libMesh
Public Types | Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | List of all members
libMesh::ParallelMesh Class Reference

#include <parallel_mesh.h>

Inheritance diagram for libMesh::ParallelMesh:
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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

 ParallelMesh (const Parallel::Communicator &comm_in, unsigned char dim=1)
 
 ParallelMesh (unsigned char dim=1)
 Constructor which takes dim, the dimension of the mesh. More...
 
 ParallelMesh (const UnstructuredMesh &other_mesh)
 
virtual UniquePtr< MeshBaseclone () const libmesh_override
 Virtual copy-constructor, creates a copy of this mesh. More...
 
 ~ParallelMesh ()
 
virtual void clear () libmesh_override
 Clear all internal data. More...
 
virtual void redistribute () libmesh_override
 Redistribute elements between processors. More...
 
virtual void update_post_partitioning () libmesh_override
 Recalculate cached data after elements and nodes have been repartitioned. More...
 
virtual bool is_serial () const libmesh_override
 
virtual bool is_serial_on_zero () const libmesh_override
 
virtual void set_distributed () libmesh_override
 Asserts that not all elements and nodes of the mesh necessarily exist on the current processor. More...
 
virtual bool is_replicated () const libmesh_override
 
template<typename T >
void libmesh_assert_valid_parallel_object_ids (const mapvector< T *, dof_id_type > &) const
 Verify id, processor_id, and if applicable unique_id consistency of a parallel objects container. More...
 
virtual void libmesh_assert_valid_parallel_ids () const libmesh_override
 Verify id and processor_id consistency of our elements and nodes containers. More...
 
void libmesh_assert_valid_parallel_p_levels () const
 Verify p_level consistency of our elements containers. More...
 
void libmesh_assert_valid_parallel_flags () const
 Verify refinement_flag and p_refinement_flag consistency of our elements containers. More...
 
template<typename T >
dof_id_type renumber_dof_objects (mapvector< T *, dof_id_type > &)
 Renumber a parallel objects container. More...
 
virtual void renumber_nodes_and_elements () libmesh_override
 Remove NULL elements from arrays. More...
 
virtual void allgather () libmesh_override
 Gathers all elements and nodes of the mesh onto every processor. More...
 
virtual void gather_to_zero () libmesh_override
 Gathers all elements and nodes of the mesh onto processor zero. More...
 
virtual void delete_remote_elements () libmesh_override
 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...
 
virtual void add_extra_ghost_elem (Elem *e)
 Inserts the element and adds it to a list of elements that should not get deleted or have their descendants deleted by delete_remote_elements. More...
 
virtual void clear_extra_ghost_elems ()
 Clears extra ghost elements. More...
 
virtual dof_id_type n_nodes () const libmesh_override
 
virtual dof_id_type max_node_id () const libmesh_override
 
virtual void reserve_nodes (const dof_id_type) libmesh_override
 Reserves space for a known number of nodes. More...
 
virtual dof_id_type n_elem () const libmesh_override
 
virtual dof_id_type n_active_elem () const libmesh_override
 
virtual dof_id_type max_elem_id () const libmesh_override
 
virtual void reserve_elem (const dof_id_type) libmesh_override
 Reserves space for a known number of elements. More...
 
virtual void update_parallel_id_counts () libmesh_override
 Updates parallel caches so that methods like n_elem() accurately reflect changes on other processors. More...
 
virtual dof_id_type parallel_n_nodes () const libmesh_override
 
dof_id_type parallel_max_node_id () const
 
virtual dof_id_type parallel_n_elem () const libmesh_override
 
dof_id_type parallel_max_elem_id () const
 
virtual unique_id_type parallel_max_unique_id () const libmesh_override
 
virtual const Pointpoint (const dof_id_type i) const libmesh_override
 
virtual const Nodenode_ptr (const dof_id_type i) const libmesh_override
 
virtual Nodenode_ptr (const dof_id_type i) libmesh_override
 
virtual const Nodequery_node_ptr (const dof_id_type i) const libmesh_override
 
virtual Nodequery_node_ptr (const dof_id_type i) libmesh_override
 
virtual const Elemelem_ptr (const dof_id_type i) const libmesh_override
 
virtual Elemelem_ptr (const dof_id_type i) libmesh_override
 
virtual const Elemquery_elem_ptr (const dof_id_type i) const libmesh_override
 
virtual Elemquery_elem_ptr (const dof_id_type i) libmesh_override
 
virtual Nodeadd_point (const Point &p, const dof_id_type id=DofObject::invalid_id, const processor_id_type proc_id=DofObject::invalid_processor_id) libmesh_override
 functions for adding /deleting nodes elements. More...
 
virtual Nodeadd_node (Node *n) libmesh_override
 Add Node n to the end of the vertex array. More...
 
virtual Nodeinsert_node (Node *n) libmesh_override
 Calls add_node(). More...
 
virtual void delete_node (Node *n) libmesh_override
 Removes the Node n from the mesh. More...
 
virtual void renumber_node (dof_id_type old_id, dof_id_type new_id) libmesh_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 Elemadd_elem (Elem *e) libmesh_override
 Add elem e to the end of the element array. More...
 
virtual Eleminsert_elem (Elem *e) libmesh_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) libmesh_override
 Removes element e from the mesh. More...
 
virtual void renumber_elem (dof_id_type old_id, dof_id_type new_id) libmesh_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 () libmesh_override
 There is no reason for a user to ever call this function. More...
 
virtual element_iterator elements_begin () libmesh_override
 Elem iterator accessor functions. More...
 
virtual const_element_iterator elements_begin () const libmesh_override
 
virtual element_iterator elements_end () libmesh_override
 
virtual const_element_iterator elements_end () const libmesh_override
 
virtual SimpleRange< element_iteratorelement_ptr_range () libmesh_override
 
virtual SimpleRange< const_element_iteratorelement_ptr_range () const libmesh_override
 
virtual element_iterator active_elements_begin () libmesh_override
 Active, local, and negation forms of the element iterators described above. More...
 
virtual const_element_iterator active_elements_begin () const libmesh_override
 
virtual element_iterator active_elements_end () libmesh_override
 
virtual const_element_iterator active_elements_end () const libmesh_override
 
virtual SimpleRange< element_iteratoractive_element_ptr_range () libmesh_override
 
virtual SimpleRange< const_element_iteratoractive_element_ptr_range () const libmesh_override
 
virtual element_iterator ancestor_elements_begin () libmesh_override
 Iterate over elements for which elem->ancestor() is true. More...
 
virtual const_element_iterator ancestor_elements_begin () const libmesh_override
 
virtual element_iterator ancestor_elements_end () libmesh_override
 
virtual const_element_iterator ancestor_elements_end () const libmesh_override
 
virtual element_iterator subactive_elements_begin () libmesh_override
 Iterate over elements for which elem->subactive() is true. More...
 
virtual const_element_iterator subactive_elements_begin () const libmesh_override
 
virtual element_iterator subactive_elements_end () libmesh_override
 
virtual const_element_iterator subactive_elements_end () const libmesh_override
 
virtual element_iterator not_active_elements_begin () libmesh_override
 
virtual const_element_iterator not_active_elements_begin () const libmesh_override
 
virtual element_iterator not_active_elements_end () libmesh_override
 
virtual const_element_iterator not_active_elements_end () const libmesh_override
 
virtual element_iterator not_ancestor_elements_begin () libmesh_override
 
virtual const_element_iterator not_ancestor_elements_begin () const libmesh_override
 
virtual element_iterator not_ancestor_elements_end () libmesh_override
 
virtual const_element_iterator not_ancestor_elements_end () const libmesh_override
 
virtual element_iterator not_subactive_elements_begin () libmesh_override
 
virtual const_element_iterator not_subactive_elements_begin () const libmesh_override
 
virtual element_iterator not_subactive_elements_end () libmesh_override
 
virtual const_element_iterator not_subactive_elements_end () const libmesh_override
 
virtual element_iterator local_elements_begin () libmesh_override
 
virtual const_element_iterator local_elements_begin () const libmesh_override
 
virtual element_iterator local_elements_end () libmesh_override
 
virtual const_element_iterator local_elements_end () const libmesh_override
 
virtual element_iterator semilocal_elements_begin () libmesh_override
 Iterate over elements for which elem->is_semilocal() is true for the current processor. More...
 
virtual const_element_iterator semilocal_elements_begin () const libmesh_override
 
virtual element_iterator semilocal_elements_end () libmesh_override
 
virtual const_element_iterator semilocal_elements_end () const libmesh_override
 
virtual element_iterator active_semilocal_elements_begin () libmesh_override
 
virtual const_element_iterator active_semilocal_elements_begin () const libmesh_override
 
virtual element_iterator active_semilocal_elements_end () libmesh_override
 
virtual const_element_iterator active_semilocal_elements_end () const libmesh_override
 
virtual element_iterator facelocal_elements_begin () libmesh_override
 Iterate over elements which are on or have a neighbor on the current processor. More...
 
virtual const_element_iterator facelocal_elements_begin () const libmesh_override
 
virtual element_iterator facelocal_elements_end () libmesh_override
 
virtual const_element_iterator facelocal_elements_end () const libmesh_override
 
virtual element_iterator not_local_elements_begin () libmesh_override
 
virtual const_element_iterator not_local_elements_begin () const libmesh_override
 
virtual element_iterator not_local_elements_end () libmesh_override
 
virtual const_element_iterator not_local_elements_end () const libmesh_override
 
virtual element_iterator active_local_elements_begin () libmesh_override
 
virtual const_element_iterator active_local_elements_begin () const libmesh_override
 
virtual element_iterator active_local_elements_end () libmesh_override
 
virtual const_element_iterator active_local_elements_end () const libmesh_override
 
virtual SimpleRange< element_iteratoractive_local_element_ptr_range () libmesh_override
 
virtual SimpleRange< const_element_iteratoractive_local_element_ptr_range () const libmesh_override
 
virtual element_iterator active_not_local_elements_begin () libmesh_override
 
virtual const_element_iterator active_not_local_elements_begin () const libmesh_override
 
virtual element_iterator active_not_local_elements_end () libmesh_override
 
virtual const_element_iterator active_not_local_elements_end () const libmesh_override
 
virtual element_iterator level_elements_begin (unsigned int level) libmesh_override
 Iterate over elements of a given level. More...
 
virtual const_element_iterator level_elements_begin (unsigned int level) const libmesh_override
 
virtual element_iterator level_elements_end (unsigned int level) libmesh_override
 
virtual const_element_iterator level_elements_end (unsigned int level) const libmesh_override
 
virtual element_iterator not_level_elements_begin (unsigned int level) libmesh_override
 
virtual const_element_iterator not_level_elements_begin (unsigned int level) const libmesh_override
 
virtual element_iterator not_level_elements_end (unsigned int level) libmesh_override
 
virtual const_element_iterator not_level_elements_end (unsigned int level) const libmesh_override
 
virtual element_iterator local_level_elements_begin (unsigned int level) libmesh_override
 
virtual const_element_iterator local_level_elements_begin (unsigned int level) const libmesh_override
 
virtual element_iterator local_level_elements_end (unsigned int level) libmesh_override
 
virtual const_element_iterator local_level_elements_end (unsigned int level) const libmesh_override
 
virtual element_iterator local_not_level_elements_begin (unsigned int level) libmesh_override
 
virtual const_element_iterator local_not_level_elements_begin (unsigned int level) const libmesh_override
 
virtual element_iterator local_not_level_elements_end (unsigned int level) libmesh_override
 
virtual const_element_iterator local_not_level_elements_end (unsigned int level) const libmesh_override
 
virtual element_iterator pid_elements_begin (processor_id_type proc_id) libmesh_override
 Iterate over all elements with a specified processor id. More...
 
virtual const_element_iterator pid_elements_begin (processor_id_type proc_id) const libmesh_override
 
virtual element_iterator pid_elements_end (processor_id_type proc_id) libmesh_override
 
virtual const_element_iterator pid_elements_end (processor_id_type proc_id) const libmesh_override
 
virtual element_iterator type_elements_begin (ElemType type) libmesh_override
 Iterate over all elements with a specified geometric type. More...
 
virtual const_element_iterator type_elements_begin (ElemType type) const libmesh_override
 
virtual element_iterator type_elements_end (ElemType type) libmesh_override
 
virtual const_element_iterator type_elements_end (ElemType type) const libmesh_override
 
virtual element_iterator active_type_elements_begin (ElemType type) libmesh_override
 
virtual const_element_iterator active_type_elements_begin (ElemType type) const libmesh_override
 
virtual element_iterator active_type_elements_end (ElemType type) libmesh_override
 
virtual const_element_iterator active_type_elements_end (ElemType type) const libmesh_override
 
virtual element_iterator active_pid_elements_begin (processor_id_type proc_id) libmesh_override
 
virtual const_element_iterator active_pid_elements_begin (processor_id_type proc_id) const libmesh_override
 
virtual element_iterator active_pid_elements_end (processor_id_type proc_id) libmesh_override
 
virtual const_element_iterator active_pid_elements_end (processor_id_type proc_id) const libmesh_override
 
virtual element_iterator unpartitioned_elements_begin () libmesh_override
 Iterate over unpartitioned elements in the Mesh. More...
 
virtual const_element_iterator unpartitioned_elements_begin () const libmesh_override
 
virtual element_iterator unpartitioned_elements_end () libmesh_override
 
virtual const_element_iterator unpartitioned_elements_end () const libmesh_override
 
virtual element_iterator active_unpartitioned_elements_begin () libmesh_override
 Iterate over active unpartitioned elements in the Mesh. More...
 
virtual const_element_iterator active_unpartitioned_elements_begin () const libmesh_override
 
virtual element_iterator active_unpartitioned_elements_end () libmesh_override
 
virtual const_element_iterator active_unpartitioned_elements_end () const libmesh_override
 
virtual element_iterator active_local_subdomain_elements_begin (subdomain_id_type subdomain_id) libmesh_override
 
virtual const_element_iterator active_local_subdomain_elements_begin (subdomain_id_type subdomain_id) const libmesh_override
 
virtual element_iterator active_local_subdomain_elements_end (subdomain_id_type subdomain_id) libmesh_override
 
virtual const_element_iterator active_local_subdomain_elements_end (subdomain_id_type subdomain_id) const libmesh_override
 
virtual element_iterator active_subdomain_elements_begin (subdomain_id_type subdomain_id) libmesh_override
 
virtual const_element_iterator active_subdomain_elements_begin (subdomain_id_type subdomain_id) const libmesh_override
 
virtual element_iterator active_subdomain_elements_end (subdomain_id_type subdomain_id) libmesh_override
 
virtual const_element_iterator active_subdomain_elements_end (subdomain_id_type subdomain_id) const libmesh_override
 
virtual element_iterator active_subdomain_set_elements_begin (std::set< subdomain_id_type > ss) libmesh_override
 
virtual const_element_iterator active_subdomain_set_elements_begin (std::set< subdomain_id_type > ss) const libmesh_override
 
virtual element_iterator active_subdomain_set_elements_end (std::set< subdomain_id_type > ss) libmesh_override
 
virtual const_element_iterator active_subdomain_set_elements_end (std::set< subdomain_id_type > ss) const libmesh_override
 
virtual element_iterator ghost_elements_begin () libmesh_override
 Iterate over "ghost" elements in the Mesh. More...
 
virtual const_element_iterator ghost_elements_begin () const libmesh_override
 
virtual element_iterator ghost_elements_end () libmesh_override
 
virtual const_element_iterator ghost_elements_end () const libmesh_override
 
virtual element_iterator evaluable_elements_begin (const DofMap &dof_map, unsigned int var_num=libMesh::invalid_uint) libmesh_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 libmesh_override
 
virtual element_iterator evaluable_elements_end (const DofMap &dof_map, unsigned int var_num=libMesh::invalid_uint) libmesh_override
 
virtual const_element_iterator evaluable_elements_end (const DofMap &dof_map, unsigned int var_num=libMesh::invalid_uint) const libmesh_override
 
virtual element_iterator flagged_elements_begin (unsigned char rflag) libmesh_override
 Iterate over all elements with a specified refinement flag. More...
 
virtual const_element_iterator flagged_elements_begin (unsigned char rflag) const libmesh_override
 
virtual element_iterator flagged_elements_end (unsigned char rflag) libmesh_override
 
virtual const_element_iterator flagged_elements_end (unsigned char rflag) const libmesh_override
 
virtual element_iterator flagged_pid_elements_begin (unsigned char rflag, processor_id_type pid) libmesh_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 libmesh_override
 
virtual element_iterator flagged_pid_elements_end (unsigned char rflag, processor_id_type pid) libmesh_override
 
virtual const_element_iterator flagged_pid_elements_end (unsigned char rflag, processor_id_type pid) const libmesh_override
 
virtual node_iterator nodes_begin () libmesh_override
 Node iterator accessor functions. More...
 
virtual const_node_iterator nodes_begin () const libmesh_override
 
virtual node_iterator nodes_end () libmesh_override
 
virtual const_node_iterator nodes_end () const libmesh_override
 
virtual SimpleRange< node_iteratornode_ptr_range () libmesh_override
 
virtual SimpleRange< const_node_iteratornode_ptr_range () const libmesh_override
 
virtual node_iterator active_nodes_begin () libmesh_override
 Iterate over only the active nodes in the Mesh. More...
 
virtual const_node_iterator active_nodes_begin () const libmesh_override
 
virtual node_iterator active_nodes_end () libmesh_override
 
virtual const_node_iterator active_nodes_end () const libmesh_override
 
virtual node_iterator local_nodes_begin () libmesh_override
 Iterate over local nodes (nodes whose processor_id() matches the current processor). More...
 
virtual const_node_iterator local_nodes_begin () const libmesh_override
 
virtual node_iterator local_nodes_end () libmesh_override
 
virtual const_node_iterator local_nodes_end () const libmesh_override
 
virtual SimpleRange< node_iteratorlocal_node_ptr_range () libmesh_override
 
virtual SimpleRange< const_node_iteratorlocal_node_ptr_range () const libmesh_override
 
virtual node_iterator pid_nodes_begin (processor_id_type proc_id) libmesh_override
 Iterate over nodes with processor_id() == proc_id. More...
 
virtual const_node_iterator pid_nodes_begin (processor_id_type proc_id) const libmesh_override
 
virtual node_iterator pid_nodes_end (processor_id_type proc_id) libmesh_override
 
virtual const_node_iterator pid_nodes_end (processor_id_type proc_id) const libmesh_override
 
virtual node_iterator bid_nodes_begin (boundary_id_type bndry_id) libmesh_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 libmesh_override
 
virtual node_iterator bid_nodes_end (boundary_id_type bndry_id) libmesh_override
 
virtual const_node_iterator bid_nodes_end (boundary_id_type bndry_id) const libmesh_override
 
virtual node_iterator bnd_nodes_begin () libmesh_override
 Iterate over nodes for which BoundaryInfo::n_boundary_ids(node) > 0. More...
 
virtual const_node_iterator bnd_nodes_begin () const libmesh_override
 
virtual node_iterator bnd_nodes_end () libmesh_override
 
virtual const_node_iterator bnd_nodes_end () const libmesh_override
 
virtual node_iterator evaluable_nodes_begin (const DofMap &dof_map, unsigned int var_num=libMesh::invalid_uint) libmesh_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 libmesh_override
 
virtual node_iterator evaluable_nodes_end (const DofMap &dof_map, unsigned int var_num=libMesh::invalid_uint) libmesh_override
 
virtual const_node_iterator evaluable_nodes_end (const DofMap &dof_map, unsigned int var_num=libMesh::invalid_uint) const libmesh_override
 
virtual void read (const std::string &name, void *mesh_data=libmesh_nullptr, bool skip_renumber_nodes_and_elements=false, bool skip_find_neighbors=false) libmesh_override
 Reads the file specified by name. More...
 
virtual void write (const std::string &name) libmesh_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 () libmesh_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) libmesh_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_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)
 Deep copy of another unstructured mesh class (used by subclass copy constructors) More...
 
virtual void find_neighbors (const bool reset_remote_elements=false, const bool reset_current_list=true) libmesh_override
 Other functions from MeshBase requiring re-definition. More...
 
virtual bool contract () libmesh_override
 Delete subactive (i.e. More...
 
virtual UniquePtr< Partitioner > & partitioner ()
 A partitioner to use at each prepare_for_use() More...
 
const BoundaryInfoget_boundary_info () const
 The information about boundary ids on the mesh. More...
 
BoundaryInfoget_boundary_info ()
 Writable information about boundary ids on the mesh. More...
 
bool is_prepared () const
 
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
 
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 Nodenode_ref (const dof_id_type i) const
 
virtual Nodenode_ref (const dof_id_type i)
 
virtual const Nodenode (const dof_id_type i) const
 
virtual Nodenode (const dof_id_type i)
 
virtual const Elemelem_ref (const dof_id_type i) const
 
virtual Elemelem_ref (const dof_id_type i)
 
virtual const Elemelem (const dof_id_type i) const
 
virtual Elemelem (const dof_id_type i)
 
virtual const Elemquery_elem (const dof_id_type i) const
 
virtual Elemquery_elem (const dof_id_type i)
 
void prepare_for_use (const bool skip_renumber_nodes_and_elements=false, const bool skip_find_neighbors=false)
 Prepare a newly created (or read) mesh for use. More...
 
virtual void partition (const unsigned int n_parts)
 Call the default partitioner (currently metis_partition()). More...
 
void partition ()
 
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_partitioning (bool skip)
 If true is passed in then this mesh will no longer 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 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...
 
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 PointLocatorBasepoint_locator () const
 
UniquePtr< PointLocatorBasesub_point_locator () 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...
 
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::Communicatorcomm () const
 
processor_id_type n_processors () const
 
processor_id_type processor_id () const
 

Public Attributes

UniquePtr< BoundaryInfoboundary_info
 This class holds the boundary information. More...
 

Protected Member Functions

unsigned intset_n_partitions ()
 

Protected Attributes

mapvector< Node *, dof_id_type_nodes
 The vertices (spatial coordinates) of the mesh. More...
 
mapvector< Elem *, dof_id_type_elements
 The elements in the mesh. More...
 
bool _is_serial
 A boolean remembering whether we're serialized or not. More...
 
bool _is_serial_on_proc_0
 A boolean remembering whether we're serialized to proc 0 or not. More...
 
dof_id_type _n_nodes
 Cached data from the last renumber_nodes_and_elements call. More...
 
dof_id_type _n_elem
 
dof_id_type _max_node_id
 
dof_id_type _max_elem_id
 
dof_id_type _next_free_local_node_id
 Guaranteed globally unused IDs for use when adding new nodes or elements. More...
 
dof_id_type _next_free_local_elem_id
 
dof_id_type _next_free_unpartitioned_node_id
 
dof_id_type _next_free_unpartitioned_elem_id
 
unique_id_type _next_unpartitioned_unique_id
 The next available unique id for assigning ids to unpartitioned DOF objects. More...
 
std::set< Elem * > _extra_ghost_elems
 These are extra ghost elements that we want to make sure not to delete when we call delete_remote_elements() More...
 
unsigned int _n_parts
 The number of partitions the mesh has. More...
 
bool _is_prepared
 Flag indicating if the mesh has been prepared for use. More...
 
UniquePtr< 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...
 
UniquePtr< 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_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...
 
UniquePtr< 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...
 
const Parallel::Communicator_communicator
 

Detailed Description

Definition at line 34 of file parallel_mesh.h.

Member Typedef Documentation

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

Definition at line 889 of file mesh_base.h.

Constructor & Destructor Documentation

libMesh::ParallelMesh::ParallelMesh ( const Parallel::Communicator comm_in,
unsigned char  dim = 1 
)
explicit

Definition at line 38 of file parallel_mesh.h.

Referenced by clone().

40  : DistributedMesh(comm_in,dim) {}
unsigned int dim
DistributedMesh(const Parallel::Communicator &comm_in, unsigned char dim=1)
Constructor.
libMesh::ParallelMesh::ParallelMesh ( unsigned char  dim = 1)
explicit

Constructor which takes dim, the dimension of the mesh.

The mesh dimension can be changed (and may automatically be changed by mesh generation/loading) later.

Deprecated:
LIBMESH_DISABLE_COMMWORLD is now the default, use the constructor that takes a Parallel::Communicator instead.

Definition at line 53 of file parallel_mesh.h.

55  {
56  libmesh_deprecated();
57  }
unsigned int dim
DistributedMesh(const Parallel::Communicator &comm_in, unsigned char dim=1)
Constructor.
libMesh::ParallelMesh::ParallelMesh ( const UnstructuredMesh other_mesh)

Definition at line 61 of file parallel_mesh.h.

61 : DistributedMesh(other_mesh) {}
DistributedMesh(const Parallel::Communicator &comm_in, unsigned char dim=1)
Constructor.
libMesh::ParallelMesh::~ParallelMesh ( )

Definition at line 66 of file parallel_mesh.h.

66 {}

Member Function Documentation

virtual SimpleRange<element_iterator> libMesh::DistributedMesh::active_element_ptr_range ( )
virtualinherited

Implements libMesh::MeshBase.

Definition at line 301 of file distributed_mesh.h.

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

Referenced by main().

virtual element_iterator active_elements_begin() libmesh_override
Active, local, and negation forms of the element iterators described above.
virtual element_iterator active_elements_end() libmesh_override
virtual SimpleRange<const_element_iterator> libMesh::DistributedMesh::active_element_ptr_range ( ) const
virtualinherited

Implements libMesh::MeshBase.

Definition at line 302 of file distributed_mesh.h.

References libMesh::DistributedMesh::active_elements_begin(), libMesh::DistributedMesh::active_elements_end(), libMesh::DistributedMesh::active_local_elements_begin(), libMesh::DistributedMesh::active_local_elements_end(), libMesh::DistributedMesh::active_semilocal_elements_begin(), libMesh::DistributedMesh::active_semilocal_elements_end(), libMesh::DistributedMesh::ancestor_elements_begin(), libMesh::DistributedMesh::ancestor_elements_end(), libMesh::DistributedMesh::facelocal_elements_begin(), libMesh::DistributedMesh::facelocal_elements_end(), libMesh::DistributedMesh::local_elements_begin(), libMesh::DistributedMesh::local_elements_end(), libMesh::DistributedMesh::not_active_elements_begin(), libMesh::DistributedMesh::not_active_elements_end(), libMesh::DistributedMesh::not_ancestor_elements_begin(), libMesh::DistributedMesh::not_ancestor_elements_end(), libMesh::DistributedMesh::not_local_elements_begin(), libMesh::DistributedMesh::not_local_elements_end(), libMesh::DistributedMesh::not_subactive_elements_begin(), libMesh::DistributedMesh::not_subactive_elements_end(), libMesh::DistributedMesh::semilocal_elements_begin(), libMesh::DistributedMesh::semilocal_elements_end(), libMesh::DistributedMesh::subactive_elements_begin(), and libMesh::DistributedMesh::subactive_elements_end().

virtual element_iterator active_elements_begin() libmesh_override
Active, local, and negation forms of the element iterators described above.
virtual element_iterator active_elements_end() libmesh_override
virtual element_iterator libMesh::DistributedMesh::active_elements_begin ( )
virtualinherited

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::DistributedMesh::active_element_ptr_range(), construct_mesh_of_active_elements(), and libMesh::DistributedMesh::element_ptr_range().

virtual const_element_iterator libMesh::DistributedMesh::active_elements_begin ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_elements_end ( )
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_elements_end ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual SimpleRange<element_iterator> libMesh::DistributedMesh::active_local_element_ptr_range ( )
virtualinherited
virtual SimpleRange<const_element_iterator> libMesh::DistributedMesh::active_local_element_ptr_range ( ) const
virtualinherited

Implements libMesh::MeshBase.

Definition at line 359 of file distributed_mesh.h.

References libMesh::DistributedMesh::active_local_elements_begin(), libMesh::DistributedMesh::active_local_elements_end(), libMesh::DistributedMesh::active_local_subdomain_elements_begin(), libMesh::DistributedMesh::active_local_subdomain_elements_end(), libMesh::DistributedMesh::active_not_local_elements_begin(), libMesh::DistributedMesh::active_not_local_elements_end(), libMesh::DistributedMesh::active_pid_elements_begin(), libMesh::DistributedMesh::active_pid_elements_end(), libMesh::DistributedMesh::active_subdomain_elements_begin(), libMesh::DistributedMesh::active_subdomain_elements_end(), libMesh::DistributedMesh::active_subdomain_set_elements_begin(), libMesh::DistributedMesh::active_subdomain_set_elements_end(), libMesh::DistributedMesh::active_type_elements_begin(), libMesh::DistributedMesh::active_type_elements_end(), libMesh::DistributedMesh::active_unpartitioned_elements_begin(), libMesh::DistributedMesh::active_unpartitioned_elements_end(), libMesh::DistributedMesh::evaluable_elements_begin(), libMesh::DistributedMesh::evaluable_elements_end(), libMesh::DistributedMesh::flagged_elements_begin(), libMesh::DistributedMesh::flagged_elements_end(), libMesh::DistributedMesh::flagged_pid_elements_begin(), libMesh::DistributedMesh::flagged_pid_elements_end(), libMesh::DistributedMesh::ghost_elements_begin(), libMesh::DistributedMesh::ghost_elements_end(), libMesh::invalid_uint, libMesh::DistributedMesh::level_elements_begin(), libMesh::DistributedMesh::level_elements_end(), libMesh::DistributedMesh::local_level_elements_begin(), libMesh::DistributedMesh::local_level_elements_end(), libMesh::DistributedMesh::local_not_level_elements_begin(), libMesh::DistributedMesh::local_not_level_elements_end(), libMesh::DistributedMesh::nodes_begin(), libMesh::DistributedMesh::nodes_end(), libMesh::DistributedMesh::not_level_elements_begin(), libMesh::DistributedMesh::not_level_elements_end(), libMesh::DistributedMesh::pid_elements_begin(), libMesh::DistributedMesh::pid_elements_end(), libMesh::DistributedMesh::type_elements_begin(), libMesh::DistributedMesh::type_elements_end(), libMesh::DistributedMesh::unpartitioned_elements_begin(), and libMesh::DistributedMesh::unpartitioned_elements_end().

virtual element_iterator active_local_elements_begin() libmesh_override
virtual element_iterator active_local_elements_end() libmesh_override
virtual element_iterator libMesh::DistributedMesh::active_local_elements_begin ( )
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_local_elements_begin ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_local_elements_end ( )
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_local_elements_end ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_local_subdomain_elements_begin ( subdomain_id_type  subdomain_id)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_local_subdomain_elements_begin ( subdomain_id_type  subdomain_id) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_local_subdomain_elements_end ( subdomain_id_type  subdomain_id)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_local_subdomain_elements_end ( subdomain_id_type  subdomain_id) const
virtualinherited

Implements libMesh::MeshBase.

virtual node_iterator libMesh::DistributedMesh::active_nodes_begin ( )
virtualinherited

Iterate over only the active nodes in the Mesh.

Implements libMesh::MeshBase.

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

virtual const_node_iterator libMesh::DistributedMesh::active_nodes_begin ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual node_iterator libMesh::DistributedMesh::active_nodes_end ( )
virtualinherited
virtual const_node_iterator libMesh::DistributedMesh::active_nodes_end ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_not_local_elements_begin ( )
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_not_local_elements_begin ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_not_local_elements_end ( )
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_not_local_elements_end ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_pid_elements_begin ( processor_id_type  proc_id)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_pid_elements_begin ( processor_id_type  proc_id) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_pid_elements_end ( processor_id_type  proc_id)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_pid_elements_end ( processor_id_type  proc_id) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_semilocal_elements_begin ( )
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_semilocal_elements_begin ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_semilocal_elements_end ( )
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_semilocal_elements_end ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_subdomain_elements_begin ( subdomain_id_type  subdomain_id)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_subdomain_elements_begin ( subdomain_id_type  subdomain_id) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_subdomain_elements_end ( subdomain_id_type  subdomain_id)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_subdomain_elements_end ( subdomain_id_type  subdomain_id) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_subdomain_set_elements_begin ( std::set< subdomain_id_type ss)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_subdomain_set_elements_begin ( std::set< subdomain_id_type ss) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_subdomain_set_elements_end ( std::set< subdomain_id_type ss)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_subdomain_set_elements_end ( std::set< subdomain_id_type ss) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_type_elements_begin ( ElemType  type)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_type_elements_begin ( ElemType  type) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_type_elements_end ( ElemType  type)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_type_elements_end ( ElemType  type) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_unpartitioned_elements_begin ( )
virtualinherited

Iterate over active unpartitioned elements in the Mesh.

Implements libMesh::MeshBase.

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

virtual const_element_iterator libMesh::DistributedMesh::active_unpartitioned_elements_begin ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::active_unpartitioned_elements_end ( )
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::active_unpartitioned_elements_end ( ) const
virtualinherited

Implements libMesh::MeshBase.

Elem * libMesh::DistributedMesh::add_elem ( Elem e)
virtualinherited

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 411 of file distributed_mesh.C.

References libMesh::DistributedMesh::_elements, libMesh::DistributedMesh::_max_elem_id, libMesh::DistributedMesh::_n_elem, libMesh::DistributedMesh::_next_free_local_elem_id, libMesh::DistributedMesh::_next_free_unpartitioned_elem_id, libMesh::MeshBase::_next_unique_id, libMesh::DistributedMesh::_next_unpartitioned_unique_id, libMesh::DofObject::id(), libMesh::DofObject::invalid_processor_id, libMesh::libmesh_assert(), std::max(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), libMesh::DofObject::processor_id(), libMesh::DofObject::set_id(), libMesh::DofObject::set_unique_id(), libMesh::DofObject::valid_id(), and libMesh::DofObject::valid_unique_id().

Referenced by libMesh::DistributedMesh::add_extra_ghost_elem(), SlitMeshTest::build_mesh(), libMesh::DistributedMesh::reserve_elem(), and BoundaryInfoTest::testShellFaceConstraints().

412 {
413  // Don't try to add NULLs!
414  libmesh_assert(e);
415 
416  // Trying to add an existing element is a no-op
417  if (e->valid_id() && _elements[e->id()] == e)
418  return e;
419 
420  const processor_id_type elem_procid = e->processor_id();
421 
422  if (!e->valid_id())
423  {
424  // We should only be creating new ids past the end of the range
425  // of existing ids
426  libmesh_assert_greater_equal(_next_free_unpartitioned_elem_id,
427  _max_elem_id);
428  libmesh_assert_greater_equal(_next_free_local_elem_id, _max_elem_id);
429 
430  // Use the unpartitioned ids for unpartitioned elems, and
431  // temporarily for ghost elems
433  if (elem_procid == this->processor_id())
434  next_id = &_next_free_local_elem_id;
435  e->set_id (*next_id);
436  }
437 
438  {
439  // Advance next_ids up high enough that each is pointing to an
440  // unused id and any subsequent increments will still point us
441  // to unused ids
443  static_cast<dof_id_type>(e->id()+1));
444 
447  ((_max_elem_id-1) / (this->n_processors() + 1) + 1) *
448  (this->n_processors() + 1) + this->n_processors();
451  ((_max_elem_id + this->n_processors() - 1) / (this->n_processors() + 1) + 1) *
452  (this->n_processors() + 1) + this->processor_id();
453 
454 #ifndef NDEBUG
455  // We need a const mapvector so we don't inadvertently create
456  // NULL entries when testing for non-NULL ones
457  const mapvector<Elem *, dof_id_type> & const_elements = _elements;
458 #endif
460  libmesh_assert(!const_elements[_next_free_local_elem_id]);
461  }
462 
463  // Don't try to overwrite existing elems
464  libmesh_assert (!_elements[e->id()]);
465 
466  _elements[e->id()] = e;
467 
468  // Try to make the cached elem data more accurate
469  if (elem_procid == this->processor_id() ||
470  elem_procid == DofObject::invalid_processor_id)
471  _n_elem++;
472 
473 #ifdef LIBMESH_ENABLE_UNIQUE_ID
474  if (!e->valid_unique_id())
475  {
476  if (processor_id() == e->processor_id())
477  {
478  e->set_unique_id() = _next_unique_id;
479  _next_unique_id += this->n_processors() + 1;
480  }
481  else
482  {
483  e->set_unique_id() = _next_unpartitioned_unique_id;
485  }
486  }
487 #endif
488 
489  // Unpartitioned elems should be added on every processor
490  // And shouldn't be added in the same batch as ghost elems
491  // But we might be just adding on processor 0 to
492  // broadcast later
493  // #ifdef DEBUG
494  // if (elem_procid == DofObject::invalid_processor_id)
495  // {
496  // dof_id_type elem_id = e->id();
497  // this->comm().max(elem_id);
498  // libmesh_assert_equal_to (elem_id, e->id());
499  // }
500  // #endif
501 
502  return e;
503 }
mapvector< Elem *, dof_id_type > _elements
The elements in the mesh.
processor_id_type n_processors() const
uint8_t processor_id_type
Definition: id_types.h:99
long double max(long double a, double b)
libmesh_assert(j)
unique_id_type _next_unique_id
The next available unique id for assigning ids to DOF objects.
Definition: mesh_base.h:1376
static const processor_id_type invalid_processor_id
An invalid processor_id to distinguish DoFs that have not been assigned to a processor.
Definition: dof_object.h:335
dof_id_type _next_free_unpartitioned_elem_id
unique_id_type _next_unpartitioned_unique_id
The next available unique id for assigning ids to unpartitioned DOF objects.
dof_id_type _next_free_local_elem_id
processor_id_type processor_id() const
uint8_t dof_id_type
Definition: id_types.h:64
void libMesh::DistributedMesh::add_extra_ghost_elem ( Elem e)
virtualinherited

Inserts the element and adds it to a list of elements that should not get deleted or have their descendants deleted by delete_remote_elements.

This is handy for inserting otherwise off-processor elements that you want to keep track of on this processor.

Definition at line 1425 of file distributed_mesh.C.

References libMesh::DistributedMesh::_extra_ghost_elems, and libMesh::DistributedMesh::add_elem().

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

1426 {
1427  // First add the elem like normal
1428  add_elem(e);
1429 
1430  // Now add it to the set that won't be deleted when we call
1431  // delete_remote_elements()
1432  _extra_ghost_elems.insert(e);
1433 }
std::set< Elem * > _extra_ghost_elems
These are extra ghost elements that we want to make sure not to delete when we call delete_remote_ele...
virtual Elem * add_elem(Elem *e) libmesh_override
Add elem e to the end of the element array.
void libMesh::MeshBase::add_ghosting_functor ( GhostingFunctor ghosting_functor)
inherited

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 786 of file mesh_base.h.

References libMesh::MeshBase::_ghosting_functors, and libMesh::MeshBase::remove_ghosting_functor().

Referenced by libMesh::DofMap::add_algebraic_ghosting_functor(), and libMesh::DofMap::add_coupling_functor().

787  { _ghosting_functors.insert(&ghosting_functor); }
std::set< GhostingFunctor * > _ghosting_functors
The list of all GhostingFunctor objects to be used when distributing a DistributedMesh.
Definition: mesh_base.h:1433
Node * libMesh::DistributedMesh::add_node ( Node n)
virtualinherited

Add Node n to the end of the vertex array.

Implements libMesh::MeshBase.

Definition at line 608 of file distributed_mesh.C.

References libMesh::DistributedMesh::_max_node_id, libMesh::DistributedMesh::_n_nodes, libMesh::DistributedMesh::_next_free_local_node_id, libMesh::DistributedMesh::_next_free_unpartitioned_node_id, libMesh::MeshBase::_next_unique_id, libMesh::DistributedMesh::_next_unpartitioned_unique_id, libMesh::DistributedMesh::_nodes, libMesh::DofObject::id(), libMesh::DofObject::invalid_processor_id, libMesh::libmesh_assert(), std::max(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), libMesh::DofObject::processor_id(), libMesh::DofObject::set_id(), libMesh::DofObject::set_unique_id(), libMesh::DofObject::valid_id(), and libMesh::DofObject::valid_unique_id().

Referenced by libMesh::DistributedMesh::add_point(), libMesh::DistributedMesh::insert_node(), and libMesh::DistributedMesh::reserve_elem().

609 {
610  // Don't try to add NULLs!
611  libmesh_assert(n);
612 
613  // Trying to add an existing node is a no-op
614  if (n->valid_id() && _nodes[n->id()] == n)
615  return n;
616 
617  const processor_id_type node_procid = n->processor_id();
618 
619  if (!n->valid_id())
620  {
621  // We should only be creating new ids past the end of the range
622  // of existing ids
623  libmesh_assert_greater_equal(_next_free_unpartitioned_node_id,
624  _max_node_id);
625  libmesh_assert_greater_equal(_next_free_local_node_id, _max_node_id);
626 
627  // Use the unpartitioned ids for unpartitioned nodes,
628  // and temporarily for ghost nodes
630  if (node_procid == this->processor_id())
631  next_id = &_next_free_local_node_id;
632  n->set_id (*next_id);
633  }
634 
635  {
636  // Advance next_ids up high enough that each is pointing to an
637  // unused id and any subsequent increments will still point us
638  // to unused ids
640  static_cast<dof_id_type>(n->id()+1));
641 
644  ((_max_node_id-1) / (this->n_processors() + 1) + 1) *
645  (this->n_processors() + 1) + this->n_processors();
648  ((_max_node_id + this->n_processors() - 1) / (this->n_processors() + 1) + 1) *
649  (this->n_processors() + 1) + this->processor_id();
650 
651 #ifndef NDEBUG
652  // We need a const mapvector so we don't inadvertently create
653  // NULL entries when testing for non-NULL ones
654  const mapvector<Node *,dof_id_type> & const_nodes = _nodes;
655 #endif
658  }
659 
660  // Don't try to overwrite existing nodes
661  libmesh_assert (!_nodes[n->id()]);
662 
663  _nodes[n->id()] = n;
664 
665  // Try to make the cached node data more accurate
666  if (node_procid == this->processor_id() ||
667  node_procid == DofObject::invalid_processor_id)
668  _n_nodes++;
669 
670 #ifdef LIBMESH_ENABLE_UNIQUE_ID
671  if (!n->valid_unique_id())
672  {
673  if (processor_id() == n->processor_id())
674  {
675  n->set_unique_id() = _next_unique_id;
676  _next_unique_id += this->n_processors();
677  }
678  else
679  {
680  n->set_unique_id() = _next_unpartitioned_unique_id;
682  }
683  }
684 #endif
685 
686 
687  // Unpartitioned nodes should be added on every processor
688  // And shouldn't be added in the same batch as ghost nodes
689  // But we might be just adding on processor 0 to
690  // broadcast later
691  // #ifdef DEBUG
692  // if (node_procid == DofObject::invalid_processor_id)
693  // {
694  // dof_id_type node_id = n->id();
695  // this->comm().max(node_id);
696  // libmesh_assert_equal_to (node_id, n->id());
697  // }
698  // #endif
699 
700  return n;
701 }
dof_id_type _n_nodes
Cached data from the last renumber_nodes_and_elements call.
dof_id_type _next_free_local_node_id
Guaranteed globally unused IDs for use when adding new nodes or elements.
processor_id_type n_processors() const
uint8_t processor_id_type
Definition: id_types.h:99
long double max(long double a, double b)
libmesh_assert(j)
unique_id_type _next_unique_id
The next available unique id for assigning ids to DOF objects.
Definition: mesh_base.h:1376
mapvector< Node *, dof_id_type > _nodes
The vertices (spatial coordinates) of the mesh.
static const processor_id_type invalid_processor_id
An invalid processor_id to distinguish DoFs that have not been assigned to a processor.
Definition: dof_object.h:335
dof_id_type _next_free_unpartitioned_node_id
unique_id_type _next_unpartitioned_unique_id
The next available unique id for assigning ids to unpartitioned DOF objects.
processor_id_type processor_id() const
uint8_t dof_id_type
Definition: id_types.h:64
Node * libMesh::DistributedMesh::add_point ( const Point p,
const dof_id_type  id = DofObject::invalid_id,
const processor_id_type  proc_id = DofObject::invalid_processor_id 
)
virtualinherited

functions for adding /deleting nodes elements.

Implements libMesh::MeshBase.

Definition at line 584 of file distributed_mesh.C.

References libMesh::DistributedMesh::_nodes, libMesh::DistributedMesh::add_node(), libMesh::Node::build(), libMesh::DofObject::id(), libMesh::libmesh_assert(), and libMesh::DofObject::processor_id().

Referenced by SlitMeshTest::build_mesh(), libMesh::DistributedMesh::reserve_elem(), BoundaryInfoTest::testShellFaceConstraints(), and triangulate_domain().

587 {
588  if (_nodes.count(id))
589  {
590  Node * n = _nodes[id];
591  libmesh_assert (n);
592  libmesh_assert_equal_to (n->id(), id);
593 
594  *n = p;
595  n->processor_id() = proc_id;
596 
597  return n;
598  }
599 
600  Node * n = Node::build(p, id).release();
601  n->processor_id() = proc_id;
602 
603  return DistributedMesh::add_node(n);
604 }
static UniquePtr< Node > build(const Node &n)
Definition: node.h:298
libmesh_assert(j)
virtual Node * add_node(Node *n) libmesh_override
Add Node n to the end of the vertex array.
mapvector< Node *, dof_id_type > _nodes
The vertices (spatial coordinates) of the mesh.
void libMesh::UnstructuredMesh::all_first_order ( )
virtualinherited

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.

Loop over the high-ordered elements. First make sure they are indeed high-order, and then replace them with an equivalent first-order element.

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 283 of file mesh_modification.C.

References libMesh::MeshBase::_is_prepared, libMesh::Elem::add_child(), libMesh::Elem::build(), libMesh::Elem::child_ptr(), libMesh::BoundaryInfo::copy_boundary_ids(), libMesh::MeshBase::delete_node(), libMesh::MeshBase::elements_begin(), libMesh::MeshBase::elements_end(), libMesh::Elem::first_order_equivalent_type(), libMesh::MeshBase::get_boundary_info(), libMesh::Elem::has_children(), libMesh::DofObject::id(), libMesh::MeshBase::insert_elem(), libMesh::libmesh_assert(), libMesh::MeshBase::max_node_id(), libMesh::Elem::n_children(), libMesh::Elem::n_sides(), libMesh::Elem::n_vertices(), libMesh::Elem::neighbor_ptr(), libMesh::Elem::node_id(), libMesh::Elem::node_ptr(), libMesh::MeshBase::nodes_begin(), libMesh::MeshBase::nodes_end(), libMesh::Elem::p_level(), libMesh::Elem::p_refinement_flag(), libMesh::Elem::parent(), libMesh::MeshBase::prepare_for_use(), libMesh::DofObject::processor_id(), libMesh::Elem::refinement_flag(), libMesh::BoundaryInfo::regenerate_id_sets(), libMesh::remote_elem, libMesh::MeshBase::renumber_nodes_and_elements(), libMesh::Elem::replace_child(), libMesh::DofObject::set_id(), libMesh::Elem::set_neighbor(), libMesh::Elem::set_node(), libMesh::Partitioner::set_node_processor_ids(), libMesh::Elem::set_p_level(), libMesh::Elem::set_p_refinement_flag(), libMesh::Elem::set_parent(), libMesh::Elem::set_refinement_flag(), libMesh::DofObject::set_unique_id(), libMesh::Elem::subdomain_id(), libMesh::Elem::type(), libMesh::DofObject::unique_id(), and libMesh::Elem::which_child_am_i().

Referenced by main().

284 {
285  /*
286  * when the mesh is not prepared,
287  * at least renumber the nodes and
288  * elements, so that the node ids
289  * are correct
290  */
291  if (!this->_is_prepared)
293 
294  START_LOG("all_first_order()", "Mesh");
295 
299  std::vector<bool> node_touched_by_me(this->max_node_id(), false);
300 
306  element_iterator endit = elements_end();
307  for (element_iterator it = elements_begin();
308  it != endit; ++it)
309  {
310  Elem * so_elem = *it;
311 
312  libmesh_assert(so_elem);
313 
314  /*
315  * build the first-order equivalent, add to
316  * the new_elements list.
317  */
318  Elem * lo_elem = Elem::build
320  (so_elem->type()), so_elem->parent()).release();
321 
322  const unsigned short n_sides = so_elem->n_sides();
323 
324  for (unsigned short s=0; s != n_sides; ++s)
325  if (so_elem->neighbor_ptr(s) == remote_elem)
326  lo_elem->set_neighbor(s, const_cast<RemoteElem *>(remote_elem));
327 
328 #ifdef LIBMESH_ENABLE_AMR
329  /*
330  * Reset the parent links of any child elements
331  */
332  if (so_elem->has_children())
333  for (unsigned int c = 0, nc = so_elem->n_children(); c != nc; ++c)
334  {
335  Elem * child = so_elem->child_ptr(c);
336  child->set_parent(lo_elem);
337  lo_elem->add_child(child, c);
338  }
339 
340  /*
341  * Reset the child link of any parent element
342  */
343  if (so_elem->parent())
344  {
345  unsigned int c =
346  so_elem->parent()->which_child_am_i(so_elem);
347  lo_elem->parent()->replace_child(lo_elem, c);
348  }
349 
350  /*
351  * Copy as much data to the new element as makes sense
352  */
353  lo_elem->set_p_level(so_elem->p_level());
354  lo_elem->set_refinement_flag(so_elem->refinement_flag());
355  lo_elem->set_p_refinement_flag(so_elem->p_refinement_flag());
356 #endif
357 
358  libmesh_assert_equal_to (lo_elem->n_vertices(), so_elem->n_vertices());
359 
360  /*
361  * By definition the vertices of the linear and
362  * second order element are identically numbered.
363  * transfer these.
364  */
365  for (unsigned int v=0; v < so_elem->n_vertices(); v++)
366  {
367  lo_elem->set_node(v) = so_elem->node_ptr(v);
368  node_touched_by_me[lo_elem->node_id(v)] = true;
369  }
370 
371  /*
372  * find_neighbors relies on remote_elem neighbor links being
373  * properly maintained.
374  */
375  for (unsigned short s=0; s != n_sides; s++)
376  {
377  if (so_elem->neighbor_ptr(s) == remote_elem)
378  lo_elem->set_neighbor(s, const_cast<RemoteElem*>(remote_elem));
379  }
380 
388  (this->get_boundary_info(), so_elem, lo_elem);
389 
390  /*
391  * The new first-order element is ready.
392  * Inserting it into the mesh will replace and delete
393  * the second-order element.
394  */
395  lo_elem->set_id(so_elem->id());
396 #ifdef LIBMESH_ENABLE_UNIQUE_ID
397  lo_elem->set_unique_id() = so_elem->unique_id();
398 #endif
399  lo_elem->processor_id() = so_elem->processor_id();
400  lo_elem->subdomain_id() = so_elem->subdomain_id();
401  this->insert_elem(lo_elem);
402  }
403 
404  const MeshBase::node_iterator nd_end = this->nodes_end();
405  MeshBase::node_iterator nd = this->nodes_begin();
406  while (nd != nd_end)
407  {
408  Node * the_node = *nd;
409  ++nd;
410  if (!node_touched_by_me[the_node->id()])
411  this->delete_node(the_node);
412  }
413 
414  // If crazy people applied boundary info to non-vertices and then
415  // deleted those non-vertices, we should make sure their boundary id
416  // caches are correct.
418 
419  STOP_LOG("all_first_order()", "Mesh");
420 
421  // On hanging nodes that used to also be second order nodes, we
422  // might now have an invalid nodal processor_id()
424 
425  // delete or renumber nodes if desired
426  this->prepare_for_use();
427 }
const BoundaryInfo & get_boundary_info() const
The information about boundary ids on the mesh.
Definition: mesh_base.h:117
static UniquePtr< Elem > build(const ElemType type, Elem *p=libmesh_nullptr)
Definition: elem.C:238
static void set_node_processor_ids(MeshBase &mesh)
This function is called after partitioning to set the processor IDs for the nodes.
Definition: partitioner.C:416
virtual dof_id_type max_node_id() const =0
libmesh_assert(j)
virtual node_iterator nodes_begin()=0
Iterate over all the nodes in the Mesh.
virtual element_iterator elements_begin()=0
Iterate over all the elements in the Mesh.
virtual element_iterator elements_end()=0
virtual void delete_node(Node *n)=0
Removes the Node n from the mesh.
void prepare_for_use(const bool skip_renumber_nodes_and_elements=false, const bool skip_find_neighbors=false)
Prepare a newly created (or read) mesh for use.
Definition: mesh_base.C:174
void regenerate_id_sets()
Clears and regenerates the cached sets of ids.
virtual Elem * insert_elem(Elem *e)=0
Insert elem e to the element array, preserving its id and replacing/deleting any existing element wit...
virtual node_iterator nodes_end()=0
void copy_boundary_ids(const BoundaryInfo &old_boundary_info, const Elem *const old_elem, const Elem *const new_elem)
bool _is_prepared
Flag indicating if the mesh has been prepared for use.
Definition: mesh_base.h:1347
static ElemType first_order_equivalent_type(const ElemType et)
Definition: elem.C:2724
virtual void renumber_nodes_and_elements()=0
After partitioning a mesh it is useful to renumber the nodes and elements so that they lie in contigu...
const RemoteElem * remote_elem
Definition: remote_elem.C:57
void libMesh::UnstructuredMesh::all_second_order ( const bool  full_ordered = true)
virtualinherited

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.

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 431 of file mesh_modification.C.

References libMesh::MeshBase::_is_prepared, libMesh::MeshBase::add_point(), libMesh::Elem::build(), libMesh::ParallelObject::comm(), libMesh::BoundaryInfo::copy_boundary_ids(), libMesh::Elem::default_order(), libMesh::MeshBase::elements_begin(), libMesh::MeshBase::elements_end(), libMesh::FIRST, libMesh::MeshBase::get_boundary_info(), libMesh::DofObject::id(), libMesh::MeshBase::insert_elem(), libMesh::DofObject::invalid_id, libMesh::MeshBase::is_serial(), libMesh::Elem::level(), libMesh::libmesh_assert(), libMesh::MeshCommunication::make_nodes_parallel_consistent(), libMesh::Parallel::Communicator::max(), libMesh::MeshBase::mesh_dimension(), libMesh::MeshBase::n_elem(), libMesh::MeshBase::n_nodes(), libMesh::Elem::n_vertices(), libMesh::Elem::neighbor_ptr(), libMesh::Elem::node_ptr(), libMesh::MeshBase::point(), libMesh::MeshBase::prepare_for_use(), libMesh::DofObject::processor_id(), libMesh::Real, libMesh::remote_elem, libMesh::MeshBase::renumber_nodes_and_elements(), libMesh::MeshBase::reserve_nodes(), libMesh::Elem::second_order_equivalent_type(), libMesh::Elem::side_index_range(), libMesh::Elem::subdomain_id(), libMesh::Elem::type(), and libMesh::DofObject::unique_id().

Referenced by libMesh::MeshTools::Generation::build_cube(), libMesh::MeshTools::Generation::build_sphere(), and main().

432 {
433  // This function must be run on all processors at once
434  parallel_object_only();
435 
436  /*
437  * when the mesh is not prepared,
438  * at least renumber the nodes and
439  * elements, so that the node ids
440  * are correct
441  */
442  if (!this->_is_prepared)
444 
445  /*
446  * If the mesh is empty
447  * then we have nothing to do
448  */
449  if (!this->n_elem())
450  return;
451 
452  /*
453  * If the mesh is already second order
454  * then we have nothing to do.
455  * We have to test for this in a round-about way to avoid
456  * a bug on distributed parallel meshes with more processors
457  * than elements.
458  */
459  bool already_second_order = false;
460  if (this->elements_begin() != this->elements_end() &&
461  (*(this->elements_begin()))->default_order() != FIRST)
462  already_second_order = true;
463  this->comm().max(already_second_order);
464  if (already_second_order)
465  return;
466 
467  START_LOG("all_second_order()", "Mesh");
468 
469  /*
470  * this map helps in identifying second order
471  * nodes. Namely, a second-order node:
472  * - edge node
473  * - face node
474  * - bubble node
475  * is uniquely defined through a set of adjacent
476  * vertices. This set of adjacent vertices is
477  * used to identify already added higher-order
478  * nodes. We are safe to use node id's since we
479  * make sure that these are correctly numbered.
480  */
481  std::map<std::vector<dof_id_type>, Node *> adj_vertices_to_so_nodes;
482 
483  /*
484  * for speed-up of the \p add_point() method, we
485  * can reserve memory. Guess the number of additional
486  * nodes for different dimensions
487  */
488  switch (this->mesh_dimension())
489  {
490  case 1:
491  /*
492  * in 1D, there can only be order-increase from Edge2
493  * to Edge3. Something like 1/2 of n_nodes() have
494  * to be added
495  */
496  this->reserve_nodes(static_cast<unsigned int>
497  (1.5*static_cast<double>(this->n_nodes())));
498  break;
499 
500  case 2:
501  /*
502  * in 2D, either refine from Tri3 to Tri6 (double the nodes)
503  * or from Quad4 to Quad8 (again, double) or Quad9 (2.25 that much)
504  */
505  this->reserve_nodes(static_cast<unsigned int>
506  (2*static_cast<double>(this->n_nodes())));
507  break;
508 
509 
510  case 3:
511  /*
512  * in 3D, either refine from Tet4 to Tet10 (factor = 2.5) up to
513  * Hex8 to Hex27 (something > 3). Since in 3D there _are_ already
514  * quite some nodes, and since we do not want to overburden the memory by
515  * a too conservative guess, use the lower bound
516  */
517  this->reserve_nodes(static_cast<unsigned int>
518  (2.5*static_cast<double>(this->n_nodes())));
519  break;
520 
521  default:
522  // Hm?
523  libmesh_error_msg("Unknown mesh dimension " << this->mesh_dimension());
524  }
525 
526 
527 
528  /*
529  * form a vector that will hold the node id's of
530  * the vertices that are adjacent to the son-th
531  * second-order node. Pull this outside of the
532  * loop so that silly compilers don't repeatedly
533  * create and destroy the vector.
534  */
535  std::vector<dof_id_type> adjacent_vertices_ids;
536 
543  element_iterator
544  it = elements_begin(),
545  endit = elements_end();
546 
547  for (; it != endit; ++it)
548  {
549  // the linear-order element
550  Elem * lo_elem = *it;
551 
552  libmesh_assert(lo_elem);
553 
554  // make sure it is linear order
555  if (lo_elem->default_order() != FIRST)
556  libmesh_error_msg("ERROR: This is not a linear element: type=" << lo_elem->type());
557 
558  // this does _not_ work for refined elements
559  libmesh_assert_equal_to (lo_elem->level (), 0);
560 
561  /*
562  * build the second-order equivalent, add to
563  * the new_elements list. Note that this here
564  * is the only point where \p full_ordered
565  * is necessary. The remaining code works well
566  * for either type of second-order equivalent, e.g.
567  * Hex20 or Hex27, as equivalents for Hex8
568  */
569  Elem * so_elem =
571  full_ordered) ).release();
572 
573  libmesh_assert_equal_to (lo_elem->n_vertices(), so_elem->n_vertices());
574 
575 
576  /*
577  * By definition the vertices of the linear and
578  * second order element are identically numbered.
579  * transfer these.
580  */
581  for (unsigned int v=0; v < lo_elem->n_vertices(); v++)
582  so_elem->set_node(v) = lo_elem->node_ptr(v);
583 
584  /*
585  * Now handle the additional mid-side nodes. This
586  * is simply handled through a map that remembers
587  * the already-added nodes. This map maps the global
588  * ids of the vertices (that uniquely define this
589  * higher-order node) to the new node.
590  * Notation: son = second-order node
591  */
592  const unsigned int son_begin = so_elem->n_vertices();
593  const unsigned int son_end = so_elem->n_nodes();
594 
595 
596  for (unsigned int son=son_begin; son<son_end; son++)
597  {
598  const unsigned int n_adjacent_vertices =
599  so_elem->n_second_order_adjacent_vertices(son);
600 
601  adjacent_vertices_ids.resize(n_adjacent_vertices);
602 
603  for (unsigned int v=0; v<n_adjacent_vertices; v++)
604  adjacent_vertices_ids[v] =
605  so_elem->node_id( so_elem->second_order_adjacent_vertex(son,v) );
606 
607  /*
608  * \p adjacent_vertices_ids is now in order of the current
609  * side. sort it, so that comparisons with the
610  * \p adjacent_vertices_ids created through other elements'
611  * sides can match
612  */
613  std::sort(adjacent_vertices_ids.begin(),
614  adjacent_vertices_ids.end());
615 
616 
617  // does this set of vertices already has a mid-node added?
618  std::pair<std::map<std::vector<dof_id_type>, Node *>::iterator,
619  std::map<std::vector<dof_id_type>, Node *>::iterator>
620  pos = adj_vertices_to_so_nodes.equal_range (adjacent_vertices_ids);
621 
622  // no, not added yet
623  if (pos.first == pos.second)
624  {
625  /*
626  * for this set of vertices, there is no
627  * second_order node yet. Add it.
628  *
629  * compute the location of the new node as
630  * the average over the adjacent vertices.
631  */
632  Point new_location = this->point(adjacent_vertices_ids[0]);
633  for (unsigned int v=1; v<n_adjacent_vertices; v++)
634  new_location += this->point(adjacent_vertices_ids[v]);
635 
636  new_location /= static_cast<Real>(n_adjacent_vertices);
637 
638  /* Add the new point to the mesh.
639  * If we are on a serialized mesh, then we're doing this
640  * all in sync, and the node processor_id will be
641  * consistent between processors.
642  * If we are on a distributed mesh, we can fix
643  * inconsistent processor ids later, but only if every
644  * processor gives new nodes a *locally* consistent
645  * processor id, so we'll give the new node the
646  * processor id of an adjacent element for now and then
647  * we'll update that later if appropriate.
648  */
649  Node * so_node = this->add_point
650  (new_location, DofObject::invalid_id,
651  lo_elem->processor_id());
652 
653  /*
654  * insert the new node with its defining vertex
655  * set into the map, and relocate pos to this
656  * new entry, so that the so_elem can use
657  * \p pos for inserting the node
658  */
659  adj_vertices_to_so_nodes.insert(pos.first,
660  std::make_pair(adjacent_vertices_ids,
661  so_node));
662 
663  so_elem->set_node(son) = so_node;
664  }
665  // yes, already added.
666  else
667  {
668  Node * so_node = pos.first->second;
669  libmesh_assert(so_node);
670 
671  so_elem->set_node(son) = so_node;
672 
673  // We need to ensure that the processor who should own a
674  // node *knows* they own the node.
675  if (so_node->processor_id() > lo_elem->processor_id())
676  so_node->processor_id() = lo_elem->processor_id();
677  }
678  }
679 
680  /*
681  * find_neighbors relies on remote_elem neighbor links being
682  * properly maintained.
683  */
684  for (auto s : lo_elem->side_index_range())
685  {
686  if (lo_elem->neighbor_ptr(s) == remote_elem)
687  so_elem->set_neighbor(s, const_cast<RemoteElem*>(remote_elem));
688  }
689 
702  (this->get_boundary_info(), lo_elem, so_elem);
703 
704  /*
705  * The new second-order element is ready.
706  * Inserting it into the mesh will replace and delete
707  * the first-order element.
708  */
709  so_elem->set_id(lo_elem->id());
710 #ifdef LIBMESH_ENABLE_UNIQUE_ID
711  so_elem->set_unique_id() = lo_elem->unique_id();
712 #endif
713  so_elem->processor_id() = lo_elem->processor_id();
714  so_elem->subdomain_id() = lo_elem->subdomain_id();
715  this->insert_elem(so_elem);
716  }
717 
718  // we can clear the map
719  adj_vertices_to_so_nodes.clear();
720 
721 
722  STOP_LOG("all_second_order()", "Mesh");
723 
724  // In a DistributedMesh our ghost node processor ids may be bad,
725  // the ids of nodes touching remote elements may be inconsistent,
726  // and unique_ids of newly added non-local nodes remain unset.
727  // make_nodes_parallel_consistent() will fix all this.
728  if (!this->is_serial())
729  MeshCommunication().make_nodes_parallel_consistent (*this);
730 
731  // renumber nodes, elements etc
732  this->prepare_for_use(/*skip_renumber =*/ false);
733 }
const BoundaryInfo & get_boundary_info() const
The information about boundary ids on the mesh.
Definition: mesh_base.h:117
virtual void reserve_nodes(const dof_id_type nn)=0
Reserves space for a known number of nodes.
virtual bool is_serial() const
Definition: mesh_base.h:140
virtual const Point & point(const dof_id_type i) const =0
static UniquePtr< Elem > build(const ElemType type, Elem *p=libmesh_nullptr)
Definition: elem.C:238
void max(T &r) const
Take a local variable and replace it with the maximum of it&#39;s values on all processors.
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)=0
Add a new Node at Point p to the end of the vertex array, with processor_id procid.
libmesh_assert(j)
virtual element_iterator elements_begin()=0
Iterate over all the elements in the Mesh.
virtual element_iterator elements_end()=0
static const dof_id_type invalid_id
An invalid id to distinguish an uninitialized DofObject.
Definition: dof_object.h:324
void prepare_for_use(const bool skip_renumber_nodes_and_elements=false, const bool skip_find_neighbors=false)
Prepare a newly created (or read) mesh for use.
Definition: mesh_base.C:174
static ElemType second_order_equivalent_type(const ElemType et, const bool full_ordered=true)
Definition: elem.C:2783
virtual Elem * insert_elem(Elem *e)=0
Insert elem e to the element array, preserving its id and replacing/deleting any existing element wit...
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
void copy_boundary_ids(const BoundaryInfo &old_boundary_info, const Elem *const old_elem, const Elem *const new_elem)
const Parallel::Communicator & comm() const
unsigned int mesh_dimension() const
Definition: mesh_base.C:148
bool _is_prepared
Flag indicating if the mesh has been prepared for use.
Definition: mesh_base.h:1347
virtual dof_id_type n_nodes() const =0
virtual dof_id_type n_elem() const =0
virtual void renumber_nodes_and_elements()=0
After partitioning a mesh it is useful to renumber the nodes and elements so that they lie in contigu...
const RemoteElem * remote_elem
Definition: remote_elem.C:57
void libMesh::DistributedMesh::allgather ( )
virtualinherited

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

Reimplemented from libMesh::MeshBase.

Definition at line 1436 of file distributed_mesh.C.

References libMesh::DistributedMesh::_is_serial, libMesh::DistributedMesh::_is_serial_on_proc_0, libMesh::MeshCommunication::allgather(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_flags(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_ids(), libMesh::DistributedMesh::max_elem_id(), libMesh::DistributedMesh::max_node_id(), libMesh::DistributedMesh::n_elem(), libMesh::DistributedMesh::n_nodes(), libMesh::DistributedMesh::parallel_max_elem_id(), libMesh::DistributedMesh::parallel_max_node_id(), libMesh::DistributedMesh::parallel_n_elem(), and libMesh::DistributedMesh::parallel_n_nodes().

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

1437 {
1438  if (_is_serial)
1439  return;
1440  MeshCommunication().allgather(*this);
1441  _is_serial = true;
1442  _is_serial_on_proc_0 = true;
1443 
1444  // Make sure our caches are up to date and our
1445  // DofObjects are well packed
1446 #ifdef DEBUG
1447  libmesh_assert_equal_to (this->n_nodes(), this->parallel_n_nodes());
1448  libmesh_assert_equal_to (this->n_elem(), this->parallel_n_elem());
1449  const dof_id_type pmax_node_id = this->parallel_max_node_id();
1450  const dof_id_type pmax_elem_id = this->parallel_max_elem_id();
1451  libmesh_assert_equal_to (this->max_node_id(), pmax_node_id);
1452  libmesh_assert_equal_to (this->max_elem_id(), pmax_elem_id);
1453 
1454  // If we've disabled renumbering we can't be sure we're contiguous
1455  // libmesh_assert_equal_to (this->n_nodes(), this->max_node_id());
1456  // libmesh_assert_equal_to (this->n_elem(), this->max_elem_id());
1457 
1458  // Make sure our neighbor links are all fine
1460 
1461  // Make sure our ids and flags are consistent
1464 #endif
1465 }
virtual dof_id_type n_elem() const libmesh_override
bool _is_serial_on_proc_0
A boolean remembering whether we&#39;re serialized to proc 0 or not.
bool _is_serial
A boolean remembering whether we&#39;re serialized or not.
dof_id_type parallel_max_elem_id() const
void libmesh_assert_valid_parallel_flags() const
Verify refinement_flag and p_refinement_flag consistency of our elements containers.
dof_id_type parallel_max_node_id() const
virtual dof_id_type n_nodes() const libmesh_override
virtual dof_id_type max_node_id() const libmesh_override
virtual dof_id_type parallel_n_nodes() const libmesh_override
void libmesh_assert_valid_neighbors(const MeshBase &mesh, bool assert_valid_remote_elems=true)
A function for verifying that neighbor connectivity is correct (each element is a neighbor of or desc...
Definition: mesh_tools.C:1713
virtual dof_id_type parallel_n_elem() const libmesh_override
virtual dof_id_type max_elem_id() const libmesh_override
uint8_t dof_id_type
Definition: id_types.h:64
virtual void libmesh_assert_valid_parallel_ids() const libmesh_override
Verify id and processor_id consistency of our elements and nodes containers.
void libMesh::MeshBase::allow_remote_element_removal ( bool  allow)
inherited

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 758 of file mesh_base.h.

References libMesh::MeshBase::_allow_remote_element_removal.

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

bool _allow_remote_element_removal
If this is false then even on DistributedMesh remote elements will not be deleted during mesh prepara...
Definition: mesh_base.h:1397
bool libMesh::MeshBase::allow_remote_element_removal ( ) const
inherited

Definition at line 759 of file mesh_base.h.

References libMesh::MeshBase::_allow_remote_element_removal.

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

bool _allow_remote_element_removal
If this is false then even on DistributedMesh remote elements will not be deleted during mesh prepara...
Definition: mesh_base.h:1397
void libMesh::MeshBase::allow_renumbering ( bool  allow)
inherited

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.

Definition at line 749 of file mesh_base.h.

References libMesh::MeshBase::_skip_renumber_nodes_and_elements.

Referenced by SlitMeshTest::build_mesh(), libMesh::UnstructuredMesh::copy_nodes_and_elements(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ErrorVector::plot_error(), libMesh::RBEIMEvaluation::RBEIMEvaluation(), libMesh::NameBasedIO::read(), libMesh::GMVIO::read(), EquationSystemsTest::testRefineThenReinitPreserveFlags(), and WriteVecAndScalar::testWrite().

bool _skip_renumber_nodes_and_elements
If this is true then renumbering will be kept to a minimum.
Definition: mesh_base.h:1389
bool libMesh::MeshBase::allow_renumbering ( ) const
inherited

Definition at line 750 of file mesh_base.h.

References libMesh::MeshBase::_skip_renumber_nodes_and_elements.

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

bool _skip_renumber_nodes_and_elements
If this is true then renumbering will be kept to a minimum.
Definition: mesh_base.h:1389
virtual element_iterator libMesh::DistributedMesh::ancestor_elements_begin ( )
virtualinherited

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

Implements libMesh::MeshBase.

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

virtual const_element_iterator libMesh::DistributedMesh::ancestor_elements_begin ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::ancestor_elements_end ( )
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::ancestor_elements_end ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual node_iterator libMesh::DistributedMesh::bid_nodes_begin ( boundary_id_type  bndry_id)
virtualinherited

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

Implements libMesh::MeshBase.

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

virtual const_node_iterator libMesh::DistributedMesh::bid_nodes_begin ( boundary_id_type  bndry_id) const
virtualinherited

Implements libMesh::MeshBase.

virtual node_iterator libMesh::DistributedMesh::bid_nodes_end ( boundary_id_type  bndry_id)
virtualinherited
virtual const_node_iterator libMesh::DistributedMesh::bid_nodes_end ( boundary_id_type  bndry_id) const
virtualinherited

Implements libMesh::MeshBase.

virtual node_iterator libMesh::DistributedMesh::bnd_nodes_begin ( )
virtualinherited

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

Implements libMesh::MeshBase.

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

virtual const_node_iterator libMesh::DistributedMesh::bnd_nodes_begin ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual node_iterator libMesh::DistributedMesh::bnd_nodes_end ( )
virtualinherited
virtual const_node_iterator libMesh::DistributedMesh::bnd_nodes_end ( ) const
virtualinherited

Implements libMesh::MeshBase.

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 612 of file mesh_base.C.

References libMesh::MeshBase::_elem_dims, libMesh::MeshBase::_spatial_dimension, libMesh::MeshBase::active_elements_begin(), libMesh::MeshBase::active_elements_end(), libMesh::ParallelObject::comm(), end, libMesh::MeshBase::mesh_dimension(), libMesh::MeshBase::node(), libMesh::MeshBase::nodes_begin(), libMesh::MeshBase::nodes_end(), and libMesh::Parallel::Communicator::set_union().

Referenced by libMesh::MeshCommunication::broadcast(), libMesh::MeshBase::get_subdomain_name_map(), and libMesh::MeshBase::prepare_for_use().

613 {
614  // This requires an inspection on every processor
615  parallel_object_only();
616 
617  // Need to clear _elem_dims first in case all elements of a
618  // particular dimension have been deleted.
619  _elem_dims.clear();
620 
621  const_element_iterator el = this->active_elements_begin();
622  const_element_iterator end = this->active_elements_end();
623 
624  for (; el!=end; ++el)
625  _elem_dims.insert((*el)->dim());
626 
627  // Some different dimension elements may only live on other processors
628  this->comm().set_union(_elem_dims);
629 
630  // If the largest element dimension found is larger than the current
631  // _spatial_dimension, increase _spatial_dimension.
632  unsigned int max_dim = this->mesh_dimension();
633  if (max_dim > _spatial_dimension)
634  _spatial_dimension = cast_int<unsigned char>(max_dim);
635 
636  // _spatial_dimension may need to increase from 1->2 or 2->3 if the
637  // mesh is full of 1D elements but they are not x-aligned, or the
638  // mesh is full of 2D elements but they are not in the x-y plane.
639  // If the mesh is x-aligned or x-y planar, we will end up checking
640  // every node's coordinates and not breaking out of the loop
641  // early...
642  if (_spatial_dimension < 3)
643  {
644  const_node_iterator node_it = this->nodes_begin();
645  const_node_iterator node_end = this->nodes_end();
646  for (; node_it != node_end; ++node_it)
647  {
648  Node & node = **node_it;
649 
650 #if LIBMESH_DIM > 1
651  // Note: the exact floating point comparison is intentional,
652  // we don't want to get tripped up by tolerances.
653  if (node(1) != 0.)
654  {
655  _spatial_dimension = 2;
656 #if LIBMESH_DIM == 2
657  // If libmesh is compiled in 2D mode, this is the
658  // largest spatial dimension possible so we can break
659  // out.
660  break;
661 #endif
662  }
663 #endif
664 
665 #if LIBMESH_DIM > 2
666  if (node(2) != 0.)
667  {
668  // Spatial dimension can't get any higher than this, so
669  // we can break out.
670  _spatial_dimension = 3;
671  break;
672  }
673 #endif
674  }
675  }
676 }
IterBase * end
Also have a polymorphic pointer to the end object, this prevents iterating past the end...
unsigned char _spatial_dimension
The "spatial dimension" of the Mesh.
Definition: mesh_base.h:1417
virtual node_iterator nodes_begin()=0
Iterate over all the nodes in the Mesh.
std::set< unsigned char > _elem_dims
We cache the dimension of the elements present in the mesh.
Definition: mesh_base.h:1411
virtual element_iterator active_elements_begin()=0
Active, local, and negation forms of the element iterators described above.
virtual element_iterator active_elements_end()=0
virtual node_iterator nodes_end()=0
const Parallel::Communicator & comm() const
unsigned int mesh_dimension() const
Definition: mesh_base.C:148
virtual const Node & node(const dof_id_type i) const
Definition: mesh_base.h:440
void set_union(T &data, const unsigned int root_id) const
Take a container of local variables on each processor, and collect their union over all processors...
void libMesh::DistributedMesh::clear ( )
virtualinherited

Clear all internal data.

Reimplemented from libMesh::MeshBase.

Definition at line 776 of file distributed_mesh.C.

References libMesh::DistributedMesh::_elements, libMesh::DistributedMesh::_is_serial, libMesh::DistributedMesh::_is_serial_on_proc_0, libMesh::DistributedMesh::_max_elem_id, libMesh::DistributedMesh::_max_node_id, libMesh::DistributedMesh::_n_elem, libMesh::DistributedMesh::_n_nodes, libMesh::DistributedMesh::_next_free_local_elem_id, libMesh::DistributedMesh::_next_free_local_node_id, libMesh::DistributedMesh::_next_free_unpartitioned_elem_id, libMesh::DistributedMesh::_next_free_unpartitioned_node_id, libMesh::DistributedMesh::_nodes, libMesh::MeshBase::clear(), end, libMesh::ParallelObject::n_processors(), and libMesh::ParallelObject::processor_id().

Referenced by libMesh::DistributedMesh::clone(), libMesh::DistributedMesh::DistributedMesh(), and libMesh::BoundaryMesh::~BoundaryMesh().

777 {
778  // Call parent clear function
779  MeshBase::clear();
780 
781 
782  // Clear our elements and nodes
783  {
784  elem_iterator_imp it = _elements.begin();
785  const elem_iterator_imp end = _elements.end();
786 
787  // There is no need to remove the elements from
788  // the BoundaryInfo data structure since we
789  // already cleared it.
790  for (; it != end; ++it)
791  delete *it;
792 
793  _elements.clear();
794  }
795 
796  // clear the nodes data structure
797  {
798  node_iterator_imp it = _nodes.begin();
799  node_iterator_imp end = _nodes.end();
800 
801  // There is no need to remove the nodes from
802  // the BoundaryInfo data structure since we
803  // already cleared it.
804  for (; it != end; ++it)
805  delete *it;
806 
807  _nodes.clear();
808  }
809 
810  // We're no longer distributed if we were before
811  _is_serial = true;
812  _is_serial_on_proc_0 = true;
813 
814  // Correct our caches
815  _n_nodes = 0;
816  _n_elem = 0;
817  _max_node_id = 0;
818  _max_elem_id = 0;
823 }
mapvector< Elem *, dof_id_type > _elements
The elements in the mesh.
bool _is_serial_on_proc_0
A boolean remembering whether we&#39;re serialized to proc 0 or not.
dof_id_type _n_nodes
Cached data from the last renumber_nodes_and_elements call.
dof_id_type _next_free_local_node_id
Guaranteed globally unused IDs for use when adding new nodes or elements.
processor_id_type n_processors() const
bool _is_serial
A boolean remembering whether we&#39;re serialized or not.
IterBase * end
Also have a polymorphic pointer to the end object, this prevents iterating past the end...
mapvector< Node *, dof_id_type >::veclike_iterator node_iterator_imp
Typedefs for the container implementation.
mapvector< Node *, dof_id_type > _nodes
The vertices (spatial coordinates) of the mesh.
virtual void clear()
Deletes all the data that are currently stored.
Definition: mesh_base.C:285
dof_id_type _next_free_unpartitioned_node_id
dof_id_type _next_free_unpartitioned_elem_id
mapvector< Elem *, dof_id_type >::veclike_iterator elem_iterator_imp
Typedefs for the container implementation.
dof_id_type _next_free_local_elem_id
processor_id_type processor_id() const
virtual void libMesh::DistributedMesh::clear_extra_ghost_elems ( )
virtualinherited

Clears extra ghost elements.

Definition at line 220 of file distributed_mesh.h.

References libMesh::DistributedMesh::_extra_ghost_elems.

220 { _extra_ghost_elems.clear(); }
std::set< Elem * > _extra_ghost_elems
These are extra ghost elements that we want to make sure not to delete when we call delete_remote_ele...
void libMesh::MeshBase::clear_point_locator ( )
inherited
virtual UniquePtr<MeshBase> libMesh::ParallelMesh::clone ( ) const
virtual

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

Reimplemented from libMesh::DistributedMesh.

Definition at line 63 of file parallel_mesh.h.

References ParallelMesh().

64  { return UniquePtr<MeshBase>(new ParallelMesh(*this)); }
ParallelMesh(const Parallel::Communicator &comm_in, unsigned char dim=1)
Definition: parallel_mesh.h:38
const Parallel::Communicator& libMesh::ParallelObject::comm ( ) const
inherited
Returns
A reference to the Parallel::Communicator object used by this mesh.

Definition at line 87 of file parallel_object.h.

References libMesh::ParallelObject::_communicator.

Referenced by libMesh::__libmesh_petsc_diff_solver_monitor(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::__libmesh_petsc_preconditioner_apply(), libMesh::__libmesh_petsc_snes_jacobian(), libMesh::__libmesh_petsc_snes_postcheck(), libMesh::__libmesh_petsc_snes_residual(), libMesh::__libmesh_tao_equality_constraints(), libMesh::__libmesh_tao_equality_constraints_jacobian(), libMesh::__libmesh_tao_gradient(), libMesh::__libmesh_tao_hessian(), libMesh::__libmesh_tao_inequality_constraints(), libMesh::__libmesh_tao_inequality_constraints_jacobian(), libMesh::__libmesh_tao_objective(), libMesh::MeshRefinement::_coarsen_elements(), libMesh::ExactSolution::_compute_error(), libMesh::ParmetisPartitioner::_do_repartition(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::PetscLinearSolver< T >::_petsc_shell_matrix_get_diagonal(), libMesh::SlepcEigenSolver< T >::_petsc_shell_matrix_get_diagonal(), libMesh::PetscLinearSolver< T >::_petsc_shell_matrix_mult(), libMesh::SlepcEigenSolver< T >::_petsc_shell_matrix_mult(), libMesh::PetscLinearSolver< T >::_petsc_shell_matrix_mult_add(), libMesh::EquationSystems::_read_impl(), libMesh::MeshRefinement::_refine_elements(), libMesh::MeshRefinement::_smooth_flags(), add_cube_convex_hull_to_mesh(), libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::ImplicitSystem::add_matrix(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), libMesh::System::add_vector(), libMesh::EigenSparseLinearSolver< T >::adjoint_solve(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), libMesh::TransientRBConstruction::assemble_affine_expansion(), libMesh::FEMSystem::assemble_qoi(), libMesh::MeshCommunication::assign_global_indices(), libMesh::ParmetisPartitioner::assign_partitioning(), libMesh::DofMap::attach_matrix(), libMesh::Parallel::BinSorter< KeyType, IdxType >::binsort(), libMesh::Parallel::Sort< KeyType, IdxType >::binsort(), libMesh::MeshCommunication::broadcast(), libMesh::SparseMatrix< T >::build(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::Parallel::Histogram< KeyType, IdxType >::build_histogram(), libMesh::PetscNonlinearSolver< T >::build_mat_null_space(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::MeshBase::cache_elem_dims(), libMesh::System::calculate_norm(), libMesh::DofMap::check_dirichlet_bcid_consistency(), libMesh::Parallel::Sort< KeyType, IdxType >::communicate_bins(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::RBConstruction::compute_max_error_bound(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBSCMConstruction::compute_SCM_bounds_on_training_set(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::MeshTools::create_bounding_box(), libMesh::MeshTools::create_nodal_bounding_box(), libMesh::MeshRefinement::create_parent_error_vector(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::MeshTools::create_subdomain_bounding_box(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::DofMap::distribute_dofs(), DMlibMeshFunction(), DMlibMeshJacobian(), DMlibMeshSetSystem_libMesh(), DMVariableBounds_libMesh(), libMesh::MeshRefinement::eliminate_unrefined_patches(), libMesh::RBEIMConstruction::enrich_RB_space(), libMesh::TransientRBConstruction::enrich_RB_space(), libMesh::RBConstruction::enrich_RB_space(), AssembleOptimization::equality_constraints(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::RBEIMConstruction::evaluate_mesh_function(), libMesh::MeshRefinement::flag_elements_by_elem_fraction(), libMesh::MeshRefinement::flag_elements_by_error_fraction(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::MeshCommunication::gather(), libMesh::MeshCommunication::gather_neighboring_elements(), libMesh::MeshfreeInterpolation::gather_remote_data(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::DofMap::get_info(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::EquationSystems::get_solution(), AssembleOptimization::inequality_constraints(), AssembleOptimization::inequality_constraints_jacobian(), libMesh::LocationMap< T >::init(), libMesh::TopologyMap::init(), libMesh::PetscDiffSolver::init(), libMesh::TimeSolver::init(), libMesh::TaoOptimizationSolver< T >::init(), libMesh::PetscNonlinearSolver< T >::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::EigenSystem::init_data(), libMesh::EigenSystem::init_matrices(), libMesh::ParmetisPartitioner::initialize(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::RBEIMConstruction::initialize_rb_construction(), integrate_function(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_flags(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_p_levels(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::MeshTools::libmesh_assert_valid_unique_ids(), libMesh::MeshRefinement::limit_level_mismatch_at_edge(), libMesh::MeshRefinement::limit_level_mismatch_at_node(), libMesh::MeshRefinement::limit_overrefined_boundary(), libMesh::MeshRefinement::limit_underrefined_boundary(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshCommunication::make_elems_parallel_consistent(), libMesh::MeshRefinement::make_flags_parallel_consistent(), libMesh::MeshCommunication::make_new_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_new_nodes_parallel_consistent(), libMesh::MeshCommunication::make_node_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_unique_ids_parallel_consistent(), libMesh::MeshCommunication::make_nodes_parallel_consistent(), libMesh::MeshCommunication::make_p_levels_parallel_consistent(), libMesh::MeshRefinement::make_refinement_compatible(), libMesh::TransientRBConstruction::mass_matrix_scaled_matvec(), libMesh::FEMSystem::mesh_position_set(), libMesh::MeshSerializer::MeshSerializer(), LinearElasticityWithContact::move_mesh(), libMesh::DistributedMesh::n_active_elem(), libMesh::MeshTools::n_active_levels(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::CondensedEigenSystem::n_global_non_condensed_dofs(), libMesh::MeshTools::n_levels(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::MeshTools::n_p_levels(), libMesh::BoundaryInfo::n_shellface_conds(), new_function_base(), libMesh::DistributedMesh::parallel_max_elem_id(), libMesh::DistributedMesh::parallel_max_node_id(), libMesh::ReplicatedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_n_elem(), libMesh::DistributedMesh::parallel_n_nodes(), libMesh::SparsityPattern::Build::parallel_sync(), libMesh::MeshTools::paranoid_n_levels(), libMesh::Partitioner::partition(), libMesh::MetisPartitioner::partition_range(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::petsc_auto_fieldsplit(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::MeshBase::prepare_for_use(), libMesh::SparseMatrix< T >::print(), FEMParameters::read(), libMesh::Nemesis_IO::read(), libMesh::CheckpointIO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::MeshBase::recalculate_n_partitions(), libMesh::MeshCommunication::redistribute(), libMesh::MeshRefinement::refine_and_coarsen_elements(), libMesh::DistributedMesh::renumber_dof_objects(), LinearElasticityWithContact::residual_and_jacobian(), libMesh::MeshCommunication::send_coarse_ghosts(), libMesh::TransientRBConstruction::set_error_temporal_data(), libMesh::RBEIMConstruction::set_explicit_sys_subvector(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::Partitioner::set_parent_processor_ids(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::Parallel::Sort< KeyType, IdxType >::sort(), libMesh::MeshBase::subdomain_ids(), libMesh::BoundaryInfo::sync(), libMesh::Parallel::sync_element_data_by_parent_id(), libMesh::Parallel::sync_node_data_by_element_id(), libMesh::MeshRefinement::test_level_one(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), libMesh::MeshRefinement::test_unflagged(), PointLocatorTest::testLocator(), BoundaryInfoTest::testMesh(), SystemsTest::testProjectCubeWithMeshFunction(), libMesh::MeshTools::total_weight(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::TransientRBConstruction::update_RB_initial_condition_all_N(), libMesh::RBEIMConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_RB_system_matrices(), libMesh::RBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), libMesh::RBConstruction::update_residual_terms(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::RBEvaluation::write_out_vectors(), libMesh::TransientRBConstruction::write_riesz_representors_to_files(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::RBDataSerialization::RBEvaluationSerialization::write_to_file(), libMesh::RBDataSerialization::TransientRBEvaluationSerialization::write_to_file(), libMesh::RBDataSerialization::RBEIMEvaluationSerialization::write_to_file(), and libMesh::RBDataSerialization::RBSCMEvaluationSerialization::write_to_file().

88  { return _communicator; }
const Parallel::Communicator & _communicator
bool libMesh::UnstructuredMesh::contract ( )
virtualinherited

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 774 of file unstructured_mesh.C.

References libMesh::Elem::active(), libMesh::Elem::ancestor(), libMesh::MeshBase::clear_point_locator(), libMesh::Elem::contract(), libMesh::MeshBase::delete_elem(), libMesh::MeshBase::elements_begin(), libMesh::MeshBase::elements_end(), end, libMesh::MeshBase::ghosting_functors_begin(), libMesh::MeshBase::ghosting_functors_end(), libMesh::libmesh_assert(), libmesh_nullptr, libMesh::GhostingFunctor::mesh_reinit(), libMesh::Elem::parent(), libMesh::MeshBase::renumber_nodes_and_elements(), and libMesh::Elem::subactive().

775 {
776  LOG_SCOPE ("contract()", "Mesh");
777 
778  // Flag indicating if this call actually changes the mesh
779  bool mesh_changed = false;
780 
781  element_iterator in = elements_begin();
782  const element_iterator end = elements_end();
783 
784 #ifdef DEBUG
785  for ( ; in != end; ++in)
786  if (*in != libmesh_nullptr)
787  {
788  Elem * el = *in;
789  libmesh_assert(el->active() || el->subactive() || el->ancestor());
790  }
791  in = elements_begin();
792 #endif
793 
794  // Loop over the elements.
795  for ( ; in != end; ++in)
796  if (*in != libmesh_nullptr)
797  {
798  Elem * el = *in;
799 
800  // Delete all the subactive ones
801  if (el->subactive())
802  {
803  // No level-0 element should be subactive.
804  // Note that we CAN'T test elem->level(), as that
805  // touches elem->parent()->dim(), and elem->parent()
806  // might have already been deleted!
807  libmesh_assert(el->parent());
808 
809  // Delete the element
810  // This just sets a pointer to NULL, and doesn't
811  // invalidate any iterators
812  this->delete_elem(el);
813 
814  // the mesh has certainly changed
815  mesh_changed = true;
816  }
817  else
818  {
819  // Compress all the active ones
820  if (el->active())
821  el->contract();
822  else
823  libmesh_assert (el->ancestor());
824  }
825  }
826 
827  // Strip any newly-created NULL voids out of the element array
829 
830  // FIXME: Need to understand why deleting subactive children
831  // invalidates the point locator. For now we will clear it explicitly
832  this->clear_point_locator();
833 
834  // Allow our GhostingFunctor objects to reinit if necessary.
835  std::set<GhostingFunctor *>::iterator gf_it = this->ghosting_functors_begin();
836  const std::set<GhostingFunctor *>::iterator gf_end = this->ghosting_functors_end();
837  for (; gf_it != gf_end; ++gf_it)
838  {
839  GhostingFunctor *gf = *gf_it;
840  libmesh_assert(gf);
841  gf->mesh_reinit();
842  }
843 
844  return mesh_changed;
845 }
const class libmesh_nullptr_t libmesh_nullptr
IterBase * end
Also have a polymorphic pointer to the end object, this prevents iterating past the end...
libmesh_assert(j)
std::set< GhostingFunctor * >::const_iterator ghosting_functors_end() const
End of range of ghosting functors.
Definition: mesh_base.h:804
virtual element_iterator elements_begin()=0
Iterate over all the elements in the Mesh.
virtual void delete_elem(Elem *e)=0
Removes element e from the mesh.
virtual element_iterator elements_end()=0
void clear_point_locator()
Releases the current PointLocator object.
Definition: mesh_base.C:555
std::set< GhostingFunctor * >::const_iterator ghosting_functors_begin() const
Beginning of range of ghosting functors.
Definition: mesh_base.h:798
virtual void renumber_nodes_and_elements()=0
After partitioning a mesh it is useful to renumber the nodes and elements so that they lie in contigu...
void libMesh::UnstructuredMesh::copy_nodes_and_elements ( const UnstructuredMesh other_mesh,
const bool  skip_find_neighbors = false 
)
virtualinherited

Deep copy of another unstructured mesh class (used by subclass copy constructors)

Definition at line 73 of file unstructured_mesh.C.

References libMesh::MeshBase::_is_prepared, libMesh::MeshBase::_n_parts, libMesh::Elem::add_child(), libMesh::MeshBase::add_elem(), libMesh::MeshBase::add_point(), libMesh::MeshBase::allow_remote_element_removal(), libMesh::MeshBase::allow_renumbering(), libMesh::Elem::build(), libMesh::MeshBase::elem_ptr(), libMesh::MeshBase::element_ptr_range(), libMesh::MeshTools::libmesh_assert_valid_amr_elem_ids(), libmesh_nullptr, libMesh::MeshBase::n_elem(), libMesh::MeshBase::n_nodes(), libMesh::Elem::neighbor_ptr(), libMesh::MeshBase::node_ptr(), libMesh::MeshBase::node_ptr_range(), libMesh::Elem::parent(), libMesh::MeshBase::prepare_for_use(), libMesh::DofObject::processor_id(), libMesh::remote_elem, libMesh::MeshBase::reserve_elem(), libMesh::MeshBase::reserve_nodes(), libMesh::Elem::set_neighbor(), libMesh::DofObject::set_unique_id(), libMesh::MeshBase::skip_partitioning(), and libMesh::Elem::subdomain_id().

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

75 {
76  LOG_SCOPE("copy_nodes_and_elements()", "UnstructuredMesh");
77 
78  // We're assuming our subclass data needs no copy
79  libmesh_assert_equal_to (_n_parts, other_mesh._n_parts);
80  libmesh_assert_equal_to (_is_prepared, other_mesh._is_prepared);
81 
82  // We're assuming the other mesh has proper element number ordering,
83  // so that we add parents before their children.
84 #ifdef DEBUG
86 #endif
87 
88  //Copy in Nodes
89  {
90  //Preallocate Memory if necessary
91  this->reserve_nodes(other_mesh.n_nodes());
92 
93  for (const auto & oldn : other_mesh.node_ptr_range())
94  {
95  // Add new nodes in old node Point locations
96 #ifdef LIBMESH_ENABLE_UNIQUE_ID
97  Node * newn =
98 #endif
99  this->add_point(*oldn, oldn->id(), oldn->processor_id());
100 
101 #ifdef LIBMESH_ENABLE_UNIQUE_ID
102  newn->set_unique_id() = oldn->unique_id();
103 #endif
104  }
105  }
106 
107  //Copy in Elements
108  {
109  //Preallocate Memory if necessary
110  this->reserve_elem(other_mesh.n_elem());
111 
112  // Declare a map linking old and new elements, needed to copy the neighbor lists
113  typedef std::unordered_map<const Elem *, Elem *> map_type;
114  map_type old_elems_to_new_elems;
115 
116  // Loop over the elements
117  for (const auto & old : other_mesh.element_ptr_range())
118  {
119  // Build a new element
120  Elem * newparent = old->parent() ?
121  this->elem_ptr(old->parent()->id()) : libmesh_nullptr;
122  UniquePtr<Elem> ap = Elem::build(old->type(), newparent);
123  Elem * el = ap.release();
124 
125  el->subdomain_id() = old->subdomain_id();
126 
127  for (auto s : old->side_index_range())
128  if (old->neighbor_ptr(s) == remote_elem)
129  el->set_neighbor(s, const_cast<RemoteElem *>(remote_elem));
130 
131 #ifdef LIBMESH_ENABLE_AMR
132  if (old->has_children())
133  for (unsigned int c = 0, nc = old->n_children(); c != nc; ++c)
134  if (old->child_ptr(c) == remote_elem)
135  el->add_child(const_cast<RemoteElem *>(remote_elem), c);
136 
137  //Create the parent's child pointers if necessary
138  if (newparent)
139  {
140  unsigned int oldc = old->parent()->which_child_am_i(old);
141  newparent->add_child(el, oldc);
142  }
143 
144  // Copy the refinement flags
145  el->set_refinement_flag(old->refinement_flag());
146 
147  // Use hack_p_level since we may not have sibling elements
148  // added yet
149  el->hack_p_level(old->p_level());
150 
151  el->set_p_refinement_flag(old->p_refinement_flag());
152 #endif // #ifdef LIBMESH_ENABLE_AMR
153 
154  //Assign all the nodes
155  for (auto i : el->node_index_range())
156  el->set_node(i) = this->node_ptr(old->node_id(i));
157 
158  // And start it off in the same subdomain
159  el->processor_id() = old->processor_id();
160 
161  // Give it the same element and unique ids
162  el->set_id(old->id());
163 
164 #ifdef LIBMESH_ENABLE_UNIQUE_ID
165  el->set_unique_id() = old->unique_id();
166 #endif
167 
168  //Hold onto it
169  if (!skip_find_neighbors)
170  {
171  this->add_elem(el);
172  }
173  else
174  {
175  Elem * new_el = this->add_elem(el);
176  old_elems_to_new_elems[old] = new_el;
177  }
178 
179  // Add the link between the original element and this copy to the map
180  if (skip_find_neighbors)
181  old_elems_to_new_elems[old] = el;
182  }
183 
184  // Loop (again) over the elements to fill in the neighbors
185  if (skip_find_neighbors)
186  {
187  for (const auto & old_elem : other_mesh.element_ptr_range())
188  {
189  Elem * new_elem = old_elems_to_new_elems[old_elem];
190  for (auto s : old_elem->side_index_range())
191  {
192  const Elem * old_neighbor = old_elem->neighbor_ptr(s);
193  Elem * new_neighbor = old_elems_to_new_elems[old_neighbor];
194  new_elem->set_neighbor(s, new_neighbor);
195  }
196  }
197  }
198  }
199 
200  //Finally prepare the new Mesh for use. Keep the same numbering and
201  //partitioning for now.
202  this->allow_renumbering(false);
203  this->allow_remote_element_removal(false);
204  this->skip_partitioning(true);
205 
206  this->prepare_for_use(false, skip_find_neighbors);
207 
208  //But in the long term, use the same renumbering and partitioning
209  //policies as our source mesh.
210  this->allow_renumbering(other_mesh.allow_renumbering());
211  this->allow_remote_element_removal(other_mesh.allow_remote_element_removal());
212  this->skip_partitioning(other_mesh.skip_partitioning());
213 }
unique_id_type & set_unique_id()
Definition: dof_object.h:662
virtual void reserve_nodes(const dof_id_type nn)=0
Reserves space for a known number of nodes.
static UniquePtr< Elem > build(const ElemType type, Elem *p=libmesh_nullptr)
Definition: elem.C:238
bool skip_partitioning() const
Definition: mesh_base.h:775
const class libmesh_nullptr_t libmesh_nullptr
virtual const Node * node_ptr(const dof_id_type i) const =0
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)=0
Add a new Node at Point p to the end of the vertex array, with processor_id procid.
unsigned int _n_parts
The number of partitions the mesh has.
Definition: mesh_base.h:1342
virtual Elem * add_elem(Elem *e)=0
Add elem e to the end of the element array.
void libmesh_assert_valid_amr_elem_ids(const MeshBase &mesh)
A function for verifying that ids of elements are correctly sorted for AMR (parents have lower ids th...
Definition: mesh_tools.C:1113
void prepare_for_use(const bool skip_renumber_nodes_and_elements=false, const bool skip_find_neighbors=false)
Prepare a newly created (or read) mesh for use.
Definition: mesh_base.C:174
bool allow_renumbering() const
Definition: mesh_base.h:750
bool _is_prepared
Flag indicating if the mesh has been prepared for use.
Definition: mesh_base.h:1347
virtual const Elem * elem_ptr(const dof_id_type i) const =0
bool allow_remote_element_removal() const
Definition: mesh_base.h:759
virtual void reserve_elem(const dof_id_type ne)=0
Reserves space for a known number of elements.
processor_id_type processor_id() const
Definition: dof_object.h:694
const RemoteElem * remote_elem
Definition: remote_elem.C:57
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 653 of file unstructured_mesh.C.

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

655 {
656 
657  // Issue a warning if the number the number of processors
658  // currently available is less that that requested for
659  // partitioning. This is not necessarily an error since
660  // you may run on one processor and still partition the
661  // mesh into several partitions.
662 #ifdef DEBUG
663  if (this->n_processors() < pid)
664  {
665  libMesh::out << "WARNING: You are creating a "
666  << "mesh for a processor id (="
667  << pid
668  << ") greater than "
669  << "the number of processors available for "
670  << "the calculation. (="
671  << this->n_processors()
672  << ")."
673  << std::endl;
674  }
675 #endif
676 
677  // Create iterators to loop over the list of elements
678  // const_active_pid_elem_iterator it(this->elements_begin(), pid);
679  // const const_active_pid_elem_iterator it_end(this->elements_end(), pid);
680 
681  const_element_iterator it = this->active_pid_elements_begin(pid);
682  const const_element_iterator it_end = this->active_pid_elements_end(pid);
683 
684  this->create_submesh (pid_mesh, it, it_end);
685 }
processor_id_type n_processors() const
void create_submesh(UnstructuredMesh &new_mesh, 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 a...
virtual element_iterator active_pid_elements_begin(processor_id_type proc_id)=0
virtual element_iterator active_pid_elements_end(processor_id_type proc_id)=0
OStreamProxy out
void libMesh::UnstructuredMesh::create_submesh ( UnstructuredMesh new_mesh,
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 693 of file unstructured_mesh.C.

References libMesh::MeshBase::add_elem(), libMesh::MeshBase::add_point(), libMesh::BoundaryInfo::add_side(), libMesh::BoundaryInfo::boundary_ids(), libMesh::Elem::build(), libMesh::MeshBase::clear(), libMesh::MeshBase::delete_remote_elements(), libMesh::MeshBase::get_boundary_info(), libMesh::DofObject::id(), libMesh::MeshBase::is_serial(), libMesh::libmesh_assert(), libMesh::MeshBase::n_elem(), libMesh::MeshBase::n_nodes(), libMesh::Elem::node_id(), libMesh::Elem::node_index_range(), libMesh::Elem::node_ptr(), libMesh::MeshBase::node_ptr(), libMesh::Elem::point(), libMesh::MeshBase::prepare_for_use(), libMesh::DofObject::processor_id(), libMesh::MeshBase::query_node_ptr(), libMesh::DofObject::set_id(), libMesh::Elem::set_node(), libMesh::DofObject::set_unique_id(), libMesh::Elem::side_index_range(), libMesh::Elem::subdomain_id(), libMesh::Elem::type(), and libMesh::DofObject::unique_id().

Referenced by construct_mesh_of_active_elements(), and libMesh::UnstructuredMesh::create_pid_mesh().

696 {
697  // Just in case the subdomain_mesh already has some information
698  // in it, get rid of it.
699  new_mesh.clear();
700 
701  // If we're not serial, our submesh isn't either.
702  // There are no remote elements to delete on an empty mesh, but
703  // calling the method to do so marks the mesh as parallel.
704  if (!this->is_serial())
705  new_mesh.delete_remote_elements();
706 
707  // Fail if (*this == new_mesh), we cannot create a submesh inside ourself!
708  // This may happen if the user accidentally passes the original mesh into
709  // this function! We will check this by making sure we did not just
710  // clear ourself.
711  libmesh_assert_not_equal_to (this->n_nodes(), 0);
712  libmesh_assert_not_equal_to (this->n_elem(), 0);
713 
714  // Container to catch boundary IDs handed back by BoundaryInfo
715  std::vector<boundary_id_type> bc_ids;
716 
717  for (; it != it_end; ++it)
718  {
719  const Elem * old_elem = *it;
720 
721  // Add an equivalent element type to the new_mesh.
722  // Copy ids for this element.
723  Elem * new_elem = Elem::build(old_elem->type()).release();
724  new_elem->set_id() = old_elem->id();
725 #ifdef LIBMESH_ENABLE_UNIQUE_ID
726  new_elem->set_unique_id() = old_elem->unique_id();
727 #endif
728  new_elem->subdomain_id() = old_elem->subdomain_id();
729  new_elem->processor_id() = old_elem->processor_id();
730 
731  new_mesh.add_elem (new_elem);
732 
733  libmesh_assert(new_elem);
734 
735  // Loop over the nodes on this element.
736  for (auto n : old_elem->node_index_range())
737  {
738  const dof_id_type this_node_id = old_elem->node_id(n);
739 
740  // Add this node to the new mesh if it's not there already
741  if (!new_mesh.query_node_ptr(this_node_id))
742  {
743 #ifdef LIBMESH_ENABLE_UNIQUE_ID
744  Node *newn =
745 #endif
746  new_mesh.add_point (old_elem->point(n),
747  this_node_id,
748  old_elem->node_ptr(n)->processor_id());
749 
750 #ifdef LIBMESH_ENABLE_UNIQUE_ID
751  newn->set_unique_id() = old_elem->node_ptr(n)->unique_id();
752 #endif
753  }
754 
755  // Define this element's connectivity on the new mesh
756  new_elem->set_node(n) = new_mesh.node_ptr(this_node_id);
757  }
758 
759  // Maybe add boundary conditions for this element
760  for (auto s : old_elem->side_index_range())
761  {
762  this->get_boundary_info().boundary_ids(old_elem, s, bc_ids);
763  new_mesh.get_boundary_info().add_side (new_elem, s, bc_ids);
764  }
765  } // end loop over elements
766 
767  // Prepare the new_mesh for use
768  new_mesh.prepare_for_use(/*skip_renumber =*/false);
769 }
const BoundaryInfo & get_boundary_info() const
The information about boundary ids on the mesh.
Definition: mesh_base.h:117
virtual bool is_serial() const
Definition: mesh_base.h:140
static UniquePtr< Elem > build(const ElemType type, Elem *p=libmesh_nullptr)
Definition: elem.C:238
libmesh_assert(j)
std::vector< boundary_id_type > boundary_ids(const Node *node) const
virtual dof_id_type n_nodes() const =0
virtual dof_id_type n_elem() const =0
uint8_t dof_id_type
Definition: id_types.h:64
void libMesh::DistributedMesh::delete_elem ( Elem e)
virtualinherited

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 541 of file distributed_mesh.C.

References libMesh::DistributedMesh::_elements, libMesh::DistributedMesh::_n_elem, libMesh::MeshBase::get_boundary_info(), libMesh::DofObject::id(), libMesh::DofObject::invalid_processor_id, libMesh::libmesh_assert(), libmesh_nullptr, libMesh::ParallelObject::processor_id(), libMesh::DofObject::processor_id(), and libMesh::BoundaryInfo::remove().

Referenced by libMesh::MeshCommunication::delete_remote_elements(), libMesh::DistributedMesh::insert_elem(), and libMesh::DistributedMesh::reserve_elem().

542 {
543  libmesh_assert (e);
544 
545  // Try to make the cached elem data more accurate
546  processor_id_type elem_procid = e->processor_id();
547  if (elem_procid == this->processor_id() ||
548  elem_procid == DofObject::invalid_processor_id)
549  _n_elem--;
550 
551  // Delete the element from the BoundaryInfo object
552  this->get_boundary_info().remove(e);
553 
554  // But not yet from the container; we might invalidate
555  // an iterator that way!
556 
557  //_elements.erase(e->id());
558 
559  // Instead, we set it to NULL for now
560 
561  _elements[e->id()] = libmesh_nullptr;
562 
563  // delete the element
564  delete e;
565 }
const BoundaryInfo & get_boundary_info() const
The information about boundary ids on the mesh.
Definition: mesh_base.h:117
mapvector< Elem *, dof_id_type > _elements
The elements in the mesh.
void remove(const Node *node)
Removes the boundary conditions associated with node node, if any exist.
uint8_t processor_id_type
Definition: id_types.h:99
const class libmesh_nullptr_t libmesh_nullptr
libmesh_assert(j)
static const processor_id_type invalid_processor_id
An invalid processor_id to distinguish DoFs that have not been assigned to a processor.
Definition: dof_object.h:335
processor_id_type processor_id() const
void libMesh::DistributedMesh::delete_node ( Node n)
virtualinherited

Removes the Node n from the mesh.

Implements libMesh::MeshBase.

Definition at line 712 of file distributed_mesh.C.

References libMesh::DistributedMesh::_n_nodes, libMesh::DistributedMesh::_nodes, libMesh::MeshBase::get_boundary_info(), libMesh::DofObject::id(), libMesh::DofObject::invalid_processor_id, libMesh::libmesh_assert(), libmesh_nullptr, libMesh::ParallelObject::processor_id(), libMesh::DofObject::processor_id(), and libMesh::BoundaryInfo::remove().

Referenced by libMesh::MeshCommunication::delete_remote_elements(), and libMesh::DistributedMesh::reserve_elem().

713 {
714  libmesh_assert(n);
715  libmesh_assert(_nodes[n->id()]);
716 
717  // Try to make the cached elem data more accurate
718  processor_id_type node_procid = n->processor_id();
719  if (node_procid == this->processor_id() ||
720  node_procid == DofObject::invalid_processor_id)
721  _n_nodes--;
722 
723  // Delete the node from the BoundaryInfo object
724  this->get_boundary_info().remove(n);
725 
726  // But not yet from the container; we might invalidate
727  // an iterator that way!
728 
729  //_nodes.erase(n->id());
730 
731  // Instead, we set it to NULL for now
732 
733  _nodes[n->id()] = libmesh_nullptr;
734 
735  // delete the node
736  delete n;
737 }
const BoundaryInfo & get_boundary_info() const
The information about boundary ids on the mesh.
Definition: mesh_base.h:117
dof_id_type _n_nodes
Cached data from the last renumber_nodes_and_elements call.
void remove(const Node *node)
Removes the boundary conditions associated with node node, if any exist.
uint8_t processor_id_type
Definition: id_types.h:99
const class libmesh_nullptr_t libmesh_nullptr
libmesh_assert(j)
mapvector< Node *, dof_id_type > _nodes
The vertices (spatial coordinates) of the mesh.
static const processor_id_type invalid_processor_id
An invalid processor_id to distinguish DoFs that have not been assigned to a processor.
Definition: dof_object.h:335
processor_id_type processor_id() const
void libMesh::DistributedMesh::delete_remote_elements ( )
virtualinherited

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 from libMesh::MeshBase.

Definition at line 1356 of file distributed_mesh.C.

References libMesh::DistributedMesh::_elements, libMesh::DistributedMesh::_extra_ghost_elems, libMesh::DistributedMesh::_is_serial, libMesh::DistributedMesh::_is_serial_on_proc_0, libMesh::DistributedMesh::_nodes, libMesh::MeshCommunication::delete_remote_elements(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_flags(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_ids(), libMesh::MeshTools::libmesh_assert_valid_refinement_tree(), libMesh::DistributedMesh::max_elem_id(), libMesh::DistributedMesh::max_node_id(), libMesh::DistributedMesh::n_elem(), libMesh::DistributedMesh::n_nodes(), libMesh::DistributedMesh::parallel_max_elem_id(), libMesh::DistributedMesh::parallel_max_node_id(), libMesh::DistributedMesh::parallel_n_elem(), libMesh::DistributedMesh::parallel_n_nodes(), and libMesh::DistributedMesh::update_parallel_id_counts().

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

1357 {
1358 #ifdef DEBUG
1359  // Make sure our neighbor links are all fine
1361 
1362  // And our child/parent links, and our flags
1364 
1365  // Make sure our ids and flags are consistent
1368 
1369  libmesh_assert_equal_to (this->n_nodes(), this->parallel_n_nodes());
1370  libmesh_assert_equal_to (this->n_elem(), this->parallel_n_elem());
1371  const dof_id_type pmax_node_id = this->parallel_max_node_id();
1372  const dof_id_type pmax_elem_id = this->parallel_max_elem_id();
1373  libmesh_assert_equal_to (this->max_node_id(), pmax_node_id);
1374  libmesh_assert_equal_to (this->max_elem_id(), pmax_elem_id);
1375 #endif
1376 
1377  _is_serial = false;
1378  _is_serial_on_proc_0 = false;
1379 
1380  MeshCommunication().delete_remote_elements(*this, _extra_ghost_elems);
1381 
1382  libmesh_assert_equal_to (this->max_elem_id(), this->parallel_max_elem_id());
1383 
1384  // Now make sure the containers actually shrink - strip
1385  // any newly-created NULL voids out of the element array
1386  mapvector<Elem *,dof_id_type>::veclike_iterator e_it = _elements.begin();
1387  const mapvector<Elem *,dof_id_type>::veclike_iterator e_end = _elements.end();
1388  for (; e_it != e_end;)
1389  if (!*e_it)
1390  _elements.erase(e_it++);
1391  else
1392  ++e_it;
1393 
1394  mapvector<Node *,dof_id_type>::veclike_iterator n_it = _nodes.begin();
1395  const mapvector<Node *,dof_id_type>::veclike_iterator n_end = _nodes.end();
1396  for (; n_it != n_end;)
1397  if (!*n_it)
1398  _nodes.erase(n_it++);
1399  else
1400  ++n_it;
1401 
1402  // We may have deleted no-longer-connected nodes or coarsened-away
1403  // elements; let's update our caches.
1404  this->update_parallel_id_counts();
1405 
1406 #ifdef DEBUG
1407  // We might not have well-packed objects if the user didn't allow us
1408  // to renumber
1409  // libmesh_assert_equal_to (this->n_nodes(), this->max_node_id());
1410  // libmesh_assert_equal_to (this->n_elem(), this->max_elem_id());
1411 
1412  // Make sure our neighbor links are all fine
1414 
1415  // And our child/parent links, and our flags
1417 
1418  // Make sure our ids and flags are consistent
1421 #endif
1422 }
mapvector< Elem *, dof_id_type > _elements
The elements in the mesh.
virtual dof_id_type n_elem() const libmesh_override
bool _is_serial_on_proc_0
A boolean remembering whether we&#39;re serialized to proc 0 or not.
void libmesh_assert_valid_refinement_tree(const MeshBase &mesh)
A function for verifying that elements on this processor have valid descendants and consistent active...
Definition: mesh_tools.C:1678
bool _is_serial
A boolean remembering whether we&#39;re serialized or not.
dof_id_type parallel_max_elem_id() const
void libmesh_assert_valid_parallel_flags() const
Verify refinement_flag and p_refinement_flag consistency of our elements containers.
virtual void update_parallel_id_counts() libmesh_override
Updates parallel caches so that methods like n_elem() accurately reflect changes on other processors...
dof_id_type parallel_max_node_id() const
mapvector< Node *, dof_id_type > _nodes
The vertices (spatial coordinates) of the mesh.
std::set< Elem * > _extra_ghost_elems
These are extra ghost elements that we want to make sure not to delete when we call delete_remote_ele...
virtual dof_id_type n_nodes() const libmesh_override
virtual dof_id_type max_node_id() const libmesh_override
virtual dof_id_type parallel_n_nodes() const libmesh_override
void libmesh_assert_valid_neighbors(const MeshBase &mesh, bool assert_valid_remote_elems=true)
A function for verifying that neighbor connectivity is correct (each element is a neighbor of or desc...
Definition: mesh_tools.C:1713
virtual dof_id_type parallel_n_elem() const libmesh_override
virtual dof_id_type max_elem_id() const libmesh_override
uint8_t dof_id_type
Definition: id_types.h:64
virtual void libmesh_assert_valid_parallel_ids() const libmesh_override
Verify id and processor_id consistency of our elements and nodes containers.
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 678 of file mesh_base.C.

References libMesh::MeshBase::active_elements_begin(), libMesh::MeshBase::active_elements_end(), libMesh::Elem::dim(), libMesh::MeshBase::elem(), libMesh::MeshBase::elem_dimensions(), libMesh::MeshBase::elem_ptr(), libMesh::MeshBase::elem_ref(), libMesh::MeshBase::elements_begin(), end, libMesh::DofObject::id(), libMesh::Elem::interior_parent(), libMesh::MeshBase::max_elem_id(), libMesh::Elem::n_vertices(), libMesh::Elem::node_id(), and libMesh::Elem::set_interior_parent().

Referenced by libMesh::MeshBase::get_subdomain_name_map(), and libMesh::MeshBase::prepare_for_use().

679 {
680  // This requires an inspection on every processor
681  parallel_object_only();
682 
683  // Check if the mesh contains mixed dimensions. If so, then set interior parents, otherwise return.
684  if (this->elem_dimensions().size() == 1)
685  return;
686 
687  //This map will be used to set interior parents
688  std::unordered_map<dof_id_type, std::vector<dof_id_type>> node_to_elem;
689 
690  const_element_iterator el = this->active_elements_begin();
691  const_element_iterator end = this->active_elements_end();
692 
693  for (; el!=end; ++el)
694  {
695  const Elem * elem = *el;
696 
697  // Populating the node_to_elem map, same as MeshTools::build_nodes_to_elem_map
698  for (unsigned int n=0; n<elem->n_vertices(); n++)
699  {
700  libmesh_assert_less (elem->id(), this->max_elem_id());
701 
702  node_to_elem[elem->node_id(n)].push_back(elem->id());
703  }
704  }
705 
706  // Automatically set interior parents
707  el = this->elements_begin();
708  for (; el!=end; ++el)
709  {
710  Elem * element = *el;
711 
712  // Ignore an 3D element or an element that already has an interior parent
713  if (element->dim()>=LIBMESH_DIM || element->interior_parent())
714  continue;
715 
716  // Start by generating a SET of elements that are dim+1 to the current
717  // element at each vertex of the current element, thus ignoring interior nodes.
718  // If one of the SET of elements is empty, then we will not have an interior parent
719  // since an interior parent must be connected to all vertices of the current element
720  std::vector<std::set<dof_id_type>> neighbors( element->n_vertices() );
721 
722  bool found_interior_parents = false;
723 
724  for (dof_id_type n=0; n < element->n_vertices(); n++)
725  {
726  std::vector<dof_id_type> & element_ids = node_to_elem[element->node_id(n)];
727  for (std::vector<dof_id_type>::iterator e_it = element_ids.begin();
728  e_it != element_ids.end(); e_it++)
729  {
730  dof_id_type eid = *e_it;
731  if (this->elem_ref(eid).dim() == element->dim()+1)
732  neighbors[n].insert(eid);
733  }
734  if (neighbors[n].size()>0)
735  {
736  found_interior_parents = true;
737  }
738  else
739  {
740  // We have found an empty set, no reason to continue
741  // Ensure we set this flag to false before the break since it could have
742  // been set to true for previous vertex
743  found_interior_parents = false;
744  break;
745  }
746  }
747 
748  // If we have successfully generated a set of elements for each vertex, we will compare
749  // the set for vertex 0 will the sets for the vertices until we find a id that exists in
750  // all sets. If found, this is our an interior parent id. The interior parent id found
751  // will be the lowest element id if there is potential for multiple interior parents.
752  if (found_interior_parents)
753  {
754  std::set<dof_id_type> & neighbors_0 = neighbors[0];
755  for (std::set<dof_id_type>::iterator e_it = neighbors_0.begin();
756  e_it != neighbors_0.end(); e_it++)
757  {
758  found_interior_parents=false;
759  dof_id_type interior_parent_id = *e_it;
760  for (dof_id_type n=1; n < element->n_vertices(); n++)
761  {
762  if (neighbors[n].find(interior_parent_id)!=neighbors[n].end())
763  {
764  found_interior_parents=true;
765  }
766  else
767  {
768  found_interior_parents=false;
769  break;
770  }
771  }
772  if (found_interior_parents)
773  {
774  element->set_interior_parent(this->elem_ptr(interior_parent_id));
775  break;
776  }
777  }
778  }
779  }
780 }
virtual const Elem * elem(const dof_id_type i) const
Definition: mesh_base.h:523
IterBase * end
Also have a polymorphic pointer to the end object, this prevents iterating past the end...
virtual element_iterator elements_begin()=0
Iterate over all the elements in the Mesh.
virtual dof_id_type max_elem_id() const =0
const std::set< unsigned char > & elem_dimensions() const
Definition: mesh_base.h:206
virtual element_iterator active_elements_begin()=0
Active, local, and negation forms of the element iterators described above.
virtual element_iterator active_elements_end()=0
virtual const Elem & elem_ref(const dof_id_type i) const
Definition: mesh_base.h:490
virtual unsigned int dim() const =0
virtual const Elem * elem_ptr(const dof_id_type i) const =0
uint8_t dof_id_type
Definition: id_types.h:64
virtual const Elem* libMesh::MeshBase::elem ( const dof_id_type  i) const
virtualinherited
Returns
A pointer to the $ i^{th} $ element, which should be present in this processor's subset of the mesh data structure.
Deprecated:
Use the less confusingly-named elem_ptr() instead.

Definition at line 523 of file mesh_base.h.

References libMesh::MeshBase::elem_ptr().

Referenced by libMesh::MeshBase::detect_interior_parents(), and libMesh::DTKAdapter::DTKAdapter().

524  {
525  libmesh_deprecated();
526  return this->elem_ptr(i);
527  }
virtual const Elem * elem_ptr(const dof_id_type i) const =0
virtual Elem* libMesh::MeshBase::elem ( const dof_id_type  i)
virtualinherited
Returns
A writable pointer to the $ i^{th} $ element, which should be present in this processor's subset of the mesh data structure.
Deprecated:
Use the less confusingly-named elem_ptr() instead.

Definition at line 538 of file mesh_base.h.

References libMesh::MeshBase::elem_ptr(), and libMesh::MeshBase::query_elem_ptr().

539  {
540  libmesh_deprecated();
541  return this->elem_ptr(i);
542  }
virtual const Elem * elem_ptr(const dof_id_type i) const =0
const std::set<unsigned char>& libMesh::MeshBase::elem_dimensions ( ) const
inherited
Returns
A const reference to a std::set of element dimensions present in the mesh.

Definition at line 206 of file mesh_base.h.

References libMesh::MeshBase::_elem_dims, libMesh::MeshBase::n_nodes(), libMesh::MeshBase::n_nodes_on_proc(), libMesh::MeshBase::parallel_n_nodes(), libMesh::MeshBase::set_spatial_dimension(), and libMesh::MeshBase::spatial_dimension().

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

207  { return _elem_dims; }
std::set< unsigned char > _elem_dims
We cache the dimension of the elements present in the mesh.
Definition: mesh_base.h:1411
const Elem * libMesh::DistributedMesh::elem_ptr ( const dof_id_type  i) const
virtualinherited
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 357 of file distributed_mesh.C.

References libMesh::DistributedMesh::_elements, and libMesh::libmesh_assert().

Referenced by libMesh::DistributedMesh::reserve_elem(), and EquationSystemsTest::testRefineThenReinitPreserveFlags().

358 {
360  libmesh_assert_equal_to (_elements[i]->id(), i);
361 
362  return _elements[i];
363 }
mapvector< Elem *, dof_id_type > _elements
The elements in the mesh.
libmesh_assert(j)
Elem * libMesh::DistributedMesh::elem_ptr ( const dof_id_type  i)
virtualinherited
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 368 of file distributed_mesh.C.

References libMesh::DistributedMesh::_elements, and libMesh::libmesh_assert().

369 {
371  libmesh_assert_equal_to (_elements[i]->id(), i);
372 
373  return _elements[i];
374 }
mapvector< Elem *, dof_id_type > _elements
The elements in the mesh.
libmesh_assert(j)
virtual const Elem& libMesh::MeshBase::elem_ref ( const dof_id_type  i) const
virtualinherited
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 490 of file mesh_base.h.

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::MeshBase::detect_interior_parents(), libMesh::SyncRefinementFlags::gather_data(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::ExodusII_IO::read(), libMesh::CheckpointIO::read_remote_elem(), libMesh::Parallel::sync_element_data_by_parent_id(), libMesh::Parallel::sync_node_data_by_element_id(), 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(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::Nemesis_IO_Helper::write_sidesets(), and libMesh::ExodusII_IO_Helper::write_sidesets().

490  {
491  return *this->elem_ptr(i);
492  }
virtual const Elem * elem_ptr(const dof_id_type i) const =0
virtual Elem& libMesh::MeshBase::elem_ref ( const dof_id_type  i)
virtualinherited
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 499 of file mesh_base.h.

References libMesh::MeshBase::elem_ptr().

499  {
500  return *this->elem_ptr(i);
501  }
virtual const Elem * elem_ptr(const dof_id_type i) const =0
virtual SimpleRange<element_iterator> libMesh::DistributedMesh::element_ptr_range ( )
virtualinherited

Implements libMesh::MeshBase.

Definition at line 294 of file distributed_mesh.h.

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

294 { return {elements_begin(), elements_end()}; }
virtual element_iterator elements_begin() libmesh_override
Elem iterator accessor functions.
virtual element_iterator elements_end() libmesh_override
virtual SimpleRange<const_element_iterator> libMesh::DistributedMesh::element_ptr_range ( ) const
virtualinherited

Implements libMesh::MeshBase.

Definition at line 295 of file distributed_mesh.h.

References libMesh::DistributedMesh::active_elements_begin(), libMesh::DistributedMesh::active_elements_end(), libMesh::DistributedMesh::elements_begin(), and libMesh::DistributedMesh::elements_end().

295 { return {elements_begin(), elements_end()}; }
virtual element_iterator elements_begin() libmesh_override
Elem iterator accessor functions.
virtual element_iterator elements_end() libmesh_override
virtual element_iterator libMesh::DistributedMesh::elements_begin ( )
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::elements_begin ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::elements_end ( )
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::elements_end ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::evaluable_elements_begin ( const DofMap dof_map,
unsigned int  var_num = libMesh::invalid_uint 
)
virtualinherited

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.

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

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

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::evaluable_elements_end ( const DofMap dof_map,
unsigned int  var_num = libMesh::invalid_uint 
)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::evaluable_elements_end ( const DofMap dof_map,
unsigned int  var_num = libMesh::invalid_uint 
) const
virtualinherited

Implements libMesh::MeshBase.

virtual node_iterator libMesh::DistributedMesh::evaluable_nodes_begin ( const DofMap dof_map,
unsigned int  var_num = libMesh::invalid_uint 
)
virtualinherited

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.

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

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

Implements libMesh::MeshBase.

virtual node_iterator libMesh::DistributedMesh::evaluable_nodes_end ( const DofMap dof_map,
unsigned int  var_num = libMesh::invalid_uint 
)
virtualinherited
virtual const_node_iterator libMesh::DistributedMesh::evaluable_nodes_end ( const DofMap dof_map,
unsigned int  var_num = libMesh::invalid_uint 
) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::facelocal_elements_begin ( )
virtualinherited

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

Implements libMesh::MeshBase.

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

virtual const_element_iterator libMesh::DistributedMesh::facelocal_elements_begin ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::facelocal_elements_end ( )
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::facelocal_elements_end ( ) const
virtualinherited

Implements libMesh::MeshBase.

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

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 NULL 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 228 of file unstructured_mesh.C.

References libMesh::Elem::active(), libMesh::Elem::ancestor(), libMesh::Elem::centroid(), libMesh::Elem::child_ptr(), libMesh::Elem::child_ref_range(), libMesh::Elem::dim(), libMesh::MeshBase::elements_begin(), libMesh::MeshBase::elements_end(), end, 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::key(), 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_nullptr, libMesh::Elem::n_children(), libMesh::MeshTools::n_levels(), libMesh::Elem::neighbor_ptr(), libMesh::Elem::neighbor_ptr_range(), libMesh::Elem::node_ref_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_index_range(), 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(), libMesh::MeshCommunication::gather(), libMesh::MeshCommunication::gather_neighboring_elements(), libMesh::DistributedMesh::redistribute(), and tetrahedralize_domain().

230 {
231  // We might actually want to run this on an empty mesh
232  // (e.g. the boundary mesh for a nonexistent bcid!)
233  // libmesh_assert_not_equal_to (this->n_nodes(), 0);
234  // libmesh_assert_not_equal_to (this->n_elem(), 0);
235 
236  // This function must be run on all processors at once
237  parallel_object_only();
238 
239  LOG_SCOPE("find_neighbors()", "Mesh");
240 
241  const element_iterator el_end = this->elements_end();
242 
243  //TODO:[BSK] This should be removed later?!
244  if (reset_current_list)
245  for (element_iterator el = this->elements_begin(); el != el_end; ++el)
246  {
247  Elem * e = *el;
248  for (auto s : e->side_index_range())
249  if (e->neighbor_ptr(s) != remote_elem ||
250  reset_remote_elements)
251  e->set_neighbor(s, libmesh_nullptr);
252  }
253 
254  // Find neighboring elements by first finding elements
255  // with identical side keys and then check to see if they
256  // are neighbors
257  {
258  // data structures -- Use the hash_multimap if available
259  typedef unsigned int key_type;
260  typedef std::pair<Elem *, unsigned char> val_type;
261  typedef std::pair<key_type, val_type> key_val_pair;
262 
263  typedef std::unordered_multimap<key_type, val_type> map_type;
264 
265  // A map from side keys to corresponding elements & side numbers
266  map_type side_to_elem_map;
267 
268 
269 
270  for (element_iterator el = this->elements_begin(); el != el_end; ++el)
271  {
272  Elem * element = *el;
273 
274  for (auto ms : element->side_index_range())
275  {
276  next_side:
277  // If we haven't yet found a neighbor on this side, try.
278  // Even if we think our neighbor is remote, that
279  // information may be out of date.
280  if (element->neighbor_ptr(ms) == libmesh_nullptr ||
281  element->neighbor_ptr(ms) == remote_elem)
282  {
283  // Get the key for the side of this element
284  const unsigned int key = element->key(ms);
285 
286  // Look for elements that have an identical side key
287  std::pair <map_type::iterator, map_type::iterator>
288  bounds = side_to_elem_map.equal_range(key);
289 
290  // May be multiple keys, check all the possible
291  // elements which _might_ be neighbors.
292  if (bounds.first != bounds.second)
293  {
294  // Get the side for this element
295  const UniquePtr<Elem> my_side(element->side_ptr(ms));
296 
297  // Look at all the entries with an equivalent key
298  while (bounds.first != bounds.second)
299  {
300  // Get the potential element
301  Elem * neighbor = bounds.first->second.first;
302 
303  // Get the side for the neighboring element
304  const unsigned int ns = bounds.first->second.second;
305  const UniquePtr<Elem> their_side(neighbor->side_ptr(ns));
306  //libmesh_assert(my_side.get());
307  //libmesh_assert(their_side.get());
308 
309  // If found a match with my side
310  //
311  // We need special tests here for 1D:
312  // since parents and children have an equal
313  // side (i.e. a node), we need to check
314  // ns != ms, and we also check level() to
315  // avoid setting our neighbor pointer to
316  // any of our neighbor's descendants
317  if ((*my_side == *their_side) &&
318  (element->level() == neighbor->level()) &&
319  ((element->dim() != 1) || (ns != ms)))
320  {
321  // So share a side. Is this a mixed pair
322  // of subactive and active/ancestor
323  // elements?
324  // If not, then we're neighbors.
325  // If so, then the subactive's neighbor is
326 
327  if (element->subactive() ==
328  neighbor->subactive())
329  {
330  // an element is only subactive if it has
331  // been coarsened but not deleted
332  element->set_neighbor (ms,neighbor);
333  neighbor->set_neighbor(ns,element);
334  }
335  else if (element->subactive())
336  {
337  element->set_neighbor(ms,neighbor);
338  }
339  else if (neighbor->subactive())
340  {
341  neighbor->set_neighbor(ns,element);
342  }
343  side_to_elem_map.erase (bounds.first);
344 
345  // get out of this nested crap
346  goto next_side;
347  }
348 
349  ++bounds.first;
350  }
351  }
352 
353  // didn't find a match...
354  // Build the map entry for this element
355  key_val_pair kvp;
356 
357  kvp.first = key;
358  kvp.second.first = element;
359  kvp.second.second = ms;
360  side_to_elem_map.insert (kvp);
361  }
362  }
363  }
364  }
365 
366 #ifdef LIBMESH_ENABLE_AMR
367 
395  const unsigned int n_levels = MeshTools::n_levels(*this);
396  for (unsigned int level = 1; level < n_levels; ++level)
397  {
398  element_iterator end = this->level_elements_end(level);
399  for (element_iterator el = this->level_elements_begin(level);
400  el != end; ++el)
401  {
402  Elem * current_elem = *el;
403  libmesh_assert(current_elem);
404  Elem * parent = current_elem->parent();
405  libmesh_assert(parent);
406  const unsigned int my_child_num = parent->which_child_am_i(current_elem);
407 
408  for (auto s : current_elem->side_index_range())
409  {
410  if (current_elem->neighbor_ptr(s) == libmesh_nullptr ||
411  (current_elem->neighbor_ptr(s) == remote_elem &&
412  parent->is_child_on_side(my_child_num, s)))
413  {
414  Elem * neigh = parent->neighbor_ptr(s);
415 
416  // If neigh was refined and had non-subactive children
417  // made remote earlier, then our current elem should
418  // actually have one of those remote children as a
419  // neighbor
420  if (neigh &&
421  (neigh->ancestor() ||
422  // If neigh has subactive children which should have
423  // matched as neighbors of the current element but
424  // did not, then those likewise must be remote
425  // children.
426  (current_elem->subactive() && neigh->has_children() &&
427  (neigh->level()+1) == current_elem->level())))
428  {
429 #ifdef DEBUG
430  // Let's make sure that "had children made remote"
431  // situation is actually the case
432  libmesh_assert(neigh->has_children());
433  bool neigh_has_remote_children = false;
434  for (auto & child : neigh->child_ref_range())
435  if (&child == remote_elem)
436  neigh_has_remote_children = true;
437  libmesh_assert(neigh_has_remote_children);
438 
439  // And let's double-check that we don't have
440  // a remote_elem neighboring an active local element
441  if (current_elem->active())
442  libmesh_assert_not_equal_to (current_elem->processor_id(),
443  this->processor_id());
444 #endif // DEBUG
445  neigh = const_cast<RemoteElem *>(remote_elem);
446  }
447  // If neigh and current_elem are more than one level
448  // apart, figuring out whether we have a remote
449  // neighbor here becomes much harder.
450  else if (neigh && (current_elem->subactive() &&
451  neigh->has_children()))
452  {
453  // Find the deepest descendant of neigh which
454  // we could consider for a neighbor. If we run
455  // out of neigh children, then that's our
456  // neighbor. If we find a potential neighbor
457  // with remote_children and we don't find any
458  // potential neighbors among its non-remote
459  // children, then our neighbor must be remote.
460  while (neigh != remote_elem &&
461  neigh->has_children())
462  {
463  bool found_neigh = false;
464  for (unsigned int c = 0, nc = neigh->n_children();
465  !found_neigh && c != nc; ++c)
466  {
467  Elem * child = neigh->child_ptr(c);
468  if (child == remote_elem)
469  continue;
470  for (auto ncn : child->neighbor_ptr_range())
471  {
472  if (ncn != remote_elem &&
473  ncn->is_ancestor_of(current_elem))
474  {
475  neigh = ncn;
476  found_neigh = true;
477  break;
478  }
479  }
480  }
481  if (!found_neigh)
482  neigh = const_cast<RemoteElem *>(remote_elem);
483  }
484  }
485  current_elem->set_neighbor(s, neigh);
486 #ifdef DEBUG
487  if (neigh != libmesh_nullptr && neigh != remote_elem)
488  // We ignore subactive elements here because
489  // we don't care about neighbors of subactive element.
490  if ((!neigh->active()) && (!current_elem->subactive()))
491  {
492  libMesh::err << "On processor " << this->processor_id()
493  << std::endl;
494  libMesh::err << "Bad element ID = " << current_elem->id()
495  << ", Side " << s << ", Bad neighbor ID = " << neigh->id() << std::endl;
496  libMesh::err << "Bad element proc_ID = " << current_elem->processor_id()
497  << ", Bad neighbor proc_ID = " << neigh->processor_id() << std::endl;
498  libMesh::err << "Bad element size = " << current_elem->hmin()
499  << ", Bad neighbor size = " << neigh->hmin() << std::endl;
500  libMesh::err << "Bad element center = " << current_elem->centroid()
501  << ", Bad neighbor center = " << neigh->centroid() << std::endl;
502  libMesh::err << "ERROR: "
503  << (current_elem->active()?"Active":"Ancestor")
504  << " Element at level "
505  << current_elem->level() << std::endl;
506  libMesh::err << "with "
507  << (parent->active()?"active":
508  (parent->subactive()?"subactive":"ancestor"))
509  << " parent share "
510  << (neigh->subactive()?"subactive":"ancestor")
511  << " neighbor at level " << neigh->level()
512  << std::endl;
513  NameBasedIO(*this).write ("bad_mesh.gmv");
514  libmesh_error_msg("Problematic mesh written to bad_mesh.gmv.");
515  }
516 #endif // DEBUG
517  }
518  }
519 
520  // We can skip to the next element if we're full-dimension
521  // and therefore don't have any interior parents
522  if (current_elem->dim() >= LIBMESH_DIM)
523  continue;
524 
525  // We have no interior parents unless we can find one later
526  current_elem->set_interior_parent(libmesh_nullptr);
527 
528  Elem * pip = parent->interior_parent();
529 
530  if (!pip)
531  continue;
532 
533  // If there's no interior_parent children, whether due to a
534  // remote element or a non-conformity, then there's no
535  // children to search.
536  if (pip == remote_elem || pip->active())
537  {
538  current_elem->set_interior_parent(pip);
539  continue;
540  }
541 
542  // For node comparisons we'll need a sensible tolerance
543  Real node_tolerance = current_elem->hmin() * TOLERANCE;
544 
545  // Otherwise our interior_parent should be a child of our
546  // parent's interior_parent.
547  for (auto & child : pip->child_ref_range())
548  {
549  // If we have a remote_elem, that might be our
550  // interior_parent. We'll set it provisionally now and
551  // keep trying to find something better.
552  if (&child == remote_elem)
553  {
554  current_elem->set_interior_parent
555  (const_cast<RemoteElem *>(remote_elem));
556  continue;
557  }
558 
559  bool child_contains_our_nodes = true;
560  for (auto & n : current_elem->node_ref_range())
561  {
562  bool child_contains_this_node = false;
563  for (auto & cn : child.node_ref_range())
564  if (cn.absolute_fuzzy_equals
565  (n, node_tolerance))
566  {
567  child_contains_this_node = true;
568  break;
569  }
570  if (!child_contains_this_node)
571  {
572  child_contains_our_nodes = false;
573  break;
574  }
575  }
576  if (child_contains_our_nodes)
577  {
578  current_elem->set_interior_parent(&child);
579  break;
580  }
581  }
582 
583  // We should have found *some* interior_parent at this
584  // point, whether semilocal or remote.
585  libmesh_assert(current_elem->interior_parent());
586  }
587  }
588 
589 #endif // AMR
590 
591 
592 #ifdef DEBUG
594  !reset_remote_elements);
596 #endif
597 }
OStreamProxy err
bool has_children() const
Definition: elem.h:2295
void libmesh_assert_valid_amr_interior_parents(const MeshBase &mesh)
A function for verifying that any interior_parent pointers on elements are consistent with AMR (paren...
Definition: mesh_tools.C:1133
bool active() const
Definition: elem.h:2257
virtual element_iterator level_elements_begin(unsigned int level)=0
Iterate over elements of a given level.
const class libmesh_nullptr_t libmesh_nullptr
static const Real TOLERANCE
IterBase * end
Also have a polymorphic pointer to the end object, this prevents iterating past the end...
libmesh_assert(j)
virtual element_iterator elements_begin()=0
Iterate over all the elements in the Mesh.
virtual element_iterator level_elements_end(unsigned int level)=0
virtual bool is_child_on_side(const unsigned int, const unsigned int) const libmesh_override
Definition: remote_elem.h:140
bool is_ancestor_of(const Elem *descendant) const
Definition: elem.h:2325
virtual element_iterator elements_end()=0
unsigned int n_levels(const MeshBase &mesh)
Definition: mesh_tools.C:603
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
void libmesh_assert_valid_neighbors(const MeshBase &mesh, bool assert_valid_remote_elems=true)
A function for verifying that neighbor connectivity is correct (each element is a neighbor of or desc...
Definition: mesh_tools.C:1713
processor_id_type processor_id() const
const RemoteElem * remote_elem
Definition: remote_elem.C:57
void libMesh::DistributedMesh::fix_broken_node_and_element_numbering ( )
virtualinherited

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 1303 of file distributed_mesh.C.

References libMesh::DistributedMesh::_elements, libMesh::DistributedMesh::_nodes, libMesh::mapvector< Val, index_t >::begin(), libMesh::mapvector< Val, index_t >::end(), end, and libmesh_nullptr.

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

1304 {
1305  // We need access to iterators for the underlying containers,
1306  // not the mapvector<> reimplementations.
1309 
1310  // Nodes first
1311  {
1312  mapvector<Node *,dof_id_type>::maptype::iterator
1313  it = nodes.begin(),
1314  end = nodes.end();
1315 
1316  for (; it != end; ++it)
1317  if (it->second != libmesh_nullptr)
1318  it->second->set_id() = it->first;
1319  }
1320 
1321  // Elements next
1322  {
1323  mapvector<Elem *,dof_id_type>::maptype::iterator
1324  it = elems.begin(),
1325  end = elems.end();
1326 
1327  for (; it != end; ++it)
1328  if (it->second != libmesh_nullptr)
1329  it->second->set_id() = it->first;
1330  }
1331 }
std::map< index_t, Val > maptype
Definition: mapvector.h:42
mapvector< Elem *, dof_id_type > _elements
The elements in the mesh.
const class libmesh_nullptr_t libmesh_nullptr
IterBase * end
Also have a polymorphic pointer to the end object, this prevents iterating past the end...
mapvector< Node *, dof_id_type > _nodes
The vertices (spatial coordinates) of the mesh.
virtual element_iterator libMesh::DistributedMesh::flagged_elements_begin ( unsigned char  rflag)
virtualinherited

Iterate over all elements with a specified refinement flag.

Implements libMesh::MeshBase.

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

virtual const_element_iterator libMesh::DistributedMesh::flagged_elements_begin ( unsigned char  rflag) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::flagged_elements_end ( unsigned char  rflag)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::flagged_elements_end ( unsigned char  rflag) const
virtualinherited

Implements libMesh::MeshBase.

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

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

Implements libMesh::MeshBase.

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

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

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::flagged_pid_elements_end ( unsigned char  rflag,
processor_id_type  pid 
)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::flagged_pid_elements_end ( unsigned char  rflag,
processor_id_type  pid 
) const
virtualinherited

Implements libMesh::MeshBase.

void libMesh::DistributedMesh::gather_to_zero ( )
virtualinherited

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

Reimplemented from libMesh::MeshBase.

Definition at line 1467 of file distributed_mesh.C.

References libMesh::DistributedMesh::_is_serial_on_proc_0, and libMesh::MeshCommunication::gather().

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

1468 {
1470  return;
1471 
1472  _is_serial_on_proc_0 = true;
1473  MeshCommunication().gather(0, *this);
1474 }
bool _is_serial_on_proc_0
A boolean remembering whether we&#39;re serialized to proc 0 or not.
const BoundaryInfo& libMesh::MeshBase::get_boundary_info ( ) const
inherited

The information about boundary ids on the mesh.

Definition at line 117 of file mesh_base.h.

References libMesh::MeshBase::boundary_info.

Referenced by libMesh::MeshRefinement::_coarsen_elements(), libMesh::MeshTools::Subdivision::add_boundary_ghosts(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), libMesh::UnstructuredMesh::all_first_order(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Subdivision::all_subdivision(), libMesh::MeshTools::Modification::all_tri(), LinearElasticity::assemble(), assemble_elasticity(), assemble_poisson(), assemble_shell(), libMesh::AbaqusIO::assign_boundary_node_ids(), libMesh::AbaqusIO::assign_sideset_ids(), AssemblyA0::boundary_assembly(), AssemblyF0::boundary_assembly(), AssemblyA1::boundary_assembly(), AssemblyF1::boundary_assembly(), AssemblyF2::boundary_assembly(), AssemblyA2::boundary_assembly(), libMesh::MeshCommunication::broadcast(), libMesh::MeshTools::Generation::build_cube(), libMesh::MeshTools::Generation::build_delaunay_square(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::MeshTools::Generation::build_sphere(), libMesh::MeshTools::Modification::change_boundary_id(), libMesh::DofMap::check_dirichlet_bcid_consistency(), libMesh::MeshBase::clear(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::FEGenericBase< OutputType >::compute_periodic_constraints(), libMesh::FEAbstract::compute_periodic_node_constraints(), libMesh::UnstructuredMesh::create_submesh(), libMesh::TetGenMeshInterface::delete_2D_hull_elements(), libMesh::ReplicatedMesh::delete_elem(), libMesh::DistributedMesh::delete_elem(), libMesh::ReplicatedMesh::delete_node(), libMesh::DistributedMesh::delete_node(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::DistributedMesh::DistributedMesh(), libMesh::MeshTools::Modification::flatten(), libMesh::UNVIO::groups_in(), libMesh::ExodusII_IO_Helper::initialize(), LinearElasticityWithContact::initialize_contact_load_paths(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), main(), AugmentSparsityOnInterface::mesh_reinit(), libMesh::BoundaryProjectSolution::operator()(), libMesh::Parallel::Packing< const Node * >::pack(), libMesh::Parallel::Packing< const Elem * >::pack(), libMesh::Parallel::Packing< const Node * >::packable_size(), libMesh::Parallel::Packing< const Elem * >::packable_size(), libMesh::TetGenMeshInterface::pointset_convexhull(), libMesh::Nemesis_IO::prepare_to_write_nodal_data(), libMesh::AbaqusIO::read(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::CheckpointIO::read_bcs(), libMesh::CheckpointIO::read_header(), libMesh::CheckpointIO::read_nodesets(), libMesh::ReplicatedMesh::renumber_nodes_and_elements(), libMesh::DistributedMesh::renumber_nodes_and_elements(), libMesh::ReplicatedMesh::ReplicatedMesh(), libMesh::ReplicatedMesh::stitching_helper(), libMesh::BoundaryInfo::sync(), AllTriTest::test_helper_2D(), AllTriTest::test_helper_3D(), BoundaryInfoTest::testEdgeBoundaryConditions(), BoundaryInfoTest::testMesh(), BoundaryInfoTest::testShellFaceConstraints(), libMesh::Elem::topological_neighbor(), libMesh::Parallel::Packing< Node * >::unpack(), libMesh::Parallel::Packing< Elem * >::unpack(), libMesh::FroIO::write(), libMesh::Nemesis_IO::write(), libMesh::ExodusII_IO::write(), libMesh::CheckpointIO::write(), libMesh::XdrIO::write(), libMesh::ExodusII_IO::write_nodal_data_common(), libMesh::Nemesis_IO_Helper::write_nodesets(), libMesh::ExodusII_IO_Helper::write_nodesets(), libMesh::Nemesis_IO_Helper::write_sidesets(), and libMesh::ExodusII_IO_Helper::write_sidesets().

117 { return *boundary_info; }
UniquePtr< BoundaryInfo > boundary_info
This class holds the boundary information.
Definition: mesh_base.h:1321
BoundaryInfo& libMesh::MeshBase::get_boundary_info ( )
inherited

Writable information about boundary ids on the mesh.

Definition at line 122 of file mesh_base.h.

References libMesh::MeshBase::boundary_info, and libMesh::MeshBase::clear().

122 { return *boundary_info; }
UniquePtr< BoundaryInfo > boundary_info
This class holds the boundary information.
Definition: mesh_base.h:1321
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 569 of file mesh_base.C.

References libMesh::MeshBase::_count_lower_dim_elems_in_point_locator.

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

570 {
572 }
bool _count_lower_dim_elems_in_point_locator
Do we count lower dimensional elements in point locator refinement? This is relevant in tree-based po...
Definition: mesh_base.h:1362
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 596 of file mesh_base.C.

References libMesh::MeshBase::_block_id_to_name, and libMesh::Elem::invalid_subdomain_id.

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

597 {
598  // Linear search over the map values.
599  std::map<subdomain_id_type, std::string>::const_iterator
600  iter = _block_id_to_name.begin(),
601  end_iter = _block_id_to_name.end();
602 
603  for ( ; iter != end_iter; ++iter)
604  if (iter->second == name)
605  return iter->first;
606 
607  // If we made it here without returning, we don't have a subdomain
608  // with the requested name, so return Elem::invalid_subdomain_id.
610 }
std::string name(const ElemQuality q)
This function returns a string containing some name for q.
Definition: elem_quality.C:39
static const subdomain_id_type invalid_subdomain_id
A static integral constant representing an invalid subdomain id.
Definition: elem.h:237
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...
Definition: mesh_base.h:1404
std::string libMesh::MeshBase::get_info ( ) const
inherited
Returns
A string containing relevant information about the mesh.

Definition at line 414 of file mesh_base.C.

References libMesh::MeshBase::_elem_dims, libMesh::MeshBase::n_active_elem(), libMesh::MeshBase::n_elem(), libMesh::MeshBase::n_local_elem(), libMesh::MeshBase::n_local_nodes(), libMesh::MeshBase::n_nodes(), libMesh::MeshBase::n_partitions(), libMesh::ParallelObject::n_processors(), libMesh::MeshBase::n_subdomains(), libMesh::n_threads(), libMesh::ParallelObject::processor_id(), and libMesh::MeshBase::spatial_dimension().

Referenced by libMesh::MeshBase::n_partitions(), and libMesh::MeshBase::print_info().

415 {
416  std::ostringstream oss;
417 
418  oss << " Mesh Information:" << '\n';
419 
420  if (!_elem_dims.empty())
421  {
422  oss << " elem_dimensions()={";
423  std::copy(_elem_dims.begin(),
424  --_elem_dims.end(), // --end() is valid if the set is non-empty
425  std::ostream_iterator<unsigned int>(oss, ", "));
426  oss << cast_int<unsigned int>(*_elem_dims.rbegin());
427  oss << "}\n";
428  }
429 
430  oss << " spatial_dimension()=" << this->spatial_dimension() << '\n'
431  << " n_nodes()=" << this->n_nodes() << '\n'
432  << " n_local_nodes()=" << this->n_local_nodes() << '\n'
433  << " n_elem()=" << this->n_elem() << '\n'
434  << " n_local_elem()=" << this->n_local_elem() << '\n'
435 #ifdef LIBMESH_ENABLE_AMR
436  << " n_active_elem()=" << this->n_active_elem() << '\n'
437 #endif
438  << " n_subdomains()=" << static_cast<std::size_t>(this->n_subdomains()) << '\n'
439  << " n_partitions()=" << static_cast<std::size_t>(this->n_partitions()) << '\n'
440  << " n_processors()=" << static_cast<std::size_t>(this->n_processors()) << '\n'
441  << " n_threads()=" << static_cast<std::size_t>(libMesh::n_threads()) << '\n'
442  << " processor_id()=" << static_cast<std::size_t>(this->processor_id()) << '\n';
443 
444  return oss.str();
445 }
virtual dof_id_type n_active_elem() const =0
unsigned int n_threads()
Definition: libmesh_base.h:125
dof_id_type n_local_nodes() const
Definition: mesh_base.h:272
unsigned int n_partitions() const
Definition: mesh_base.h:833
processor_id_type n_processors() const
std::set< unsigned char > _elem_dims
We cache the dimension of the elements present in the mesh.
Definition: mesh_base.h:1411
unsigned int spatial_dimension() const
Definition: mesh_base.C:157
dof_id_type n_local_elem() const
Definition: mesh_base.h:372
subdomain_id_type n_subdomains() const
Definition: mesh_base.C:334
virtual dof_id_type n_nodes() const =0
virtual dof_id_type n_elem() const =0
processor_id_type processor_id() const
const std::map<subdomain_id_type, std::string>& libMesh::MeshBase::get_subdomain_name_map ( ) const
inherited

Definition at line 1295 of file mesh_base.h.

References libMesh::MeshBase::_block_id_to_name, libMesh::MeshBase::cache_elem_dims(), and libMesh::MeshBase::detect_interior_parents().

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

1296  { return _block_id_to_name; }
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...
Definition: mesh_base.h:1404
virtual element_iterator libMesh::DistributedMesh::ghost_elements_begin ( )
virtualinherited

Iterate over "ghost" elements in the Mesh.

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

Implements libMesh::MeshBase.

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

virtual const_element_iterator libMesh::DistributedMesh::ghost_elements_begin ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::ghost_elements_end ( )
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::ghost_elements_end ( ) const
virtualinherited

Implements libMesh::MeshBase.

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

Beginning of range of ghosting functors.

Definition at line 798 of file mesh_base.h.

References libMesh::MeshBase::_ghosting_functors.

Referenced by libMesh::UnstructuredMesh::contract(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::MeshBase::prepare_for_use(), libMesh::query_ghosting_functors(), libMesh::MeshCommunication::redistribute(), and libMesh::MeshCommunication::send_coarse_ghosts().

799  { return _ghosting_functors.begin(); }
std::set< GhostingFunctor * > _ghosting_functors
The list of all GhostingFunctor objects to be used when distributing a DistributedMesh.
Definition: mesh_base.h:1433
std::set<GhostingFunctor *>::const_iterator libMesh::MeshBase::ghosting_functors_end ( ) const
inherited
Elem * libMesh::DistributedMesh::insert_elem ( Elem e)
virtualinherited

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 507 of file distributed_mesh.C.

References libMesh::DistributedMesh::_elements, libMesh::DistributedMesh::_n_elem, libMesh::MeshBase::_next_unique_id, libMesh::DistributedMesh::_next_unpartitioned_unique_id, libMesh::DistributedMesh::delete_elem(), libMesh::DofObject::id(), libMesh::DofObject::invalid_processor_id, libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), libMesh::DofObject::processor_id(), libMesh::DofObject::set_unique_id(), and libMesh::DofObject::valid_unique_id().

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

508 {
509  if (_elements[e->id()])
510  this->delete_elem(_elements[e->id()]);
511 
512 #ifdef LIBMESH_ENABLE_UNIQUE_ID
513  if (!e->valid_unique_id())
514  {
515  if (processor_id() == e->processor_id())
516  {
517  e->set_unique_id() = _next_unique_id;
518  _next_unique_id += this->n_processors() + 1;
519  }
520  else
521  {
522  e->set_unique_id() = _next_unpartitioned_unique_id;
524  }
525  }
526 #endif
527 
528  // Try to make the cached elem data more accurate
529  processor_id_type elem_procid = e->processor_id();
530  if (elem_procid == this->processor_id() ||
531  elem_procid == DofObject::invalid_processor_id)
532  _n_elem++;
533 
534  _elements[e->id()] = e;
535 
536  return e;
537 }
mapvector< Elem *, dof_id_type > _elements
The elements in the mesh.
processor_id_type n_processors() const
uint8_t processor_id_type
Definition: id_types.h:99
unique_id_type _next_unique_id
The next available unique id for assigning ids to DOF objects.
Definition: mesh_base.h:1376
static const processor_id_type invalid_processor_id
An invalid processor_id to distinguish DoFs that have not been assigned to a processor.
Definition: dof_object.h:335
unique_id_type _next_unpartitioned_unique_id
The next available unique id for assigning ids to unpartitioned DOF objects.
virtual void delete_elem(Elem *e) libmesh_override
Removes element e from the mesh.
processor_id_type processor_id() const
Node * libMesh::DistributedMesh::insert_node ( Node n)
virtualinherited

Calls add_node().

Implements libMesh::MeshBase.

Definition at line 705 of file distributed_mesh.C.

References libMesh::DistributedMesh::add_node().

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

706 {
707  return DistributedMesh::add_node(n);
708 }
virtual Node * add_node(Node *n) libmesh_override
Add Node n to the end of the vertex array.
bool libMesh::MeshBase::is_prepared ( ) const
inherited
Returns
true if the mesh has been prepared via a call to prepare_for_use, false otherwise.

Definition at line 133 of file mesh_base.h.

References libMesh::MeshBase::_is_prepared.

Referenced by libMesh::DofMap::build_sparsity(), libMesh::DofMap::create_dof_constraints(), libMesh::DofMap::distribute_dofs(), and libMesh::DofMap::reinit().

134  { return _is_prepared; }
bool _is_prepared
Flag indicating if the mesh has been prepared for use.
Definition: mesh_base.h:1347
virtual bool libMesh::DistributedMesh::is_replicated ( ) const
virtualinherited
virtual bool libMesh::DistributedMesh::is_serial ( ) const
virtualinherited
Returns
true if all elements and nodes of the mesh exist on the current processor, false otherwise

Reimplemented from libMesh::MeshBase.

Definition at line 123 of file distributed_mesh.h.

References libMesh::DistributedMesh::_is_serial.

Referenced by libMesh::MeshCommunication::delete_remote_elements(), libMesh::MeshCommunication::redistribute(), libMesh::DistributedMesh::redistribute(), PointLocatorTest::testLocator(), and BoundaryInfoTest::testMesh().

124  { return _is_serial; }
bool _is_serial
A boolean remembering whether we&#39;re serialized or not.
virtual bool libMesh::DistributedMesh::is_serial_on_zero ( ) const
virtualinherited
Returns
true if all elements and nodes of the mesh exist on the processor 0, false otherwise

Reimplemented from libMesh::MeshBase.

Definition at line 130 of file distributed_mesh.h.

References libMesh::DistributedMesh::_is_serial, and libMesh::DistributedMesh::_is_serial_on_proc_0.

131  { return _is_serial || _is_serial_on_proc_0; }
bool _is_serial_on_proc_0
A boolean remembering whether we&#39;re serialized to proc 0 or not.
bool _is_serial
A boolean remembering whether we&#39;re serialized or not.
virtual element_iterator libMesh::DistributedMesh::level_elements_begin ( unsigned int  level)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::level_elements_begin ( unsigned int  level) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::level_elements_end ( unsigned int  level)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::level_elements_end ( unsigned int  level) const
virtualinherited

Implements libMesh::MeshBase.

void libMesh::DistributedMesh::libmesh_assert_valid_parallel_flags ( ) const
inherited

Verify refinement_flag and p_refinement_flag consistency of our elements containers.

Calls libmesh_assert() on each possible failure.

Definition at line 955 of file distributed_mesh.C.

References libMesh::DistributedMesh::_elements, libMesh::Elem::active(), libMesh::ParallelObject::comm(), libMesh::invalid_uint, libMesh::libmesh_assert(), libmesh_nullptr, libMesh::Elem::p_refinement_flag(), libMesh::DistributedMesh::parallel_max_elem_id(), and libMesh::Elem::refinement_flag().

Referenced by libMesh::DistributedMesh::allgather(), libMesh::DistributedMesh::delete_remote_elements(), libMesh::DistributedMesh::is_replicated(), and libMesh::DistributedMesh::renumber_nodes_and_elements().

956 {
957 #if defined(LIBMESH_ENABLE_AMR) && !defined(NDEBUG)
958  // This function must be run on all processors at once
959  parallel_object_only();
960 
961  dof_id_type pmax_elem_id = this->parallel_max_elem_id();
962 
963  for (dof_id_type i=0; i != pmax_elem_id; ++i)
964  {
965  Elem * el = _elements[i]; // Returns NULL if there's no map entry
966 
967  unsigned int refinement_flag = el ?
968  static_cast<unsigned int> (el->refinement_flag()) : libMesh::invalid_uint;
969  unsigned int p_refinement_flag = el ?
970  static_cast<unsigned int> (el->p_refinement_flag()) : libMesh::invalid_uint;
971 
972  libmesh_assert(this->comm().semiverify(el ? &refinement_flag : libmesh_nullptr));
973 
974  // p refinement flags aren't always kept correct on inactive
975  // ghost elements
976  libmesh_assert(this->comm().semiverify((el && el->active()) ? &p_refinement_flag : libmesh_nullptr));
977  }
978 #endif // LIBMESH_ENABLE_AMR
979 }
mapvector< Elem *, dof_id_type > _elements
The elements in the mesh.
const unsigned int invalid_uint
A number which is used quite often to represent an invalid or uninitialized value.
Definition: libmesh.h:184
const class libmesh_nullptr_t libmesh_nullptr
dof_id_type parallel_max_elem_id() const
libmesh_assert(j)
const Parallel::Communicator & comm() const
uint8_t dof_id_type
Definition: id_types.h:64
void libMesh::DistributedMesh::libmesh_assert_valid_parallel_ids ( ) const
virtualinherited

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

Calls libmesh_assert() on each possible failure.

Reimplemented from libMesh::MeshBase.

Definition at line 924 of file distributed_mesh.C.

References libMesh::DistributedMesh::_elements, libMesh::DistributedMesh::_nodes, and libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids().

Referenced by libMesh::BoundaryInfo::add_elements(), libMesh::DistributedMesh::allgather(), libMesh::DistributedMesh::delete_remote_elements(), libMesh::DistributedMesh::is_replicated(), and libMesh::DistributedMesh::renumber_nodes_and_elements().

925 {
928 }
mapvector< Elem *, dof_id_type > _elements
The elements in the mesh.
mapvector< Node *, dof_id_type > _nodes
The vertices (spatial coordinates) of the mesh.
void libmesh_assert_valid_parallel_object_ids(const mapvector< T *, dof_id_type > &) const
Verify id, processor_id, and if applicable unique_id consistency of a parallel objects container...
template<typename T >
void libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids ( const mapvector< T *, dof_id_type > &  objects) const
inherited

Verify id, processor_id, and if applicable unique_id consistency of a parallel objects container.

Calls libmesh_assert() on each possible failure in that container.

Definition at line 868 of file distributed_mesh.C.

References libMesh::ParallelObject::comm(), libMesh::DofObject::invalid_id, libMesh::DofObject::invalid_processor_id, libMesh::libmesh_assert(), libmesh_nullptr, std::max(), libMesh::Parallel::Communicator::min(), libMesh::DistributedMesh::parallel_max_elem_id(), libMesh::DistributedMesh::parallel_max_node_id(), and libMesh::ParallelObject::processor_id().

Referenced by libMesh::DistributedMesh::is_replicated(), and libMesh::DistributedMesh::libmesh_assert_valid_parallel_ids().

869 {
870  // This function must be run on all processors at once
871  parallel_object_only();
872 
873  const dof_id_type pmax_node_id = this->parallel_max_node_id();
874  const dof_id_type pmax_elem_id = this->parallel_max_elem_id();
875  const dof_id_type pmax_id = std::max(pmax_node_id, pmax_elem_id);
876 
877  for (dof_id_type i=0; i != pmax_id; ++i)
878  {
879  T * obj = objects[i]; // Returns NULL if there's no map entry
880 
881  // Local lookups by id should return the requested object
882  libmesh_assert(!obj || obj->id() == i);
883 
884  // All processors with an object should agree on id
885 #ifndef NDEBUG
886  const dof_id_type dofid = obj && obj->valid_id() ?
887  obj->id() : DofObject::invalid_id;
888  libmesh_assert(this->comm().semiverify(obj ? &dofid : libmesh_nullptr));
889 #endif
890 
891  // All processors with an object should agree on processor id
892  const dof_id_type procid = obj && obj->valid_processor_id() ?
893  obj->processor_id() : DofObject::invalid_processor_id;
894  libmesh_assert(this->comm().semiverify(obj ? &procid : libmesh_nullptr));
895 
896  dof_id_type min_procid = procid;
897  this->comm().min(min_procid);
898 
899  // Either:
900  // 1.) I own this elem (min_procid == this->processor_id()) *and* I have a valid pointer to it (obj != NULL)
901  // or
902  // 2.) I don't own this elem (min_procid != this->processor_id()). (In this case I may or may not have a valid pointer to it.)
903 
904  // Original assert logic
905  // libmesh_assert (min_procid != this->processor_id() || obj);
906 
907  // More human-understandable logic...
909  ((min_procid == this->processor_id()) && obj)
910  ||
911  (min_procid != this->processor_id())
912  );
913 
914 #if defined(LIBMESH_ENABLE_UNIQUE_ID) && !defined(NDEBUG)
915  // All processors with an object should agree on unique id
916  const unique_id_type uniqueid = obj ? obj->unique_id() : 0;
917  libmesh_assert(this->comm().semiverify(obj ? &uniqueid : libmesh_nullptr));
918 #endif
919  }
920 }
void min(T &r) const
Take a local variable and replace it with the minimum of it&#39;s values on all processors.
const class libmesh_nullptr_t libmesh_nullptr
dof_id_type parallel_max_elem_id() const
long double max(long double a, double b)
libmesh_assert(j)
dof_id_type parallel_max_node_id() const
static const processor_id_type invalid_processor_id
An invalid processor_id to distinguish DoFs that have not been assigned to a processor.
Definition: dof_object.h:335
static const dof_id_type invalid_id
An invalid id to distinguish an uninitialized DofObject.
Definition: dof_object.h:324
const Parallel::Communicator & comm() const
uint8_t unique_id_type
Definition: id_types.h:79
processor_id_type processor_id() const
uint8_t dof_id_type
Definition: id_types.h:64
void libMesh::DistributedMesh::libmesh_assert_valid_parallel_p_levels ( ) const
inherited

Verify p_level consistency of our elements containers.

Calls libmesh_assert() on each possible failure.

Definition at line 932 of file distributed_mesh.C.

References libMesh::DistributedMesh::_elements, libMesh::Elem::active(), libMesh::ParallelObject::comm(), libMesh::invalid_uint, libMesh::libmesh_assert(), libmesh_nullptr, libMesh::Elem::p_level(), and libMesh::DistributedMesh::parallel_max_elem_id().

Referenced by libMesh::DistributedMesh::is_replicated(), and libMesh::DistributedMesh::renumber_nodes_and_elements().

933 {
934 #ifndef NDEBUG
935  // This function must be run on all processors at once
936  parallel_object_only();
937 
938  dof_id_type pmax_elem_id = this->parallel_max_elem_id();
939 
940  for (dof_id_type i=0; i != pmax_elem_id; ++i)
941  {
942  Elem * el = _elements[i]; // Returns NULL if there's no map entry
943 
944  unsigned int p_level = el ? (el->p_level()) : libMesh::invalid_uint;
945 
946  // All processors with an active element should agree on p level
947  libmesh_assert(this->comm().semiverify((el && el->active()) ? &p_level : libmesh_nullptr));
948  }
949 #endif
950 }
mapvector< Elem *, dof_id_type > _elements
The elements in the mesh.
const unsigned int invalid_uint
A number which is used quite often to represent an invalid or uninitialized value.
Definition: libmesh.h:184
const class libmesh_nullptr_t libmesh_nullptr
dof_id_type parallel_max_elem_id() const
libmesh_assert(j)
const Parallel::Communicator & comm() const
uint8_t dof_id_type
Definition: id_types.h:64
virtual element_iterator libMesh::DistributedMesh::local_elements_begin ( )
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::local_elements_begin ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::local_elements_end ( )
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::local_elements_end ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::local_level_elements_begin ( unsigned int  level)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::local_level_elements_begin ( unsigned int  level) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::local_level_elements_end ( unsigned int  level)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::local_level_elements_end ( unsigned int  level) const
virtualinherited

Implements libMesh::MeshBase.

virtual SimpleRange<node_iterator> libMesh::DistributedMesh::local_node_ptr_range ( )
virtualinherited

Implements libMesh::MeshBase.

Definition at line 487 of file distributed_mesh.h.

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

487 { return {local_nodes_begin(), local_nodes_end()}; }
virtual node_iterator local_nodes_end() libmesh_override
virtual node_iterator local_nodes_begin() libmesh_override
Iterate over local nodes (nodes whose processor_id() matches the current processor).
virtual SimpleRange<const_node_iterator> libMesh::DistributedMesh::local_node_ptr_range ( ) const
virtualinherited
virtual node_iterator libMesh::DistributedMesh::local_nodes_begin ( )
virtualinherited

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

Implements libMesh::MeshBase.

Referenced by libMesh::DistributedMesh::local_node_ptr_range(), main(), and libMesh::DistributedMesh::node_ptr_range().

virtual const_node_iterator libMesh::DistributedMesh::local_nodes_begin ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual node_iterator libMesh::DistributedMesh::local_nodes_end ( )
virtualinherited
virtual const_node_iterator libMesh::DistributedMesh::local_nodes_end ( ) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::local_not_level_elements_begin ( unsigned int  level)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::local_not_level_elements_begin ( unsigned int  level) const
virtualinherited

Implements libMesh::MeshBase.

virtual element_iterator libMesh::DistributedMesh::local_not_level_elements_end ( unsigned int  level)
virtualinherited
virtual const_element_iterator libMesh::DistributedMesh::local_not_level_elements_end ( unsigned int  level) const
virtualinherited

Implements libMesh::MeshBase.

virtual dof_id_type libMesh::DistributedMesh::max_elem_id ( ) const
virtualinherited
virtual dof_id_type libMesh::DistributedMesh::max_node_id ( ) const
virtualinherited
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 148 of file mesh_base.C.

References libMesh::MeshBase::_elem_dims.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), 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_shell(), assemble_stokes(), assemble_wave(), libMesh::MeshTools::Generation::build_cube(), libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::MeshTools::Generation::build_sphere(), libMesh::EquationSystems::build_variable_names(), libMesh::MeshBase::cache_elem_dims(), compute_stresses(), LinearElasticity::compute_stresses(), libMesh::DofMap::create_dof_constraints(), libMesh::MeshBase::delete_remote_elements(), libMesh::MeshTools::Modification::distort(), SolidSystem::element_time_derivative(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::MeshRefinement::flag_elements_by_elem_fraction(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::LaplaceMeshSmoother::init(), libMesh::PointLocatorTree::init(), SolidSystem::init_data(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::RBEIMAssembly::initialize_fe(), integrate_function(), LaplaceYoung::jacobian(), main(), libMesh::FEInterface::n_vec_dim(), libMesh::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::PatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::BoundaryProjectSolution::operator()(), libMesh::GMVIO::read(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::VTKIO::read(), libMesh::XdrIO::read_serialized_connectivity(), LaplaceYoung::residual(), SolidSystem::save_initial_mesh(), libMesh::HPCoarsenTest::select_refinement(), setup(), libMesh::MeshTools::Modification::smooth(), MeshSpatialDimensionTest::test1D(), MeshSpatialDimensionTest::test2D(), 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_nodal_data(), libMesh::EnsightIO::write_scalar_ascii(), libMesh::GnuPlotIO::write_solution(), and libMesh::EnsightIO::write_vector_ascii().

149 {
150  if (!_elem_dims.empty())
151  return cast_int<unsigned int>(*_elem_dims.rbegin());
152  return 0;
153 }
std::set< unsigned char > _elem_dims
We cache the dimension of the elements present in the mesh.
Definition: mesh_base.h:1411
dof_id_type libMesh::DistributedMesh::n_active_elem ( ) const
virtualinherited
Returns
The number of active elements in the mesh.

Implemented in terms of active_element_iterators.

Implements libMesh::MeshBase.

Definition at line 1335 of file distributed_mesh.C.

References libMesh::DistributedMesh::active_local_elements_begin(), libMesh::DistributedMesh::active_local_elements_end(), libMesh::DistributedMesh::active_pid_elements_begin(), libMesh::DistributedMesh::active_pid_elements_end(), libMesh::ParallelObject::comm(), distance(), libMesh::DofObject::invalid_processor_id, and libMesh::Parallel::Communicator::sum().

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

1336 {
1337  parallel_object_only();
1338 
1339  // Get local active elements first
1340  dof_id_type active_elements =
1342  this->active_local_elements_end()));
1343  this->comm().sum(active_elements);
1344 
1345  // Then add unpartitioned active elements, which should exist on
1346  // every processor
1347  active_elements +=
1348  static_cast<dof_id_type>(std::distance
1351  return active_elements;
1352 }
virtual element_iterator active_local_elements_begin() libmesh_override
virtual element_iterator active_local_elements_end() libmesh_override
Real distance(const Point &p)
static const processor_id_type invalid_processor_id
An invalid processor_id to distinguish DoFs that have not been assigned to a processor.
Definition: dof_object.h:335
virtual element_iterator active_pid_elements_begin(processor_id_type proc_id) libmesh_override
const Parallel::Communicator & comm() const
void sum(T &r) const
Take a local variable and replace it with the sum of it&#39;s values on all processors.
uint8_t dof_id_type
Definition: id_types.h:64
virtual element_iterator active_pid_elements_end(processor_id_type proc_id) libmesh_override
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 375 of file mesh_base.C.

References libMesh::MeshBase::active_pid_elements_begin(), libMesh::MeshBase::active_pid_elements_end(), distance(), and libMesh::ParallelObject::n_processors().

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

376 {
377  libmesh_assert_less (proc_id, this->n_processors());
378  return static_cast<dof_id_type>(std::distance (this->active_pid_elements_begin(proc_id),
379  this->active_pid_elements_end (proc_id)));
380 }
processor_id_type n_processors() const
Real distance(const Point &p)
virtual element_iterator active_pid_elements_begin(processor_id_type proc_id)=0
virtual element_iterator active_pid_elements_end(processor_id_type proc_id)=0
uint8_t dof_id_type
Definition: id_types.h:64
dof_id_type libMesh::MeshBase::n_active_local_elem ( ) const
inherited
dof_id_type libMesh::MeshBase::n_active_sub_elem ( ) const
inherited

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

Definition at line 399 of file mesh_base.C.

References libMesh::MeshBase::active_elements_begin(), libMesh::MeshBase::active_elements_end(), and end.

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

400 {
401  dof_id_type ne=0;
402 
403  const_element_iterator el = this->active_elements_begin();
404  const const_element_iterator end = this->active_elements_end();
405 
406  for (; el!=end; ++el)
407  ne += (*el)->n_sub_elem();
408 
409  return ne;
410 }
IterBase * end
Also have a polymorphic pointer to the end object, this prevents iterating past the end...
virtual element_iterator active_elements_begin()=0
Active, local, and negation forms of the element iterators described above.
virtual element_iterator active_elements_end()=0
uint8_t dof_id_type
Definition: id_types.h:64
virtual dof_id_type libMesh::DistributedMesh::n_elem ( ) const
virtualinherited
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 226 of file distributed_mesh.h.

References libMesh::DistributedMesh::_n_elem, and libMesh::DistributedMesh::n_active_elem().

Referenced by libMesh::DistributedMesh::allgather(), libMesh::DistributedMesh::delete_remote_elements(), libMesh::DistributedMesh::DistributedMesh(), libMesh::MeshCommunication::gather(), main(), libMesh::DistributedMesh::renumber_nodes_and_elements(), and SlitMeshTest::testMesh().

226 { return _n_elem; }
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 362 of file mesh_base.C.

References distance(), libMesh::DofObject::invalid_processor_id, libMesh::libmesh_assert(), libMesh::ParallelObject::n_processors(), libMesh::MeshBase::pid_elements_begin(), and libMesh::MeshBase::pid_elements_end().

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

363 {
364  // We're either counting a processor's elements or unpartitioned
365  // elements
366  libmesh_assert (proc_id < this->n_processors() ||
368 
369  return static_cast<dof_id_type>(std::distance (this->pid_elements_begin(proc_id),
370  this->pid_elements_end (proc_id)));
371 }
processor_id_type n_processors() const
Real distance(const Point &p)
libmesh_assert(j)
static const processor_id_type invalid_processor_id
An invalid processor_id to distinguish DoFs that have not been assigned to a processor.
Definition: dof_object.h:335
virtual element_iterator pid_elements_begin(processor_id_type proc_id)=0
Iterate over all elements with a specified processor id.
uint8_t dof_id_type
Definition: id_types.h:64
virtual element_iterator pid_elements_end(processor_id_type proc_id)=0
dof_id_type libMesh::MeshBase::n_local_elem ( ) const
inherited
Returns
The number of elements on the local processor.

Definition at line 372 of file mesh_base.h.

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

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

373  { return this->n_elem_on_proc (this->processor_id()); }
dof_id_type n_elem_on_proc(const processor_id_type proc) const
Definition: mesh_base.C:362
processor_id_type processor_id() const
dof_id_type libMesh::MeshBase::n_local_nodes ( ) const
inherited
Returns
The number of nodes on the local processor.

Definition at line 272 of file mesh_base.h.

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

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

273  { return this->n_nodes_on_proc (this->processor_id()); }
dof_id_type n_nodes_on_proc(const processor_id_type proc) const
Definition: mesh_base.C:349
processor_id_type processor_id() const
virtual dof_id_type libMesh::DistributedMesh::n_nodes ( ) const
virtualinherited
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 223 of file distributed_mesh.h.

References libMesh::DistributedMesh::_n_nodes.

Referenced by libMesh::DistributedMesh::allgather(), libMesh::DistributedMesh::delete_remote_elements(), libMesh::DistributedMesh::DistributedMesh(), libMesh::MeshCommunication::gather(), libMesh::DistributedMesh::renumber_nodes_and_elements(), and SlitMeshTest::testMesh().

223 { return _n_nodes; }
dof_id_type _n_nodes
Cached data from the last renumber_nodes_and_elements call.
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 349 of file mesh_base.C.

References distance(), libMesh::DofObject::invalid_processor_id, libMesh::libmesh_assert(), libMesh::ParallelObject::n_processors(), libMesh::MeshBase::pid_nodes_begin(), and libMesh::MeshBase::pid_nodes_end().

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

350 {
351  // We're either counting a processor's nodes or unpartitioned
352  // nodes
353  libmesh_assert (proc_id < this->n_processors() ||
355 
356  return static_cast<dof_id_type>(std::distance (this->pid_nodes_begin(proc_id),
357  this->pid_nodes_end (proc_id)));
358 }
virtual node_iterator pid_nodes_end(processor_id_type proc_id)=0
processor_id_type n_processors() const
Real distance(const Point &p)
libmesh_assert(j)
static const processor_id_type invalid_processor_id
An invalid processor_id to distinguish DoFs that have not been assigned to a processor.
Definition: dof_object.h:335
virtual node_iterator pid_nodes_begin(processor_id_type proc_id)=0
Iterate over nodes with processor_id() == proc_id.
uint8_t dof_id_type
Definition: id_types.h:64
unsigned int libMesh::MeshBase::n_partitions ( ) const
inherited
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 833 of file mesh_base.h.

References libMesh::MeshBase::_n_parts, libMesh::MeshBase::all_first_order(), libMesh::MeshBase::all_second_order(), libMesh::MeshBase::get_info(), libmesh_nullptr, libMesh::Quality::name(), libMesh::MeshBase::operator<<, libMesh::out, libMesh::MeshBase::print_info(), libMesh::MeshBase::read(), and libMesh::MeshBase::write().

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

834  { return _n_parts; }
unsigned int _n_parts
The number of partitions the mesh has.
Definition: mesh_base.h:1342
processor_id_type libMesh::ParallelObject::n_processors ( ) const
inherited