libMesh
Public Member Functions | Static Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes | Static Protected Attributes | Friends | List of all members
libMesh::SparseMatrix< T > Class Template Referenceabstract

Generic sparse matrix. More...

#include <dof_map.h>

Inheritance diagram for libMesh::SparseMatrix< T >:
[legend]

Public Member Functions

 SparseMatrix (const Parallel::Communicator &comm LIBMESH_CAN_DEFAULT_TO_COMMWORLD)
 Constructor; initializes the matrix to be empty, without any structure, i.e. More...
 
virtual ~SparseMatrix ()
 Destructor. More...
 
virtual bool initialized () const
 
void attach_dof_map (const DofMap &dof_map)
 Get a pointer to the DofMap to use. More...
 
virtual bool need_full_sparsity_pattern () const
 
virtual void update_sparsity_pattern (const SparsityPattern::Graph &)
 Updates the matrix sparsity pattern. More...
 
virtual void init (const numeric_index_type m, const numeric_index_type n, const numeric_index_type m_l, const numeric_index_type n_l, const numeric_index_type nnz=30, const numeric_index_type noz=10, const numeric_index_type blocksize=1)=0
 Initialize SparseMatrix with the specified sizes. More...
 
virtual void init ()=0
 Initialize this matrix using the sparsity structure computed by dof_map. More...
 
virtual void clear ()=0
 Restores the SparseMatrix<T> to a pristine state. More...
 
virtual void zero ()=0
 Set all entries to 0. More...
 
virtual void zero_rows (std::vector< numeric_index_type > &rows, T diag_value=0.0)
 Sets all row entries to 0 then puts diag_value in the diagonal entry. More...
 
virtual void close ()=0
 Calls the SparseMatrix's internal assembly routines, ensuring that the values are consistent across processors. More...
 
virtual void flush ()
 For PETSc matrix , this function is similar to close but without shrinking memory. More...
 
virtual numeric_index_type m () const =0
 
virtual numeric_index_type n () const =0
 
virtual numeric_index_type row_start () const =0
 
virtual numeric_index_type row_stop () const =0
 
virtual void set (const numeric_index_type i, const numeric_index_type j, const T value)=0
 Set the element (i,j) to value. More...
 
virtual void add (const numeric_index_type i, const numeric_index_type j, const T value)=0
 Add value to the element (i,j). More...
 
virtual void add_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols)=0
 Add the full matrix dm to the SparseMatrix. More...
 
virtual void add_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &dof_indices)=0
 Same as add_matrix, but assumes the row and column maps are the same. More...
 
virtual void add_block_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &brows, const std::vector< numeric_index_type > &bcols)
 Add the full matrix dm to the SparseMatrix. More...
 
virtual void add_block_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &dof_indices)
 Same as add_block_matrix(), but assumes the row and column maps are the same. More...
 
virtual void add (const T a, SparseMatrix< T > &X)=0
 Compute $ A \leftarrow A + a*X $ for scalar a, matrix X. More...
 
virtual T operator() (const numeric_index_type i, const numeric_index_type j) const =0
 
virtual Real l1_norm () const =0
 
virtual Real linfty_norm () const =0
 
virtual bool closed () const =0
 
void print (std::ostream &os=libMesh::out, const bool sparse=false) const
 Print the contents of the matrix to the screen in a uniform style, regardless of matrix/solver package being used. More...
 
virtual void print_personal (std::ostream &os=libMesh::out) const =0
 Print the contents of the matrix to the screen in a package-personalized style, if available. More...
 
virtual void print_matlab (const std::string &="") const
 Print the contents of the matrix in Matlab's sparse matrix format. More...
 
virtual void create_submatrix (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) const
 This function creates a matrix called "submatrix" which is defined by the row and column indices given in the "rows" and "cols" entries. More...
 
virtual void reinit_submatrix (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) const
 This function is similar to the one above, but it allows you to reuse the existing sparsity pattern of "submatrix" instead of reallocating it again. More...
 
void vector_mult (NumericVector< T > &dest, const NumericVector< T > &arg) const
 Multiplies the matrix by the NumericVector arg and stores the result in NumericVector dest. More...
 
void vector_mult_add (NumericVector< T > &dest, const NumericVector< T > &arg) const
 Multiplies the matrix by the NumericVector arg and adds the result to the NumericVector dest. More...
 
virtual void get_diagonal (NumericVector< T > &dest) const =0
 Copies the diagonal part of the matrix into dest. More...
 
virtual void get_transpose (SparseMatrix< T > &dest) const =0
 Copies the transpose of the matrix into dest, which may be *this. More...
 
template<>
void print (std::ostream &os, const bool sparse) const
 
const Parallel::Communicatorcomm () const
 
processor_id_type n_processors () const
 
processor_id_type processor_id () const
 

Static Public Member Functions

static UniquePtr< SparseMatrix< T > > build (const Parallel::Communicator &comm, const SolverPackage solver_package=libMesh::default_solver_package())
 Builds a SparseMatrix<T> using the linear solver package specified by solver_package. More...
 
static std::string get_info ()
 Gets a string containing the reference information. More...
 
static void print_info (std::ostream &out=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

virtual void _get_submatrix (SparseMatrix< T > &, const std::vector< numeric_index_type > &, const std::vector< numeric_index_type > &, const bool) const
 Protected implementation of the create_submatrix and reinit_submatrix routines. More...
 
void increment_constructor_count (const std::string &name)
 Increments the construction counter. More...
 
void increment_destructor_count (const std::string &name)
 Increments the destruction counter. More...
 

Protected Attributes

DofMap const * _dof_map
 The DofMap object associated with this object. More...
 
bool _is_initialized
 Flag indicating whether or not the matrix has 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...
 

Friends

std::ostream & operator<< (std::ostream &os, const SparseMatrix< T > &m)
 Same as the print method above, but allows you to print to a stream in the standard syntax. More...
 

Detailed Description

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

Generic sparse matrix.

This class contains pure virtual members that must be overridden in derived classes. Using a common base class allows for uniform access to sparse matrices from various different solver packages in different formats.

Author
Benjamin S. Kirk
Date
2003

Definition at line 65 of file dof_map.h.

Member Typedef Documentation

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

template<typename T>
libMesh::SparseMatrix< T >::SparseMatrix ( const Parallel::Communicator &comm  LIBMESH_CAN_DEFAULT_TO_COMMWORLD)
explicit

Constructor; initializes the matrix to be empty, without any structure, i.e.

the matrix is not usable at all. This constructor is therefore only useful for matrices which are members of a class. All other matrices should be created at a point in the data flow where all necessary information is available.

You have to initialize the matrix before usage with init(...).

Definition at line 43 of file sparse_matrix.C.

43  :
44  ParallelObject(comm_in),
46  _is_initialized(false)
47 {}
ParallelObject(const Parallel::Communicator &comm_in)
Constructor.
const class libmesh_nullptr_t libmesh_nullptr
bool _is_initialized
Flag indicating whether or not the matrix has been initialized.
DofMap const * _dof_map
The DofMap object associated with this object.
template<typename T >
libMesh::SparseMatrix< T >::~SparseMatrix ( )
virtual

Destructor.

Free all memory, but do not release the memory of the sparsity structure.

Definition at line 53 of file sparse_matrix.C.

54 {}

Member Function Documentation

template<typename T>
virtual void libMesh::SparseMatrix< T >::_get_submatrix ( SparseMatrix< T > &  ,
const std::vector< numeric_index_type > &  ,
const std::vector< numeric_index_type > &  ,
const bool   
) const
protectedvirtual

Protected implementation of the create_submatrix and reinit_submatrix routines.

Note
This function must be overridden in derived classes for it to work properly!

Reimplemented in libMesh::libmesh_final< T >.

Definition at line 410 of file sparse_matrix.h.

414  {
415  libmesh_not_implemented();
416  }
template<typename T>
virtual void libMesh::SparseMatrix< T >::add ( const numeric_index_type  i,
const numeric_index_type  j,
const T  value 
)
pure virtual
template<typename T>
virtual void libMesh::SparseMatrix< T >::add ( const T  a,
SparseMatrix< T > &  X 
)
pure virtual
template<typename T>
void libMesh::SparseMatrix< T >::add_block_matrix ( const DenseMatrix< T > &  dm,
const std::vector< numeric_index_type > &  brows,
const std::vector< numeric_index_type > &  bcols 
)
virtual

Add the full matrix dm to the SparseMatrix.

This is useful for adding an element matrix at assembly time. The matrix is assumed blocked, and brow, bcol correspond to the block row and column indices.

Reimplemented in libMesh::libmesh_final< T >.

Definition at line 61 of file sparse_matrix.C.

References libMesh::SparseMatrix< T >::add_matrix(), libMesh::DenseMatrixBase< T >::m(), and libMesh::DenseMatrixBase< T >::n().

64 {
65  libmesh_assert_equal_to (dm.m() / brows.size(), dm.n() / bcols.size());
66 
67  const numeric_index_type blocksize = cast_int<numeric_index_type>
68  (dm.m() / brows.size());
69 
70  libmesh_assert_equal_to (dm.m()%blocksize, 0);
71  libmesh_assert_equal_to (dm.n()%blocksize, 0);
72 
73  std::vector<numeric_index_type> rows, cols;
74 
75  rows.reserve(blocksize*brows.size());
76  cols.reserve(blocksize*bcols.size());
77 
78  for (std::size_t ib=0; ib<brows.size(); ib++)
79  {
80  numeric_index_type i=brows[ib]*blocksize;
81 
82  for (unsigned int v=0; v<blocksize; v++)
83  rows.push_back(i++);
84  }
85 
86  for (std::size_t jb=0; jb<bcols.size(); jb++)
87  {
88  numeric_index_type j=bcols[jb]*blocksize;
89 
90  for (unsigned int v=0; v<blocksize; v++)
91  cols.push_back(j++);
92  }
93 
94  this->add_matrix (dm, rows, cols);
95 }
virtual void add_matrix(const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols)=0
Add the full matrix dm to the SparseMatrix.
dof_id_type numeric_index_type
Definition: id_types.h:92
template<typename T>
virtual void libMesh::SparseMatrix< T >::add_block_matrix ( const DenseMatrix< T > &  dm,
const std::vector< numeric_index_type > &  dof_indices 
)
virtual

Same as add_block_matrix(), but assumes the row and column maps are the same.

Thus the matrix dm must be square.

Reimplemented in libMesh::libmesh_final< T >.

Definition at line 249 of file sparse_matrix.h.

251  { this->add_block_matrix (dm, dof_indices, dof_indices); }
virtual void add_block_matrix(const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &brows, const std::vector< numeric_index_type > &bcols)
Add the full matrix dm to the SparseMatrix.
Definition: sparse_matrix.C:61
template<typename T>
virtual void libMesh::SparseMatrix< T >::add_matrix ( const DenseMatrix< T > &  dm,
const std::vector< numeric_index_type > &  rows,
const std::vector< numeric_index_type > &  cols 
)
pure virtual
template<typename T>
virtual void libMesh::SparseMatrix< T >::add_matrix ( const DenseMatrix< T > &  dm,
const std::vector< numeric_index_type > &  dof_indices 
)
pure virtual

Same as add_matrix, but assumes the row and column maps are the same.

Thus the matrix dm must be square.

Implemented in libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, and libMesh::libmesh_final< T >.

template<typename T>
void libMesh::SparseMatrix< T >::attach_dof_map ( const DofMap dof_map)

Get a pointer to the DofMap to use.

Definition at line 105 of file sparse_matrix.h.

Referenced by libMesh::DofMap::attach_matrix().

106  { _dof_map = &dof_map; }
DofMap const * _dof_map
The DofMap object associated with this object.
template<typename T >
UniquePtr< SparseMatrix< T > > libMesh::SparseMatrix< T >::build ( const Parallel::Communicator comm,
const SolverPackage  solver_package = libMesh::default_solver_package() 
)
static

Builds a SparseMatrix<T> using the linear solver package specified by solver_package.

Definition at line 135 of file sparse_matrix.C.

References libMesh::ParallelObject::comm(), libMesh::EIGEN_SOLVERS, libMesh::LASPACK_SOLVERS, libMesh::libmesh_ignore(), libMesh::PETSC_SOLVERS, and libMesh::TRILINOS_SOLVERS.

Referenced by libMesh::ImplicitSystem::add_matrix(), libMesh::TransientRBConstruction::allocate_data_structures(), and libMesh::RBConstruction::allocate_data_structures().

137 {
138  // Avoid unused parameter warnings when no solver packages are enabled.
140 
141  // Build the appropriate vector
142  switch (solver_package)
143  {
144 
145 #ifdef LIBMESH_HAVE_LASPACK
146  case LASPACK_SOLVERS:
147  return UniquePtr<SparseMatrix<T>>(new LaspackMatrix<T>(comm));
148 #endif
149 
150 
151 #ifdef LIBMESH_HAVE_PETSC
152  case PETSC_SOLVERS:
153  return UniquePtr<SparseMatrix<T>>(new PetscMatrix<T>(comm));
154 #endif
155 
156 
157 #ifdef LIBMESH_TRILINOS_HAVE_EPETRA
158  case TRILINOS_SOLVERS:
159  return UniquePtr<SparseMatrix<T>>(new EpetraMatrix<T>(comm));
160 #endif
161 
162 
163 #ifdef LIBMESH_HAVE_EIGEN
164  case EIGEN_SOLVERS:
165  return UniquePtr<SparseMatrix<T>>(new EigenSparseMatrix<T>(comm));
166 #endif
167 
168  default:
169  libmesh_error_msg("ERROR: Unrecognized solver package: " << solver_package);
170  }
171 
172  libmesh_error_msg("We'll never get here!");
173  return UniquePtr<SparseMatrix<T>>();
174 }
void libmesh_ignore(const T &)
const Parallel::Communicator & comm() const
template<typename T>
virtual void libMesh::SparseMatrix< T >::clear ( )
pure virtual
template<typename T>
virtual void libMesh::SparseMatrix< T >::close ( )
pure virtual
template<typename T>
virtual bool libMesh::SparseMatrix< T >::closed ( ) const
pure virtual
Returns
true if the matrix has been assembled.

Implemented in libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, and libMesh::libmesh_final< T >.

const Parallel::Communicator& libMesh::ParallelObject::comm ( ) const
inherited
Returns
A reference to the Parallel::Communicator object used by this mesh.

Definition at line 87 of file parallel_object.h.

References libMesh::ParallelObject::_communicator.

Referenced by libMesh::__libmesh_petsc_diff_solver_monitor(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::__libmesh_petsc_preconditioner_apply(), libMesh::__libmesh_petsc_snes_jacobian(), libMesh::__libmesh_petsc_snes_postcheck(), libMesh::__libmesh_petsc_snes_residual(), libMesh::__libmesh_tao_equality_constraints(), libMesh::__libmesh_tao_equality_constraints_jacobian(), libMesh::__libmesh_tao_gradient(), libMesh::__libmesh_tao_hessian(), libMesh::__libmesh_tao_inequality_constraints(), libMesh::__libmesh_tao_inequality_constraints_jacobian(), libMesh::__libmesh_tao_objective(), libMesh::MeshRefinement::_coarsen_elements(), libMesh::ExactSolution::_compute_error(), libMesh::ParmetisPartitioner::_do_repartition(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::PetscLinearSolver< T >::_petsc_shell_matrix_get_diagonal(), libMesh::SlepcEigenSolver< T >::_petsc_shell_matrix_get_diagonal(), libMesh::PetscLinearSolver< T >::_petsc_shell_matrix_mult(), libMesh::SlepcEigenSolver< T >::_petsc_shell_matrix_mult(), libMesh::PetscLinearSolver< T >::_petsc_shell_matrix_mult_add(), libMesh::EquationSystems::_read_impl(), libMesh::MeshRefinement::_refine_elements(), libMesh::MeshRefinement::_smooth_flags(), add_cube_convex_hull_to_mesh(), libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::ImplicitSystem::add_matrix(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), libMesh::System::add_vector(), libMesh::EigenSparseLinearSolver< T >::adjoint_solve(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), libMesh::TransientRBConstruction::assemble_affine_expansion(), libMesh::FEMSystem::assemble_qoi(), libMesh::MeshCommunication::assign_global_indices(), libMesh::ParmetisPartitioner::assign_partitioning(), libMesh::DofMap::attach_matrix(), libMesh::Parallel::BinSorter< KeyType, IdxType >::binsort(), libMesh::Parallel::Sort< KeyType, IdxType >::binsort(), libMesh::MeshCommunication::broadcast(), libMesh::SparseMatrix< T >::build(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::Parallel::Histogram< KeyType, IdxType >::build_histogram(), libMesh::PetscNonlinearSolver< T >::build_mat_null_space(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::MeshBase::cache_elem_dims(), libMesh::System::calculate_norm(), libMesh::DofMap::check_dirichlet_bcid_consistency(), libMesh::Parallel::Sort< KeyType, IdxType >::communicate_bins(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::RBConstruction::compute_max_error_bound(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBSCMConstruction::compute_SCM_bounds_on_training_set(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::MeshTools::create_bounding_box(), libMesh::MeshTools::create_nodal_bounding_box(), libMesh::MeshRefinement::create_parent_error_vector(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::MeshTools::create_subdomain_bounding_box(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::DofMap::distribute_dofs(), DMlibMeshFunction(), DMlibMeshJacobian(), DMlibMeshSetSystem_libMesh(), DMVariableBounds_libMesh(), libMesh::MeshRefinement::eliminate_unrefined_patches(), libMesh::RBEIMConstruction::enrich_RB_space(), libMesh::TransientRBConstruction::enrich_RB_space(), libMesh::RBConstruction::enrich_RB_space(), AssembleOptimization::equality_constraints(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::RBEIMConstruction::evaluate_mesh_function(), libMesh::MeshRefinement::flag_elements_by_elem_fraction(), libMesh::MeshRefinement::flag_elements_by_error_fraction(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::MeshCommunication::gather(), libMesh::MeshCommunication::gather_neighboring_elements(), libMesh::MeshfreeInterpolation::gather_remote_data(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::DofMap::get_info(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::EquationSystems::get_solution(), AssembleOptimization::inequality_constraints(), AssembleOptimization::inequality_constraints_jacobian(), libMesh::LocationMap< T >::init(), libMesh::TopologyMap::init(), libMesh::PetscDiffSolver::init(), libMesh::TimeSolver::init(), libMesh::TaoOptimizationSolver< T >::init(), libMesh::PetscNonlinearSolver< T >::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::EigenSystem::init_data(), libMesh::EigenSystem::init_matrices(), libMesh::ParmetisPartitioner::initialize(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::RBEIMConstruction::initialize_rb_construction(), integrate_function(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_flags(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_p_levels(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::MeshTools::libmesh_assert_valid_unique_ids(), libMesh::MeshRefinement::limit_level_mismatch_at_edge(), libMesh::MeshRefinement::limit_level_mismatch_at_node(), libMesh::MeshRefinement::limit_overrefined_boundary(), libMesh::MeshRefinement::limit_underrefined_boundary(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshCommunication::make_elems_parallel_consistent(), libMesh::MeshRefinement::make_flags_parallel_consistent(), libMesh::MeshCommunication::make_new_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_new_nodes_parallel_consistent(), libMesh::MeshCommunication::make_node_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_unique_ids_parallel_consistent(), libMesh::MeshCommunication::make_nodes_parallel_consistent(), libMesh::MeshCommunication::make_p_levels_parallel_consistent(), libMesh::MeshRefinement::make_refinement_compatible(), libMesh::TransientRBConstruction::mass_matrix_scaled_matvec(), libMesh::FEMSystem::mesh_position_set(), libMesh::MeshSerializer::MeshSerializer(), LinearElasticityWithContact::move_mesh(), libMesh::DistributedMesh::n_active_elem(), libMesh::MeshTools::n_active_levels(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::CondensedEigenSystem::n_global_non_condensed_dofs(), libMesh::MeshTools::n_levels(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::MeshTools::n_p_levels(), libMesh::BoundaryInfo::n_shellface_conds(), new_function_base(), libMesh::DistributedMesh::parallel_max_elem_id(), libMesh::DistributedMesh::parallel_max_node_id(), libMesh::ReplicatedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_n_elem(), libMesh::DistributedMesh::parallel_n_nodes(), libMesh::SparsityPattern::Build::parallel_sync(), libMesh::MeshTools::paranoid_n_levels(), libMesh::Partitioner::partition(), libMesh::MetisPartitioner::partition_range(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::petsc_auto_fieldsplit(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::MeshBase::prepare_for_use(), libMesh::SparseMatrix< T >::print(), FEMParameters::read(), libMesh::Nemesis_IO::read(), libMesh::CheckpointIO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::MeshBase::recalculate_n_partitions(), libMesh::MeshCommunication::redistribute(), libMesh::MeshRefinement::refine_and_coarsen_elements(), libMesh::DistributedMesh::renumber_dof_objects(), LinearElasticityWithContact::residual_and_jacobian(), libMesh::MeshCommunication::send_coarse_ghosts(), libMesh::TransientRBConstruction::set_error_temporal_data(), libMesh::RBEIMConstruction::set_explicit_sys_subvector(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::Partitioner::set_parent_processor_ids(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::Parallel::Sort< KeyType, IdxType >::sort(), libMesh::MeshBase::subdomain_ids(), libMesh::BoundaryInfo::sync(), libMesh::Parallel::sync_element_data_by_parent_id(), libMesh::Parallel::sync_node_data_by_element_id(), libMesh::MeshRefinement::test_level_one(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), libMesh::MeshRefinement::test_unflagged(), PointLocatorTest::testLocator(), BoundaryInfoTest::testMesh(), SystemsTest::testProjectCubeWithMeshFunction(), libMesh::MeshTools::total_weight(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::TransientRBConstruction::update_RB_initial_condition_all_N(), libMesh::RBEIMConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_RB_system_matrices(), libMesh::RBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), libMesh::RBConstruction::update_residual_terms(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::RBEvaluation::write_out_vectors(), libMesh::TransientRBConstruction::write_riesz_representors_to_files(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::RBDataSerialization::RBEvaluationSerialization::write_to_file(), libMesh::RBDataSerialization::TransientRBEvaluationSerialization::write_to_file(), libMesh::RBDataSerialization::RBEIMEvaluationSerialization::write_to_file(), and libMesh::RBDataSerialization::RBSCMEvaluationSerialization::write_to_file().

88  { return _communicator; }
const Parallel::Communicator & _communicator
template<typename T>
virtual void libMesh::SparseMatrix< T >::create_submatrix ( SparseMatrix< T > &  submatrix,
const std::vector< numeric_index_type > &  rows,
const std::vector< numeric_index_type > &  cols 
) const
virtual

This function creates a matrix called "submatrix" which is defined by the row and column indices given in the "rows" and "cols" entries.

Currently this operation is only defined for the PetscMatrix type.

Definition at line 350 of file sparse_matrix.h.

353  {
354  this->_get_submatrix(submatrix,
355  rows,
356  cols,
357  false); // false means DO NOT REUSE submatrix
358  }
virtual void _get_submatrix(SparseMatrix< T > &, const std::vector< numeric_index_type > &, const std::vector< numeric_index_type > &, const bool) const
Protected implementation of the create_submatrix and reinit_submatrix routines.
void libMesh::ReferenceCounter::disable_print_counter_info ( )
staticinherited

Definition at line 107 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

Referenced by libMesh::LibMeshInit::LibMeshInit(), and libMesh::ReferenceCounter::n_objects().

108 {
109  _enable_print_counter = false;
110  return;
111 }
static bool _enable_print_counter
Flag to control whether reference count information is printed when print_info is called...
void libMesh::ReferenceCounter::enable_print_counter_info ( )
staticinherited

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

Definition at line 101 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

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

102 {
103  _enable_print_counter = true;
104  return;
105 }
static bool _enable_print_counter
Flag to control whether reference count information is printed when print_info is called...
template<typename T>
virtual void libMesh::SparseMatrix< T >::flush ( )
virtual

For PETSc matrix , this function is similar to close but without shrinking memory.

This is useful when we want to switch between ADD_VALUES and INSERT_VALUES. close should be called before using the matrix.

Reimplemented in libMesh::libmesh_final< T >.

Definition at line 178 of file sparse_matrix.h.

178 { close(); }
virtual void close()=0
Calls the SparseMatrix&#39;s internal assembly routines, ensuring that the values are consistent across p...
template<typename T>
virtual void libMesh::SparseMatrix< T >::get_diagonal ( NumericVector< T > &  dest) const
pure virtual

Copies the diagonal part of the matrix into dest.

Implemented in libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, and libMesh::libmesh_final< T >.

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().

48 {
49 #if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)
50 
51  std::ostringstream oss;
52 
53  oss << '\n'
54  << " ---------------------------------------------------------------------------- \n"
55  << "| Reference count information |\n"
56  << " ---------------------------------------------------------------------------- \n";
57 
58  for (Counts::iterator it = _counts.begin();
59  it != _counts.end(); ++it)
60  {
61  const std::string name(it->first);
62  const unsigned int creations = it->second.first;
63  const unsigned int destructions = it->second.second;
64 
65  oss << "| " << name << " reference count information:\n"
66  << "| Creations: " << creations << '\n'
67  << "| Destructions: " << destructions << '\n';
68  }
69 
70  oss << " ---------------------------------------------------------------------------- \n";
71 
72  return oss.str();
73 
74 #else
75 
76  return "";
77 
78 #endif
79 }
std::string name(const ElemQuality q)
This function returns a string containing some name for q.
Definition: elem_quality.C:39
static Counts _counts
Actually holds the data.
template<typename T>
virtual void libMesh::SparseMatrix< T >::get_transpose ( SparseMatrix< T > &  dest) const
pure virtual
void libMesh::ReferenceCounter::increment_constructor_count ( const std::string &  name)
protectedinherited

Increments the construction counter.

Should be called in the constructor of any derived class that will be reference counted.

Definition at line 185 of file reference_counter.h.

References libMesh::ReferenceCounter::_counts, libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

Referenced by libMesh::ReferenceCounter::n_objects(), and libMesh::ReferenceCountedObject< RBParametrized >::ReferenceCountedObject().

186 {
187  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
188  std::pair<unsigned int, unsigned int> & p = _counts[name];
189 
190  p.first++;
191 }
std::string name(const ElemQuality q)
This function returns a string containing some name for q.
Definition: elem_quality.C:39
spin_mutex spin_mtx
A convenient spin mutex object which can be used for obtaining locks.
Definition: threads.C:29
static Counts _counts
Actually holds the data.
void libMesh::ReferenceCounter::increment_destructor_count ( const std::string &  name)
protectedinherited

Increments the destruction counter.

Should be called in the destructor of any derived class that will be reference counted.

Definition at line 198 of file reference_counter.h.

References libMesh::ReferenceCounter::_counts, libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

Referenced by libMesh::ReferenceCounter::n_objects(), and libMesh::ReferenceCountedObject< RBParametrized >::~ReferenceCountedObject().

199 {
200  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
201  std::pair<unsigned int, unsigned int> & p = _counts[name];
202 
203  p.second++;
204 }
std::string name(const ElemQuality q)
This function returns a string containing some name for q.
Definition: elem_quality.C:39
spin_mutex spin_mtx
A convenient spin mutex object which can be used for obtaining locks.
Definition: threads.C:29
static Counts _counts
Actually holds the data.
template<typename T>
virtual void libMesh::SparseMatrix< T >::init ( const numeric_index_type  m,
const numeric_index_type  n,
const numeric_index_type  m_l,
const numeric_index_type  n_l,
const numeric_index_type  nnz = 30,
const numeric_index_type  noz = 10,
const numeric_index_type  blocksize = 1 
)
pure virtual

Initialize SparseMatrix with the specified sizes.

Parameters
mThe global number of rows.
nThe global number of columns.
m_lThe local number of rows.
n_lThe local number of columns.
nnzThe number of on-diagonal nonzeros per row (defaults to 30).
nozThe number of off-diagonal nonzeros per row (defaults to 10).
blocksizeOptional value indicating dense coupled blocks for systems with multiple variables all of the same type.

Implemented in libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, and libMesh::libmesh_final< T >.

template<typename T>
virtual void libMesh::SparseMatrix< T >::init ( )
pure virtual

Initialize this matrix using the sparsity structure computed by dof_map.

Implemented in libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, and libMesh::libmesh_final< T >.

template<typename T>
virtual bool libMesh::SparseMatrix< T >::initialized ( ) const
virtual
Returns
true if the matrix has been initialized, false otherwise.

Definition at line 100 of file sparse_matrix.h.

Referenced by libMesh::ImplicitSystem::assemble(), libMesh::ImplicitSystem::init_matrices(), and libMesh::SparseMatrix< T >::print().

100 { return _is_initialized; }
bool _is_initialized
Flag indicating whether or not the matrix has been initialized.
template<typename T>
virtual Real libMesh::SparseMatrix< T >::l1_norm ( ) const
pure virtual
Returns
The $ \ell_1 $-norm of the matrix, that is the max column sum: $ |M|_1 = \max_{j} \sum_{i} |M_{ij}| $

This is the natural matrix norm that is compatible with the $ \ell_1 $-norm for vectors, i.e. $ |Mv|_1 \leq |M|_1 |v|_1 $. (cf. Haemmerlin-Hoffmann : Numerische Mathematik)

Implemented in libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, and libMesh::libmesh_final< T >.

Referenced by libMesh::FEMSystem::assembly().

template<typename T>
virtual Real libMesh::SparseMatrix< T >::linfty_norm ( ) const
pure virtual
Returns
The $ \ell_{\infty} $-norm of the matrix, that is the max row sum:

$ |M|_{\infty} = \max_{i} \sum_{j} |M_{ij}| $

This is the natural matrix norm that is compatible to the $ \ell_{\infty} $-norm of vectors, i.e. $ |Mv|_{\infty} \leq |M|_{\infty} |v|_{\infty} $. (cf. Haemmerlin-Hoffmann : Numerische Mathematik)

Implemented in libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, and libMesh::libmesh_final< T >.

template<typename T>
virtual numeric_index_type libMesh::SparseMatrix< T >::m ( ) const
pure virtual
template<typename T>
virtual numeric_index_type libMesh::SparseMatrix< T >::n ( ) const
pure virtual
static unsigned int libMesh::ReferenceCounter::n_objects ( )
staticinherited
processor_id_type libMesh::ParallelObject::n_processors ( ) const
inherited
Returns
The number of processors in the group.

Definition at line 93 of file parallel_object.h.

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

Referenced by libMesh::ParmetisPartitioner::_do_repartition(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::DistributedMesh::add_elem(), libMesh::DistributedMesh::add_node(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::FEMSystem::assembly(), libMesh::ParmetisPartitioner::assign_partitioning(), libMesh::AztecLinearSolver< T >::AztecLinearSolver(), libMesh::MeshCommunication::broadcast(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::DistributedMesh::clear(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::UnstructuredMesh::create_pid_mesh(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::DistributedMesh::DistributedMesh(), libMesh::EnsightIO::EnsightIO(), libMesh::MeshCommunication::gather(), libMesh::MeshCommunication::gather_neighboring_elements(), libMesh::MeshBase::get_info(), libMesh::EquationSystems::get_solution(), libMesh::SystemSubsetBySubdomain::init(), libMesh::ParmetisPartitioner::initialize(), libMesh::Nemesis_IO_Helper::initialize(), libMesh::DistributedMesh::insert_elem(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::DofMap::local_variable_indices(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshBase::n_active_elem_on_proc(), libMesh::MeshBase::n_elem_on_proc(), libMesh::MeshBase::n_nodes_on_proc(), libMesh::SparsityPattern::Build::parallel_sync(), libMesh::Partitioner::partition(), libMesh::MeshBase::partition(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::PetscLinearSolver< T >::PetscLinearSolver(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::SparseMatrix< T >::print(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::CheckpointIO::read(), libMesh::CheckpointIO::read_connectivity(), libMesh::XdrIO::read_header(), libMesh::CheckpointIO::read_nodes(), libMesh::MeshCommunication::redistribute(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::Partitioner::repartition(), libMesh::MeshCommunication::send_coarse_ghosts(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::Parallel::Sort< KeyType, IdxType >::sort(), WriteVecAndScalar::testWrite(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), and libMesh::XdrIO::write_serialized_nodesets().

94  { return cast_int<processor_id_type>(_communicator.size()); }
unsigned int size() const
Definition: parallel.h:726
const Parallel::Communicator & _communicator
template<typename T>
virtual bool libMesh::SparseMatrix< T >::need_full_sparsity_pattern ( ) const
virtual
Returns
true if this sparse matrix format needs to be fed the graph of the sparse matrix.

This is true for LaspackMatrix, but not PetscMatrix. In the case where the full graph is not required, we can efficiently approximate it to provide a good estimate of the required size of the sparse matrix.

Reimplemented in libMesh::libmesh_final< T >, and libMesh::libmesh_final< T >.

Definition at line 117 of file sparse_matrix.h.

Referenced by libMesh::DofMap::attach_matrix().

118  { return false; }
template<typename T>
virtual T libMesh::SparseMatrix< T >::operator() ( const numeric_index_type  i,
const numeric_index_type  j 
) const
pure virtual
Returns
A copy of matrix entry (i,j).
Note
This may be an expensive operation, and you should always be careful where you call this function.

Implemented in libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, and libMesh::libmesh_final< T >.

template<>
void libMesh::SparseMatrix< Complex >::print ( std::ostream &  os,
const bool  sparse 
) const

Definition at line 101 of file sparse_matrix.C.

References libMesh::SparseMatrix< T >::m(), and libMesh::SparseMatrix< T >::n().

102 {
103  // std::complex<>::operator<<() is defined, but use this form
104 
105  if (sparse)
106  {
107  libmesh_not_implemented();
108  }
109 
110  os << "Real part:" << std::endl;
111  for (numeric_index_type i=0; i<this->m(); i++)
112  {
113  for (numeric_index_type j=0; j<this->n(); j++)
114  os << std::setw(8) << (*this)(i,j).real() << " ";
115  os << std::endl;
116  }
117 
118  os << std::endl << "Imaginary part:" << std::endl;
119  for (numeric_index_type i=0; i<this->m(); i++)
120  {
121  for (numeric_index_type j=0; j<this->n(); j++)
122  os << std::setw(8) << (*this)(i,j).imag() << " ";
123  os << std::endl;
124  }
125 }
virtual numeric_index_type n() const =0
virtual numeric_index_type m() const =0
dof_id_type numeric_index_type
Definition: id_types.h:92
template<typename T >
void libMesh::SparseMatrix< T >::print ( std::ostream &  os = libMesh::out,
const bool  sparse = false 
) const

Print the contents of the matrix to the screen in a uniform style, regardless of matrix/solver package being used.

Definition at line 208 of file sparse_matrix.C.

References libMesh::SparseMatrix< T >::_dof_map, libMesh::ParallelObject::comm(), libMesh::DofMap::end_dof(), libMesh::DofMap::first_dof(), libMesh::SparseMatrix< T >::initialized(), libMesh::libmesh_assert(), libMesh::SparseMatrix< T >::m(), libMesh::SparseMatrix< T >::n(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), libMesh::Parallel::Communicator::receive(), and libMesh::Parallel::Communicator::send().

209 {
210  parallel_object_only();
211 
212  libmesh_assert (this->initialized());
213 
214  if (!this->_dof_map)
215  libmesh_error_msg("Error! Trying to print a matrix with no dof_map set!");
216 
217  // We'll print the matrix from processor 0 to make sure
218  // it's serialized properly
219  if (this->processor_id() == 0)
220  {
221  libmesh_assert_equal_to (this->_dof_map->first_dof(), 0);
222  for (numeric_index_type i=this->_dof_map->first_dof();
223  i!=this->_dof_map->end_dof(); ++i)
224  {
225  if (sparse)
226  {
227  for (numeric_index_type j=0; j<this->n(); j++)
228  {
229  T c = (*this)(i,j);
230  if (c != static_cast<T>(0.0))
231  {
232  os << i << " " << j << " " << c << std::endl;
233  }
234  }
235  }
236  else
237  {
238  for (numeric_index_type j=0; j<this->n(); j++)
239  os << (*this)(i,j) << " ";
240  os << std::endl;
241  }
242  }
243 
244  std::vector<numeric_index_type> ibuf, jbuf;
245  std::vector<T> cbuf;
246  numeric_index_type currenti = this->_dof_map->end_dof();
247  for (processor_id_type p=1; p < this->n_processors(); ++p)
248  {
249  this->comm().receive(p, ibuf);
250  this->comm().receive(p, jbuf);
251  this->comm().receive(p, cbuf);
252  libmesh_assert_equal_to (ibuf.size(), jbuf.size());
253  libmesh_assert_equal_to (ibuf.size(), cbuf.size());
254 
255  if (ibuf.empty())
256  continue;
257  libmesh_assert_greater_equal (ibuf.front(), currenti);
258  libmesh_assert_greater_equal (ibuf.back(), ibuf.front());
259 
260  std::size_t currentb = 0;
261  for (;currenti <= ibuf.back(); ++currenti)
262  {
263  if (sparse)
264  {
265  for (numeric_index_type j=0; j<this->n(); j++)
266  {
267  if (currentb < ibuf.size() &&
268  ibuf[currentb] == currenti &&
269  jbuf[currentb] == j)
270  {
271  os << currenti << " " << j << " " << cbuf[currentb] << std::endl;
272  currentb++;
273  }
274  }
275  }
276  else
277  {
278  for (numeric_index_type j=0; j<this->n(); j++)
279  {
280  if (currentb < ibuf.size() &&
281  ibuf[currentb] == currenti &&
282  jbuf[currentb] == j)
283  {
284  os << cbuf[currentb] << " ";
285  currentb++;
286  }
287  else
288  os << static_cast<T>(0.0) << " ";
289  }
290  os << std::endl;
291  }
292  }
293  }
294  if (!sparse)
295  {
296  for (; currenti != this->m(); ++currenti)
297  {
298  for (numeric_index_type j=0; j<this->n(); j++)
299  os << static_cast<T>(0.0) << " ";
300  os << std::endl;
301  }
302  }
303  }
304  else
305  {
306  std::vector<numeric_index_type> ibuf, jbuf;
307  std::vector<T> cbuf;
308 
309  // We'll assume each processor has access to entire
310  // matrix rows, so (*this)(i,j) is valid if i is a local index.
311  for (numeric_index_type i=this->_dof_map->first_dof();
312  i!=this->_dof_map->end_dof(); ++i)
313  {
314  for (numeric_index_type j=0; j<this->n(); j++)
315  {
316  T c = (*this)(i,j);
317  if (c != static_cast<T>(0.0))
318  {
319  ibuf.push_back(i);
320  jbuf.push_back(j);
321  cbuf.push_back(c);
322  }
323  }
324  }
325  this->comm().send(0,ibuf);
326  this->comm().send(0,jbuf);
327  this->comm().send(0,cbuf);
328  }
329 }
virtual numeric_index_type n() const =0
virtual numeric_index_type m() const =0
processor_id_type n_processors() const
uint8_t processor_id_type
Definition: id_types.h:99
libmesh_assert(j)
virtual bool initialized() const
dof_id_type first_dof(const processor_id_type proc) const
Definition: dof_map.h:535
dof_id_type end_dof(const processor_id_type proc) const
Definition: dof_map.h:577
dof_id_type numeric_index_type
Definition: id_types.h:92
void send(const unsigned int dest_processor_id, const T &buf, const MessageTag &tag=no_tag) const
Blocking-send to one processor with data-defined type.
DofMap const * _dof_map
The DofMap object associated with this object.
const Parallel::Communicator & comm() const
Status receive(const unsigned int dest_processor_id, T &buf, const MessageTag &tag=any_tag) const
Blocking-receive from one processor with data-defined type.
processor_id_type processor_id() const
void libMesh::ReferenceCounter::print_info ( std::ostream &  out = libMesh::out)
staticinherited

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

Definition at line 88 of file reference_counter.C.

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

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

89 {
91  out_stream << ReferenceCounter::get_info();
92 }
static std::string get_info()
Gets a string containing the reference information.
static bool _enable_print_counter
Flag to control whether reference count information is printed when print_info is called...
template<typename T>
virtual void libMesh::SparseMatrix< T >::print_matlab ( const std::string &  = "") const
virtual

Print the contents of the matrix in Matlab's sparse matrix format.

Optionally prints the matrix to the file named name. If name is not specified it is dumped to the screen.

Reimplemented in libMesh::libmesh_final< T >, and libMesh::libmesh_final< T >.

Definition at line 340 of file sparse_matrix.h.

341  {
342  libmesh_not_implemented();
343  }
template<typename T>
virtual void libMesh::SparseMatrix< T >::print_personal ( std::ostream &  os = libMesh::out) const
pure virtual

Print the contents of the matrix to the screen in a package-personalized style, if available.

Implemented in libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, and libMesh::libmesh_final< T >.

processor_id_type libMesh::ParallelObject::processor_id ( ) const
inherited
Returns
The rank of this processor in the group.

Definition at line 99 of file parallel_object.h.

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

Referenced by libMesh::BoundaryInfo::_find_id_maps(), libMesh::EquationSystems::_read_impl(), libMesh::DistributedMesh::add_elem(), libMesh::BoundaryInfo::add_elements(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::MeshRefinement::add_node(), libMesh::MeshTools::Modification::all_tri(), libMesh::FEMSystem::assembly(), libMesh::ParmetisPartitioner::assign_partitioning(), libMesh::MeshCommunication::broadcast(), libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::Nemesis_IO_Helper::build_element_and_node_maps(), libMesh::ParmetisPartitioner::build_graph(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::DofMap::build_sparsity(), libMesh::DistributedMesh::clear(), libMesh::ExodusII_IO_Helper::close(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::compute_communication_map_parameters(), libMesh::Nemesis_IO_Helper::compute_internal_and_border_elems_and_internal_nodes(), libMesh::RBConstruction::compute_max_error_bound(), libMesh::Nemesis_IO_Helper::compute_node_communication_maps(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::ExodusII_IO_Helper::create(), libMesh::DistributedMesh::delete_elem(), libMesh::DistributedMesh::delete_node(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::DistributedMesh::DistributedMesh(), libMesh::EnsightIO::EnsightIO(), libMesh::RBEIMConstruction::evaluate_mesh_function(), libMesh::MeshFunction::find_element(), libMesh::MeshFunction::find_elements(), libMesh::UnstructuredMesh::find_neighbors(), libMesh::MeshCommunication::gather(), libMesh::MeshCommunication::gather_neighboring_elements(), libMesh::Nemesis_IO_Helper::get_cmap_params(), libMesh::Nemesis_IO_Helper::get_eb_info_global(), libMesh::Nemesis_IO_Helper::get_elem_cmap(), libMesh::Nemesis_IO_Helper::get_elem_map(), libMesh::MeshBase::get_info(), libMesh::DofMap::get_info(), libMesh::Nemesis_IO_Helper::get_init_global(), libMesh::Nemesis_IO_Helper::get_init_info(), libMesh::Nemesis_IO_Helper::get_loadbal_param(), libMesh::Nemesis_IO_Helper::get_node_cmap(), libMesh::Nemesis_IO_Helper::get_node_map(), libMesh::Nemesis_IO_Helper::get_ns_param_global(), libMesh::EquationSystems::get_solution(), libMesh::Nemesis_IO_Helper::get_ss_param_global(), libMesh::SparsityPattern::Build::handle_vi_vj(), libMesh::SystemSubsetBySubdomain::init(), HeatSystem::init_data(), libMesh::ParmetisPartitioner::initialize(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize_element_variables(), libMesh::ExodusII_IO_Helper::initialize_global_variables(), libMesh::ExodusII_IO_Helper::initialize_nodal_variables(), libMesh::DistributedMesh::insert_elem(), libMesh::DofMap::is_evaluable(), libMesh::SparsityPattern::Build::join(), libMesh::TransientRBEvaluation::legacy_write_offline_data_to_files(), libMesh::RBEIMEvaluation::legacy_write_offline_data_to_files(), libMesh::RBEvaluation::legacy_write_offline_data_to_files(), libMesh::RBSCMEvaluation::legacy_write_offline_data_to_files(), libMesh::RBEIMEvaluation::legacy_write_out_interpolation_points_elem(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DofMap::local_variable_indices(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), AugmentSparsityOnInterface::mesh_reinit(), libMesh::MeshBase::n_active_local_elem(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::System::n_local_dofs(), libMesh::MeshBase::n_local_elem(), libMesh::MeshBase::n_local_nodes(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::SparsityPattern::Build::operator()(), libMesh::PatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::SparsityPattern::Build::parallel_sync(), libMesh::MetisPartitioner::partition_range(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::SparseMatrix< T >::print(), libMesh::NumericVector< T >::print_global(), libMesh::Nemesis_IO_Helper::put_cmap_params(), libMesh::Nemesis_IO_Helper::put_elem_cmap(), libMesh::Nemesis_IO_Helper::put_elem_map(), libMesh::Nemesis_IO_Helper::put_loadbal_param(), libMesh::Nemesis_IO_Helper::put_node_cmap(), libMesh::Nemesis_IO_Helper::put_node_map(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::CheckpointIO::read(), libMesh::XdrIO::read(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::ExodusII_IO_Helper::read_node_num_map(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::MeshCommunication::redistribute(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::MeshCommunication::send_coarse_ghosts(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::LaplaceMeshSmoother::smooth(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), BoundaryInfoTest::testShellFaceConstraints(), WriteVecAndScalar::testWrite(), libMesh::MeshTools::total_weight(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::Parallel::Packing< Node * >::unpack(), libMesh::Parallel::Packing< Elem * >::unpack(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::DTKAdapter::update_variable_values(), libMesh::MeshTools::weight(), libMesh::NameBasedIO::write(), libMesh::CheckpointIO::write(), libMesh::XdrIO::write(), libMesh::EquationSystems::write(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO::write_element_data(), libMesh::ExodusII_IO_Helper::write_element_values(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO::write_global_data(), libMesh::ExodusII_IO_Helper::write_global_values(), libMesh::ExodusII_IO::write_information_records(), libMesh::ExodusII_IO_Helper::write_information_records(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::UCDIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data_discontinuous(), libMesh::ExodusII_IO_Helper::write_nodal_values(), libMesh::Nemesis_IO_Helper::write_nodesets(), libMesh::ExodusII_IO_Helper::write_nodesets(), libMesh::RBEvaluation::write_out_vectors(), write_output_solvedata(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::XdrIO::write_serialized_bc_names(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::XdrIO::write_serialized_subdomain_names(), libMesh::Nemesis_IO_Helper::write_sidesets(), libMesh::ExodusII_IO_Helper::write_sidesets(), libMesh::ExodusII_IO::write_timestep(), and libMesh::ExodusII_IO_Helper::write_timestep().

100  { return cast_int<processor_id_type>(_communicator.rank()); }
const Parallel::Communicator & _communicator
unsigned int rank() const
Definition: parallel.h:724
template<typename T>
virtual void libMesh::SparseMatrix< T >::reinit_submatrix ( SparseMatrix< T > &  submatrix,
const std::vector< numeric_index_type > &  rows,
const std::vector< numeric_index_type > &  cols 
) const
virtual

This function is similar to the one above, but it allows you to reuse the existing sparsity pattern of "submatrix" instead of reallocating it again.

This should hopefully be more efficient if you are frequently extracting submatrices of the same size.

Definition at line 366 of file sparse_matrix.h.

369  {
370  this->_get_submatrix(submatrix,
371  rows,
372  cols,
373  true); // true means REUSE submatrix
374  }
virtual void _get_submatrix(SparseMatrix< T > &, const std::vector< numeric_index_type > &, const std::vector< numeric_index_type > &, const bool) const
Protected implementation of the create_submatrix and reinit_submatrix routines.
template<typename T>
virtual numeric_index_type libMesh::SparseMatrix< T >::row_start ( ) const
pure virtual
Returns
The index of the first matrix row stored on this processor.

Implemented in libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, and libMesh::libmesh_final< T >.

template<typename T>
virtual numeric_index_type libMesh::SparseMatrix< T >::row_stop ( ) const
pure virtual
Returns
The index of the last matrix row (+1) stored on this processor.

Implemented in libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, and libMesh::libmesh_final< T >.

template<typename T>
virtual void libMesh::SparseMatrix< T >::set ( const numeric_index_type  i,
const numeric_index_type  j,
const T  value 
)
pure virtual

Set the element (i,j) to value.

Throws an error if the entry does not exist. Zero values can be "stored" in non-existent fields.

Implemented in libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, libMesh::libmesh_final< T >, and libMesh::libmesh_final< T >.

Referenced by AssembleOptimization::equality_constraints_jacobian(), and AssembleOptimization::inequality_constraints_jacobian().

template<typename T>
virtual void libMesh::SparseMatrix< T >::update_sparsity_pattern ( const SparsityPattern::Graph )
virtual

Updates the matrix sparsity pattern.

When your SparseMatrix<T> implementation does not need this data, simply do not override this method.

Reimplemented in libMesh::libmesh_final< T >, and libMesh::libmesh_final< T >.

Definition at line 125 of file sparse_matrix.h.

Referenced by libMesh::DofMap::attach_matrix().

125 {}
template<typename T>
void libMesh::SparseMatrix< T >::vector_mult ( NumericVector< T > &  dest,
const NumericVector< T > &  arg 
) const
template<typename T>
void libMesh::SparseMatrix< T >::vector_mult_add ( NumericVector< T > &  dest,
const NumericVector< T > &  arg 
) const

Multiplies the matrix by the NumericVector arg and adds the result to the NumericVector dest.

Definition at line 188 of file sparse_matrix.C.

References libMesh::NumericVector< T >::add_vector().

Referenced by libMesh::SparseMatrix< T >::vector_mult(), and libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve().

190 {
191  /* This functionality is actually implemented in the \p
192  NumericVector class. */
193  dest.add_vector(arg,*this);
194 }
template<typename T>
virtual void libMesh::SparseMatrix< T >::zero ( )
pure virtual
template<typename T>
void libMesh::SparseMatrix< T >::zero_rows ( std::vector< numeric_index_type > &  rows,
diag_value = 0.0 
)
virtual

Sets all row entries to 0 then puts diag_value in the diagonal entry.

Reimplemented in libMesh::libmesh_final< T >.

Definition at line 199 of file sparse_matrix.C.

200 {
201  /* This functionality isn't implemented or stubbed in every subclass yet */
202  libmesh_not_implemented();
203 }

Friends And Related Function Documentation

template<typename T>
std::ostream& operator<< ( std::ostream &  os,
const SparseMatrix< T > &  m 
)
friend

Same as the print method above, but allows you to print to a stream in the standard syntax.

template <typename U>
friend std::ostream & operator << (std::ostream & os, const SparseMatrix<U> & m);
Note
The above syntax, which does not require any prior declaration of operator<<, declares any instantiation of SparseMatrix<X> is friend to any instantiation of operator<<(ostream &, SparseMatrix<Y> &). It would not happen in practice, but in principle it means that SparseMatrix<Complex> would be friend to operator<<(ostream &, SparseMatrix<Real>).
The form below, which requires a previous declaration of the operator<<(stream &, SparseMatrix<T> &) function (see top of this file), means that any instantiation of SparseMatrix<T> is friend to the specialization operator<<(ostream &, SparseMatrix<T> &), but e.g. SparseMatrix<U> is not friend to the same function. So this is slightly different to the form above...

This method seems to be the "preferred" technique, see http://www.parashift.com/c++-faq-lite/template-friends.html

Definition at line 440 of file sparse_matrix.h.

441 {
442  m.print(os);
443  return os;
444 }
virtual numeric_index_type m() const =0

Member Data Documentation

const Parallel::Communicator& libMesh::ParallelObject::_communicator
protectedinherited
ReferenceCounter::Counts libMesh::ReferenceCounter::_counts
staticprotectedinherited
template<typename T>
DofMap const* libMesh::SparseMatrix< T >::_dof_map
protected

The DofMap object associated with this object.

Definition at line 421 of file sparse_matrix.h.

Referenced by libMesh::SparseMatrix< T >::print().

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().

template<typename T>
bool libMesh::SparseMatrix< T >::_is_initialized
protected

Flag indicating whether or not the matrix has been initialized.

Definition at line 426 of file sparse_matrix.h.

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.

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().


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