libMesh::EigenSparseMatrix< T > Class Template Reference

#include <eigen_sparse_matrix.h>

Inheritance diagram for libMesh::EigenSparseMatrix< T >:

Public Types

typedef EigenSM DataType
 
typedef Eigen::Triplet< T, eigen_idx_typeTripletType
 

Public Member Functions

 EigenSparseMatrix (const Parallel::Communicator &comm LIBMESH_CAN_DEFAULT_TO_COMMWORLD)
 
 ~EigenSparseMatrix ()
 
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) libmesh_override
 
virtual void init () libmesh_override
 
virtual void clear () libmesh_override
 
virtual void zero () libmesh_override
 
virtual void close () libmesh_override
 
virtual numeric_index_type m () const libmesh_override
 
virtual numeric_index_type n () const libmesh_override
 
virtual numeric_index_type row_start () const libmesh_override
 
virtual numeric_index_type row_stop () const libmesh_override
 
virtual void set (const numeric_index_type i, const numeric_index_type j, const T value) libmesh_override
 
virtual void add (const numeric_index_type i, const numeric_index_type j, const T value) libmesh_override
 
virtual void add_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) libmesh_override
 
virtual void add_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &dof_indices) libmesh_override
 
virtual void add (const T a, SparseMatrix< T > &X) libmesh_override
 
virtual T operator() (const numeric_index_type i, const numeric_index_type j) const libmesh_override
 
virtual Real l1_norm () const libmesh_override
 
virtual Real linfty_norm () const libmesh_override
 
virtual bool closed () const libmesh_override
 
virtual void print_personal (std::ostream &os=libMesh::out) const libmesh_override
 
virtual void get_diagonal (NumericVector< T > &dest) const libmesh_override
 
virtual void get_transpose (SparseMatrix< T > &dest) const libmesh_override
 
virtual bool initialized () const
 
void attach_dof_map (const DofMap &dof_map)
 
virtual bool need_full_sparsity_pattern () const
 
virtual void update_sparsity_pattern (const SparsityPattern::Graph &)
 
virtual void zero_rows (std::vector< numeric_index_type > &rows, T diag_value=0.0)
 
virtual void flush ()
 
virtual void add_block_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &brows, const std::vector< numeric_index_type > &bcols)
 
virtual void add_block_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &dof_indices)
 
void print (std::ostream &os=libMesh::out, const bool sparse=false) const
 
template<>
void print (std::ostream &os, const bool sparse) const
 
virtual void print_matlab (const std::string &="") const
 
virtual void create_submatrix (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) const
 
virtual void reinit_submatrix (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) const
 
void vector_mult (NumericVector< T > &dest, const NumericVector< T > &arg) const
 
void vector_mult_add (NumericVector< T > &dest, const NumericVector< T > &arg) const
 
const Parallel::Communicatorcomm () const
 
processor_id_type n_processors () const
 
processor_id_type processor_id () const
 

Static Public Member Functions

static std::unique_ptr< SparseMatrix< T > > build (const Parallel::Communicator &comm, const SolverPackage solver_package=libMesh::default_solver_package())
 
static std::string get_info ()
 
static void print_info (std::ostream &out=libMesh::out)
 
static unsigned int n_objects ()
 
static void enable_print_counter_info ()
 
static void disable_print_counter_info ()
 

Protected Types

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

Protected Member Functions

virtual void _get_submatrix (SparseMatrix< T > &, const std::vector< numeric_index_type > &, const std::vector< numeric_index_type > &, const bool) const
 
void increment_constructor_count (const std::string &name)
 
void increment_destructor_count (const std::string &name)
 

Protected Attributes

DofMap const * _dof_map
 
bool _is_initialized
 
const Parallel::Communicator_communicator
 

Static Protected Attributes

static Counts _counts
 
static Threads::atomic< unsigned int > _n_objects
 
static Threads::spin_mutex _mutex
 
static bool _enable_print_counter = true
 

Private Attributes

DataType _mat
 
bool _closed
 

Friends

class EigenSparseVector< T >
 
class EigenSparseLinearSolver< T >
 

Detailed Description

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

The EigenSparseMatrix class wraps a sparse matrix object from the Eigen library. All overridden virtual functions are documented in sparse_matrix.h.

Author
Benjamin S. Kirk
Date
2013

Definition at line 54 of file eigen_sparse_matrix.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.

template<typename T>
typedef EigenSM libMesh::EigenSparseMatrix< T >::DataType

Convenient typedefs

Definition at line 80 of file eigen_sparse_matrix.h.

template<typename T>
typedef Eigen::Triplet<T,eigen_idx_type> libMesh::EigenSparseMatrix< T >::TripletType

Definition at line 81 of file eigen_sparse_matrix.h.

Constructor & Destructor Documentation

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

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 161 of file eigen_sparse_matrix.C.

161  :
162  SparseMatrix<T>(comm_in),
163  _closed (false)
164 {
165 }
template<typename T >
libMesh::EigenSparseMatrix< T >::~EigenSparseMatrix ( )

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

Definition at line 170 of file eigen_sparse_matrix.C.

References libMesh::EigenSparseMatrix< T >::clear().

171 {
172  this->clear ();
173 }
virtual void clear() libmesh_override

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
inlineprotectedvirtualinherited

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::PetscMatrix< T >.

Definition at line 411 of file sparse_matrix.h.

415  {
416  libmesh_not_implemented();
417  }
template<typename T >
void libMesh::EigenSparseMatrix< T >::add ( const numeric_index_type  i,
const numeric_index_type  j,
const T  value 
)
virtual

Add value to the element (i,j). Throws an error if the entry does not exist. Zero values can be "added" to non-existent entries.

Implements libMesh::SparseMatrix< T >.

Definition at line 247 of file eigen_sparse_matrix.C.

References libMesh::EigenSparseMatrix< T >::_mat, libMesh::SparseMatrix< T >::initialized(), libMesh::EigenSparseMatrix< T >::m(), libMesh::EigenSparseMatrix< T >::n(), and value.

Referenced by libMesh::EigenSparseMatrix< T >::close().

250 {
251  libmesh_assert (this->initialized());
252  libmesh_assert_less (i, this->m());
253  libmesh_assert_less (j, this->n());
254 
255  _mat.coeffRef(i,j) += value;
256 }
virtual bool initialized() const
virtual numeric_index_type n() const libmesh_override
static const bool value
Definition: xdr_io.C:108
virtual numeric_index_type m() const libmesh_override
template<typename T >
void libMesh::EigenSparseMatrix< T >::add ( const T  a,
SparseMatrix< T > &  X 
)
virtual

Compute $ A \leftarrow A + a*X $ for scalar a, matrix X.

Implements libMesh::SparseMatrix< T >.

Definition at line 270 of file eigen_sparse_matrix.C.

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

271 {
272  libmesh_assert (this->initialized());
273  libmesh_assert_equal_to (this->m(), X_in.m());
274  libmesh_assert_equal_to (this->n(), X_in.n());
275 
276  EigenSparseMatrix<T> & X = cast_ref<EigenSparseMatrix<T> &> (X_in);
277 
278  _mat += X._mat*a_in;
279 }
virtual bool initialized() const
virtual numeric_index_type n() const libmesh_override
virtual numeric_index_type m() const libmesh_override
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 
)
virtualinherited

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::PetscMatrix< T >.

Definition at line 62 of file sparse_matrix.C.

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

65 {
66  libmesh_assert_equal_to (dm.m() / brows.size(), dm.n() / bcols.size());
67 
68  const numeric_index_type blocksize = cast_int<numeric_index_type>
69  (dm.m() / brows.size());
70 
71  libmesh_assert_equal_to (dm.m()%blocksize, 0);
72  libmesh_assert_equal_to (dm.n()%blocksize, 0);
73 
74  std::vector<numeric_index_type> rows, cols;
75 
76  rows.reserve(blocksize*brows.size());
77  cols.reserve(blocksize*bcols.size());
78 
79  for (std::size_t ib=0; ib<brows.size(); ib++)
80  {
81  numeric_index_type i=brows[ib]*blocksize;
82 
83  for (unsigned int v=0; v<blocksize; v++)
84  rows.push_back(i++);
85  }
86 
87  for (std::size_t jb=0; jb<bcols.size(); jb++)
88  {
89  numeric_index_type j=bcols[jb]*blocksize;
90 
91  for (unsigned int v=0; v<blocksize; v++)
92  cols.push_back(j++);
93  }
94 
95  this->add_matrix (dm, rows, cols);
96 }
virtual void add_matrix(const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols)=0
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 
)
inlinevirtualinherited

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::PetscMatrix< T >.

Definition at line 250 of file sparse_matrix.h.

252  { 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)
Definition: sparse_matrix.C:62
template<typename T >
void libMesh::EigenSparseMatrix< T >::add_matrix ( const DenseMatrix< T > &  dm,
const std::vector< numeric_index_type > &  rows,
const std::vector< numeric_index_type > &  cols 
)
virtual

Add the full matrix dm to the SparseMatrix. This is useful for adding an element matrix at assembly time.

Implements libMesh::SparseMatrix< T >.

Definition at line 121 of file eigen_sparse_matrix.C.

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

Referenced by libMesh::EigenSparseMatrix< T >::add_matrix(), and libMesh::EigenSparseMatrix< T >::close().

125 {
126  libmesh_assert (this->initialized());
127  unsigned int n_rows = cast_int<unsigned int>(rows.size());
128  unsigned int n_cols = cast_int<unsigned int>(cols.size());
129  libmesh_assert_equal_to (dm.m(), n_rows);
130  libmesh_assert_equal_to (dm.n(), n_cols);
131 
132 
133  for (unsigned int i=0; i<n_rows; i++)
134  for (unsigned int j=0; j<n_cols; j++)
135  this->add(rows[i],cols[j],dm(i,j));
136 }
virtual bool initialized() const
virtual void add(const numeric_index_type i, const numeric_index_type j, const T value) libmesh_override
template<typename T >
void libMesh::EigenSparseMatrix< T >::add_matrix ( const DenseMatrix< T > &  dm,
const std::vector< numeric_index_type > &  dof_indices 
)
virtual

Same as add_matrix, but assumes the row and column maps are the same. Thus the matrix dm must be square.

Implements libMesh::SparseMatrix< T >.

Definition at line 261 of file eigen_sparse_matrix.C.

References libMesh::EigenSparseMatrix< T >::add_matrix().

263 {
264  this->add_matrix (dm, dof_indices, dof_indices);
265 }
virtual void add_matrix(const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) libmesh_override
template<typename T>
void libMesh::SparseMatrix< T >::attach_dof_map ( const DofMap dof_map)
inlineinherited

Get a pointer to the DofMap to use.

Definition at line 106 of file sparse_matrix.h.

Referenced by libMesh::__libmesh_tao_hessian(), and libMesh::DofMap::attach_matrix().

107  { _dof_map = &dof_map; }
DofMap const * _dof_map
template<typename T >
std::unique_ptr< SparseMatrix< T > > libMesh::SparseMatrix< T >::build ( const Parallel::Communicator comm,
const SolverPackage  solver_package = libMesh::default_solver_package() 
)
staticinherited

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

Definition at line 136 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::EigenSystem::init_data(), and libMesh::EigenSystem::init_matrices().

138 {
139  // Avoid unused parameter warnings when no solver packages are enabled.
141 
142  // Build the appropriate vector
143  switch (solver_package)
144  {
145 
146 #ifdef LIBMESH_HAVE_LASPACK
147  case LASPACK_SOLVERS:
148  return libmesh_make_unique<LaspackMatrix<T>>(comm);
149 #endif
150 
151 
152 #ifdef LIBMESH_HAVE_PETSC
153  case PETSC_SOLVERS:
154  return libmesh_make_unique<PetscMatrix<T>>(comm);
155 #endif
156 
157 
158 #ifdef LIBMESH_TRILINOS_HAVE_EPETRA
159  case TRILINOS_SOLVERS:
160  return libmesh_make_unique<EpetraMatrix<T>>(comm);
161 #endif
162 
163 
164 #ifdef LIBMESH_HAVE_EIGEN
165  case EIGEN_SOLVERS:
166  return libmesh_make_unique<EigenSparseMatrix<T>>(comm);
167 #endif
168 
169  default:
170  libmesh_error_msg("ERROR: Unrecognized solver package: " << solver_package);
171  }
172 }
EIGEN_SOLVERS
Definition: libmesh.C:261
TRILINOS_SOLVERS
Definition: libmesh.C:259
LASPACK_SOLVERS
Definition: libmesh.C:263
void libmesh_ignore(const T &)
const Parallel::Communicator & comm() const
template<typename T >
void libMesh::EigenSparseMatrix< T >::clear ( )
virtual

Restores the SparseMatrix<T> to a pristine state.

Implements libMesh::SparseMatrix< T >.

Definition at line 178 of file eigen_sparse_matrix.C.

References libMesh::EigenSparseMatrix< T >::_closed, libMesh::SparseMatrix< T >::_is_initialized, and libMesh::EigenSparseMatrix< T >::_mat.

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

179 {
180  _mat.resize(0,0);
181 
182  _closed = false;
183  this->_is_initialized = false;
184 }
template<typename T>
virtual bool libMesh::EigenSparseMatrix< T >::closed ( ) const
inlinevirtual
Returns
true if the matrix has been assembled.

Implements libMesh::SparseMatrix< T >.

Definition at line 131 of file eigen_sparse_matrix.h.

References libMesh::EigenSparseMatrix< T >::_closed.

const Parallel::Communicator& libMesh::ParallelObject::comm ( ) const
inlineinherited
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_jacobian(), libMesh::__libmesh_petsc_diff_solver_monitor(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::__libmesh_petsc_snes_fd_residual(), libMesh::__libmesh_petsc_snes_jacobian(), libMesh::__libmesh_petsc_snes_mffd_residual(), 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(), libMesh::ImplicitSystem::add_matrix(), libMesh::System::add_vector(), libMesh::EigenSparseLinearSolver< T >::adjoint_solve(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::LaplaceMeshSmoother::allgather_graph(), 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::DistributedVector< T >::clone(), libMesh::EigenSparseVector< T >::clone(), libMesh::LaspackVector< T >::clone(), libMesh::EpetraVector< T >::clone(), libMesh::PetscVector< T >::clone(), libMesh::EpetraVector< T >::close(), libMesh::Parallel::Sort< KeyType, IdxType >::communicate_bins(), 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::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::EpetraVector< T >::EpetraVector(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), 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::CondensedEigenSystem::get_eigenpair(), libMesh::DofMap::get_info(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::EquationSystems::get_solution(), libMesh::LocationMap< T >::init(), libMesh::TopologyMap::init(), libMesh::TimeSolver::init(), libMesh::TaoOptimizationSolver< T >::init(), libMesh::PetscNonlinearSolver< T >::init(), libMesh::DistributedVector< T >::init(), libMesh::EpetraVector< T >::init(), libMesh::PetscVector< 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::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::libmesh_petsc_snes_residual_helper(), libMesh::MeshRefinement::limit_level_mismatch_at_edge(), libMesh::MeshRefinement::limit_level_mismatch_at_node(), libMesh::MeshRefinement::limit_overrefined_boundary(), libMesh::MeshRefinement::limit_underrefined_boundary(), 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::DistributedVector< T >::max(), libMesh::FEMSystem::mesh_position_set(), libMesh::MeshSerializer::MeshSerializer(), libMesh::DistributedVector< T >::min(), 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(), 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::LinearPartitioner::partition_range(), 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(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), 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(), libMesh::CheckpointIO::select_split_config(), libMesh::MeshCommunication::send_coarse_ghosts(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::Partitioner::set_parent_processor_ids(), libMesh::PetscDiffSolver::setup_petsc_data(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::Parallel::Sort< KeyType, IdxType >::sort(), libMesh::split_mesh(), 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(), libMesh::MeshRefinement::test_unflagged(), libMesh::MeshTools::total_weight(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::DistributedVector< T >::zero_clone(), libMesh::EigenSparseVector< T >::zero_clone(), libMesh::LaspackVector< T >::zero_clone(), libMesh::EpetraVector< T >::zero_clone(), and libMesh::PetscVector< T >::zero_clone().

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
inlinevirtualinherited

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 351 of file sparse_matrix.h.

354  {
355  this->_get_submatrix(submatrix,
356  rows,
357  cols,
358  false); // false means DO NOT REUSE submatrix
359  }
virtual void _get_submatrix(SparseMatrix< T > &, const std::vector< numeric_index_type > &, const std::vector< numeric_index_type > &, const bool) const
void libMesh::ReferenceCounter::disable_print_counter_info ( )
staticinherited
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 }
template<typename T>
virtual void libMesh::SparseMatrix< T >::flush ( )
inlinevirtualinherited

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::PetscMatrix< T >.

Definition at line 179 of file sparse_matrix.h.

179 { close(); }
virtual void close()=0
template<typename T >
void libMesh::EigenSparseMatrix< T >::get_diagonal ( NumericVector< T > &  dest) const
virtual

Copies the diagonal part of the matrix into dest.

Implements libMesh::SparseMatrix< T >.

Definition at line 141 of file eigen_sparse_matrix.C.

References libMesh::EigenSparseVector< T >::_vec.

Referenced by libMesh::EigenSparseMatrix< T >::print_personal().

142 {
143  EigenSparseVector<T> & dest = cast_ref<EigenSparseVector<T> &>(dest_in);
144 
145  dest._vec = _mat.diagonal();
146 }
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)
Definition: elem_quality.C:39
template<typename T >
void libMesh::EigenSparseMatrix< T >::get_transpose ( SparseMatrix< T > &  dest) const
virtual

Copies the transpose of the matrix into dest, which may be *this.

Implements libMesh::SparseMatrix< T >.

Definition at line 151 of file eigen_sparse_matrix.C.

References libMesh::EigenSparseMatrix< T >::_mat.

Referenced by libMesh::EigenSparseMatrix< T >::print_personal().

152 {
153  EigenSparseMatrix<T> & dest = cast_ref<EigenSparseMatrix<T> &>(dest_in);
154 
155  dest._mat = _mat.transpose();
156 }
void libMesh::ReferenceCounter::increment_constructor_count ( const std::string &  name)
inlineprotectedinherited

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)
Definition: elem_quality.C:39
spin_mutex spin_mtx
Definition: threads.C:29
void libMesh::ReferenceCounter::increment_destructor_count ( const std::string &  name)
inlineprotectedinherited

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)
Definition: elem_quality.C:39
spin_mutex spin_mtx
Definition: threads.C:29
template<typename T>
virtual void libMesh::EigenSparseMatrix< 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 
)
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.

Implements libMesh::SparseMatrix< T >.

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

Initialize this matrix using the sparsity structure computed by dof_map.

Implements libMesh::SparseMatrix< T >.

Definition at line 63 of file eigen_sparse_matrix.C.

References libMesh::libMeshPrivateData::_is_initialized, and libMesh::initialized().

64 {
65  // Ignore calls on initialized objects
66  if (this->initialized())
67  return;
68 
69  // We need the DofMap for this!
70  libmesh_assert(this->_dof_map);
71 
72  // Clear initialized matrices
73  if (this->initialized())
74  this->clear();
75 
76  const numeric_index_type n_rows = this->_dof_map->n_dofs();
77  const numeric_index_type n_cols = n_rows;
78 
79 #ifndef NDEBUG
80  // The following variables are only used for assertions,
81  // so avoid declaring them when asserts are inactive.
82  const numeric_index_type n_l = this->_dof_map->n_dofs_on_processor(0);
83  const numeric_index_type m_l = n_l;
84 #endif
85 
86  // Laspack Matrices only work for uniprocessor cases
87  libmesh_assert_equal_to (n_rows, n_cols);
88  libmesh_assert_equal_to (m_l, n_rows);
89  libmesh_assert_equal_to (n_l, n_cols);
90 
91  const std::vector<numeric_index_type> & n_nz = this->_dof_map->get_n_nz();
92 
93 #ifndef NDEBUG
94  // The following variables are only used for assertions,
95  // so avoid declaring them when asserts are inactive.
96  const std::vector<numeric_index_type> & n_oz = this->_dof_map->get_n_oz();
97 #endif
98 
99  // Make sure the sparsity pattern isn't empty
100  libmesh_assert_equal_to (n_nz.size(), n_l);
101  libmesh_assert_equal_to (n_oz.size(), n_l);
102 
103  if (n_rows==0)
104  {
105  _mat.resize(0,0);
106  return;
107  }
108 
109  _mat.resize(n_rows,n_cols);
110  _mat.reserve(n_nz);
111 
112  this->_is_initialized = true;
113 
114  libmesh_assert_equal_to (n_rows, this->m());
115  libmesh_assert_equal_to (n_cols, this->n());
116 }
dof_id_type n_dofs() const
Definition: dof_map.h:519
dof_id_type n_dofs_on_processor(const processor_id_type proc) const
Definition: dof_map.h:535
virtual bool initialized() const
virtual void clear() libmesh_override
dof_id_type numeric_index_type
Definition: id_types.h:92
virtual numeric_index_type n() const libmesh_override
const std::vector< dof_id_type > & get_n_oz() const
Definition: dof_map.h:417
DofMap const * _dof_map
virtual numeric_index_type m() const libmesh_override
const std::vector< dof_id_type > & get_n_nz() const
Definition: dof_map.h:404
template<typename T >
Real libMesh::EigenSparseMatrix< T >::l1_norm ( ) const
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)

Implements libMesh::SparseMatrix< T >.

Definition at line 298 of file eigen_sparse_matrix.C.

References libMesh::EigenSparseMatrix< T >::_mat, std::abs(), libMesh::EigenSparseMatrix< T >::m(), and libMesh::EigenSparseMatrix< T >::n().

Referenced by libMesh::EigenSparseMatrix< T >::close().

299 {
300  // There does not seem to be a straightforward way to iterate over
301  // the columns of an EigenSparseMatrix. So we use some extra
302  // storage and keep track of the column sums while going over the
303  // row entries...
304  std::vector<Real> abs_col_sums(this->n());
305 
306  // For a row-major Eigen SparseMatrix like we're using, the
307  // InnerIterator iterates over the non-zero entries of rows.
308  for (unsigned row=0; row<this->m(); ++row)
309  {
310  EigenSM::InnerIterator it(_mat, row);
311  for (; it; ++it)
312  abs_col_sums[it.col()] += std::abs(it.value());
313  }
314 
315  return *(std::max_element(abs_col_sums.begin(), abs_col_sums.end()));
316 }
double abs(double a)
virtual numeric_index_type n() const libmesh_override
virtual numeric_index_type m() const libmesh_override
template<typename T >
Real libMesh::EigenSparseMatrix< T >::linfty_norm ( ) const
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)

Implements libMesh::SparseMatrix< T >.

Definition at line 321 of file eigen_sparse_matrix.C.

References libMesh::EigenSparseMatrix< T >::_mat, std::abs(), libMesh::EigenSparseMatrix< T >::m(), std::max(), and libMesh::Real.

Referenced by libMesh::EigenSparseMatrix< T >::close().

322 {
323  Real max_abs_row_sum = 0.;
324 
325  // For a row-major Eigen SparseMatrix like we're using, the
326  // InnerIterator iterates over the non-zero entries of rows.
327  for (unsigned row=0; row<this->m(); ++row)
328  {
329  Real current_abs_row_sum = 0.;
330  EigenSM::InnerIterator it(_mat, row);
331  for (; it; ++it)
332  current_abs_row_sum += std::abs(it.value());
333 
334  max_abs_row_sum = std::max(max_abs_row_sum, current_abs_row_sum);
335  }
336 
337  return max_abs_row_sum;
338 }
double abs(double a)
long double max(long double a, double b)
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
virtual numeric_index_type m() const libmesh_override
static unsigned int libMesh::ReferenceCounter::n_objects ( )
inlinestaticinherited
processor_id_type libMesh::ParallelObject::n_processors ( ) const
inlineinherited
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::DistributedVector< T >::init(), 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(), 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:725
const Parallel::Communicator & _communicator
template<typename T>
virtual bool libMesh::SparseMatrix< T >::need_full_sparsity_pattern ( ) const
inlinevirtualinherited
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::EpetraMatrix< T >, and libMesh::LaspackMatrix< T >.

Definition at line 118 of file sparse_matrix.h.

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

119  { return false; }
template<typename T >
T libMesh::EigenSparseMatrix< T >::operator() ( const numeric_index_type  i,
const numeric_index_type  j 
) const
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.

Implements libMesh::SparseMatrix< T >.

Definition at line 285 of file eigen_sparse_matrix.C.

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

Referenced by libMesh::EigenSparseMatrix< T >::close().

287 {
288  libmesh_assert (this->initialized());
289  libmesh_assert_less (i, this->m());
290  libmesh_assert_less (j, this->n());
291 
292  return _mat.coeff(i,j);
293 }
virtual bool initialized() const
virtual numeric_index_type n() const libmesh_override
virtual numeric_index_type m() const libmesh_override
template<>
void libMesh::SparseMatrix< Complex >::print ( std::ostream &  os,
const bool  sparse 
) const
inherited

Definition at line 102 of file sparse_matrix.C.

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

103 {
104  // std::complex<>::operator<<() is defined, but use this form
105 
106  if (sparse)
107  {
108  libmesh_not_implemented();
109  }
110 
111  os << "Real part:" << std::endl;
112  for (numeric_index_type i=0; i<this->m(); i++)
113  {
114  for (numeric_index_type j=0; j<this->n(); j++)
115  os << std::setw(8) << (*this)(i,j).real() << " ";
116  os << std::endl;
117  }
118 
119  os << std::endl << "Imaginary part:" << std::endl;
120  for (numeric_index_type i=0; i<this->m(); i++)
121  {
122  for (numeric_index_type j=0; j<this->n(); j++)
123  os << std::setw(8) << (*this)(i,j).imag() << " ";
124  os << std::endl;
125  }
126 }
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
inherited

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

Definition at line 206 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::SparseMatrix< T >::m(), libMesh::SparseMatrix< T >::n(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), libMesh::Parallel::Communicator::receive(), and libMesh::Parallel::Communicator::send().

Referenced by libMesh::EigenSparseMatrix< T >::print_personal(), and libMesh::LaspackMatrix< T >::print_personal().

207 {
208  parallel_object_only();
209 
210  libmesh_assert (this->initialized());
211 
212  if (!this->_dof_map)
213  libmesh_error_msg("Error! Trying to print a matrix with no dof_map set!");
214 
215  // We'll print the matrix from processor 0 to make sure
216  // it's serialized properly
217  if (this->processor_id() == 0)
218  {
219  libmesh_assert_equal_to (this->_dof_map->first_dof(), 0);
220  for (numeric_index_type i=this->_dof_map->first_dof();
221  i!=this->_dof_map->end_dof(); ++i)
222  {
223  if (sparse)
224  {
225  for (numeric_index_type j=0; j<this->n(); j++)
226  {
227  T c = (*this)(i,j);
228  if (c != static_cast<T>(0.0))
229  {
230  os << i << " " << j << " " << c << std::endl;
231  }
232  }
233  }
234  else
235  {
236  for (numeric_index_type j=0; j<this->n(); j++)
237  os << (*this)(i,j) << " ";
238  os << std::endl;
239  }
240  }
241 
242  std::vector<numeric_index_type> ibuf, jbuf;
243  std::vector<T> cbuf;
244  numeric_index_type currenti = this->_dof_map->end_dof();
245  for (processor_id_type p=1; p < this->n_processors(); ++p)
246  {
247  this->comm().receive(p, ibuf);
248  this->comm().receive(p, jbuf);
249  this->comm().receive(p, cbuf);
250  libmesh_assert_equal_to (ibuf.size(), jbuf.size());
251  libmesh_assert_equal_to (ibuf.size(), cbuf.size());
252 
253  if (ibuf.empty())
254  continue;
255  libmesh_assert_greater_equal (ibuf.front(), currenti);
256  libmesh_assert_greater_equal (ibuf.back(), ibuf.front());
257 
258  std::size_t currentb = 0;
259  for (;currenti <= ibuf.back(); ++currenti)
260  {
261  if (sparse)
262  {
263  for (numeric_index_type j=0; j<this->n(); j++)
264  {
265  if (currentb < ibuf.size() &&
266  ibuf[currentb] == currenti &&
267  jbuf[currentb] == j)
268  {
269  os << currenti << " " << j << " " << cbuf[currentb] << std::endl;
270  currentb++;
271  }
272  }
273  }
274  else
275  {
276  for (numeric_index_type j=0; j<this->n(); j++)
277  {
278  if (currentb < ibuf.size() &&
279  ibuf[currentb] == currenti &&
280  jbuf[currentb] == j)
281  {
282  os << cbuf[currentb] << " ";
283  currentb++;
284  }
285  else
286  os << static_cast<T>(0.0) << " ";
287  }
288  os << std::endl;
289  }
290  }
291  }
292  if (!sparse)
293  {
294  for (; currenti != this->m(); ++currenti)
295  {
296  for (numeric_index_type j=0; j<this->n(); j++)
297  os << static_cast<T>(0.0) << " ";
298  os << std::endl;
299  }
300  }
301  }
302  else
303  {
304  std::vector<numeric_index_type> ibuf, jbuf;
305  std::vector<T> cbuf;
306 
307  // We'll assume each processor has access to entire
308  // matrix rows, so (*this)(i,j) is valid if i is a local index.
309  for (numeric_index_type i=this->_dof_map->first_dof();
310  i!=this->_dof_map->end_dof(); ++i)
311  {
312  for (numeric_index_type j=0; j<this->n(); j++)
313  {
314  T c = (*this)(i,j);
315  if (c != static_cast<T>(0.0))
316  {
317  ibuf.push_back(i);
318  jbuf.push_back(j);
319  cbuf.push_back(c);
320  }
321  }
322  }
323  this->comm().send(0,ibuf);
324  this->comm().send(0,jbuf);
325  this->comm().send(0,cbuf);
326  }
327 }
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
virtual bool initialized() const
dof_id_type first_dof(const processor_id_type proc) const
Definition: dof_map.h:544
dof_id_type end_dof(const processor_id_type proc) const
Definition: dof_map.h:586
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
DofMap const * _dof_map
const Parallel::Communicator & comm() const
Status receive(const unsigned int dest_processor_id, T &buf, const MessageTag &tag=any_tag) const
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()
template<typename T>
virtual void libMesh::SparseMatrix< T >::print_matlab ( const std::string &  = "") const
inlinevirtualinherited

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::PetscMatrix< T >.

Definition at line 341 of file sparse_matrix.h.

342  {
343  libmesh_not_implemented();
344  }
template<typename T>
virtual void libMesh::EigenSparseMatrix< T >::print_personal ( std::ostream &  os = libMesh::out) const
inlinevirtual

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

Implements libMesh::SparseMatrix< T >.

Definition at line 133 of file eigen_sparse_matrix.h.

References libMesh::EigenSparseMatrix< T >::get_diagonal(), libMesh::EigenSparseMatrix< T >::get_transpose(), and libMesh::SparseMatrix< T >::print().

133 { this->print(os); }
void print(std::ostream &os=libMesh::out, const bool sparse=false) const
processor_id_type libMesh::ParallelObject::processor_id ( ) const
inlineinherited
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::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::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::DistributedVector< T >::init(), libMesh::SystemSubsetBySubdomain::init(), 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::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(), libMesh::MeshRefinement::make_coarsening_compatible(), 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::XdrIO::read(), libMesh::CheckpointIO::read(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::read_global_values(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::ExodusII_IO_Helper::read_node_num_map(), 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::CheckpointIO::select_split_config(), libMesh::MeshCommunication::send_coarse_ghosts(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::LaplaceMeshSmoother::smooth(), 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::MeshTools::weight(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::CheckpointIO::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::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(), libMesh::ExodusII_IO_Helper::write_timestep(), and libMesh::ExodusII_IO::write_timestep_discontinuous().

100  { return cast_int<processor_id_type>(_communicator.rank()); }
const Parallel::Communicator & _communicator
unsigned int rank() const
Definition: parallel.h:723
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
inlinevirtualinherited

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 367 of file sparse_matrix.h.

370  {
371  this->_get_submatrix(submatrix,
372  rows,
373  cols,
374  true); // true means REUSE submatrix
375  }
virtual void _get_submatrix(SparseMatrix< T > &, const std::vector< numeric_index_type > &, const std::vector< numeric_index_type > &, const bool) const
template<typename T >
numeric_index_type libMesh::EigenSparseMatrix< T >::row_start ( ) const
virtual
Returns
The index of the first matrix row stored on this processor.

Implements libMesh::SparseMatrix< T >.

Definition at line 217 of file eigen_sparse_matrix.C.

Referenced by libMesh::EigenSparseMatrix< T >::close().

218 {
219  return 0;
220 }
template<typename T >
numeric_index_type libMesh::EigenSparseMatrix< T >::row_stop ( ) const
virtual
Returns
The index of the last matrix row (+1) stored on this processor.

Implements libMesh::SparseMatrix< T >.

Definition at line 225 of file eigen_sparse_matrix.C.

References libMesh::EigenSparseMatrix< T >::m().

Referenced by libMesh::EigenSparseMatrix< T >::close().

226 {
227  return this->m();
228 }
virtual numeric_index_type m() const libmesh_override
template<typename T >
void libMesh::EigenSparseMatrix< T >::set ( const numeric_index_type  i,
const numeric_index_type  j,
const T  value 
)
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.

Implements libMesh::SparseMatrix< T >.

Definition at line 233 of file eigen_sparse_matrix.C.

References libMesh::EigenSparseMatrix< T >::_mat, libMesh::SparseMatrix< T >::initialized(), libMesh::EigenSparseMatrix< T >::m(), libMesh::EigenSparseMatrix< T >::n(), and value.

236 {
237  libmesh_assert (this->initialized());
238  libmesh_assert_less (i, this->m());
239  libmesh_assert_less (j, this->n());
240 
241  _mat.coeffRef(i,j) = value;
242 }
virtual bool initialized() const
virtual numeric_index_type n() const libmesh_override
static const bool value
Definition: xdr_io.C:108
virtual numeric_index_type m() const libmesh_override
template<typename T>
virtual void libMesh::SparseMatrix< T >::update_sparsity_pattern ( const SparsityPattern::Graph )
inlinevirtualinherited

Updates the matrix sparsity pattern. When your SparseMatrix<T> implementation does not need this data, simply do not override this method.

Reimplemented in libMesh::EpetraMatrix< T >, and libMesh::LaspackMatrix< T >.

Definition at line 126 of file sparse_matrix.h.

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

126 {}
template<typename T>
void libMesh::SparseMatrix< T >::vector_mult ( NumericVector< T > &  dest,
const NumericVector< T > &  arg 
) const
inherited

Multiplies the matrix by the NumericVector arg and stores the result in NumericVector dest.

Definition at line 176 of file sparse_matrix.C.

References libMesh::SparseMatrix< T >::vector_mult_add(), and libMesh::NumericVector< T >::zero().

Referenced by libMesh::ImplicitSystem::qoi_parameter_hessian(), and libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product().

178 {
179  dest.zero();
180  this->vector_mult_add(dest,arg);
181 }
void vector_mult_add(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
inherited

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

Definition at line 186 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().

188 {
189  /* This functionality is actually implemented in the \p
190  NumericVector class. */
191  dest.add_vector(arg,*this);
192 }
template<typename T >
void libMesh::EigenSparseMatrix< T >::zero ( )
virtual

Set all entries to 0.

Implements libMesh::SparseMatrix< T >.

Definition at line 189 of file eigen_sparse_matrix.C.

References libMesh::EigenSparseMatrix< T >::_mat.

190 {
191  _mat.setZero();
192 }
template<typename T>
void libMesh::SparseMatrix< T >::zero_rows ( std::vector< numeric_index_type > &  rows,
diag_value = 0.0 
)
virtualinherited

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 197 of file sparse_matrix.C.

198 {
199  /* This functionality isn't implemented or stubbed in every subclass yet */
200  libmesh_not_implemented();
201 }

Friends And Related Function Documentation

template<typename T>
friend class EigenSparseLinearSolver< T >
friend

Definition at line 155 of file eigen_sparse_matrix.h.

template<typename T>
friend class EigenSparseVector< T >
friend

Make other Eigen datatypes friends

Definition at line 154 of file eigen_sparse_matrix.h.

Member Data Documentation

template<typename T>
bool libMesh::EigenSparseMatrix< T >::_closed
private

Flag indicating if the matrix has been closed yet.

Definition at line 149 of file eigen_sparse_matrix.h.

Referenced by libMesh::EigenSparseMatrix< T >::clear(), libMesh::EigenSparseMatrix< T >::close(), and libMesh::EigenSparseMatrix< T >::closed().

ReferenceCounter::Counts libMesh::ReferenceCounter::_counts
staticprotectedinherited
template<typename T>
DofMap const* libMesh::SparseMatrix< T >::_dof_map
protectedinherited

The DofMap object associated with this object.

Definition at line 422 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
protectedinherited

Flag indicating whether or not the matrix has been initialized.

Definition at line 427 of file sparse_matrix.h.

Referenced by libMesh::PetscMatrix< T >::_get_submatrix(), libMesh::EigenSparseMatrix< T >::clear(), libMesh::LaspackMatrix< T >::clear(), and libMesh::PetscMatrix< T >::get_transpose().

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: