libMesh
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This abstract base class defines the interface by which library code and user code can report associations between elements. More...
#include <ghosting_functor.h>
Public Types | |
typedef std::map< const Elem *, const CouplingMatrix *, CompareDofObjectsByPIDAndThenID > | map_type |
What elements do we care about and what variables do we care about on each element? More... | |
Public Member Functions | |
GhostingFunctor () | |
Constructor. More... | |
GhostingFunctor (const MeshBase &mesh) | |
Constructor using mesh. More... | |
GhostingFunctor (const GhostingFunctor &other) | |
Copy Constructor. More... | |
virtual | ~GhostingFunctor ()=default |
Virtual destructor; this is an abstract base class. More... | |
virtual std::unique_ptr< GhostingFunctor > | clone () const |
A clone() is needed because GhostingFunctor can not be shared between different meshes. More... | |
virtual void | set_mesh (const MeshBase *mesh) |
It should be called after cloning a ghosting functor. More... | |
virtual void | set_periodic_boundaries (const PeriodicBoundaries *) |
const MeshBase * | get_mesh () const |
Return the mesh associated with ghosting functor. More... | |
virtual void | operator() (const MeshBase::const_element_iterator &range_begin, const MeshBase::const_element_iterator &range_end, processor_id_type p, map_type &coupled_elements)=0 |
For the specified range of active elements, what other elements currently living (whether local or ghosted) on this processor need to be coupled/ghosted to accommodate them? Don't bother to return any results which already have processor_id p. More... | |
virtual void | mesh_reinit () |
GhostingFunctor subclasses which cache data will need to initialize that cache. More... | |
virtual void | dofmap_reinit () |
For algebraic ghosting or coupling functors we also call dofmap_reinit() later, after dofs have been distributed on the new mesh but before the functors have been queried for send_list or sparsity pattern calculations. More... | |
virtual void | redistribute () |
GhostingFunctor subclasses with relatively long-lasting caches may want to redistribute those caches whenever the relevant Mesh is redistributed; we will give them an opportunity when that happens. More... | |
virtual void | delete_remote_elements () |
GhostingFunctor subclasses with relatively long-lasting caches may want to delete the no-longer-relevant parts of those caches after a redistribution is complete. More... | |
Static Public Member Functions | |
static std::string | get_info () |
Gets a string containing the reference information. More... | |
static void | print_info (std::ostream &out_stream=libMesh::out) |
Prints the reference information, by default to libMesh::out . More... | |
static unsigned int | n_objects () |
Prints the number of outstanding (created, but not yet destroyed) objects. More... | |
static void | enable_print_counter_info () |
Methods to enable/disable the reference counter output from print_info() More... | |
static void | disable_print_counter_info () |
Protected Types | |
typedef std::map< std::string, std::pair< unsigned int, unsigned int > > | Counts |
Data structure to log the information. More... | |
Protected Member Functions | |
void | increment_constructor_count (const std::string &name) noexcept |
Increments the construction counter. More... | |
void | increment_destructor_count (const std::string &name) noexcept |
Increments the destruction counter. More... | |
Protected Attributes | |
const MeshBase * | _mesh |
Static Protected Attributes | |
static Counts | _counts |
Actually holds the data. More... | |
static Threads::atomic< unsigned int > | _n_objects |
The number of objects. More... | |
static Threads::spin_mutex | _mutex |
Mutual exclusion object to enable thread-safe reference counting. More... | |
static bool | _enable_print_counter = true |
Flag to control whether reference count information is printed when print_info is called. More... | |
This abstract base class defines the interface by which library code and user code can report associations between elements.
These associations between elements may be used to keep copies of non-local elements retained on a distributed mesh, may be used to keep element degrees of freedom properly communicated on a distributed vector, and/or may be used to insert coupling entries between elements' degrees of freedom to a sparsity matrix.
We can think of three levels of "element dependencies". An element K1 has a coupling dependency on K2 if the dofs on K1 might (modulo the coupling matrix) need sparsity pattern entries for dofs on K2. An element K1 has an algebraic dependency on K2 if a processor which owns K1 might need to examine the solution dof values on K2. An element K1 has a geometric dependency on K2 if a processor which owns K1 might need to examine the geometry of K2. For any element K, we could call the set of coupling-ghosted ("coupled") elements C(K), call the set of algebraic-ghosted ("evaluable") elements E(K), and call the set of geometry-ghosted ("ghosted") elements G(K).
It should be safe to assume that, for any element K, C(K) implies E(K) implies G(K). These will be one-way implications in some problems and equality relations in others.
We can think of these as operators on sets of elements in the obvious way, e.g.: G({K}) = {G(Ki) for all Ki in {K}}.
The user should omit from their implementations relations which we already have enough information to understand implicitly. For instance, K is obviously in C(K), so a GhostingFunctor should never bother telling us so. We pass a processor_id_type parameter to the GhostingFunctor::operator(), e.g. when determining what ghosted elements need to be sent to that processor while redistributing, and a GhostingFunctor should not return any elements which already have that processor_id. We determine what ancestor elements should be ghosted based on what active elements are being ghosted, and a GhostingFunctor should not return any elements which are not active.
We may have a PeriodicBoundary, a hanging node constraint equation, or a user-defined constraint equation which creates a dependency between two elements; if so then we don't need the user to also tell us about that relation. The DefaultCoupling functor will make both direct and periodic neighbor elements algebraically ghosted by default.
However, note that geometric ghosting information needs to all be inferrable (e.g. with PeriodicBoundary objects already all attached) before a mesh is prepared for use; otherwise ghost elements may be prematurely deleted and become unrecoverable.
For iterating over ghosted elements:
MeshBase::active_elements_begin() gives the first iterator to all geometrically ghosted elements. (this means all elements on any mesh which isn't distributed)
MeshBase::evaluable_elements_begin() gives the first iterator to all algebraically evaluable elements, which is a superset of all algebraically ghosted elements. (rarely a strict superset, but low order geometrically ghosted elements surrounded by enough algebraically ghosted elements may become evaluable "by accident")
Users may only care about a subset of variables in distant evaluable elements, so we could imagine defining E_v(K) for each variable number v, in which case E(K) under our previous definition is the union of E_v(K) forall v, and this is what would be included in G(K) when deciding what to ghost, but our send_list would only include the subset of variables we need, so communication and memory use would be much reduced. However, for efficiency and API simplicity, we instead define the isomorphic operator E'(K) which gives a set of ordered pairs of elements and variable-number-sets, from which a consistent E(K) would be derived by ignoring the variable-number-sets.
For C(K), there are similar issues: e.g. we may want some discontinuous variables to couple only within their own element but other discontinuous variables to couple in a DG/FVM way. This could extend to more than one variable index: i.e. a dof for variable v1 in element K1 would depend on a dof for variable v2 in element K2 iff K2 is in C_v1_v2(K1). This would induce a consistent E_v(K) = union of C_w_v(K) forall variable indices w. Again, the equivalent API alternative we use here is for C'(K) to return a set of ordered pairs of elements and variable-number-pair-sets.
We return variable-stuff-sets as pointers to CouplingMatrix. That way, in the common case where the user cares about all variables and couple to all variables, all the functor needs to return for variable-number-sets and variable-number-pair-sets is nullptr (which as in other libMesh APIs will be interpreted and documented to mean the full set). In the common case where the user wants coupling between elements to match coupling within elements, the functor can return the same pointer as DofMap::_coupling_matrix. Even in the less common cases, the user can store common variable-number-sets and variable-number-pair sets as CouplingMatrix members of a functor object of their subclass, and setting up a few of those matrices then setting lots of those pointers is cheap.
The definition of the CouplingMatrix for a variable-dependent E' should be consistent with the requirements that would have been imposed had that matrix been used for a C'. In other words, if the returned CouplingMatrix CM has CM(i,j)==true for any i, then variable j will be evaluable on the algebraically ghosted element.
After a GhostingFunctor has been created, a reference to it can be passed to MeshBase::add_ghosting_functor to expand geometric ghosting, or to DofMap::add_algebraic_ghosting_functor to expand both algebraic and geometric ghosting, or to DofMap::add_coupling_functor to expand coupling along with both types of ghosting.
Note that when an element is specified in algebraic ghosting or coupling queries, only degrees of freedom for the variables supported on that element are thereby ghosted and/or coupled. Any unsupported variable dofs associated with the element's nodes (e.g. subdomain-restricted variables on a neighboring subdomain) will be unaffected.
Typical usage of the GhostingFunctor would be to add a geometric ghosting functor before the mesh preparation is completed; progmatically, this would be before MeshBase::prepare_for_use() is called, but many different libMesh idioms internally call this function. The algebraic and coupling ghosting functors normally are added before EquationSystems::init() is called. However, in some circumstances, solution evaluation may be needed within the GhostingFunctor in order to determine the ghosting, in which case the appropriate functor would need to be added after EquationSystems::init(). In this case, the user will need to reinitialize certain parts of the DofMap for algebraic and coupling functors. For algebraic ghosting functors, the user will need to call DofMap::reinit_send_list() and then reinitialize any NumericVectors that are GHOSTED, e.g. the System::current_local_solution. For coupling ghosting, the user will also need to recompute the sparsity pattern via DofMap::clear_sparsity() and then DofMap::compute_sparsity() and then reinitialize any SparseMatrix objects attached to the System, e.g. the system.get_system_matrix().
Definition at line 184 of file ghosting_functor.h.
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protectedinherited |
Data structure to log the information.
The log is identified by the class name.
Definition at line 119 of file reference_counter.h.
typedef std::map<const Elem*, const CouplingMatrix*, CompareDofObjectsByPIDAndThenID> libMesh::GhostingFunctor::map_type |
What elements do we care about and what variables do we care about on each element?
Definition at line 241 of file ghosting_functor.h.
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inline |
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inline |
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inline |
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virtualdefault |
Virtual destructor; this is an abstract base class.
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inlinevirtual |
A clone() is needed because GhostingFunctor can not be shared between different meshes.
The operations in GhostingFunctor are mesh dependent.
Reimplemented in libMesh::DefaultCoupling, libMesh::PointNeighborCoupling, and libMesh::SiblingCoupling.
Definition at line 215 of file ghosting_functor.h.
Referenced by libMesh::MeshBase::MeshBase().
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inlinevirtual |
GhostingFunctor subclasses with relatively long-lasting caches may want to delete the no-longer-relevant parts of those caches after a redistribution is complete.
Reimplemented in libMesh::PointNeighborCoupling, libMesh::DefaultCoupling, and libMesh::GhostPointNeighbors.
Definition at line 291 of file ghosting_functor.h.
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staticinherited |
Definition at line 100 of file reference_counter.C.
References libMesh::ReferenceCounter::_enable_print_counter.
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inlinevirtual |
For algebraic ghosting or coupling functors we also call dofmap_reinit() later, after dofs have been distributed on the new mesh but before the functors have been queried for send_list or sparsity pattern calculations.
Definition at line 272 of file ghosting_functor.h.
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staticinherited |
Methods to enable/disable the reference counter output from print_info()
Definition at line 94 of file reference_counter.C.
References libMesh::ReferenceCounter::_enable_print_counter.
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staticinherited |
Gets a string containing the reference information.
Definition at line 47 of file reference_counter.C.
References libMesh::ReferenceCounter::_counts, and libMesh::Quality::name().
Referenced by libMesh::ReferenceCounter::print_info().
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inline |
Return the mesh associated with ghosting functor.
Definition at line 235 of file ghosting_functor.h.
References _mesh, and libMesh::libmesh_assert().
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inlineprotectednoexceptinherited |
Increments the construction counter.
Should be called in the constructor of any derived class that will be reference counted.
Definition at line 183 of file reference_counter.h.
References libMesh::err, libMesh::BasicOStreamProxy< charT, traits >::get(), libMesh::Quality::name(), and libMesh::Threads::spin_mtx.
Referenced by libMesh::ReferenceCountedObject< RBParametrized >::ReferenceCountedObject().
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inlineprotectednoexceptinherited |
Increments the destruction counter.
Should be called in the destructor of any derived class that will be reference counted.
Definition at line 207 of file reference_counter.h.
References libMesh::err, libMesh::BasicOStreamProxy< charT, traits >::get(), libMesh::Quality::name(), and libMesh::Threads::spin_mtx.
Referenced by libMesh::ReferenceCountedObject< RBParametrized >::~ReferenceCountedObject().
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inlinevirtual |
GhostingFunctor subclasses which cache data will need to initialize that cache.
We call mesh_reinit() whenever the relevant Mesh has changed, but before remote elements on a distributed mesh are deleted.
Reimplemented in AugmentSparsityOnNodes, libMesh::PointNeighborCoupling, libMesh::DefaultCoupling, and AugmentSparsityOnInterface.
Definition at line 264 of file ghosting_functor.h.
Referenced by libMesh::GhostPointNeighbors::delete_remote_elements().
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inlinestaticinherited |
Prints the number of outstanding (created, but not yet destroyed) objects.
Definition at line 85 of file reference_counter.h.
References libMesh::ReferenceCounter::_n_objects.
Referenced by libMesh::LibMeshInit::~LibMeshInit().
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pure virtual |
For the specified range of active elements, what other elements currently living (whether local or ghosted) on this processor need to be coupled/ghosted to accommodate them? Don't bother to return any results which already have processor_id p.
This API is new, and we should replace "ignoring those on processor p" with "ignoring those which match a predicate functor" eventually.
Implemented in libMesh::DefaultCoupling, libMesh::PointNeighborCoupling, libMesh::GhostPointNeighbors, AugmentSparsityOnNodes, libMesh::SiblingCoupling, and OverlappingCouplingFunctor.
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staticinherited |
Prints the reference information, by default to libMesh::out
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Definition at line 81 of file reference_counter.C.
References libMesh::ReferenceCounter::_enable_print_counter, and libMesh::ReferenceCounter::get_info().
Referenced by libMesh::LibMeshInit::~LibMeshInit().
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inlinevirtual |
GhostingFunctor subclasses with relatively long-lasting caches may want to redistribute those caches whenever the relevant Mesh is redistributed; we will give them an opportunity when that happens.
At the point in the code where this is called, element processor ids have been set to their new destinations, and those elements have been copied to their new destinations, but the elements have not yet been deleted by the processors which previously held them..
Reimplemented in AugmentSparsityOnNodes, libMesh::PointNeighborCoupling, libMesh::DefaultCoupling, and AugmentSparsityOnInterface.
Definition at line 284 of file ghosting_functor.h.
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inlinevirtual |
It should be called after cloning a ghosting functor.
Ghosting functor is mesh dependent
Definition at line 225 of file ghosting_functor.h.
Referenced by libMesh::DofMap::add_algebraic_ghosting_functor(), and libMesh::DofMap::add_coupling_functor().
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inlinevirtual |
Reimplemented in libMesh::PointNeighborCoupling, and libMesh::DefaultCoupling.
Definition at line 229 of file ghosting_functor.h.
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staticprotectedinherited |
Actually holds the data.
Definition at line 124 of file reference_counter.h.
Referenced by libMesh::ReferenceCounter::get_info().
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staticprotectedinherited |
Flag to control whether reference count information is printed when print_info is called.
Definition at line 143 of file reference_counter.h.
Referenced by libMesh::ReferenceCounter::disable_print_counter_info(), libMesh::ReferenceCounter::enable_print_counter_info(), and libMesh::ReferenceCounter::print_info().
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protected |
Definition at line 291 of file ghosting_functor.h.
Referenced by get_mesh(), libMesh::DefaultCoupling::mesh_reinit(), libMesh::PointNeighborCoupling::mesh_reinit(), and set_mesh().
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staticprotectedinherited |
Mutual exclusion object to enable thread-safe reference counting.
Definition at line 137 of file reference_counter.h.
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staticprotectedinherited |
The number of objects.
Print the reference count information when the number returns to 0.
Definition at line 132 of file reference_counter.h.
Referenced by libMesh::ReferenceCounter::n_objects(), libMesh::ReferenceCounter::ReferenceCounter(), and libMesh::ReferenceCounter::~ReferenceCounter().