#include <mesh.h>

Collaboration diagram for Mesh:

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Public Types
enum	{ x_coord =0, y_coord =1, z_coord =2 }

Public Member Functions
	TYPEDEF_ERR_INFO (EI_ElemLast, int)

	TYPEDEF_ERR_INFO (EI_ElemNew, int)

	TYPEDEF_ERR_INFO (EI_RegLast, std::string)

	TYPEDEF_ERR_INFO (EI_RegNew, std::string)

	DECLARE_EXCEPTION (ExcDuplicateBoundary,<< "Duplicate boundary elements! \n"<< "Element id: "<< EI_ElemLast::val<< " on region name: "<< EI_RegLast::val<< "\n"<< "Element id: "<< EI_ElemNew::val<< " on region name: "<< EI_RegNew::val<< "\n")

	Mesh (const std::string &input_str="{mesh_file=\"\"}", MPI_Comm com=MPI_COMM_WORLD)

	Mesh (Input::Record in_record, MPI_Comm com=MPI_COMM_WORLD)

void	reinit (Input::Record in_record)

	~Mesh ()
	Destructor. More...

unsigned int	n_nodes () const

unsigned int	n_elements () const

unsigned int	n_boundaries () const

unsigned int	n_edges () const

unsigned int	n_corners ()

const RegionDB &	region_db () const

Partitioning *	get_part ()

Distribution *	get_el_ds () const

int *	get_row_4_el () const

int *	get_el_4_loc () const

MPI_Comm	get_comm () const

void	make_intersec_elements ()

unsigned int	n_sides ()

unsigned int	n_vb_neighbours () const

unsigned int	max_edge_sides (unsigned int dim) const

void	read_gmsh_from_stream (istream &in)

void	init_from_input ()

vector< int > const &	elements_id_maps (bool boundary_domain) const

ElementAccessor< 3 >	element_accessor (unsigned int idx, bool boundary=false)

void	read_regions_from_input (Input::Array region_list)

void	check_and_finish ()

Static Public Member Functions
static const Input::Type::Record &	get_input_type ()

Public Attributes
NodeVector	node_vector
	Vector of nodes of the mesh. More...

ElementVector	element
	Vector of elements of the mesh. More...

vector< Boundary >	boundary_

ElementVector	bc_elements

std::vector< Edge >	edges
	Vector of MH edges, this should not be part of the geometrical mesh. More...

vector< Intersection >	intersections

vector< vector< unsigned int > >	master_elements

vector< Neighbour >	vb_neighbours_

int	n_insides

int	n_exsides

int	n_sides_

int	n_lines

int	n_triangles

int	n_tetrahedras

vector< vector< vector< unsigned int > > >	side_nodes

Static Public Attributes
static const unsigned int	undef_idx =-1

Protected Member Functions
void	make_neighbours_and_edges ()

void	make_edge_permutations ()

void	create_node_element_lists ()

void	intersect_element_lists (vector< unsigned int > const &nodes_list, vector< unsigned int > &intersection_element_list)

bool	find_lower_dim_element (ElementVector &elements, vector< unsigned int > &element_list, unsigned int dim, unsigned int &element_idx)

bool	same_sides (const SideIter &si, vector< unsigned int > &side_nodes)

void	setup_topology ()

void	element_to_neigh_vb ()

void	count_element_types ()

void	count_side_types ()

void	modify_element_ids (const RegionDB::MapElementIDToRegionID &map)

Protected Attributes
unsigned int	n_bb_neigh

unsigned int	n_vb_neigh

vector< int >	bulk_elements_id_

vector< int >	boundary_elements_id_

unsigned int	n_all_input_elements_
	Number of elements read from input. More...

vector< vector< unsigned int > >	node_elements

unsigned int	max_edge_sides_ [3]
	Maximal number of sides per one edge in the actual mesh (set in make_neighbours_and_edges()). More...

RegionDB	region_db_

boost::shared_ptr< Partitioning >	part_

Input::Record	in_record_

MPI_Comm	comm_

Private Attributes
int *	row_4_el
	Index set assigning to global element index the local index used in parallel vectors. More...

int *	el_4_loc
	Index set assigning to local element index its global index. More...

Distribution *	el_ds
	Parallel distribution of elements. More...

Friends
class	GmshMeshReader

class	RegionSetBase

Detailed Description

Definition at line 99 of file mesh.h.

Member Enumeration Documentation

anonymous enum

Labels for coordinate indexes in arma::vec3 representing vectors and points.

Enumerator
x_coord
y_coord
z_coord

Definition at line 118 of file mesh.h.

Constructor & Destructor Documentation

Mesh::Mesh	(	const std::string &	input_str = `"{mesh_file=\"\"}"`,
		MPI_Comm	com = `MPI_COMM_WORLD`
	)

Constructor with input record given by string. Aimed for testing purpose. Do not process input record. That is done in init_from_input.

Definition at line 76 of file mesh.cc.

Mesh::Mesh	(	Input::Record	in_record,
		MPI_Comm	com = `MPI_COMM_WORLD`
	)

Constructor from an input record. Do not process input record. That is done in init_from_input.

Definition at line 91 of file mesh.cc.

Mesh::~Mesh ( )

Destructor.

Definition at line 148 of file mesh.cc.

Member Function Documentation

void Mesh::check_and_finish ( )

Check usage of regions, set regions to elements defined by user, close RegionDB

Definition at line 751 of file mesh.cc.

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void Mesh::count_element_types ( )

protected

Definition at line 201 of file mesh.cc.

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void Mesh::count_side_types ( )

protected

Definition at line 290 of file mesh.cc.

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void Mesh::create_node_element_lists ( )

protected

Create element lists for nodes in Mesh::nodes_elements.

Definition at line 303 of file mesh.cc.

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Mesh::DECLARE_EXCEPTION	(	ExcDuplicateBoundary	,
		<< "Duplicate boundary elements! \n"<< "Element id: "<< EI_ElemLast::val<< " on region name: "<< EI_RegLast::val<< "\n"<< "Element id: "<< EI_ElemNew::val<< " on region name: "<< EI_RegNew::val<< "\n"
	)

ElementAccessor< 3 > Mesh::element_accessor	(	unsigned int	idx,
		bool	boundary = `false`
	)

Definition at line 700 of file mesh.cc.

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void Mesh::element_to_neigh_vb ( )

protected

Definition at line 626 of file mesh.cc.

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vector< int > const & Mesh::elements_id_maps ( bool boundary_domain ) const

Returns vector of ID numbers of elements, either bulk or bc elemnts.

Definition at line 706 of file mesh.cc.

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bool Mesh::find_lower_dim_element	(	ElementVector &	elements,
		vector< unsigned int > &	element_list,
		unsigned int	dim,
		unsigned int &	element_idx
	)

protected

Remove elements with dimension not equal to dim from element_list. Index of the first element of dimension dim-1, is returned in element_idx. If no such element is found the method returns false, if one such element is found the method returns true, if more elements are found we report an user input error.

Definition at line 344 of file mesh.cc.

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MPI_Comm Mesh::get_comm ( ) const

inline

Returns MPI communicator of the mesh.

Definition at line 177 of file mesh.h.

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int* Mesh::get_el_4_loc ( ) const

inline

Definition at line 171 of file mesh.h.

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Distribution* Mesh::get_el_ds ( ) const

inline

Definition at line 165 of file mesh.h.

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const IT::Record & Mesh::get_input_type ( )

static

Definition at line 58 of file mesh.cc.

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Partitioning * Mesh::get_part ( )

Returns pointer to partitioning object. Partitioning is created during setup_topology.

Definition at line 192 of file mesh.cc.

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int* Mesh::get_row_4_el ( ) const

inline

Definition at line 168 of file mesh.h.

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void Mesh::init_from_input ( )

Reads input record, creates regions, read the mesh, setup topology. creates region sets.

Definition at line 231 of file mesh.cc.

void Mesh::intersect_element_lists	(	vector< unsigned int > const &	nodes_list,
		vector< unsigned int > &	intersection_element_list
	)

protected

Find intersection of element lists given by Mesh::node_elements for elements givne by nodes_list parameter. The result is placed into vector intersection_element_list. If the node_list is empty, and empty intersection is returned.

Definition at line 316 of file mesh.cc.

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void Mesh::make_edge_permutations ( )

protected

On edges sharing sides of many elements it may happen that each side has its nodes ordered in a different way. This method finds the permutation for each side so as to obtain the ordering of side 0.

Definition at line 555 of file mesh.cc.

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void Mesh::make_intersec_elements ( )

Definition at line 661 of file mesh.cc.

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void Mesh::make_neighbours_and_edges ( )

protected

This replaces read_neighbours() in order to avoid using NGH preprocessor.

TODO:

Avoid maps:

4) replace EdgeVector by std::vector<Edge> (need not to know the size)

5) need not to have temporary array for Edges, only postpone setting pointers in elements and set them after edges are found; we can temporary save Edge index instead of pointer in Neigbours and elements

6) Try replace Edge * by indexes in Neigbours and elements (anyway we have mesh pointer in elements so it is accessible also from Neigbours)

TODO:

use std::is_any for setting is_neigbour
possibly make appropriate constructors for Edge and Neighbour
check side!=-1 when searching neigbouring element
process bc_elements first, there should be no Neigh, but check it set Edge and boundary there

Definition at line 381 of file mesh.cc.

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unsigned int Mesh::max_edge_sides ( unsigned int dim ) const

inline

Returns maximal number of sides of one edge, which connects elements of dimension dim.

Parameters

dim	Dimension of elements sharing the edge.

Definition at line 192 of file mesh.h.

void Mesh::modify_element_ids ( const RegionDB::MapElementIDToRegionID & map )

protected

Possibly modify region id of elements sets by user in "regions" part of input file.

TODO: This method needs check in issue 'Review mesh setting'. Changes have been done during generalized region key and may be causing problems during the further development.

Definition at line 252 of file mesh.cc.

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unsigned int Mesh::n_boundaries ( ) const

inline

Definition at line 146 of file mesh.h.

unsigned int Mesh::n_corners ( )

Definition at line 182 of file mesh.cc.

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unsigned int Mesh::n_edges ( ) const

inline

Definition at line 150 of file mesh.h.

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unsigned int Mesh::n_elements ( ) const

inline

Definition at line 142 of file mesh.h.

unsigned int Mesh::n_nodes ( ) const

inline

Definition at line 138 of file mesh.h.

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unsigned int Mesh::n_sides ( )

Definition at line 173 of file mesh.cc.

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unsigned int Mesh::n_vb_neighbours ( ) const

inline

Definition at line 184 of file mesh.h.

void Mesh::read_gmsh_from_stream ( istream & in )

Reads mesh from stream.

Method is especially used in unit tests.

Definition at line 217 of file mesh.cc.

void Mesh::read_regions_from_input ( Input::Array region_list )

Reads elements and their affiliation to regions and region sets defined by user in input file Format of input record is defined in method RegionSetBase::get_input_type()

Parameters

region_list Array input AbstractRecords which define regions, region sets and elements

Definition at line 741 of file mesh.cc.

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const RegionDB& Mesh::region_db ( ) const

inline

Definition at line 156 of file mesh.h.

void Mesh::reinit ( Input::Record in_record )

Common part of both previous constructors and way how to reinitialize a mesh from the given input record.

Definition at line 103 of file mesh.cc.

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bool Mesh::same_sides	(	const SideIter &	si,
		vector< unsigned int > &	side_nodes
	)

protected

Returns true if side si has same nodes as in the list side_nodes.

Definition at line 364 of file mesh.cc.

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void Mesh::setup_topology ( )

protected

Initialize all mesh structures from raw information about nodes and elements (including boundary elements). Namely: create remaining boundary elements and Boundary objects, find edges and compatible neighborings.

Definition at line 262 of file mesh.cc.

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Mesh::TYPEDEF_ERR_INFO	(	EI_ElemLast	,
		int
	)

Mesh::TYPEDEF_ERR_INFO	(	EI_ElemNew	,
		int
	)

Mesh::TYPEDEF_ERR_INFO	(	EI_RegLast	,
		std::string
	)

Mesh::TYPEDEF_ERR_INFO	(	EI_RegNew	,
		std::string
	)

Friends And Related Function Documentation

friend class GmshMeshReader

friend

Definition at line 384 of file mesh.h.

friend class RegionSetBase

friend

Definition at line 385 of file mesh.h.

Member Data Documentation

ElementVector Mesh::bc_elements

vector of boundary elements - should replace 'boundary' TODO: put both bulk and bc elements (on zero level) to the same vector or make better map id->element for field inputs that use element IDs the avoid usage of ElementVector etc.

Definition at line 233 of file mesh.h.

vector<Boundary> Mesh::boundary_

Vector of boundary sides where is prescribed boundary condition. TODO: apply all boundary conditions in the main assembling cycle over elements and remove this Vector.

Definition at line 229 of file mesh.h.

vector<int> Mesh::boundary_elements_id_

mutableprotected

Definition at line 355 of file mesh.h.

vector<int> Mesh::bulk_elements_id_

mutableprotected

Vector of both bulk and boundary IDs. Bulk elements come first, then boundary elements, but only the portion that appears in input mesh file and has ID assigned.

TODO: Rather should be part of GMSH reader, but in such case we need store pointer to it in the mesh (good idea, but need more general interface for readers)

Definition at line 355 of file mesh.h.

MPI_Comm Mesh::comm_

protected

MPI communicator used for partitioning and ...

Definition at line 382 of file mesh.h.

std::vector<Edge> Mesh::edges

Vector of MH edges, this should not be part of the geometrical mesh.

Definition at line 236 of file mesh.h.

int* Mesh::el_4_loc

private

Index set assigning to local element index its global index.

Definition at line 393 of file mesh.h.

Distribution* Mesh::el_ds

private

Parallel distribution of elements.

Definition at line 395 of file mesh.h.

intersections array for every intersection in which El is master Mesh::element

Vector of elements of the mesh.

For every element El we have vector of indices into This is necessary for true mortar.

Definition at line 225 of file mesh.h.

Input::Record Mesh::in_record_

protected

Accessor to the input record for the mesh.

Definition at line 377 of file mesh.h.

vector<Intersection> Mesh::intersections

Vector of individual intersections of two elements. This is enough for local mortar.

Definition at line 244 of file mesh.h.

vector<vector<unsigned int> > Mesh::master_elements

Definition at line 250 of file mesh.h.

unsigned int Mesh::max_edge_sides_[3]

protected

Maximal number of sides per one edge in the actual mesh (set in make_neighbours_and_edges()).

Definition at line 363 of file mesh.h.

unsigned int Mesh::n_all_input_elements_

protected

Number of elements read from input.

Definition at line 357 of file mesh.h.

unsigned int Mesh::n_bb_neigh

protected

Definition at line 349 of file mesh.h.

int Mesh::n_exsides

Definition at line 258 of file mesh.h.

int Mesh::n_insides

Definition at line 257 of file mesh.h.

int Mesh::n_lines

Definition at line 261 of file mesh.h.

int Mesh::n_sides_

Definition at line 259 of file mesh.h.

int Mesh::n_tetrahedras

Definition at line 263 of file mesh.h.

int Mesh::n_triangles

Definition at line 262 of file mesh.h.

unsigned int Mesh::n_vb_neigh

protected

Definition at line 349 of file mesh.h.

vector<vector<unsigned int> > Mesh::node_elements

protected

Definition at line 360 of file mesh.h.

NodeVector Mesh::node_vector

Vector of nodes of the mesh.

Definition at line 223 of file mesh.h.

boost::shared_ptr<Partitioning> Mesh::part_

protected

Mesh partitioning. Created in setup_topology.

Definition at line 373 of file mesh.h.

RegionDB Mesh::region_db_

protected

Database of regions (both bulk and boundary) of the mesh. Regions are logical parts of the domain that allows setting of different data and boundary conditions on them.

Definition at line 369 of file mesh.h.

int* Mesh::row_4_el

private

Index set assigning to global element index the local index used in parallel vectors.

Definition at line 391 of file mesh.h.

vector< vector< vector<unsigned int> > > Mesh::side_nodes

Definition at line 274 of file mesh.h.

const unsigned int Mesh::undef_idx =-1

static

Definition at line 112 of file mesh.h.

vector<Neighbour> Mesh::vb_neighbours_

Vector of compatible neighbourings.

Definition at line 255 of file mesh.h.

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

/home/cygwin64/F123-windows-release/flow123d/src/mesh/mesh.h
/home/cygwin64/F123-windows-release/flow123d/src/mesh/mesh.cc

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Friends

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation