#include <Mesh.h>

Inheritance diagram for dolfin::Mesh:

[legend]

Collaboration diagram for dolfin::Mesh:

Public Member Functions
	Mesh ()
	Create empty mesh.

	Mesh (MPI_Comm comm)
	Create empty mesh.

	Mesh (const Mesh &mesh)

	Mesh (std::string filename)

	Mesh (MPI_Comm comm, std::string filename)

	Mesh (MPI_Comm comm, LocalMeshData &local_mesh_data)

	~Mesh ()
	Destructor.

const Mesh &	operator= (const Mesh &mesh)

std::size_t	num_vertices () const

std::size_t	num_edges () const

std::size_t	num_faces () const

std::size_t	num_facets () const

std::size_t	num_cells () const

std::size_t	num_entities (std::size_t d) const

std::vector< double > &	coordinates ()

const std::vector< double > &	coordinates () const

const std::vector< unsigned int > &	cells () const

std::size_t	num_entities_global (std::size_t dim) const

MeshTopology &	topology ()

const MeshTopology &	topology () const

MeshGeometry &	geometry ()

const MeshGeometry &	geometry () const

MeshDomains &	domains ()

const MeshDomains &	domains () const

std::shared_ptr< BoundingBoxTree >	bounding_box_tree () const

MeshData &	data ()

const MeshData &	data () const

CellType &	type ()

const CellType &	type () const
	Get mesh cell type (const version).

std::size_t	init (std::size_t dim) const

void	init (std::size_t d0, std::size_t d1) const

void	init () const
	Compute all entities and connectivity.

void	init_global (std::size_t dim) const
	Compute global indices for entity dimension dim.

void	clean ()

void	order ()

bool	ordered () const

Mesh	renumber_by_color () const

void	scale (double factor)

void	translate (const Point &point)

void	rotate (double angle, std::size_t axis=2)

void	rotate (double angle, std::size_t axis, const Point &point)

void	smooth (std::size_t num_iterations=1)

void	smooth_boundary (std::size_t num_iterations=1, bool harmonic_smoothing=true)

void	snap_boundary (const SubDomain &sub_domain, bool harmonic_smoothing=true)

const std::vector< std::size_t > &	color (std::string coloring_type) const

const std::vector< std::size_t > &	color (std::vector< std::size_t > coloring_type) const

double	hmin () const

double	hmax () const

double	rmin () const

double	rmax () const

std::size_t	hash () const

std::string	str (bool verbose) const

const std::vector< int > &	cell_orientations () const

void	init_cell_orientations (const Expression &global_normal)

MPI_Comm	mpi_comm () const

std::string	ghost_mode () const

Public Member Functions inherited from dolfin::Variable
	Variable ()
	Create unnamed variable.

	Variable (const std::string name, const std::string label)
	Create variable with given name and label.

	Variable (const Variable &variable)
	Copy constructor.

virtual	~Variable ()
	Destructor.

const Variable &	operator= (const Variable &variable)
	Assignment operator.

void	rename (const std::string name, const std::string label)
	Rename variable.

std::string	name () const
	Return name.

std::string	label () const
	Return label (description)

std::size_t	id () const

Public Member Functions inherited from dolfin::Hierarchical< Mesh >
	Hierarchical (Mesh &self)
	Constructor.

virtual	~Hierarchical ()
	Destructor.

std::size_t	depth () const

bool	has_parent () const

bool	has_child () const

Mesh &	parent ()

const Mesh &	parent () const
	Return parent in hierarchy (const version).

std::shared_ptr< Mesh >	parent_shared_ptr ()

std::shared_ptr< const Mesh >	parent_shared_ptr () const
	Return shared pointer to parent (const version).

Mesh &	child ()

const Mesh &	child () const
	Return child in hierarchy (const version).

std::shared_ptr< Mesh >	child_shared_ptr ()

std::shared_ptr< const Mesh >	child_shared_ptr () const
	Return shared pointer to child (const version).

Mesh &	root_node ()

const Mesh &	root_node () const
	Return root node object in hierarchy (const version).

std::shared_ptr< Mesh >	root_node_shared_ptr ()

std::shared_ptr< const Mesh >	root_node_shared_ptr () const
	Return shared pointer to root node object in hierarchy (const version).

Mesh &	leaf_node ()

const Mesh &	leaf_node () const
	Return leaf node object in hierarchy (const version).

std::shared_ptr< Mesh >	leaf_node_shared_ptr ()

std::shared_ptr< const Mesh >	leaf_node_shared_ptr () const
	Return shared pointer to leaf node object in hierarchy (const version).

void	set_parent (std::shared_ptr< Mesh > parent)
	Set parent.

void	clear_child ()
	Clear child.

void	set_child (std::shared_ptr< Mesh > child)
	Set child.

const Hierarchical &	operator= (const Hierarchical &hierarchical)
	Assignment operator.

void	_debug () const
	Function useful for debugging the hierarchy.

Friends
class	MeshEditor

class	TopologyComputation

class	MeshPartitioning

Mesh	create_mesh (Function &coordinates)

Additional Inherited Members
Public Attributes inherited from dolfin::Variable
Parameters	parameters
	Parameters.

Detailed Description

A Mesh consists of a set of connected and numbered mesh entities.

Both the representation and the interface are dimension-independent, but a concrete interface is also provided for standard named mesh entities:

Entity	Dimension	Codimension
Vertex	0
Edge	1
Face	2
Facet		1
Cell		0

When working with mesh iterators, all entities and connectivity are precomputed automatically the first time an iterator is created over any given topological dimension or connectivity.

Note that for efficiency, only entities of dimension zero (vertices) and entities of the maximal dimension (cells) exist when creating a Mesh. Other entities must be explicitly created by calling init(). For example, all edges in a mesh may be created by a call to mesh.init(1). Similarly, connectivities such as all edges connected to a given vertex must also be explicitly created (in this case by a call to mesh.init(0, 1)).

Constructor & Destructor Documentation

◆ Mesh() [1/4]

Mesh::Mesh ( const Mesh & mesh )

Copy constructor.

Parameters

mesh	(Mesh) Object to be copied.

◆ Mesh() [2/4]

Mesh::Mesh ( std::string filename )

explicit

Create mesh from data file.

Parameters

filename (std::string) Name of file to load.

◆ Mesh() [3/4]

Mesh::Mesh	(	MPI_Comm	comm,
		std::string	filename
	)

Create mesh from data file.

Parameters

comm	(MPI_Comm) The MPI communicator
filename	(std::string) Name of file to load.

◆ Mesh() [4/4]

Mesh::Mesh	(	MPI_Comm	comm,
		LocalMeshData &	local_mesh_data
	)

Create a distributed mesh from local (per process) data.

Parameters

comm	(MPI_Comm) MPI communicator for the mesh.
local_mesh_data	(LocalMeshData) Data from which to build the mesh.

Member Function Documentation

◆ bounding_box_tree()

std::shared_ptr< BoundingBoxTree > Mesh::bounding_box_tree ( ) const

Get bounding box tree for mesh. The bounding box tree is initialized and built upon the first call to this function. The bounding box tree can be used to compute collisions between the mesh and other objects. It is the responsibility of the caller to use (and possibly rebuild) the tree. It is stored as a (mutable) member of the mesh to enable sharing of the bounding box tree data structure.

Returns: std::shared_ptr<BoundingBoxTree>

◆ cell_orientations()

const std::vector< int > & Mesh::cell_orientations ( ) const

Return cell_orientations (const version)

Returns

std::vector<int>

    Map from cell index to orientation of cell. Is empty
    if cell orientations have not been computed.

◆ cells()

const std::vector<unsigned int>& dolfin::Mesh::cells ( ) const

inline

Get cell connectivity.

Returns: std::vector<unsigned int>& Connectivity for all cells.

◆ clean()

void Mesh::clean ( )

Clean out all auxiliary topology data. This clears all topological data, except the connectivity between cells and vertices.

◆ color() [1/2]

const std::vector< std::size_t > & Mesh::color ( std::string coloring_type ) const

Color the cells of the mesh such that no two neighboring cells share the same color. A colored mesh keeps a MeshFunction<std::size_t> named "cell colors" as mesh data which holds the colors of the mesh.

Parameters

coloring_type (std::string) Coloring type, specifying what relation makes two cells neighbors, can be one of "vertex", "edge" or "facet".

Returns: std::vector<std::size_t>& The colors as a mesh function over the cells of the mesh.

◆ color() [2/2]

const std::vector< std::size_t > & Mesh::color ( std::vector< std::size_t > coloring_type ) const

Color the cells of the mesh such that no two neighboring cells share the same color. A colored mesh keeps a MeshFunction<std::size_t> named "cell colors" as mesh data which holds the colors of the mesh.

Parameters

coloring_type (std::vector<std::size_t>&) Coloring type given as list of topological dimensions, specifying what relation makes two mesh entities neighbors.

Returns: std::vector<std::size_t>& The colors as a mesh function over entities of the mesh.

◆ coordinates() [1/2]

std::vector<double>& dolfin::Mesh::coordinates ( )

inline

Get vertex coordinates.

Returns: std::vector<double>& Coordinates of all vertices.

◆ coordinates() [2/2]

const std::vector<double>& dolfin::Mesh::coordinates ( ) const

inline

Return coordinates of all vertices (const version).

Returns: std::vector<double>& Coordinates of all vertices.

◆ data() [1/2]

MeshData & Mesh::data ( )

Get mesh data.

Returns: MeshData& The mesh data object associated with the mesh.

◆ data() [2/2]

const MeshData & Mesh::data ( ) const

Get mesh data (const version).

Returns: MeshData& The mesh data object associated with the mesh.

◆ domains() [1/2]

MeshDomains& dolfin::Mesh::domains ( )

inline

Get mesh (sub)domains.

Returns: MeshDomains The (sub)domains associated with the mesh.

◆ domains() [2/2]

const MeshDomains& dolfin::Mesh::domains ( ) const

inline

Get mesh (sub)domains (const).

Returns: MeshDomains The (sub)domains associated with the mesh.

◆ geometry() [1/2]

MeshGeometry& dolfin::Mesh::geometry ( )

inline

Get mesh geometry.

Returns: MeshGeometry The geometry object associated with the mesh.

◆ geometry() [2/2]

const MeshGeometry& dolfin::Mesh::geometry ( ) const

inline

Get mesh geometry (const version).

Returns: MeshGeometry The geometry object associated with the mesh.

◆ ghost_mode()

std::string Mesh::ghost_mode ( ) const

Ghost mode used for partitioning. Possible values are same as parameters["ghost_mode"]. WARNING: the interface may change in future without deprecation; the method is now intended for internal library use.

◆ hash()

std::size_t Mesh::hash ( ) const

Compute hash of mesh, currently based on the has of the mesh geometry and mesh topology.

Returns: std::size_t A tree-hashed value of the coordinates over all MPI processes

◆ hmax()

double Mesh::hmax ( ) const

Compute maximum cell size in mesh, measured greatest distance between any two vertices of a cell.

Returns: double The maximum cell size. The size is computed using Cell::h()

◆ hmin()

double Mesh::hmin ( ) const

Compute minimum cell size in mesh, measured greatest distance between any two vertices of a cell.

Returns: double The minimum cell size. The size is computed using Cell::h()

◆ init() [1/2]

std::size_t Mesh::init ( std::size_t dim ) const

Compute entities of given topological dimension.

Parameters

dim	(std::size_t) Topological dimension.

Returns: std::size_t Number of created entities.

◆ init() [2/2]

void Mesh::init	(	std::size_t	d0,
		std::size_t	d1
	)		const

Compute connectivity between given pair of dimensions.

Parameters

d0	(std::size_t) Topological dimension.
d1	(std::size_t) Topological dimension.

◆ init_cell_orientations()

void Mesh::init_cell_orientations ( const Expression & global_normal )

Compute and initialize cell_orientations relative to a given global outward direction/normal/orientation. Only defined if mesh is orientable.

Parameters

global_normal (Expression) A global normal direction to the mesh

◆ mpi_comm()

MPI_Comm dolfin::Mesh::mpi_comm ( ) const

inline

Mesh MPI communicator

Returns: MPI_Comm

◆ num_cells()

std::size_t dolfin::Mesh::num_cells ( ) const

inline

Get number of cells in mesh.

Returns: std::size_t Number of cells.

◆ num_edges()

std::size_t dolfin::Mesh::num_edges ( ) const

inline

Get number of edges in mesh.

Returns: std::size_t Number of edges.

◆ num_entities()

std::size_t dolfin::Mesh::num_entities ( std::size_t d ) const

inline

Get number of entities of given topological dimension.

Parameters

d	(std::size_t) Topological dimension.

Returns: std::size_t Number of entities of topological dimension d.

◆ num_entities_global()

std::size_t dolfin::Mesh::num_entities_global ( std::size_t dim ) const

inline

Get global number of entities of given topological dimension.

Parameters

dim	(std::size_t) Topological dimension.

Returns: std::size_t Global number of entities of topological dimension d.

◆ num_faces()

std::size_t dolfin::Mesh::num_faces ( ) const

inline

Get number of faces in mesh.

Returns: std::size_t Number of faces.

◆ num_facets()

std::size_t dolfin::Mesh::num_facets ( ) const

inline

Get number of facets in mesh.

Returns: std::size_t Number of facets.

◆ num_vertices()

std::size_t dolfin::Mesh::num_vertices ( ) const

inline

Get number of vertices in mesh.

Returns: std::size_t Number of vertices.

◆ operator=()

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

Assignment operator

Parameters

mesh	(Mesh) Another Mesh object.

◆ order()

void Mesh::order ( )

Order all mesh entities.

See also: UFC documentation (put link here!)

◆ ordered()

bool Mesh::ordered ( ) const

Check if mesh is ordered according to the UFC numbering convention.

Returns: bool The return values is true iff the mesh is ordered.

◆ renumber_by_color()

dolfin::Mesh Mesh::renumber_by_color ( ) const

Renumber mesh entities by coloring. This function is currently restricted to renumbering by cell coloring. The cells (cell-vertex connectivity) and the coordinates of the mesh are renumbered to improve the locality within each color. It is assumed that the mesh has already been colored and that only cell-vertex connectivity exists as part of the mesh.

Returns: Mesh

◆ rmax()

double Mesh::rmax ( ) const

Compute maximum cell inradius.

Returns: double The maximum of cells' inscribed sphere radii

◆ rmin()

double Mesh::rmin ( ) const

Compute minimum cell inradius.

Returns: double The minimum of cells' inscribed sphere radii

◆ rotate() [1/2]

void Mesh::rotate	(	double	angle,
		std::size_t	axis = `2`
	)

Rotate mesh around a coordinate axis through center of mass of all mesh vertices

Parameters

angle	(double) The number of degrees (0-360) of rotation.
axis	(std::size_t) The coordinate axis around which to rotate the mesh.

◆ rotate() [2/2]

void Mesh::rotate	(	double	angle,
		std::size_t	axis,
		const Point &	point
	)

Rotate mesh around a coordinate axis through a given point

Parameters

angle	(double) The number of degrees (0-360) of rotation.
axis	(std::size_t) The coordinate axis around which to rotate the mesh.
point	(Point) The point around which to rotate the mesh.

◆ scale()

void Mesh::scale ( double factor )

Scale mesh coordinates with given factor.

Arguments factor (double) The factor defining the scaling.

◆ smooth()

void Mesh::smooth ( std::size_t num_iterations = 1 )

Smooth internal vertices of mesh by local averaging.

Parameters

num_iterations (std::size_t) Number of iterations to perform smoothing, default value is 1.

◆ smooth_boundary()

void Mesh::smooth_boundary	(	std::size_t	num_iterations = `1`,
		bool	harmonic_smoothing = `true`
	)

Smooth boundary vertices of mesh by local averaging.

Parameters

num_iterations	(std::size_t) Number of iterations to perform smoothing, default value is 1.
harmonic_smoothing	(bool) Flag to turn on harmonics smoothing, default value is true.

◆ snap_boundary()

void Mesh::snap_boundary	(	const SubDomain &	sub_domain,
		bool	harmonic_smoothing = `true`
	)

Snap boundary vertices of mesh to match given sub domain.

Parameters

sub_domain	(SubDomain) A SubDomain object.
harmonic_smoothing	(bool) Flag to turn on harmonics smoothing, default value is true.

◆ str()

std::string Mesh::str ( bool verbose ) const

virtual

Informal string representation.

Parameters

verbose (bool) Flag to turn on additional output.

Returns: std::string An informal representation of the mesh.

Reimplemented from dolfin::Variable.

◆ topology() [1/2]

MeshTopology& dolfin::Mesh::topology ( )

inline

Get mesh topology.

Returns: MeshTopology The topology object associated with the mesh.

◆ topology() [2/2]

const MeshTopology& dolfin::Mesh::topology ( ) const

inline

Get mesh topology (const version).

Returns: MeshTopology The topology object associated with the mesh.

◆ translate()

void Mesh::translate ( const Point & point )

Translate mesh according to a given vector.

Parameters

point (Point) The vector defining the translation.

◆ type()

CellType& dolfin::Mesh::type ( )

inline

Get mesh cell type.

Returns: CellType& The cell type object associated with the mesh.

Friends And Related Function Documentation

◆ create_mesh

Mesh create_mesh ( Function & coordinates )

friend

Creates mesh from coordinate function

Topology is given by underlying mesh of the function space and geometry is given by function values. Hence resulting mesh geometry has a degree of the function space degree. Geometry of function mesh is ignored.

Mesh connectivities d-0, d-1, ..., d-r are built on function mesh (where d is topological dimension of the mesh and r is maximal dimension of entity associated with any coordinate node). Consider clearing unneeded connectivities when finished.

Parameters

coordinates (Function) Vector Lagrange function of any degree

Returns: Mesh The mesh

The documentation for this class was generated from the following files:

/home/fenics/shared/dolfin/dolfin/mesh/Mesh.h
/home/fenics/shared/dolfin/dolfin/mesh/Mesh.cpp

Public Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Mesh() [1/4]

◆ Mesh() [2/4]

◆ Mesh() [3/4]

◆ Mesh() [4/4]

Member Function Documentation

◆ bounding_box_tree()

◆ cell_orientations()

◆ cells()

◆ clean()

◆ color() [1/2]

◆ color() [2/2]

◆ coordinates() [1/2]

◆ coordinates() [2/2]

◆ data() [1/2]

◆ data() [2/2]

◆ domains() [1/2]

◆ domains() [2/2]

◆ geometry() [1/2]

◆ geometry() [2/2]

◆ ghost_mode()

◆ hash()

◆ hmax()

◆ hmin()

◆ init() [1/2]

◆ init() [2/2]

◆ init_cell_orientations()

◆ mpi_comm()

◆ num_cells()

◆ num_edges()

◆ num_entities()

◆ num_entities_global()

◆ num_faces()

◆ num_facets()

◆ num_vertices()

◆ operator=()

◆ order()

◆ ordered()

◆ renumber_by_color()

◆ rmax()

◆ rmin()

◆ rotate() [1/2]

◆ rotate() [2/2]

◆ scale()

◆ smooth()

◆ smooth_boundary()

◆ snap_boundary()

◆ str()

◆ topology() [1/2]

◆ topology() [2/2]

◆ translate()

◆ type()

Friends And Related Function Documentation

◆ create_mesh