This class provides an interface to the suite of preconditioners available from PETSc. More...

#include <petsc_preconditioner.h>

Inheritance diagram for libMesh::PetscPreconditioner< T >:

Public Member Functions
	PetscPreconditioner (const libMesh::Parallel::Communicator &comm_in)
	Constructor. More...

virtual	~PetscPreconditioner ()=default

virtual void	apply (const NumericVector< T > &x, NumericVector< T > &y) override
	Computes the preconditioned vector `y` based on input vector `x`. More...

virtual void	clear () override
	Release all memory and clear data structures. More...

virtual void	init () override
	Initialize data structures if not done so already. More...

PC	pc ()

virtual bool	initialized () const

virtual void	setup ()
	This is called every time the "operator might have changed". More...

virtual void	zero ()
	Can be used to zero items relevant to the preconditioner. More...

void	set_matrix (SparseMatrix< Number > &mat)
	Sets the matrix to be preconditioned. More...

PreconditionerType	type () const

void	set_type (const PreconditionerType pct)
	Sets the type of preconditioner to use. More...

const Parallel::Communicator &	comm () const

processor_id_type	n_processors () const

processor_id_type	processor_id () const

Static Public Member Functions
static void	set_petsc_preconditioner_type (const PreconditionerType &preconditioner_type, PC &pc)
	Tells PETSc to use the user-specified preconditioner. More...

static void	set_petsc_aux_data (PC &pc, System &sys, const unsigned v=0)
	Builds PETSc auxiliary data needed by preconditioners such as hypre ams/ads. More...

static void	set_hypre_ams_data (PC &pc, System &sys, const unsigned v)

static void	set_hypre_ads_data (PC &pc, System &sys, const unsigned v)

static void	set_petsc_aux_data (PC &, System &, const unsigned=0)

static std::unique_ptr< Preconditioner< T > >	build_preconditioner (const libMesh::Parallel::Communicator &comm, const SolverPackage solver_package=libMesh::default_solver_package())
	Builds a `Preconditioner` using the linear solver package specified by `solver_package`, returning the result wrapped in a std::unique_ptr for safety. More...

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
WrappedPetsc< PC >	_pc
	Preconditioner context. More...

Mat	_mat
	PETSc Mat pulled out of the _matrix object during init(). More...

SparseMatrix< T > *	_matrix
	The matrix P... More...

PreconditionerType	_preconditioner_type
	Enum stating with type of preconditioner to use. More...

bool	_is_initialized
	Flag indicating if the data structures have been initialized. More...

const Parallel::Communicator &	_communicator

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...

Detailed Description

template<typename T>
class libMesh::PetscPreconditioner< T >

This class provides an interface to the suite of preconditioners available from PETSc.

All overridden virtual functions are documented in preconditioner.h.

Author: Derek Gaston

Date: 2009

Definition at line 57 of file petsc_preconditioner.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.

Constructor & Destructor Documentation

◆ PetscPreconditioner()

template<typename T >

libMesh::PetscPreconditioner< T >::PetscPreconditioner ( const libMesh::Parallel::Communicator & comm_in )

Constructor.

Initializes PetscPreconditioner data structures

Definition at line 37 of file petsc_preconditioner.C.

                                                                                         :
   Preconditioner<T>(comm_in)
 {}

◆ ~PetscPreconditioner()

template<typename T >

virtual libMesh::PetscPreconditioner< T >::~PetscPreconditioner ( )

virtualdefault

Member Function Documentation

◆ apply()

template<typename T >

void libMesh::PetscPreconditioner< T >::apply	(	const NumericVector< T > &	x,
		NumericVector< T > &	y
	)

overridevirtual

Computes the preconditioned vector y based on input vector x.

This is usually done by solving \( Py=x \) to get the action of \( P^-1 x \).

Implements libMesh::Preconditioner< T >.

Definition at line 44 of file petsc_preconditioner.C.

References libMesh::PetscVector< T >::vec().

 {
   PetscVector<T> & x_pvec = cast_ref<PetscVector<T> &>(const_cast<NumericVector<T> &>(x));
   PetscVector<T> & y_pvec = cast_ref<PetscVector<T> &>(const_cast<NumericVector<T> &>(y));
 
   Vec x_vec = x_pvec.vec();
   Vec y_vec = y_pvec.vec();
 
   LibmeshPetscCall(PCApply(_pc, x_vec, y_vec));
 }

◆ build_preconditioner()

template<typename T >

std::unique_ptr< Preconditioner< T > > libMesh::Preconditioner< T >::build_preconditioner	(	const libMesh::Parallel::Communicator &	comm,
		const SolverPackage	solver_package = `libMesh::default_solver_package()`
	)

staticinherited

Builds a Preconditioner using the linear solver package specified by solver_package, returning the result wrapped in a std::unique_ptr for safety.

Definition at line 50 of file preconditioner.C.

 {
   // Avoid unused parameter warnings when no solver packages are enabled.
   libmesh_ignore(comm);
 
   // Build and return the appropriate Preconditioner object.
   switch (solver_package)
     {
 
 #ifdef LIBMESH_HAVE_PETSC
     case PETSC_SOLVERS:
       {
         return std::make_unique<PetscPreconditioner<T>>(comm);
       }
 #endif
 
 #ifdef LIBMESH_TRILINOS_HAVE_EPETRA
     case TRILINOS_SOLVERS:
       return std::make_unique<TrilinosPreconditioner<T>>(comm);
 #endif
 
 #ifdef LIBMESH_HAVE_EIGEN
     case EIGEN_SOLVERS:
       return std::make_unique<EigenPreconditioner<T>>(comm);
 #endif
 
     default:
       libmesh_error_msg("ERROR:  Unrecognized solver package: " << solver_package);
     }
 }

◆ clear()

template<typename T >

void libMesh::PetscPreconditioner< T >::clear ( )

overridevirtual

Release all memory and clear data structures.

Reimplemented from libMesh::Preconditioner< T >.

Definition at line 93 of file petsc_preconditioner.C.

 {
   // Calls custom deleter
   _pc.destroy();
 }

◆ comm()

const Parallel::Communicator& libMesh::ParallelObject::comm ( ) const

inlineinherited

Returns: A reference to the Parallel::Communicator object used by this mesh.

Definition at line 97 of file parallel_object.h.

References libMesh::ParallelObject::_communicator.

98 { return _communicator; }

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:120

◆ 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;
 }

◆ 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
 }

◆ 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();
   }
 }

◆ init()

template<typename T >

void libMesh::PetscPreconditioner< T >::init ( )

overridevirtual

Initialize data structures if not done so already.

Note: This MUST be called before the preconditioning object is used.

Reimplemented from libMesh::Preconditioner< T >.

Definition at line 59 of file petsc_preconditioner.C.

References libMesh::libMeshPrivateData::_is_initialized.

 {
   libmesh_error_msg_if(!this->_matrix, "ERROR: No matrix set for PetscPreconditioner, but init() called");
 
   // Clear the preconditioner in case it has been created in the past
   if (!this->_is_initialized)
     {
       // Should probably use PCReset(), but it's not working at the moment so we'll destroy instead
       if (_pc)
         _pc.destroy();
 
       LibmeshPetscCall(PCCreate(this->comm().get(), _pc.get()));
 
       auto pmatrix = cast_ptr<PetscMatrixBase<T> *>(this->_matrix);
       _mat = pmatrix->mat();
     }
 
   LibmeshPetscCall(PCSetOperators(_pc, _mat, _mat));
 
   // Set the PCType.  Note: this used to be done *before* the call to
   // PCSetOperators(), and only when !_is_initialized, but
   // 1.) Some preconditioners (those employing sub-preconditioners,
   // for example) have to call PCSetUp(), and can only do this after
   // the operators have been set.
   // 2.) It should be safe to call set_petsc_preconditioner_type()
   // multiple times.
   set_petsc_preconditioner_type(this->_preconditioner_type, *_pc);
 
   this->_is_initialized = true;
 }

◆ initialized()

template<typename T>

virtual bool libMesh::Preconditioner< T >::initialized ( ) const

inlinevirtualinherited

Returns: true if the data structures are initialized, false otherwise.

Reimplemented in libMesh::StaticCondensationPreconditioner.

Definition at line 84 of file preconditioner.h.

Referenced by libMesh::libmesh_petsc_preconditioner_setup().

84 { return _is_initialized; }

libMesh::Preconditioner::_is_initialized

bool _is_initialized

Flag indicating if the data structures have been initialized.

Definition: preconditioner.h:148

◆ 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().

86 { return _n_objects; }

libMesh::ReferenceCounter::_n_objects

static Threads::atomic< unsigned int > _n_objects

The number of objects.

Definition: reference_counter.h:132

◆ n_processors()

processor_id_type libMesh::ParallelObject::n_processors ( ) const

inlineinherited

Returns: The number of processors in the group.

Definition at line 103 of file parallel_object.h.

References libMesh::ParallelObject::_communicator, libMesh::libmesh_assert(), and TIMPI::Communicator::size().

   {
     processor_id_type returnval =
       cast_int<processor_id_type>(_communicator.size());
     libmesh_assert(returnval); // We never have an empty comm
     return returnval;
   }

◆ pc()

template<typename T >

PC libMesh::PetscPreconditioner< T >::pc ( )

Returns: The PETSc PC object. Can be useful for implementing more advanced algorithms.

Definition at line 102 of file petsc_preconditioner.C.

 {
   return _pc;
 }

◆ 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();
 }

◆ processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const

inlineinherited

Returns: The rank of this processor in the group.

Definition at line 114 of file parallel_object.h.

References libMesh::ParallelObject::_communicator, and TIMPI::Communicator::rank().

115 { return cast_int<processor_id_type>(_communicator.rank()); }

TIMPI::Communicator::rank

processor_id_type rank() const

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:120

◆ set_hypre_ads_data()

template<typename T >

void libMesh::PetscPreconditioner< T >::set_hypre_ads_data	(	PC &	pc,
		System &	sys,
		const unsigned	v
	)

static

Definition at line 345 of file petsc_preconditioner.C.

References libMesh::EquationSystems::add_system(), libMesh::System::add_variable(), libMesh::CG, libMesh::PetscMatrixBase< T >::close(), dim, distance(), libMesh::DofObject::dof_number(), libMesh::FIRST, libMesh::DofMapBase::first_dof(), libMesh::System::get_dof_map(), libMesh::System::get_equation_systems(), libMesh::System::get_mesh(), libMesh::global_processor_id(), libMesh::System::hide_output(), libMesh::libmesh_assert(), libMesh::DofMap::local_variable_indices(), libMesh::make_range(), libMesh::PetscMatrixBase< T >::mat(), libMesh::PetscMatrix< T >::matrix_matrix_mult(), libMesh::MeshBase::mesh_dimension(), libMesh::System::n_dofs(), libMesh::DofMap::n_dofs_per_processor(), libMesh::DofMap::n_local_dofs(), libMesh::System::n_local_dofs(), libMesh::NEDELEC_ONE, libMesh::System::number(), libMesh::on_command_line(), libMesh::Real, libMesh::System::reinit_mesh(), libMesh::PetscMatrixBase< T >::row_start(), libMesh::PetscMatrixBase< T >::row_stop(), libMesh::PetscMatrix< T >::set(), and libMesh::Elem::type_to_n_sides_map.

 {
   // Get the communicator from the PETSc object
   Parallel::communicator comm;
   PetscErrorCode ierr = PetscObjectGetComm((PetscObject)pc, &comm);
   libmesh_error_msg_if(ierr != LIBMESH_PETSC_SUCCESS,
                        "Error retrieving communicator");
   Parallel::Communicator Comm(comm);
 
   // The mesh/problem dimension
   const unsigned dim = sys.get_mesh().mesh_dimension();
 
   // Dummy Lagrange and Nédélec systems defined over the same mesh so we can
   // enumerate the vertices and edges, respectively
   System & lagrange_sys = sys.get_equation_systems().add_system<System>("__hypre_ads_vertices");
   lagrange_sys.hide_output() = true;
   lagrange_sys.add_variable("__lagrange");
   lagrange_sys.reinit_mesh();
   System & nedelec_sys = sys.get_equation_systems().add_system<System>("__hypre_ads_edges");
   nedelec_sys.hide_output() = true;
   nedelec_sys.add_variable("__nedelec", FIRST, NEDELEC_ONE);
   nedelec_sys.reinit_mesh();
 
   // Global (i.e. total) and local (i.e. to this processor) number of faces,
   // edges and vertices
   const std::vector<dof_id_type> n_all_faces = sys.get_dof_map().n_dofs_per_processor(v);
   const dof_id_type n_glb_faces = std::accumulate(n_all_faces.begin(), n_all_faces.end(), 0);
   const dof_id_type n_loc_faces = n_all_faces[global_processor_id()];
   const dof_id_type n_glb_edges = nedelec_sys.n_dofs();
   const dof_id_type n_loc_edges = nedelec_sys.n_local_dofs();
   const dof_id_type n_glb_verts = lagrange_sys.n_dofs();
   const dof_id_type n_loc_verts = lagrange_sys.n_local_dofs();
 
   // We require local indexing through the vertices and contiguous indexing
   // through the edges and faces: since the vertices are enumerated on their own
   // system, a local index can simply be obtained by subtracting those vertices
   // in all preceding processors; since the edges are enumerated on their own
   // system, we already have contiguous indexing; for the faces, if the system
   // we are given by the user has multiple variables/splits, we effectively need
   // to add local face numbers to those faces in all preceding processors
 
   // The number of vertices and faces in all preceding processors
   dof_id_signed_type vert_offset = -lagrange_sys.get_dof_map().first_dof();
   dof_id_signed_type face_offset =
     std::accumulate(n_all_faces.begin(), n_all_faces.begin() + global_processor_id(), 0);
 
   // Whether dofs are in variable-major or node-major order
   bool var_major = !libMesh::on_command_line("--node-major-dofs");
 
   // If variable-major order, we need only subtract all the preceding dofs; but
   // if node-major order, we need to enumerate the dofs on this processor
   std::vector<dof_id_type> idx_faces;
   if (var_major)
   {
     face_offset -= sys.get_dof_map().first_dof();
     for (auto i : make_range(v))
       face_offset -= sys.get_dof_map().n_local_dofs(i);
   }
   else
     sys.get_dof_map().local_variable_indices(idx_faces, sys.get_mesh(), v);
 
   // Create the discrete grandient matrix, representing the edges in terms of its vertices
   // Preallocate 2 diagonal + 2 off-diagonal nonzeros as the vertices could fall on either
   PetscMatrix<Real> G(Comm, n_glb_edges, n_glb_verts, n_loc_edges, n_loc_verts, 2, 2);
 
   // Create the discrete curl matrix, representing the faces in terms of its edges
   // Preallocate 4 diagonal + 4 off-diagonal nonzeros as the edges could fall on either
   PetscMatrix<Real> C(Comm, n_glb_faces, n_glb_edges, n_loc_faces, n_loc_edges, 4, 4);
 
   // Create array for the coordinates of the local vertices
   PetscReal * coords;
   LibmeshPetscCallA(comm, PetscMalloc1(dim * n_loc_verts, &coords));
 
   // Populate the discrete gradient matrix and the coordinates array
   for (const auto & elem : sys.get_mesh().active_local_element_ptr_range())
     for (auto face : make_range(elem->n_faces()))
     {
       // The number of edges on this face
       const unsigned n_face_edges = Elem::type_to_n_sides_map[elem->side_type(face)];
 
       // The faces's three/four edges
       std::vector<dof_id_type> edge_dofs(n_face_edges);
       std::vector<bool> edge_orients(n_face_edges);
       for (auto face_edge : make_range(n_face_edges))
       {
         // Convert from face-wise to element-wise edge id
         const unsigned edge = elem->local_side_node(face, n_face_edges + face_edge)
                             - elem->n_vertices();
         libmesh_assert(elem->is_edge_on_side(edge, face));
 
         // The edge's two vertices
         dof_id_type vert_dofs[2];
         for (auto vert : make_range(2))
         {
           const unsigned loc_vert_node_id = elem->local_edge_node(edge, vert);
           libmesh_assert(elem->is_vertex(loc_vert_node_id));
 
           const Node & vert_node = elem->node_ref(loc_vert_node_id);
           vert_dofs[vert] = vert_node.dof_number(lagrange_sys.number(), 0, 0);
 
           // If owned, populate coordinates array
           if (vert_node.processor_id() == global_processor_id())
           {
             const dof_id_type loc_vert_dof = vert_offset + vert_dofs[vert];
             libmesh_assert(loc_vert_dof <  n_loc_verts);
 
             for (auto d : make_range(dim))
               coords[dim * loc_vert_dof + d] = vert_node(d);
           }
         }
 
         // The edge's (middle) node
         const unsigned loc_edge_node_id = elem->local_edge_node(edge, 2);
         libmesh_assert(elem->is_edge(loc_edge_node_id));
 
         const Node & edge_node = elem->node_ref(loc_edge_node_id);
         edge_dofs[face_edge] = edge_node.dof_number(nedelec_sys.number(), 0, 0);
         edge_orients[face_edge] = elem->positive_edge_orientation(edge) ^
                                   elem->relative_edge_face_order(edge, face);
 
         // If owned, populate discrete gradient matrix
         if (edge_node.processor_id() == global_processor_id())
         {
           const Real sign = elem->positive_edge_orientation(edge) ? 1 : -1;
 
           libmesh_assert(edge_dofs[face_edge] >= G.row_start());
           libmesh_assert(edge_dofs[face_edge] <  G.row_stop());
           G.set(edge_dofs[face_edge], vert_dofs[0],  sign);
           G.set(edge_dofs[face_edge], vert_dofs[1], -sign);
         }
       }
 
       // The faces's (middle) node
       const unsigned loc_face_node_id = elem->local_side_node(face, 2 * n_face_edges);
       libmesh_assert(elem->is_face(loc_face_node_id));
 
       const Node & face_node = elem->node_ref(loc_face_node_id);
 
       // If owned, populate discrete curl matrix
       if (face_node.processor_id() == global_processor_id())
       {
         const dof_id_type face_dof = face_node.dof_number(sys.number(), v, 0);
 
         const dof_id_type cont_face_dof = face_offset +
           (var_major ? face_dof
                      : std::distance(idx_faces.begin(),
                        std::find(idx_faces.begin(), idx_faces.end(), face_dof)));
 
         const bool face_orient = elem->positive_face_orientation(face);
 
         for (auto face_edge : make_range(n_face_edges))
         {
           const Real sign = face_orient ^ edge_orients[face_edge] ? 1 : -1;
 
           libmesh_assert(cont_face_dof >= C.row_start());
           libmesh_assert(cont_face_dof <  C.row_stop());
           C.set(cont_face_dof, edge_dofs[face_edge], sign);
         }
       }
     }
 
   // Assemble the discrete gradient and discrete curl matrices
   G.close();
   C.close();
 
 #ifndef NDEBUG
   // The product CG of the two matrices should be the zero matrix
   PetscMatrix<Real> CG(Comm);
   C.matrix_matrix_mult(G, CG);
   libmesh_assert(CG.linfty_norm() == 0);
 #endif
 
   // Hand over the matrices and coordinates array
   LibmeshPetscCallA(comm, PCHYPRESetDiscreteGradient(pc, G.mat()));
   LibmeshPetscCallA(comm, PCHYPRESetDiscreteCurl(pc, C.mat()));
   LibmeshPetscCallA(comm, PCSetCoordinates(pc, dim, n_loc_verts, coords));
 
   // Free allocated memory for the coordinates array
   LibmeshPetscCallA(comm, PetscFree(coords));
 }

◆ set_hypre_ams_data()

template<typename T >

void libMesh::PetscPreconditioner< T >::set_hypre_ams_data	(	PC &	pc,
		System &	sys,
		const unsigned	v
	)

static

Definition at line 221 of file petsc_preconditioner.C.

References libMesh::EquationSystems::add_system(), libMesh::System::add_variable(), libMesh::PetscMatrixBase< T >::close(), dim, distance(), libMesh::DofObject::dof_number(), libMesh::DofMapBase::first_dof(), libMesh::System::get_dof_map(), libMesh::System::get_equation_systems(), libMesh::System::get_mesh(), libMesh::global_processor_id(), libMesh::System::hide_output(), libMesh::libmesh_assert(), libMesh::DofMap::local_variable_indices(), libMesh::make_range(), libMesh::PetscMatrixBase< T >::mat(), libMesh::MeshBase::mesh_dimension(), libMesh::System::n_dofs(), libMesh::DofMap::n_dofs_per_processor(), libMesh::DofMap::n_local_dofs(), libMesh::System::n_local_dofs(), libMesh::System::number(), libMesh::on_command_line(), libMesh::Real, libMesh::System::reinit_mesh(), libMesh::PetscMatrixBase< T >::row_start(), libMesh::PetscMatrixBase< T >::row_stop(), and libMesh::PetscMatrix< T >::set().

 {
   // Get the communicator from the PETSc object
   Parallel::communicator comm;
   PetscErrorCode ierr = PetscObjectGetComm((PetscObject)pc, &comm);
   libmesh_error_msg_if(ierr != LIBMESH_PETSC_SUCCESS,
                        "Error retrieving communicator");
   Parallel::Communicator Comm(comm);
 
   // The mesh/problem dimension
   const unsigned dim = sys.get_mesh().mesh_dimension();
 
   // Dummy Lagrange system defined over the same mesh so we can enumerate the vertices
   System & lagrange_sys = sys.get_equation_systems().add_system<System>("__hypre_ams_vertices");
   lagrange_sys.hide_output() = true;
   lagrange_sys.add_variable("__lagrange");
   lagrange_sys.reinit_mesh();
 
   // Global (i.e. total) and local (i.e. to this processor) number of edges and vertices
   const std::vector<dof_id_type> n_all_edges = sys.get_dof_map().n_dofs_per_processor(v);
   const dof_id_type n_glb_edges = std::accumulate(n_all_edges.begin(), n_all_edges.end(), 0);
   const dof_id_type n_loc_edges = n_all_edges[global_processor_id()];
   const dof_id_type n_glb_verts = lagrange_sys.n_dofs();
   const dof_id_type n_loc_verts = lagrange_sys.n_local_dofs();
 
   // We require local indexing through the vertices and contiguous indexing
   // through the edges: since the vertices are enumerated on their own system,
   // a local index can simply be obtained by subtracting those vertices in all
   // preceding processors; for the edges, if the system we are given by the
   // user has multiple variables/splits, we effectively need to add local edge
   // numbers to those edges in all preceding processors
 
   // The number of vertices and edges in all preceding processors
   dof_id_signed_type vert_offset = -lagrange_sys.get_dof_map().first_dof();
   dof_id_signed_type edge_offset =
     std::accumulate(n_all_edges.begin(), n_all_edges.begin() + global_processor_id(), 0);
 
   // Whether dofs are in variable-major or node-major order
   bool var_major = !libMesh::on_command_line("--node-major-dofs");
 
   // If variable-major order, we need only subtract all the preceding dofs; but
   // if node-major order, we need to enumerate the dofs on this processor
   std::vector<dof_id_type> idx_edges;
   if (var_major)
   {
     edge_offset -= sys.get_dof_map().first_dof();
     for (auto i : make_range(v))
       edge_offset -= sys.get_dof_map().n_local_dofs(i);
   }
   else
     sys.get_dof_map().local_variable_indices(idx_edges, sys.get_mesh(), v);
 
   // Create the discrete grandient matrix, representing the edges in terms of its vertices
   // Preallocate 2 diagonal + 2 off-diagonal nonzeros as the vertices could fall on either
   PetscMatrix<Real> G(Comm, n_glb_edges, n_glb_verts, n_loc_edges, n_loc_verts, 2, 2);
 
   // Create array for the coordinates of the local vertices
   PetscReal * coords;
   LibmeshPetscCallA(comm, PetscMalloc1(dim * n_loc_verts, &coords));
 
   // Populate the discrete gradient matrix and the coordinates array
   for (const auto & elem : sys.get_mesh().active_local_element_ptr_range())
     for (auto edge : make_range(elem->n_edges()))
     {
       // The edge's two vertices
       dof_id_type vert_dofs[2];
       for (auto vert : make_range(2))
       {
         const unsigned loc_vert_node_id = elem->local_edge_node(edge, vert);
         libmesh_assert(elem->is_vertex(loc_vert_node_id));
 
         const Node & vert_node = elem->node_ref(loc_vert_node_id);
         vert_dofs[vert] = vert_node.dof_number(lagrange_sys.number(), 0, 0);
 
         // If owned, populate coordinates array
         if (vert_node.processor_id() == global_processor_id())
         {
           const dof_id_type loc_vert_dof = vert_offset + vert_dofs[vert];
           libmesh_assert(loc_vert_dof <  n_loc_verts);
 
           for (auto d : make_range(dim))
             coords[dim * loc_vert_dof + d] = vert_node(d);
         }
       }
 
       // The edge's (middle) node
       const unsigned loc_edge_node_id = elem->local_edge_node(edge, 2);
       libmesh_assert(elem->is_edge(loc_edge_node_id));
 
       const Node & edge_node = elem->node_ref(loc_edge_node_id);
 
       // If owned, populate discrete gradient matrix
       if (edge_node.processor_id() == global_processor_id())
       {
         const dof_id_type edge_dof = edge_node.dof_number(sys.number(), v, 0);
 
         const dof_id_type cont_edge_dof = edge_offset +
           (var_major ? edge_dof
                      : std::distance(idx_edges.begin(),
                        std::find(idx_edges.begin(), idx_edges.end(), edge_dof)));
 
         const Real sign = elem->positive_edge_orientation(edge) ? 1 : -1;
 
         libmesh_assert(cont_edge_dof >= G.row_start());
         libmesh_assert(cont_edge_dof <  G.row_stop());
         G.set(cont_edge_dof, vert_dofs[0],  sign);
         G.set(cont_edge_dof, vert_dofs[1], -sign);
       }
     }
 
   // Assemble the discrete gradient matrix
   G.close();
 
   // Hand over the matrix and coordinates array
   LibmeshPetscCallA(comm, PCHYPRESetDiscreteGradient(pc, G.mat()));
   LibmeshPetscCallA(comm, PCSetCoordinates(pc, dim, n_loc_verts, coords));
 
   // Free allocated memory for the coordinates array
   LibmeshPetscCallA(comm, PetscFree(coords));
 }

◆ set_matrix()

template<typename T >

void libMesh::Preconditioner< T >::set_matrix ( SparseMatrix< Number > & mat )

inherited

Sets the matrix to be preconditioned.

Definition at line 164 of file preconditioner.h.

 {
   //If the matrix is changing then we (probably) need to reinitialize.
   _is_initialized = false;
   _matrix = &mat;
 }

◆ set_petsc_aux_data() [1/2]

template<typename T >

void libMesh::PetscPreconditioner< T >::set_petsc_aux_data	(	PC &	pc,
		System &	sys,
		const unsigned	v = `0`
	)

static

Builds PETSc auxiliary data needed by preconditioners such as hypre ams/ads.

Definition at line 161 of file petsc_preconditioner.C.

References libMesh::System::get_mesh(), libMesh::MeshBase::mesh_dimension(), libMesh::System::n_vars(), libMesh::NEDELEC_ONE, libMesh::RAVIART_THOMAS, libMesh::Variable::type(), and libMesh::System::variable().

 {
   // Get the communicator from the PETSc object
   Parallel::communicator comm;
   PetscErrorCode ierr = PetscObjectGetComm((PetscObject)pc, &comm);
   libmesh_error_msg_if(ierr != LIBMESH_PETSC_SUCCESS,
                        "Error retrieving communicator");
 
   // Make sure the preconditioner options are set
   LibmeshPetscCallA(comm, PCSetFromOptions(pc));
 
   // Get the type of preconditioner we are using
   PCType pc_type = nullptr;
   LibmeshPetscCallA(comm, PCGetType(pc, &pc_type));
 
   // Check if hypre ams/ads, otherwise we quit with nothing to do
   if (pc_type && std::string(pc_type) == PCHYPRE)
   {
     // Get the hypre preconditioner we are using
     PCType hypre_type = nullptr;
     LibmeshPetscCallA(comm, PCHYPREGetType(pc, &hypre_type));
 
     // If not ams/ads, we quit with nothing to do
     if (std::string(hypre_type) == "ams")
     {
       // If multiple variables, we error out as senseless
       libmesh_error_msg_if(sys.n_vars() > 1,
                            "Error applying hypre AMS to a system with multiple "
                            "variables");
       // If not a 1st order Nédélec or a 2d 1st order Raviart-Thomas system, we
       // error out as we do not support anything else at the moment
       libmesh_error_msg_if(sys.variable(v).type() != FEType(1, NEDELEC_ONE) &&
                           (sys.variable(v).type() != FEType(1, RAVIART_THOMAS) ||
                            sys.get_mesh().mesh_dimension() != 2),
                            "Error applying hypre AMS to a system "
                            "whose variable is not 1st order Nedelec or 1st "
                            "order Raviart-Thomas on a 2d mesh");
       set_hypre_ams_data(pc, sys, v);
     }
     else if (std::string(hypre_type) == "ads")
     {
       // If multiple variables, we error out as senseless
       libmesh_error_msg_if(sys.n_vars() > 1,
                            "Error applying hypre ADS to a system with multiple "
                            "variables");
       // If not a 3d 1st order Raviart-Thomas system, we error out as we do not
       // support anything else at the moment
       libmesh_error_msg_if(sys.variable(v).type() != FEType(1, RAVIART_THOMAS) ||
                            sys.get_mesh().mesh_dimension() != 3,
                            "Error applying hypre ADS to a system "
                            "whose variable is not 1st "
                            "order Raviart-Thomas on a 3d mesh");
       set_hypre_ads_data(pc, sys, v);
     }
   }
 }

◆ set_petsc_aux_data() [2/2]

template<typename T >

static void libMesh::PetscPreconditioner< T >::set_petsc_aux_data	(	PC &	,
		System &	,
		const unsigned	= `0`
	)

inlinestatic

Definition at line 93 of file petsc_preconditioner.h.

93 {}

◆ set_petsc_preconditioner_type()

template<typename T >

void libMesh::PetscPreconditioner< T >::set_petsc_preconditioner_type	(	const PreconditionerType &	preconditioner_type,
		PC &	pc
	)

static

Tells PETSc to use the user-specified preconditioner.

Definition at line 110 of file petsc_preconditioner.C.

References libMesh::AMG_PRECOND, libMesh::ASM_PRECOND, libMesh::BLOCK_JACOBI_PRECOND, libMesh::CHOLESKY_PRECOND, libMesh::EISENSTAT_PRECOND, libMesh::Utility::enum_to_string(), libMesh::err, libMesh::ICC_PRECOND, libMesh::IDENTITY_PRECOND, libMesh::ILU_PRECOND, libMesh::JACOBI_PRECOND, libMesh::LU_PRECOND, libMesh::SHELL_PRECOND, libMesh::SOR_PRECOND, libMesh::SVD_PRECOND, and libMesh::USER_PRECOND.

 {
   // get the communicator from the PETSc object
   Parallel::communicator comm;
   PetscErrorCode ierr = PetscObjectGetComm((PetscObject)pc, & comm);
   if (ierr != LIBMESH_PETSC_SUCCESS)
     libmesh_error_msg("Error retrieving communicator");
 
   #define CasePCSetType(PreconditionerType, PCType)                       \
   case PreconditionerType:                                                \
     LibmeshPetscCallA(comm, PCSetType (pc, const_cast<KSPType>(PCType))); \
     break;
 
   switch (preconditioner_type)
     {
     CasePCSetType(IDENTITY_PRECOND,     PCNONE)
     CasePCSetType(CHOLESKY_PRECOND,     PCCHOLESKY)
     CasePCSetType(ICC_PRECOND,          PCICC)
     CasePCSetType(ILU_PRECOND,          PCILU)
     CasePCSetType(LU_PRECOND,           PCLU)
     CasePCSetType(ASM_PRECOND,          PCASM)
     CasePCSetType(JACOBI_PRECOND,       PCJACOBI)
     CasePCSetType(BLOCK_JACOBI_PRECOND, PCBJACOBI)
     CasePCSetType(SOR_PRECOND,          PCSOR)
     CasePCSetType(EISENSTAT_PRECOND,    PCEISENSTAT)
     CasePCSetType(AMG_PRECOND,          PCHYPRE)
     CasePCSetType(SVD_PRECOND,          PCSVD)
     CasePCSetType(USER_PRECOND,         PCMAT)
     CasePCSetType(SHELL_PRECOND,        PCSHELL)
 
     default:
       libMesh::err << "ERROR:  Unsupported PETSC Preconditioner: "
                    << Utility::enum_to_string(preconditioner_type) << std::endl
                    << "Continuing with PETSC defaults" << std::endl;
     }
 
   // Set additional options if we are doing AMG and
   // HYPRE is available
 #ifdef LIBMESH_HAVE_PETSC_HYPRE
   if (preconditioner_type == AMG_PRECOND)
     LibmeshPetscCallA(comm, PCHYPRESetType(pc, "boomeramg"));
 #endif
 
   // Let the commandline override stuff
   LibmeshPetscCallA(comm, PCSetFromOptions(pc));
 }

◆ set_type()

template<typename T >

void libMesh::Preconditioner< T >::set_type ( const PreconditionerType pct )

inherited

Sets the type of preconditioner to use.

Definition at line 173 of file preconditioner.h.

 {
   //If the preconditioner type changes we (probably) need to reinitialize.
   _is_initialized = false;
   _preconditioner_type = pct;
 }

◆ setup()

template<typename T>

virtual void libMesh::Preconditioner< T >::setup ( )

inlinevirtualinherited

This is called every time the "operator might have changed".

This is where you need to fill in your preconditioning matrix.

Reimplemented in libMesh::StaticCondensationPreconditioner.

Definition at line 110 of file preconditioner.h.

Referenced by libMesh::libmesh_petsc_preconditioner_setup().

110 {}

◆ type()

template<typename T>

PreconditionerType libMesh::Preconditioner< T >::type ( ) const

inlineinherited

Returns: The type of preconditioner to use.

Definition at line 125 of file preconditioner.h.

125 { return _preconditioner_type; }

libMesh::Preconditioner::_preconditioner_type

PreconditionerType _preconditioner_type

Enum stating with type of preconditioner to use.

Definition: preconditioner.h:143

◆ zero()

template<typename T>

virtual void libMesh::Preconditioner< T >::zero ( )

inlinevirtualinherited

Can be used to zero items relevant to the preconditioner.

Reimplemented in libMesh::StaticCondensationPreconditioner.

Definition at line 115 of file preconditioner.h.

115 {}

Member Data Documentation

◆ _communicator

const Parallel::Communicator& libMesh::ParallelObject::_communicator

protectedinherited

Definition at line 120 of file parallel_object.h.

Referenced by libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::StaticCondensation::close(), libMesh::ParallelObject::comm(), libMesh::CondensedEigenSystem::initialize_condensed_matrices(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::operator=(), libMesh::ParallelObject::processor_id(), libMesh::BoundaryInfo::regenerate_id_sets(), libMesh::StaticCondensationDofMap::reinit(), and libMesh::BoundaryInfo::synchronize_global_id_set().

◆ _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().

◆ _is_initialized

template<typename T>

bool libMesh::Preconditioner< T >::_is_initialized

protectedinherited

Flag indicating if the data structures have been initialized.

Definition at line 148 of file preconditioner.h.

Referenced by libMesh::Preconditioner< Number >::initialized().

◆ _mat

template<typename T >

Mat libMesh::PetscPreconditioner< T >::_mat

protected

PETSc Mat pulled out of the _matrix object during init().

We aren't responsible for cleaning up this one.

Definition at line 107 of file petsc_preconditioner.h.

◆ _matrix

template<typename T>

SparseMatrix<T>* libMesh::Preconditioner< T >::_matrix

protectedinherited

The matrix P...

ie the matrix to be preconditioned. This is often the actual system matrix of a linear system.

Definition at line 138 of file preconditioner.h.

◆ _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().

◆ _pc

template<typename T >

WrappedPetsc<PC> libMesh::PetscPreconditioner< T >::_pc

protected

Preconditioner context.

Definition at line 101 of file petsc_preconditioner.h.

◆ _preconditioner_type

template<typename T>

PreconditionerType libMesh::Preconditioner< T >::_preconditioner_type

protectedinherited

Enum stating with type of preconditioner to use.

Definition at line 143 of file preconditioner.h.

Referenced by libMesh::Preconditioner< Number >::type().

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

include/numerics/petsc_preconditioner.h
src/numerics/petsc_preconditioner.C

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

template<typename T> class libMesh::PetscPreconditioner< T >

Member Typedef Documentation

◆ Counts

Constructor & Destructor Documentation

◆ PetscPreconditioner()

◆ ~PetscPreconditioner()

Member Function Documentation

◆ apply()

◆ build_preconditioner()

◆ clear()

◆ comm()

◆ disable_print_counter_info()

◆ enable_print_counter_info()

◆ get_info()

◆ increment_constructor_count()

◆ increment_destructor_count()

◆ init()

◆ initialized()

◆ n_objects()

◆ n_processors()

◆ pc()

◆ print_info()

◆ processor_id()

◆ set_hypre_ads_data()

◆ set_hypre_ams_data()

◆ set_matrix()

◆ set_petsc_aux_data() [1/2]

◆ set_petsc_aux_data() [2/2]

◆ set_petsc_preconditioner_type()

◆ set_type()

◆ setup()

◆ type()

◆ zero()

Member Data Documentation

◆ _communicator

◆ _counts

◆ _enable_print_counter

◆ _is_initialized

◆ _mat

◆ _matrix

◆ _mutex

◆ _n_objects

◆ _pc

◆ _preconditioner_type

template<typename T>
class libMesh::PetscPreconditioner< T >