Collaboration diagram for GIMLI::Mesh:

Public Types
typedef std::vector< RegionMarker >	RegionMarkerList

typedef RVector3	HoleMarker

typedef PosVector	HoleMarkerList

Public Member Functions
	Mesh (Index dim=2, bool isGeometry=false)

	Mesh (const std::string &filename, bool createNeighborInfos=true)

	Mesh (const Mesh &mesh)

Mesh &	operator= (const Mesh &mesh)

	~Mesh ()

void	clear ()

void	setStaticGeometry (bool stat)

bool	staticGeometry () const

void	setGeometry (bool b)

bool	isGeometry () const

void	geometryChanged ()

void	setDimension (uint dim)

uint	dimension () const

uint	dim () const

Node *	createNode (double x, double y, double z, int marker=0)

Node *	createNode (const Node &node)

Node *	createNode (const RVector3 &pos, int marker=0)

Node *	createSecondaryNode (const RVector3 &pos, double tol=-1)

Node *	createNodeWithCheck (const RVector3 &pos, double tol=1e-6, bool warn=false, bool edgeCheck=false)

Boundary *	createBoundary (std::vector< Node * > &nodes, int marker=0, bool check=true)

Boundary *	createBoundary (const IndexArray &nodes, int marker=0, bool check=true)

Boundary *	createBoundary (const Boundary &bound, bool check=true)

Boundary *	createBoundary (const Cell &cell, bool check=true)

Boundary *	createNodeBoundary (Node &n1, int marker=0, bool check=true)

Boundary *	createEdge (Node &n1, Node &n2, int marker=0, bool check=true)

Boundary *	createEdge3 (Node &n1, Node &n2, Node &n3, int marker=0, bool check=true)

Boundary *	createTriangleFace (Node &n1, Node &n2, Node &n3, int marker=0, bool check=true)

Boundary *	createQuadrangleFace (Node &n1, Node &n2, Node &n3, Node &n4, int marker=0, bool check=true)

Boundary *	createPolygonFace (std::vector< Node * > &nodes, int marker, bool check=true)

Cell *	createCell (int marker=0)

Cell *	createCell (std::vector< Node * > &nodes, int marker=0)

Cell *	createCell (const IndexArray &nodes, int marker=0)

Cell *	createCell (const Cell &cell)

Cell *	createTriangle (Node &n1, Node &n2, Node &n3, int marker=0)

Cell *	createQuadrangle (Node &n1, Node &n2, Node &n3, Node &n4, int marker=0)

Cell *	createTetrahedron (Node &n1, Node &n2, Node &n3, Node &n4, int marker=0)

Cell *	copyCell (const Cell &cell, double tol=1e-6)

Boundary *	copyBoundary (const Boundary &bound, double tol=1e-6, bool check=true)

void	create1DGrid (const RVector &x)

void	create2DGrid (const RVector &x, const RVector &y, int markerType=0, bool worldBoundaryMarker=false)

void	create3DGrid (const RVector &x, const RVector &y, const RVector &z, int markerType=0, bool worldBoundaryMarker=false)

void	createGrid (const RVector &x)

void	createGrid (const RVector &x, const RVector &y, int markerType=0, bool worldBoundaryMarker=false)

void	createGrid (const RVector &x, const RVector &y, const RVector &z, int markerType=0, bool worldBoundaryMarker=false)

void	createHull_ (const Mesh &mesh)

Mesh	createHull () const

Mesh	createH2 () const

Mesh	createP2 () const

void	createMeshByCells (const Mesh &mesh, const std::vector< Cell * > &cells)

void	createMeshByBoundaries (const Mesh &mesh, const std::vector< Boundary * > &bounds)

Mesh	createMeshByCellIdx (const IndexArray &idxList)

void	createMeshByCellIdx (const Mesh &mesh, const IndexArray &idxList)

void	createMeshByMarker (const Mesh &mesh, int from, int to=-1)

Mesh	createSubMesh (const std::vector< Cell * > &cells) const

Mesh	createSubMesh (const std::vector< Boundary * > &bounds) const

Mesh	createSubMesh (const std::vector< Node * > &nodes) const

void	showInfos ()
	Show some infos.

const std::vector< Node * > &	nodes () const

const std::vector< Cell * > &	cells () const

const std::vector< Boundary * > &	boundaries () const

std::vector< Node * >	nodes (const IndexArray &ids) const

std::vector< Node * >	nodes (const BVector &b) const

std::vector< Cell * >	cells (const IndexArray &ids) const

std::vector< Cell * >	cells (const BVector &b) const

std::vector< Boundary * >	boundaries (const IndexArray &ids) const

std::vector< Boundary * >	boundaries (const BVector &b) const

Index	nodeCount (bool withSecNodes=false) const

Node &	node (Index i) const

Node &	node (Index i)

Index	secondaryNodeCount () const

Node &	secondaryNode (Index id) const

Node &	secondaryNode (Index id)

IndexArray	nodeIDs (bool withSecNodes=false) const

void	setNodeIDs (IndexArray &ids)

Index	cellCount () const

Cell &	cell (Index i) const

Cell &	cell (Index i)

Index	boundaryCount () const

Boundary &	boundary (Index i) const

Boundary &	boundary (Index i)

PosVector	positions (bool withSecNodes=false) const

PosVector	positions (const IndexArray &idx) const

PosVector	cellCenters () const

PosVector	cellCenter () const

PosVector	boundaryCenters () const

RVector &	cellSizes () const

RVector &	boundarySizes () const

PosVector &	boundarySizedNormals () const

void	setBoundaryMarkers (const IndexArray &ids, int marker)

void	setBoundaryMarkers (const IVector &marker)

IVector	boundaryMarkers () const

IVector	nodeMarkers () const

IndexArray	findNodesIdxByMarker (int marker) const

std::vector< Boundary * >	findBoundaryByMarker (int marker) const

std::vector< Boundary * >	findBoundaryByMarker (int from, int to) const

Cell *	findCell (const RVector3 &pos, size_t &counter, bool extensive) const

Cell *	findCell (const RVector3 &pos, bool extensive=true) const

Index	findNearestNode (const RVector3 &pos)

std::vector< Cell * >	findCellByMarker (int from, int to=0) const

std::vector< Cell * >	findCellByAttribute (double from, double to=0.0) const

std::vector< Cell * >	findCellsAlongRay (const RVector3 &start, const RVector3 &dir, PosVector &pos) const

void	prolongateEmptyCellsValues (RVector &vals, double background=-9e99) const

void	recountNodes ()

void	sortNodes (const IndexArray &perm)

bool	neighborsKnown () const

void	cleanNeighborInfos ()

void	createNeighborInfos (bool force=false)

void	createNeighborInfosCell_ (Cell *c)

void	relax ()

void	smooth (bool nodeMoving=true, bool edgeSwapping=true, uint smoothFunction=1, uint smoothIteration=10)

Mesh &	scale (const RVector3 &s)

Mesh &	scale (const double &s)

Mesh &	translate (const RVector3 &t)

Mesh &	rotate (const RVector3 &r)

Mesh &	transform (const RMatrix &mat)

Mesh &	deform (const R3Vector &eps, double magnify=1.0)

Mesh &	deform (const RVector &eps, double magnify=1.0)

void	swapCoordinates (Index i, Index j)

int	save (const std::string &fileName, IOFormat format=Binary) const

int	saveAscii (const std::string &fileName) const

int	saveBinary (const std::string &fileName) const

void	load (const std::string &fileName, bool createNeighbors=true, IOFormat format=Binary)

void	loadAscii (const std::string &fileName)

void	importMod (const std::string &fileName)

void	importVTK (const std::string &fbody)

void	importVTU (const std::string &fbody)

void	importSTL (const std::string &fileName, bool isBinary=false, double snap=1e-3)

void	loadBinary (const std::string &fileName)

void	saveBinaryV2 (const std::string &fbody) const

void	loadBinaryV2 (const std::string &fbody)

int	exportSimple (const std::string &fbody, const RVector &data) const

int	exportMidCellValue (const std::string &fileName, const RVector &data1, const RVector &data2) const

int	exportMidCellValue (const std::string &fileName, const RVector &data1) const

void	exportVTK (const std::string &fbody, const std::map< std::string, RVector > &data, const PosVector &vec, bool writeCells=true) const

void	exportVTK (const std::string &fbody, const std::map< std::string, RVector > &data, bool writeCells=true) const

void	exportVTK (const std::string &fbody, bool writeCells=true) const

void	exportVTK (const std::string &fbody, const PosVector &vec, bool writeCells=true) const

void	exportVTK (const std::string &fbody, const RVector &arr) const

void	readVTKPoints_ (std::fstream &file, const std::vector< std::string > &row)

void	readVTKCells_ (std::fstream &file, const std::vector< std::string > &row)

void	readVTKScalars_ (std::fstream &file, const std::vector< std::string > &row)

void	readVTKPolygons_ (std::fstream &file, const std::vector< std::string > &row)

void	exportVTU (const std::string &filename, bool binary=false) const

void	exportBoundaryVTU (const std::string &fbody, bool binary=false) const

void	addVTUPiece_ (std::fstream &file, const Mesh &mesh, const std::map< std::string, RVector > &data) const

void	exportAsTetgenPolyFile (const std::string &filename)

void	fixBoundaryDirections ()

void	addData (const std::string &name, const CVector &data)

void	addData (const std::string &name, const RVector &data)

void	addData (const std::string &name, const PosVector &data)

RVector	data (const std::string &name) const

bool	haveData (const std::string &name) const

const std::map< std::string, RVector > &	dataMap () const

void	setDataMap (const std::map< std::string, RVector > m)

void	dataInfo () const

void	clearData ()

void	setCommentString (const std::string &commentString)

const std::string &	commentString () const

void	mapCellAttributes (const std::map< float, float > &aMap)

void	mapBoundaryMarker (const std::map< int, int > &aMap)

void	setCellAttributes (const RVector &attribute)

void	setCellAttributes (double attribute)

RVector	cellAttributes () const

void	setCellMarkers (const IndexArray &ids, int marker)

void	setCellMarkers (const IVector &marker)

void	setCellMarkers (const RVector &attribute)

IVector	cellMarkers () const

double	xMin () const

double	yMin () const

double	zMin () const

double	xMax () const

double	yMax () const

double	zMax () const

const BoundingBox	boundingBox () const

RSparseMapMatrix	interpolationMatrix (const PosVector &q)

void	interpolationMatrix (const PosVector &q, RSparseMapMatrix &I)

RSparseMapMatrix &	cellToBoundaryInterpolation () const

RVector	divergence (const PosVector &V) const

PosVector	boundaryDataToCellGradient (const RVector &boundaryData) const

PosVector	cellDataToBoundaryGradient (const RVector &cellData) const

PosVector	cellDataToBoundaryGradient (const RVector &cellData, const PosVector &cellGradient) const

void	addRegionMarker (const RVector3 &pos, int marker, double area=0)

void	addRegionMarker (const RegionMarker &reg)

const RegionMarkerList &	regionMarkers () const

RegionMarker *	regionMarker (SIndex i)

void	addHoleMarker (const RVector3 &pos)

const HoleMarkerList &	holeMarker () const

Index	hash () const

Protected Member Functions
void	copy_ (const Mesh &mesh)

void	findRange_ () const

Node *	createNodeGC_ (const RVector3 &pos, int marker)

Node *	createNode_ (const RVector3 &pos, int marker)

Node *	createSecondaryNode_ (const RVector3 &pos)

template<class B >
Boundary *	createBoundary_ (std::vector< Node * > &nodes, int marker, int id)

template<class B >
Boundary *	createBoundaryChecked_ (std::vector< Node * > &nodes, int marker, bool check=true)

template<class C >
Cell *	createCell_ (std::vector< Node * > &nodes, int marker, int id)

Node *	createRefinementNode_ (Node n0, Node n1, std::map< std::pair< Index, Index >, Node * > &nodeMatrix)

void	createRefined_ (const Mesh &mesh, bool p2, bool r2)

Cell *	findCellBySlopeSearch_ (const RVector3 &pos, Cell *start, size_t &count, bool tagging) const

void	fillKDTree_ () const

Protected Attributes
std::vector< Node * >	nodeVector_

std::vector< Node * >	secNodeVector_

std::vector< Boundary * >	boundaryVector_

std::vector< Cell * >	cellVector_

uint	dimension_

RVector3	minRange_

RVector3	maxRange_

bool	rangesKnown_

bool	neighborsKnown_

KDTreeWrapper *	tree_

bool	staticGeometry_

bool	isGeometry_

RVector	cellSizesCache_

RVector	boundarySizesCache_

PosVector	boundarySizedNormCache_

RSparseMapMatrix *	cellToBoundaryInterpolationCache_

bool	oldTet10NumberingStyle_

std::map< std::string, RVector >	dataMap_

std::string	commentString_

RegionMarkerList	regionMarker_

HoleMarkerList	holeMarker_

Constructor & Destructor Documentation

◆ Mesh() [1/3]

GIMLI::Mesh::Mesh	(	Index	dim = `2`,
		bool	isGeometry = `false`
	)

Default constructor, create empty mesh with dimension dim If this mesh is supposed to be a geometry definition, all created nodes will be checked for duplicates.

References GIMLI::load().

◆ Mesh() [2/3]

GIMLI::Mesh::Mesh	(	const std::string &	filename,
		bool	createNeighborInfos = `true`
	)

Constructor, read mesh from filename

◆ Mesh() [3/3]

GIMLI::Mesh::Mesh ( const Mesh & mesh )

Copy constructor.

◆ ~Mesh()

GIMLI::Mesh::~Mesh ( )

Default destructor.

Member Function Documentation

◆ addData() [1/2]

void GIMLI::Mesh::addData	(	const std::string &	name,
		const PosVector &	data
	)

inline

Add data to the mesh that will be saved with by using the binary mesh format v.2. or exported with the appropriate name in VTK format, if the size of data equals the amount of nodes, cells or boundaries.

◆ addData() [2/2]

void GIMLI::Mesh::addData	(	const std::string &	name,
		const RVector &	data
	)

Add data to the mesh that will be saved with by using the binary mesh format v.2. or exported with the appropriate name in VTK format, if the size of data equals the amount of nodes, cells or boundaries.

◆ addHoleMarker()

void GIMLI::Mesh::addHoleMarker ( const RVector3 & pos )

Add a hole marker for tetgen or triangle creation if the mesh is a PLC

References GIMLI::Vector< ValueType >::addVal(), and GIMLI::MeshEntity::ids().

◆ addRegionMarker()

void GIMLI::Mesh::addRegionMarker	(	const RVector3 &	pos,
		int	marker,
		double	area = `0`
	)

Add a region marker for tetgen or triangle creation if the mesh is a PLC, if area is < 0 a hole is added.

References GIMLI::MeshEntity::N(), GIMLI::Vector< ValueType >::resize(), and GIMLI::Shape::rst().

◆ addVTUPiece_()

void GIMLI::Mesh::addVTUPiece_	(	std::fstream &	file,
		const Mesh &	mesh,
		const std::map< std::string, RVector > &	data
	)		const

Internal function for exporting VTU

◆ boundaries() [1/3]

const std::vector< Boundary * >& GIMLI::Mesh::boundaries ( ) const

inline

Return const reference to all boundaries

Referenced by GIMLI::RegionManager::permuteParameterMarker().

◆ boundaries() [2/3]

std::vector< Boundary * > GIMLI::Mesh::boundaries ( const BVector & b ) const

Return a vector of boundary ptrs matching BVector b.

◆ boundaries() [3/3]

std::vector< Boundary * > GIMLI::Mesh::boundaries ( const IndexArray & ids ) const

Return vector of boundaries from index list

◆ boundaryCenters()

PosVector GIMLI::Mesh::boundaryCenters ( ) const

Return a vector of all center positions for all boundaries

◆ boundaryDataToCellGradient()

PosVector GIMLI::Mesh::boundaryDataToCellGradient ( const RVector & boundaryData ) const

Interpolate boundary based values to cell based gradients.

◆ boundaryMarkers()

IVector GIMLI::Mesh::boundaryMarkers ( ) const

Return a vector of all boundary marker

◆ boundarySizedNormals()

PosVector & GIMLI::Mesh::boundarySizedNormals ( ) const

Return the reference to the vector of scaled normal directions for each boundary. Cached for static geometry and will be build on first call. Not thread safe, perhaps not python GC safe. Return $\{A_i \vec{n}_i\} \forall i = [0..N_B]$ . Where $ A_i$ is the size and $\vec{n}_i$ the normal direction for the i-th boundary. If you want to use this, i.e. for the calculation of inside or outside flow through the boundary, you need to recognize the orientation of this boundary to the cell the flow goes into or comes from. For the left cell neighbor the normal direction should be always the outer normal.

◆ boundarySizes()

RVector & GIMLI::Mesh::boundarySizes ( ) const

Return the reference to a RVector of all boundary sizes. Cached for static geometry.

References GIMLI::Vector< ValueType >::resize(), and GIMLI::MeshEntity::size().

◆ cellAttributes()

RVector GIMLI::Mesh::cellAttributes ( ) const

Return a RVector of all cell attributes

◆ cellCenters()

PosVector GIMLI::Mesh::cellCenters ( ) const

Return a vector of all cell center positions

References GIMLI::Vector< ValueType >::resize().

◆ cellDataToBoundaryGradient() [1/2]

PosVector GIMLI::Mesh::cellDataToBoundaryGradient ( const RVector & cellData ) const

Interpolate cell based values to boundary based gradients.

◆ cellDataToBoundaryGradient() [2/2]

PosVector GIMLI::Mesh::cellDataToBoundaryGradient	(	const RVector &	cellData,
		const PosVector &	cellGradient
	)		const

Interpolate cell based values to boundary based gradients with a given cell Gradient.

◆ cellMarkers()

IVector GIMLI::Mesh::cellMarkers ( ) const

Return a vector of all cell marker

◆ cells() [1/2]

std::vector< Cell * > GIMLI::Mesh::cells ( const BVector & b ) const

Return a vector of cells ptrs matching BVector b.

◆ cells() [2/2]

std::vector< Cell * > GIMLI::Mesh::cells ( const IndexArray & ids ) const

Return vector of cells from index list

References GIMLI::find().

◆ cellSizes()

RVector & GIMLI::Mesh::cellSizes ( ) const

Return the reference to a RVector of all cell sizes. Cached for static geometry.

◆ cellToBoundaryInterpolation()

RSparseMapMatrix & GIMLI::Mesh::cellToBoundaryInterpolation ( ) const

Return the reference to the matrix for cell value to boundary value interpolation matrix.

References GIMLI::BaseEntity::id().

◆ cleanNeighborInfos()

void GIMLI::Mesh::cleanNeighborInfos ( )

Remove from each boundary the ptr to the corresponding left and right cell

◆ clear()

void GIMLI::Mesh::clear ( )

Clear all data, inclusive all caches.

Referenced by GIMLI::RegionManager::region(), and GIMLI::TriangleWrapper::transformTriangleToMesh_().

◆ clearData()

void GIMLI::Mesh::clearData ( )

Empty the data map.

◆ commentString()

const std::string& GIMLI::Mesh::commentString ( ) const

inline

Return comment for VTK Ascii export headline.

◆ copyBoundary()

Boundary * GIMLI::Mesh::copyBoundary	(	const Boundary &	bound,
		double	tol = `1e-6`,
		bool	check = `true`
	)

Create a boundary as a copy of a boundary from an alternative mesh. Each node of the new cell will be created with duplication check and reused if there is already a node withing the tolerance distance tol. tol=-1 disables this duplication check.

◆ copyCell()

Cell * GIMLI::Mesh::copyCell	(	const Cell &	cell,
		double	tol = `1e-6`
	)

Create a cell as a copy of a cell from an alternative mesh. Each node of the new cell will be created with duplication check and reused if there is already a node withing the tolerance distance tol. tol=-1 disables this duplication check.

◆ create2DGrid()

void GIMLI::Mesh::create2DGrid	(	const RVector &	x,
		const RVector &	y,
		int	markerType = `0`,
		bool	worldBoundaryMarker = `false`
	)

Default boundary marker are -x[1], +x[2], +z[3], -z[4]. If worldBoundaryMarker is set it becomes +z[-1], else[-2].

References GIMLI::x(), and GIMLI::y().

◆ create3DGrid()

void GIMLI::Mesh::create3DGrid	(	const RVector &	x,
		const RVector &	y,
		const RVector &	z,
		int	markerType = `0`,
		bool	worldBoundaryMarker = `false`
	)

Default boundary marker are -x[1], +x[2], +z[3], -z[4], -y[5], +z[6]. If worldBoundaryMarker is set it becomes +z[-1], else[-2]. You can exportBoundaryVTU and take a look with Paraview.

References GIMLI::x(), GIMLI::y(), and GIMLI::z().

◆ createBoundary()

Boundary * GIMLI::Mesh::createBoundary	(	const IndexArray &	nodes,
		int	marker = `0`,
		bool	check = `true`
	)

Create a boundary from the given node indices

◆ createCell() [1/2]

Cell * GIMLI::Mesh::createCell	(	const IndexArray &	nodes,
		int	marker = `0`
	)

Create a cell from the given node indices

◆ createCell() [2/2]

Cell * GIMLI::Mesh::createCell ( int marker = 0 )

Create empty cell without a node or a shape.

◆ createGrid() [1/3]

void GIMLI::Mesh::createGrid ( const RVector & x )

inline

Create one dimensional grid. Boundary on the domain border will get marker: 1,2 for: left, right.

Referenced by GIMLI::createGrid().

◆ createGrid() [2/3]

void GIMLI::Mesh::createGrid	(	const RVector &	x,
		const RVector &	y,
		const RVector &	z,
		int	markerType = `0`,
		bool	worldBoundaryMarker = `false`
	)

inline

Create three dimensional grid. Boundaries on the domain border will get the markers: 1,2,3,4,5,6 for: left, right, bottom, top, front, back

◆ createGrid() [3/3]

void GIMLI::Mesh::createGrid	(	const RVector &	x,
		const RVector &	y,
		int	markerType = `0`,
		bool	worldBoundaryMarker = `false`
	)

inline

Create two dimensional grid. Boundaries on the domain border will get the markers: 1,2,3,4 for: left, right, bottom, top.

◆ createH2()

Mesh GIMLI::Mesh::createH2 ( ) const

Create and copy global H2 mesh of this mesh.

◆ createHull()

Mesh GIMLI::Mesh::createHull ( ) const

Create 3D mesh with 3D boundary elements from this 2D mesh cells. Increase mesh dimension. Mesh should contain 2D cells.

◆ createMeshByBoundaries()

void GIMLI::Mesh::createMeshByBoundaries	(	const Mesh &	mesh,
		const std::vector< Boundary * > &	bounds
	)

Create a partly mesh without cells from mesh, based on a vector of ptrs to boundaries

Create new boundaries

◆ createMeshByCellIdx() [1/2]

Mesh GIMLI::Mesh::createMeshByCellIdx ( const IndexArray & idxList )

Create a new mesh that is a part from this mesh, based on cell-ids

◆ createMeshByCellIdx() [2/2]

void GIMLI::Mesh::createMeshByCellIdx	(	const Mesh &	mesh,
		const IndexArray &	idxList
	)

Create a partly mesh from mesh, based on cell-ids

◆ createMeshByCells()

void GIMLI::Mesh::createMeshByCells	(	const Mesh &	mesh,
		const std::vector< Cell * > &	cells
	)

Create a partly mesh without cells from mesh, based on a vector of ptrs to boundaries

Create new cells

copy all boundary with marker != 0

check that all nodes have a common cell

Copy data if available

Create all remaining boundaries

◆ createMeshByMarker()

void GIMLI::Mesh::createMeshByMarker	(	const Mesh &	mesh,
		int	from,
		int	to = `-1`
	)

Create a partly mesh from mesh, based on meshs attributes. For a single attribute set to to 0, for unlimited set to to -1

◆ createNeighborInfos()

void GIMLI::Mesh::createNeighborInfos ( bool force = false )

Search and set to each boundary the corresponding left and right cell.

References GIMLI::Boundary::leftCell(), GIMLI::Boundary::normShowsOutside(), and GIMLI::Boundary::swapNorm().

◆ createNeighborInfosCell_()

void GIMLI::Mesh::createNeighborInfosCell_ ( Cell * c )

Create and store boundaries and neighboring information for this cell.

◆ createNodeGC_()

Node * GIMLI::Mesh::createNodeGC_	(	const RVector3 &	pos,
		int	marker
	)

protected

Ensure is geometry check

◆ createNodeWithCheck()

Node * GIMLI::Mesh::createNodeWithCheck	(	const RVector3 &	pos,
		double	tol = `1e-6`,
		bool	warn = `false`,
		bool	edgeCheck = `false`
	)

Create new Node with duplication checks. Returns the already existing node when its within a tolerance distance to pos. If edgeCheck is set, any 2d (p1) boundary edges will be checked for any intersection with pos and splitted if necessary.

◆ createP2()

Mesh GIMLI::Mesh::createP2 ( ) const

Create and copy global P2 mesh of this mesh.

References GIMLI::BaseEntity::id().

◆ createRefined_()

void GIMLI::Mesh::createRefined_	(	const Mesh &	mesh,
		bool	p2,
		bool	r2
	)

protected

Copy data if available

copy original marker into the new mesh

◆ createSecondaryNode()

Node * GIMLI::Mesh::createSecondaryNode	(	const RVector3 &	pos,
		double	tol = `-1`
	)

Create a secondary node, which is stored in an additional list for additional use. If tolerance tol set to a value > 0, then it will be checked if there is already a node at this position and return a ptr to the existing node instead of creating a new.

◆ createSubMesh() [1/3]

Mesh GIMLI::Mesh::createSubMesh ( const std::vector< Boundary * > & bounds ) const

Syntactic sugar to extract a part of the mesh based on boundaries.

◆ createSubMesh() [2/3]

Mesh GIMLI::Mesh::createSubMesh ( const std::vector< Cell * > & cells ) const

Syntactic sugar to extract a part of the mesh based on cells.

◆ createSubMesh() [3/3]

Mesh GIMLI::Mesh::createSubMesh ( const std::vector< Node * > & nodes ) const

Syntactic sugar to extract a part of the mesh based on nodes with associated cells and boundaries.

◆ data()

RVector GIMLI::Mesh::data ( const std::string & name ) const

Return the data with a given name. If there is no such data an exception is thrown.

◆ dataInfo()

void GIMLI::Mesh::dataInfo ( ) const

Print data map info.

◆ dataMap()

const std::map< std::string, RVector >& GIMLI::Mesh::dataMap ( ) const

inline

Return the full data map read only.

◆ deform() [1/2]

Mesh & GIMLI::Mesh::deform	(	const R3Vector &	eps,
		double	magnify = `1.0`
	)

Apply deformation epsilon to all nodes. Optional magnify the deformation. Returns a reference to the mesh (no copy).

◆ deform() [2/2]

Mesh & GIMLI::Mesh::deform	(	const RVector &	eps,
		double	magnify = `1.0`
	)

Apply deformation epsilon (with squeezed array) to all nodes. Optional magnify the deformation. Returns a reference to the mesh (no copy).

◆ dim()

uint GIMLI::Mesh::dim ( ) const

inline

Shortcut for dimension.

◆ dimension()

uint GIMLI::Mesh::dimension ( ) const

inline

Return the dimension of this mesh.

◆ divergence()

RVector GIMLI::Mesh::divergence ( const PosVector & V ) const

Return the divergence for each cell of a given vector field for each boundary. The divergence is calculated by simple 1 point boundary integration over each cell. $d(cell) = \sum_boundaries V(boundary center) \cdot n(boundary)$ Higher order integration needs to be implemented. Contact the author if you need this.

◆ exportBoundaryVTU()

void GIMLI::Mesh::exportBoundaryVTU	(	const std::string &	fbody,
		bool	binary = `false`
	)		const

Export the boundary of this mesh in vtu format: Visualization Toolkit Unstructured Points Data (http://www.vtk.org) Set Binary to true writes the datacontent in binary format. The file suffix .vtu will be added or substituted if .vtu or .vtk is found.

◆ exportMidCellValue()

int GIMLI::Mesh::exportMidCellValue	(	const std::string &	fileName,
		const RVector &	data1,
		const RVector &	data2
	)		const

Very simple export filter. Write to file fileName: x_0 y_0 [z_0] data1_0 [data2]_0
x_n y_n [z_n] data1_n [data2]_n
with n = number of cells, and x y [z] == cell center

References GIMLI::BaseEntity::id().

◆ exportVTK() [1/3]

void GIMLI::Mesh::exportVTK	(	const std::string &	fbody,
		bool	writeCells = `true`
	)		const

Export mesh and whole data map

◆ exportVTK() [2/3]

void GIMLI::Mesh::exportVTK	(	const std::string &	fbody,
		const PosVector &	vec,
		bool	writeCells = `true`
	)		const

Export mesh and whole data map and vector data in vec

◆ exportVTK() [3/3]

void GIMLI::Mesh::exportVTK	(	const std::string &	fbody,
		const RVector &	arr
	)		const

Export mesh with one additional array that will called 'arr'

◆ exportVTU()

void GIMLI::Mesh::exportVTU	(	const std::string &	filename,
		bool	binary = `false`
	)		const

Export the mesh in filename using vtu format: Visualization Toolkit Unstructured Points Data (http://www.vtk.org) Set binary to true writes the data content in binary format. The file suffix .vtu will be added or substituted if .vtu or .vtk is found. data, cell.markers and cell.attribute will be exported as data.

◆ findBoundaryByMarker() [1/2]

std::vector< Boundary * > GIMLI::Mesh::findBoundaryByMarker	(	int	from,
		int	to
	)		const

Return a vector of boundary ptrs with the boundary marker between [from and to).
for to equal open end set to = MAX_INT

◆ findBoundaryByMarker() [2/2]

std::vector< Boundary * > GIMLI::Mesh::findBoundaryByMarker ( int marker ) const

Return an index list of all nodes that match the marker *‍/ std::list < Index > findListNodesIdxByMarker(int marker) const;

/*! Return a vector of boundary ptrs with the boundary marker equal marker.

◆ findCell() [1/2]

Cell* GIMLI::Mesh::findCell	(	const RVector3 &	pos,
		bool	extensive = `true`
	)		const

inline

Shortcut for findCell(const RVector3 & pos, size_t & counter, bool extensive)

◆ findCell() [2/2]

Cell * GIMLI::Mesh::findCell	(	const RVector3 &	pos,
		size_t &	counter,
		bool	extensive
	)		const

Return ptr to the cell that match position pos, counter holds amount of touch tests. Searching is done first by nearest-neighbor-kd-tree search, followed by slope-search if extensive is set. Return NULL if no cell can be found.

** *sigh, no luck with simple kd-tree search, try more expensive full slope search

◆ findCellByAttribute()

std::vector< Cell * > GIMLI::Mesh::findCellByAttribute	(	double	from,
		double	to = `0.0`
	)		const

Return vector of cell ptrs with attribute match the range [from .. to).
For single attribute match to is set to 0.0, for open end set to = -1.0

◆ findCellByMarker()

std::vector< Cell * > GIMLI::Mesh::findCellByMarker	(	int	from,
		int	to = `0`
	)		const

Return vector of cell ptrs with marker match the range [from .. to).
For single marker match to is set to 0, for open end set to = -1

Referenced by GIMLI::Region::setFixValue().

◆ findCellsAlongRay()

std::vector< Cell * > GIMLI::Mesh::findCellsAlongRay	(	const RVector3 &	start,
		const RVector3 &	dir,
		PosVector &	pos
	)		const

Return vector of cells that are intersected with a given ray from start to end. Intersecting positions, i.e., the travel path are stored in pos. Note this will not yet check if the ray lies completely along a boundary. This will probably fail and need to be implemented.

References GIMLI::Cell::boundary(), and GIMLI::Shape::intersectRay().

◆ findNearestNode()

Index GIMLI::Mesh::findNearestNode ( const RVector3 & pos )

Return the index to the node of this mesh with the smallest distance to pos.

Referenced by GIMLI::TravelTimeDijkstraModelling::updateMeshDependency_().

◆ findNodesIdxByMarker()

IndexArray GIMLI::Mesh::findNodesIdxByMarker ( int marker ) const

Return an index vector of all nodes that match the marker

◆ fixBoundaryDirections()

void GIMLI::Mesh::fixBoundaryDirections ( )

All outer boundaries, i.e., all boundaries with only one cell (the left) need to be sorted that the norm vector shows outside the mesh.

◆ geometryChanged()

void GIMLI::Mesh::geometryChanged ( )

Some parts of the geometry changed so the mesh is supposed to be dynamic.

◆ haveData()

bool GIMLI::Mesh::haveData ( const std::string & name ) const

inline

Return True if date with such a name exists.

◆ holeMarker()

const HoleMarkerList& GIMLI::Mesh::holeMarker ( ) const

inline

Return read only reference for all defined hole regions.

Referenced by GIMLI::TriangleWrapper::transformMeshToTriangle_().

◆ importSTL()

void GIMLI::Mesh::importSTL	(	const std::string &	fileName,
		bool	isBinary = `false`,
		double	snap = `1e-3`
	)

Import Ascii STL as 3D mesh and save triangles as Boundary Faces. Node positions can be snap to a tolerance.

◆ interpolationMatrix() [1/2]

RSparseMapMatrix GIMLI::Mesh::interpolationMatrix ( const PosVector & q )

Return the interpolation matrix I from all node positions to the query points q. I is a (len(q) x nodeCount()) SparseMapMatrix. To perform the interpolation just calculate the matrix vector product. uInterpolated = I.mult(uPerNode) or uInterpolated = I * uPerNode

◆ interpolationMatrix() [2/2]

void GIMLI::Mesh::interpolationMatrix	(	const PosVector &	q,
		RSparseMapMatrix &	I
	)

Inplace version of interpolationMatrix(const PosVector & q)

◆ isGeometry()

bool GIMLI::Mesh::isGeometry ( ) const

inline

Return if the mesh is a geometry definition.

◆ load()

void GIMLI::Mesh::load	(	const std::string &	fileName,
		bool	createNeighbors = `true`,
		IOFormat	format = `Binary`
	)

Load Mesh from file and try to import fileformat regarding file suffix. If createNeighborInfos is set, the mesh is checked for consistency and missing boundaries will be created.

◆ loadBinary()

void GIMLI::Mesh::loadBinary ( const std::string & fileName )

Be carefull with interchanging binary meshs between 32-64bit architecture. Atm we save fixed int for counter and idx. We have to replace and test it with uint32 or uint16

◆ loadBinaryV2()

void GIMLI::Mesh::loadBinaryV2 ( const std::string & fbody )

Load mesh in binary format v.2.0. should be possible to interchange on all little endian platforms. Format see saveBinaryV2. If something goes wrong while reading, an exception is thrown.

References setGeometry().

◆ mapBoundaryMarker()

void GIMLI::Mesh::mapBoundaryMarker ( const std::map< int, int > & aMap )

Change all boundary marker that match bMap.first to bMap.second.

◆ neighborsKnown()

bool GIMLI::Mesh::neighborsKnown ( ) const

inline

Return true if createNeighborInfos is called once

◆ nodeIDs()

IndexArray GIMLI::Mesh::nodeIDs ( bool withSecNodes = false ) const

Return ids for all nodes. Optionally including for secondary ndoes.

◆ nodeMarkers()

IVector GIMLI::Mesh::nodeMarkers ( ) const

Return a vector of all node marker

◆ nodes() [1/2]

std::vector< Node * > GIMLI::Mesh::nodes ( const BVector & b ) const

Return a vector of nodes ptrs matching BVector b.

◆ nodes() [2/2]

std::vector< Node * > GIMLI::Mesh::nodes ( const IndexArray & ids ) const

Return vector of node from index list

References GIMLI::find().

◆ operator=()

Mesh & GIMLI::Mesh::operator= ( const Mesh & mesh )

Copy assignment operator.

◆ positions() [1/2]

PosVector GIMLI::Mesh::positions ( bool withSecNodes = false ) const

Return a vector of all node positions

◆ positions() [2/2]

PosVector GIMLI::Mesh::positions ( const IndexArray & idx ) const

Return a vector of node positions for an index vector

◆ prolongateEmptyCellsValues()

void GIMLI::Mesh::prolongateEmptyCellsValues	(	RVector &	vals,
		double	background = `-9e99`
	)		const

Prolongate the empty (lower than TOLERANCE.) cell values in vals from its neighboring cells. This function is called recursively until all zero-attribute-values in vals are filled with an attribute greater than Zero. RVector vals need to be of size cellCount(). If Background is unequal -9e99 all empty values will be set to background.

◆ regionMarker()

RegionMarker * GIMLI::Mesh::regionMarker ( SIndex i )

Return the pointer to region marker with the marker is i or throws an exception of there is no such marker.

◆ rotate()

Mesh & GIMLI::Mesh::rotate ( const RVector3 & r )

Rotates the mesh the with RVector3 r, r in radian. If you want to rotate in degree, use degToRad(const RVector3 & deg). Returns a reference to the mesh (no copy).

◆ saveBinary()

int GIMLI::Mesh::saveBinary ( const std::string & fileName ) const

Be carefull with interchanging binary meshs between 32-64bit architecture. Atm we save fixed int for counter and idx. We have to replace and test it with uint32 or uint16

write vertex dummy-infos;

write cell dummy-infos

◆ saveBinaryV2()

void GIMLI::Mesh::saveBinaryV2 ( const std::string & fbody ) const

Save mesh in binary format v.2.0. should be possible to interchange on all little endian platforms. Contains all export data, marker an attribute. If something goes wrong while writing, an exception is thrown. sizes uint8 (1 byte), uint16 (2 byte), uint32 (4 byte), uint64 (8 byte) Format:

◆ scale() [1/2]

Mesh& GIMLI::Mesh::scale ( const double & s )

inline

Scales the mesh with s. Shortcut for scale(RVector3(s,s,s)) Returns a reference to the mesh (no copy).

◆ scale() [2/2]

Mesh & GIMLI::Mesh::scale ( const RVector3 & s )

Scales the mesh with RVector3 s. Returns a reference to the mesh (no copy).

◆ setBoundaryMarkers() [1/2]

void GIMLI::Mesh::setBoundaryMarkers	(	const IndexArray &	ids,
		int	marker
	)

Set the marker to all boundaries in index array.

◆ setBoundaryMarkers() [2/2]

void GIMLI::Mesh::setBoundaryMarkers ( const IVector & marker )

Set all cell marker the values in attribute.

◆ setCellAttributes() [1/2]

void GIMLI::Mesh::setCellAttributes ( const RVector & attribute )

Set all cell attributes to the values in vector attribute.

◆ setCellAttributes() [2/2]

void GIMLI::Mesh::setCellAttributes ( double attribute )

Set all cell attributes to the scalar value: attribute

◆ setCellMarkers() [1/3]

void GIMLI::Mesh::setCellMarkers	(	const IndexArray &	ids,
		int	marker
	)

Set the cell marker of all indices in ids to marker.

Referenced by GIMLI::createGrid().

◆ setCellMarkers() [2/3]

void GIMLI::Mesh::setCellMarkers ( const IVector & marker )

Set all cell marker the values in attribute.

◆ setCellMarkers() [3/3]

void GIMLI::Mesh::setCellMarkers ( const RVector & attribute )

Set all cell marker the values in attribute (casting to int)

◆ setCommentString()

void GIMLI::Mesh::setCommentString ( const std::string & commentString )

inline

Set the comment for VTK Ascii export headline.

◆ setDataMap()

void GIMLI::Mesh::setDataMap ( const std::map< std::string, RVector > m )

inline

Replace the datamap by m

◆ setDimension()

void GIMLI::Mesh::setDimension ( uint dim )

inline

Set the dimension of the mesh. [Default = 2]

◆ setGeometry()

void GIMLI::Mesh::setGeometry ( bool b )

Mesh is marked as geometry definition or PLC so createNode will allways with check.

Referenced by loadBinaryV2().

◆ setNodeIDs()

void GIMLI::Mesh::setNodeIDs ( IndexArray & ids )

Set all node ids. Size of IndexArray indicated if it should be set the secondary nodes too.

◆ setStaticGeometry()

void GIMLI::Mesh::setStaticGeometry ( bool stat )

If the mesh is static in geometry and shape some useful information are cached. (cell sizes, boundary sizes, ...) For dynamic meshes, i.e., node positions can be moved, you have to set staticGeometry to false to avoid any caching.

◆ smooth()

void GIMLI::Mesh::smooth	(	bool	nodeMoving = `true`,
		bool	edgeSwapping = `true`,
		uint	smoothFunction = `1`,
		uint	smoothIteration = `10`
	)

Smooth the mesh via moving all free nodes into the average of all neighboring nodes. Repeat this smoothIteration times. There is currently only this smoothFunction. EdgeSwapping is deactivated.

◆ staticGeometry()

bool GIMLI::Mesh::staticGeometry ( ) const

inline

Return true if this mesh have static geometry. [Default=True]

◆ swapCoordinates()

void GIMLI::Mesh::swapCoordinates	(	Index	i,
		Index	j
	)

Swap coordinate i with j for i and j lower then dimension of the mesh. Returns a reference to the mesh (no copy).

◆ transform()

Mesh & GIMLI::Mesh::transform ( const RMatrix & mat )

Apply a 4x4 transformation matrix to the whole mesh. Returns a reference to the mesh (no copy).

◆ translate()

Mesh & GIMLI::Mesh::translate ( const RVector3 & t )

Translates the mesh with RVector3 t. Returns a reference to the mesh (no copy).

Member Data Documentation

◆ staticGeometry_

bool GIMLI::Mesh::staticGeometry_

protected

A static geometry mesh caches geometry informations.

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

◆ Mesh() [1/3]

◆ Mesh() [2/3]

◆ Mesh() [3/3]

◆ ~Mesh()

Member Function Documentation

◆ addData() [1/2]

◆ addData() [2/2]

◆ addHoleMarker()

◆ addRegionMarker()

◆ addVTUPiece_()

◆ boundaries() [1/3]

◆ boundaries() [2/3]

◆ boundaries() [3/3]

◆ boundaryCenters()

◆ boundaryDataToCellGradient()

◆ boundaryMarkers()

◆ boundarySizedNormals()

◆ boundarySizes()

◆ cellAttributes()

◆ cellCenters()

◆ cellDataToBoundaryGradient() [1/2]

◆ cellDataToBoundaryGradient() [2/2]

◆ cellMarkers()

◆ cells() [1/2]

◆ cells() [2/2]

◆ cellSizes()

◆ cellToBoundaryInterpolation()

◆ cleanNeighborInfos()

◆ clear()

◆ clearData()

◆ commentString()

◆ copyBoundary()

◆ copyCell()

◆ create2DGrid()

◆ create3DGrid()

◆ createBoundary()

◆ createCell() [1/2]

◆ createCell() [2/2]

◆ createGrid() [1/3]

◆ createGrid() [2/3]

◆ createGrid() [3/3]

◆ createH2()

◆ createHull()

◆ createMeshByBoundaries()

◆ createMeshByCellIdx() [1/2]

◆ createMeshByCellIdx() [2/2]

◆ createMeshByCells()

◆ createMeshByMarker()

◆ createNeighborInfos()

◆ createNeighborInfosCell_()

◆ createNodeGC_()

◆ createNodeWithCheck()

◆ createP2()

◆ createRefined_()

◆ createSecondaryNode()

◆ createSubMesh() [1/3]

◆ createSubMesh() [2/3]

◆ createSubMesh() [3/3]

◆ data()

◆ dataInfo()

◆ dataMap()

◆ deform() [1/2]

◆ deform() [2/2]

◆ dim()

◆ dimension()

◆ divergence()

◆ exportBoundaryVTU()

◆ exportMidCellValue()

◆ exportVTK() [1/3]

◆ exportVTK() [2/3]

◆ exportVTK() [3/3]

◆ exportVTU()

◆ findBoundaryByMarker() [1/2]

◆ findBoundaryByMarker() [2/2]

◆ findCell() [1/2]