation.

Definition at line 120 of file DisContField3D.h.

Referenced by DisContField3D(), SetUpDG(), v_AddFwdBwdTraceIntegral(), v_AddTraceIntegral(), v_ExtractTracePhys(), and v_GetFwdBwdTracePhys().

std::vector<int> Nektar::MultiRegions::DisContField3D::m_periodicBwdCopy
protected

Definition at line 154 of file DisContField3D.h.

Referenced by SetUpDG(), and v_GetFwdBwdTracePhys().

PeriodicMap Nektar::MultiRegions::DisContField3D::m_periodicEdges
protected

A map which identifies groups of periodic edges.

Definition at line 135 of file DisContField3D.h.

Referenced by Nektar::MultiRegions::ContField3D::ContField3D(), DisContField3D(), FindPeriodicFaces(), and v_GetPeriodicEntities().

PeriodicMap Nektar::MultiRegions::DisContField3D::m_periodicFaces
protected

A map which identifies pairs of periodic faces.

Definition at line 130 of file DisContField3D.h.

Referenced by Nektar::MultiRegions::ContField3D::ContField3D(), DisContField3D(), FindPeriodicFaces(), IsLeftAdjacentFace(), SetUpDG(), and v_GetPeriodicEntities().

std::vector<int> Nektar::MultiRegions::DisContField3D::m_periodicFwdCopy
protected

A vector indicating degress of freedom which need to be copied from forwards to backwards space in case of a periodic boundary condition.

Definition at line 153 of file DisContField3D.h.

Referenced by SetUpDG(), and v_GetFwdBwdTracePhys().

PeriodicMap Nektar::MultiRegions::DisContField3D::m_periodicVerts
protected

A map which identifies groups of periodic vertices.

Definition at line 140 of file DisContField3D.h.

Referenced by Nektar::MultiRegions::ContField3D::ContField3D(), DisContField3D(), FindPeriodicFaces(), and v_GetPeriodicEntities().

ExpListSharedPtr Nektar::MultiRegions::DisContField3D::m_trace
protected
AssemblyMapDGSharedPtr Nektar::MultiRegions::DisContField3D::m_traceMap
protected