libMesh::GhostPointNeighbors Class Reference

This class implements the original default geometry ghosting requirements in libMesh: point neighbors on the same manifold, including across periodic boundaries, and interior_parent elements. More...

#include <ghost_point_neighbors.h>

Inheritance diagram for libMesh::GhostPointNeighbors:

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
virtual void	delete_remote_elements () override
	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...
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) override
	For the specified range of active elements, find their point neighbors and interior_parent elements, ignoring those on processor p. More...
virtual std::unique_ptr< GhostingFunctor >	clone () const =0
	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	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...

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 ()

Public Attributes
virtual GhostPointNeighbors(const MeshBase &mesh) void	redistribute () override
	Constructor. More...
return	nullptr { libmesh_deprecated()

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...

Private Attributes
const PeriodicBoundaries *	_periodic_bcs

Detailed Description

This class implements the original default geometry ghosting requirements in libMesh: point neighbors on the same manifold, including across periodic boundaries, and interior_parent elements.

Author

Roy H. Stogner

Date

2016

Definition at line 43 of file ghost_point_neighbors.h.

Member Typedef Documentation

Counts

typedef std::map<std::string, std::pair<unsigned int, unsigned int> > libMesh::ReferenceCounter::Counts

protectedinherited

Data structure to log the information.

The log is identified by the class name.

Definition at line 119 of file reference_counter.h.

map_type

typedef std::map<const Elem*, const CouplingMatrix*, CompareDofObjectsByPIDAndThenID> libMesh::GhostingFunctor::map_type

inherited

What elements do we care about and what variables do we care about on each element?

Definition at line 243 of file ghosting_functor.h.

Member Function Documentation

clone()

virtual std::unique_ptr<GhostingFunctor> libMesh::GhostingFunctor::clone ( ) const

pure virtualinherited

A clone() is needed because GhostingFunctor can not be shared between different meshes.

The operations in GhostingFunctor are mesh dependent.

Implemented in libMesh::NonManifoldGhostingFunctor, libMesh::DefaultCoupling, libMesh::PointNeighborCoupling, libMesh::SiblingCoupling, libMesh::OverlapCoupling, AugmentSparsityOnNodes, OverlappingCouplingFunctor, and AugmentSparsityOnInterface.

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

delete_remote_elements()

virtual void libMesh::GhostPointNeighbors::delete_remote_elements ( )

inlineoverridevirtual

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 from libMesh::GhostingFunctor.

Definition at line 94 of file ghost_point_neighbors.h.

References libMesh::GhostingFunctor::mesh_reinit().

  { this->mesh_reinit(); }

disable_print_counter_info()

void libMesh::ReferenceCounter::disable_print_counter_info ( )

staticinherited

Definition at line 100 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

{
  _enable_print_counter = false;
  return;
}

dofmap_reinit()

virtual void libMesh::GhostingFunctor::dofmap_reinit ( )

inlinevirtualinherited

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 274 of file ghosting_functor.h.

{};

enable_print_counter_info()

void libMesh::ReferenceCounter::enable_print_counter_info ( )

staticinherited

Methods to enable/disable the reference counter output from print_info().

Enabled by default.

Definition at line 94 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

Referenced by libMesh::LibMeshInit::~LibMeshInit().

{
  _enable_print_counter = true;
  return;
}

get_info()

std::string libMesh::ReferenceCounter::get_info ( )

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().

{
#if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)

  std::ostringstream oss;

  oss << '\n'
      << " ---------------------------------------------------------------------------- \n"
      << "| Reference count information                                                |\n"
      << " ---------------------------------------------------------------------------- \n";

  for (const auto & [name, cd] : _counts)
    oss << "| " << name << " reference count information:\n"
        << "|  Creations:    " << cd.first    << '\n'
        << "|  Destructions: " << cd.second << '\n';

  oss << " ---------------------------------------------------------------------------- \n";

  return oss.str();

#else

  return "";

#endif
}

get_mesh()

const MeshBase* libMesh::GhostingFunctor::get_mesh ( ) const

inlineinherited

Return the mesh associated with ghosting functor.

Definition at line 237 of file ghosting_functor.h.

References libMesh::GhostingFunctor::_mesh, and libMesh::libmesh_assert().

{ libmesh_assert(_mesh); return _mesh; }

increment_constructor_count()

void libMesh::ReferenceCounter::increment_constructor_count ( const std::string &  name )

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().

{
  libmesh_try
  {
    Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
    std::pair<unsigned int, unsigned int> & p = _counts[name];
    p.first++;
  }
  libmesh_catch (...)
  {
    auto stream = libMesh::err.get();
    stream->exceptions(stream->goodbit); // stream must not throw
    libMesh::err << "Encountered unrecoverable error while calling "
                 << "ReferenceCounter::increment_constructor_count() "
                 << "for a(n) " << name << " object." << std::endl;
    std::terminate();
  }
}

increment_destructor_count()

void libMesh::ReferenceCounter::increment_destructor_count ( const std::string &  name )

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().

{
  libmesh_try
  {
    Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
    std::pair<unsigned int, unsigned int> & p = _counts[name];
    p.second++;
  }
  libmesh_catch (...)
  {
    auto stream = libMesh::err.get();
    stream->exceptions(stream->goodbit); // stream must not throw
    libMesh::err << "Encountered unrecoverable error while calling "
                 << "ReferenceCounter::increment_destructor_count() "
                 << "for a(n) " << name << " object." << std::endl;
    std::terminate();
  }
}

mesh_reinit()

virtual void libMesh::GhostingFunctor::mesh_reinit ( )

inlinevirtualinherited

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, libMesh::NonManifoldGhostingFunctor, libMesh::OverlapCoupling, and AugmentSparsityOnInterface.

Definition at line 266 of file ghosting_functor.h.

Referenced by delete_remote_elements().

{};

n_objects()

static unsigned int libMesh::ReferenceCounter::n_objects ( )

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().

  { return _n_objects; }

operator()()

void libMesh::GhostPointNeighbors::operator() ( const MeshBase::const_element_iterator &  range_begin, const MeshBase::const_element_iterator &  range_end, processor_id_type  p, GhostPointNeighbors::map_type &  coupled_elements  )

overridevirtual

For the specified range of active elements, find their point neighbors and interior_parent elements, ignoring those on processor p.

Implements libMesh::GhostingFunctor.

Definition at line 38 of file ghost_point_neighbors.C.

References libMesh::Elem::active_family_tree_by_topological_neighbor(), libMesh::as_range(), libMesh::BoundaryInfo::boundary_ids(), libMesh::Elem::find_point_neighbors(), libMesh::DofObject::id(), libMesh::Elem::interior_parent(), libMesh::invalid_uint, libMesh::libmesh_assert(), libMesh::DofObject::processor_id(), libMesh::remote_elem, and libMesh::Elem::topological_neighbor().

{
  libmesh_assert(_mesh);

#ifdef LIBMESH_ENABLE_PERIODIC
  const bool check_periodic_bcs =
    (_periodic_bcs && !_periodic_bcs->empty());

  auto * db = _mesh->get_disjoint_neighbor_boundary_pairs();
  const bool check_disjoint_bcs = (db && !db->empty());

  std::unique_ptr<PointLocatorBase> point_locator;
  if (check_periodic_bcs || check_disjoint_bcs)
      point_locator = _mesh->sub_point_locator();

  std::set<const Elem *> periodic_elems_examined;
  const BoundaryInfo & binfo = _mesh->get_boundary_info();
  std::vector<boundary_id_type> appn_bcids;
  std::vector<const Elem *> active_periodic_neighbors;
#endif

  // Using a connected_nodes set rather than point_neighbors() would
  // give us correct results even in corner cases, such as where two
  // elements meet only at a corner.  ;-)
  //
  // std::unordered_set<const Node *> connected_nodes;
  //
  // Unfortunately, it's not a *fast* enough test to use on a
  // ReplicatedMesh (where it's O(Nprocs) times slower), or as a
  // coupling functor (where it's O(Nelem/Nprocs) times slower), or as
  // a coupling functor on a ReplicatedMesh (where you might as well
  // just give up now)

  // Links between boundary and interior elements on mixed
  // dimensional meshes also give us correct ghosting in this way.
  std::unordered_set<const Elem *> interior_parents;

  // We also preserve neighbors and their neighboring children for
  // active local elements - in most cases this is redundant with the
  // node check, but for non-conforming Tet4 meshes and
  // non-level-one-conforming 2D+3D meshes it is possible for an
  // element and its coarse neighbor to not share any vertices.
  //
  // We also preserve interior parents for active pid elements


  // This code is just for geometric coupling, so we use a null
  // CouplingMatrix pointer.  We'll declare that here so as to avoid
  // confusing the insert() calls later.
  CouplingMatrix * nullcm = nullptr;

  for (const auto & elem : as_range(range_begin, range_end))
    {
      libmesh_assert(_mesh->query_elem_ptr(elem->id()) == elem);

      if (elem->processor_id() != p)
        coupled_elements.emplace(elem, nullcm);

      std::set<const Elem *> elem_point_neighbors;
      elem->find_point_neighbors(elem_point_neighbors);

      for (const auto & neigh : elem_point_neighbors)
        if (neigh->processor_id() != p)
          coupled_elements.emplace(neigh, nullcm);

      // An interior_parent isn't on the same manifold so won't be
      // found as a point neighbor, and it may not share nodes so we
      // can't use a connected_nodes test.
      //
      // Trying to preserve interior_parent() only works if it's on
      // the same Mesh, which is *not* guaranteed!  So we'll
      // double-check.
      const Elem * ip = elem->interior_parent();
      if (ip && ip->processor_id() != p &&
          _mesh->query_elem_ptr(ip->id()) == ip)
        coupled_elements.emplace(ip, nullcm);

#ifdef LIBMESH_ENABLE_PERIODIC
      if (check_periodic_bcs)
        {
          for (const auto s : elem->side_index_range())
            {
              if (elem->neighbor_ptr(s))
                continue;

              const Elem * const equal_level_periodic_neigh = elem->topological_neighbor
                (s, *_mesh, *point_locator, _periodic_bcs);

              if (!equal_level_periodic_neigh || equal_level_periodic_neigh == remote_elem)
                continue;

#ifdef LIBMESH_ENABLE_AMR
              equal_level_periodic_neigh->active_family_tree_by_topological_neighbor(
                active_periodic_neighbors,
                elem,
                *_mesh,
                *point_locator,
                _periodic_bcs,
                /*reset=*/true);
#else
              active_periodic_neighbors = { equal_level_periodic_neigh };
#endif

              for (const Elem * const active_periodic_neigh : active_periodic_neighbors)
                {
                  std::set <const Elem *> active_periodic_point_neighbors;

                  // This fills point neighbors *including*
                  // active_periodic_neigh. The documentation for this method
                  // states that this will return *active* point neighbors
                  active_periodic_neigh->find_point_neighbors(active_periodic_point_neighbors);

                  for (const Elem * const appn : active_periodic_point_neighbors)
                    {
                      // Don't need to ghost RemoteElem or an element we already own or an
                      // element we've already examined
                      if (appn == remote_elem || appn->processor_id() == p ||
                          periodic_elems_examined.count(appn))
                        continue;

                      // We only need to keep point neighbors that are along the periodic boundaries
                      bool on_periodic_boundary = false;
                      for (const auto appn_s : appn->side_index_range())
                        {
                          binfo.boundary_ids(appn, appn_s, appn_bcids);
                          for (const auto appn_bcid : appn_bcids)
                            if (_periodic_bcs->find(appn_bcid) != _periodic_bcs->end())
                              {
                                on_periodic_boundary = true;
                                goto jump;
                              }
                        }
                      jump:
                        if (on_periodic_boundary)
                          coupled_elements.emplace(appn, nullcm);

                        periodic_elems_examined.insert(appn);
                    }
                }
            }
        }

      if (check_disjoint_bcs)
        {
          // Also ghost their disjoint neighbors
          for (auto s : elem->side_index_range())
          {
            for (const auto & [id, boundary_ptr] : *db)
            {
              if (!_mesh->get_boundary_info().has_boundary_id(elem, s, id))
                continue;

              unsigned int neigh_side = invalid_uint;
              const Elem * neigh =
                  db->neighbor(id, *point_locator, elem, s, &neigh_side);

              if (!neigh || neigh == remote_elem)
                continue;

              if (neigh->processor_id() != p)
                coupled_elements.emplace(neigh, nullcm);
            }
          }
        }

#endif // LIBMESH_ENABLE_PERIODIC
    }
}

print_info()

void libMesh::ReferenceCounter::print_info ( std::ostream &  out_stream = libMesh::out )

staticinherited

Prints the reference information, by default to libMesh::out.

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().

{
  if (_enable_print_counter)
    out_stream << ReferenceCounter::get_info();
}

redistribute()

virtual void libMesh::GhostingFunctor::redistribute ( )

inlinevirtualinherited

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, libMesh::NonManifoldGhostingFunctor, AugmentSparsityOnInterface, and libMesh::OverlapCoupling.

Definition at line 286 of file ghosting_functor.h.

{};

set_mesh()

virtual void libMesh::GhostingFunctor::set_mesh ( const MeshBase *  mesh )

inlinevirtualinherited

It should be called after cloning a ghosting functor.

Ghosting functor is mesh dependent

Definition at line 227 of file ghosting_functor.h.

References libMesh::GhostingFunctor::_mesh, and mesh.

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

{ _mesh = mesh; }

set_periodic_boundaries()

virtual void libMesh::GhostingFunctor::set_periodic_boundaries ( const PeriodicBoundaries *  )

inlinevirtualinherited

Reimplemented in libMesh::PointNeighborCoupling, and libMesh::DefaultCoupling.

Definition at line 231 of file ghosting_functor.h.

{}

Member Data Documentation

_counts

ReferenceCounter::Counts libMesh::ReferenceCounter::_counts

staticprotectedinherited

Actually holds the data.

Definition at line 124 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::get_info().

_enable_print_counter

bool libMesh::ReferenceCounter::_enable_print_counter = true

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().

_mesh

const MeshBase* libMesh::GhostingFunctor::_mesh

protectedinherited

Definition at line 293 of file ghosting_functor.h.

Referenced by libMesh::GhostingFunctor::get_mesh(), libMesh::OverlapCoupling::mesh_reinit(), libMesh::NonManifoldGhostingFunctor::mesh_reinit(), libMesh::DefaultCoupling::mesh_reinit(), libMesh::PointNeighborCoupling::mesh_reinit(), and libMesh::GhostingFunctor::set_mesh().

_mutex

Threads::spin_mutex libMesh::ReferenceCounter::_mutex

staticprotectedinherited

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 137 of file reference_counter.h.

_n_objects

Threads::atomic< unsigned int > libMesh::ReferenceCounter::_n_objects

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().

_periodic_bcs

const PeriodicBoundaries* libMesh::GhostPointNeighbors::_periodic_bcs

private

Definition at line 109 of file ghost_point_neighbors.h.

nullptr

return libMesh::GhostingFunctor::nullptr { libmesh_deprecated()

inherited

Definition at line 220 of file ghosting_functor.h.

redistribute

virtual GhostPointNeighbors (const MeshBase & mesh) void libMesh::GhostPointNeighbors::redistribute() override

inlineoverride

Constructor.

Constructor. A clone() is needed because GhostingFunctor can not be shared between different meshes. The operations in GhostingFunctor are mesh dependent. If we have periodic boundaries, then we'll need the mesh to have an updated point locator whenever we're about to query them.

Definition at line 91 of file ghost_point_neighbors.h.

  { this->mesh_reinit(); }

---

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

• include/ghosting/ghost_point_neighbors.h
• src/ghosting/ghost_point_neighbors.C