Nektar::SpatialDomains::MeshGraph1D Class Reference

#include <MeshGraph1D.h>

Inheritance diagram for Nektar::SpatialDomains::MeshGraph1D:

Collaboration diagram for Nektar::SpatialDomains::MeshGraph1D:

Public Member Functions
	MeshGraph1D ()
	MeshGraph1D (const LibUtilities::SessionReaderSharedPtr &pSession, const DomainRangeShPtr &rng=NullDomainRangeShPtr)
virtual	~MeshGraph1D ()
void	ReadGeometry (const std::string &infilename)
	Read will read the meshgraph vertices given a filename. More...
void	ReadGeometry (TiXmlDocument &doc)
	Read will read the meshgraph vertices given a TiXmlDocument. More...
void	ReadElements (TiXmlDocument &doc)
void	ReadComposites (TiXmlDocument &doc)
void	ResolveGeomRef (const std::string &prevToken, const std::string &token, Composite &composite)
int	GetCoordim (void)
const SegGeomMap &	GetSeggeoms (void) const
int	GetVidFromElmt (const int vert, const int elmt) const
Public Member Functions inherited from Nektar::SpatialDomains::MeshGraph
	MeshGraph ()
	MeshGraph (unsigned int meshDimension, unsigned int spaceDimension)
	MeshGraph (const LibUtilities::SessionReaderSharedPtr &pSession, const DomainRangeShPtr &rng=NullDomainRangeShPtr)
virtual	~MeshGraph ()
void	ReadGeometryInfo (const std::string &infilename)
	Read geometric information from a file. More...
void	ReadGeometryInfo (TiXmlDocument &doc)
	Read geometric information from an XML document. More...
void	ReadExpansions (const std::string &infilename)
	Read the expansions given the XML file path. More...
void	ReadExpansions (TiXmlDocument &doc)
	Read the expansions given the XML document reference. More...
void	ReadDomain (TiXmlDocument &doc)
void	ReadCurves (TiXmlDocument &doc)
void	ReadCurves (std::string &infilename)
void	WriteGeometry (std::string &outfilename)
	Write out an XML file containing the GEOMETRY block representing this MeshGraph instance inside a NEKTAR tag. More...
void	WriteGeometry (TiXmlDocument &doc)
	Populate a TinyXML document with a GEOMETRY tag inside the NEKTAR tag. More...
int	GetMeshDimension () const
	Dimension of the mesh (can be a 1D curve in 3D space). More...
int	GetSpaceDimension () const
	Dimension of the space (can be a 1D curve in 3D space). More...
void	SetDomainRange (NekDouble xmin, NekDouble xmax, NekDouble ymin=NekConstants::kNekUnsetDouble, NekDouble ymax=NekConstants::kNekUnsetDouble, NekDouble zmin=NekConstants::kNekUnsetDouble, NekDouble zmax=NekConstants::kNekUnsetDouble)
bool	CheckRange (Geometry2D &geom)
	Check if goemetry is in range definition if activated. More...
bool	CheckRange (Geometry3D &geom)
	Check if goemetry is in range definition if activated. More...
Composite	GetComposite (int whichComposite) const
GeometrySharedPtr	GetCompositeItem (int whichComposite, int whichItem)
void	GetCompositeList (const std::string &compositeStr, CompositeMap &compositeVector) const
const CompositeMap &	GetComposites () const
const std::vector< CompositeMap > &	GetDomain (void) const
const CompositeMap &	GetDomain (int domain) const
const ExpansionMap &	GetExpansions ()
const ExpansionMap &	GetExpansions (const std::string variable)
ExpansionShPtr	GetExpansion (GeometrySharedPtr geom, const std::string variable="DefaultVar")
void	SetExpansions (std::vector< LibUtilities::FieldDefinitionsSharedPtr > &fielddef)
	Sets expansions given field definitions. More...
void	SetExpansions (std::vector< LibUtilities::FieldDefinitionsSharedPtr > &fielddef, std::vector< std::vector< LibUtilities::PointsType > > &pointstype)
	Sets expansions given field definition, quadrature points. More...
void	SetExpansionsToEvenlySpacedPoints (int npoints=0)
	Sets expansions to have equispaced points. More...
void	SetExpansionsToPolyOrder (int nmodes)
	Reset expansion to have specified polynomial order nmodes. More...
void	SetExpansions (const std::string variable, ExpansionMapShPtr &exp)
	This function sets the expansion #exp in map with entry #variable. More...
void	SetBasisKey (LibUtilities::ShapeType shape, LibUtilities::BasisKeyVector &keys, std::string var="DefaultVar")
	Sets the basis key for all expansions of the given shape. More...
bool	SameExpansions (const std::string var1, const std::string var2)
bool	CheckForGeomInfo (std::string parameter)
const std::string	GetGeomInfo (std::string parameter)
LibUtilities::BasisKeyVector	DefineBasisKeyFromExpansionTypeHomo (GeometrySharedPtr in, ExpansionType type_x, ExpansionType type_y, ExpansionType type_z, const int nummodes_x, const int nummodes_y, const int nummodes_z)
int	GetNvertices () const
PointGeomSharedPtr	GetVertex (int id)
PointGeomSharedPtr	AddVertex (NekDouble x, NekDouble y, NekDouble z)
	Adds a vertex to the with the next available ID. More...
SegGeomSharedPtr	AddEdge (PointGeomSharedPtr v0, PointGeomSharedPtr v1, CurveSharedPtr curveDefinition=CurveSharedPtr())
	Adds an edge between two points. If curveDefinition is null, then the edge is straight, otherwise it is curved according to the curveDefinition. More...
SegGeomSharedPtr	GetEdge (unsigned int id)
TriGeomSharedPtr	AddTriangle (SegGeomSharedPtr edges[], StdRegions::Orientation orient[])
QuadGeomSharedPtr	AddQuadrilateral (SegGeomSharedPtr edges[], StdRegions::Orientation orient[])
TetGeomSharedPtr	AddTetrahedron (TriGeomSharedPtr tfaces[TetGeom::kNtfaces])
PyrGeomSharedPtr	AddPyramid (TriGeomSharedPtr tfaces[PyrGeom::kNtfaces], QuadGeomSharedPtr qfaces[PyrGeom::kNqfaces])
PrismGeomSharedPtr	AddPrism (TriGeomSharedPtr tfaces[PrismGeom::kNtfaces], QuadGeomSharedPtr qfaces[PrismGeom::kNqfaces])
HexGeomSharedPtr	AddHexahedron (QuadGeomSharedPtr qfaces[HexGeom::kNqfaces])
const PointGeomMap &	GetVertSet () const
CurveMap &	GetCurvedEdges ()
CurveMap &	GetCurvedFaces ()
const SegGeomMap &	GetAllSegGeoms () const
const TriGeomMap &	GetAllTriGeoms () const
const QuadGeomMap &	GetAllQuadGeoms () const
const TetGeomMap &	GetAllTetGeoms () const
const PyrGeomMap &	GetAllPyrGeoms () const
const PrismGeomMap &	GetAllPrismGeoms () const
const HexGeomMap &	GetAllHexGeoms () const
template<typename ElementType >
const std::map< int, boost::shared_ptr< ElementType > > &	GetAllElementsOfType () const
	Convenience method for ElVis. More...
template<>
const std::map< int, boost::shared_ptr< HexGeom > > &	GetAllElementsOfType () const
template<>
const std::map< int, boost::shared_ptr< PrismGeom > > &	GetAllElementsOfType () const
template<>
const std::map< int, boost::shared_ptr< TetGeom > > &	GetAllElementsOfType () const
template<>
const std::map< int, boost::shared_ptr< PyrGeom > > &	GetAllElementsOfType () const

Additional Inherited Members
Static Public Member Functions inherited from Nektar::SpatialDomains::MeshGraph
static boost::shared_ptr< MeshGraph >	Read (const LibUtilities::SessionReaderSharedPtr &pSession, DomainRangeShPtr &rng=NullDomainRangeShPtr)
static boost::shared_ptr< MeshGraph >	Read (const std::string &infilename, bool pReadExpansions=true)
static LibUtilities::BasisKeyVector	DefineBasisKeyFromExpansionType (GeometrySharedPtr in, ExpansionType type, const int order)
Protected Member Functions inherited from Nektar::SpatialDomains::MeshGraph
ExpansionMapShPtr	SetUpExpansionMap (void)
Protected Attributes inherited from Nektar::SpatialDomains::MeshGraph
LibUtilities::SessionReaderSharedPtr	m_session
PointGeomMap	m_vertSet
InterfaceCompList	m_iComps
CurveMap	m_curvedEdges
CurveMap	m_curvedFaces
SegGeomMap	m_segGeoms
TriGeomMap	m_triGeoms
QuadGeomMap	m_quadGeoms
TetGeomMap	m_tetGeoms
PyrGeomMap	m_pyrGeoms
PrismGeomMap	m_prismGeoms
HexGeomMap	m_hexGeoms
int	m_meshDimension
int	m_spaceDimension
int	m_partition
bool	m_meshPartitioned
CompositeMap	m_meshComposites
std::vector< CompositeMap >	m_domain
DomainRangeShPtr	m_domainRange
ExpansionMapShPtrMap	m_expansionMapShPtrMap
GeomInfoMap	m_geomInfo

Detailed Description

Definition at line 47 of file MeshGraph1D.h.

Constructor & Destructor Documentation

Nektar::SpatialDomains::MeshGraph1D::MeshGraph1D

(

)

Definition at line 46 of file MeshGraph1D.cpp.

        {
        }

Nektar::SpatialDomains::MeshGraph1D::MeshGraph1D	(	const LibUtilities::SessionReaderSharedPtr &	pSession,
		const DomainRangeShPtr &	rng = NullDomainRangeShPtr
	)

Definition at line 50 of file MeshGraph1D.cpp.

References Nektar::SpatialDomains::MeshGraph::ReadExpansions(), and ReadGeometry().

            : MeshGraph(pSession,rng)
        {
            ReadGeometry  (pSession->GetDocument());
            ReadExpansions(pSession->GetDocument());
        }

Nektar::SpatialDomains::MeshGraph1D::~MeshGraph1D ( )

virtual

Definition at line 58 of file MeshGraph1D.cpp.

        {
        }

Member Function Documentation

int Nektar::SpatialDomains::MeshGraph1D::GetCoordim ( void  )

inline

Definition at line 62 of file MeshGraph1D.h.

References Nektar::SpatialDomains::MeshGraph::GetSpaceDimension().

            {
                return GetSpaceDimension();
            }

const SegGeomMap& Nektar::SpatialDomains::MeshGraph1D::GetSeggeoms ( void  ) const

inline

Definition at line 67 of file MeshGraph1D.h.

References Nektar::SpatialDomains::MeshGraph::m_segGeoms.

            {
                return m_segGeoms;
            }

int Nektar::SpatialDomains::MeshGraph1D::GetVidFromElmt ( const int  vert, const int  elmt  ) const

inline

Definition at line 72 of file MeshGraph1D.h.

References ASSERTL2, and Nektar::SpatialDomains::MeshGraph::m_segGeoms.

            {
                ASSERTL2((elmt >=0)&&(elmt < m_segGeoms.size()),
                    "eid is out of range");

                //return m_segGeoms[elmt]->GetVid(vert);
                return m_segGeoms.find(elmt)->second->GetVid(vert);
            }

void Nektar::SpatialDomains::MeshGraph1D::ReadComposites

(

TiXmlDocument &

doc

)

We know we have it since we made it this far.

Look for elements in ELEMENT block.

All elements are of the form: "<? ID="#"> ... </?>", with ? being the element type.

Parse out the element components corresponding to type of element.

Keep looking for additional composite definitions.

Definition at line 170 of file MeshGraph1D.cpp.

References ASSERTL0, ErrorUtil::efatal, Nektar::SpatialDomains::MeshGraph::m_meshComposites, NEKERROR, and ResolveGeomRef().

Referenced by ReadGeometry().

        {
            TiXmlHandle docHandle(&doc);

            /// We know we have it since we made it this far.
            TiXmlElement* mesh = docHandle.FirstChildElement("NEKTAR").FirstChildElement("GEOMETRY").Element();
            TiXmlElement* field = NULL;

            ASSERTL0(mesh, "Unable to find GEOMETRY tag in file.");

            /// Look for elements in ELEMENT block.
            field = mesh->FirstChildElement("COMPOSITE");

            ASSERTL0(field, "Unable to find COMPOSITE tag in file.");

            TiXmlElement *node = field->FirstChildElement("C");

            // Sequential counter for the composite numbers.
            int nextCompositeNumber = -1;

            while (node)
            {
                /// All elements are of the form: "<? ID="#"> ... </?>", with
                /// ? being the element type.

                nextCompositeNumber++;

                int indx;
                int err = node->QueryIntAttribute("ID", &indx);
                ASSERTL0(err == TIXML_SUCCESS, "Unable to read attribute ID.");
                //ASSERTL0(indx == nextCompositeNumber, "Composite IDs must begin with zero and be sequential.");

                TiXmlNode* compositeChild = node->FirstChild();
                // This is primarily to skip comments that may be present.
                // Comments appear as nodes just like elements.
                // We are specifically looking for text in the body
                // of the definition.
                while(compositeChild && compositeChild->Type() != TiXmlNode::TINYXML_TEXT)
                {
                    compositeChild = compositeChild->NextSibling();
                }

                ASSERTL0(compositeChild, "Unable to read composite definition body.");
                std::string compositeStr = compositeChild->ToText()->ValueStr();

                /// Parse out the element components corresponding to type of element.

                std::istringstream compositeDataStrm(compositeStr.c_str());

                try
                {
                    bool first = true;
                    std::string prevCompositeElementStr;

                    while (!compositeDataStrm.fail())
                    {
                        std::string compositeElementStr;
                        compositeDataStrm >> compositeElementStr;

                        if (!compositeDataStrm.fail())
                        {
                            if (first)
                            {
                                first = false;

                                Composite curVector = MemoryManager<std::vector<GeometrySharedPtr> >::AllocateSharedPtr();
                                m_meshComposites[indx] = curVector;
                            }

                            if (compositeElementStr.length() > 0)
                            {
                                ResolveGeomRef(prevCompositeElementStr, compositeElementStr, m_meshComposites[indx]);
                            }
                            prevCompositeElementStr = compositeElementStr;
                        }
                    }
                }
                catch(...)
                {
                    NEKERROR(ErrorUtil::efatal,
                        (std::string("Unable to read COMPOSITE data for composite: ") + compositeStr).c_str());
                }

                /// Keep looking for additional composite definitions.
                node = node->NextSiblingElement("C");
            }

            ASSERTL0(nextCompositeNumber >= 0, "At least one composite must be specified.");
        }

void Nektar::SpatialDomains::MeshGraph1D::ReadElements

(

TiXmlDocument &

doc

)

We know we have it since we made it this far.

Look for elements in ELEMENT block.

All elements are of the form: "<S ID = n> ... </S>", with ? being the element type.

Parse out the element components corresponding to type of element. Read two vertex numbers

Keep looking for additional segments

Definition at line 97 of file MeshGraph1D.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, ErrorUtil::efatal, Nektar::SpatialDomains::MeshGraph::GetVertex(), Nektar::iterator, Nektar::SpatialDomains::MeshGraph::m_curvedEdges, Nektar::SpatialDomains::MeshGraph::m_segGeoms, Nektar::SpatialDomains::MeshGraph::m_spaceDimension, and NEKERROR.

Referenced by ReadGeometry().

        {
            /// We know we have it since we made it this far.
            TiXmlHandle docHandle(&doc);
            TiXmlElement* mesh = docHandle.FirstChildElement("NEKTAR").FirstChildElement("GEOMETRY").Element();
            TiXmlElement* field = NULL;

            /// Look for elements in ELEMENT block.
            field = mesh->FirstChildElement("ELEMENT");

            ASSERTL0(field, "Unable to find ELEMENT tag in file.");

            /// All elements are of the form: "<S ID = n> ... </S>", with
            /// ? being the element type.

            TiXmlElement *segment = field->FirstChildElement("S");
            CurveMap::iterator it;

            while (segment)
            {
                int indx;
                int err = segment->QueryIntAttribute("ID", &indx);
                ASSERTL0(err == TIXML_SUCCESS, "Unable to read element attribute ID.");

                TiXmlNode* elementChild = segment->FirstChild();
                while(elementChild && elementChild->Type() != TiXmlNode::TINYXML_TEXT)
                {
                    elementChild = elementChild->NextSibling();
                }

                ASSERTL0(elementChild, "Unable to read element description body.");
                std::string elementStr = elementChild->ToText()->ValueStr();

                /// Parse out the element components corresponding to type of element.
                /// Read two vertex numbers
                int vertex1, vertex2;
                std::istringstream elementDataStrm(elementStr.c_str());

                try
                {
                    elementDataStrm >> vertex1;
                    elementDataStrm >> vertex2;

                    ASSERTL0(!elementDataStrm.fail(), (std::string("Unable to read element data for SEGMENT: ") + elementStr).c_str());

                    PointGeomSharedPtr vertices[2] = {GetVertex(vertex1), GetVertex(vertex2)};
                    SegGeomSharedPtr seg;
                    it = m_curvedEdges.find(indx);

                    if (it == m_curvedEdges.end())
                    {
                        seg = MemoryManager<SegGeom>::AllocateSharedPtr(indx, m_spaceDimension, vertices);
                        seg->SetGlobalID(indx); // Set global mesh id
                    }
                    else
                    {
                        seg = MemoryManager<SegGeom>::AllocateSharedPtr(indx, m_spaceDimension, vertices, it->second);
                        seg->SetGlobalID(indx); //Set global mesh id
                    }
                    seg->SetGlobalID(indx);
                    m_segGeoms[indx] = seg;
                }
                catch(...)
                {
                    NEKERROR(ErrorUtil::efatal,
                        (std::string("Unable to read element data for segment: ") + elementStr).c_str());
                }

                /// Keep looking for additional segments
                segment = segment->NextSiblingElement("S");
            }
        }

void Nektar::SpatialDomains::MeshGraph1D::ReadGeometry ( const std::string &  infilename )

virtual

Read will read the meshgraph vertices given a filename.

Reimplemented from Nektar::SpatialDomains::MeshGraph.

Definition at line 63 of file MeshGraph1D.cpp.

References ASSERTL0.

Referenced by MeshGraph1D().

        {
            TiXmlDocument doc(infilename);

            bool loadOkay = doc.LoadFile();
            std::stringstream errstr;
            errstr << "Unable to load file: " << infilename << "\n";
            errstr << doc.ErrorDesc() << " (Line " << doc.ErrorRow()
                   << ", Column " << doc.ErrorCol() << ")";
            ASSERTL0(loadOkay, errstr.str());

            ReadGeometry(doc);
        }

void Nektar::SpatialDomains::MeshGraph1D::ReadGeometry ( TiXmlDocument &  doc )

virtual

Read will read the meshgraph vertices given a TiXmlDocument.

Look for all geometry related data in GEOMETRY block.

Error value returned by TinyXML.

Reimplemented from Nektar::SpatialDomains::MeshGraph.

Definition at line 78 of file MeshGraph1D.cpp.

References ASSERTL0, ReadComposites(), Nektar::SpatialDomains::MeshGraph::ReadCurves(), Nektar::SpatialDomains::MeshGraph::ReadDomain(), ReadElements(), and Nektar::SpatialDomains::MeshGraph::ReadGeometry().

        {
             // Read mesh first
            MeshGraph::ReadGeometry(doc);
            TiXmlHandle docHandle(&doc);

            TiXmlElement* mesh = NULL;

            /// Look for all geometry related data in GEOMETRY block.
            mesh = docHandle.FirstChildElement("NEKTAR").FirstChildElement("GEOMETRY").Element();

            ASSERTL0(mesh, "Unable to find GEOMETRY tag in file.");

            ReadCurves(doc);
            ReadElements(doc);
            ReadComposites(doc);
            ReadDomain(doc);
        }

void Nektar::SpatialDomains::MeshGraph1D::ResolveGeomRef	(	const std::string &	prevToken,
		const std::string &	token,
		Composite &	composite
	)

Definition at line 265 of file MeshGraph1D.cpp.

References ASSERTL0, ErrorUtil::efatal, ErrorUtil::ewarning, Nektar::ParseUtils::GenerateSeqVector(), Nektar::iterator, Nektar::SpatialDomains::MeshGraph::m_segGeoms, Nektar::SpatialDomains::MeshGraph::m_vertSet, and NEKERROR.

Referenced by ReadComposites().

        {
            try
            {
                std::istringstream tokenStream(token);
                std::istringstream prevTokenStream(prevToken);

                char type;
                char prevType;

                tokenStream >> type;

                std::string::size_type indxBeg = token.find_first_of('[') + 1;
                std::string::size_type indxEnd = token.find_last_of(']') - 1;

                ASSERTL0(indxBeg <= indxEnd, (std::string("Error reading index definition:") + token).c_str());

                std::string indxStr = token.substr(indxBeg, indxEnd - indxBeg + 1);

                typedef vector<unsigned int> SeqVectorType;
                SeqVectorType seqVector;

                if (!ParseUtils::GenerateSeqVector(indxStr.c_str(), seqVector))
                {
                    NEKERROR(ErrorUtil::efatal, (std::string("Ill-formed sequence definition: ") + indxStr).c_str());
                }

                prevTokenStream >> prevType;

                // All composites must be of the same dimension.
                bool validSequence = (prevToken.empty() ||         // No previous, then current is just fine.
                    (type == 'V' && prevType == 'V') ||
                    (type == 'S' && prevType == 'S'));

                ASSERTL0(validSequence, (std::string("Invalid combination of composite items: ")
                    + type + " and " + prevType + ".").c_str());

                switch(type)
                {
                case 'V':   // Vertex
                    for (SeqVectorType::iterator iter=seqVector.begin(); iter!=seqVector.end(); ++iter)
                    {
                        if (m_vertSet.find(*iter) == m_vertSet.end())
                        {
                            char errStr[16] = "";
                            ::sprintf(errStr, "%d", *iter);
                            NEKERROR(ErrorUtil::ewarning, (std::string("Unknown vertex index: ") + errStr).c_str());
                        }
                        else
                        {
                            composite->push_back(m_vertSet[*iter]);
                        }
                    }
                    break;

                case 'S':   // Segment
                    for (SeqVectorType::iterator iter=seqVector.begin(); iter!=seqVector.end(); ++iter)
                    {
                        if (m_segGeoms.find(*iter) == m_segGeoms.end())
                        {
                            char errStr[16] = "";
                            ::sprintf(errStr, "%d", *iter);
                            NEKERROR(ErrorUtil::ewarning, (std::string("Unknown segment index: ") + errStr).c_str());
                        }
                        else
                        {
                            composite->push_back(m_segGeoms[*iter]);
                        }
                    }
                    break;

                default:
                    NEKERROR(ErrorUtil::efatal, (std::string("Unrecognized composite token: ") + token).c_str());
                }
            }
            catch(...)
            {
                NEKERROR(ErrorUtil::efatal, (std::string("Problem processing composite token: ") + token).c_str());
            }

            return;
        }