libMesh::DefaultCoupling Class Reference

This class implements the default algebraic coupling in libMesh: elements couple to themselves, but may also couple to neighbors both locally and across periodic boundary conditions. More...

#include <default_coupling.h>

Inheritance diagram for libMesh::DefaultCoupling:

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?

Public Member Functions
	DefaultCoupling ()
	Constructor.
	DefaultCoupling (const DefaultCoupling &other)
	Constructor.
virtual std::unique_ptr< GhostingFunctor >	clone () const override
	A clone() is needed because GhostingFunctor can not be shared between different meshes.
void	set_dof_coupling (const CouplingMatrix *dof_coupling)
unsigned int	n_levels ()
void	set_n_levels (unsigned int n_levels)
void	set_periodic_boundaries (const PeriodicBoundaries *periodic_bcs) override
virtual void	mesh_reinit () override
	If we have periodic boundaries, then we'll need the mesh to have an updated point locator whenever we're about to query them.
virtual void	redistribute () override
	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.
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.
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 the elements which will be coupled to them in the sparsity pattern.
virtual void	set_mesh (const MeshBase *mesh)
	It should be called after cloning a ghosting functor.
const MeshBase *	get_mesh () const
	Return the mesh associated with ghosting functor.
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.

Static Public Member Functions
static std::string	get_info ()
	Gets a string containing the reference information.
static void	print_info (std::ostream &out_stream=libMesh::out)
	Prints the reference information, by default to libMesh::out.
static unsigned int	n_objects ()
	Prints the number of outstanding (created, but not yet destroyed) objects.
static void	enable_print_counter_info ()
	Methods to enable/disable the reference counter output from print_info().
static void	disable_print_counter_info ()

Public Attributes
return	nullptr { libmesh_deprecated()

Protected Types
typedef std::map< std::string, std::pair< unsigned int, unsigned int > >	Counts
	Data structure to log the information.

Protected Member Functions
void	increment_constructor_count (const std::string &name) noexcept
	Increments the construction counter.
void	increment_destructor_count (const std::string &name) noexcept
	Increments the destruction counter.

Protected Attributes
const MeshBase *	_mesh

Static Protected Attributes
static Counts	_counts
	Actually holds the data.
static Threads::atomic< unsigned int >	_n_objects
	The number of objects.
static Threads::spin_mutex	_mutex
	Mutual exclusion object to enable thread-safe reference counting.
static bool	_enable_print_counter = true
	Flag to control whether reference count information is printed when print_info is called.

Private Attributes
const CouplingMatrix *	_dof_coupling
const PeriodicBoundaries *	_periodic_bcs
unsigned int	_n_levels

Detailed Description

This class implements the default algebraic coupling in libMesh: elements couple to themselves, but may also couple to neighbors both locally and across periodic boundary conditions.

Author

Roy H. Stogner

Date

2016

Definition at line 44 of file default_coupling.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.

Constructor & Destructor Documentation

DefaultCoupling() [1/2]

libMesh::DefaultCoupling::DefaultCoupling ( )

inline

Constructor.

Definition at line 51 of file default_coupling.h.

                    :
    _dof_coupling(nullptr),
#ifdef LIBMESH_ENABLE_PERIODIC
    _periodic_bcs(nullptr),
#endif
    _n_levels(0)
  {}

DefaultCoupling() [2/2]

libMesh::DefaultCoupling::DefaultCoupling ( const DefaultCoupling &  other )

inline

Constructor.

Definition at line 62 of file default_coupling.h.

                                                 :
    GhostingFunctor(other),
    _dof_coupling(other._dof_coupling),
#ifdef LIBMESH_ENABLE_PERIODIC
    _periodic_bcs(other._periodic_bcs),
#endif
    _n_levels(other._n_levels)
  {}

Member Function Documentation

clone()

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

inlineoverridevirtual

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

The operations in GhostingFunctor are mesh dependent.

Implements libMesh::GhostingFunctor.

Definition at line 75 of file default_coupling.h.

  { return std::make_unique<DefaultCoupling>(*this); }

delete_remote_elements()

virtual void libMesh::DefaultCoupling::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 104 of file default_coupling.h.

  { this->mesh_reinit(); }

References mesh_reinit().

disable_print_counter_info()

void libMesh::ReferenceCounter::disable_print_counter_info ( )

staticinherited

Definition at line 100 of file reference_counter.C.

{
  _enable_print_counter = false;
  return;
}

References libMesh::ReferenceCounter::_enable_print_counter.

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.

{
  _enable_print_counter = true;
  return;
}

References libMesh::ReferenceCounter::_enable_print_counter.

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

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.

{
#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
}

References libMesh::ReferenceCounter::_counts.

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

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.

{ libmesh_assert(_mesh); return _mesh; }

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

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.

{
  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();
  }
}

References libMesh::err, libMesh::BasicOStreamProxy< charT, traits >::get(), and libMesh::Threads::spin_mtx.

Referenced by libMesh::ReferenceCountedObject< T >::ReferenceCountedObject(), libMesh::ReferenceCountedObject< T >::ReferenceCountedObject(), and libMesh::ReferenceCountedObject< T >::ReferenceCountedObject().

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.

{
  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();
  }
}

References libMesh::err, libMesh::BasicOStreamProxy< charT, traits >::get(), and libMesh::Threads::spin_mtx.

Referenced by libMesh::ReferenceCountedObject< T >::~ReferenceCountedObject().

mesh_reinit()

void libMesh::DefaultCoupling::mesh_reinit ( )

overridevirtual

If we have periodic boundaries, then we'll need the mesh to have an updated point locator whenever we're about to query them.

Reimplemented from libMesh::GhostingFunctor.

Definition at line 53 of file default_coupling.C.

{
  // Unless we have periodic boundary conditions, we don't need
  // anything precomputed.
#ifdef LIBMESH_ENABLE_PERIODIC
  if (!_periodic_bcs || _periodic_bcs->empty())
    return;
#endif
 
  // If we do have periodic boundary conditions, we'll need a master
  // point locator, so we'd better have a mesh to build it on.
  libmesh_assert(_mesh);
 
  // Make sure an up-to-date master point locator has been
  // constructed; we'll need to grab sub-locators soon.
  _mesh->sub_point_locator();
}

References libMesh::GhostingFunctor::_mesh, _periodic_bcs, libMesh::libmesh_assert(), and libMesh::MeshBase::sub_point_locator().

Referenced by delete_remote_elements(), and redistribute().

n_levels()

unsigned int libMesh::DefaultCoupling::n_levels ( )

inline

Definition at line 82 of file default_coupling.h.

  { return _n_levels; }

References _n_levels.

Referenced by set_n_levels().

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.

  { return _n_objects; }

References libMesh::ReferenceCounter::_n_objects.

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

operator()()

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

overridevirtual

For the specified range of active elements, find the elements which will be coupled to them in the sparsity pattern.

This will be only the elements themselves by default, but will include side neighbors if an all-discontinuous-variable system is detected and/or if the user specified –implicit_neighbor_dofs on the command line or used set_implicit_neighbor_dofs() in their code.

Implements libMesh::GhostingFunctor.

Definition at line 73 of file default_coupling.C.

{
  LOG_SCOPE("operator()", "DefaultCoupling");
 
  // Let us not do assertion at this moment for API upgrade.
  // There is a functor inside of ElementSideNeighborLayers.
  // We can not set mesh for that functor because there is no handle
  // in libmesh. We need to override set_mesh in moose for setting a mesh for the functor.
  // The set_mesh overridden will not happen until the current change gets in.
  //libmesh_assert(_mesh);
 
#ifdef LIBMESH_ENABLE_PERIODIC
  bool check_periodic_bcs =
    (_periodic_bcs && !_periodic_bcs->empty());
 
  std::unique_ptr<PointLocatorBase> point_locator;
  if (check_periodic_bcs)
    {
      libmesh_assert(_mesh);
      point_locator = _mesh->sub_point_locator();
    }
#endif
 
  if (!this->_n_levels)
    {
      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, _dof_coupling);
      }
      return;
    }
 
  typedef std::unordered_set<const Elem*> set_type;
  set_type next_elements_to_check(range_begin, range_end);
  set_type elements_to_check;
  set_type elements_checked;
 
  for (unsigned int i=0; i != this->_n_levels; ++i)
    {
      elements_to_check.swap(next_elements_to_check);
      next_elements_to_check.clear();
      elements_checked.insert(elements_to_check.begin(), elements_to_check.end());
 
      for (const auto & elem : elements_to_check)
        {
          std::vector<const Elem *> active_neighbors;
 
          //libmesh_assert(_mesh->query_elem_ptr(elem->id()) ==elem);
 
          if (elem->processor_id() != p)
            coupled_elements.emplace(elem, _dof_coupling);
 
          for (auto s : elem->side_index_range())
            {
              const Elem * neigh = elem->neighbor_ptr(s);
 
#ifdef LIBMESH_ENABLE_PERIODIC
              // We might still have a periodic neighbor here
              if (!neigh && check_periodic_bcs)
                {
                  libmesh_assert(_mesh);
 
                  neigh = elem->topological_neighbor
                    (s, *_mesh, *point_locator, _periodic_bcs);
                }
#endif
 
              // With no regular *or* periodic neighbors we have nothing
              // to do. *Or* Mesh ghosting might ask us about what we want to
              // distribute along with non-local elements, and those
              // non-local elements might have remote neighbors, and
              // if they do then we can't say anything about them.
              if (!neigh || neigh == remote_elem)
                continue;
 
              // With any kind of neighbor, we need to couple to all the
              // active descendants on our side.
#ifdef LIBMESH_ENABLE_AMR
              if (neigh == elem->neighbor_ptr(s))
                neigh->active_family_tree_by_neighbor(active_neighbors,elem);
#  ifdef LIBMESH_ENABLE_PERIODIC
              else
                neigh->active_family_tree_by_topological_neighbor
                  (active_neighbors,elem,*_mesh,*point_locator,_periodic_bcs);
#  endif
#else
              active_neighbors.clear();
              active_neighbors.push_back(neigh);
#endif
 
              for (const auto & neighbor : active_neighbors)
                {
                  if (!elements_checked.count(neighbor))
                    next_elements_to_check.insert(neighbor);
 
                  if (neighbor->processor_id() != p)
                    coupled_elements.emplace(neighbor, _dof_coupling);
                }
            }
        }
    }
}

References libMesh::Elem::active_family_tree_by_neighbor(), libMesh::Elem::active_family_tree_by_topological_neighbor(), libMesh::as_range(), libMesh::libmesh_assert(), libMesh::Elem::neighbor_ptr(), libMesh::remote_elem, and libMesh::Elem::topological_neighbor().

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.

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

References libMesh::ReferenceCounter::_enable_print_counter, and libMesh::ReferenceCounter::get_info().

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

redistribute()

virtual void libMesh::DefaultCoupling::redistribute ( )

inlineoverridevirtual

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 from libMesh::GhostingFunctor.

Definition at line 101 of file default_coupling.h.

  { this->mesh_reinit(); }

References mesh_reinit().

set_dof_coupling()

void libMesh::DefaultCoupling::set_dof_coupling

(

const CouplingMatrix *

dof_coupling

)

Definition at line 35 of file default_coupling.C.

{
  // We used to treat an empty 0x0 _dof_coupling matrix as if it
  // were an NxN all-ones matrix.  We'd like to stop supporting this
  // behavior, but for now we'll just warn about it, while supporting
  // it via the preferred mechanism: a nullptr _dof_coupling
  // matrix pointer is interpreted as a full coupling matrix.
  if (dof_coupling && dof_coupling->empty())
    {
      libmesh_deprecated();
      _dof_coupling = nullptr;
    }
  else
    _dof_coupling = dof_coupling;
}

References _dof_coupling, and libMesh::CouplingMatrix::empty().

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.

{ _mesh = mesh; }

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

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

set_n_levels()

void libMesh::DefaultCoupling::set_n_levels ( unsigned int  n_levels )

inline

Definition at line 86 of file default_coupling.h.

  { _n_levels = n_levels; }

References _n_levels, and n_levels().

Referenced by main(), and DefaultCouplingTest::testCoupling().

set_periodic_boundaries()

void libMesh::DefaultCoupling::set_periodic_boundaries ( const PeriodicBoundaries *  periodic_bcs )

inlineoverridevirtual

Reimplemented from libMesh::GhostingFunctor.

Definition at line 91 of file default_coupling.h.

  { _periodic_bcs = periodic_bcs; }

References _periodic_bcs.

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().

_dof_coupling

const CouplingMatrix* libMesh::DefaultCoupling::_dof_coupling

private

Definition at line 124 of file default_coupling.h.

Referenced by set_dof_coupling().

_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 296 of file ghosting_functor.h.

Referenced by libMesh::GhostingFunctor::get_mesh(), mesh_reinit(), libMesh::NonManifoldGhostingFunctor::mesh_reinit(), libMesh::OverlapCoupling::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_levels

unsigned int libMesh::DefaultCoupling::_n_levels

private

Definition at line 128 of file default_coupling.h.

Referenced by n_levels(), and set_n_levels().

_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(), libMesh::ReferenceCounter::ReferenceCounter(), libMesh::ReferenceCounter::ReferenceCounter(), and libMesh::ReferenceCounter::~ReferenceCounter().

_periodic_bcs

const PeriodicBoundaries* libMesh::DefaultCoupling::_periodic_bcs

private

Definition at line 126 of file default_coupling.h.

Referenced by mesh_reinit(), and set_periodic_boundaries().

nullptr

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

inherited

Definition at line 220 of file ghosting_functor.h.

---

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

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