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Reference documentation for deal.II version 9.1.1
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#include <deal.II/distributed/tria.h>
Classes | |
struct | CellAttachedData |
class | DataTransfer |
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 std::string &file_basename) const |
unsigned int | get_checksum () const |
void | save (const std::string &filename) const |
void | load (const std::string &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 |
const ::internal::p4est::types< dim >::forest * | get_p4est () const |
virtual void | add_periodicity (const std::vector<::GridTools::PeriodicFacePair< cell_iterator >> &) override |
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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 |
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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 | |
Triangulation & | operator= (Triangulation< dim, spacedim > &&tria) noexcept |
virtual void | set_mesh_smoothing (const MeshSmoothing mesh_smoothing) |
virtual const MeshSmoothing & | get_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_id > | get_boundary_ids () const |
std::vector< types::manifold_id > | get_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_iterator > | cell_iterators () const |
IteratorRange< active_cell_iterator > | active_cell_iterators () const |
IteratorRange< cell_iterator > | cell_iterators_on_level (const unsigned int level) const |
IteratorRange< active_cell_iterator > | active_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_iterator > | active_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 |
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Subscriptor () | |
Subscriptor (const Subscriptor &) | |
Subscriptor (Subscriptor &&) noexcept | |
virtual | ~Subscriptor () |
Subscriptor & | operator= (const Subscriptor &) |
Subscriptor & | operator= (Subscriptor &&) noexcept |
void | subscribe (std::atomic< bool > *const validity, const std::string &identifier="") const |
void | unsubscribe (std::atomic< bool > *const validity, const std::string &identifier="") 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_t > | local_quadrant_cell_relations |
std::vector< types::global_dof_index > | coarse_cell_to_p4est_tree_permutation |
Additional Inherited Members | |
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static ::ExceptionBase & | ExcInvalidLevel (int arg1, int arg2) |
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) |
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static ::ExceptionBase & | ExcInUse (int arg1, std::string arg2, std::string arg3) |
static ::ExceptionBase & | ExcNoSubscriber (std::string arg1, std::string arg2) |
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Signals | signals |
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static const unsigned int | dimension = dim |
static const unsigned int | space_dimension = spacedim |
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void | fill_level_ghost_owners () |
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void | update_periodic_face_map () |
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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) |
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MPI_Comm | mpi_communicator |
types::subdomain_id | my_subdomain |
types::subdomain_id | n_subdomains |
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MeshSmoothing | smooth_grid |
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.
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:
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:
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.
Definition at line 46 of file p4est_wrappers.h.
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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().
enum parallel::distributed::Triangulation::Settings |
Configuration flags for distributed Triangulations to be set in the constructor. Settings can be combined using bitwise OR.
Enumerator | |
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default_setting | Default settings, other options are disabled. |
mesh_reconstruction_after_repartitioning | If set, the deal.II mesh will be reconstructed from the coarse mesh every time a repartitioning in p4est happens. This can be a bit more expensive, but guarantees the same memory layout and therefore cell ordering in the deal.II mesh. As assembly is done in the deal.II cell ordering, this flag is required to get reproducible behaviour after snapshot/resume. |
construct_multigrid_hierarchy | This flags needs to be set to use the geometric multigrid functionality. This option requires additional computation and communication. Note: geometric multigrid is still a work in progress. |
no_automatic_repartitioning | Setting this flag will disable automatic repartitioning of the cells after a refinement cycle. It can be executed manually by calling repartition(). |
Triangulation< dim, spacedim >::Triangulation | ( | MPI_Comm | mpi_communicator, |
const typename ::Triangulation< dim, spacedim >::MeshSmoothing | smooth_grid = (::Triangulation<dim, spacedim>::none) , |
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const Settings | settings = default_setting |
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) |
Constructor.
mpi_communicator | denotes the MPI communicator to be used for the triangulation. |
smooth_grid | Degree 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. |
settings | See the description of the Settings enumerator. Providing construct_multigrid_hierarchy enforces Triangulation::limit_level_difference_at_vertices for smooth_grid. |
check_for_distorted_cells
argument provided by the base class.
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overridevirtual |
Destructor.
Reimplemented from parallel::Triangulation< dim, spacedim >.
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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 >.
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overridevirtual |
Implementation of the same function as in the base class.
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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 >.
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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.
Reimplemented from Triangulation< dim, spacedim >.
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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 not be more than 2:1.
Reimplemented from Triangulation< dim, 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.).
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
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.
vertex_locally_moved
argument may not contain vertices that aren't at least on ghost cells.vertex_locally_moved | A 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(). |
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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 >.
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overridevirtual |
Return the local memory consumption in bytes.
Reimplemented from parallel::Triangulation< dim, spacedim >.
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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.
void Triangulation< dim, spacedim >::write_mesh_vtk | ( | const std::string & | file_basename | ) | const |
unsigned int Triangulation< dim, spacedim >::get_checksum | ( | ) | const |
void Triangulation< dim, spacedim >::save | ( | const std::string & | 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().
void Triangulation< dim, spacedim >::load | ( | const std::string & | filename, |
const bool | autopartition = true |
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) |
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).
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 transferred 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
.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
).
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().)
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.
const std::vector< types::global_dof_index > & Triangulation< dim, spacedim >::get_coarse_cell_to_p4est_tree_permutation | ( | ) | const |
const ::internal::p4est::types< dim >::forest * Triangulation< dim, spacedim >::get_p4est | ( | ) | const |
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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.
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Override the function to update the number cache so we can fill data like level_ghost_owners
.
Reimplemented from parallel::Triangulation< dim, spacedim >.
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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.
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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.
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Internal function notifying all registered slots to provide their weights before repartitioning occurs. Called from execute_coarsening_and_refinement() and repartition().
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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 >.
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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
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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.
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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.