Reference documentation for deal.II version Git 3fe3ec1 2018-08-21 21:05:51 -0400
Classes | Public Types | Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
parallel::distributed::Triangulation< dim, spacedim > Class Template Reference

#include <deal.II/distributed/tria.h>

Inheritance diagram for parallel::distributed::Triangulation< dim, spacedim >:
[legend]

Classes

struct  CellAttachedData
 
class  DataTransfer
 

Public Types

enum  Settings { default_setting = 0x0, mesh_reconstruction_after_repartitioning = 0x1, construct_multigrid_hierarchy = 0x2, no_automatic_repartitioning = 0x4 }
 
using cell_iterator = typename::Triangulation< dim, spacedim >::cell_iterator
 
using active_cell_iterator = typename::Triangulation< dim, spacedim >::active_cell_iterator
 
- Public Types inherited from Triangulation< dim, spacedim >
enum  MeshSmoothing {
  none = 0x0, limit_level_difference_at_vertices = 0x1, eliminate_unrefined_islands = 0x2, patch_level_1 = 0x4,
  coarsest_level_1 = 0x8, allow_anisotropic_smoothing = 0x10, eliminate_refined_inner_islands = 0x100, eliminate_refined_boundary_islands = 0x200,
  do_not_produce_unrefined_islands = 0x400, smoothing_on_refinement, smoothing_on_coarsening, maximum_smoothing = 0xffff ^ allow_anisotropic_smoothing
}
 
using cell_iterator = TriaIterator< CellAccessor< dim, spacedim >>
 
using active_cell_iterator = TriaActiveIterator< CellAccessor< dim, spacedim >>
 
using face_iterator = TriaIterator< TriaAccessor< dim-1, dim, spacedim >>
 
using active_face_iterator = TriaActiveIterator< TriaAccessor< dim-1, dim, spacedim >>
 
using vertex_iterator = TriaIterator<::TriaAccessor< 0, dim, spacedim >>
 
using active_vertex_iterator = TriaActiveIterator<::TriaAccessor< 0, dim, spacedim >>
 
enum  CellStatus { CELL_PERSIST, CELL_REFINE, CELL_COARSEN, CELL_INVALID }
 

Public Member Functions

 Triangulation (MPI_Comm mpi_communicator, const typename::Triangulation< dim, spacedim >::MeshSmoothing smooth_grid=(::Triangulation< dim, spacedim >::none), const Settings settings=default_setting)
 
virtual ~Triangulation () override
 
virtual void clear () override
 
virtual void copy_triangulation (const ::Triangulation< dim, spacedim > &other_tria) override
 
virtual void create_triangulation (const std::vector< Point< spacedim >> &vertices, const std::vector< CellData< dim >> &cells, const SubCellData &subcelldata) override
 
virtual void execute_coarsening_and_refinement () override
 
virtual bool prepare_coarsening_and_refinement () override
 
void repartition ()
 
void communicate_locally_moved_vertices (const std::vector< bool > &vertex_locally_moved)
 
virtual bool has_hanging_nodes () const override
 
virtual std::size_t memory_consumption () const override
 
virtual std::size_t memory_consumption_p4est () const
 
void write_mesh_vtk (const char *file_basename) const
 
unsigned int get_checksum () const
 
void save (const char *filename) const
 
void load (const char *filename, const bool autopartition=true)
 
unsigned int register_data_attach (const std::function< std::vector< char >(const cell_iterator &, const CellStatus)> &pack_callback, const bool returns_variable_size_data)
 
void notify_ready_to_unpack (const unsigned int handle, const std::function< void(const cell_iterator &, const CellStatus, const boost::iterator_range< std::vector< char >::const_iterator > &)> &unpack_callback)
 
const std::vector< types::global_dof_index > & get_p4est_tree_to_coarse_cell_permutation () const
 
const std::vector< types::global_dof_index > & get_coarse_cell_to_p4est_tree_permutation () const
 
virtual void add_periodicity (const std::vector<::GridTools::PeriodicFacePair< cell_iterator >> &) override
 
- Public Member Functions inherited from parallel::Triangulation< dim, spacedim >
 Triangulation (MPI_Comm mpi_communicator, const typename::Triangulation< dim, spacedim >::MeshSmoothing smooth_grid=(::Triangulation< dim, spacedim >::none), const bool check_for_distorted_cells=false)
 
virtual MPI_Comm get_communicator () const
 
virtual void copy_triangulation (const ::Triangulation< dim, spacedim > &old_tria) override
 
const std::vector< unsigned int > & n_locally_owned_active_cells_per_processor () const
 
unsigned int n_locally_owned_active_cells () const
 
virtual types::global_dof_index n_global_active_cells () const override
 
virtual unsigned int n_global_levels () const override
 
types::subdomain_id locally_owned_subdomain () const override
 
const std::set< types::subdomain_id > & ghost_owners () const
 
const std::set< types::subdomain_id > & level_ghost_owners () const
 
- Public Member Functions inherited from Triangulation< dim, spacedim >
 Triangulation (const MeshSmoothing smooth_grid=none, const bool check_for_distorted_cells=false)
 
 Triangulation (const Triangulation< dim, spacedim > &)=delete
 
 Triangulation (Triangulation< dim, spacedim > &&tria) noexcept
 
Triangulationoperator= (Triangulation< dim, spacedim > &&tria) noexcept
 
virtual void set_mesh_smoothing (const MeshSmoothing mesh_smoothing)
 
virtual const MeshSmoothingget_mesh_smoothing () const
 
void set_manifold (const types::manifold_id number, const Manifold< dim, spacedim > &manifold_object)
 
void set_manifold (const types::manifold_id number)
 
void reset_manifold (const types::manifold_id manifold_number)
 
void reset_all_manifolds ()
 
void set_all_manifold_ids (const types::manifold_id number)
 
void set_all_manifold_ids_on_boundary (const types::manifold_id number)
 
void set_all_manifold_ids_on_boundary (const types::boundary_id b_id, const types::manifold_id number)
 
const Manifold< dim, spacedim > & get_manifold (const types::manifold_id number) const
 
std::vector< types::boundary_idget_boundary_ids () const
 
std::vector< types::manifold_idget_manifold_ids () const
 
virtual void copy_triangulation (const Triangulation< dim, spacedim > &other_tria)
 
virtual void create_triangulation_compatibility (const std::vector< Point< spacedim >> &vertices, const std::vector< CellData< dim >> &cells, const SubCellData &subcelldata)
 
void flip_all_direction_flags ()
 
void set_all_refine_flags ()
 
void refine_global (const unsigned int times=1)
 
void save_refine_flags (std::ostream &out) const
 
void save_refine_flags (std::vector< bool > &v) const
 
void load_refine_flags (std::istream &in)
 
void load_refine_flags (const std::vector< bool > &v)
 
void save_coarsen_flags (std::ostream &out) const
 
void save_coarsen_flags (std::vector< bool > &v) const
 
void load_coarsen_flags (std::istream &out)
 
void load_coarsen_flags (const std::vector< bool > &v)
 
bool get_anisotropic_refinement_flag () const
 
void clear_user_flags ()
 
void save_user_flags (std::ostream &out) const
 
void save_user_flags (std::vector< bool > &v) const
 
void load_user_flags (std::istream &in)
 
void load_user_flags (const std::vector< bool > &v)
 
void clear_user_flags_line ()
 
void save_user_flags_line (std::ostream &out) const
 
void save_user_flags_line (std::vector< bool > &v) const
 
void load_user_flags_line (std::istream &in)
 
void load_user_flags_line (const std::vector< bool > &v)
 
void clear_user_flags_quad ()
 
void save_user_flags_quad (std::ostream &out) const
 
void save_user_flags_quad (std::vector< bool > &v) const
 
void load_user_flags_quad (std::istream &in)
 
void load_user_flags_quad (const std::vector< bool > &v)
 
void clear_user_flags_hex ()
 
void save_user_flags_hex (std::ostream &out) const
 
void save_user_flags_hex (std::vector< bool > &v) const
 
void load_user_flags_hex (std::istream &in)
 
void load_user_flags_hex (const std::vector< bool > &v)
 
void clear_user_data ()
 
void save_user_indices (std::vector< unsigned int > &v) const
 
void load_user_indices (const std::vector< unsigned int > &v)
 
void save_user_pointers (std::vector< void * > &v) const
 
void load_user_pointers (const std::vector< void * > &v)
 
void save_user_indices_line (std::vector< unsigned int > &v) const
 
void load_user_indices_line (const std::vector< unsigned int > &v)
 
void save_user_indices_quad (std::vector< unsigned int > &v) const
 
void load_user_indices_quad (const std::vector< unsigned int > &v)
 
void save_user_indices_hex (std::vector< unsigned int > &v) const
 
void load_user_indices_hex (const std::vector< unsigned int > &v)
 
void save_user_pointers_line (std::vector< void * > &v) const
 
void load_user_pointers_line (const std::vector< void * > &v)
 
void save_user_pointers_quad (std::vector< void * > &v) const
 
void load_user_pointers_quad (const std::vector< void * > &v)
 
void save_user_pointers_hex (std::vector< void * > &v) const
 
void load_user_pointers_hex (const std::vector< void * > &v)
 
cell_iterator begin (const unsigned int level=0) const
 
active_cell_iterator begin_active (const unsigned int level=0) const
 
cell_iterator end () const
 
cell_iterator end (const unsigned int level) const
 
active_cell_iterator end_active (const unsigned int level) const
 
cell_iterator last () const
 
active_cell_iterator last_active () const
 
IteratorRange< cell_iteratorcell_iterators () const
 
IteratorRange< active_cell_iteratoractive_cell_iterators () const
 
IteratorRange< cell_iteratorcell_iterators_on_level (const unsigned int level) const
 
IteratorRange< active_cell_iteratoractive_cell_iterators_on_level (const unsigned int level) const
 
face_iterator begin_face () const
 
active_face_iterator begin_active_face () const
 
face_iterator end_face () const
 
IteratorRange< active_face_iteratoractive_face_iterators () const
 
vertex_iterator begin_vertex () const
 
active_vertex_iterator begin_active_vertex () const
 
vertex_iterator end_vertex () const
 
unsigned int n_lines () const
 
unsigned int n_lines (const unsigned int level) const
 
unsigned int n_active_lines () const
 
unsigned int n_active_lines (const unsigned int level) const
 
unsigned int n_quads () const
 
unsigned int n_quads (const unsigned int level) const
 
unsigned int n_active_quads () const
 
unsigned int n_active_quads (const unsigned int level) const
 
unsigned int n_hexs () const
 
unsigned int n_hexs (const unsigned int level) const
 
unsigned int n_active_hexs () const
 
unsigned int n_active_hexs (const unsigned int level) const
 
unsigned int n_cells () const
 
unsigned int n_cells (const unsigned int level) const
 
unsigned int n_active_cells () const
 
unsigned int n_active_cells (const unsigned int level) const
 
unsigned int n_faces () const
 
unsigned int n_active_faces () const
 
unsigned int n_levels () const
 
unsigned int n_vertices () const
 
const std::vector< Point< spacedim > > & get_vertices () const
 
unsigned int n_used_vertices () const
 
bool vertex_used (const unsigned int index) const
 
const std::vector< bool > & get_used_vertices () const
 
unsigned int max_adjacent_cells () const
 
Triangulation< dim, spacedim > & get_triangulation ()
 
const Triangulation< dim, spacedim > & get_triangulation () const
 
unsigned int n_raw_lines () const
 
unsigned int n_raw_lines (const unsigned int level) const
 
unsigned int n_raw_quads () const
 
unsigned int n_raw_quads (const unsigned int level) const
 
unsigned int n_raw_hexs (const unsigned int level) const
 
unsigned int n_raw_cells (const unsigned int level) const
 
unsigned int n_raw_faces () const
 
template<class Archive >
void save (Archive &ar, const unsigned int version) const
 
template<class Archive >
void load (Archive &ar, const unsigned int version)
 
virtual void add_periodicity (const std::vector< GridTools::PeriodicFacePair< cell_iterator >> &)
 
const std::map< std::pair< cell_iterator, unsigned int >, std::pair< std::pair< cell_iterator, unsigned int >, std::bitset< 3 > > > & get_periodic_face_map () const
 
- Public Member Functions inherited from Subscriptor
 Subscriptor ()
 
 Subscriptor (const Subscriptor &)
 
 Subscriptor (Subscriptor &&) noexcept
 
virtual ~Subscriptor ()
 
Subscriptoroperator= (const Subscriptor &)
 
Subscriptoroperator= (Subscriptor &&) noexcept
 
void subscribe (const char *identifier=nullptr) const
 
void unsubscribe (const char *identifier=nullptr) const
 
unsigned int n_subscriptions () const
 
template<typename StreamType >
void list_subscribers (StreamType &stream) const
 
void list_subscribers () const
 
template<class Archive >
void serialize (Archive &ar, const unsigned int version)
 

Private Types

using quadrant_cell_relation_t = typename std::tuple< typename::internal::p4est::types< dim >::quadrant *, CellStatus, cell_iterator >
 

Private Member Functions

virtual void update_number_cache () override
 
void update_quadrant_cell_relations ()
 
typename::internal::p4est::types< dim >::tree * init_tree (const int dealii_coarse_cell_index) const
 
void setup_coarse_cell_to_p4est_tree_permutation ()
 
void copy_new_triangulation_to_p4est (std::integral_constant< int, 2 >)
 
void copy_local_forest_to_triangulation ()
 
std::vector< unsigned int > get_cell_weights () const
 
virtual std::map< unsigned int, std::set<::types::subdomain_id > > compute_vertices_with_ghost_neighbors () const override
 
std::vector< bool > mark_locally_active_vertices_on_level (const int level) const
 

Private Attributes

Settings settings
 
bool triangulation_has_content
 
typename::internal::p4est::types< dim >::connectivity * connectivity
 
typename::internal::p4est::types< dim >::forest * parallel_forest
 
typename::internal::p4est::types< dim >::ghost * parallel_ghost
 
std::vector< quadrant_cell_relation_tlocal_quadrant_cell_relations
 
std::vector< types::global_dof_indexcoarse_cell_to_p4est_tree_permutation
 

Additional Inherited Members

- Static Public Member Functions inherited from Triangulation< dim, spacedim >
static::ExceptionBase & ExcInvalidLevel (int arg1)
 
static::ExceptionBase & ExcTriangulationNotEmpty (int arg1, int arg2)
 
static::ExceptionBase & ExcGridReadError ()
 
static::ExceptionBase & ExcFacesHaveNoLevel ()
 
static::ExceptionBase & ExcEmptyLevel (int arg1)
 
static::ExceptionBase & ExcNonOrientableTriangulation ()
 
static::ExceptionBase & ExcBoundaryIdNotFound (types::boundary_id arg1)
 
- Static Public Member Functions inherited from Subscriptor
static::ExceptionBase & ExcInUse (int arg1, std::string arg2, std::string arg3)
 
static::ExceptionBase & ExcNoSubscriber (std::string arg1, std::string arg2)
 
- Public Attributes inherited from Triangulation< dim, spacedim >
Signals signals
 
- Static Public Attributes inherited from Triangulation< dim, spacedim >
static const unsigned int dimension = dim
 
static const unsigned int space_dimension = spacedim
 
- Protected Member Functions inherited from parallel::Triangulation< dim, spacedim >
void fill_level_ghost_owners ()
 
- Protected Member Functions inherited from Triangulation< dim, spacedim >
void update_periodic_face_map ()
 
- Static Protected Member Functions inherited from Triangulation< dim, spacedim >
static void write_bool_vector (const unsigned int magic_number1, const std::vector< bool > &v, const unsigned int magic_number2, std::ostream &out)
 
static void read_bool_vector (const unsigned int magic_number1, std::vector< bool > &v, const unsigned int magic_number2, std::istream &in)
 
- Protected Attributes inherited from parallel::Triangulation< dim, spacedim >
MPI_Comm mpi_communicator
 
types::subdomain_id my_subdomain
 
types::subdomain_id n_subdomains
 
- Protected Attributes inherited from Triangulation< dim, spacedim >
MeshSmoothing smooth_grid
 

Detailed Description

template<int dim, int spacedim = dim>
class parallel::distributed::Triangulation< dim, spacedim >

This class acts like the Triangulation class, but it distributes the mesh across a number of different processors when using MPI. The class's interface does not add a lot to the Triangulation class but there are a number of difficult algorithms under the hood that ensure we always have a load-balanced, fully distributed mesh. Use of this class is explained in step-40, step-32, the Parallel computing with multiple processors using distributed memory documentation module, as well as the distributed_paper. See there for more information. This class satisfies the MeshType concept.

Note
This class does not support anisotropic refinement, because it relies on the p4est library that does not support this. Attempts to refine cells anisotropically will result in errors.
There is currently no support for distributing 1d triangulations.

Interaction with boundary description

Refining and coarsening a distributed triangulation is a complicated process because cells may have to be migrated from one processor to another. On a single processor, materializing that part of the global mesh that we want to store here from what we have stored before therefore may involve several cycles of refining and coarsening the locally stored set of cells until we have finally gotten from the previous to the next triangulation. This process is described in more detail in the distributed_paper. Unfortunately, in this process, some information can get lost relating to flags that are set by user code and that are inherited from mother to child cell but that are not moved along with a cell if that cell is migrated from one processor to another.

An example are boundary indicators. Assume, for example, that you start with a single cell that is refined once globally, yielding four children. If you have four processors, each one owns one cell. Assume now that processor 1 sets the boundary indicators of the external boundaries of the cell it owns to 42. Since processor 0 does not own this cell, it doesn't set the boundary indicators of its ghost cell copy of this cell. Now, assume we do several mesh refinement cycles and end up with a configuration where this processor suddenly finds itself as the owner of this cell. If boundary indicator 42 means that we need to integrate Neumann boundary conditions along this boundary, then processor 0 will forget to do so because it has never set the boundary indicator along this cell's boundary to 42.

The way to avoid this dilemma is to make sure that things like setting boundary indicators or material ids is done immediately every time a parallel triangulation is refined. This is not necessary for sequential triangulations because, there, these flags are inherited from mother to child cell and remain with a cell even if it is refined and the children are later coarsened again, but this does not hold for distributed triangulations. It is made even more difficult by the fact that in the process of refining a parallel distributed triangulation, the triangulation may call Triangulation::execute_coarsening_and_refinement multiple times and this function needs to know about boundaries. In other words, it is not enough to just set boundary indicators on newly created faces only after calling distributed::parallel::Triangulation::execute_coarsening_and_refinement: it actually has to happen while that function is still running.

The way to do this is by writing a function that sets boundary indicators and that will be called by the Triangulation class. The triangulation does not provide a pointer to itself to the function being called, nor any other information, so the trick is to get this information into the function. C++ provides a nice mechanism for this that is best explained using an example:

#include <functional>
template <int dim>
void set_boundary_ids (
{
... set boundary indicators on the triangulation object ...
}
template <int dim>
void
MyClass<dim>::create_coarse_mesh (
{
... create the coarse mesh ...
coarse_grid.signals.post_refinement.connect(
std::bind (&set_boundary_ids<dim>, std::ref(coarse_grid)));
}

What the call to std::bind does is to produce an object that can be called like a function with no arguments. It does so by taking the address of a function that does, in fact, take an argument but permanently fix this one argument to a reference to the coarse grid triangulation. After each refinement step, the triangulation will then call the object so created which will in turn call set_boundary_ids<dim> with the reference to the coarse grid as argument.

This approach can be generalized. In the example above, we have used a global function that will be called. However, sometimes it is necessary that this function is in fact a member function of the class that generates the mesh, for example because it needs to access run-time parameters. This can be achieved as follows: assuming the set_boundary_ids() function has been declared as a (non- static, but possibly private) member function of the MyClass class, then the following will work:

#include <functional>
template <int dim>
void
MyClass<dim>::set_boundary_ids (
{
... set boundary indicators on the triangulation object ...
}
template <int dim>
void
MyClass<dim>::create_coarse_mesh (
{
... create the coarse mesh ...
coarse_grid.signals.post_refinement.connect(
std::bind (&MyGeometry<dim>::set_boundary_ids,
std::cref(*this),
std::ref(coarse_grid)));
}

Here, like any other member function, set_boundary_ids implicitly takes a pointer or reference to the object it belongs to as first argument. std::bind again creates an object that can be called like a global function with no arguments, and this object in turn calls set_boundary_ids with a pointer to the current object and a reference to the triangulation to work on. Note that because the create_coarse_mesh function is declared as const, it is necessary that the set_boundary_ids function is also declared const.

Note:For reasons that have to do with the way the parallel::distributed::Triangulation is implemented, functions that have been attached to the post-refinement signal of the triangulation are called more than once, sometimes several times, every time the triangulation is actually refined.

Author
Wolfgang Bangerth, Timo Heister 2008, 2009, 2010, 2011

Definition at line 46 of file p4est_wrappers.h.

Member Typedef Documentation

template<int dim, int spacedim = dim>
using parallel::distributed::Triangulation< dim, spacedim >::quadrant_cell_relation_t = typename std::tuple< typename ::internal::p4est::types<dim>::quadrant *, CellStatus, cell_iterator>
private

This auxiliary data structure stores the relation between a p4est quadrant, a deal.II cell and its current CellStatus. For an extensive description of the latter, see the documentation for the member function register_data_attach().

Definition at line 922 of file tria.h.

Constructor & Destructor Documentation

template<int dim, int spacedim>
Triangulation< dim, spacedim >::Triangulation ( MPI_Comm  mpi_communicator,
const typename::Triangulation< dim, spacedim >::MeshSmoothing  smooth_grid = (::Triangulation<dim, spacedim>::none),
const Settings  settings = default_setting 
)

Constructor.

Parameters
mpi_communicatordenotes the MPI communicator to be used for the triangulation.
smooth_gridDegree and kind of mesh smoothing to be applied to the mesh. See the Triangulation class for a description of the kinds of smoothing operations that can be applied.
settingsSee the description of the Settings enumerator. Providing construct_multigrid_hierarchy enforces Triangulation::limit_level_difference_at_vertices for smooth_grid.
Note
This class does not currently support the check_for_distorted_cells argument provided by the base class.
While it is possible to pass all of the mesh smoothing flags listed in the base class to objects of this type, it is not always possible to honor all of these smoothing options if they would require knowledge of refinement/coarsening flags on cells not locally owned by this processor. As a consequence, for some of these flags, the ultimate number of cells of the parallel triangulation may depend on the number of processors into which it is partitioned. On the other hand, if no smoothing flags are passed, if you always mark the same cells of the mesh, you will always get the exact same refined mesh independent of the number of processors into which the triangulation is partitioned.

Definition at line 2142 of file tria.cc.

template<int dim, int spacedim>
Triangulation< dim, spacedim >::~Triangulation ( )
overridevirtual

Destructor.

Reimplemented from parallel::Triangulation< dim, spacedim >.

Definition at line 2172 of file tria.cc.

Member Function Documentation

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::clear ( )
overridevirtual

Reset this triangulation into a virgin state by deleting all data.

Note that this operation is only allowed if no subscriptions to this object exist any more, such as DoFHandler objects using it.

Reimplemented from Triangulation< dim, spacedim >.

Definition at line 2588 of file tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::copy_triangulation ( const ::Triangulation< dim, spacedim > &  other_tria)
overridevirtual

Implementation of the same function as in the base class.

Note
This function cannot copy a triangulation that has been refined.
This function can be used to copy a serial Triangulation to a parallel::distributed::Triangulation but only if the serial Triangulation has never been refined.

Definition at line 4770 of file tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::create_triangulation ( const std::vector< Point< spacedim >> &  vertices,
const std::vector< CellData< dim >> &  cells,
const SubCellData subcelldata 
)
overridevirtual

Create a triangulation as documented in the base class.

This function also sets up the various data structures necessary to distribute a mesh across a number of processors. This will be necessary once the mesh is being refined, though we will always keep the entire coarse mesh that is generated by this function on all processors.

Reimplemented from Triangulation< dim, spacedim >.

Definition at line 2193 of file tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::execute_coarsening_and_refinement ( )
overridevirtual

Coarsen and refine the mesh according to refinement and coarsening flags set.

Since the current processor only has control over those cells it owns (i.e. the ones for which cell->subdomain_id() == this->locally_owned_subdomain()), refinement and coarsening flags are only respected for those locally owned cells. Flags may be set on other cells as well (and may often, in fact, if you call Triangulation::prepare_coarsening_and_refinement()) but will be largely ignored: the decision to refine the global mesh will only be affected by flags set on locally owned cells.

Note
This function by default partitions the mesh in such a way that the number of cells on all processors is roughly equal. If you want to set weights for partitioning, e.g. because some cells are more expensive to compute than others, you can use the signal cell_weight as documented in the Triangulation class. This function will check whether a function is connected to the signal and if so use it. If you prefer to repartition the mesh yourself at user-defined intervals only, you can create your triangulation object by passing the parallel::distributed::Triangulation::no_automatic_repartitioning flag to the constructor, which ensures that calling the current function only refines and coarsens the triangulation, but doesn't partition it. You can then call the repartition() function manually. The usage of the cell_weights signal is identical in both cases, if a function is connected to the signal it will be used to balance the calculated weights, otherwise the number of cells is balanced.

Reimplemented from Triangulation< dim, spacedim >.

Definition at line 3808 of file tria.cc.

template<int dim, int spacedim>
bool Triangulation< dim, spacedim >::prepare_coarsening_and_refinement ( )
overridevirtual

Override the implementation of prepare_coarsening_and_refinement from the base class. This is necessary if periodic boundaries are enabled and the level difference over vertices over the periodic boundary must be not more than 2:1.

Reimplemented from Triangulation< dim, spacedim >.

Definition at line 3418 of file tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::repartition ( )

Manually repartition the active cells between processors. Normally this repartitioning will happen automatically when calling execute_coarsening_and_refinement() (or refine_global()) unless the no_automatic_repartitioning is set in the constructor. Setting the flag and then calling repartition() gives the same result.

If you want to transfer data (using SolutionTransfer or manually with register_data_attach() and notify_ready_to_unpack()), you need to set it up twice: once when calling execute_coarsening_and_refinement(), which will handle coarsening and refinement but obviously won't ship any data between processors, and a second time when calling repartition(). Here, no coarsening and refinement will be done but information will be packed and shipped to different processors. In other words, you probably want to treat a call to repartition() in the same way as execute_coarsening_and_refinement() with respect to dealing with data movement (SolutionTransfer, etc.).

Note
If no function is connected to the cell_weight signal described in the Triangulation class, this function will balance the number of cells on each processor. If one or more functions are connected, it will calculate the sum of the weights and balance the weights across processors. The only requirement on the weights is that every cell's weight is positive and that the sum over all weights on all processors can be formed using a 64-bit integer. Beyond that, it is your choice how you want to interpret the weights. A common approach is to consider the weights proportional to the cost of doing computations on a cell, e.g., by summing the time for assembly and solving. In practice, determining this cost is of course not trivial since we don't solve on isolated cells, but on the entire mesh. In such cases, one could, for example, choose the weight equal to the number of unknowns per cell (in the context of hp finite element methods), or using a heuristic that estimates the cost on each cell depending on whether, for example, one has to run some expensive algorithm on some cells but not others (such as forming boundary integrals during the assembly only on cells that are actually at the boundary, or computing expensive nonlinear terms only on some cells but not others, e.g., in the elasto-plastic problem in step-42).

Definition at line 4073 of file tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::communicate_locally_moved_vertices ( const std::vector< bool > &  vertex_locally_moved)

When vertices have been moved locally, for example using code like

cell->vertex(0) = new_location;

then this function can be used to update the location of vertices between MPI processes.

All the vertices that have been moved and might be in the ghost layer of a process have to be reported in the vertex_locally_moved argument. This ensures that that part of the information that has to be send between processes is actually sent. Additionally, it is quite important that vertices on the boundary between processes are reported on exactly one process (e.g. the one with the highest id). Otherwise we could expect undesirable results if multiple processes move a vertex differently. A typical strategy is to let processor \(i\) move those vertices that are adjacent to cells whose owners include processor \(i\) but no other processor \(j\) with \(j<i\); in other words, for vertices at the boundary of a subdomain, the processor with the lowest subdomain id "owns" a vertex.

Note
It only makes sense to move vertices that are either located on locally owned cells or on cells in the ghost layer. This is because you can be sure that these vertices indeed exist on the finest mesh aggregated over all processors, whereas vertices on artificial cells but not at least in the ghost layer may or may not exist on the globally finest mesh. Consequently, the vertex_locally_moved argument may not contain vertices that aren't at least on ghost cells.
This function moves vertices in such a way that on every processor, the vertices of every locally owned and ghost cell is consistent with the corresponding location of these cells on other processors. On the other hand, the locations of artificial cells will in general be wrong since artificial cells may or may not exist on other processors and consequently it is not possible to determine their location in any way. This is not usually a problem since one never does anything on artificial cells. However, it may lead to problems if the mesh with moved vertices is refined in a later step. If that's what you want to do, the right way to do it is to save the offset applied to every vertex, call this function, and before refining or coarsening the mesh apply the opposite offset and call this function again.
Parameters
vertex_locally_movedA bitmap indicating which vertices have been moved. The size of this array must be equal to Triangulation::n_vertices() and must be a subset of those vertices flagged by GridTools::get_locally_owned_vertices().
See also
This function is used, for example, in GridTools::distort_random().

Definition at line 4169 of file tria.cc.

template<int dim, int spacedim>
bool Triangulation< dim, spacedim >::has_hanging_nodes ( ) const
overridevirtual

Return true if the triangulation has hanging nodes.

In the context of parallel distributed triangulations, every processor stores only that part of the triangulation it locally owns. However, it also stores the entire coarse mesh, and to guarantee the 2:1 relationship between cells, this may mean that there are hanging nodes between cells that are not locally owned or ghost cells (i.e., between ghost cells and artificial cells, or between artificial and artificial cells; see the glossary). One is not typically interested in this case, so the function returns whether there are hanging nodes between any two cells of the "global" mesh, i.e., the union of locally owned cells on all processors.

Reimplemented from Triangulation< dim, spacedim >.

Definition at line 2627 of file tria.cc.

template<int dim, int spacedim>
std::size_t Triangulation< dim, spacedim >::memory_consumption ( ) const
overridevirtual

Return the local memory consumption in bytes.

Reimplemented from parallel::Triangulation< dim, spacedim >.

Definition at line 4730 of file tria.cc.

template<int dim, int spacedim>
std::size_t Triangulation< dim, spacedim >::memory_consumption_p4est ( ) const
virtual

Return the local memory consumption contained in the p4est data structures alone. This is already contained in memory_consumption() but made available separately for debugging purposes.

Definition at line 4758 of file tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::write_mesh_vtk ( const char *  file_basename) const

A collective operation that produces a sequence of output files with the given file base name that contain the mesh in VTK format.

More than anything else, this function is useful for debugging the interface between deal.II and p4est.

Definition at line 2675 of file tria.cc.

template<int dim, int spacedim>
unsigned int Triangulation< dim, spacedim >::get_checksum ( ) const

Produce a check sum of the triangulation. This is a collective operation and is mostly useful for debugging purposes.

Definition at line 2878 of file tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::save ( const char *  filename) const

Save the refinement information from the coarse mesh into the given file. This file needs to be reachable from all nodes in the computation on a shared network file system. See the SolutionTransfer class on how to store solution vectors into this file. Additional cell-based data can be saved using register_data_attach().

Definition at line 2689 of file tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::load ( const char *  filename,
const bool  autopartition = true 
)

Load the refinement information saved with save() back in. The mesh must contain the same coarse mesh that was used in save() before calling this function.

You do not need to load with the same number of MPI processes that you saved with. Rather, if a mesh is loaded with a different number of MPI processes than used at the time of saving, the mesh is repartitioned appropriately. Cell-based data that was saved with register_data_attach() can be read in with notify_ready_to_unpack() after calling load().

If you use p4est version > 0.3.4.2 the autopartition flag tells p4est to ignore the partitioning that the triangulation had when it was saved and make it uniform upon loading. If autopartition is set to false, the triangulation is only repartitioned if needed (i.e. if a different number of MPI processes is encountered).

Definition at line 2765 of file tria.cc.

template<int dim, int spacedim>
unsigned int Triangulation< dim, spacedim >::register_data_attach ( const std::function< std::vector< char >(const cell_iterator &, const CellStatus)> &  pack_callback,
const bool  returns_variable_size_data 
)

Register a function that can be used to attach data of fixed size to cells. This is useful for two purposes: (i) Upon refinement and coarsening of a triangulation (in parallel::distributed::Triangulation::execute_coarsening_and_refinement()), one needs to be able to store one or more data vectors per cell that characterizes the solution values on the cell so that this data can then be transferred to the new owning processor of the cell (or its parent/children) when the mesh is re-partitioned; (ii) when serializing a computation to a file, it is necessary to attach data to cells so that it can be saved (in parallel::distributed::Triangulation::save()) along with the cell's other information and, if necessary, later be reloaded from disk with a different subdivision of cells among the processors.

The way this function works is that it allows any number of interest parties to register their intent to attach data to cells. One example of classes that do this is parallel::distributed::SolutionTransfer where each parallel::distributed::SolutionTransfer object that works on the current Triangulation object then needs to register its intent. Each of these parties registers a callback function (the second argument here, pack_callback) that will be called whenever the triangulation's execute_coarsening_and_refinement() or save() functions are called.

The current function then returns an integer handle that corresponds to the number of data set that the callback provided here will attach. While this number could be given a precise meaning, this is not important: You will never actually have to do anything with this number except return it to the notify_ready_to_unpack() function. In other words, each interested party (i.e., the caller of the current function) needs to store their respective returned handle for later use when unpacking data in the callback provided to notify_ready_to_unpack().

Whenever pack_callback is then called by execute_coarsening_and_refinement() or load() on a given cell, it receives a number of arguments. In particular, the first argument passed to the callback indicates the cell for which it is supposed to attach data. This is always an active cell.

The second, CellStatus, argument provided to the callback function will tell you if the given cell will be coarsened, refined, or will persist as is. (This status may be different than the refinement or coarsening flags set on that cell, to accommodate things such as the "one hanging node per edge" rule.). These flags need to be read in context with the p4est quadrant they belong to, as their relations are gathered in local_quadrant_cell_relations.

Specifically, the values for this argument mean the following:

  • CELL_PERSIST: The cell won't be refined/coarsened, but might be moved to a different processor. If this is the case, the callback will want to pack up the data on this cell into an array and store it at the provided address for later unpacking wherever this cell may land.
  • CELL_REFINE: This cell will be refined into 4 or 8 cells (in 2d and 3d, respectively). However, because these children don't exist yet, you cannot access them at the time when the callback is called. Thus, in local_quadrant_cell_relations, the corresponding p4est quadrants of the children cells are linked to the deal.II cell which is going to be refined. To be specific, only the very first child is marked with CELL_REFINE, whereas the others will be marked with CELL_INVALID, which indicates that these cells will be ignored by default during the packing or unpacking process. This ensures that data is only transfered once onto or from the parent cell. If the callback is called with CELL_REFINE, the callback will want to pack up the data on this cell into an array and store it at the provided address for later unpacking in a way so that it can then be transferred to the children of the cell that will then be available. In other words, if the data the callback will want to pack up corresponds to a finite element field, then the prolongation from parent to (new) children will have to happen during unpacking.
  • CELL_COARSEN: The children of this cell will be coarsened into the given cell. These children still exist, so if this is the value given to the callback as second argument, the callback will want to transfer data from the children to the current parent cell and pack it up so that it can later be unpacked again on a cell that then no longer has any children (and may also be located on a different processor). In other words, if the data the callback will want to pack up corresponds to a finite element field, then it will need to do the restriction from children to parent at this point.
  • CELL_INVALID: See CELL_REFINE.
Note
If this function is used for serialization of data using save() and load(), then the cell status argument with which the callback is called will always be CELL_PERSIST.

The callback function is expected to return a memory chunk of the format std::vector<char>, representing the packed data on a certain cell.

The second parameter returns_variable_size_data indicates whether the returned size of the memory region from the callback function varies by cell (=true) or stays constant on each one throughout the whole domain (=false).

Note
The purpose of this function is to register intent to attach data for a single, subsequent call to execute_coarsening_and_refinement() and notify_ready_to_unpack(), save(), load(). Consequently, notify_ready_to_unpack(), save(), and load() all forget the registered callbacks once these callbacks have been called, and you will have to re-register them with a triangulation if you want them to be active for another call to these functions.

Definition at line 4340 of file tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::notify_ready_to_unpack ( const unsigned int  handle,
const std::function< void(const cell_iterator &, const CellStatus, const boost::iterator_range< std::vector< char >::const_iterator > &)> &  unpack_callback 
)

This function is the opposite of register_data_attach(). It is called after the execute_coarsening_and_refinement() or save()/load() functions are done when classes and functions that have previously attached data to a triangulation for either transfer to other processors, across mesh refinement, or serialization of data to a file are ready to receive that data back. The important part about this process is that the triangulation cannot do this right away from the end of execute_coarsening_and_refinement() or load() via a previously attached callback function (as the register_data_attach() function does) because the classes that eventually want the data back may need to do some setup between the point in time where the mesh has been recreated and when the data can actually be received. An example is the parallel::distributed::SolutionTransfer class that can really only receive the data once not only the mesh is completely available again on the current processor, but only after a DoFHandler has been reinitialized and distributed degrees of freedom. In other words, there is typically a significant amount of set up that needs to happen in user space before the classes that can receive data attached to cell are ready to actually do so. When they are, they use the current function to tell the triangulation object that now is the time when they are ready by calling the current function.

The supplied callback function is then called for each newly locally owned cell. The first argument to the callback is an iterator that designates the cell; the second argument indicates the status of the cell in question; and the third argument localizes a memory area by two iterators that contains the data that was previously saved from the callback provided to register_data_attach().

The CellStatus will indicate if the cell was refined, coarsened, or persisted unchanged. The cell_iterator argument to the callback will then either be an active, locally owned cell (if the cell was not refined), or the immediate parent if it was refined during execute_coarsening_and_refinement(). Therefore, contrary to during register_data_attach(), you can now access the children if the status is CELL_REFINE but no longer for callbacks with status CELL_COARSEN.

The first argument to this function, handle, corresponds to the return value of register_data_attach(). (The precise meaning of what the numeric value of this handle is supposed to represent is neither important, nor should you try to use it for anything other than transmit information between a call to register_data_attach() to the corresponding call to notify_ready_to_unpack().)

Definition at line 4370 of file tria.cc.

template<int dim, int spacedim>
const std::vector< types::global_dof_index > & Triangulation< dim, spacedim >::get_p4est_tree_to_coarse_cell_permutation ( ) const

Return a permutation vector for the order the coarse cells are handed off to p4est. For example the value of the \(i\)th element in this vector is the index of the deal.II coarse cell (counting from begin(0)) that corresponds to the \(i\)th tree managed by p4est.

Definition at line 4452 of file tria.cc.

template<int dim, int spacedim>
const std::vector< types::global_dof_index > & Triangulation< dim, spacedim >::get_coarse_cell_to_p4est_tree_permutation ( ) const

Return a permutation vector for the mapping from the coarse deal cells to the p4est trees. This is the inverse of get_p4est_tree_to_coarse_cell_permutation.

Definition at line 4462 of file tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::add_periodicity ( const std::vector<::GridTools::PeriodicFacePair< cell_iterator >> &  periodicity_vector)
overridevirtual

In addition to the action in the base class Triangulation, this function joins faces in the p4est forest for periodic boundary conditions. As a result, each pair of faces will differ by at most one refinement level and ghost neighbors will be available across these faces.

The vector can be filled by the function GridTools::collect_periodic_faces.

For more information on periodic boundary conditions see GridTools::collect_periodic_faces, DoFTools::make_periodicity_constraints and step-45.

Note
Before this function can be used the Triangulation has to be initialized and must not be refined. Calling this function more than once is possible, but not recommended: The function destroys and rebuilds the p4est forest each time it is called.

Definition at line 4561 of file tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::update_number_cache ( )
overrideprivatevirtual

Override the function to update the number cache so we can fill data like level_ghost_owners.

Reimplemented from parallel::Triangulation< dim, spacedim >.

Definition at line 2890 of file tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::update_quadrant_cell_relations ( )
private

Go through all p4est trees and store the relations between locally owned quadrants and cells in the private member local_quadrant_cell_relations.

The stored vector will be ordered by the occurrence of quadrants in the corresponding local sc_array of the parallel_forest. p4est requires this specific ordering for its transfer functions.

Definition at line 4837 of file tria.cc.

template<int dim, int spacedim>
typename::internal::p4est::types< dim >::tree * Triangulation< dim, spacedim >::init_tree ( const int  dealii_coarse_cell_index) const
private

Return a pointer to the p4est tree that belongs to the given dealii_coarse_cell_index()

Definition at line 2902 of file tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::setup_coarse_cell_to_p4est_tree_permutation ( )
private

The function that computes the permutation between the two data storage schemes.

Definition at line 2658 of file tria.cc.

template<int dim, int spacedim = dim>
void parallel::distributed::Triangulation< dim, spacedim >::copy_new_triangulation_to_p4est ( std::integral_constant< int, 2 >  )
private

Take the contents of a newly created triangulation we are attached to and copy it to p4est data structures.

This function exists in 2d and 3d variants.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::copy_local_forest_to_triangulation ( )
private

Copy the local part of the refined forest from p4est into the attached triangulation.

Definition at line 3448 of file tria.cc.

template<int dim, int spacedim>
std::vector< unsigned int > Triangulation< dim, spacedim >::get_cell_weights ( ) const
private

Internal function notifying all registered slots to provide their weights before repartitioning occurs. Called from execute_coarsening_and_refinement() and repartition().

Returns
A vector of unsigned integers representing the weight or computational load of every cell after the refinement/coarsening/ repartition cycle. Note that the number of entries does not need to be equal to either n_active_cells or n_locally_owned_active_cells, because the triangulation is not updated yet. The weights are sorted in the order that p4est will encounter them while iterating over them.

Definition at line 4874 of file tria.cc.

template<int dim, int spacedim>
std::map< unsigned int, std::set<::types::subdomain_id > > Triangulation< dim, spacedim >::compute_vertices_with_ghost_neighbors ( ) const
overrideprivatevirtual

Override the implementation in parallel::Triangulation because we can ask p4est about ghost neighbors across periodic boundaries.

Specifically, this function determines the neighboring subdomains that are adjacent to each vertex.

Reimplemented from parallel::Triangulation< dim, spacedim >.

Definition at line 4472 of file tria.cc.

template<int dim, int spacedim>
std::vector< bool > Triangulation< dim, spacedim >::mark_locally_active_vertices_on_level ( const int  level) const
private

This method returns a bit vector of length tria.n_vertices() indicating the locally active vertices on a level, i.e., the vertices touched by the locally owned level cells for use in geometric multigrid (possibly including the vertices due to periodic boundary conditions) are marked by true.

Used by DoFHandler::Policy::ParallelDistributed.

ensure that if one of the two vertices on a periodic face is marked as active (i.e., belonging to an owned level cell), also the other one is active

Definition at line 4485 of file tria.cc.

Member Data Documentation

template<int dim, int spacedim = dim>
Settings parallel::distributed::Triangulation< dim, spacedim >::settings
private

store the Settings.

Definition at line 854 of file tria.h.

template<int dim, int spacedim = dim>
bool parallel::distributed::Triangulation< dim, spacedim >::triangulation_has_content
private

A flag that indicates whether the triangulation has actual content.

Definition at line 859 of file tria.h.

template<int dim, int spacedim = dim>
typename ::internal::p4est::types<dim>::connectivity* parallel::distributed::Triangulation< dim, spacedim >::connectivity
private

A data structure that holds the connectivity between trees. Since each tree is rooted in a coarse grid cell, this data structure holds the connectivity between the cells of the coarse grid.

Definition at line 866 of file tria.h.

template<int dim, int spacedim = dim>
typename ::internal::p4est::types<dim>::forest* parallel::distributed::Triangulation< dim, spacedim >::parallel_forest
private

A data structure that holds the local part of the global triangulation.

Definition at line 872 of file tria.h.

template<int dim, int spacedim = dim>
typename ::internal::p4est::types<dim>::ghost* parallel::distributed::Triangulation< dim, spacedim >::parallel_ghost
private

A data structure that holds some information about the ghost cells of the triangulation.

Definition at line 878 of file tria.h.

template<int dim, int spacedim = dim>
std::vector<quadrant_cell_relation_t> parallel::distributed::Triangulation< dim, spacedim >::local_quadrant_cell_relations
private

Vector of tuples, which each contain a p4est quadrant, a deal.II cell and their relation after refinement. To update its contents, use the compute_quadrant_cell_relations member function.

The size of this vector is assumed to be equal to the number of locally owned quadrants in the parallel_forest object.

Definition at line 932 of file tria.h.

template<int dim, int spacedim = dim>
std::vector<types::global_dof_index> parallel::distributed::Triangulation< dim, spacedim >::coarse_cell_to_p4est_tree_permutation
private

Two arrays that store which p4est tree corresponds to which coarse grid cell and vice versa. We need these arrays because p4est goes with the original order of coarse cells when it sets up its forest, and then applies the Morton ordering within each tree. But if coarse grid cells are badly ordered this may mean that individual parts of the forest stored on a local machine may be split across coarse grid cells that are not geometrically close. Consequently, we apply a hierarchical preordering according to SparsityTools::reorder_hierarchical() to ensure that the part of the forest stored by p4est is located on geometrically close coarse grid cells.

Definition at line 1136 of file tria.h.


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