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Nektar::SolverUtils::EquationSystem Class Reference

A base class for describing how to solve specific equations. More...

#include <EquationSystem.h>

Inheritance diagram for Nektar::SolverUtils::EquationSystem:
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Public Member Functions

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

Protected Types

enum  HomogeneousType { eHomogeneous1D, eHomogeneous2D, eHomogeneous3D, eNotHomogeneous }
 Parameter for homogeneous expansions. More...
 

Protected Member Functions

SOLVER_UTILS_EXPORT EquationSystem (const LibUtilities::SessionReaderSharedPtr &pSession)
 Initialises EquationSystem class members. More...
 
int nocase_cmp (const std::string &s1, const std::string &s2)
 
virtual SOLVER_UTILS_EXPORT void v_InitObject ()
 Initialisation object for EquationSystem. More...
 
virtual SOLVER_UTILS_EXPORT void v_DoInitialise ()
 Virtual function for initialisation implementation. More...
 
virtual SOLVER_UTILS_EXPORT void v_DoSolve ()
 Virtual function for solve implementation. More...
 
virtual SOLVER_UTILS_EXPORT
NekDouble 
v_LinfError (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray)
 Virtual function for the L_inf error computation between fields and a given exact solution. More...
 
virtual SOLVER_UTILS_EXPORT
NekDouble 
v_L2Error (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray, bool Normalised=false)
 Virtual function for the L_2 error computation between fields and a given exact solution. More...
 
virtual SOLVER_UTILS_EXPORT void v_TransCoeffToPhys ()
 Virtual function for transformation to physical space. More...
 
virtual SOLVER_UTILS_EXPORT void v_TransPhysToCoeff ()
 Virtual function for transformation to coefficient space. More...
 
virtual SOLVER_UTILS_EXPORT void v_GenerateSummary (SummaryList &l)
 Virtual function for generating summary information. More...
 
virtual SOLVER_UTILS_EXPORT void v_SetInitialConditions (NekDouble initialtime=0.0, bool dumpInitialConditions=true, const int domain=0)
 
virtual SOLVER_UTILS_EXPORT void v_EvaluateExactSolution (unsigned int field, Array< OneD, NekDouble > &outfield, const NekDouble time)
 
SOLVER_UTILS_EXPORT void EvaluateFunctionExp (std::string pFieldName, Array< OneD, NekDouble > &pArray, const std::string &pFunctionName, const NekDouble &pTime=0.0, const int domain=0)
 
SOLVER_UTILS_EXPORT void EvaluateFunctionFld (std::string pFieldName, Array< OneD, NekDouble > &pArray, const std::string &pFunctionName, const NekDouble &pTime=0.0, const int domain=0)
 
SOLVER_UTILS_EXPORT void EvaluateFunctionPts (std::string pFieldName, Array< OneD, NekDouble > &pArray, const std::string &pFunctionName, const NekDouble &pTime=0.0, const int domain=0)
 
SOLVER_UTILS_EXPORT void LoadPts (std::string funcFilename, std::string filename, Nektar::LibUtilities::PtsFieldSharedPtr &outPts)
 
SOLVER_UTILS_EXPORT void SetUpBaseFields (SpatialDomains::MeshGraphSharedPtr &mesh)
 
SOLVER_UTILS_EXPORT void ImportFldBase (std::string pInfile, SpatialDomains::MeshGraphSharedPtr pGraph)
 
virtual SOLVER_UTILS_EXPORT void v_Output (void)
 
virtual SOLVER_UTILS_EXPORT
MultiRegions::ExpListSharedPtr 
v_GetPressure (void)
 
virtual SOLVER_UTILS_EXPORT void v_ExtraFldOutput (std::vector< Array< OneD, NekDouble > > &fieldcoeffs, std::vector< std::string > &variables)
 

Protected Attributes

LibUtilities::CommSharedPtr m_comm
 Communicator. More...
 
LibUtilities::SessionReaderSharedPtr m_session
 The session reader. More...
 
LibUtilities::FieldIOSharedPtr m_fld
 Field input/output. More...
 
std::map< std::string,
FieldUtils::Interpolator
m_interpolators
 Map of interpolator objects. More...
 
std::map< std::string,
std::pair< std::string,
LibUtilities::PtsFieldSharedPtr > > 
m_loadedPtsFields
 pts fields we already read from disk: {funcFilename: (filename, ptsfield)} More...
 
std::map< std::string,
std::pair< std::string,
loadedFldField > > 
m_loadedFldFields
 
Array< OneD,
MultiRegions::ExpListSharedPtr
m_fields
 Array holding all dependent variables. More...
 
Array< OneD,
MultiRegions::ExpListSharedPtr
m_base
 Base fields. More...
 
Array< OneD,
MultiRegions::ExpListSharedPtr
m_derivedfields
 Array holding all dependent variables. More...
 
SpatialDomains::BoundaryConditionsSharedPtr m_boundaryConditions
 Pointer to boundary conditions object. More...
 
SpatialDomains::MeshGraphSharedPtr m_graph
 Pointer to graph defining mesh. More...
 
std::string m_sessionName
 Name of the session. More...
 
NekDouble m_time
 Current time of simulation. More...
 
int m_initialStep
 Number of the step where the simulation should begin. More...
 
NekDouble m_fintime
 Finish time of the simulation. More...
 
NekDouble m_timestep
 Time step size. More...
 
NekDouble m_lambda
 Lambda constant in real system if one required. More...
 
NekDouble m_checktime
 Time between checkpoints. More...
 
int m_nchk
 Number of checkpoints written so far. More...
 
int m_steps
 Number of steps to take. More...
 
int m_checksteps
 Number of steps between checkpoints. More...
 
int m_spacedim
 Spatial dimension (>= expansion dim). More...
 
int m_expdim
 Expansion dimension. More...
 
bool m_singleMode
 Flag to determine if single homogeneous mode is used. More...
 
bool m_halfMode
 Flag to determine if half homogeneous mode is used. More...
 
bool m_multipleModes
 Flag to determine if use multiple homogenenous modes are used. More...
 
bool m_useFFT
 Flag to determine if FFT is used for homogeneous transform. More...
 
bool m_homogen_dealiasing
 Flag to determine if dealiasing is used for homogeneous simulations. More...
 
bool m_specHP_dealiasing
 Flag to determine if dealisising is usde for the Spectral/hp element discretisation. More...
 
enum MultiRegions::ProjectionType m_projectionType
 Type of projection; e.g continuous or discontinuous. More...
 
Array< OneD, Array< OneD,
NekDouble > > 
m_traceNormals
 Array holding trace normals for DG simulations in the forwards direction. More...
 
Array< OneD, Array< OneD,
Array< OneD, NekDouble > > > 
m_gradtan
 1 x nvariable x nq More...
 
Array< OneD, Array< OneD,
Array< OneD, NekDouble > > > 
m_tanbasis
 2 x m_spacedim x nq More...
 
Array< OneD, bool > m_checkIfSystemSingular
 Flag to indicate if the fields should be checked for singularity. More...
 
LibUtilities::FieldMetaDataMap m_fieldMetaDataMap
 Map to identify relevant solver info to dump in output fields. More...
 
int m_NumQuadPointsError
 Number of Quadrature points used to work out the error. More...
 
enum HomogeneousType m_HomogeneousType
 
NekDouble m_LhomX
 physical length in X direction (if homogeneous) More...
 
NekDouble m_LhomY
 physical length in Y direction (if homogeneous) More...
 
NekDouble m_LhomZ
 physical length in Z direction (if homogeneous) More...
 
int m_npointsX
 number of points in X direction (if homogeneous) More...
 
int m_npointsY
 number of points in Y direction (if homogeneous) More...
 
int m_npointsZ
 number of points in Z direction (if homogeneous) More...
 
int m_HomoDirec
 number of homogenous directions More...
 

Private Member Functions

virtual SOLVER_UTILS_EXPORT
Array< OneD, bool > 
v_GetSystemSingularChecks ()
 
virtual SOLVER_UTILS_EXPORT void v_GetFluxVector (const int i, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &flux)
 
virtual SOLVER_UTILS_EXPORT void v_GetFluxVector (const int i, const int j, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &flux)
 
virtual SOLVER_UTILS_EXPORT void v_GetFluxVector (const int i, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &fluxX, Array< OneD, Array< OneD, NekDouble > > &fluxY)
 
virtual SOLVER_UTILS_EXPORT void v_NumericalFlux (Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numflux)
 
virtual SOLVER_UTILS_EXPORT void v_NumericalFlux (Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numfluxX, Array< OneD, Array< OneD, NekDouble > > &numfluxY)
 
virtual SOLVER_UTILS_EXPORT void v_NumFluxforScalar (const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &uflux)
 
virtual SOLVER_UTILS_EXPORT void v_NumFluxforVector (const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &qfield, Array< OneD, Array< OneD, NekDouble > > &qflux)
 
SOLVER_UTILS_EXPORT void PrintProgressbar (const int position, const int goal) const
 

Detailed Description

A base class for describing how to solve specific equations.

This class is a base class for all solver implementations. It provides the underlying generic functionality and interface for solving equations.

To solve a steady-state equation, create a derived class from this class and reimplement the virtual functions to provide custom implementation for the problem.

To solve unsteady problems, derive from the UnsteadySystem class instead which provides general time integration.

Definition at line 75 of file EquationSystem.h.

Member Enumeration Documentation

Parameter for homogeneous expansions.

Enumerator
eHomogeneous1D 
eHomogeneous2D 
eHomogeneous3D 
eNotHomogeneous 

Definition at line 536 of file EquationSystem.h.

Constructor & Destructor Documentation

Nektar::SolverUtils::EquationSystem::~EquationSystem ( )
virtual

Destructor.

Destructor for class EquationSystem.

Definition at line 674 of file EquationSystem.cpp.

675  {
676  LibUtilities::NekManager<LocalRegions::MatrixKey,
677  DNekScalMat, LocalRegions::MatrixKey::opLess>::ClearManager();
678  LibUtilities::NekManager<LocalRegions::MatrixKey,
679  DNekScalBlkMat, LocalRegions::MatrixKey::opLess>::ClearManager();
680  }
NekMatrix< NekMatrix< NekMatrix< NekDouble, StandardMatrixTag >, ScaledMatrixTag >, BlockMatrixTag > DNekScalBlkMat
Definition: NekTypeDefs.hpp:66
NekMatrix< NekMatrix< NekDouble, StandardMatrixTag >, ScaledMatrixTag > DNekScalMat
Nektar::SolverUtils::EquationSystem::EquationSystem ( const LibUtilities::SessionReaderSharedPtr pSession)
protected

Initialises EquationSystem class members.

This constructor is protected as the objects of this class are never instantiated directly.

Parameters
pSessionThe session reader holding problem parameters.

Definition at line 97 of file EquationSystem.cpp.

References m_fieldMetaDataMap, and m_session.

99  : m_comm (pSession->GetComm()),
100  m_session (pSession),
101  m_lambda (0),
103  {
104  // set up session names in fieldMetaDataMap
105  const vector<std::string> filenames = m_session->GetFilenames();
106 
107  for(int i = 0; i < filenames.size(); ++i)
108  {
109  string sessionname = "SessionName";
110  sessionname += boost::lexical_cast<std::string>(i);
111  m_fieldMetaDataMap[sessionname] = filenames[i];
112  m_fieldMetaDataMap["ChkFileNum"] = boost::lexical_cast<std::string>(0);
113  }
114 
115  }
NekDouble m_lambda
Lambda constant in real system if one required.
LibUtilities::CommSharedPtr m_comm
Communicator.
LibUtilities::FieldMetaDataMap m_fieldMetaDataMap
Map to identify relevant solver info to dump in output fields.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
static FieldMetaDataMap NullFieldMetaDataMap
Definition: FieldIO.h:55

Member Function Documentation

void Nektar::SolverUtils::EquationSystem::AdvectionNonConservativeForm ( const Array< OneD, Array< OneD, NekDouble > > &  V,
const Array< OneD, const NekDouble > &  u,
Array< OneD, NekDouble > &  outarray,
Array< OneD, NekDouble > &  wk = NullNekDouble1DArray 
)

Compute the non-conservative advection.

Calculate the inner product $ V\cdot \nabla u $

Parameters
VFields.
uFields.
outarrayStorage for result.
wkWorkspace.

Definition at line 1802 of file EquationSystem.cpp.

References ASSERTL0, m_fields, Vmath::Vmul(), and Vmath::Vvtvp().

Referenced by Nektar::CFLtester::DoOdeRhs(), Nektar::EigenValuesAdvection::v_DoSolve(), and WeakAdvectionNonConservativeForm().

1807  {
1808  // Use dimension of Velocity vector to dictate dimension of operation
1809  int ndim = V.num_elements();
1810  //int ndim = m_expdim;
1811 
1812  // ToDo: here we should add a check that V has right dimension
1813 
1814  int nPointsTot = m_fields[0]->GetNpoints();
1815  Array<OneD, NekDouble> grad0,grad1,grad2;
1816 
1817  // Check to see if wk space is defined
1818  if (wk.num_elements())
1819  {
1820  grad0 = wk;
1821  }
1822  else
1823  {
1824  grad0 = Array<OneD, NekDouble> (nPointsTot);
1825  }
1826 
1827  // Evaluate V\cdot Grad(u)
1828  switch(ndim)
1829  {
1830  case 1:
1831  m_fields[0]->PhysDeriv(u,grad0);
1832  Vmath::Vmul(nPointsTot, grad0, 1, V[0], 1, outarray,1);
1833  break;
1834  case 2:
1835  grad1 = Array<OneD, NekDouble> (nPointsTot);
1836  m_fields[0]->PhysDeriv(u, grad0, grad1);
1837  Vmath::Vmul (nPointsTot, grad0, 1, V[0], 1, outarray, 1);
1838  Vmath::Vvtvp(nPointsTot, grad1, 1, V[1], 1,
1839  outarray, 1, outarray, 1);
1840  break;
1841  case 3:
1842  grad1 = Array<OneD, NekDouble> (nPointsTot);
1843  grad2 = Array<OneD, NekDouble> (nPointsTot);
1844  m_fields[0]->PhysDeriv(u,grad0,grad1,grad2);
1845  Vmath::Vmul (nPointsTot, grad0, 1, V[0], 1, outarray, 1);
1846  Vmath::Vvtvp(nPointsTot, grad1, 1, V[1], 1,
1847  outarray, 1, outarray, 1);
1848  Vmath::Vvtvp(nPointsTot, grad2, 1, V[2], 1,
1849  outarray, 1, outarray, 1);
1850  break;
1851  default:
1852  ASSERTL0(false,"dimension unknown");
1853  }
1854  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
void Vvtvp(int n, const T *w, const int incw, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
vvtvp (vector times vector plus vector): z = w*x + y
Definition: Vmath.cpp:442
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
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
template<class T >
boost::shared_ptr<T> Nektar::SolverUtils::EquationSystem::as ( )
inline

Definition at line 112 of file EquationSystem.h.

References ASSERTL1, and CellMLToNektar.cellml_metadata::p.

113  {
114 #if defined __INTEL_COMPILER && BOOST_VERSION > 105200
115  typedef typename boost::shared_ptr<T>::element_type E;
116  E * p = dynamic_cast< E* >( shared_from_this().get() );
117  ASSERTL1(p, "Cannot perform cast");
118  return boost::shared_ptr<T>( shared_from_this(), p );
119 #else
120  return boost::dynamic_pointer_cast<T>( shared_from_this() );
121 #endif
122  }
#define ASSERTL1(condition, msg)
Assert Level 1 – Debugging which is used whether in FULLDEBUG or DEBUG compilation mode...
Definition: ErrorUtil.hpp:228
void Nektar::SolverUtils::EquationSystem::Checkpoint_BaseFlow ( const int  n)

Write base flow file of m_fields.

Write the n-th base flow into a .chk file

Parameters
nThe index of the base flow file.

Definition at line 2168 of file EquationSystem.cpp.

References m_sessionName, and WriteFld().

2169  {
2170  std::string outname = m_sessionName + "_BaseFlow_" +
2171  boost::lexical_cast<std::string>(n);
2172 
2173  WriteFld(outname + ".chk");
2174  }
std::string m_sessionName
Name of the session.
SOLVER_UTILS_EXPORT void WriteFld(const std::string &outname)
Write field data to the given filename.
void Nektar::SolverUtils::EquationSystem::Checkpoint_Output ( const int  n)

Write checkpoint file of m_fields.

Write the n-th checkpoint file.

Parameters
nThe index of the checkpoint file.

Definition at line 2142 of file EquationSystem.cpp.

References m_sessionName, and WriteFld().

Referenced by Nektar::SolverUtils::UnsteadySystem::v_DoSolve(), Nektar::CoupledLinearNS::v_DoSolve(), Nektar::IsentropicVortex::v_SetInitialConditions(), Nektar::NonlinearPeregrine::v_SetInitialConditions(), Nektar::CompressibleFlowSystem::v_SetInitialConditions(), and v_SetInitialConditions().

2143  {
2144  std::string outname = m_sessionName + "_" +
2145  boost::lexical_cast<std::string>(n);
2146  WriteFld(outname + ".chk");
2147  }
std::string m_sessionName
Name of the session.
SOLVER_UTILS_EXPORT void WriteFld(const std::string &outname)
Write field data to the given filename.
void Nektar::SolverUtils::EquationSystem::Checkpoint_Output ( const int  n,
MultiRegions::ExpListSharedPtr field,
std::vector< Array< OneD, NekDouble > > &  fieldcoeffs,
std::vector< std::string > &  variables 
)

Write checkpoint file of custom data fields.

Write the n-th checkpoint file.

Parameters
nThe index of the checkpoint file.

Definition at line 2153 of file EquationSystem.cpp.

References m_sessionName, and WriteFld().

2158  {
2159  std::string outname = m_sessionName + "_" +
2160  boost::lexical_cast<std::string>(n);
2161  WriteFld(outname, field, fieldcoeffs, variables);
2162  }
std::string m_sessionName
Name of the session.
SOLVER_UTILS_EXPORT void WriteFld(const std::string &outname)
Write field data to the given filename.
void Nektar::SolverUtils::EquationSystem::CopyFromPhysField ( const int  i,
Array< OneD, NekDouble > &  output 
)
inline

Definition at line 935 of file EquationSystem.h.

References m_fields, and Vmath::Vcopy().

937  {
938  Vmath::Vcopy(output.num_elements(), m_fields[i]->GetPhys(), 1, output, 1 );
939  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
void Vcopy(int n, const T *x, const int incx, T *y, const int incy)
Definition: Vmath.cpp:1061
void Nektar::SolverUtils::EquationSystem::CopyToPhysField ( const int  i,
Array< OneD, NekDouble > &  output 
)
inline

Definition at line 941 of file EquationSystem.h.

References m_fields, and Vmath::Vcopy().

943  {
944  Vmath::Vcopy(output.num_elements(), output, 1, m_fields[i]->UpdatePhys(), 1 );
945  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
void Vcopy(int n, const T *x, const int incx, T *y, const int incy)
Definition: Vmath.cpp:1061
std::string Nektar::SolverUtils::EquationSystem::DescribeFunction ( std::string  pFieldName,
const std::string &  pFunctionName,
const int  domain 
)

Provide a description of a function for a given field name.

Parameters
pFieldNameField name.
pFunctionNameFunction name.

Definition at line 1119 of file EquationSystem.cpp.

References ASSERTL0, Nektar::LibUtilities::eFunctionTypeExpression, Nektar::LibUtilities::eFunctionTypeFile, and m_session.

Referenced by v_SetInitialConditions().

1123  {
1124  ASSERTL0(m_session->DefinesFunction(pFunctionName),
1125  "Function '" + pFunctionName + "' does not exist.");
1126 
1127  std::string retVal;
1129 
1130  vType = m_session->GetFunctionType(pFunctionName, pFieldName);
1132  {
1134  = m_session->GetFunction(pFunctionName, pFieldName,domain);
1135  retVal = ffunc->GetExpression();
1136  }
1137  else if (vType == LibUtilities::eFunctionTypeFile)
1138  {
1139  std::string filename
1140  = m_session->GetFunctionFilename(pFunctionName, pFieldName,domain);
1141  retVal = "from file " + filename;
1142  }
1143 
1144  return retVal;
1145  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
boost::shared_ptr< Equation > EquationSharedPtr
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
void Nektar::SolverUtils::EquationSystem::DoInitialise ( )
inline

Perform any initialisation necessary before solving the problem.

This allows initialisation of the solver which cannot be completed during object construction (such as setting of initial conditions).

Public interface routine to virtual function implementation.

Definition at line 715 of file EquationSystem.h.

References v_DoInitialise().

716  {
717  v_DoInitialise();
718  }
virtual SOLVER_UTILS_EXPORT void v_DoInitialise()
Virtual function for initialisation implementation.
void Nektar::SolverUtils::EquationSystem::DoSolve ( void  )
inline

Solve the problem.

Performs the actual solve.

Public interface routine to virtual function implementation.

Definition at line 747 of file EquationSystem.h.

References v_DoSolve().

748  {
749  v_DoSolve();
750  }
virtual SOLVER_UTILS_EXPORT void v_DoSolve()
Virtual function for solve implementation.
Array< OneD, NekDouble > Nektar::SolverUtils::EquationSystem::ErrorExtraPoints ( unsigned int  field)

Compute error (L2 and L_inf) over an larger set of quadrature points return [L2 Linf].

Compute the error in the L2-norm, L-inf for a larger number of quadrature points.

Parameters
fieldThe field to compare.
Returns
Error in the L2-norm and L-inf norm.

Definition at line 1279 of file EquationSystem.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), Nektar::LibUtilities::eGaussLobattoLegendre, Nektar::LibUtilities::eGaussRadauMAlpha1Beta0, Nektar::LibUtilities::eModified_A, Nektar::LibUtilities::eModified_B, GetNumExpModes(), m_fields, m_graph, m_NumQuadPointsError, m_session, and m_time.

Referenced by v_L2Error(), and v_LinfError().

1281  {
1282  int NumModes = GetNumExpModes();
1283  Array<OneD,NekDouble> L2INF(2);
1284 
1285  const LibUtilities::PointsKey PkeyT1(
1287  const LibUtilities::PointsKey PkeyT2(
1289  const LibUtilities::PointsKey PkeyQ1(
1291  const LibUtilities::PointsKey PkeyQ2(
1293  const LibUtilities::BasisKey BkeyT1(
1294  LibUtilities::eModified_A,NumModes, PkeyT1);
1295  const LibUtilities::BasisKey BkeyT2(
1296  LibUtilities::eModified_B, NumModes, PkeyT2);
1297  const LibUtilities::BasisKey BkeyQ1(
1298  LibUtilities::eModified_A, NumModes, PkeyQ1);
1299  const LibUtilities::BasisKey BkeyQ2(
1300  LibUtilities::eModified_A, NumModes, PkeyQ2);
1301 
1304  m_session, BkeyT1, BkeyT2, BkeyQ1, BkeyQ2, m_graph);
1305 
1306  int ErrorCoordim = ErrorExp->GetCoordim(0);
1307  int ErrorNq = ErrorExp->GetTotPoints();
1308 
1309  Array<OneD,NekDouble> ErrorXc0(ErrorNq, 0.0);
1310  Array<OneD,NekDouble> ErrorXc1(ErrorNq, 0.0);
1311  Array<OneD,NekDouble> ErrorXc2(ErrorNq, 0.0);
1312 
1313  switch(ErrorCoordim)
1314  {
1315  case 1:
1316  ErrorExp->GetCoords(ErrorXc0);
1317  break;
1318  case 2:
1319  ErrorExp->GetCoords(ErrorXc0, ErrorXc1);
1320  break;
1321  case 3:
1322  ErrorExp->GetCoords(ErrorXc0, ErrorXc1, ErrorXc2);
1323  break;
1324  }
1326  m_session->GetFunction("ExactSolution", field);
1327 
1328  // Evaluate the exact solution
1329  Array<OneD,NekDouble> ErrorSol(ErrorNq);
1330 
1331  exSol->Evaluate(ErrorXc0,ErrorXc1,ErrorXc2,m_time,ErrorSol);
1332 
1333  // Calcualte spectral/hp approximation on the quadrature points
1334  // of this new expansion basis
1335  ErrorExp->BwdTrans_IterPerExp(m_fields[field]->GetCoeffs(),
1336  ErrorExp->UpdatePhys());
1337 
1338  L2INF[0] = ErrorExp->L2 (ErrorExp->GetPhys(), ErrorSol);
1339  L2INF[1] = ErrorExp->Linf(ErrorExp->GetPhys(), ErrorSol);
1340 
1341  return L2INF;
1342  }
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
NekDouble m_time
Current time of simulation.
Principle Modified Functions .
Definition: BasisType.h:49
SOLVER_UTILS_EXPORT int GetNumExpModes()
Gauss Radau pinned at x=-1, .
Definition: PointsType.h:59
Principle Modified Functions .
Definition: BasisType.h:50
boost::shared_ptr< ExpList2D > ExpList2DSharedPtr
Shared pointer to an ExpList2D object.
Definition: ExpList2D.h:49
boost::shared_ptr< Equation > EquationSharedPtr
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
SpatialDomains::MeshGraphSharedPtr m_graph
Pointer to graph defining mesh.
int m_NumQuadPointsError
Number of Quadrature points used to work out the error.
1D Gauss-Lobatto-Legendre quadrature points
Definition: PointsType.h:52
void Nektar::SolverUtils::EquationSystem::EvaluateExactSolution ( int  field,
Array< OneD, NekDouble > &  outfield,
const NekDouble  time 
)
inline

Evaluates an exact solution.

Definition at line 826 of file EquationSystem.h.

References v_EvaluateExactSolution().

829  {
830  v_EvaluateExactSolution(field, outfield, time);
831  }
virtual SOLVER_UTILS_EXPORT void v_EvaluateExactSolution(unsigned int field, Array< OneD, NekDouble > &outfield, const NekDouble time)
void Nektar::SolverUtils::EquationSystem::EvaluateFunction ( Array< OneD, Array< OneD, NekDouble > > &  pArray,
std::string  pFunctionName,
const NekDouble  pTime = 0.0,
const int  domain = 0 
)

Evaluates a function as specified in the session file.

Evaluates a physical function at each quadrature point in the domain.

Parameters
pArrayThe array into which to write the values.
pEqnThe equation to evaluate.

Definition at line 688 of file EquationSystem.cpp.

References ASSERTL0, and m_session.

Referenced by Nektar::CoupledLinearNS::DefineForcingTerm(), Nektar::ShallowWaterSystem::EvaluateCoriolis(), EvaluateFunction(), Nektar::ShallowWaterSystem::EvaluateWaterDepth(), InitialiseBaseFlow(), Nektar::SteadyAdvectionDiffusion::v_DoInitialise(), Nektar::CoupledLinearNS::v_DoInitialise(), Nektar::LinearElasticSystem::v_DoSolve(), v_EvaluateExactSolution(), Nektar::Poisson::v_InitObject(), Nektar::EigenValuesAdvection::v_InitObject(), Nektar::Projection::v_InitObject(), Nektar::BidomainRoth::v_InitObject(), Nektar::Monodomain::v_InitObject(), Nektar::APE::v_InitObject(), Nektar::UnsteadyAdvection::v_InitObject(), Nektar::CFLtester::v_InitObject(), Nektar::UnsteadyAdvectionDiffusion::v_InitObject(), Nektar::PulseWaveSystem::v_InitObject(), Nektar::PulseWaveSystem::v_L2Error(), v_L2Error(), Nektar::PulseWaveSystem::v_LinfError(), v_LinfError(), Nektar::APE::v_PreIntegrate(), and v_SetInitialConditions().

693  {
694  ASSERTL0(m_session->DefinesFunction(pFunctionName),
695  "Function '" + pFunctionName + "' does not exist.");
696 
697  std::vector<std::string> vFieldNames = m_session->GetVariables();
698 
699  for(int i = 0 ; i < vFieldNames.size(); i++)
700  {
701  EvaluateFunction(vFieldNames[i], pArray[i], pFunctionName,
702  pTime, domain);
703  }
704  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
SOLVER_UTILS_EXPORT void EvaluateFunction(Array< OneD, Array< OneD, NekDouble > > &pArray, std::string pFunctionName, const NekDouble pTime=0.0, const int domain=0)
Evaluates a function as specified in the session file.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
void Nektar::SolverUtils::EquationSystem::EvaluateFunction ( std::vector< std::string >  pFieldNames,
Array< OneD, Array< OneD, NekDouble > > &  pFields,
const std::string &  pFunctionName,
const NekDouble pTime = 0.0,
const int  domain = 0 
)

Populate given fields with the function from session.

Populates a forcing function for each of the dependent variables using the expression provided by the BoundaryConditions object.

Parameters
forceArray of fields to assign forcing.

Definition at line 711 of file EquationSystem.cpp.

References ASSERTL0, ASSERTL1, EvaluateFunction(), and m_session.

717  {
718  ASSERTL1(pFieldNames.size() == pFields.num_elements(),
719  "Function '" + pFunctionName +
720  "' variable list size mismatch with array storage.");
721  ASSERTL0(m_session->DefinesFunction(pFunctionName),
722  "Function '" + pFunctionName + "' does not exist.");
723 
724  for (int i = 0; i < pFieldNames.size(); i++)
725  {
726  EvaluateFunction(pFieldNames[i], pFields[i], pFunctionName, pTime,
727  domain);
728  }
729  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
SOLVER_UTILS_EXPORT void EvaluateFunction(Array< OneD, Array< OneD, NekDouble > > &pArray, std::string pFunctionName, const NekDouble pTime=0.0, const int domain=0)
Evaluates a function as specified in the session file.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
#define ASSERTL1(condition, msg)
Assert Level 1 – Debugging which is used whether in FULLDEBUG or DEBUG compilation mode...
Definition: ErrorUtil.hpp:228
void Nektar::SolverUtils::EquationSystem::EvaluateFunction ( std::vector< std::string >  pFieldNames,
Array< OneD, MultiRegions::ExpListSharedPtr > &  pFields,
const std::string &  pFunctionName,
const NekDouble pTime = 0.0,
const int  domain = 0 
)

Populate given fields with the function from session.

Populates a function for each of the dependent variables using the expression or filenames provided by the SessionReader object.

Parameters
forceArray of fields to assign forcing.

Definition at line 736 of file EquationSystem.cpp.

References ASSERTL0, EvaluateFunction(), and m_session.

742  {
743  ASSERTL0(m_session->DefinesFunction(pFunctionName),
744  "Function '" + pFunctionName + "' does not exist.");
745  ASSERTL0(pFieldNames.size() == pFields.num_elements(),
746  "Field list / name list size mismatch.");
747 
748  for (int i = 0; i < pFieldNames.size(); i++)
749  {
750  EvaluateFunction(pFieldNames[i], pFields[i]->UpdatePhys(),
751  pFunctionName, pTime, domain);
752  pFields[i]->FwdTrans_IterPerExp(pFields[i]->GetPhys(),
753  pFields[i]->UpdateCoeffs());
754  }
755  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
SOLVER_UTILS_EXPORT void EvaluateFunction(Array< OneD, Array< OneD, NekDouble > > &pArray, std::string pFunctionName, const NekDouble pTime=0.0, const int domain=0)
Evaluates a function as specified in the session file.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
void Nektar::SolverUtils::EquationSystem::EvaluateFunction ( std::string  pFieldName,
Array< OneD, NekDouble > &  pArray,
const std::string &  pFunctionName,
const NekDouble pTime = 0.0,
const int  domain = 0 
)

Definition at line 757 of file EquationSystem.cpp.

References ASSERTL0, Nektar::LibUtilities::eFunctionTypeExpression, Nektar::LibUtilities::eFunctionTypeFile, Nektar::LibUtilities::eFunctionTypeTransientFile, EvaluateFunctionExp(), EvaluateFunctionFld(), EvaluateFunctionPts(), and m_session.

762  {
763  ASSERTL0(m_session->DefinesFunction(pFunctionName),
764  "Function '" + pFunctionName + "' does not exist.");
765 
767  vType = m_session->GetFunctionType(pFunctionName, pFieldName, domain);
769  {
770  EvaluateFunctionExp(pFieldName, pArray, pFunctionName, pTime, domain);
771  }
772  else if (vType == LibUtilities::eFunctionTypeFile ||
774  {
775  std::string filename =
776  m_session->GetFunctionFilename(pFunctionName, pFieldName, domain);
777 
778  if (boost::filesystem::path(filename).extension() != ".pts")
779  {
780  EvaluateFunctionFld(pFieldName, pArray, pFunctionName, pTime,
781  domain);
782  }
783  else
784  {
785  EvaluateFunctionPts(pFieldName, pArray, pFunctionName, pTime,
786  domain);
787  }
788  }
789  }
SOLVER_UTILS_EXPORT void EvaluateFunctionPts(std::string pFieldName, Array< OneD, NekDouble > &pArray, const std::string &pFunctionName, const NekDouble &pTime=0.0, const int domain=0)
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
SOLVER_UTILS_EXPORT void EvaluateFunctionExp(std::string pFieldName, Array< OneD, NekDouble > &pArray, const std::string &pFunctionName, const NekDouble &pTime=0.0, const int domain=0)
SOLVER_UTILS_EXPORT void EvaluateFunctionFld(std::string pFieldName, Array< OneD, NekDouble > &pArray, const std::string &pFunctionName, const NekDouble &pTime=0.0, const int domain=0)
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
void Nektar::SolverUtils::EquationSystem::EvaluateFunctionExp ( std::string  pFieldName,
Array< OneD, NekDouble > &  pArray,
const std::string &  pFunctionName,
const NekDouble pTime = 0.0,
const int  domain = 0 
)
protected

Definition at line 791 of file EquationSystem.cpp.

References ASSERTL0, Nektar::LibUtilities::eFunctionTypeExpression, m_fields, and m_session.

Referenced by EvaluateFunction().

796  {
797  ASSERTL0(m_session->DefinesFunction(pFunctionName),
798  "Function '" + pFunctionName + "' does not exist.");
799 
800  unsigned int nq = m_fields[0]->GetNpoints();
801  if (pArray.num_elements() < nq)
802  {
803  pArray = Array<OneD, NekDouble>(nq);
804  }
805 
807  vType = m_session->GetFunctionType(pFunctionName, pFieldName, domain);
809  "vType not eFunctionTypeExpression");
810 
811  Array<OneD, NekDouble> x0(nq);
812  Array<OneD, NekDouble> x1(nq);
813  Array<OneD, NekDouble> x2(nq);
814 
815  // Get the coordinates (assuming all fields have the same
816  // discretisation)
817  m_fields[0]->GetCoords(x0, x1, x2);
819  m_session->GetFunction(pFunctionName, pFieldName, domain);
820 
821  ffunc->Evaluate(x0, x1, x2, pTime, pArray);
822  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
boost::shared_ptr< Equation > EquationSharedPtr
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
void Nektar::SolverUtils::EquationSystem::EvaluateFunctionFld ( std::string  pFieldName,
Array< OneD, NekDouble > &  pArray,
const std::string &  pFunctionName,
const NekDouble pTime = 0.0,
const int  domain = 0 
)
protected

Definition at line 824 of file EquationSystem.cpp.

References ASSERTL0, Nektar::LibUtilities::FieldIO::CreateForFile(), Nektar::LibUtilities::eFunctionTypeFile, Nektar::LibUtilities::eFunctionTypeTransientFile, CellMLToNektar.pycml::format, GetNcoeffs(), m_fields, m_loadedFldFields, m_session, and Nektar::LibUtilities::NullFieldMetaDataMap.

Referenced by EvaluateFunction().

829  {
830 
831  ASSERTL0(m_session->DefinesFunction(pFunctionName),
832  "Function '" + pFunctionName + "' does not exist.");
833 
834  unsigned int nq = m_fields[0]->GetNpoints();
835  if (pArray.num_elements() < nq)
836  {
837  pArray = Array<OneD, NekDouble>(nq);
838  }
839 
841  vType = m_session->GetFunctionType(pFunctionName, pFieldName, domain);
844  "vType not eFunctionTypeFile or eFunctionTypeTransientFile");
845 
846  std::string filename =
847  m_session->GetFunctionFilename(pFunctionName, pFieldName, domain);
848  std::string fileVar = m_session->GetFunctionFilenameVariable(
849  pFunctionName, pFieldName, domain);
850 
851  if (fileVar.length() == 0)
852  {
853  fileVar = pFieldName;
854  }
855 
856  // In case of eFunctionTypeTransientFile, generate filename from
857  // format string
859  {
860  try
861  {
862 #if (defined _WIN32 && _MSC_VER < 1900)
863  // We need this to make sure boost::format has always
864  // two digits in the exponents of Scientific notation.
865  unsigned int old_exponent_format;
866  old_exponent_format = _set_output_format(_TWO_DIGIT_EXPONENT);
867  filename = boost::str(boost::format(filename) % pTime);
868  _set_output_format(old_exponent_format);
869 #else
870  filename = boost::str(boost::format(filename) % pTime);
871 #endif
872  }
873  catch (...)
874  {
875  ASSERTL0(false, "Invalid Filename in function \"" + pFunctionName +
876  "\", variable \"" + fileVar + "\"")
877  }
878  }
879 
880  std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef;
881  std::vector<std::vector<NekDouble> > FieldData;
882 
883  // Define list of global element ids
884  int numexp = m_fields[0]->GetExpSize();
885  Array<OneD, int> ElementGIDs(numexp);
886  for (int i = 0; i < numexp; ++i)
887  {
888  ElementGIDs[i] = m_fields[0]->GetExp(i)->GetGeom()->GetGlobalID();
889  }
890 
891  // check if we already loaded this file. For transient files,
892  // funcFilename != filename so we can make sure we only keep the
893  // latest field per funcFilename.
894  std::string funcFilename =
895  m_session->GetFunctionFilename(pFunctionName, pFieldName, domain);
896  if (m_loadedFldFields.find(funcFilename) != m_loadedFldFields.end())
897  {
898  // found
899  if (m_loadedFldFields[funcFilename].first == filename)
900  {
901  // found
902  FieldDef = m_loadedFldFields[funcFilename].second.fieldDef;
903  FieldData = m_loadedFldFields[funcFilename].second.fieldData;
904  }
905  else
906  {
909  pts_fld->Import(filename, FieldDef, FieldData,
911  ElementGIDs);
912  }
913  }
914  else
915  {
918  pts_fld->Import(filename, FieldDef, FieldData,
920  ElementGIDs);
921  }
922  // Now we overwrite the field we had in
923  // m_loadedFldFields[funcFilename] before, making sure we only keep
924  // one field per funcFilename in memory
925  m_loadedFldFields[funcFilename].first = filename;
926  m_loadedFldFields[funcFilename].second.fieldDef = FieldDef;
927  m_loadedFldFields[funcFilename].second.fieldData = FieldData;
928 
929  int idx = -1;
930  Array<OneD, NekDouble> vCoeffs(m_fields[0]->GetNcoeffs(), 0.0);
931  // Loop over all the expansions
932  for (int i = 0; i < FieldDef.size(); ++i)
933  {
934  // Find the index of the required field in the
935  // expansion segment
936  for (int j = 0; j < FieldDef[i]->m_fields.size(); ++j)
937  {
938  if (FieldDef[i]->m_fields[j] == fileVar)
939  {
940  idx = j;
941  }
942  }
943 
944  if (idx >= 0)
945  {
946  m_fields[0]->ExtractDataToCoeffs(
947  FieldDef[i], FieldData[i], FieldDef[i]->m_fields[idx], vCoeffs);
948  }
949  else
950  {
951  cout << "Field " + fileVar + " not found." << endl;
952  }
953  }
954 
955  m_fields[0]->BwdTrans_IterPerExp(vCoeffs, pArray);
956  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
std::map< std::string, std::pair< std::string, loadedFldField > > m_loadedFldFields
boost::shared_ptr< FieldIO > FieldIOSharedPtr
Definition: FieldIO.h:309
static boost::shared_ptr< FieldIO > CreateForFile(const LibUtilities::SessionReaderSharedPtr session, const std::string &filename)
Construct a FieldIO object for a given input filename.
Definition: FieldIO.cpp:212
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
SOLVER_UTILS_EXPORT int GetNcoeffs()
static FieldMetaDataMap NullFieldMetaDataMap
Definition: FieldIO.h:55
void Nektar::SolverUtils::EquationSystem::EvaluateFunctionPts ( std::string  pFieldName,
Array< OneD, NekDouble > &  pArray,
const std::string &  pFunctionName,
const NekDouble pTime = 0.0,
const int  domain = 0 
)
protected

Definition at line 958 of file EquationSystem.cpp.

References ASSERTL0, Nektar::LibUtilities::eFunctionTypeFile, Nektar::LibUtilities::eFunctionTypeTransientFile, CellMLToNektar.pycml::format, LoadPts(), m_fields, m_loadedPtsFields, and m_session.

Referenced by EvaluateFunction().

963  {
964 
965  ASSERTL0(m_session->DefinesFunction(pFunctionName),
966  "Function '" + pFunctionName + "' does not exist.");
967 
968  unsigned int nq = m_fields[0]->GetNpoints();
969  if (pArray.num_elements() < nq)
970  {
971  pArray = Array<OneD, NekDouble>(nq);
972  }
973 
975  vType = m_session->GetFunctionType(pFunctionName, pFieldName, domain);
978  "vType not eFunctionTypeFile or eFunctionTypeTransientFile");
979 
980  std::string filename =
981  m_session->GetFunctionFilename(pFunctionName, pFieldName, domain);
982  std::string fileVar = m_session->GetFunctionFilenameVariable(
983  pFunctionName, pFieldName, domain);
984 
985  if (fileVar.length() == 0)
986  {
987  fileVar = pFieldName;
988  }
989 
990  // In case of eFunctionTypeTransientFile, generate filename from
991  // format string
993  {
994  try
995  {
996 #if (defined _WIN32 && _MSC_VER < 1900)
997  // We need this to make sure boost::format has always
998  // two digits in the exponents of Scientific notation.
999  unsigned int old_exponent_format;
1000  old_exponent_format = _set_output_format(_TWO_DIGIT_EXPONENT);
1001  filename = boost::str(boost::format(filename) % pTime);
1002  _set_output_format(old_exponent_format);
1003 #else
1004  filename = boost::str(boost::format(filename) % pTime);
1005 #endif
1006  }
1007  catch (...)
1008  {
1009  ASSERTL0(false, "Invalid Filename in function \"" + pFunctionName +
1010  "\", variable \"" + fileVar + "\"")
1011  }
1012  }
1013 
1015  // check if we already loaded this file. For transient files,
1016  // funcFilename != filename so we can make sure we only keep the
1017  // latest pts field per funcFilename.
1018  std::string funcFilename =
1019  m_session->GetFunctionFilename(pFunctionName, pFieldName, domain);
1020 
1021  if (m_loadedPtsFields.find(funcFilename) != m_loadedPtsFields.end())
1022  {
1023  // found
1024  if (m_loadedPtsFields[funcFilename].first == filename)
1025  {
1026  // found
1027  outPts = m_loadedPtsFields[funcFilename].second;
1028  }
1029  else
1030  {
1031  LoadPts(funcFilename, filename, outPts);
1032  }
1033  }
1034  else
1035  {
1036  LoadPts(funcFilename, filename, outPts);
1037  }
1038  // Now we overwrite the field we had in
1039  // m_loadedPtsFields[funcFilename] before, making sure we only keep
1040  // one field per funcFilename in memory
1041  m_loadedPtsFields[funcFilename].first = filename;
1042  m_loadedPtsFields[funcFilename].second = outPts;
1043 
1044  int fieldInd;
1045  vector<string> fieldNames = outPts->GetFieldNames();
1046  for (fieldInd = 0; fieldInd < fieldNames.size(); ++fieldInd)
1047  {
1048  if (outPts->GetFieldName(fieldInd) == pFieldName)
1049  {
1050  break;
1051  }
1052  }
1053  ASSERTL0(fieldInd != fieldNames.size(), "field not found");
1054 
1055  pArray = outPts->GetPts(fieldInd + outPts->GetDim());
1056  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
SOLVER_UTILS_EXPORT void LoadPts(std::string funcFilename, std::string filename, Nektar::LibUtilities::PtsFieldSharedPtr &outPts)
std::map< std::string, std::pair< std::string, LibUtilities::PtsFieldSharedPtr > > m_loadedPtsFields
pts fields we already read from disk: {funcFilename: (filename, ptsfield)}
boost::shared_ptr< PtsField > PtsFieldSharedPtr
Definition: PtsField.h:178
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
void Nektar::SolverUtils::EquationSystem::FwdTransFields ( void  )

FwdTrans the m_fields members

Definition at line 1708 of file EquationSystem.cpp.

References m_fields.

1709  {
1710  for (int i = 0; i < m_fields.num_elements(); i++)
1711  {
1712  m_fields[i]->FwdTrans(m_fields[i]->GetPhys(),
1713  m_fields[i]->UpdateCoeffs());
1714  m_fields[i]->SetPhysState(false);
1715  }
1716  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
SOLVER_UTILS_EXPORT int Nektar::SolverUtils::EquationSystem::GetCheckpointNumber ( )
inline

Definition at line 416 of file EquationSystem.h.

References m_nchk.

417  {
418  return m_nchk;
419  }
int m_nchk
Number of checkpoints written so far.
SOLVER_UTILS_EXPORT int Nektar::SolverUtils::EquationSystem::GetCheckpointSteps ( )
inline

Definition at line 426 of file EquationSystem.h.

References m_checksteps.

427  {
428  return m_checksteps;
429  }
int m_checksteps
Number of steps between checkpoints.
int Nektar::SolverUtils::EquationSystem::GetCoeff_Offset ( int  n)
inline

Definition at line 895 of file EquationSystem.h.

References m_fields.

896  {
897  return m_fields[0]->GetCoeff_Offset(n);
898  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
int Nektar::SolverUtils::EquationSystem::GetExpSize ( void  )
inline

Definition at line 885 of file EquationSystem.h.

References m_fields.

Referenced by Nektar::CompressibleFlowSystem::GetStabilityLimitVector(), and Nektar::UnsteadyAdvectionDiffusion::SubStepAdvance().

886  {
887  return m_fields[0]->GetExpSize();
888  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
NekDouble Nektar::SolverUtils::EquationSystem::GetFinalTime ( )
inline

Return final time.

Definition at line 839 of file EquationSystem.h.

References m_time.

840  {
841  return m_time;
842  }
NekDouble m_time
Current time of simulation.
void Nektar::SolverUtils::EquationSystem::GetFluxVector ( const int  i,
Array< OneD, Array< OneD, NekDouble > > &  physfield,
Array< OneD, Array< OneD, NekDouble > > &  flux 
)
inline

Definition at line 947 of file EquationSystem.h.

References v_GetFluxVector().

Referenced by WeakDGAdvection(), and WeakDGDiffusion().

950  {
951  v_GetFluxVector(i,physfield, flux);
952  }
virtual SOLVER_UTILS_EXPORT void v_GetFluxVector(const int i, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &flux)
void Nektar::SolverUtils::EquationSystem::GetFluxVector ( const int  i,
Array< OneD, Array< OneD, NekDouble > > &  physfield,
Array< OneD, Array< OneD, NekDouble > > &  fluxX,
Array< OneD, Array< OneD, NekDouble > > &  fluxY 
)
inline

Definition at line 954 of file EquationSystem.h.

References v_GetFluxVector().

958  {
959  v_GetFluxVector(i,physfield, fluxX, fluxY);
960  }
virtual SOLVER_UTILS_EXPORT void v_GetFluxVector(const int i, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &flux)
void Nektar::SolverUtils::EquationSystem::GetFluxVector ( const int  i,
const int  j,
Array< OneD, Array< OneD, NekDouble > > &  physfield,
Array< OneD, Array< OneD, NekDouble > > &  flux 
)
inline

Definition at line 962 of file EquationSystem.h.

References v_GetFluxVector().

965  {
966  v_GetFluxVector(i,j,physfield,flux);
967  }
virtual SOLVER_UTILS_EXPORT void v_GetFluxVector(const int i, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &flux)
int Nektar::SolverUtils::EquationSystem::GetNcoeffs ( void  )
inline
int Nektar::SolverUtils::EquationSystem::GetNcoeffs ( const int  eid)
inline

Definition at line 849 of file EquationSystem.h.

References m_fields.

850  {
851  return m_fields[0]->GetNcoeffs(eid);
852  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
int Nektar::SolverUtils::EquationSystem::GetNpoints ( void  )
inline

Definition at line 910 of file EquationSystem.h.

References m_fields.

Referenced by Nektar::ImageWarpingSystem::DoOdeProjection(), Nektar::NonlinearSWE::DoOdeProjection(), Nektar::LinearSWE::DoOdeProjection(), Nektar::UnsteadyInviscidBurger::DoOdeProjection(), Nektar::UnsteadyDiffusion::DoOdeProjection(), Nektar::UnsteadyAdvection::DoOdeProjection(), Nektar::NonlinearPeregrine::DoOdeProjection(), Nektar::UnsteadyAdvectionDiffusion::DoOdeProjection(), Nektar::CFLtester::DoOdeProjection(), Nektar::UnsteadyViscousBurgers::DoOdeProjection(), Nektar::CompressibleFlowSystem::DoOdeProjection(), Nektar::ImageWarpingSystem::DoOdeRhs(), Nektar::UnsteadyInviscidBurger::DoOdeRhs(), Nektar::UnsteadyAdvection::DoOdeRhs(), Nektar::UnsteadyAdvectionDiffusion::DoOdeRhs(), Nektar::CFLtester::DoOdeRhs(), Nektar::UnsteadyViscousBurgers::DoOdeRhs(), Nektar::CompressibleFlowSystem::DoOdeRhs(), Nektar::UnsteadyInviscidBurger::GetFluxVector(), Nektar::UnsteadyDiffusion::GetFluxVector(), Nektar::UnsteadyAdvectionDiffusion::GetFluxVectorDiff(), Nektar::UnsteadyViscousBurgers::GetFluxVectorDiff(), Nektar::UnsteadyInviscidBurger::GetNormalVelocity(), Nektar::SolverUtils::UnsteadySystem::v_AppendOutput1D(), Nektar::NavierStokesCFE::v_DoDiffusion(), Nektar::EigenValuesAdvection::v_DoSolve(), Nektar::LinearElasticSystem::v_DoSolve(), Nektar::EigenValuesAdvection::v_GetFluxVector(), Nektar::ImageWarpingSystem::v_GetFluxVector(), Nektar::CFLtester::v_GetFluxVector(), Nektar::IncNavierStokes::v_GetFluxVector(), Nektar::PulseWaveSystem::v_L2Error(), v_L2Error(), Nektar::PulseWaveSystem::v_LinfError(), v_LinfError(), WeakDGAdvection(), WeakDGDiffusion(), and ZeroPhysFields().

911  {
912  return m_fields[0]->GetNpoints();
913  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
int Nektar::SolverUtils::EquationSystem::GetNumElmVelocity ( void  )
inline

Definition at line 915 of file EquationSystem.h.

References m_fields.

916  {
917  return (m_fields.num_elements() - 1);
918  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
int Nektar::SolverUtils::EquationSystem::GetNumExpModes ( void  )
inline

Definition at line 854 of file EquationSystem.h.

References m_graph.

Referenced by ErrorExtraPoints().

855  {
856  return m_graph->GetExpansions().begin()->second->m_basisKeyVector[0]
857  .GetNumModes();
858  }
SpatialDomains::MeshGraphSharedPtr m_graph
Pointer to graph defining mesh.
const Array< OneD, int > Nektar::SolverUtils::EquationSystem::GetNumExpModesPerExp ( void  )
inline

Definition at line 860 of file EquationSystem.h.

References m_fields.

Referenced by Nektar::APE::GetCFLEstimate(), Nektar::IncNavierStokes::GetElmtCFLVals(), and Nektar::CompressibleFlowSystem::v_GetTimeStep().

861  {
862  return m_fields[0]->EvalBasisNumModesMaxPerExp();
863  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
int Nektar::SolverUtils::EquationSystem::GetNvariables ( void  )
inline

Definition at line 865 of file EquationSystem.h.

References m_session.

Referenced by ImportFldToMultiDomains().

866  {
867  return m_session->GetVariables().size();
868  }
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
int Nektar::SolverUtils::EquationSystem::GetPhys_Offset ( int  n)
inline

Definition at line 890 of file EquationSystem.h.

References m_fields.

Referenced by Nektar::IncNavierStokes::SetRadiationBoundaryForcing(), Nektar::NonlinearSWE::WallBoundary(), Nektar::LinearSWE::WallBoundary(), Nektar::SolverUtils::UnsteadySystem::WeakPenaltyforScalar(), and Nektar::SolverUtils::UnsteadySystem::WeakPenaltyforVector().

891  {
892  return m_fields[0]->GetPhys_Offset(n);
893  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
MultiRegions::ExpListSharedPtr Nektar::SolverUtils::EquationSystem::GetPressure ( void  )
inline

Get pressure field if available.

Get Pressure field if available

Definition at line 782 of file EquationSystem.h.

References v_GetPressure().

783  {
784  return v_GetPressure();
785  }
virtual SOLVER_UTILS_EXPORT MultiRegions::ExpListSharedPtr v_GetPressure(void)
SOLVER_UTILS_EXPORT LibUtilities::SessionReaderSharedPtr Nektar::SolverUtils::EquationSystem::GetSession ( )
inline

Get Session name.

Definition at line 131 of file EquationSystem.h.

References m_session.

Referenced by LoadPts().

132  {
133  return m_session;
134  }
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
SOLVER_UTILS_EXPORT std::string Nektar::SolverUtils::EquationSystem::GetSessionName ( )
inline

Get Session name.

Definition at line 106 of file EquationSystem.h.

References m_sessionName.

107  {
108  return m_sessionName;
109  }
std::string m_sessionName
Name of the session.
int Nektar::SolverUtils::EquationSystem::GetSteps ( void  )
inline

Definition at line 920 of file EquationSystem.h.

References m_steps.

921  {
922  return m_steps;
923  }
int m_steps
Number of steps to take.
NekDouble Nektar::SolverUtils::EquationSystem::GetTimeStep ( void  )
inline

Definition at line 925 of file EquationSystem.h.

References m_timestep.

Referenced by Nektar::SolverUtils::UnsteadySystem::v_DoSolve().

926  {
927  return m_timestep;
928  }
NekDouble m_timestep
Time step size.
int Nektar::SolverUtils::EquationSystem::GetTotPoints ( void  )
inline

Definition at line 900 of file EquationSystem.h.

References m_fields.

Referenced by Nektar::NonlinearSWE::AddCoriolis(), Nektar::LinearSWE::AddCoriolis(), Nektar::NonlinearPeregrine::AddCoriolis(), Nektar::NonlinearSWE::AddVariableDepth(), Nektar::NonlinearPeregrine::AddVariableDepth(), Nektar::CompressibleFlowSystem::CalcSteadyState(), Nektar::NonlinearSWE::ConservativeToPrimitive(), Nektar::LinearSWE::ConservativeToPrimitive(), Nektar::NonlinearPeregrine::ConservativeToPrimitive(), Nektar::NonlinearSWE::DoOdeRhs(), Nektar::LinearSWE::DoOdeRhs(), Nektar::NonlinearPeregrine::DoOdeRhs(), Nektar::APE::DoOdeRhs(), Nektar::RinglebFlow::GetExactRinglebFlow(), Nektar::CFLtester::GetStdVelocity(), Nektar::CompressibleFlowSystem::GetStdVelocity(), Nektar::NonlinearPeregrine::LaitoneSolitaryWave(), Nektar::NonlinearSWE::PrimitiveToConservative(), Nektar::LinearSWE::PrimitiveToConservative(), Nektar::NonlinearPeregrine::PrimitiveToConservative(), Nektar::CoupledLinearNS::SetUpCoupledMatrix(), Nektar::NonlinearSWE::v_ConservativeToPrimitive(), Nektar::LinearSWE::v_ConservativeToPrimitive(), Nektar::NonlinearPeregrine::v_ConservativeToPrimitive(), Nektar::IsentropicVortex::v_EvaluateExactSolution(), Nektar::ShallowWaterSystem::v_InitObject(), Nektar::APE::v_InitObject(), Nektar::NonlinearSWE::v_PrimitiveToConservative(), Nektar::LinearSWE::v_PrimitiveToConservative(), Nektar::NonlinearPeregrine::v_PrimitiveToConservative(), Nektar::IsentropicVortex::v_SetInitialConditions(), and Nektar::NonlinearPeregrine::WCESolve().

901  {
902  return m_fields[0]->GetNpoints();
903  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
int Nektar::SolverUtils::EquationSystem::GetTotPoints ( int  n)
inline

Definition at line 905 of file EquationSystem.h.

References m_fields.

906  {
907  return m_fields[0]->GetTotPoints(n);
908  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
int Nektar::SolverUtils::EquationSystem::GetTraceNpoints ( void  )
inline
int Nektar::SolverUtils::EquationSystem::GetTraceTotPoints ( void  )
inline
const std::string Nektar::SolverUtils::EquationSystem::GetVariable ( unsigned int  i)
inline

Definition at line 870 of file EquationSystem.h.

References m_session.

871  {
872  return m_session->GetVariable(i);
873  }
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
void Nektar::SolverUtils::EquationSystem::ImportFld ( const std::string &  infile,
Array< OneD, MultiRegions::ExpListSharedPtr > &  pFields 
)

Input field data from the given file.

Import field from infile and load into m_fields. This routine will also perform a BwdTrans to ensure data is in both the physical and coefficient storage.

Parameters
infileFilename to read.

Definition at line 2270 of file EquationSystem.cpp.

References ASSERTL1, Nektar::LibUtilities::FieldIO::CreateForFile(), GetNcoeffs(), m_fields, m_session, and Vmath::Zero().

2273  {
2274  std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef;
2275  std::vector<std::vector<NekDouble> > FieldData;
2276  LibUtilities::FieldIOSharedPtr field_fld =
2278  field_fld->Import(infile,FieldDef,FieldData);
2279 
2280  // Copy FieldData into m_fields
2281  for(int j = 0; j < pFields.num_elements(); ++j)
2282  {
2283  Vmath::Zero(pFields[j]->GetNcoeffs(),
2284  pFields[j]->UpdateCoeffs(),1);
2285 
2286  for(int i = 0; i < FieldDef.size(); ++i)
2287  {
2288  ASSERTL1(FieldDef[i]->m_fields[j] ==
2289  m_session->GetVariable(j),
2290  std::string("Order of ") + infile
2291  + std::string(" data and that defined in "
2292  "m_boundaryconditions differs"));
2293 
2294  pFields[j]->ExtractDataToCoeffs(FieldDef[i], FieldData[i],
2295  FieldDef[i]->m_fields[j],
2296  pFields[j]->UpdateCoeffs());
2297  }
2298  pFields[j]->BwdTrans(pFields[j]->GetCoeffs(),
2299  pFields[j]->UpdatePhys());
2300  }
2301  }
boost::shared_ptr< FieldIO > FieldIOSharedPtr
Definition: FieldIO.h:309
static boost::shared_ptr< FieldIO > CreateForFile(const LibUtilities::SessionReaderSharedPtr session, const std::string &filename)
Construct a FieldIO object for a given input filename.
Definition: FieldIO.cpp:212
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
SOLVER_UTILS_EXPORT int GetNcoeffs()
void Zero(int n, T *x, const int incx)
Zero vector.
Definition: Vmath.cpp:373
#define ASSERTL1(condition, msg)
Assert Level 1 – Debugging which is used whether in FULLDEBUG or DEBUG compilation mode...
Definition: ErrorUtil.hpp:228
void Nektar::SolverUtils::EquationSystem::ImportFld ( const std::string &  infile,
std::vector< std::string > &  fieldStr,
Array< OneD, Array< OneD, NekDouble > > &  coeffs 
)

Output a field. Input field data into array from the given file.

Import field from infile and load into the array coeffs.

Parameters
infileFilename to read.
fieldStran array of string identifying fields to be imported
coeffsand array of array of coefficients to store imported data

Definition at line 2396 of file EquationSystem.cpp.

References ASSERTL0, Nektar::LibUtilities::FieldIO::CreateForFile(), m_fields, m_session, and Vmath::Zero().

2400  {
2401 
2402  ASSERTL0(fieldStr.size() <= coeffs.num_elements(),
2403  "length of fieldstr should be the same as pFields");
2404 
2405  std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef;
2406  std::vector<std::vector<NekDouble> > FieldData;
2407 
2408  LibUtilities::FieldIOSharedPtr field_fld =
2410  field_fld->Import(infile,FieldDef,FieldData);
2411 
2412  // Copy FieldData into m_fields
2413  for(int j = 0; j < fieldStr.size(); ++j)
2414  {
2415  Vmath::Zero(coeffs[j].num_elements(),coeffs[j],1);
2416  for(int i = 0; i < FieldDef.size(); ++i)
2417  {
2418  m_fields[0]->ExtractDataToCoeffs(FieldDef[i], FieldData[i],
2419  fieldStr[j], coeffs[j]);
2420  }
2421  }
2422  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
boost::shared_ptr< FieldIO > FieldIOSharedPtr
Definition: FieldIO.h:309
static boost::shared_ptr< FieldIO > CreateForFile(const LibUtilities::SessionReaderSharedPtr session, const std::string &filename)
Construct a FieldIO object for a given input filename.
Definition: FieldIO.cpp:212
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
void Zero(int n, T *x, const int incx)
Zero vector.
Definition: Vmath.cpp:373
void Nektar::SolverUtils::EquationSystem::ImportFld ( const std::string &  infile,
MultiRegions::ExpListSharedPtr pField,
std::string &  pFieldName 
)

Output a field. Input field data into ExpList from the given file.

Import field from infile and load into pField. This routine will also perform a BwdTrans to ensure data is in both the physical and coefficient storage.

Definition at line 2355 of file EquationSystem.cpp.

References ASSERTL1, Nektar::LibUtilities::FieldIO::CreateForFile(), m_fields, m_session, and Vmath::Zero().

2359  {
2360  std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef;
2361  std::vector<std::vector<NekDouble> > FieldData;
2362 
2363  LibUtilities::FieldIOSharedPtr field_fld =
2365  field_fld->Import(infile,FieldDef,FieldData);
2366  int idx = -1;
2367 
2368  Vmath::Zero(pField->GetNcoeffs(),pField->UpdateCoeffs(),1);
2369 
2370  for(int i = 0; i < FieldDef.size(); ++i)
2371  {
2372  // find the index of the required field in the file.
2373  for(int j = 0; j < FieldData.size(); ++j)
2374  {
2375  if (FieldDef[i]->m_fields[j] == pFieldName)
2376  {
2377  idx = j;
2378  }
2379  }
2380  ASSERTL1(idx >= 0, "Field " + pFieldName + " not found.");
2381 
2382  pField->ExtractDataToCoeffs(FieldDef[i], FieldData[i],
2383  FieldDef[i]->m_fields[idx],
2384  pField->UpdateCoeffs());
2385  }
2386  pField->BwdTrans(pField->GetCoeffs(), pField->UpdatePhys());
2387  }
boost::shared_ptr< FieldIO > FieldIOSharedPtr
Definition: FieldIO.h:309
static boost::shared_ptr< FieldIO > CreateForFile(const LibUtilities::SessionReaderSharedPtr session, const std::string &filename)
Construct a FieldIO object for a given input filename.
Definition: FieldIO.cpp:212
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
void Zero(int n, T *x, const int incx)
Zero vector.
Definition: Vmath.cpp:373
#define ASSERTL1(condition, msg)
Assert Level 1 – Debugging which is used whether in FULLDEBUG or DEBUG compilation mode...
Definition: ErrorUtil.hpp:228
void Nektar::SolverUtils::EquationSystem::ImportFldBase ( std::string  pInfile,
SpatialDomains::MeshGraphSharedPtr  pGraph 
)
protected

Definition at line 1607 of file EquationSystem.cpp.

References ASSERTL0, Nektar::LibUtilities::FieldIO::CreateForFile(), m_base, m_fields, and m_session.

1610  {
1611  std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef;
1612  std::vector<std::vector<NekDouble> > FieldData;
1613 
1614  //Get Homogeneous
1617  base_fld->Import(pInfile,FieldDef,FieldData);
1618 
1619  int nvar = m_session->GetVariables().size();
1620  if (m_session->DefinesSolverInfo("HOMOGENEOUS"))
1621  {
1622  std::string HomoStr = m_session->GetSolverInfo("HOMOGENEOUS");
1623  }
1624  // copy FieldData into m_fields
1625  for (int j = 0; j < nvar; ++j)
1626  {
1627  for(int i = 0; i < FieldDef.size(); ++i)
1628  {
1629  bool flag = FieldDef[i]->m_fields[j] ==
1630  m_session->GetVariable(j);
1631  ASSERTL0(flag, (std::string("Order of ") + pInfile
1632  + std::string(" data and that defined in "
1633  "the session differs")).c_str());
1634 
1635  m_base[j]->ExtractDataToCoeffs(FieldDef[i], FieldData[i],
1636  FieldDef[i]->m_fields[j],
1637  m_base[j]->UpdateCoeffs());
1638  }
1639  }
1640  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
boost::shared_ptr< FieldIO > FieldIOSharedPtr
Definition: FieldIO.h:309
static boost::shared_ptr< FieldIO > CreateForFile(const LibUtilities::SessionReaderSharedPtr session, const std::string &filename)
Construct a FieldIO object for a given input filename.
Definition: FieldIO.cpp:212
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Array< OneD, MultiRegions::ExpListSharedPtr > m_base
Base fields.
void Nektar::SolverUtils::EquationSystem::ImportFldToMultiDomains ( const std::string &  infile,
Array< OneD, MultiRegions::ExpListSharedPtr > &  pFields,
const int  ndomains 
)

Input field data from the given file to multiple domains.

Import field from infile and load into m_fields. This routine will also perform a BwdTrans to ensure data is in both the physical and coefficient storage.

Parameters
infileFilename to read. If optionan ndomains is specified it assumes we loop over nodmains for each nvariables.

Definition at line 2312 of file EquationSystem.cpp.

References ASSERTL0, ASSERTL1, GetNcoeffs(), GetNvariables(), Nektar::LibUtilities::Import(), m_fields, m_session, and Vmath::Zero().

2316  {
2317  std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef;
2318  std::vector<std::vector<NekDouble> > FieldData;
2319 
2320  LibUtilities::Import(infile,FieldDef,FieldData);
2321 
2322  int nvariables = GetNvariables();
2323 
2324  ASSERTL0(ndomains*nvariables == pFields.num_elements(),"Number of fields does not match the number of variables and domains");
2325 
2326  // Copy FieldData into m_fields
2327  for(int j = 0; j < ndomains; ++j)
2328  {
2329  for(int i = 0; i < nvariables; ++i)
2330  {
2331  Vmath::Zero(pFields[j*nvariables+i]->GetNcoeffs(),pFields[j*nvariables+i]->UpdateCoeffs(),1);
2332 
2333  for(int n = 0; n < FieldDef.size(); ++n)
2334  {
2335  ASSERTL1(FieldDef[n]->m_fields[i] == m_session->GetVariable(i),
2336  std::string("Order of ") + infile
2337  + std::string(" data and that defined in "
2338  "m_boundaryconditions differs"));
2339 
2340  pFields[j*nvariables+i]->ExtractDataToCoeffs(FieldDef[n], FieldData[n],
2341  FieldDef[n]->m_fields[i],
2342  pFields[j*nvariables+i]->UpdateCoeffs());
2343  }
2344  pFields[j*nvariables+i]->BwdTrans(pFields[j*nvariables+i]->GetCoeffs(),
2345  pFields[j*nvariables+i]->UpdatePhys());
2346  }
2347  }
2348  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
void Import(const std::string &infilename, std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble > > &fielddata, FieldMetaDataMap &fieldinfomap, const Array< OneD, int > &ElementIDs)
This function allows for data to be imported from an FLD file when a session and/or communicator is n...
Definition: FieldIO.cpp:279
SOLVER_UTILS_EXPORT int GetNvariables()
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
SOLVER_UTILS_EXPORT int GetNcoeffs()
void Zero(int n, T *x, const int incx)
Zero vector.
Definition: Vmath.cpp:373
#define ASSERTL1(condition, msg)
Assert Level 1 – Debugging which is used whether in FULLDEBUG or DEBUG compilation mode...
Definition: ErrorUtil.hpp:228
void Nektar::SolverUtils::EquationSystem::InitialiseBaseFlow ( Array< OneD, Array< OneD, NekDouble > > &  base)

Perform initialisation of the base flow.

Definition at line 1427 of file EquationSystem.cpp.

References EvaluateFunction(), m_graph, m_spacedim, and SetUpBaseFields().

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

1429  {
1430  base = Array<OneD, Array<OneD, NekDouble> >(m_spacedim);
1431  std::vector<std::string> vel;
1432  vel.push_back("Vx");
1433  vel.push_back("Vy");
1434  vel.push_back("Vz");
1435  vel.resize(m_spacedim);
1437  EvaluateFunction(vel, base, "BaseFlow");
1438  }
SOLVER_UTILS_EXPORT void SetUpBaseFields(SpatialDomains::MeshGraphSharedPtr &mesh)
int m_spacedim
Spatial dimension (>= expansion dim).
SOLVER_UTILS_EXPORT void EvaluateFunction(Array< OneD, Array< OneD, NekDouble > > &pArray, std::string pFunctionName, const NekDouble pTime=0.0, const int domain=0)
Evaluates a function as specified in the session file.
SpatialDomains::MeshGraphSharedPtr m_graph
Pointer to graph defining mesh.
void Nektar::SolverUtils::EquationSystem::InitObject ( )
inline

Initialises the members of this object.

This is the second part of the two-phase initialisation process. Calls to virtual functions will correctly resolve to the derived class during this phase of the construction.

Definition at line 703 of file EquationSystem.h.

References v_InitObject().

704  {
705  v_InitObject();
706  }
virtual SOLVER_UTILS_EXPORT void v_InitObject()
Initialisation object for EquationSystem.
NekDouble Nektar::SolverUtils::EquationSystem::L2Error ( unsigned int  field,
const Array< OneD, NekDouble > &  exactsoln,
bool  Normalised = false 
)
inline

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

L_2 Error computation Public interface routine to virtual function implementation.

Definition at line 774 of file EquationSystem.h.

References v_L2Error().

Referenced by L2Error().

775  {
776  return v_L2Error(field, exactsoln, Normalised);
777  }
virtual SOLVER_UTILS_EXPORT NekDouble v_L2Error(unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray, bool Normalised=false)
Virtual function for the L_2 error computation between fields and a given exact solution.
SOLVER_UTILS_EXPORT NekDouble Nektar::SolverUtils::EquationSystem::L2Error ( unsigned int  field,
bool  Normalised = false 
)
inline

Compute the L2 error of the fields.

Definition at line 206 of file EquationSystem.h.

References L2Error(), and Nektar::NullNekDouble1DArray.

209  {
210  return L2Error(field,NullNekDouble1DArray,Normalised);
211  }
static Array< OneD, NekDouble > NullNekDouble1DArray
SOLVER_UTILS_EXPORT NekDouble L2Error(unsigned int field, const Array< OneD, NekDouble > &exactsoln, bool Normalised=false)
Compute the L2 error between fields and a given exact solution.
NekDouble Nektar::SolverUtils::EquationSystem::LinfError ( unsigned int  field,
const Array< OneD, NekDouble > &  exactsoln = NullNekDouble1DArray 
)
inline

Linf error computation.

L_inf Error computation Public interface routine to virtual function implementation.

Definition at line 765 of file EquationSystem.h.

References v_LinfError().

766  {
767  return v_LinfError(field, exactsoln);
768  }
virtual SOLVER_UTILS_EXPORT NekDouble v_LinfError(unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray)
Virtual function for the L_inf error computation between fields and a given exact solution...
void Nektar::SolverUtils::EquationSystem::LoadPts ( std::string  funcFilename,
std::string  filename,
Nektar::LibUtilities::PtsFieldSharedPtr outPts 
)
protected

Definition at line 1058 of file EquationSystem.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), Nektar::FieldUtils::eShepard, GetSession(), Nektar::LibUtilities::PtsIO::Import(), m_comm, m_fields, m_interpolators, m_session, and PrintProgressbar().

Referenced by EvaluateFunctionPts().

1061  {
1062  unsigned int nq = m_fields[0]->GetNpoints();
1063 
1065  LibUtilities::PtsIO ptsIO(m_session->GetComm());
1066  ptsIO.Import(filename, inPts);
1067 
1068  Array<OneD, Array<OneD, NekDouble> > pts(inPts->GetDim() +
1069  inPts->GetNFields());
1070  for (int i = 0; i < inPts->GetDim() + inPts->GetNFields(); ++i)
1071  {
1072  pts[i] = Array<OneD, NekDouble>(nq);
1073  }
1074  if (inPts->GetDim() == 1)
1075  {
1076  m_fields[0]->GetCoords(pts[0]);
1077  }
1078  else if (inPts->GetDim() == 2)
1079  {
1080  m_fields[0]->GetCoords(pts[0], pts[1]);
1081  }
1082  else if (inPts->GetDim() == 3)
1083  {
1084  m_fields[0]->GetCoords(pts[0], pts[1], pts[2]);
1085  }
1087  inPts->GetDim(), inPts->GetFieldNames(), pts);
1088 
1089  // check if we already have an interolator for this funcFilename
1090  if (m_interpolators.find(funcFilename) == m_interpolators.end())
1091  {
1092  m_interpolators[funcFilename] =
1093  FieldUtils::Interpolator(Nektar::FieldUtils::eShepard);
1094  if (m_comm->GetRank() == 0)
1095  {
1096  m_interpolators[funcFilename].SetProgressCallback(
1098  }
1099  m_interpolators[funcFilename].CalcWeights(inPts, outPts);
1100  if (m_comm->GetRank() == 0)
1101  {
1102  cout << endl;
1103  if (GetSession()->DefinesCmdLineArgument("verbose"))
1104  {
1105  m_interpolators[funcFilename].PrintStatistics();
1106  }
1107  }
1108  }
1109  m_interpolators[funcFilename].Interpolate(inPts, outPts);
1110  }
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
SOLVER_UTILS_EXPORT void PrintProgressbar(const int position, const int goal) const
boost::shared_ptr< PtsField > PtsFieldSharedPtr
Definition: PtsField.h:178
LibUtilities::CommSharedPtr m_comm
Communicator.
SOLVER_UTILS_EXPORT LibUtilities::SessionReaderSharedPtr GetSession()
Get Session name.
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
std::map< std::string, FieldUtils::Interpolator > m_interpolators
Map of interpolator objects.
int Nektar::SolverUtils::EquationSystem::nocase_cmp ( const std::string &  s1,
const std::string &  s2 
)
inlineprotected

Definition at line 563 of file EquationSystem.h.

References NoCaseStringCompare().

564  {
565  return NoCaseStringCompare(s1,s2);
566  }
SOLVER_UTILS_EXPORT int NoCaseStringCompare(const std::string &s1, const std::string &s2)
Perform a case-insensitive string comparison.
int Nektar::SolverUtils::EquationSystem::NoCaseStringCompare ( const std::string &  s1,
const std::string &  s2 
)

Perform a case-insensitive string comparison.

Performs a case-insensitive string comparison (from web).

Parameters
s1First string to compare.
s2Second string to compare.
Returns
0 if the strings match.

Definition at line 2519 of file EquationSystem.cpp.

Referenced by nocase_cmp().

2522  {
2523  //if (s1.size() < s2.size()) return -1;
2524  //if (s1.size() > s2.size()) return 1;
2525 
2526  string::const_iterator it1=s1.begin();
2527  string::const_iterator it2=s2.begin();
2528 
2529  // Stop when either string's end has been reached
2530  while ( (it1!=s1.end()) && (it2!=s2.end()) )
2531  {
2532  if(::toupper(*it1) != ::toupper(*it2)) //letters differ?
2533  {
2534  // Return -1 to indicate smaller than, 1 otherwise
2535  return (::toupper(*it1) < ::toupper(*it2)) ? -1 : 1;
2536  }
2537 
2538  // Proceed to the next character in each string
2539  ++it1;
2540  ++it2;
2541  }
2542 
2543  size_t size1=s1.size();
2544  size_t size2=s2.size();// cache lengths
2545 
2546  // Return -1, 0 or 1 according to strings' lengths
2547  if (size1==size2)
2548  {
2549  return 0;
2550  }
2551 
2552  return (size1 < size2) ? -1 : 1;
2553  }
void Nektar::SolverUtils::EquationSystem::NumericalFlux ( Array< OneD, Array< OneD, NekDouble > > &  physfield,
Array< OneD, Array< OneD, NekDouble > > &  numflux 
)
inline

Definition at line 969 of file EquationSystem.h.

References v_NumericalFlux().

Referenced by WeakDGAdvection().

971  {
972  v_NumericalFlux(physfield, numflux);
973  }
virtual SOLVER_UTILS_EXPORT void v_NumericalFlux(Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numflux)
void Nektar::SolverUtils::EquationSystem::NumericalFlux ( Array< OneD, Array< OneD, NekDouble > > &  physfield,
Array< OneD, Array< OneD, NekDouble > > &  numfluxX,
Array< OneD, Array< OneD, NekDouble > > &  numfluxY 
)
inline

Definition at line 975 of file EquationSystem.h.

References v_NumericalFlux().

978  {
979  v_NumericalFlux(physfield, numfluxX, numfluxY);
980  }
virtual SOLVER_UTILS_EXPORT void v_NumericalFlux(Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numflux)
void Nektar::SolverUtils::EquationSystem::NumFluxforScalar ( const Array< OneD, Array< OneD, NekDouble > > &  ufield,
Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &  uflux 
)
inline

Definition at line 982 of file EquationSystem.h.

References v_NumFluxforScalar().

Referenced by WeakDGDiffusion().

985  {
986  v_NumFluxforScalar(ufield, uflux);
987  }
virtual SOLVER_UTILS_EXPORT void v_NumFluxforScalar(const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &uflux)
void Nektar::SolverUtils::EquationSystem::NumFluxforVector ( const Array< OneD, Array< OneD, NekDouble > > &  ufield,
Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &  qfield,
Array< OneD, Array< OneD, NekDouble > > &  qflux 
)
inline

Definition at line 989 of file EquationSystem.h.

References v_NumFluxforVector().

Referenced by WeakDGDiffusion().

993  {
994  v_NumFluxforVector(ufield, qfield, qflux);
995  }
virtual SOLVER_UTILS_EXPORT void v_NumFluxforVector(const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &qfield, Array< OneD, Array< OneD, NekDouble > > &qflux)
void Nektar::SolverUtils::EquationSystem::Output ( void  )
inline

Perform output operations after solve.

Perform output operations after solve.

Definition at line 756 of file EquationSystem.h.

References v_Output().

757  {
758  v_Output();
759  }
virtual SOLVER_UTILS_EXPORT void v_Output(void)
SOLVER_UTILS_EXPORT void Nektar::SolverUtils::EquationSystem::PrintProgressbar ( const int  position,
const int  goal 
) const
inlineprivate

Definition at line 690 of file EquationSystem.h.

References Nektar::LibUtilities::PrintProgressbar().

Referenced by LoadPts().

692  {
693  LibUtilities::PrintProgressbar(position, goal, "Interpolating");
694  }
int PrintProgressbar(const int position, const int goal, const string message, int lastprogress=-1)
Prints a progressbar.
Definition: Progressbar.hpp:69
void Nektar::SolverUtils::EquationSystem::PrintSummary ( std::ostream &  out)
inline

Print a summary of parameters and solver characteristics.

Prints a summary of variables and problem parameters.

Public interface routine to virtual function implementation.

Parameters
outThe ostream object to write to.

Definition at line 794 of file EquationSystem.h.

References m_session, and v_GenerateSummary().

795  {
796  if (m_session->GetComm()->GetRank() == 0)
797  {
798  std::vector<std::pair<std::string, std::string> > vSummary;
799  v_GenerateSummary(vSummary);
800 
801  out << "=======================================================================" << std::endl;
802  SummaryList::const_iterator x;
803  for (x = vSummary.begin(); x != vSummary.end(); ++x)
804  {
805  out << "\t";
806  out.width(20);
807  out << x->first << ": " << x->second << std::endl;
808  }
809  out << "=======================================================================" << std::endl;
810  }
811  }
virtual SOLVER_UTILS_EXPORT void v_GenerateSummary(SummaryList &l)
Virtual function for generating summary information.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
SOLVER_UTILS_EXPORT void Nektar::SolverUtils::EquationSystem::ResetSessionName ( std::string  newname)
inline

Reset Session name.

Definition at line 125 of file EquationSystem.h.

References m_sessionName.

126  {
127  m_sessionName = newname;
128  }
std::string m_sessionName
Name of the session.
SOLVER_UTILS_EXPORT void Nektar::SolverUtils::EquationSystem::ScanForHistoryPoints ( )

Builds map of which element holds each history point.

void Nektar::SolverUtils::EquationSystem::SessionSummary ( SummaryList s)

Write out a session summary.

Write out a summary of the session data.

Parameters
outOutput stream to write data to.

Definition at line 2428 of file EquationSystem.cpp.

References Nektar::SolverUtils::AddSummaryItem(), Nektar::MultiRegions::eDiscontinuous, Nektar::MultiRegions::eGalerkin, eHomogeneous1D, eHomogeneous2D, Nektar::MultiRegions::eMixed_CG_Discontinuous, Nektar::SolverUtils::GetAdvectionFactory(), Nektar::SolverUtils::GetDiffusionFactory(), m_expdim, m_fields, m_halfMode, m_HomogeneousType, m_LhomY, m_LhomZ, m_multipleModes, m_npointsY, m_npointsZ, m_projectionType, m_session, m_sessionName, m_singleMode, m_spacedim, and m_useFFT.

Referenced by Nektar::Projection::v_GenerateSummary(), Nektar::Laplace::v_GenerateSummary(), Nektar::LinearElasticSystem::v_GenerateSummary(), and v_GenerateSummary().

2429  {
2430  AddSummaryItem(s, "EquationType", m_session->GetSolverInfo("EQTYPE"));
2431  AddSummaryItem(s, "Session Name", m_sessionName);
2432  AddSummaryItem(s, "Spatial Dim.", m_spacedim);
2433  AddSummaryItem(s, "Max SEM Exp. Order", m_fields[0]->EvalBasisNumModesMax());
2434 
2435  if (m_session->GetComm()->GetSize() > 1)
2436  {
2437  AddSummaryItem(s, "Num. Processes",
2438  m_session->GetComm()->GetSize());
2439  }
2440 
2442  {
2443  AddSummaryItem(s, "Quasi-3D", "Homogeneous in z-direction");
2444  AddSummaryItem(s, "Expansion Dim.", m_expdim + 1);
2445  AddSummaryItem(s, "Num. Hom. Modes (z)", m_npointsZ);
2446  AddSummaryItem(s, "Hom. length (LZ)", m_LhomZ);
2447  AddSummaryItem(s, "FFT Type", m_useFFT ? "FFTW" : "MVM");
2448  if (m_halfMode)
2449  {
2450  AddSummaryItem(s, "ModeType", "Half Mode");
2451  }
2452  else if (m_singleMode)
2453  {
2454  AddSummaryItem(s, "ModeType", "Single Mode");
2455  }
2456  else if (m_multipleModes)
2457  {
2458  AddSummaryItem(s, "ModeType", "Multiple Modes");
2459  }
2460  }
2461  else if(m_HomogeneousType == eHomogeneous2D)
2462  {
2463  AddSummaryItem(s, "Quasi-3D", "Homogeneous in yz-plane");
2464  AddSummaryItem(s, "Expansion Dim.", m_expdim + 2);
2465  AddSummaryItem(s, "Num. Hom. Modes (y)", m_npointsY);
2466  AddSummaryItem(s, "Num. Hom. Modes (z)", m_npointsZ);
2467  AddSummaryItem(s, "Hom. length (LY)", m_LhomY);
2468  AddSummaryItem(s, "Hom. length (LZ)", m_LhomZ);
2469  AddSummaryItem(s, "FFT Type", m_useFFT ? "FFTW" : "MVM");
2470  }
2471  else
2472  {
2473  AddSummaryItem(s, "Expansion Dim.", m_expdim);
2474  }
2475 
2476  if (m_session->DefinesSolverInfo("UpwindType"))
2477  {
2478  AddSummaryItem(s, "Riemann Solver",
2479  m_session->GetSolverInfo("UpwindType"));
2480  }
2481 
2482  if (m_session->DefinesSolverInfo("AdvectionType"))
2483  {
2484  std::string AdvectionType;
2485  AdvectionType = m_session->GetSolverInfo("AdvectionType");
2486  AddSummaryItem(s, "Advection Type", GetAdvectionFactory().
2487  GetClassDescription(AdvectionType));
2488  }
2489 
2491  {
2492  AddSummaryItem(s, "Projection Type", "Continuous Galerkin");
2493  }
2495  {
2496  AddSummaryItem(s, "Projection Type", "Discontinuous Galerkin");
2497  }
2499  {
2500  AddSummaryItem(s, "Projection Type",
2501  "Mixed Continuous Galerkin and Discontinuous");
2502  }
2503 
2504  if (m_session->DefinesSolverInfo("DiffusionType"))
2505  {
2506  std::string DiffusionType;
2507  DiffusionType = m_session->GetSolverInfo("DiffusionType");
2508  AddSummaryItem(s, "Diffusion Type", GetDiffusionFactory().
2509  GetClassDescription(DiffusionType));
2510  }
2511  }
bool m_singleMode
Flag to determine if single homogeneous mode is used.
bool m_halfMode
Flag to determine if half homogeneous mode is used.
NekDouble m_LhomZ
physical length in Z direction (if homogeneous)
int m_expdim
Expansion dimension.
DiffusionFactory & GetDiffusionFactory()
Definition: Diffusion.cpp:42
enum MultiRegions::ProjectionType m_projectionType
Type of projection; e.g continuous or discontinuous.
bool m_useFFT
Flag to determine if FFT is used for homogeneous transform.
NekDouble m_LhomY
physical length in Y direction (if homogeneous)
int m_npointsZ
number of points in Z direction (if homogeneous)
std::string m_sessionName
Name of the session.
bool m_multipleModes
Flag to determine if use multiple homogenenous modes are used.
int m_npointsY
number of points in Y direction (if homogeneous)
void AddSummaryItem(SummaryList &l, const std::string &name, const std::string &value)
Adds a summary item to the summary info list.
Definition: Misc.cpp:50
int m_spacedim
Spatial dimension (>= expansion dim).
AdvectionFactory & GetAdvectionFactory()
Gets the factory for initialising advection objects.
Definition: Advection.cpp:46
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
enum HomogeneousType m_HomogeneousType
void Nektar::SolverUtils::EquationSystem::SetBoundaryConditions ( NekDouble  time)

Evaluates the boundary conditions at the given time.

If boundary conditions are time-dependent, they will be evaluated at the time specified.

Parameters
timeThe time at which to evaluate the BCs

Definition at line 1152 of file EquationSystem.cpp.

References m_fields, and m_session.

Referenced by Nektar::UnsteadyAdvectionDiffusion::DoImplicitSolve(), Nektar::UnsteadyViscousBurgers::DoImplicitSolve(), Nektar::ImageWarpingSystem::DoOdeProjection(), Nektar::NonlinearSWE::DoOdeProjection(), Nektar::LinearSWE::DoOdeProjection(), Nektar::UnsteadyInviscidBurger::DoOdeProjection(), Nektar::UnsteadyDiffusion::DoOdeProjection(), Nektar::UnsteadyAdvection::DoOdeProjection(), Nektar::NonlinearPeregrine::DoOdeProjection(), Nektar::UnsteadyAdvectionDiffusion::DoOdeProjection(), Nektar::CFLtester::DoOdeProjection(), Nektar::UnsteadyViscousBurgers::DoOdeProjection(), Nektar::PulseWavePropagation::SetPulseWaveBoundaryConditions(), and Nektar::SolverUtils::UnsteadySystem::v_DoInitialise().

1153  {
1154  std::string varName;
1155  int nvariables = m_fields.num_elements();
1156  for (int i = 0; i < nvariables; ++i)
1157  {
1158  varName = m_session->GetVariable(i);
1159  m_fields[i]->EvaluateBoundaryConditions(time, varName);
1160  }
1161  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
SOLVER_UTILS_EXPORT void Nektar::SolverUtils::EquationSystem::SetCheckpointNumber ( int  num)
inline

Definition at line 421 of file EquationSystem.h.

References m_nchk.

422  {
423  m_nchk = num;
424  }
int m_nchk
Number of checkpoints written so far.
SOLVER_UTILS_EXPORT void Nektar::SolverUtils::EquationSystem::SetCheckpointSteps ( int  num)
inline

Definition at line 431 of file EquationSystem.h.

References m_checksteps.

432  {
433  m_checksteps = num;
434  }
int m_checksteps
Number of steps between checkpoints.
void Nektar::SolverUtils::EquationSystem::SetInitialConditions ( NekDouble  initialtime = 0.0,
bool  dumpInitialConditions = true,
const int  domain = 0 
)
inline

Initialise the data in the dependent fields.

Definition at line 818 of file EquationSystem.h.

References v_SetInitialConditions().

Referenced by main(), Nektar::SolverUtils::UnsteadySystem::v_DoInitialise(), Nektar::PulseWaveSystem::v_DoInitialise(), and Nektar::CoupledLinearNS::v_DoInitialise().

821  {
822  v_SetInitialConditions(initialtime,dumpInitialConditions,domain);
823  }
virtual SOLVER_UTILS_EXPORT void v_SetInitialConditions(NekDouble initialtime=0.0, bool dumpInitialConditions=true, const int domain=0)
SOLVER_UTILS_EXPORT void Nektar::SolverUtils::EquationSystem::SetInitialStep ( const int  step)
inline

Definition at line 442 of file EquationSystem.h.

References m_initialStep.

444  {
445  m_initialStep = step;
446  }
int m_initialStep
Number of the step where the simulation should begin.
void Nektar::SolverUtils::EquationSystem::SetLambda ( NekDouble  lambda)
inline

Set parameter m_lambda.

Definition at line 813 of file EquationSystem.h.

References m_lambda.

814  {
815  m_lambda = lambda;
816  }
NekDouble m_lambda
Lambda constant in real system if one required.
SOLVER_UTILS_EXPORT void Nektar::SolverUtils::EquationSystem::SetModifiedBasis ( const bool  modbasis)
inline
void Nektar::SolverUtils::EquationSystem::SetSteps ( const int  steps)
inline

Definition at line 930 of file EquationSystem.h.

References m_steps.

931  {
932  m_steps = steps;
933  }
int m_steps
Number of steps to take.
SOLVER_UTILS_EXPORT void Nektar::SolverUtils::EquationSystem::SetTime ( const NekDouble  time)
inline

Definition at line 436 of file EquationSystem.h.

References m_time.

438  {
439  m_time = time;
440  }
NekDouble m_time
Current time of simulation.
void Nektar::SolverUtils::EquationSystem::SetUpBaseFields ( SpatialDomains::MeshGraphSharedPtr mesh)
protected

Definition at line 1440 of file EquationSystem.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, Nektar::LibUtilities::eFourier, Nektar::LibUtilities::eFourierEvenlySpaced, Nektar::LibUtilities::eFourierHalfModeRe, Nektar::LibUtilities::eFourierSingleModeSpaced, Nektar::MultiRegions::eGalerkin, eHomogeneous1D, Nektar::MultiRegions::eMixed_CG_Discontinuous, m_base, m_expdim, m_graph, m_halfMode, m_homogen_dealiasing, m_HomogeneousType, m_LhomZ, m_npointsZ, m_projectionType, m_session, m_singleMode, and m_useFFT.

Referenced by InitialiseBaseFlow().

1442  {
1443  int i;
1444 
1445  // The number of variables can be different from the dimension
1446  // of the base flow
1447  int nvariables = m_session->GetVariables().size();
1448  m_base = Array<OneD, MultiRegions::ExpListSharedPtr>(nvariables);
1451  {
1452  switch (m_expdim)
1453  {
1454  case 1:
1455  {
1456  for(i = 0; i < m_base.num_elements(); i++)
1457  {
1460  m_session->GetVariable(0));
1461  }
1462  }
1463  break;
1464  case 2:
1465  {
1467  {
1468  if (m_singleMode)
1469  {
1470  const LibUtilities::PointsKey PkeyZ(m_npointsZ,
1472  const LibUtilities::BasisKey BkeyZ(
1474  m_npointsZ,PkeyZ);
1475 
1476  for (i = 0 ; i < m_base.num_elements(); i++)
1477  {
1478  m_base[i] = MemoryManager<MultiRegions
1479  ::ContField3DHomogeneous1D>
1480  ::AllocateSharedPtr(
1481  m_session, BkeyZ, m_LhomZ,
1483  m_graph,
1484  m_session->GetVariable(i));
1485  m_base[i]->SetWaveSpace(true);
1486  }
1487  }
1488  else if (m_halfMode)
1489  {
1490  //1 plane field (half mode expansion)
1491  const LibUtilities::PointsKey PkeyZ(m_npointsZ,
1493  const LibUtilities::BasisKey BkeyZ(
1495  m_npointsZ,PkeyZ);
1496 
1497  for (i = 0 ; i < m_base.num_elements(); i++)
1498  {
1499  m_base[i] = MemoryManager<MultiRegions
1500  ::ContField3DHomogeneous1D>
1501  ::AllocateSharedPtr(
1502  m_session, BkeyZ, m_LhomZ,
1504  m_graph,
1505  m_session->GetVariable(i));
1506  m_base[i]->SetWaveSpace(true);
1507  }
1508  }
1509  else
1510  {
1511  const LibUtilities::PointsKey PkeyZ(m_npointsZ,
1513  const LibUtilities::BasisKey BkeyZ(
1515  PkeyZ);
1516 
1517  for (i = 0 ; i < m_base.num_elements(); i++)
1518  {
1519  m_base[i] = MemoryManager<MultiRegions
1520  ::ContField3DHomogeneous1D>
1521  ::AllocateSharedPtr(
1522  m_session, BkeyZ, m_LhomZ,
1524  m_graph,
1525  m_session->GetVariable(i));
1526  m_base[i]->SetWaveSpace(false);
1527  }
1528  }
1529  }
1530  else
1531  {
1532  i = 0;
1536  m_session->GetVariable(i));
1537  m_base[0]=firstbase;
1538 
1539  for (i = 1 ; i < m_base.num_elements(); i++)
1540  {
1541  m_base[i] = MemoryManager<MultiRegions::
1542  ContField2D>::AllocateSharedPtr(
1543  *firstbase,mesh,
1544  m_session->GetVariable(i));
1545  }
1546  }
1547  }
1548  break;
1549  case 3:
1550  {
1554  m_session->GetVariable(0));
1555  m_base[0] = firstbase;
1556  for (i = 1 ; i < m_base.num_elements(); i++)
1557  {
1559  ::AllocateSharedPtr(*firstbase, m_graph,
1560  m_session->GetVariable(0));
1561  }
1562  }
1563  break;
1564  default:
1565  ASSERTL0(false,"Expansion dimension not recognised");
1566  break;
1567  }
1568  }
1569  else
1570  {
1571  switch(m_expdim)
1572  {
1573  case 1:
1574  {
1575  // need to use zero for variable as may be more base
1576  // flows than variables
1577  for(i = 0 ; i < m_base.num_elements(); i++)
1578  {
1579  m_base[i] = MemoryManager<MultiRegions
1580  ::DisContField1D>
1581  ::AllocateSharedPtr(m_session, m_graph,
1582  m_session->GetVariable(0));
1583  }
1584  break;
1585  }
1586  case 2:
1587  {
1588  for(i = 0 ; i < m_base.num_elements(); i++)
1589  {
1590  m_base[i] = MemoryManager<MultiRegions::
1591  DisContField2D>::AllocateSharedPtr(
1593  m_session->GetVariable(0));
1594  }
1595  break;
1596  }
1597  case 3:
1598  ASSERTL0(false, "3 D not set up");
1599  default:
1600  ASSERTL0(false, "Expansion dimension not recognised");
1601  break;
1602  }
1603  }
1604  }
bool m_singleMode
Flag to determine if single homogeneous mode is used.
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
bool m_halfMode
Flag to determine if half homogeneous mode is used.
NekDouble m_LhomZ
physical length in Z direction (if homogeneous)
int m_expdim
Expansion dimension.
enum MultiRegions::ProjectionType m_projectionType
Type of projection; e.g continuous or discontinuous.
bool m_useFFT
Flag to determine if FFT is used for homogeneous transform.
boost::shared_ptr< ContField2D > ContField2DSharedPtr
Definition: ContField2D.h:287
Fourier Expansion .
Definition: BasisType.h:52
int m_npointsZ
number of points in Z direction (if homogeneous)
1D Evenly-spaced points using Fourier Fit
Definition: PointsType.h:66
Fourier Modified expansions with just the real part of the first mode .
Definition: BasisType.h:59
bool m_homogen_dealiasing
Flag to determine if dealiasing is used for homogeneous simulations.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Array< OneD, MultiRegions::ExpListSharedPtr > m_base
Base fields.
1D Non Evenly-spaced points for Single Mode analysis
Definition: PointsType.h:67
SpatialDomains::MeshGraphSharedPtr m_graph
Pointer to graph defining mesh.
boost::shared_ptr< ContField3D > ContField3DSharedPtr
Definition: ContField3D.h:206
enum HomogeneousType m_HomogeneousType
SOLVER_UTILS_EXPORT void Nektar::SolverUtils::EquationSystem::SetUpTraceNormals ( void  )
void Nektar::SolverUtils::EquationSystem::TransCoeffToPhys ( void  )
inline

Transform from coefficient to physical space.

Performs the transformation from coefficient to physical space.

Public interface routine to virtual function implementation.

Definition at line 726 of file EquationSystem.h.

References v_TransCoeffToPhys().

727  {
729  }
virtual SOLVER_UTILS_EXPORT void v_TransCoeffToPhys()
Virtual function for transformation to physical space.
void Nektar::SolverUtils::EquationSystem::TransPhysToCoeff ( void  )
inline

Transform from physical to coefficient space.

Performs the transformation from physical to coefficient space.

Public interface routine to virtual function implementation.

Definition at line 736 of file EquationSystem.h.

References v_TransPhysToCoeff().

737  {
739  }
virtual SOLVER_UTILS_EXPORT void v_TransPhysToCoeff()
Virtual function for transformation to coefficient space.
SOLVER_UTILS_EXPORT LibUtilities::FieldMetaDataMap& Nektar::SolverUtils::EquationSystem::UpdateFieldMetaDataMap ( )
inline

Get hold of FieldInfoMap so it can be updated.

Array< OneD, MultiRegions::ExpListSharedPtr > & Nektar::SolverUtils::EquationSystem::UpdateFields ( void  )
inline

Definition at line 833 of file EquationSystem.h.

References m_fields.

834  {
835  return m_fields;
836  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
void Nektar::SolverUtils::EquationSystem::v_DoInitialise ( void  )
protectedvirtual

Virtual function for initialisation implementation.

By default, nothing needs initialising at the EquationSystem level.

Reimplemented in Nektar::CoupledLinearNS, Nektar::PulseWaveSystem, Nektar::VelocityCorrectionScheme, Nektar::SolverUtils::UnsteadySystem, Nektar::VCSMapping, Nektar::SteadyAdvectionDiffusion, and Nektar::EigenValuesAdvection.

Definition at line 1421 of file EquationSystem.cpp.

Referenced by DoInitialise().

1422  {
1423 
1424  }
void Nektar::SolverUtils::EquationSystem::v_DoSolve ( void  )
protectedvirtual
void Nektar::SolverUtils::EquationSystem::v_EvaluateExactSolution ( unsigned int  field,
Array< OneD, NekDouble > &  outfield,
const NekDouble  time 
)
protectedvirtual

Reimplemented in Nektar::IsentropicVortex, and Nektar::RinglebFlow.

Definition at line 1402 of file EquationSystem.cpp.

References ASSERTL0, EvaluateFunction(), m_fields, m_session, and Vmath::Zero().

Referenced by EvaluateExactSolution().

1406  {
1407  ASSERTL0 (outfield.num_elements() == m_fields[field]->GetNpoints(),
1408  "ExactSolution array size mismatch.");
1409  Vmath::Zero(outfield.num_elements(), outfield, 1);
1410  if (m_session->DefinesFunction("ExactSolution"))
1411  {
1412  EvaluateFunction(m_session->GetVariable(field), outfield,
1413  "ExactSolution", time);
1414  }
1415  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
SOLVER_UTILS_EXPORT void EvaluateFunction(Array< OneD, Array< OneD, NekDouble > > &pArray, std::string pFunctionName, const NekDouble pTime=0.0, const int domain=0)
Evaluates a function as specified in the session file.
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
void Zero(int n, T *x, const int incx)
Zero vector.
Definition: Vmath.cpp:373
void Nektar::SolverUtils::EquationSystem::v_ExtraFldOutput ( std::vector< Array< OneD, NekDouble > > &  fieldcoeffs,
std::vector< std::string > &  variables 
)
protectedvirtual

Reimplemented in Nektar::CompressibleFlowSystem, Nektar::LinearElasticSystem, and Nektar::APE.

Definition at line 2629 of file EquationSystem.cpp.

Referenced by WriteFld().

2632  {
2633  }
void Nektar::SolverUtils::EquationSystem::v_GenerateSummary ( SummaryList l)
protectedvirtual
void Nektar::SolverUtils::EquationSystem::v_GetFluxVector ( const int  i,
Array< OneD, Array< OneD, NekDouble > > &  physfield,
Array< OneD, Array< OneD, NekDouble > > &  flux 
)
privatevirtual

Reimplemented in Nektar::IncNavierStokes, Nektar::CFLtester, Nektar::PulseWavePropagation, Nektar::ImageWarpingSystem, and Nektar::EigenValuesAdvection.

Definition at line 2560 of file EquationSystem.cpp.

References ASSERTL0.

Referenced by GetFluxVector().

2564  {
2565  ASSERTL0(false, "v_GetFluxVector: This function is not valid "
2566  "for the Base class");
2567  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
void Nektar::SolverUtils::EquationSystem::v_GetFluxVector ( const int  i,
const int  j,
Array< OneD, Array< OneD, NekDouble > > &  physfield,
Array< OneD, Array< OneD, NekDouble > > &  flux 
)
privatevirtual

Definition at line 2569 of file EquationSystem.cpp.

References ASSERTL0.

2573  {
2574  ASSERTL0(false, "v_GetqFluxVector: This function is not valid "
2575  "for the Base class");
2576  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
void Nektar::SolverUtils::EquationSystem::v_GetFluxVector ( const int  i,
Array< OneD, Array< OneD, NekDouble > > &  physfield,
Array< OneD, Array< OneD, NekDouble > > &  fluxX,
Array< OneD, Array< OneD, NekDouble > > &  fluxY 
)
privatevirtual

Definition at line 2578 of file EquationSystem.cpp.

References ASSERTL0.

2583  {
2584  ASSERTL0(false, "v_GetFluxVector: This function is not valid "
2585  "for the Base class");
2586  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
MultiRegions::ExpListSharedPtr Nektar::SolverUtils::EquationSystem::v_GetPressure ( void  )
protectedvirtual

Reimplemented in Nektar::IncNavierStokes.

Definition at line 2622 of file EquationSystem.cpp.

References ASSERTL0.

Referenced by GetPressure().

2623  {
2624  ASSERTL0(false, "This function is not valid for the Base class");
2626  return null;
2627  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
boost::shared_ptr< ExpList > ExpListSharedPtr
Shared pointer to an ExpList object.
Array< OneD, bool > Nektar::SolverUtils::EquationSystem::v_GetSystemSingularChecks ( )
privatevirtual

Reimplemented in Nektar::VelocityCorrectionScheme, Nektar::Laplace, Nektar::Helmholtz, and Nektar::Poisson.

Definition at line 2555 of file EquationSystem.cpp.

References m_session.

Referenced by v_InitObject().

2556  {
2557  return Array<OneD, bool>(m_session->GetVariables().size(), false);
2558  }
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
void Nektar::SolverUtils::EquationSystem::v_InitObject ( )
protectedvirtual

Initialisation object for EquationSystem.

Continuous field

Setting up the normals

Setting up the normals

Reimplemented in Nektar::CoupledLinearNS, Nektar::IncNavierStokes, Nektar::PulseWaveSystem, Nektar::UnsteadyViscousBurgers, Nektar::UnsteadyAdvectionDiffusion, Nektar::LinearElasticSystem, Nektar::CFLtester, Nektar::CompressibleFlowSystem, Nektar::UnsteadyAdvection, Nektar::SolverUtils::UnsteadySystem, Nektar::UnsteadyInviscidBurger, Nektar::APE, Nektar::ShallowWaterSystem, Nektar::NonlinearPeregrine, Nektar::IterativeElasticSystem, Nektar::PulseWavePropagation, Nektar::ImageWarpingSystem, Nektar::UnsteadyDiffusion, Nektar::Monodomain, Nektar::Bidomain, Nektar::BidomainRoth, Nektar::VCSMapping, Nektar::LinearSWE, Nektar::NonlinearSWE, Nektar::PulseWaveSystemOutput, Nektar::Laplace, Nektar::SteadyAdvectionDiffusion, Nektar::Projection, Nektar::NavierStokesCFE, Nektar::EigenValuesAdvection, Nektar::Helmholtz, Nektar::SteadyAdvectionDiffusionReaction, Nektar::VelocityCorrectionScheme, Nektar::Poisson, and Nektar::SolverUtils::AdvectionSystem.

Definition at line 120 of file EquationSystem.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, Nektar::LibUtilities::FieldIO::CreateDefault(), Nektar::MultiRegions::eDiscontinuous, Nektar::LibUtilities::eFourier, Nektar::LibUtilities::eFourierEvenlySpaced, Nektar::LibUtilities::eFourierHalfModeIm, Nektar::LibUtilities::eFourierHalfModeRe, Nektar::LibUtilities::eFourierSingleMode, Nektar::LibUtilities::eFourierSingleModeSpaced, Nektar::MultiRegions::eGalerkin, eHomogeneous1D, eHomogeneous2D, eHomogeneous3D, Nektar::MultiRegions::eMixed_CG_Discontinuous, eNotHomogeneous, GetTraceNpoints(), m_boundaryConditions, m_checkIfSystemSingular, m_checksteps, m_checktime, m_expdim, m_fields, m_fintime, m_fld, m_graph, m_halfMode, m_HomoDirec, m_homogen_dealiasing, m_HomogeneousType, m_LhomY, m_LhomZ, m_multipleModes, m_nchk, m_npointsY, m_npointsZ, m_NumQuadPointsError, m_projectionType, m_session, m_sessionName, m_singleMode, m_spacedim, m_specHP_dealiasing, m_steps, m_time, m_timestep, m_traceNormals, m_useFFT, Nektar::SpatialDomains::MeshGraph::Read(), v_GetSystemSingularChecks(), and ZeroPhysFields().

Referenced by InitObject(), Nektar::EigenValuesAdvection::v_InitObject(), Nektar::Projection::v_InitObject(), Nektar::SteadyAdvectionDiffusion::v_InitObject(), Nektar::Laplace::v_InitObject(), Nektar::SolverUtils::UnsteadySystem::v_InitObject(), and Nektar::LinearElasticSystem::v_InitObject().

121  {
122  // Save the basename of input file name for output details
123  m_sessionName = m_session->GetSessionName();
124 
125  // Instantiate a field reader/writer
127 
128  // Read the geometry and the expansion information
130 
131  // Also read and store the boundary conditions
135 
136  // Set space dimension for use in class
137  m_spacedim = m_graph->GetSpaceDimension();
138 
139  // Setting parameteres for homogenous problems
140  m_HomoDirec = 0;
141  m_useFFT = false;
142  m_homogen_dealiasing = false;
143  m_singleMode = false;
144  m_halfMode = false;
145  m_multipleModes = false;
147 
148  if (m_session->DefinesSolverInfo("HOMOGENEOUS"))
149  {
150  std::string HomoStr = m_session->GetSolverInfo("HOMOGENEOUS");
151  m_spacedim = 3;
152 
153  if ((HomoStr == "HOMOGENEOUS1D") || (HomoStr == "Homogeneous1D")
154  || (HomoStr == "1D") || (HomoStr == "Homo1D"))
155  {
157  m_session->LoadParameter("LZ", m_LhomZ);
158  m_HomoDirec = 1;
159 
160  if(m_session->DefinesSolverInfo("ModeType"))
161  {
162  m_session->MatchSolverInfo("ModeType", "SingleMode",
163  m_singleMode, false);
164  m_session->MatchSolverInfo("ModeType", "HalfMode",
165  m_halfMode, false);
166  m_session->MatchSolverInfo("ModeType", "MultipleModes",
167  m_multipleModes, false);
168  }
169 
170  // Stability Analysis flags
171  if (m_session->DefinesSolverInfo("ModeType"))
172  {
173  if(m_singleMode)
174  {
175  m_npointsZ = 2;
176  }
177  else if(m_halfMode)
178  {
179  m_npointsZ = 1;
180  }
181  else if(m_multipleModes)
182  {
183  m_npointsZ = m_session->GetParameter("HomModesZ");
184  }
185  else
186  {
187  ASSERTL0(false, "SolverInfo ModeType not valid");
188  }
189  }
190  else
191  {
192  m_npointsZ = m_session->GetParameter("HomModesZ");
193  }
194  }
195 
196  if ((HomoStr == "HOMOGENEOUS2D") || (HomoStr == "Homogeneous2D")
197  || (HomoStr == "2D") || (HomoStr == "Homo2D"))
198  {
200  m_session->LoadParameter("HomModesY", m_npointsY);
201  m_session->LoadParameter("LY", m_LhomY);
202  m_session->LoadParameter("HomModesZ", m_npointsZ);
203  m_session->LoadParameter("LZ", m_LhomZ);
204  m_HomoDirec = 2;
205  }
206 
207  if ((HomoStr == "HOMOGENEOUS3D") || (HomoStr == "Homogeneous3D")
208  || (HomoStr == "3D") || (HomoStr == "Homo3D"))
209  {
211  m_session->LoadParameter("HomModesY", m_npointsY);
212  m_session->LoadParameter("LY", m_LhomY);
213  m_session->LoadParameter("HomModesZ", m_npointsZ);
214  m_session->LoadParameter("LZ", m_LhomZ);
215  m_HomoDirec = 2;
216  }
217 
218  m_session->MatchSolverInfo("USEFFT", "FFTW", m_useFFT, false);
219 
220  m_session->MatchSolverInfo("DEALIASING", "True",
221  m_homogen_dealiasing, false);
222  if(m_homogen_dealiasing == false)
223  {
224  m_session->MatchSolverInfo("DEALIASING", "On",
225  m_homogen_dealiasing, false);
226  }
227  }
228  else
229  {
230  // set to default value so can use to identify 2d or 3D
231  // (homogeneous) expansions
232  m_npointsZ = 1;
233  }
234 
235  m_session->MatchSolverInfo("SPECTRALHPDEALIASING", "True",
236  m_specHP_dealiasing, false);
237  if (m_specHP_dealiasing == false)
238  {
239  m_session->MatchSolverInfo("SPECTRALHPDEALIASING", "On",
240  m_specHP_dealiasing, false);
241  }
242 
243  // Options to determine type of projection from file or directly
244  // from constructor
245  if (m_session->DefinesSolverInfo("PROJECTION"))
246  {
247  std::string ProjectStr = m_session->GetSolverInfo("PROJECTION");
248 
249  if ((ProjectStr == "Continuous") || (ProjectStr == "Galerkin") ||
250  (ProjectStr == "CONTINUOUS") || (ProjectStr == "GALERKIN"))
251  {
253  }
254  else if ((ProjectStr == "MixedCGDG") ||
255  (ProjectStr == "Mixed_CG_Discontinuous"))
256  {
258  }
259  else if(ProjectStr == "DisContinuous")
260  {
262  }
263  else
264  {
265  ASSERTL0(false,"PROJECTION value not recognised");
266  }
267  }
268  else
269  {
270  cerr << "Projection type not specified in SOLVERINFO,"
271  "defaulting to continuous Galerkin" << endl;
273  }
274 
275  // Enforce singularity check for some problems
277 
278  int i;
279  int nvariables = m_session->GetVariables().size();
280  bool DeclareCoeffPhysArrays = true;
281 
282 
283  m_fields = Array<OneD, MultiRegions::ExpListSharedPtr>(nvariables);
284  m_spacedim = m_graph->GetSpaceDimension()+m_HomoDirec;
285  m_expdim = m_graph->GetMeshDimension();
286 
287  /// Continuous field
290  {
291  switch(m_expdim)
292  {
293  case 1:
294  {
297  {
298  const LibUtilities::PointsKey PkeyY
300  const LibUtilities::BasisKey BkeyY
302  const LibUtilities::PointsKey PkeyZ
304  const LibUtilities::BasisKey
305  BkeyZ(LibUtilities::eFourier, m_npointsZ, PkeyZ);
306 
307  for (i = 0; i < m_fields.num_elements(); i++)
308  {
309  m_fields[i] = MemoryManager<MultiRegions
310  ::ContField3DHomogeneous2D>
311  ::AllocateSharedPtr(
312  m_session, BkeyY, BkeyZ, m_LhomY,
313  m_LhomZ, m_useFFT,
315  m_session->GetVariable(i));
316  }
317  }
318  else
319  {
320  for (i = 0; i < m_fields.num_elements(); i++)
321  {
322  m_fields[i] = MemoryManager
323  <MultiRegions::ContField1D>::
324  AllocateSharedPtr(
326  m_session->GetVariable(i));
327  }
328  }
329  break;
330  }
331  case 2:
332  {
334  {
335  // Fourier single mode stability analysis
336  if (m_singleMode)
337  {
338  const LibUtilities::PointsKey PkeyZ(
339  m_npointsZ,
341 
342  const LibUtilities::BasisKey BkeyZ(
344  m_npointsZ,
345  PkeyZ);
346 
347  for(i = 0; i < m_fields.num_elements(); i++)
348  {
349  m_fields[i] = MemoryManager<MultiRegions
350  ::ContField3DHomogeneous1D>
351  ::AllocateSharedPtr(
352  m_session, BkeyZ, m_LhomZ,
354  m_graph,
355  m_session->GetVariable(i),
357  }
358  }
359  // Half mode stability analysis
360  else if(m_halfMode)
361  {
362  const LibUtilities::PointsKey PkeyZ(
363  m_npointsZ,
365 
366  const LibUtilities::BasisKey BkeyZR(
368  m_npointsZ, PkeyZ);
369 
370  const LibUtilities::BasisKey BkeyZI(
372  m_npointsZ, PkeyZ);
373 
374 
375  for (i = 0; i < m_fields.num_elements(); i++)
376  {
377  if(m_session->GetVariable(i).compare("w")
378  == 0)
379  {
380  m_fields[i] = MemoryManager<MultiRegions
381  ::ContField3DHomogeneous1D>
382  ::AllocateSharedPtr(
383  m_session, BkeyZI, m_LhomZ,
384  m_useFFT,
386  m_graph,
387  m_session->GetVariable(i),
389  }
390  else
391  {
392  m_fields[i] = MemoryManager<MultiRegions
393  ::ContField3DHomogeneous1D>
394  ::AllocateSharedPtr(
395  m_session, BkeyZR, m_LhomZ,
397  m_graph,
398  m_session->GetVariable(i),
400  }
401 
402 
403  }
404  }
405  // Normal homogeneous 1D
406  else
407  {
408  const LibUtilities::PointsKey PkeyZ(
409  m_npointsZ,
411  const LibUtilities::BasisKey BkeyZ(
413 
414  for (i = 0; i < m_fields.num_elements(); i++)
415  {
416  m_fields[i] = MemoryManager<MultiRegions
417  ::ContField3DHomogeneous1D>
418  ::AllocateSharedPtr(
419  m_session, BkeyZ, m_LhomZ,
421  m_graph,
422  m_session->GetVariable(i),
424  }
425  }
426  }
427  else
428  {
429  i = 0;
431  firstfield = MemoryManager<MultiRegions::
432  ContField2D>::AllocateSharedPtr(
434  m_session->GetVariable(i),
435  DeclareCoeffPhysArrays,
437  m_fields[0] = firstfield;
438  for (i = 1; i < m_fields.num_elements(); i++)
439  {
440  if (m_graph->
441  SameExpansions(m_session->GetVariable(0),
442  m_session->GetVariable(i)))
443  {
444  m_fields[i] = MemoryManager<MultiRegions::
445  ContField2D>::AllocateSharedPtr(
446  *firstfield, m_graph,
447  m_session->GetVariable(i),
448  DeclareCoeffPhysArrays,
450  }
451  else
452  {
453  m_fields[i] = MemoryManager<MultiRegions
454  ::ContField2D>::AllocateSharedPtr(
455  m_session, m_graph,
456  m_session->GetVariable(i),
457  DeclareCoeffPhysArrays,
459  }
460  }
461 
462  if (m_projectionType ==
464  {
465  /// Setting up the normals
467  Array<OneD, Array<OneD, NekDouble> >
468  (m_spacedim);
469 
470  for (i = 0; i < m_spacedim; ++i)
471  {
472  m_traceNormals[i] = Array<OneD, NekDouble>
473  (GetTraceNpoints());
474  }
475 
476  m_fields[0]->GetTrace()->
477  GetNormals(m_traceNormals);
478  }
479 
480  }
481 
482  break;
483  }
484  case 3:
485  {
486  i = 0;
490  m_session->GetVariable(i),
492 
493  m_fields[0] = firstfield;
494  for (i = 1; i < m_fields.num_elements(); i++)
495  {
496  if(m_graph->SameExpansions(
497  m_session->GetVariable(0),
498  m_session->GetVariable(i)))
499  {
500  m_fields[i] = MemoryManager<MultiRegions
501  ::ContField3D>::AllocateSharedPtr(
502  *firstfield, m_graph,
503  m_session->GetVariable(i),
505  }
506  else
507  {
508  m_fields[i] = MemoryManager<MultiRegions
509  ::ContField3D>::AllocateSharedPtr(
510  m_session, m_graph,
511  m_session->GetVariable(i),
513  }
514  }
515 
516  if (m_projectionType ==
518  {
519  /// Setting up the normals
521  Array<OneD, Array<OneD, NekDouble> >
522  (m_spacedim);
523  for(i = 0; i < m_spacedim; ++i)
524  {
525  m_traceNormals[i] =
526  Array<OneD, NekDouble> (GetTraceNpoints());
527  }
528 
529  m_fields[0]->GetTrace()->GetNormals(m_traceNormals);
530  // Call the trace on all fields to ensure DG setup.
531  for(i = 1; i < m_fields.num_elements(); ++i)
532  {
533  m_fields[i]->GetTrace();
534  }
535  }
536  break;
537  }
538  default:
539  ASSERTL0(false,"Expansion dimension not recognised");
540  break;
541  }
542  }
543  // Discontinuous field
544  else
545  {
546  switch(m_expdim)
547  {
548  case 1:
549  {
552  {
553  const LibUtilities::PointsKey PkeyY(
555  const LibUtilities::BasisKey BkeyY(
557  const LibUtilities::PointsKey PkeyZ(
559  const LibUtilities::BasisKey BkeyZ(
561 
562  for (i = 0; i < m_fields.num_elements(); i++)
563  {
564  m_fields[i] = MemoryManager<MultiRegions
565  ::DisContField3DHomogeneous2D>
566  ::AllocateSharedPtr(
567  m_session, BkeyY, BkeyZ, m_LhomY,
568  m_LhomZ, m_useFFT,
570  m_session->GetVariable(i));
571  }
572  }
573  else
574  {
575  for (i = 0; i < m_fields.num_elements(); i++)
576  {
577  m_fields[i] = MemoryManager<MultiRegions::
578  DisContField1D>::AllocateSharedPtr(
580  m_session->GetVariable(i));
581  }
582  }
583 
584  break;
585  }
586  case 2:
587  {
589  {
590  const LibUtilities::PointsKey PkeyZ(
592  const LibUtilities::BasisKey BkeyZ(
594 
595  for (i = 0; i < m_fields.num_elements(); i++)
596  {
597  m_fields[i] = MemoryManager<MultiRegions
598  ::DisContField3DHomogeneous1D>
599  ::AllocateSharedPtr(
600  m_session, BkeyZ, m_LhomZ, m_useFFT,
602  m_session->GetVariable(i));
603  }
604  }
605  else
606  {
607  for (i = 0; i < m_fields.num_elements(); i++)
608  {
609  m_fields[i] = MemoryManager<MultiRegions::
610  DisContField2D>::AllocateSharedPtr(
612  m_session->GetVariable(i));
613  }
614  }
615 
616  break;
617  }
618  case 3:
619  {
621  {
622  ASSERTL0(false,
623  "3D fully periodic problems not implemented yet");
624  }
625  else
626  {
627  for (i = 0; i < m_fields.num_elements(); i++)
628  {
629  m_fields[i] = MemoryManager<MultiRegions::
630  DisContField3D>::AllocateSharedPtr(
632  m_session->GetVariable(i));
633  }
634  }
635  break;
636  }
637  default:
638  ASSERTL0(false, "Expansion dimension not recognised");
639  break;
640  }
641 
642  // Setting up the normals
644  Array<OneD, Array<OneD, NekDouble> >(m_spacedim);
645 
646  for (i = 0; i < m_spacedim; ++i)
647  {
648  m_traceNormals[i] =
649  Array<OneD, NekDouble> (GetTraceNpoints(), 0.0);
650  }
651 
652  m_fields[0]->GetTrace()->GetNormals(m_traceNormals);
653  }
654 
655  // Set Default Parameter
656  m_session->LoadParameter("Time", m_time, 0.0);
657  m_session->LoadParameter("TimeStep", m_timestep, 0.01);
658  m_session->LoadParameter("NumSteps", m_steps, 0);
659  m_session->LoadParameter("IO_CheckSteps", m_checksteps, 0);
660  m_session->LoadParameter("IO_CheckTime", m_checktime, 0.0);
661  m_session->LoadParameter("FinTime", m_fintime, 0);
662  m_session->LoadParameter("NumQuadPointsError",
664 
665  m_nchk = 0;
666 
667  // Zero all physical fields initially
668  ZeroPhysFields();
669  }
bool m_singleMode
Flag to determine if single homogeneous mode is used.
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
static boost::shared_ptr< MeshGraph > Read(const LibUtilities::SessionReaderSharedPtr &pSession, DomainRangeShPtr &rng=NullDomainRangeShPtr)
Definition: MeshGraph.cpp:124
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
NekDouble m_time
Current time of simulation.
NekDouble m_timestep
Time step size.
bool m_halfMode
Flag to determine if half homogeneous mode is used.
NekDouble m_LhomZ
physical length in Z direction (if homogeneous)
Array< OneD, bool > m_checkIfSystemSingular
Flag to indicate if the fields should be checked for singularity.
int m_expdim
Expansion dimension.
enum MultiRegions::ProjectionType m_projectionType
Type of projection; e.g continuous or discontinuous.
NekDouble m_checktime
Time between checkpoints.
bool m_useFFT
Flag to determine if FFT is used for homogeneous transform.
NekDouble m_LhomY
physical length in Y direction (if homogeneous)
boost::shared_ptr< ContField2D > ContField2DSharedPtr
Definition: ContField2D.h:287
bool m_specHP_dealiasing
Flag to determine if dealisising is usde for the Spectral/hp element discretisation.
Fourier Expansion .
Definition: BasisType.h:52
int m_npointsZ
number of points in Z direction (if homogeneous)
std::string m_sessionName
Name of the session.
int m_nchk
Number of checkpoints written so far.
int m_checksteps
Number of steps between checkpoints.
NekDouble m_fintime
Finish time of the simulation.
int m_steps
Number of steps to take.
Array< OneD, Array< OneD, NekDouble > > m_traceNormals
Array holding trace normals for DG simulations in the forwards direction.
int m_HomoDirec
number of homogenous directions
1D Evenly-spaced points using Fourier Fit
Definition: PointsType.h:66
bool m_multipleModes
Flag to determine if use multiple homogenenous modes are used.
Fourier Modified expansions with just the real part of the first mode .
Definition: BasisType.h:59
virtual SOLVER_UTILS_EXPORT Array< OneD, bool > v_GetSystemSingularChecks()
int m_npointsY
number of points in Y direction (if homogeneous)
SpatialDomains::BoundaryConditionsSharedPtr m_boundaryConditions
Pointer to boundary conditions object.
int m_spacedim
Spatial dimension (>= expansion dim).
bool m_homogen_dealiasing
Flag to determine if dealiasing is used for homogeneous simulations.
Fourier Modified expansions with just the imaginary part of the first mode .
Definition: BasisType.h:60
static boost::shared_ptr< FieldIO > CreateDefault(const LibUtilities::SessionReaderSharedPtr session)
Returns an object for the default FieldIO method.
Definition: FieldIO.cpp:181
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Fourier ModifiedExpansion with just the first mode .
Definition: BasisType.h:58
SOLVER_UTILS_EXPORT int GetTraceNpoints()
1D Non Evenly-spaced points for Single Mode analysis
Definition: PointsType.h:67
LibUtilities::FieldIOSharedPtr m_fld
Field input/output.
SOLVER_UTILS_EXPORT void ZeroPhysFields()
SpatialDomains::MeshGraphSharedPtr m_graph
Pointer to graph defining mesh.
boost::shared_ptr< ContField3D > ContField3DSharedPtr
Definition: ContField3D.h:206
int m_NumQuadPointsError
Number of Quadrature points used to work out the error.
enum HomogeneousType m_HomogeneousType
NekDouble Nektar::SolverUtils::EquationSystem::v_L2Error ( unsigned int  field,
const Array< OneD, NekDouble > &  exactsoln = NullNekDouble1DArray,
bool  Normalised = false 
)
protectedvirtual

Virtual function for the L_2 error computation between fields and a given exact solution.

Compute the error in the L2-norm.

Parameters
fieldThe field to compare.
exactsolnThe exact solution to compare with.
NormalisedNormalise L2-error.
Returns
Error in the L2-norm.

Reimplemented in Nektar::PulseWaveSystem.

Definition at line 1170 of file EquationSystem.cpp.

References ErrorExtraPoints(), EvaluateFunction(), GetNpoints(), m_comm, m_fields, m_NumQuadPointsError, m_session, m_time, and Nektar::LibUtilities::ReduceSum.

Referenced by L2Error().

1174  {
1175  NekDouble L2error = -1.0;
1176 
1177  if (m_NumQuadPointsError == 0)
1178  {
1179  if (m_fields[field]->GetPhysState() == false)
1180  {
1181  m_fields[field]->BwdTrans(m_fields[field]->GetCoeffs(),
1182  m_fields[field]->UpdatePhys());
1183  }
1184 
1185  if (exactsoln.num_elements())
1186  {
1187  L2error = m_fields[field]->L2(m_fields[field]->GetPhys(), exactsoln);
1188  }
1189  else if (m_session->DefinesFunction("ExactSolution"))
1190  {
1191  Array<OneD, NekDouble>
1192  exactsoln(m_fields[field]->GetNpoints());
1193 
1194  EvaluateFunction(m_session->GetVariable(field), exactsoln,
1195  "ExactSolution", m_time);
1196 
1197  L2error = m_fields[field]->L2(m_fields[field]->GetPhys(), exactsoln);
1198  }
1199  else
1200  {
1201  L2error = m_fields[field]->L2(m_fields[field]->GetPhys());
1202  }
1203 
1204  if (Normalised == true)
1205  {
1206  Array<OneD, NekDouble> one(m_fields[field]->GetNpoints(),
1207  1.0);
1208 
1209  NekDouble Vol = m_fields[field]->PhysIntegral(one);
1210  m_comm->AllReduce(Vol, LibUtilities::ReduceSum);
1211 
1212  L2error = sqrt(L2error*L2error/Vol);
1213  }
1214  }
1215  else
1216  {
1217  Array<OneD,NekDouble> L2INF(2);
1218  L2INF = ErrorExtraPoints(field);
1219  L2error = L2INF[0];
1220  }
1221  return L2error;
1222  }
NekDouble m_time
Current time of simulation.
SOLVER_UTILS_EXPORT Array< OneD, NekDouble > ErrorExtraPoints(unsigned int field)
Compute error (L2 and L_inf) over an larger set of quadrature points return [L2 Linf].
LibUtilities::CommSharedPtr m_comm
Communicator.
double NekDouble
SOLVER_UTILS_EXPORT void EvaluateFunction(Array< OneD, Array< OneD, NekDouble > > &pArray, std::string pFunctionName, const NekDouble pTime=0.0, const int domain=0)
Evaluates a function as specified in the session file.
SOLVER_UTILS_EXPORT int GetNpoints()
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
int m_NumQuadPointsError
Number of Quadrature points used to work out the error.
NekDouble Nektar::SolverUtils::EquationSystem::v_LinfError ( unsigned int  field,
const Array< OneD, NekDouble > &  exactsoln = NullNekDouble1DArray 
)
protectedvirtual

Virtual function for the L_inf error computation between fields and a given exact solution.

Compute the error in the L_inf-norm

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

Reimplemented in Nektar::PulseWaveSystem.

Definition at line 1230 of file EquationSystem.cpp.

References ErrorExtraPoints(), EvaluateFunction(), GetNpoints(), m_fields, m_NumQuadPointsError, m_session, and m_time.

Referenced by LinfError().

1233  {
1234  NekDouble Linferror = -1.0;
1235 
1236  if (m_NumQuadPointsError == 0)
1237  {
1238  if (m_fields[field]->GetPhysState() == false)
1239  {
1240  m_fields[field]->BwdTrans(m_fields[field]->GetCoeffs(),
1241  m_fields[field]->UpdatePhys());
1242  }
1243 
1244  if (exactsoln.num_elements())
1245  {
1246  Linferror = m_fields[field]->Linf(m_fields[field]->GetPhys(), exactsoln);
1247  }
1248  else if (m_session->DefinesFunction("ExactSolution"))
1249  {
1250  Array<OneD, NekDouble>
1251  exactsoln(m_fields[field]->GetNpoints());
1252 
1253  EvaluateFunction(m_session->GetVariable(field), exactsoln,
1254  "ExactSolution", m_time);
1255 
1256  Linferror = m_fields[field]->Linf(m_fields[field]->GetPhys(), exactsoln);
1257  }
1258  else
1259  {
1260  Linferror = m_fields[field]->Linf(m_fields[field]->GetPhys());
1261  }
1262  }
1263  else
1264  {
1265  Array<OneD,NekDouble> L2INF(2);
1266  L2INF = ErrorExtraPoints(field);
1267  Linferror = L2INF[1];
1268  }
1269 
1270  return Linferror;
1271  }
NekDouble m_time
Current time of simulation.
SOLVER_UTILS_EXPORT Array< OneD, NekDouble > ErrorExtraPoints(unsigned int field)
Compute error (L2 and L_inf) over an larger set of quadrature points return [L2 Linf].
double NekDouble
SOLVER_UTILS_EXPORT void EvaluateFunction(Array< OneD, Array< OneD, NekDouble > > &pArray, std::string pFunctionName, const NekDouble pTime=0.0, const int domain=0)
Evaluates a function as specified in the session file.
SOLVER_UTILS_EXPORT int GetNpoints()
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
int m_NumQuadPointsError
Number of Quadrature points used to work out the error.
bool Nektar::SolverUtils::EquationSystem::v_NegatedOp ( void  )
virtual

Virtual function to identify if operator is negated in DoSolve.

Virtual function to define if operator in DoSolve is negated with regard to the strong form. This is currently only used in Arnoldi solves. Default is false.

Reimplemented in Nektar::CoupledLinearNS.

Definition at line 1655 of file EquationSystem.cpp.

1656  {
1657  return false;
1658  }
void Nektar::SolverUtils::EquationSystem::v_NumericalFlux ( Array< OneD, Array< OneD, NekDouble > > &  physfield,
Array< OneD, Array< OneD, NekDouble > > &  numflux 
)
privatevirtual

Reimplemented in Nektar::IncNavierStokes, Nektar::CFLtester, Nektar::SolverUtils::UnsteadySystem, Nektar::PulseWavePropagation, Nektar::ImageWarpingSystem, and Nektar::EigenValuesAdvection.

Definition at line 2588 of file EquationSystem.cpp.

References ASSERTL0.

Referenced by NumericalFlux().

2591  {
2592  ASSERTL0(false, "v_NumericalFlux: This function is not valid "
2593  "for the Base class");
2594  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
void Nektar::SolverUtils::EquationSystem::v_NumericalFlux ( Array< OneD, Array< OneD, NekDouble > > &  physfield,
Array< OneD, Array< OneD, NekDouble > > &  numfluxX,
Array< OneD, Array< OneD, NekDouble > > &  numfluxY 
)
privatevirtual

Reimplemented in Nektar::SolverUtils::UnsteadySystem.

Definition at line 2596 of file EquationSystem.cpp.

References ASSERTL0.

2600  {
2601  ASSERTL0(false, "v_NumericalFlux: This function is not valid "
2602  "for the Base class");
2603  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
void Nektar::SolverUtils::EquationSystem::v_NumFluxforScalar ( const Array< OneD, Array< OneD, NekDouble > > &  ufield,
Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &  uflux 
)
privatevirtual

Reimplemented in Nektar::SolverUtils::UnsteadySystem.

Definition at line 2605 of file EquationSystem.cpp.

References ASSERTL0.

Referenced by NumFluxforScalar().

2608  {
2609  ASSERTL0(false, "v_NumFluxforScalar: This function is not valid "
2610  "for the Base class");
2611  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
void Nektar::SolverUtils::EquationSystem::v_NumFluxforVector ( const Array< OneD, Array< OneD, NekDouble > > &  ufield,
Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &  qfield,
Array< OneD, Array< OneD, NekDouble > > &  qflux 
)
privatevirtual

Reimplemented in Nektar::SolverUtils::UnsteadySystem.

Definition at line 2613 of file EquationSystem.cpp.

References ASSERTL0.

Referenced by NumFluxforVector().

2617  {
2618  ASSERTL0(false, "v_NumFluxforVector: This function is not valid "
2619  "for the Base class");
2620  }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
void Nektar::SolverUtils::EquationSystem::v_Output ( void  )
protectedvirtual

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

Reimplemented in Nektar::CoupledLinearNS, and Nektar::PulseWaveSystem.

Definition at line 1688 of file EquationSystem.cpp.

References m_sessionName, and WriteFld().

Referenced by Output().

1689  {
1690  WriteFld(m_sessionName + ".fld");
1691  }
std::string m_sessionName
Name of the session.
SOLVER_UTILS_EXPORT void WriteFld(const std::string &outname)
Write field data to the given filename.
void Nektar::SolverUtils::EquationSystem::v_SetInitialConditions ( NekDouble  initialtime = 0.0,
bool  dumpInitialConditions = true,
const int  domain = 0 
)
protectedvirtual

Set the physical fields based on a restart file, or a function describing the initial condition given in the session.

Parameters
initialtimeTime at which to evaluate the function.
dumpInitialConditionsWrite the initial condition to file?

Reimplemented in Nektar::CompressibleFlowSystem, Nektar::NonlinearPeregrine, Nektar::Monodomain, Nektar::Bidomain, Nektar::BidomainRoth, and Nektar::IsentropicVortex.

Definition at line 1351 of file EquationSystem.cpp.

References Checkpoint_Output(), DescribeFunction(), EvaluateFunction(), GetNcoeffs(), m_checksteps, m_fields, m_nchk, m_session, m_time, and Vmath::Zero().

Referenced by SetInitialConditions(), Nektar::Bidomain::v_SetInitialConditions(), Nektar::BidomainRoth::v_SetInitialConditions(), Nektar::Monodomain::v_SetInitialConditions(), Nektar::NonlinearPeregrine::v_SetInitialConditions(), and Nektar::CompressibleFlowSystem::v_SetInitialConditions().

1354  {
1355  if (m_session->GetComm()->GetRank() == 0)
1356  {
1357  cout << "Initial Conditions:" << endl;
1358  }
1359 
1360  if (m_session->DefinesFunction("InitialConditions"))
1361  {
1362  EvaluateFunction(m_session->GetVariables(), m_fields,
1363  "InitialConditions", m_time, domain);
1364 
1365  if (m_session->GetComm()->GetRank() == 0)
1366  {
1367 
1368  for (int i = 0; i < m_fields.num_elements(); ++i)
1369  {
1370  std::string varName = m_session->GetVariable(i);
1371  cout << " - Field " << varName << ": "
1372  << DescribeFunction(varName, "InitialConditions",domain)
1373  << endl;
1374  }
1375  }
1376  }
1377  else
1378  {
1379  int nq = m_fields[0]->GetNpoints();
1380  for (int i = 0; i < m_fields.num_elements(); i++)
1381  {
1382  Vmath::Zero(nq, m_fields[i]->UpdatePhys(), 1);
1383  m_fields[i]->SetPhysState(true);
1385  m_fields[i]->UpdateCoeffs(), 1);
1386  if (m_session->GetComm()->GetRank() == 0)
1387  {
1388  cout << " - Field " << m_session->GetVariable(i)
1389  << ": 0 (default)" << endl;
1390  }
1391  }
1392 
1393  }
1394 
1395  if (dumpInitialConditions && m_checksteps)
1396  {
1398  m_nchk++;
1399  }
1400  }
SOLVER_UTILS_EXPORT std::string DescribeFunction(std::string pFieldName, const std::string &pFunctionName, const int domain)
Provide a description of a function for a given field name.
NekDouble m_time
Current time of simulation.
SOLVER_UTILS_EXPORT void Checkpoint_Output(const int n)
Write checkpoint file of m_fields.
int m_nchk
Number of checkpoints written so far.
int m_checksteps
Number of steps between checkpoints.
SOLVER_UTILS_EXPORT void EvaluateFunction(Array< OneD, Array< OneD, NekDouble > > &pArray, std::string pFunctionName, const NekDouble pTime=0.0, const int domain=0)
Evaluates a function as specified in the session file.
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
SOLVER_UTILS_EXPORT int GetNcoeffs()
void Zero(int n, T *x, const int incx)
Zero vector.
Definition: Vmath.cpp:373
void Nektar::SolverUtils::EquationSystem::v_TransCoeffToPhys ( void  )
protectedvirtual

Virtual function for transformation to physical space.

Reimplemented in Nektar::IncNavierStokes, Nektar::CoupledLinearNS, and Nektar::VelocityCorrectionScheme.

Definition at line 1663 of file EquationSystem.cpp.

Referenced by TransCoeffToPhys().

1664  {
1665 
1666  }
void Nektar::SolverUtils::EquationSystem::v_TransPhysToCoeff ( void  )
protectedvirtual

Virtual function for transformation to coefficient space.

Reimplemented in Nektar::IncNavierStokes, Nektar::CoupledLinearNS, and Nektar::VelocityCorrectionScheme.

Definition at line 1671 of file EquationSystem.cpp.

Referenced by TransPhysToCoeff().

1672  {
1673 
1674  }
void Nektar::SolverUtils::EquationSystem::WeakAdvectionDivergenceForm ( const Array< OneD, Array< OneD, NekDouble > > &  F,
Array< OneD, NekDouble > &  outarray 
)

Compute the inner product $ (\phi, \nabla \cdot F) $.

Calculate Inner product of the divergence advection form $(\phi, \nabla \cdot F)$, where for example $ F = uV $.

Parameters
FFields.
outarrayStorage for result.

Definition at line 1741 of file EquationSystem.cpp.

References Nektar::MultiRegions::DirCartesianMap, m_fields, and Vmath::Vadd().

1744  {
1745  // Use dimension of Velocity vector to dictate dimension of operation
1746  int ndim = F.num_elements();
1747  int nPointsTot = m_fields[0]->GetNpoints();
1748  Array<OneD, NekDouble> tmp(nPointsTot);
1749  Array<OneD, NekDouble> div(nPointsTot, 0.0);
1750 
1751  // Evaluate the divergence
1752  for (int i = 0; i < ndim; ++i)
1753  {
1754  //m_fields[0]->PhysDeriv(i,F[i],tmp);
1755  m_fields[0]->PhysDeriv(MultiRegions::DirCartesianMap[i],F[i],tmp);
1756  Vmath::Vadd(nPointsTot, tmp, 1, div, 1, div, 1);
1757  }
1758 
1759  m_fields[0]->IProductWRTBase(div, outarray);
1760  }
MultiRegions::Direction const DirCartesianMap[]
Definition: ExpList.h:86
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
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::SolverUtils::EquationSystem::WeakAdvectionGreensDivergenceForm ( const Array< OneD, Array< OneD, NekDouble > > &  F,
Array< OneD, NekDouble > &  outarray 
)

Compute the inner product $ (\nabla \phi \cdot F) $.

Computes the weak Green form of advection terms (without boundary integral), i.e. $ (\nabla \phi \cdot F) $ where for example $ F=uV $.

Parameters
FFields.
outarrayStorage for result.
Note
Assuming all fields are of the same expansion and order so that we can use the parameters of m_fields[0].

Definition at line 1728 of file EquationSystem.cpp.

References m_fields.

Referenced by WeakDGAdvection(), and WeakDGDiffusion().

1731  {
1732  m_fields[0]->IProductWRTDerivBase(F,outarray);
1733  }
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
void Nektar::SolverUtils::EquationSystem::WeakAdvectionNonConservativeForm ( const Array< OneD, Array< OneD, NekDouble > > &  V,
const Array< OneD, const NekDouble > &  u,
Array< OneD, NekDouble > &  outarray,
bool  UseContCoeffs = false 
)

Compute the inner product $ (\phi, V\cdot \nabla u) $.

Calculate Inner product of the divergence advection form $ (\phi, V\cdot \nabla u) $

Parameters
VFields.
uFields.
outarrayStorage for result.

Definition at line 1769 of file EquationSystem.cpp.

References AdvectionNonConservativeForm(), Nektar::MultiRegions::eGlobal, and m_fields.

1774  {
1775  // use dimension of Velocity vector to dictate dimension of operation
1776  int ndim = V.num_elements();
1777 
1778  int nPointsTot = m_fields[0]->GetNpoints();
1779  Array<OneD, NekDouble> tmp(nPointsTot);
1780  Array<OneD, NekDouble> wk(ndim * nPointsTot, 0.0);
1781 
1782  AdvectionNonConservativeForm(V, u, tmp, wk);
1783 
1784  if (UseContCoeffs)
1785  {
1786  m_fields[0]->IProductWRTBase(tmp, outarray,
1788  }
1789  else
1790  {
1791  m_fields[0]->IProductWRTBase_IterPerExp(tmp, outarray);
1792  }
1793  }
f SOLVER_UTILS_EXPORT void AdvectionNonConservativeForm(const Array< OneD, Array< OneD, NekDouble > > &V, const Array< OneD, const NekDouble > &u, Array< OneD, NekDouble > &outarray, Array< OneD, NekDouble > &wk=NullNekDouble1DArray)
Compute the non-conservative advection.
Global coefficients.
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
void Nektar::SolverUtils::EquationSystem::WeakDGAdvection ( const Array< OneD, Array< OneD, NekDouble > > &  InField,
Array< OneD, Array< OneD, NekDouble > > &  OutField,
bool  NumericalFluxIncludesNormal = true,
bool  InFieldIsInPhysSpace = false,
int  nvariables = 0 
)

Calculate the weak discontinuous Galerkin advection.

Calculate weak DG advection in the form $ \langle\phi, \hat{F}\cdot n\rangle - (\nabla \phi \cdot F) $.

Parameters
InFieldFields.
OutFieldStorage for result.
NumericalFluxIncludesNormalDefault: true.
InFieldIsPhysSpaceDefault: false.
nvariablesNumber of fields.

Definition at line 1866 of file EquationSystem.cpp.

References GetFluxVector(), GetNcoeffs(), GetNpoints(), GetTraceNpoints(), m_expdim, m_fields, Vmath::Neg(), NumericalFlux(), and WeakAdvectionGreensDivergenceForm().

Referenced by Nektar::ImageWarpingSystem::DoOdeRhs(), Nektar::PulseWavePropagation::DoOdeRhs(), Nektar::CFLtester::DoOdeRhs(), and Nektar::EigenValuesAdvection::v_DoSolve().

1872  {
1873  int i;
1874  int nVelDim = m_expdim;
1875  int nPointsTot = GetNpoints();
1876  int ncoeffs = GetNcoeffs();
1877  int nTracePointsTot = GetTraceNpoints();
1878 
1879  if (!nvariables)
1880  {
1881  nvariables = m_fields.num_elements();
1882  }
1883 
1884  Array<OneD, Array<OneD, NekDouble> > fluxvector(nVelDim);
1885  Array<OneD, Array<OneD, NekDouble> > physfield (nvariables);
1886 
1887  for(i = 0; i < nVelDim; ++i)
1888  {
1889  fluxvector[i] = Array<OneD, NekDouble>(nPointsTot);
1890  }
1891 
1892  // Get the variables in physical space
1893  // already in physical space
1894  if (InFieldIsInPhysSpace == true)
1895  {
1896  for (i = 0; i < nvariables; ++i)
1897  {
1898  physfield[i] = InField[i];
1899  }
1900  }
1901  // otherwise do a backward transformation
1902  else
1903  {
1904  for(i = 0; i < nvariables; ++i)
1905  {
1906  // Could make this point to m_fields[i]->UpdatePhys();
1907  physfield[i] = Array<OneD, NekDouble>(nPointsTot);
1908  m_fields[i]->BwdTrans(InField[i],physfield[i]);
1909  }
1910  }
1911 
1912  // Get the advection part (without numerical flux)
1913  for (i = 0; i < nvariables; ++i)
1914  {
1915  // Get the ith component of the flux vector in (physical space)
1916  GetFluxVector(i, physfield, fluxvector);
1917 
1918  // Calculate the i^th value of (\grad_i \phi, F)
1919  WeakAdvectionGreensDivergenceForm(fluxvector,OutField[i]);
1920  }
1921 
1922  // Get the numerical flux and add to the modal coeffs
1923  // if the NumericalFluxs function already includes the
1924  // normal in the output
1925  if (NumericalFluxIncludesNormal == true)
1926  {
1927  Array<OneD, Array<OneD, NekDouble> > numflux (nvariables);
1928 
1929  for (i = 0; i < nvariables; ++i)
1930  {
1931  numflux[i] = Array<OneD, NekDouble>(nTracePointsTot);
1932  }
1933 
1934  // Evaluate numerical flux in physical space which may in
1935  // general couple all component of vectors
1936  NumericalFlux(physfield, numflux);
1937 
1938  // Evaulate <\phi, \hat{F}\cdot n> - OutField[i]
1939  for (i = 0; i < nvariables; ++i)
1940  {
1941  Vmath::Neg(ncoeffs,OutField[i],1);
1942  m_fields[i]->AddTraceIntegral(numflux[i],OutField[i]);
1943  m_fields[i]->SetPhysState(false);
1944  }
1945  }
1946  // if the NumericalFlux function does not include the
1947  // normal in the output
1948  else
1949  {
1950  Array<OneD, Array<OneD, NekDouble> > numfluxX (nvariables);
1951  Array<OneD, Array<OneD, NekDouble> > numfluxY (nvariables);
1952 
1953  for (i = 0; i < nvariables; ++i)
1954  {
1955  numfluxX[i] = Array<OneD, NekDouble>(nTracePointsTot);
1956  numfluxY[i] = Array<OneD, NekDouble>(nTracePointsTot);
1957  }
1958 
1959  // Evaluate numerical flux in physical space which may in
1960  // general couple all component of vectors
1961  NumericalFlux(physfield, numfluxX, numfluxY);
1962 
1963  // Evaulate <\phi, \hat{F}\cdot n> - OutField[i]
1964  for(i = 0; i < nvariables; ++i)
1965  {
1966  Vmath::Neg(ncoeffs,OutField[i],1);
1967  m_fields[i]->AddTraceIntegral(numfluxX[i], numfluxY[i],
1968  OutField[i]);
1969  m_fields[i]->SetPhysState(false);
1970  }
1971  }
1972  }
int m_expdim
Expansion dimension.
SOLVER_UTILS_EXPORT void WeakAdvectionGreensDivergenceForm(const Array< OneD, Array< OneD, NekDouble > > &F, Array< OneD, NekDouble > &outarray)
Compute the inner product .
SOLVER_UTILS_EXPORT void NumericalFlux(Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numflux)
void Neg(int n, T *x, const int incx)
Negate x = -x.
Definition: Vmath.cpp:396
SOLVER_UTILS_EXPORT void GetFluxVector(const int i, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &flux)
SOLVER_UTILS_EXPORT int GetNpoints()
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
SOLVER_UTILS_EXPORT int GetTraceNpoints()
SOLVER_UTILS_EXPORT int GetNcoeffs()
void Nektar::SolverUtils::EquationSystem::WeakDGDiffusion ( const Array< OneD, Array< OneD, NekDouble > > &  InField,
Array< OneD, Array< OneD, NekDouble > > &  OutField,
bool  NumericalFluxIncludesNormal = true,
bool  InFieldIsInPhysSpace = false 
)

Calculate weak DG Diffusion in the LDG form.

Calculate weak DG Diffusion in the LDG form $ \langle\psi, \hat{u}\cdot n\rangle - \langle\nabla\psi \cdot u\rangle \langle\phi, \hat{q}\cdot n\rangle - (\nabla \phi \cdot q) \rangle $

Definition at line 1980 of file EquationSystem.cpp.

References GetFluxVector(), GetNcoeffs(), GetNpoints(), GetTraceNpoints(), m_fields, m_spacedim, m_tanbasis, Vmath::Neg(), NumFluxforScalar(), NumFluxforVector(), Vmath::Vadd(), Vmath::Vcopy(), Vmath::Vmul(), and WeakAdvectionGreensDivergenceForm().

1985  {
1986  int i, j, k;
1987  int nPointsTot = GetNpoints();
1988  int ncoeffs = GetNcoeffs();
1989  int nTracePointsTot = GetTraceNpoints();
1990  int nvariables = m_fields.num_elements();
1991  int nqvar = 2;
1992 
1993  Array<OneD, NekDouble> qcoeffs (ncoeffs);
1994  Array<OneD, NekDouble> temp (ncoeffs);
1995 
1996  Array<OneD, Array<OneD, NekDouble> > fluxvector (m_spacedim);
1997  Array<OneD, Array<OneD, NekDouble> > ufield (nvariables);
1998 
1999  Array<OneD, Array<OneD, Array<OneD, NekDouble> > > flux (nqvar);
2000  Array<OneD, Array<OneD, Array<OneD, NekDouble> > > qfield (nqvar);
2001 
2002  for (j = 0; j < nqvar; ++j)
2003  {
2004  qfield[j] = Array<OneD, Array<OneD, NekDouble> >(nqvar);
2005  flux[j] = Array<OneD, Array<OneD, NekDouble> >(nqvar);
2006 
2007  for (i = 0; i< nvariables; ++i)
2008  {
2009  ufield[i] = Array<OneD, NekDouble>(nPointsTot, 0.0);
2010  qfield[j][i] = Array<OneD, NekDouble>(nPointsTot, 0.0);
2011  flux[j][i] = Array<OneD, NekDouble>(nTracePointsTot, 0.0);
2012  }
2013  }
2014 
2015  for (k = 0; k < m_spacedim; ++k)
2016  {
2017  fluxvector[k] = Array<OneD, NekDouble>(nPointsTot, 0.0);
2018  }
2019 
2020  // Get the variables in physical space already in physical space
2021  if (InFieldIsInPhysSpace == true)
2022  {
2023  for (i = 0; i < nvariables; ++i)
2024  {
2025  ufield[i] = InField[i];
2026  }
2027  }
2028  // Otherwise do a backward transformation
2029  else
2030  {
2031  for (i = 0; i < nvariables; ++i)
2032  {
2033  // Could make this point to m_fields[i]->UpdatePhys();
2034  ufield[i] = Array<OneD, NekDouble>(nPointsTot);
2035  m_fields[i]->BwdTrans(InField[i],ufield[i]);
2036  }
2037  }
2038 
2039  // ##########################################################
2040  // Compute q_{\eta} and q_{\xi} from su
2041  // Obtain Numerical Fluxes
2042  // ##########################################################
2043  NumFluxforScalar(ufield, flux);
2044 
2045  for (j = 0; j < nqvar; ++j)
2046  {
2047  for (i = 0; i < nvariables; ++i)
2048  {
2049  // Get the ith component of the flux vector in
2050  // (physical space) fluxvector = m_tanbasis * u,
2051  // where m_tanbasis = 2 by m_spacedim by nPointsTot
2052  if (m_tanbasis.num_elements())
2053  {
2054  for (k = 0; k < m_spacedim; ++k)
2055  {
2056  Vmath::Vmul(nPointsTot, m_tanbasis[j][k], 1,
2057  ufield[i], 1, fluxvector[k], 1);
2058  }
2059  }
2060  else
2061  {
2062  GetFluxVector(i, j, ufield, fluxvector);
2063  }
2064 
2065  // Calculate the i^th value of (\grad_i \phi, F)
2066  WeakAdvectionGreensDivergenceForm(fluxvector, qcoeffs);
2067 
2068  Vmath::Neg(ncoeffs,qcoeffs,1);
2069  m_fields[i]->AddTraceIntegral(flux[j][i], qcoeffs);
2070  m_fields[i]->SetPhysState(false);
2071 
2072  // Add weighted mass matrix = M ( \nabla \cdot Tanbasis )
2073 // if(m_gradtan.num_elements())
2074 // {
2075 // MultiRegions::GlobalMatrixKey key(StdRegions::eMass,
2076 // m_gradtan[j]);
2077 // m_fields[i]->MultiRegions::ExpList::GeneralMatrixOp(key,
2078 // InField[i], temp);
2079 // Vmath::Svtvp(ncoeffs, -1.0, temp, 1, qcoeffs, 1,
2080 // qcoeffs, 1);
2081 // }
2082 
2083  //Multiply by the inverse of mass matrix
2084  m_fields[i]->MultiplyByElmtInvMass(qcoeffs, qcoeffs);
2085 
2086  // Back to physical space
2087  m_fields[i]->BwdTrans(qcoeffs, qfield[j][i]);
2088  }
2089  }
2090 
2091 
2092  // ##########################################################
2093  // Compute u from q_{\eta} and q_{\xi}
2094  // ##########################################################
2095 
2096  // Obtain Numerical Fluxes
2097  NumFluxforVector(ufield, qfield, flux[0]);
2098 
2099  for (i = 0; i < nvariables; ++i)
2100  {
2101  // L = L(tan_eta) q_eta + L(tan_xi) q_xi
2102  OutField[i] = Array<OneD, NekDouble>(ncoeffs, 0.0);
2103  temp = Array<OneD, NekDouble>(ncoeffs, 0.0);
2104 
2105  if (m_tanbasis.num_elements())
2106  {
2107  for (j = 0; j < nqvar; ++j)
2108  {
2109  for (k = 0; k < m_spacedim; ++k)
2110  {
2111  Vmath::Vmul(nPointsTot, m_tanbasis[j][k], 1,
2112  qfield[j][i], 1, fluxvector[k], 1);
2113  }
2114 
2115  WeakAdvectionGreensDivergenceForm(fluxvector, temp);
2116  Vmath::Vadd(ncoeffs, temp, 1, OutField[i], 1,
2117  OutField[i], 1);
2118  }
2119  }
2120  else
2121  {
2122  for (k = 0; k < m_spacedim; ++k)
2123  {
2124  Vmath::Vcopy(nPointsTot, qfield[k][i], 1,
2125  fluxvector[k], 1);
2126  }
2127 
2128  WeakAdvectionGreensDivergenceForm(fluxvector, OutField[i]);
2129  }
2130 
2131  // Evaulate <\phi, \hat{F}\cdot n> - OutField[i]
2132  Vmath::Neg(ncoeffs,OutField[i],1);
2133  m_fields[i]->AddTraceIntegral(flux[0][i], OutField[i]);
2134  m_fields[i]->SetPhysState(false);
2135  }
2136  }
SOLVER_UTILS_EXPORT void NumFluxforScalar(const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &uflux)
SOLVER_UTILS_EXPORT void WeakAdvectionGreensDivergenceForm(const Array< OneD, Array< OneD, NekDouble > > &F, Array< OneD, NekDouble > &outarray)
Compute the inner product .
Array< OneD, Array< OneD, Array< OneD, NekDouble > > > m_tanbasis
2 x m_spacedim x nq
int m_spacedim
Spatial dimension (>= expansion dim).
void Neg(int n, T *x, const int incx)
Negate x = -x.
Definition: Vmath.cpp:396
SOLVER_UTILS_EXPORT void GetFluxVector(const int i, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &flux)
SOLVER_UTILS_EXPORT int GetNpoints()
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
SOLVER_UTILS_EXPORT int GetTraceNpoints()
SOLVER_UTILS_EXPORT int GetNcoeffs()
SOLVER_UTILS_EXPORT void NumFluxforVector(const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &qfield, Array< OneD, Array< OneD, NekDouble > > &qflux)
void Vcopy(int n, const T *x, const int incx, T *y, const int incy)
Definition: Vmath.cpp:1061
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 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::SolverUtils::EquationSystem::WriteFld ( const std::string &  outname)

Write field data to the given filename.

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

Parameters
outnameFilename to write to.

Definition at line 2180 of file EquationSystem.cpp.

References GetNcoeffs(), m_boundaryConditions, m_fields, and v_ExtraFldOutput().

Referenced by Checkpoint_BaseFlow(), Checkpoint_Output(), Nektar::BidomainRoth::v_InitObject(), Nektar::Monodomain::v_InitObject(), Nektar::CoupledLinearNS::v_Output(), and v_Output().

2181  {
2182  std::vector<Array<OneD, NekDouble> > fieldcoeffs(
2183  m_fields.num_elements());
2184  std::vector<std::string> variables(m_fields.num_elements());
2185 
2186  for (int i = 0; i < m_fields.num_elements(); ++i)
2187  {
2188  if (m_fields[i]->GetNcoeffs() == m_fields[0]->GetNcoeffs())
2189  {
2190  fieldcoeffs[i] = m_fields[i]->UpdateCoeffs();
2191  }
2192  else
2193  {
2194  fieldcoeffs[i] = Array<OneD,NekDouble>(m_fields[0]->
2195  GetNcoeffs());
2196  m_fields[0]->ExtractCoeffsToCoeffs(m_fields[i],
2197  m_fields[i]->GetCoeffs(),
2198  fieldcoeffs[i]);
2199  }
2200  variables[i] = m_boundaryConditions->GetVariable(i);
2201  }
2202 
2203  v_ExtraFldOutput(fieldcoeffs, variables);
2204 
2205  WriteFld(outname, m_fields[0], fieldcoeffs, variables);
2206  }
virtual SOLVER_UTILS_EXPORT void v_ExtraFldOutput(std::vector< Array< OneD, NekDouble > > &fieldcoeffs, std::vector< std::string > &variables)
SpatialDomains::BoundaryConditionsSharedPtr m_boundaryConditions
Pointer to boundary conditions object.
SOLVER_UTILS_EXPORT void WriteFld(const std::string &outname)
Write field data to the given filename.
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
SOLVER_UTILS_EXPORT int GetNcoeffs()
void Nektar::SolverUtils::EquationSystem::WriteFld ( const std::string &  outname,
MultiRegions::ExpListSharedPtr field,
std::vector< Array< OneD, NekDouble > > &  fieldcoeffs,
std::vector< std::string > &  variables 
)

Write input fields to the given filename.

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

Parameters
outnameFilename to write to.
fieldExpList on which data is based.
fieldcoeffsAn array of array of expansion coefficients.
variablesAn array of variable names.

Definition at line 2217 of file EquationSystem.cpp.

References Nektar::GlobalMapping::Mapping::Load(), m_fieldMetaDataMap, m_fld, m_nchk, m_session, m_time, and Nektar::GlobalMapping::MappingSharedPtr.

2222  {
2223  std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef
2224  = field->GetFieldDefinitions();
2225  std::vector<std::vector<NekDouble> > FieldData(FieldDef.size());
2226 
2227  // Copy Data into FieldData and set variable
2228  for(int j = 0; j < fieldcoeffs.size(); ++j)
2229  {
2230  for(int i = 0; i < FieldDef.size(); ++i)
2231  {
2232  // Could do a search here to find correct variable
2233  FieldDef[i]->m_fields.push_back(variables[j]);
2234  field->AppendFieldData(FieldDef[i], FieldData[i],
2235  fieldcoeffs[j]);
2236  }
2237  }
2238 
2239  // Update time in field info if required
2240  if(m_fieldMetaDataMap.find("Time") != m_fieldMetaDataMap.end())
2241  {
2242  m_fieldMetaDataMap["Time"] = boost::lexical_cast<std::string>(m_time);
2243  }
2244 
2245  // Update step in field info if required
2246  if(m_fieldMetaDataMap.find("ChkFileNum") != m_fieldMetaDataMap.end())
2247  {
2248  m_fieldMetaDataMap["ChkFileNum"] = boost::lexical_cast<std::string>(m_nchk);
2249  }
2250 
2251  // If necessary, add mapping information to metadata
2252  // and output mapping coordinates
2253  Array<OneD, MultiRegions::ExpListSharedPtr> fields(1);
2254  fields[0] = field;
2258  mapping->Output( fieldMetaDataMap, outname);
2259 
2260  m_fld->Write(outname, FieldDef, FieldData, fieldMetaDataMap, true);
2261  }
NekDouble m_time
Current time of simulation.
int m_nchk
Number of checkpoints written so far.
std::map< std::string, std::string > FieldMetaDataMap
Definition: FieldIO.h:54
LibUtilities::FieldMetaDataMap m_fieldMetaDataMap
Map to identify relevant solver info to dump in output fields.
GLOBAL_MAPPING_EXPORT typedef boost::shared_ptr< Mapping > MappingSharedPtr
A shared pointer to a Mapping object.
Definition: Mapping.h:51
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
LibUtilities::FieldIOSharedPtr m_fld
Field input/output.
static GLOBAL_MAPPING_EXPORT MappingSharedPtr Load(const LibUtilities::SessionReaderSharedPtr &pSession, const Array< OneD, MultiRegions::ExpListSharedPtr > &pFields)
Return a pointer to the mapping, creating it on first call.
Definition: Mapping.cpp:265
SOLVER_UTILS_EXPORT void Nektar::SolverUtils::EquationSystem::WriteHistoryData ( std::ostream &  out)

Probe each history point and write to file.

void Nektar::SolverUtils::EquationSystem::ZeroPhysFields ( void  )

Zero the physical fields.

Definition at line 1696 of file EquationSystem.cpp.

References GetNpoints(), m_fields, and Vmath::Zero().

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

1697  {
1698  for (int i = 0; i < m_fields.num_elements(); i++)
1699  {
1701  m_fields[i]->UpdatePhys(),1);
1702  }
1703  }
SOLVER_UTILS_EXPORT int GetNpoints()
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
void Zero(int n, T *x, const int incx)
Zero vector.
Definition: Vmath.cpp:373

Member Data Documentation

Array<OneD, MultiRegions::ExpListSharedPtr> Nektar::SolverUtils::EquationSystem::m_base
protected

Base fields.

Definition at line 470 of file EquationSystem.h.

Referenced by ImportFldBase(), and SetUpBaseFields().

SpatialDomains::BoundaryConditionsSharedPtr Nektar::SolverUtils::EquationSystem::m_boundaryConditions
protected
Array<OneD, bool> Nektar::SolverUtils::EquationSystem::m_checkIfSystemSingular
protected

Flag to indicate if the fields should be checked for singularity.

Definition at line 528 of file EquationSystem.h.

Referenced by v_InitObject().

int Nektar::SolverUtils::EquationSystem::m_checksteps
protected
NekDouble Nektar::SolverUtils::EquationSystem::m_checktime
protected

Time between checkpoints.

Definition at line 490 of file EquationSystem.h.

Referenced by Nektar::SolverUtils::UnsteadySystem::v_DoSolve(), and v_InitObject().

LibUtilities::CommSharedPtr Nektar::SolverUtils::EquationSystem::m_comm
protected
Array<OneD, MultiRegions::ExpListSharedPtr> Nektar::SolverUtils::EquationSystem::m_derivedfields
protected

Array holding all dependent variables.

Definition at line 472 of file EquationSystem.h.

int Nektar::SolverUtils::EquationSystem::m_expdim
protected
LibUtilities::FieldMetaDataMap Nektar::SolverUtils::EquationSystem::m_fieldMetaDataMap
protected
Array<OneD, MultiRegions::ExpListSharedPtr> Nektar::SolverUtils::EquationSystem::m_fields
protected

Array holding all dependent variables.

Definition at line 468 of file EquationSystem.h.

Referenced by Nektar::UnsteadyAdvectionDiffusion::AddAdvectionPenaltyFlux(), Nektar::NonlinearSWE::AddCoriolis(), Nektar::LinearSWE::AddCoriolis(), Nektar::NonlinearPeregrine::AddCoriolis(), Nektar::NonlinearSWE::AddVariableDepth(), Nektar::NonlinearPeregrine::AddVariableDepth(), AdvectionNonConservativeForm(), Nektar::VCSMapping::ApplyIncNSMappingForcing(), Nektar::LinearElasticSystem::BuildMatrixSystem(), Nektar::CompressibleFlowSystem::CalcSteadyState(), Nektar::IncNavierStokes::CalcSteadyState(), Nektar::SolverUtils::UnsteadySystem::CheckForRestartTime(), Nektar::CoupledLinearNS::Continuation(), Nektar::ShallowWaterSystem::CopyBoundaryTrace(), CopyFromPhysField(), CopyToPhysField(), Nektar::CoupledLinearNS::DefineForcingTerm(), Nektar::CompressibleFlowSystem::DoAdvection(), Nektar::Bidomain::DoImplicitSolve(), Nektar::BidomainRoth::DoImplicitSolve(), Nektar::Monodomain::DoImplicitSolve(), Nektar::UnsteadyDiffusion::DoImplicitSolve(), Nektar::UnsteadyAdvectionDiffusion::DoImplicitSolve(), Nektar::UnsteadyViscousBurgers::DoImplicitSolve(), Nektar::NonlinearSWE::DoOdeProjection(), Nektar::LinearSWE::DoOdeProjection(), Nektar::UnsteadyInviscidBurger::DoOdeProjection(), Nektar::UnsteadyDiffusion::DoOdeProjection(), Nektar::UnsteadyAdvection::DoOdeProjection(), Nektar::NonlinearPeregrine::DoOdeProjection(), Nektar::APE::DoOdeProjection(), Nektar::UnsteadyAdvectionDiffusion::DoOdeProjection(), Nektar::CFLtester::DoOdeProjection(), Nektar::PulseWavePropagation::DoOdeRhs(), Nektar::ImageWarpingSystem::DoOdeRhs(), Nektar::NonlinearSWE::DoOdeRhs(), Nektar::UnsteadyInviscidBurger::DoOdeRhs(), Nektar::LinearSWE::DoOdeRhs(), Nektar::Bidomain::DoOdeRhs(), Nektar::UnsteadyDiffusion::DoOdeRhs(), Nektar::BidomainRoth::DoOdeRhs(), Nektar::UnsteadyAdvection::DoOdeRhs(), Nektar::NonlinearPeregrine::DoOdeRhs(), Nektar::APE::DoOdeRhs(), Nektar::UnsteadyAdvectionDiffusion::DoOdeRhs(), Nektar::CFLtester::DoOdeRhs(), Nektar::UnsteadyViscousBurgers::DoOdeRhs(), Nektar::CompressibleFlowSystem::DoOdeRhs(), ErrorExtraPoints(), Nektar::CoupledLinearNS::EvaluateAdvection(), Nektar::IncNavierStokes::EvaluateAdvectionTerms(), EvaluateFunctionExp(), EvaluateFunctionFld(), EvaluateFunctionPts(), Nektar::CoupledLinearNS::EvaluateNewtonRHS(), FwdTransFields(), Nektar::APE::GetBasefield(), Nektar::APE::GetCFLEstimate(), Nektar::IncNavierStokes::GetCFLEstimate(), GetCoeff_Offset(), Nektar::IncNavierStokes::GetElmtCFLVals(), Nektar::RinglebFlow::GetExactRinglebFlow(), GetExpSize(), Nektar::NonlinearSWE::GetFluxVector(), Nektar::LinearSWE::GetFluxVector(), Nektar::NonlinearPeregrine::GetFluxVector(), Nektar::CompressibleFlowSystem::GetFluxVector(), Nektar::UnsteadyAdvectionDiffusion::GetFluxVectorAdv(), Nektar::UnsteadyViscousBurgers::GetFluxVectorAdv(), Nektar::UnsteadyAdvection::GetFluxVectorDeAlias(), Nektar::CompressibleFlowSystem::GetFluxVectorDeAlias(), Nektar::UnsteadyAdvectionDiffusion::GetMaxStdVelocity(), GetNcoeffs(), Nektar::UnsteadyAdvectionDiffusion::GetNormalVel(), Nektar::UnsteadyInviscidBurger::GetNormalVelocity(), Nektar::UnsteadyAdvection::GetNormalVelocity(), Nektar::UnsteadyViscousBurgers::GetNormalVelocity(), GetNpoints(), GetNumElmVelocity(), GetNumExpModesPerExp(), GetPhys_Offset(), Nektar::CompressibleFlowSystem::GetStabilityLimitVector(), Nektar::APE::GetStdVelocity(), Nektar::CFLtester::GetStdVelocity(), Nektar::CompressibleFlowSystem::GetStdVelocity(), Nektar::UnsteadyAdvectionDiffusion::GetSubstepTimeStep(), GetTotPoints(), GetTraceNpoints(), Nektar::NavierStokesCFE::GetViscousFluxVector(), Nektar::NavierStokesCFE::GetViscousFluxVectorDeAlias(), ImportFld(), ImportFldBase(), ImportFldToMultiDomains(), Nektar::CompressibleFlowSystem::InitAdvection(), Nektar::CompressibleFlowSystem::InitializeSteadyState(), Nektar::NonlinearPeregrine::LaitoneSolitaryWave(), LoadPts(), Nektar::VCSMapping::MappingAccelerationCorrection(), Nektar::VCSMapping::MappingAdvectionCorrection(), Nektar::VCSMapping::MappingPressureCorrection(), Nektar::NonlinearPeregrine::NumericalFluxConsVariables(), Nektar::NonlinearPeregrine::NumericalFluxForcing(), SessionSummary(), Nektar::NonlinearSWE::SetBoundaryConditions(), Nektar::LinearSWE::SetBoundaryConditions(), Nektar::APE::SetBoundaryConditions(), Nektar::CompressibleFlowSystem::SetBoundaryConditions(), Nektar::NonlinearPeregrine::SetBoundaryConditions(), Nektar::IncNavierStokes::SetBoundaryConditions(), SetBoundaryConditions(), Nektar::NonlinearPeregrine::SetBoundaryConditionsContVariables(), Nektar::NonlinearPeregrine::SetBoundaryConditionsForcing(), Nektar::IncNavierStokes::SetRadiationBoundaryForcing(), Nektar::CoupledLinearNS::SetUpCoupledMatrix(), Nektar::IncNavierStokes::SetWomersleyBoundary(), Nektar::IncNavierStokes::SetZeroNormalVelocity(), Nektar::CoupledLinearNS::Solve(), Nektar::CoupledLinearNS::SolveLinearNS(), Nektar::CoupledLinearNS::SolveSteadyNavierStokes(), Nektar::CoupledLinearNS::SolveUnsteadyStokesSystem(), Nektar::UnsteadyAdvectionDiffusion::SubStepAdvance(), Nektar::UnsteadyAdvectionDiffusion::SubStepAdvection(), Nektar::SolverUtils::UnsteadySystem::SVVVarDiffCoeff(), UpdateFields(), Nektar::SolverUtils::UnsteadySystem::v_AppendOutput1D(), Nektar::NonlinearSWE::v_ConservativeToPrimitive(), Nektar::LinearSWE::v_ConservativeToPrimitive(), Nektar::NonlinearPeregrine::v_ConservativeToPrimitive(), Nektar::NavierStokesCFE::v_DoDiffusion(), Nektar::SteadyAdvectionDiffusion::v_DoInitialise(), Nektar::VCSMapping::v_DoInitialise(), Nektar::VelocityCorrectionScheme::v_DoInitialise(), Nektar::PulseWaveSystem::v_DoInitialise(), Nektar::CoupledLinearNS::v_DoInitialise(), Nektar::EigenValuesAdvection::v_DoSolve(), Nektar::Projection::v_DoSolve(), Nektar::Laplace::v_DoSolve(), Nektar::SteadyAdvectionDiffusion::v_DoSolve(), Nektar::IterativeElasticSystem::v_DoSolve(), Nektar::SolverUtils::UnsteadySystem::v_DoSolve(), Nektar::LinearElasticSystem::v_DoSolve(), Nektar::PulseWaveSystem::v_DoSolve(), Nektar::VCSMapping::v_EvaluateAdvection_SetPressureBCs(), Nektar::VelocityCorrectionScheme::v_EvaluateAdvection_SetPressureBCs(), Nektar::IsentropicVortex::v_EvaluateExactSolution(), v_EvaluateExactSolution(), Nektar::LinearElasticSystem::v_ExtraFldOutput(), Nektar::CompressibleFlowSystem::v_ExtraFldOutput(), Nektar::Poisson::v_GenerateSummary(), Nektar::Projection::v_GenerateSummary(), Nektar::IncNavierStokes::v_GetFluxVector(), Nektar::CFLtester::v_GetTimeStep(), Nektar::CompressibleFlowSystem::v_GetTimeStep(), Nektar::Poisson::v_InitObject(), Nektar::VelocityCorrectionScheme::v_InitObject(), Nektar::Projection::v_InitObject(), Nektar::NavierStokesCFE::v_InitObject(), Nektar::NonlinearSWE::v_InitObject(), Nektar::LinearSWE::v_InitObject(), Nektar::VCSMapping::v_InitObject(), Nektar::Bidomain::v_InitObject(), Nektar::BidomainRoth::v_InitObject(), Nektar::Monodomain::v_InitObject(), Nektar::UnsteadyDiffusion::v_InitObject(), Nektar::ImageWarpingSystem::v_InitObject(), Nektar::IterativeElasticSystem::v_InitObject(), Nektar::NonlinearPeregrine::v_InitObject(), Nektar::ShallowWaterSystem::v_InitObject(), Nektar::APE::v_InitObject(), Nektar::UnsteadyInviscidBurger::v_InitObject(), Nektar::UnsteadyAdvection::v_InitObject(), Nektar::CompressibleFlowSystem::v_InitObject(), Nektar::LinearElasticSystem::v_InitObject(), Nektar::UnsteadyAdvectionDiffusion::v_InitObject(), Nektar::UnsteadyViscousBurgers::v_InitObject(), Nektar::PulseWaveSystem::v_InitObject(), Nektar::IncNavierStokes::v_InitObject(), Nektar::CoupledLinearNS::v_InitObject(), v_InitObject(), v_L2Error(), v_LinfError(), Nektar::EigenValuesAdvection::v_NumericalFlux(), Nektar::ImageWarpingSystem::v_NumericalFlux(), Nektar::CFLtester::v_NumericalFlux(), Nektar::IncNavierStokes::v_NumericalFlux(), Nektar::SolverUtils::UnsteadySystem::v_NumFluxforScalar(), Nektar::SolverUtils::UnsteadySystem::v_NumFluxforVector(), Nektar::CoupledLinearNS::v_Output(), Nektar::NonlinearSWE::v_PrimitiveToConservative(), Nektar::LinearSWE::v_PrimitiveToConservative(), Nektar::NonlinearPeregrine::v_PrimitiveToConservative(), Nektar::IsentropicVortex::v_SetInitialConditions(), Nektar::CompressibleFlowSystem::v_SetInitialConditions(), v_SetInitialConditions(), Nektar::VCSWeakPressure::v_SetUpPressureForcing(), Nektar::VCSMapping::v_SetUpPressureForcing(), Nektar::VelocityCorrectionScheme::v_SetUpPressureForcing(), Nektar::VCSMapping::v_SetUpViscousForcing(), Nektar::VelocityCorrectionScheme::v_SetUpViscousForcing(), Nektar::VCSMapping::v_SolvePressure(), Nektar::VCSMapping::v_SolveViscous(), Nektar::VelocityCorrectionScheme::v_SolveViscous(), Nektar::VelocityCorrectionScheme::v_TransCoeffToPhys(), Nektar::CoupledLinearNS::v_TransCoeffToPhys(), Nektar::VelocityCorrectionScheme::v_TransPhysToCoeff(), Nektar::CoupledLinearNS::v_TransPhysToCoeff(), Nektar::APE::WallBC(), Nektar::NonlinearSWE::WallBoundary(), Nektar::LinearSWE::WallBoundary(), Nektar::NonlinearPeregrine::WallBoundary(), Nektar::NonlinearSWE::WallBoundary2D(), Nektar::LinearSWE::WallBoundary2D(), Nektar::NonlinearPeregrine::WallBoundary2D(), Nektar::NonlinearPeregrine::WallBoundaryContVariables(), Nektar::NonlinearPeregrine::WallBoundaryForcing(), Nektar::NonlinearPeregrine::WCESolve(), WeakAdvectionDivergenceForm(), WeakAdvectionGreensDivergenceForm(), WeakAdvectionNonConservativeForm(), WeakDGAdvection(), WeakDGDiffusion(), Nektar::SolverUtils::UnsteadySystem::WeakPenaltyforScalar(), Nektar::SolverUtils::UnsteadySystem::WeakPenaltyforVector(), WriteFld(), Nektar::IterativeElasticSystem::WriteGeometry(), and ZeroPhysFields().

NekDouble Nektar::SolverUtils::EquationSystem::m_fintime
protected

Finish time of the simulation.

Definition at line 484 of file EquationSystem.h.

Referenced by Nektar::SolverUtils::UnsteadySystem::v_DoSolve(), Nektar::PulseWaveSystem::v_InitObject(), and v_InitObject().

LibUtilities::FieldIOSharedPtr Nektar::SolverUtils::EquationSystem::m_fld
protected

Field input/output.

Definition at line 460 of file EquationSystem.h.

Referenced by v_InitObject(), and WriteFld().

Array<OneD, Array<OneD, Array<OneD,NekDouble> > > Nektar::SolverUtils::EquationSystem::m_gradtan
protected

1 x nvariable x nq

Definition at line 524 of file EquationSystem.h.

SpatialDomains::MeshGraphSharedPtr Nektar::SolverUtils::EquationSystem::m_graph
protected
bool Nektar::SolverUtils::EquationSystem::m_halfMode
protected

Flag to determine if half homogeneous mode is used.

Definition at line 504 of file EquationSystem.h.

Referenced by SessionSummary(), SetUpBaseFields(), and v_InitObject().

int Nektar::SolverUtils::EquationSystem::m_HomoDirec
protected

number of homogenous directions

Definition at line 556 of file EquationSystem.h.

Referenced by v_InitObject().

bool Nektar::SolverUtils::EquationSystem::m_homogen_dealiasing
protected

Flag to determine if dealiasing is used for homogeneous simulations.

Definition at line 513 of file EquationSystem.h.

Referenced by SetUpBaseFields(), Nektar::VCSWeakPressure::v_GenerateSummary(), Nektar::VelocityCorrectionScheme::v_GenerateSummary(), Nektar::CoupledLinearNS::v_InitObject(), and v_InitObject().

enum HomogeneousType Nektar::SolverUtils::EquationSystem::m_HomogeneousType
protected
int Nektar::SolverUtils::EquationSystem::m_initialStep
protected

Number of the step where the simulation should begin.

Definition at line 482 of file EquationSystem.h.

Referenced by SetInitialStep(), Nektar::SolverUtils::UnsteadySystem::v_DoSolve(), and Nektar::SolverUtils::UnsteadySystem::v_InitObject().

std::map<std::string, FieldUtils::Interpolator > Nektar::SolverUtils::EquationSystem::m_interpolators
protected

Map of interpolator objects.

Definition at line 462 of file EquationSystem.h.

Referenced by LoadPts().

NekDouble Nektar::SolverUtils::EquationSystem::m_lambda
protected

Lambda constant in real system if one required.

Definition at line 488 of file EquationSystem.h.

Referenced by SetLambda(), and Nektar::CoupledLinearNS::v_DoInitialise().

NekDouble Nektar::SolverUtils::EquationSystem::m_LhomX
protected

physical length in X direction (if homogeneous)

Definition at line 548 of file EquationSystem.h.

NekDouble Nektar::SolverUtils::EquationSystem::m_LhomY
protected

physical length in Y direction (if homogeneous)

Definition at line 549 of file EquationSystem.h.

Referenced by SessionSummary(), and v_InitObject().

NekDouble Nektar::SolverUtils::EquationSystem::m_LhomZ
protected

physical length in Z direction (if homogeneous)

Definition at line 550 of file EquationSystem.h.

Referenced by SessionSummary(), SetUpBaseFields(), Nektar::CoupledLinearNS::SetUpCoupledMatrix(), Nektar::CoupledLinearNS::v_InitObject(), and v_InitObject().

std::map<std::string, std::pair<std::string, loadedFldField> > Nektar::SolverUtils::EquationSystem::m_loadedFldFields
protected

Definition at line 466 of file EquationSystem.h.

Referenced by EvaluateFunctionFld().

std::map<std::string, std::pair<std::string, LibUtilities::PtsFieldSharedPtr> > Nektar::SolverUtils::EquationSystem::m_loadedPtsFields
protected

pts fields we already read from disk: {funcFilename: (filename, ptsfield)}

Definition at line 464 of file EquationSystem.h.

Referenced by EvaluateFunctionPts().

bool Nektar::SolverUtils::EquationSystem::m_multipleModes
protected

Flag to determine if use multiple homogenenous modes are used.

Definition at line 506 of file EquationSystem.h.

Referenced by SessionSummary(), and v_InitObject().

int Nektar::SolverUtils::EquationSystem::m_nchk
protected
int Nektar::SolverUtils::EquationSystem::m_npointsX
protected

number of points in X direction (if homogeneous)

Definition at line 552 of file EquationSystem.h.

int Nektar::SolverUtils::EquationSystem::m_npointsY
protected

number of points in Y direction (if homogeneous)

Definition at line 553 of file EquationSystem.h.

Referenced by SessionSummary(), and v_InitObject().

int Nektar::SolverUtils::EquationSystem::m_npointsZ
protected
int Nektar::SolverUtils::EquationSystem::m_NumQuadPointsError
protected
enum MultiRegions::ProjectionType Nektar::SolverUtils::EquationSystem::m_projectionType
protected

Type of projection; e.g continuous or discontinuous.

Definition at line 520 of file EquationSystem.h.

Referenced by Nektar::NonlinearSWE::AddCoriolis(), Nektar::LinearSWE::AddCoriolis(), Nektar::NonlinearPeregrine::AddCoriolis(), Nektar::NonlinearSWE::AddVariableDepth(), Nektar::NonlinearPeregrine::AddVariableDepth(), Nektar::UnsteadyAdvectionDiffusion::DoImplicitSolve(), Nektar::ImageWarpingSystem::DoOdeProjection(), Nektar::NonlinearSWE::DoOdeProjection(), Nektar::LinearSWE::DoOdeProjection(), Nektar::UnsteadyInviscidBurger::DoOdeProjection(), Nektar::UnsteadyDiffusion::DoOdeProjection(), Nektar::UnsteadyAdvection::DoOdeProjection(), Nektar::NonlinearPeregrine::DoOdeProjection(), Nektar::UnsteadyAdvectionDiffusion::DoOdeProjection(), Nektar::CFLtester::DoOdeProjection(), Nektar::UnsteadyViscousBurgers::DoOdeProjection(), Nektar::CompressibleFlowSystem::DoOdeProjection(), Nektar::ImageWarpingSystem::DoOdeRhs(), Nektar::NonlinearSWE::DoOdeRhs(), Nektar::LinearSWE::DoOdeRhs(), Nektar::NonlinearPeregrine::DoOdeRhs(), Nektar::CFLtester::DoOdeRhs(), Nektar::UnsteadyViscousBurgers::DoOdeRhs(), Nektar::CompressibleFlowSystem::GetStabilityLimit(), Nektar::CompressibleFlowSystem::InitAdvection(), SessionSummary(), SetUpBaseFields(), Nektar::EigenValuesAdvection::v_DoSolve(), Nektar::NonlinearSWE::v_InitObject(), Nektar::LinearSWE::v_InitObject(), Nektar::UnsteadyDiffusion::v_InitObject(), Nektar::NonlinearPeregrine::v_InitObject(), Nektar::ShallowWaterSystem::v_InitObject(), Nektar::APE::v_InitObject(), Nektar::UnsteadyInviscidBurger::v_InitObject(), Nektar::UnsteadyAdvection::v_InitObject(), Nektar::UnsteadyAdvectionDiffusion::v_InitObject(), Nektar::UnsteadyViscousBurgers::v_InitObject(), Nektar::PulseWaveSystem::v_InitObject(), and v_InitObject().

LibUtilities::SessionReaderSharedPtr Nektar::SolverUtils::EquationSystem::m_session
protected

The session reader.

Definition at line 458 of file EquationSystem.h.

Referenced by Nektar::LinearElasticSystem::BuildMatrixSystem(), Nektar::CompressibleFlowSystem::CalcSteadyState(), Nektar::SolverUtils::UnsteadySystem::CheckForRestartTime(), Nektar::CoupledLinearNS::DefineForcingTerm(), DescribeFunction(), Nektar::Bidomain::DoImplicitSolve(), Nektar::ImageWarpingSystem::DoOdeRhs(), Nektar::BidomainRoth::DoOdeRhs(), Nektar::Bidomain::DoOdeRhs(), EquationSystem(), ErrorExtraPoints(), EvaluateFunction(), EvaluateFunctionExp(), EvaluateFunctionFld(), EvaluateFunctionPts(), GetNvariables(), GetSession(), Nektar::UnsteadyAdvectionDiffusion::GetSubstepTimeStep(), GetVariable(), Nektar::Helmholtz::Helmholtz(), ImportFld(), ImportFldBase(), ImportFldToMultiDomains(), Nektar::CompressibleFlowSystem::InitAdvection(), Nektar::CompressibleFlowSystem::InitialiseParameters(), Nektar::CompressibleFlowSystem::InitializeSteadyState(), LoadPts(), PrintSummary(), SessionSummary(), Nektar::NonlinearSWE::SetBoundaryConditions(), Nektar::LinearSWE::SetBoundaryConditions(), Nektar::APE::SetBoundaryConditions(), Nektar::IncNavierStokes::SetBoundaryConditions(), SetBoundaryConditions(), Nektar::PulseWavePropagation::SetPulseWaveBoundaryConditions(), SetUpBaseFields(), Nektar::CoupledLinearNS::SetUpCoupledMatrix(), Nektar::UnsteadyAdvectionDiffusion::SubStepAdvance(), Nektar::SteadyAdvectionDiffusion::v_DoInitialise(), Nektar::PulseWaveSystem::v_DoInitialise(), Nektar::CoupledLinearNS::v_DoInitialise(), Nektar::IterativeElasticSystem::v_DoSolve(), Nektar::SolverUtils::UnsteadySystem::v_DoSolve(), Nektar::LinearElasticSystem::v_DoSolve(), Nektar::PulseWaveSystem::v_DoSolve(), v_EvaluateExactSolution(), Nektar::APE::v_ExtraFldOutput(), Nektar::CompressibleFlowSystem::v_ExtraFldOutput(), Nektar::Poisson::v_GenerateSummary(), Nektar::Projection::v_GenerateSummary(), Nektar::LinearSWE::v_GenerateSummary(), Nektar::Monodomain::v_GenerateSummary(), Nektar::SolverUtils::UnsteadySystem::v_GenerateSummary(), Nektar::VelocityCorrectionScheme::v_GetForceDimension(), Nektar::CoupledLinearNS::v_GetForceDimension(), Nektar::Poisson::v_GetSystemSingularChecks(), Nektar::Helmholtz::v_GetSystemSingularChecks(), Nektar::Laplace::v_GetSystemSingularChecks(), Nektar::VelocityCorrectionScheme::v_GetSystemSingularChecks(), v_GetSystemSingularChecks(), Nektar::Poisson::v_InitObject(), Nektar::SteadyAdvectionDiffusionReaction::v_InitObject(), Nektar::VelocityCorrectionScheme::v_InitObject(), Nektar::NavierStokesCFE::v_InitObject(), Nektar::Projection::v_InitObject(), Nektar::PulseWaveSystemOutput::v_InitObject(), Nektar::NonlinearSWE::v_InitObject(), Nektar::VCSMapping::v_InitObject(), Nektar::LinearSWE::v_InitObject(), Nektar::Bidomain::v_InitObject(), Nektar::BidomainRoth::v_InitObject(), Nektar::Monodomain::v_InitObject(), Nektar::UnsteadyDiffusion::v_InitObject(), Nektar::ImageWarpingSystem::v_InitObject(), Nektar::PulseWavePropagation::v_InitObject(), Nektar::IterativeElasticSystem::v_InitObject(), Nektar::NonlinearPeregrine::v_InitObject(), Nektar::ShallowWaterSystem::v_InitObject(), Nektar::APE::v_InitObject(), Nektar::SolverUtils::UnsteadySystem::v_InitObject(), Nektar::UnsteadyInviscidBurger::v_InitObject(), Nektar::UnsteadyAdvection::v_InitObject(), Nektar::CompressibleFlowSystem::v_InitObject(), Nektar::LinearElasticSystem::v_InitObject(), Nektar::UnsteadyAdvectionDiffusion::v_InitObject(), Nektar::UnsteadyViscousBurgers::v_InitObject(), Nektar::PulseWaveSystem::v_InitObject(), Nektar::IncNavierStokes::v_InitObject(), Nektar::CoupledLinearNS::v_InitObject(), v_InitObject(), Nektar::PulseWaveSystem::v_L2Error(), v_L2Error(), Nektar::PulseWaveSystem::v_LinfError(), v_LinfError(), Nektar::CompressibleFlowSystem::v_SetInitialConditions(), v_SetInitialConditions(), Nektar::VCSMapping::v_SolvePressure(), Nektar::VCSMapping::v_SolveViscous(), Nektar::SolverUtils::UnsteadySystem::WeakPenaltyforScalar(), Nektar::SolverUtils::UnsteadySystem::WeakPenaltyforVector(), WriteFld(), Nektar::IterativeElasticSystem::WriteGeometry(), and Nektar::PulseWaveSystem::WriteVessels().

std::string Nektar::SolverUtils::EquationSystem::m_sessionName
protected
bool Nektar::SolverUtils::EquationSystem::m_singleMode
protected
int Nektar::SolverUtils::EquationSystem::m_spacedim
protected

Spatial dimension (>= expansion dim).

Definition at line 498 of file EquationSystem.h.

Referenced by Nektar::NonlinearSWE::AddVariableDepth(), Nektar::NonlinearPeregrine::AddVariableDepth(), Nektar::CompressibleFlowSystem::DoAdvection(), Nektar::Bidomain::DoImplicitSolve(), Nektar::NonlinearSWE::DoOdeRhs(), Nektar::LinearSWE::DoOdeRhs(), Nektar::APE::DoOdeRhs(), Nektar::IsentropicVortex::EvaluateIsentropicVortex(), Nektar::APE::GetBasefield(), Nektar::NonlinearSWE::GetFluxVector(), Nektar::LinearSWE::GetFluxVector(), Nektar::APE::GetFluxVector(), Nektar::NonlinearPeregrine::GetFluxVector(), Nektar::CompressibleFlowSystem::GetFluxVector(), Nektar::UnsteadyAdvection::GetFluxVectorDeAlias(), Nektar::CompressibleFlowSystem::GetFluxVectorDeAlias(), Nektar::UnsteadyInviscidBurger::GetNormalVelocity(), Nektar::APE::GetStdVelocity(), Nektar::CompressibleFlowSystem::GetStdVelocity(), Nektar::NonlinearSWE::GetVelocityVector(), Nektar::LinearSWE::GetVelocityVector(), Nektar::NonlinearPeregrine::GetVelocityVector(), Nektar::NavierStokesCFE::GetViscousFluxVector(), Nektar::NavierStokesCFE::GetViscousFluxVectorDeAlias(), InitialiseBaseFlow(), Nektar::CompressibleFlowSystem::InitialiseParameters(), SessionSummary(), Nektar::IncNavierStokes::SetZeroNormalVelocity(), Nektar::SolverUtils::UnsteadySystem::v_DoSolve(), Nektar::IsentropicVortex::v_EvaluateExactSolution(), Nektar::APE::v_ExtraFldOutput(), Nektar::EigenValuesAdvection::v_InitObject(), Nektar::SteadyAdvectionDiffusion::v_InitObject(), Nektar::Bidomain::v_InitObject(), Nektar::BidomainRoth::v_InitObject(), Nektar::Monodomain::v_InitObject(), Nektar::ImageWarpingSystem::v_InitObject(), Nektar::ShallowWaterSystem::v_InitObject(), Nektar::APE::v_InitObject(), Nektar::UnsteadyAdvection::v_InitObject(), Nektar::CompressibleFlowSystem::v_InitObject(), Nektar::CFLtester::v_InitObject(), Nektar::UnsteadyAdvectionDiffusion::v_InitObject(), Nektar::IncNavierStokes::v_InitObject(), v_InitObject(), Nektar::EigenValuesAdvection::v_NumericalFlux(), Nektar::ImageWarpingSystem::v_NumericalFlux(), Nektar::CFLtester::v_NumericalFlux(), Nektar::IncNavierStokes::v_NumericalFlux(), Nektar::APE::v_PreIntegrate(), Nektar::IsentropicVortex::v_SetInitialConditions(), Nektar::APE::WallBC(), Nektar::NonlinearSWE::WallBoundary(), Nektar::LinearSWE::WallBoundary(), Nektar::NonlinearPeregrine::WallBoundary(), and WeakDGDiffusion().

bool Nektar::SolverUtils::EquationSystem::m_specHP_dealiasing
protected
int Nektar::SolverUtils::EquationSystem::m_steps
protected
Array<OneD, Array<OneD, Array<OneD,NekDouble> > > Nektar::SolverUtils::EquationSystem::m_tanbasis
protected

2 x m_spacedim x nq

Definition at line 526 of file EquationSystem.h.

Referenced by WeakDGDiffusion().

NekDouble Nektar::SolverUtils::EquationSystem::m_time
protected
NekDouble Nektar::SolverUtils::EquationSystem::m_timestep
protected
Array<OneD, Array<OneD, NekDouble> > Nektar::SolverUtils::EquationSystem::m_traceNormals
protected
bool Nektar::SolverUtils::EquationSystem::m_useFFT
protected

Flag to determine if FFT is used for homogeneous transform.

Definition at line 508 of file EquationSystem.h.

Referenced by SessionSummary(), SetUpBaseFields(), Nektar::CoupledLinearNS::v_InitObject(), and v_InitObject().