#include <serial_mesh.h>

Inheritance diagram for libMesh::SerialMesh:

Public Types
typedef Predicates::multi_predicate	Predicate
	We need an empty, generic class to act as a predicate for this and derived mesh classes. More...

Public Member Functions
	SerialMesh (const Parallel::Communicator &comm_in, unsigned char dim=1)

	SerialMesh (const UnstructuredMesh &other_mesh)

virtual std::unique_ptr< MeshBase >	clone () const override
	Virtual copy-constructor, creates a copy of this mesh. More...

	~SerialMesh ()

virtual void	clear () override
	Clear all internal data. More...

virtual void	renumber_nodes_and_elements () override
	Remove nullptr elements from arrays. More...

virtual dof_id_type	n_nodes () const override

virtual dof_id_type	parallel_n_nodes () const override

virtual dof_id_type	max_node_id () const override

virtual void	reserve_nodes (const dof_id_type nn) override
	Reserves space for a known number of nodes. More...

virtual dof_id_type	n_elem () const override

virtual dof_id_type	parallel_n_elem () const override

virtual dof_id_type	n_active_elem () const override

virtual dof_id_type	max_elem_id () const override

virtual unique_id_type	parallel_max_unique_id () const override

virtual void	reserve_elem (const dof_id_type ne) override
	Reserves space for a known number of elements. More...

virtual void	update_parallel_id_counts () override
	Updates parallel caches so that methods like n_elem() accurately reflect changes on other processors. More...

virtual const Point &	point (const dof_id_type i) const override

virtual const Node *	node_ptr (const dof_id_type i) const override

virtual Node *	node_ptr (const dof_id_type i) override

virtual const Node *	query_node_ptr (const dof_id_type i) const override

virtual Node *	query_node_ptr (const dof_id_type i) override

virtual const Elem *	elem_ptr (const dof_id_type i) const override

virtual Elem *	elem_ptr (const dof_id_type i) override

virtual const Elem *	query_elem_ptr (const dof_id_type i) const override

virtual Elem *	query_elem_ptr (const dof_id_type i) override

virtual Node *	add_point (const Point &p, const dof_id_type id=DofObject::invalid_id, const processor_id_type proc_id=DofObject::invalid_processor_id) override
	functions for adding /deleting nodes elements. More...

virtual Node *	add_node (Node *n) override
	Add `Node` `n` to the end of the vertex array. More...

virtual Node *	insert_node (Node *n) override
	Insert `Node` `n` into the Mesh at a location consistent with n->id(), allocating extra storage if necessary. More...

virtual void	delete_node (Node *n) override
	Removes the Node n from the mesh. More...

virtual void	renumber_node (dof_id_type old_id, dof_id_type new_id) override
	Changes the id of node `old_id`, both by changing node(old_id)->id() and by moving node(old_id) in the mesh's internal container. More...

virtual Elem *	add_elem (Elem *e) override
	Add elem `e` to the end of the element array. More...

virtual Elem *	insert_elem (Elem *e) override
	Insert elem `e` to the element array, preserving its id and replacing/deleting any existing element with the same id. More...

virtual void	delete_elem (Elem *e) override
	Removes element `e` from the mesh. More...

virtual void	renumber_elem (dof_id_type old_id, dof_id_type new_id) override
	Changes the id of element `old_id`, both by changing elem(old_id)->id() and by moving elem(old_id) in the mesh's internal container. More...

virtual void	fix_broken_node_and_element_numbering () override
	There is no reason for a user to ever call this function. More...

void	stitch_meshes (const ReplicatedMesh &other_mesh, boundary_id_type this_mesh_boundary, boundary_id_type other_mesh_boundary, Real tol=TOLERANCE, bool clear_stitched_boundary_ids=false, bool verbose=true, bool use_binary_search=true, bool enforce_all_nodes_match_on_boundaries=false)
	Stitch `other_mesh` to this mesh so that this mesh is the union of the two meshes. More...

void	stitch_surfaces (boundary_id_type boundary_id_1, boundary_id_type boundary_id_2, Real tol=TOLERANCE, bool clear_stitched_boundary_ids=false, bool verbose=true, bool use_binary_search=true, bool enforce_all_nodes_match_on_boundaries=false)
	Similar to stitch_meshes, except that we stitch two adjacent surfaces within this mesh. More...

std::vector< dof_id_type >	get_disconnected_subdomains (std::vector< subdomain_id_type > *subdomain_ids=nullptr) const
	Return IDs of representative elements of all disconnected subdomains. More...

std::unordered_map< dof_id_type, std::vector< std::vector< Point > > >	get_boundary_points () const
	Return all points on boundary. More...

virtual element_iterator	elements_begin () override
	Elem iterator accessor functions. More...

virtual const_element_iterator	elements_begin () const override

virtual element_iterator	elements_end () override

virtual const_element_iterator	elements_end () const override

virtual SimpleRange< element_iterator >	element_ptr_range () override

virtual SimpleRange< const_element_iterator >	element_ptr_range () const override

virtual element_iterator	active_elements_begin () override
	Active, local, and negation forms of the element iterators described above. More...

virtual const_element_iterator	active_elements_begin () const override

virtual element_iterator	active_elements_end () override

virtual const_element_iterator	active_elements_end () const override

virtual SimpleRange< element_iterator >	active_element_ptr_range () override

virtual SimpleRange< const_element_iterator >	active_element_ptr_range () const override

virtual element_iterator	ancestor_elements_begin () override
	Iterate over elements for which elem->ancestor() is true. More...

virtual const_element_iterator	ancestor_elements_begin () const override

virtual element_iterator	ancestor_elements_end () override

virtual const_element_iterator	ancestor_elements_end () const override

virtual element_iterator	subactive_elements_begin () override
	Iterate over elements for which elem->subactive() is true. More...

virtual const_element_iterator	subactive_elements_begin () const override

virtual element_iterator	subactive_elements_end () override

virtual const_element_iterator	subactive_elements_end () const override

virtual element_iterator	not_active_elements_begin () override

virtual const_element_iterator	not_active_elements_begin () const override

virtual element_iterator	not_active_elements_end () override

virtual const_element_iterator	not_active_elements_end () const override

virtual element_iterator	not_ancestor_elements_begin () override

virtual const_element_iterator	not_ancestor_elements_begin () const override

virtual element_iterator	not_ancestor_elements_end () override

virtual const_element_iterator	not_ancestor_elements_end () const override

virtual element_iterator	not_subactive_elements_begin () override

virtual const_element_iterator	not_subactive_elements_begin () const override

virtual element_iterator	not_subactive_elements_end () override

virtual const_element_iterator	not_subactive_elements_end () const override

virtual element_iterator	local_elements_begin () override

virtual const_element_iterator	local_elements_begin () const override

virtual element_iterator	local_elements_end () override

virtual const_element_iterator	local_elements_end () const override

virtual element_iterator	semilocal_elements_begin () override
	Iterate over elements for which elem->is_semilocal() is true for the current processor. More...

virtual const_element_iterator	semilocal_elements_begin () const override

virtual element_iterator	semilocal_elements_end () override

virtual const_element_iterator	semilocal_elements_end () const override

virtual element_iterator	active_semilocal_elements_begin () override

virtual const_element_iterator	active_semilocal_elements_begin () const override

virtual element_iterator	active_semilocal_elements_end () override

virtual const_element_iterator	active_semilocal_elements_end () const override

virtual element_iterator	facelocal_elements_begin () override
	Iterate over elements which are on or have a neighbor on the current processor. More...

virtual const_element_iterator	facelocal_elements_begin () const override

virtual element_iterator	facelocal_elements_end () override

virtual const_element_iterator	facelocal_elements_end () const override

virtual element_iterator	not_local_elements_begin () override

virtual const_element_iterator	not_local_elements_begin () const override

virtual element_iterator	not_local_elements_end () override

virtual const_element_iterator	not_local_elements_end () const override

virtual element_iterator	active_local_elements_begin () override

virtual const_element_iterator	active_local_elements_begin () const override

virtual element_iterator	active_local_elements_end () override

virtual const_element_iterator	active_local_elements_end () const override

virtual SimpleRange< element_iterator >	active_local_element_ptr_range () override

virtual SimpleRange< const_element_iterator >	active_local_element_ptr_range () const override

virtual element_iterator	active_not_local_elements_begin () override

virtual const_element_iterator	active_not_local_elements_begin () const override

virtual element_iterator	active_not_local_elements_end () override

virtual const_element_iterator	active_not_local_elements_end () const override

virtual element_iterator	level_elements_begin (unsigned int level) override
	Iterate over elements of a given level. More...

virtual const_element_iterator	level_elements_begin (unsigned int level) const override

virtual element_iterator	level_elements_end (unsigned int level) override

virtual const_element_iterator	level_elements_end (unsigned int level) const override

virtual element_iterator	not_level_elements_begin (unsigned int level) override

virtual const_element_iterator	not_level_elements_begin (unsigned int level) const override

virtual element_iterator	not_level_elements_end (unsigned int level) override

virtual const_element_iterator	not_level_elements_end (unsigned int level) const override

virtual element_iterator	local_level_elements_begin (unsigned int level) override

virtual const_element_iterator	local_level_elements_begin (unsigned int level) const override

virtual element_iterator	local_level_elements_end (unsigned int level) override

virtual const_element_iterator	local_level_elements_end (unsigned int level) const override

virtual element_iterator	local_not_level_elements_begin (unsigned int level) override

virtual const_element_iterator	local_not_level_elements_begin (unsigned int level) const override

virtual element_iterator	local_not_level_elements_end (unsigned int level) override

virtual const_element_iterator	local_not_level_elements_end (unsigned int level) const override

virtual element_iterator	pid_elements_begin (processor_id_type proc_id) override
	Iterate over all elements with a specified processor id. More...

virtual const_element_iterator	pid_elements_begin (processor_id_type proc_id) const override

virtual element_iterator	pid_elements_end (processor_id_type proc_id) override

virtual const_element_iterator	pid_elements_end (processor_id_type proc_id) const override

virtual element_iterator	type_elements_begin (ElemType type) override
	Iterate over all elements with a specified geometric type. More...

virtual const_element_iterator	type_elements_begin (ElemType type) const override

virtual element_iterator	type_elements_end (ElemType type) override

virtual const_element_iterator	type_elements_end (ElemType type) const override

virtual element_iterator	active_type_elements_begin (ElemType type) override

virtual const_element_iterator	active_type_elements_begin (ElemType type) const override

virtual element_iterator	active_type_elements_end (ElemType type) override

virtual const_element_iterator	active_type_elements_end (ElemType type) const override

virtual element_iterator	active_pid_elements_begin (processor_id_type proc_id) override

virtual const_element_iterator	active_pid_elements_begin (processor_id_type proc_id) const override

virtual element_iterator	active_pid_elements_end (processor_id_type proc_id) override

virtual const_element_iterator	active_pid_elements_end (processor_id_type proc_id) const override

virtual element_iterator	unpartitioned_elements_begin () override
	Iterate over unpartitioned elements in the Mesh. More...

virtual const_element_iterator	unpartitioned_elements_begin () const override

virtual element_iterator	unpartitioned_elements_end () override

virtual const_element_iterator	unpartitioned_elements_end () const override

virtual element_iterator	active_unpartitioned_elements_begin () override
	Iterate over active unpartitioned elements in the Mesh. More...

virtual const_element_iterator	active_unpartitioned_elements_begin () const override

virtual element_iterator	active_unpartitioned_elements_end () override

virtual const_element_iterator	active_unpartitioned_elements_end () const override

virtual element_iterator	active_local_subdomain_elements_begin (subdomain_id_type subdomain_id) override

virtual const_element_iterator	active_local_subdomain_elements_begin (subdomain_id_type subdomain_id) const override

virtual element_iterator	active_local_subdomain_elements_end (subdomain_id_type subdomain_id) override

virtual const_element_iterator	active_local_subdomain_elements_end (subdomain_id_type subdomain_id) const override

virtual SimpleRange< element_iterator >	active_local_subdomain_elements_ptr_range (subdomain_id_type subdomain_id) override

virtual SimpleRange< const_element_iterator >	active_local_subdomain_elements_ptr_range (subdomain_id_type subdomain_id) const override

virtual element_iterator	active_subdomain_elements_begin (subdomain_id_type subdomain_id) override

virtual const_element_iterator	active_subdomain_elements_begin (subdomain_id_type subdomain_id) const override

virtual element_iterator	active_subdomain_elements_end (subdomain_id_type subdomain_id) override

virtual const_element_iterator	active_subdomain_elements_end (subdomain_id_type subdomain_id) const override

virtual SimpleRange< element_iterator >	active_subdomain_elements_ptr_range (subdomain_id_type subdomain_id) override

virtual SimpleRange< const_element_iterator >	active_subdomain_elements_ptr_range (subdomain_id_type subdomain_id) const override

virtual element_iterator	active_subdomain_set_elements_begin (std::set< subdomain_id_type > ss) override

virtual const_element_iterator	active_subdomain_set_elements_begin (std::set< subdomain_id_type > ss) const override

virtual element_iterator	active_subdomain_set_elements_end (std::set< subdomain_id_type > ss) override

virtual const_element_iterator	active_subdomain_set_elements_end (std::set< subdomain_id_type > ss) const override

virtual SimpleRange< element_iterator >	active_subdomain_set_elements_ptr_range (std::set< subdomain_id_type > ss) override

virtual SimpleRange< const_element_iterator >	active_subdomain_set_elements_ptr_range (std::set< subdomain_id_type > ss) const override

virtual element_iterator	ghost_elements_begin () override
	Iterate over "ghost" elements in the Mesh. More...

virtual const_element_iterator	ghost_elements_begin () const override

virtual element_iterator	ghost_elements_end () override

virtual const_element_iterator	ghost_elements_end () const override

virtual element_iterator	evaluable_elements_begin (const DofMap &dof_map, unsigned int var_num=libMesh::invalid_uint) override
	Iterate over elements in the Mesh where the solution (as distributed by the given DofMap) can be evaluated, for the given variable var_num, or for all variables by default. More...

virtual const_element_iterator	evaluable_elements_begin (const DofMap &dof_map, unsigned int var_num=libMesh::invalid_uint) const override

virtual element_iterator	evaluable_elements_end (const DofMap &dof_map, unsigned int var_num=libMesh::invalid_uint) override

virtual const_element_iterator	evaluable_elements_end (const DofMap &dof_map, unsigned int var_num=libMesh::invalid_uint) const override

virtual element_iterator	flagged_elements_begin (unsigned char rflag) override
	Iterate over all elements with a specified refinement flag. More...

virtual const_element_iterator	flagged_elements_begin (unsigned char rflag) const override

virtual element_iterator	flagged_elements_end (unsigned char rflag) override

virtual const_element_iterator	flagged_elements_end (unsigned char rflag) const override

virtual element_iterator	flagged_pid_elements_begin (unsigned char rflag, processor_id_type pid) override
	Iterate over all elements with a specified refinement flag on a specified processor. More...

virtual const_element_iterator	flagged_pid_elements_begin (unsigned char rflag, processor_id_type pid) const override

virtual element_iterator	flagged_pid_elements_end (unsigned char rflag, processor_id_type pid) override

virtual const_element_iterator	flagged_pid_elements_end (unsigned char rflag, processor_id_type pid) const override

virtual node_iterator	nodes_begin () override
	Node iterator accessor functions. More...

virtual const_node_iterator	nodes_begin () const override

virtual node_iterator	nodes_end () override

virtual const_node_iterator	nodes_end () const override

virtual SimpleRange< node_iterator >	node_ptr_range () override

virtual SimpleRange< const_node_iterator >	node_ptr_range () const override

virtual node_iterator	active_nodes_begin () override
	Iterate over only the active nodes in the Mesh. More...

virtual const_node_iterator	active_nodes_begin () const override

virtual node_iterator	active_nodes_end () override

virtual const_node_iterator	active_nodes_end () const override

virtual node_iterator	local_nodes_begin () override
	Iterate over local nodes (nodes whose processor_id() matches the current processor). More...

virtual const_node_iterator	local_nodes_begin () const override

virtual node_iterator	local_nodes_end () override

virtual const_node_iterator	local_nodes_end () const override

virtual SimpleRange< node_iterator >	local_node_ptr_range () override

virtual SimpleRange< const_node_iterator >	local_node_ptr_range () const override

virtual node_iterator	pid_nodes_begin (processor_id_type proc_id) override
	Iterate over nodes with processor_id() == proc_id. More...

virtual const_node_iterator	pid_nodes_begin (processor_id_type proc_id) const override

virtual node_iterator	pid_nodes_end (processor_id_type proc_id) override

virtual const_node_iterator	pid_nodes_end (processor_id_type proc_id) const override

virtual node_iterator	bid_nodes_begin (boundary_id_type bndry_id) override
	Iterate over nodes for which BoundaryInfo::has_boundary_id(node, bndry_id) is true. More...

virtual const_node_iterator	bid_nodes_begin (boundary_id_type bndry_id) const override

virtual node_iterator	bid_nodes_end (boundary_id_type bndry_id) override

virtual const_node_iterator	bid_nodes_end (boundary_id_type bndry_id) const override

virtual node_iterator	bnd_nodes_begin () override
	Iterate over nodes for which BoundaryInfo::n_boundary_ids(node) > 0. More...

virtual const_node_iterator	bnd_nodes_begin () const override

virtual node_iterator	bnd_nodes_end () override

virtual const_node_iterator	bnd_nodes_end () const override

virtual node_iterator	evaluable_nodes_begin (const DofMap &dof_map, unsigned int var_num=libMesh::invalid_uint) override
	Iterate over nodes in the Mesh where the solution (as distributed by the given DofMap) can be evaluated, for the given variable var_num, or for all variables by default. More...

virtual const_node_iterator	evaluable_nodes_begin (const DofMap &dof_map, unsigned int var_num=libMesh::invalid_uint) const override

virtual node_iterator	evaluable_nodes_end (const DofMap &dof_map, unsigned int var_num=libMesh::invalid_uint) override

virtual const_node_iterator	evaluable_nodes_end (const DofMap &dof_map, unsigned int var_num=libMesh::invalid_uint) const override

virtual void	read (const std::string &name, void *mesh_data=nullptr, bool skip_renumber_nodes_and_elements=false, bool skip_find_neighbors=false) override
	Reads the file specified by `name`. More...

virtual void	write (const std::string &name) override
	Write the file specified by `name`. More...

void	write (const std::string &name, const std::vector< Number > &values, const std::vector< std::string > &variable_names)
	Write to the file specified by `name`. More...

virtual void	all_first_order () override
	Converts a mesh with higher-order elements into a mesh with linear elements. More...

virtual void	all_second_order (const bool full_ordered=true) override
	Converts a (conforming, non-refined) mesh with linear elements into a mesh with second-order elements. More...

void	create_pid_mesh (UnstructuredMesh &pid_mesh, const processor_id_type pid) const
	Generates a new mesh containing all the elements which are assigned to processor `pid`. More...

void	create_submesh (UnstructuredMesh &new_mesh, const const_element_iterator &it, const const_element_iterator &it_end) const
	Constructs a mesh called "new_mesh" from the current mesh by iterating over the elements between it and it_end and adding them to the new mesh. More...

virtual void	copy_nodes_and_elements (const UnstructuredMesh &other_mesh, const bool skip_find_neighbors=false, dof_id_type element_id_offset=0, dof_id_type node_id_offset=0, unique_id_type unique_id_offset=0)
	Deep copy of nodes and elements from another unstructured mesh class (used by subclass copy constructors and by mesh merging operations) More...

virtual void	find_neighbors (const bool reset_remote_elements=false, const bool reset_current_list=true) override
	Other functions from MeshBase requiring re-definition. More...

virtual bool	contract () override
	Delete subactive (i.e. More...

virtual std::unique_ptr< Partitioner > &	partitioner ()
	A partitioner to use at each prepare_for_use() More...

const BoundaryInfo &	get_boundary_info () const
	The information about boundary ids on the mesh. More...

BoundaryInfo &	get_boundary_info ()
	Writable information about boundary ids on the mesh. More...

bool	is_prepared () const

virtual bool	is_serial () const

virtual bool	is_serial_on_zero () const

virtual void	set_distributed ()
	Asserts that not all elements and nodes of the mesh necessarily exist on the current processor. More...

virtual bool	is_replicated () const

virtual void	allgather ()
	Gathers all elements and nodes of the mesh onto every processor. More...

virtual void	gather_to_zero ()
	Gathers all elements and nodes of the mesh onto processor zero. More...

virtual void	delete_remote_elements ()
	When supported, deletes all nonlocal elements of the mesh except for "ghosts" which touch a local element, and deletes all nodes which are not part of a local or ghost element. More...

unsigned int	mesh_dimension () const

void	set_mesh_dimension (unsigned char d)
	Resets the logical dimension of the mesh. More...

const std::set< unsigned char > &	elem_dimensions () const

void	set_elem_dimensions (const std::set< unsigned char > &elem_dims)
	Most of the time you should not need to call this, as the element dimensions will be set automatically by a call to cache_elem_dims(), therefore only call this if you know what you're doing. More...

unsigned int	spatial_dimension () const

void	set_spatial_dimension (unsigned char d)
	Sets the "spatial dimension" of the Mesh. More...

dof_id_type	n_nodes_on_proc (const processor_id_type proc) const

dof_id_type	n_local_nodes () const

dof_id_type	n_unpartitioned_nodes () const

unique_id_type	next_unique_id ()

void	set_next_unique_id (unique_id_type id)
	Sets the next unique id to be used. More...

dof_id_type	n_elem_on_proc (const processor_id_type proc) const

dof_id_type	n_local_elem () const

dof_id_type	n_unpartitioned_elem () const

dof_id_type	n_active_elem_on_proc (const processor_id_type proc) const

dof_id_type	n_active_local_elem () const

dof_id_type	n_sub_elem () const

dof_id_type	n_active_sub_elem () const
	Same as `n_sub_elem()`, but only counts active elements. More...

virtual const Node &	node_ref (const dof_id_type i) const

virtual Node &	node_ref (const dof_id_type i)

virtual const Node &	node (const dof_id_type i) const

virtual Node &	node (const dof_id_type i)

virtual const Elem &	elem_ref (const dof_id_type i) const

virtual Elem &	elem_ref (const dof_id_type i)

virtual const Elem *	elem (const dof_id_type i) const

virtual Elem *	elem (const dof_id_type i)

virtual const Elem *	query_elem (const dof_id_type i) const

virtual Elem *	query_elem (const dof_id_type i)

virtual void	own_node (Node &)
	Takes ownership of node `n` on this partition of a distributed mesh, by setting n.processor_id() to this->processor_id(), as well as changing n.id() and moving it in the mesh's internal container to give it a new authoritative id. More...

ElemMappingType	default_mapping_type () const
	Returns the default master space to physical space mapping basis functions to be used on newly added elements. More...

void	set_default_mapping_type (const ElemMappingType type)
	Set the default master space to physical space mapping basis functions to be used on newly added elements. More...

unsigned char	default_mapping_data () const
	Returns any default data value used by the master space to physical space mapping. More...

void	set_default_mapping_data (const unsigned char data)
	Set the default master space to physical space mapping basis functions to be used on newly added elements. More...

unsigned int	add_elem_integer (const std::string &name, bool allocate_data=true)
	Register an integer datum (of type dof_id_type) to be added to each element in the mesh. More...

std::vector< unsigned int >	add_elem_integers (const std::vector< std::string > &names, bool allocate_data=true)
	Register integer data (of type dof_id_type) to be added to each element in the mesh, one string name for each new integer. More...

unsigned int	get_elem_integer_index (const std::string &name) const

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

const std::string &	get_elem_integer_name (unsigned int i) const

unsigned int	n_elem_integers () const

template<typename T >
unsigned int	add_elem_datum (const std::string &name, bool allocate_data=true)
	Register a datum (of type T) to be added to each element in the mesh. More...

template<typename T >
std::vector< unsigned int >	add_elem_data (const std::vector< std::string > &names, bool allocate_data=true)
	Register data (of type T) to be added to each element in the mesh. More...

unsigned int	add_node_integer (const std::string &name, bool allocate_data=true)
	Register an integer datum (of type dof_id_type) to be added to each node in the mesh. More...

std::vector< unsigned int >	add_node_integers (const std::vector< std::string > &names, bool allocate_data=true)
	Register integer data (of type dof_id_type) to be added to each node in the mesh. More...

unsigned int	get_node_integer_index (const std::string &name) const

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

const std::string &	get_node_integer_name (unsigned int i) const

unsigned int	n_node_integers () const

template<typename T >
unsigned int	add_node_datum (const std::string &name, bool allocate_data=true)
	Register a datum (of type T) to be added to each node in the mesh. More...

template<typename T >
std::vector< unsigned int >	add_node_data (const std::vector< std::string > &name, bool allocate_data=true)
	Register data (of type T) to be added to each node in the mesh. More...

void	prepare_for_use (const bool skip_renumber_nodes_and_elements=false, const bool skip_find_neighbors=false)
	Prepare a newly ecreated (or read) mesh for use. More...

virtual void	partition (const unsigned int n_parts)
	Call the default partitioner (currently `metis_partition()`). More...

void	partition ()

virtual void	redistribute ()
	Redistribute elements between processors. More...

virtual void	update_post_partitioning ()
	Recalculate any cached data after elements and nodes have been repartitioned. More...

void	allow_renumbering (bool allow)
	If false is passed in then this mesh will no longer be renumbered when being prepared for use. More...

bool	allow_renumbering () const

void	allow_remote_element_removal (bool allow)
	If false is passed in then this mesh will no longer have remote elements deleted when being prepared for use; i.e. More...

bool	allow_remote_element_removal () const

void	skip_noncritical_partitioning (bool skip)
	If true is passed in then the elements on this mesh will no longer be (re)partitioned, and the nodes on this mesh will only be repartitioned if they are found "orphaned" via coarsening or other removal of the last element responsible for their node/element processor id consistency. More...

bool	skip_noncritical_partitioning () const

void	skip_partitioning (bool skip)
	If true is passed in then nothing on this mesh will be (re)partitioned. More...

bool	skip_partitioning () const

void	add_ghosting_functor (GhostingFunctor &ghosting_functor)
	Adds a functor which can specify ghosting requirements for use on distributed meshes. More...

void	add_ghosting_functor (std::shared_ptr< GhostingFunctor > ghosting_functor)
	Adds a functor which can specify ghosting requirements for use on distributed meshes. More...

void	remove_ghosting_functor (GhostingFunctor &ghosting_functor)
	Removes a functor which was previously added to the set of ghosting functors. More...

std::set< GhostingFunctor * >::const_iterator	ghosting_functors_begin () const
	Beginning of range of ghosting functors. More...

std::set< GhostingFunctor * >::const_iterator	ghosting_functors_end () const
	End of range of ghosting functors. More...

GhostingFunctor &	default_ghosting ()
	Default ghosting functor. More...

void	subdomain_ids (std::set< subdomain_id_type > &ids) const
	Constructs a list of all subdomain identifiers in the global mesh. More...

subdomain_id_type	n_subdomains () const

unsigned int	n_partitions () const

std::string	get_info () const

void	print_info (std::ostream &os=libMesh::out) const
	Prints relevant information about the mesh. More...

unsigned int	recalculate_n_partitions ()
	In a few (very rare) cases, the user may have manually tagged the elements with specific processor IDs by hand, without using a partitioner. More...

const PointLocatorBase &	point_locator () const

std::unique_ptr< PointLocatorBase >	sub_point_locator () const

void	set_point_locator_close_to_point_tol (Real val)
	Set value used by PointLocatorBase::close_to_point_tol(). More...

Real	get_point_locator_close_to_point_tol () const

void	clear_point_locator ()
	Releases the current `PointLocator` object. More...

void	set_count_lower_dim_elems_in_point_locator (bool count_lower_dim_elems)
	In the point locator, do we count lower dimensional elements when we refine point locator regions? This is relevant in tree-based point locators, for example. More...

bool	get_count_lower_dim_elems_in_point_locator () const
	Get the current value of _count_lower_dim_elems_in_point_locator. More...

virtual void	libmesh_assert_valid_parallel_ids () const
	Verify id and processor_id consistency of our elements and nodes containers. More...

std::string &	subdomain_name (subdomain_id_type id)

const std::string &	subdomain_name (subdomain_id_type id) const

subdomain_id_type	get_id_by_name (const std::string &name) const

std::map< subdomain_id_type, std::string > &	set_subdomain_name_map ()

const std::map< subdomain_id_type, std::string > &	get_subdomain_name_map () const

void	cache_elem_dims ()
	Search the mesh and cache the different dimensions of the elements present in the mesh. More...

void	detect_interior_parents ()
	Search the mesh for elements that have a neighboring element of dim+1 and set that element as the interior parent. More...

const Parallel::Communicator &	comm () const

processor_id_type	n_processors () const

processor_id_type	processor_id () const

Public Attributes
std::unique_ptr< BoundaryInfo >	boundary_info
	This class holds the boundary information. More...

Protected Member Functions
unsigned int &	set_n_partitions ()

void	size_elem_extra_integers ()
	Size extra-integer arrays of all elements in the mesh. More...

void	size_node_extra_integers ()
	Size extra-integer arrays of all nodes in the mesh. More...

std::pair< std::vector< unsigned int >, std::vector< unsigned int > >	merge_extra_integer_names (const MeshBase &other)
	Merge extra-integer arrays from an `other` mesh. More...

Protected Attributes
std::vector< Node * >	_nodes
	The vertices (spatial coordinates) of the mesh. More...

std::vector< Elem * >	_elements
	The elements in the mesh. More...

unsigned int	_n_parts
	The number of partitions the mesh has. More...

ElemMappingType	_default_mapping_type
	The default mapping type (typically Lagrange) between master and physical space to assign to newly added elements. More...

unsigned char	_default_mapping_data
	The default mapping data (unused with Lagrange, used for nodal weight lookup index with rational bases) to assign to newly added elements. More...

bool	_is_prepared
	Flag indicating if the mesh has been prepared for use. More...

std::unique_ptr< PointLocatorBase >	_point_locator
	A `PointLocator` class for this mesh. More...

bool	_count_lower_dim_elems_in_point_locator
	Do we count lower dimensional elements in point locator refinement? This is relevant in tree-based point locators, for example. More...

std::unique_ptr< Partitioner >	_partitioner
	A partitioner to use at each prepare_for_use(). More...

unique_id_type	_next_unique_id
	The next available unique id for assigning ids to DOF objects. More...

bool	_skip_noncritical_partitioning
	If this is true then no partitioning should be done with the possible exception of orphaned nodes. More...

bool	_skip_all_partitioning
	If this is true then no partitioning should be done. More...

bool	_skip_renumber_nodes_and_elements
	If this is true then renumbering will be kept to a minimum. More...

bool	_allow_remote_element_removal
	If this is false then even on DistributedMesh remote elements will not be deleted during mesh preparation. More...

std::map< subdomain_id_type, std::string >	_block_id_to_name
	This structure maintains the mapping of named blocks for file formats that support named blocks. More...

std::set< unsigned char >	_elem_dims
	We cache the dimension of the elements present in the mesh. More...

unsigned char	_spatial_dimension
	The "spatial dimension" of the Mesh. More...

std::vector< std::string >	_elem_integer_names
	The array of names for integer data associated with each element in the mesh. More...

std::vector< std::string >	_node_integer_names
	The array of names for integer data associated with each node in the mesh. More...

std::unique_ptr< GhostingFunctor >	_default_ghosting
	The default geometric GhostingFunctor, used to implement standard libMesh element ghosting behavior. More...

std::set< GhostingFunctor * >	_ghosting_functors
	The list of all GhostingFunctor objects to be used when distributing a DistributedMesh. More...

std::map< GhostingFunctor *, std::shared_ptr< GhostingFunctor > >	_shared_functors
	Hang on to references to any GhostingFunctor objects we were passed in shared_ptr form. More...

Real	_point_locator_close_to_point_tol
	If nonzero, we will call PointLocatorBase::set_close_to_point_tol() on any PointLocators that we create. More...

const Parallel::Communicator &	_communicator

Private Types
typedef std::vector< Elem * >::iterator	elem_iterator_imp
	Typedefs for the container implementation. More...

typedef std::vector< Elem * >::const_iterator	const_elem_iterator_imp

typedef std::vector< Node * >::iterator	node_iterator_imp
	Typedefs for the container implementation. More...

typedef std::vector< Node * >::const_iterator	const_node_iterator_imp

Private Member Functions
void	stitching_helper (const ReplicatedMesh *other_mesh, boundary_id_type boundary_id_1, boundary_id_type boundary_id_2, Real tol, bool clear_stitched_boundary_ids, bool verbose, bool use_binary_search, bool enforce_all_nodes_match_on_boundaries, bool skip_find_neighbors)
	Helper function for stitch_meshes and stitch_surfaces that does the mesh stitching. More...

Detailed Description

Definition at line 34 of file serial_mesh.h.

Member Typedef Documentation

◆ const_elem_iterator_imp

typedef std::vector<Elem *>::const_iterator libMesh::ReplicatedMesh::const_elem_iterator_imp

privateinherited

Definition at line 536 of file replicated_mesh.h.

◆ const_node_iterator_imp

typedef std::vector<Node *>::const_iterator libMesh::ReplicatedMesh::const_node_iterator_imp

privateinherited

Definition at line 543 of file replicated_mesh.h.

◆ elem_iterator_imp

typedef std::vector<Elem *>::iterator libMesh::ReplicatedMesh::elem_iterator_imp

privateinherited

Typedefs for the container implementation.

In this case, it's just a std::vector<Elem *>.

Definition at line 535 of file replicated_mesh.h.

◆ node_iterator_imp

typedef std::vector<Node *>::iterator libMesh::ReplicatedMesh::node_iterator_imp

privateinherited

Typedefs for the container implementation.

In this case, it's just a std::vector<Node *>.

Definition at line 542 of file replicated_mesh.h.

◆ Predicate

typedef Predicates::multi_predicate libMesh::MeshBase::Predicate

inherited

We need an empty, generic class to act as a predicate for this and derived mesh classes.

Definition at line 1209 of file mesh_base.h.

Constructor & Destructor Documentation

◆ SerialMesh() [1/2]

libMesh::SerialMesh::SerialMesh	(	const Parallel::Communicator &	comm_in,
		unsigned char	dim = `1`
	)

inlineexplicit

Definition at line 38 of file serial_mesh.h.

40 : ReplicatedMesh(comm_in,dim) {}

◆ SerialMesh() [2/2]

libMesh::SerialMesh::SerialMesh ( const UnstructuredMesh & other_mesh )

inline

Definition at line 42 of file serial_mesh.h.

42 : ReplicatedMesh(other_mesh) {}

◆ ~SerialMesh()

libMesh::SerialMesh::~SerialMesh ( )

inline

Definition at line 47 of file serial_mesh.h.

47 {}

Member Function Documentation

◆ active_element_ptr_range() [1/2]

virtual SimpleRange<const_element_iterator> libMesh::ReplicatedMesh::active_element_ptr_range ( ) const

inlineoverridevirtualinherited

Implements libMesh::MeshBase.

Definition at line 274 of file replicated_mesh.h.

274 { return {active_elements_begin(), active_elements_end()}; }

References libMesh::ReplicatedMesh::active_elements_begin(), and libMesh::ReplicatedMesh::active_elements_end().

◆ active_element_ptr_range() [2/2]

virtual SimpleRange<element_iterator> libMesh::ReplicatedMesh::active_element_ptr_range ( )

inlineoverridevirtualinherited

Implements libMesh::MeshBase.

Definition at line 273 of file replicated_mesh.h.

273 { return {active_elements_begin(), active_elements_end()}; }

References libMesh::ReplicatedMesh::active_elements_begin(), and libMesh::ReplicatedMesh::active_elements_end().

Referenced by libMesh::ReplicatedMesh::get_boundary_points(), libMesh::ReplicatedMesh::get_disconnected_subdomains(), and libMesh::ReplicatedMesh::stitching_helper().

◆ active_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_elements_begin ( )

overridevirtualinherited

Active, local, and negation forms of the element iterators described above.

An "active" element is an element without children (i.e. has not been refined). A "local" element is one whose processor_id() matches the current processor.

Implements libMesh::MeshBase.

Referenced by libMesh::ReplicatedMesh::active_element_ptr_range(), and libMesh::ReplicatedMesh::n_active_elem().

◆ active_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

Referenced by libMesh::ReplicatedMesh::active_element_ptr_range(), and libMesh::ReplicatedMesh::n_active_elem().

◆ active_local_element_ptr_range() [1/2]

virtual SimpleRange<const_element_iterator> libMesh::ReplicatedMesh::active_local_element_ptr_range ( ) const

inlineoverridevirtualinherited

Implements libMesh::MeshBase.

Definition at line 331 of file replicated_mesh.h.

331 { return {active_local_elements_begin(), active_local_elements_end()}; }

References libMesh::ReplicatedMesh::active_local_elements_begin(), and libMesh::ReplicatedMesh::active_local_elements_end().

◆ active_local_element_ptr_range() [2/2]

virtual SimpleRange<element_iterator> libMesh::ReplicatedMesh::active_local_element_ptr_range ( )

inlineoverridevirtualinherited

Implements libMesh::MeshBase.

Definition at line 330 of file replicated_mesh.h.

330 { return {active_local_elements_begin(), active_local_elements_end()}; }

References libMesh::ReplicatedMesh::active_local_elements_begin(), and libMesh::ReplicatedMesh::active_local_elements_end().

◆ active_local_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_local_elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_local_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_local_elements_begin ( )

overridevirtualinherited

Implements libMesh::MeshBase.

Referenced by libMesh::ReplicatedMesh::active_local_element_ptr_range().

◆ active_local_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_local_elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_local_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_local_elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

Referenced by libMesh::ReplicatedMesh::active_local_element_ptr_range().

◆ active_local_subdomain_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_local_subdomain_elements_begin ( subdomain_id_type subdomain_id ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_local_subdomain_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_local_subdomain_elements_begin ( subdomain_id_type subdomain_id )

overridevirtualinherited

Implements libMesh::MeshBase.

Referenced by libMesh::ReplicatedMesh::active_local_subdomain_elements_ptr_range().

◆ active_local_subdomain_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_local_subdomain_elements_end ( subdomain_id_type subdomain_id ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_local_subdomain_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_local_subdomain_elements_end ( subdomain_id_type subdomain_id )

overridevirtualinherited

Implements libMesh::MeshBase.

Referenced by libMesh::ReplicatedMesh::active_local_subdomain_elements_ptr_range().

◆ active_local_subdomain_elements_ptr_range() [1/2]

virtual SimpleRange<const_element_iterator> libMesh::ReplicatedMesh::active_local_subdomain_elements_ptr_range ( subdomain_id_type subdomain_id ) const

inlineoverridevirtualinherited

Implements libMesh::MeshBase.

Definition at line 394 of file replicated_mesh.h.

395 { return {active_local_subdomain_elements_begin(subdomain_id), active_local_subdomain_elements_end(subdomain_id)}; }

References libMesh::ReplicatedMesh::active_local_subdomain_elements_begin(), and libMesh::ReplicatedMesh::active_local_subdomain_elements_end().

◆ active_local_subdomain_elements_ptr_range() [2/2]

virtual SimpleRange<element_iterator> libMesh::ReplicatedMesh::active_local_subdomain_elements_ptr_range ( subdomain_id_type subdomain_id )

inlineoverridevirtualinherited

Implements libMesh::MeshBase.

Definition at line 392 of file replicated_mesh.h.

393 { return {active_local_subdomain_elements_begin(subdomain_id), active_local_subdomain_elements_end(subdomain_id)}; }

References libMesh::ReplicatedMesh::active_local_subdomain_elements_begin(), and libMesh::ReplicatedMesh::active_local_subdomain_elements_end().

◆ active_nodes_begin() [1/2]

virtual const_node_iterator libMesh::ReplicatedMesh::active_nodes_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_nodes_begin() [2/2]

virtual node_iterator libMesh::ReplicatedMesh::active_nodes_begin ( )

overridevirtualinherited

Iterate over only the active nodes in the Mesh.

Implements libMesh::MeshBase.

◆ active_nodes_end() [1/2]

virtual const_node_iterator libMesh::ReplicatedMesh::active_nodes_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_nodes_end() [2/2]

virtual node_iterator libMesh::ReplicatedMesh::active_nodes_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_not_local_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_not_local_elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_not_local_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_not_local_elements_begin ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_not_local_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_not_local_elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_not_local_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_not_local_elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_pid_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_pid_elements_begin ( processor_id_type proc_id ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_pid_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_pid_elements_begin ( processor_id_type proc_id )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_pid_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_pid_elements_end ( processor_id_type proc_id ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_pid_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_pid_elements_end ( processor_id_type proc_id )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_semilocal_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_semilocal_elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_semilocal_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_semilocal_elements_begin ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_semilocal_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_semilocal_elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_semilocal_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_semilocal_elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_subdomain_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_subdomain_elements_begin ( subdomain_id_type subdomain_id ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_subdomain_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_subdomain_elements_begin ( subdomain_id_type subdomain_id )

overridevirtualinherited

Implements libMesh::MeshBase.

Referenced by libMesh::ReplicatedMesh::active_subdomain_elements_ptr_range().

◆ active_subdomain_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_subdomain_elements_end ( subdomain_id_type subdomain_id ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_subdomain_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_subdomain_elements_end ( subdomain_id_type subdomain_id )

overridevirtualinherited

Implements libMesh::MeshBase.

Referenced by libMesh::ReplicatedMesh::active_subdomain_elements_ptr_range().

◆ active_subdomain_elements_ptr_range() [1/2]

virtual SimpleRange<const_element_iterator> libMesh::ReplicatedMesh::active_subdomain_elements_ptr_range ( subdomain_id_type subdomain_id ) const

inlineoverridevirtualinherited

Implements libMesh::MeshBase.

Definition at line 403 of file replicated_mesh.h.

404 { return {active_subdomain_elements_begin(subdomain_id), active_subdomain_elements_end(subdomain_id)}; }

References libMesh::ReplicatedMesh::active_subdomain_elements_begin(), and libMesh::ReplicatedMesh::active_subdomain_elements_end().

◆ active_subdomain_elements_ptr_range() [2/2]

virtual SimpleRange<element_iterator> libMesh::ReplicatedMesh::active_subdomain_elements_ptr_range ( subdomain_id_type subdomain_id )

inlineoverridevirtualinherited

Implements libMesh::MeshBase.

Definition at line 401 of file replicated_mesh.h.

402 { return {active_subdomain_elements_begin(subdomain_id), active_subdomain_elements_end(subdomain_id)}; }

References libMesh::ReplicatedMesh::active_subdomain_elements_begin(), and libMesh::ReplicatedMesh::active_subdomain_elements_end().

◆ active_subdomain_set_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_subdomain_set_elements_begin ( std::set< subdomain_id_type > ss ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_subdomain_set_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_subdomain_set_elements_begin ( std::set< subdomain_id_type > ss )

overridevirtualinherited

Implements libMesh::MeshBase.

Referenced by libMesh::ReplicatedMesh::active_subdomain_set_elements_ptr_range().

◆ active_subdomain_set_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_subdomain_set_elements_end ( std::set< subdomain_id_type > ss ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_subdomain_set_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_subdomain_set_elements_end ( std::set< subdomain_id_type > ss )

overridevirtualinherited

Implements libMesh::MeshBase.

Referenced by libMesh::ReplicatedMesh::active_subdomain_set_elements_ptr_range().

◆ active_subdomain_set_elements_ptr_range() [1/2]

virtual SimpleRange<const_element_iterator> libMesh::ReplicatedMesh::active_subdomain_set_elements_ptr_range ( std::set< subdomain_id_type > ss ) const

inlineoverridevirtualinherited

Implements libMesh::MeshBase.

Definition at line 412 of file replicated_mesh.h.

413 { return {active_subdomain_set_elements_begin(ss), active_subdomain_set_elements_end(ss)}; }

References libMesh::ReplicatedMesh::active_subdomain_set_elements_begin(), and libMesh::ReplicatedMesh::active_subdomain_set_elements_end().

◆ active_subdomain_set_elements_ptr_range() [2/2]

virtual SimpleRange<element_iterator> libMesh::ReplicatedMesh::active_subdomain_set_elements_ptr_range ( std::set< subdomain_id_type > ss )

inlineoverridevirtualinherited

Implements libMesh::MeshBase.

Definition at line 410 of file replicated_mesh.h.

411 { return {active_subdomain_set_elements_begin(ss), active_subdomain_set_elements_end(ss)}; }

References libMesh::ReplicatedMesh::active_subdomain_set_elements_begin(), and libMesh::ReplicatedMesh::active_subdomain_set_elements_end().

◆ active_type_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_type_elements_begin ( ElemType type ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_type_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_type_elements_begin ( ElemType type )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_type_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_type_elements_end ( ElemType type ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_type_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_type_elements_end ( ElemType type )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_unpartitioned_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_unpartitioned_elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_unpartitioned_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_unpartitioned_elements_begin ( )

overridevirtualinherited

Iterate over active unpartitioned elements in the Mesh.

Implements libMesh::MeshBase.

◆ active_unpartitioned_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::active_unpartitioned_elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ active_unpartitioned_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::active_unpartitioned_elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ add_elem()

Elem * libMesh::ReplicatedMesh::add_elem ( Elem * e )

overridevirtualinherited

Add elem e to the end of the element array.

To add an element locally, set e->processor_id() before adding it. To ensure a specific element id, call e->set_id() before adding it; only do this in parallel if you are manually keeping ids consistent.

Users should call MeshBase::prepare_for_use() after elements are added to and/or deleted from the mesh.

Implements libMesh::MeshBase.

Definition at line 282 of file replicated_mesh.C.

 {
   libmesh_assert(e);
  
   // We no longer merely append elements with ReplicatedMesh
  
   // If the user requests a valid id that doesn't correspond to an
   // existing element, let's give them that id, resizing the elements
   // container if necessary.
   if (!e->valid_id())
     e->set_id (cast_int<dof_id_type>(_elements.size()));
  
 #ifdef LIBMESH_ENABLE_UNIQUE_ID
   if (!e->valid_unique_id())
     e->set_unique_id() = _next_unique_id++;
   else
    _next_unique_id = std::max(_next_unique_id, e->unique_id()+1);
 #endif
  
   const dof_id_type id = e->id();
  
   if (id < _elements.size())
     {
       // Overwriting existing elements is still probably a mistake.
       libmesh_assert(!_elements[id]);
     }
   else
     {
       _elements.resize(id+1, nullptr);
     }
  
   _elements[id] = e;
  
   // Make sure any new element is given space for any extra integers
   // we've requested
   e->add_extra_integers(_elem_integer_names.size());
  
   // And set mapping type and data on any new element
   e->set_mapping_type(this->default_mapping_type());
   e->set_mapping_data(this->default_mapping_data());
  
   return e;
 }

References libMesh::MeshBase::_elem_integer_names, libMesh::ReplicatedMesh::_elements, libMesh::MeshBase::_next_unique_id, libMesh::DofObject::add_extra_integers(), libMesh::MeshBase::default_mapping_data(), libMesh::MeshBase::default_mapping_type(), libMesh::DofObject::id(), libMesh::libmesh_assert(), libMesh::DofObject::set_id(), libMesh::Elem::set_mapping_data(), libMesh::Elem::set_mapping_type(), libMesh::DofObject::set_unique_id(), libMesh::DofObject::unique_id(), libMesh::DofObject::valid_id(), and libMesh::DofObject::valid_unique_id().

Referenced by GetBoundaryPointsTest::build_mesh(), MixedDimensionMeshTest::build_mesh(), MeshfunctionDFEM::build_mesh(), MixedDimensionNonUniformRefinement::build_mesh(), MixedDimensionNonUniformRefinementTriangle::build_mesh(), MixedDimensionNonUniformRefinement3D::build_mesh(), and libMesh::RBEIMEvaluation::legacy_write_out_interpolation_points_elem().

◆ add_elem_data()

template<typename T >

std::vector< unsigned int > libMesh::MeshBase::add_elem_data	(	const std::vector< std::string > &	names,
		bool	allocate_data = `true`
	)

inlineinherited

Register data (of type T) to be added to each element in the mesh.

If the mesh already has elements, data is allocated in each.

Returns: The starting index number for the new data, or for the existing data if one by the same name has already been added.

If type T is larger than dof_id_type, each datum will end up spanning multiple index values, but will be queried with the starting index number.

No type checking is done with this function! If you add data of type T, don't try to access it with a call specifying type U.

Definition at line 1992 of file mesh_base.h.

 {
   std::vector<unsigned int> returnval(names.size());
  
   const std::size_t old_size = _elem_integer_names.size();
  
   for (auto i : index_range(names))
     returnval[i] = this->add_elem_datum<T>(names[i], false);
  
   if (allocate_data && old_size != _elem_integer_names.size())
     this->size_elem_extra_integers();
  
   return returnval;
 }

References libMesh::MeshBase::_elem_integer_names, libMesh::index_range(), and libMesh::MeshBase::size_elem_extra_integers().

◆ add_elem_datum()

template<typename T >

unsigned int libMesh::MeshBase::add_elem_datum	(	const std::string &	name,
		bool	allocate_data = `true`
	)

inlineinherited

Register a datum (of type T) to be added to each element in the mesh.

If the mesh already has elements, data by default is allocated in each of them. This may be expensive to do repeatedly; use add_elem_data instead.

Returns: The index numbers for the new data, and/or for existing data if data by some of the same names has already been added.

If type T is larger than dof_id_type, its data will end up spanning multiple index values, but will be queried with the starting index number.

No type checking is done with this function! If you add data of type T, don't try to access it with a call specifying type U.

Definition at line 1973 of file mesh_base.h.

 {
   const std::size_t old_size = _elem_integer_names.size();
  
   unsigned int start_idx = this->add_elem_integer(name, false);
   unsigned int n_more_integers = (sizeof(T)-1)/sizeof(dof_id_type);
   for (unsigned int i=0; i != n_more_integers; ++i)
     this->add_elem_integer(name+"__"+std::to_string(i));
  
   if (allocate_data && old_size != _elem_integer_names.size())
     this->size_elem_extra_integers();
  
   return start_idx;
 }

References libMesh::MeshBase::_elem_integer_names, libMesh::MeshBase::add_elem_integer(), and libMesh::MeshBase::size_elem_extra_integers().

Referenced by ExtraIntegersTest::build_mesh().

◆ add_elem_integer()

unsigned int libMesh::MeshBase::add_elem_integer	(	const std::string &	name,
		bool	allocate_data = `true`
	)

inherited

Register an integer datum (of type dof_id_type) to be added to each element in the mesh.

If the mesh already has elements, data by default is allocated in each of them. This may be expensive to do repeatedly; use add_elem_integers instead.

Returns: The index number for the new datum, or for the existing datum if one by the same name has already been added.

Definition at line 176 of file mesh_base.C.

 {
   for (auto i : index_range(_elem_integer_names))
     if (_elem_integer_names[i] == name)
       return i;
  
   _elem_integer_names.push_back(name);
   if (allocate_data)
     this->size_elem_extra_integers();
   return _elem_integer_names.size()-1;
 }

References libMesh::MeshBase::_elem_integer_names, libMesh::index_range(), libMesh::Quality::name(), and libMesh::MeshBase::size_elem_extra_integers().

Referenced by libMesh::MeshBase::add_elem_datum(), ExtraIntegersTest::build_mesh(), ExtraIntegersTest::checkpoint_helper(), libMesh::CheckpointIO::read_header(), and ExtraIntegersTest::test_helper().

◆ add_elem_integers()

std::vector< unsigned int > libMesh::MeshBase::add_elem_integers	(	const std::vector< std::string > &	names,
		bool	allocate_data = `true`
	)

inherited

Register integer data (of type dof_id_type) to be added to each element in the mesh, one string name for each new integer.

If the mesh already has elements, data by default is allocated in each of them.

Returns: The index numbers for the new data, and/or for existing data if data by some of the same names has already been added.

Definition at line 191 of file mesh_base.C.

 {
   std::unordered_map<std::string, std::size_t> name_indices;
   for (auto i : index_range(_elem_integer_names))
     name_indices[_elem_integer_names[i]] = i;
  
   std::vector<unsigned int> returnval(names.size());
  
   bool added_an_integer = false;
   for (auto i : index_range(names))
     {
       const std::string & name = names[i];
       auto it = name_indices.find(name);
       if (it != name_indices.end())
         returnval[i] = it->second;
       else
         {
           returnval[i] = _elem_integer_names.size();
           name_indices[name] = returnval[i];
           _elem_integer_names.push_back(name);
           added_an_integer = true;
         }
     }
  
   if (allocate_data && added_an_integer)
     this->size_elem_extra_integers();
  
   return returnval;
 }

References libMesh::MeshBase::_elem_integer_names, libMesh::index_range(), and libMesh::Quality::name().

Referenced by MeshStitchTest::testMeshStitch().

◆ add_ghosting_functor() [1/2]

void libMesh::MeshBase::add_ghosting_functor ( GhostingFunctor & ghosting_functor )

inlineinherited

Adds a functor which can specify ghosting requirements for use on distributed meshes.

Multiple ghosting functors can be added; any element which is required by any functor will be ghosted.

GhostingFunctor memory must be managed by the code which calls this function; the GhostingFunctor lifetime is expected to extend until either the functor is removed or the Mesh is destructed.

Definition at line 1089 of file mesh_base.h.

1090 { _ghosting_functors.insert(&ghosting_functor); }

References libMesh::MeshBase::_ghosting_functors.

Referenced by libMesh::DofMap::add_algebraic_ghosting_functor(), libMesh::DofMap::add_coupling_functor(), libMesh::MeshBase::add_ghosting_functor(), main(), and EquationSystemsTest::testDisableDefaultGhosting().

◆ add_ghosting_functor() [2/2]

void libMesh::MeshBase::add_ghosting_functor ( std::shared_ptr< GhostingFunctor > ghosting_functor )

inlineinherited

Adds a functor which can specify ghosting requirements for use on distributed meshes.

Multiple ghosting functors can be added; any element which is required by any functor will be ghosted.

GhostingFunctor memory when using this method is managed by the shared_ptr mechanism.

Definition at line 1100 of file mesh_base.h.

1101 { _shared_functors[ghosting_functor.get()] = ghosting_functor;

1102 this->add_ghosting_functor(*ghosting_functor); }

References libMesh::MeshBase::_shared_functors, and libMesh::MeshBase::add_ghosting_functor().

◆ add_node()

Node * libMesh::ReplicatedMesh::add_node ( Node * n )

overridevirtualinherited

Add Node n to the end of the vertex array.

Implements libMesh::MeshBase.

Definition at line 472 of file replicated_mesh.C.

 {
   libmesh_assert(n);
   // We only append points with ReplicatedMesh
   libmesh_assert(!n->valid_id() || n->id() == _nodes.size());
  
   n->set_id (cast_int<dof_id_type>(_nodes.size()));
  
 #ifdef LIBMESH_ENABLE_UNIQUE_ID
   if (!n->valid_unique_id())
     n->set_unique_id() = _next_unique_id++;
 #endif
  
   n->add_extra_integers(_node_integer_names.size());
  
   _nodes.push_back(n);
  
   return n;
 }

References libMesh::MeshBase::_next_unique_id, libMesh::MeshBase::_node_integer_names, libMesh::ReplicatedMesh::_nodes, libMesh::DofObject::add_extra_integers(), libMesh::DofObject::id(), libMesh::libmesh_assert(), libMesh::DofObject::set_id(), libMesh::DofObject::set_unique_id(), libMesh::DofObject::valid_id(), and libMesh::DofObject::valid_unique_id().

◆ add_node_data()

template<typename T >

std::vector< unsigned int > libMesh::MeshBase::add_node_data	(	const std::vector< std::string > &	name,
		bool	allocate_data = `true`
	)

inlineinherited

Register data (of type T) to be added to each node in the mesh.

If the mesh already has nodes, data by default is allocated in each.

Returns: The starting index number for the new data, or for the existing data if one by the same name has already been added.

If type T is larger than dof_id_type, its data will end up spanning multiple index values, but will be queried with the starting index number.

No type checking is done with this function! If you add data of type T, don't try to access it with a call specifying type U.

Definition at line 2030 of file mesh_base.h.

 {
   std::vector<unsigned int> returnval(names.size());
  
   const std::size_t old_size = _node_integer_names.size();
  
   for (auto i : index_range(names))
     returnval[i] = this->add_node_datum<T>(names[i], false);
  
   if (allocate_data && old_size != _node_integer_names.size())
     this->size_node_extra_integers();
  
   return returnval;
 }

References libMesh::MeshBase::_node_integer_names, libMesh::index_range(), and libMesh::MeshBase::size_node_extra_integers().

◆ add_node_datum()

template<typename T >

unsigned int libMesh::MeshBase::add_node_datum	(	const std::string &	name,
		bool	allocate_data = `true`
	)

inlineinherited

Register a datum (of type T) to be added to each node in the mesh.

If the mesh already has nodes, data by default is allocated in each of them. This may be expensive to do repeatedly; use add_node_data instead.

Returns: The starting index number for the new datum, or for the existing datum if one by the same name has already been added.

If type T is larger than dof_id_type, its data will end up spanning multiple index values, but will be queried with the starting index number.

No type checking is done with this function! If you add data of type T, don't try to access it with a call specifying type U.

Definition at line 2011 of file mesh_base.h.

 {
   const std::size_t old_size = _node_integer_names.size();
  
   unsigned int start_idx = this->add_node_integer(name, false);
   unsigned int n_more_integers = (sizeof(T)-1)/sizeof(dof_id_type);
   for (unsigned int i=0; i != n_more_integers; ++i)
     this->add_node_integer(name+"__"+std::to_string(i), false);
  
   if (allocate_data && old_size != _node_integer_names.size())
     this->size_node_extra_integers();
  
   return start_idx;
 }

References libMesh::MeshBase::_node_integer_names, libMesh::MeshBase::add_node_integer(), and libMesh::MeshBase::size_node_extra_integers().

Referenced by ExtraIntegersTest::build_mesh(), libMesh::DynaIO::read_mesh(), RationalMapTest< elem_type >::setUp(), and FETest< order, family, elem_type >::setUp().

◆ add_node_integer()

unsigned int libMesh::MeshBase::add_node_integer	(	const std::string &	name,
		bool	allocate_data = `true`
	)

inherited

Register an integer datum (of type dof_id_type) to be added to each node in the mesh.

If the mesh already has nodes, data by default is allocated in each of them. This may be expensive to do repeatedly; use add_node_integers instead.

Returns: The index number for the new datum, or for the existing datum if one by the same name has already been added.

Definition at line 247 of file mesh_base.C.

 {
   for (auto i : index_range(_node_integer_names))
     if (_node_integer_names[i] == name)
       return i;
  
   _node_integer_names.push_back(name);
   if (allocate_data)
     this->size_node_extra_integers();
   return _node_integer_names.size()-1;
 }

References libMesh::index_range(), and libMesh::Quality::name().

Referenced by libMesh::MeshBase::add_node_datum(), ExtraIntegersTest::build_mesh(), ExtraIntegersTest::checkpoint_helper(), libMesh::CheckpointIO::read_header(), RationalMapTest< elem_type >::setUp(), FETest< order, family, elem_type >::setUp(), and ExtraIntegersTest::test_helper().

◆ add_node_integers()

std::vector< unsigned int > libMesh::MeshBase::add_node_integers	(	const std::vector< std::string > &	names,
		bool	allocate_data = `true`
	)

inherited

Register integer data (of type dof_id_type) to be added to each node in the mesh.

If the mesh already has nodes, data by default is allocated in each.

Returns: The index numbers for the new data, and/or for existing data if data by some of the same names has already been added.

Definition at line 262 of file mesh_base.C.

 {
   std::unordered_map<std::string, std::size_t> name_indices;
   for (auto i : index_range(_node_integer_names))
     name_indices[_node_integer_names[i]] = i;
  
   std::vector<unsigned int> returnval(names.size());
  
   bool added_an_integer = false;
   for (auto i : index_range(names))
     {
       const std::string & name = names[i];
       auto it = name_indices.find(name);
       if (it != name_indices.end())
         returnval[i] = it->second;
       else
         {
           returnval[i] = _node_integer_names.size();
           name_indices[name] = returnval[i];
           _node_integer_names.push_back(name);
           added_an_integer = true;
         }
     }
  
   if (allocate_data && added_an_integer)
     this->size_node_extra_integers();
  
   return returnval;
 }

References libMesh::index_range(), and libMesh::Quality::name().

Referenced by MeshStitchTest::testMeshStitch().

◆ add_point()

Node * libMesh::ReplicatedMesh::add_point	(	const Point &	p,
		const dof_id_type	id = `DofObject::invalid_id`,
		const processor_id_type	proc_id = `DofObject::invalid_processor_id`
	)

overridevirtualinherited

functions for adding /deleting nodes elements.

Implements libMesh::MeshBase.

Definition at line 417 of file replicated_mesh.C.

 {
   //   // We only append points with ReplicatedMesh
   //   libmesh_assert(id == DofObject::invalid_id || id == _nodes.size());
   //   Node *n = Node::build(p, _nodes.size()).release();
   //   n->processor_id() = proc_id;
   //   _nodes.push_back (n);
  
   Node * n = nullptr;
  
   // If the user requests a valid id, either
   // provide the existing node or resize the container
   // to fit the new node.
   if (id != DofObject::invalid_id)
     if (id < _nodes.size())
       n = _nodes[id];
     else
       _nodes.resize(id+1);
   else
     _nodes.push_back (static_cast<Node *>(nullptr));
  
   // if the node already exists, then assign new (x,y,z) values
   if (n)
     *n = p;
   // otherwise build a new node, put it in the right spot, and return
   // a valid pointer.
   else
     {
       n = Node::build(p, (id == DofObject::invalid_id) ?
                       cast_int<dof_id_type>(_nodes.size()-1) : id).release();
       n->processor_id() = proc_id;
  
       n->add_extra_integers(_node_integer_names.size());
  
 #ifdef LIBMESH_ENABLE_UNIQUE_ID
       if (!n->valid_unique_id())
         n->set_unique_id() = _next_unique_id++;
 #endif
  
       if (id == DofObject::invalid_id)
         _nodes.back() = n;
       else
         _nodes[id] = n;
     }
  
   // better not pass back a nullptr.
   libmesh_assert (n);
  
   return n;
 }

References libMesh::MeshBase::_next_unique_id, libMesh::MeshBase::_node_integer_names, libMesh::ReplicatedMesh::_nodes, libMesh::DofObject::add_extra_integers(), libMesh::Node::build(), libMesh::DofObject::invalid_id, libMesh::libmesh_assert(), libMesh::DofObject::processor_id(), libMesh::DofObject::set_unique_id(), and libMesh::DofObject::valid_unique_id().

Referenced by GetBoundaryPointsTest::build_mesh(), MixedDimensionMeshTest::build_mesh(), MeshfunctionDFEM::build_mesh(), MixedDimensionNonUniformRefinement::build_mesh(), MixedDimensionNonUniformRefinementTriangle::build_mesh(), MixedDimensionNonUniformRefinement3D::build_mesh(), and libMesh::RBEIMEvaluation::legacy_write_out_interpolation_points_elem().

◆ all_first_order()

void libMesh::UnstructuredMesh::all_first_order ( )

overridevirtualinherited

Converts a mesh with higher-order elements into a mesh with linear elements.

For example, a mesh consisting of Tet10 will be converted to a mesh with Tet4 etc.

Prepare to identify (and then delete) a bunch of no-longer-used nodes.

If the second order element had any boundary conditions they should be transferred to the first-order element. The old boundary conditions will be removed from the BoundaryInfo data structure by insert_elem.

Implements libMesh::MeshBase.

Definition at line 860 of file unstructured_mesh.C.

 {
   /*
    * when the mesh is not prepared,
    * at least renumber the nodes and
    * elements, so that the node ids
    * are correct
    */
   if (!this->_is_prepared)
     this->renumber_nodes_and_elements ();
  
   START_LOG("all_first_order()", "Mesh");
  
   std::vector<bool> node_touched_by_me(this->max_node_id(), false);
  
   // Loop over the high-ordered elements.
   // First make sure they _are_ indeed high-order, and then replace
   // them with an equivalent first-order element.
   for (auto & so_elem : element_ptr_range())
     {
       libmesh_assert(so_elem);
  
       /*
        * build the first-order equivalent, add to
        * the new_elements list.
        */
       Elem * lo_elem = Elem::build
         (Elem::first_order_equivalent_type
          (so_elem->type()), so_elem->parent()).release();
  
       const unsigned short n_sides = so_elem->n_sides();
  
       for (unsigned short s=0; s != n_sides; ++s)
         if (so_elem->neighbor_ptr(s) == remote_elem)
           lo_elem->set_neighbor(s, const_cast<RemoteElem *>(remote_elem));
  
 #ifdef LIBMESH_ENABLE_AMR
       /*
        * Reset the parent links of any child elements
        */
       if (so_elem->has_children())
         for (unsigned int c = 0, nc = so_elem->n_children(); c != nc; ++c)
           {
             Elem * child = so_elem->child_ptr(c);
             if (child != remote_elem)
               child->set_parent(lo_elem);
             lo_elem->add_child(child, c);
           }
  
       /*
        * Reset the child link of any parent element
        */
       if (so_elem->parent())
         {
           unsigned int c =
             so_elem->parent()->which_child_am_i(so_elem);
           lo_elem->parent()->replace_child(lo_elem, c);
         }
  
       /*
        * Copy as much data to the new element as makes sense
        */
       lo_elem->set_p_level(so_elem->p_level());
       lo_elem->set_refinement_flag(so_elem->refinement_flag());
       lo_elem->set_p_refinement_flag(so_elem->p_refinement_flag());
 #endif
  
       libmesh_assert_equal_to (lo_elem->n_vertices(), so_elem->n_vertices());
  
       /*
        * By definition the vertices of the linear and
        * second order element are identically numbered.
        * transfer these.
        */
       for (unsigned int v=0, snv=so_elem->n_vertices(); v < snv; v++)
         {
           lo_elem->set_node(v) = so_elem->node_ptr(v);
           node_touched_by_me[lo_elem->node_id(v)] = true;
         }
  
       /*
        * find_neighbors relies on remote_elem neighbor links being
        * properly maintained.
        */
       for (unsigned short s=0; s != n_sides; s++)
         {
           if (so_elem->neighbor_ptr(s) == remote_elem)
             lo_elem->set_neighbor(s, const_cast<RemoteElem*>(remote_elem));
         }
  
       this->get_boundary_info().copy_boundary_ids
         (this->get_boundary_info(), so_elem, lo_elem);
  
       /*
        * The new first-order element is ready.
        * Inserting it into the mesh will replace and delete
        * the second-order element.
        */
       lo_elem->set_id(so_elem->id());
 #ifdef LIBMESH_ENABLE_UNIQUE_ID
       lo_elem->set_unique_id() = so_elem->unique_id();
 #endif
       lo_elem->processor_id() = so_elem->processor_id();
       lo_elem->subdomain_id() = so_elem->subdomain_id();
       this->insert_elem(lo_elem);
     }
  
   // Deleting nodes does not invalidate iterators, so this is safe.
   for (const auto & node : this->node_ptr_range())
     if (!node_touched_by_me[node->id()])
       this->delete_node(node);
  
   // If crazy people applied boundary info to non-vertices and then
   // deleted those non-vertices, we should make sure their boundary id
   // caches are correct.
   this->get_boundary_info().regenerate_id_sets();
  
   STOP_LOG("all_first_order()", "Mesh");
  
   // On hanging nodes that used to also be second order nodes, we
   // might now have an invalid nodal processor_id()
   Partitioner::set_node_processor_ids(*this);
  
   // delete or renumber nodes if desired
   this->prepare_for_use();
 }

◆ all_second_order()

void libMesh::UnstructuredMesh::all_second_order ( const bool full_ordered = true )

overridevirtualinherited

Converts a (conforming, non-refined) mesh with linear elements into a mesh with second-order elements.

For example, a mesh consisting of Tet4 will be converted to a mesh with Tet10 etc.

Note: For some elements like Hex8 there exist two higher order equivalents, Hex20 and Hex27. When full_ordered is true (default), then Hex27 is built. Otherwise, Hex20 is built. The same holds obviously for Quad4, Prism6, etc.

On distributed meshes we currently only support unpartitioned meshes (where we'll add every node in sync) or completely-partitioned meshes (where we'll sync nodes later); let's keep track to make sure we're not in any in-between state.

Loop over the low-ordered elements in the elements vector. First make sure they _are indeed low-order, and then replace them with an equivalent second-order element. Don't forget to delete the low-order element, or else it will leak!

If the linear element had any boundary conditions they should be transferred to the second-order element. The old boundary conditions will be removed from the BoundaryInfo data structure by insert_elem.

Also, prepare_for_use() will reconstruct most of our neighbor links, but if we have any remote_elem links in a distributed mesh, they need to be preserved. We do that in the same loop here.

Implements libMesh::MeshBase.

Definition at line 998 of file unstructured_mesh.C.

 {
   // This function must be run on all processors at once
   parallel_object_only();
  
   /*
    * when the mesh is not prepared,
    * at least renumber the nodes and
    * elements, so that the node ids
    * are correct
    */
   if (!this->_is_prepared)
     this->renumber_nodes_and_elements ();
  
   /*
    * If the mesh is empty
    * then we have nothing to do
    */
   if (!this->n_elem())
     return;
  
   /*
    * If the mesh is already second order
    * then we have nothing to do.
    * We have to test for this in a round-about way to avoid
    * a bug on distributed parallel meshes with more processors
    * than elements.
    */
   bool already_second_order = false;
   if (this->elements_begin() != this->elements_end() &&
       (*(this->elements_begin()))->default_order() != FIRST)
     already_second_order = true;
   this->comm().max(already_second_order);
   if (already_second_order)
     return;
  
   START_LOG("all_second_order()", "Mesh");
  
   /*
    * this map helps in identifying second order
    * nodes.  Namely, a second-order node:
    * - edge node
    * - face node
    * - bubble node
    * is uniquely defined through a set of adjacent
    * vertices.  This set of adjacent vertices is
    * used to identify already added higher-order
    * nodes.  We are safe to use node id's since we
    * make sure that these are correctly numbered.
    */
   std::map<std::vector<dof_id_type>, Node *> adj_vertices_to_so_nodes;
  
   /*
    * for speed-up of the \p add_point() method, we
    * can reserve memory.  Guess the number of additional
    * nodes for different dimensions
    */
   switch (this->mesh_dimension())
     {
     case 1:
       /*
        * in 1D, there can only be order-increase from Edge2
        * to Edge3.  Something like 1/2 of n_nodes() have
        * to be added
        */
       this->reserve_nodes(static_cast<unsigned int>
                           (1.5*static_cast<double>(this->n_nodes())));
       break;
  
     case 2:
       /*
        * in 2D, either refine from Tri3 to Tri6 (double the nodes)
        * or from Quad4 to Quad8 (again, double) or Quad9 (2.25 that much)
        */
       this->reserve_nodes(static_cast<unsigned int>
                           (2*static_cast<double>(this->n_nodes())));
       break;
  
  
     case 3:
       /*
        * in 3D, either refine from Tet4 to Tet10 (factor = 2.5) up to
        * Hex8 to Hex27 (something  > 3).  Since in 3D there _are_ already
        * quite some nodes, and since we do not want to overburden the memory by
        * a too conservative guess, use the lower bound
        */
       this->reserve_nodes(static_cast<unsigned int>
                           (2.5*static_cast<double>(this->n_nodes())));
       break;
  
     default:
       // Hm?
       libmesh_error_msg("Unknown mesh dimension " << this->mesh_dimension());
     }
  
  
  
   /*
    * form a vector that will hold the node id's of
    * the vertices that are adjacent to the son-th
    * second-order node.  Pull this outside of the
    * loop so that silly compilers don't repeatedly
    * create and destroy the vector.
    */
   std::vector<dof_id_type> adjacent_vertices_ids;
  
   dof_id_type n_unpartitioned_elem = 0,
               n_partitioned_elem = 0;
   const processor_id_type my_pid = this->processor_id();
  
   element_iterator
     it = elements_begin(),
     endit = elements_end();
  
   for (; it != endit; ++it)
     {
       // the linear-order element
       Elem * lo_elem = *it;
  
       libmesh_assert(lo_elem);
  
       // make sure it is linear order
       if (lo_elem->default_order() != FIRST)
         libmesh_error_msg("ERROR: This is not a linear element: type=" << lo_elem->type());
  
       // this does _not_ work for refined elements
       libmesh_assert_equal_to (lo_elem->level (), 0);
  
       const processor_id_type lo_pid = lo_elem->processor_id();
  
       if (lo_pid == DofObject::invalid_processor_id)
         ++n_unpartitioned_elem;
       else
         ++n_partitioned_elem;
  
       /*
        * build the second-order equivalent, add to
        * the new_elements list.  Note that this here
        * is the only point where \p full_ordered
        * is necessary.  The remaining code works well
        * for either type of second-order equivalent, e.g.
        * Hex20 or Hex27, as equivalents for Hex8
        */
       Elem * so_elem =
         Elem::build (Elem::second_order_equivalent_type(lo_elem->type(),
                                                         full_ordered) ).release();
  
       libmesh_assert_equal_to (lo_elem->n_vertices(), so_elem->n_vertices());
  
  
       /*
        * By definition the vertices of the linear and
        * second order element are identically numbered.
        * transfer these.
        */
       for (unsigned int v=0, lnv=lo_elem->n_vertices(); v < lnv; v++)
         so_elem->set_node(v) = lo_elem->node_ptr(v);
  
       /*
        * Now handle the additional mid-side nodes.  This
        * is simply handled through a map that remembers
        * the already-added nodes.  This map maps the global
        * ids of the vertices (that uniquely define this
        * higher-order node) to the new node.
        * Notation: son = second-order node
        */
       const unsigned int son_begin = so_elem->n_vertices();
       const unsigned int son_end   = so_elem->n_nodes();
  
  
       for (unsigned int son=son_begin; son<son_end; son++)
         {
           const unsigned int n_adjacent_vertices =
             so_elem->n_second_order_adjacent_vertices(son);
  
           adjacent_vertices_ids.resize(n_adjacent_vertices);
  
           for (unsigned int v=0; v<n_adjacent_vertices; v++)
             adjacent_vertices_ids[v] =
               so_elem->node_id( so_elem->second_order_adjacent_vertex(son,v) );
  
           /*
            * \p adjacent_vertices_ids is now in order of the current
            * side.  sort it, so that comparisons  with the
            * \p adjacent_vertices_ids created through other elements'
            * sides can match
            */
           std::sort(adjacent_vertices_ids.begin(),
                     adjacent_vertices_ids.end());
  
  
           // does this set of vertices already have a mid-node added?
           auto pos = adj_vertices_to_so_nodes.equal_range (adjacent_vertices_ids);
  
           // no, not added yet
           if (pos.first == pos.second)
             {
               /*
                * for this set of vertices, there is no
                * second_order node yet.  Add it.
                *
                * compute the location of the new node as
                * the average over the adjacent vertices.
                */
               Point new_location = this->point(adjacent_vertices_ids[0]);
               for (unsigned int v=1; v<n_adjacent_vertices; v++)
                 new_location += this->point(adjacent_vertices_ids[v]);
  
               new_location /= static_cast<Real>(n_adjacent_vertices);
  
               /* Add the new point to the mesh.
                * If we are on a serialized mesh, then we're doing this
                * all in sync, and the node processor_id will be
                * consistent between processors.
                * If we are on a distributed mesh, we can fix
                * inconsistent processor ids later, but only if every
                * processor gives new nodes a *locally* consistent
                * processor id, so we'll give the new node the
                * processor id of an adjacent element for now and then
                * we'll update that later if appropriate.
                */
               Node * so_node = this->add_point
                 (new_location, DofObject::invalid_id, lo_pid);
  
               /*
                * insert the new node with its defining vertex
                * set into the map, and relocate pos to this
                * new entry, so that the so_elem can use
                * \p pos for inserting the node
                */
               adj_vertices_to_so_nodes.insert(pos.first,
                                               std::make_pair(adjacent_vertices_ids,
                                                              so_node));
  
               so_elem->set_node(son) = so_node;
             }
           // yes, already added.
           else
             {
               Node * so_node = pos.first->second;
               libmesh_assert(so_node);
  
               so_elem->set_node(son) = so_node;
  
               // We need to ensure that the processor who should own a
               // node *knows* they own the node.  And because
               // Node::choose_processor_id() may depend on Node id,
               // which may not yet be authoritative, we still have to
               // use a dumb-but-id-independent partitioning heuristic.
               processor_id_type chosen_pid =
                 std::min (so_node->processor_id(), lo_pid);
  
               // Plus, if we just discovered that we own this node,
               // then on a distributed mesh we need to make sure to
               // give it a valid id, not just a placeholder id!
               if (!this->is_replicated() &&
                   so_node->processor_id() != my_pid &&
                   chosen_pid == my_pid)
                 this->own_node(*so_node);
  
               so_node->processor_id() = chosen_pid;
             }
         }
  
       /*
        * find_neighbors relies on remote_elem neighbor links being
        * properly maintained.
        */
       for (auto s : lo_elem->side_index_range())
         {
           if (lo_elem->neighbor_ptr(s) == remote_elem)
             so_elem->set_neighbor(s, const_cast<RemoteElem*>(remote_elem));
         }
  
       this->get_boundary_info().copy_boundary_ids
         (this->get_boundary_info(), lo_elem, so_elem);
  
       /*
        * The new second-order element is ready.
        * Inserting it into the mesh will replace and delete
        * the first-order element.
        */
       so_elem->set_id(lo_elem->id());
 #ifdef LIBMESH_ENABLE_UNIQUE_ID
       so_elem->set_unique_id() = lo_elem->unique_id();
 #endif
       so_elem->processor_id() = lo_pid;
       so_elem->subdomain_id() = lo_elem->subdomain_id();
       this->insert_elem(so_elem);
     }
  
   // we can clear the map
   adj_vertices_to_so_nodes.clear();
  
  
   STOP_LOG("all_second_order()", "Mesh");
  
   // On a DistributedMesh our ghost node processor ids may be bad,
   // the ids of nodes touching remote elements may be inconsistent,
   // unique_ids of newly added non-local nodes remain unset, and our
   // partitioning of new nodes may not be well balanced.
   //
   // make_nodes_parallel_consistent() will fix all this.
   if (!this->is_replicated())
     {
       dof_id_type max_unpartitioned_elem = n_unpartitioned_elem;
       this->comm().max(max_unpartitioned_elem);
       if (max_unpartitioned_elem)
         {
           // We'd better be effectively serialized here.  In theory we
           // could support more complicated cases but in practice we
           // only support "completely partitioned" and/or "serialized"
           if (!this->comm().verify(n_unpartitioned_elem) ||
               !this->comm().verify(n_partitioned_elem) ||
               !this->is_serial())
             libmesh_not_implemented();
         }
       else
         {
           MeshCommunication().make_nodes_parallel_consistent (*this);
         }
     }
  
   // renumber nodes, elements etc
   this->prepare_for_use(/*skip_renumber =*/ false);
 }

◆ allgather()

virtual void libMesh::MeshBase::allgather ( )

inlinevirtualinherited

Gathers all elements and nodes of the mesh onto every processor.

Reimplemented in libMesh::DistributedMesh.

Definition at line 188 of file mesh_base.h.

188 {}

Referenced by libMesh::EquationSystems::allgather(), libMesh::MeshSerializer::MeshSerializer(), and PartitionerTest< PartitionerSubclass, MeshClass >::testPartition().

◆ allow_remote_element_removal() [1/2]

bool libMesh::MeshBase::allow_remote_element_removal ( ) const

inlineinherited

Definition at line 1035 of file mesh_base.h.

1035 { return _allow_remote_element_removal; }

References libMesh::MeshBase::_allow_remote_element_removal.

Referenced by libMesh::UnstructuredMesh::copy_nodes_and_elements().

◆ allow_remote_element_removal() [2/2]

void libMesh::MeshBase::allow_remote_element_removal ( bool allow )

inlineinherited

If false is passed in then this mesh will no longer have remote elements deleted when being prepared for use; i.e.

even a DistributedMesh will remain (if it is already) serialized. This may adversely affect performance and memory use.

Definition at line 1034 of file mesh_base.h.

1034 { _allow_remote_element_removal = allow; }

References libMesh::MeshBase::_allow_remote_element_removal.

Referenced by libMesh::DynaIO::add_spline_constraints(), AllSecondOrderTest::allSecondOrder(), libMesh::UnstructuredMesh::copy_nodes_and_elements(), main(), MeshInputTest::testDynaReadElem(), and MeshInputTest::testDynaReadPatch().

◆ allow_renumbering() [1/2]

bool libMesh::MeshBase::allow_renumbering ( ) const

inlineinherited

Definition at line 1026 of file mesh_base.h.

1026 { return !_skip_renumber_nodes_and_elements; }

References libMesh::MeshBase::_skip_renumber_nodes_and_elements.

Referenced by libMesh::UnstructuredMesh::copy_nodes_and_elements(), and libMesh::UnstructuredMesh::read().

◆ allow_renumbering() [2/2]

void libMesh::MeshBase::allow_renumbering ( bool allow )

inlineinherited

If false is passed in then this mesh will no longer be renumbered when being prepared for use.

This may slightly adversely affect performance during subsequent element access, particularly when using a distributed mesh.

Important! When allow_renumbering(false) is set, ReplicatedMesh::n_elem() and ReplicatedMesh::n_nodes() will return wrong values whenever adaptive refinement is followed by adaptive coarsening. (Uniform refinement followed by uniform coarsening is OK.) This is due to the fact that n_elem() and n_nodes() are currently O(1) functions that just return the size of the respective underlying vectors, and this size is wrong when the numbering includes "gaps" from nodes and elements that have been deleted. We plan to implement a caching mechanism in the near future that will fix this incorrect behavior.

Definition at line 1025 of file mesh_base.h.

1025 { _skip_renumber_nodes_and_elements = !allow; }

References libMesh::MeshBase::_skip_renumber_nodes_and_elements.

Referenced by libMesh::DynaIO::add_spline_constraints(), GetBoundaryPointsTest::build_mesh(), SlitMeshTest::build_mesh(), libMesh::UnstructuredMesh::copy_nodes_and_elements(), main(), libMesh::RBEIMEvaluation::RBEIMEvaluation(), libMesh::NameBasedIO::read(), libMesh::GMVIO::read(), MeshInputTest::testDynaReadElem(), MeshInputTest::testDynaReadPatch(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), SystemsTest::testProjectMatrix3D(), EquationSystemsTest::testRefineThenReinitPreserveFlags(), EquationSystemsTest::testRepartitionThenReinit(), WriteSidesetData::testWrite(), and WriteVecAndScalar::testWrite().

◆ ancestor_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::ancestor_elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ ancestor_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::ancestor_elements_begin ( )

overridevirtualinherited

Iterate over elements for which elem->ancestor() is true.

Implements libMesh::MeshBase.

◆ ancestor_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::ancestor_elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ ancestor_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::ancestor_elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ bid_nodes_begin() [1/2]

virtual const_node_iterator libMesh::ReplicatedMesh::bid_nodes_begin ( boundary_id_type bndry_id ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ bid_nodes_begin() [2/2]

virtual node_iterator libMesh::ReplicatedMesh::bid_nodes_begin ( boundary_id_type bndry_id )

overridevirtualinherited

Iterate over nodes for which BoundaryInfo::has_boundary_id(node, bndry_id) is true.

Implements libMesh::MeshBase.

◆ bid_nodes_end() [1/2]

virtual const_node_iterator libMesh::ReplicatedMesh::bid_nodes_end ( boundary_id_type bndry_id ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ bid_nodes_end() [2/2]

virtual node_iterator libMesh::ReplicatedMesh::bid_nodes_end ( boundary_id_type bndry_id )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ bnd_nodes_begin() [1/2]

virtual const_node_iterator libMesh::ReplicatedMesh::bnd_nodes_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ bnd_nodes_begin() [2/2]

virtual node_iterator libMesh::ReplicatedMesh::bnd_nodes_begin ( )

overridevirtualinherited

Iterate over nodes for which BoundaryInfo::n_boundary_ids(node) > 0.

Implements libMesh::MeshBase.

◆ bnd_nodes_end() [1/2]

virtual const_node_iterator libMesh::ReplicatedMesh::bnd_nodes_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ bnd_nodes_end() [2/2]

virtual node_iterator libMesh::ReplicatedMesh::bnd_nodes_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ cache_elem_dims()

void libMesh::MeshBase::cache_elem_dims ( )

inherited

Search the mesh and cache the different dimensions of the elements present in the mesh.

This is done in prepare_for_use(), but can be done manually by other classes after major mesh modifications.

Definition at line 753 of file mesh_base.C.

 {
   // This requires an inspection on every processor
   parallel_object_only();
  
   // Need to clear _elem_dims first in case all elements of a
   // particular dimension have been deleted.
   _elem_dims.clear();
  
   for (const auto & elem : this->active_element_ptr_range())
     _elem_dims.insert(cast_int<unsigned char>(elem->dim()));
  
   // Some different dimension elements may only live on other processors
   this->comm().set_union(_elem_dims);
  
   // If the largest element dimension found is larger than the current
   // _spatial_dimension, increase _spatial_dimension.
   unsigned int max_dim = this->mesh_dimension();
   if (max_dim > _spatial_dimension)
     _spatial_dimension = cast_int<unsigned char>(max_dim);
  
   // _spatial_dimension may need to increase from 1->2 or 2->3 if the
   // mesh is full of 1D elements but they are not x-aligned, or the
   // mesh is full of 2D elements but they are not in the x-y plane.
   // If the mesh is x-aligned or x-y planar, we will end up checking
   // every node's coordinates and not breaking out of the loop
   // early...
 #if LIBMESH_DIM > 1
   if (_spatial_dimension < 3)
     {
       for (const auto & node : this->node_ptr_range())
         {
           // Note: the exact floating point comparison is intentional,
           // we don't want to get tripped up by tolerances.
           if ((*node)(1) != 0.)
             {
               _spatial_dimension = 2;
 #if LIBMESH_DIM == 2
               // If libmesh is compiled in 2D mode, this is the
               // largest spatial dimension possible so we can break
               // out.
               break;
 #endif
             }
  
 #if LIBMESH_DIM > 2
           if ((*node)(2) != 0.)
             {
               // Spatial dimension can't get any higher than this, so
               // we can break out.
               _spatial_dimension = 3;
               break;
             }
 #endif
         }
     }
 #endif // LIBMESH_DIM > 1
 }

Referenced by libMesh::MeshBase::set_elem_dimensions().

◆ clear()

void libMesh::ReplicatedMesh::clear ( )

overridevirtualinherited

Clear all internal data.

Reimplemented from libMesh::MeshBase.

Definition at line 593 of file replicated_mesh.C.

 {
   // Call parent clear function
   MeshBase::clear();
  
   // Clear our elements and nodes
   // There is no need to remove the elements from
   // the BoundaryInfo data structure since we
   // already cleared it.
   for (auto & elem : _elements)
     delete elem;
  
   _elements.clear();
  
   // clear the nodes data structure
   // There is no need to remove the nodes from
   // the BoundaryInfo data structure since we
   // already cleared it.
   for (auto & node : _nodes)
     delete node;
  
   _nodes.clear();
 }

References libMesh::ReplicatedMesh::_elements, libMesh::ReplicatedMesh::_nodes, libMesh::MeshBase::clear(), libMesh::MeshBase::elem(), and libMesh::MeshBase::node().

Referenced by libMesh::RBEIMEvaluation::clear(), libMesh::RBEIMEvaluation::legacy_write_out_interpolation_points_elem(), libMesh::RBDataDeserialization::load_rb_eim_evaluation_data(), and libMesh::ReplicatedMesh::~ReplicatedMesh().

◆ clear_point_locator()

void libMesh::MeshBase::clear_point_locator ( )

inherited

Releases the current PointLocator object.

Definition at line 696 of file mesh_base.C.

 {
   _point_locator.reset(nullptr);
 }

Referenced by libMesh::UnstructuredMesh::contract(), and libMesh::MeshCommunication::delete_remote_elements().

◆ clone()

virtual std::unique_ptr<MeshBase> libMesh::SerialMesh::clone ( ) const

inlineoverridevirtual

Virtual copy-constructor, creates a copy of this mesh.

Reimplemented from libMesh::ReplicatedMesh.

Definition at line 44 of file serial_mesh.h.

45 { return libmesh_make_unique<SerialMesh>(*this); }

◆ comm()

const Parallel::Communicator& libMesh::ParallelObject::comm ( ) const

inlineinherited

Returns: A reference to the Parallel::Communicator object used by this mesh.

Definition at line 94 of file parallel_object.h.

95 { return _communicator; }

References libMesh::ParallelObject::_communicator.

◆ contract()

bool libMesh::UnstructuredMesh::contract ( )

overridevirtualinherited

Delete subactive (i.e.

children of coarsened) elements. This removes all elements descended from currently active elements in the mesh.

Implements libMesh::MeshBase.

Definition at line 797 of file unstructured_mesh.C.

 {
   LOG_SCOPE ("contract()", "Mesh");
  
   // Flag indicating if this call actually changes the mesh
   bool mesh_changed = false;
  
 #ifdef DEBUG
   for (const auto & elem : this->element_ptr_range())
     libmesh_assert(elem->active() || elem->subactive() || elem->ancestor());
 #endif
  
   // Loop over the elements.
   for (auto & elem : this->element_ptr_range())
     {
       // Delete all the subactive ones
       if (elem->subactive())
         {
           // No level-0 element should be subactive.
           // Note that we CAN'T test elem->level(), as that
           // touches elem->parent()->dim(), and elem->parent()
           // might have already been deleted!
           libmesh_assert(elem->parent());
  
           // Delete the element
           // This just sets a pointer to nullptr, and doesn't
           // invalidate any iterators
           this->delete_elem(elem);
  
           // the mesh has certainly changed
           mesh_changed = true;
         }
       else
         {
           // Compress all the active ones
           if (elem->active())
             elem->contract();
           else
             libmesh_assert (elem->ancestor());
         }
     }
  
   // Strip any newly-created nullptr voids out of the element array
   this->renumber_nodes_and_elements();
  
   // FIXME: Need to understand why deleting subactive children
   // invalidates the point locator.  For now we will clear it explicitly
   this->clear_point_locator();
  
   // Allow our GhostingFunctor objects to reinit if necessary.
   for (auto & gf : as_range(this->ghosting_functors_begin(),
                             this->ghosting_functors_end()))
     {
       libmesh_assert(gf);
       gf->mesh_reinit();
     }
  
   return mesh_changed;
 }

References libMesh::Elem::active(), libMesh::Elem::ancestor(), libMesh::as_range(), libMesh::MeshBase::clear_point_locator(), libMesh::Elem::contract(), libMesh::MeshBase::delete_elem(), libMesh::MeshBase::elem(), libMesh::MeshBase::element_ptr_range(), libMesh::MeshBase::ghosting_functors_begin(), libMesh::MeshBase::ghosting_functors_end(), libMesh::libmesh_assert(), libMesh::Elem::parent(), libMesh::MeshBase::renumber_nodes_and_elements(), and libMesh::Elem::subactive().

◆ copy_nodes_and_elements()

void libMesh::UnstructuredMesh::copy_nodes_and_elements	(	const UnstructuredMesh &	other_mesh,
		const bool	skip_find_neighbors = `false`,
		dof_id_type	element_id_offset = `0`,
		dof_id_type	node_id_offset = `0`,
		unique_id_type	unique_id_offset = `0`
	)

virtualinherited

Deep copy of nodes and elements from another unstructured mesh class (used by subclass copy constructors and by mesh merging operations)

This will not copy most "high level" data in the mesh; that is done separately by constructors. An exception is that, if the other_mesh has element or node extra_integer data, any names for that data which do not already exist on this mesh are added so that all such data can be copied.

Definition at line 61 of file unstructured_mesh.C.

 {
   LOG_SCOPE("copy_nodes_and_elements()", "UnstructuredMesh");
  
   std::pair<std::vector<unsigned int>, std::vector<unsigned int>>
     extra_int_maps = this->merge_extra_integer_names(other_mesh);
  
   const unsigned int n_old_node_ints = extra_int_maps.second.size(),
                      n_new_node_ints = _node_integer_names.size(),
                      n_old_elem_ints = extra_int_maps.first.size(),
                      n_new_elem_ints = _elem_integer_names.size();
  
   // If we are partitioned into fewer parts than the incoming mesh,
   // then we need to "wrap" the other Mesh's processor ids to fit
   // within our range. This can happen, for example, while stitching
   // ReplicatedMeshes with small numbers of elements in parallel...
   bool wrap_proc_ids = (_n_parts < other_mesh._n_parts);
  
   // We're assuming our subclass data needs no copy
   libmesh_assert_equal_to (_is_prepared, other_mesh._is_prepared);
  
   // We're assuming the other mesh has proper element number ordering,
   // so that we add parents before their children, and that the other
   // mesh is consistently partitioned.
 #ifdef DEBUG
   MeshTools::libmesh_assert_valid_amr_elem_ids(other_mesh);
   MeshTools::libmesh_assert_valid_procids<Node>(other_mesh);
 #endif
  
   //Copy in Nodes
   {
     //Preallocate Memory if necessary
     this->reserve_nodes(other_mesh.n_nodes());
  
     for (const auto & oldn : other_mesh.node_ptr_range())
       {
         processor_id_type added_pid = cast_int<processor_id_type>
           (wrap_proc_ids ? oldn->processor_id() % _n_parts : oldn->processor_id());
  
         // Add new nodes in old node Point locations
         Node * newn =
           this->add_point(*oldn,
                           oldn->id() + node_id_offset,
                           added_pid);
  
         newn->add_extra_integers(n_new_node_ints);
         for (unsigned int i = 0; i != n_old_node_ints; ++i)
           newn->set_extra_integer(extra_int_maps.second[i],
                                   oldn->get_extra_integer(i));
  
 #ifdef LIBMESH_ENABLE_UNIQUE_ID
         newn->set_unique_id() =
           oldn->unique_id() + unique_id_offset;
 #endif
       }
   }
  
   //Copy in Elements
   {
     //Preallocate Memory if necessary
     this->reserve_elem(other_mesh.n_elem());
  
     // Declare a map linking old and new elements, needed to copy the neighbor lists
     typedef std::unordered_map<const Elem *, Elem *> map_type;
     map_type old_elems_to_new_elems;
  
     // Loop over the elements
     for (const auto & old : other_mesh.element_ptr_range())
       {
         // Build a new element
         Elem * newparent = old->parent() ?
           this->elem_ptr(old->parent()->id() + element_id_offset) :
           nullptr;
         std::unique_ptr<Elem> ap = Elem::build(old->type(), newparent);
         Elem * el = ap.release();
  
         el->subdomain_id() = old->subdomain_id();
  
 #ifdef LIBMESH_ENABLE_AMR
         if (old->has_children())
           for (unsigned int c = 0, nc = old->n_children(); c != nc; ++c)
             if (old->child_ptr(c) == remote_elem)
               el->add_child(const_cast<RemoteElem *>(remote_elem), c);
  
         //Create the parent's child pointers if necessary
         if (newparent)
           {
             unsigned int oldc = old->parent()->which_child_am_i(old);
             newparent->add_child(el, oldc);
           }
  
         // Copy the refinement flags
         el->set_refinement_flag(old->refinement_flag());
  
         // Use hack_p_level since we may not have sibling elements
         // added yet
         el->hack_p_level(old->p_level());
  
         el->set_p_refinement_flag(old->p_refinement_flag());
 #endif // #ifdef LIBMESH_ENABLE_AMR
  
         //Assign all the nodes
         for (auto i : el->node_index_range())
           el->set_node(i) =
             this->node_ptr(old->node_id(i) + node_id_offset);
  
         // And start it off with the same processor id (mod _n_parts).
         el->processor_id() = cast_int<processor_id_type>
           (wrap_proc_ids ? old->processor_id() % _n_parts : old->processor_id());
  
         // Give it the same element and unique ids
         el->set_id(old->id() + element_id_offset);
  
         el->add_extra_integers(n_new_elem_ints);
         for (unsigned int i = 0; i != n_old_elem_ints; ++i)
           el->set_extra_integer(extra_int_maps.first[i],
                                 old->get_extra_integer(i));
  
 #ifdef LIBMESH_ENABLE_UNIQUE_ID
         el->set_unique_id() =
           old->unique_id() + unique_id_offset;
 #endif
  
         //Hold onto it
         if (!skip_find_neighbors)
           {
             for (auto s : old->side_index_range())
               if (old->neighbor_ptr(s) == remote_elem)
                 el->set_neighbor(s, const_cast<RemoteElem *>(remote_elem));
             this->add_elem(el);
           }
         else
           {
             Elem * new_el = this->add_elem(el);
             old_elems_to_new_elems[old] = new_el;
           }
       }
  
     // Loop (again) over the elements to fill in the neighbors
     if (skip_find_neighbors)
       {
         old_elems_to_new_elems[remote_elem] = const_cast<RemoteElem*>(remote_elem);
  
         for (const auto & old_elem : other_mesh.element_ptr_range())
           {
             Elem * new_elem = old_elems_to_new_elems[old_elem];
             for (auto s : old_elem->side_index_range())
               {
                 const Elem * old_neighbor = old_elem->neighbor_ptr(s);
                 Elem * new_neighbor = old_elems_to_new_elems[old_neighbor];
                 new_elem->set_neighbor(s, new_neighbor);
               }
           }
       }
   }
  
   //Finally prepare the new Mesh for use.  Keep the same numbering and
   //partitioning for now.
   this->allow_renumbering(false);
   this->allow_remote_element_removal(false);
  
   // We should generally be able to skip *all* partitioning here
   // because we're only adding one already-consistent mesh to another.
   this->skip_partitioning(true);
  
   this->prepare_for_use(false, skip_find_neighbors);
  
   //But in the long term, use the same renumbering and partitioning
   //policies as our source mesh.
   this->allow_renumbering(other_mesh.allow_renumbering());
   this->allow_remote_element_removal(other_mesh.allow_remote_element_removal());
   this->skip_partitioning(other_mesh._skip_all_partitioning);
   this->skip_noncritical_partitioning(other_mesh._skip_noncritical_partitioning);
 }

Referenced by libMesh::DistributedMesh::DistributedMesh(), libMesh::ReplicatedMesh::ReplicatedMesh(), and libMesh::ReplicatedMesh::stitching_helper().

◆ create_pid_mesh()

void libMesh::UnstructuredMesh::create_pid_mesh	(	UnstructuredMesh &	pid_mesh,
		const processor_id_type	pid
	)		const

inherited

Generates a new mesh containing all the elements which are assigned to processor pid.

This mesh is written to the pid_mesh reference which you must create and pass to the function.

Definition at line 672 of file unstructured_mesh.C.

 {
  
   // Issue a warning if the number the number of processors
   // currently available is less that that requested for
   // partitioning.  This is not necessarily an error since
   // you may run on one processor and still partition the
   // mesh into several partitions.
 #ifdef DEBUG
   if (this->n_processors() < pid)
     {
       libMesh::out << "WARNING:  You are creating a "
                    << "mesh for a processor id (="
                    << pid
                    << ") greater than "
                    << "the number of processors available for "
                    << "the calculation. (="
                    << this->n_processors()
                    << ")."
                    << std::endl;
     }
 #endif
  
   this->create_submesh (pid_mesh,
                         this->active_pid_elements_begin(pid),
                         this->active_pid_elements_end(pid));
 }

References libMesh::MeshBase::active_pid_elements_begin(), libMesh::MeshBase::active_pid_elements_end(), libMesh::UnstructuredMesh::create_submesh(), libMesh::ParallelObject::n_processors(), and libMesh::out.

◆ create_submesh()

void libMesh::UnstructuredMesh::create_submesh	(	UnstructuredMesh &	new_mesh,
		const const_element_iterator &	it,
		const const_element_iterator &	it_end
	)		const

inherited

Constructs a mesh called "new_mesh" from the current mesh by iterating over the elements between it and it_end and adding them to the new mesh.

Definition at line 707 of file unstructured_mesh.C.

 {
   // Just in case the subdomain_mesh already has some information
   // in it, get rid of it.
   new_mesh.clear();
  
   // If we're not serial, our submesh isn't either.
   // There are no remote elements to delete on an empty mesh, but
   // calling the method to do so marks the mesh as parallel.
   if (!this->is_serial())
     new_mesh.delete_remote_elements();
  
   // Fail if (*this == new_mesh), we cannot create a submesh inside ourself!
   // This may happen if the user accidentally passes the original mesh into
   // this function!  We will check this by making sure we did not just
   // clear ourself.
   libmesh_assert_not_equal_to (this->n_nodes(), 0);
   libmesh_assert_not_equal_to (this->n_elem(), 0);
  
   // Container to catch boundary IDs handed back by BoundaryInfo
   std::vector<boundary_id_type> bc_ids;
  
   // Put any extra integers on the new mesh too
   new_mesh.merge_extra_integer_names(*this);
   const unsigned int n_node_ints = _node_integer_names.size(),
                      n_elem_ints = _elem_integer_names.size();
  
   for (const auto & old_elem : as_range(it, it_end))
     {
       // Add an equivalent element type to the new_mesh.
       // Copy ids for this element.
       Elem * new_elem = Elem::build(old_elem->type()).release();
       new_elem->set_id() = old_elem->id();
 #ifdef LIBMESH_ENABLE_UNIQUE_ID
       new_elem->set_unique_id() = old_elem->unique_id();
 #endif
       new_elem->subdomain_id() = old_elem->subdomain_id();
       new_elem->processor_id() = old_elem->processor_id();
  
       new_elem->add_extra_integers(n_elem_ints);
       for (unsigned int i = 0; i != n_elem_ints; ++i)
         new_elem->set_extra_integer(i, old_elem->get_extra_integer(i));
  
       new_mesh.add_elem (new_elem);
  
       libmesh_assert(new_elem);
  
       // Loop over the nodes on this element.
       for (auto n : old_elem->node_index_range())
         {
           const dof_id_type this_node_id = old_elem->node_id(n);
  
           // Add this node to the new mesh if it's not there already
           if (!new_mesh.query_node_ptr(this_node_id))
             {
               Node * newn =
                 new_mesh.add_point (old_elem->point(n),
                                     this_node_id,
                                     old_elem->node_ptr(n)->processor_id());
  
               newn->add_extra_integers(n_node_ints);
               for (unsigned int i = 0; i != n_node_ints; ++i)
                 newn->set_extra_integer(i, old_elem->node_ptr(n)->get_extra_integer(i));
  
 #ifdef LIBMESH_ENABLE_UNIQUE_ID
               newn->set_unique_id() = old_elem->node_ptr(n)->unique_id();
 #endif
             }
  
           // Define this element's connectivity on the new mesh
           new_elem->set_node(n) = new_mesh.node_ptr(this_node_id);
         }
  
       // Maybe add boundary conditions for this element
       for (auto s : old_elem->side_index_range())
         {
           this->get_boundary_info().boundary_ids(old_elem, s, bc_ids);
           new_mesh.get_boundary_info().add_side (new_elem, s, bc_ids);
         }
     } // end loop over elements
  
   // Prepare the new_mesh for use
   new_mesh.prepare_for_use(/*skip_renumber =*/false);
 }

Referenced by libMesh::UnstructuredMesh::create_pid_mesh().

◆ default_ghosting()

GhostingFunctor& libMesh::MeshBase::default_ghosting ( )

inlineinherited

Default ghosting functor.

Definition at line 1125 of file mesh_base.h.

1125 { return *_default_ghosting; }

References libMesh::MeshBase::_default_ghosting.

◆ default_mapping_data()

unsigned char libMesh::MeshBase::default_mapping_data ( ) const

inlineinherited

Returns any default data value used by the master space to physical space mapping.

Definition at line 724 of file mesh_base.h.

                                               {
     return _default_mapping_data;
   }

References libMesh::MeshBase::_default_mapping_data.

Referenced by libMesh::ReplicatedMesh::add_elem(), libMesh::DistributedMesh::add_elem(), libMesh::ReplicatedMesh::insert_elem(), libMesh::DistributedMesh::insert_elem(), MeshInputTest::testDynaReadElem(), and MeshInputTest::testDynaReadPatch().

◆ default_mapping_type()

ElemMappingType libMesh::MeshBase::default_mapping_type ( ) const

inlineinherited

Returns the default master space to physical space mapping basis functions to be used on newly added elements.

Definition at line 708 of file mesh_base.h.

                                                 {
     return _default_mapping_type;
   }

References libMesh::MeshBase::_default_mapping_type.

Referenced by libMesh::ReplicatedMesh::add_elem(), libMesh::DistributedMesh::add_elem(), libMesh::ReplicatedMesh::insert_elem(), libMesh::DistributedMesh::insert_elem(), MeshInputTest::testDynaReadElem(), and MeshInputTest::testDynaReadPatch().

◆ delete_elem()

void libMesh::ReplicatedMesh::delete_elem ( Elem * e )

overridevirtualinherited

Removes element e from the mesh.

This method must be implemented in derived classes in such a way that it does not invalidate element iterators. Users should call MeshBase::prepare_for_use() after elements are added to and/or deleted from the mesh.

Note: Calling this method may produce isolated nodes, i.e. nodes not connected to any element.

Implements libMesh::MeshBase.

Definition at line 360 of file replicated_mesh.C.

 {
   libmesh_assert(e);
  
   // Initialize an iterator to eventually point to the element we want to delete
   std::vector<Elem *>::iterator pos = _elements.end();
  
   // In many cases, e->id() gives us a clue as to where e
   // is located in the _elements vector.  Try that first
   // before trying the O(n_elem) search.
   libmesh_assert_less (e->id(), _elements.size());
  
   if (_elements[e->id()] == e)
     {
       // We found it!
       pos = _elements.begin();
       std::advance(pos, e->id());
     }
  
   else
     {
       // This search is O(n_elem)
       pos = std::find (_elements.begin(),
                        _elements.end(),
                        e);
     }
  
   // Huh? Element not in the vector?
   libmesh_assert (pos != _elements.end());
  
   // Remove the element from the BoundaryInfo object
   this->get_boundary_info().remove(e);
  
   // delete the element
   delete e;
  
   // explicitly zero the pointer
   *pos = nullptr;
 }

References libMesh::ReplicatedMesh::_elements, libMesh::MeshBase::get_boundary_info(), libMesh::DofObject::id(), libMesh::libmesh_assert(), and libMesh::BoundaryInfo::remove().

Referenced by libMesh::ReplicatedMesh::insert_elem().

◆ delete_node()

void libMesh::ReplicatedMesh::delete_node ( Node * n )

overridevirtualinherited

Removes the Node n from the mesh.

Implements libMesh::MeshBase.

Definition at line 539 of file replicated_mesh.C.

 {
   libmesh_assert(n);
   libmesh_assert_less (n->id(), _nodes.size());
  
   // Initialize an iterator to eventually point to the element we want
   // to delete
   std::vector<Node *>::iterator pos;
  
   // In many cases, e->id() gives us a clue as to where e
   // is located in the _elements vector.  Try that first
   // before trying the O(n_elem) search.
   if (_nodes[n->id()] == n)
     {
       pos = _nodes.begin();
       std::advance(pos, n->id());
     }
   else
     {
       pos = std::find (_nodes.begin(),
                        _nodes.end(),
                        n);
     }
  
   // Huh? Node not in the vector?
   libmesh_assert (pos != _nodes.end());
  
   // Delete the node from the BoundaryInfo object
   this->get_boundary_info().remove(n);
  
   // delete the node
   delete n;
  
   // explicitly zero the pointer
   *pos = nullptr;
 }

References libMesh::ReplicatedMesh::_nodes, libMesh::MeshBase::get_boundary_info(), libMesh::DofObject::id(), libMesh::libmesh_assert(), and libMesh::BoundaryInfo::remove().

Referenced by libMesh::ReplicatedMesh::stitching_helper().

◆ delete_remote_elements()

virtual void libMesh::MeshBase::delete_remote_elements ( )

inlinevirtualinherited

When supported, deletes all nonlocal elements of the mesh except for "ghosts" which touch a local element, and deletes all nodes which are not part of a local or ghost element.

Reimplemented in libMesh::DistributedMesh.

Definition at line 201 of file mesh_base.h.

201 {}

Referenced by libMesh::MeshTools::Generation::build_extrusion(), libMesh::UnstructuredMesh::create_submesh(), libMesh::Nemesis_IO::read(), libMesh::BoundaryInfo::sync(), and libMesh::MeshSerializer::~MeshSerializer().

◆ detect_interior_parents()

void libMesh::MeshBase::detect_interior_parents ( )

inherited

Search the mesh for elements that have a neighboring element of dim+1 and set that element as the interior parent.

Definition at line 812 of file mesh_base.C.

 {
   // This requires an inspection on every processor
   parallel_object_only();
  
   // Check if the mesh contains mixed dimensions. If so, then set interior parents, otherwise return.
   if (this->elem_dimensions().size() == 1)
     return;
  
   //This map will be used to set interior parents
   std::unordered_map<dof_id_type, std::vector<dof_id_type>> node_to_elem;
  
   for (const auto & elem : this->active_element_ptr_range())
     {
       // Populating the node_to_elem map, same as MeshTools::build_nodes_to_elem_map
       for (auto n : IntRange<unsigned int>(0, elem->n_vertices()))
         {
           libmesh_assert_less (elem->id(), this->max_elem_id());
  
           node_to_elem[elem->node_id(n)].push_back(elem->id());
         }
     }
  
   // Automatically set interior parents
   for (const auto & element : this->element_ptr_range())
     {
       // Ignore an 3D element or an element that already has an interior parent
       if (element->dim()>=LIBMESH_DIM || element->interior_parent())
         continue;
  
       // Start by generating a SET of elements that are dim+1 to the current
       // element at each vertex of the current element, thus ignoring interior nodes.
       // If one of the SET of elements is empty, then we will not have an interior parent
       // since an interior parent must be connected to all vertices of the current element
       std::vector<std::set<dof_id_type>> neighbors( element->n_vertices() );
  
       bool found_interior_parents = false;
  
       for (auto n : IntRange<unsigned int>(0, element->n_vertices()))
         {
           std::vector<dof_id_type> & element_ids = node_to_elem[element->node_id(n)];
           for (const auto & eid : element_ids)
             if (this->elem_ref(eid).dim() == element->dim()+1)
               neighbors[n].insert(eid);
  
           if (neighbors[n].size()>0)
             {
               found_interior_parents = true;
             }
           else
             {
               // We have found an empty set, no reason to continue
               // Ensure we set this flag to false before the break since it could have
               // been set to true for previous vertex
               found_interior_parents = false;
               break;
             }
         }
  
       // If we have successfully generated a set of elements for each vertex, we will compare
       // the set for vertex 0 will the sets for the vertices until we find a id that exists in
       // all sets.  If found, this is our an interior parent id.  The interior parent id found
       // will be the lowest element id if there is potential for multiple interior parents.
       if (found_interior_parents)
         {
           std::set<dof_id_type> & neighbors_0 = neighbors[0];
           for (const auto & interior_parent_id : neighbors_0)
             {
               found_interior_parents = false;
               for (auto n : IntRange<unsigned int>(1, element->n_vertices()))
                 {
                   if (neighbors[n].find(interior_parent_id)!=neighbors[n].end())
                     {
                       found_interior_parents=true;
                     }
                   else
                     {
                       found_interior_parents=false;
                       break;
                     }
                 }
               if (found_interior_parents)
                 {
                   element->set_interior_parent(this->elem_ptr(interior_parent_id));
                   break;
                 }
             }
         }
     }
 }

References dim.

◆ elem() [1/2]

virtual Elem* libMesh::MeshBase::elem ( const dof_id_type i )

inlinevirtualinherited

Returns: A writable pointer to the \( i^{th} \) element, which should be present in this processor's subset of the mesh data structure.

Definition at line 569 of file mesh_base.h.

   {
     libmesh_deprecated();
     return this->elem_ptr(i);
   }

References libMesh::MeshBase::elem_ptr().

◆ elem() [2/2]

virtual const Elem* libMesh::MeshBase::elem ( const dof_id_type i ) const

inlinevirtualinherited

Returns: A pointer to the \( i^{th} \) element, which should be present in this processor's subset of the mesh data structure.

Definition at line 554 of file mesh_base.h.

   {
     libmesh_deprecated();
     return this->elem_ptr(i);
   }

References libMesh::MeshBase::elem_ptr().

Referenced by libMesh::ReplicatedMesh::clear(), libMesh::DistributedMesh::clear(), libMesh::UnstructuredMesh::contract(), libMesh::DistributedMesh::DistributedMesh(), libMesh::ReplicatedMesh::get_boundary_points(), libMesh::ReplicatedMesh::get_disconnected_subdomains(), libMesh::DistributedMesh::renumber_nodes_and_elements(), and libMesh::ReplicatedMesh::stitching_helper().

◆ elem_dimensions()

const std::set<unsigned char>& libMesh::MeshBase::elem_dimensions ( ) const

inlineinherited

Returns: A const reference to a std::set of element dimensions present in the mesh.

Definition at line 225 of file mesh_base.h.

226 { return _elem_dims; }

References libMesh::MeshBase::_elem_dims.

Referenced by libMesh::System::calculate_norm(), and libMesh::TreeNode< N >::insert().

◆ elem_ptr() [1/2]

const Elem * libMesh::ReplicatedMesh::elem_ptr ( const dof_id_type i ) const

overridevirtualinherited

Returns: A pointer to the \( i^{th} \) element, which should be present in this processor's subset of the mesh data structure.

Implements libMesh::MeshBase.

Definition at line 232 of file replicated_mesh.C.

 {
   libmesh_assert_less (i, this->n_elem());
   libmesh_assert(_elements[i]);
   libmesh_assert_equal_to (_elements[i]->id(), i); // This will change soon
  
   return _elements[i];
 }

References libMesh::ReplicatedMesh::_elements, libMesh::libmesh_assert(), and libMesh::ReplicatedMesh::n_elem().

Referenced by libMesh::RBEIMEvaluation::legacy_read_in_interpolation_points_elem(), libMesh::ReplicatedMesh::stitching_helper(), MixedDimensionMeshTest::testDofOrdering(), MixedDimensionNonUniformRefinement::testDofOrdering(), MixedDimensionNonUniformRefinementTriangle::testDofOrdering(), MixedDimensionNonUniformRefinement3D::testDofOrdering(), MixedDimensionNonUniformRefinement::testMesh(), MixedDimensionNonUniformRefinementTriangle::testMesh(), and MixedDimensionNonUniformRefinement3D::testMesh().

◆ elem_ptr() [2/2]

Elem * libMesh::ReplicatedMesh::elem_ptr ( const dof_id_type i )

overridevirtualinherited

Returns: A writable pointer to the \( i^{th} \) element, which should be present in this processor's subset of the mesh data structure.

Implements libMesh::MeshBase.

Definition at line 244 of file replicated_mesh.C.

 {
   libmesh_assert_less (i, this->n_elem());
   libmesh_assert(_elements[i]);
   libmesh_assert_equal_to (_elements[i]->id(), i); // This will change soon
  
   return _elements[i];
 }

References libMesh::ReplicatedMesh::_elements, libMesh::libmesh_assert(), and libMesh::ReplicatedMesh::n_elem().

◆ elem_ref() [1/2]

virtual Elem& libMesh::MeshBase::elem_ref ( const dof_id_type i )

inlinevirtualinherited

Returns: A writable reference to the \( i^{th} \) element, which should be present in this processor's subset of the mesh data structure.

Definition at line 530 of file mesh_base.h.

                                                 {
     return *this->elem_ptr(i);
   }

References libMesh::MeshBase::elem_ptr().

◆ elem_ref() [2/2]

virtual const Elem& libMesh::MeshBase::elem_ref ( const dof_id_type i ) const

inlinevirtualinherited

Returns: A reference to the \( i^{th} \) element, which should be present in this processor's subset of the mesh data structure.

Definition at line 521 of file mesh_base.h.

                                                             {
     return *this->elem_ptr(i);
   }

References libMesh::MeshBase::elem_ptr().

Referenced by libMesh::SyncRefinementFlags::act_on_data(), libMesh::AbaqusIO::assign_sideset_ids(), libMesh::AbaqusIO::assign_subdomain_ids(), libMesh::Nemesis_IO_Helper::build_element_and_node_maps(), libMesh::InfElemBuilder::build_inf_elem(), MixedDimensionNonUniformRefinement::build_mesh(), MixedDimensionNonUniformRefinementTriangle::build_mesh(), MixedDimensionNonUniformRefinement3D::build_mesh(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::SubFunctor::find_dofs_to_send(), libMesh::SyncRefinementFlags::gather_data(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::ExodusII_IO::read(), libMesh::CheckpointIO::read_remote_elem(), SystemsTest::testDofCouplingWithVarGroups(), MeshExtruderTest::testExtruder(), MixedDimensionMeshTest::testMesh(), SlitMeshTest::testMesh(), MixedDimensionNonUniformRefinement::testMesh(), MixedDimensionNonUniformRefinementTriangle::testMesh(), MixedDimensionNonUniformRefinement3D::testMesh(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::FroIO::write(), libMesh::Nemesis_IO_Helper::write_elements(), and libMesh::GmshIO::write_mesh().

◆ element_ptr_range() [1/2]

virtual SimpleRange<const_element_iterator> libMesh::ReplicatedMesh::element_ptr_range ( ) const

inlineoverridevirtualinherited

Implements libMesh::MeshBase.

Definition at line 267 of file replicated_mesh.h.

267 { return {elements_begin(), elements_end()}; }

References libMesh::ReplicatedMesh::elements_begin(), and libMesh::ReplicatedMesh::elements_end().

◆ element_ptr_range() [2/2]

virtual SimpleRange<element_iterator> libMesh::ReplicatedMesh::element_ptr_range ( )

inlineoverridevirtualinherited

Implements libMesh::MeshBase.

Definition at line 266 of file replicated_mesh.h.

266 { return {elements_begin(), elements_end()}; }

References libMesh::ReplicatedMesh::elements_begin(), and libMesh::ReplicatedMesh::elements_end().

Referenced by libMesh::ReplicatedMesh::stitching_helper().

◆ elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::elements_begin ( )

overridevirtualinherited

Elem iterator accessor functions.

Implements libMesh::MeshBase.

Referenced by libMesh::ReplicatedMesh::element_ptr_range().

◆ elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

Referenced by libMesh::ReplicatedMesh::element_ptr_range().

◆ evaluable_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::evaluable_elements_begin	(	const DofMap &	dof_map,
		unsigned int	var_num = `libMesh::invalid_uint`
	)		const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ evaluable_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::evaluable_elements_begin	(	const DofMap &	dof_map,
		unsigned int	var_num = `libMesh::invalid_uint`
	)

overridevirtualinherited

Iterate over elements in the Mesh where the solution (as distributed by the given DofMap) can be evaluated, for the given variable var_num, or for all variables by default.

Implements libMesh::MeshBase.

◆ evaluable_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::evaluable_elements_end	(	const DofMap &	dof_map,
		unsigned int	var_num = `libMesh::invalid_uint`
	)		const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ evaluable_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::evaluable_elements_end	(	const DofMap &	dof_map,
		unsigned int	var_num = `libMesh::invalid_uint`
	)

overridevirtualinherited

Implements libMesh::MeshBase.

◆ evaluable_nodes_begin() [1/2]

virtual const_node_iterator libMesh::ReplicatedMesh::evaluable_nodes_begin	(	const DofMap &	dof_map,
		unsigned int	var_num = `libMesh::invalid_uint`
	)		const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ evaluable_nodes_begin() [2/2]

virtual node_iterator libMesh::ReplicatedMesh::evaluable_nodes_begin	(	const DofMap &	dof_map,
		unsigned int	var_num = `libMesh::invalid_uint`
	)

overridevirtualinherited

Iterate over nodes in the Mesh where the solution (as distributed by the given DofMap) can be evaluated, for the given variable var_num, or for all variables by default.

Implements libMesh::MeshBase.

◆ evaluable_nodes_end() [1/2]

virtual const_node_iterator libMesh::ReplicatedMesh::evaluable_nodes_end	(	const DofMap &	dof_map,
		unsigned int	var_num = `libMesh::invalid_uint`
	)		const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ evaluable_nodes_end() [2/2]

virtual node_iterator libMesh::ReplicatedMesh::evaluable_nodes_end	(	const DofMap &	dof_map,
		unsigned int	var_num = `libMesh::invalid_uint`
	)

overridevirtualinherited

Implements libMesh::MeshBase.

◆ facelocal_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::facelocal_elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ facelocal_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::facelocal_elements_begin ( )

overridevirtualinherited

Iterate over elements which are on or have a neighbor on the current processor.

Implements libMesh::MeshBase.

◆ facelocal_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::facelocal_elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ facelocal_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::facelocal_elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ find_neighbors()

void libMesh::UnstructuredMesh::find_neighbors	(	const bool	reset_remote_elements = `false`,
		const bool	reset_current_list = `true`
	)

overridevirtualinherited

Other functions from MeshBase requiring re-definition.

Here we look at all of the child elements which don't already have valid neighbors.

If a child element has a nullptr neighbor it is either because it is on the boundary or because its neighbor is at a different level. In the latter case we must get the neighbor from the parent.

If a child element has a remote_elem neighbor on a boundary it shares with its parent, that info may have become out-dated through coarsening of the neighbor's parent. In this case, if the parent's neighbor is active then the child should share it.

Furthermore, that neighbor better be active, otherwise we missed a child somewhere.

We also need to look through children ordered by increasing refinement level in order to add new interior_parent() links in boundary elements which have just been generated by refinement, and fix links in boundary elements whose previous interior_parent() has just been coarsened away.

Implements libMesh::MeshBase.

Definition at line 257 of file unstructured_mesh.C.

 {
   // We might actually want to run this on an empty mesh
   // (e.g. the boundary mesh for a nonexistent bcid!)
   // libmesh_assert_not_equal_to (this->n_nodes(), 0);
   // libmesh_assert_not_equal_to (this->n_elem(), 0);
  
   // This function must be run on all processors at once
   parallel_object_only();
  
   LOG_SCOPE("find_neighbors()", "Mesh");
  
   //TODO:[BSK] This should be removed later?!
   if (reset_current_list)
     for (const auto & e : this->element_ptr_range())
       for (auto s : e->side_index_range())
         if (e->neighbor_ptr(s) != remote_elem || reset_remote_elements)
           e->set_neighbor(s, nullptr);
  
   // Find neighboring elements by first finding elements
   // with identical side keys and then check to see if they
   // are neighbors
   {
     // data structures -- Use the hash_multimap if available
     typedef unsigned int                    key_type;
     typedef std::pair<Elem *, unsigned char> val_type;
     typedef std::pair<key_type, val_type>   key_val_pair;
  
     typedef std::unordered_multimap<key_type, val_type> map_type;
  
     // A map from side keys to corresponding elements & side numbers
     map_type side_to_elem_map;
  
     // Pull objects out of the loop to reduce heap operations
     std::unique_ptr<Elem> my_side, their_side;
  
     for (const auto & element : this->element_ptr_range())
       {
         for (auto ms : element->side_index_range())
           {
           next_side:
             // If we haven't yet found a neighbor on this side, try.
             // Even if we think our neighbor is remote, that
             // information may be out of date.
             if (element->neighbor_ptr(ms) == nullptr ||
                 element->neighbor_ptr(ms) == remote_elem)
               {
                 // Get the key for the side of this element
                 const unsigned int key = element->key(ms);
  
                 // Look for elements that have an identical side key
                 auto bounds = side_to_elem_map.equal_range(key);
  
                 // May be multiple keys, check all the possible
                 // elements which _might_ be neighbors.
                 if (bounds.first != bounds.second)
                   {
                     // Get the side for this element
                     element->side_ptr(my_side, ms);
  
                     // Look at all the entries with an equivalent key
                     while (bounds.first != bounds.second)
                       {
                         // Get the potential element
                         Elem * neighbor = bounds.first->second.first;
  
                         // Get the side for the neighboring element
                         const unsigned int ns = bounds.first->second.second;
                         neighbor->side_ptr(their_side, ns);
                         //libmesh_assert(my_side.get());
                         //libmesh_assert(their_side.get());
  
                         // If found a match with my side
                         //
                         // We need special tests here for 1D:
                         // since parents and children have an equal
                         // side (i.e. a node), we need to check
                         // ns != ms, and we also check level() to
                         // avoid setting our neighbor pointer to
                         // any of our neighbor's descendants
                         if ((*my_side == *their_side) &&
                             (element->level() == neighbor->level()) &&
                             ((element->dim() != 1) || (ns != ms)))
                           {
                             // So share a side.  Is this a mixed pair
                             // of subactive and active/ancestor
                             // elements?
                             // If not, then we're neighbors.
                             // If so, then the subactive's neighbor is
  
                             if (element->subactive() ==
                                 neighbor->subactive())
                               {
                                 // an element is only subactive if it has
                                 // been coarsened but not deleted
                                 element->set_neighbor (ms,neighbor);
                                 neighbor->set_neighbor(ns,element);
                               }
                             else if (element->subactive())
                               {
                                 element->set_neighbor(ms,neighbor);
                               }
                             else if (neighbor->subactive())
                               {
                                 neighbor->set_neighbor(ns,element);
                               }
                             side_to_elem_map.erase (bounds.first);
  
                             // get out of this nested crap
                             goto next_side;
                           }
  
                         ++bounds.first;
                       }
                   }
  
                 // didn't find a match...
                 // Build the map entry for this element
                 key_val_pair kvp;
  
                 kvp.first         = key;
                 kvp.second.first  = element;
                 kvp.second.second = cast_int<unsigned char>(ms);
                 side_to_elem_map.insert (kvp);
               }
           }
       }
   }
  
 #ifdef LIBMESH_ENABLE_AMR
  
   const unsigned int n_levels = MeshTools::n_levels(*this);
   for (unsigned int level = 1; level < n_levels; ++level)
     {
       for (auto & current_elem : as_range(level_elements_begin(level),
                                           level_elements_end(level)))
         {
           libmesh_assert(current_elem);
           Elem * parent = current_elem->parent();
           libmesh_assert(parent);
           const unsigned int my_child_num = parent->which_child_am_i(current_elem);
  
           for (auto s : current_elem->side_index_range())
             {
               if (current_elem->neighbor_ptr(s) == nullptr ||
                   (current_elem->neighbor_ptr(s) == remote_elem &&
                    parent->is_child_on_side(my_child_num, s)))
                 {
                   Elem * neigh = parent->neighbor_ptr(s);
  
                   // If neigh was refined and had non-subactive children
                   // made remote earlier, then our current elem should
                   // actually have one of those remote children as a
                   // neighbor
                   if (neigh &&
                       (neigh->ancestor() ||
                        // If neigh has subactive children which should have
                        // matched as neighbors of the current element but
                        // did not, then those likewise must be remote
                        // children.
                        (current_elem->subactive() && neigh->has_children() &&
                         (neigh->level()+1) == current_elem->level())))
                     {
 #ifdef DEBUG
                       // Let's make sure that "had children made remote"
                       // situation is actually the case
                       libmesh_assert(neigh->has_children());
                       bool neigh_has_remote_children = false;
                       for (auto & child : neigh->child_ref_range())
                         if (&child == remote_elem)
                           neigh_has_remote_children = true;
                       libmesh_assert(neigh_has_remote_children);
  
                       // And let's double-check that we don't have
                       // a remote_elem neighboring an active local element
                       if (current_elem->active())
                         libmesh_assert_not_equal_to (current_elem->processor_id(),
                                                      this->processor_id());
 #endif // DEBUG
                       neigh = const_cast<RemoteElem *>(remote_elem);
                     }
                   // If neigh and current_elem are more than one level
                   // apart, figuring out whether we have a remote
                   // neighbor here becomes much harder.
                   else if (neigh && (current_elem->subactive() &&
                                      neigh->has_children()))
                     {
                       // Find the deepest descendant of neigh which
                       // we could consider for a neighbor.  If we run
                       // out of neigh children, then that's our
                       // neighbor.  If we find a potential neighbor
                       // with remote_children and we don't find any
                       // potential neighbors among its non-remote
                       // children, then our neighbor must be remote.
                       while (neigh != remote_elem &&
                              neigh->has_children())
                         {
                           bool found_neigh = false;
                           for (unsigned int c = 0, nc = neigh->n_children();
                                !found_neigh && c != nc; ++c)
                             {
                               Elem * child = neigh->child_ptr(c);
                               if (child == remote_elem)
                                 continue;
                               for (auto ncn : child->neighbor_ptr_range())
                                 {
                                   if (ncn != remote_elem &&
                                       ncn->is_ancestor_of(current_elem))
                                     {
                                       neigh = ncn;
                                       found_neigh = true;
                                       break;
                                     }
                                 }
                             }
                           if (!found_neigh)
                             neigh = const_cast<RemoteElem *>(remote_elem);
                         }
                     }
                   current_elem->set_neighbor(s, neigh);
 #ifdef DEBUG
                   if (neigh != nullptr && neigh != remote_elem)
                     // We ignore subactive elements here because
                     // we don't care about neighbors of subactive element.
                     if ((!neigh->active()) && (!current_elem->subactive()))
                       {
                         libMesh::err << "On processor " << this->processor_id()
                                      << std::endl;
                         libMesh::err << "Bad element ID = " << current_elem->id()
                                      << ", Side " << s << ", Bad neighbor ID = " << neigh->id() << std::endl;
                         libMesh::err << "Bad element proc_ID = " << current_elem->processor_id()
                                      << ", Bad neighbor proc_ID = " << neigh->processor_id() << std::endl;
                         libMesh::err << "Bad element size = " << current_elem->hmin()
                                      << ", Bad neighbor size = " << neigh->hmin() << std::endl;
                         libMesh::err << "Bad element center = " << current_elem->centroid()
                                      << ", Bad neighbor center = " << neigh->centroid() << std::endl;
                         libMesh::err << "ERROR: "
                                      << (current_elem->active()?"Active":"Ancestor")
                                      << " Element at level "
                                      << current_elem->level() << std::endl;
                         libMesh::err << "with "
                                      << (parent->active()?"active":
                                          (parent->subactive()?"subactive":"ancestor"))
                                      << " parent share "
                                      << (neigh->subactive()?"subactive":"ancestor")
                                      << " neighbor at level " << neigh->level()
                                      << std::endl;
                         NameBasedIO(*this).write ("bad_mesh.gmv");
                         libmesh_error_msg("Problematic mesh written to bad_mesh.gmv.");
                       }
 #endif // DEBUG
                 }
             }
  
           // We can skip to the next element if we're full-dimension
           // and therefore don't have any interior parents
           if (current_elem->dim() >= LIBMESH_DIM)
             continue;
  
           // We have no interior parents unless we can find one later
           current_elem->set_interior_parent(nullptr);
  
           Elem * pip = parent->interior_parent();
  
           if (!pip)
             continue;
  
           // If there's no interior_parent children, whether due to a
           // remote element or a non-conformity, then there's no
           // children to search.
           if (pip == remote_elem || pip->active())
             {
               current_elem->set_interior_parent(pip);
               continue;
             }
  
           // For node comparisons we'll need a sensible tolerance
           Real node_tolerance = current_elem->hmin() * TOLERANCE;
  
           // Otherwise our interior_parent should be a child of our
           // parent's interior_parent.
           for (auto & child : pip->child_ref_range())
             {
               // If we have a remote_elem, that might be our
               // interior_parent.  We'll set it provisionally now and
               // keep trying to find something better.
               if (&child == remote_elem)
                 {
                   current_elem->set_interior_parent
                     (const_cast<RemoteElem *>(remote_elem));
                   continue;
                 }
  
               bool child_contains_our_nodes = true;
               for (auto & n : current_elem->node_ref_range())
                 {
                   bool child_contains_this_node = false;
                   for (auto & cn : child.node_ref_range())
                     if (cn.absolute_fuzzy_equals
                         (n, node_tolerance))
                       {
                         child_contains_this_node = true;
                         break;
                       }
                   if (!child_contains_this_node)
                     {
                       child_contains_our_nodes = false;
                       break;
                     }
                 }
               if (child_contains_our_nodes)
                 {
                   current_elem->set_interior_parent(&child);
                   break;
                 }
             }
  
           // We should have found *some* interior_parent at this
           // point, whether semilocal or remote.
           libmesh_assert(current_elem->interior_parent());
         }
     }
  
 #endif // AMR
  
  
 #ifdef DEBUG
   MeshTools::libmesh_assert_valid_neighbors(*this,
                                             !reset_remote_elements);
   MeshTools::libmesh_assert_valid_amr_interior_parents(*this);
 #endif
 }

References libMesh::Elem::active(), libMesh::Elem::ancestor(), libMesh::as_range(), libMesh::Elem::centroid(), libMesh::Elem::child_ptr(), libMesh::Elem::child_ref_range(), libMesh::MeshBase::element_ptr_range(), libMesh::err, libMesh::Elem::has_children(), libMesh::Elem::hmin(), libMesh::DofObject::id(), libMesh::Elem::interior_parent(), libMesh::Elem::is_ancestor_of(), libMesh::Elem::is_child_on_side(), libMesh::Elem::level(), libMesh::MeshBase::level_elements_begin(), libMesh::MeshBase::level_elements_end(), libMesh::libmesh_assert(), libMesh::MeshTools::libmesh_assert_valid_amr_interior_parents(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::Elem::n_children(), libMesh::MeshTools::n_levels(), libMesh::Elem::neighbor_ptr(), libMesh::Elem::neighbor_ptr_range(), libMesh::Elem::parent(), libMesh::ParallelObject::processor_id(), libMesh::DofObject::processor_id(), libMesh::Real, libMesh::remote_elem, libMesh::Elem::set_interior_parent(), libMesh::Elem::set_neighbor(), libMesh::Elem::side_ptr(), libMesh::Elem::subactive(), libMesh::TOLERANCE, libMesh::Elem::which_child_am_i(), and libMesh::NameBasedIO::write().

Referenced by libMesh::TriangleWrapper::copy_tri_to_mesh(), and libMesh::DistributedMesh::redistribute().

◆ fix_broken_node_and_element_numbering()

void libMesh::ReplicatedMesh::fix_broken_node_and_element_numbering ( )

overridevirtualinherited

There is no reason for a user to ever call this function.

This function restores a previously broken element/node numbering such that mesh.node_ref(n).id() == n.

Implements libMesh::MeshBase.

Definition at line 798 of file replicated_mesh.C.

 {
   // Nodes first
   for (auto n : index_range(_nodes))
     if (this->_nodes[n] != nullptr)
       this->_nodes[n]->set_id() = cast_int<dof_id_type>(n);
  
   // Elements next
   for (auto e : index_range(_elements))
     if (this->_elements[e] != nullptr)
       this->_elements[e]->set_id() = cast_int<dof_id_type>(e);
 }

References libMesh::ReplicatedMesh::_elements, libMesh::ReplicatedMesh::_nodes, and libMesh::index_range().

◆ flagged_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::flagged_elements_begin ( unsigned char rflag ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ flagged_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::flagged_elements_begin ( unsigned char rflag )

overridevirtualinherited

Iterate over all elements with a specified refinement flag.

Implements libMesh::MeshBase.

◆ flagged_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::flagged_elements_end ( unsigned char rflag ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ flagged_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::flagged_elements_end ( unsigned char rflag )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ flagged_pid_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::flagged_pid_elements_begin	(	unsigned char	rflag,
		processor_id_type	pid
	)		const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ flagged_pid_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::flagged_pid_elements_begin	(	unsigned char	rflag,
		processor_id_type	pid
	)

overridevirtualinherited

Iterate over all elements with a specified refinement flag on a specified processor.

Implements libMesh::MeshBase.

◆ flagged_pid_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::flagged_pid_elements_end	(	unsigned char	rflag,
		processor_id_type	pid
	)		const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ flagged_pid_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::flagged_pid_elements_end	(	unsigned char	rflag,
		processor_id_type	pid
	)

overridevirtualinherited

Implements libMesh::MeshBase.

◆ gather_to_zero()

virtual void libMesh::MeshBase::gather_to_zero ( )

inlinevirtualinherited

Gathers all elements and nodes of the mesh onto processor zero.

Reimplemented in libMesh::DistributedMesh.

Definition at line 194 of file mesh_base.h.

194 {}

Referenced by libMesh::MeshSerializer::MeshSerializer().

◆ get_boundary_info() [1/2]

BoundaryInfo& libMesh::MeshBase::get_boundary_info ( )

inlineinherited

Writable information about boundary ids on the mesh.

Definition at line 137 of file mesh_base.h.

137 { return *boundary_info; }

References libMesh::MeshBase::boundary_info.

◆ get_boundary_info() [2/2]

const BoundaryInfo& libMesh::MeshBase::get_boundary_info ( ) const

inlineinherited

The information about boundary ids on the mesh.

Definition at line 132 of file mesh_base.h.

132 { return *boundary_info; }

References libMesh::MeshBase::boundary_info.

◆ get_boundary_points()

std::unordered_map< dof_id_type, std::vector< std::vector< Point > > > libMesh::ReplicatedMesh::get_boundary_points ( ) const

inherited

Return all points on boundary.

The key of the returned unordered map is the ID of a representative element of all disconnected subdomains. Subdomains are considered connected only when they are sharing at least one d-1 dimensional object (side in 2D), where d is the mesh dimension. The size of the unordered map value is the number of disconnected boundaries for a subdomain. Boundaries are considered connected only when they are sharing a d-2 dimensional object. This function currently only works for 2D meshes. The points of each boundary are ordered to form an enclosure.

Definition at line 1498 of file replicated_mesh.C.

 {
   if (mesh_dimension() != 2)
     libmesh_error_msg("Error: get_boundary_points only works for 2D now");
  
   // find number of disconnected subdomains
   // subdomains will hold the IDs of disconnected subdomains for all elements.
   std::vector<subdomain_id_type> subdomains;
   std::vector<dof_id_type> elem_ids = get_disconnected_subdomains(&subdomains);
  
   std::unordered_map<dof_id_type, std::vector<std::vector<Point>>> boundary_points;
  
   // get all boundary sides that are to be erased later during visiting
   // use a comparison functor to avoid run-time randomness due to pointers
   struct boundary_side_compare
   {
     bool operator()(const std::pair<const Elem *, unsigned int> & lhs,
                     const std::pair<const Elem *, unsigned int> & rhs) const
       {
         if (lhs.first->id() < rhs.first->id())
           return true;
         else if (lhs.first->id() == rhs.first->id())
         {
           if (lhs.second < rhs.second)
             return true;
         }
         return false;
       }
   };
   std::set<std::pair<const Elem *, unsigned int>, boundary_side_compare> boundary_elements;
   for (const auto & elem : active_element_ptr_range())
     for (auto s : elem->side_index_range())
       if (elem->neighbor_ptr(s) == nullptr)
         boundary_elements.insert(std::pair<const Elem *, unsigned int>(elem, s));
  
   while (!boundary_elements.empty())
   {
     // get the first entry as the seed
     const Elem * eseed = boundary_elements.begin()->first;
     unsigned int sseed = boundary_elements.begin()->second;
  
     // get the subdomain ID that these boundary sides attached to
     subdomain_id_type subdomain_id = subdomains[eseed->id()];
  
     // start visiting the mesh to find all boundary nodes with the seed
     std::vector<Point> bpoints;
     const Elem * elem = eseed;
     unsigned int s = sseed;
     std::vector<unsigned int> local_side_nodes = elem->nodes_on_side(s);
     while (true)
     {
       std::pair<const Elem *, unsigned int> side(elem, s);
       libmesh_assert(boundary_elements.find(side) != boundary_elements.end());
       boundary_elements.erase(side);
  
       // push all nodes on the side except the node on the other end of the side (index 1)
       for (auto i : index_range(local_side_nodes))
         if (i != 1)
           bpoints.push_back(*static_cast<const Point *>(elem->node_ptr(local_side_nodes[i])));
  
       // use the last node to find next element and side
       const Node * node = elem->node_ptr(local_side_nodes[1]);
       std::set<const Elem *> neighbors;
       elem->find_point_neighbors(*node, neighbors);
  
       // if only one neighbor is found (itself), this node is a cornor node on boundary
       if (neighbors.size() != 1)
         neighbors.erase(elem);
  
       // find the connecting side
       bool found = false;
       for (const auto & neighbor : neighbors)
       {
         for (auto ss : neighbor->side_index_range())
           if (neighbor->neighbor_ptr(ss) == nullptr && !(elem == neighbor && s == ss))
           {
             local_side_nodes = neighbor->nodes_on_side(ss);
             // we expect the starting point of the side to be the same as the end of the previous side
             if (neighbor->node_ptr(local_side_nodes[0]) == node)
             {
               elem = neighbor;
               s = ss;
               found = true;
               break;
             }
             else if (neighbor->node_ptr(local_side_nodes[1]) == node)
             {
               elem = neighbor;
               s = ss;
               found = true;
               // flip nodes in local_side_nodes because the side is in an opposite direction
               auto temp(local_side_nodes);
               local_side_nodes[0] = temp[1];
               local_side_nodes[1] = temp[0];
               for (unsigned int i = 2; i < temp.size(); ++i)
                 local_side_nodes[temp.size() + 1 - i] = temp[i];
               break;
             }
           }
         if (found)
           break;
       }
       if (!found)
         libmesh_error_msg("ERROR: mesh topology error on visiting boundary sides");
  
       // exit if we reach the starting point
       if (elem == eseed && s == sseed)
         break;
     }
     boundary_points[elem_ids[subdomain_id]].push_back(bpoints);
   }
  
   return boundary_points;
 }

References libMesh::ReplicatedMesh::active_element_ptr_range(), libMesh::MeshBase::elem(), libMesh::Elem::find_point_neighbors(), libMesh::ReplicatedMesh::get_disconnected_subdomains(), libMesh::DofObject::id(), libMesh::index_range(), libMesh::libmesh_assert(), libMesh::MeshBase::mesh_dimension(), libMesh::Elem::neighbor_ptr(), libMesh::MeshBase::node(), libMesh::Elem::node_ptr(), libMesh::Elem::nodes_on_side(), and libMesh::Elem::side_index_range().

Referenced by GetBoundaryPointsTest::testMesh().

◆ get_count_lower_dim_elems_in_point_locator()

bool libMesh::MeshBase::get_count_lower_dim_elems_in_point_locator ( ) const

inherited

Get the current value of _count_lower_dim_elems_in_point_locator.

Definition at line 710 of file mesh_base.C.

 {
   return _count_lower_dim_elems_in_point_locator;
 }

Referenced by libMesh::TreeNode< N >::insert().

◆ get_disconnected_subdomains()

std::vector< dof_id_type > libMesh::ReplicatedMesh::get_disconnected_subdomains ( std::vector< subdomain_id_type > * subdomain_ids = nullptr ) const

inherited

Return IDs of representative elements of all disconnected subdomains.

Subdomains are considered connected only when they are sharing at least one d-1 dimensional object (side in 2D, face in 3D), where d is the mesh dimension. The optional argument can be used for getting the subdomain IDs of all elements with element IDs as the index. This function cannot be called for a mesh with hanging nodes from adaptive mesh refinement.

Definition at line 1431 of file replicated_mesh.C.

 {
   // find number of disconnected subdomains
   std::vector<dof_id_type> representative_elem_ids;
  
   // use subdomain_ids as markers for all elements to indicate if the elements
   // have been visited. Note: here subdomain ID is unrelated with element
   // subdomain_id().
   std::vector<subdomain_id_type> subdomains;
   if (!subdomain_ids)
     subdomain_ids = &subdomains;
   subdomain_ids->clear();
   subdomain_ids->resize(max_elem_id() + 1, Elem::invalid_subdomain_id);
  
   // counter of disconnected subdomains
   subdomain_id_type subdomain_counter = 0;
  
   // a stack for visiting elements, make its capacity sufficiently large to avoid
   // memory allocation and deallocation when the vector size changes
   std::vector<Elem *> list;
   list.reserve(n_elem());
  
   // counter of visited elements
   dof_id_type visited = 0;
   dof_id_type n_active = n_active_elem();
   do
   {
     for (const auto & elem : active_element_ptr_range())
       if ((*subdomain_ids)[elem->id()] == Elem::invalid_subdomain_id)
       {
         list.push_back(elem);
         (*subdomain_ids)[elem->id()] = subdomain_counter;
         break;
       }
     // we should be able to find a seed here
     libmesh_assert(list.size() > 0);
  
     dof_id_type min_id = std::numeric_limits<dof_id_type>::max();
     while (list.size() > 0)
     {
       // pop up an element
       Elem * elem = list.back(); list.pop_back(); ++visited;
  
       min_id = std::min(elem->id(), min_id);
  
       for (auto s : elem->side_index_range())
       {
         Elem * neighbor = elem->neighbor_ptr(s);
         if (neighbor != nullptr && (*subdomain_ids)[neighbor->id()] == Elem::invalid_subdomain_id)
         {
           // neighbor must be active
           libmesh_assert(neighbor->active());
           list.push_back(neighbor);
           (*subdomain_ids)[neighbor->id()] = subdomain_counter;
         }
       }
     }
  
     representative_elem_ids.push_back(min_id);
     subdomain_counter++;
   }
   while (visited != n_active);
  
   return representative_elem_ids;
 }

References libMesh::Elem::active(), libMesh::ReplicatedMesh::active_element_ptr_range(), libMesh::MeshBase::elem(), libMesh::DofObject::id(), libMesh::Elem::invalid_subdomain_id, libMesh::libmesh_assert(), libMesh::ReplicatedMesh::max_elem_id(), libMesh::ReplicatedMesh::n_active_elem(), libMesh::ReplicatedMesh::n_elem(), libMesh::Elem::neighbor_ptr(), libMesh::Elem::side_index_range(), and libMesh::MeshBase::subdomain_ids().

Referenced by libMesh::ReplicatedMesh::get_boundary_points().

◆ get_elem_integer_index()

unsigned int libMesh::MeshBase::get_elem_integer_index ( const std::string & name ) const

inherited

Definition at line 224 of file mesh_base.C.

 {
   for (auto i : index_range(_elem_integer_names))
     if (_elem_integer_names[i] == name)
       return i;
  
   libmesh_error_msg("Unknown elem integer " << name);
   return libMesh::invalid_uint;
 }

References libMesh::index_range(), libMesh::invalid_uint, and libMesh::Quality::name().

◆ get_elem_integer_name()

const std::string& libMesh::MeshBase::get_elem_integer_name ( unsigned int i ) const

inlineinherited

Definition at line 818 of file mesh_base.h.

819 { return _elem_integer_names[i]; }

References libMesh::MeshBase::_elem_integer_names.

Referenced by libMesh::CheckpointIO::write().

◆ get_id_by_name()

subdomain_id_type libMesh::MeshBase::get_id_by_name ( const std::string & name ) const

inherited

Returns: The id of the named subdomain if it exists, Elem::invalid_subdomain_id otherwise.

Definition at line 737 of file mesh_base.C.

 {
   // Linear search over the map values.
   std::map<subdomain_id_type, std::string>::const_iterator
     iter = _block_id_to_name.begin(),
     end_iter = _block_id_to_name.end();
  
   for ( ; iter != end_iter; ++iter)
     if (iter->second == name)
       return iter->first;
  
   // If we made it here without returning, we don't have a subdomain
   // with the requested name, so return Elem::invalid_subdomain_id.
   return Elem::invalid_subdomain_id;
 }

References libMesh::Quality::name().

◆ get_info()

std::string libMesh::MeshBase::get_info ( ) const

inherited

Returns: A string containing relevant information about the mesh.

Definition at line 551 of file mesh_base.C.

 {
   std::ostringstream oss;
  
   oss << " Mesh Information:"                                  << '\n';
  
   if (!_elem_dims.empty())
     {
       oss << "  elem_dimensions()={";
       std::copy(_elem_dims.begin(),
                 --_elem_dims.end(), // --end() is valid if the set is non-empty
                 std::ostream_iterator<unsigned int>(oss, ", "));
       oss << cast_int<unsigned int>(*_elem_dims.rbegin());
       oss << "}\n";
     }
  
   oss << "  spatial_dimension()=" << this->spatial_dimension() << '\n'
       << "  n_nodes()="           << this->n_nodes()           << '\n'
       << "    n_local_nodes()="   << this->n_local_nodes()     << '\n'
       << "  n_elem()="            << this->n_elem()            << '\n'
       << "    n_local_elem()="    << this->n_local_elem()      << '\n'
 #ifdef LIBMESH_ENABLE_AMR
       << "    n_active_elem()="   << this->n_active_elem()     << '\n'
 #endif
       << "  n_subdomains()="      << static_cast<std::size_t>(this->n_subdomains()) << '\n'
       << "  n_partitions()="      << static_cast<std::size_t>(this->n_partitions()) << '\n'
       << "  n_processors()="      << static_cast<std::size_t>(this->n_processors()) << '\n'
       << "  n_threads()="         << static_cast<std::size_t>(libMesh::n_threads()) << '\n'
       << "  processor_id()="      << static_cast<std::size_t>(this->processor_id()) << '\n';
  
   return oss.str();
 }

References libMesh::MeshTools::n_elem(), n_nodes, and libMesh::n_threads().

◆ get_node_integer_index()

unsigned int libMesh::MeshBase::get_node_integer_index ( const std::string & name ) const

inherited

Definition at line 295 of file mesh_base.C.

 {
   for (auto i : index_range(_node_integer_names))
     if (_node_integer_names[i] == name)
       return i;
  
   libmesh_error_msg("Unknown node integer " << name);
   return libMesh::invalid_uint;
 }

References libMesh::index_range(), libMesh::invalid_uint, and libMesh::Quality::name().

◆ get_node_integer_name()

const std::string& libMesh::MeshBase::get_node_integer_name ( unsigned int i ) const

inlineinherited

Definition at line 915 of file mesh_base.h.

916 { return _node_integer_names[i]; }

References libMesh::MeshBase::_node_integer_names.

Referenced by libMesh::CheckpointIO::write().

◆ get_point_locator_close_to_point_tol()

Real libMesh::MeshBase::get_point_locator_close_to_point_tol ( ) const

inherited

Definition at line 919 of file mesh_base.C.

 {
   return _point_locator_close_to_point_tol;
 }

◆ get_subdomain_name_map()

const std::map<subdomain_id_type, std::string>& libMesh::MeshBase::get_subdomain_name_map ( ) const

inlineinherited

Definition at line 1633 of file mesh_base.h.

1634 { return _block_id_to_name; }

References libMesh::MeshBase::_block_id_to_name.

Referenced by libMesh::DistributedMesh::DistributedMesh(), libMesh::ReplicatedMesh::ReplicatedMesh(), libMesh::XdrIO::write_serialized_subdomain_names(), and libMesh::CheckpointIO::write_subdomain_names().

◆ ghost_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::ghost_elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ ghost_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::ghost_elements_begin ( )

overridevirtualinherited

Iterate over "ghost" elements in the Mesh.

A ghost element is one which is not local, but is semilocal.

Implements libMesh::MeshBase.

◆ ghost_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::ghost_elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ ghost_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::ghost_elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ ghosting_functors_begin()

std::set<GhostingFunctor *>::const_iterator libMesh::MeshBase::ghosting_functors_begin ( ) const

inlineinherited

Beginning of range of ghosting functors.

Definition at line 1113 of file mesh_base.h.

1114 { return _ghosting_functors.begin(); }

References libMesh::MeshBase::_ghosting_functors.

Referenced by libMesh::UnstructuredMesh::contract(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::query_ghosting_functors(), and EquationSystemsTest::testDisableDefaultGhosting().

◆ ghosting_functors_end()

std::set<GhostingFunctor *>::const_iterator libMesh::MeshBase::ghosting_functors_end ( ) const

inlineinherited

End of range of ghosting functors.

Definition at line 1119 of file mesh_base.h.

1120 { return _ghosting_functors.end(); }

References libMesh::MeshBase::_ghosting_functors.

Referenced by libMesh::UnstructuredMesh::contract(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::query_ghosting_functors(), and EquationSystemsTest::testDisableDefaultGhosting().

◆ has_elem_integer()

bool libMesh::MeshBase::has_elem_integer ( const std::string & name ) const

inherited

Definition at line 236 of file mesh_base.C.

 {
   for (auto & entry : _elem_integer_names)
     if (entry == name)
       return true;
  
   return false;
 }

References libMesh::Quality::name().

◆ has_node_integer()

bool libMesh::MeshBase::has_node_integer ( const std::string & name ) const

inherited

Definition at line 307 of file mesh_base.C.

 {
   for (auto & entry : _node_integer_names)
     if (entry == name)
       return true;
  
   return false;
 }

References libMesh::Quality::name().

◆ insert_elem()

Elem * libMesh::ReplicatedMesh::insert_elem ( Elem * e )

overridevirtualinherited

Insert elem e to the element array, preserving its id and replacing/deleting any existing element with the same id.

Users should call MeshBase::prepare_for_use() after elements are added to and/or deleted from the mesh.

Implements libMesh::MeshBase.

Definition at line 328 of file replicated_mesh.C.

 {
 #ifdef LIBMESH_ENABLE_UNIQUE_ID
   if (!e->valid_unique_id())
     e->set_unique_id() = _next_unique_id++;
 #endif
  
   dof_id_type eid = e->id();
   libmesh_assert_less (eid, _elements.size());
   Elem * oldelem = _elements[eid];
  
   if (oldelem)
     {
       libmesh_assert_equal_to (oldelem->id(), eid);
       this->delete_elem(oldelem);
     }
  
   _elements[e->id()] = e;
  
   // Make sure any new element is given space for any extra integers
   // we've requested
   e->add_extra_integers(_elem_integer_names.size());
  
   // And set mapping type and data on any new element
   e->set_mapping_type(this->default_mapping_type());
   e->set_mapping_data(this->default_mapping_data());
  
   return e;
 }

References libMesh::MeshBase::_elem_integer_names, libMesh::ReplicatedMesh::_elements, libMesh::MeshBase::_next_unique_id, libMesh::DofObject::add_extra_integers(), libMesh::MeshBase::default_mapping_data(), libMesh::MeshBase::default_mapping_type(), libMesh::ReplicatedMesh::delete_elem(), libMesh::DofObject::id(), libMesh::Elem::set_mapping_data(), libMesh::Elem::set_mapping_type(), libMesh::DofObject::set_unique_id(), and libMesh::DofObject::valid_unique_id().

◆ insert_node()

Node * libMesh::ReplicatedMesh::insert_node ( Node * n )

overridevirtualinherited

Insert Node n into the Mesh at a location consistent with n->id(), allocating extra storage if necessary.

Throws an error if: .) n==nullptr .) n->id() == DofObject::invalid_id .) A node already exists in position n->id().

This function differs from the ReplicatedMesh::add_node() function, which is only capable of appending nodes at the end of the nodes storage.

Implements libMesh::MeshBase.

Definition at line 494 of file replicated_mesh.C.

 {
   if (!n)
     libmesh_error_msg("Error, attempting to insert nullptr node.");
  
   if (n->id() == DofObject::invalid_id)
     libmesh_error_msg("Error, cannot insert node with invalid id.");
  
   if (n->id() < _nodes.size())
     {
       // Don't allow inserting on top of an existing Node.
  
       // Doing so doesn't have to be *error*, in the case where a
       // redundant insert is done, but when that happens we ought to
       // always be able to make the code more efficient by avoiding
       // the redundant insert, so let's keep screaming "Error" here.
       if (_nodes[ n->id() ] != nullptr)
         libmesh_error_msg("Error, cannot insert node on top of existing node.");
     }
   else
     {
       // Allocate just enough space to store the new node.  This will
       // cause highly non-ideal memory allocation behavior if called
       // repeatedly...
       _nodes.resize(n->id() + 1);
     }
  
 #ifdef LIBMESH_ENABLE_UNIQUE_ID
   if (!n->valid_unique_id())
     n->set_unique_id() = _next_unique_id++;
 #endif
  
   n->add_extra_integers(_node_integer_names.size());
  
   // We have enough space and this spot isn't already occupied by
   // another node, so go ahead and add it.
   _nodes[ n->id() ] = n;
  
   // If we made it this far, we just inserted the node the user handed
   // us, so we can give it right back.
   return n;
 }

References libMesh::MeshBase::_next_unique_id, libMesh::MeshBase::_node_integer_names, libMesh::ReplicatedMesh::_nodes, libMesh::DofObject::add_extra_integers(), libMesh::DofObject::id(), libMesh::DofObject::invalid_id, libMesh::DofObject::set_unique_id(), and libMesh::DofObject::valid_unique_id().

◆ is_prepared()

bool libMesh::MeshBase::is_prepared ( ) const

inlineinherited

Returns: true if the mesh has been prepared via a call to prepare_for_use, false otherwise.

Definition at line 152 of file mesh_base.h.

153 { return _is_prepared; }

References libMesh::MeshBase::_is_prepared.

Referenced by libMesh::MeshRefinement::_refine_elements(), and libMesh::DofMap::create_dof_constraints().

◆ is_replicated()

virtual bool libMesh::MeshBase::is_replicated ( ) const

inlinevirtualinherited

Returns: true if new elements and nodes can and should be created in synchronization on all processors, false otherwise

Reimplemented in libMesh::DistributedMesh.

Definition at line 181 of file mesh_base.h.

182 { return true; }

Referenced by libMesh::MeshRefinement::_refine_elements(), libMesh::DynaIO::add_spline_constraints(), libMesh::UnstructuredMesh::all_second_order(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::CheckpointIO::read(), and libMesh::MeshRefinement::uniformly_coarsen().

◆ is_serial()

virtual bool libMesh::MeshBase::is_serial ( ) const

inlinevirtualinherited

Returns: true if all elements and nodes of the mesh exist on the current processor, false otherwise

Reimplemented in libMesh::DistributedMesh.

Definition at line 159 of file mesh_base.h.

160 { return true; }

Referenced by libMesh::MeshRefinement::_coarsen_elements(), libMesh::MeshRefinement::_smooth_flags(), libMesh::BoundaryInfo::add_elements(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::EquationSystems::allgather(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::DofMap::create_dof_constraints(), libMesh::UnstructuredMesh::create_submesh(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::LocationMap< T >::init(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshSerializer::MeshSerializer(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::Nemesis_IO::read(), libMesh::DofMap::scatter_constraints(), libMesh::BoundaryInfo::sync(), PointLocatorTest::testLocator(), BoundaryInfoTest::testMesh(), WriteSidesetData::testWrite(), libMesh::MeshTools::total_weight(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::CheckpointIO::write(), and libMesh::XdrIO::write_parallel().

◆ is_serial_on_zero()

virtual bool libMesh::MeshBase::is_serial_on_zero ( ) const

inlinevirtualinherited

Returns: true if all elements and nodes of the mesh exist on the processor 0, false otherwise

Reimplemented in libMesh::DistributedMesh.

Definition at line 166 of file mesh_base.h.

167 { return true; }

◆ level_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::level_elements_begin ( unsigned int level ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ level_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::level_elements_begin ( unsigned int level )

overridevirtualinherited

Iterate over elements of a given level.

Implements libMesh::MeshBase.

◆ level_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::level_elements_end ( unsigned int level ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ level_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::level_elements_end ( unsigned int level )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ libmesh_assert_valid_parallel_ids()

virtual void libMesh::MeshBase::libmesh_assert_valid_parallel_ids ( ) const

inlinevirtualinherited

Verify id and processor_id consistency of our elements and nodes containers.

Calls libmesh_assert() on each possible failure. Currently only implemented on DistributedMesh; a serial data structure is much harder to get out of sync.

Reimplemented in libMesh::DistributedMesh.

Definition at line 1297 of file mesh_base.h.

1297 {}

Referenced by libMesh::MeshRefinement::_refine_elements(), libMesh::InfElemBuilder::build_inf_elem(), and libMesh::MeshRefinement::refine_and_coarsen_elements().

◆ local_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::local_elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ local_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::local_elements_begin ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ local_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::local_elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ local_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::local_elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ local_level_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::local_level_elements_begin ( unsigned int level ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ local_level_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::local_level_elements_begin ( unsigned int level )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ local_level_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::local_level_elements_end ( unsigned int level ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ local_level_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::local_level_elements_end ( unsigned int level )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ local_node_ptr_range() [1/2]

virtual SimpleRange<const_node_iterator> libMesh::ReplicatedMesh::local_node_ptr_range ( ) const

inlineoverridevirtualinherited

Implements libMesh::MeshBase.

Definition at line 472 of file replicated_mesh.h.

472 { return {local_nodes_begin(), local_nodes_end()}; }

References libMesh::ReplicatedMesh::local_nodes_begin(), and libMesh::ReplicatedMesh::local_nodes_end().

◆ local_node_ptr_range() [2/2]

virtual SimpleRange<node_iterator> libMesh::ReplicatedMesh::local_node_ptr_range ( )

inlineoverridevirtualinherited

Implements libMesh::MeshBase.

Definition at line 471 of file replicated_mesh.h.

471 { return {local_nodes_begin(), local_nodes_end()}; }

References libMesh::ReplicatedMesh::local_nodes_begin(), and libMesh::ReplicatedMesh::local_nodes_end().

◆ local_nodes_begin() [1/2]

virtual const_node_iterator libMesh::ReplicatedMesh::local_nodes_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ local_nodes_begin() [2/2]

virtual node_iterator libMesh::ReplicatedMesh::local_nodes_begin ( )

overridevirtualinherited

Iterate over local nodes (nodes whose processor_id() matches the current processor).

Implements libMesh::MeshBase.

Referenced by libMesh::ReplicatedMesh::local_node_ptr_range().

◆ local_nodes_end() [1/2]

virtual const_node_iterator libMesh::ReplicatedMesh::local_nodes_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ local_nodes_end() [2/2]

virtual node_iterator libMesh::ReplicatedMesh::local_nodes_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

Referenced by libMesh::ReplicatedMesh::local_node_ptr_range().

◆ local_not_level_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::local_not_level_elements_begin ( unsigned int level ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ local_not_level_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::local_not_level_elements_begin ( unsigned int level )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ local_not_level_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::local_not_level_elements_end ( unsigned int level ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ local_not_level_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::local_not_level_elements_end ( unsigned int level )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ max_elem_id()

virtual dof_id_type libMesh::ReplicatedMesh::max_elem_id ( ) const

inlineoverridevirtualinherited

Returns: A number greater than or equal to the maximum element id in the mesh.

Implements libMesh::MeshBase.

Definition at line 124 of file replicated_mesh.h.

125 { return cast_int<dof_id_type>(_elements.size()); }

References libMesh::ReplicatedMesh::_elements.

Referenced by libMesh::ReplicatedMesh::get_disconnected_subdomains(), and libMesh::ReplicatedMesh::stitching_helper().

◆ max_node_id()

virtual dof_id_type libMesh::ReplicatedMesh::max_node_id ( ) const

inlineoverridevirtualinherited

Returns: A number greater than or equal to the maximum node id in the mesh.

Implements libMesh::MeshBase.

Definition at line 110 of file replicated_mesh.h.

111 { return cast_int<dof_id_type>(_nodes.size()); }

References libMesh::ReplicatedMesh::_nodes.

Referenced by libMesh::ReplicatedMesh::stitching_helper().

◆ merge_extra_integer_names()

std::pair< std::vector< unsigned int >, std::vector< unsigned int > > libMesh::MeshBase::merge_extra_integer_names ( const MeshBase & other )

protectedinherited

Merge extra-integer arrays from an other mesh.

Returns two mappings from index values in other to (possibly newly created) index values with the same string name in this mesh, the first for element integers and the second for node integers.

Definition at line 944 of file mesh_base.C.

 {
   std::pair<std::vector<unsigned int>, std::vector<unsigned int>> returnval;
   returnval.first = this->add_elem_integers(other._elem_integer_names);
   returnval.second = this->add_node_integers(other._node_integer_names);
   return returnval;
 }

References libMesh::MeshBase::_elem_integer_names, and libMesh::MeshBase::_node_integer_names.

Referenced by libMesh::UnstructuredMesh::copy_nodes_and_elements(), and libMesh::UnstructuredMesh::create_submesh().

◆ mesh_dimension()

unsigned int libMesh::MeshBase::mesh_dimension ( ) const

inherited

Returns: The logical dimension of the mesh; i.e. the manifold dimension of the elements in the mesh. If we ever support multi-dimensional meshes (e.g. hexes and quads in the same mesh) then this will return the largest such dimension.

Definition at line 135 of file mesh_base.C.

 {
   if (!_elem_dims.empty())
     return cast_int<unsigned int>(*_elem_dims.rbegin());
   return 0;
 }

References libMesh::MeshBase::_elem_dims.

Referenced by libMesh::HPCoarsenTest::add_projection(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), assemble(), LinearElasticity::assemble(), assemble_1D(), AssembleOptimization::assemble_A_and_F(), assemble_biharmonic(), assemble_cd(), assemble_elasticity(), assemble_ellipticdg(), assemble_helmholtz(), assemble_laplace(), assemble_mass(), assemble_matrices(), assemble_poisson(), assemble_SchroedingerEquation(), assemble_shell(), assemble_stokes(), assemble_wave(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::EquationSystems::build_variable_names(), compute_jacobian(), compute_residual(), LinearElasticityWithContact::compute_stresses(), LinearElasticity::compute_stresses(), compute_stresses(), LargeDeformationElasticity::compute_stresses(), libMesh::DofMap::create_dof_constraints(), libMesh::MeshTools::Modification::distort(), SolidSystem::element_time_derivative(), libMesh::MeshRefinement::flag_elements_by_elem_fraction(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::ReplicatedMesh::get_boundary_points(), libMesh::LaplaceMeshSmoother::init(), libMesh::PointLocatorTree::init(), SolidSystem::init_data(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::RBEIMAssembly::initialize_fe(), integrate_function(), LaplaceYoung::jacobian(), LargeDeformationElasticity::jacobian(), main(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::GMVIO::read(), libMesh::VTKIO::read(), libMesh::System::read_header(), libMesh::UCDIO::read_implementation(), libMesh::XdrIO::read_serialized_connectivity(), LaplaceYoung::residual(), LargeDeformationElasticity::residual(), LinearElasticityWithContact::residual_and_jacobian(), SolidSystem::save_initial_mesh(), setup(), libMesh::MeshTools::Modification::smooth(), MeshSpatialDimensionTest::test1D(), MeshSpatialDimensionTest::test2D(), InfFERadialTest::testSingleOrder(), libMesh::BoundaryVolumeSolutionTransfer::transfer(), libMesh::DTKSolutionTransfer::transfer(), libMesh::DofMap::use_coupled_neighbor_dofs(), libMesh::PostscriptIO::write(), libMesh::CheckpointIO::write(), libMesh::TecplotIO::write_binary(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::UCDIO::write_implementation(), libMesh::UCDIO::write_nodal_data(), libMesh::EnsightIO::write_scalar_ascii(), libMesh::GnuPlotIO::write_solution(), and libMesh::EnsightIO::write_vector_ascii().

◆ n_active_elem()

dof_id_type libMesh::ReplicatedMesh::n_active_elem ( ) const

overridevirtualinherited

Returns: The number of active elements in the mesh.

Implemented in terms of active_element_iterators.

Implements libMesh::MeshBase.

Definition at line 1424 of file replicated_mesh.C.

 {
   return static_cast<dof_id_type>(std::distance (this->active_elements_begin(),
                                                  this->active_elements_end()));
 }

References libMesh::ReplicatedMesh::active_elements_begin(), libMesh::ReplicatedMesh::active_elements_end(), and distance().

Referenced by libMesh::ReplicatedMesh::get_disconnected_subdomains(), MixedDimensionNonUniformRefinement::testMesh(), MixedDimensionNonUniformRefinementTriangle::testMesh(), and MixedDimensionNonUniformRefinement3D::testMesh().

◆ n_active_elem_on_proc()

dof_id_type libMesh::MeshBase::n_active_elem_on_proc ( const processor_id_type proc ) const

inherited

Returns: The number of active elements on processor proc.

Definition at line 518 of file mesh_base.C.

 {
   libmesh_assert_less (proc_id, this->n_processors());
   return static_cast<dof_id_type>(std::distance (this->active_pid_elements_begin(proc_id),
                                                  this->active_pid_elements_end  (proc_id)));
 }

References distance().

Referenced by libMesh::MeshBase::n_active_local_elem().

◆ n_active_local_elem()

dof_id_type libMesh::MeshBase::n_active_local_elem ( ) const

inlineinherited

Returns: The number of active elements on the local processor.

Definition at line 420 of file mesh_base.h.

421 { return this->n_active_elem_on_proc (this->processor_id()); }

References libMesh::MeshBase::n_active_elem_on_proc(), and libMesh::ParallelObject::processor_id().

Referenced by libMesh::VTKIO::cells_to_vtk().

◆ n_active_sub_elem()

dof_id_type libMesh::MeshBase::n_active_sub_elem ( ) const

inherited

Same as n_sub_elem(), but only counts active elements.

Definition at line 539 of file mesh_base.C.

 {
   dof_id_type ne=0;
  
   for (const auto & elem : this->active_element_ptr_range())
     ne += elem->n_sub_elem();
  
   return ne;
 }

Referenced by libMesh::TecplotIO::write_ascii(), libMesh::GMVIO::write_ascii_old_impl(), and libMesh::TecplotIO::write_binary().

◆ n_elem()

virtual dof_id_type libMesh::ReplicatedMesh::n_elem ( ) const

inlineoverridevirtualinherited

Returns: The number of elements in the mesh.

The standard n_elem() function may return a cached value on distributed meshes, and so can be called by any processor at any time.

Implements libMesh::MeshBase.

Definition at line 116 of file replicated_mesh.h.

117 { return cast_int<dof_id_type>(_elements.size()); }

References libMesh::ReplicatedMesh::_elements.

Referenced by libMesh::ReplicatedMesh::elem_ptr(), libMesh::ReplicatedMesh::get_disconnected_subdomains(), libMesh::RBEIMEvaluation::legacy_write_out_interpolation_points_elem(), libMesh::ReplicatedMesh::query_elem_ptr(), MixedDimensionMeshTest::testMesh(), MixedDimensionNonUniformRefinement::testMesh(), MixedDimensionNonUniformRefinementTriangle::testMesh(), and MixedDimensionNonUniformRefinement3D::testMesh().

◆ n_elem_integers()

unsigned int libMesh::MeshBase::n_elem_integers ( ) const

inlineinherited

Definition at line 829 of file mesh_base.h.

829 { return _elem_integer_names.size(); }

References libMesh::MeshBase::_elem_integer_names.

Referenced by libMesh::CheckpointIO::read_connectivity(), and libMesh::CheckpointIO::write().

◆ n_elem_on_proc()

dof_id_type libMesh::MeshBase::n_elem_on_proc ( const processor_id_type proc ) const

inherited

Returns: The number of elements on processor proc.

Definition at line 505 of file mesh_base.C.

 {
   // We're either counting a processor's elements or unpartitioned
   // elements
   libmesh_assert (proc_id < this->n_processors() ||
                   proc_id == DofObject::invalid_processor_id);
  
   return static_cast<dof_id_type>(std::distance (this->pid_elements_begin(proc_id),
                                                  this->pid_elements_end  (proc_id)));
 }

References distance(), and libMesh::libmesh_assert().

Referenced by libMesh::MeshBase::n_local_elem(), and libMesh::MeshBase::n_unpartitioned_elem().

◆ n_local_elem()

dof_id_type libMesh::MeshBase::n_local_elem ( ) const

inlineinherited

Returns: The number of elements on the local processor.

Definition at line 403 of file mesh_base.h.

404 { return this->n_elem_on_proc (this->processor_id()); }

References libMesh::MeshBase::n_elem_on_proc(), and libMesh::ParallelObject::processor_id().

Referenced by libMesh::DTKAdapter::DTKAdapter(), and libMesh::DistributedMesh::parallel_n_elem().

◆ n_local_nodes()

dof_id_type libMesh::MeshBase::n_local_nodes ( ) const

inlineinherited

Returns: The number of nodes on the local processor.

Definition at line 303 of file mesh_base.h.

304 { return this->n_nodes_on_proc (this->processor_id()); }

References libMesh::MeshBase::n_nodes_on_proc(), and libMesh::ParallelObject::processor_id().

Referenced by libMesh::VTKIO::nodes_to_vtk(), and libMesh::DistributedMesh::parallel_n_nodes().

◆ n_node_integers()

unsigned int libMesh::MeshBase::n_node_integers ( ) const

inlineinherited

Definition at line 926 of file mesh_base.h.

926 { return _node_integer_names.size(); }

References libMesh::MeshBase::_node_integer_names.

Referenced by libMesh::CheckpointIO::read_nodes(), and libMesh::CheckpointIO::write().

◆ n_nodes()

virtual dof_id_type libMesh::ReplicatedMesh::n_nodes ( ) const

inlineoverridevirtualinherited

Returns: The number of nodes in the mesh.

This function and others must be defined in derived classes since the MeshBase class has no specific storage for nodes or elements. The standard n_nodes() function may return a cached value on distributed meshes, and so can be called by any processor at any time.

Implements libMesh::MeshBase.

Definition at line 104 of file replicated_mesh.h.

105 { return cast_int<dof_id_type>(_nodes.size()); }

References libMesh::ReplicatedMesh::_nodes.

Referenced by libMesh::ReplicatedMesh::node_ptr(), libMesh::ReplicatedMesh::query_node_ptr(), MixedDimensionMeshTest::testMesh(), MixedDimensionNonUniformRefinement::testMesh(), MixedDimensionNonUniformRefinementTriangle::testMesh(), and MixedDimensionNonUniformRefinement3D::testMesh().

◆ n_nodes_on_proc()

dof_id_type libMesh::MeshBase::n_nodes_on_proc ( const processor_id_type proc ) const

inherited

Returns: The number of nodes on processor proc.

Definition at line 492 of file mesh_base.C.

 {
   // We're either counting a processor's nodes or unpartitioned
   // nodes
   libmesh_assert (proc_id < this->n_processors() ||
                   proc_id == DofObject::invalid_processor_id);
  
   return static_cast<dof_id_type>(std::distance (this->pid_nodes_begin(proc_id),
                                                  this->pid_nodes_end  (proc_id)));
 }

References distance(), and libMesh::libmesh_assert().

Referenced by libMesh::MeshBase::n_local_nodes(), and libMesh::MeshBase::n_unpartitioned_nodes().

◆ n_partitions()

unsigned int libMesh::MeshBase::n_partitions ( ) const

inlineinherited

Returns: The number of partitions which have been defined via a call to either mesh.partition() or by building a Partitioner object and calling partition.

Note: The partitioner object is responsible for setting this value.

Definition at line 1153 of file mesh_base.h.

1154 { return _n_parts; }

References libMesh::MeshBase::_n_parts.

Referenced by libMesh::BoundaryInfo::sync(), libMesh::NameBasedIO::write(), libMesh::GMVIO::write_ascii_new_impl(), and libMesh::GMVIO::write_ascii_old_impl().

◆ n_processors()

processor_id_type libMesh::ParallelObject::n_processors ( ) const

inlineinherited

Returns: The number of processors in the group.

Definition at line 100 of file parallel_object.h.

101 { return cast_int<processor_id_type>(_communicator.size()); }

References libMesh::ParallelObject::_communicator.

◆ n_sub_elem()

dof_id_type libMesh::MeshBase::n_sub_elem ( ) const

inherited

Returns: The number of elements that will be written out in certain I/O formats.

For example, a 9-noded quadrilateral will be broken into 4 linear sub-elements for plotting purposes. Thus, for a mesh of 2 QUAD9 elements n_tecplot_elem() will return 8. Implemented in terms of element_iterators.

Definition at line 527 of file mesh_base.C.

 {
   dof_id_type ne=0;
  
   for (const auto & elem : this->element_ptr_range())
     ne += elem->n_sub_elem();
  
   return ne;
 }

◆ n_subdomains()

subdomain_id_type libMesh::MeshBase::n_subdomains ( ) const

inherited

Returns: The number of subdomains in the global mesh. Subdomains correspond to separate subsets of the mesh which could correspond e.g. to different materials in a solid mechanics application, or regions where different physical processes are important. The subdomain mapping is independent from the parallel decomposition.

Definition at line 477 of file mesh_base.C.

 {
   // This requires an inspection on every processor
   parallel_object_only();
  
   std::set<subdomain_id_type> ids;
  
   this->subdomain_ids (ids);
  
   return cast_int<subdomain_id_type>(ids.size());
 }

Referenced by libMesh::XdrIO::write(), and libMesh::NameBasedIO::write_nodal_data().

◆ n_unpartitioned_elem()

dof_id_type libMesh::MeshBase::n_unpartitioned_elem ( ) const

inlineinherited

Returns: The number of elements owned by no processor.

Definition at line 409 of file mesh_base.h.

410 { return this->n_elem_on_proc (DofObject::invalid_processor_id); }

References libMesh::DofObject::invalid_processor_id, and libMesh::MeshBase::n_elem_on_proc().

Referenced by libMesh::UnstructuredMesh::all_second_order(), and libMesh::DistributedMesh::parallel_n_elem().

◆ n_unpartitioned_nodes()

dof_id_type libMesh::MeshBase::n_unpartitioned_nodes ( ) const

inlineinherited

Returns: The number of nodes owned by no processor.

Definition at line 309 of file mesh_base.h.

310 { return this->n_nodes_on_proc (DofObject::invalid_processor_id); }

References libMesh::DofObject::invalid_processor_id, and libMesh::MeshBase::n_nodes_on_proc().

Referenced by libMesh::DistributedMesh::parallel_n_nodes().

◆ next_unique_id()

unique_id_type libMesh::MeshBase::next_unique_id ( )

inlineinherited

Returns: The next unique id to be used.

Definition at line 322 of file mesh_base.h.

322 { return _next_unique_id; }

References libMesh::MeshBase::_next_unique_id.

◆ node() [1/2]

virtual Node& libMesh::MeshBase::node ( const dof_id_type i )

inlinevirtualinherited

Returns: A reference to the \( i^{th} \) node, which should be present in this processor's subset of the mesh data structure.

Definition at line 485 of file mesh_base.h.

   {
     libmesh_deprecated();
     return *this->node_ptr(i);
   }

References libMesh::MeshBase::node_ptr().

◆ node() [2/2]

virtual const Node& libMesh::MeshBase::node ( const dof_id_type i ) const

inlinevirtualinherited

Returns: A constant reference (for reading only) to the \( i^{th} \) node, which should be present in this processor's subset of the mesh data structure.

Definition at line 471 of file mesh_base.h.

   {
     libmesh_deprecated();
     return *this->node_ptr(i);
   }

References libMesh::MeshBase::node_ptr().

Referenced by libMesh::UnstructuredMesh::all_first_order(), libMesh::ReplicatedMesh::clear(), libMesh::DistributedMesh::clear(), libMesh::ReplicatedMesh::get_boundary_points(), libMesh::ReplicatedMesh::renumber_nodes_and_elements(), libMesh::DistributedMesh::renumber_nodes_and_elements(), and libMesh::ReplicatedMesh::stitching_helper().

◆ node_ptr() [1/2]

const Node * libMesh::ReplicatedMesh::node_ptr ( const dof_id_type i ) const

overridevirtualinherited

Returns: A pointer to the \( i^{th} \) node, which should be present in this processor's subset of the mesh data structure.

Implements libMesh::MeshBase.

Definition at line 182 of file replicated_mesh.C.

 {
   libmesh_assert_less (i, this->n_nodes());
   libmesh_assert(_nodes[i]);
   libmesh_assert_equal_to (_nodes[i]->id(), i); // This will change soon
  
   return _nodes[i];
 }

References libMesh::ReplicatedMesh::_nodes, libMesh::libmesh_assert(), and libMesh::ReplicatedMesh::n_nodes().

Referenced by GetBoundaryPointsTest::build_mesh(), MixedDimensionMeshTest::build_mesh(), MeshfunctionDFEM::build_mesh(), MixedDimensionNonUniformRefinement::build_mesh(), MixedDimensionNonUniformRefinementTriangle::build_mesh(), MixedDimensionNonUniformRefinement3D::build_mesh(), libMesh::RBEIMEvaluation::legacy_write_out_interpolation_points_elem(), and libMesh::ReplicatedMesh::stitching_helper().

◆ node_ptr() [2/2]

Node * libMesh::ReplicatedMesh::node_ptr ( const dof_id_type i )

overridevirtualinherited

Returns: A writable pointer to the \( i^{th} \) node, which should be present in this processor's subset of the mesh data structure.

Implements libMesh::MeshBase.

Definition at line 194 of file replicated_mesh.C.

 {
   libmesh_assert_less (i, this->n_nodes());
   libmesh_assert(_nodes[i]);
   libmesh_assert_equal_to (_nodes[i]->id(), i); // This will change soon
  
   return _nodes[i];
 }

References libMesh::ReplicatedMesh::_nodes, libMesh::libmesh_assert(), and libMesh::ReplicatedMesh::n_nodes().

◆ node_ptr_range() [1/2]

virtual SimpleRange<const_node_iterator> libMesh::ReplicatedMesh::node_ptr_range ( ) const

inlineoverridevirtualinherited

Implements libMesh::MeshBase.

Definition at line 460 of file replicated_mesh.h.

460 { return {nodes_begin(), nodes_end()}; }

References libMesh::ReplicatedMesh::nodes_begin(), and libMesh::ReplicatedMesh::nodes_end().

◆ node_ptr_range() [2/2]

virtual SimpleRange<node_iterator> libMesh::ReplicatedMesh::node_ptr_range ( )

inlineoverridevirtualinherited

Implements libMesh::MeshBase.

Definition at line 459 of file replicated_mesh.h.

459 { return {nodes_begin(), nodes_end()}; }

References libMesh::ReplicatedMesh::nodes_begin(), and libMesh::ReplicatedMesh::nodes_end().

◆ node_ref() [1/2]

virtual Node& libMesh::MeshBase::node_ref ( const dof_id_type i )

inlinevirtualinherited

Returns: A reference to the \( i^{th} \) node, which should be present in this processor's subset of the mesh data structure.

Definition at line 459 of file mesh_base.h.

                                                 {
     return *this->node_ptr(i);
   }

References libMesh::MeshBase::node_ptr().

◆ node_ref() [2/2]

virtual const Node& libMesh::MeshBase::node_ref ( const dof_id_type i ) const

inlinevirtualinherited

Returns: A constant reference (for reading only) to the \( i^{th} \) node, which should be present in this processor's subset of the mesh data structure.

Definition at line 451 of file mesh_base.h.

                                                             {
     return *this->node_ptr(i);
   }

References libMesh::MeshBase::node_ptr().

Referenced by libMesh::SyncNodalPositions::act_on_data(), LinearElasticityWithContact::add_contact_edge_elements(), libMesh::DynaIO::add_spline_constraints(), assemble_matrix_and_rhs(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::DTKAdapter::DTKAdapter(), fill_dirichlet_bc(), main(), libMesh::ReplicatedMesh::point(), libMesh::DistributedMesh::point(), libMesh::XdrIO::read_serialized_nodes(), LinearElasticityWithContact::residual_and_jacobian(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::MeshTools::Modification::smooth(), libMesh::ReplicatedMesh::stitching_helper(), libMesh::DTKAdapter::update_variable_values(), and libMesh::GmshIO::write_mesh().

◆ nodes_begin() [1/2]

virtual const_node_iterator libMesh::ReplicatedMesh::nodes_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ nodes_begin() [2/2]

virtual node_iterator libMesh::ReplicatedMesh::nodes_begin ( )

overridevirtualinherited

Node iterator accessor functions.

Implements libMesh::MeshBase.

Referenced by libMesh::ReplicatedMesh::node_ptr_range().

◆ nodes_end() [1/2]

virtual const_node_iterator libMesh::ReplicatedMesh::nodes_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ nodes_end() [2/2]

virtual node_iterator libMesh::ReplicatedMesh::nodes_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

Referenced by libMesh::ReplicatedMesh::node_ptr_range().

◆ not_active_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::not_active_elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_active_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::not_active_elements_begin ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_active_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::not_active_elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_active_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::not_active_elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_ancestor_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::not_ancestor_elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_ancestor_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::not_ancestor_elements_begin ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_ancestor_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::not_ancestor_elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_ancestor_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::not_ancestor_elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_level_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::not_level_elements_begin ( unsigned int level ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_level_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::not_level_elements_begin ( unsigned int level )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_level_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::not_level_elements_end ( unsigned int level ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_level_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::not_level_elements_end ( unsigned int level )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_local_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::not_local_elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_local_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::not_local_elements_begin ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_local_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::not_local_elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_local_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::not_local_elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_subactive_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::not_subactive_elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_subactive_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::not_subactive_elements_begin ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_subactive_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::not_subactive_elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ not_subactive_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::not_subactive_elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ own_node()

virtual void libMesh::MeshBase::own_node ( Node & )

inlinevirtualinherited

Takes ownership of node n on this partition of a distributed mesh, by setting n.processor_id() to this->processor_id(), as well as changing n.id() and moving it in the mesh's internal container to give it a new authoritative id.

Reimplemented in libMesh::DistributedMesh.

Definition at line 656 of file mesh_base.h.

656 {}

Referenced by libMesh::UnstructuredMesh::all_second_order().

◆ parallel_max_unique_id()

unique_id_type libMesh::ReplicatedMesh::parallel_max_unique_id ( ) const

overridevirtualinherited

Returns: A number greater than or equal to the maximum unique_id in the mesh.

Implements libMesh::MeshBase.

Definition at line 629 of file replicated_mesh.C.

 {
   // This function must be run on all processors at once
   parallel_object_only();
  
   unique_id_type max_local = _next_unique_id;
   this->comm().max(max_local);
   return max_local;
 }

References libMesh::MeshBase::_next_unique_id, and libMesh::ParallelObject::comm().

Referenced by libMesh::ReplicatedMesh::stitching_helper(), and libMesh::ReplicatedMesh::update_parallel_id_counts().

◆ parallel_n_elem()

virtual dof_id_type libMesh::ReplicatedMesh::parallel_n_elem ( ) const

inlineoverridevirtualinherited

Returns: The number of elements in the mesh.

The parallel_n_elem() function computes a parallel-synchronized value on distributed meshes, and so must be called in parallel only.

Implements libMesh::MeshBase.

Definition at line 119 of file replicated_mesh.h.

120 { return cast_int<dof_id_type>(_elements.size()); }

References libMesh::ReplicatedMesh::_elements.

◆ parallel_n_nodes()

virtual dof_id_type libMesh::ReplicatedMesh::parallel_n_nodes ( ) const

inlineoverridevirtualinherited

Returns: The number of nodes in the mesh.

This function and others must be overridden in derived classes since the MeshBase class has no specific storage for nodes or elements. The parallel_n_nodes() function computes a parallel-synchronized value on distributed meshes, and so must be called in parallel only.

Implements libMesh::MeshBase.

Definition at line 107 of file replicated_mesh.h.

108 { return cast_int<dof_id_type>(_nodes.size()); }

References libMesh::ReplicatedMesh::_nodes.

◆ partition() [1/2]

void libMesh::MeshBase::partition ( )

inlineinherited

Definition at line 992 of file mesh_base.h.

993 { this->partition(this->n_processors()); }

References libMesh::ParallelObject::n_processors().

◆ partition() [2/2]

void libMesh::MeshBase::partition ( const unsigned int n_parts )

virtualinherited

Call the default partitioner (currently metis_partition()).

Definition at line 599 of file mesh_base.C.

 {
   // If we get here and we have unpartitioned elements, we need that
   // fixed.
   if (this->n_unpartitioned_elem() > 0)
     {
       libmesh_assert (partitioner().get());
       libmesh_assert (this->is_serial());
       partitioner()->partition (*this, n_parts);
     }
   // A nullptr partitioner or a skip_partitioning(true) call or a
   // skip_noncritical_partitioning(true) call means don't repartition;
   // skip_noncritical_partitioning() checks all these.
   else if (!skip_noncritical_partitioning())
     {
       partitioner()->partition (*this, n_parts);
     }
   else
     {
       // Adaptive coarsening may have "orphaned" nodes on processors
       // whose elements no longer share them.  We need to check for
       // and possibly fix that.
       MeshTools::correct_node_proc_ids(*this);
  
       // Make sure locally cached partition count is correct
       this->recalculate_n_partitions();
  
       // Make sure any other locally cached data is correct
       this->update_post_partitioning();
     }
 }

References libMesh::MeshTools::correct_node_proc_ids(), libMesh::ReferenceElem::get(), and libMesh::libmesh_assert().

Referenced by main(), libMesh::split_mesh(), ExtraIntegersTest::test_helper(), MappedSubdomainPartitionerTest::testMappedSubdomainPartitioner(), EquationSystemsTest::testRepartitionThenReinit(), and CheckpointIOTest::testSplitter().

◆ partitioner()

virtual std::unique_ptr<Partitioner>& libMesh::MeshBase::partitioner ( )

inlinevirtualinherited

A partitioner to use at each prepare_for_use()

Definition at line 127 of file mesh_base.h.

127 { return _partitioner; }

References libMesh::MeshBase::_partitioner.

Referenced by main(), libMesh::BoundaryInfo::sync(), MappedSubdomainPartitionerTest::testMappedSubdomainPartitioner(), and MeshInputTest::testMeshMoveConstructor().

◆ pid_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::pid_elements_begin ( processor_id_type proc_id ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ pid_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::pid_elements_begin ( processor_id_type proc_id )

overridevirtualinherited

Iterate over all elements with a specified processor id.

Implements libMesh::MeshBase.

◆ pid_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::pid_elements_end ( processor_id_type proc_id ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ pid_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::pid_elements_end ( processor_id_type proc_id )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ pid_nodes_begin() [1/2]

virtual const_node_iterator libMesh::ReplicatedMesh::pid_nodes_begin ( processor_id_type proc_id ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ pid_nodes_begin() [2/2]

virtual node_iterator libMesh::ReplicatedMesh::pid_nodes_begin ( processor_id_type proc_id )

overridevirtualinherited

Iterate over nodes with processor_id() == proc_id.

Implements libMesh::MeshBase.

◆ pid_nodes_end() [1/2]

virtual const_node_iterator libMesh::ReplicatedMesh::pid_nodes_end ( processor_id_type proc_id ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ pid_nodes_end() [2/2]

virtual node_iterator libMesh::ReplicatedMesh::pid_nodes_end ( processor_id_type proc_id )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ point()

const Point & libMesh::ReplicatedMesh::point ( const dof_id_type i ) const

overridevirtualinherited

Returns: A constant reference (for reading only) to the \( i^{th} \) point, which should be present in this processor's subset of the mesh data structure.

Implements libMesh::MeshBase.

Definition at line 174 of file replicated_mesh.C.

 {
   return this->node_ref(i);
 }

References libMesh::MeshBase::node_ref().

Referenced by libMesh::ReplicatedMesh::stitching_helper().

◆ point_locator()

const PointLocatorBase & libMesh::MeshBase::point_locator ( ) const

inherited

Returns: A pointer to a PointLocatorBase object for this mesh, constructing a master PointLocator first if necessary.

Definition at line 652 of file mesh_base.C.

 {
   libmesh_deprecated();
  
   if (_point_locator.get() == nullptr)
     {
       // PointLocator construction may not be safe within threads
       libmesh_assert(!Threads::in_threads);
  
       _point_locator = PointLocatorBase::build(TREE_ELEMENTS, *this);
  
       if (_point_locator_close_to_point_tol > 0.)
         _point_locator->set_close_to_point_tol(_point_locator_close_to_point_tol);
     }
  
   return *_point_locator;
 }

References libMesh::Threads::in_threads, libMesh::libmesh_assert(), and libMesh::TREE_ELEMENTS.

◆ prepare_for_use()

void libMesh::MeshBase::prepare_for_use	(	const bool	skip_renumber_nodes_and_elements = `false`,
		const bool	skip_find_neighbors = `false`
	)

inherited

Prepare a newly ecreated (or read) mesh for use.

This involves 4 steps: 1.) call find_neighbors() 2.) call partition() 3.) call renumber_nodes_and_elements() 4.) call cache_elem_dims()

The argument to skip renumbering is now deprecated - to prevent a mesh from being renumbered, set allow_renumbering(false).

If this is a distributed mesh, local copies of remote elements will be deleted here - to keep those elements replicated during preparation, set allow_remote_element_removal(false).

Definition at line 318 of file mesh_base.C.

 {
   LOG_SCOPE("prepare_for_use()", "MeshBase");
  
   parallel_object_only();
  
   libmesh_assert(this->comm().verify(this->is_serial()));
  
   // A distributed mesh may have processors with no elements (or
   // processors with no elements of higher dimension, if we ever
   // support mixed-dimension meshes), but we want consistent
   // mesh_dimension anyways.
   //
   // cache_elem_dims() should get the elem_dimensions() and
   // mesh_dimension() correct later, and we don't need it earlier.
  
  
   // Renumber the nodes and elements so that they in contiguous
   // blocks.  By default, _skip_renumber_nodes_and_elements is false.
   //
   // We may currently change that by passing
   // skip_renumber_nodes_and_elements==true to this function, but we
   // should use the allow_renumbering() accessor instead.
   //
   // Instances where you if prepare_for_use() should not renumber the nodes
   // and elements include reading in e.g. an xda/r or gmv file. In
   // this case, the ordering of the nodes may depend on an accompanying
   // solution, and the node ordering cannot be changed.
  
   if (skip_renumber_nodes_and_elements)
     {
       libmesh_deprecated();
       this->allow_renumbering(false);
     }
  
   // Mesh modification operations might not leave us with consistent
   // id counts, but our partitioner might need that consistency.
   if (!_skip_renumber_nodes_and_elements)
     this->renumber_nodes_and_elements();
   else
     this->update_parallel_id_counts();
  
   // Let all the elements find their neighbors
   if (!skip_find_neighbors)
     this->find_neighbors();
  
   // The user may have set boundary conditions.  We require that the
   // boundary conditions were set consistently.  Because we examine
   // neighbors when evaluating non-raw boundary condition IDs, this
   // assert is only valid when our neighbor links are in place.
 #ifdef DEBUG
   MeshTools::libmesh_assert_valid_boundary_ids(*this);
 #endif
  
   // Search the mesh for all the dimensions of the elements
   // and cache them.
   this->cache_elem_dims();
  
   // Search the mesh for elements that have a neighboring element
   // of dim+1 and set that element as the interior parent
   this->detect_interior_parents();
  
   // Fix up node unique ids in case mesh generation code didn't take
   // exceptional care to do so.
   //  MeshCommunication().make_node_unique_ids_parallel_consistent(*this);
  
   // We're going to still require that mesh generation code gets
   // element unique ids consistent.
 #if defined(DEBUG) && defined(LIBMESH_ENABLE_UNIQUE_ID)
   MeshTools::libmesh_assert_valid_unique_ids(*this);
 #endif
  
   // Reset our PointLocator.  Any old locator is invalidated any time
   // the elements in the underlying elements in the mesh have changed,
   // so we clear it here.
   this->clear_point_locator();
  
   // Allow our GhostingFunctor objects to reinit if necessary.
   // Do this before partitioning and redistributing, and before
   // deleting remote elements.
   for (auto & gf : _ghosting_functors)
     {
       libmesh_assert(gf);
       gf->mesh_reinit();
     }
  
   // Partition the mesh unless *all* partitioning is to be skipped.
   // If only noncritical partitioning is to be skipped, the
   // partition() call will still check for orphaned nodes.
   if (!skip_partitioning())
     this->partition();
  
   // If we're using DistributedMesh, we'll probably want it
   // parallelized.
   if (this->_allow_remote_element_removal)
     this->delete_remote_elements();
  
   if (!_skip_renumber_nodes_and_elements)
     this->renumber_nodes_and_elements();
  
   // The mesh is now prepared for use.
   _is_prepared = true;
  
 #if defined(DEBUG) && defined(LIBMESH_ENABLE_UNIQUE_ID)
   MeshTools::libmesh_assert_valid_boundary_ids(*this);
   MeshTools::libmesh_assert_valid_unique_ids(*this);
 #endif
 }

References libMesh::libmesh_assert(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), and libMesh::MeshTools::libmesh_assert_valid_unique_ids().

Referenced by LinearElasticityWithContact::add_contact_edge_elements(), libMesh::UnstructuredMesh::all_first_order(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Subdivision::all_subdivision(), libMesh::MeshTools::Modification::all_tri(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::InfElemBuilder::build_inf_elem(), GetBoundaryPointsTest::build_mesh(), MixedDimensionMeshTest::build_mesh(), MeshfunctionDFEM::build_mesh(), SlitMeshTest::build_mesh(), MixedDimensionNonUniformRefinement::build_mesh(), MixedDimensionNonUniformRefinementTriangle::build_mesh(), MixedDimensionNonUniformRefinement3D::build_mesh(), libMesh::MeshRefinement::coarsen_elements(), libMesh::UnstructuredMesh::copy_nodes_and_elements(), libMesh::UnstructuredMesh::create_submesh(), libMesh::MeshTools::Modification::flatten(), main(), libMesh::MeshTools::Subdivision::prepare_subdivision_mesh(), libMesh::GMVIO::read(), libMesh::UnstructuredMesh::read(), libMesh::MeshRefinement::refine_and_coarsen_elements(), libMesh::MeshRefinement::refine_elements(), libMesh::ReplicatedMesh::stitching_helper(), libMesh::BoundaryInfo::sync(), MeshSpatialDimensionTest::test1D(), MeshSpatialDimensionTest::test2D(), SystemsTest::testBlockRestrictedVarNDofs(), SystemsTest::testDofCouplingWithVarGroups(), MeshInputTest::testDynaReadElem(), MeshInputTest::testDynaReadPatch(), MeshInputTest::testExodusCopyElementSolution(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), EquationSystemsTest::testPostInitAddElem(), SystemsTest::testProjectMatrix3D(), EquationSystemsTest::testReinitWithNodeElem(), BoundaryInfoTest::testShellFaceConstraints(), WriteVecAndScalar::testWrite(), tetrahedralize_domain(), libMesh::TriangleInterface::triangulate(), libMesh::MeshRefinement::uniformly_coarsen(), and libMesh::MeshRefinement::uniformly_refine().

◆ print_info()

void libMesh::MeshBase::print_info ( std::ostream & os = libMesh::out ) const

inherited

Prints relevant information about the mesh.

Definition at line 585 of file mesh_base.C.

 {
   os << this->get_info()
      << std::endl;
 }

Referenced by assemble_and_solve(), libMesh::InfElemBuilder::build_inf_elem(), main(), and libMesh::operator<<().

◆ processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const

inlineinherited

Returns: The rank of this processor in the group.

Definition at line 106 of file parallel_object.h.

107 { return cast_int<processor_id_type>(_communicator.rank()); }

References libMesh::ParallelObject::_communicator.

◆ query_elem() [1/2]

virtual Elem* libMesh::MeshBase::query_elem ( const dof_id_type i )

inlinevirtualinherited

Returns: A writable pointer to the \( i^{th} \) element, or nullptr if no such element exists in this processor's mesh data structure.

Definition at line 609 of file mesh_base.h.

   {
     libmesh_deprecated();
     return this->query_elem_ptr(i);
   }

References libMesh::MeshBase::query_elem_ptr().

◆ query_elem() [2/2]

virtual const Elem* libMesh::MeshBase::query_elem ( const dof_id_type i ) const

inlinevirtualinherited

Returns: A pointer to the \( i^{th} \) element, or nullptr if no such element exists in this processor's mesh data structure.

Definition at line 595 of file mesh_base.h.

   {
     libmesh_deprecated();
     return this->query_elem_ptr(i);
   }

References libMesh::MeshBase::query_elem_ptr().

◆ query_elem_ptr() [1/2]

const Elem * libMesh::ReplicatedMesh::query_elem_ptr ( const dof_id_type i ) const

overridevirtualinherited

Returns: A pointer to the \( i^{th} \) element, or nullptr if no such element exists in this processor's mesh data structure.

Implements libMesh::MeshBase.

Definition at line 256 of file replicated_mesh.C.

 {
   if (i >= this->n_elem())
     return nullptr;
   libmesh_assert (_elements[i] == nullptr ||
                   _elements[i]->id() == i); // This will change soon
  
   return _elements[i];
 }

References libMesh::ReplicatedMesh::_elements, libMesh::libmesh_assert(), and libMesh::ReplicatedMesh::n_elem().

◆ query_elem_ptr() [2/2]

Elem * libMesh::ReplicatedMesh::query_elem_ptr ( const dof_id_type i )

overridevirtualinherited

Returns: A writable pointer to the \( i^{th} \) element, or nullptr if no such element exists in this processor's mesh data structure.

Implements libMesh::MeshBase.

Definition at line 269 of file replicated_mesh.C.

 {
   if (i >= this->n_elem())
     return nullptr;
   libmesh_assert (_elements[i] == nullptr ||
                   _elements[i]->id() == i); // This will change soon
  
   return _elements[i];
 }

References libMesh::ReplicatedMesh::_elements, libMesh::libmesh_assert(), and libMesh::ReplicatedMesh::n_elem().

◆ query_node_ptr() [1/2]

const Node * libMesh::ReplicatedMesh::query_node_ptr ( const dof_id_type i ) const

overridevirtualinherited

Returns: A pointer to the \( i^{th} \) node, or nullptr if no such node exists in this processor's mesh data structure.

Implements libMesh::MeshBase.

Definition at line 206 of file replicated_mesh.C.

 {
   if (i >= this->n_nodes())
     return nullptr;
   libmesh_assert (_nodes[i] == nullptr ||
                   _nodes[i]->id() == i); // This will change soon
  
   return _nodes[i];
 }

References libMesh::ReplicatedMesh::_nodes, libMesh::libmesh_assert(), and libMesh::ReplicatedMesh::n_nodes().

◆ query_node_ptr() [2/2]

Node * libMesh::ReplicatedMesh::query_node_ptr ( const dof_id_type i )

overridevirtualinherited

Returns: A writable pointer to the \( i^{th} \) node, or nullptr if no such node exists in this processor's mesh data structure.

Implements libMesh::MeshBase.

Definition at line 219 of file replicated_mesh.C.

 {
   if (i >= this->n_nodes())
     return nullptr;
   libmesh_assert (_nodes[i] == nullptr ||
                   _nodes[i]->id() == i); // This will change soon
  
   return _nodes[i];
 }

References libMesh::ReplicatedMesh::_nodes, libMesh::libmesh_assert(), and libMesh::ReplicatedMesh::n_nodes().

◆ read()

void libMesh::UnstructuredMesh::read	(	const std::string &	name,
		void *	mesh_data = `nullptr`,
		bool	skip_renumber_nodes_and_elements = `false`,
		bool	skip_find_neighbors = `false`
	)

overridevirtualinherited

Reads the file specified by name.

Attempts to figure out the proper method by the file extension. This is now the only way to read a mesh. The UnstructuredMesh then initializes its data structures and is ready for use.

The skip_renumber_nodes_and_elements argument is now deprecated - to disallow renumbering, set MeshBase::allow_renumbering(false).

Set skip_find_neighbors=true to skip the find-neighbors operation during prepare_for_use. This operation isn't always necessary and it can be time-consuming, which is why we provide an option to skip it.

Implements libMesh::MeshBase.

Definition at line 620 of file unstructured_mesh.C.

 {
   // Set the skip_renumber_nodes_and_elements flag on all processors
   // if necessary.
   // This ensures that renumber_nodes_and_elements is *not* called
   // during prepare_for_use() for certain types of mesh files.
   // This is required in cases where there is an associated solution
   // file which expects a certain ordering of the nodes.
   if (name.rfind(".gmv") + 4 == name.size())
     this->allow_renumbering(false);
  
   NameBasedIO(*this).read(name);
  
   if (skip_renumber_nodes_and_elements)
     {
       // Use MeshBase::allow_renumbering() yourself instead.
       libmesh_deprecated();
       this->allow_renumbering(false);
     }
  
   // Done reading the mesh.  Now prepare it for use.
   this->prepare_for_use(/*skip_renumber (deprecated)*/ false,
                         skip_find_neighbors);
 }

References libMesh::MeshBase::allow_renumbering(), libMesh::Quality::name(), libMesh::MeshBase::prepare_for_use(), and libMesh::NameBasedIO::read().

Referenced by ExtraIntegersTest::checkpoint_helper(), libMesh::RBEIMEvaluation::legacy_read_in_interpolation_points_elem(), main(), and SlitMeshRefinedSystemTest::testRestart().

◆ recalculate_n_partitions()

unsigned int libMesh::MeshBase::recalculate_n_partitions ( )

inherited

In a few (very rare) cases, the user may have manually tagged the elements with specific processor IDs by hand, without using a partitioner.

In this case, the Mesh will not know that the total number of partitions, _n_parts, has changed, unless you call this function. This is an O(N active elements) calculation. The return value is the number of partitions, and _n_parts is also set by this function.

Definition at line 631 of file mesh_base.C.

 {
   // This requires an inspection on every processor
   parallel_object_only();
  
   unsigned int max_proc_id=0;
  
   for (const auto & elem : this->active_local_element_ptr_range())
     max_proc_id = std::max(max_proc_id, static_cast<unsigned int>(elem->processor_id()));
  
   // The number of partitions is one more than the max processor ID.
   _n_parts = max_proc_id+1;
  
   this->comm().max(_n_parts);
  
   return _n_parts;
 }

◆ redistribute()

virtual void libMesh::MeshBase::redistribute ( )

inlinevirtualinherited

Redistribute elements between processors.

This gets called automatically by the Partitioner, and is a no-op in the case of a ReplicatedMesh or serialized DistributedMesh

Reimplemented in libMesh::DistributedMesh.

Definition at line 1000 of file mesh_base.h.

1000 {}

◆ remove_ghosting_functor()

void libMesh::MeshBase::remove_ghosting_functor ( GhostingFunctor & ghosting_functor )

inherited

Removes a functor which was previously added to the set of ghosting functors.

Definition at line 450 of file mesh_base.C.

 {
   _ghosting_functors.erase(&ghosting_functor);
  
   auto it = _shared_functors.find(&ghosting_functor);
   if (it != _shared_functors.end())
     _shared_functors.erase(it);
 }

Referenced by libMesh::DofMap::clear(), libMesh::DofMap::remove_algebraic_ghosting_functor(), libMesh::DofMap::remove_coupling_functor(), EquationSystemsTest::testDisableDefaultGhosting(), and libMesh::DofMap::~DofMap().

◆ renumber_elem()

void libMesh::ReplicatedMesh::renumber_elem	(	dof_id_type	old_id,
		dof_id_type	new_id
	)

overridevirtualinherited

Changes the id of element old_id, both by changing elem(old_id)->id() and by moving elem(old_id) in the mesh's internal container.

No element with the id new_id should already exist.

Implements libMesh::MeshBase.

Definition at line 402 of file replicated_mesh.C.

 {
   // This doesn't get used in serial yet
   Elem * el = _elements[old_id];
   libmesh_assert (el);
  
   el->set_id(new_id);
   libmesh_assert (!_elements[new_id]);
   _elements[new_id] = el;
   _elements[old_id] = nullptr;
 }

References libMesh::ReplicatedMesh::_elements, libMesh::libmesh_assert(), and libMesh::DofObject::set_id().

◆ renumber_node()

void libMesh::ReplicatedMesh::renumber_node	(	dof_id_type	old_id,
		dof_id_type	new_id
	)

overridevirtualinherited

Changes the id of node old_id, both by changing node(old_id)->id() and by moving node(old_id) in the mesh's internal container.

No element with the id new_id should already exist.

Implements libMesh::MeshBase.

Definition at line 578 of file replicated_mesh.C.

 {
   // This doesn't get used in serial yet
   Node * nd = _nodes[old_id];
   libmesh_assert (nd);
  
   nd->set_id(new_id);
   libmesh_assert (!_nodes[new_id]);
   _nodes[new_id] = nd;
   _nodes[old_id] = nullptr;
 }

References libMesh::ReplicatedMesh::_nodes, libMesh::libmesh_assert(), and libMesh::DofObject::set_id().

◆ renumber_nodes_and_elements()

void libMesh::ReplicatedMesh::renumber_nodes_and_elements ( )

overridevirtualinherited

Remove nullptr elements from arrays.

Implements libMesh::MeshBase.

Definition at line 642 of file replicated_mesh.C.

 {
   LOG_SCOPE("renumber_nodes_and_elem()", "Mesh");
  
   // node and element id counters
   dof_id_type next_free_elem = 0;
   dof_id_type next_free_node = 0;
  
   // Will hold the set of nodes that are currently connected to elements
   std::unordered_set<Node *> connected_nodes;
  
   // Loop over the elements.  Note that there may
   // be nullptrs in the _elements vector from the coarsening
   // process.  Pack the elements in to a contiguous array
   // and then trim any excess.
   {
     std::vector<Elem *>::iterator in        = _elements.begin();
     std::vector<Elem *>::iterator out_iter  = _elements.begin();
     const std::vector<Elem *>::iterator end = _elements.end();
  
     for (; in != end; ++in)
       if (*in != nullptr)
         {
           Elem * el = *in;
  
           *out_iter = *in;
           ++out_iter;
  
           // Increment the element counter
           el->set_id (next_free_elem++);
  
           if (_skip_renumber_nodes_and_elements)
             {
               // Add this elements nodes to the connected list
               for (auto & n : el->node_ref_range())
                 connected_nodes.insert(&n);
             }
           else  // We DO want node renumbering
             {
               // Loop over this element's nodes.  Number them,
               // if they have not been numbered already.  Also,
               // position them in the _nodes vector so that they
               // are packed contiguously from the beginning.
               for (auto & n : el->node_ref_range())
                 if (n.id() == next_free_node)    // don't need to process
                   next_free_node++;                      // [(src == dst) below]
  
                 else if (n.id() > next_free_node) // need to process
                   {
                     // The source and destination indices
                     // for this node
                     const dof_id_type src_idx = n.id();
                     const dof_id_type dst_idx = next_free_node++;
  
                     // ensure we want to swap a valid nodes
                     libmesh_assert(_nodes[src_idx]);
  
                     // Swap the source and destination nodes
                     std::swap(_nodes[src_idx],
                               _nodes[dst_idx] );
  
                     // Set proper indices where that makes sense
                     if (_nodes[src_idx] != nullptr)
                       _nodes[src_idx]->set_id (src_idx);
                     _nodes[dst_idx]->set_id (dst_idx);
                   }
             }
         }
  
     // Erase any additional storage. These elements have been
     // copied into nullptr voids by the procedure above, and are
     // thus repeated and unnecessary.
     _elements.erase (out_iter, end);
   }
  
  
   if (_skip_renumber_nodes_and_elements)
     {
       // Loop over the nodes.  Note that there may
       // be nullptrs in the _nodes vector from the coarsening
       // process.  Pack the nodes in to a contiguous array
       // and then trim any excess.
  
       std::vector<Node *>::iterator in        = _nodes.begin();
       std::vector<Node *>::iterator out_iter  = _nodes.begin();
       const std::vector<Node *>::iterator end = _nodes.end();
  
       for (; in != end; ++in)
         if (*in != nullptr)
           {
             // This is a reference so that if we change the pointer it will change in the vector
             Node * & nd = *in;
  
             // If this node is still connected to an elem, put it in the list
             if (connected_nodes.find(nd) != connected_nodes.end())
               {
                 *out_iter = nd;
                 ++out_iter;
  
                 // Increment the node counter
                 nd->set_id (next_free_node++);
               }
             else // This node is orphaned, delete it!
               {
                 this->get_boundary_info().remove (nd);
  
                 // delete the node
                 delete nd;
                 nd = nullptr;
               }
           }
  
       // Erase any additional storage.  Whatever was
       _nodes.erase (out_iter, end);
     }
   else // We really DO want node renumbering
     {
       // Any nodes in the vector >= _nodes[next_free_node]
       // are not connected to any elements and may be deleted
       // if desired.
  
       // Now, delete the unused nodes
       {
         std::vector<Node *>::iterator nd        = _nodes.begin();
         const std::vector<Node *>::iterator end = _nodes.end();
  
         std::advance (nd, next_free_node);
  
         for (auto & node : as_range(nd, end))
           {
             // Mesh modification code might have already deleted some
             // nodes
             if (node == nullptr)
               continue;
  
             // remove any boundary information associated with
             // this node
             this->get_boundary_info().remove (node);
  
             // delete the node
             delete node;
             node = nullptr;
           }
  
         _nodes.erase (nd, end);
       }
     }
  
   libmesh_assert_equal_to (next_free_elem, _elements.size());
   libmesh_assert_equal_to (next_free_node, _nodes.size());
  
   this->update_parallel_id_counts();
 }

References libMesh::ReplicatedMesh::_elements, libMesh::ReplicatedMesh::_nodes, libMesh::MeshBase::_skip_renumber_nodes_and_elements, libMesh::as_range(), end, libMesh::MeshBase::get_boundary_info(), libMesh::libmesh_assert(), libMesh::MeshBase::node(), libMesh::Elem::node_ref_range(), libMesh::BoundaryInfo::remove(), libMesh::DofObject::set_id(), swap(), and libMesh::ReplicatedMesh::update_parallel_id_counts().

◆ reserve_elem()

virtual void libMesh::ReplicatedMesh::reserve_elem ( const dof_id_type ne )

inlineoverridevirtualinherited

Reserves space for a known number of elements.

Note: This method may or may not do anything, depending on the actual Mesh implementation. If you know the number of elements you will add and call this method before repeatedly calling add_point() the implementation will be more efficient.

Implements libMesh::MeshBase.

Definition at line 131 of file replicated_mesh.h.

132 { _elements.reserve (ne); }

References libMesh::ReplicatedMesh::_elements.

◆ reserve_nodes()

virtual void libMesh::ReplicatedMesh::reserve_nodes ( const dof_id_type nn )

inlineoverridevirtualinherited

Reserves space for a known number of nodes.

Note: This method may or may not do anything, depending on the actual Mesh implementation. If you know the number of nodes you will add and call this method before repeatedly calling add_point() the implementation will be more efficient.

Implements libMesh::MeshBase.

Definition at line 113 of file replicated_mesh.h.

114 { _nodes.reserve (nn); }

References libMesh::ReplicatedMesh::_nodes.

◆ semilocal_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::semilocal_elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ semilocal_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::semilocal_elements_begin ( )

overridevirtualinherited

Iterate over elements for which elem->is_semilocal() is true for the current processor.

Implements libMesh::MeshBase.

◆ semilocal_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::semilocal_elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ semilocal_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::semilocal_elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ set_count_lower_dim_elems_in_point_locator()

void libMesh::MeshBase::set_count_lower_dim_elems_in_point_locator ( bool count_lower_dim_elems )

inherited

In the point locator, do we count lower dimensional elements when we refine point locator regions? This is relevant in tree-based point locators, for example.

Definition at line 703 of file mesh_base.C.

 {
   _count_lower_dim_elems_in_point_locator = count_lower_dim_elems;
 }

◆ set_default_mapping_data()

void libMesh::MeshBase::set_default_mapping_data ( const unsigned char data )

inlineinherited

Set the default master space to physical space mapping basis functions to be used on newly added elements.

Definition at line 732 of file mesh_base.h.

                                                            {
     _default_mapping_data = data;
   }

References libMesh::MeshBase::_default_mapping_data, and data.

Referenced by libMesh::DynaIO::read_mesh(), RationalMapTest< elem_type >::setUp(), and FETest< order, family, elem_type >::setUp().

◆ set_default_mapping_type()

void libMesh::MeshBase::set_default_mapping_type ( const ElemMappingType type )

inlineinherited

Set the default master space to physical space mapping basis functions to be used on newly added elements.

Definition at line 716 of file mesh_base.h.

                                                              {
     _default_mapping_type = type;
   }

References libMesh::MeshBase::_default_mapping_type.

Referenced by libMesh::DynaIO::read_mesh(), and RationalMapTest< elem_type >::setUp().

◆ set_distributed()

virtual void libMesh::MeshBase::set_distributed ( )

inlinevirtualinherited

Asserts that not all elements and nodes of the mesh necessarily exist on the current processor.

Only valid to call on classes which can be created in a distributed form.

Reimplemented in libMesh::DistributedMesh.

Definition at line 174 of file mesh_base.h.

175 { libmesh_error(); }

Referenced by libMesh::CheckpointIO::read().

◆ set_elem_dimensions()

void libMesh::MeshBase::set_elem_dimensions ( const std::set< unsigned char > & elem_dims )

inherited

Most of the time you should not need to call this, as the element dimensions will be set automatically by a call to cache_elem_dims(), therefore only call this if you know what you're doing.

In some specialized situations, for example when adding a single Elem on all procs, it can be faster to skip calling cache_elem_dims() and simply specify the element dimensions manually, which is why this setter exists.

Definition at line 144 of file mesh_base.C.

 {
 #ifdef DEBUG
   // In debug mode, we call cache_elem_dims() and then make sure
   // the result actually agrees with what the user specified.
   parallel_object_only();
  
   this->cache_elem_dims();
   libmesh_assert_msg(_elem_dims == elem_dims, \
                      "Specified element dimensions does not match true element dimensions!");
 #endif
  
   _elem_dims = elem_dims;
 }

References libMesh::MeshBase::_elem_dims, and libMesh::MeshBase::cache_elem_dims().

◆ set_mesh_dimension()

void libMesh::MeshBase::set_mesh_dimension ( unsigned char d )

inlineinherited

Resets the logical dimension of the mesh.

If the mesh has elements of multiple dimensions, this should be set to the largest dimension. E.g. if the mesh has 1D and 2D elements, this should be set to 2. If the mesh has 2D and 3D elements, this should be set to 3.

Definition at line 218 of file mesh_base.h.

219 { _elem_dims.clear(); _elem_dims.insert(d); }

References libMesh::MeshBase::_elem_dims.

Referenced by libMesh::MeshTools::Generation::build_delaunay_square(), MixedDimensionMeshTest::build_mesh(), MeshfunctionDFEM::build_mesh(), SlitMeshTest::build_mesh(), MixedDimensionNonUniformRefinement::build_mesh(), MixedDimensionNonUniformRefinementTriangle::build_mesh(), MixedDimensionNonUniformRefinement3D::build_mesh(), libMesh::TriangleWrapper::copy_tri_to_mesh(), libMesh::AbaqusIO::read(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::GMVIO::read(), libMesh::VTKIO::read(), libMesh::CheckpointIO::read_connectivity(), libMesh::CheckpointIO::read_header(), libMesh::UCDIO::read_implementation(), libMesh::GmshIO::read_mesh(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::OFFIO::read_stream(), libMesh::MatlabIO::read_stream(), and libMesh::TriangleInterface::triangulate().

◆ set_n_partitions()

unsigned int& libMesh::MeshBase::set_n_partitions ( )

inlineprotectedinherited

Returns: A writable reference to the number of partitions.

Definition at line 1667 of file mesh_base.h.

1668 { return _n_parts; }

References libMesh::MeshBase::_n_parts.

Referenced by libMesh::BoundaryInfo::sync().

◆ set_next_unique_id()

void libMesh::MeshBase::set_next_unique_id ( unique_id_type id )

inlineinherited

Sets the next unique id to be used.

Definition at line 327 of file mesh_base.h.

327 { _next_unique_id = id; }

References libMesh::MeshBase::_next_unique_id.

◆ set_point_locator_close_to_point_tol()

void libMesh::MeshBase::set_point_locator_close_to_point_tol ( Real val )

inherited

Set value used by PointLocatorBase::close_to_point_tol().

Defaults to 0.0. If nonzero, calls close_to_point_tol() whenever a new PointLocator is built for use by this Mesh. Since the Mesh controls the creation and destruction of the PointLocator, if there are any parameters we need to customize on it, the Mesh will need to know about them.

Definition at line 905 of file mesh_base.C.

 {
   _point_locator_close_to_point_tol = val;
   if (_point_locator)
     {
       if (val > 0.)
         _point_locator->set_close_to_point_tol(val);
       else
         _point_locator->unset_close_to_point_tol();
     }
 }

◆ set_spatial_dimension()

void libMesh::MeshBase::set_spatial_dimension ( unsigned char d )

inherited

Sets the "spatial dimension" of the Mesh.

See the documentation for Mesh::spatial_dimension() for more information.

Definition at line 166 of file mesh_base.C.

 {
   // The user can set the _spatial_dimension however they wish,
   // libMesh will only *increase* the spatial dimension, however,
   // never decrease it.
   _spatial_dimension = d;
 }

References libMesh::MeshBase::_spatial_dimension.

Referenced by MeshSpatialDimensionTest::test2D().

◆ set_subdomain_name_map()

std::map<subdomain_id_type, std::string>& libMesh::MeshBase::set_subdomain_name_map ( )

inlineinherited

Returns: A writable reference to the whole subdomain name map

Definition at line 1631 of file mesh_base.h.

1632 { return _block_id_to_name; }

References libMesh::MeshBase::_block_id_to_name.

Referenced by libMesh::DistributedMesh::DistributedMesh(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::CheckpointIO::read_subdomain_names(), and libMesh::ReplicatedMesh::ReplicatedMesh().

◆ size_elem_extra_integers()

void libMesh::MeshBase::size_elem_extra_integers ( )

protectedinherited

Size extra-integer arrays of all elements in the mesh.

Definition at line 926 of file mesh_base.C.

 {
   const std::size_t new_size = _elem_integer_names.size();
   for (auto elem : this->element_ptr_range())
     elem->add_extra_integers(new_size);
 }

Referenced by libMesh::MeshBase::add_elem_data(), libMesh::MeshBase::add_elem_datum(), and libMesh::MeshBase::add_elem_integer().

◆ size_node_extra_integers()

void libMesh::MeshBase::size_node_extra_integers ( )

protectedinherited

Size extra-integer arrays of all nodes in the mesh.

Definition at line 935 of file mesh_base.C.

 {
   const std::size_t new_size = _node_integer_names.size();
   for (auto node : this->node_ptr_range())
     node->add_extra_integers(new_size);
 }

Referenced by libMesh::MeshBase::add_node_data(), and libMesh::MeshBase::add_node_datum().

◆ skip_noncritical_partitioning() [1/2]

bool libMesh::MeshBase::skip_noncritical_partitioning ( ) const

inlineinherited

Definition at line 1061 of file mesh_base.h.

1062 { return _skip_noncritical_partitioning || _skip_all_partitioning || !_partitioner.get(); }

References libMesh::MeshBase::_partitioner, libMesh::MeshBase::_skip_all_partitioning, and libMesh::MeshBase::_skip_noncritical_partitioning.

Referenced by libMesh::UnstructuredMesh::copy_nodes_and_elements().

◆ skip_noncritical_partitioning() [2/2]

void libMesh::MeshBase::skip_noncritical_partitioning ( bool skip )

inlineinherited

If true is passed in then the elements on this mesh will no longer be (re)partitioned, and the nodes on this mesh will only be repartitioned if they are found "orphaned" via coarsening or other removal of the last element responsible for their node/element processor id consistency.

Note: It would probably be a bad idea to call this on a DistributedMesh before the first partitioning has happened... because no elements would get assigned to your processor pool.; Skipping partitioning can have adverse effects on your performance when using AMR... i.e. you could get large load imbalances. However you might still want to use this if the communication and computation of the rebalance and repartition is too high for your application.

It is also possible, for backwards-compatibility purposes, to skip noncritical partitioning by resetting the partitioner() pointer for this mesh.

Definition at line 1058 of file mesh_base.h.

1059 { _skip_noncritical_partitioning = skip; }

References libMesh::MeshBase::_skip_noncritical_partitioning.

Referenced by libMesh::MeshTools::correct_node_proc_ids().

◆ skip_partitioning() [1/2]

bool libMesh::MeshBase::skip_partitioning ( ) const

inlineinherited

Definition at line 1078 of file mesh_base.h.

1078 { return _skip_all_partitioning; }

References libMesh::MeshBase::_skip_all_partitioning.

Referenced by libMesh::UnstructuredMesh::copy_nodes_and_elements().

◆ skip_partitioning() [2/2]

void libMesh::MeshBase::skip_partitioning ( bool skip )

inlineinherited

If true is passed in then nothing on this mesh will be (re)partitioned.

Note: The caveats for skip_noncritical_partitioning() still apply, and removing elements from a mesh with this setting enabled can leave node processor ids in an inconsistent state (not matching any attached element), causing failures in other library code. Do not use this setting along with element deletion or coarsening.

Definition at line 1076 of file mesh_base.h.

1076 { _skip_all_partitioning = skip; }

References libMesh::MeshBase::_skip_all_partitioning.

◆ spatial_dimension()

unsigned int libMesh::MeshBase::spatial_dimension ( ) const

inherited

Returns: The "spatial dimension" of the mesh.

The spatial dimension is defined as:

1 - for an exactly x-aligned mesh of 1D elements 2 - for an exactly x-y planar mesh of 2D elements 3 - otherwise

No tolerance checks are performed to determine whether the Mesh is x-aligned or x-y planar, only strict equality with zero in the higher dimensions is checked. Also, x-z and y-z planar meshes are considered to have spatial dimension == 3.

The spatial dimension is updated during prepare_for_use() based on the dimensions of the various elements present in the Mesh, but is never automatically decreased by this function.

For example, if the user calls set_spatial_dimension(2) and then later inserts 3D elements into the mesh, Mesh::spatial_dimension() will return 3 after the next call to prepare_for_use(). On the other hand, if the user calls set_spatial_dimension(3) and then inserts only x-aligned 1D elements into the Mesh, mesh.spatial_dimension() will remain 3.

Definition at line 159 of file mesh_base.C.

 {
   return cast_int<unsigned int>(_spatial_dimension);
 }

References libMesh::MeshBase::_spatial_dimension.

Referenced by MeshSpatialDimensionTest::test1D(), and MeshSpatialDimensionTest::test2D().

◆ stitch_meshes()

void libMesh::ReplicatedMesh::stitch_meshes	(	const ReplicatedMesh &	other_mesh,
		boundary_id_type	this_mesh_boundary,
		boundary_id_type	other_mesh_boundary,
		Real	tol = `TOLERANCE`,
		bool	clear_stitched_boundary_ids = `false`,
		bool	verbose = `true`,
		bool	use_binary_search = `true`,
		bool	enforce_all_nodes_match_on_boundaries = `false`
	)

inherited

Stitch other_mesh to this mesh so that this mesh is the union of the two meshes.

this_mesh_boundary and other_mesh_boundary are used to specify a dim-1 dimensional surface on which we seek to merge any "overlapping" nodes, where we use the parameter tol as a relative tolerance (relative to the smallest edge length on the surfaces being stitched) to determine whether or not nodes are overlapping. If clear_stitched_boundary_ids==true, this function clears boundary_info IDs in this mesh associated this_mesh_boundary and other_mesh_boundary. If use_binary_search is true, we use an optimized "sort then binary search" algorithm for finding matching nodes. Otherwise we use a N^2 algorithm (which can be more reliable at dealing with slightly misaligned meshes). If enforce_all_nodes_match_on_boundaries is true, we throw an error if the number of nodes on the specified boundaries don't match the number of nodes that were merged. This is a helpful error check in some cases. If skip_find_neighbors is true, a faster stitching method is used, where the lists of neighbors for each elements are copied as well and patched, without calling the time-consuming find_neighbors() function.

Note that the element IDs for elements in the stitched mesh corresponding to "this" mesh will be unchanged. The IDs for elements corresponding to other_mesh will be incremented by this->max_elem_id().

There is no simple a priori relationship between node IDs in "this" mesh and other_mesh and node IDs in the stitched mesh because the number of nodes (and hence the node IDs) in the stitched mesh depend on how many nodes are stitched.

Definition at line 812 of file replicated_mesh.C.

 {
   LOG_SCOPE("stitch_meshes()", "ReplicatedMesh");
   stitching_helper(&other_mesh,
                    this_mesh_boundary_id,
                    other_mesh_boundary_id,
                    tol,
                    clear_stitched_boundary_ids,
                    verbose,
                    use_binary_search,
                    enforce_all_nodes_match_on_boundaries,
                    true);
 }

References libMesh::ReplicatedMesh::stitching_helper().

◆ stitch_surfaces()

void libMesh::ReplicatedMesh::stitch_surfaces	(	boundary_id_type	boundary_id_1,
		boundary_id_type	boundary_id_2,
		Real	tol = `TOLERANCE`,
		bool	clear_stitched_boundary_ids = `false`,
		bool	verbose = `true`,
		bool	use_binary_search = `true`,
		bool	enforce_all_nodes_match_on_boundaries = `false`
	)

inherited

Similar to stitch_meshes, except that we stitch two adjacent surfaces within this mesh.

Definition at line 833 of file replicated_mesh.C.

 {
   stitching_helper(nullptr,
                    boundary_id_1,
                    boundary_id_2,
                    tol,
                    clear_stitched_boundary_ids,
                    verbose,
                    use_binary_search,
                    enforce_all_nodes_match_on_boundaries,
                    true);
 }

References libMesh::ReplicatedMesh::stitching_helper().

◆ stitching_helper()

void libMesh::ReplicatedMesh::stitching_helper	(	const ReplicatedMesh *	other_mesh,
		boundary_id_type	boundary_id_1,
		boundary_id_type	boundary_id_2,
		Real	tol,
		bool	clear_stitched_boundary_ids,
		bool	verbose,
		bool	use_binary_search,
		bool	enforce_all_nodes_match_on_boundaries,
		bool	skip_find_neighbors
	)

privateinherited

Helper function for stitch_meshes and stitch_surfaces that does the mesh stitching.

Definition at line 852 of file replicated_mesh.C.

 {
   std::map<dof_id_type, dof_id_type> node_to_node_map, other_to_this_node_map; // The second is the inverse map of the first
   std::map<dof_id_type, std::vector<dof_id_type>> node_to_elems_map;
  
   typedef dof_id_type                     key_type;
   typedef std::pair<Elem *, unsigned char> val_type;
   typedef std::pair<key_type, val_type>   key_val_pair;
   typedef std::unordered_multimap<key_type, val_type> map_type;
   // Mapping between all side keys in this mesh and elements+side numbers relevant to the boundary in this mesh as well.
   map_type side_to_elem_map;
  
   // If there is only one mesh (i.e. other_mesh == nullptr), then loop over this mesh twice
   if (!other_mesh)
     {
       other_mesh = this;
     }
  
   if ((this_mesh_boundary_id  != BoundaryInfo::invalid_id) &&
       (other_mesh_boundary_id != BoundaryInfo::invalid_id))
     {
       LOG_SCOPE("stitch_meshes node merging", "ReplicatedMesh");
  
       // While finding nodes on the boundary, also find the minimum edge length
       // of all faces on both boundaries.  This will later be used in relative
       // distance checks when stitching nodes.
       Real h_min = std::numeric_limits<Real>::max();
       bool h_min_updated = false;
  
       // Loop below fills in these sets for the two meshes.
       std::set<dof_id_type> this_boundary_node_ids, other_boundary_node_ids;
  
       // Pull objects out of the loop to reduce heap operations
       std::unique_ptr<Elem> side;
  
       {
         // Make temporary fixed-size arrays for loop
         boundary_id_type id_array[2]         = {this_mesh_boundary_id, other_mesh_boundary_id};
         std::set<dof_id_type> * set_array[2] = {&this_boundary_node_ids, &other_boundary_node_ids};
         const ReplicatedMesh * mesh_array[2] = {this, other_mesh};
  
         for (unsigned i=0; i<2; ++i)
           {
             // First we deal with node boundary IDs.
             // We only enter this loop if we have at least one
             // nodeset.
             if (mesh_array[i]->get_boundary_info().n_nodeset_conds() > 0)
               {
                 // build_node_list() returns a vector of (node-id, bc-id) tuples
                 for (const auto & t : mesh_array[i]->get_boundary_info().build_node_list())
                   {
                     boundary_id_type node_bc_id = std::get<1>(t);
                     if (node_bc_id == id_array[i])
                       {
                         dof_id_type this_node_id = std::get<0>(t);
                         set_array[i]->insert( this_node_id );
  
                         // We need to set h_min to some value. It's too expensive to
                         // search for the element that actually contains this node,
                         // since that would require a PointLocator. As a result, we
                         // just use the first (non-NodeElem!) element in the mesh to
                         // give us hmin if it's never been set before.
                         if (!h_min_updated)
                           {
                             for (const auto & elem : mesh_array[i]->active_element_ptr_range())
                               {
                                 Real current_h_min = elem->hmin();
                                 if (current_h_min > 0.)
                                   {
                                     h_min = current_h_min;
                                     h_min_updated = true;
                                     break;
                                   }
                               }
  
                             // If, after searching all the active elements, we did not update
                             // h_min, give up and set h_min to 1 so that we don't repeat this
                             // fruitless search
                             if (!h_min_updated)
                               {
                                 h_min_updated = true;
                                 h_min = 1.0;
                               }
                           }
                       }
                   }
               }
  
             // Container to catch boundary IDs passed back from BoundaryInfo.
             std::vector<boundary_id_type> bc_ids;
  
             for (auto & el : mesh_array[i]->element_ptr_range())
               {
                 // Now check whether elem has a face on the specified boundary
                 for (auto side_id : el->side_index_range())
                   if (el->neighbor_ptr(side_id) == nullptr)
                     {
                       // Get *all* boundary IDs on this side, not just the first one!
                       mesh_array[i]->get_boundary_info().boundary_ids (el, side_id, bc_ids);
  
                       if (std::find(bc_ids.begin(), bc_ids.end(), id_array[i]) != bc_ids.end())
                         {
                           el->build_side_ptr(side, side_id);
                           for (auto & n : side->node_ref_range())
                             set_array[i]->insert(n.id());
  
                           h_min = std::min(h_min, side->hmin());
                           h_min_updated = true;
  
                           // This side is on the boundary, add its information to side_to_elem
                           if (skip_find_neighbors && (i==0))
                             {
                               key_type key = el->key(side_id);
                               val_type val;
                               val.first = el;
                               val.second = cast_int<unsigned char>(side_id);
  
                               key_val_pair kvp;
                               kvp.first = key;
                               kvp.second = val;
                               side_to_elem_map.insert (kvp);
                             }
                         }
  
                       // Also, check the edges on this side. We don't have to worry about
                       // updating neighbor info in this case since elements don't store
                       // neighbor info on edges.
                       for (auto edge_id : el->edge_index_range())
                         {
                           if (el->is_edge_on_side(edge_id, side_id))
                             {
                               // Get *all* boundary IDs on this edge, not just the first one!
                               mesh_array[i]->get_boundary_info().edge_boundary_ids (el, edge_id, bc_ids);
  
                               if (std::find(bc_ids.begin(), bc_ids.end(), id_array[i]) != bc_ids.end())
                                 {
                                   std::unique_ptr<Elem> edge (el->build_edge_ptr(edge_id));
                                   for (auto & n : edge->node_ref_range())
                                     set_array[i]->insert( n.id() );
  
                                   h_min = std::min(h_min, edge->hmin());
                                   h_min_updated = true;
                                 }
                             }
                         }
                     }
               }
           }
       }
  
       if (verbose)
         {
           libMesh::out << "In ReplicatedMesh::stitch_meshes:\n"
                        << "This mesh has "  << this_boundary_node_ids.size()
                        << " nodes on boundary " << this_mesh_boundary_id  << ".\n"
                        << "Other mesh has " << other_boundary_node_ids.size()
                        << " nodes on boundary " << other_mesh_boundary_id << ".\n";
  
           if (h_min_updated)
             {
               libMesh::out << "Minimum edge length on both surfaces is " << h_min << ".\n";
             }
           else
             {
               libMesh::out << "No elements on specified surfaces." << std::endl;
             }
         }
  
       // We require nanoflann for the "binary search" (really kd-tree)
       // option to work. If it's not available, turn that option off,
       // warn the user, and fall back on the N^2 search algorithm.
       if (use_binary_search)
         {
 #ifndef LIBMESH_HAVE_NANOFLANN
           use_binary_search = false;
           libmesh_warning("The use_binary_search option in the "
                           "ReplicatedMesh stitching algorithms requires nanoflann "
                           "support. Falling back on N^2 search algorithm.");
 #endif
         }
  
       if (this_boundary_node_ids.size())
       {
         if (use_binary_search)
         {
 #ifdef LIBMESH_HAVE_NANOFLANN
           typedef nanoflann::KDTreeSingleIndexAdaptor<nanoflann::L2_Simple_Adaptor<Real, VectorOfNodesAdaptor>, VectorOfNodesAdaptor, 3> kd_tree_t;
  
           // Create the dataset needed to build the kd tree with nanoflann
           std::vector<std::pair<Point, dof_id_type>> this_mesh_nodes(this_boundary_node_ids.size());
           std::set<dof_id_type>::iterator current_node = this_boundary_node_ids.begin(),
                                           node_ids_end = this_boundary_node_ids.end();
           for (unsigned int ctr = 0; current_node != node_ids_end; ++current_node, ++ctr)
           {
             this_mesh_nodes[ctr].first = this->point(*current_node);
             this_mesh_nodes[ctr].second = *current_node;
           }
  
           VectorOfNodesAdaptor vec_nodes_adaptor(this_mesh_nodes);
  
           kd_tree_t this_kd_tree(3, vec_nodes_adaptor, 10);
           this_kd_tree.buildIndex();
  
           // Storage for nearest neighbor in the loop below
           std::vector<size_t> ret_index(1);
           std::vector<Real> ret_dist_sqr(1);
  
           // Loop over other mesh. For each node, find its nearest neighbor in this mesh, and fill in the maps.
           for (auto node : other_boundary_node_ids)
           {
             const Real query_pt[] = {other_mesh->point(node)(0), other_mesh->point(node)(1), other_mesh->point(node)(2)};
             this_kd_tree.knnSearch(&query_pt[0], 1, &ret_index[0], &ret_dist_sqr[0]);
             if (ret_dist_sqr[0] < TOLERANCE*TOLERANCE)
             {
               node_to_node_map[this_mesh_nodes[ret_index[0]].second] = node;
               other_to_this_node_map[node] = this_mesh_nodes[ret_index[0]].second;
             }
           }
  
           // If the 2 maps don't have the same size, it means we have overwritten a value in node_to_node_map
           // It means one node in this mesh is the nearest neighbor of several nodes in other mesh.
           // Not possible !
           if (node_to_node_map.size() != other_to_this_node_map.size())
             libmesh_error_msg("Error: Found multiple matching nodes in stitch_meshes");
 #endif
         }
         else
         {
           // In the unlikely event that two meshes composed entirely of
           // NodeElems are being stitched together, we will not have
           // selected a valid h_min value yet, and the distance
           // comparison below will be true for essentially any two
           // nodes. In this case we simply fall back on an absolute
           // distance check.
           if (!h_min_updated)
             {
               libmesh_warning("No valid h_min value was found, falling back on "
                               "absolute distance check in the N^2 search algorithm.");
               h_min = 1.;
             }
  
           // Otherwise, use a simple N^2 search to find the closest matching points. This can be helpful
           // in the case that we have tolerance issues which cause mismatch between the two surfaces
           // that are being stitched.
           for (const auto & this_node_id : this_boundary_node_ids)
           {
             Node & this_node = this->node_ref(this_node_id);
  
             bool found_matching_nodes = false;
  
             for (const auto & other_node_id : other_boundary_node_ids)
             {
               const Node & other_node = other_mesh->node_ref(other_node_id);
  
               Real node_distance = (this_node - other_node).norm();
  
               if (node_distance < tol*h_min)
               {
                 // Make sure we didn't already find a matching node!
                 if (found_matching_nodes)
                   libmesh_error_msg("Error: Found multiple matching nodes in stitch_meshes");
  
                 node_to_node_map[this_node_id] = other_node_id;
                 other_to_this_node_map[other_node_id] = this_node_id;
  
                 found_matching_nodes = true;
               }
             }
           }
         }
       }
  
       // Build up the node_to_elems_map, using only one loop over other_mesh
       for (auto & el : other_mesh->element_ptr_range())
         {
           // For each node on the element, find the corresponding node
           // on "this" Mesh, 'this_node_id', if it exists, and push
           // the current element ID back onto node_to_elems_map[this_node_id].
           // For that we will use the reverse mapping we created at
           // the same time as the forward mapping.
           for (auto & n : el->node_ref_range())
             {
               dof_id_type other_node_id = n.id();
               std::map<dof_id_type, dof_id_type>::iterator it =
                 other_to_this_node_map.find(other_node_id);
  
               if (it != other_to_this_node_map.end())
                 {
                   dof_id_type this_node_id = it->second;
                   node_to_elems_map[this_node_id].push_back( el->id() );
                 }
             }
         }
  
       if (verbose)
         {
           libMesh::out << "In ReplicatedMesh::stitch_meshes:\n"
                        << "Found " << node_to_node_map.size()
                        << " matching nodes.\n"
                        << std::endl;
         }
  
       if (enforce_all_nodes_match_on_boundaries)
         {
           std::size_t n_matching_nodes = node_to_node_map.size();
           std::size_t this_mesh_n_nodes = this_boundary_node_ids.size();
           std::size_t other_mesh_n_nodes = other_boundary_node_ids.size();
           if ((n_matching_nodes != this_mesh_n_nodes) || (n_matching_nodes != other_mesh_n_nodes))
             libmesh_error_msg("Error: We expected the number of nodes to match.");
         }
     }
   else
     {
       if (verbose)
         {
           libMesh::out << "Skip node merging in ReplicatedMesh::stitch_meshes:" << std::endl;
         }
     }
  
   dof_id_type node_delta = this->max_node_id();
   dof_id_type elem_delta = this->max_elem_id();
  
   unique_id_type unique_delta =
 #ifdef LIBMESH_ENABLE_UNIQUE_ID
     this->parallel_max_unique_id();
 #else
     0;
 #endif
  
   // If other_mesh != nullptr, then we have to do a bunch of work
   // in order to copy it to this mesh
   if (this!=other_mesh)
     {
       LOG_SCOPE("stitch_meshes copying", "ReplicatedMesh");
  
       // Increment the node_to_node_map and node_to_elems_map
       // to account for id offsets
       for (auto & pr : node_to_node_map)
         pr.second += node_delta;
  
       for (auto & pr : node_to_elems_map)
         for (auto & entry : pr.second)
           entry += elem_delta;
  
       // Copy mesh data. If we skip the call to find_neighbors(), the lists
       // of neighbors will be copied verbatim from the other mesh
       this->copy_nodes_and_elements(*other_mesh, skip_find_neighbors,
                                     elem_delta, node_delta,
                                     unique_delta);
  
       // Copy BoundaryInfo from other_mesh too.  We do this via the
       // list APIs rather than element-by-element for speed.
       BoundaryInfo & boundary = this->get_boundary_info();
       const BoundaryInfo & other_boundary = other_mesh->get_boundary_info();
  
       for (const auto & t : other_boundary.build_node_list())
         boundary.add_node(std::get<0>(t) + node_delta,
                           std::get<1>(t));
  
       for (const auto & t : other_boundary.build_side_list())
         boundary.add_side(std::get<0>(t) + elem_delta,
                           std::get<1>(t),
                           std::get<2>(t));
  
       for (const auto & t : other_boundary.build_edge_list())
         boundary.add_edge(std::get<0>(t) + elem_delta,
                           std::get<1>(t),
                           std::get<2>(t));
  
       for (const auto & t : other_boundary.build_shellface_list())
         boundary.add_shellface(std::get<0>(t) + elem_delta,
                                std::get<1>(t),
                                std::get<2>(t));
  
     } // end if (other_mesh)
  
   // Finally, we need to "merge" the overlapping nodes
   // We do this by iterating over node_to_elems_map and updating
   // the elements so that they "point" to the nodes that came
   // from this mesh, rather than from other_mesh.
   // Then we iterate over node_to_node_map and delete the
   // duplicate nodes that came from other_mesh.
  
   {
     LOG_SCOPE("stitch_meshes node updates", "ReplicatedMesh");
  
     // Container to catch boundary IDs passed back from BoundaryInfo.
     std::vector<boundary_id_type> bc_ids;
  
     for (const auto & pr : node_to_elems_map)
       {
         dof_id_type target_node_id = pr.first;
         dof_id_type other_node_id = node_to_node_map[target_node_id];
         Node & target_node = this->node_ref(target_node_id);
  
         std::size_t n_elems = pr.second.size();
         for (std::size_t i=0; i<n_elems; i++)
           {
             dof_id_type elem_id = pr.second[i];
             Elem * el = this->elem_ptr(elem_id);
  
             // find the local node index that we want to update
             unsigned int local_node_index = el->local_node(other_node_id);
             libmesh_assert_not_equal_to(local_node_index, libMesh::invalid_uint);
  
             // We also need to copy over the nodeset info here,
             // because the node will get deleted below
             this->get_boundary_info().boundary_ids(el->node_ptr(local_node_index), bc_ids);
             el->set_node(local_node_index) = &target_node;
             this->get_boundary_info().add_node(&target_node, bc_ids);
           }
       }
   }
  
   {
     LOG_SCOPE("stitch_meshes node deletion", "ReplicatedMesh");
     for (const auto & pr : node_to_node_map)
       {
         // In the case that this==other_mesh, the two nodes might be the same (e.g. if
         // we're stitching a "sliver"), hence we need to skip node deletion in that case.
         if ((this == other_mesh) && (pr.second == pr.first))
           continue;
  
         dof_id_type this_node_id = pr.second;
         this->delete_node( this->node_ptr(this_node_id) );
       }
   }
  
   // If find_neighbors() wasn't called in prepare_for_use(), we need to
   // manually loop once more over all elements adjacent to the stitched boundary
   // and fix their lists of neighbors.
   // This is done according to the following steps:
   //   1. Loop over all copied elements adjacent to the boundary using node_to_elems_map (trying to avoid duplicates)
   //   2. Look at all their sides with a nullptr neighbor and update them using side_to_elem_map if necessary
   //   3. Update the corresponding side in side_to_elem_map as well
   if (skip_find_neighbors)
     {
       LOG_SCOPE("stitch_meshes neighbor fixes", "ReplicatedMesh");
  
       // Pull objects out of the loop to reduce heap operations
       std::unique_ptr<Elem> my_side, their_side;
  
       std::set<dof_id_type> fixed_elems;
       for (const auto & pr : node_to_elems_map)
         {
           std::size_t n_elems = pr.second.size();
           for (std::size_t i=0; i<n_elems; i++)
             {
               dof_id_type elem_id = pr.second[i];
               if (fixed_elems.find(elem_id) == fixed_elems.end())
                 {
                   Elem * el = this->elem_ptr(elem_id);
                   fixed_elems.insert(elem_id);
                   for (auto s : el->side_index_range())
                     {
                       if (el->neighbor_ptr(s) == nullptr)
                         {
                           key_type key = el->key(s);
                           auto bounds = side_to_elem_map.equal_range(key);
  
                           if (bounds.first != bounds.second)
                             {
                               // Get the side for this element
                               el->side_ptr(my_side, s);
  
                               // Look at all the entries with an equivalent key
                               while (bounds.first != bounds.second)
                                 {
                                   // Get the potential element
                                   Elem * neighbor = bounds.first->second.first;
  
                                   // Get the side for the neighboring element
                                   const unsigned int ns = bounds.first->second.second;
                                   neighbor->side_ptr(their_side, ns);
                                   //libmesh_assert(my_side.get());
                                   //libmesh_assert(their_side.get());
  
                                   // If found a match with my side
                                   //
                                   // We need special tests here for 1D:
                                   // since parents and children have an equal
                                   // side (i.e. a node), we need to check
                                   // ns != ms, and we also check level() to
                                   // avoid setting our neighbor pointer to
                                   // any of our neighbor's descendants
                                   if ((*my_side == *their_side) &&
                                       (el->level() == neighbor->level()) &&
                                       ((el->dim() != 1) || (ns != s)))
                                     {
                                       // So share a side.  Is this a mixed pair
                                       // of subactive and active/ancestor
                                       // elements?
                                       // If not, then we're neighbors.
                                       // If so, then the subactive's neighbor is
  
                                       if (el->subactive() ==
                                           neighbor->subactive())
                                         {
                                           // an element is only subactive if it has
                                           // been coarsened but not deleted
                                           el->set_neighbor (s,neighbor);
                                           neighbor->set_neighbor(ns,el);
                                         }
                                       else if (el->subactive())
                                         {
                                           el->set_neighbor(s,neighbor);
                                         }
                                       else if (neighbor->subactive())
                                         {
                                           neighbor->set_neighbor(ns,el);
                                         }
                                       // It's OK to invalidate the
                                       // bounds.first iterator here,
                                       // as we are immediately going
                                       // to break out of this while
                                       // loop. bounds.first will
                                       // therefore not be used for
                                       // anything else.
                                       side_to_elem_map.erase (bounds.first);
                                       break;
                                     }
  
                                   ++bounds.first;
                                 }
                             }
                         }
                     }
                 }
             }
         }
     }
  
   this->prepare_for_use( /*skip_renumber_nodes_and_elements= */ false, skip_find_neighbors);
  
   // After the stitching, we may want to clear boundary IDs from element
   // faces that are now internal to the mesh
   if (clear_stitched_boundary_ids)
     {
       LOG_SCOPE("stitch_meshes clear bcids", "ReplicatedMesh");
  
       // Container to catch boundary IDs passed back from BoundaryInfo.
       std::vector<boundary_id_type> bc_ids;
  
       for (auto & el : element_ptr_range())
         for (auto side_id : el->side_index_range())
           if (el->neighbor_ptr(side_id) != nullptr)
             {
               // Completely remove the side from the boundary_info object if it has either
               // this_mesh_boundary_id or other_mesh_boundary_id.
               this->get_boundary_info().boundary_ids (el, side_id, bc_ids);
  
               if (std::find(bc_ids.begin(), bc_ids.end(), this_mesh_boundary_id) != bc_ids.end() ||
                   std::find(bc_ids.begin(), bc_ids.end(), other_mesh_boundary_id) != bc_ids.end())
                 this->get_boundary_info().remove_side(el, side_id);
             }
  
       // Removing stitched-away boundary ids might have removed an id
       // *entirely*, so we need to recompute boundary id sets to check
       // for that.
       this->get_boundary_info().regenerate_id_sets();
     }
 }

Referenced by libMesh::ReplicatedMesh::stitch_meshes(), and libMesh::ReplicatedMesh::stitch_surfaces().

◆ sub_point_locator()

std::unique_ptr< PointLocatorBase > libMesh::MeshBase::sub_point_locator ( ) const

inherited

Returns: A pointer to a subordinate PointLocatorBase object for this mesh, constructing a master PointLocator first if necessary. This should not be used in threaded or non-parallel_only code unless the master has already been constructed.

Definition at line 672 of file mesh_base.C.

 {
   // If there's no master point locator, then we need one.
   if (_point_locator.get() == nullptr)
     {
       // PointLocator construction may not be safe within threads
       libmesh_assert(!Threads::in_threads);
  
       // And it may require parallel communication
       parallel_object_only();
  
       _point_locator = PointLocatorBase::build(TREE_ELEMENTS, *this);
  
       if (_point_locator_close_to_point_tol > 0.)
         _point_locator->set_close_to_point_tol(_point_locator_close_to_point_tol);
     }
  
   // Otherwise there was a master point locator, and we can grab a
   // sub-locator easily.
   return PointLocatorBase::build(TREE_ELEMENTS, *this, _point_locator.get());
 }

References libMesh::Threads::in_threads, libMesh::libmesh_assert(), and libMesh::TREE_ELEMENTS.

Referenced by MeshfunctionDFEM::build_mesh(), libMesh::DofMap::create_dof_constraints(), libMesh::MeshFunction::init(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshRefinement::make_refinement_compatible(), libMesh::DefaultCoupling::mesh_reinit(), libMesh::PointNeighborCoupling::mesh_reinit(), libMesh::MeshRefinement::test_level_one(), PointLocatorTest::testLocator(), MixedDimensionMeshTest::testPointLocatorTree(), SystemsTest::testProjectCube(), SystemsTest::testProjectLine(), and SystemsTest::testProjectSquare().

◆ subactive_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::subactive_elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ subactive_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::subactive_elements_begin ( )

overridevirtualinherited

Iterate over elements for which elem->subactive() is true.

Implements libMesh::MeshBase.

◆ subactive_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::subactive_elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ subactive_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::subactive_elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ subdomain_ids()

void libMesh::MeshBase::subdomain_ids ( std::set< subdomain_id_type > & ids ) const

inherited

Constructs a list of all subdomain identifiers in the global mesh.

Subdomains correspond to separate subsets of the mesh which could correspond e.g. to different materials in a solid mechanics application, or regions where different physical processes are important. The subdomain mapping is independent from the parallel decomposition.

Definition at line 461 of file mesh_base.C.

 {
   // This requires an inspection on every processor
   parallel_object_only();
  
   ids.clear();
  
   for (const auto & elem : this->active_local_element_ptr_range())
     ids.insert(elem->subdomain_id());
  
   // Some subdomains may only live on other processors
   this->comm().set_union(ids);
 }

Referenced by libMesh::ReplicatedMesh::get_disconnected_subdomains(), and libMesh::TecplotIO::TecplotIO().

◆ subdomain_name() [1/2]

std::string & libMesh::MeshBase::subdomain_name ( subdomain_id_type id )

inherited

Returns: A writable reference for getting/setting an optional name for a subdomain.

Definition at line 717 of file mesh_base.C.

 {
   return _block_id_to_name[id];
 }

Referenced by libMesh::AbaqusIO::assign_subdomain_ids(), DMlibMeshSetSystem_libMesh(), libMesh::UNVIO::groups_in(), libMesh::ExodusII_IO::read(), libMesh::GmshIO::read_mesh(), and libMesh::TecplotIO::write_binary().

◆ subdomain_name() [2/2]

const std::string & libMesh::MeshBase::subdomain_name ( subdomain_id_type id ) const

inherited

Definition at line 722 of file mesh_base.C.

 {
   // An empty string to return when no matching subdomain name is found
   static const std::string empty;
  
   std::map<subdomain_id_type, std::string>::const_iterator iter = _block_id_to_name.find(id);
   if (iter == _block_id_to_name.end())
     return empty;
   else
     return iter->second;
 }

◆ type_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::type_elements_begin ( ElemType type ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ type_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::type_elements_begin ( ElemType type )

overridevirtualinherited

Iterate over all elements with a specified geometric type.

Implements libMesh::MeshBase.

◆ type_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::type_elements_end ( ElemType type ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ type_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::type_elements_end ( ElemType type )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ unpartitioned_elements_begin() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::unpartitioned_elements_begin ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ unpartitioned_elements_begin() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::unpartitioned_elements_begin ( )

overridevirtualinherited

Iterate over unpartitioned elements in the Mesh.

Implements libMesh::MeshBase.

◆ unpartitioned_elements_end() [1/2]

virtual const_element_iterator libMesh::ReplicatedMesh::unpartitioned_elements_end ( ) const

overridevirtualinherited

Implements libMesh::MeshBase.

◆ unpartitioned_elements_end() [2/2]

virtual element_iterator libMesh::ReplicatedMesh::unpartitioned_elements_end ( )

overridevirtualinherited

Implements libMesh::MeshBase.

◆ update_parallel_id_counts()

void libMesh::ReplicatedMesh::update_parallel_id_counts ( )

overridevirtualinherited

Updates parallel caches so that methods like n_elem() accurately reflect changes on other processors.

Implements libMesh::MeshBase.

Definition at line 619 of file replicated_mesh.C.

 {
 #ifdef LIBMESH_ENABLE_UNIQUE_ID
   _next_unique_id = this->parallel_max_unique_id();
 #endif
 }

References libMesh::MeshBase::_next_unique_id, and libMesh::ReplicatedMesh::parallel_max_unique_id().

Referenced by libMesh::ReplicatedMesh::renumber_nodes_and_elements().

◆ update_post_partitioning()

virtual void libMesh::MeshBase::update_post_partitioning ( )

inlinevirtualinherited

Recalculate any cached data after elements and nodes have been repartitioned.

Reimplemented in libMesh::DistributedMesh.

Definition at line 1006 of file mesh_base.h.

1006 {}

Referenced by libMesh::Nemesis_IO::read().

◆ write() [1/2]

void libMesh::UnstructuredMesh::write ( const std::string & name )

overridevirtualinherited

Write the file specified by name.

Attempts to figure out the proper method by the file extension.

Implements libMesh::MeshBase.

Definition at line 650 of file unstructured_mesh.C.

 {
   LOG_SCOPE("write()", "Mesh");
  
   NameBasedIO(*this).write(name);
 }

References libMesh::Quality::name(), and libMesh::NameBasedIO::write().

Referenced by libMesh::RBEIMEvaluation::legacy_write_out_interpolation_points_elem(), and main().

◆ write() [2/2]

void libMesh::UnstructuredMesh::write	(	const std::string &	name,
		const std::vector< Number > &	values,
		const std::vector< std::string > &	variable_names
	)

inherited

Write to the file specified by name.

Attempts to figure out the proper method by the file extension. Also writes data.

Definition at line 659 of file unstructured_mesh.C.

 {
   LOG_SCOPE("write()", "Mesh");
  
   NameBasedIO(*this).write_nodal_data(name, v, vn);
 }

References libMesh::Quality::name(), and libMesh::NameBasedIO::write_nodal_data().

Member Data Documentation

◆ _allow_remote_element_removal

bool libMesh::MeshBase::_allow_remote_element_removal

protectedinherited

If this is false then even on DistributedMesh remote elements will not be deleted during mesh preparation.

This is true by default.

Definition at line 1754 of file mesh_base.h.

Referenced by libMesh::MeshBase::allow_remote_element_removal().

◆ _block_id_to_name

std::map<subdomain_id_type, std::string> libMesh::MeshBase::_block_id_to_name

protectedinherited

This structure maintains the mapping of named blocks for file formats that support named blocks.

Currently this is only implemented for ExodusII

Definition at line 1761 of file mesh_base.h.

Referenced by libMesh::MeshBase::get_subdomain_name_map(), and libMesh::MeshBase::set_subdomain_name_map().

◆ _communicator

const Parallel::Communicator& libMesh::ParallelObject::_communicator

protectedinherited

Definition at line 112 of file parallel_object.h.

Referenced by libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::ParallelObject::comm(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::operator=(), and libMesh::ParallelObject::processor_id().

◆ _count_lower_dim_elems_in_point_locator

bool libMesh::MeshBase::_count_lower_dim_elems_in_point_locator

protectedinherited

Do we count lower dimensional elements in point locator refinement? This is relevant in tree-based point locators, for example.

Definition at line 1713 of file mesh_base.h.

◆ _default_ghosting

std::unique_ptr<GhostingFunctor> libMesh::MeshBase::_default_ghosting

protectedinherited

The default geometric GhostingFunctor, used to implement standard libMesh element ghosting behavior.

We use a base class pointer here to avoid dragging in more header dependencies.

Definition at line 1812 of file mesh_base.h.

Referenced by libMesh::MeshBase::default_ghosting(), and libMesh::MeshBase::MeshBase().

◆ _default_mapping_data

unsigned char libMesh::MeshBase::_default_mapping_data

protectedinherited

The default mapping data (unused with Lagrange, used for nodal weight lookup index with rational bases) to assign to newly added elements.

Definition at line 1693 of file mesh_base.h.

Referenced by libMesh::MeshBase::default_mapping_data(), and libMesh::MeshBase::set_default_mapping_data().

◆ _default_mapping_type

ElemMappingType libMesh::MeshBase::_default_mapping_type

protectedinherited

The default mapping type (typically Lagrange) between master and physical space to assign to newly added elements.

Definition at line 1686 of file mesh_base.h.

Referenced by libMesh::MeshBase::default_mapping_type(), and libMesh::MeshBase::set_default_mapping_type().

◆ _elem_dims

std::set<unsigned char> libMesh::MeshBase::_elem_dims

protectedinherited

We cache the dimension of the elements present in the mesh.

So, if we have a mesh with 1D and 2D elements, this structure will contain 1 and 2.

Definition at line 1768 of file mesh_base.h.

Referenced by libMesh::MeshBase::elem_dimensions(), libMesh::MeshBase::mesh_dimension(), libMesh::MeshBase::MeshBase(), libMesh::MeshBase::set_elem_dimensions(), and libMesh::MeshBase::set_mesh_dimension().

◆ _elem_integer_names

std::vector<std::string> libMesh::MeshBase::_elem_integer_names

protectedinherited

The array of names for integer data associated with each element in the mesh.

Definition at line 1780 of file mesh_base.h.

Referenced by libMesh::ReplicatedMesh::add_elem(), libMesh::DistributedMesh::add_elem(), libMesh::MeshBase::add_elem_data(), libMesh::MeshBase::add_elem_datum(), libMesh::MeshBase::add_elem_integer(), libMesh::MeshBase::add_elem_integers(), libMesh::UnstructuredMesh::copy_nodes_and_elements(), libMesh::UnstructuredMesh::create_submesh(), libMesh::MeshBase::get_elem_integer_name(), libMesh::ReplicatedMesh::insert_elem(), libMesh::DistributedMesh::insert_elem(), libMesh::MeshBase::merge_extra_integer_names(), and libMesh::MeshBase::n_elem_integers().

◆ _elements

std::vector<Elem *> libMesh::ReplicatedMesh::_elements

protectedinherited

The elements in the mesh.

Definition at line 513 of file replicated_mesh.h.

◆ _ghosting_functors

std::set<GhostingFunctor *> libMesh::MeshBase::_ghosting_functors

protectedinherited

The list of all GhostingFunctor objects to be used when distributing a DistributedMesh.

Basically unused by ReplicatedMesh for now, but belongs to MeshBase because the cost is trivial.

Definition at line 1821 of file mesh_base.h.

Referenced by libMesh::MeshBase::add_ghosting_functor(), libMesh::MeshBase::ghosting_functors_begin(), libMesh::MeshBase::ghosting_functors_end(), and libMesh::MeshBase::MeshBase().

◆ _is_prepared

bool libMesh::MeshBase::_is_prepared

protectedinherited

Flag indicating if the mesh has been prepared for use.

Definition at line 1698 of file mesh_base.h.

Referenced by libMesh::UnstructuredMesh::all_first_order(), libMesh::UnstructuredMesh::all_second_order(), libMesh::UnstructuredMesh::copy_nodes_and_elements(), and libMesh::MeshBase::is_prepared().

◆ _n_parts

unsigned int libMesh::MeshBase::_n_parts

protectedinherited

The number of partitions the mesh has.

This is set by the partitioners, and may not be changed directly by the user.

Note: The number of partitions need not equal this->n_processors(), consider for example the case where you simply want to partition a mesh on one processor and view the result in GMV.

Definition at line 1680 of file mesh_base.h.

Referenced by libMesh::UnstructuredMesh::copy_nodes_and_elements(), libMesh::MeshBase::n_partitions(), and libMesh::MeshBase::set_n_partitions().

◆ _next_unique_id

unique_id_type libMesh::MeshBase::_next_unique_id

protectedinherited

The next available unique id for assigning ids to DOF objects.

Definition at line 1727 of file mesh_base.h.

Referenced by libMesh::ReplicatedMesh::add_elem(), libMesh::DistributedMesh::add_elem(), libMesh::ReplicatedMesh::add_node(), libMesh::DistributedMesh::add_node(), libMesh::ReplicatedMesh::add_point(), libMesh::DistributedMesh::DistributedMesh(), libMesh::ReplicatedMesh::insert_elem(), libMesh::DistributedMesh::insert_elem(), libMesh::ReplicatedMesh::insert_node(), libMesh::MeshBase::next_unique_id(), libMesh::ReplicatedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_max_unique_id(), libMesh::ReplicatedMesh::ReplicatedMesh(), libMesh::MeshBase::set_next_unique_id(), libMesh::ReplicatedMesh::update_parallel_id_counts(), and libMesh::DistributedMesh::update_parallel_id_counts().

◆ _node_integer_names

std::vector<std::string> libMesh::MeshBase::_node_integer_names

protectedinherited

The array of names for integer data associated with each node in the mesh.

Definition at line 1786 of file mesh_base.h.

Referenced by libMesh::ReplicatedMesh::add_node(), libMesh::DistributedMesh::add_node(), libMesh::MeshBase::add_node_data(), libMesh::MeshBase::add_node_datum(), libMesh::ReplicatedMesh::add_point(), libMesh::UnstructuredMesh::copy_nodes_and_elements(), libMesh::UnstructuredMesh::create_submesh(), libMesh::MeshBase::get_node_integer_name(), libMesh::ReplicatedMesh::insert_node(), libMesh::MeshBase::merge_extra_integer_names(), and libMesh::MeshBase::n_node_integers().

◆ _nodes

std::vector<Node *> libMesh::ReplicatedMesh::_nodes

protectedinherited

The vertices (spatial coordinates) of the mesh.

Definition at line 508 of file replicated_mesh.h.

◆ _partitioner

std::unique_ptr<Partitioner> libMesh::MeshBase::_partitioner

protectedinherited

A partitioner to use at each prepare_for_use().

This will be built in the constructor of each derived class, but can be replaced by the user through the partitioner() accessor.

Definition at line 1721 of file mesh_base.h.

Referenced by libMesh::DistributedMesh::DistributedMesh(), libMesh::MeshBase::MeshBase(), libMesh::MeshBase::partitioner(), libMesh::ReplicatedMesh::ReplicatedMesh(), and libMesh::MeshBase::skip_noncritical_partitioning().

◆ _point_locator

std::unique_ptr<PointLocatorBase> libMesh::MeshBase::_point_locator

mutableprotectedinherited

A PointLocator class for this mesh.

This will not actually be built unless needed. Further, since we want our point_locator() method to be const (yet do the dynamic allocating) this needs to be mutable. Since the PointLocatorBase::build() member is used, and it operates on a constant reference to the mesh, this is OK.

Definition at line 1707 of file mesh_base.h.

◆ _point_locator_close_to_point_tol

Real libMesh::MeshBase::_point_locator_close_to_point_tol

protectedinherited

If nonzero, we will call PointLocatorBase::set_close_to_point_tol() on any PointLocators that we create.

Definition at line 1833 of file mesh_base.h.

◆ _shared_functors

std::map<GhostingFunctor *, std::shared_ptr<GhostingFunctor> > libMesh::MeshBase::_shared_functors

protectedinherited

Hang on to references to any GhostingFunctor objects we were passed in shared_ptr form.

Definition at line 1827 of file mesh_base.h.

Referenced by libMesh::MeshBase::add_ghosting_functor().

◆ _skip_all_partitioning

bool libMesh::MeshBase::_skip_all_partitioning

protectedinherited

If this is true then no partitioning should be done.

Definition at line 1739 of file mesh_base.h.

Referenced by libMesh::UnstructuredMesh::copy_nodes_and_elements(), libMesh::MeshBase::skip_noncritical_partitioning(), and libMesh::MeshBase::skip_partitioning().

◆ _skip_noncritical_partitioning

bool libMesh::MeshBase::_skip_noncritical_partitioning

protectedinherited

If this is true then no partitioning should be done with the possible exception of orphaned nodes.

Definition at line 1734 of file mesh_base.h.

Referenced by libMesh::UnstructuredMesh::copy_nodes_and_elements(), and libMesh::MeshBase::skip_noncritical_partitioning().

◆ _skip_renumber_nodes_and_elements

bool libMesh::MeshBase::_skip_renumber_nodes_and_elements

protectedinherited

If this is true then renumbering will be kept to a minimum.

This is set when prepare_for_use() is called.

Definition at line 1746 of file mesh_base.h.

Referenced by libMesh::MeshBase::allow_renumbering(), libMesh::ReplicatedMesh::renumber_nodes_and_elements(), and libMesh::DistributedMesh::renumber_nodes_and_elements().

◆ _spatial_dimension

unsigned char libMesh::MeshBase::_spatial_dimension

protectedinherited

The "spatial dimension" of the Mesh.

See the documentation for Mesh::spatial_dimension() for more information.

Definition at line 1774 of file mesh_base.h.

Referenced by libMesh::MeshBase::set_spatial_dimension(), and libMesh::MeshBase::spatial_dimension().

◆ boundary_info

std::unique_ptr<BoundaryInfo> libMesh::MeshBase::boundary_info

inherited

This class holds the boundary information.

It can store nodes, edges, and faces with a corresponding id that facilitates setting boundary conditions.

Direct access to this class will be removed in future libMesh versions. Use the get_boundary_info() accessor instead.

Definition at line 1659 of file mesh_base.h.

Referenced by libMesh::MeshBase::get_boundary_info(), and MeshInputTest::testMeshMoveConstructor().

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

include/mesh/serial_mesh.h

Public Types

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Types

Private Member Functions

Detailed Description

Member Typedef Documentation

◆ const_elem_iterator_imp

◆ const_node_iterator_imp

◆ elem_iterator_imp

◆ node_iterator_imp

◆ Predicate

Constructor & Destructor Documentation

◆ SerialMesh() [1/2]

◆ SerialMesh() [2/2]

◆ ~SerialMesh()

Member Function Documentation

◆ active_element_ptr_range() [1/2]

◆ active_element_ptr_range() [2/2]

◆ active_elements_begin() [1/2]

◆ active_elements_begin() [2/2]

◆ active_elements_end() [1/2]

◆ active_elements_end() [2/2]

◆ active_local_element_ptr_range() [1/2]

◆ active_local_element_ptr_range() [2/2]

◆ active_local_elements_begin() [1/2]

◆ active_local_elements_begin() [2/2]

◆ active_local_elements_end() [1/2]

◆ active_local_elements_end() [2/2]

◆ active_local_subdomain_elements_begin() [1/2]

◆ active_local_subdomain_elements_begin() [2/2]

◆ active_local_subdomain_elements_end() [1/2]

◆ active_local_subdomain_elements_end() [2/2]

◆ active_local_subdomain_elements_ptr_range() [1/2]

◆ active_local_subdomain_elements_ptr_range() [2/2]

◆ active_nodes_begin() [1/2]

◆ active_nodes_begin() [2/2]

◆ active_nodes_end() [1/2]

◆ active_nodes_end() [2/2]

◆ active_not_local_elements_begin() [1/2]

◆ active_not_local_elements_begin() [2/2]

◆ active_not_local_elements_end() [1/2]

◆ active_not_local_elements_end() [2/2]

◆ active_pid_elements_begin() [1/2]

◆ active_pid_elements_begin() [2/2]

◆ active_pid_elements_end() [1/2]

◆ active_pid_elements_end() [2/2]

◆ active_semilocal_elements_begin() [1/2]

◆ active_semilocal_elements_begin() [2/2]

◆ active_semilocal_elements_end() [1/2]

◆ active_semilocal_elements_end() [2/2]

◆ active_subdomain_elements_begin() [1/2]

◆ active_subdomain_elements_begin() [2/2]

◆ active_subdomain_elements_end() [1/2]

◆ active_subdomain_elements_end() [2/2]

◆ active_subdomain_elements_ptr_range() [1/2]

◆ active_subdomain_elements_ptr_range() [2/2]

◆ active_subdomain_set_elements_begin() [1/2]

◆ active_subdomain_set_elements_begin() [2/2]

◆ active_subdomain_set_elements_end() [1/2]

◆ active_subdomain_set_elements_end() [2/2]

◆ active_subdomain_set_elements_ptr_range() [1/2]

◆ active_subdomain_set_elements_ptr_range() [2/2]

◆ active_type_elements_begin() [1/2]

◆ active_type_elements_begin() [2/2]

◆ active_type_elements_end() [1/2]

◆ active_type_elements_end() [2/2]

◆ active_unpartitioned_elements_begin() [1/2]

◆ active_unpartitioned_elements_begin() [2/2]

◆ active_unpartitioned_elements_end() [1/2]

◆ active_unpartitioned_elements_end() [2/2]

◆ add_elem()

◆ add_elem_data()

◆ add_elem_datum()

◆ add_elem_integer()

◆ add_elem_integers()

◆ add_ghosting_functor() [1/2]

◆ add_ghosting_functor() [2/2]