#include <unstructured_mesh.h>

Inheritance diagram for libMesh::UnstructuredMesh:

Public Types
typedef Predicates::multi_predicate	Predicate
Public Member Functions
	UnstructuredMesh (const Parallel::Communicator &comm_in, unsigned char dim=1)
	UnstructuredMesh (unsigned char dim=1)
virtual	~UnstructuredMesh ()
void	read (const std::string &name, MeshData *mesh_data=NULL, bool skip_renumber_nodes_and_elements=false)
void	write (const std::string &name, MeshData *mesh_data=NULL)
void	write (const std::string &name, const std::vector< Number > &values, const std::vector< std::string > &variable_names)
virtual void	all_first_order ()
virtual void	all_second_order (const bool full_ordered=true)
void	create_pid_mesh (UnstructuredMesh &pid_mesh, const processor_id_type pid) const
void	create_submesh (UnstructuredMesh &new_mesh, const_element_iterator &it, const const_element_iterator &it_end) const
virtual void	copy_nodes_and_elements (const UnstructuredMesh &other_mesh, const bool skip_find_neighbors=false)
virtual void	find_neighbors (const bool reset_remote_elements=false, const bool reset_current_list=true)
virtual bool	contract ()
virtual UniquePtr< MeshBase >	clone () const =0
virtual UniquePtr< Partitioner > &	partitioner ()
const BoundaryInfo &	get_boundary_info () const
BoundaryInfo &	get_boundary_info ()
virtual void	clear ()
bool	is_prepared () const
virtual bool	is_serial () const
virtual void	allgather ()
virtual void	delete_remote_elements ()
unsigned int	mesh_dimension () const
void	set_mesh_dimension (unsigned char d)
const std::set< unsigned char > &	elem_dimensions () const
unsigned int	spatial_dimension () const
virtual dof_id_type	n_nodes () const =0
virtual dof_id_type	parallel_n_nodes () const =0
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
virtual dof_id_type	max_node_id () const =0
unique_id_type	next_unique_id ()
void	set_next_unique_id (unique_id_type id)
virtual void	reserve_nodes (const dof_id_type nn)=0
virtual dof_id_type	n_elem () const =0
virtual dof_id_type	parallel_n_elem () const =0
virtual dof_id_type	max_elem_id () const =0
virtual void	reserve_elem (const dof_id_type ne)=0
virtual void	update_parallel_id_counts ()=0
virtual dof_id_type	n_active_elem () const =0
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
virtual const Point &	point (const dof_id_type i) const =0
virtual const Node &	node (const dof_id_type i) const =0
virtual Node &	node (const dof_id_type i)=0
virtual const Node *	node_ptr (const dof_id_type i) const =0
virtual Node *	node_ptr (const dof_id_type i)=0
virtual const Node *	query_node_ptr (const dof_id_type i) const =0
virtual Node *	query_node_ptr (const dof_id_type i)=0
virtual const Elem *	elem (const dof_id_type i) const =0
virtual Elem *	elem (const dof_id_type i)=0
virtual const Elem *	query_elem (const dof_id_type i) const =0
virtual Elem *	query_elem (const dof_id_type i)=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
virtual Node *	add_node (Node *n)=0
virtual Node *	insert_node (Node *n)=0
virtual void	delete_node (Node *n)=0
virtual void	renumber_node (dof_id_type old_id, dof_id_type new_id)=0
virtual Elem *	add_elem (Elem *e)=0
virtual Elem *	insert_elem (Elem *e)=0
virtual void	delete_elem (Elem *e)=0
virtual void	renumber_elem (dof_id_type old_id, dof_id_type new_id)=0
virtual void	renumber_nodes_and_elements ()=0
virtual void	fix_broken_node_and_element_numbering ()=0
void	prepare_for_use (const bool skip_renumber_nodes_and_elements=false, const bool skip_find_neighbors=false)
virtual void	partition (const unsigned int n_parts)
void	partition ()
virtual void	redistribute ()
virtual void	update_post_partitioning ()
void	allow_renumbering (bool allow)
bool	allow_renumbering () const
void	skip_partitioning (bool skip)
bool	skip_partitioning () const
void	subdomain_ids (std::set< subdomain_id_type > &ids) const
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
unsigned int	recalculate_n_partitions ()
const PointLocatorBase &	point_locator () const
UniquePtr< PointLocatorBase >	sub_point_locator () const
void	clear_point_locator ()
virtual void	libmesh_assert_valid_parallel_ids () const
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
virtual element_iterator	elements_begin ()=0
virtual const_element_iterator	elements_begin () const =0
virtual element_iterator	elements_end ()=0
virtual const_element_iterator	elements_end () const =0
virtual element_iterator	active_elements_begin ()=0
virtual const_element_iterator	active_elements_begin () const =0
virtual element_iterator	active_elements_end ()=0
virtual const_element_iterator	active_elements_end () const =0
virtual element_iterator	ancestor_elements_begin ()=0
virtual const_element_iterator	ancestor_elements_begin () const =0
virtual element_iterator	ancestor_elements_end ()=0
virtual const_element_iterator	ancestor_elements_end () const =0
virtual element_iterator	subactive_elements_begin ()=0
virtual const_element_iterator	subactive_elements_begin () const =0
virtual element_iterator	subactive_elements_end ()=0
virtual const_element_iterator	subactive_elements_end () const =0
virtual element_iterator	not_active_elements_begin ()=0
virtual const_element_iterator	not_active_elements_begin () const =0
virtual element_iterator	not_active_elements_end ()=0
virtual const_element_iterator	not_active_elements_end () const =0
virtual element_iterator	not_ancestor_elements_begin ()=0
virtual const_element_iterator	not_ancestor_elements_begin () const =0
virtual element_iterator	not_ancestor_elements_end ()=0
virtual const_element_iterator	not_ancestor_elements_end () const =0
virtual element_iterator	not_subactive_elements_begin ()=0
virtual const_element_iterator	not_subactive_elements_begin () const =0
virtual element_iterator	not_subactive_elements_end ()=0
virtual const_element_iterator	not_subactive_elements_end () const =0
virtual element_iterator	local_elements_begin ()=0
virtual const_element_iterator	local_elements_begin () const =0
virtual element_iterator	local_elements_end ()=0
virtual const_element_iterator	local_elements_end () const =0
virtual element_iterator	semilocal_elements_begin ()=0
virtual const_element_iterator	semilocal_elements_begin () const =0
virtual element_iterator	semilocal_elements_end ()=0
virtual const_element_iterator	semilocal_elements_end () const =0
virtual element_iterator	facelocal_elements_begin ()=0
virtual const_element_iterator	facelocal_elements_begin () const =0
virtual element_iterator	facelocal_elements_end ()=0
virtual const_element_iterator	facelocal_elements_end () const =0
virtual element_iterator	not_local_elements_begin ()=0
virtual const_element_iterator	not_local_elements_begin () const =0
virtual element_iterator	not_local_elements_end ()=0
virtual const_element_iterator	not_local_elements_end () const =0
virtual element_iterator	active_local_elements_begin ()=0
virtual const_element_iterator	active_local_elements_begin () const =0
virtual element_iterator	active_local_elements_end ()=0
virtual const_element_iterator	active_local_elements_end () const =0
virtual element_iterator	active_not_local_elements_begin ()=0
virtual const_element_iterator	active_not_local_elements_begin () const =0
virtual element_iterator	active_not_local_elements_end ()=0
virtual const_element_iterator	active_not_local_elements_end () const =0
virtual element_iterator	level_elements_begin (const unsigned int level)=0
virtual const_element_iterator	level_elements_begin (const unsigned int level) const =0
virtual element_iterator	level_elements_end (const unsigned int level)=0
virtual const_element_iterator	level_elements_end (const unsigned int level) const =0
virtual element_iterator	not_level_elements_begin (const unsigned int level)=0
virtual const_element_iterator	not_level_elements_begin (const unsigned int level) const =0
virtual element_iterator	not_level_elements_end (const unsigned int level)=0
virtual const_element_iterator	not_level_elements_end (const unsigned int level) const =0
virtual element_iterator	local_level_elements_begin (const unsigned int level)=0
virtual const_element_iterator	local_level_elements_begin (const unsigned int level) const =0
virtual element_iterator	local_level_elements_end (const unsigned int level)=0
virtual const_element_iterator	local_level_elements_end (const unsigned int level) const =0
virtual element_iterator	local_not_level_elements_begin (const unsigned int level)=0
virtual const_element_iterator	local_not_level_elements_begin (const unsigned int level) const =0
virtual element_iterator	local_not_level_elements_end (const unsigned int level)=0
virtual const_element_iterator	local_not_level_elements_end (const unsigned int level) const =0
virtual element_iterator	pid_elements_begin (const processor_id_type proc_id)=0
virtual const_element_iterator	pid_elements_begin (const processor_id_type proc_id) const =0
virtual element_iterator	pid_elements_end (const processor_id_type proc_id)=0
virtual const_element_iterator	pid_elements_end (const processor_id_type proc_id) const =0
virtual element_iterator	type_elements_begin (const ElemType type)=0
virtual const_element_iterator	type_elements_begin (const ElemType type) const =0
virtual element_iterator	type_elements_end (const ElemType type)=0
virtual const_element_iterator	type_elements_end (const ElemType type) const =0
virtual element_iterator	active_type_elements_begin (const ElemType type)=0
virtual const_element_iterator	active_type_elements_begin (const ElemType type) const =0
virtual element_iterator	active_type_elements_end (const ElemType type)=0
virtual const_element_iterator	active_type_elements_end (const ElemType type) const =0
virtual element_iterator	active_pid_elements_begin (const processor_id_type proc_id)=0
virtual const_element_iterator	active_pid_elements_begin (const processor_id_type proc_id) const =0
virtual element_iterator	active_pid_elements_end (const processor_id_type proc_id)=0
virtual const_element_iterator	active_pid_elements_end (const processor_id_type proc_id) const =0
virtual element_iterator	unpartitioned_elements_begin ()=0
virtual const_element_iterator	unpartitioned_elements_begin () const =0
virtual element_iterator	unpartitioned_elements_end ()=0
virtual const_element_iterator	unpartitioned_elements_end () const =0
virtual element_iterator	active_local_subdomain_elements_begin (const subdomain_id_type subdomain_id)=0
virtual const_element_iterator	active_local_subdomain_elements_begin (const subdomain_id_type subdomain_id) const =0
virtual element_iterator	active_local_subdomain_elements_end (const subdomain_id_type subdomain_id)=0
virtual const_element_iterator	active_local_subdomain_elements_end (const subdomain_id_type subdomain_id) const =0
virtual element_iterator	active_subdomain_elements_begin (const subdomain_id_type subdomain_id)=0
virtual const_element_iterator	active_subdomain_elements_begin (const subdomain_id_type subdomain_id) const =0
virtual element_iterator	active_subdomain_elements_end (const subdomain_id_type subdomain_id)=0
virtual const_element_iterator	active_subdomain_elements_end (const subdomain_id_type subdomain_id) const =0
virtual node_iterator	nodes_begin ()=0
virtual const_node_iterator	nodes_begin () const =0
virtual node_iterator	nodes_end ()=0
virtual const_node_iterator	nodes_end () const =0
virtual node_iterator	active_nodes_begin ()=0
virtual const_node_iterator	active_nodes_begin () const =0
virtual node_iterator	active_nodes_end ()=0
virtual const_node_iterator	active_nodes_end () const =0
virtual node_iterator	local_nodes_begin ()=0
virtual const_node_iterator	local_nodes_begin () const =0
virtual node_iterator	local_nodes_end ()=0
virtual const_node_iterator	local_nodes_end () const =0
virtual node_iterator	pid_nodes_begin (const processor_id_type proc_id)=0
virtual const_node_iterator	pid_nodes_begin (const processor_id_type proc_id) const =0
virtual node_iterator	pid_nodes_end (const processor_id_type proc_id)=0
virtual const_node_iterator	pid_nodes_end (const processor_id_type proc_id) const =0
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 ()
const Parallel::Communicator &	comm () const
processor_id_type	n_processors () const
processor_id_type	processor_id () const
Public Attributes
UniquePtr< BoundaryInfo >	boundary_info
Protected Member Functions
virtual void	assign_unique_ids ()=0
unsigned int &	set_n_partitions ()
Protected Attributes
unsigned int	_n_parts
bool	_is_prepared
UniquePtr< PointLocatorBase >	_point_locator
UniquePtr< Partitioner >	_partitioner
unique_id_type	_next_unique_id
bool	_skip_partitioning
bool	_skip_renumber_nodes_and_elements
std::map< subdomain_id_type, std::string >	_block_id_to_name
std::set< unsigned char >	_elem_dims
const Parallel::Communicator &	_communicator
Friends
class	Partitioner
class	MeshInput< MeshBase >
class	BoundaryInfo
std::ostream &	operator<< (std::ostream &os, const MeshBase &m)

Detailed Description

The UnstructuredMesh class is derived from the MeshBase class. The user will typically want to instantiate and use the Mesh class in her applications, which is currently a simple derived class of UnstructuredMesh. In order to use the adaptive mesh refinment capabilities of the library, first instantiate a MeshRefinement object with a reference to this class. Then call the appropriate refinement functions from that object. To interact with the boundary, instantiate a BoundaryMesh with a reference to this class, and then use that object's functionality.

Definition at line 51 of file unstructured_mesh.h.

Member Typedef Documentation

typedef Predicates::multi_predicate libMesh::MeshBase::Predicate [inherited]

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

Definition at line 647 of file mesh_base.h.

Constructor & Destructor Documentation

libMesh::UnstructuredMesh::UnstructuredMesh	(	const Parallel::Communicator &	comm_in,
		unsigned char	dim = `1`
	)		`[explicit]`

Constructor. Takes dim, the dimension of the mesh. The mesh dimension can be changed (and may automatically be changed by mesh generation/loading) later.

Definition at line 54 of file unstructured_mesh.C.

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

                                                     :
  MeshBase (comm_in,d)
{
  libmesh_assert (libMesh::initialized());
}

libMesh::UnstructuredMesh::UnstructuredMesh ( unsigned char dim = 1 )

Deprecated constructor. Takes dim, the dimension of the mesh. The mesh dimension can be changed (and may automatically be changed by mesh generation/loading) later.

Definition at line 64 of file unstructured_mesh.C.

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

                                                   :
  MeshBase (d)
{
  libmesh_assert (libMesh::initialized());
}

libMesh::UnstructuredMesh::~UnstructuredMesh ( ) [virtual]

Destructor.

Definition at line 210 of file unstructured_mesh.C.

References libMesh::closed().

{
  //  this->clear ();  // Nothing to clear at this level

  libmesh_exceptionless_assert (!libMesh::closed());
}

Member Function Documentation

virtual element_iterator libMesh::MeshBase::active_elements_begin ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::active_elements_begin ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::active_elements_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::active_elements_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::active_local_elements_begin ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::FEMSystem::assemble_qoi(), libMesh::FEMSystem::assemble_qoi_derivative(), libMesh::FEMSystem::assembly(), libMesh::Nemesis_IO_Helper::build_element_and_node_maps(), libMesh::ParmetisPartitioner::build_graph(), libMesh::EquationSystems::build_solution_vector(), libMesh::DofMap::build_sparsity(), libMesh::MeshBase::cache_elem_dims(), libMesh::System::calculate_norm(), libMesh::VTKIO::cells_to_vtk(), libMesh::Nemesis_IO_Helper::compute_internal_and_border_elems_and_internal_nodes(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::MeshTools::find_hanging_nodes_and_parents(), libMesh::MeshRefinement::flag_elements_by_elem_fraction(), libMesh::MeshRefinement::flag_elements_by_error_fraction(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::EquationSystems::get_solution(), libMesh::LaplaceMeshSmoother::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::ParmetisPartitioner::initialize(), libMesh::MeshTools::libmesh_assert_valid_procids< Node >(), libMesh::System::local_dof_indices(), libMesh::DofMap::local_variable_indices(), libMesh::DofMap::max_constraint_error(), libMesh::FEMSystem::mesh_position_get(), libMesh::FEMSystem::mesh_position_set(), libMesh::MeshTools::n_active_local_levels(), libMesh::PointLocatorTree::perform_linear_search(), libMesh::ErrorVector::plot_error(), libMesh::FEMSystem::postprocess(), libMesh::System::project_vector(), libMesh::MeshBase::recalculate_n_partitions(), libMesh::HPSingularity::select_refinement(), libMesh::HPCoarsenTest::select_refinement(), libMesh::MeshBase::subdomain_ids(), libMesh::MeshRefinement::test_level_one(), libMesh::MeshRefinement::test_unflagged(), libMesh::Tree< N >::Tree(), libMesh::Nemesis_IO_Helper::write_exodus_initialization_info(), libMesh::EnsightIO::write_geometry_ascii(), libMesh::EnsightIO::write_scalar_ascii(), libMesh::EnsightIO::write_vector_ascii(), and libMesh::System::zero_variable().

virtual const_element_iterator libMesh::MeshBase::active_local_elements_begin ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::active_local_elements_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::FEMSystem::assemble_qoi(), libMesh::FEMSystem::assemble_qoi_derivative(), libMesh::FEMSystem::assembly(), libMesh::Nemesis_IO_Helper::build_element_and_node_maps(), libMesh::ParmetisPartitioner::build_graph(), libMesh::EquationSystems::build_solution_vector(), libMesh::DofMap::build_sparsity(), libMesh::MeshBase::cache_elem_dims(), libMesh::System::calculate_norm(), libMesh::VTKIO::cells_to_vtk(), libMesh::Nemesis_IO_Helper::compute_internal_and_border_elems_and_internal_nodes(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::MeshTools::find_hanging_nodes_and_parents(), libMesh::MeshRefinement::flag_elements_by_elem_fraction(), libMesh::MeshRefinement::flag_elements_by_error_fraction(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::EquationSystems::get_solution(), libMesh::LaplaceMeshSmoother::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::ParmetisPartitioner::initialize(), libMesh::MeshTools::libmesh_assert_valid_procids< Node >(), libMesh::System::local_dof_indices(), libMesh::DofMap::local_variable_indices(), libMesh::DofMap::max_constraint_error(), libMesh::FEMSystem::mesh_position_get(), libMesh::FEMSystem::mesh_position_set(), libMesh::MeshTools::n_active_local_levels(), libMesh::PointLocatorTree::perform_linear_search(), libMesh::ErrorVector::plot_error(), libMesh::FEMSystem::postprocess(), libMesh::MeshBase::recalculate_n_partitions(), libMesh::HPSingularity::select_refinement(), libMesh::HPCoarsenTest::select_refinement(), libMesh::MeshBase::subdomain_ids(), libMesh::MeshRefinement::test_level_one(), libMesh::MeshRefinement::test_unflagged(), libMesh::Tree< N >::Tree(), libMesh::Nemesis_IO_Helper::write_exodus_initialization_info(), libMesh::EnsightIO::write_geometry_ascii(), libMesh::EnsightIO::write_scalar_ascii(), libMesh::EnsightIO::write_vector_ascii(), and libMesh::System::zero_variable().

virtual const_element_iterator libMesh::MeshBase::active_local_elements_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::active_local_subdomain_elements_begin ( const subdomain_id_type subdomain_id ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by DMCreateDomainDecomposition_libMesh(), and DMCreateFieldDecomposition_libMesh().

virtual const_element_iterator libMesh::MeshBase::active_local_subdomain_elements_begin ( const subdomain_id_type subdomain_id ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::active_local_subdomain_elements_end ( const subdomain_id_type subdomain_id ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by DMCreateDomainDecomposition_libMesh(), and DMCreateFieldDecomposition_libMesh().

virtual const_element_iterator libMesh::MeshBase::active_local_subdomain_elements_end ( const subdomain_id_type subdomain_id ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual node_iterator libMesh::MeshBase::active_nodes_begin ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_node_iterator libMesh::MeshBase::active_nodes_begin ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual node_iterator libMesh::MeshBase::active_nodes_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_node_iterator libMesh::MeshBase::active_nodes_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::active_not_local_elements_begin ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::DofMap::allgather_recursive_constraints(), and libMesh::DofMap::scatter_constraints().

virtual const_element_iterator libMesh::MeshBase::active_not_local_elements_begin ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::active_not_local_elements_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::DofMap::allgather_recursive_constraints(), and libMesh::DofMap::scatter_constraints().

virtual const_element_iterator libMesh::MeshBase::active_not_local_elements_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::active_pid_elements_begin ( const processor_id_type proc_id ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by create_pid_mesh(), libMesh::ParmetisPartitioner::initialize(), and libMesh::MeshBase::n_active_elem_on_proc().

virtual const_element_iterator libMesh::MeshBase::active_pid_elements_begin ( const processor_id_type proc_id ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::active_pid_elements_end ( const processor_id_type proc_id ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by create_pid_mesh(), libMesh::ParmetisPartitioner::initialize(), and libMesh::MeshBase::n_active_elem_on_proc().

virtual const_element_iterator libMesh::MeshBase::active_pid_elements_end ( const processor_id_type proc_id ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::active_subdomain_elements_begin ( const subdomain_id_type subdomain_id ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::TecplotIO::write_binary().

virtual const_element_iterator libMesh::MeshBase::active_subdomain_elements_begin ( const subdomain_id_type subdomain_id ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::active_subdomain_elements_end ( const subdomain_id_type subdomain_id ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::TecplotIO::write_binary().

virtual const_element_iterator libMesh::MeshBase::active_subdomain_elements_end ( const subdomain_id_type subdomain_id ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::active_type_elements_begin ( const ElemType type ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshTools::n_active_elem_of_type().

virtual const_element_iterator libMesh::MeshBase::active_type_elements_begin ( const ElemType type ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::active_type_elements_end ( const ElemType type ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshTools::n_active_elem_of_type().

virtual const_element_iterator libMesh::MeshBase::active_type_elements_end ( const ElemType type ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual Elem* libMesh::MeshBase::add_elem ( Elem * e ) [pure virtual, inherited]

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.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::GMVIO::_read_one_cell(), libMesh::MeshTools::Subdivision::add_boundary_ghosts(), libMesh::MeshRefinement::add_elem(), libMesh::MeshTools::Modification::all_tri(), libMesh::MeshTools::Generation::build_cube(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::TriangleWrapper::copy_tri_to_mesh(), create_submesh(), libMesh::UNVIO::elements_in(), libMesh::MeshTools::Modification::flatten(), libMesh::mesh_inserter_iterator< T >::operator=(), libMesh::TetGenMeshInterface::pointset_convexhull(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::VTKIO::read(), libMesh::CheckpointIO::read_connectivity(), libMesh::AbaqusIO::read_elements(), libMesh::GmshIO::read_mesh(), libMesh::LegacyXdrIO::read_mesh(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::OFFIO::read_stream(), libMesh::MatlabIO::read_stream(), libMesh::BoundaryInfo::sync(), libMesh::TetGenMeshInterface::triangulate_conformingDelaunayMesh_carvehole(), and libMesh::TetGenMeshInterface::triangulate_pointset().

virtual Node* libMesh::MeshBase::add_node ( Node * n ) [pure virtual, inherited]

Add Node n to the end of the vertex array.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual Node* libMesh::MeshBase::add_point	(	const Point &	p,
		const dof_id_type	id = `DofObject::invalid_id`,
		const processor_id_type	proc_id = `DofObject::invalid_processor_id`
	)		`[pure virtual, inherited]`

Add a new Node at Point p to the end of the vertex array, with processor_id procid. Use DofObject::invalid_processor_id (default) to add a node to all processors, or this->processor_id() to add a node to the local processor only. If adding a node locally, passing an id other than DofObject::invalid_id will set that specific node id. Only do this in parallel if you are manually keeping ids consistent.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::GMVIO::_read_nodes(), libMesh::MeshTools::Subdivision::add_boundary_ghosts(), libMesh::MeshRefinement::add_point(), all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::MeshTools::Generation::build_cube(), libMesh::MeshTools::Generation::build_delaunay_square(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::TriangleWrapper::copy_tri_to_mesh(), create_submesh(), libMesh::UNVIO::nodes_in(), libMesh::mesh_inserter_iterator< T >::operator=(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::VTKIO::read(), libMesh::GmshIO::read_mesh(), libMesh::LegacyXdrIO::read_mesh(), libMesh::AbaqusIO::read_nodes(), libMesh::CheckpointIO::read_nodes(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::OFFIO::read_stream(), libMesh::MatlabIO::read_stream(), libMesh::BoundaryInfo::sync(), libMesh::TriangleInterface::triangulate(), and libMesh::TetGenMeshInterface::triangulate_conformingDelaunayMesh_carvehole().

void libMesh::UnstructuredMesh::all_first_order ( ) [virtual]

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 transfered 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 293 of file mesh_modification.C.

{
  /*
   * when the mesh is not prepared,
   * at least renumber the nodes and
   * elements, so that the node ids
   * are correct
   */
  if (!this->_is_prepared)
    this->renumber_nodes_and_elements ();

  START_LOG("all_first_order()", "Mesh");

  std::vector<bool> node_touched_by_me(this->max_node_id(), false);

  element_iterator endit = elements_end();
  for (element_iterator it = elements_begin();
       it != endit; ++it)
    {
      Elem* so_elem = *it;

      libmesh_assert(so_elem);

      /*
       * build the first-order equivalent, add to
       * the new_elements list.
       */
      Elem* lo_elem = Elem::build
        (Elem::first_order_equivalent_type
         (so_elem->type()), so_elem->parent()).release();

      for (unsigned int s=0; s != so_elem->n_sides(); ++s)
        if (so_elem->neighbor(s) == remote_elem)
          lo_elem->set_neighbor(s, const_cast<RemoteElem*>(remote_elem));

#ifdef LIBMESH_ENABLE_AMR
      /*
       * Reset the parent links of any child elements
       */
      if (so_elem->has_children())
        for (unsigned int c=0; c != so_elem->n_children(); ++c)
          {
            so_elem->child(c)->set_parent(lo_elem);
            lo_elem->add_child(so_elem->child(c), c);
          }

      /*
       * Reset the child link of any parent element
       */
      if (so_elem->parent())
        {
          unsigned int c =
            so_elem->parent()->which_child_am_i(so_elem);
          lo_elem->parent()->replace_child(lo_elem, c);
        }

      /*
       * Copy as much data to the new element as makes sense
       */
      lo_elem->set_p_level(so_elem->p_level());
      lo_elem->set_refinement_flag(so_elem->refinement_flag());
      lo_elem->set_p_refinement_flag(so_elem->p_refinement_flag());
#endif

      libmesh_assert_equal_to (lo_elem->n_vertices(), so_elem->n_vertices());

      /*
       * By definition the vertices of the linear and
       * second order element are identically numbered.
       * transfer these.
       */
      for (unsigned int v=0; v < so_elem->n_vertices(); v++)
        {
          lo_elem->set_node(v) = so_elem->get_node(v);
          node_touched_by_me[lo_elem->node(v)] = true;
        }

      libmesh_assert_equal_to (lo_elem->n_sides(), so_elem->n_sides());

      for (unsigned short s=0; s<so_elem->n_sides(); s++)
        {
          const std::vector<boundary_id_type> boundary_ids =
            this->get_boundary_info().raw_boundary_ids (so_elem, s);

          this->get_boundary_info().add_side (lo_elem, s, boundary_ids);
        }

      /*
       * The new first-order element is ready.
       * Inserting it into the mesh will replace and delete
       * the second-order element.
       */
      lo_elem->set_id(so_elem->id());
      lo_elem->processor_id() = so_elem->processor_id();
      lo_elem->subdomain_id() = so_elem->subdomain_id();
      this->insert_elem(lo_elem);
    }

  const MeshBase::node_iterator nd_end = this->nodes_end();
  MeshBase::node_iterator nd = this->nodes_begin();
  while (nd != nd_end)
    {
      Node *the_node = *nd;
      ++nd;
      if (!node_touched_by_me[the_node->id()])
        this->delete_node(the_node);
    }

  STOP_LOG("all_first_order()", "Mesh");

  // On hanging nodes that used to also be second order nodes, we
  // might now have an invalid nodal processor_id()
  Partitioner::set_node_processor_ids(*this);

  // delete or renumber nodes, etc
  this->prepare_for_use(/*skip_renumber =*/ false);
}

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

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 that 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 ...

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 transfered 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 427 of file mesh_modification.C.

Referenced by libMesh::MeshTools::Generation::build_cube().

{
  // This function must be run on all processors at once
  parallel_object_only();

  /*
   * when the mesh is not prepared,
   * at least renumber the nodes and
   * elements, so that the node ids
   * are correct
   */
  if (!this->_is_prepared)
    this->renumber_nodes_and_elements ();

  /*
   * If the mesh is empty
   * then we have nothing to do
   */
  if (!this->n_elem())
    return;

  /*
   * If the mesh is already second order
   * then we have nothing to do.
   * We have to test for this in a round-about way to avoid
   * a bug on distributed parallel meshes with more processors
   * than elements.
   */
  bool already_second_order = false;
  if (this->elements_begin() != this->elements_end() &&
      (*(this->elements_begin()))->default_order() != FIRST)
    already_second_order = true;
  this->comm().max(already_second_order);
  if (already_second_order)
    return;

  START_LOG("all_second_order()", "Mesh");

  /*
   * this map helps in identifying second order
   * nodes.  Namely, a second-order node:
   * - edge node
   * - face node
   * - bubble node
   * is uniquely defined through a set of adjacent
   * vertices.  This set of adjacent vertices is
   * used to identify already added higher-order
   * nodes.  We are safe to use node id's since we
   * make sure that these are correctly numbered.
   */
  std::map<std::vector<dof_id_type>, Node*> adj_vertices_to_so_nodes;

  /*
   * for speed-up of the \p add_point() method, we
   * can reserve memory.  Guess the number of additional
   * nodes for different dimensions
   */
  switch (this->mesh_dimension())
    {
    case 1:
      /*
       * in 1D, there can only be order-increase from Edge2
       * to Edge3.  Something like 1/2 of n_nodes() have
       * to be added
       */
      this->reserve_nodes(static_cast<unsigned int>
                          (1.5*static_cast<double>(this->n_nodes())));
      break;

    case 2:
      /*
       * in 2D, either refine from Tri3 to Tri6 (double the nodes)
       * or from Quad4 to Quad8 (again, double) or Quad9 (2.25 that much)
       */
      this->reserve_nodes(static_cast<unsigned int>
                          (2*static_cast<double>(this->n_nodes())));
      break;


    case 3:
      /*
       * in 3D, either refine from Tet4 to Tet10 (factor = 2.5) up to
       * Hex8 to Hex27 (something  > 3).  Since in 3D there _are_ already
       * quite some nodes, and since we do not want to overburden the memory by
       * a too conservative guess, use the lower bound
       */
      this->reserve_nodes(static_cast<unsigned int>
                          (2.5*static_cast<double>(this->n_nodes())));
      break;

    default:
      // Hm?
      libmesh_error_msg("Unknown mesh dimension " << this->mesh_dimension());
    }



  /*
   * form a vector that will hold the node id's of
   * the vertices that are adjacent to the son-th
   * second-order node.  Pull this outside of the
   * loop so that silly compilers don't repeatedly
   * create and destroy the vector.
   */
  std::vector<dof_id_type> adjacent_vertices_ids;

  const_element_iterator endit = elements_end();
  for (const_element_iterator it = elements_begin();
       it != endit; ++it)
    {
      // the linear-order element
      const Elem* lo_elem = *it;

      libmesh_assert(lo_elem);

      // make sure it is linear order
      if (lo_elem->default_order() != FIRST)
        libmesh_error_msg("ERROR: This is not a linear element: type=" << lo_elem->type());

      // this does _not_ work for refined elements
      libmesh_assert_equal_to (lo_elem->level (), 0);

      /*
       * build the second-order equivalent, add to
       * the new_elements list.  Note that this here
       * is the only point where \p full_ordered
       * is necessary.  The remaining code works well
       * for either type of seconrd-order equivalent, e.g.
       * Hex20 or Hex27, as equivalents for Hex8
       */
      Elem* so_elem =
        Elem::build (Elem::second_order_equivalent_type(lo_elem->type(),
                                                        full_ordered) ).release();

      libmesh_assert_equal_to (lo_elem->n_vertices(), so_elem->n_vertices());


      /*
       * By definition the vertices of the linear and
       * second order element are identically numbered.
       * transfer these.
       */
      for (unsigned int v=0; v < lo_elem->n_vertices(); v++)
        so_elem->set_node(v) = lo_elem->get_node(v);

      /*
       * Now handle the additional mid-side nodes.  This
       * is simply handled through a map that remembers
       * the already-added nodes.  This map maps the global
       * ids of the vertices (that uniquely define this
       * higher-order node) to the new node.
       * Notation: son = second-order node
       */
      const unsigned int son_begin = so_elem->n_vertices();
      const unsigned int son_end   = so_elem->n_nodes();


      for (unsigned int son=son_begin; son<son_end; son++)
        {
          const unsigned int n_adjacent_vertices =
            so_elem->n_second_order_adjacent_vertices(son);

          adjacent_vertices_ids.resize(n_adjacent_vertices);

          for (unsigned int v=0; v<n_adjacent_vertices; v++)
            adjacent_vertices_ids[v] =
              so_elem->node( so_elem->second_order_adjacent_vertex(son,v) );

          /*
           * \p adjacent_vertices_ids is now in order of the current
           * side.  sort it, so that comparisons  with the
           * \p adjacent_vertices_ids created through other elements'
           * sides can match
           */
          std::sort(adjacent_vertices_ids.begin(),
                    adjacent_vertices_ids.end());


          // does this set of vertices already has a mid-node added?
          std::pair<std::map<std::vector<dof_id_type>, Node*>::iterator,
            std::map<std::vector<dof_id_type>, Node*>::iterator>
            pos = adj_vertices_to_so_nodes.equal_range (adjacent_vertices_ids);

          // no, not added yet
          if (pos.first == pos.second)
            {
              /*
               * for this set of vertices, there is no
               * second_order node yet.  Add it.
               *
               * compute the location of the new node as
               * the average over the adjacent vertices.
               */
              Point new_location = this->point(adjacent_vertices_ids[0]);
              for (unsigned int v=1; v<n_adjacent_vertices; v++)
                new_location += this->point(adjacent_vertices_ids[v]);

              new_location /= static_cast<Real>(n_adjacent_vertices);

              /* Add the new point to the mesh, giving it a globally
               * well-defined processor id.
               */
              Node* so_node = this->add_point
                (new_location, DofObject::invalid_id,
                 this->node(adjacent_vertices_ids[0]).processor_id());

              /*
               * insert the new node with its defining vertex
               * set into the map, and relocate pos to this
               * new entry, so that the so_elem can use
               * \p pos for inserting the node
               */
              adj_vertices_to_so_nodes.insert(pos.first,
                                              std::make_pair(adjacent_vertices_ids,
                                                             so_node));

              so_elem->set_node(son) = so_node;
            }
          // yes, already added.
          else
            {
              libmesh_assert(pos.first->second);

              so_elem->set_node(son) = pos.first->second;
            }
        }


      libmesh_assert_equal_to (lo_elem->n_sides(), so_elem->n_sides());

      for (unsigned short s=0; s<lo_elem->n_sides(); s++)
        {
          const std::vector<boundary_id_type> boundary_ids =
            this->get_boundary_info().raw_boundary_ids (lo_elem, s);

          this->get_boundary_info().add_side (so_elem, s, boundary_ids);

          if (lo_elem->neighbor(s) == remote_elem)
            so_elem->set_neighbor(s, const_cast<RemoteElem*>(remote_elem));
        }

      /*
       * The new second-order element is ready.
       * Inserting it into the mesh will replace and delete
       * the first-order element.
       */
      so_elem->set_id(lo_elem->id());
      so_elem->processor_id() = lo_elem->processor_id();
      so_elem->subdomain_id() = lo_elem->subdomain_id();
      this->insert_elem(so_elem);
    }

  // we can clear the map
  adj_vertices_to_so_nodes.clear();


  STOP_LOG("all_second_order()", "Mesh");

  // In a ParallelMesh our ghost node processor ids may be bad and
  // the ids of nodes touching remote elements may be inconsistent.
  // Fix them.
  if (!this->is_serial())
    MeshCommunication().make_nodes_parallel_consistent (*this);

  // renumber nodes, elements etc
  this->prepare_for_use(/*skip_renumber =*/ false);
}

virtual void libMesh::MeshBase::allgather ( ) [inline, virtual, inherited]

Gathers all elements and nodes of the mesh onto every processor

Reimplemented in libMesh::ParallelMesh.

Definition at line 145 of file mesh_base.h.

Referenced by libMesh::EquationSystems::allgather(), and libMesh::MeshSerializer::MeshSerializer().

{}

void libMesh::MeshBase::allow_renumbering ( bool allow ) [inline, 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, particulary when using a distributed mesh.

Definition at line 551 of file mesh_base.h.

References libMesh::MeshBase::_skip_renumber_nodes_and_elements.

Referenced by copy_nodes_and_elements(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ErrorVector::plot_error(), and libMesh::NameBasedIO::read().

{ _skip_renumber_nodes_and_elements = !allow; }

bool libMesh::MeshBase::allow_renumbering ( ) const [inline, inherited]

Definition at line 552 of file mesh_base.h.

References libMesh::MeshBase::_skip_renumber_nodes_and_elements.

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

{ return !_skip_renumber_nodes_and_elements; }

virtual element_iterator libMesh::MeshBase::ancestor_elements_begin ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::ancestor_elements_begin ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::ancestor_elements_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::ancestor_elements_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual void libMesh::MeshBase::assign_unique_ids ( ) [protected, pure virtual, inherited]

Assign globally unique IDs to all DOF objects (Elements and Nodes) if the library has been configured with unique_id support.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

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

void libMesh::MeshBase::cache_elem_dims ( ) [inherited]

Search the mesh and cache the different dimenions 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 497 of file mesh_base.C.

References libMesh::MeshBase::_elem_dims, libMesh::MeshBase::active_local_elements_begin(), libMesh::MeshBase::active_local_elements_end(), libMesh::ParallelObject::comm(), end, and libMesh::Parallel::Communicator::set_union().

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

{
  // This requires an inspection on every processor
  parallel_object_only();

  const_element_iterator el  = this->active_local_elements_begin();
  const_element_iterator end = this->active_local_elements_end();

  for (; el!=end; ++el)
    _elem_dims.insert((*el)->dim());

  // Some different dimension elements may only live on other processors
  this->comm().set_union(_elem_dims);
}

void libMesh::MeshBase::clear ( ) [virtual, inherited]

Deletes all the data that are currently stored.

Reimplemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Definition at line 196 of file mesh_base.C.

References libMesh::MeshBase::_elem_dims, libMesh::MeshBase::_is_prepared, libMesh::MeshBase::_n_parts, libMesh::BoundaryInfo::clear(), libMesh::MeshBase::clear_point_locator(), and libMesh::MeshBase::get_boundary_info().

Referenced by libMesh::MeshTools::Generation::build_cube(), libMesh::MeshTools::Generation::build_delaunay_square(), libMesh::TriangleWrapper::copy_tri_to_mesh(), create_submesh(), libMesh::AbaqusIO::read(), libMesh::ExodusII_IO::read(), libMesh::GMVIO::read(), libMesh::VTKIO::read(), libMesh::LegacyXdrIO::read_ascii(), libMesh::GmshIO::read_mesh(), libMesh::LegacyXdrIO::read_mesh(), libMesh::OFFIO::read_stream(), libMesh::MatlabIO::read_stream(), libMesh::BoundaryInfo::sync(), libMesh::TriangleInterface::triangulate(), and libMesh::MeshBase::~MeshBase().

{
  // Reset the number of partitions
  _n_parts = 1;

  // Reset the _is_prepared flag
  _is_prepared = false;

  // Clear boundary information
  this->get_boundary_info().clear();

  // Clear element dimensions
  _elem_dims.clear();

  // Clear our point locator.
  this->clear_point_locator();
}

void libMesh::MeshBase::clear_point_locator ( ) [inherited]

Releases the current PointLocator object.

Definition at line 454 of file mesh_base.C.

References libMesh::MeshBase::_point_locator.

Referenced by libMesh::MeshBase::clear(), contract(), and libMesh::MeshBase::prepare_for_use().

{
  _point_locator.reset(NULL);
}

virtual UniquePtr<MeshBase> libMesh::MeshBase::clone ( ) const [pure virtual, inherited]

Virtual "copy constructor"

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::ErrorVector::plot_error().

const Parallel::Communicator& libMesh::ParallelObject::comm ( ) const [inline, inherited]

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

Definition at line 86 of file parallel_object.h.

References libMesh::ParallelObject::_communicator.

  { return _communicator; }

bool libMesh::UnstructuredMesh::contract ( ) [virtual]

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 694 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::libmesh_assert(), libMesh::Elem::parent(), libMesh::MeshBase::renumber_nodes_and_elements(), libMesh::START_LOG(), and libMesh::Elem::subactive().

{
  START_LOG ("contract()", "Mesh");

  // Flag indicating if this call actually changes the mesh
  bool mesh_changed = false;

  element_iterator in        = elements_begin();
  const element_iterator end = elements_end();

#ifdef DEBUG
  for ( ; in != end; ++in)
    if (*in != NULL)
      {
        Elem* el = *in;
        libmesh_assert(el->active() || el->subactive() || el->ancestor());
      }
  in = elements_begin();
#endif

  // Loop over the elements.
  for ( ; in != end; ++in)
    if (*in != NULL)
      {
        Elem* el = *in;

        // Delete all the subactive ones
        if (el->subactive())
          {
            // No level-0 element should be subactive.
            // Note that we CAN'T test elem->level(), as that
            // touches elem->parent()->dim(), and elem->parent()
            // might have already been deleted!
            libmesh_assert(el->parent());

            // Delete the element
            // This just sets a pointer to NULL, and doesn't
            // invalidate any iterators
            this->delete_elem(el);

            // the mesh has certainly changed
            mesh_changed = true;
          }
        else
          {
            // Compress all the active ones
            if (el->active())
              el->contract();
            else
              libmesh_assert (el->ancestor());
          }
      }

  // Strip any newly-created NULL voids out of the element array
  this->renumber_nodes_and_elements();

  // FIXME: Need to understand why deleting subactive children
  // invalidates the point locator.  For now we will clear it explicitly
  this->clear_point_locator();

  STOP_LOG ("contract()", "Mesh");

  return mesh_changed;
}

void libMesh::UnstructuredMesh::copy_nodes_and_elements	(	const UnstructuredMesh &	other_mesh,
		const bool	skip_find_neighbors = `false`
	)		`[virtual]`

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

Definition at line 74 of file unstructured_mesh.C.

Referenced by libMesh::ParallelMesh::ParallelMesh(), libMesh::SerialMesh::SerialMesh(), and libMesh::SerialMesh::stitching_helper().

{
  // We're assuming our subclass data needs no copy
  libmesh_assert_equal_to (_n_parts, other_mesh._n_parts);
  libmesh_assert (std::equal(_elem_dims.begin(), _elem_dims.end(), other_mesh._elem_dims.begin()));
  libmesh_assert_equal_to (_is_prepared, other_mesh._is_prepared);

  // We're assuming the other mesh has proper element number ordering,
  // so that we add parents before their children.
#ifdef DEBUG
  MeshTools::libmesh_assert_valid_amr_elem_ids(other_mesh);
#endif

  //Copy in Nodes
  {
    //Preallocate Memory if necessary
    this->reserve_nodes(other_mesh.n_nodes());

    const_node_iterator it = other_mesh.nodes_begin();
    const_node_iterator end = other_mesh.nodes_end();

    for (; it != end; ++it)
      {
        const Node *oldn = *it;

        // Add new nodes in old node Point locations
        /*Node *newn =*/ this->add_point(*oldn, oldn->id(), oldn->processor_id());

        // And start them off in the same subdomain
        //        newn->processor_id() = oldn->processor_id();
      }
  }

  //Copy in Elements
  {
    //Preallocate Memory if necessary
    this->reserve_elem(other_mesh.n_elem());

    // Declare a map linking old and new elements, needed to copy the neighbor lists
    std::map<const Elem*, Elem*> old_elems_to_new_elems;

    // Loop over the elements
    MeshBase::const_element_iterator it = other_mesh.elements_begin();
    const MeshBase::const_element_iterator end = other_mesh.elements_end();

    // FIXME: Where do we set element IDs??
    for (; it != end; ++it)
      {
        //Look at the old element
        const Elem *old = *it;
        //Build a new element
        Elem *newparent = old->parent() ?
          this->elem(old->parent()->id()) : NULL;
        UniquePtr<Elem> ap = Elem::build(old->type(), newparent);
        Elem * el = ap.release();

        el->subdomain_id() = old->subdomain_id();

        for (unsigned int s=0; s != old->n_sides(); ++s)
          if (old->neighbor(s) == remote_elem)
            el->set_neighbor(s, const_cast<RemoteElem*>(remote_elem));

#ifdef LIBMESH_ENABLE_AMR
        if (old->has_children())
          for (unsigned int c=0; c != old->n_children(); ++c)
            if (old->child(c) == remote_elem)
              el->add_child(const_cast<RemoteElem*>(remote_elem), c);

        //Create the parent's child pointers if necessary
        if (newparent)
          {
            unsigned int oldc = old->parent()->which_child_am_i(old);
            newparent->add_child(el, oldc);
          }

        // Copy the refinement flags
        el->set_refinement_flag(old->refinement_flag());
        el->set_p_refinement_flag(old->p_refinement_flag());
#endif // #ifdef LIBMESH_ENABLE_AMR

        //Assign all the nodes
        for(unsigned int i=0;i<el->n_nodes();i++)
          el->set_node(i) = &this->node(old->node(i));

        // And start it off in the same subdomain
        el->processor_id() = old->processor_id();

        // Give it the same id
        el->set_id(old->id());

        //Hold onto it
        if(!skip_find_neighbors)
          {
            this->add_elem(el);
          }
        else
          {
            Elem* new_el = this->add_elem(el);
            old_elems_to_new_elems[old] = new_el;
          }

        // Add the link between the original element and this copy to the map
        if(skip_find_neighbors)
          old_elems_to_new_elems[old] = el;
      }

    // Loop (again) over the elements to fill in the neighbors
    if(skip_find_neighbors)
      {
        it = other_mesh.elements_begin();
        for (; it != end; ++it)
          {
            Elem* old_elem = *it;
            Elem* new_elem = old_elems_to_new_elems[old_elem];
            for (unsigned int s=0; s != old_elem->n_neighbors(); ++s)
              {
                const Elem* old_neighbor = old_elem->neighbor(s);
                Elem* new_neighbor = old_elems_to_new_elems[old_neighbor];
                new_elem->set_neighbor(s, new_neighbor);
              }
          }
      }
  }

  //Finally prepare the new Mesh for use.  Keep the same numbering and
  //partitioning but also the same renumbering and partitioning
  //policies as our source mesh.
  this->allow_renumbering(false);
  this->skip_partitioning(true);
  this->prepare_for_use(false, skip_find_neighbors);
  this->allow_renumbering(other_mesh.allow_renumbering());
  this->skip_partitioning(other_mesh.skip_partitioning());
}

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

Definition at line 560 of file unstructured_mesh.C.

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

{

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

  // Create iterators to loop over the list of elements
  //   const_active_pid_elem_iterator       it(this->elements_begin(),   pid);
  //   const const_active_pid_elem_iterator it_end(this->elements_end(), pid);

  const_element_iterator       it     = this->active_pid_elements_begin(pid);
  const const_element_iterator it_end = this->active_pid_elements_end(pid);

  this->create_submesh (pid_mesh, it, it_end);
}

void libMesh::UnstructuredMesh::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.

Definition at line 600 of file unstructured_mesh.C.

Referenced by create_pid_mesh().

{
  // Just in case the subdomain_mesh already has some information
  // in it, get rid of it.
  new_mesh.clear();

  // Fail if (*this == new_mesh), we cannot create a submesh inside ourself!
  // This may happen if the user accidently passes the original mesh into
  // this function!  We will check this by making sure we did not just
  // clear ourself.
  libmesh_assert_not_equal_to (this->n_nodes(), 0);
  libmesh_assert_not_equal_to (this->n_elem(), 0);

  // How the nodes on this mesh will be renumbered to nodes
  // on the new_mesh.
  std::vector<dof_id_type> new_node_numbers (this->n_nodes());

  std::fill (new_node_numbers.begin(),
             new_node_numbers.end(),
             DofObject::invalid_id);



  // the number of nodes on the new mesh, will be incremented
  dof_id_type n_new_nodes = 0;
  dof_id_type n_new_elem  = 0;

  for (; it != it_end; ++it)
    {
      // increment the new element counter
      n_new_elem++;

      const Elem* old_elem = *it;

      // Add an equivalent element type to the new_mesh
      Elem* new_elem =
        new_mesh.add_elem (Elem::build(old_elem->type()).release());

      libmesh_assert(new_elem);

      // Loop over the nodes on this element.
      for (unsigned int n=0; n<old_elem->n_nodes(); n++)
        {
          libmesh_assert_less (old_elem->node(n), new_node_numbers.size());

          if (new_node_numbers[old_elem->node(n)] == DofObject::invalid_id)
            {
              new_node_numbers[old_elem->node(n)] = n_new_nodes;

              // Add this node to the new mesh
              new_mesh.add_point (old_elem->point(n));

              // Increment the new node counter
              n_new_nodes++;
            }

          // Define this element's connectivity on the new mesh
          libmesh_assert_less (new_node_numbers[old_elem->node(n)], new_mesh.n_nodes());

          new_elem->set_node(n) = new_mesh.node_ptr (new_node_numbers[old_elem->node(n)]);
        }

      // Copy ids for this element
      new_elem->subdomain_id() = old_elem->subdomain_id();
      new_elem->processor_id() = old_elem->processor_id();

      // Maybe add boundary conditions for this element
      for (unsigned short s=0; s<old_elem->n_sides(); s++)
        // We're supporting boundary ids on internal sides now
        //if (old_elem->neighbor(s) == NULL)
        {
          const std::vector<boundary_id_type>& bc_ids =
            this->get_boundary_info().boundary_ids(old_elem, s);
          for (std::vector<boundary_id_type>::const_iterator id_it=bc_ids.begin(); id_it!=bc_ids.end(); ++id_it)
            {
              const boundary_id_type bc_id = *id_it;
              if (bc_id != this->get_boundary_info().invalid_id)
                new_mesh.get_boundary_info().add_side (new_elem, s,
                                                       bc_id);
            }
        }
    } // end loop over elements


  // Prepare the new_mesh for use
  new_mesh.prepare_for_use(/*skip_renumber =*/false);

}

virtual void libMesh::MeshBase::delete_elem ( Elem * e ) [pure virtual, inherited]

Removes element e from the mesh. Note that calling this method may produce isolated nodes, i.e. nodes not connected to any element. This method must be implemented in derived classes in such a way that it does not invalidate element iterators.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshTools::Modification::all_tri(), libMesh::MeshTools::Generation::build_cube(), contract(), libMesh::TetGenMeshInterface::delete_2D_hull_elements(), libMesh::MeshTools::Modification::flatten(), libMesh::TetGenMeshInterface::pointset_convexhull(), libMesh::AbaqusIO::read(), libMesh::UNVIO::read_implementation(), and libMesh::GmshIO::read_mesh().

virtual void libMesh::MeshBase::delete_node ( Node * n ) [pure virtual, inherited]

Removes the Node n from the mesh.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by all_first_order().

virtual void libMesh::MeshBase::delete_remote_elements ( ) [inline, virtual, inherited]

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

Reimplemented in libMesh::ParallelMesh.

Definition at line 152 of file mesh_base.h.

Referenced by libMesh::MeshTools::Generation::build_extrusion(), libMesh::EquationSystems::init(), libMesh::MeshBase::prepare_for_use(), libMesh::Nemesis_IO::read(), libMesh::BoundaryInfo::sync(), and libMesh::MeshSerializer::~MeshSerializer().

{}

virtual const Elem* libMesh::MeshBase::elem ( const dof_id_type i ) const [pure virtual, inherited]

Return a pointer to the $i^{th}$ element, which should be present in this processor's subset of the mesh data structure.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::GMVIO::_read_materials(), libMesh::MeshTools::Subdivision::add_boundary_ghosts(), libMesh::BoundaryInfo::add_edge(), libMesh::BoundaryInfo::add_side(), libMesh::AbaqusIO::assign_sideset_ids(), libMesh::AbaqusIO::assign_subdomain_ids(), libMesh::Nemesis_IO_Helper::build_element_and_node_maps(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::DofMap::elem_ptr(), libMesh::MeshData::foreign_id_to_elem(), libMesh::UNVIO::groups_in(), libMesh::ErrorVector::is_active_elem(), libMesh::BoundaryInfo::operator=(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::CheckpointIO::read_connectivity(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::MeshTools::subdomain_bounding_box(), libMesh::BoundaryInfo::sync(), libMesh::Parallel::sync_element_data_by_parent_id(), libMesh::Parallel::sync_node_data_by_element_id(), libMesh::Elem::topological_neighbor(), libMesh::Parallel::unpack(), libMesh::FroIO::write(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::Nemesis_IO_Helper::write_elements(), libMesh::LegacyXdrIO::write_mesh(), libMesh::ExodusII_IO_Helper::write_sidesets(), libMesh::Nemesis_IO_Helper::write_sidesets(), and libMesh::DivaIO::write_stream().

virtual Elem* libMesh::MeshBase::elem ( const dof_id_type i ) [pure virtual, inherited]

Return a writeable pointer to the $i^{th}$ element, which should be present in this processor's subset of the mesh data structure.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

const std::set<unsigned char>& libMesh::MeshBase::elem_dimensions ( ) const [inline, inherited]

Returns:: set of dimensions of elements present in the mesh.

Definition at line 175 of file mesh_base.h.

References libMesh::MeshBase::_elem_dims.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::FEMContext::FEMContext(), and libMesh::MeshBase::get_info().

  { return _elem_dims; }

virtual element_iterator libMesh::MeshBase::elements_begin ( ) [pure virtual, inherited]

Elem iterator accessor functions. These must be defined in Concrete base classes.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::elements_begin ( ) const [pure virtual, inherited]

const Elem iterator accessor functions.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::elements_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::elements_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::facelocal_elements_begin ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::facelocal_elements_begin ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::facelocal_elements_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::facelocal_elements_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

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

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.

Implements libMesh::MeshBase.

Definition at line 221 of file unstructured_mesh.C.

References libMesh::Elem::active(), libMesh::Elem::ancestor(), libMesh::Elem::centroid(), libMesh::Elem::child(), 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::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_neighbors(), libMesh::Elem::n_children(), libMesh::MeshTools::n_levels(), libMesh::Elem::n_neighbors(), libMesh::Elem::neighbor(), libMesh::Elem::parent(), libMesh::ParallelObject::processor_id(), libMesh::DofObject::processor_id(), libMesh::remote_elem, libMesh::Elem::set_neighbor(), libMesh::Elem::side(), libMesh::START_LOG(), libMesh::Elem::subactive(), libMesh::Elem::which_child_am_i(), and libMesh::NameBasedIO::write().

Referenced by libMesh::TriangleWrapper::copy_tri_to_mesh().

{
  // We might actually want to run this on an empty mesh
  // (e.g. the boundary mesh for a nonexistant bcid!)
  // libmesh_assert_not_equal_to (this->n_nodes(), 0);
  // libmesh_assert_not_equal_to (this->n_elem(), 0);

  // This function must be run on all processors at once
  parallel_object_only();

  START_LOG("find_neighbors()", "Mesh");

  const element_iterator el_end = this->elements_end();

  //TODO:[BSK] This should be removed later?!
  if (reset_current_list)
    for (element_iterator el = this->elements_begin(); el != el_end; ++el)
      {
        Elem* e = *el;
        for (unsigned int s=0; s<e->n_neighbors(); s++)
          if (e->neighbor(s) != remote_elem ||
              reset_remote_elements)
            e->set_neighbor(s,NULL);
      }

  // Find neighboring elements by first finding elements
  // with identical side keys and then check to see if they
  // are neighbors
  {
    // data structures -- Use the hash_multimap if available
    typedef unsigned int                    key_type;
    typedef std::pair<Elem*, unsigned char> val_type;
    typedef std::pair<key_type, val_type>   key_val_pair;

    typedef LIBMESH_BEST_UNORDERED_MULTIMAP<key_type, val_type> map_type;

    // A map from side keys to corresponding elements & side numbers
    map_type side_to_elem_map;



    for (element_iterator el = this->elements_begin(); el != el_end; ++el)
      {
        Elem* element = *el;

        for (unsigned char ms=0; ms<element->n_neighbors(); ms++)
          {
          next_side:
            // If we haven't yet found a neighbor on this side, try.
            // Even if we think our neighbor is remote, that
            // information may be out of date.
            if (element->neighbor(ms) == NULL ||
                element->neighbor(ms) == remote_elem)
              {
                // Get the key for the side of this element
                const unsigned int key = element->key(ms);

                // Look for elements that have an identical side key
                std::pair <map_type::iterator, map_type::iterator>
                  bounds = side_to_elem_map.equal_range(key);

                // May be multiple keys, check all the possible
                // elements which _might_ be neighbors.
                if (bounds.first != bounds.second)
                  {
                    // Get the side for this element
                    const UniquePtr<Elem> my_side(element->side(ms));

                    // Look at all the entries with an equivalent key
                    while (bounds.first != bounds.second)
                      {
                        // Get the potential element
                        Elem* neighbor = bounds.first->second.first;

                        // Get the side for the neighboring element
                        const unsigned int ns = bounds.first->second.second;
                        const UniquePtr<Elem> their_side(neighbor->side(ns));
                        //libmesh_assert(my_side.get());
                        //libmesh_assert(their_side.get());

                        // If found a match with my side
                        //
                        // We need special tests here for 1D:
                        // since parents and children have an equal
                        // side (i.e. a node), we need to check
                        // ns != ms, and we also check level() to
                        // avoid setting our neighbor pointer to
                        // any of our neighbor's descendants
                        if( (*my_side == *their_side) &&
                            (element->level() == neighbor->level()) &&
                            ((element->dim() != 1) || (ns != ms)) )
                          {
                            // So share a side.  Is this a mixed pair
                            // of subactive and active/ancestor
                            // elements?
                            // If not, then we're neighbors.
                            // If so, then the subactive's neighbor is

                            if (element->subactive() ==
                                neighbor->subactive())
                              {
                                // an element is only subactive if it has
                                // been coarsened but not deleted
                                element->set_neighbor (ms,neighbor);
                                neighbor->set_neighbor(ns,element);
                              }
                            else if (element->subactive())
                              {
                                element->set_neighbor(ms,neighbor);
                              }
                            else if (neighbor->subactive())
                              {
                                neighbor->set_neighbor(ns,element);
                              }
                            side_to_elem_map.erase (bounds.first);

                            // get out of this nested crap
                            goto next_side;
                          }

                        ++bounds.first;
                      }
                  }

                // didn't find a match...
                // Build the map entry for this element
                key_val_pair kvp;

                kvp.first         = key;
                kvp.second.first  = element;
                kvp.second.second = ms;

                // use the lower bound as a hint for
                // where to put it.
#if defined(LIBMESH_HAVE_UNORDERED_MAP) || defined(LIBMESH_HAVE_TR1_UNORDERED_MAP) || defined(LIBMESH_HAVE_HASH_MAP) || defined(LIBMESH_HAVE_EXT_HASH_MAP)
                side_to_elem_map.insert (kvp);
#else
                side_to_elem_map.insert (bounds.first,kvp);
#endif
              }
          }
      }
  }

#ifdef LIBMESH_ENABLE_AMR

  const unsigned int n_levels = MeshTools::n_levels(*this);
  for (unsigned int level = 1; level < n_levels; ++level)
    {
      element_iterator end = this->level_elements_end(level);
      for (element_iterator el = this->level_elements_begin(level);
           el != end; ++el)
        {
          Elem* current_elem = *el;
          libmesh_assert(current_elem);
          Elem* parent = current_elem->parent();
          libmesh_assert(parent);
          const unsigned int my_child_num = parent->which_child_am_i(current_elem);

          for (unsigned int s=0; s < current_elem->n_neighbors(); s++)
            {
              if (current_elem->neighbor(s) == NULL ||
                  (current_elem->neighbor(s) == remote_elem &&
                   parent->is_child_on_side(my_child_num, s)))
                {
                  Elem *neigh = parent->neighbor(s);

                  // If neigh was refined and had non-subactive children
                  // made remote earlier, then a non-subactive elem should
                  // actually have one of those remote children as a
                  // neighbor
                  if (neigh && (neigh->ancestor()) && (!current_elem->subactive()))
                    {
#ifdef DEBUG
                      // Let's make sure that "had children made remote"
                      // situation is actually the case
                      libmesh_assert(neigh->has_children());
                      bool neigh_has_remote_children = false;
                      for (unsigned int c = 0; c != neigh->n_children(); ++c)
                        {
                          if (neigh->child(c) == remote_elem)
                            neigh_has_remote_children = true;
                        }
                      libmesh_assert(neigh_has_remote_children);

                      // And let's double-check that we don't have
                      // a remote_elem neighboring a local element
                      libmesh_assert_not_equal_to (current_elem->processor_id(),
                                                   this->processor_id());
#endif // DEBUG
                      neigh = const_cast<RemoteElem*>(remote_elem);
                    }

                  current_elem->set_neighbor(s, neigh);
#ifdef DEBUG
                  if (neigh != NULL && neigh != remote_elem)
                    // We ignore subactive elements here because
                    // we don't care about neighbors of subactive element.
                    if ((!neigh->active()) && (!current_elem->subactive()))
                      {
                        libMesh::err << "On processor " << this->processor_id()
                                     << std::endl;
                        libMesh::err << "Bad element ID = " << current_elem->id()
                                     << ", Side " << s << ", Bad neighbor ID = " << neigh->id() << std::endl;
                        libMesh::err << "Bad element proc_ID = " << current_elem->processor_id()
                                     << ", Bad neighbor proc_ID = " << neigh->processor_id() << std::endl;
                        libMesh::err << "Bad element size = " << current_elem->hmin()
                                     << ", Bad neighbor size = " << neigh->hmin() << std::endl;
                        libMesh::err << "Bad element center = " << current_elem->centroid()
                                     << ", Bad neighbor center = " << neigh->centroid() << std::endl;
                        libMesh::err << "ERROR: "
                                     << (current_elem->active()?"Active":"Ancestor")
                                     << " Element at level "
                                     << current_elem->level() << std::endl;
                        libMesh::err << "with "
                                     << (parent->active()?"active":
                                         (parent->subactive()?"subactive":"ancestor"))
                                     << " parent share "
                                     << (neigh->subactive()?"subactive":"ancestor")
                                     << " neighbor at level " << neigh->level()
                                     << std::endl;
                        NameBasedIO(*this).write ("bad_mesh.gmv");
                        libmesh_error_msg("Problematic mesh written to bad_mesh.gmv.");
                      }
#endif // DEBUG
                }
            }
        }
    }

#endif // AMR


#ifdef DEBUG
  MeshTools::libmesh_assert_valid_neighbors(*this);
#endif

  STOP_LOG("find_neighbors()", "Mesh");
}

virtual void libMesh::MeshBase::fix_broken_node_and_element_numbering ( ) [pure virtual, inherited]

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(n)->id() == n.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::EquationSystems::_read_impl().

const BoundaryInfo& libMesh::MeshBase::get_boundary_info ( ) const [inline, inherited]

The information about boundary ids on the mesh

Definition at line 115 of file mesh_base.h.

References libMesh::MeshBase::boundary_info.

{ return *boundary_info; }

BoundaryInfo& libMesh::MeshBase::get_boundary_info ( ) [inline, inherited]

Writeable information about boundary ids on the mesh

Definition at line 120 of file mesh_base.h.

References libMesh::MeshBase::boundary_info.

{ return *boundary_info; }

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 481 of file mesh_base.C.

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

{
  // Linear search over the map values.
  std::map<subdomain_id_type, std::string>::const_iterator
    iter = _block_id_to_name.begin(),
    end_iter = _block_id_to_name.end();

  for ( ; iter != end_iter; ++iter)
    if (iter->second == name)
      return iter->first;

  // If we made it here without returning, we don't have a subdomain
  // with the requested name, so return Elem::invalid_subdomain_id.
  return Elem::invalid_subdomain_id;
}

std::string libMesh::MeshBase::get_info ( ) const [inherited]

Returns:: a string containing relevant information about the mesh.

Definition at line 315 of file mesh_base.C.

References libMesh::MeshBase::elem_dimensions(), end, 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::print_info().

{
  std::ostringstream oss;

  oss << " Mesh Information:"                                  << '\n'
      << "  elem_dimensions()={";
  {
    std::set<unsigned char>::const_iterator it =
      this->elem_dimensions().begin();
    if (it != this->elem_dimensions().end())
      oss << *it;
    for (; it != this->elem_dimensions().end(); ++it)
      oss << ',' << *it;
  }
  oss << "  spatial_dimension()=" << this->spatial_dimension() << '\n'
      << "  n_nodes()="           << this->n_nodes()           << '\n'
      << "    n_local_nodes()="   << this->n_local_nodes()     << '\n'
      << "  n_elem()="            << this->n_elem()            << '\n'
      << "    n_local_elem()="    << this->n_local_elem()      << '\n'
#ifdef LIBMESH_ENABLE_AMR
      << "    n_active_elem()="   << this->n_active_elem()     << '\n'
#endif
      << "  n_subdomains()="      << static_cast<std::size_t>(this->n_subdomains()) << '\n'
      << "  n_partitions()="      << static_cast<std::size_t>(this->n_partitions()) << '\n'
      << "  n_processors()="      << static_cast<std::size_t>(this->n_processors()) << '\n'
      << "  n_threads()="         << static_cast<std::size_t>(libMesh::n_threads()) << '\n'
      << "  processor_id()="      << static_cast<std::size_t>(this->processor_id()) << '\n';

  return oss.str();
}

const std::map<subdomain_id_type, std::string>& libMesh::MeshBase::get_subdomain_name_map ( ) const [inline, inherited]

Definition at line 862 of file mesh_base.h.

References libMesh::MeshBase::_block_id_to_name.

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

  { return _block_id_to_name; }

virtual Elem* libMesh::MeshBase::insert_elem ( Elem * e ) [pure virtual, inherited]

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

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by all_first_order(), all_second_order(), and libMesh::MeshTools::Subdivision::all_subdivision().

virtual Node* libMesh::MeshBase::insert_node ( Node * n ) [pure virtual, inherited]

Insert Node n into the Mesh at a location consistent with n->id(), allocating extra storage if necessary. Will error rather than overwriting an existing Node. Primarily intended for use with the mesh_inserter_iterator, only use if you know what you are doing...

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::mesh_inserter_iterator< T >::operator=().

bool libMesh::MeshBase::is_prepared ( ) const [inline, inherited]

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

Definition at line 131 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().

  { return _is_prepared; }

virtual bool libMesh::MeshBase::is_serial ( ) const [inline, virtual, inherited]

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

Reimplemented in libMesh::ParallelMesh.

Definition at line 138 of file mesh_base.h.

Referenced by libMesh::MeshRefinement::_coarsen_elements(), libMesh::MetisPartitioner::_do_partition(), libMesh::MeshRefinement::_refine_elements(), all_second_order(), libMesh::EquationSystems::allgather(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::MeshRefinement::coarsen_elements(), libMesh::DofMap::create_dof_constraints(), libMesh::LocationMap< T >::init(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshSerializer::MeshSerializer(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::MeshBase::partition(), libMesh::MeshBase::prepare_for_use(), libMesh::Nemesis_IO::read(), libMesh::MeshRefinement::refine_and_coarsen_elements(), libMesh::MeshRefinement::refine_elements(), libMesh::DofMap::scatter_constraints(), libMesh::BoundaryInfo::sync(), libMesh::MeshTools::total_weight(), libMesh::EquationSystems::write(), libMesh::LegacyXdrIO::write_mesh(), and libMesh::XdrIO::write_parallel().

  { return true; }

virtual element_iterator libMesh::MeshBase::level_elements_begin ( const unsigned int level ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshTools::Modification::change_boundary_id(), find_neighbors(), libMesh::MeshRefinement::make_coarsening_compatible(), and libMesh::MeshTools::Modification::smooth().

virtual const_element_iterator libMesh::MeshBase::level_elements_begin ( const unsigned int level ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::level_elements_end ( const unsigned int level ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshTools::Modification::change_boundary_id(), find_neighbors(), libMesh::MeshRefinement::make_coarsening_compatible(), and libMesh::MeshTools::Modification::smooth().

virtual const_element_iterator libMesh::MeshBase::level_elements_end ( const unsigned int level ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual void libMesh::MeshBase::libmesh_assert_valid_parallel_ids ( ) const [inline, virtual, inherited]

Verify id and processor_id consistency of our elements and nodes containers. Calls libmesh_assert() on each possible failure. Currently only implemented on ParallelMesh; a serial data structure is much harder to get out of sync.

Reimplemented in libMesh::ParallelMesh.

Definition at line 707 of file mesh_base.h.

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

{}

virtual element_iterator libMesh::MeshBase::local_elements_begin ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshCommunication::assign_global_indices(), libMesh::DofMap::create_dof_constraints(), libMesh::EquationSystems::get_solution(), libMesh::MeshTools::libmesh_assert_valid_remote_elems(), libMesh::MeshTools::n_local_levels(), and libMesh::MeshTools::n_p_levels().

virtual const_element_iterator libMesh::MeshBase::local_elements_begin ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::local_elements_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshCommunication::assign_global_indices(), libMesh::DofMap::create_dof_constraints(), libMesh::EquationSystems::get_solution(), libMesh::MeshTools::libmesh_assert_valid_remote_elems(), libMesh::MeshTools::n_local_levels(), libMesh::MeshTools::n_p_levels(), and libMesh::XdrIO::write_serialized_connectivity().

virtual const_element_iterator libMesh::MeshBase::local_elements_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::local_level_elements_begin ( const unsigned int level ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::XdrIO::write_serialized_connectivity().

virtual const_element_iterator libMesh::MeshBase::local_level_elements_begin ( const unsigned int level ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::local_level_elements_end ( const unsigned int level ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::XdrIO::write_serialized_connectivity().

virtual const_element_iterator libMesh::MeshBase::local_level_elements_end ( const unsigned int level ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual node_iterator libMesh::MeshBase::local_nodes_begin ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshCommunication::assign_global_indices(), libMesh::MeshTools::bounding_box(), libMesh::EquationSystems::build_solution_vector(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::MeshTools::libmesh_assert_valid_procids< Node >(), libMesh::DofMap::local_variable_indices(), libMesh::VTKIO::nodes_to_vtk(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::XdrIO::write_serialized_nodes(), and libMesh::System::zero_variable().

virtual const_node_iterator libMesh::MeshBase::local_nodes_begin ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual node_iterator libMesh::MeshBase::local_nodes_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshCommunication::assign_global_indices(), libMesh::MeshTools::bounding_box(), libMesh::EquationSystems::build_solution_vector(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::MeshTools::libmesh_assert_valid_procids< Node >(), libMesh::DofMap::local_variable_indices(), libMesh::VTKIO::nodes_to_vtk(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::XdrIO::write_serialized_nodes(), and libMesh::System::zero_variable().

virtual const_node_iterator libMesh::MeshBase::local_nodes_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::local_not_level_elements_begin ( const unsigned int level ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::local_not_level_elements_begin ( const unsigned int level ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::local_not_level_elements_end ( const unsigned int level ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::local_not_level_elements_end ( const unsigned int level ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual dof_id_type libMesh::MeshBase::max_elem_id ( ) const [pure virtual, inherited]

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

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::EquationSystems::get_solution(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_procids< Elem >(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), and libMesh::ErrorVector::plot_error().

virtual dof_id_type libMesh::MeshBase::max_node_id ( ) const [pure virtual, inherited]

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

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::DofMap::add_neighbors_to_send_list(), all_first_order(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::EquationSystems::build_solution_vector(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_procids< Node >(), libMesh::ErrorVector::plot_error(), and libMesh::GMVIO::write_ascii_old_impl().

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 118 of file mesh_base.C.

References libMesh::MeshBase::_elem_dims, and libMesh::libmesh_assert().

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::HPCoarsenTest::add_projection(), all_second_order(), libMesh::MeshTools::Generation::build_cube(), libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::EquationSystems::build_solution_vector(), libMesh::EquationSystems::build_variable_names(), libMesh::System::calculate_norm(), libMesh::DofMap::create_dof_constraints(), libMesh::MeshTools::Modification::distort(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::MeshRefinement::flag_elements_by_elem_fraction(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::LaplaceMeshSmoother::init(), libMesh::PointLocatorTree::init(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::FEInterface::n_vec_dim(), libMesh::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::PatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::ProjectSolution::operator()(), libMesh::BoundaryProjectSolution::operator()(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::GMVIO::read(), libMesh::VTKIO::read(), libMesh::System::read_header(), libMesh::LegacyXdrIO::read_mesh(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::HPCoarsenTest::select_refinement(), libMesh::MeshTools::Modification::smooth(), libMesh::DofMap::use_coupled_neighbor_dofs(), libMesh::PostscriptIO::write(), libMesh::GMVIO::write_ascii_old_impl(), 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(), libMesh::DivaIO::write_stream(), and libMesh::EnsightIO::write_vector_ascii().

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

virtual dof_id_type libMesh::MeshBase::n_active_elem ( ) const [pure virtual, inherited]

Returns the number of active elements in the mesh. Implemented in terms of active_element_iterators.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::LinearPartitioner::_do_partition(), libMesh::MetisPartitioner::_do_partition(), libMesh::SFCPartitioner::_do_partition(), libMesh::MeshRefinement::flag_elements_by_error_tolerance(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::MeshTools::Modification::flatten(), libMesh::MeshBase::get_info(), libMesh::PointLocatorList::init(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::VariationalMeshSmoother::metr_data_gen(), libMesh::Partitioner::partition(), libMesh::Partitioner::repartition(), libMesh::VariationalMeshSmoother::smooth(), libMesh::GMVIO::write_ascii_new_impl(), libMesh::GMVIO::write_ascii_old_impl(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::GmshIO::write_mesh(), and libMesh::GnuPlotIO::write_solution().

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 276 of file mesh_base.C.

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

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

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

dof_id_type libMesh::MeshBase::n_active_local_elem ( ) const [inline, inherited]

Returns the number of active elements on the local processor.

Definition at line 314 of file mesh_base.h.

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

Referenced by libMesh::ParmetisPartitioner::assign_partitioning(), libMesh::ParmetisPartitioner::build_graph(), libMesh::VTKIO::cells_to_vtk(), and libMesh::ParmetisPartitioner::initialize().

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

dof_id_type libMesh::MeshBase::n_active_sub_elem ( ) const [inherited]

Same, but only counts active elements.

Definition at line 300 of file mesh_base.C.

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

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

{
  dof_id_type ne=0;

  const_element_iterator       el  = this->active_elements_begin();
  const const_element_iterator end = this->active_elements_end();

  for (; el!=end; ++el)
    ne += (*el)->n_sub_elem();

  return ne;
}

virtual dof_id_type libMesh::MeshBase::n_elem ( ) const [pure virtual, inherited]

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.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

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 263 of file mesh_base.C.

References 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(), and libMesh::MeshBase::n_unpartitioned_elem().

{
  // We're either counting a processor's elements or unpartitioned
  // elements
  libmesh_assert (proc_id < this->n_processors() ||
                  proc_id == DofObject::invalid_processor_id);

  return static_cast<dof_id_type>(std::distance (this->pid_elements_begin(proc_id),
                                                 this->pid_elements_end  (proc_id)));
}

dof_id_type libMesh::MeshBase::n_local_elem ( ) const [inline, inherited]

Returns the number of elements on the local processor.

Definition at line 297 of file mesh_base.h.

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

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

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

dof_id_type libMesh::MeshBase::n_local_nodes ( ) const [inline, inherited]

Returns the number of nodes on the local processor.

Definition at line 211 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::ParallelMesh::parallel_n_nodes().

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

virtual dof_id_type libMesh::MeshBase::n_nodes ( ) const [pure virtual, inherited]

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.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

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 250 of file mesh_base.C.

References 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::n_local_nodes(), and libMesh::MeshBase::n_unpartitioned_nodes().

{
  // We're either counting a processor's nodes or unpartitioned
  // nodes
  libmesh_assert (proc_id < this->n_processors() ||
                  proc_id == DofObject::invalid_processor_id);

  return static_cast<dof_id_type>(std::distance (this->pid_nodes_begin(proc_id),
                                                 this->pid_nodes_end  (proc_id)));
}

unsigned int libMesh::MeshBase::n_partitions ( ) const [inline, 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 that the partitioner objects are responsible for setting this value.

Definition at line 593 of file mesh_base.h.

References libMesh::MeshBase::_n_parts.

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().

  { return _n_parts; }

processor_id_type libMesh::ParallelObject::n_processors ( ) const [inline, inherited]

Returns:: the number of processors in the group.

Definition at line 92 of file parallel_object.h.

References libMesh::ParallelObject::_communicator, and libMesh::Parallel::Communicator::size().

Referenced by libMesh::ParmetisPartitioner::_do_repartition(), libMesh::ParallelMesh::add_elem(), libMesh::ParallelMesh::add_node(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::FEMSystem::assembly(), libMesh::ParmetisPartitioner::assign_partitioning(), libMesh::ParallelMesh::assign_unique_ids(), libMesh::AztecLinearSolver< T >::AztecLinearSolver(), libMesh::ParallelMesh::clear(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), create_pid_mesh(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::EnsightIO::EnsightIO(), libMesh::MeshBase::get_info(), libMesh::EquationSystems::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::ParmetisPartitioner::initialize(), libMesh::Nemesis_IO_Helper::initialize(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_procids< Elem >(), libMesh::MeshTools::libmesh_assert_valid_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::DofMap::local_variable_indices(), libMesh::MeshBase::n_active_elem_on_proc(), libMesh::MeshBase::n_elem_on_proc(), libMesh::MeshBase::n_nodes_on_proc(), libMesh::Partitioner::partition(), libMesh::MeshBase::partition(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::PetscLinearSolver< T >::PetscLinearSolver(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::MeshTools::processor_bounding_box(), libMesh::System::project_vector(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::CheckpointIO::read(), libMesh::XdrIO::read(), libMesh::System::read_parallel_data(), libMesh::System::read_SCALAR_dofs(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::System::read_serialized_vector(), libMesh::Partitioner::repartition(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::BoundaryInfo::sync(), libMesh::ParallelMesh::update_parallel_id_counts(), libMesh::CheckpointIO::write(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::System::write_parallel_data(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), and libMesh::XdrIO::write_serialized_nodesets().

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

dof_id_type libMesh::MeshBase::n_sub_elem ( ) const [inherited]

This function returns the number of elements that will be written out in the Tecplot format. For example, a 9-noded quadrilateral will be broken into 4 linear sub-elements for plotting purposes. Thus, for a mesh of 2 QUAD9 elements n_tecplot_elem() will return 8. Implemented in terms of element_iterators.

Definition at line 285 of file mesh_base.C.

References libMesh::MeshBase::elements_begin(), libMesh::MeshBase::elements_end(), and end.

{
  dof_id_type ne=0;

  const_element_iterator       el  = this->elements_begin();
  const const_element_iterator end = this->elements_end();

  for (; el!=end; ++el)
    ne += (*el)->n_sub_elem();

  return ne;
}

subdomain_id_type libMesh::MeshBase::n_subdomains ( ) const [inherited]

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

Definition at line 235 of file mesh_base.C.

References libMesh::MeshBase::subdomain_ids().

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

{
  // This requires an inspection on every processor
  parallel_object_only();

  std::set<subdomain_id_type> ids;

  this->subdomain_ids (ids);

  return cast_int<subdomain_id_type>(ids.size());
}

dof_id_type libMesh::MeshBase::n_unpartitioned_elem ( ) const [inline, inherited]

Returns the number of elements owned by no processor.

Definition at line 303 of file mesh_base.h.

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

Referenced by libMesh::ParallelMesh::parallel_n_elem(), and libMesh::MeshBase::partition().

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

dof_id_type libMesh::MeshBase::n_unpartitioned_nodes ( ) const [inline, inherited]

Returns the number of nodes owned by no processor.

Definition at line 217 of file mesh_base.h.

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

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

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

unique_id_type libMesh::MeshBase::next_unique_id ( ) [inline, inherited]

Returns the next unique id to be used.

Definition at line 230 of file mesh_base.h.

References libMesh::MeshBase::_next_unique_id.

{ return _next_unique_id; }

virtual const Node& libMesh::MeshBase::node ( const dof_id_type i ) const [pure virtual, inherited]

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

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::MeshTools::Generation::build_cube(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::MeshTools::Modification::smooth(), libMesh::GmshIO::write_mesh(), and libMesh::LegacyXdrIO::write_mesh().

virtual Node& libMesh::MeshBase::node ( const dof_id_type i ) [pure virtual, inherited]

Return a reference to the $i^{th}$ node, which should be present in this processor's subset of the mesh data structure.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const Node* libMesh::MeshBase::node_ptr ( const dof_id_type i ) const [pure virtual, inherited]

Return a pointer to the $i^{th}$ node, which should be present in this processor's subset of the mesh data structure.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::GMVIO::_read_one_cell(), libMesh::SyncNodalPositions::act_on_data(), libMesh::BoundaryInfo::add_node(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::AbaqusIO::assign_boundary_node_ids(), libMesh::TetGenMeshInterface::assign_nodes_to_elem(), libMesh::MeshTools::Generation::build_cube(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::VTKIO::cells_to_vtk(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::GMVIO::copy_nodal_solution(), libMesh::TriangleWrapper::copy_tri_to_mesh(), create_submesh(), libMesh::MeshTools::Modification::distort(), libMesh::UNVIO::elements_in(), libMesh::MeshData::foreign_id_to_node(), libMesh::SyncNodalPositions::gather_data(), libMesh::DofMap::node_ptr(), libMesh::BoundaryInfo::operator=(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::VTKIO::read(), libMesh::CheckpointIO::read_connectivity(), libMesh::AbaqusIO::read_elements(), libMesh::GmshIO::read_mesh(), libMesh::LegacyXdrIO::read_mesh(), libMesh::OFFIO::read_stream(), libMesh::MatlabIO::read_stream(), libMesh::DofMap::scatter_constraints(), libMesh::Partitioner::set_node_processor_ids(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::BoundaryInfo::sync(), libMesh::Parallel::unpack(), and libMesh::Nemesis_IO_Helper::write_nodal_coordinates().

virtual Node* libMesh::MeshBase::node_ptr ( const dof_id_type i ) [pure virtual, inherited]

Return a writeable pointer to the $i^{th}$ node, which should be present in this processor's subset of the mesh data structure.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual node_iterator libMesh::MeshBase::nodes_begin ( ) [pure virtual, inherited]

non-const Node iterator accessor functions.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_node_iterator libMesh::MeshBase::nodes_begin ( ) const [pure virtual, inherited]

const Node iterator accessor functions.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual node_iterator libMesh::MeshBase::nodes_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_node_iterator libMesh::MeshBase::nodes_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::not_active_elements_begin ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::Partitioner::set_node_processor_ids().

virtual const_element_iterator libMesh::MeshBase::not_active_elements_begin ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::not_active_elements_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::Partitioner::set_node_processor_ids().

virtual const_element_iterator libMesh::MeshBase::not_active_elements_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::not_ancestor_elements_begin ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::not_ancestor_elements_begin ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::not_ancestor_elements_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::not_ancestor_elements_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::not_level_elements_begin ( const unsigned int level ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::not_level_elements_begin ( const unsigned int level ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::not_level_elements_end ( const unsigned int level ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::not_level_elements_end ( const unsigned int level ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::not_local_elements_begin ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::not_local_elements_begin ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::not_local_elements_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::not_local_elements_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::not_subactive_elements_begin ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::not_subactive_elements_begin ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::not_subactive_elements_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::not_subactive_elements_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual dof_id_type libMesh::MeshBase::parallel_n_elem ( ) const [pure virtual, inherited]

Returns the number of elements in the mesh. The parallel_n_elem() function returns a newly calculated parallel-synchronized value on distributed meshes, and so must be called in parallel only.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::Nemesis_IO_Helper::initialize(), and libMesh::Nemesis_IO::read().

virtual dof_id_type libMesh::MeshBase::parallel_n_nodes ( ) const [pure virtual, inherited]

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 parallel_n_nodes() function returns a newly calculated parallel-synchronized value on distributed meshes, and so must be called in parallel only.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::Nemesis_IO_Helper::initialize(), and libMesh::Nemesis_IO::read().

void libMesh::MeshBase::partition ( const unsigned int n_parts ) [virtual, inherited]

Call the default partitioner (currently metis_partition()).

Definition at line 361 of file mesh_base.C.

References libMesh::MeshBase::is_serial(), libMesh::libmesh_assert(), libMesh::MeshBase::n_unpartitioned_elem(), libMesh::MeshBase::partitioner(), libMesh::MeshBase::recalculate_n_partitions(), libMesh::Partitioner::set_node_processor_ids(), libMesh::MeshBase::skip_partitioning(), and libMesh::MeshBase::update_post_partitioning().

{
  // If we get here and we have unpartitioned elements, we need that
  // fixed.
  if (this->n_unpartitioned_elem() > 0)
    {
      libmesh_assert (partitioner().get());
      libmesh_assert (this->is_serial());
      partitioner()->partition (*this, n_parts);
    }
  // NULL partitioner means don't repartition
  // Non-serial meshes may not be ready for repartitioning here.
  else if(!skip_partitioning() &&
          partitioner().get() &&
          this->is_serial())
    {
      partitioner()->partition (*this, n_parts);
    }
  else
    {
      // Adaptive coarsening may have "orphaned" nodes on processors
      // whose elements no longer share them.  We need to check for
      // and possibly fix that.
      Partitioner::set_node_processor_ids(*this);

      // Make sure locally cached partition count
      this->recalculate_n_partitions();

      // Make sure any other locally cached data is correct
      this->update_post_partitioning();
    }
}

void libMesh::MeshBase::partition ( ) [inline, inherited]

Definition at line 529 of file mesh_base.h.

References libMesh::ParallelObject::n_processors(), and libMesh::MeshBase::partition().

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

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

virtual UniquePtr<Partitioner>& libMesh::MeshBase::partitioner ( ) [inline, virtual, inherited]

A partitioner to use at each prepare_for_use()

Definition at line 110 of file mesh_base.h.

References libMesh::MeshBase::_partitioner.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::MeshBase::partition(), and libMesh::BoundaryInfo::sync().

{ return _partitioner; }

virtual element_iterator libMesh::MeshBase::pid_elements_begin ( const processor_id_type proc_id ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshBase::n_elem_on_proc(), libMesh::MeshTools::processor_bounding_box(), libMesh::BoundaryInfo::sync(), and libMesh::MeshTools::weight().

virtual const_element_iterator libMesh::MeshBase::pid_elements_begin ( const processor_id_type proc_id ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::pid_elements_end ( const processor_id_type proc_id ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshBase::n_elem_on_proc(), libMesh::MeshTools::processor_bounding_box(), libMesh::BoundaryInfo::sync(), and libMesh::MeshTools::weight().

virtual const_element_iterator libMesh::MeshBase::pid_elements_end ( const processor_id_type proc_id ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual node_iterator libMesh::MeshBase::pid_nodes_begin ( const processor_id_type proc_id ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshTools::bounding_box(), and libMesh::MeshBase::n_nodes_on_proc().

virtual const_node_iterator libMesh::MeshBase::pid_nodes_begin ( const processor_id_type proc_id ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual node_iterator libMesh::MeshBase::pid_nodes_end ( const processor_id_type proc_id ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshTools::bounding_box(), and libMesh::MeshBase::n_nodes_on_proc().

virtual const_node_iterator libMesh::MeshBase::pid_nodes_end ( const processor_id_type proc_id ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const Point& libMesh::MeshBase::point ( const dof_id_type i ) const [pure virtual, inherited]

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

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by all_second_order(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::MeshTools::subdomain_bounding_box(), libMesh::FroIO::write(), libMesh::TetGenIO::write(), libMesh::MEDITIO::write_ascii(), libMesh::TecplotIO::write_ascii(), libMesh::GMVIO::write_ascii_new_impl(), libMesh::GMVIO::write_ascii_old_impl(), libMesh::TecplotIO::write_binary(), libMesh::GMVIO::write_binary(), libMesh::GnuPlotIO::write_solution(), and libMesh::DivaIO::write_stream().

const PointLocatorBase & libMesh::MeshBase::point_locator ( ) const [inherited]

returns a pointer to a PointLocatorBase object for this mesh, constructing a master PointLocator first if necessary. This should never be used in threaded or non-parallel_only code, and so is deprecated.

Definition at line 417 of file mesh_base.C.

References libMesh::MeshBase::_point_locator, libMesh::PointLocatorBase::build(), libMesh::Threads::in_threads, libMesh::libmesh_assert(), and libMesh::TREE_ELEMENTS.

{
  libmesh_deprecated();

  if (_point_locator.get() == NULL)
    {
      // PointLocator construction may not be safe within threads
      libmesh_assert(!Threads::in_threads);

      _point_locator.reset (PointLocatorBase::build(TREE_ELEMENTS, *this).release());
    }

  return *_point_locator;
}

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

Prepare a newly created (or read) mesh for use. This involves 4 steps: 1.) call find_neighbors() 2.) call partition() 3.) call renumber_nodes_and_elements() 4.) call cache_elem_dims()

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

Definition at line 124 of file mesh_base.C.

Referenced by all_first_order(), all_second_order(), libMesh::MeshTools::Subdivision::all_subdivision(), libMesh::MeshTools::Modification::all_tri(), libMesh::MeshTools::Generation::build_cube(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::MeshRefinement::coarsen_elements(), create_submesh(), libMesh::MeshTools::Modification::flatten(), libMesh::MeshTools::Subdivision::prepare_subdivision_mesh(), libMesh::GMVIO::read(), read(), libMesh::MeshRefinement::refine_and_coarsen_elements(), libMesh::MeshRefinement::refine_elements(), libMesh::SerialMesh::stitching_helper(), libMesh::BoundaryInfo::sync(), libMesh::MeshRefinement::uniformly_coarsen(), and libMesh::MeshRefinement::uniformly_refine().

{
  parallel_object_only();

  libmesh_assert(this->comm().verify(this->is_serial()));

  // A distributed mesh may have processors with no elements (or
  // processors with no elements of higher dimension, if we ever
  // support mixed-dimension meshes), but we want consistent
  // mesh_dimension anyways.
  //
  // cache_elem_dims() should get the elem_dimensions() and
  // mesh_dimension() correct later, and we don't need it earlier.


  // Renumber the nodes and elements so that they in contiguous
  // blocks.  By default, _skip_renumber_nodes_and_elements is false.
  //
  // We may currently change that by passing
  // skip_renumber_nodes_and_elements==true to this function, but we
  // should use the allow_renumbering() accessor instead.
  //
  // Instances where you if prepare_for_use() should not renumber the nodes
  // and elements include reading in e.g. an xda/r or gmv file. In
  // this case, the ordering of the nodes may depend on an accompanying
  // solution, and the node ordering cannot be changed.

  if (skip_renumber_nodes_and_elements)
    {
      libmesh_deprecated();
      this->allow_renumbering(false);
    }

  // Mesh modification operations might not leave us with consistent
  // id counts, but our partitioner might need that consistency.
  if(!_skip_renumber_nodes_and_elements)
    this->renumber_nodes_and_elements();
  else
    this->update_parallel_id_counts();

  // Let all the elements find their neighbors
  if(!skip_find_neighbors)
    this->find_neighbors();

  // Partition the mesh.
  this->partition();

  // If we're using ParallelMesh, we'll want it parallelized.
  this->delete_remote_elements();

#ifdef LIBMESH_ENABLE_UNIQUE_ID
  // Assign DOF object unique ids
  this->assign_unique_ids();
#endif

  if(!_skip_renumber_nodes_and_elements)
    this->renumber_nodes_and_elements();

  // Search the mesh for all the dimensions of the elements
  // and cache them.
  this->cache_elem_dims();

  // Reset our PointLocator.  This needs to happen any time the elements
  // in the underlying elements in the mesh have changed, so we do it here.
  this->clear_point_locator();

  // The mesh is now prepared for use.
  _is_prepared = true;
}

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

Prints relevant information about the mesh.

Definition at line 347 of file mesh_base.C.

References libMesh::MeshBase::get_info().

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

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

processor_id_type libMesh::ParallelObject::processor_id ( ) const [inline, inherited]

Returns:: the rank of this processor in the group.

Definition at line 98 of file parallel_object.h.

References libMesh::ParallelObject::_communicator, and libMesh::Parallel::Communicator::rank().

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

virtual const Elem* libMesh::MeshBase::query_elem ( const dof_id_type i ) const [pure virtual, inherited]

Return a pointer to the $i^{th}$ element, or NULL if no such element exists in this processor's mesh data structure.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_procids< Elem >(), and libMesh::Parallel::unpack().

virtual Elem* libMesh::MeshBase::query_elem ( const dof_id_type i ) [pure virtual, inherited]

Return a writeable pointer to the $i^{th}$ element, or NULL if no such element exists in this processor's mesh data structure.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const Node* libMesh::MeshBase::query_node_ptr ( const dof_id_type i ) const [pure virtual, inherited]

Return a pointer to the $i^{th}$ node, or NULL if no such node exists in this processor's mesh data structure.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_procids< Node >(), and libMesh::Parallel::unpack().

virtual Node* libMesh::MeshBase::query_node_ptr ( const dof_id_type i ) [pure virtual, inherited]

Return a writeable pointer to the $i^{th}$ node, or NULL if no such node exists in this processor's mesh data structure.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

void libMesh::UnstructuredMesh::read	(	const std::string &	name,
		MeshData *	mesh_data = `NULL`,
		bool	skip_renumber_nodes_and_elements = `false`
	)		`[virtual]`

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

In order to read the UNV and TetGen file types, you must also pass a separate pointer to the MeshData object you will use with this mesh, since these read methods expect it.

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

Implements libMesh::MeshBase.

Definition at line 484 of file unstructured_mesh.C.

References libMesh::MeshBase::allow_renumbering(), libMesh::MeshBase::prepare_for_use(), libMesh::NameBasedIO::read(), libMesh::TetGenIO::read(), and libMesh::UNVIO::read().

{
  // Set the skip_renumber_nodes_and_elements flag on all processors
  // if necessary.
  // This ensures that renumber_nodes_and_elements is *not* called
  // during prepare_for_use() for certain types of mesh files.
  // This is required in cases where there is an associated solution
  // file which expects a certain ordering of the nodes.
  if(name.rfind(".gmv")+4==name.size())
    {
      skip_renumber_nodes_and_elements =  true;
    }

  if (mesh_data)
    {
      libmesh_deprecated();
      if (name.rfind(".unv") < name.size())
        UNVIO(*this, mesh_data).read (name);
      else if ((name.rfind(".node")  < name.size()) ||
               (name.rfind(".ele")   < name.size()))
        TetGenIO(*this,mesh_data).read (name);
    }
  else
    NameBasedIO(*this).read(name);

  if (skip_renumber_nodes_and_elements)
    {
      // Use MeshBase::allow_renumbering() yourself instead.
      libmesh_deprecated();
      this->allow_renumbering(false);
    }

  // Done reading the mesh.  Now prepare it for use.
  this->prepare_for_use();
}

unsigned int libMesh::MeshBase::recalculate_n_partitions ( ) [inherited]

In a few (very rare) cases, the user may have manually tagged the elements with specific processor IDs by hand, without using a partitioner. In this case, the Mesh will not know that the total number of partitions, _n_parts, has changed, unless you call this function. This is an O(N active elements) calculation. The return value is the number of partitions, and _n_parts is also set by this function.

Definition at line 394 of file mesh_base.C.

References libMesh::MeshBase::_n_parts, libMesh::MeshBase::active_local_elements_begin(), libMesh::MeshBase::active_local_elements_end(), libMesh::ParallelObject::comm(), end, std::max(), and libMesh::Parallel::Communicator::max().

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

{
  // This requires an inspection on every processor
  parallel_object_only();

  const_element_iterator el  = this->active_local_elements_begin();
  const_element_iterator end = this->active_local_elements_end();

  unsigned int max_proc_id=0;

  for (; el!=end; ++el)
    max_proc_id = std::max(max_proc_id, static_cast<unsigned int>((*el)->processor_id()));

  // The number of partitions is one more than the max processor ID.
  _n_parts = max_proc_id+1;

  this->comm().max(_n_parts);

  return _n_parts;
}

virtual void libMesh::MeshBase::redistribute ( ) [inline, virtual, inherited]

Redistribute elements between processors. This gets called automatically by the Partitioner, and is a no-op in the case of a SerialMesh or serialized ParallelMesh

Reimplemented in libMesh::ParallelMesh.

Definition at line 537 of file mesh_base.h.

Referenced by libMesh::Partitioner::partition().

{}

virtual void libMesh::MeshBase::renumber_elem	(	dof_id_type	old_id,
		dof_id_type	new_id
	)		`[pure virtual, inherited]`

Changes the id of element old_id, both by changing elem(old_id)->id() and by moving elem(old_id) in the mesh's internal container. No element with the id new_id should already exist.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual void libMesh::MeshBase::renumber_node	(	dof_id_type	old_id,
		dof_id_type	new_id
	)		`[pure virtual, inherited]`

Changes the id of node old_id, both by changing node(old_id)->id() and by moving node(old_id) in the mesh's internal container. No element with the id new_id should already exist.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual void libMesh::MeshBase::renumber_nodes_and_elements ( ) [pure virtual, inherited]

After partitoning a mesh it is useful to renumber the nodes and elements so that they lie in contiguous blocks on the processors. This method does just that.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by all_first_order(), all_second_order(), contract(), libMesh::ErrorVector::plot_error(), and libMesh::MeshBase::prepare_for_use().

virtual void libMesh::MeshBase::reserve_elem ( const dof_id_type ne ) [pure virtual, inherited]

Reserves space for a known number of elements. Note that this method may or may not do anything, depending on the actual Mesh implementation. If you know the number of elements you will add and call this method before repeatedly calling add_point() the implementation will be more efficient.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshTools::Generation::build_cube(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::ExodusII_IO::read(), libMesh::XdrIO::read(), libMesh::GmshIO::read_mesh(), and libMesh::LegacyXdrIO::read_mesh().

virtual void libMesh::MeshBase::reserve_nodes ( const dof_id_type nn ) [pure virtual, inherited]

Reserves space for a known number of nodes. Note that this method may or may not do anything, depending on the actual Mesh implementation. If you know the number of nodes you will add and call this method before repeatedly calling add_point() the implementation will be more efficient.

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by all_second_order(), libMesh::MeshTools::Generation::build_cube(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::ExodusII_IO::read(), libMesh::XdrIO::read(), libMesh::GmshIO::read_mesh(), and libMesh::LegacyXdrIO::read_mesh().

virtual element_iterator libMesh::MeshBase::semilocal_elements_begin ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::semilocal_elements_begin ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::semilocal_elements_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual const_element_iterator libMesh::MeshBase::semilocal_elements_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

void libMesh::MeshBase::set_mesh_dimension ( unsigned char d ) [inline, inherited]

Resets the logical dimension of the mesh. If the mesh has elements of multiple dimensions, this should be set to the largest dimension. E.g. if the mesh has 1D and 2D elements, this should be set to 2. If the mesh has 2D and 3D elements, this should be set to 3.

Definition at line 169 of file mesh_base.h.

References libMesh::MeshBase::_elem_dims.

Referenced by libMesh::MeshTools::Generation::build_cube(), libMesh::MeshTools::Generation::build_delaunay_square(), libMesh::TriangleWrapper::copy_tri_to_mesh(), libMesh::AbaqusIO::read(), libMesh::TetGenIO::read(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::GMVIO::read(), libMesh::VTKIO::read(), libMesh::CheckpointIO::read_connectivity(), libMesh::UNVIO::read_implementation(), libMesh::GmshIO::read_mesh(), libMesh::LegacyXdrIO::read_mesh(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::OFFIO::read_stream(), libMesh::MatlabIO::read_stream(), and libMesh::TriangleInterface::triangulate().

  { _elem_dims.clear(); _elem_dims.insert(d); }

unsigned int& libMesh::MeshBase::set_n_partitions ( ) [inline, protected, inherited]

Returns a writeable reference to the number of partitions.

Definition at line 898 of file mesh_base.h.

References libMesh::MeshBase::_n_parts.

Referenced by libMesh::Partitioner::partition(), libMesh::Partitioner::repartition(), and libMesh::BoundaryInfo::sync().

  { return _n_parts; }

void libMesh::MeshBase::set_next_unique_id ( unique_id_type id ) [inline, inherited]

Sets the next unique id to be used.

Definition at line 235 of file mesh_base.h.

References libMesh::MeshBase::_next_unique_id.

{ _next_unique_id = id; }

std::map<subdomain_id_type, std::string>& libMesh::MeshBase::set_subdomain_name_map ( ) [inline, inherited]

Return a writeable reference to the whole subdomain name map

Definition at line 860 of file mesh_base.h.

References libMesh::MeshBase::_block_id_to_name.

Referenced by libMesh::XdrIO::read_serialized_subdomain_names(), and libMesh::CheckpointIO::read_subdomain_names().

  { return _block_id_to_name; }

void libMesh::MeshBase::skip_partitioning ( bool skip ) [inline, inherited]

If true is passed in then this mesh will no longer be (re)partitioned. It would probably be a bad idea to call this on a Serial Mesh _before_ the first partitioning has happened... because no elements would get assigned to your processor pool.

Note that turning on skip_partitioning() can have adverse effects on your performance when using AMR... ie you could get large load imbalances.

However you might still want to use this if the communication and computation of the rebalance and repartition is too high for your application.

Definition at line 566 of file mesh_base.h.

References libMesh::MeshBase::_skip_partitioning.

Referenced by copy_nodes_and_elements().

{ _skip_partitioning = skip; }

bool libMesh::MeshBase::skip_partitioning ( ) const [inline, inherited]

Definition at line 567 of file mesh_base.h.

References libMesh::MeshBase::_skip_partitioning.

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

{ return _skip_partitioning; }

unsigned int libMesh::MeshBase::spatial_dimension ( ) const [inline, inherited]

Returns the spatial dimension of the mesh. Note that this is defined at compile time in the header libmesh_common.h.

Definition at line 182 of file mesh_base.h.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::MeshBase::get_info(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::UNVIO::nodes_out(), libMesh::MeshTools::Modification::scale(), libMesh::MeshTools::subdomain_bounding_box(), and libMesh::Nemesis_IO_Helper::write_exodus_initialization_info().

  { return cast_int<unsigned int>(LIBMESH_DIM); }

UniquePtr< PointLocatorBase > libMesh::MeshBase::sub_point_locator ( ) const [inherited]

returns a pointer to a subordinate PointLocatorBase object for this mesh, constructing a master PointLocator first if necessary. This should not be used in threaded or non-parallel_only code unless the master has already been constructed.

Definition at line 433 of file mesh_base.C.

References libMesh::MeshBase::_point_locator, libMesh::PointLocatorBase::build(), libMesh::Threads::in_threads, libMesh::libmesh_assert(), and libMesh::TREE_ELEMENTS.

Referenced by libMesh::DofMap::create_dof_constraints(), libMesh::MeshFunction::init(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshRefinement::make_refinement_compatible(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::SerialMesh::stitching_helper(), and libMesh::MeshRefinement::test_level_one().

{
  // If there's no master point locator, then we need one.
  if (_point_locator.get() == NULL)
    {
      // PointLocator construction may not be safe within threads
      libmesh_assert(!Threads::in_threads);

      // And it may require parallel communication
      parallel_object_only();

      _point_locator.reset (PointLocatorBase::build(TREE_ELEMENTS, *this).release());
    }

  // Otherwise there was a master point locator, and we can grab a
  // sub-locator easily.
  return PointLocatorBase::build(TREE_ELEMENTS, *this, _point_locator.get());
}

virtual element_iterator libMesh::MeshBase::subactive_elements_begin ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::Partitioner::set_node_processor_ids().

virtual const_element_iterator libMesh::MeshBase::subactive_elements_begin ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::subactive_elements_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::Partitioner::set_node_processor_ids().

virtual const_element_iterator libMesh::MeshBase::subactive_elements_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

void libMesh::MeshBase::subdomain_ids ( std::set< subdomain_id_type > & ids ) const [inherited]

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

Definition at line 216 of file mesh_base.C.

References libMesh::MeshBase::active_local_elements_begin(), libMesh::MeshBase::active_local_elements_end(), libMesh::ParallelObject::comm(), end, and libMesh::Parallel::Communicator::set_union().

Referenced by libMesh::MeshBase::n_subdomains(), and libMesh::TecplotIO::TecplotIO().

{
  // This requires an inspection on every processor
  parallel_object_only();

  ids.clear();

  const_element_iterator el  = this->active_local_elements_begin();
  const_element_iterator end = this->active_local_elements_end();

  for (; el!=end; ++el)
    ids.insert((*el)->subdomain_id());

  // Some subdomains may only live on other processors
  this->comm().set_union(ids);
}

std::string & libMesh::MeshBase::subdomain_name ( subdomain_id_type id ) [inherited]

Returns a writable reference for getting/setting an optional name for a subdomain.

Definition at line 461 of file mesh_base.C.

References libMesh::MeshBase::_block_id_to_name.

Referenced by libMesh::AbaqusIO::assign_subdomain_ids(), DMlibMeshSetSystem_libMesh(), libMesh::UNVIO::groups_in(), libMesh::ExodusII_IO::read(), libMesh::TecplotIO::write_binary(), and libMesh::ExodusII_IO_Helper::write_elements().

{
  return _block_id_to_name[id];
}

const std::string & libMesh::MeshBase::subdomain_name ( subdomain_id_type id ) const [inherited]

Definition at line 466 of file mesh_base.C.

References libMesh::MeshBase::_block_id_to_name.

{
  // An empty string to return when no matching subdomain name is found
  static const std::string empty;

  std::map<subdomain_id_type, std::string>::const_iterator iter = _block_id_to_name.find(id);
  if (iter == _block_id_to_name.end())
    return empty;
  else
    return iter->second;
}

virtual element_iterator libMesh::MeshBase::type_elements_begin ( const ElemType type ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshTools::n_elem_of_type(), and libMesh::MeshTools::n_non_subactive_elem_of_type_at_level().

virtual const_element_iterator libMesh::MeshBase::type_elements_begin ( const ElemType type ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::type_elements_end ( const ElemType type ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshTools::n_elem_of_type(), and libMesh::MeshTools::n_non_subactive_elem_of_type_at_level().

virtual const_element_iterator libMesh::MeshBase::type_elements_end ( const ElemType type ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::unpartitioned_elements_begin ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshTools::n_active_levels(), libMesh::MeshTools::n_levels(), libMesh::MeshTools::n_p_levels(), libMesh::Partitioner::partition_unpartitioned_elements(), and libMesh::Partitioner::set_node_processor_ids().

virtual const_element_iterator libMesh::MeshBase::unpartitioned_elements_begin ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual element_iterator libMesh::MeshBase::unpartitioned_elements_end ( ) [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshTools::n_active_levels(), libMesh::MeshTools::n_levels(), libMesh::MeshTools::n_p_levels(), libMesh::Partitioner::partition_unpartitioned_elements(), and libMesh::Partitioner::set_node_processor_ids().

virtual const_element_iterator libMesh::MeshBase::unpartitioned_elements_end ( ) const [pure virtual, inherited]

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

virtual void libMesh::MeshBase::update_parallel_id_counts ( ) [pure virtual, inherited]

Updates parallel caches so that methods like n_elem() accurately reflect changes on other processors

Implemented in libMesh::ParallelMesh, and libMesh::SerialMesh.

Referenced by libMesh::MeshRefinement::_coarsen_elements(), libMesh::MeshRefinement::_refine_elements(), and libMesh::MeshBase::prepare_for_use().

virtual void libMesh::MeshBase::update_post_partitioning ( ) [inline, virtual, inherited]

Recalculate any cached data after elements and nodes have been repartitioned.

Reimplemented in libMesh::ParallelMesh.

Definition at line 543 of file mesh_base.h.

Referenced by libMesh::Partitioner::partition(), libMesh::MeshBase::partition(), and libMesh::Nemesis_IO::read().

{}

void libMesh::UnstructuredMesh::write	(	const std::string &	name,
		MeshData *	mesh_data = `NULL`
	)		`[virtual]`

Write the file specified by name. Attempts to figure out the proper method by the file extension.

In order to write the UNV and TetGen file types, you must also pass a separate pointer to the MeshData object you have been using with this mesh, since these write methods expect it.

Implements libMesh::MeshBase.

Definition at line 524 of file unstructured_mesh.C.

References libMesh::START_LOG(), libMesh::NameBasedIO::write(), and libMesh::UNVIO::write().

{
  START_LOG("write()", "Mesh");

  if (mesh_data)
    {
      libmesh_deprecated();
      if (name.rfind(".unv") < name.size())
        UNVIO(*this, mesh_data).write (name);
      else
        libmesh_error_msg("Only UNV output supports MeshData");
    }

  NameBasedIO(*this).write(name);

  STOP_LOG("write()", "Mesh");
}

void libMesh::UnstructuredMesh::write	(	const std::string &	name,
		const std::vector< Number > &	values,
		const std::vector< std::string > &	variable_names
	)

Write to the file specified by name. Attempts to figure out the proper method by the file extension. Also writes data.

Definition at line 545 of file unstructured_mesh.C.

References libMesh::START_LOG(), and libMesh::NameBasedIO::write_nodal_data().

{
  START_LOG("write()", "Mesh");

  NameBasedIO(*this).write_nodal_data(name, v, vn);

  STOP_LOG("write()", "Mesh");
}

Friends And Related Function Documentation

friend class BoundaryInfo [friend, inherited]

Make the BoundaryInfo class a friend so that it can create and interact with BoundaryMesh.

Definition at line 983 of file mesh_base.h.

friend class MeshInput< MeshBase > [friend, inherited]

The MeshInput classes are friends so that they can set the number of partitions.

Definition at line 977 of file mesh_base.h.

std::ostream& operator<<	(	std::ostream &	os,
		const MeshBase &	m
	)		`[friend, inherited]`

Equivalent to calling print_info() above, but now you can write: Mesh mesh; libMesh::out << mesh << std::endl;

Definition at line 354 of file mesh_base.C.

{
  m.print_info(os);
  return os;
}

friend class Partitioner [friend, inherited]

The partitioner class is a friend so that it can set the number of partitions.

Definition at line 971 of file mesh_base.h.

Member Data Documentation

std::map<subdomain_id_type, std::string> libMesh::MeshBase::_block_id_to_name [protected, inherited]

This structure maintains the mapping of named blocks for file formats that support named blocks. Currently this is only implemented for ExodusII

Definition at line 958 of file mesh_base.h.

Referenced by libMesh::MeshBase::get_id_by_name(), libMesh::MeshBase::get_subdomain_name_map(), libMesh::MeshBase::set_subdomain_name_map(), and libMesh::MeshBase::subdomain_name().

const Parallel::Communicator& libMesh::ParallelObject::_communicator [protected, inherited]

Definition at line 104 of file parallel_object.h.

Referenced by libMesh::EquationSystems::build_solution_vector(), libMesh::ParallelObject::comm(), libMesh::EquationSystems::get_solution(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::operator=(), and libMesh::ParallelObject::processor_id().

std::set<unsigned char> libMesh::MeshBase::_elem_dims [protected, inherited]

We cache the dimension of the elements present in the mesh. So, if we have a mesh with 1D and 2D elements, this structure will contain 1 and 2.

Definition at line 965 of file mesh_base.h.

Referenced by libMesh::MeshBase::cache_elem_dims(), libMesh::MeshBase::clear(), copy_nodes_and_elements(), libMesh::MeshBase::elem_dimensions(), libMesh::MeshBase::mesh_dimension(), libMesh::MeshBase::MeshBase(), and libMesh::MeshBase::set_mesh_dimension().

bool libMesh::MeshBase::_is_prepared [protected, inherited]

Flag indicating if the mesh has been prepared for use.

Definition at line 915 of file mesh_base.h.

Referenced by all_first_order(), all_second_order(), libMesh::MeshBase::clear(), copy_nodes_and_elements(), libMesh::MeshBase::is_prepared(), and libMesh::MeshBase::prepare_for_use().

unsigned int libMesh::MeshBase::_n_parts [protected, inherited]

The number of partitions the mesh has. This is set by the partitioners, and may not be changed directly by the user. **NOTE** The number of partitions *need not* equal this->n_processors(), consider for example the case where you simply want to partition a mesh on one processor and view the result in GMV.

Definition at line 910 of file mesh_base.h.

Referenced by libMesh::MeshBase::clear(), copy_nodes_and_elements(), libMesh::MeshBase::n_partitions(), libMesh::MeshBase::recalculate_n_partitions(), and libMesh::MeshBase::set_n_partitions().

unique_id_type libMesh::MeshBase::_next_unique_id [protected, inherited]

The next available unique id for assigning ids to DOF objects

Definition at line 938 of file mesh_base.h.

Referenced by libMesh::SerialMesh::add_elem(), libMesh::ParallelMesh::add_elem(), libMesh::SerialMesh::add_node(), libMesh::ParallelMesh::add_node(), libMesh::SerialMesh::assign_unique_ids(), libMesh::ParallelMesh::assign_unique_ids(), libMesh::MeshBase::next_unique_id(), libMesh::ParallelMesh::ParallelMesh(), libMesh::SerialMesh::SerialMesh(), and libMesh::MeshBase::set_next_unique_id().

UniquePtr<Partitioner> libMesh::MeshBase::_partitioner [protected, inherited]

A partitioner to use at each prepare_for_use().

This will be built in the constructor of each derived class, but can be replaced by the user through the partitioner() accessor.

Definition at line 932 of file mesh_base.h.

Referenced by libMesh::MeshBase::MeshBase(), libMesh::ParallelMesh::ParallelMesh(), libMesh::MeshBase::partitioner(), and libMesh::SerialMesh::SerialMesh().

UniquePtr<PointLocatorBase> libMesh::MeshBase::_point_locator [mutable, protected, inherited]

A PointLocator class for this mesh. This will not actually be built unless needed. Further, since we want our point_locator() method to be const (yet do the dynamic allocating) this needs to be mutable. Since the PointLocatorBase::build() member is used, and it operates on a constant reference to the mesh, this is OK.

Definition at line 924 of file mesh_base.h.

Referenced by libMesh::MeshBase::clear_point_locator(), libMesh::MeshBase::point_locator(), and libMesh::MeshBase::sub_point_locator().

bool libMesh::MeshBase::_skip_partitioning [protected, inherited]

If this is true then no partitioning should be done.

Definition at line 944 of file mesh_base.h.

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

bool libMesh::MeshBase::_skip_renumber_nodes_and_elements [protected, inherited]

If this is true then renumbering will be kept to a miniumum.

This is set when prepare_for_use() is called.

Definition at line 951 of file mesh_base.h.

Referenced by libMesh::MeshBase::allow_renumbering(), libMesh::MeshBase::prepare_for_use(), libMesh::SerialMesh::renumber_nodes_and_elements(), and libMesh::ParallelMesh::renumber_nodes_and_elements().