#include <mesh.h>

Inheritance diagram for Mesh:

Collaboration diagram for Mesh:

[legend]

Classes
struct	ElementTmpData

Public Types
enum	IntersectionSearch { BIHsearch = 1, BIHonly = 2, BBsearch = 3 }
	Types of search algorithm for finding intersection candidates. More...

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

typedef enum Mesh::IntersectionSearch	IntersectionSearch
	Types of search algorithm for finding intersection candidates. More...

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)

	TYPEDEF_ERR_INFO (EI_ElemId, int)

	TYPEDEF_ERR_INFO (EI_ElemIdOther, int)

	TYPEDEF_ERR_INFO (EI_Region, std::string)

	TYPEDEF_ERR_INFO (EI_RegIdx, unsigned int)

	TYPEDEF_ERR_INFO (EI_Dim, unsigned int)

	TYPEDEF_ERR_INFO (EI_DimOther, unsigned int)

	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")

	DECLARE_EXCEPTION (ExcElmWrongOrder,<< "Element IDs in non-increasing order, ID: "<< EI_ElemId::val<< "\n")

	DECLARE_EXCEPTION (ExcRegionElmDiffDim,<< "User defined region "<< EI_Region::qval<< " (id "<< EI_RegIdx::val<< ") by 'From_Elements' cannot have elements of different dimensions.\n"<< "Thrown due to: dim "<< EI_Dim::val<< " neq dim "<< EI_DimOther::val<< " (ele id "<< EI_ElemId::val<< ").\n"<< "Split elements by dim, create separate regions and then possibly use Union.\n")

	DECLARE_EXCEPTION (ExcTooMatchingIds,<< "Mesh: Duplicate dim-join lower dim elements: "<< EI_ElemId::val<< ", "<< EI_ElemIdOther::val<< ".\n")

	DECLARE_EXCEPTION (ExcBdrElemMatchRegular,<< "Boundary element (id: "<< EI_ElemId::val<< ") match a regular element (id: "<< EI_ElemIdOther::val<< ") of lower dimension.\n")

	Mesh ()

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

virtual	~Mesh ()
	Destructor. More...

virtual unsigned int	n_nodes () const

unsigned int	n_boundaries () const

unsigned int	n_edges () const

Edge	edge (uint edge_idx) const

Boundary	boundary (uint edge_idx) const

unsigned int	n_corners ()

const RegionDB &	region_db () const

virtual Partitioning *	get_part ()

virtual const LongIdx *	get_local_part ()

Distribution *	get_el_ds () const

LongIdx *	get_row_4_el () const

LongIdx *	get_el_4_loc () const

Distribution *	get_node_ds () const

LongIdx *	get_node_4_loc () const

unsigned int	n_local_nodes () const

MPI_Comm	get_comm () const

MixedMeshIntersections &	mixed_intersections ()

unsigned int	n_sides () const

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 ()

void	setup_topology ()

void	elements_id_maps (vector< LongIdx > &bulk_elements_id, vector< LongIdx > &boundary_elements_id) const

virtual std::shared_ptr< std::vector< LongIdx > >	check_compatible_mesh (Mesh &input_mesh)

virtual std::shared_ptr< std::vector< LongIdx > >	check_compatible_discont_mesh (Mesh &input_mesh)

virtual ElementAccessor< 3 >	element_accessor (unsigned int idx) const
	Create and return ElementAccessor to element of given idx. More...

NodeAccessor< 3 >	node (unsigned int idx) const
	Create and return NodeAccessor to node of given idx. More...

void	read_regions_from_input (Input::Array region_list)

const vector< vector< unsigned int > > &	node_elements ()

void	check_and_finish ()

std::vector< BoundingBox >	get_element_boxes ()
	Compute bounding boxes of elements contained in mesh. More...

const BIHTree &	get_bih_tree ()
	Getter for BIH. Creates and compute BIH at first call. More...

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

void	add_node (unsigned int node_id, arma::vec3 coords)
	Add new node of given id and coordinates to mesh. More...

void	add_element (unsigned int elm_id, unsigned int dim, unsigned int region_id, unsigned int partition_id, std::vector< unsigned int > node_ids)
	Add new element of given id to mesh. More...

void	add_physical_name (unsigned int dim, unsigned int id, std::string name)
	Add new node of given id and coordinates to mesh. More...

FilePath	mesh_file ()
	Return FilePath object representing "mesh_file" input key. More...

IntersectionSearch	get_intersection_search ()
	Getter for input type selection for intersection search algorithm. More...

double	global_snap_radius () const
	Maximal distance of observe point from Mesh relative to its size. More...

void	init_element_vector (unsigned int size)
	Initialize element_vec_, set size and reset counters of boundary and bulk elements. More...

void	init_node_vector (unsigned int size)
	Initialize node_vec_, set size. More...

virtual Range< ElementAccessor< 3 > >	elements_range () const
	Returns range of bulk elements. More...

Range< NodeAccessor< 3 > >	node_range () const
	Returns range of nodes. More...

Range< Edge >	edge_range () const
	Returns range of edges. More...

virtual unsigned int	n_elements () const
	Returns count of boundary or bulk elements. More...

int	elem_index (int elem_id) const
	For element of given elem_id returns index in element_vec_ or (-1) if element doesn't exist. More...

int	find_elem_id (unsigned int pos) const
	Return element id (in GMSH file) of element of given position in element vector. More...

const std::vector< unsigned int > &	element_permutations () const
	Return permutation vector of elements. More...

int	node_index (int node_id) const
	For node of given node_id returns index in element_vec_ or (-1) if node doesn't exist. More...

int	find_node_id (unsigned int pos) const
	Return node id (in GMSH file) of node of given position in node vector. More...

const std::vector< unsigned int > &	node_permutations () const
	Return permutation vector of nodes. More...

void	check_element_size (unsigned int elem_idx) const
	Check if given index is in element_vec_. More...

unsigned int	create_boundary_elements ()
	Create boundary elements from data of temporary structure, this method MUST be call after read mesh from file, return number of read boundary elements. More...

void	permute_tetrahedron (unsigned int elm_idx, std::vector< unsigned int > permutation_vec)
	Permute nodes of 3D elements of given elm_idx. More...

void	permute_triangle (unsigned int elm_idx, std::vector< unsigned int > permutation_vec)
	Permute nodes of 2D elements of given elm_idx. More...

BCMesh *	get_bc_mesh ()
	Create boundary mesh if doesn't exist and return it. More...

Static Public Member Functions
static const Input::Type::Selection &	get_input_intersection_variant ()
	The definition of input record for selection of variant of file format. More...

static const Input::Type::Record &	get_input_type ()

Public Attributes
vector< BoundaryData >	boundary_

std::shared_ptr< MixedMeshIntersections >	intersections

vector< vector< unsigned int > >	master_elements

DuplicateNodes *	tree

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

vector< vector< unsigned int > >	node_elements_
	For each node the vector contains a list of elements that use this node. More...

Static Public Attributes
static const unsigned int	undef_idx =-1

Protected Member Functions
void	init ()

void	make_neighbours_and_edges ()

void	make_edge_permutations ()

void	create_node_element_lists ()

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

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

void	element_to_neigh_vb ()

void	count_element_types ()

void	count_side_types ()

void	check_mesh_on_read ()

void	modify_element_ids (const RegionDB::MapElementIDToRegionID &map)

Element *	add_element_to_vector (int id)
	Adds element to mesh data structures (element_vec_, element_ids_), returns pointer to this element. More...

void	init_element (Element *ele, unsigned int elm_id, unsigned int dim, RegionIdx region_idx, unsigned int partition_id, std::vector< unsigned int > node_ids)
	Initialize element. More...

void	output_internal_ngh_data ()
	Output of neighboring data into raw output. More...

void	optimize ()

void	sort_permuted_nodes_elements (std::vector< int > new_node_ids, std::vector< int > new_elem_ids)
	Sort elements and nodes by order stored in permutation vectors. More...

Protected Attributes
unsigned int	n_bb_neigh

unsigned int	n_vb_neigh

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

bool	optimize_memory_locality

RegionDB	region_db_

std::shared_ptr< Partitioning >	part_

std::shared_ptr< BIHTree >	bih_tree_

Input::Record	in_record_

MPI_Comm	comm_

vector< Element >	element_vec_

vector< ElementTmpData >	bc_element_tmp_
	Hold data of boundary elements during reading mesh (allow to preserve correct order during reading of mix bulk-boundary element) More...

unsigned int	bulk_size_
	Count of bulk elements. More...

unsigned int	boundary_loaded_size_
	Count of boundary elements loaded from mesh file. More...

BidirectionalMap< int >	element_ids_
	Maps element ids to indexes into vector element_vec_. More...

Armor::Array< double >	nodes_

BidirectionalMap< int >	node_ids_
	Maps node ids to indexes into vector node_vec_. More...

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

std::vector< unsigned int >	node_permutation_
	Vector of node permutations of optimized mesh (see class MeshOptimizer) More...

std::vector< unsigned int >	elem_permutation_
	Vector of element permutations of optimized mesh (see class MeshOptimizer) More...

Private Member Functions
void	distribute_nodes ()
	Fill array node_4_loc_ and create object node_ds_ according to element distribution. More...

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

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

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

LongIdx *	node_4_loc_
	Index set assigning to local node index its global index. More...

Distribution *	node_ds_
	Parallel distribution of nodes. Depends on elements distribution. More...

unsigned int	n_local_nodes_
	Hold number of local nodes (own + ghost), value is equal with size of node_4_loc array. More...

BCMesh *	bc_mesh_
	Boundary mesh, object is created only if it's necessary. More...

Friends
class	Edge

class	Side

class	RegionSetBase

class	Element

class	BIHTree

class	Boundary

class	BCMesh

template<int spacedim>
class	ElementAccessor

template<int spacedim>
class	NodeAccessor

Detailed Description

Definition at line 77 of file mesh.h.

Member Typedef Documentation

◆ IntersectionSearch

typedef enum Mesh::IntersectionSearch Mesh::IntersectionSearch

Types of search algorithm for finding intersection candidates.

Member Enumeration Documentation

◆ anonymous enum

anonymous enum

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

Enumerator
x_coord
y_coord
z_coord

Definition at line 126 of file mesh.h.

◆ IntersectionSearch

enum Mesh::IntersectionSearch

Types of search algorithm for finding intersection candidates.

Enumerator
BIHsearch
BIHonly
BBsearch

Definition at line 110 of file mesh.h.

Constructor & Destructor Documentation

◆ Mesh() [1/2]

Mesh::Mesh ( )

Empty constructor.

Use only for unit tests!!!

Definition at line 103 of file mesh.cc.

◆ Mesh() [2/2]

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 120 of file mesh.cc.

◆ ~Mesh()

Mesh::~Mesh ( )

virtual

Destructor.

Definition at line 200 of file mesh.cc.

Member Function Documentation

◆ add_element()

void Mesh::add_element	(	unsigned int	elm_id,
		unsigned int	dim,
		unsigned int	region_id,
		unsigned int	partition_id,
		std::vector< unsigned int >	node_ids
	)

Add new element of given id to mesh.

Definition at line 1237 of file mesh.cc.

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◆ add_element_to_vector()

Element * Mesh::add_element_to_vector ( int id )

protected

Adds element to mesh data structures (element_vec_, element_ids_), returns pointer to this element.

Definition at line 1312 of file mesh.cc.

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◆ add_node()

void Mesh::add_node	(	unsigned int	node_id,
		arma::vec3	coords
	)

Add new node of given id and coordinates to mesh.

Definition at line 1229 of file mesh.cc.

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◆ add_physical_name()

void Mesh::add_physical_name	(	unsigned int	dim,
		unsigned int	id,
		std::string	name
	)

Add new node of given id and coordinates to mesh.

Definition at line 1224 of file mesh.cc.

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◆ boundary()

Boundary Mesh::boundary ( uint edge_idx ) const

Definition at line 255 of file mesh.cc.

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◆ check_and_finish()

void Mesh::check_and_finish ( )

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

Definition at line 1181 of file mesh.cc.

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◆ check_compatible_discont_mesh()

std::shared_ptr< std::vector< LongIdx > > Mesh::check_compatible_discont_mesh ( Mesh & input_mesh )

virtual

Reimplemented in BCMesh.

Definition at line 1101 of file mesh.cc.

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◆ check_compatible_mesh()

std::shared_ptr< std::vector< LongIdx > > Mesh::check_compatible_mesh ( Mesh & input_mesh )

virtual

Reimplemented in BCMesh.

Definition at line 966 of file mesh.cc.

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◆ check_element_size()

void Mesh::check_element_size ( unsigned int elem_idx ) const

inline

Check if given index is in element_vec_.

Definition at line 1338 of file mesh.cc.

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◆ check_mesh_on_read()

void Mesh::check_mesh_on_read ( )

protected

Check the element quality and remove unused nodes.

Definition at line 316 of file mesh.cc.

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◆ count_element_types()

void Mesh::count_element_types ( )

protected

Definition at line 274 of file mesh.cc.

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◆ count_side_types()

void Mesh::count_side_types ( )

protected

Definition at line 454 of file mesh.cc.

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◆ create_boundary_elements()

unsigned int Mesh::create_boundary_elements ( )

Create boundary elements from data of temporary structure, this method MUST be call after read mesh from file, return number of read boundary elements.

Definition at line 1441 of file mesh.cc.

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◆ create_node_element_lists()

void Mesh::create_node_element_lists ( )

protected

Create element lists for nodes in Mesh::nodes_elements.

Definition at line 468 of file mesh.cc.

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◆ DECLARE_EXCEPTION() [1/5]

Mesh::DECLARE_EXCEPTION	(	ExcBdrElemMatchRegular	,
		<< "Boundary element (id: "<< EI_ElemId::val<< ") match a regular element (id: "<< EI_ElemIdOther::val<< ") of lower dimension.\n"
	)

◆ DECLARE_EXCEPTION() [2/5]

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"
	)

◆ DECLARE_EXCEPTION() [3/5]

Mesh::DECLARE_EXCEPTION	(	ExcElmWrongOrder	,
		<< "Element IDs in non-increasing	order,
		ID:"<< EI_ElemId::val<< "\n"
	)

◆ DECLARE_EXCEPTION() [4/5]

Mesh::DECLARE_EXCEPTION	(	ExcRegionElmDiffDim	,
		<< "User defined region "<< EI_Region::qval<< " (id "<< EI_RegIdx::val<< ") by 'From_Elements' cannot have elements of different dimensions.\n"<< "Thrown due to: dim "<< EI_Dim::val<< " neq dim "<< EI_DimOther::val<< " (ele id "<< EI_ElemId::val<< ").\n"<< "Split elements by	dim,
		create separate regions and then possibly use Union.\n"
	)

◆ DECLARE_EXCEPTION() [5/5]

Mesh::DECLARE_EXCEPTION	(	ExcTooMatchingIds	,
		<< "Mesh: Duplicate dim-join lower dim elements: "<< EI_ElemId::val<< "	,
		"<< EI_ElemIdOther::val<< ".\n"
	)

◆ distribute_nodes()

void Mesh::distribute_nodes ( )

private

Fill array node_4_loc_ and create object node_ds_ according to element distribution.

Definition at line 1495 of file mesh.cc.

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◆ edge()

Edge Mesh::edge ( uint edge_idx ) const

Definition at line 249 of file mesh.cc.

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◆ edge_range()

Range< Edge > Mesh::edge_range ( ) const

Returns range of edges.

Definition at line 1332 of file mesh.cc.

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◆ elem_index()

int Mesh::elem_index ( int elem_id ) const

inline

For element of given elem_id returns index in element_vec_ or (-1) if element doesn't exist.

Definition at line 381 of file mesh.h.

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◆ element_accessor()

ElementAccessor< 3 > Mesh::element_accessor ( unsigned int idx ) const

virtual

Create and return ElementAccessor to element of given idx.

Reimplemented in BCMesh.

Definition at line 913 of file mesh.cc.

◆ element_permutations()

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

inline

Return permutation vector of elements.

Definition at line 393 of file mesh.h.

◆ element_to_neigh_vb()

void Mesh::element_to_neigh_vb ( )

protected

Definition at line 863 of file mesh.cc.

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◆ elements_id_maps()

void Mesh::elements_id_maps	(	vector< LongIdx > &	bulk_elements_id,
		vector< LongIdx > &	boundary_elements_id
	)		const

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

Definition at line 925 of file mesh.cc.

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◆ elements_range()

Range< ElementAccessor< 3 > > Mesh::elements_range ( ) const

virtual

Returns range of bulk elements.

Reimplemented in BCMesh.

Definition at line 1320 of file mesh.cc.

◆ find_elem_id()

int Mesh::find_elem_id ( unsigned int pos ) const

inline

Return element id (in GMSH file) of element of given position in element vector.

Definition at line 387 of file mesh.h.

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◆ find_lower_dim_element()

bool Mesh::find_lower_dim_element	(	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 513 of file mesh.cc.

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◆ find_node_id()

int Mesh::find_node_id ( unsigned int pos ) const

inline

Return node id (in GMSH file) of node of given position in node vector.

Definition at line 405 of file mesh.h.

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◆ get_bc_mesh()

BCMesh * Mesh::get_bc_mesh ( )

Create boundary mesh if doesn't exist and return it.

Definition at line 1489 of file mesh.cc.

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◆ get_bih_tree()

const BIHTree & Mesh::get_bih_tree ( )

Getter for BIH. Creates and compute BIH at first call.

Definition at line 1211 of file mesh.cc.

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◆ get_comm()

MPI_Comm Mesh::get_comm ( ) const

inline

Returns MPI communicator of the mesh.

Definition at line 192 of file mesh.h.

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◆ get_el_4_loc()

LongIdx* Mesh::get_el_4_loc ( ) const

inline

Definition at line 177 of file mesh.h.

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◆ get_el_ds()

Distribution* Mesh::get_el_ds ( ) const

inline

Definition at line 171 of file mesh.h.

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◆ get_element_boxes()

std::vector< BoundingBox > Mesh::get_element_boxes ( )

Compute bounding boxes of elements contained in mesh.

Definition at line 1196 of file mesh.cc.

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◆ get_input_intersection_variant()

const Input::Type::Selection & Mesh::get_input_intersection_variant ( )

static

The definition of input record for selection of variant of file format.

Definition at line 64 of file mesh.cc.

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◆ get_input_type()

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

static

Definition at line 75 of file mesh.cc.

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◆ get_intersection_search()

Mesh::IntersectionSearch Mesh::get_intersection_search ( )

Getter for input type selection for intersection search algorithm.

Definition at line 138 of file mesh.cc.

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◆ get_local_part()

const LongIdx * Mesh::get_local_part ( )

virtual

Reimplemented in BCMesh.

Definition at line 265 of file mesh.cc.

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◆ get_node_4_loc()

LongIdx* Mesh::get_node_4_loc ( ) const

inline

Definition at line 183 of file mesh.h.

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◆ get_node_ds()

Distribution* Mesh::get_node_ds ( ) const

inline

Definition at line 180 of file mesh.h.

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◆ get_part()

Partitioning * Mesh::get_part ( )

virtual

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

Reimplemented in BCMesh.

Definition at line 261 of file mesh.cc.

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◆ get_row_4_el()

LongIdx* Mesh::get_row_4_el ( ) const

inline

Definition at line 174 of file mesh.h.

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◆ global_snap_radius()

double Mesh::global_snap_radius ( ) const

Maximal distance of observe point from Mesh relative to its size.

Definition at line 1220 of file mesh.cc.

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◆ init()

void Mesh::init ( )

protected

Part of the constructor whichdoes not depedn on input record. Initializes node-side numbering according to RefElement.

Definition at line 144 of file mesh.cc.

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◆ init_element()

void Mesh::init_element	(	Element *	ele,
		unsigned int	elm_id,
		unsigned int	dim,
		RegionIdx	region_idx,
		unsigned int	partition_id,
		std::vector< unsigned int >	node_ids
	)

protected

Initialize element.

Definition at line 1260 of file mesh.cc.

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◆ init_element_vector()

void Mesh::init_element_vector ( unsigned int size )

Initialize element_vec_, set size and reset counters of boundary and bulk elements.

Definition at line 1289 of file mesh.cc.

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◆ init_from_input()

void Mesh::init_from_input ( )

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

◆ init_node_vector()

void Mesh::init_node_vector ( unsigned int size )

Initialize node_vec_, set size.

Definition at line 1303 of file mesh.cc.

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◆ intersect_element_lists()

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

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 481 of file mesh.cc.

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◆ make_edge_permutations()

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 743 of file mesh.cc.

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◆ make_neighbours_and_edges()

void Mesh::make_neighbours_and_edges ( )

protected

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

TODO:

Avoid maps:

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 boundary elements first, there should be no Neigh, but check it set Edge and boundary there

Definition at line 549 of file mesh.cc.

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◆ max_edge_sides()

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 205 of file mesh.h.

◆ mesh_file()

FilePath Mesh::mesh_file ( )

inline

Return FilePath object representing "mesh_file" input key.

Definition at line 347 of file mesh.h.

◆ mixed_intersections()

MixedMeshIntersections & Mesh::mixed_intersections ( )

Definition at line 896 of file mesh.cc.

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◆ modify_element_ids()

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 291 of file mesh.cc.

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◆ n_boundaries()

unsigned int Mesh::n_boundaries ( ) const

inline

Definition at line 147 of file mesh.h.

◆ n_corners()

unsigned int Mesh::n_corners ( )

Definition at line 239 of file mesh.cc.

◆ n_edges()

unsigned int Mesh::n_edges ( ) const

inline

Definition at line 151 of file mesh.h.

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◆ n_elements()

virtual unsigned int Mesh::n_elements ( ) const

inlinevirtual

Returns count of boundary or bulk elements.

Reimplemented in BCMesh.

Definition at line 373 of file mesh.h.

◆ n_local_nodes()

unsigned int Mesh::n_local_nodes ( ) const

inline

Definition at line 186 of file mesh.h.

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◆ n_nodes()

virtual unsigned int Mesh::n_nodes ( ) const

inlinevirtual

Reimplemented in BCMesh.

Definition at line 143 of file mesh.h.

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◆ n_sides()

unsigned int Mesh::n_sides ( ) const

Definition at line 225 of file mesh.cc.

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◆ n_vb_neighbours()

unsigned int Mesh::n_vb_neighbours ( ) const

Definition at line 234 of file mesh.cc.

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◆ node()

NodeAccessor< 3 > Mesh::node ( unsigned int idx ) const

Create and return NodeAccessor to node of given idx.

Definition at line 919 of file mesh.cc.

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◆ node_elements()

const vector< vector< unsigned int > > & Mesh::node_elements ( )

Returns nodes_elements vector, if doesn't exist creates its.

Definition at line 1281 of file mesh.cc.

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◆ node_index()

int Mesh::node_index ( int node_id ) const

inline

For node of given node_id returns index in element_vec_ or (-1) if node doesn't exist.

Definition at line 399 of file mesh.h.

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◆ node_permutations()

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

inline

Return permutation vector of nodes.

Definition at line 411 of file mesh.h.

◆ node_range()

Range< NodeAccessor< 3 > > Mesh::node_range ( ) const

Returns range of nodes.

Definition at line 1326 of file mesh.cc.

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◆ optimize()

void Mesh::optimize ( )

protected

Apply functionality of MeshOptimizer to sort nodes and elements.

Use Hilbert curve, need call sort_permuted_nodes_elements method.

Definition at line 417 of file mesh.cc.

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◆ output_internal_ngh_data()

void Mesh::output_internal_ngh_data ( )

protected

Output of neighboring data into raw output.

Definition at line 1346 of file mesh.cc.

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◆ permute_tetrahedron()

void Mesh::permute_tetrahedron	(	unsigned int	elm_idx,
		std::vector< unsigned int >	permutation_vec
	)

Permute nodes of 3D elements of given elm_idx.

Definition at line 1455 of file mesh.cc.

◆ permute_triangle()

void Mesh::permute_triangle	(	unsigned int	elm_idx,
		std::vector< unsigned int >	permutation_vec
	)

Permute nodes of 2D elements of given elm_idx.

Definition at line 1472 of file mesh.cc.

◆ read_gmsh_from_stream()

void Mesh::read_gmsh_from_stream ( istream & in )

Reads mesh from stream.

Method is especially used in unit tests.

◆ read_regions_from_input()

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 1171 of file mesh.cc.

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◆ region_db()

const RegionDB& Mesh::region_db ( ) const

inline

Definition at line 160 of file mesh.h.

◆ same_sides()

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 532 of file mesh.cc.

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◆ setup_topology()

void Mesh::setup_topology ( )

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 381 of file mesh.cc.

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◆ sort_permuted_nodes_elements()

void Mesh::sort_permuted_nodes_elements	(	std::vector< int >	new_node_ids,
		std::vector< int >	new_elem_ids
	)

protected

Sort elements and nodes by order stored in permutation vectors.

Definition at line 427 of file mesh.cc.

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◆ TYPEDEF_ERR_INFO() [1/10]

Mesh::TYPEDEF_ERR_INFO	(	EI_Dim	,
		unsigned int
	)

◆ TYPEDEF_ERR_INFO() [2/10]

Mesh::TYPEDEF_ERR_INFO	(	EI_DimOther	,
		unsigned int
	)

◆ TYPEDEF_ERR_INFO() [3/10]

Mesh::TYPEDEF_ERR_INFO	(	EI_ElemId	,
		int
	)

◆ TYPEDEF_ERR_INFO() [4/10]

Mesh::TYPEDEF_ERR_INFO	(	EI_ElemIdOther	,
		int
	)

◆ TYPEDEF_ERR_INFO() [5/10]

Mesh::TYPEDEF_ERR_INFO	(	EI_ElemLast	,
		int
	)

◆ TYPEDEF_ERR_INFO() [6/10]

Mesh::TYPEDEF_ERR_INFO	(	EI_ElemNew	,
		int
	)

◆ TYPEDEF_ERR_INFO() [7/10]

Mesh::TYPEDEF_ERR_INFO	(	EI_RegIdx	,
		unsigned int
	)

◆ TYPEDEF_ERR_INFO() [8/10]

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

◆ TYPEDEF_ERR_INFO() [9/10]

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

◆ TYPEDEF_ERR_INFO() [10/10]

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

Friends And Related Function Documentation

◆ BCMesh

friend class BCMesh

friend

Definition at line 611 of file mesh.h.

◆ BIHTree

friend class BIHTree

friend

Definition at line 609 of file mesh.h.

◆ Boundary

friend class Boundary

friend

Definition at line 610 of file mesh.h.

◆ Edge

friend class Edge

friend

Definition at line 605 of file mesh.h.

◆ Element

friend class Element

friend

Definition at line 608 of file mesh.h.

◆ ElementAccessor

template<int spacedim>

friend class ElementAccessor

friend

Definition at line 612 of file mesh.h.

◆ NodeAccessor

template<int spacedim>

friend class NodeAccessor

friend

Definition at line 613 of file mesh.h.

◆ RegionSetBase

friend class RegionSetBase

friend

Definition at line 607 of file mesh.h.

◆ Side

friend class Side

friend

Definition at line 606 of file mesh.h.

Member Data Documentation

◆ bc_element_tmp_

vector<ElementTmpData> Mesh::bc_element_tmp_

protected

Hold data of boundary elements during reading mesh (allow to preserve correct order during reading of mix bulk-boundary element)

Definition at line 576 of file mesh.h.

◆ bc_mesh_

BCMesh* Mesh::bc_mesh_

private

Boundary mesh, object is created only if it's necessary.

Definition at line 635 of file mesh.h.

◆ bih_tree_

std::shared_ptr<BIHTree> Mesh::bih_tree_

protected

BIH Tree for intersection and observe points lookup.

Definition at line 555 of file mesh.h.

◆ boundary_

vector<BoundaryData> Mesh::boundary_

mutable

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 275 of file mesh.h.

◆ boundary_loaded_size_

unsigned int Mesh::boundary_loaded_size_

protected

Count of boundary elements loaded from mesh file.

Definition at line 582 of file mesh.h.

◆ bulk_size_

unsigned int Mesh::bulk_size_

protected

Count of bulk elements.

Definition at line 579 of file mesh.h.

◆ comm_

MPI_Comm Mesh::comm_

protected

MPI communicator used for partitioning and ...

Definition at line 566 of file mesh.h.

◆ edges

std::vector<EdgeData> Mesh::edges

protected

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

Definition at line 596 of file mesh.h.

◆ el_4_loc

LongIdx* Mesh::el_4_loc

private

Index set assigning to local element index its global index.

Definition at line 625 of file mesh.h.

◆ el_ds

Distribution* Mesh::el_ds

private

Parallel distribution of elements.

Definition at line 627 of file mesh.h.

◆ elem_permutation_

std::vector<unsigned int> Mesh::elem_permutation_

protected

Vector of element permutations of optimized mesh (see class MeshOptimizer)

Definition at line 602 of file mesh.h.

◆ element_ids_

BidirectionalMap<int> Mesh::element_ids_

protected

Maps element ids to indexes into vector element_vec_.

Definition at line 585 of file mesh.h.

◆ element_vec_

vector<Element> Mesh::element_vec_

protected

Vector of elements of the mesh.

Store all elements of the mesh in order bulk elements - boundary elements

Definition at line 573 of file mesh.h.

◆ in_record_

Input::Record Mesh::in_record_

protected

Accessor to the input record for the mesh.

Definition at line 561 of file mesh.h.

◆ intersections

std::shared_ptr<MixedMeshIntersections> Mesh::intersections

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

Definition at line 283 of file mesh.h.

◆ master_elements

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

Definition at line 289 of file mesh.h.

◆ max_edge_sides_

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 521 of file mesh.h.

◆ n_bb_neigh

unsigned int Mesh::n_bb_neigh

protected

Definition at line 518 of file mesh.h.

◆ n_exsides

int Mesh::n_exsides

Definition at line 299 of file mesh.h.

◆ n_insides

int Mesh::n_insides

Definition at line 298 of file mesh.h.

◆ n_lines

int Mesh::n_lines

Definition at line 302 of file mesh.h.

◆ n_local_nodes_

unsigned int Mesh::n_local_nodes_

private

Hold number of local nodes (own + ghost), value is equal with size of node_4_loc array.

Definition at line 633 of file mesh.h.

◆ n_sides_

int Mesh::n_sides_

mutable

Definition at line 300 of file mesh.h.

◆ n_tetrahedras

int Mesh::n_tetrahedras

Definition at line 304 of file mesh.h.

◆ n_triangles

int Mesh::n_triangles

Definition at line 303 of file mesh.h.

◆ n_vb_neigh

unsigned int Mesh::n_vb_neigh

protected

Definition at line 518 of file mesh.h.

◆ node_4_loc_

LongIdx* Mesh::node_4_loc_

private

Index set assigning to local node index its global index.

Definition at line 629 of file mesh.h.

◆ node_ds_

Distribution* Mesh::node_ds_

private

Parallel distribution of nodes. Depends on elements distribution.

Definition at line 631 of file mesh.h.

◆ node_elements_

vector<vector<unsigned int> > Mesh::node_elements_

For each node the vector contains a list of elements that use this node.

Definition at line 378 of file mesh.h.

◆ node_ids_

BidirectionalMap<int> Mesh::node_ids_

protected

Maps node ids to indexes into vector node_vec_.

Definition at line 593 of file mesh.h.

◆ node_permutation_

std::vector<unsigned int> Mesh::node_permutation_

protected

Vector of node permutations of optimized mesh (see class MeshOptimizer)

Definition at line 599 of file mesh.h.

◆ nodes_

Armor::Array<double> Mesh::nodes_

protected

Vector of nodes of the mesh.

Definition at line 590 of file mesh.h.

◆ optimize_memory_locality

bool Mesh::optimize_memory_locality

protected

Flag for optimization perfomed at the beginning of setup_topology. Default true, can be set to flase by the optimize_mesh key of the input recoed.

Definition at line 540 of file mesh.h.

◆ part_

std::shared_ptr<Partitioning> Mesh::part_

protected

Mesh partitioning. Created in setup_topology.

Definition at line 550 of file mesh.h.

◆ region_db_

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 546 of file mesh.h.

◆ row_4_el

LongIdx* Mesh::row_4_el

private

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

Definition at line 623 of file mesh.h.

◆ side_nodes

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

Definition at line 316 of file mesh.h.

◆ tree

DuplicateNodes* Mesh::tree

Definition at line 291 of file mesh.h.

◆ undef_idx

const unsigned int Mesh::undef_idx =-1

static

Definition at line 121 of file mesh.h.

◆ vb_neighbours_

vector<Neighbour> Mesh::vb_neighbours_

Vector of compatible neighbourings.

Definition at line 296 of file mesh.h.

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

/opt/flow123d/flow123d/src/mesh/mesh.h
/opt/flow123d/flow123d/src/mesh/mesh.cc

Classes

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ IntersectionSearch

Member Enumeration Documentation

◆ anonymous enum

◆ IntersectionSearch

Constructor & Destructor Documentation

◆ Mesh() [1/2]

◆ Mesh() [2/2]

◆ ~Mesh()

Member Function Documentation

◆ add_element()

◆ add_element_to_vector()

◆ add_node()

◆ add_physical_name()

◆ boundary()

◆ check_and_finish()

◆ check_compatible_discont_mesh()

◆ check_compatible_mesh()

◆ check_element_size()

◆ check_mesh_on_read()

◆ count_element_types()

◆ count_side_types()

◆ create_boundary_elements()

◆ create_node_element_lists()

◆ DECLARE_EXCEPTION() [1/5]

◆ DECLARE_EXCEPTION() [2/5]

◆ DECLARE_EXCEPTION() [3/5]

◆ DECLARE_EXCEPTION() [4/5]

◆ DECLARE_EXCEPTION() [5/5]

◆ distribute_nodes()

◆ edge()

◆ edge_range()

◆ elem_index()

◆ element_accessor()

◆ element_permutations()

◆ element_to_neigh_vb()

◆ elements_id_maps()

◆ elements_range()

◆ find_elem_id()

◆ find_lower_dim_element()

◆ find_node_id()

◆ get_bc_mesh()

◆ get_bih_tree()

◆ get_comm()

◆ get_el_4_loc()

◆ get_el_ds()

◆ get_element_boxes()

◆ get_input_intersection_variant()

◆ get_input_type()

◆ get_intersection_search()

◆ get_local_part()

◆ get_node_4_loc()

◆ get_node_ds()

◆ get_part()

◆ get_row_4_el()

◆ global_snap_radius()

◆ init()

◆ init_element()

◆ init_element_vector()

◆ init_from_input()

◆ init_node_vector()

◆ intersect_element_lists()

◆ make_edge_permutations()

◆ make_neighbours_and_edges()

◆ max_edge_sides()

◆ mesh_file()

◆ mixed_intersections()

◆ modify_element_ids()